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Sample GSM1406413 Query DataSets for GSM1406413
Status Public on Dec 08, 2015
Title R EtOH rep1 hyb2
Sample type RNA
 
Source name ESCs
Organism Mus musculus
Characteristics treatment: EtOH
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
R1EtOH.Detection Pval
R1EtOH.BEAD_STDERR
R1EtOH.Avg_NBEADS

Data table
ID_REF VALUE R1EtOH.Detection Pval R1EtOH.BEAD_STDERR R1EtOH.Avg_NBEADS
ILMN_1212607 162.9597705 0.3258145 6.885111 36
ILMN_1212612 148.6054798 0.7807018 4.623923 42
ILMN_1212619 189.0054938 0.05388471 6.56036 34
ILMN_1212628 158.1648662 0.3558897 5.837996 44
ILMN_1212632 340.8450142 0 15.22974 46
ILMN_1212636 6267.982085 0 219.5836 39
ILMN_1212637 987.296036 0 89.07771 34
ILMN_1212645 175.9198173 0.1716792 4.85287 29
ILMN_1212648 394.8794683 0 15.66575 48
ILMN_1212653 196.8230685 0.01754386 7.081522 39
ILMN_1212672 812.7060494 0 42.13557 36
ILMN_1212682 171.6899524 0.1741855 7.704802 34
ILMN_1212683 145.7497306 0.9135338 5.249639 33
ILMN_1212685 147.3208115 0.9110276 5.222793 40
ILMN_1212692 211.7781249 0.04135338 7.213077 44
ILMN_1212693 159.0465664 0.5701754 6.699139 35
ILMN_1212695 154.1876783 0.5588973 5.822763 40
ILMN_1212698 148.8651238 0.8897243 3.950505 48
ILMN_1212702 166.1116993 0.3884712 7.164681 39
ILMN_1212703 181.7432719 0.09022556 5.674967 36

Total number of rows: 25697

Table truncated, full table size 1092 Kbytes.




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

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