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Sample GSM1406402 Query DataSets for GSM1406402
Status Public on Dec 08, 2015
Title dY EtOH rep3 hyb1
Sample type RNA
 
Source name EpiLCs
Organism Mus musculus
Characteristics treatment: EtOH
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
dY3-EtOH.Detection Pval
dY3-EtOH.BEAD_STDERR
dY3-EtOH.Avg_NBEADS

Data table
ID_REF VALUE dY3-EtOH.Detection Pval dY3-EtOH.BEAD_STDERR dY3-EtOH.Avg_NBEADS
ILMN_1212607 148.792565 0.8170426 3.076396 32
ILMN_1212612 165.1809139 0.2844611 5.357201 39
ILMN_1212619 508.460972 0 14.91638 35
ILMN_1212628 149.5422427 0.8734336 3.630386 34
ILMN_1212632 306.931832 0 6.662611 47
ILMN_1212636 7376.458676 0 231.5501 35
ILMN_1212637 865.6957823 0 28.62255 38
ILMN_1212645 179.9128646 0.05263158 4.175458 41
ILMN_1212648 684.3256854 0 19.48303 47
ILMN_1212653 179.3987287 0.07393484 5.498838 29
ILMN_1212672 1267.843234 0 37.38224 33
ILMN_1212682 173.471605 0.1353384 6.42945 33
ILMN_1212683 146.8584999 0.8834587 4.040883 48
ILMN_1212685 166.1373199 0.2192982 4.868926 39
ILMN_1212692 548.6653488 0 15.90514 48
ILMN_1212693 199.6149959 0.0112782 7.936564 33
ILMN_1212695 143.3144293 0.9511278 3.198742 33
ILMN_1212698 148.184354 0.7619048 3.797427 34
ILMN_1212702 191.5862827 0.01378446 6.554125 34
ILMN_1212703 205.9176928 0.00877193 7.106407 42

Total number of rows: 25697

Table truncated, full table size 1098 Kbytes.




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

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