|
| Status |
Public on Feb 06, 2018 |
| Title |
cardiacFibro-PE2_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
cardiac fibroblasts (heart tissue)
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: cardiac fibroblasts
passage: 2
growth medium: serum free medium with phenylephrine (10µM)
|
| Treatment protocol |
Cell culture meduim was replaced 24h after plating to serum free medium for 'cardioSFM' and 'cardiacFibro-SFM',or to serum free medium + phenylephrine for 'cardiacPE' and 'cardiacFibro-PE'
|
| 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 |
total RNA |
| Extraction protocol |
RNA was extracted from isolated cardiomyocytes and cardiac fibroblasts by NucleoSpin RNA kit (Macherey-Negal)
1000ng of total RNA was processed using the TruSeq RNA Sample Preparation Kit v2 protocol (Illumina, Part # 15026495). Sequencing libraries were constructed with barcodes to allow multiplexing of 10 samples on one lane
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads containing Illumina adapters were trimmed using cutadapt.
TopHat (v2.0.10) was used to align the reads to the rat genome (Rnor 6.0, from Ensembl)
Counting reads on genes (Ensembl release 83) was done with HTSeq-count (version 0.6.1p1)
Differential expression analysis was performed using DESeq2 (1.6.3)
For expression level comparison, DEseq2 counts were normalized to exon length.
Genome_build: Rn6
Supplementary_files_format_and_content: abundance measurements (for all samples)
|
| |
|
| 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) |
| GSE102531 |
Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [RNA-Seq] |
| GSE102532 |
Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families |
|
| Relations |
| BioSample |
SAMN07498479 |
| SRA |
SRX3087677 |
