Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissue [snRNA-Seq]
Single-nucleus RNA-seq · human · 11 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
- 11 samples: 5 × SAT vs 2 × SAT1, vs 2 × SAT2, vs 2 × SAT3,Groups 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
- Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissueNature genetics · 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 GSE297258_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 PRJNA1263400. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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.
- GSM8987150 SAT1, biological rep 1 SAT1,
- GSM8987151 SAT1, biological rep 2 SAT1,
- GSM8987152 SAT2, biological rep 1 SAT2,
- GSM8987153 SAT2, biological rep 2 SAT2,
- GSM8987154 SAT3, biological rep 1 SAT3,
- GSM8987155 SAT3, biological rep 2 SAT3,
- GSM8987156 SAT4 SAT
- GSM8987157 SAT5 SAT
- GSM8987158 SAT6 SAT
- GSM8987159 SAT7 SAT
- GSM8987160 SAT8 SAT
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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.