publication of RPKMs of select genes from transcriptome study

Question

[oakie]

Hi,

I wonder if it would it be OK to publish only data of select genes from an RNA-seq study? So, I would not include all the metadata, only the RPKM data from the genes that I want to talk about. The journals under consideration are PlosOne, and Scientific Reports. I do not find clear information in the journal's guidelines.

The alternative would be to use the samples for RT-QPCR but I want to now if it's OK to do the above.

Anyone has some clues?

Thanks.

Answer 1

[Benn]

No, it is not okay. You'll have to submit raw data, please follow GEO guidelines (that's where your data end). And as a side note, RPKM is not useful for many statistics, so to submit only RPKM would frustrate a lot of users and Biostars moderaters who would have to tell those users not to use RPKM values.

[ATpoint]

This all comes down to reproducibility. Raw data must be available to download, which means un-manipulated data as they come from the sequencer. This will allow everyone not only to reproduce the data but also to use them with their custom pipelines, and maybe in a different context for their scientific question. Public data are important as not everyone can create every dataset one might need and it is great for confirmation purposes to demonstrate that your own findings can be reproduced with a totally independent dataset (or not, this would also be informative). All these journals require upload of raw data to a public repository, but you can password-protect e.g. the accession numbers you get from NCBI for your data until the paper is fully published.