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Mapping genotypes to chromatin accessibility profiles in single cells [Genotyping GoT-ChA amplicon]

GSE204911 Homo sapiens (human) Single-cell RNA-seq 27 samples Submitted 2024/05/08 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 27 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
27 samples: 27 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.
Paper
Mapping genotypes to chromatin accessibility profiles in single cellsNature · 2024
Summary (written by the submitters)
Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments
Published in
Mapping genotypes to chromatin accessibility profiles in single cells
Izzo F, Myers RM, Ganesan S et al. · Nature 2024 · PMID 38720070 · doi:10.1038/s41586-024-07388-y
This dataset
Open GSE204911 in finder → Find more human datasets →
Download · which file do I need?

Direct links to NCBI, 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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE204911_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

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 PRJNA842709. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38720070) ↗
Study design
27 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 27 sample titles: 27 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.

Samples in this study
Datasets on a similar topic

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