|
| Status |
Public on Mar 18, 2020 |
| Title |
P1MID3 |
| 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
surgery performed at developmental age: P1
sample collected at post-surgical day: day 3
surgery type: MI
cell type: cardiomyocytes
|
| 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 injury. Ventricle tissues below LAD ligation plane from MI hearts, and ventricle tissues at similar region from sham 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 Single Cell 3’ Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol.
Single Cell RNA-Seq (Single Nucleus RNA-Seq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
P1_8_AllCM.txt
|
| 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 premRNA reference genome to generated gene-barcode matrix.
R package Seurat was used for downstream quality filtering and data analysis. Potential cell doublets 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.
Normalized expression matrix was output from Seurat R object.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files of normalized gene expression value for nuclei analyzed; 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 |
May 03, 2019 |
| Last update date |
Mar 19, 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) |
| GSE130699 |
Single nucleus RNA-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 |
SAMN11570054 |
| SRA |
SRX5786030 |
