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Sample GSM8110557 Query DataSets for GSM8110557
Status Public on Feb 25, 2024
Title AI13-3
Sample type RNA
 
Source name Ankrd11-ncko
Organism Mus musculus
Characteristics genotype: Ankrd11-ncko
age: E11.5
Extracted molecule total RNA
Extraction protocol Vizgen provided protocols for requisite tissue type were utilized to conduct data acquisition
Label N/A
Label protocol N/A
 
Hybridization protocol N/A
Scan protocol N/A
Description merscope instrument
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
 
Submission date Feb 25, 2024
Last update date Feb 25, 2024
Contact name Anastassia Voronova
E-mail(s) voronova@ualberta.ca
Organization name University of Alberta
Department Department of Medical Genetics
Street address 8-39 Medical Sciences Building
City Edmonton
State/province Alberta
ZIP/Postal code T6G2H7
Country Canada
 
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]

Supplementary file Size Download File type/resource
GSM8110557_AI13-3-mat.tar.gz 6.1 Mb (ftp)(http) TAR

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