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Sample GSM7120224 Query DataSets for GSM7120224
Status Public on Feb 09, 2024
Title Susceptible
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics tissue: brain
strain: C57BL/6J
Sex: male
age: 8 weeks
sample group: Susceptible
Extracted molecule total RNA
Extraction protocol The brains were coronally cryosectioned at a thickness of 10 μm by Cryostat Microtome (Leica CM1950, Germany). Then 5-10 sections were selected to be stained with HE, photographed and tested for RNA integrity number (RIN) value
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing Spatial Transcriptomics
bcl2fastq command line tool was used for base calling Sequence reads were trimmed for adapter sequence and polyA homopolymers using cutadapt
Reads were mapped, annotated and demultiplexed using the spaceranger v1.0.0 command line tool
Annotated reads were quantified and mapped to the Hematoxylin and Eosin image using the spaceranger v1.0.0 command line tool
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: raw.zip include matrix with raw counts for every gene and every spot and spatial informations
Library strategy: Spatial Transcriptomics (Visium)
 
Submission date Mar 28, 2023
Last update date Feb 09, 2024
Contact name TING WANG
Organization name Beijing Institute of Basic Medical Sciences
Street address Haidian District, Beijing
City Beijing
ZIP/Postal code 100850
Country China
 
Platform ID GPL24247
Series (1)
GSE228394 Characterization of stress-susceptible cells and gene in mouse brain via Spatial Transcriptomics
Relations
BioSample SAMN33952600
SRA SRX19795828

Supplementary file Size Download File type/resource
GSM7120224_WT_Sus.tar.gz 58.9 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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