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Sample GSM718702 Query DataSets for GSM718702
Status Public on May 03, 2011
Title ESC Rep 1
Sample type RNA
 
Source name mES cells Sox1-GFP
Organism Mus musculus
Characteristics treatment: untreated
cell line: 46C mES cells Sox1-GFP
differentiation state: Pluripotent
Treatment protocol ESC: N2B27 media containing LIF and BMP without serum as described previously (Ying and Smith, 2003; Ying et al., 2008). ES cell media was supplemented with the FGF receptor inhibitor PD173074 (Sigma, StemGent) at 100 nM. 48 hr: ES cells were trypsinized, washed, and replated into N2B27 only media for 48 hours.
Growth protocol Mouse embryonic stem cells were maintained and passaged on gelatin coated plates without feeder cells in N2B27 media containing LIF and BMP without serum as described previously (Ying and Smith, 2003; Ying et al., 2008). ES cell media was supplemented with the FGF receptor inhibitor PD173074 (Sigma, StemGent) at 100 nM to suppress background differentiation. Similar results were obtained using the MEK inhibitor PD0325901 (Sigma, StemGent) at 1 µM. Cells were routinely propagated by trypsinization and re-plating every two to three days, with a split ratio of 1 in 10. N2B27 was prepared with B27 without vitamin A.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol, phenol:chloroform extraction, and isopropanol precipitation.
Label Biotin
Label protocol Biotinylated and amplified cRNA was prepared by the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion).
 
Hybridization protocol Biotinylated cRNA was hybridized onto Illumina Mouse-Ref8 BeadChip microarrays, according to the manufacturer’s protocol.
Scan protocol Microarrays were analyzed by an Illumina BeadArray Reader
Data processing raw data were normalized in BeadStudio
 
Submission date May 02, 2011
Last update date May 03, 2011
Contact name Matt Thomson
E-mail(s) thomson@post.harvard.edu
Organization name Harvard University
Department MCB
Lab Ramanathan
Street address 52 Oxford Street 368
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL6885
Series (1)
GSE29005 Gene expression microarray for mouse ES cells vs. mouse ES cells treated with 48 hr N2B27

Data table header descriptions
ID_REF
VALUE quantile normalized
1ESC.Detection Pval

Data table
ID_REF VALUE 1ESC.Detection Pval
ILMN_1248788 60.74062 0.3245614
ILMN_2707227 63.98435 0.131579
ILMN_2896528 1126.313 0
ILMN_2721178 295.8877 0
ILMN_1227723 221.7089 0
ILMN_3033922 183.3866 0
ILMN_3092673 588.9035 0
ILMN_2730714 1266.016 0
ILMN_3162224 951.5677 0
ILMN_2816356 67.08845 0.03634085
ILMN_2808939 409.445 0
ILMN_2634564 236.3165 0
ILMN_1216623 276.6968 0
ILMN_1215157 424.7549 0
ILMN_1228777 57.12928 0.6278195
ILMN_2737647 58.70397 0.4912281
ILMN_1216425 62.78908 0.1967418
ILMN_2734484 237.6221 0
ILMN_2652961 61.07458 0.3082707
ILMN_2952292 92.95985 0

Total number of rows: 25697

Table truncated, full table size 727 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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