|
| Status |
Public on Nov 22, 2021 |
| Title |
female_sham |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
Sex: Female
tissue: Kidney
treatment: Sham control
timepoint: 2 days after sham surgery
platform: 10X Visium
|
| Treatment protocol |
Kidney injury was elicited in C57BL6 female mice (8-10 weeks of age) using a bilateral ischemia reperfusion injury paradigm where renal pedicles were clamped for 34 minutes under 1.8% isoflurane.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized according to approved IACUC protocols and kidney tissues were collected at four time points following injury, plus from one sham control mouse. All tissues were frozen and processed according to 10X Visium instructions.
Spatial RNA libraries were generated using standard protocol from 10X Visium.
Spatial RNA libraries from individual kidney slices (n=1 per timepoint).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Spatial transcriptomics
mRNA
|
| Data processing |
SpaceRanger: FASTQ files were aligned to mm10 reference and manually aligned to respective H&E stain images using 10X Genomics Space Ranger count (spatial 3’ v1; spaceranger-1.2.1). Aligned sequencing libraries from all time point samples were integrated using agg.
Data generation: Resulting image aligned sequencing files from SpaceRanger were loaded into (1) Seurat - Version 4.0.3 - https://satijalab.org/seurat/articles/spatial_vignette.html, (2) SPOTlight - https://marcelosua.github.io/SPOTlight/#07_Visualization, and (3) Giotto - http://spatialgiotto.rc.fas.harvard.edu/giotto.dataset.example.html. All reference data was previously published by Kirita et al., 2020 and available on http://humphreyslab.com/SingleCell/.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_processed.tar.gz: Each processed spatial data file includes the outputs of SpaceRanger - cloupe, molecule_info.h5, filtered_feature_matrix.h5, metrics_summary.csv, molecule_info.h5, raw_feature_bc_matrix.h5, and all spatial images (jpg and png) with scale factors and tissue positions.
|
| |
|
| Submission date |
Aug 27, 2021 |
| Last update date |
Nov 22, 2021 |
| Contact name |
Eryn E Dixon |
| E-mail(s) |
d.eryn@wustl.edu
|
| Phone |
3143621575
|
| Organization name |
Washington University in St. Louis
|
| Department |
Renal Division/Internal Medicine
|
| Lab |
Benjamin D. Humphreys
|
| Street address |
600 S Euclid Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE182939 |
Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model |
|
| Relations |
| BioSample |
SAMN21024014 |
| SRA |
SRX11951881 |
