|
| Status |
Public on Feb 06, 2018 |
| Title |
cardioSFM2_ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
cardiomyocytes (heart tissue)
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: neonatal rat ventricular myocytes
passage: none
growth medium: serum free medium
|
| Treatment protocol |
Cell culture meduim was replaced 24h after plating to serum free medium for 'cardioSFM', serum free medium + phenylephrine for 'cardiacPE', serum free medium + infection with adenovirus expressing WT GATA4 gene for 'cardioGata4'
|
| Growth protocol |
Neonatal rat ventricular cardiomyocytes and cardiac fibroblasts were obtained from 1-3 days old rats using an enzymatic neonatal cardiomyocyte isolation system (Worthington Biochemical Corp). We used a Percoll (sigma) density centrifugation, to isolate cardiomyocytes and fibroblasts fractions. 1.5-2X106 live cardiomyocytes were plated on 10cm dishes, while fibroblasts were plated without counting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
25000 cells from each sample were centrifugated and resuspended with lysis buffer, followed by transposition reaction using Tn5 transposase (Nextera kit).
Nextera DNA preparation kit Illumina,Catalog number-FC-121-1030
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads containing Nextera transposase or RNA PCR primer were trimmed using cutadapt
The reads were aligned uniquely to the rat genome (Rnor 6.0, from Ensembl) using bowtie (version 1.0.0)
Mitochondrial reads were filtered, and duplicated reads were removed using Picard tools
The two biological replicates were correlated and combined
Peaks were called using Macs2 callpeak --nomodel --extsize 100 --shift -46
Genome_build: Rn6
Supplementary_files_format_and_content: Bedgraph. In each file- peaks present in all biological replicates ('common peaks')
|
| |
|
| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Izhak Kehat |
| E-mail(s) |
ikehat@technion.ac.il
|
| Organization name |
Technion - Israel's Institute of Technology
|
| Street address |
Efron St.
|
| City |
Haifa |
| ZIP/Postal code |
3525422 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE102529 |
Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [ATAC-Seq] |
| GSE102532 |
Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families |
|
| Relations |
| BioSample |
SAMN07498474 |
| SRA |
SRX3087665 |
