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Sample GSM1406411 Query DataSets for GSM1406411
Status Public on Dec 08, 2015
Title dY Tam rep2 hyb2
Sample type RNA
 
Source name EpiLCs
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
dY2Tam.Detection Pval
dY2Tam.BEAD_STDERR
dY2Tam.Avg_NBEADS

Data table
ID_REF VALUE dY2Tam.Detection Pval dY2Tam.BEAD_STDERR dY2Tam.Avg_NBEADS
ILMN_1212607 148.9821541 0.7781955 3.747358 51
ILMN_1212612 146.9849377 0.8070176 4.720915 27
ILMN_1212619 330.5540963 0 9.600171 37
ILMN_1212628 153.434151 0.4611529 4.988451 34
ILMN_1212632 401.6075781 0 23.8583 33
ILMN_1212636 7418.832656 0 278.5581 29
ILMN_1212637 1025.641706 0 74.62209 44
ILMN_1212645 181.6918143 0.06265664 5.92002 35
ILMN_1212648 660.3176479 0 26.1722 55
ILMN_1212653 163.5963199 0.1942356 6.294468 32
ILMN_1212672 1035.318723 0 46.80212 40
ILMN_1212682 161.4428267 0.3120301 5.856629 28
ILMN_1212683 161.8619573 0.2380952 6.434488 40
ILMN_1212685 154.2132071 0.6390978 5.896148 49
ILMN_1212692 366.4646107 0 16.31 47
ILMN_1212693 188.8566704 0.02756892 6.92258 42
ILMN_1212695 165.9442481 0.1691729 6.871106 40
ILMN_1212698 153.1779134 0.7042606 4.2336 35
ILMN_1212702 181.0318473 0.08646616 6.750738 32
ILMN_1212703 207.2032883 0.002506266 9.071059 47

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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