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Sample GSM520530 Query DataSets for GSM520530
Status Public on Mar 16, 2010
Title Vector EZH2 promoter 1
Sample type genomic
 
Channel 1
Source name EZH2 ChIP DNA from MDA-MB-231 Vector
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
ab: anti-EZH2
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from MDA-MB-231 Vector or HOTAIR cells and amplifed using the Sigma Whole Genome Amplification Kit
Label Cy5
Label protocol Amplified DNA was labeled according to standard Nimblegen protocols
 
Channel 2
Source name Input DNA
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
ab: none
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from MDA-MB-231 Vector or HOTAIR cells and amplifed using the Sigma Whole Genome Amplification Kit
Label Cy3
Label protocol Amplified DNA was labeled according to standard Nimblegen protocols
 
 
Hybridization protocol Labeled DNA was hybridized to Nimblegen promoter arrays according to standard Nimblegen protocols
Scan protocol Slides were scanned using a Axon 4000B scanner
Description EZH2 ChIP DNA from MDA-MB-231 Vector
Data processing Experimental/input (Cy5/C3) ratio files were generated and peaks filtered with FDR less than or equal to 0.2
 
Submission date Mar 10, 2010
Last update date Mar 12, 2010
Contact name Rajnish Gupta
Organization name Stanford University
Street address CCSR Room 2155
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL6325
Series (1)
GSE20737 Long non-coding RNA HOTAIR reprograms chromatin state to promote breast cancer metastasis

Data table header descriptions
ID_REF
VALUE Nimblescan software was used for data processing based on standard protocols. Values represent scaled log2 ratio, which is the ratio of the input signals for the experimental (IP) and control (input) samples co- hybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Centering is performed by subtracting the bi-weight mean for the log-ratio values for all features on the array from each log-ratio value

Data table
ID_REF VALUE
CHR10P001020948 0.47
CHR10P001021048 0.3
CHR10P001026162 -0.49
CHR10P001022248 -0.19
CHR10P001023448 -0.02
CHR10P001023148 -1.1
CHR10P001026962 0
CHR10P001021248 -0.97
CHR10P001021748 -0.7
CHR10P001024348 0.19
CHR10P001026062 -1.04
CHR10P001021648 -0.57
CHR10P001023548 -0.5
CHR10P001023248 -1.27
CHR10P001027262 -0.52
CHR10P001022548 -0.48
CHR10P001025462 -0.71
CHR10P001026762 0.7
CHR10P001027562 -0.28
CHR10P001021348 -0.76

Total number of rows: 378943

Table truncated, full table size 7910 Kbytes.




Supplementary file Size Download File type/resource
GSM520530_HG18-1_179073_overlap_532.pair.gz 7.0 Mb (ftp)(http) PAIR
GSM520530_HG18-1_179073_overlap_635.pair.gz 7.0 Mb (ftp)(http) PAIR
GSM520530_HG18-1_179073_overlap_635_ratio_peaks.gff.gz 104.6 Kb (ftp)(http) GFF
Processed data included within Sample table
Processed data provided as supplementary file

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