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Sample GSM461961 Query DataSets for GSM461961
Status Public on Oct 01, 2010
Title HCT116_siATF3_24hr
Sample type RNA
 
Source name HCT116 cells, siATF3, 24hr, replicate 1
Organism Homo sapiens
Characteristics tissue: colorectal cancer
cell line: HCT116
protocol: ATF3 knockdown
time: 24hr
Treatment protocol HCT116 cells pre-transfected with siRNA were stimulated by methyl methanesulfonate (MMS) at 50 ng/ml for 0, 6, 12, and 24 hours.
Growth protocol HCT116 cells were cultured in 0.25% FCS for 24 hours, transfected with either control siRNA or siRNA for ATF3 knockdown, and after further 24 hours stimulated with MMS.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from MMS-treated HCT116 cells by using Sepasol RNA I Super (nacalai tesque, Japan).
Label Cy3
Label protocol RNA was labelled with Cy3 according to One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) Ver. 5.7 (Agilent, Japan).
 
Hybridization protocol Probes were hybridized to Whole Human Genome Microarray Kit, 4 x 44K according to One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) Ver. 5.7 (Agilent, Japan).
Scan protocol Arrays were scanned by Agilent DNA Microarray Scanner using Feature Extraction 9.5.3 (Agilent, Japan).
Description Gene expression in HCT116 cells transfected with siRNA against ATF3 and stimulated with methyl methanesulfonate (MMS) for 24 hr.
Data processing Normalization between arrays was done by using average signals of seven house keeping genes (RPS13, RPL27, RPS20, RPL30, RPL13A, RPL9, and SRP14) according to de Jonge HJ et al. Evidence based selection of housekeeping genes. PLoS One. 2007 Sep 19;2(9):e898.
 
Submission date Oct 14, 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 GPL4133
Series (1)
GSE18457 ChIP-chip from HCT116 cells treated with MMS and LNCaP cells with ATF3

Data table header descriptions
ID_REF
VALUE processed Cy3 signal intensity

Data table
ID_REF VALUE
1 8.834495e+004
2 5.960672e+000
3 7.529646e+000
4 5.259800e+000
5 5.754480e+000
6 7.136201e+000
7 5.190954e+000
8 6.622167e+000
9 2.897939e+000
10 9.260857e+000
11 9.201533e+000
12 6.783395e+002
13 2.224835e+001
14 8.794646e+001
15 1.305317e+001
16 2.169337e+004
17 1.337360e+001
18 6.851830e+001
19 3.054123e+004
20 1.429324e+001

Total number of rows: 45015

Table truncated, full table size 868 Kbytes.




Supplementary file Size Download File type/resource
GSM461961.txt.gz 7.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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