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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 04, 2024 |
| Title |
Mesenchymal glioma stem cells trigger vasectasia, a distinct neovascularization process mediated by extracellular vesicles carrying EGFR [scRNA-seq] |
| Organisms |
Homo sapiens; Mus musculus; synthetic construct |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
To investigate the functional role of EGFR in the formation of large vessels, we established a mesenchymal glioma stem cell line (GSC83) with intact EGFR and knocked down EGFR by Crispr-Cas9.
We then performed single cells gene expression profiling analysis using data obtained from RNA-seq of 2 different tumours, derived by injection of GSC83 WT or GSC83 KO in NSG mice. In addition, GSC83 WT or GSC83 KO tumours in NSG mice were subjected to spatial gene expression profiling in situ using GeoMX platform.
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| Overall design |
Comparative single cells gene expression profiling analysis of RNA-seq data for 83 wild type EGFR and its EGFR knockdown derivative (GSC83 WT vs. GSC83 KO).
For GeoMX spatial analysis, regions-of-interest were designated using anti-CD31 immunofluorescent tissue staining. Cells within/proximal to CD31-positive areas were profiled for mRNA expression.
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| Web link |
https://www.nature.com/articles/s41467-024-46597-x
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| Contributor(s) |
Spinelli C, Adnani L, Meehan B, Montermini L, Huang S, Kim M, Nishimura T, Croul SE, Nakano I, Riazalhosseini Y, Rak J |
| Citation(s) |
38570528 |
| Submission date |
Jul 01, 2022 |
| Last update date |
Apr 05, 2024 |
| Contact name |
Janusz Rak |
| E-mail(s) |
janusz.rak@mcgill.ca
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| Organization name |
McGill University
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| Department |
Department of Pediatrics
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| Lab |
Lab or Dr. Janusz Rak
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| Street address |
1001 Decarie Blvd. Room E01.4366
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4A 3J1 |
| Country |
Canada |
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| Platforms (3) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL25431 |
Illumina HiSeq 4000 (Homo sapiens; Mus musculus) |
| GPL26526 |
Illumina NovaSeq 6000 (synthetic construct) |
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| Samples (45)
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| GSM6284971 |
Mesenchymal glioma stem cells with intact EGFR (scRNA-seq) |
| GSM6284972 |
Mesenchymal glioma stem cells with depleted EGFR (scRNA-seq) |
| GSM8120929 |
No Template Control (GeoMx) |
| GSM8120930 |
Mouse1, KO, Small (GeoMx) |
| GSM8120931 |
Mouse2, WT, Large_1 (GeoMx) |
| GSM8120932 |
Mouse2, WT, Large_3 (GeoMx) |
| GSM8120933 |
Mouse2, WT, Large_4 (GeoMx) |
| GSM8120934 |
Mouse2, WT, Small-WT_1 (GeoMx) |
| GSM8120935 |
Mouse2, WT, Small-WT_2 (GeoMx) |
| GSM8120936 |
Mouse3, KO, Small_1 (GeoMx) |
| GSM8120937 |
Mouse2, WT, Small-WT_3 (GeoMx) |
| GSM8120938 |
Mouse3, KO, Small_2 (GeoMx) |
| GSM8120939 |
Mouse3, KO, Small_3 (GeoMx) |
| GSM8120940 |
Mouse4, WT, Large_1 (GeoMx) |
| GSM8120941 |
Mouse3, KO, Large-KO_1 (GeoMx) |
| GSM8120942 |
Mouse3, KO, Large-KO_2 (GeoMx) |
| GSM8120943 |
Mouse4, WT, Large_2 (GeoMx) |
| GSM8120944 |
Mouse4, WT, Large_3 (GeoMx) |
| GSM8120945 |
Mouse4, WT, Large_4 (GeoMx) |
| GSM8120946 |
Mouse4, WT, Small-WT_1 (GeoMx) |
| GSM8120947 |
Mouse4, WT, Small-WT_2 (GeoMx) |
| GSM8120948 |
Mouse4, WT, Small-WT_3 (GeoMx) |
| GSM8120949 |
Mouse4, WT, Small-WT_4 (GeoMx) |
| GSM8120950 |
Mouse2, WT, Large_2 (GeoMx) |
| GSM8120951 |
Mouse5, WT, Large_1 (GeoMx) |
| GSM8120952 |
Mouse5, WT, Large_2 (GeoMx) |
| GSM8120954 |
Mouse5, WT, Small-WT_1 (GeoMx) |
| GSM8120956 |
Mouse5, WT, Large_3 (GeoMx) |
| GSM8120958 |
Mouse5, WT, Small-WT_2 (GeoMx) |
| GSM8120960 |
Mouse5, WT, Small-WT_3 (GeoMx) |
| GSM8120962 |
Mouse6, KO, Small_1 (GeoMx) |
| GSM8120964 |
Mouse6, KO, Large-KO_1 (GeoMx) |
| GSM8120966 |
Mouse6, KO, Large-KO_2 (GeoMx) |
| GSM8120969 |
Mouse6, KO, Small_2 (GeoMx) |
| GSM8120971 |
Mouse7, CTRL, Small-CTRL_3 (GeoMx) |
| GSM8120973 |
Mouse7, CTRL, Large-CTRL_1 (GeoMx) |
| GSM8120975 |
Mouse5, WT, Outside_1 (GeoMx) |
| GSM8120977 |
Mouse5, WT, Outside_2 (GeoMx) |
| GSM8120979 |
Mouse5, WT, Outside_3 (GeoMx) |
| GSM8120981 |
Mouse6, KO, Outside_1 (GeoMx) |
| GSM8120983 |
Mouse6, KO , Outside_1 (GeoMx) |
| GSM8120985 |
Mouse6, KO, Outside_2 (GeoMx) |
| GSM8120987 |
Mouse7, CTRL, Large-CTRL_2 (GeoMx) |
| GSM8120989 |
Mouse7, CTRL, Small-CTRL_4 (GeoMx) |
| GSM8120991 |
Mouse7, CTRL, Small-CTRL_5 (GeoMx) |
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| Relations |
| BioProject |
PRJNA854923 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE207360_Human_Mouse_filtered.rds.gz |
3.9 Gb |
(ftp)(http) |
RDS |
| GSE207360_Human_Mouse_unfiltered.rds.gz |
19.3 Mb |
(ftp)(http) |
RDS |
| GSE207360_Mm_R_NGS_WTA_v1.0.pkc.gz |
1.8 Mb |
(ftp)(http) |
PKC |
| GSE207360_Q3_5__Filtered.xlsx |
3.8 Mb |
(ftp)(http) |
XLSX |
| GSE207360_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of DCC, TAR) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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