We have just published a very detailed guide to submitting RNA-Seq data to NCBI's SRA, and transcriptome assemblies to TSA. We have often felt the need for a detailed, all-in-one-place, presentation of the steps required to submit RNA-Seq reads and assemblies to NCBI, so we decided to create one! Having often searched Biostars for help on this and similar topics, we would like to share with the community.
The manuscript: Feindt, W., Oppenheim, S. J., DeSalle, R., & Mehr, S. (2018). Good citizenship made easy: A step-by-step guide to submitting RNA-Seq data to NCBI. Current Protocols in Bioinformatics, e67. doi: 10.1002/cpbi.67 (if you don't have access, please visit https://www.researchgate.net/profile/Wiebke_Feindt to request full text from the authors)
The companion website: http://desalle.amnh.org/good_citizenship_rna/
We hope it is of use!