BioProject
KAP200004
BioProject Title
Discovery of 3D-nucleome biomarker in liver/breast cancer patients
(DDBJ: PRJDB19217)
Common Fields
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BioProject
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KAP200004 |
|---|---|
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Strategy
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MNase-Seq
,
RAD-Seq
,
ChIA-PET
,
RNA-Seq
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Source
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GENOMIC
,
TRANSCRIPTOMIC
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Selection
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Restriction Digest , other , PolyA |
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Layout
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single
,
paired
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Instrument
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Illumina HiSeq 2500
,
Illumina NovaSeq 6000
,
Illumina HiSeq 4000
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|
Submission date
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2021-03-22 |
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Experiments
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96 |
Accession
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Runs
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All runs [96] |
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BioSamples
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All samples [60] |
Experiment Metadata
(96 cases)
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EXPERIMENT ID
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Identifier
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BIOSAMPLE ID
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sample_name
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library_name
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title | library_strategy | library_source | library_selection | library_layout | platform | instrument_model | design_description | library_construction_protocol | library_strandedness | insert_size | Submission dateSubmission date | Registration date |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| KAE21103420 | DRA: DRX650180 | KAS21009682 | BT549_rep2 | BT549_rep2-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009682 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103410 | DRA: DRX650179 | KAS21009681 | BT549_rep1 | BT549_rep1-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009681 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103400 | DRA: DRX650178 | KAS21009680 | HCC70_rep2 | HCC70_rep2-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009680 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103390 | DRA: DRX650177 | KAS21009679 | HCC70_rep1 | HCC70_rep1-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009679 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103380 | DRA: DRX650176 | KAS21009678 | HCC1954_rep2 | HCC1954_rep2-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009678 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103370 | DRA: DRX650175 | KAS21009677 | HCC1954_rep1 | HCC1954_rep1-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009677 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103360 | DRA: DRX650174 | KAS21009676 | ZR7530_rep2 | ZR7530_rep2-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009676 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103350 | DRA: DRX650173 | KAS21009675 | ZR7530_rep1 | ZR7530_rep1-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009675 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103340 | DRA: DRX650172 | KAS21009674 | T47D_rep2 | T47D_rep2-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009674 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103330 | DRA: DRX650171 | KAS21009673 | T47D_rep1 | T47D_rep1-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009673 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103320 | DRA: DRX650170 | KAS21009672 | HMEC_rep2 | HMEC_rep2-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009672 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103310 | DRA: DRX650169 | KAS21009671 | HMEC_rep1 | HMEC_rep1-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009671 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103300 | DRA: DRX650168 | KAS21009682 | BT549_rep2 | BT549_rep2-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009682 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103290 | DRA: DRX650167 | KAS21009681 | BT549_rep1 | BT549_rep1-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009681 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103280 | DRA: DRX650166 | KAS21009680 | HCC70_rep2 | HCC70_rep2-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009680 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103270 | DRA: DRX650165 | KAS21009679 | HCC70_rep1 | HCC70_rep1-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009679 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103260 | DRA: DRX650164 | KAS21009678 | HCC1954_rep2 | HCC1954_rep2-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009678 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103250 | DRA: DRX650163 | KAS21009677 | HCC1954_rep1 | HCC1954_rep1-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009677 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103240 | DRA: DRX650162 | KAS21009676 | ZR7530_rep2 | ZR7530_rep2-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009676 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103230 | DRA: DRX650161 | KAS21009675 | ZR7530_rep1 | ZR7530_rep1-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009675 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103220 | DRA: DRX650160 | KAS21009674 | T47D_rep2 | T47D_rep2-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009674 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103210 | DRA: DRX650159 | KAS21009673 | T47D_rep1 | T47D_rep1-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009673 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103200 | DRA: DRX650158 | KAS21009672 | HMEC_rep2 | HMEC_rep2-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009672 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103190 | DRA: DRX650157 | KAS21009671 | HMEC_rep1 | HMEC_rep1-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009671 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103180 | DRA: DRX650156 | KAS21009682 | BT549_rep2 | BT549_rep2-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009682 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103170 | DRA: DRX650155 | KAS21009681 | BT549_rep1 | BT549_rep1-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009681 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103160 | DRA: DRX650154 | KAS21009680 | HCC70_rep2 | HCC70_rep2-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009680 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103150 | DRA: DRX650153 | KAS21009679 | HCC70_rep1 | HCC70_rep1-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009679 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103140 | DRA: DRX650152 | KAS21009678 | HCC1954_rep2 | HCC1954_rep2-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009678 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103130 | DRA: DRX650151 | KAS21009677 | HCC1954_rep1 | HCC1954_rep1-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009677 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103120 | DRA: DRX650150 | KAS21009676 | ZR7530_rep2 | ZR7530_rep2-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009676 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103110 | DRA: DRX650149 | KAS21009675 | ZR7530_rep1 | ZR7530_rep1-001_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009675 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103100 | DRA: DRX650148 | KAS21009674 | T47D_rep2 | T47D_rep2-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009674 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103090 | DRA: DRX650147 | KAS21009673 | T47D_rep1 | T47D_rep1-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009673 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103080 | DRA: DRX650146 | KAS21009672 | HMEC_rep2 | HMEC_rep2-003_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009672 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21103070 | DRA: DRX650145 | KAS21009671 | HMEC_rep1 | HMEC_rep1-002_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS21009671 | MNase-Seq | GENOMIC | Restriction Digest | single | ILLUMINA | Illumina HiSeq 2500 | The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at room temperature RT. The crosslinking was quenched with 125 mM glycine for 5 min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer 50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA. Following, the suspended chromatin was sheared using an ultrasonicator Covaris S220 and incubated overnight with the relavant antibodies against anti-CTCF Millipore; 07-729, anti-H3K27ac Abcam; ab4729, and Protein A, G sepharose GE Healthcare; 17-1279-03 and 17-0618-05 at 4degree Celsius with agitation. The immune complexes were washed sequentially with low-salt wash buffer 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, high-salt wash buffer 20 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and LiCl wash buffer, and finally washed twice with TE buffer. The washed immune complexes were eluted with elution buffer 1% SDS, 0.1 M NaHCO3 and de-crosslinked overnight at 68degree Celsius. The immunoprecipitated DNA was treated with proteinase K and RNase A, and collected by phenol-chloroform-isoamyl alcohol precipitation. Libraries were prepared using an Accel-NGS 2S Plus DNA Library Kit SWIFT; 21024 according to the manufactureru0026's guidelines. The libraries were sequenced using an Illumina Hiseq2500 system with the single method 50 bp. | 2021-12-02 | 2021-12-02 | |||
| KAE21051390 | DRA: DRX649307 | KAS20000438 | SNU449_HiC_rep2 | SNU449_HiC_rep2_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000438 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051380 | DRA: DRX649306 | KAS20000437 | SNU449_HiC_rep1 | SNU449_HiC_rep1_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000437 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051370 | DRA: DRX649305 | KAS20000436 | Huh7_HiC_rep2 | Huh7_HiC_rep2_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000436 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051360 | DRA: DRX649304 | KAS20000435 | Huh7_HiC_rep1 | Huh7_HiC_rep1_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000435 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051350 | DRA: DRX649303 | KAS20000434 | Huh1_HiC_rep2 | Huh1_HiC_rep2_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000434 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051340 | DRA: DRX649302 | KAS20000433 | Huh1_HiC_rep1 | Huh1_HiC_rep1_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000433 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051330 | DRA: DRX649301 | KAS20000432 | Hep3B_HiC_rep2 | Hep3B_HiC_rep2_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000432 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051320 | DRA: DRX649300 | KAS20000431 | Hep3B_HiC_rep1 | Hep3B_HiC_rep1_Hi-C | Illumina NovaSeq 6000 paired Sequencing of KAS20000431 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 2,000,000 cells were crosslinked using 36.5% formaldehyde. In situ Hi-C was performed using the Arima-HiC kit Arima Genomics Inc and sequenced using a Illumina Novaseq 6000 150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051310 | DRA: DRX649299 | KAS20000430 | SNU449_ATAC_rep2 | SNU449_ATAC_rep2_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000430 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 SNU449 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051300 | DRA: DRX649298 | KAS20000429 | SNU449_ATAC_rep1 | SNU449_ATAC_rep1_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000429 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 SNU449 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051290 | DRA: DRX649297 | KAS20000428 | Huh7_ATAC_rep2 | Huh7_ATAC_rep2_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000428 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 Huh7 