|
| Status |
Public on Jan 30, 2023 |
| Title |
ATAC_V2 |
| Sample type |
SRA |
| |
|
| Source name |
ventricle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ventricle
cell type: cardiomyocytes
genotype: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The optimized-ATACSeq (omni-ATACSeq) libraries were generated from the isolated cardiomyocytes (two biological replicates) using the author’s recommended lysis steps and transposition protocol. Corces MR, et al. Nat Methods. 2017.
The DNA fragments were amplified with NEBNext High-fidelity 2x PCR master mix. Purify amplified library using Qiagen MinElute PCR Purification kit.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC_vCM_rep2
|
| Data processing |
Fastq files were aligned to mouse genome assembly mm10 using Bowtie2 v2.3.4.3.
PCR duplicates were removed and peak calling for each sample was performed with MACS2 v2.2.6.
Wig files were generated as described for bioChIP-seq data, and then normalized using Danpos2.
Assembly: mm10
Supplementary files format and content: bigWig files
|
| |
|
| Submission date |
Oct 07, 2022 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Xiaoran Zhang |
| E-mail(s) |
xiaoran.zhang@childrens.harvard.edu
|
| Phone |
8574259855
|
| Organization name |
Boston Children's Hospital
|
| Department |
Cardiology
|
| Lab |
Pu lab
|
| Street address |
14 Perkins Square, Apt 11
|
| City |
Jamaica Plain |
| State/province |
MA |
| ZIP/Postal code |
02130 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE215031 |
Transposase-accessible chromatin with high-throughput sequencing for purified neonatal aCMs and vCMs |
| GSE215065 |
Regulation of mouse chamber selective enhancers |
|
| Relations |
| BioSample |
SAMN31208371 |
| SRA |
SRX17827924 |
