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| Status |
Public on Mar 29, 2015 |
| Title |
HDF51iPS7_ECMENZ_P25 |
| Sample type |
genomic |
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| Source name |
induced Pluripotent Stem Cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: induced Pluripotent Stem Cell
cell line: HDF51iPS7
passage number: P25
condition: enzymatic passaging,
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| Treatment protocol |
HDF51iPS1, HDF51iPS7, and HDF51iPS11 cells were cultured at 37ºC and 5% CO2 on extracellular matrix (GeltrexTM ; Life Technologies) or irradiated mouse embryonic fibroblasts (MEFs). Cells on feeder layers were cultured in standard hPSC medium, consisting of DMEM/F12 with 20% Knockout Serum Replacement, 1 mM GlutaMAXTM, 0.1 mM non-essential amino acids (NEAA), and 12 ng/ml basic FGF (all from Life Technologies) and passaged mechanically enzymatically dissociated (MefEnz) with Accutase® (Life Technologies). Cells cultured on Geltrex in StemPro® hESC SFM (Life Technologies) with 0.1 mM β-mercaptoethanol and 12 ng/ml basic FGF, were passaged mechanically (EcmMech) or enzymatically (EcmEnz) with Accutase.
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| Growth protocol |
The HDF51iPS1, HDF51iPS7, and HDF51iPS11 lines were three independent hiPSC clones reprogrammed from human fetal dermal fibroblasts using the standard reprogramming factors (OCT4/POU5F1, SOX2, KLF4, and MYC) carried by retroviral vectors.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
All DNA was isolated (QIAGEN Gentra Puregene Cell Kit) except the sperm sample (PicoPure DNA Extraction Kit, Life Technologies, Inc.), and quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) according to the manufacturer’s protocol.
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| Label |
C-Bio and A-DNP
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| Label protocol |
Standard Illumina Protocol
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| Hybridization protocol |
Standard Illumina Protocol
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| Scan protocol |
Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting
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| Description |
Retro-Virus Derived
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| Data processing |
Genotyping calls were made with GenomeStudio (Illumina, Inc.) via the cluster files provided by the manufacturer. The GenCall (v. 6.3.0) threshold was set to 0.15, and the call rates were greater than 0.998. Reproducibility and heritability were calculated in GenomeStudio (Illumina, Inc.).
Header definitions of Series supplementary files: Name is the SNP ID, Chr (Chromosome), Position (location on Chr), Genotype: AA,AB,BB,or NC (No Call), Score, Theta, R, B Allele, Log R Ratio
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| Submission date |
Apr 16, 2014 |
| Last update date |
Mar 29, 2015 |
| Contact name |
Francesca Boscolo |
| E-mail(s) |
francesca.boscolo@gmail.com
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| Organization name |
UCSD
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| Department |
Reproductive Medicine
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| Lab |
Marianna Alperin
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
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| Platform ID |
GPL14157 |
| Series (2) |
| GSE56834 |
Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions II |
| GSE56851 |
Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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