|
| Status |
Public on Feb 09, 2024 |
| Title |
Control |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
strain: C57BL/6J
Sex: male
age: 8 weeks
sample group: Control
|
| 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 |
SAMN33952602 |
| SRA |
SRX19795826 |
