|
| Status |
Public on Feb 05, 2019 |
| Title |
PAs-S1-3h |
| Sample type |
SRA |
| |
|
| Source name |
PANC-1_PA for 3hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PANC-1
cell type: pancreatic cancer cells
passage: 3-5
exposed to: 20 μg/ml Proanthocyanidins (PA) for 3hrs
|
| Treatment protocol |
PANC-1 cells were harvested at the indicated time post Proanthocyanidins (20μg/ml) or DMSO exposure.
|
| Growth protocol |
PANC-1 cells were cultured as monolayers in Dulbecco's Modified Eagle Medium (Gibco, USA) containing 10% fetal bovine serum (Hyclone, USA).Cells were incubated and maintained in a chamber with 95% air and 5% CO2 at 37℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following treatment of PANC-1 cells with or without Proanthocyanidins the cells were harvested, washed with cold PBS, and lysed with ice-cold Trizol reagent.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
3h PAs exposure
|
| Data processing |
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
mapped using tophat2 --microexon-search --no-coverage-search --b2-N 1
detecting different expression gene using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
|
| Department |
Center for Genome Analysis
|
| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE85610 |
Gene expression profiles in response to proanthocyanidins in pancreatic cancer cells |
|
| Relations |
| BioSample |
SAMN05574892 |
| SRA |
SRX2023095 |
