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Sample GSM1406415 Query DataSets for GSM1406415
Status Public on Dec 08, 2015
Title R EtOH rep2 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
R2EtOH.Detection Pval
R2EtOH.BEAD_STDERR
R2EtOH.Avg_NBEADS

Data table
ID_REF VALUE R2EtOH.Detection Pval R2EtOH.BEAD_STDERR R2EtOH.Avg_NBEADS
ILMN_1212607 161.6910648 0.3446115 4.765257 37
ILMN_1212612 149.1007998 0.7694235 5.179553 33
ILMN_1212619 202.67625 0.01879699 5.097491 44
ILMN_1212628 152.8766008 0.5413534 5.746308 47
ILMN_1212632 337.3332275 0 14.90264 40
ILMN_1212636 5944.13544 0 338.109 29
ILMN_1212637 984.550144 0 75.40421 35
ILMN_1212645 162.6234184 0.3884712 4.944602 34
ILMN_1212648 351.6884246 0 12.06965 49
ILMN_1212653 188.6077682 0.02882206 6.80378 38
ILMN_1212672 767.0278485 0 40.24987 32
ILMN_1212682 182.3503779 0.07518797 7.964437 29
ILMN_1212683 155.4469774 0.5413534 5.474245 44
ILMN_1212685 148.9413572 0.8546366 4.370502 44
ILMN_1212692 213.8800165 0.02882206 7.865309 43
ILMN_1212693 161.5245931 0.4912281 5.418828 44
ILMN_1212695 146.6939962 0.8345864 6.526248 32
ILMN_1212698 147.0650832 0.9197995 4.773785 35
ILMN_1212702 188.7282428 0.07769424 8.164655 41
ILMN_1212703 193.244058 0.02882206 6.624004 48

Total number of rows: 25697

Table truncated, full table size 1108 Kbytes.




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

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