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Sample GSM1406416 Query DataSets for GSM1406416
Status Public on Dec 08, 2015
Title R Tam rep2 hyb2
Sample type RNA
 
Source name ESCs
Organism Mus musculus
Characteristics treatment: 1uM tamoxifen
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
R2Tam.Detection Pval
R2Tam.BEAD_STDERR
R2Tam.Avg_NBEADS

Data table
ID_REF VALUE R2Tam.Detection Pval R2Tam.BEAD_STDERR R2Tam.Avg_NBEADS
ILMN_1212607 153.175931 0.6077694 3.945277 45
ILMN_1212612 152.8571702 0.5802005 7.232308 33
ILMN_1212619 198.8532901 0.0112782 8.652205 40
ILMN_1212628 161.8554013 0.245614 8.905313 34
ILMN_1212632 393.3690383 0 16.80659 47
ILMN_1212636 6299.489144 0 333.1167 38
ILMN_1212637 918.1451674 0 47.94614 45
ILMN_1212645 185.6749752 0.05639098 7.904099 35
ILMN_1212648 350.5689863 0 13.82884 50
ILMN_1212653 181.8409376 0.04385965 7.620528 47
ILMN_1212672 821.0408417 0 38.84829 43
ILMN_1212682 173.0173665 0.1303258 6.730683 38
ILMN_1212683 141.5474131 0.9699248 4.66133 38
ILMN_1212685 155.0173842 0.60401 6.700274 38
ILMN_1212692 232.1070075 0.003759399 8.951627 35
ILMN_1212693 168.5814733 0.2506266 8.360301 31
ILMN_1212695 159.2533235 0.3345865 8.405899 31
ILMN_1212698 169.5761981 0.1867168 7.988318 46
ILMN_1212702 188.7368749 0.05263158 7.677433 43
ILMN_1212703 194.2713801 0.02130326 7.776082 38

Total number of rows: 25697

Table truncated, full table size 1095 Kbytes.




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

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