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Series GSE170763 Query DataSets for GSE170763
Status Public on Feb 07, 2023
Title Whole-genome genotyping of human islets using Illumina infinium chips
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Genomic DNA was extracted from human islets using Dneasy Blood & Tissue Kit (QIAGEN) with RNase A treatment. 200-500ng DNA was genotyped using InfiniumOmni2-5-8v Genotyping BeadChips (Illumina).DNA was isolated from human islet cells from various donors. DNA was genotyped using Illumina Infinium whole-genome genotyping array. Genotypes were called with GenomeStudio (v.2.0.4) using default settings. Genotypes that passed quality filters (missing<0.05, minor allele frequency (MAF>0.01), non-ambiguous alleles defined by AT/GC variants with MAF>40%) were exported.
 
Overall design Whole-genome genotyping of human islets from non-diabetic (n=12), pre-diabetic (n=9) and type 2 diabetes (n=15) individuals.
 
Contributor(s) Sander M
Citation(s) 36711922, 37231096
Submission date Mar 27, 2021
Last update date Oct 18, 2023
Contact name Maike Sander
E-mail(s) masander@ucsd.edu
Organization name UC San Diego
Street address 2880 Torrey Pines Scenic Dr.
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL16104 Illumina HumanOmni2.5-8 BeadChip
Samples (36)
GSM5215384 SAMP-1613: Pre-T2D
GSM5215385 SAMP-1134: Non-diabetic
GSM5215386 SAMP-1144: T2D
This SubSeries is part of SuperSeries:
GSE171153 Integration of human genetics with single cell accessible chromatin profiles across phenotypes identifies islet cell type-specific regulatory programs of type 2 diabetes progression
Relations
BioProject PRJNA717969

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE170763_RAW.tar 1.2 Gb (http)(custom) TAR (of IDAT)
GSE170763_plink_files.tar.gz 33.9 Mb (ftp)(http) TAR
Processed data are available on Series record

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