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3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution

GSE195611 Homo sapiens (human) Single-cell RNA-seq 410 samples Submitted 2024/08/14 Platform GPL24676Platform GPL21290
At a glance

Single-cell RNA-seq · human · 410 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
410 samples: 10 conditions, mostly in duplicateGroups 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
Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulationsNature communications · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations
Zhou Y, Li T, Choppavarapu L et al. · Nature communications 2024 · PMID 39333113 · doi:10.1038/s41467-024-52440-0
This dataset
Open GSE195611 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

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, or the whole study as GSE195611_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA801481 and SRA study SRP356610. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39333113) ↗
Study design
10 conditions, mostly in duplicate
breast cancer single cell A ×293 breast cancer single cell CL4 ×21 breast cancer single cell CL2 ×19 breast cancer single cell CL5 ×19 breast cancer single cell CL3 ×17 breast cancer single cell CL1 ×14 breast cancer single cell CL6 ×5 breast cancer MCF7 ×2 +8 more

Supports a between-group comparison across 394 samples.

How we read this: 10 replicated groups read from the first 400 of 410 sample titles; they account for 394 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.

Samples in this study

+ 370 more — browse all 410 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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