A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 56 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)
- Samples
- 56 samples: 44 distinct titles, 10 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
- A cycling, progenitor-like cell population at the base of atypical teratoid rhabdoid tumor subtype differentiation trajectoriesNeuro-oncology · 2025
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 GSE283843_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 PRJNA1195879. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 56 sample titles: 44 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.
- GSM8672828 ATRT-05 (ATRT-SHH)
- GSM8672829 ATRT-15-RV4 (ATRT-TYR)
- GSM8672830 ATRT-173 (ATRT-SHH)
- GSM8672831 ATRT-207 (ATRT-MYC)
- GSM8672832 ATRT-243 (ATRT-MYC)
- GSM8672833 ATRT-256 (ATRT-SHH)
- GSM8672834 ATRT-340 (ATRT-TYR)
- GSM8672835 AT-SHH04 tumoroid model treated with DMSO replicate 1
- GSM8672836 AT-SHH04 tumoroid model treated with DMSO replicate 2
- GSM8672837 AT-SHH04 tumoroid model treated with Entinostat replicate 1
- GSM8672838 AT-SHH04 tumoroid model treated with Entinostat replicate 2
- GSM8672839 AT-SHH04 tumoroid model treated with RO31-8220 mesylate replicate 1
- GSM8672840 AT-SHH04 tumoroid model treated with RO31-8220 mesylate replicate 2
- GSM8672841 AT-SHH04 tumoroid model treated with Thiostrepton replicate 1
- GSM8672842 AT-SHH04 tumoroid model treated with Thiostrepton replicate 2
- GSM8672843 AT-MYC08 tumoroid model treated with DMSO replicate 1
- GSM8672844 AT-MYC08 tumoroid model treated with DMSO replicate 2
- GSM8672845 AT-MYC08 tumoroid model treated with Entinostat replicate 1
- GSM8672846 AT-MYC08 tumoroid model treated with Entinostat replicate 2
- GSM8672847 AT-MYC08 tumoroid model treated with RO31-8220 mesylate replicate 1
- GSM8672848 AT-MYC08 tumoroid model treated with RO31-8220 mesylate replicate 2
- GSM8672849 AT-MYC08 tumoroid model treated with Thiostrepton replicate 1
- GSM8672850 AT-MYC08 tumoroid model treated with Thiostrepton replicate 2
- GSM8672929 ATRT TYR-5 patient tissue viably frozen
- GSM8672930 ATRT TYR-6 patient tissue viably frozen
- GSM8672931 ATRT SHH-6 patient tissue viably frozen
- GSM8672932 ATRT SHH-7 patient tissue viably frozen
- GSM8672933 ATRT SHH-8 patient tissue viably frozen
- GSM8672934 ATRT SHH-9 patient tissue viably frozen
- GSM8672935 ATRT SHH-10 patient tissue viably frozen
- GSM8672936 ATRT MYC-4 patient tissue viably frozen
- GSM8672945 scRNA-seq part of multiome data AT-SHH04
- GSM8672946 scRNA-seq part of multiome data AT-SHH05
- GSM8672947 scRNA-seq part of multiome data AT-SHH15
- GSM8672948 scATAC-seq part of multiome data AT-SHH04
- GSM8672949 scATAC-seq part of multiome data AT-SHH05
- GSM8672950 scATAC-seq part of multiome data AT-SHH15
- GSM8672951 ATRT-TYR-1 fresh frozen tumor tissue
- GSM8672952 ATRT-TYR-2 fresh frozen tumor tissue
- GSM8672953 ATRT-TYR-3 fresh frozen tumor tissue
+ 16 more — browse all 56 samples with per-sample file links →
- GSE283833 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [bulk RNA-Seq] 16 samples shares progenitor-like, trajectories, population, atypical, teratoid, rhabdoid, cycling, subtype
- GSE283832 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [Xenium Spatial_Transcriptomics] 7 samples shares progenitor-like, trajectories, population, atypical, teratoid, rhabdoid, cycling, subtype
- GSE282972 An in vitro pharmacogenomic approach reveals subtype-specific therapeutic vulnerabilities in atypical teratoid/rhabdoid tumors (AT/RT) [RNASeq] 13 samples shares atypical, teratoid, rhabdoid, subtype
- GSE230742 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [I] 21 samples shares atypical, teratoid, rhabdoid
- GSE276501 Atypical Teratoid Rhabdoid Tumours Are Susceptible to Panobinostat-Mediated Differentiation Therapy 18 samples shares atypical, teratoid, rhabdoid
- GSE213249 Inhibiting EZH2 Targets Atypical Teratoid Rhabdoid Tumor by Triggering Viral Mimicry via Both RNA and DNA Sensing Pathways [RNA-Seq] 12 samples shares atypical, teratoid, rhabdoid
- GSE296682 Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease 9 samples shares trajectories, population
- GSE246521 Chronic Lymphocytic Leukemia in African Ancestry Population is Characterized by Increased Genomic Instability 350 samples shares population
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.