|
| Status |
Public on Mar 18, 2020 |
| Title |
P1D3MI |
| Sample type |
SRA |
| |
|
| Source name |
Cardiomyocyte nuclei isolated from ventricle tissue below left anterior descending artery ligation plane
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR/CD1
|
| Treatment protocol |
Neonatal P1 mice were subjected to myocardial infarction, induced by permanent ligation of LAD coronary artery.
|
| Growth protocol |
Animals were housed in a 12 h light/dark cycle in a temperature-controlled room in the Animal Research Center of UT Southwestern, with ad libitum access to water and food.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mice were euthanized at 3d post injury. Ventricle tissues below LAD ligation plane from MI hearts were collected for nuclei extraction. Extracted nuclei were stained with cardiac nuclear membrane marker PCM1 antibody and PCM1+ cardiomyocyte nuclei were sorted by FACS.
Sorted cardiomyocyte nuclei were subjected to single nucleus RNA-sequencing using 10xGenomics platform. Library preparation was performed using Chromium Single Cell ATAC library & Gel Bead Kit V1.0 (10xGenomics) according to the manufacturer’s protocol.
single cell ATAC-seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The CellRanger ATAC v1.1.0 was used for primary analysis of the scATAC-seq data.
Raw base call (BCL) files were converted to FASTQ files and filtered reads were aligned to the mouse mm10 reference genome.
Transposase cut sites in each cell were quantified using barcoded UMIs and 10x cell barcode sequences.
Count matrix for accessible chromatin peaks was generated for downstream analysis using the R package Signac (v0.1.6).
Genome_build: mm10
Supplementary_files_format_and_content: csv file documenting single cell barcodes and QC information, tsv file documenting accessible chromatin fragments, h5 file documenting open chromatin peak x cell matrix, tsv file for cell barcodes, mtx file for peak x cell matrix, and bed file for open chromatin peak regions generated from CellRanger-atac primary analysis of the raw sequencing data.
|
| |
|
| Submission date |
Dec 19, 2019 |
| Last update date |
Mar 18, 2020 |
| Contact name |
Zhaoning Wang |
| E-mail(s) |
zhw063@health.ucsd.edu
|
| Organization name |
UC San Diego
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Bing Ren Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE142365 |
Single cell ATAC-seq of cardiomyocytes from neonatal mouse hearts after injury |
| GSE142366 |
Dynamic transcriptional responses to injury of regenerative and non-regenerative cardiomyocytes revealed by single-nucleus RNA sequencing |
|
| Relations |
| BioSample |
SAMN13635359 |
| SRA |
SRX7416645 |
