Where can I get both total RNA-seq & Chip-seq data,

Question

[dlyedms1019]

Hi,

I want to get both total RNA data and chip data of Human. Total RNA literally means all RNA sequenced data, not just mRNA. When searching for "total RNA seq" AND "Chip" in the GEO database, only 40 results were obtained, and even that was not appropriate. Is there a DB where I can get both data? The more I do not need accession, the better.

Thanks.

[ATpoint]

You will probably not find it with a simple query. Depending on the scentific question you have to do the annoying work and search through the literature. What exactly do you need? RNA-seq and ChIP-seq is available in many studies. Which organism, does it need to be the same donor or just the same condition, e.g. littermate mice? Does it really need to be "total" RNA? Which additional info do you get compared to polyA-enriched RNA?

[Papyrus]

Additionally, often "total" RNA-seq is called "bulk" RNA-seq, and you may have additional results using that nomenclature.

Answer 1

[i.sudbery]

Depends on what you mean by "total RNA seq". You can find samples that have both polyA+ and polyA- data, but you will not find datasets that contain both long and short RNA, as it is impossible to sequence both well at once.

You will find matched ChIP-seq and RNA-seq in some of the big functional genomics projects. Notably ENCODE, Blueprint and Epigenetics Roadmap.

But I wouldn't go thinking that "only 40" isn't that much. Such datasets are difficult to produce, and I wouldn't expect to find 100s of them.