|
Status |
Public on Nov 06, 2015 |
Title |
ChIP-Seq_H3K27ac_intestine |
Sample type |
SRA |
|
|
Source name |
Intestine
|
Organism |
Danio rerio |
Characteristics |
tissue: Whole intestine chip antibody: H3K27ac ChIP grade (abcam)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
phenol/chloroform Ovation Ultralow Library System V2 Workflow (NuGEN)
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
data was mapped using bowtie 1.1.1 Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling. Cisgenome v.2 software package was used for peak-calling (FDR < 0.05). In the case of the Atac-Seq the called peaks were not used in the manuscript, however the provided BED file for the ATAC-seq sample was used to generate the figure. Genome_build: zv9 Supplementary_files_format_and_content: cod files with called peaks. The BED files for the H3K4me2 ChIP and ATAC-sq samples were used to generate figures.
|
|
|
Submission date |
Oct 21, 2015 |
Last update date |
May 15, 2019 |
Contact name |
lucas kaaij |
E-mail(s) |
l.kaaij@imb-mainz.de
|
Organization name |
IMB
|
Department |
RNA silencing
|
Lab |
Rene Ketting
|
Street address |
ackermannweg 4
|
City |
mainz |
ZIP/Postal code |
55128 |
Country |
Germany |
|
|
Platform ID |
GPL18413 |
Series (2) |
GSE74231 |
Enhancers reside in a unique epigenetic environment during early zebrafish development [ChIP-seq & ATAC-seq] |
GSE74617 |
Enhancers reside in a unique epigenetic environment during early zebrafish development |
|
Relations |
BioSample |
SAMN04201222 |
SRA |
SRX1360667 |