Epigenomic profiling of stemness, differentiation and primary tissues in human glioblastoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 49 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- GlioblastomaThis series is part of our curated briefing on it.
- Samples
- 49 samples: 10 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.
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 GSE54792_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA237652. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 27 samples.
How we read this: 10 replicated groups read from 49 sample titles; they account for 27 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.
- GSM1306339 MGG4TPC H3K27ac
- GSM1306340 MGG6TPC H3K27ac
- GSM1306341 MGG8TPC H3K27ac
- GSM1306342 MGG4DGC H3K27ac
- GSM1306343 MGG6DGC H3K27ac
- GSM1306344 MGG8DGC H3K27ac
- GSM1306345 MGG8 DGC + empty vector H3K27ac
- GSM1306346 MGG8 DGC + POU3F2 cDNA H3K27ac
- GSM1306347 MGG8 DGC + SOX2 cDNA H3K27ac
- GSM1306348 MGG8 DGC + SALL2 cDNA H3K27ac
- GSM1306349 MGG8 DGC + OLIG2 cDNA H3K27ac
- GSM1306351 MGG8 DGC + POU3F2 and SOX2 cDNA H3K27ac
- GSM1306352 MGG8 DGC + POU3F2, SOX2 and SALL2 cDNA H3K27ac
- GSM1306354 MGG8 iTPC POU3F2 SOX2 SALL2 OLIG2 H3K27ac
- GSM1306355 MGG8 iTPC POU3F2 SOX2 SALL2 OLIG2 replicate H3K27ac
- GSM1306358 MGG8TPC POU3F2
- GSM1306360 MGG8TPC SOX2 r1 MGG8TPC SOX2
- GSM1306362 MGG8TPC SOX2 r2 MGG8TPC SOX2
- GSM1306364 MGG8TPC SALL2
- GSM1306365 MGG8TPC OLIG2 r1 MGG8TPC OLIG2
- GSM1306367 MGG8TPC OLIG2 r2 MGG8TPC OLIG2
- GSM1306369 MGG27 primary tumor H3K27ac
- GSM1306371 MGG28 primary tumor H3K27ac
- GSM1306373 MGG30 primary tumor H3K27ac
- GSM1306375 MGG4 iTPC POU3F2 SOX2 SALL2 OLIG2 H3K27ac
- GSM1306377 MGG4 DGC + empty vector H3K27ac
- GSM1324075 MGG4TPC_1 MGG4TPC
- GSM1324076 MGG4TPC_2 MGG4TPC
- GSM1324077 MGG4TPC_3 MGG4TPC
- GSM1324078 MGG6TPC_1 MGG6TPC
- GSM1324079 MGG6TPC_2 MGG6TPC
- GSM1324080 MGG6TPC_3 MGG6TPC
- GSM1324081 MGG8TPC_1 MGG8TPC
- GSM1324082 MGG8TPC_2 MGG8TPC
- GSM1324083 MGG8TPC_3 MGG8TPC
- GSM1324084 MGG4DGC_1 MGG4DGC
- GSM1324085 MGG4DGC_2 MGG4DGC
- GSM1324086 MGG4DGC_3 MGG4DGC
- GSM1324087 MGG6DGC_1 MGG6DGC
- GSM1324088 MGG6DGC_2 MGG6DGC
+ 9 more — browse all 49 samples with per-sample file links →
- 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
- 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
- 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
- GSE10878 Integrative Genome-wide Analysis of Glioblastoma. 60 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.