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Array-based functional genomics data
KSE102929
Title
Genomics data from diabetic serum

Study
Study Fields - Title, Summary, Experimental design, Experimental type, Organism, Source name, Contributor(s) Citation, Submission type
Title
Genomics data from diabetic serum
Summary
For this study, we analyzed genomic variation profiles from 330 individuals, including patients with diabetes and healthy controls. DNA was extracted from each sample and hybridized on high-density genomic microarrays to detect single nucleotide polymorphisms (SNPs). To ensure accurate comparisons, individuals were carefully categorized into diabetes and control groups based on clinical criteria, allowing for a comprehensive analysis of genomic differences associated with diabetes.
Experimental design
case control design
Experimental type
comparative genomic hybridization by array
Organism
Human
Source name
human_serum_Diabetes , human_serum_Normal
Contributor(s)
-
Submission type
Complete

Protocols
Protocols - Accession, Type, Description
Accession
Type
Description
KSP10028400 Nucleic acid labeling protocol
Labelled DNA were prepared according to the standard Affymetrix protocol.
KSP10028401 Nucleic acid hybridization to array protocol
DNA were hybridized for 24 hr. Arrays were processed in the GeneTitan.
KSP10028402 Array scanning and feature extraction protocol
Arrays were scanned using the GeneTitan scanner using Standard Affymetrix procedures.
KSP10028398 Sample collection protocol
missing
KSP10028399 Nucleic acid extraction protocol
DNA were extracted using Dneasy Blood&Tissue kit according to the manufacturer's instruction.
KSP10028403 Normalization data transformation protocol
The Best Practices Genotyping Analysis Workflow begins by grouping samples into batches, followed by generating Dish QC (DQC) values. Samples with DQC values greater than 0.82 are selected for quality control (QC). DQC is a QC metric that evaluates the overlap between the two homozygous peaks (AT and GC) in contrast space using normalized intensities from control non-polymorphic probes. Samples with DQC values below the threshold are excluded from further analysis. Next, sample QC call rates are generated using AxiomGT1.Step1, and samples are filtered based on a QC SNP set, retaining only those with a QC call rate of 88% or higher. Plate QC is then performed to ensure that the average plate call rate is at least 97%, with a plate pass rate of ≥95% for tissue, blood, or cell line samples, and ≥93% for saliva samples. Plates meeting these criteria are considered high-quality. Following this, samples and plates that passed QC are co-clustered and genotyped using the AxiomGT1.Step2 algorithm. Finally, SNP QC is performed by categorizing SNPs into six groups. SNPs that do not fall into the recommended classes for the genome type are excluded from downstream analysis.

