|
| Status |
Public on Aug 10, 2024 |
| Title |
28day_4 |
| Sample type |
other |
| |
|
| Source name |
Glioblastoma
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: Ntva-INK4a_ARF−/−
grade: Grade IV
time point: D28
replicate: 4
|
| Treatment protocol |
3 mice were sacraficed at this time point prior to the initiation of treatment. 10 mice were treated daily with 200 mg/kg BLZ945 (Novartis), 3 were sacraficed 7-days post treatment, 4 at 28-days and 3 after rebound.
|
| Growth protocol |
Gliobastomas were induced in mice using the RCAS model system at 5-weeks of age. Mice were monitored by MRI over the next 6 weeks until tumors developed that were at least 30 mm3 in volume.
|
| Extracted molecule |
other |
| Extraction protocol |
Mice were euthanised with pentobarbitol, intercardiacally perfused with cold PBS and PLP, and brains were extracted. Brains were embedded in OCT and cryosectioned onto Xenium slides. Slides were processed and labelled with the 10X Mouse Brain gene probe panel plus a 100-plex add on gene panel following the 10X Xenium workflow. Single-cell gene expression was measured for each slide on the Xenium Analyzer.
|
| Label |
n/a
|
| Label protocol |
n/a
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
Image pre-processing, puncta detection, transcript decoding and quality score assignment was perofrmed via on-board analysis software Xenium Analyzer.
|
| Data processing |
Xenium analyzer performed read quantification and generated cell by gene count matrix.
matrix.mtx.gz: Gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes.
features.tsv.gz: Gene feature info
barcodes.tsv.gz: Barcode sequences that correspond to column indices in matrix.mtx.
transcript.csv.gz: Transcript quality and localization info
cells.csv.gz: Cell summary and transcript count info for each identified cell
gene_panel.json.gz: JSON file
|
| |
|
| Submission date |
May 07, 2024 |
| Last update date |
Aug 10, 2024 |
| Contact name |
Nadine Fournier |
| E-mail(s) |
nadine.fournier@sib.swiss
|
| Organization name |
Agora Cancer Research Center & Swiss Institute of Bioinformatics
|
| Lab |
Translational Data Science Facility
|
| Street address |
Agora Cancer Research Center, Bugon 25A
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1000 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL33896 |
| Series (2) |
| GSE266969 |
Spatial transcriptomics profile at single cell level of murine glioblastomas treated with and without anti-CSF-1R inhibitors. |
| GSE266971 |
Spatial and scRNAseq profiling of murine glioblastomas treated with and without anti-CSF-1R inhibitors |
|
