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Sample GSM456586 Query DataSets for GSM456586
Status Public on Nov 04, 2009
Title MEF rep2
Sample type RNA
 
Source name Mouse embryonic fibroblasts (MEFs)
Organism Mus musculus
Characteristics cell type: Embryonic Fibroblast Cells
Treatment protocol Cells were treated with small molecules as described in Ichida et al. (Cell Stem Cell, 2009).
Growth protocol Cells were grown in a monolayer on gelatin-coated plates, either with or without an irradiated mouse embryonic fibroblast (MEF) feeder layer. They were given standard mES media containing either fetal bovine serum (FBS) or knock-out serum replacement (KSR).
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent in accordance with the prescribed protocol.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion Illumina Total Prep RNA Amp kit.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Non-normalized data file: RAW_2.txt
Data processing The data were normalized using cubic-spline normalization with BeadStudio.
 
Submission date Sep 25, 2009
Last update date Sep 25, 2009
Contact name Esther Yesde Son
E-mail(s) son@fas.harvard.edu
Phone 617-496-5611
Fax 617-384-5611
Organization name Harvard University
Department Stem Cells and Regenerative Biology
Lab Eggan
Street address 7 Divinity Avenue
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL6885
Series (1)
GSE18286 Global gene expression analysis of (1) chemically reprogrammed iPS cells, and (2) chemical-treated cells

Data table header descriptions
ID_REF
VALUE Cubic-spline normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 1060.705 0
ILMN_2721178 227.1625 0
ILMN_3033922 547.2267 0
ILMN_3092673 2388.2 0
ILMN_2816356 31.77006 0.007518797
ILMN_2808939 425.1965 0
ILMN_2634564 322.835 0
ILMN_2737647 2.901952 0.2756892
ILMN_2734484 364.0217 0
ILMN_2952292 35.53797 0.005012531
ILMN_2699078 -3.314162 0.7468672
ILMN_1213681 64.46876 0
ILMN_2735413 3.006315 0.273183
ILMN_2735415 5.001774 0.1967418
ILMN_2891688 396.8596 0
ILMN_2637698 546.9896 0
ILMN_2674228 88.94186 0
ILMN_2601546 11.24397 0.0839599
ILMN_1230831 -1.281767 0.556391
ILMN_2848071 22.05561 0.01754386

Total number of rows: 25697

Table truncated, full table size 749 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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