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Sample GSM1406417 Query DataSets for GSM1406417
Status Public on Dec 08, 2015
Title R EtOH rep3 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
R3EtOH.Detection Pval
R3EtOH.BEAD_STDERR
R3EtOH.Avg_NBEADS

Data table
ID_REF VALUE R3EtOH.Detection Pval R3EtOH.BEAD_STDERR R3EtOH.Avg_NBEADS
ILMN_1212607 159.750057 0.4022556 4.842383 46
ILMN_1212612 159.4538699 0.358396 4.108586 32
ILMN_1212619 213.7110309 0.006265664 7.409969 39
ILMN_1212628 150.1967752 0.6027569 4.675187 40
ILMN_1212632 369.1153209 0 12.63205 37
ILMN_1212636 6017.141842 0 195.6781 32
ILMN_1212637 919.9285839 0 50.1153 45
ILMN_1212645 180.191798 0.1378446 6.597106 44
ILMN_1212648 397.3622498 0 12.59828 46
ILMN_1212653 198.7257208 0.01378446 8.000842 34
ILMN_1212672 809.7803059 0 36.62957 38
ILMN_1212682 159.0351745 0.4223058 6.557852 27
ILMN_1212683 156.3454198 0.4548872 4.654568 48
ILMN_1212685 148.0217006 0.8796992 4.263069 40
ILMN_1212692 209.0319312 0.05012531 5.9509 34
ILMN_1212693 161.5205954 0.4473684 4.847222 33
ILMN_1212695 155.8980033 0.4649123 5.293087 42
ILMN_1212698 145.7633041 0.9423559 5.820887 43
ILMN_1212702 172.5155881 0.264411 5.0075 44
ILMN_1212703 201.6656321 0.01378446 7.691302 39

Total number of rows: 25697

Table truncated, full table size 1099 Kbytes.




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

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