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Sample GSM1406406 Query DataSets for GSM1406406
Status Public on Dec 08, 2015
Title R Tam rep2 hyb1
Sample type RNA
 
Source name ESCs
Organism Mus musculus
Characteristics treatment: 1uM tamoxifen
hyb number: 1
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
R2-Tam.Detection Pval
R2-Tam.BEAD_STDERR
R2-Tam.Avg_NBEADS

Data table
ID_REF VALUE R2-Tam.Detection Pval R2-Tam.BEAD_STDERR R2-Tam.Avg_NBEADS
ILMN_1212607 160.0290563 0.3433584 4.782415 46
ILMN_1212612 167.0213737 0.2105263 6.005961 32
ILMN_1212619 205.5762639 0.002506266 7.335384 43
ILMN_1212628 140.9970861 0.9962406 4.25027 30
ILMN_1212632 406.0927038 0 13.47877 40
ILMN_1212636 5773.395441 0 219.7529 45
ILMN_1212637 929.4417693 0 39.65833 42
ILMN_1212645 189.7689959 0.01378446 7.273894 40
ILMN_1212648 405.7600983 0 13.78011 49
ILMN_1212653 201.2165307 0.00877193 7.891157 33
ILMN_1212672 845.4903457 0 37.04822 32
ILMN_1212682 169.8824701 0.1629073 6.73869 31
ILMN_1212683 153.3238587 0.6340852 4.831715 40
ILMN_1212685 151.6980734 0.6390978 4.527284 42
ILMN_1212692 193.4256489 0.006265664 6.015497 30
ILMN_1212693 167.5305521 0.1503759 4.41194 45
ILMN_1212695 166.7234758 0.2042606 5.610208 44
ILMN_1212698 152.1891141 0.593985 4.557092 47
ILMN_1212702 180.107387 0.04385965 5.021407 38
ILMN_1212703 182.6709813 0.04010025 5.620547 33

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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