|
| Status |
Public on Jun 26, 2012 |
| Title |
HepG2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: transformed cells
cell type: Liver carcinoma cells
|
| Growth protocol |
Cells are grown according to ENCODE standards
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Oligo-dT was used to prime batch RNA. 96-well PCR was then conducted using junction-specific primers on the resulting cDNA. The resultant RT-PCR products were pooled according to cell line and sequenced on the Roche 454 FLX.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX |
| |
|
| Description |
pooled RT-PCR products
|
| Data processing |
The reads were mapped with BLAT v.34 with defaults parameters = blat.out.psl
Genome_build: hg19
Supplementary_files_format_and_content: PSL files contain the BLAT mapping of the 454 reads on the human genome (hg19 build)
|
| |
|
| Submission date |
Jun 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Julien Lagarde |
| E-mail(s) |
julienlag@gmail.com
|
| Organization name |
CRG
|
| Department |
Bioinformatics and Genomics
|
| Lab |
Computational Biology of RNA Processing
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9186 |
| Series (1) |
| GSE38886 |
Targeted RT-PCR assays spanning unannotated splice junctions sequenced by Roche 454. |
|
| Relations |
| SRA |
SRX155656 |
| BioSample |
SAMN01057248 |