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051280 | DRA: DRX649296 | KAS20000427 | Huh7_ATAC_rep1 | Huh7_ATAC_rep1_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000427 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 Huh7 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051270 | DRA: DRX649295 | KAS20000426 | Huh1_ATAC_rep2 | Huh1_ATAC_rep2_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000426 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 Huh1 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051260 | DRA: DRX649294 | KAS20000425 | Huh1_ATAC_rep1 | Huh1_ATAC_rep1_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000425 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 Huh1 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051250 | DRA: DRX649293 | KAS20000424 | Hep3B_ATAC_rep2 | Hep3B_ATAC_rep2_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000424 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 Hep3B cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21051240 | DRA: DRX649292 | KAS20000423 | Hep3B_ATAC_rep1 | Hep3B_ATAC_rep1_ATAC-Seq | Illumina NovaSeq 6000 paired Sequencing of KAS20000423 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina NovaSeq 6000 | Total 50,000 Hep3B cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a NovaSeq2500 system150bp with the paired method. | 2021-03-31 | 2021-03-31 | |||
| KAE21040660 | DRA: DRX649327 | KAS20000276 | TCPS150-rep2 | TCPS150-rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000276 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040650 | DRA: DRX649326 | KAS20000275 | TCPS150-rep1 | TCPS150-rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000275 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040640 | DRA: DRX649325 | KAS20000274 | TCPS20-rep2 | TCPS20-rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000274 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040630 | DRA: DRX649324 | KAS20000273 | TCPS20-rep1 | TCPS20-rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000273 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040620 | DRA: DRX649323 | KAS20000272 | pV4D4150-rep2 | pV4D4150-rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000272 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040610 | DRA: DRX649322 | KAS20000271 | pV4D4150-rep1 | pV4D4150-rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000271 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040600 | DRA: DRX649321 | KAS20000270 | pV4D420-rep2 | pV4D420-rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000270 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040590 | DRA: DRX649320 | KAS20000269 | pV4D420-rep1 | pV4D420-rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000269 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040580 | DRA: DRX649319 | KAS20000268 | pCHMA150-rep2 | pCHMA150-rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000268 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040570 | DRA: DRX649318 | KAS20000267 | pCHMA150-rep1 | pCHMA150-rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000267 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040560 | DRA: DRX649317 | KAS20000266 | pCHMA20-rep2 | pCHMA20-rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000266 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040550 | DRA: DRX649316 | KAS20000265 | pCHMA20-rep1 | pCHMA20-rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000265 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from mESCs using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, mESCs cultured in 6-well plates were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 2 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 10 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040540 | DRA: DRX649315 | KAS20000264 | T47D_TCPS_Deep_rep2 | T47D_TCPS_Deep_rep2_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000264 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040530 | DRA: DRX649314 | KAS20000263 | T47D_TCPS_Deep_rep1 | T47D_TCPS_Deep_rep1_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000263 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040520 | DRA: DRX649313 | KAS20000262 | T47D_V4D4_Deep_rep2 | T47D_V4D4_Deep_rep2_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000262 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040510 | DRA: DRX649312 | KAS20000261 | T47D_V4D4_Deep_rep1 | T47D_V4D4_Deep_rep1_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000261 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040500 | DRA: DRX649311 | KAS20000260 | T47D_TCPS_rep2 | T47D_TCPS_rep2_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000260 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040490 | DRA: DRX649310 | KAS20000259 | T47D_TCPS_rep1 | T47D_TCPS_rep1_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000259 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040480 | DRA: DRX649309 | KAS20000258 | T47D_V4D4_rep2 | T47D_V4D4_rep2_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000258 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040470 | DRA: DRX649308 | KAS20000257 | T47D_V4D4_rep1 | T47D_V4D4_rep1_GENOMIC | Illumina HiSeq 4000 paired Sequencing of KAS20000257 | RAD-Seq | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 4000 | In-situ Hi-C was performed as previously described Rao et al., 2014. Briefly: T47D cells were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI R0147, NEB; 5??ends were filled by incorporation of biotinylated-dCTP 19524-016, Life Technologies; proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads 65601, Life Technologies; and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040240 | DRA: DRX649291 | KAS20000288 | ZR7530_rep2 | ZR7530_rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000288 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040230 | DRA: DRX649290 | KAS20000286 | T47D_rep2 | T47D_rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000286 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040220 | DRA: DRX649289 | KAS20000284 | HMEC_rep2 | HMEC_rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000284 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040210 | DRA: DRX649288 | KAS20000280 | HCC70_rep2 | HCC70_rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000280 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040200 | DRA: DRX649287 | KAS20000282 | HCC1954_rep2 | HCC1954_rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000282 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040190 | DRA: DRX649286 | KAS20000278 | BT549_rep2 | BT549_rep2_TRANSCRIPTOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000278 | RNA-Seq | TRANSCRIPTOMIC | PolyA | single | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040180 | DRA: DRX649285 | KAS20000288 | ZR7530_rep2 | ZR7530_rep2_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000288 | ChIA-PET | GENOMIC | other | single | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040170 | DRA: DRX649284 | KAS20000286 | T47D_rep2 | T47D_rep2_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000286 | ChIA-PET | GENOMIC | other | single | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040160 | DRA: DRX649283 | KAS20000284 | HMEC_rep2 | HMEC_rep2_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000284 | ChIA-PET | GENOMIC | other | single | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040150 | DRA: DRX649282 | KAS20000280 | HCC70_rep2 | HCC70_rep2_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000280 | ChIA-PET | GENOMIC | other | single | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040140 | DRA: DRX649281 | KAS20000282 | HCC1954_rep2 | HCC1954_rep2_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000282 | ChIA-PET | GENOMIC | other | single | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040130 | DRA: DRX649280 | KAS20000278 | BT549_rep2 | BT549_rep2_GENOMIC | Illumina HiSeq 2500 single Sequencing of KAS20000278 | ChIA-PET | GENOMIC | other | single | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040120 | DRA: DRX649279 | KAS20000287 | ZR7530_rep1 | ZR7530_rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000287 | RNA-Seq | TRANSCRIPTOMIC | PolyA | paired | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040110 | DRA: DRX649278 | KAS20000285 | T47D_rep1 | T47D_rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000285 | RNA-Seq | TRANSCRIPTOMIC | PolyA | paired | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040100 | DRA: DRX649277 | KAS20000283 | HMEC_rep1 | HMEC_rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000283 | RNA-Seq | TRANSCRIPTOMIC | PolyA | paired | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040090 | DRA: DRX649276 | KAS20000279 | HCC70_rep1 | HCC70_rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000279 | RNA-Seq | TRANSCRIPTOMIC | PolyA | paired | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040080 | DRA: DRX649275 | KAS20000281 | HCC1954_rep1 | HCC1954_rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000281 | RNA-Seq | TRANSCRIPTOMIC | PolyA | paired | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040070 | DRA: DRX649274 | KAS20000277 | BT549_rep1 | BT549_rep1_TRANSCRIPTOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000277 | RNA-Seq | TRANSCRIPTOMIC | PolyA | paired | ILLUMINA | Illumina HiSeq 2500 | Total RNAs were purified from BT549 using the TRIzol reagent Invitrogen according to the manufactureru0026's protocol. Briefly, BT549 cultured in 100mm cultured dishonly 500,000 cells were used were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform 200 microliter/sample was added, and the samples were mixed vigorously by hand for 15 sec and incubated at 25degree Celsius for 3 min. The mixtures were centrifuged at 12,000 rpm for 15 min at 4degree Celsius, and 500 microliter of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25degree Celsius for 15 min to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 min at 4degree Celsius, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 min at 4degree Celsius. The RNA pellets were dried and dissolved in RNase-free water. For mRNA-seq library preparation, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit E7490, NEB, and libraries were prepared using a NEXTflex apid directional RNA-seq kit E7760, NEB. The libraries were sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates. | 2021-03-22 | 2021-03-22 | |||
| KAE21040060 | DRA: DRX649273 | KAS20000287 | ZR7530_rep1 | ZR7530_rep1_GENOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000287 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040050 | DRA: DRX649272 | KAS20000285 | T47D_rep1 | T47D_rep1_GENOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000285 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040040 | DRA: DRX649271 | KAS20000283 | HMEC_rep1 | HMEC_rep1_GENOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000283 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040030 | DRA: DRX649270 | KAS20000279 | HCC70_rep1 | HCC70_rep1_GENOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000279 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040020 | DRA: DRX649269 | KAS20000281 | HCC1954_rep1 | HCC1954_rep1_GENOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000281 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 | |||
| KAE21040010 | DRA: DRX649268 | KAS20000277 | BT549_rep1 | BT549_rep1_GENOMIC | Illumina HiSeq 2500 paired Sequencing of KAS20000277 | ChIA-PET | GENOMIC | other | paired | ILLUMINA | Illumina HiSeq 2500 | Total 50,000 BT549 cells were washed two times with 50ul cold PBS, and resuspended with 50ul cold lysis buffer10 mM Tris-Cl, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40. After centrifugation at 2,000 rpm for 10 min at 4?? nuclei were incubated in fresh 25ul TD Buffer 10mM Tris-HCl pH8.0, 5mM MgCl2, 10% dimethylformamide with 2.5ul Tn5 Transposase and 23ul DW at 37degree Celsius for 30min. QIAquick PCR purification kitQiagen; cat. no. 28106 was used to purify DNA fragments. We used HiFi HotStart ReadyMix KAPA; KK2601 for library amplification following provided manual except number of PCR cycle: we performed 15 cycle for PCR amplification. The amplified library was purified with a QIAquick PCR purification kit Qiagen; cat. no. 28106 and sequenced using a Hiseq2500 system50bp with the paired method. | 2021-03-22 | 2021-03-22 |