|
Status |
Public on Jun 16, 2019 |
Title |
NeuroD1FSK |
Sample type |
SRA |
|
|
Source name |
NeuroD1_ChIPseq
|
Organism |
Rattus norvegicus |
Characteristics |
cell line: INS-1 cell type: insulinoma cells sample treatment: 1 hour 10 uM forskolin chip antibody: Goat anti-NeuroD1 (Santa Cruz sc-1086X)
|
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 |
NeuroD1FSK-2-1-CGATGT_CGATGT_L001 processed data file: CREBNeuroD1cobound.bed CREBNeuroD1PDX1cobound.bed CREBnoNeuroD1PDX1.bed CREBPDX1cobound.bed NeuroD1noCREB.bed PDX1NeuroD1noCREB.bed PDX1noCREB.bed
|
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 |
SAMN10935165 |
SRA |
SRX5375039 |