|
| Status |
Public on Feb 14, 2023 |
| Title |
iPSC_TOB0220 |
| Sample type |
genomic |
| |
|
| Source name |
iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
|
| Treatment protocol |
NA
|
| Growth protocol |
1mL aliquots of each of the iPSC line were thawed and plated in StemFlex media (Life Technologies; Catalog Number: A3349401; Lot Number: 2093181) complete with StemFlex Supplement (Life Technologies, Catalog Number: A33492-01; Lot Number: 2090179) with Rock inhibitor Y-27632 (10µM final concentration; Stem Cell Technologies; Catalog Number: 72304) on Costar non-treated 6 well polystyrene plates (Catalog Number: 3736; Lot Number: 30417038) coated with Vitronectin XF (Stem Cell Technologies; Catalog Number: 07180; Lot Number: 18B87584) diluted in CellAdhere Buffer (Stem Cell Technologies, Catalog Number: 07183; Lot Number: 18M979058). Cells were subcultured once a week with ReLeSR (Stem Cell Technologies; Catalog Number: 05872) until sample collection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with the QIAGEN DNeasy Blood & Tissue Kit
|
| Label |
biotin
|
| Label protocol |
NA
|
| |
|
| Hybridization protocol |
NA
|
| Scan protocol |
NA
|
| Data processing |
SNPs were filtered for low-quality SNPs in Axiom Suite. Genotyped SNPs were then imputed using hg38 1000G v3 using an in-house pipeline described and available on github: https://github.com/powellgenomicslab/SNP_imputation_1000g_hg38/wiki/SNP-Genotype-Imputation-Using-1000G-hg38-Reference.
Processed data is provided in two vcf files - one that contains the iPSC lines in the 18-line village (18 of the samples) and one that contains iPSC lines from the 3-line village (3 samples)
|
| |
|
| Submission date |
Feb 09, 2023 |
| Last update date |
Feb 15, 2023 |
| Contact name |
Drew Neavin |
| E-mail(s) |
d.neavin@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Cellular Science
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
New South Wales |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL33111 |
| Series (2) |
| GSE224950 |
Village In a Dish: A Model System for Population-scale hiPSC Studies [Affymetrix] |
| GSE225282 |
Village In a Dish: A Model System for Population-scale hiPSC Studies |
|
