Question

RNA-Seq database for immune cells

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6.7 years ago

Daiwei Tang ▴ 10

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!

gene RNA-Seq • 7.1k views

ADD COMMENT • link updated 2.1 years ago by shweta.johari13 ▴ 30 • written 6.7 years ago by Daiwei Tang ▴ 10

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

ADD REPLY • link 6.7 years ago by GenoMax 146k

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

ADD REPLY • link 6.7 years ago by Daiwei Tang ▴ 10

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That link is under the Read heading.

ADD REPLY • link 6.7 years ago by GenoMax 146k

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Gotcha Thanks a lot!

ADD REPLY • link 6.7 years ago by Daiwei Tang ▴ 10

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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

ADD REPLY • link 2.1 years ago by shweta.johari13 ▴ 30

score 1 · Answer 1 · 2018-02-02

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6.7 years ago

Charles Warden 8.3k

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

ADD COMMENT • link 6.7 years ago by Charles Warden 8.3k

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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.

ADD REPLY • link 6.7 years ago by Daiwei Tang ▴ 10

score 1 · Answer 2 · 2018-02-03

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6.7 years ago

Arup Ghosh 3.2k

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.

ADD COMMENT • link 6.7 years ago by Arup Ghosh 3.2k

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

ADD REPLY • link 6.7 years ago by Daiwei Tang ▴ 10

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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?

ADD REPLY • link 6.7 years ago by Daiwei Tang ▴ 10

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Try EBI Expression Atlas

Example

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

ADD REPLY • link 6.7 years ago by Arup Ghosh 3.2k

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Thanks a lot man, let me check this out

ADD REPLY • link 6.7 years ago by Daiwei Tang ▴ 10

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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.