Metabolic regulation of the glioblastoma stem cell epitranscriptome by malate dehydrogenase 2 (MDH2)
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
- GlioblastomaThis series is part of our curated briefing on it.
- Samples
- 18 samples: 9 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
- Metabolic regulation of the glioblastoma stem cell epitranscriptome by malate dehydrogenase 2Cell metabolism · 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 GSE255535_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 PRJNA1075313 and SRA study SRP489237. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 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.
- GSM8074017 GSCs, shCONT set 1 GSCs, shCONT
- GSM8074018 GSCs, shMDH2-03_set 1 GSCs, shMDH2-03
- GSM8074019 GSCs, ShMDH2-63_set 1 GSCs, ShMDH2-63
- GSM8074020 GSCs, shCONT set 2 GSCs, shCONT
- GSM8074021 GSCs, shMDH2-03_set 2 GSCs, shMDH2-03
- GSM8074022 GSCs, ShMDH2-63_set 2 GSCs, ShMDH2-63
- GSM8291331 GSCs, shCONT_in01 GSCs, shCONT_in
- GSM8291332 GSCs, shCONT_in02 GSCs, shCONT_in
- GSM8291333 GSCs, shCONT_IP01 GSCs, shCONT_IP
- GSM8291334 GSCs, shCONT_IP02 GSCs, shCONT_IP
- GSM8291335 GSCs, shMDH2_03_in01 GSCs, shMDH2_03_in
- GSM8291336 GSCs, shMDH2_03_in02 GSCs, shMDH2_03_in
- GSM8291337 GSCs, shMDH2_03_IP01 GSCs, shMDH2_03_IP
- GSM8291338 GSCs, shMDH2_03_IP02 GSCs, shMDH2_03_IP
- GSM8291339 GSCs, shMDH2_63_in01 GSCs, shMDH2_63_in
- GSM8291340 GSCs, shMDH2_63_in02 GSCs, shMDH2_63_in
- GSM8291341 GSCs, shMDH2_63_IP01 GSCs, shMDH2_63_IP
- GSM8291342 GSCs, shMDH2_63_IP02 GSCs, shMDH2_63_IP
- 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.