|
| Status |
Public on Jan 17, 2024 |
| Title |
cartana_iri12h_male |
| Sample type |
RNA |
| |
|
| Source name |
cartana_iri12h_male
|
| Organism |
Mus musculus |
| Characteristics |
genotype: C57BL/6
Sex: male
surgery: IRI 12 hours
tissue: Kidney
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA hybridization-based in situ sequencing protocol: Fresh kidneys were incubated in 2-methylbutane (Millipore, Sigma) equilibrated in liquid nitrogen to maintain RNA integrity. Tissues were then stored at −80°C and embedded in cryomolds using OCT (Tissue-Tek 4583) on dry ice. For frozen sectioning, OCT blocks were equilibrated to −18°C, and 10 μm-thick sections were mounted onto the glass slides (1358W; Globe Scientific). Libraries were prepared using the high sensitivity (HS) library preparation kit provided by CARTANA (Sweden) per manufacturer’s instruction. In brief, slides were fixed in freshly prepared formaldehyde diluted in 0.01% DEPC treated PBS, followed by permeabilization in 0.1M HCl (DEPC treated). After dehydration and rehydration in series of alcohol gradients, slides were incubated in RM1-mix (provided by the library kit) overnight at 37°C. Kidney sections were incubated in WB4 (library kit) at 37°C for 30 min. Gene probes were ligated in ligases dissolved in RM2 (library kit) at 37°C for 2 hours. Transcripts were amplified in RM3-mix (library kit) at 30°C overnight. Slides were stained with DAPI for quality control imaging and shipped to 10x Genomics for in situ sequencing.
|
| Label |
not applicable
|
| Label protocol |
not applicable
|
| |
|
| Hybridization protocol |
not applicable
|
| Scan protocol |
not applicable
|
| Description |
ISS by Cartana
|
| Data processing |
ISS data processing: ISS data was processed using our in-house pipeline called CellScopes https://github.com/TheHumphreysLab/CellScopes.jl.
Cell segmentation: Cell segmentation was performed using Baysor https://github.com/kharchenkolab/Baysor.
genome assembly: mm10
|
| |
|
| Submission date |
Mar 09, 2023 |
| Last update date |
Jan 17, 2024 |
| Contact name |
Haojia Wu |
| E-mail(s) |
haojiawu@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Renal Division/Internal Medicine
|
| Lab |
Humphreys Lab
|
| Street address |
600 S Euclid Ave
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
MO 63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL33238 |
| Series (2) |
| GSE227044 |
High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing [ISS, Cartana] |
| GSE227046 |
High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing |
|
