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Sample GSM1406410 Query DataSets for GSM1406410
Status Public on Dec 08, 2015
Title dY Tam rep1 hyb1
Sample type RNA
 
Source name EpiLCs
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
dY1-Tam.Detection Pval
dY1-Tam.BEAD_STDERR
dY1-Tam.Avg_NBEADS

Data table
ID_REF VALUE dY1-Tam.Detection Pval dY1-Tam.BEAD_STDERR dY1-Tam.Avg_NBEADS
ILMN_1212607 162.1615943 0.2418546 6.698423 34
ILMN_1212612 146.0815916 0.9160401 4.182508 33
ILMN_1212619 375.1770811 0 12.63847 50
ILMN_1212628 159.2149806 0.4260652 6.714095 39
ILMN_1212632 391.631203 0 15.74396 34
ILMN_1212636 7158.034511 0 390.629 33
ILMN_1212637 966.1477984 0 45.45627 39
ILMN_1212645 186.4622021 0.03007519 4.823866 44
ILMN_1212648 647.1775664 0 29.85325 39
ILMN_1212653 174.5493167 0.1002506 5.372793 39
ILMN_1212672 1200.633258 0 45.73563 37
ILMN_1212682 152.6831205 0.6654136 4.287242 31
ILMN_1212683 156.5662001 0.4874687 5.050254 34
ILMN_1212685 152.1662332 0.6215539 5.624599 36
ILMN_1212692 494.3832339 0 24.60483 39
ILMN_1212693 184.0552348 0.03508772 5.13034 43
ILMN_1212695 158.8863791 0.4072682 4.920135 32
ILMN_1212698 153.9441339 0.4962406 5.157712 42
ILMN_1212702 172.7357341 0.07769424 6.747446 25
ILMN_1212703 201.0275596 0.00877193 6.599422 38

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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