Array-based functional genomics data
KSE102929
Title
Genomics data from diabetic serum
Study
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Title
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Genomics data from diabetic serum |
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Summary
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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.
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Experimental design
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case control design
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Experimental type
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comparative genomic hybridization by array
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Organism
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Human |
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Source name
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human_serum_Diabetes , human_serum_Normal |
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Contributor(s)
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- |
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Submission type
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Complete |
Protocols
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Accession
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Type
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Description
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| KSP10028400 | Nucleic acid labeling protocol |
Labelled DNA were prepared according to the standard Affymetrix protocol.
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| KSP10028401 | Nucleic acid hybridization to array protocol |
DNA were hybridized for 24 hr. Arrays were processed in the GeneTitan.
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| KSP10028402 | Array scanning and feature extraction protocol |
Arrays were scanned using the GeneTitan scanner using Standard Affymetrix procedures.
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| KSP10028398 | Sample collection protocol |
missing
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| KSP10028399 | Nucleic acid extraction protocol |
DNA were extracted using Dneasy Blood&Tissue kit according to the manufacturer's instruction.
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| 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.
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Detailed Experiment information
Toggle table
Accession
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BioSamples
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BioProject
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KAP241439 |
| File Name | Sample IDS | Size | Format | File type | Release date | Download | |
|---|---|---|---|---|---|---|---|
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GD_001_5507694400697091521772_A01_Axiom_KORV1_1.CEL
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28,592,810 28,592,810 | CEL |
Raw data file
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2025-02-10 | |||
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Output.vcf
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1,037,732,310 1,037,732,310 | vcf |
Variant analysis file
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2025-02-10 | |||
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GD_002_5507694400697091521772_B01_Axiom_KORV1_1.CEL
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28,652,386 28,652,386 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_003_5507694400697091521772_C01_Axiom_KORV1_1.CEL
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28,626,798 28,626,798 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_004_5507694400697091521772_D01_Axiom_KORV1_1.CEL
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28,635,730 28,635,730 | CEL |
Raw data file
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2025-02-10 | |||
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GD_005_5507694400697091521772_E01_Axiom_KORV1_1.CEL
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28,651,566 28,651,566 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_007_5507694400697091521772_F01_Axiom_KORV1_1.CEL
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28,639,690 28,639,690 | CEL |
Raw data file
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2025-02-10 | |||
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GD_009_5507694400697091521772_G01_Axiom_KORV1_1.CEL
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28,626,062 28,626,062 | CEL |
Raw data file
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2025-02-10 | |||
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GD_010_5507694400697091521772_H01_Axiom_KORV1_1.CEL
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28,617,546 28,617,546 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_011_5507694400697091521772_A02_Axiom_KORV1_1.CEL
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28,606,646 28,606,646 | CEL |
Raw data file
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2025-02-10 | |||
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GD_012_5507694400697091521772_B02_Axiom_KORV1_1.CEL
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28,621,210 28,621,210 | CEL |
Raw data file
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2025-02-10 | |||
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GD_013_5507694400697091521772_C02_Axiom_KORV1_1.CEL
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28,620,046 28,620,046 | CEL |
Raw data file
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2025-02-10 | |||
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GD_014_5507694400697091521772_D02_Axiom_KORV1_1.CEL
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28,624,094 28,624,094 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_015_5507694400697091521772_E02_Axiom_KORV1_1.CEL
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28,645,166 28,645,166 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_016_5507694400697091521772_F02_Axiom_KORV1_1.CEL
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28,610,906 28,610,906 | CEL |
Raw data file
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2025-02-10 | |||
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GD_017_5507694400697091521772_G02_Axiom_KORV1_1.CEL
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28,631,638 28,631,638 | CEL |
Raw data file
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2025-02-10 | |||
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GD_018_5507694400697091521772_H02_Axiom_KORV1_1.CEL
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28,620,214 28,620,214 | CEL |
Raw data file
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2025-02-10 | |||
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GD_019_5507694400697091521772_A03_Axiom_KORV1_1.CEL
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28,606,430 28,606,430 | CEL |
Raw data file
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2025-02-10 | |||
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GD_020_5507694400697091521772_B03_Axiom_KORV1_1.CEL
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28,616,806 28,616,806 | CEL |
Raw data file
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2025-02-10 | |||
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GD_021_5507694400697091521772_C03_Axiom_KORV1_1.CEL
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28,620,834 28,620,834 | CEL |
Raw data file
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2025-02-10 | |||
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GD_022_5507694400697091521772_D03_Axiom_KORV1_1.CEL
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28,631,318 28,631,318 | CEL |
Raw data file
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2025-02-10 | |||
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GD_024_5507694400697091521772_E03_Axiom_KORV1_1.CEL
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28,607,006 28,607,006 | CEL |
Raw data file
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2025-02-10 | |||
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GD_025_5507694400697091521772_F03_Axiom_KORV1_1.CEL
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28,609,954 28,609,954 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_029_5507694400697091521772_G03_Axiom_KORV1_1.CEL
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28,662,082 28,662,082 | CEL |
Raw data file
|
2025-02-10 | |||
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GD_030_5507694400697091521772_H03_Axiom_KORV1_1.CEL
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28,642,758 28,642,758 | CEL |
Raw data file
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2025-02-10 |