Detailed Experiment information
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Showing 1-25 of 330
Validations details list
Accession ID BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file BioSample accession ID Sample name Organism NCBI taxonomy ID sampleGroup Complete Reference data ID type Reference data ID Detailed sample title Source name Molecule Label Description Platform ID Protocols Factor value Raw data file Abundance matrix file Epigenomic analysis file Variant analysis file Others Primary analysis file
KAX10004012 KAS24109511 GD_001 Human 9606 Complete Diabetes_patient GD001 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028401, KSP10028402, KSP10028403 GD_001_5507694400697091521772_A01_Axiom_KORV1_1.CEL Output.vcf
KAX10004013 KAS24109512 GD_002 Human 9606 Complete Diabetes_patient GD002 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028401, KSP10028402, KSP10028403 GD_002_5507694400697091521772_B01_Axiom_KORV1_1.CEL Output.vcf
KAX10004014 KAS24109513 GD_003 Human 9606 Complete Diabetes_patient GD003 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_003_5507694400697091521772_C01_Axiom_KORV1_1.CEL Output.vcf
KAX10004015 KAS24109514 GD_004 Human 9606 Complete Diabetes_patient GD004 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_004_5507694400697091521772_D01_Axiom_KORV1_1.CEL Output.vcf
KAX10004016 KAS24109515 GD_005 Human 9606 Complete Diabetes_patient GD005 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_005_5507694400697091521772_E01_Axiom_KORV1_1.CEL Output.vcf
KAX10004017 KAS24109516 GD_007 Human 9606 Complete Diabetes_patient GD007 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_007_5507694400697091521772_F01_Axiom_KORV1_1.CEL Output.vcf
KAX10004018 KAS24109517 GD_009 Human 9606 Complete Diabetes_patient GD009 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_009_5507694400697091521772_G01_Axiom_KORV1_1.CEL Output.vcf
KAX10004019 KAS24109518 GD_010 Human 9606 Complete Diabetes_patient GD010 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_010_5507694400697091521772_H01_Axiom_KORV1_1.CEL Output.vcf
KAX10004020 KAS24109519 GD_011 Human 9606 Complete Diabetes_patient GD011 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_011_5507694400697091521772_A02_Axiom_KORV1_1.CEL Output.vcf
KAX10004021 KAS24109520 GD_012 Human 9606 Complete Diabetes_patient GD012 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_012_5507694400697091521772_B02_Axiom_KORV1_1.CEL Output.vcf
KAX10004022 KAS24109521 GD_013 Human 9606 Complete Diabetes_patient GD013 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_013_5507694400697091521772_C02_Axiom_KORV1_1.CEL Output.vcf
KAX10004023 KAS24109522 GD_014 Human 9606 Complete Diabetes_patient GD014 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_014_5507694400697091521772_D02_Axiom_KORV1_1.CEL Output.vcf
KAX10004024 KAS24109523 GD_015 Human 9606 Complete Diabetes_patient GD015 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_015_5507694400697091521772_E02_Axiom_KORV1_1.CEL Output.vcf
KAX10004025 KAS24109524 GD_016 Human 9606 Complete Diabetes_patient GD016 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_016_5507694400697091521772_F02_Axiom_KORV1_1.CEL Output.vcf
KAX10004026 KAS24109525 GD_017 Human 9606 Complete Diabetes_patient GD017 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_017_5507694400697091521772_G02_Axiom_KORV1_1.CEL Output.vcf
KAX10004027 KAS24109526 GD_018 Human 9606 Complete Diabetes_patient GD018 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_018_5507694400697091521772_H02_Axiom_KORV1_1.CEL Output.vcf
KAX10004028 KAS24109527 GD_019 Human 9606 Complete Diabetes_patient GD019 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_019_5507694400697091521772_A03_Axiom_KORV1_1.CEL Output.vcf
KAX10004029 KAS24109528 GD_020 Human 9606 Complete Diabetes_patient GD020 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_020_5507694400697091521772_B03_Axiom_KORV1_1.CEL Output.vcf
KAX10004030 KAS24109529 GD_021 Human 9606 Complete Diabetes_patient GD021 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_021_5507694400697091521772_C03_Axiom_KORV1_1.CEL Output.vcf
KAX10004031 KAS24109530 GD_022 Human 9606 Complete Diabetes_patient GD022 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_022_5507694400697091521772_D03_Axiom_KORV1_1.CEL Output.vcf
KAX10004032 KAS24109531 GD_024 Human 9606 Complete Diabetes_patient GD024 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_024_5507694400697091521772_E03_Axiom_KORV1_1.CEL Output.vcf
KAX10004033 KAS24109532 GD_025 Human 9606 Complete Diabetes_patient GD025 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_025_5507694400697091521772_F03_Axiom_KORV1_1.CEL Output.vcf
KAX10004034 KAS24109533 GD_029 Human 9606 Complete Diabetes_patient GD029 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_029_5507694400697091521772_G03_Axiom_KORV1_1.CEL Output.vcf
KAX10004035 KAS24109534 GD_030 Human 9606 Complete Diabetes_patient GD030 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_030_5507694400697091521772_H03_Axiom_KORV1_1.CEL Output.vcf
KAX10004036 KAS24109535 GD_031 Human 9606 Complete Diabetes_patient GD031 human_serum_Diabetes genomic DNA biotin Genomic variation data from blood samples of patients diagnosed with diabetes, used for the comparative analysis of SNP differences. GPL24321 KSP10028399, KSP10028400, KSP10028402, KSP10028403 GD_031_5507694400697091521772_A04_Axiom_KORV1_1.CEL Output.vcf

