|
| Status |
Public on Jan 01, 2025 |
| Title |
Endpoint_rep_4 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
genotype: NestinCre/+; p53f/f; Ptenf/+; R26td/+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1) Tumourigenesis atlas samples: fresh brain tissue was harvested from mutant mice at four MRI-defined stages: the “preneoplastic” stage at which the brain imaging shows no signs of neoplastic lesion development; the “early lesion” stage characterized by small abnormalities seen on T2/FLAIR MRI sequences; the “mid-lesion” stage when the lesion has reached a larger size as indicated by T2/FLAIR-bright mass in asymptomatic animals and occupies a significant fraction of the brain hemisphere; and, finally, the “endpoint” stage when mice develop symptoms of raised intracranial pressure or focal neurologic abnormalities, with the tumour extending over a large portion of the brain hemisphere(s), typically with midline shift. Each brain sample was dissociated followed by fluorescent activated cell sorting to separate the mutant (tdTomato+) cells from non-mutant (tdTomato-) cells. Following sorting, both populations were characterized by scRNA-seq using the 10X Genomics platform. 2) Brain injury samples: we removed the cannula on day 5 and collected brain samples at the 5-days post-implantation (5dpi) timepoint as well as 7 days following the removal of the cannula (12dpi timepoint). For each timepoint, we processed the ipsilateral (IP) and contralateral (CR) hemispheres separately so the latter could serve as an internal control. Each sample was dissociated into single cells followed by FACS sorting of the GFP+ and GFP- cells and then each processed for scRNA-seq using the 10X Genomics platform.
We used the 10X Genomics platform according to the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
tumourigenesis.atlas.RData
malignant.cells.Sox2CEPPT.and.NestinCPPT.models.RData
|
| Data processing |
Raw sequencing data were aligned to the mm10 mouse reference using Cell Ranger (v3.1.0). Doublets and multiplets were identified by scDblFinder (v1.4.0), and low-quality cells (percent of mitochondrial > 12%; number of genes detected per cell < 800; number of Unique Molecular Identifier (UMI) per cell < 500) were removed as part of the QC process. Seurat (v4.5) was used to cluster data from all samples together and perform the downstream analyses.
Assembly: mm10
Supplementary files format and content: Seurat RData - tumourigenesis atlas samples
Supplementary files format and content: Seurat RData - malignant cells from the Sox2CEPPT and NestinCPPT mouse models samples (isolated from the tumourigenesis atlas)
Supplementary files format and content: Seurat RData - brain injury samples (Sox2eGFP mice)
|
| |
|
| Submission date |
Jun 03, 2024 |
| Last update date |
Jan 01, 2025 |
| Contact name |
Akram Hamed |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Toronto
|
| Department |
Molecular Genetics
|
| Street address |
NA
|
| City |
Toronto |
| ZIP/Postal code |
NA |
| Country |
Canada |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE278511 |
Gliomagenesis mimics an injury response orchestrated by neural crest-like cells |
|
| Relations |
| BioSample |
SAMN41610482 |
| SRA |
SRX24761022 |
