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Sample GSM459761 Query DataSets for GSM459761
Status Public on Oct 01, 2010
Title HCT116+MMS HG18 (ChIP-chip)
Sample type genomic
 
Channel 1
Source name ATF3 ChIP DNA from HCT116 cells treated with MMS
Organism Homo sapiens
Characteristics disease state: colorectal cancer
cell line: HCT116
agent: MMS
antibody: anti-ATF3 antibody
Treatment protocol Treated with MMS at 50 ng/ml for 6 hours.
Growth protocol HCT116 cells were cultured in medium containing 0.25% FCS for 24 hours and then stimulated with 50 ng/ml methyl methanesulfonate (MMS).
Extracted molecule genomic DNA
Extraction protocol HCT116 cells were fixed with 0.01% formaldehyde for 10 min at RT and the reaction was stopped by glycine. After a wash PBS, cells were lysed and DNA was fragmented by 12 cycles of sonication at high power for 30 seconds using BioRuptor.
Label Cy5
Label protocol According to NimbleGen's protocol (http://www.nimblegen.com/products/lit/lit.html).
 
Channel 2
Source name Whole cell extract DNA from HCT116 cells treated with MMS (control)
Organism Homo sapiens
Characteristics disease state: colorectal cancer
cell line: HCT116
agent: MMS
antibody: none
Treatment protocol Treated with MMS at 50 ng/ml for 6 hours.
Growth protocol HCT116 cells were cultured in medium containing 0.25% FCS for 24 hours and then stimulated with 50 ng/ml methyl methanesulfonate (MMS).
Extracted molecule genomic DNA
Extraction protocol HCT116 cells were fixed with 0.01% formaldehyde for 10 min at RT and the reaction was stopped by glycine. After a wash PBS, cells were lysed and DNA was fragmented by 12 cycles of sonication at high power for 30 seconds using BioRuptor.
Label Cy3
Label protocol According to NimbleGen's protocol (http://www.nimblegen.com/products/lit/lit.html).
 
 
Hybridization protocol According to NimbleGen's protocol (http://www.nimblegen.com/products/lit/lit.html).
Scan protocol Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
Description ChIP-chip for ATF3 in HCT116 cells treated with 50 ng/ml MMS for 6 hours.
Data processing Peak calling was carried out using MA2C software using 500 bp window, scoring by trimmed mean, lower-bound of false discovery rate at 0.2%, and default setting for else (Song J.S., et al., Model-based analysis of two-color arrays (MA2C), Genome Biology 2007, 8:R178, doi:10.1186/gb-2007-8-8-r178).

1. MA2C $fCHIP IDg.bed, MA2C $fCHIP IDg.gff, MA2C $fCHIP IDg.xls, MA2C $fCHIP IDg.pdf, and MA2C $fCHIP IDg FDRtable.txt for peak locations and quality control. In MA2C $fCHIP IDg.xls, the column \Peak Pos" contains the location of peak with respect to the peak starting position. In some cases, two enriched regions may overlap and cause problems with some genome browsers, we resolve this issue by merging the overlapping peak regions, if necessary.
2. MA2C $fCHIP IDg.ratio.bar contains normalized probe ratios.
3. MA2C $fCHIP IDg.MA2Cscore.bar contains MA2C scores.
 
Submission date Oct 07, 2009
Last update date Oct 14, 2009
Contact name Yujiro Tanaka
E-mail(s) yujirotanaka@gmail.com
Organization name Tokyo Medical and Dental University
Department School of Biomedical Science
Lab Genome Structure and Regulation
Street address 2-3-10 Kandasurugadai
City Chiyodaku
State/province Tokyo
ZIP/Postal code 101-0062
Country Japan
 
Platform ID GPL9448
Series (1)
GSE18457 ChIP-chip from HCT116 cells treated with MMS and LNCaP cells with ATF3

Data table header descriptions
ID_REF
VALUE Normalized Log2 (Cy5/Cy3) Ratio

Data table
ID_REF VALUE
CHR01P000056753 0.182657253
CHR01P000056853 -0.808267955
CHR01P000056953 0.399392328
CHR01P000057053 -0.466021371
CHR01P000057153 -0.233093731
CHR01P000057253 0.320700423
CHR01P000057353 -0.468434184
CHR01P000057453 0.370847675
CHR01P000057553 0.12683991
CHR01P000057753 0.135784862
CHR01P000057853 -0.003299958
CHR01P000057953 -0.630882704
CHR01P000058053 -0.356570046
CHR01P000058153 0.68625437
CHR01P000058253 0.78624695
CHR01P000058353 0.082498345
CHR01P000058556 -0.828968432
CHR01P000058656 0.504236382
CHR01P000058756 1.069899494
CHR01P000058956 -0.857495314

Total number of rows: 386230

Table truncated, full table size 10651 Kbytes.




Supplementary file Size Download File type/resource
GSM459761_100263_532.pair.gz 7.0 Mb (ftp)(http) PAIR
GSM459761_100263_635.pair.gz 7.0 Mb (ftp)(http) PAIR
GSM459761_100263_trim_2E-3_500.MA2Cscore.bar.gz 2.6 Mb (ftp)(http) BAR
GSM459761_100263_trim_2E-3_500.bed.gz 146.0 Kb (ftp)(http) BED
GSM459761_100263_trim_2E-3_500.gff.gz 189.1 Kb (ftp)(http) GFF
GSM459761_100263_trim_2E-3_500.pdf.gz 298.6 Kb (ftp)(http) PDF
GSM459761_100263_trim_2E-3_500.ratio.bar.gz 2.8 Mb (ftp)(http) BAR
GSM459761_100263_trim_2E-3_500.xls.gz 192.3 Kb (ftp)(http) XLS
GSM459761_100263_trim_2E-3_500_FDRtable.txt.gz 9.3 Kb (ftp)(http) TXT
GSM459761_100263_trim_2E-3_500_neg.xls.gz 856 b (ftp)(http) XLS
Processed data included within Sample table
Processed data provided as supplementary file

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