|
| Status |
Public on Sep 16, 2022 |
| Title |
M195845_m_band |
| Sample type |
SRA |
| |
|
| Source name |
Feline heart left ventricle
|
| Organism |
Felis catus |
| Characteristics |
tissue: Heart
Sex: Male
treatment: Banded
|
| Treatment protocol |
Aortic constriction (banding operation) or sham surgery (normal)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated from flash frozen post-mortem cardiac tissue for microfluidic encapsulation using 10X Genomics' 10X Genomics Chromium Controller v3.1 Next GEM Single Cell 3'. Approximately 100mg of tissue was sectioned to a thickness of 100um then subjected to differential centrifugation and filtering.
10X Genomics Chromium Controller v3.1 Next GEM Single Cell 3'
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: single nuclei RNA-seq
Cellranger 6.0.0 mkfastq to generate FASTQ
CutAdapt v2.8 to trim template switch oligo sequence and its complement, and homopolymers (A30, T30, G30, C30)
CellRanger Count v12 to generate count matrices
CellBender v2.0 to filter ambient RNA byproducts
Scrinvex v13 to filter likely cytoplasmic transcripts
Scrublet to remove doublets
Genome_build: Felis_catus_9.0
Supplementary_files_format_and_content: Normalized and log scale count matrix
|
| |
|
| Submission date |
Sep 17, 2021 |
| Last update date |
Sep 16, 2022 |
| Contact name |
Nathan Tucker |
| E-mail(s) |
ntucker@mmri.edu
|
| Organization name |
Masonic Medical Research Institute
|
| Street address |
2150 Bleecker St
|
| City |
Utica |
| State/province |
NY |
| ZIP/Postal code |
13501 |
| Country |
USA |
| |
|
| Platform ID |
GPL28702 |
| Series (1) |
| GSE184328 |
Cardiopulmonary Phenotyping of Sex-Based Differences in a Feline Model of HFpEF |
|
| Relations |
| BioSample |
SAMN21468805 |
| SRA |
SRX12219228 |
