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Sample GSM338409 Query DataSets for GSM338409
Status Public on Nov 05, 2008
Title ING4 PHD mutant ChIP-chip
Sample type genomic
 
Channel 1
Source name ChIP DNA
Organism Homo sapiens
Characteristics HT1080 cell line stably expressing ING4-D213A
Biomaterial provider Gozani Laboratory
Growth protocol DMEM + 10% FBS
Extracted molecule genomic DNA
Extraction protocol ChIP samples collected as in http://www.genomecenter.ucdavis.edu/farnham/pdf/FarnhamLabChIP%20Protocol.pdf
Label cy5
Label protocol Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension)
 
Channel 2
Source name Input DNA
Organism Homo sapiens
Characteristics HT1080 cell line stably expressing ING4-D213A
Biomaterial provider Gozani Laboratory
Growth protocol DMEM + 10% FBS
Extracted molecule genomic DNA
Extraction protocol ChIP samples collected as in http://www.genomecenter.ucdavis.edu/farnham/pdf/FarnhamLabChIP%20Protocol.pdf
Label cy3
Label protocol Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension)
 
 
Hybridization protocol standard manufacturer's protocol
Scan protocol Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols
Description HG18 array 1 of 2
Data processing Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction
 
Submission date Oct 30, 2008
Last update date Nov 04, 2008
Contact name Tiffany Hung
E-mail(s) tiffany.hung@stanford.edu
Organization name Stanford University
Street address 371 SERRA MALL
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL6325
Series (1)
GSE13412 ING4 ChIP-chip in HT1080 cells

Data table header descriptions
ID_REF
VALUE Log2Ratio ChIP/Input DNA

Data table
ID_REF VALUE
CHR10P001020948 0.25
CHR10P001021048 0.23
CHR10P001026162 0.17
CHR10P001022248 0.24
CHR10P001023448 0.84
CHR10P001023148 0.16
CHR10P001026962 0.74
CHR10P001021248 -0.5
CHR10P001021748 -0.38
CHR10P001024348 -0.05
CHR10P001026062 0.2
CHR10P001021648 0.29
CHR10P001023548 0.16
CHR10P001023248 0.23
CHR10P001027262 0.31
CHR10P001022548 -0.16
CHR10P001025462 1.04
CHR10P001026762 0.7
CHR10P001027562 -0.34
CHR10P001021348 0.34

Total number of rows: 378943

Table truncated, full table size 7909 Kbytes.




Supplementary file Size Download File type/resource
GSM338409.tif.gz 13.5 Mb (ftp)(http) TIFF
GSM338409_532.pair.gz 6.8 Mb (ftp)(http) PAIR
GSM338409_635.pair.gz 6.8 Mb (ftp)(http) PAIR
Processed data included within Sample table

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