Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [ATACme]
DNA methylation · human · 18 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE271127_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 PRJNA1130011 and SRA study SRP517083. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM8370134 ATAC-Me, H9, 0 day NPCdiff A
- GSM8370135 ATAC-Me, H9, 0 day NPCdiff B
- GSM8370136 ATAC-Me, H9, 6 hour NPCdiff A
- GSM8370137 ATAC-Me, H9, 6 hour NPCdiff B
- GSM8370138 ATAC-Me, H9, 12 hour NPCdiff A
- GSM8370139 ATAC-Me, H9, 12 hour NPCdiff B
- GSM8370140 ATAC-Me, H9, 1 day NPCdiff A
- GSM8370141 ATAC-Me, H9, 1 day NPCdiff B
- GSM8370142 ATAC-Me, H9, 2 day NPCdiff A
- GSM8370143 ATAC-Me, H9, 2 day NPCdiff B
- GSM8370144 ATAC-Me, H9, 3 day NPCdiff A
- GSM8370145 ATAC-Me, H9, 3 day NPCdiff B
- GSM8370146 ATAC-Me, H9, 4.5 day NPCdiff A
- GSM8370147 ATAC-Me, H9, 4.5 day NPCdiff B
- GSM8370148 ATAC-Me, H9, 6 day NPCdiff A
- GSM8370149 ATAC-Me, H9, 6 day NPCdiff B
- GSM8370150 ATAC-Me, H9, 12 day NPCdiff A
- GSM8370151 ATAC-Me, H9, 12 day NPCdiff B
- GSE256316 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ChIP-Seq] 121 samples shares accessibility, chromatin, enhancer
- GSE285741 LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair ChIP-seq 32 samples shares demethylation, accessibility, chromatin
- GSE256317 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ATAC-Seq] 32 samples shares accessibility, chromatin, enhancer
- GSE329420 Endothelial exosomes remodel chromatin accessibility and superenhancer in cancer cells to promote liver metastatic colonization 26 samples shares accessibility, chromatin, enhancer
- GSE277922 Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids 25 samples shares accessibility, chromatin, dynamics
- GSE285742 LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair [ATAC-seq] 20 samples shares demethylation, accessibility, chromatin
- GSE268580 Highly multiplexed single cell chromatin regulator and accessibility profiling elucidates chromatin dynamics in human B cell development and oncogenesis, and reveals an adverse prognostic gene expression signature in B lymphoblastic leukemias 15 samples shares accessibility, chromatin, dynamics
- GSE277921 Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids [ATAC-seq] 13 samples shares accessibility, chromatin, dynamics
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.