Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome sequencing of human hepatocellular carcinoma

ABSTRACT: Deep high-throughput transcriptome sequencing (RNA-seq) performed on 3 pairs of matched tumor and adjacent non-tumorours (NT) tissues from HCC patients of Chinese origin generated 183.6-million reads that could be aligned. We discovered a number of differentially expressed genes and multiple types of somatic single nucleotide variations (SNVs) in expressed genes. After the removal of the error alignments, high-quality reads were mapped to the human reference sequence (GRCh37/hg19) using three different softwares TopHat, Burrows-Wheeler Aligner (BWA) and CLC Genomics Workbench (CLC). The high-quality variants were identified using VarScan with the following parameters: minimum coverage depth of 10, variation frequency of more than 30% and base quality of more than 15. A total of 568, 545 and 494 potential somatic single nucleotide variants (SNVs), including 94, 89 and 101 coding somatic SNVs (cSNVs), were identified in 3 tumor samples HCC448T, HCC473T and HCC510T, respectively. Validation analysis was carried out for 10 of the intersected cSNVs (all are non-synonymous substitutions) within selected genes of interests with the majority confirmed. Examination of 3 paired human hepatocellular carcinoma and matched non-tumor tissues

ORGANISM(S): Homo sapiens

SUBMITTER: Chi Ho Lin

PROVIDER: E-GEOD-33294 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma.

Chan Tim Hon Man TH Lin Chi Ho CH Qi Lihua L Fei Jing J Li Yan Y Yong Kol Jia KJ Liu Ming M Song Yangyang Y Chow Raymond Kwok Kei RK Ng Vanessa Hui En VH Yuan Yun-Fei YF Tenen Daniel G DG Guan Xin-Yuan XY Chen Leilei L

Gut 20130613 5

<h4>Objective</h4>Hepatocellular carcinoma (HCC) is a heterogeneous tumour displaying a complex variety of genetic and epigenetic changes. In human cancers, aberrant post-transcriptional modifications, such as alternative splicing and RNA editing, may lead to tumour specific transcriptome diversity.<h4>Design</h4>By utilising large scale transcriptome sequencing of three paired HCC clinical specimens and their adjacent non-tumour (NT) tissue counterparts at depth, we discovered an average of 20 ...[more]

PMID: 23766440

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Dataset Information

Transcriptome sequencing of human hepatocellular carcinoma

Publications

A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma.

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