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Sample GSM874650 Query DataSets for GSM874650
Status Public on May 30, 2012
Title V6.5 ESC Utx WT
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 (WT)
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 Feb 09, 2015
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
Reanalyzed by GSM1606116

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

Data table
10344614 7.248991
10344622 7.332388
10344624 11.1387
10344633 10.47208
10344637 9.164618
10344658 7.535557
10344707 8.647099
10344713 11.38959
10344723 8.067898
10344725 7.336524
10344741 10.17429
10344750 6.873222
10344789 8.685166
10344797 7.659029
10344799 9.435943
10344801 9.098541
10344803 8.592794
10344805 8.325826
10344807 8.760727
10344809 8.41824

Total number of rows: 21811

Table truncated, full table size 381 Kbytes.

Supplementary file Size Download File type/resource
GSM874650.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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