Where can I find public Single Cell RNA-seq data?

Question

[309772486]

Hi everyone,

I am trying to find some public RNAseq data from single cells. Do you know any of them? Thanks for the help!

[tan]

We developed BioTuring Browser, a modern application for free accessing to published sequencing data, focusing on single-cell transcriptomics. Many brain single-cell datasets have been indexed, including DropViz, which has more than 690,000 cells.

You can download it here: https://bioturing.com/product/bbrowser.

Some screen-shots

[Arup Ghosh]

Try http://www.cellatlassearch.com/ if you are looking for human scRNA-seq samples.

Answer 1

[Cumol]

Here you will find one: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59739

It is from this publication: Usoskin, D. et al. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nat Neurosci 18, 145–153 (2015).

Answer 2

[fusion.slope]

Check the last Work of Jeff Leek:

https://jhubiostatistics.shinyapps.io/recount/

and type "Single Cells" you will find a lot of Public available RNA-seq data-sets that you can download with SRA Toolkiit

Answer 3

[User 59]

There's a few datasets from the 10X Genomics platform here:

http://support.10xgenomics.com/single-cell/datasets

Answer 4

[Mike]

There is one more database for single cell RNAseq: scRNASeqDB

scRNASeqDB a database for gene expression profiling in human single cell by RNA-seq

https://bioinfo.uth.edu/scrnaseqdb/

Answer 5

[Friederike]

The Broad's Single Cell Portal currently houses 70 single cell data sets which can be perused. They also offer neat functions like showing you the expression of your favorite gene in all those publicly available data sets that they host etc.

Answer 6

[of]

Another one that could be useful:

https://panglaodb.se/

Answer 7

[Denise CS]

In Single Cell Expression Atlas.

If there are studies you would like them to include, get in touch with their Support team. Their major requirement for inclusion is to have access to the raw data.

Answer 8

[hannah.johnson]

Interesting data just published by Dolomite Bio here

Answer 9

[Min Dai]

More than 20 human and mouse scRNA-seq datasets are collected by the Hemberg Group: https://hemberg-lab.github.io/scRNA.seq.datasets/

[Friederike]

The R package scRNAseq provides them in ready-to-use SingleCellExperiment objects: https://www.bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.html#available-data-sets

[Min Dai]

This is so cool! thanks

Answer 10

[Aqsa]

Elucidata's platform Polly has 1880+ single cell RNA-seq datasets which have been aggregated from 8 different public repositories. These have been meticulously curated and are ready for analysis.

You can check it out here- https://www.elucidata.io/data/single-cell-omix-atlas