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Sample GSM349763 Query DataSets for GSM349763
Status Public on Dec 11, 2008
Title SW48 p53 NULL Colorectal cancer cells_12 Gy gamma radiation
Sample type RNA
 
Channel 1
Source name SW48 Colorectal cancer cell line, exposed to 12Gy gamma radiation and incubated 24 hours before sample collection
Organism Homo sapiens
Characteristics Cell Line: SW48, p53 status: -/-, Treatment: 12 Gy gamma radiation
Treatment protocol Exposure to 12 Gy gamma radiation
Growth protocol Cells grown to 70% confluence in T75 flasks
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen RNeasy Plant kit according to manufacturer's instructions
Label Cy5
Label protocol cDNA was used as a template for in vitro transcription using T7 RNA polymerase and Cy-3 and Cy-5 labeled CTP
 
Channel 2
Source name SW48 Colorectal cancer cell line, nonirradiated and incubated for same time as irradiated samples
Organism Homo sapiens
Characteristics Cell Line: SW48, p53 status: -/-, Treatment: No radiation
Treatment protocol Exposure to 12 Gy gamma radiation
Growth protocol Cells grown to 70% confluence in T75 flasks
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen RNeasy Plant kit according to manufacturer's instructions
Label Cy3
Label protocol cDNA was used as a template for in vitro transcription using T7 RNA polymerase and Cy-3 and Cy-5 labeled CTP
 
 
Hybridization protocol Samples from the same cell line with and without gamma irradiation were hybridized to the same slide. Labeled cRNA samples were used for hybridization to Agilent 4x44K microarrays and scanned as directed by the manufacurer.
Scan protocol Agilent microarray scanner,as according to manufacturer
Description colorectal cancer cell lines that differ only with respect to their endogenous TP53 status
Data processing Data were extracted using Feature Extraction software v8.1 (Agilent Technologies) under default settings for normalization. Microarrays with higher than 5 percent feature of local background region outliers were excluded. Distributions of signal and background intensity of both red and green channels were examined with boxplot and maPlot using the Bioconductor package. The ratios of each feature were calculated after background subtraction and normalization. Features exhibiting signifcant changes of gene expression were selected based on PValueLogRatio calculated from the feature extraction software.
 
Submission date Dec 09, 2008
Last update date Dec 11, 2008
Contact name Raymond Anthony Pagliarini
Organization name NIBRI
Department Oncology
Street address 250 Massachusetts Ave. Room 3C-292
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL4133
Series (1)
GSE13886 Response of p53 isogenic colorectal cancer panel to 12 Gy gamma irradiation

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing irradiated/nonirradiated cell line
PRE_VALUE ratio (Cy5/Cy3) representing irradiated/nonirradiated cell line

Data table
ID_REF VALUE PRE_VALUE
1 0.4293 1.3466
2 -2.9062 0.1334
3 -2.0221 0.2462
4 -2.0110 0.2481
5 -2.0012 0.2498
6 -1.9914 0.2515
7 -1.9834 0.2529
8 -1.9760 0.2542
9 -1.9697 0.2553
10 -1.9635 0.2564
11 -1.9585 0.2573
12 0.2535 1.1921
13 -0.0098 0.9932
14 -0.2216 0.8576
15 -0.3804 0.7682
16 0.0571 1.0404
17 -0.0258 0.9823
18 0.1833 1.1355
19 0.1164 1.0840
20 -0.0130 0.9910

Total number of rows: 45015

Table truncated, full table size 891 Kbytes.




Supplementary file Size Download File type/resource
GSM349763.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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