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Sample GSM1406408 Query DataSets for GSM1406408
Status Public on Dec 08, 2015
Title R Tam rep3 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
R3-Tam.Detection Pval
R3-Tam.BEAD_STDERR
R3-Tam.Avg_NBEADS

Data table
ID_REF VALUE R3-Tam.Detection Pval R3-Tam.BEAD_STDERR R3-Tam.Avg_NBEADS
ILMN_1212607 155.1247558 0.5639098 2.622844 58
ILMN_1212612 165.1050132 0.2706767 5.542488 39
ILMN_1212619 208.1905438 0.005012531 6.637556 34
ILMN_1212628 153.5022724 0.7005013 4.671556 38
ILMN_1212632 377.3474161 0 11.87938 40
ILMN_1212636 5930.991612 0 219.0477 33
ILMN_1212637 853.8421505 0 42.85266 36
ILMN_1212645 179.6187427 0.05764411 4.231263 43
ILMN_1212648 444.5047495 0 15.67317 41
ILMN_1212653 201.9333246 0.01253133 5.363012 39
ILMN_1212672 771.02198 0 26.61314 32
ILMN_1212682 173.0746017 0.1328321 4.925666 45
ILMN_1212683 156.0740803 0.537594 4.49401 36
ILMN_1212685 154.526244 0.5338346 4.968721 42
ILMN_1212692 198.8514216 0.003759399 5.663733 52
ILMN_1212693 159.0550221 0.3508772 5.10115 34
ILMN_1212695 152.1664408 0.7142857 3.933185 32
ILMN_1212698 158.0328791 0.3909774 4.418969 41
ILMN_1212702 202.3102055 0.006265664 9.554685 34
ILMN_1212703 192.8886865 0.02631579 5.158496 31

Total number of rows: 25697

Table truncated, full table size 1101 Kbytes.




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

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