|
| Status |
Public on Feb 06, 2018 |
| Title |
input_cardioSFM1_ChIPseq |
| 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
chip antibody: none
|
| Treatment protocol |
Cell culture meduim was replaced 24h after plating to serum free medium for 'cardioSFM',or to serum free medium + phenylephrine for 'cardiacPE'
|
| 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 |
according to MAGnify™ Chromatin Immunoprecipitation System (Invitrogen) protocol.
Libraries were prepared according to Blecher-Gonen et al.2013. Briefly, the ChIP product was subjected to end repair, A base addition, adapter ligation and PCR amplification to create libraries. The adaptors contain different barcodes to allow multiplexing of 12 samples in one pool.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapters were removed from all samples using the cutadapt tool
Reads that had a length less than 40 bases after the adapter trimming were discarded (cutadapt option –m 40).
Reads for each sample were mapped independently using Bowtie version (v 0.12.9) against the Rattus norvegicus genome. Genome assembly: Rnor_6.0, Ensembl release 83
Peaks were called using Macs2 callpeak --nomodel --extsize 146.
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) |
| GSE102530 |
Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [ChIP-Seq] |
| GSE102532 |
Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families |
|
| Relations |
| BioSample |
SAMN07498463 |
| SRA |
SRX3087688 |
