STAG2 mutations and 3D genome organization, chromatin loops, and polycomb signaling in glioblastoma multiforme
RNA-seq (gene expression) · human · 20 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
- GlioblastomaThis series is part of our curated briefing on it.
- Samples
- 20 samples: 16 distinct titles, 4 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
- STAG2 mutations regulate 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiformeThe Journal of biological chemistry · 2024
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE240343_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1003411 and SRA study SRP454002. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 20 sample titles: 16 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.
- GSM7696517 H4 parental replicate 1
- GSM7696518 H4 parental replicate 2
- GSM7696519 H4 88-1 replicate 1
- GSM7696520 H4 88-1 replicate 2
- GSM7696521 42MGBA parental replicate 1
- GSM7696522 42MGBA parental replicate 2
- GSM7696523 42MGBA 53-1 replicate 1
- GSM7696524 42MGBA 53-1 replicate 2
- GSM7698149 H4 parental replicate 1 [RNA-seq]
- GSM7698150 H4 parental replicate 2 [RNA-seq]
- GSM7698151 H4 parental replicate 3 [RNA-seq]
- GSM7698152 H4 88-1 replicate 1 [RNA-seq]
- GSM7698153 H4 88-1 replicate 2 [RNA-seq]
- GSM7698154 H4 88-1 replicate 3 [RNA-seq]
- GSM7698155 42MGBA parental replicate 1 [RNA-seq]
- GSM7698156 42MGBA parental replicate 2 [RNA-seq]
- GSM7698157 42MGBA parental replicate 3 [RNA-seq]
- GSM7698158 42MGBA 53-1 replicate 1 [RNA-seq]
- GSM7698159 42MGBA 53-1 replicate 2 [RNA-seq]
- GSM7698160 42MGBA 53-1 replicate 3 [RNA-seq]
- GSE107560 Ivy Glioblastoma Atlas Project 305 samples same disease briefing · shares glioblastoma
- GSE13041 Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age 267 samples same disease briefing · shares glioblastoma
- GSE10878 Integrative Genome-wide Analysis of Glioblastoma. 60 samples same disease briefing · shares glioblastoma
- GSE112650 SOX4/11 Enhances NGN2 Reprogramming Glioblastoma Cells into Neuron Cells by Modulating RhoA and CDC42/RAC1 Pathway Activity 30 samples same disease briefing · shares glioblastoma
- GSE112648 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 18 samples same disease briefing · shares glioblastoma
- GSE112645 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 12 samples same disease briefing · shares glioblastoma
- GSE115459 Exosome-transmitted RVT1 from reactive astrocytes promotes recurrence glioblastoma proliferation 9 samples same disease briefing · shares glioblastoma
- GSE131928 single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas 2 samples same disease briefing · shares glioblastoma
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.