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Sample GSM2279683 Query DataSets for GSM2279683
Status Public on Feb 05, 2019
Title PAs-S2-3h
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 SAMN05574893
SRA SRX2023096

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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