Finding sets of Ribo-Seq, mRNA-Seq, and RNC-Seq data

Question

[plberry]

I am running into a problem trying to find complete datasets for human cell lines that contain mRNA-Seq, Ribo-Seq, and RNC-Seq data. Is there a way to search for this in GEO or other public sequencing databases? Right now I am finding I have to look up each paper every dataset is associated with and try to figure out whether they did all three or only 1 or 2. Some that come up under RNC-Seq turn out to actually be done with a different method (RIP-seq, etc). Am I missing something really obvious in how to find these datasets?

[seidel]

Have you tried the GEO search interface with those specific terms? I mean, have you checked if those specific terms exist for each method? e.g. "expression profiling by high throughput sequencing[DataSet Type] AND high throughput sequencing[Platform Technology Type]" Sometimes you have to dig deep to see if the specific terms exist. For instance on this page: https://www.ncbi.nlm.nih.gov/gds/advanced/ you can select DataSet Type, and then show the index list to see if your sequencing type is listed. Just wondering if you've tried that approach.

[plberry]

Yes, I tried that - unfortunately it doesn't seem to distinguish between various types of RNA-sequencing strategies, and as far as I can tell just lumps them all under "expression profiling by high throughput sequencing." So far what I've been doing is searching for papers that mention RNC-seq, but even then I get a lot of other RNA-seq strategies like RIP-seq, etc. or the papers just briefly mention RNC-seq but they didn't actually do it. Here's the one paper with a complete data set I was able to find for human cells after many hours of searching yesterday: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771717/ and they only have the complete set for HeLa cells, not any of their other cell lines.

Answer 1

[plberry]

Going through the advanced search again I found how to do it! Also there are <5 studies listed that are even on humans, so that answers that why I was having such trouble finding them. I'm writing it out here in case anyone in the future misses the specific options to click on the advanced search like I did:

1. Dataset Type: expression profiling by high-throughput sequencing

2. AND Description: type in "RNC" then hit "refresh index". I missed that button before and the fact that not all of the terms appear on the scroll bar, there's a limit of 200 terms.