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Sample GSM1406418 Query DataSets for GSM1406418
Status Public on Dec 08, 2015
Title R Tam rep3 hyb2
Sample type RNA
 
Source name ESCs
Organism Mus musculus
Characteristics treatment: 1uM tamoxifen
hyb number: 2
Treatment protocol Tamoxifen was added at 1uM for 36h to induce knockout
Growth protocol All cells were grown in Knockout DMEM with 15%FBS, Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).
Extracted molecule total RNA
Extraction protocol RNA was extracted with the standard Trizol protocol
Label biotin
Label protocol Standard Illumina protocol
 
Hybridization protocol Standard Illumina protocol - a subset of the RNA was hybed on two separate chips at different times and used as such on Sample Network (see hyb#)
Scan protocol Standard Illumina protocol
Data processing Using RGui, the data was processed by Sample Network (ref) and subsequently quantile normalized. Differential gene expression was performed using the limma package, with a cutoff of adjusted p-value < 0.05.
 
Submission date Jun 09, 2014
Last update date Dec 08, 2015
Contact name Raga Krishnakumar
E-mail(s) raga.krishnakumar@gmail.com
Organization name UCSF
Lab Blelloch
Street address 912E RMB, 35 Medical Center Way
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL6885
Series (2)
GSE58317 Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [expression array]
GSE58408 Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation

Data table header descriptions
ID_REF
VALUE Sample Network and Quantile Normalization
R3Tam.Detection Pval
R3Tam.BEAD_STDERR
R3Tam.Avg_NBEADS

Data table
ID_REF VALUE R3Tam.Detection Pval R3Tam.BEAD_STDERR R3Tam.Avg_NBEADS
ILMN_1212607 159.0062246 0.3984962 4.245789 52
ILMN_1212612 151.9885862 0.6203008 7.003408 36
ILMN_1212619 213.8311429 0 12.84053 40
ILMN_1212628 147.5532029 0.6829574 7.559398 34
ILMN_1212632 396.1570601 0 19.95825 42
ILMN_1212636 5861.734979 0 512.6093 27
ILMN_1212637 869.726062 0 57.5696 49
ILMN_1212645 193.7928182 0.03759398 10.13316 38
ILMN_1212648 423.2985041 0 20.28056 40
ILMN_1212653 196.0829015 0.01503759 9.225388 35
ILMN_1212672 794.3866493 0 43.55294 41
ILMN_1212682 168.7912408 0.1817043 6.529599 43
ILMN_1212683 152.8302706 0.5776942 6.717718 52
ILMN_1212685 158.1852436 0.4736842 7.267814 41
ILMN_1212692 219.3012192 0.01503759 6.99635 43
ILMN_1212693 171.8907176 0.1992481 12.14511 32
ILMN_1212695 145.7644587 0.8295739 6.068248 35
ILMN_1212698 154.9929727 0.6215539 5.425213 44
ILMN_1212702 182.3814023 0.0989975 6.757534 40
ILMN_1212703 179.5772767 0.09273183 7.363227 42

Total number of rows: 25697

Table truncated, full table size 1093 Kbytes.




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

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