GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM874651 Query DataSets for GSM874651
Status Public on May 30, 2012
Title V6.5 ESC Utx KO
Sample type RNA
Source name V6.5 ESC Utx -/Y
Organism Mus musculus
Characteristics cell type: Mouse Embryonic Stem Cell (ESC)
genotype/variation: UTX-/Y (KO)
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 Feb 13, 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 8.448315
10344622 7.28248
10344624 11.33918
10344633 10.58318
10344637 9.241122
10344658 7.425567
10344707 8.646092
10344713 11.47457
10344723 8.639774
10344725 7.774065
10344741 10.4834
10344750 6.205554
10344789 8.741244
10344797 7.791883
10344799 9.298201
10344801 9.07511
10344803 8.596759
10344805 8.436608
10344807 8.809686
10344809 8.456645

Total number of rows: 21811

Table truncated, full table size 381 Kbytes.

Supplementary file Size Download File type/resource
GSM874651.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap