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Sample GSM1406409 Query DataSets for GSM1406409
Status Public on Dec 08, 2015
Title dY EtOH rep1 hyb1
Sample type RNA
 
Source name EpiLCs
Organism Mus musculus
Characteristics treatment: EtOH
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-EtOH.Detection Pval
dY1-EtOH.BEAD_STDERR
dY1-EtOH.Avg_NBEADS

Data table
ID_REF VALUE dY1-EtOH.Detection Pval dY1-EtOH.BEAD_STDERR dY1-EtOH.Avg_NBEADS
ILMN_1212607 157.4814024 0.4561403 3.712252 47
ILMN_1212612 155.226816 0.5964912 4.742581 43
ILMN_1212619 515.9043506 0 15.02127 46
ILMN_1212628 153.8157893 0.7243108 4.935987 38
ILMN_1212632 314.3032978 0 10.79766 36
ILMN_1212636 7525.91832 0 307.5959 33
ILMN_1212637 1102.53277 0 45.31524 41
ILMN_1212645 173.2401821 0.0914787 4.334824 41
ILMN_1212648 635.4181933 0 20.75001 39
ILMN_1212653 164.4797682 0.2957394 4.847823 48
ILMN_1212672 1093.842575 0 38.69094 27
ILMN_1212682 163.5759876 0.2794486 7.156243 33
ILMN_1212683 151.30886 0.7418546 5.495445 32
ILMN_1212685 152.0622562 0.6729323 3.819284 48
ILMN_1212692 522.3504781 0 19.76172 37
ILMN_1212693 206.607964 0.003759399 5.584358 30
ILMN_1212695 150.911036 0.7593985 3.510413 39
ILMN_1212698 144.875156 0.8796992 4.874293 31
ILMN_1212702 177.2152327 0.05263158 5.64433 38
ILMN_1212703 211.185981 0.003759399 8.447167 35

Total number of rows: 25697

Table truncated, full table size 1104 Kbytes.




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

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