|
| Status |
Public on Dec 08, 2020 |
| Title |
scRNA-seq_P8_1Sham |
| Sample type |
SRA |
| |
|
| Source name |
Single cells isolated from ventricle tissue below left anterior descending artery ligation plane
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR/CD1
tissue: ventricle
surgery performed at developmental age: P8
sample collected at post-surgical day: day1
surgery type: Sham
|
| Treatment protocol |
Neonatal P1 or P8 mice were subjected to myocardial infarction, induced by permanent ligation of LAD coronary artery, or sham surgery.
|
| 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 |
total RNA |
| Extraction protocol |
Mice were euthanized at 1d or 3d post surgery. Ventricle tissues below LAD ligation plane from MI hearts, and ventricle tissues from similar region of sham hearts, were collected and digested into single cell suspension.
Single cells digested from the tissue were subjected to single cell RNA-sequencing using 10xGenomics platform. Library preparation was performed using Single Cell 3’ Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
P8+1 dps
|
| Data processing |
The Cell Ranger Single-Cell Software Suit (10xGenomics) was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.
The cDNA reads were aligned to the mm10/GRCm38 mRNA reference genome to generated gene-barcode matrix.
R package Seurat was used for downstream quality filtering and data analysis. Potential cell doublets, red blood cells, and low quality cells were removed from the data.
Data were normalized and scaled, taken number of genes (nGene) and unique molecular/ identifiers (nUMI) into consideration.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated value (tsv) files and matrix (mtx) files for filtered gene barcode matrices generated from CellRanger primary analysis from raw sequencing data.
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Dec 08, 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) |
| GSE153480 |
Single cell RNA-seq of neonatal heart regeneration |
| GSE153481 |
Cell-type-specific gene regulatory networks underlying murine neonatal heart regeneration at single-cell resolution |
|
| Relations |
| BioSample |
SAMN15398546 |
| SRA |
SRX8632242 |
