|
| Status |
Public on Jun 19, 2021 |
| Title |
Tbx18 Sham (Heart) |
| Sample type |
SRA |
| |
|
| Source name |
Ventricles of the heart
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart
strain: Tbx18CreER/+;Rosa26tdT/+
treatment: Sham Surgery
|
| Treatment protocol |
LAD ligation in the heart tissue. Photothrombosis in the brain tissue.
|
| Growth protocol |
Intraperitoneal tamoxifen administration for 4 days followed by week washout period.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In the heart, atria were removed, and enzymatic digestion was performed using a Collagenase (Worthington) and Dispase (Sigma) mix. Cells were then sorted for tdT expression using fluorescence activated cell sorting. In the brain, cortical tissue was dissected and digested using the Miltenyi® Adult Brain Dissociation Kit. Cells were sorted for tdT expression using fluorescence activated cell sorting.
RNA libraries were prepared for sequencing using 3' 10X Genomics v.3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CellRanger mkfastq was used to demultiplex the base call files
CellRanger (v3.0.2) count with mm10 genome reference was used to perform read alignment and UMI counting and generate filtered feature barcode matrices
Filtering cells (Seurat v3): minimum features >500
Filtering features (Seurat v3): minimum cells >3
Normalization (Seurat v3): logNormalization
Number of variable features: (Brain) 7500; (Heart) 2000
Scaling (Seurat v3, default): ScaleData
Batch correction (Seurat v3): FindIntegrationAnchors & IntegrateData; Heart(dim=20, anchor.features=2000); Brain(dim=75, anchor.features=7500)
Dimensional reduction (Seurat v3): RunPCA; Heart (pca, dim = 30); Brain (pca, dim = 50)
Clustering (Seurat v3): FindNeighbors (Heart: dim = 20; Brain: dim = 50); FindClusters (resolution = 0.5)
Differential expression (Seurat v3):FindMarkers (min.pct=0.25)
Genome_build: mm10
Supplementary_files_format_and_content: Data is from filtered feature-barcode matrices generated by cellranger count. mtx (matrix table of count values for genes and samples) and tsv files (features/cellular barcodes)
|
| |
|
| Submission date |
Jun 18, 2021 |
| Last update date |
Jul 13, 2021 |
| Contact name |
Reza Ardehali |
| E-mail(s) |
RArdehali@mednet.ucla.edu
|
| Phone |
310-825-0819
|
| Organization name |
David Geffen School of Medicine at UCLA
|
| Department |
Internal Medicine, Division of Cardiology
|
| Lab |
MacDonald Research Laboratories (MRL) Bldg 3579
|
| Street address |
675 Charles E Young Dr S
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE178469 |
Pericytes exhibit a parallel pro-fibrotic response after vascular injury in the heart and brain |
|
| Relations |
| BioSample |
SAMN19775008 |
