|
| Status |
Public on Apr 02, 2013 |
| Title |
Transcriptome sequencing of human hepatocellular carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
|
| |
|
| Overall design |
Examination of 3 paired human hepatocellular carcinoma and matched non-tumor tissues
|
| |
|
| Contributor(s) |
Lin CH, Lok S |
| Citation(s) |
23766440 |
| Submission date |
Oct 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Chi Ho Lin |
| E-mail(s) |
nicklin.cpos@hku.hk
|
| Phone |
+852 2831 5511
|
| Organization name |
The University of Hong Kong
|
| Department |
Centre for PanorOmic Sciences
|
| Street address |
6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam
|
| City |
Hong Kong |
| ZIP/Postal code |
Hong Kong |
| Country |
Hong Kong |
| |
|
| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
|
| Samples (6)
|
|
| Relations |
| SRA |
SRP009123 |
| BioProject |
PRJNA149267 |
Less...
More...