|
| Status |
Public on Jul 08, 2014 |
| Title |
Sample6_hESO8 |
| Sample type |
genomic |
| |
|
| Source name |
Human Embryonic Stem Cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Pluripotent Stem Cell
cell line: IVF Derived
|
| 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.
|
| 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)).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated (QIAGEN Gentra Puregene Cell Kit), quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) and bisulfite converted (EZDNA Methylation Kit, Zymo Research) according to the manufacturer’s protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting
|
| Description |
8769527127_R06C01
|
| Data processing |
We performed preprocessing and normalization utilizing the statistical programming language R (http://www.r-project.org/) (version 3.0.1) and the R package minfi (v.1.6.0). Briefly, IDATs files were control normalized and probes with detection p-values > 0.01 in at least one sample were discarded. The samples were then normalized using the SWAN normalization option in the minfi package and M-values were exported. The R script, ComBat was used to eliminate batch effects.
|
| |
|
| Submission date |
Dec 06, 2013 |
| Last update date |
Jul 08, 2014 |
| Contact name |
Robert E Morey |
| E-mail(s) |
robmoreyucsd@gmail.com, remorey@health.ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Pathology
|
| Lab |
Parast
|
| Street address |
2880 Torrey Pines Scenic Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE53060 |
Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [methylation array] |
| GSE53096 |
Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms |
|
