← BioTransfer GEO Dataset Finder
GEO series

Single-nucleus RNA-sequencing (snRNA-Seq) of brain cells from tumor-bearing C57BL/6 mice

GSE246154 Mus musculus (mouse) Single-nucleus RNA-seq 19 samples Submitted 2024/03/28 Platform GPL30172Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 19 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Mus musculus (mouse)
Samples
19 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.
Summary (written by the submitters)
GL261-derived glioblastoma stem cells (GSCs) form aggressive tumors when implanted into the brains of C57BL/6 mice. We used snRNA-Seq to analyze GL261 and GL261-GSCs as well as tumor samples of 7 and 28 days of development.
This dataset
Open GSE246154 in finder → Find more mouse 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 GSE246154_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 PRJNA1031664 and SRA study SRP468204. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 conditions, mostly in triplicate
GL261-GSCs ×3 Mouse GL261-GSC glioblastoma peptide 7d ×3 Mouse GL261-GSC glioblastoma TMZ 7d ×3 Mouse GL261-GSC glioblastoma TMZ 28d ×3 GL261 cells ×2 Mouse GL261-GSC glioblastoma control 7d ×2 Mouse GL261-GSC glioblastoma control 28d ×2 Mouse GL261-GSC glioblastoma peptide 28d ×1

Supports a between-group comparison across 18 samples.

How we read this: 7 replicated groups read from 19 sample titles; they account for 18 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

Search all mouse 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.