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Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

GSE85755 Danio rerio (zebrafish) Single-cell RNA-seq 21 samples Submitted 2017/09/28 Platform GPL19057Platform GPL20828
At a glance

Single-cell RNA-seq · zebrafish · 21 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Danio rerio (zebrafish)
Samples
21 samples
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.
Summary (written by the submitters)
In many gene expression studies, cells are extracted by tissue dissociation and Fluorescence-Activated Cell Sorting (FACS), but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here, we applied single-cell mRNA sequencing (scRNA-seq) to muscle stem cells, and unexpectedly found a subpopulation that is strongly affected by the widely-used dissociation protocol that we employed.
Read the full summary ↓
One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly, we detected similar subpopulations in other single-cell datasets, suggesting that cells from other tissues might be affected by this artefact as well.
This dataset
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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 GSE85755_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 PRJNA339266 and SRA study SRP082370. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28960196) ↗
Samples in this study

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