|
| Status |
Public on Mar 04, 2024 |
| Title |
Mesenchymal glioma stem cells with depleted EGFR (scRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
83
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: 83
cell type: mesenchymal glioma stem cells
genotype: KO
treatment: human 83 cells injected in brain of NSG mouse
time: Day 90
|
| Treatment protocol |
The cells were injected in the brain of NSG mice.
|
| Growth protocol |
83 GSC WT and KO mesenchymal cells were maintained in DMEM-F12 supplemented with 100μg/ml EGF, 100μg/ml FGF, 0.2% Heparin, 1X B27 serum free supplement, 1% Glutamax and antibiotics in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole-tumor cells were dissociated and isolated using Collagenase/Dispase and resuspended in PBS for single-cell capture.
Following the Chromium Single Cell 3’ Reagent Kits v3 User Guide, a single-cell RNA library was generated using the GemCode Single-Cell Instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10x Genomics 3' CellPlex Multiplexing single cell
scRNA
Human_Mouse_filtered.rds
Human_Mouse_unfiltered.rds
|
| Data processing |
We used Cell Ranger v3.0.1 (10x Genomics) to demultiplex the raw sequencing reads to FASTQ files and align the reads to human and mouse reference hg19 and mm10 to quantify gene counts for each origin of species.
We loaded the gene count data using the Seurat package and separate the object to human and mouse ones for further quality controls.
Doublets were filtered out in each object, and cells were annotated based on consistent expression of lineage-specific markers.
Assembly: hg19, mm10
Supplementary files format and content: There are two forms of processed data: Gene count matrix by CellRanger (.tar) and Seurat analysis results (.rds). Each format of processed data include both unfiltered and filtered versions.
|
| |
|
| Submission date |
Jul 01, 2022 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Janusz Rak |
| E-mail(s) |
janusz.rak@mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Department of Pediatrics
|
| Lab |
Lab or Dr. Janusz Rak
|
| Street address |
1001 Decarie Blvd. Room E01.4366
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4A 3J1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL25431 |
| Series (1) |
| GSE207360 |
Mesenchymal glioma stem cells trigger vasectasia, a distinct neovascularization process mediated by extracellular vesicles carrying EGFR [scRNA-seq] |
|
| Relations |
| BioSample |
SAMN29472985 |
| SRA |
SRX15971698 |
