RNA-Seq database for immune cells

Question

[Daiwei Tang]

Hi all, I'm wondering is there any database/datasets that have pure immune cell lines' RNA-Seq data (i.e., B cells, T cells, macrophages). I was only able to find those with collection of microarray data. Thanks!

[GenoMax]

EBI-ENA. Click on "experiments" at left. Do additional searches as needed.

[Daiwei Tang]

Thanks for your reply. I'm pretty new to this site, sorry I didn't see any experiments link at left ?

[GenoMax]

That link is under the Read heading.

[Daiwei Tang]

Gotcha Thanks a lot!

[shweta.johari13]

Hey, I have bulk RNA Sequencing datasets from tumro and tumor infiltating immune cells but fro mouse. I am also checking for some way to distinguish between them. Can I please ask how you did it and what did you use?

Thank you.

Kind Regards, Shweta Johari

Answer 1

[Charles Warden]

Immune cell signatures defined from microarray datasets have been applied to RNA-Seq data, so it may still be worth considering the microarray gene expression datasets.

While I would also be curious to know about comparable RNA-Seq datasets, you could keep an eye on citations for these fairly popular microarray datasets:

Abbas et al 2005: GSE22886

Novershtern et al. 2011: GSE24759

[Daiwei Tang]

Thanks for your suggestion Charles. Actually I'm particularly interested in some genes that exclusively expressed in one or several immune cell types, it seems that microarray does worse in correctly reporting those non-expressing genes.

Answer 2

[Arup Ghosh]

ImmGen has a large collection of MicroArray as well as RNA-seq datasets. Check expression of a gene in several immune-associated cell lines from the Gene Skyline browser.

[Daiwei Tang]

Thank you so much! ImmuneGen seems like what I'm looking for, I will check it out.

[Daiwei Tang]

Oh I forgot to mention, actually I'm looking for some database like this for Human instead of mouse, do you have to know any?

[Arup Ghosh]

Try EBI Expression Atlas

Example

Enable Cell type * checkbox in *Filter your results section.

[Daiwei Tang]

Thanks a lot man, let me check this out

[Charles Warden]

This is a good suggestion!

If looking for raw ImmGen RNA-Seq data, the GEO entry (and link to SRA reads) is GSE109125.

This is for mouse sorted cells. While I should probably learn more about ImmGene / Gene Skyline, I didn't see RNA-Seq data from human cells.

[Daiwei Tang]

I think for ImmGen it is only for mouse