Dataset features

Specifications


Dataset type: Genome variation profiling by array
Number of samples: 30
Release date: Dec 12 2018
Last update date: Dec 13 2018
Access: Public
Dataset link RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [SNP]

Experimental Protocol


To detect copy number variations (CNVs) for the 15 ICCs in discovery stage, we performed genome-wide single nucleotide polymorphisms (SNPs) genotyping by Affymetrix Genome-Wide Human SNP Array 6.0, which includes more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes. Copy-number estimation using Robust Multichip Analysis (CRMA, v2) method was used to pre-process the probe signal intensities from each raw .CEL file. This procedure consists of a calibration for offset and global crosstalk between alleles, and normalized for probe sequence effects. Once the data has been preprocessed using CRMA, fragment-length effects were normalized. Next, raw copy numbers was calculated by paired analysis, which takes the matched non-tumor liver tissue as reference for each tumor. Segmented copy number profiles were analyzed using Circular binary segmentation (CBS) algorithm with default parameters in the R package “DNA-copy”.

Repositories


GEO

GSE119335

BioProject

PRJNA488804

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Contact


Pengbo Cao