looking for human PBMC bulk cell seq data and scRNA data

Question

[Emily]

Where can I find publicly available PBMC bulk cell seq and scRNA seq data that are from control samples (or samples from healthy patients subjects).

Thanks in advance!

[GenoMax]

Are you asking for bulk (i.e normal) or scRNA seq data? You are using tags for both. In any case searching https://sra-explorer.info/ is one option.

[Emily]

Im looking for both bulk RNA-seq data and scRNA seq data of PBMC

Answer 1

[Friederike]

For processed bulk RNA-seq data in Robjects, see celldex, especially the Human Protein Cell Atlas data set.

For count matrices of single-cell RNA-seq data, see Bioconductor's singlecellRNAseq package.

For obtaining raw reads of either of these data sets, follow GenoMax' advice via sra-explorer or directly in GEO.

[Emily]

Is it human protein cell atlas or human primary cell atlas? couldn't find the one that was protein atlas...

[Friederike]

Yes, excuse my typo. But you may also read the descriptions of the data sets yourself and decide which ones are a good fit.

[GenoMax]

10x has single-cell PBMC datasets you can download. You will need to provide an email address.

[Emily]

I also need bulk cell data from the same study/sample but most publications do either just bulk or scRNA, never the both

[Friederike]

Then you should have specified that from the get-go.

[Athena]

My apologies. Are there any dataset (s) that has both bulk and scRNA seq from the same sample? Seems like most just use one type of (bulk or single cell) and publish rathet than doing both

[Friederike]

That's probably correct; but you can check some of the older publications (2016, 2017) where single-cell assays still had to prove themselves

[Emily]

Thank you, i will go hunt for those papers then. Cheers!