← BioTransfer GEO Dataset Finder
GEO series

PolyA RNA-seq from Medulloblastoma cells ± EYA2 knockdown

GSE230865 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/04/28 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 18 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
MedulloblastomaThis series is part of our curated briefing on it.
Samples
18 samples: 6 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
EYA2 tyrosine phosphatase inhibition reduces MYC and prevents medulloblastoma progressionNeuro-oncology · 2023
Summary (written by the submitters)
Analysis of steady-state mRNA levels in two medulloblastoma-derived cell lines.
Published in
EYA2 tyrosine phosphatase inhibition reduces MYC and prevents medulloblastoma progression
Wolin AR, Vincent MY, Hotz T et al. · Neuro-oncology 2023 · PMID 37486991 · doi:10.1093/neuonc/noad128
This dataset
Open GSE230865 in finder → Find more human RNA-seq datasets → Medulloblastoma 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 GSE230865_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA962875 and SRA study SRP435044. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37486991) ↗
Study design
6 conditions, mostly in triplicate
Group 3 MB D425 cells, non-targeting control, ×3 Group 3 MB D425 cells, EYA2 shRNA#6, ×3 Group 3 MB D425 cells, EYA2 shRNA#8, ×3 Group 3 MB D458 cells, non-targeting control, ×3 Group 3 MB D458 cells, EYA2 shRNA#7 ×3 Group 3 MB D458 cells, EYA2 shRNA#8, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 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
More Medulloblastoma datasets

Search all human 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.