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| Status |
Public on Jul 08, 2014 |
| Title |
Sample16_iPSS4 |
| Sample type |
genomic |
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| Source name |
induced Pluripotent Stem Cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Pluripotent Stem Cell
cell line: Sendai-Virus Derived
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| Treatment protocol |
Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Genetically matched iPSCs were generated by transductions of the same HDF culture with retroviral or Sendai virus vectors carrying OCT4, SOX2, KLF4, and MYC. Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)).
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| Growth protocol |
Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Cells were transduced by retro virus-based iPSC vectors as previously reported (Lowry, W. E. et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proceedings of the National Academy of Sciences of the United States of America 105, 2883-2888, doi:10.1073/pnas.0711983105 (2008)). Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)).
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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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| 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.). CNVs were identified using the cnvPartition Plug-in v 3.2.0 in GenomeStudio (Illumina, Inc.). The cnvPartition confidence threshold was set at 100, with a minimum number of SNPs per CNV region of 10. All CNVs were visually verified by assessing both the B-allele-frequency and Log R ratios.
Name is the SNP ID, Chr (Chromosome), Position (location on Chr), Genotype: AA,AB,BB,or NC (No Call), Score, Thera, R, B Allele, Log R Ratio
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| Submission date |
May 02, 2014 |
| Last update date |
Jul 08, 2014 |
| Contact name |
Robert E Morey |
| E-mail(s) |
robmoreyucsd@gmail.com, remorey@health.ucsd.edu
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| Organization name |
UCSD
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| Department |
Pathology
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| Lab |
Parast
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| Street address |
2880 Torrey Pines Scenic Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL14157 |
| Series (2) |
| GSE53096 |
Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms |
| GSE53141 |
Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [SNP array] |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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