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Sample GSM568485 Query DataSets for GSM568485
Status Public on Apr 17, 2011
Title Hepatocyte-iPS, Rep 2
Sample type RNA
 
Source name Hepatocyte-derived iPS cell
Organism Homo sapiens
Characteristics cell type: hepatocyte-derived iPS cell
passage: 6
Treatment protocol iPS cells were generated by overexpressing the human transcription factors OCT4, SOX2, C-MYC, KLF4, and NANOG using a doxycycline-inducible lentivirus transgene system that has been previously documented to faithfully reprogram both human fibroblasts and keratinocytes to an hESC-like state (Maherali et al, 2008; Hockemeyer et al., 2008).
Growth protocol The hepatocytes were obtained from Lonza (reference #: CC-2703W6). The newborn foreskin (BJ) fibroblasts were obtained from ATCC (reference #: CRL-2522). The melanocytes were obtained from Promocell (reference #: C-12402).

Somatic cells were grown in 425 mls High-glucose DMEM, 50 mls Atlanta FBS (10%), 5 mls L-glutamine, 10 mls Penicillin/Streptomycin, 5 mls Non-essential amino acids, 5 mls Sodium pyruvate, and 2 μl Beta-mercaptoethanol. ES and iPS cells were grown in a hES-KSR Basal Medium of 382.5 mls DMEM/F12 containing Hepes, 100 mls Knockout Serum ment (KSR), 2.5 mls L-glutamine, 5 mls Non-essential amino acids, 10 mls Penicillin/Streptomycin, and 3.5 μl Beta-mercaptoethanol.
Extracted molecule total RNA
Extraction protocol RNeasy Mini RNA isolation kit (Qiagen).
Label biotin
Label protocol Biotinylated cRNA were prepared using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay.
 
Hybridization protocol Hybridization was performed according to the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay Manual.
Scan protocol Arrays were scanned with GCS3000 using the standard procedures recommended by Affymetrix.
Description Expression profile of human hepatocyte-derived iPS cell (passage number 6).
Data processing The data were normalized using RMA in R 2.10.1 and a CDF file that maps the Affymetrix probes to RefSeq genes.
 
Submission date Jul 20, 2010
Last update date Apr 17, 2011
Contact name Jun S Song
Organization name UCSF
Department Institute for Human Genetics
Street address 513 Parnassus Avenue, Box 0794
City San Francisco
State/province CA
ZIP/Postal code 94143-0794
Country USA
 
Platform ID GPL10666
Series (1)
GSE23034 Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

Data table header descriptions
ID_REF
VALUE RMA normalized RefSeq expression index

Data table
ID_REF VALUE
NM_000014_at 5.314
NM_000015_at 4.043
NM_000016_at 10.85
NM_000017_at 6.646
NM_000018_at 9.088
NM_000019_at 8.823
NM_000020_at 6.065
NM_000021_at 9.803
NM_000022_at 8.008
NM_000023_at 6.326
NM_000024_at 5.965
NM_000025_at 5.269
NM_000026_at 9.785
NM_000027_at 7.581
NM_000028_at 9.728
NM_000029_at 5.175
NM_000030_at 6.069
NM_000031_at 6.768
NM_000032_at 5.884
NM_000033_at 6.395

Total number of rows: 28312

Table truncated, full table size 544 Kbytes.




Supplementary file Size Download File type/resource
GSM568485.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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