|
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 |