|
| Status |
Public on Oct 03, 2014 |
| Title |
PSC from non-cancer control [DI4] |
| Sample type |
SRA |
| |
|
| Source name |
human PSCs
|
| Organism |
Homo sapiens |
| Characteristics |
strain: C57Bl6/J
cell type: human pancreatic stellate cells
condition/treatment: primary PSCs from control patient
|
| Treatment protocol |
Cells were treated with calcipotriol at a concentration of 100nM.
|
| Growth protocol |
Human PSCs, mouse PSCs, and MiaPaCa2 cells were cultured in DMEM containing 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was with Trizol per manufacturer's instructions. Standard Illumina RNA library construction with multiplexing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file available on Series record: DI.bw
PSC from non-cancer control
|
| Data processing |
Read alignment and junction mapping was accomplished using TopHat2 v2.0.4 using a 25 bp 5’ segment seed for initial mapping followed by differential gene expression analysis using Cuffdiff v2.0.2 to map reads to the reference genome annotation.
BEDTools was used to generate bedGraphs from the bam files generated from TopHat2.
Bigwig files were generated from bedGraphs using the bedGraph to bigwig command from UCSC.
Genome_build: NCBI mouse build 37.2 and human build 37.2.
Supplementary_files_format_and_content: Bigwig files for UCSC browser viewing
|
| |
|
| Submission date |
Jan 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruth T Yu |
| Organization name |
Salk Institute
|
| Department |
Gene Expression Lab
|
| Lab |
Ronald Evans
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE43770 |
Vitamin d receptor-mediated stromal reprogramming suppresses pancreatitis and enhances pancreatic cancer therapy |
|
| Relations |
| SRA |
SRX219908 |
| BioSample |
SAMN01902516 |
