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Series GSE43369 Query DataSets for GSE43369
Status Public on May 27, 2013
Title DNA Methylation Biomarkers for Noninvasive Diagnosis of Colorectal Cancer
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed.
 
Overall design Bisulphite converted DNA from 92 colorectal tumor samples and paired adjacent normal mucosa were hybridised to the Illumina GoldenGate Methylation Cancer Panel I. Additionally, replicates were hybridised for five tumor tissue and their corresponding normal mucosa for reproducibility purposes, totalling 194 samples. Three samples (SAMPLEs 49, 51, and 162) and 50 loci did not reach the quality criteria required regarding the signal-to-noise ratio and were therefore excluded from further analysis. One additional non-tumoral sample (SAMPLE 15) was removed because it exhibited a methylation pattern quiet different from that shown by the rest of normal specimens, which could be indicative of hybridization errors. These Samples and loci are included in the raw data matrix to allow other investigators to use them if different criteria are applied. They have been also included in the Sample tables with missing values in order to preserve the structure of the data across records/files (See 'data processing' section for more details).
 
Contributor(s) Moreno V, Esteller M
Citation(s) 23694962
Submission date Jan 09, 2013
Last update date Sep 09, 2014
Contact name Antonio Berenguer-Llergo
E-mail(s) toniberenguer@iconcologia.net
Organization name Catalan Institute of Oncology (ICO)
Department Cancer Prevention Program
Lab Biomarkers and Susceptibility Unit (UBS)
Street address Gran Via 199-203
City L'Hospitalet del Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
 
Platforms (1)
GPL9183 Illumina GoldenGate Methylation Cancer Panel I
Samples (194)
GSM1061244 genomic DNA from paired normal mucosa adjacent to colorectal tumor 1
GSM1061245 genomic DNA from colorectal tumor 2
GSM1061246 genomic DNA from paired normal mucosa adjacent to colorectal tumor 3
Relations
BioProject PRJNA185764

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43369.txt.gz 880 b (ftp)(http) TXT
GSE43369_Matrix_signal_intensities.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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