|
| Status |
Public on Dec 26, 2018 |
| Title |
CM-JAKi biological rep2 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic stellate cell line (PSC5-I)_pancreatic tumor organoid conditioned media 2 with JAK inhibitor
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Pancreata
cell type: WT PSC cells
cell line: PSC5
|
| Treatment protocol |
Treated cells were cultured with 500 nM JAKi for 4 days. JAKi = AZD1480 from Selleck, catalog number S2162.
|
| Growth protocol |
Cells were cultured in 5%FBS DMEM control media (MG-CM) or tumor organoid conditioned media (CM) for 4 days in the presence or absence of JAKi. An independent source of CM was used for each cohort.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the PureLink RNA mini kit (Thermo Fisher Scientific)
TruSeq Stranded Total RNA Kit with RiboZero Human/Mouse/Rat (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribosomal RNA-depleted RNA
Sample name in processed data file: Samp.298865
|
| Data processing |
Illumina NextSeq platform
Paired-end sequenced reads were mapped to Gencode mouse (vM1/NCBIM37) whole genome using STAR program (v2.5.1b) with parameters from ENCODE 3 STAR-RSEM pipeline. Gene/Transcript expressions were quantified using RSEM program (v1.2.29).
Differential expression analysis was conducted using DESeq2 program and customized R script
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data in tab-delimited text format.
|
| |
|
| Submission date |
Apr 24, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Giulia Biffi |
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE113615 |
RNA-Seq comparison of pancreatic stellate cells (PSCs) cultured with control media or tumor organoid conditioned media in the presence or absence of JAKi |
|
| Relations |
| BioSample |
SAMN08977738 |
| SRA |
SRX3992126 |
