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Sample GSM938430 Query DataSets for GSM938430
Status Public on May 30, 2012
Title OSKM_MEF_Nanog_KO
Sample type RNA
Source name OSKM_MEF_Nanog_KO
Organism Mus musculus
Characteristics cell type: Mouse Embryonic Fibroblast Cells (MEF) generated from Nanog-/- ESCs (Mitsui et al. Cell 2003)
genotype/variation: transduced with OSKM lentivirus for 8 days
Treatment protocol Cells were washed with PBS and then harvested by trypsinization for RNA extraction
Growth protocol N2B27 2i/LIF mouse ESC media
Extracted molecule total RNA
Extraction protocol mRNA was extracted byTRIZOL reagent (invitogene) according to manufacturer's instructions
Label Biotin
Label protocol 250 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
Hybridization protocol Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Scan protocol Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
Description Gene expression data of the indicated cell line
Data processing The data were analyzed with Affy Expression Console software, using RMA method. Probes were further filtered to include only probes that have at least one call > 6 (in log2-scale)
Submission date May 29, 2012
Last update date May 30, 2012
Contact name Noa Novershtern
Organization name Weizmann Institute of Science
Department Molecular Genetics
Street address Weizmann Institute
City Rehovot
ZIP/Postal code 7610001
Country Israel
Platform ID GPL6246
Series (2)
GSE35775 The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency [Affymetrix gene expression]
GSE37822 The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency

Data table header descriptions
VALUE Log 2 signal intensity, after RMA normalization

Data table
10344614 7.583449
10344622 7.993355
10344624 10.53841
10344633 10.96952
10344637 9.197466
10344658 8.442436
10344707 9.430798
10344713 11.51429
10344723 7.088974
10344725 7.458991
10344741 9.948124
10344750 8.188953
10344789 7.926525
10344797 8.926434
10344799 8.63818
10344801 8.278915
10344803 7.712641
10344805 7.485467
10344807 7.712313
10344809 7.43886

Total number of rows: 21811

Table truncated, full table size 380 Kbytes.

Supplementary file Size Download File type/resource
GSM938430_OSKM_MEF_Nanog_KO.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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