|
| Status |
Public on Jun 16, 2019 |
| Title |
hepaFSK_rep2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
hepa_FSK
|
| Organism |
Mus musculus |
| Characteristics |
strain: Wild-type black6 mice
cell type: cultured mouse primary hepatocytes
treatment: 2 hours 10 uM forskolin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cultured cells or tissue with Trizol/chloroform and cleaned up with Rneasy mini columns (Qiagen)
Libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
hepaFSKrep2
processed data file:
mousehepaRNAseqrepeat.xlsx
|
| Data processing |
FASTQ files were aligned against the mouse mm10 or rat rn6 genome builds using Tophat v2.0.9 or STAR
For differential expression analysis, raw read count tables of two biological replicates from control and FSK treated material were generated using Homer(analyzeRepeats.pl with option –raw). Differential expression and adjusted p-values for significance calculated with Homer (getDiffExpression.pl using DESeq2)
Genome_build: mm10 or rn6
|
| |
|
| Submission date |
Feb 14, 2019 |
| Last update date |
Jun 16, 2019 |
| Contact name |
Sam Van de Velde |
| Organization name |
Salk Institute
|
| Department |
PBL
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE126557 |
CREB mediates transient and sustained genomic responses to cAMP via distinct mechanisms [RNA-seq] |
| GSE126558 |
CREB mediates transient and sustained genomic responses to cAMP via distinct mechanisms |
|
| Relations |
| BioSample |
SAMN10935155 |
| SRA |
SRX5375079 |
