Looking for publicly available dataset.

Question

[KVC_bioinfo]

Hello All,

I am trying to find a gene expression dataset which is publicly available? I am looking for gene counts coming from HTSeq like tools for different genes. This is not specific to any genes. It can be from human/mouse. I want the dataset only to test few statistical tests.

The purpose of this is for use in a project at University.

Could someone help me suggesting sources for such datasets?

Thanks!

[WouterDeCoster]

Have a look at the recount2 R package, lot's of data readily available.

[rice.researcher]

ArrayExpress has number of processed data and filtering option may show dataset you are looking for.

[KVC_bioinfo]

Thank you so much. I will look into it.

[KVC_bioinfo]

No. But I will definitely look into it.

[bunnyslope]

Hi! I am new to RNA-Seq. ARCHS4 seems a great platform. May I ask a naive question? For the gene counts data that we download from ARCHS4, do I have to convert them to FPKM, RPKM or TPM before I do gene expression analysis between different samples?

Thank you!

[mark.ziemann]

Best to open a new question - I'm sure the community can help you with your request :)

Answer 1

[mark.ziemann]

2 good options:

recount2 https://jhubiostatistics.shinyapps.io/recount/

ARCHS4 http://amp.pharm.mssm.edu/archs4/

Also many GEO series include count matrices although these are generated by various pipelines.