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Sample GSM1406407 Query DataSets for GSM1406407
Status Public on Dec 08, 2015
Title R EtOH rep3 hyb1
Sample type RNA
 
Source name ESCs
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
R3-EtOH.Detection Pval
R3-EtOH.BEAD_STDERR
R3-EtOH.Avg_NBEADS

Data table
ID_REF VALUE R3-EtOH.Detection Pval R3-EtOH.BEAD_STDERR R3-EtOH.Avg_NBEADS
ILMN_1212607 154.9338928 0.5789474 3.301222 51
ILMN_1212612 148.3214283 0.8521304 3.09531 41
ILMN_1212619 183.38309 0.07894737 3.846348 40
ILMN_1212628 154.7672321 0.6566416 4.09312 48
ILMN_1212632 346.2065834 0 10.39694 27
ILMN_1212636 6035.554809 0 184.4497 35
ILMN_1212637 866.4846139 0 26.41291 40
ILMN_1212645 166.4967348 0.2255639 3.435027 37
ILMN_1212648 400.9502343 0 6.297677 52
ILMN_1212653 204.8829282 0.01754386 5.768397 36
ILMN_1212672 855.0389401 0 27.51856 32
ILMN_1212682 184.8516124 0.07017544 4.948369 42
ILMN_1212683 160.8298767 0.4072682 4.78886 33
ILMN_1212685 156.016739 0.4849624 3.935611 43
ILMN_1212692 214.3518089 0.002506266 7.132559 41
ILMN_1212693 180.5964147 0.08145364 6.033013 37
ILMN_1212695 153.9934819 0.6215539 3.591688 42
ILMN_1212698 148.1211336 0.7756892 2.281065 27
ILMN_1212702 171.57892 0.1428571 4.335894 37
ILMN_1212703 194.3800797 0.02882206 3.808797 41

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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