|
| Status |
Public on Jan 28, 2022 |
| Title |
Amputation 3dpa-3 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish epicardial cell
|
| Organism |
Danio rerio |
| Characteristics |
strain: EK
tissue: heart epicardium
age: 6 month
treatment: 3 days after heart apex amputation injury
|
| Treatment protocol |
Heart apex amputation injury
|
| Growth protocol |
Zebrafih were maintained in standard conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction and library making was done as described (reference: PMID: 24097267)
Library making was done as described (reference: PMID: 24097267)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
3 days after heart apex amputation injury, replicate 3
|
| Data processing |
Illumina Casava 1.8 software was used for basecalling.
Reads were trimmed for adaptors using Cutadapt
Trimmed reads were alignned to the DanRer10 genome using Bowtie with parameters “-n 2 -m 4”
Reads mapped to mitochondrial DNA were removed and alignments were filtered for PCR artifacts
Peaks were called using MACS2 with parameters “-q 0.01 --nomodel --shift -100 --ext 200 --bdg”
Genome_build: DanRer10
Supplementary_files_format_and_content: bigWig files were generated using wigToBigWig with standard settings.
|
| |
|
| Submission date |
Nov 02, 2016 |
| Last update date |
Jan 28, 2022 |
| Contact name |
Jingli Cao |
| E-mail(s) |
jic4001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Cell & Developmental Biology
|
| Lab |
Jingli Cao
|
| Street address |
413 E 69th ST, BRB-518
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE89444 |
Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration |
|
| Relations |
| BioSample |
SAMN05968591 |
| SRA |
SRX2322869 |
