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Bulk and single cell RNA sequencing analyses of GBM Primary and Recurrent, early and late passages, DMSO / TMZ treatment.

GSE278154 Homo sapiens (human) Single-cell RNA-seq 37 samples Submitted 2024/11/22 Platform GPL24676Platform GPL16791
At a glance

Single-cell RNA-seq · human · 37 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
37 samples: 36 distinct titles, 1 of them repeatedGroups 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.
Paper
Glioblastoma functional heterogeneity and enrichment of cancer stem cells with tumor recurrenceNeuron · 2024
Summary (written by the submitters)
We used bulk RNA sequencing to analyze unsupervised clustering of early and late passages of four GBM PDXs. Single cell RNAseq data was used to study transcriptional profiles of DMSO and TMZ, Primary and Recurrent as well as early and late passages of GBM PDXs.
Published in
Glioblastoma functional heterogeneity and enrichment of cancer stem cells with tumor recurrence
Xie XP, Ganbold M, Li J et al. · Neuron 2024 · PMID 39510072 · doi:10.1016/j.neuron.2024.10.012
This dataset
Open GSE278154 in finder → Find more human RNA-seq datasets →
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 GSE278154_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 PRJNA1165770 and SRA study SRP535250. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39510072) ↗
Study design
36 distinct titles, 1 of them repeated
180327-I-PO-I ×2

How we read this: Read from 37 sample titles: 36 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
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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