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Sample GSM556140 Query DataSets for GSM556140
Status Public on Jun 16, 2010
Title Heterozygous Chd7 Null replicate 1
Sample type RNA
 
Source name mouse ES cells
Organism Mus musculus
Characteristics strain: C3HeB/FeJ
cell type: mouse ES cells
genotype/variation: Heterozygous Chd7 Null
Growth protocol ES cells were cultured using feeder MEFs according to standard procotols.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol. The ratio of ES to feeder cells was estimated at 5:1.
Label biotin
Label protocol RNA was labeled and hybridized to Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays according to the manufacturer’s instructions
 
Hybridization protocol RNA was labeled and hybridized to Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays according to the manufacturer’s instructions
Scan protocol Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays were scanned according to the manufacturer’s instructions.
Description replicate 1
Data processing Raw data were background subtracted and quantile normalized using Illumina Bead Studio software version 3
Unnormalized data are signal intensity with background subtracted; normailized data are signal intensity with background subtracted and quantile normalized using Illumina Bead Studio software
 
Submission date Jun 14, 2010
Last update date Jun 15, 2010
Contact name Mike Paul Schnetz
E-mail(s) mps35@case.edu
Phone 216.368.1256
Organization name Case Western Reserve University
Department Genetics
Lab Scacheri
Street address 10900 Eulid Ave
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL6885
Series (1)
GSE22341 CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.

Data table header descriptions
ID_REF
VALUE quantile normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1243637 -12.5 0.93686
ILMN_2604666 9.4 0.15335
ILMN_2727423 -11.5 0.91753
ILMN_2920454 -5.9 0.70619
ILMN_2726412 -0.4 0.46005
ILMN_2919124 2.1 0.36856
ILMN_3162205 -9.6 0.86598
ILMN_2931500 12.2 0.10954
ILMN_2680398 10.7 0.12629
ILMN_2943387 -4.3 0.63273
ILMN_3017615 3.6 0.3183
ILMN_2692868 5 0.27448
ILMN_3028463 -10.9 0.90335
ILMN_3049961 -1.7 0.50515
ILMN_2665238 -9.4 0.85438
ILMN_2796264 3.8 0.30928
ILMN_2861445 9.5 0.15206
ILMN_2747623 26.8 0.00129
ILMN_3093817 25.1 0.00515
ILMN_2860932 82.4 0

Total number of rows: 25697

Table truncated, full table size 583 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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