Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 74 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
- 74 samples: 72 distinct titles, 2 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
- Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programsNature communications · 2024
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 GSE229966_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 PRJNA956900. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 74 sample titles: 72 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.
- GSM7181938 G1-HiC
- GSM7181939 G120-HiC
- GSM7181940 G148-HiC
- GSM7181941 G163-HiC
- GSM7181942 G171-HiC
- GSM7181943 G181-HiC
- GSM7181944 G208-HiC biorep1
- GSM7181945 G208-HiC biorep2
- GSM7181946 G213-HiC biorep1
- GSM7181947 G213-HiC biorep2
- GSM7181948 G23-HiC
- GSM7181949 G275-HiC
- GSM7181950 G275R-HiC
- GSM7181951 G28-HiC
- GSM7181952 G318-HiC
- GSM7181953 G323-HiC
- GSM7181954 G351-HiC
- GSM7181955 G390-HiC
- GSM7181956 G394-HiC
- GSM7181957 G402-HiC
- GSM7181958 G402R-HiC
- GSM7181959 G412-HiC
- GSM7181960 G412R-HiC
- GSM7181961 G450-HiC
- GSM7181962 G452C-HiC
- GSM7181963 G452P-HiC
- GSM7181964 G457-HiC
- GSM7181965 G61-HiC
- GSM7181966 G62-HiC
- GSM7181967 G83-HiC
- GSM7182016 G275_H3K27ac
- GSM7182017 G275R_H3K27ac
- GSM7182018 G412R_H3K27ac
- GSM7182019 G402R_H3K27ac
- GSM7182020 G402_H3K27ac
- GSM7182021 G412_H3K27ac
- GSM7182022 G452C_H3K27ac
- GSM7182023 G394_H3K27ac
- GSM7182024 G148_H3K27ac
- GSM7182025 G450_H3K27ac
+ 34 more — browse all 74 samples with per-sample file links →
- 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.