|
| Status |
Public on Jul 22, 2019 |
| Title |
ATAC-sham-7dpi |
| Sample type |
SRA |
| |
|
| Source name |
Myh6-MerCrMer;nTnG sorted nuclei from sham operated left ventricular tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
stress: sham operation
tissue: sham operated left ventricular nuclei
time: 7 days post-stress
sample type: SH800 flow cytometer sorted nuclei
|
| Treatment protocol |
Tamoxifen (20 mg/kg) was administrated i.p. one week prior to t=0 and repeated the two following days. Myocardial infarction was performed as described previously in Sergeeva et al., 2013.
|
| Growth protocol |
Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATAC-seq, isolated nuclei were GFP sorted on a SH800 flow cytometer (Sony). Samples were gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. A total of 50.000 nuclei per sample was collected and successively washed with PBS and used as input for ATAC-seq. Prior to sequencing, a quality check was performed to assure cardiomyocyte-specific open chromatin.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC-non-diff-7dpi-peak.bed
ATAC-sham-7dpi
|
| Data processing |
Reads were mapped to mm9 build of the mouse genome using BWA (Li et al., 2009) using default settings.
The BEDTools suite (Quinlan et al., 2010) was used to distribute the genome wide signal into bins of 500bp. To allow for differential peak calling between datasets, quantile normalization was applied using the deepTools2 suite (Ramirez et al., 2016). Peaks overlapping with TSS (Biomart) were removed.
Genome_build: mm9 (ATAC-seq)
Supplementary_files_format_and_content: ATAC-seq: BED files (peaks called differential or stable between BZ and sham at 4, 7 or 14 days post myocardial infarction).
|
| |
|
| Submission date |
Feb 06, 2018 |
| Last update date |
Jul 22, 2019 |
| Contact name |
Vincent M. Christoffels |
| E-mail(s) |
v.m.christoffels@amsterdamumc.nl
|
| Phone |
0205667821
|
| Organization name |
Amsterdam UMC
|
| Department |
Medical Biology
|
| Lab |
Vincent Christoffels
|
| Street address |
Meibergdreef 15 K2-159
|
| City |
Amsterdam |
| State/province |
N/A (NA) |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE110209 |
Spatiotemporal pattern of the transcriptional regulatory landscape of the mouse ventricle after myocardial infarction |
|
| Relations |
| BioSample |
SAMN08471540 |
| SRA |
SRX3653348 |
