Single-nucleus chromatin accessibility profiling identifies cell types and functional variants contributing to major depression
Single-nucleus RNA-seq · human · 42 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Homo sapiens (human)
- Samples
- 42 samples: 42 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 GSE246443_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1032938 and SRA study SRP468905. 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 42 sample titles: 42 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.
- GSM7868917 atac_A4B4 female and male
- GSM7868918 atac_A1B1 female and male
- GSM7868919 atac_A26B26 female and male
- GSM7868920 atac_A9B9 female and male
- GSM7868921 atac_A30B30 female and male
- GSM7868922 atac_A18B18 female and male
- GSM7868923 atac_A36B36 female and male
- GSM7868924 atac_A10B10 female and male
- GSM7868925 atac_A27B27 female and male
- GSM7868926 atac_A2B2 female and male
- GSM7868927 atac_A13B13 female and male
- GSM7868928 atac_A15B15 female and male
- GSM7868929 atac_A21B21 female and male
- GSM7868930 atac_A11B11 female and male
- GSM7868931 atac_A3B3 female and male
- GSM7868932 atac_A37B37 female and male
- GSM7868933 atac_A31B31 female and male
- GSM7868934 atac_A12B12 female and male
- GSM7868935 atac_A22B22 female and male
- GSM7868936 atac_A8B8 female and male
- GSM7868937 atac_A32B32 male
- GSM7868938 atac_A23B23 female and male
- GSM7868939 atac_A20B20 female and male
- GSM7868940 atac_A33B33 female and male
- GSM7868941 atac_A24B24 female and male
- GSM7868942 atac_A16B16 female and male
- GSM7868943 atac_A34B34 female and male
- GSM7868944 atac_A14B14 female and male
- GSM7868945 atac_A40B40 female and male
- GSM7868946 atac_A6B6 female and male
- GSM7868947 atac_A5B5 female and male
- GSM7868948 atac_A38B38 female and male
- GSM7868949 atac_A17B17 female and male
- GSM7868950 atac_A39B39 female and male
- GSM7868951 atac_A35B35 female and male
- GSM7868952 atac_A29B29 female and male
- GSM7868953 atac_A41B41 female and male
- GSM7868954 atac_A19B19 female and male
- GSM7868955 atac_A25B25 female and male
- GSM7868956 atac_A7B7 female and male
+ 2 more — browse all 42 samples with per-sample file links →
- GSE278910 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN] 30 samples shares single-nucleus, accessibility, chromatin
- GSE204912 Mapping genotypes to chromatin accessibility profiles in single cells 55 samples shares accessibility, chromatin, types
- GSE204911 Mapping genotypes to chromatin accessibility profiles in single cells [Genotyping GoT-ChA amplicon] 27 samples shares accessibility, chromatin, types
- GSE273054 Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation 119 samples shares accessibility, chromatin
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares accessibility, chromatin
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares accessibility, chromatin
- GSE325835 BATF3 regulates chromatin accessibility during CD8+ T lymphocyte differentiation 36 samples shares accessibility, chromatin
- GSE301512 Chromatin topology dynamics of dexamethasone-treated trabecular meshwork identifies 78 causal genes for intraocular pressure and primary open angle glaucoma [CUT&Run] 30 samples shares identifies, 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.