Single cell RNA-seq analysis of IDH-mutant astrocytoma
Single-cell RNA-seq · human · 6341 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- Lower-grade gliomaThis series is part of our curated briefing on it.
- Samples
- 6341 samples: 43 conditions, mostly with about 9 replicates eachGroups 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.
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 GSE89567_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: 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 PRJNA352580. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 399 samples.
How we read this: 43 replicated groups read from the first 400 of 6341 sample titles; they account for 399 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.
- GSM2377571 MGH42_P7_A01 MGH42_P7_A
- GSM2377572 MGH42_P7_A02 MGH42_P7_A
- GSM2377573 MGH42_P7_A03 MGH42_P7_A
- GSM2377574 MGH42_P7_A04 MGH42_P7_A
- GSM2377575 MGH42_P7_A05 MGH42_P7_A
- GSM2377576 MGH42_P7_A07 MGH42_P7_A
- GSM2377577 MGH42_P7_A09 MGH42_P7_A
- GSM2377578 MGH42_P7_A11 MGH42_P7_A
- GSM2377579 MGH42_P7_A12 MGH42_P7_A
- GSM2377580 MGH42_P7_B02 MGH42_P7_B
- GSM2377581 MGH42_P7_B03 MGH42_P7_B
- GSM2377582 MGH42_P7_B05 MGH42_P7_B
- GSM2377583 MGH42_P7_B06 MGH42_P7_B
- GSM2377584 MGH42_P7_B07 MGH42_P7_B
- GSM2377585 MGH42_P7_B08 MGH42_P7_B
- GSM2377586 MGH42_P7_B09 MGH42_P7_B
- GSM2377587 MGH42_P7_B12 MGH42_P7_B
- GSM2377588 MGH42_P7_C01 MGH42_P7_C
- GSM2377589 MGH42_P7_C02 MGH42_P7_C
- GSM2377590 MGH42_P7_C03 MGH42_P7_C
- GSM2377591 MGH42_P7_C05 MGH42_P7_C
- GSM2377592 MGH42_P7_C06 MGH42_P7_C
- GSM2377593 MGH42_P7_C07 MGH42_P7_C
- GSM2377594 MGH42_P7_C08 MGH42_P7_C
- GSM2377595 MGH42_P7_C09 MGH42_P7_C
- GSM2377596 MGH42_P7_C11 MGH42_P7_C
- GSM2377597 MGH42_P7_C12 MGH42_P7_C
- GSM2377598 MGH42_P7_D03 MGH42_P7_D
- GSM2377599 MGH42_P7_D04 MGH42_P7_D
- GSM2377600 MGH42_P7_D05 MGH42_P7_D
- GSM2377601 MGH42_P7_D06 MGH42_P7_D
- GSM2377602 MGH42_P7_D07 MGH42_P7_D
- GSM2377603 MGH42_P7_D10 MGH42_P7_D
- GSM2377604 MGH42_P7_D11 MGH42_P7_D
- GSM2377605 MGH42_P7_D12 MGH42_P7_D
- GSM2377606 MGH42_P7_E01 MGH42_P7_E
- GSM2377607 MGH42_P7_E02 MGH42_P7_E
- GSM2377608 MGH42_P7_E04 MGH42_P7_E
- GSM2377609 MGH42_P7_E05 MGH42_P7_E
- GSM2377610 MGH42_P7_E06 MGH42_P7_E
+ 6301 more — browse all 6341 samples with per-sample file links →
- GSE326221 Acquired genetic and cell state changes in IDH-mutant glioma progression [snRNA-seq] 75 samples same disease briefing · shares idh-mutant, rna-seq
- GSE70630 Single cell RNA-seq analysis of oligodendroglioma 4825 samples same disease briefing · shares rna-seq
- GSE260997 Mutant IDH inhibitors induce lineage differentiation in IDH-mutant Oligodendroglioma III 2458 samples same disease briefing · shares idh-mutant
- GSE244433 Human single cell RNA-sequencing reveals a targetable CD8+ exhausted T cell population that maintains murine low-grade glioma growth 16 samples same disease briefing · shares rna-seq
- GSE270109 Single-Cell Sequencing of IDH-Mutant Glioma 4 samples same disease briefing · shares idh-mutant
- GSE226321 Multimodal integration of transcriptomics, proteomics and radiomics improves prediction of recurrence in patients with IDH-mutant Glioma 59 samples same disease briefing · shares idh-mutant
- GSE308634 Transcriptional changes mediated by the HDACi panobinostat in IDH-wildtype and IDH-mutant gliomas 54 samples same disease briefing · shares idh-mutant
- GSE308636 Transcriptional changes mediated by the HDACi belinostat in IDH-mutant glioma cultures with YAP and TAZ overexpression 36 samples same disease briefing · shares idh-mutant
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.