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Sample GSM456608 Query DataSets for GSM456608
Status Public on Nov 04, 2009
Title OKMS6 RepSox 48h rep3
Sample type RNA
 
Source name Partially reprogrammed cell line derived from virally transduced MEFs
Organism Mus musculus
Characteristics cell type: Partially reprogrammed Embryonic Stem Cells
cell line: OKMS6
genome/variation: viral Sox2
small molecule treatment: RepSox at 48 hours
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 1108.243 0
ILMN_2721178 190.5154 0
ILMN_3033922 459.1943 0
ILMN_3092673 1867.641 0
ILMN_2816356 54.70884 0
ILMN_2808939 386.1981 0
ILMN_2634564 248.2498 0
ILMN_2737647 -0.6936295 0.4937343
ILMN_2734484 385.5948 0
ILMN_2952292 41.40272 0
ILMN_2699078 -4.071053 0.8195488
ILMN_1213681 135.0582 0
ILMN_2735413 -1.552438 0.5538847
ILMN_2735415 8.639641 0.1065163
ILMN_2891688 525.2253 0
ILMN_2637698 1047.732 0
ILMN_2674228 155.9691 0
ILMN_2601546 8.160625 0.1140351
ILMN_1230831 9.712017 0.08646616
ILMN_2848071 12.22894 0.04761905

Total number of rows: 25697

Table truncated, full table size 740 Kbytes.




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

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