Chromatin accessibility mapping for functional GWAS risk variants of neuropsychiatric and neurodegenerative disorders in hiPSC-derived neural cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 141 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
- 141 samples: 5 conditions, mostly with about 38 replicates eachGroups 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
- Alzheimer's disease protective allele of Clusterin modulates neuronal excitability through lipid-droplet-mediated neuron-glia communicationmedRxiv : the preprint server for health sciences · 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 GSE263804_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 PRJNA1099272 and SRA study SRP501338. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 141 samples.
How we read this: 5 replicated groups read from 141 sample titles; they account for 141 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.
- GSM8199303 MG-02 MG
- GSM8199304 MG-03 MG
- GSM8199305 MG-04 MG
- GSM8199306 MG-05 MG
- GSM8199307 MG-06 MG
- GSM8199308 MG-08 MG
- GSM8199309 MG-09 MG
- GSM8199310 MG-12 MG
- GSM8199311 MG-13 MG
- GSM8199312 MG-14 MG
- GSM8199313 MG-15 MG
- GSM8199314 MG-16 MG
- GSM8199315 MG-17 MG
- GSM8199316 MG-19 MG
- GSM8199317 MG-20 MG
- GSM8199318 MG-21 MG
- GSM8199319 MG-28 MG
- GSM8199320 MG-29 MG
- GSM8199321 MG-30 MG
- GSM8199322 MG-31 MG
- GSM8199323 MG-32 MG
- GSM8199324 MG-33 MG
- GSM8199325 MG-34 MG
- GSM8199326 MG-35 MG
- GSM8199327 MG-50 MG
- GSM8199328 MG-51 MG
- GSM8199329 MG-52 MG
- GSM8199330 MG-53 MG
- GSM8199331 MG-55 MG
- GSM8199332 MG-57 MG
- GSM8199333 MG-58 MG
- GSM8199334 MG-60 MG
- GSM8199335 MG-61 MG
- GSM8199336 MG-62 MG
- GSM8199337 MG-63 MG
- GSM8199338 MG-64 MG
- GSM8199339 MG-65 MG
- GSM8199340 MG-66 MG
- GSM8199341 Ast-31 Ast
- GSM8199342 Ast-32 Ast
+ 101 more — browse all 141 samples with per-sample file links →
- GSE246443 Single-nucleus chromatin accessibility profiling identifies cell types and functional variants contributing to major depression 42 samples shares accessibility, chromatin, variants
- GSE285390 Incorporating histone H2B variants into chromatin modifies chromatin accessibility to induce the epithelial-to-mesenchymal transition in breast cancer [CUT&RUN] 32 samples shares accessibility, chromatin, variants
- GSE293119 Integration of Alzheimer’s GWAS, 3D genomics, and single-cell CRISPRi non-coding screen implicates causal variants in a microglial enhancer regulating TSPAN14. [RNA-Seq] 18 samples shares gwas, variants
- GSE264684 Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits 477 samples shares accessibility, chromatin
- GSE281464 Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [Perturb-seq] 7 samples shares gwas, chromatin
- GSE99172 Single-cell chromatin accessibility data from K562 cells using scATAC-seq 288 samples shares accessibility, chromatin
- GSE277774 Expanded chromatin accessibility mapping explains genetic variation associated with complex traits in liver 189 samples shares accessibility, chromatin
- GSE291386 Chromatin accessibility profiling of HSPC-derived erythroblast differentiation [ATAC-seq] 165 samples shares accessibility, chromatin
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.