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Sample GSM1406400 Query DataSets for GSM1406400
Status Public on Dec 08, 2015
Title dY EtOH rep2 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
dY2-EtOH.Detection Pval
dY2-EtOH.BEAD_STDERR
dY2-EtOH.Avg_NBEADS

Data table
ID_REF VALUE dY2-EtOH.Detection Pval dY2-EtOH.BEAD_STDERR dY2-EtOH.Avg_NBEADS
ILMN_1212607 151.0831752 0.7030075 4.360862 47
ILMN_1212612 153.0836687 0.6691729 6.730135 26
ILMN_1212619 513.4709107 0 16.75792 36
ILMN_1212628 163.79106 0.2982456 5.092672 39
ILMN_1212632 318.464097 0 10.85264 38
ILMN_1212636 7232.469212 0 286.4432 29
ILMN_1212637 990.2421121 0 45.67513 39
ILMN_1212645 189.2870439 0.01503759 6.009735 38
ILMN_1212648 633.1495496 0 15.17955 60
ILMN_1212653 173.192814 0.1065163 5.196952 29
ILMN_1212672 1225.857664 0 46.03106 39
ILMN_1212682 166.1737133 0.2055138 4.363628 33
ILMN_1212683 151.0583281 0.7205514 3.798583 47
ILMN_1212685 159.6000016 0.3471178 4.835058 41
ILMN_1212692 408.9481674 0 15.09431 40
ILMN_1212693 196.6289746 0.007518797 7.213105 33
ILMN_1212695 155.9773508 0.5426065 5.065452 31
ILMN_1212698 153.6168739 0.547619 5.54572 36
ILMN_1212702 165.6510733 0.1541353 3.884306 54
ILMN_1212703 186.4232163 0.02631579 5.344331 35

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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