Papers with just RNA-Seq data

[billstevens]

Hi guys,

So I'm a grad student who really wants to graduate. Truly, that is all I want. I am tired of being here. I badly need a publication to do so.

I have five biological replicates of RNA-Seq data. I aligned with TopHat and I used DESeq to come up with differential expression. The most important cytokine that I thought was interesting had a 20 fold change difference in RNA data (2000 counts versus 100). So I did the same experiment with an ELISA. It did not show up as differentially expressed. I suppose there are all sorts of reasons for this: post-transcriptionally it does something, maybe the cytokines are ABOUT to be translated, maybe the cytokines have been translated but haven't left the cell into the media yet.

However, I'm tired and sad. I'm trying qPCR on a few genes, including the important one. If they come out ok, is that enough for a publication? Do people publish with JUST RNA-Seq data? I'm the only one in my lab who's doing this stuff, and I want to be done with it. Please, please, any and all advice would be greatly appreciated.

[jimmybee]

However, I'm tired and sad. I'm trying qPCR on a few genes, including the important one. If they come out ok, is that enough for a publication? Do people publish with JUST RNA-Seq data? I'm the only one in my lab who's doing this stuff, and I want to be done with it. Please, please, any and all advice would be greatly appreciated.

You should really discuss this with your supervisor or at least someone in your lab who has a good background in what you have been doing. I don't think anyone here could give you any direction with only minor background information.

[honey]

RNA-seq

billstevens,
Dont give up. Take it as a learning step. I dont know much of your labs focus however, I believe Confirm a bunch of genes by RT PCR, then show with few immunofluoresence/ western or something like that and then do the pathway analysis and focus on your hypothesis. That may work to certain level.
Good luck

[JackieBadger]

I have never heard of a publication being a requirement to get a degree. Write your thesis and graduate if that's all you want to do.

[masterpiece]

JackieBadger,

Nowdays, more and more universities required student to publish at least a paper as a requirement for the student to graduate. Same thing happen in a lot of places, for example in China.

http://www.bbc.co.uk/news/science-environment-12885271

billsteven,

I might be wrong, from my knowledge I haven't seen yet any paper publish DE analysis with just RNAseq data. My suggestion you can try qPCR at least several candidate of genes. I pretty sure you can get some of them corresponding to your RNAseq data.

wish u all the best!!!

[magnoseq]

You can publish with just RNA seq data provided you validate at least 10 genes that are up or down-regulated from your data set. Validate your genes by qRT-PCR. Hope this helps!

[mbblack]

err, so what was the point of this experiment in the first place? Surely that should guide you as to what points you wish to make with the data?

Of course you can publish a paper with just RNA-Seq data. People have been publishing papers with just array data for many years (or just isozyme data, or just RFLP data, or whatever). The point of a publication is to pose an interesting scientific question, and attempt to answer it with the data in hand. If your question is one that can be addressed with just your RNA-Seq data, then write it up.

Publishing data just for the sake of justifying having generated it in the first place is not a strategy for success. Publishing data because it provides valuable insight into some biologically interesting question will be a much simpler to put to paper as the question itself will guide you to how to analyze and present the data.

In other words, the easiest science to write up is query drive science, not data driven science (data in search of a question will always be a nightmare to write up).