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.
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.
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