|
| Status |
Public on Feb 09, 2023 |
| Title |
RNAPII_DMEM_siCtrl_3 |
| Sample type |
SRA |
| |
|
| Source name |
cardiac fibroblasts
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: Neonatal
treatment: DMEM/50 nM siCtrl
|
| Treatment protocol |
Cardiac fibroblasts were treated for 75 min with 1 μM Ang II
|
| Growth protocol |
Cardiac fibroblasts were isolated from 1-3 day old Sprague-Dawley rats.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cardiac fibroblasts were fixed with 1% formaldehyde and the fixed chromatin sonicated for 18 cycles (30 seconds on/30 seconds off) in a Diagenode BioRuptor UCD-200
Libraries were prepared with the NEBNext® UltraTM II DNA Library Prep kit for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Sheared chromain
Cardiac fibroblasts were treated 72 h after transfection with 50 nM siRNA. S. pombe chromatin was combined with the rat chromatin and immunoprecipitated with an anti-Rpb1 (8WG16) antibody
RNAPII_DMEM_siCtrl.bw
|
| Data processing |
Fastq files were trimmed with TrimGalore (v0.6.0) with the settings --phred33 --length 36 -q 5 --stringency 1 -e 0.1
Processed reads were aligned to the custom combined rat and S. pombe genome with Bowtie2 (v2.3.5)
Low-quality mapped reads (MAPQ < 10) and reads mapped to non-standard chromosomes were removed wtih SAMtools (v1.9)
Duplicate reads were removed with Picard tools (v2.20.6, Broad Institute)
Aligned reads were separated into individual files for the rat or S. pombe genome respectively
Input reads subtracted with the deepTools (v3.3.1) function bamCompare (--scaleFactorsMethod SES) and negative values set to 0
Values were converted to RPM with library size adjusted by the total number of reads aligned to the S. pombe genome
Genome_build: Rattus_norvegicus.Rnor_6.0.94 and Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: bigwig file of merged biological replicates
|
| |
|
| Submission date |
Mar 23, 2020 |
| Last update date |
Feb 09, 2023 |
| Contact name |
Terence Hébert |
| E-mail(s) |
terence.hebert@mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Pharmacology and Therapeutics
|
| Street address |
3655 Promenade Sir William Osler
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE147416 |
An interaction between Gβγ and RNA polymerase II regulates transcription in cardiac fibroblasts |
|
| Relations |
| BioSample |
SAMN14428326 |
| SRA |
SRX7973269 |
