Question: RNA-Seq database for immune cells
1
gravatar for Daiwei Tang
14 months ago by
Daiwei Tang10
New Haven, Yale University
Daiwei Tang10 wrote:

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!

rna-seq gene • 2.9k views
ADD COMMENTlink modified 14 months ago by arup1.1k • written 14 months ago by Daiwei Tang10

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

ADD REPLYlink written 14 months ago by genomax65k

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

ADD REPLYlink written 14 months ago by Daiwei Tang10

That link is under the Read heading.

ADD REPLYlink written 14 months ago by genomax65k

Gotcha Thanks a lot!

ADD REPLYlink written 14 months ago by Daiwei Tang10
1
gravatar for Charles Warden
14 months ago by
Charles Warden6.5k
Duarte, CA
Charles Warden6.5k wrote:

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 COMMENTlink written 14 months ago by Charles Warden6.5k

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 REPLYlink written 14 months ago by Daiwei Tang10
1
gravatar for arup
14 months ago by
arup1.1k
India
arup1.1k wrote:

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 COMMENTlink written 14 months ago by arup1.1k

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

ADD REPLYlink written 14 months ago by Daiwei Tang10

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 REPLYlink written 14 months ago by Daiwei Tang10

Try EBI Expression Atlas

Example

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

ADD REPLYlink written 14 months ago by arup1.1k

Thanks a lot man, let me check this out

ADD REPLYlink written 14 months ago by Daiwei Tang10

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.

ADD REPLYlink written 14 months ago by Charles Warden6.5k

I think for ImmGen it is only for mouse

ADD REPLYlink written 14 months ago by Daiwei Tang10
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