GEO series

Glioblastoma-cortical organoids recapitulate cell state heterogeneity and intercellular transfer

GSE276838 Homo sapiens (human) Single-cell RNA-seq 29 samples Submitted 2024/10/01 Platform GPL30172Platform GPL30173

At a glance

Single-cell RNA-seq · human · 29 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Topic: GlioblastomaThis series is part of our curated briefing on it.
Samples: 29 samples: 29 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Glioblastoma is characterized by heterogeneous malignant cells that are functionally integrated within the neuroglial microenvironment. Here, we model this ecosystem by growing glioblastoma into long-term cultured human cortical organoids that contain the major neuroglial cell types found in the cerebral cortex. Single-cell RNA-seq analysis suggests that, compared to matched gliomasphere models, glioblastoma cortical organoids (GCO) more faithfully recapitulate the diversity and expression programs of malignant cell states found in patient tumors.

Read the full summary ↓

Additionally, we observe widespread transfer of glioblastoma transcripts and GFP proteins to non-malignant cells in the organoids. Mechanistically, this transfer involves extracellular vesicles and is biased towards defined glioblastoma cell states and astroglia cell types. These results extend previous glioblastoma-organoid modeling efforts and suggest widespread intercellular transfer in the glioblastoma neuroglial microenvironment.

This dataset

Open GSE276838 in finder → Find more RNA-seq datasets → Glioblastoma landscape →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE276838_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1159203 and SRA study SRP531862. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

29 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 29 sample titles: 29 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8506473 purified EVs from m005_11A GCOs, bulk RNA-seq
GSM8506474 purified EVs from 11A cortical organoids, bulk RNA-seq
GSM8506475 purified EVs from m005 cell line, bulk RNA-seq
GSM8506476 m005 GCO, GFPpos (FACS), scRNA-seq
GSM8506477 m005 GCO, GFPneg (FACS), scRNA-seq
GSM8506478 MDA-231 GCO, GFPpos (FACS), scRNA-seq
GSM8506479 MDA-231 GCO, GFPneg (FACS), scRNA-seq
GSM8506480 MGG101 GCO, GFPpos and GFPneg gene expression
GSM8506481 MGG101 GCO, GFPpos and GFPneg feature barcoding
GSM8506482 MGG123 GCO, GFPpos (FACS), scRNA-seq
GSM8506483 MGG123 GCO, GFPneg (FACS), scRNA-seq
GSM8506484 MGG125 GCO, GFPpos (FACS), scRNA-seq
GSM8506485 MGG125 GCO, GFPneg (FACS), scRNA-seq
GSM8506486 MGG23_H1 GCO, GFPpos (FACS), scRNA-seq
GSM8506487 MGG23_H1 GCO, GFPneg (FACS), scRNA-seq
GSM8506488 MGG23_11A GCO, GFPpos and GFPneg gene expression
GSM8506489 MGG23_11A GCO, GFPpos and GFPneg feature barcoding
GSM8506490 MGG23_PGP1 GCO, GFPpos (FACS), scRNA-seq
GSM8506491 MGG23_PGP1 GCO, GFPneg (FACS), scRNA-seq
GSM8506492 MGG65 GCO, GFPpos (FACS), scRNA-seq
GSM8506493 MGG65 GCO, GFPneg (FACS), scRNA-seq
GSM8506494 MGG70 GCO, GFPpos (FACS), scRNA-seq
GSM8506495 MGG70 GCO, GFPneg (FACS), scRNA-seq
GSM8506496 MGG75 GCO, GFPpos (FACS), scRNA-seq
GSM8506497 MGG75 GCO, GFPneg (FACS), scRNA-seq
GSM8506498 MGG87 GCO, tdTpos (FACS), scRNA-seq
GSM8506499 MGG87 GCO, tdTneg (FACS), scRNA-seq
GSM8506500 MGH143 GCO, GFPpos (FACS), scRNA-seq
GSM8506501 MGH143 GCO, GFPneg (FACS), scRNA-seq

More Glioblastoma datasets

GSE231555 Splicing and gene expression changes in cell lines treated with splicing switching oligonucleotide targeting TRA2B 46 samples same disease briefing
GSE112648 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 18 samples same disease briefing
GSE131928 single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas 2 samples same disease briefing
GSE107560 Ivy Glioblastoma Atlas Project 305 samples same disease briefing
GSE13041 Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age 267 samples same disease briefing
GSE112650 SOX4/11 Enhances NGN2 Reprogramming Glioblastoma Cells into Neuron Cells by Modulating RhoA and CDC42/RAC1 Pathway Activity 30 samples same disease briefing
GSE112645 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 12 samples same disease briefing
GSE10878 Integrative Genome-wide Analysis of Glioblastoma. 60 samples same disease briefing

Search all RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.