Accession
Accession - RUNs, BIOSAMPLEs
BioSamples
KAS24109511 , KAS24109512 , KAS24109513 , KAS24109514 , KAS24109515 , KAS24109516 , KAS24109517 , KAS24109518 , KAS24109519 , KAS24109520 , KAS24109521 , KAS24109522 , KAS24109523 , KAS24109524 , KAS24109525 , KAS24109526 , KAS24109527 , KAS24109528
312 more
less
BioProject
KAP241439

Files
KEA file 목록
File Name Sample IDS Size Format File type Release date Download
GD_001_5507694400697091521772_A01_Axiom_KORV1_1.CEL
28,592,810 28,592,810 CEL
Raw data file
2025-02-10
Output.vcf
KAS24109511 KAS24109512
328 more
less
1,037,732,310 1,037,732,310 vcf
Variant analysis file
2025-02-10
GD_002_5507694400697091521772_B01_Axiom_KORV1_1.CEL
28,652,386 28,652,386 CEL
Raw data file
2025-02-10
GD_003_5507694400697091521772_C01_Axiom_KORV1_1.CEL
28,626,798 28,626,798 CEL
Raw data file
2025-02-10
GD_004_5507694400697091521772_D01_Axiom_KORV1_1.CEL
28,635,730 28,635,730 CEL
Raw data file
2025-02-10
GD_005_5507694400697091521772_E01_Axiom_KORV1_1.CEL
28,651,566 28,651,566 CEL
Raw data file
2025-02-10
GD_007_5507694400697091521772_F01_Axiom_KORV1_1.CEL
28,639,690 28,639,690 CEL
Raw data file
2025-02-10
GD_009_5507694400697091521772_G01_Axiom_KORV1_1.CEL
28,626,062 28,626,062 CEL
Raw data file
2025-02-10
GD_010_5507694400697091521772_H01_Axiom_KORV1_1.CEL
28,617,546 28,617,546 CEL
Raw data file
2025-02-10
GD_011_5507694400697091521772_A02_Axiom_KORV1_1.CEL
28,606,646 28,606,646 CEL
Raw data file
2025-02-10
GD_012_5507694400697091521772_B02_Axiom_KORV1_1.CEL
28,621,210 28,621,210 CEL
Raw data file
2025-02-10
GD_013_5507694400697091521772_C02_Axiom_KORV1_1.CEL
28,620,046 28,620,046 CEL
Raw data file
2025-02-10
GD_014_5507694400697091521772_D02_Axiom_KORV1_1.CEL
28,624,094 28,624,094 CEL
Raw data file
2025-02-10
GD_015_5507694400697091521772_E02_Axiom_KORV1_1.CEL
28,645,166 28,645,166 CEL
Raw data file
2025-02-10
GD_016_5507694400697091521772_F02_Axiom_KORV1_1.CEL
28,610,906 28,610,906 CEL
Raw data file
2025-02-10
GD_017_5507694400697091521772_G02_Axiom_KORV1_1.CEL
28,631,638 28,631,638 CEL
Raw data file
2025-02-10
GD_018_5507694400697091521772_H02_Axiom_KORV1_1.CEL
28,620,214 28,620,214 CEL
Raw data file
2025-02-10
GD_019_5507694400697091521772_A03_Axiom_KORV1_1.CEL
28,606,430 28,606,430 CEL
Raw data file
2025-02-10
GD_020_5507694400697091521772_B03_Axiom_KORV1_1.CEL
28,616,806 28,616,806 CEL
Raw data file
2025-02-10
GD_021_5507694400697091521772_C03_Axiom_KORV1_1.CEL
28,620,834 28,620,834 CEL
Raw data file
2025-02-10
GD_022_5507694400697091521772_D03_Axiom_KORV1_1.CEL
28,631,318 28,631,318 CEL
Raw data file
2025-02-10
GD_024_5507694400697091521772_E03_Axiom_KORV1_1.CEL
28,607,006 28,607,006 CEL
Raw data file
2025-02-10
GD_025_5507694400697091521772_F03_Axiom_KORV1_1.CEL
28,609,954 28,609,954 CEL
Raw data file
2025-02-10
GD_029_5507694400697091521772_G03_Axiom_KORV1_1.CEL
28,662,082 28,662,082 CEL
Raw data file
2025-02-10
GD_030_5507694400697091521772_H03_Axiom_KORV1_1.CEL
28,642,758 28,642,758 CEL
Raw data file
2025-02-10