E-GEOD-33294 - Transcriptome sequencing of human hepatocellular carcinoma

Released on 2 April 2013, last updated on 4 August 2015
Homo sapiens
Samples (6)
Protocols (3)
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
Experiment type
RNA-seq of coding RNA 
A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma. Chan TH, Lin CH, Qi L, Fei J, Li Y, Yong KJ, Liu M, Song Y, Chow RK, Ng VH, Yuan YF, Tenen DG, Guan XY, Chen L.
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-33294.idf.txt
Sample and data relationshipE-GEOD-33294.sdrf.txt
Processed data (1)E-GEOD-33294.processed.1.zip