|
| Status |
Public on Jun 08, 2024 |
| Title |
Vehicle, Spatial Transcriptomics |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
condition: unilateral ureteral obstruction (UUO) surgery
treatment: Vehicle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh frozen tissue were OCT embedded, and 10 μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Assembly: mm10
Supplementary files format and content: barcodes.tsv: lust of spatial barcodes
Supplementary files format and content: genes.tsv: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
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 tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Jun 04, 2024 |
| Last update date |
Jun 08, 2024 |
| Contact name |
Yao Xu |
| E-mail(s) |
yao.xu@med.uni-greifswald.de
|
| Organization name |
University Medicine Greifswald
|
| Street address |
Felix-Hausdorff-Straße 3
|
| City |
Greifswald |
| State/province |
State |
| ZIP/Postal code |
17487 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE269063 |
scRNA-Seq reveals anti-fibrotic mechanisms of TRPC6 inhibition [Spatial Transcriptomics] |
|
| Relations |
| BioSample |
SAMN41673855 |
| SRA |
SRX24798096 |
