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Sample GSM488139 Query DataSets for GSM488139
Status Public on Apr 08, 2011
Title Oct4 shRNA replicate 2
Sample type RNA
 
Source name Oct4 shRNA replicate 2
Organism Mus musculus
Characteristics cell type: Embryonic Stem Cell
transfection: Oct4 shRNA
Growth protocol Mouse CCE or E14T stem cells were maintained on primary mouse embryonic fibroblasts with DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 103 U ml-1 of LIF (Chemicon) and doxycycline (1ug/ml)
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label Cy3
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Expressing Oct4 shRNA
Data processing Data was VST normalized in R using LUMI and LIMMA packages
 
Submission date Dec 20, 2009
Last update date Apr 08, 2011
Contact name Jonathan Monk
E-mail(s) jonathan.m.monk@gmail.com
Phone 9716457785
Organization name Mt. Sinai School of Medicine
Department Gene and Cell Medicine
Lab Lemischka
Street address One Gustave L. Levy Place
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL6481
Series (1)
GSE19588 Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network (2)

Data table header descriptions
ID_REF
VALUE VST normalized

Data table
ID_REF VALUE
10243 7.924104596
10280 7.855422798
10575 7.88148307
20048 7.804742807
20296 12.15472296
20343 7.869014391
20373 7.742228457
20431 12.63776117
50014 7.615270593
50017 7.706153095
50019 7.990830921
50020 7.662334769
50022 7.576643794
50025 7.587865813
50026 7.542010527
50035 7.585499359
50037 7.99625281
50039 8.239198291
50040 7.599734562
50041 7.897850664

Total number of rows: 46643

Table truncated, full table size 945 Kbytes.




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

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