|
| Status |
Public on Jun 16, 2019 |
| Title |
PolIIACREBFSK |
| Sample type |
SRA |
| |
|
| Source name |
RNA PolII_ChIPseq
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: INS-1
cell type: insulinoma cells
sample treatment: Ad-ACREB/1 hour 10 uM forskolin
chip antibody: rabbit anti-RPB1 (Cell Signaling 2629)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
ChIP-seq libraries were constructed with NEBNext ChIPseq library kit (NEB) according to manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: FSKupgenesRNA.bed
PolIIACREBFSK_S28
|
| Data processing |
genome build: rn5
Reads were aligned to the mouse (mm10) or rat (rn5, rn6) genomes using bowtie2 or STAR
Binding peaks were called using Homer
Homer peak files were converted to BED files using Homer
Co-occupancy of binding sites was performed using Homer (mergePeak command -prefix option)
Super-enhancers were identified based on H3AcK27 occupancy with HOMER (findPeaks –style super –L 0, maximum distance to stitch peaks together: 12.5 kb).
|
| |
|
| 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 |
GPL18694 |
| Series (2) |
| GSE126556 |
CREB mediates transient and sustained genomic responses to cAMP via distinct mechanisms [ChIP-seq] |
| GSE126558 |
CREB mediates transient and sustained genomic responses to cAMP via distinct mechanisms |
|
| Relations |
| BioSample |
SAMN10935213 |
| SRA |
SRX5375015 |
