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Single-cell RNA sequencing of patient-derived xenograft meningiomas

GSE239795 Homo sapiens (human) Single-cell RNA-seq 23 samples Submitted 2024/05/03 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 23 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
23 samples: 7 conditions, mostly in triplicateGroups 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
Perivascular NOTCH3+ Stem Cells Drive Meningioma Tumorigenesis and Resistance to RadiotherapyCancer discovery · 2024
Summary (written by the submitters)
We report single-cell RNA sequencing of 23 PDX meningiomas that underwent radiation therapy, were treated with a Notch3 neutralizing antibody, or overexpressed Notch3.
Published in
Perivascular NOTCH3+ Stem Cells Drive Meningioma Tumorigenesis and Resistance to Radiotherapy
Choudhury A, Cady MA, Lucas CG et al. · Cancer discovery 2024 · PMID 38742767 · doi:10.1158/2159-8290.CD-23-1459
This dataset
Open GSE239795 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 GSE239795_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 PRJNA1000978 and SRA study SRP452657. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38742767) ↗
Study design
7 conditions, mostly in triplicate
PDX meningioma, control, no radiation, ×5 PDX meningioma, Notch3 OE, no radiation, ×3 PDX meningioma, Notch3 OE, early radiation, ×3 PDX meningioma, Notch3 OE, late radiation, ×3 PDX meningioma, Notch3 ab, no radiation, ×3 PDX meningioma, control, early radiation, ×3 PDX meningioma, control, late radiation, ×3

Supports a between-group comparison across 23 samples.

How we read this: 7 replicated groups read from 23 sample titles; they account for 23 of them. 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

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