|
| Status |
Public on Oct 14, 2023 |
| Title |
Control Male |
| Sample type |
RNA |
| |
|
| Source name |
Control_Male
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ascending aorta
disease state: control (non-aneurysmal)
Sex: Male
age: 59
ascending aorta diameter: Non-aneurysmal
number of cells: 6753
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Surgically resected ascending aorta samples from two non-aneurysmal (Control) subjects and three TAA subjects with ascending aneurysms were embedded and frozen in Optimal cutting temperature compound (OCT). OCT-embedded ascending aorta samples were cut into 10 μm sections and adhered onto the imageable area of Vizgen slides. The slides were fixed in pre-heated 4% paraformaldehyde for 30 minutes in an incubator. Subsequent slide processing was performed according to Fresh Frozen Tissue preparation protocol by Vizgen. Hybridization of custom MERFISH probes targeting 140 genes were performed by Vizgen according to the MERSCOPE User Guide.
|
| Label |
N/A
|
| Label protocol |
https://vizgen.com/technology/#merfish
|
| |
|
| Hybridization protocol |
https://vizgen.com/technology/#merfish
|
| Scan protocol |
N/A
|
| Data processing |
Cell segmentation boundaries were determined using the default MERFISH approach (Zhang et al., 2021). The Vizgen MERSCOPE data and cell boundaries were inputted to Seurat 4.2 (R package) using LoadVizgen function. Cells with less than 20 molecules were discarded. SCTransform function was used to normalize the data. Unsupervised clustering and dimensionality reduction were performed using Seurat to identify spatially-resolved cell types on the merged dataset of two control and three TAA samples.
*Molecules.txt are raw data files that contain spatial coordinates for each molecule
*Segmentation.txt are processed data files that contain spatial coordinates describing segmentation of each cell
*Matrix.txt are processed data files that contain detected transcripts in each cell.
|
| |
|
| Submission date |
Aug 29, 2023 |
| Last update date |
Oct 14, 2023 |
| Contact name |
Dogukan Mizrak |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Department |
Cardiac Surgery
|
| Street address |
NCRC Building 26, 263S
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL33428 |
| Series (1) |
| GSE241870 |
MERSCOPE profiling of non-aneurysmal and aneurysmal human ascending aorta |
|
