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Sample GSM1406404 Query DataSets for GSM1406404
Status Public on Dec 08, 2015
Title R Tam rep1 hyb1
Sample type RNA
 
Source name ESCs
Organism Mus musculus
Characteristics treatment: 1uM tamoxifen
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
R1-Tam.Detection Pval
R1-Tam.BEAD_STDERR
R1-Tam.Avg_NBEADS

Data table
ID_REF VALUE R1-Tam.Detection Pval R1-Tam.BEAD_STDERR R1-Tam.Avg_NBEADS
ILMN_1212607 160.323533 0.358396 5.242324 47
ILMN_1212612 149.2205024 0.8383459 3.845409 32
ILMN_1212619 201.8737105 0.007518797 5.239621 31
ILMN_1212628 148.7377554 0.8784461 4.847102 36
ILMN_1212632 431.0829717 0 16.06639 38
ILMN_1212636 7647.679574 0 360.5369 34
ILMN_1212637 994.2616131 0 44.36189 44
ILMN_1212645 181.4223305 0.04511278 4.840452 31
ILMN_1212648 359.7079985 0 17.88241 32
ILMN_1212653 176.4481951 0.1265664 5.474123 33
ILMN_1212672 641.7504721 0 21.46397 43
ILMN_1212682 162.0223707 0.3421053 5.330459 36
ILMN_1212683 148.2682487 0.8458647 3.805407 45
ILMN_1212685 149.9067749 0.7393484 3.661737 33
ILMN_1212692 222.2928852 0 8.253638 49
ILMN_1212693 160.6506702 0.3057644 6.026717 33
ILMN_1212695 150.7269826 0.7807018 4.477148 43
ILMN_1212698 148.4626363 0.783208 3.796113 56
ILMN_1212702 201.8184263 0.002506266 6.714819 52
ILMN_1212703 182.030061 0.05263158 5.786077 43

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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