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Series GSE119335 Query DataSets for GSE119335
Status Public on Dec 12, 2018
Title RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [SNP]
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Alteration in RNA editing has been connected to tumor progression and many other important human diseases. However, the role of RNA editing in intrahepatic cholangiocarcinoma (ICC) remains unclear. Here we conducted a transcriptome-wide investigation in ICCs, and revealed ADAR-associated over-editing occurred uniformly in ICCs. Collectively, these results reveal a previously unrecognized role of RNA editing in malignant transformation into ICC, and ADAR1 inhibition may obviate progression and relapse of this malignancy.
 
Overall design 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”.
 
Contributor(s) Zhou G, Cao P, Li Y
Citation(s) 36476255
Submission date Aug 31, 2018
Last update date Jan 04, 2023
Contact name Pengbo Cao
E-mail(s) icaopb@gmail.com
Organization name Beijing Institute of Radiation Medicine
Street address 27 Taiping Road
City Beijing
ZIP/Postal code 100850
Country China
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (30)
GSM3370095 90608N
GSM3370096 90608T
GSM3370097 98699N
This SubSeries is part of SuperSeries:
GSE119337 RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma
Relations
BioProject PRJNA488804

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
GSE119335_RAW.tar 835.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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