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Sample GSM1146805 Query DataSets for GSM1146805
Status Public on Sep 01, 2013
Title Colorectal Normal Tissue-033112-01NB-CytoScanHD
Sample type genomic
Source name Colorectal Normal Tissue-033112-01NB
Organism Homo sapiens
Characteristics cell type: Adjacent Normal
gender: Male
age: 56
tissue: Sigmoid
tnm: T3N0M0
Stage: II
Treatment protocol NONE
Growth protocol NONE (Tissue samples were used)
Extracted molecule genomic DNA
Extraction protocol DNA and RNA were extracted from the same tissue using Macherey Nagel trio kit (Germany).10-30mg of tissue sample was homogenized using Qiagen Tissue lyzer. The lysate was loaded on centrifuge columns. After washing nucleic acids were eluted as per the manufacturers protocol.
Label Biotin
Label protocol CytoScanHD kit and Reagent kit bundle from Affymetrix
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.
Description 033112-01NB
Hybridized to CytoScanHD
Data processing Nexus Copy Number 6.0 (Biodiscovery, Inc., CA, USA) was used to assess genome wide copy number frequencies for the 15 patients. Aroma.affymetrix - another CBS implemented as part of BioConductor’s DNACopy library- and the underlying TumorBoost algorithm were also used to identify genomic events and normalize allele specific copy number with paired normals
Primary data description: CNV calls, LOH (see supplementary file linked on Series record)
Submission date May 22, 2013
Last update date Sep 01, 2013
Contact name Sathish Periyasamy
Phone 0966503921073
Organization name NGHA
Department Bioinformatics
Street address P.O. Box 22490
City Riyadh
State/province Select a State or Province
ZIP/Postal code 11426
Country Saudi Arabia
Platform ID GPL16131
Series (1)
GSE47204 CytoScanHD array Data for Colerectal Tumor and Normal Samples

Supplementary file Size Download File type/resource
GSM1146805_033112-01NB.CEL.gz 31.4 Mb (ftp)(http) CEL
Processed data are available on Series record

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