|
| Status |
Public on Jun 19, 2024 |
| Title |
uninjure, caudal 1mm from epicenter |
| Sample type |
SRA |
| |
|
| Source name |
spinal cord
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spinal cord
treatment: sham
|
| Treatment protocol |
a complete transection of the spinal cord of C57BL/6J mice at the tenth thoracic vertebra was performed.
|
| Growth protocol |
Adult female mice of 8-9 weeks old were used in the SCI.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Four consecutive spinal cord cryosections were cut at 20-μm thickness each and attached to one of the four capture areas of the Visium Spatial Gene Expression slides (10x Genomics, 1000184).
The spatial transcriptomics library was constructed according to the Visium Spatial Gene Expression Reagent Kits User Guide (10x Genomics, CG000239 Rev D).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Fresh frozen Spatial transcriptome sequencing
|
| Data processing |
The raw Visium spatial RNA-seq data and histological H&E images were processed using the Space Ranger pipeline (v.1.0.0, 10x Genomics) to align and summarize unique molecular identifier (UMI) counts according to the reference genome “Mouse Genome mm10”.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count of each tissue spot in Hierarchical Data Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tiisue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the coordinates specifying spots
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Feb 22, 2024 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Guangdun Peng |
| Organization name |
Chinese Academy of Sciences
|
| Department |
Guangzhou Institute of Biomedicine and Health
|
| Lab |
Guangdun Peng's lab
|
| Street address |
Kaiyuan Ave 190
|
| City |
Guangzhou |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE256397 |
A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2 |
|
| Relations |
| BioSample |
SAMN40043395 |
| SRA |
SRX23708662 |
