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| Status |
Public on Feb 25, 2024 |
| Title |
AH50-1 |
| Sample type |
RNA |
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| Source name |
Ankrd11-ncko
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| Organism |
Mus musculus |
| Characteristics |
genotype: Ankrd11-ncko
age: E11.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
Vizgen provided protocols for requisite tissue type were utilized to conduct data acquisition
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| Label |
N/A
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| Label protocol |
N/A
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| Hybridization protocol |
N/A
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| Scan protocol |
N/A
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| Description |
merscope instrument
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| Data processing |
Following generation of MERSCOPE outputs and cell segmentation via Cellpose, gene count matrices and cell centroid definitions were defined using squidpy (v1.3.1).
Cells were categorized as within our outside the heart for the purpose of this study via their spatial position, utilizing user input to define a bounding box around the heart.
Data and metadata generated previously was then analyzed using the Seurat library (v5.0.1), conducting blind clustering to determine cell identities, then determining DEGs between experimental conditions for relevant conditions.
processed data files format and content
*-mat.tar.gz: gzipped tar archive folder containing 3 files: bb.csv, a table defining the bounding box used to categorize cells as outside or within the heart; centroids.csv, a table containing x and y coordinates for centroids defining each cell boundary; counts.csv, a table containing raw counts of RNA levels for each cell (rows - gene symbols, columns - cell IDs)
metadata.csv: table defining per-cell metadata values, including clustering assignments, sample name, localization
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| Submission date |
Feb 25, 2024 |
| Last update date |
Feb 25, 2024 |
| Contact name |
Anastassia Voronova |
| E-mail(s) |
voronova@ualberta.ca
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| Organization name |
University of Alberta
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| Department |
Department of Medical Genetics
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| Street address |
8-39 Medical Sciences Building
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| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G2H7 |
| Country |
Canada |
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| Platform ID |
GPL31217 |
| Series (1) |
| GSE258835 |
Ankrd11, a chromatin regulator and a KBG syndrome risk gene, is a critical regulator of cardiac neural crest cell biology and heart development [MERSCOPE] |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM8110555_AH50-1-mat.tar.gz |
5.7 Mb |
(ftp)(http) |
TAR |
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