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Sample GSM6284972 Query DataSets for GSM6284972
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
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
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]
BioSample SAMN29472985
SRA SRX15971698

Supplementary file Size Download File type/resource
GSM6284972_83KO_hg19_mm10.tar.gz 626.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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