Finding matched RNA-seq and Ribo-seq datasets for Nicotiana benthamiana under the same condition

[Farshid]

Hello, I am working on translation efficiency analysis in Nicotiana benthamiana. To do this properly, I need paired RNA-seq and Ribo-seq datasets collected under the same biological condition (same tissue, treatment, and time point).

What is the best way to find such matched datasets specifically for N. benthamiana? Are there databases, repositories, or projects you would recommend? Or should I manually search places like NCBI GEO or ENA? Also, are there specific metadata fields I should check to make sure RNA-seq and Ribo-seq samples are compatible?

I would appreciate any advice or pointers. Thank you very much!

[ehaag]

Instead of manually searching separate databases, you can search the NIAID Data Ecosystem which aggregates the metadata across all these repositories in one place and points you to where the data exists. For example, I just tried using the Advanced Search tool to build this query: "Nicotiana benthamiana" AND ("ribosome profiling" OR "ribo-seq"). I got a few results but not a ton (https://data.niaid.nih.gov/search?q=...ribo-seq%22%29) but you can play around with constructing your query or starting broad and using the filters