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Run
KAR21103150
Experiment Title
Illumina HiSeq 2500 single Sequencing of KAS21009679 (PRJDB19217)

Common Fields
Common Fields - BioProject, Data Type, Submission date, Access, Release date, Runs
Experiment
Accession KAE21103150
library name HCC70_rep1-002_GENOMIC
platform ILLUMINA
strategy MNase-Seq
source GENOMIC
selection Restriction Digest
layout single
BioSample
Accession KAS21009679
Sample name HCC70_rep1
Organism Homo sapiens
BioProject
Accession KAP200004
Project title Discovery of 3D-nucleome biomarker in liver/breast cancer patients

Run Metadata
Primary
(1 cases)
Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
file type
location
file name
bytes
total sequences (bp)
sequence lengh (bp) Release date Access type
fastq KBDS-KRA 1,134,500,846 1,134,500,846 2021-12-03 PUBLIC

library_construction_protocol
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.

Analysis
(0 cases)
Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
analysis type
file type
location
File name
bytes
Release date Access type
No Run data.

Reference
(0 cases)
Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
reference type RefSeq accession ID File name
No Run data.