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Sample GSM307296 Query DataSets for GSM307296
Status Public on Oct 21, 2008
Title tumor sample 204
Sample type RNA
 
Channel 1
Source name tumor sample
Organism Homo sapiens
Characteristics Rectal tumor tissue
TEM treated
Group: AA
Stage: T0N0
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy5
Label protocol Two ug of total RNA was amplified and labeled using Ambion's Amino Allyl MessageAmp™ aRNA kit and protocol (Ambion Inc., Austin, TX). For each microarray experiment, 2.0-μg aliquots of aRNA were labeled with Cy5 (Amersham Biosciences, Buckinghamshire, UK). The labeled aRNAs were mixed with equal amounts of Cy3-labeled reference aRNA. To the mixture of labeled reference and sample RNA, 20 μg human COT-1 DNA (Invitrogen, Carlsbad, CA), 8 μg yeast tRNA (Invitrogen) and 20 μg polyadenylic acid (Sigma-Aldrich, St. Louis, MO) were added.
 
Channel 2
Source name Reference material consisting of pooled RNAs isolated from five colorectal cancer cell lines (HCT116, LS411N, SW480, HCT15, Caco2) and five normal rectum samples.
Organism Homo sapiens
Characteristics reference
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy3
Label protocol Two ug of total RNA was amplified and labeled using Ambion's Amino Allyl MessageAmp™ aRNA kit and protocol (Ambion Inc., Austin, TX). For each microarray experiment, 2.0-μg aliquots of aRNA were labeled with Cy5 (Amersham Biosciences, Buckinghamshire, UK). The labeled aRNAs were mixed with equal amounts of Cy3-labeled reference aRNA. To the mixture of labeled reference and sample RNA, 20 μg human COT-1 DNA (Invitrogen, Carlsbad, CA), 8 μg yeast tRNA (Invitrogen) and 20 μg polyadenylic acid (Sigma-Aldrich, St. Louis, MO) were added.
 
 
Hybridization protocol Preheated hybridization buffer (25% formamide, 5× SSC, 0.1% SDS) was added and arrays were hybridised overnight 42°C to human 35K oligo microarrays
Scan protocol Scanned on an Agilent G2565BA scanner.
Description Expanded descriptions of Channel 1 'Characteristics':
TEM: transanal endoscopic microsurgical resection. TME: total mesorectal excision
AA: pure adenomas(in paper A/A), AC: adenoma fraction from cases with a carcinoma focus(in paper A/C), CA: tumor fractions consisting of a mixture of adenoma and carcinoma tissue(in paper AC/C), CC: carcinomas without lymph node metastasis(in paper C/C), CC(N): carcinomas with lymph node metastasis(in paper C/C(N+)).
The stages (T1N0) represent the TNM classification of colorectal tumors (International Union Against Cancer (UICC)).
Data processing Images were quantified using Genepix 5.1 Software. The Limma (linear models for microarray data) package of Bioconductor (http://www.bioconductor.org) was used for importing the data, normalizing the arrays and identifying differentially expressed genes. Control spots and spots with more than 10% saturation, a diameter smaller than 60 μm or signal intensity less than 20 counts above background were excluded from the analysis. Data were corrected for local background (method normexp) and normalized within arrays by print-tip loess normalization and between arrays by quantile normalization.
 
Submission date Jul 24, 2008
Last update date Oct 21, 2008
Contact name Esther Lips
E-mail(s) e.lips@nki.nl
Phone +31-20-5122039
Organization name NKI-AVL
Department Molecular Pathology
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
 
Platform ID GPL3676
Series (1)
GSE12225 Integrating chromosomal aberrations and gene expression profiles to dissect rectal cancer

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 -0.189
2 -0.395
3 -0.144
5 0.102
6 0.058
7 -0.004
8 -0.035
9 -0.28
10 -0.433
11 -0.257
12 -1.68
13 -0.613
14 -0.35
16 -0.343
17 0.28
18 0.534
19 -0.268
20 -0.297
21 0.046
23 0.158

Total number of rows: 33091

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM307296.gpr.gz 4.0 Mb (ftp)(http) GPR
Processed data included within Sample table

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