← BioTransfer GEO Dataset Finder
GEO series

CLIP (NOVA1 & AGO) and RNAseq (control & NOVA1KD) in human GBM cells

GSE242124 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2024/03/06 Platform GPL24676Platform GPL15520
At a glance

RNA-seq (gene expression) · human · 36 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)
Samples
36 samples: 17 conditions, mostly in duplicateGroups 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
NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cellsProceedings of the National Academy of Sciences of the United States of America · 2024
Summary (written by the submitters)
GBM cells derived from a patient were subjected to CLIP and RNAseq assays to for transcriptome analysis (CLIP and RNAseq).
Published in
NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cells
Saito Y, Yang Y, Saito M et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 38416679 · doi:10.1073/pnas.2314695121
This dataset
Open GSE242124 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 GSE242124_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 PRJNA1011395 and SRA study SRP457903. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38416679) ↗
Study design
17 conditions, mostly in duplicate
CLIP_AGO_GBM ×4 CLIP_NOVA1_GBM1 ×2 CLIP_NOVA1_GBM2 ×2 CLIP_NOVA1_GBM3 ×2 CLIP_NOVA1_GBM4 ×2 RNAseq_GBM1_shControl ×2 RNAseq_GBM1_shNOVA1KD1 ×2 RNAseq_GBM1_shNOVA1KD2 ×2 +9 more

Supports a between-group comparison across 36 samples.

How we read this: 17 replicated groups read from 36 sample titles; they account for 36 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 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.