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Sample GSM1976743 Query DataSets for GSM1976743
Status Public on Jun 27, 2017
Title CCA Non-Tumor Tissue LCS_674B
Sample type genomic
 
Source name CCA Non-Tumor Tissue
Organism Homo sapiens
Characteristics tissue: Liver Non-Tumor Tissue
disease state: Cholangiocarcinoma (CCA)
sample name matched with transcriptome data: LCS_674B
individual: LCS_674
Extracted molecule genomic DNA
Extraction protocol Total DNA was extracted from frozen tissue using Phenol/Chloroform extraction protocol. Samples with sufficient amount of double-stranded DNA as confirmed by Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) were included for array studies.
Label biotin
Label protocol Standard Affymetrix procedures
 
Hybridization protocol Standard Affymetrix procedures
Scan protocol Standard Affymetrix procedures using GeneChip Scanner 3000 uisng AGCC software
Data processing PARTEK Genomic suite (6.6) was used to import allele intensity from the CEL files. Interrogating probes was imported without filtering probes. Adjusmentt for fragment length and probe sequence was performed using the Partek default option. Post import values were corrected for localized GC content using the inbuilt Partek feature based on methods described in Diskin et al. (Nucleic Acids Research. 2008. 36:19). Copy number data was estimated from signal intensity on Affmetrix SNP 6.0 arrays. Copy number ratio values were generated in Partek Genomics Suite (v 6.6) using a paired non-tumor sample as reference following the paired workflow.
Copy number ratio values of tumor sample using a paired non-tumor sample as reference (total 153 columns)
 
Submission date Dec 21, 2015
Last update date Jun 27, 2017
Contact name Xin Wei Wang
E-mail(s) xw3u@nih.gov
Phone 240-760-6858
Organization name National Cancer Institute
Department Laboratory of Human Carcinogenesis
Lab Liver Carcinogenesis Unit
Street address 37 Convent Drive
City Bethesda
State/province MD
ZIP/Postal code 20892-4255
Country USA
 
Platform ID GPL6801
Series (2)
GSE76213 Copy Number Variation of human hepatocellular carcinoma (HCC) and Cholangiocarcinoma (CCA) from the Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC)
GSE76311 Human hepatocellular carcinoma (HCC) and Cholangiocarcinoma (CCA) from Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC)

Supplementary file Size Download File type/resource
GSM1976743_N197.CEL.gz 27.7 Mb (ftp)(http) CEL
Processed data are available on Series record

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