Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors
DNA methylation · human · 31 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 31 samples: 24 distinct titles, 3 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
- Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumorsLife science alliance · 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 GSE197569_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 beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA810995. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 31 sample titles: 24 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.
- GSM5920695 4_DNA, A1
- GSM5920696 3_DNA, A2
- GSM5920697 18_DNA, M1
- GSM5920698 20_DNA, M2
- GSM5920699 15_DNA, M3
- GSM5920700 1_DNA, P1
- GSM5920701 2_DNA, P2
- GSM5920702 16_DNA, P3
- GSM5920703 5_DNA, P4
- GSM5920704 21_DNA, P5
- GSM5920705 A1
- GSM5920706 A2
- GSM5920707 M1
- GSM5920708 M2
- GSM5920709 M3
- GSM5920710 P1
- GSM5920711 P2
- GSM5920712 P3
- GSM5920713 P4
- GSM5920714 P5
- GSM8065048 CRL-3020, rep A, NEUROD1 (CUT&RUN)
- GSM8065049 CRL-3020, rep B, NEUROD1 (CUT&RUN)
- GSM8065050 CRL-3036, rep A, NEUROD1 (CUT&RUN)
- GSM8065051 CRL-3036, rep B, NEUROD1 (CUT&RUN)
- GSM8065052 CRL-3038, rep A, NEUROD1 (CUT&RUN)
- GSM8065053 CRL-3038, rep B, NEUROD1 (CUT&RUN)
- GSM8065054 CRL-3021, rep A, NEUROD1 (CUT&RUN)
- GSM8065055 CRL-3021, rep B, NEUROD1 (CUT&RUN)
- GSM8065056 CRL-3021, positive control
- GSM8065057 CRL-3021, negative control
- GSM8065058 CRL-3038, positive control
- GSE283843 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories 56 samples shares trajectories, atypical, teratoid, rhabdoid
- GSE283832 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [Xenium Spatial_Transcriptomics] 7 samples shares trajectories, atypical, teratoid, rhabdoid
- GSE256353 Upregulated cholesterol biosynthesis facilitates the survival of methylation-retaining AML cells following decitabine treatment [single_colony_TEM-Seq] 1728 samples shares methylation
- GSE74193 Mapping DNA methylation across development, genotype, and schizophrenia in the human frontal cortex 675 samples shares methylation
- GSE73801 DNA methylation data from CNS-PNETs and various other brain tumor samples 593 samples shares methylation
- GSE93646 Microarray-based DNA methylation profiles of primary medulloblastomas 428 samples shares methylation
- GSE72680 DNA Methylation of African Americans from the Grady Trauma Project 422 samples shares methylation
- GSE275610 scRNA-seq and snATAC-seq reveal differentiation trajectories of several pancreatic islet induction protocols 341 samples shares trajectories
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.