PRJNA997229 - https://www.ncbi.nlm.nih.gov/bioproject/PRJNA997229
SRP450893 - https://trace.ncbi.nlm.nih.gov/Traces/?view=study&acc=SRP450893
Publication - https://elifesciences.org/reviewed-preprints/92621

Link to table in Google Drive: https://docs.google.com/spreadsheets/d/1G_54-aa2INHQ54d823-YkDhmEfw3XmkK9vXDXlLjF_w/edit?usp=sharing

Dr. Goldstein mentioned several of his RNA-Seq datasets should be available online. Paige Kulzer - can you please email Dr. Goldstein and ask about the location online.

Nowlan Freese and Paige Kulzer - before you do that, let's inventory the datasets that are available in the Sequence Read Archive for the two key species Bob mentioned - H. exemplaris and Ramazzottius varieornatus.

Here is a link to the genome data from NCBI for R. varieornatus: https://www.ncbi.nlm.nih.gov/datasets/taxonomy/947166/.

For a reference about a developmental time series dataset, see Bob's review article: https://cshprotocols.cshlp.org/content/2018/11/pdb.emo102301.full

I've created a spreadsheet listing the various RNA-seq datasets I could find in the Sequence Read Archive (and elsewhere). It's likely not exhaustive, but Bob did confirm with me via email that most of the RNA-seq datasets he's aware of came from the Arikawa lab at Keio University which does match with what I've compiled. Here's a link to that sheet.

Bob also mentioned that his next RNA-seq dataset is being published online this week with his manuscript that's being published. I will keep an eye out for that data and update the spreadsheet accordingly.

I ran the above SRR samples through the rna-seq pipeline version that we had on the cluster at UNC Charlotte. I made alignment (bam) and coverage graph (bedgraph) files and deployed them at https://data.bioviz.org/tardigrade.

Dr. Goldstein has just had a new RNA-Seq dataset published alongside his paper, so I've updated the Tardigrade RNA-Seq Data Mastersheet with links to that new data.

For review, please take a look around NCBI, GEO, ENA, etc. to make sure that I haven't missed any datasets for our key species. Once that's done, I suggest we close this ticket and create a new ticket that focuses on deploying tardigrade RNA-Seq data as quickloads.

I looked in the SRA by running queries on the Web site. I didn't find anything else besides what we already found.

However, I think that if we truly want to make sure, we ought to write some type of automatic query script that can search the database for new accessions that we do not already have. Doing this manually is very hard!

Update:

• I made this git repository in bitbucket, with "main" as the default branch: https://bitbucket.org/lorainelab/tardigrade/src/main/
• I added a tab-separated copy of the google tardigrade sheet as: tardigrade/SRA/Tardigrade-RNASeq-Data-SRA-datasets.txt

Paige Kulzer: Please check over the repository and make sure it makes sense. If it's all good, please close the ticket. Otherwise, let me know if you advise me to make any changes.

Here are some thoughts I had while I was looking through the new git repo in BitBucket:

1. We may want to include a copy of Dr. Goldstein's newest publication in the ForTeaching folder. It is currently behind a paywall online but he sent me a pdf copy via email that I will attach to this ticket.
2. Only the SRA folder currently has a README document, but I think the ForTeaching folder might benefit from having one, too. Ideally, this would describe what each of those documents are and how they're being used for teaching. Also, similarly to my above comment, it might be nice to include a copy of the article related to SRP450893 in this folder.
3. Is there a reason that SRP383198 only has an accession list saved in the SRA folder? It appears that all of the SRPs in this folder have full metadata saved. I'm able to access the Run Selector for that SRP, here's a link. I recommend we keep it consistent and update this file so that it contains all of the metadata from that SRP.
4. There are several other SRP numbers that were present in the mastersheet that aren't being represented in the SRA folder: SRP098563, SRP306097, SRP395413, SRP267838, SRP193253, SRP454305. I think we ought to include all of the datasets present in the mastersheet in this folder, or at least the datasets derived from the species whose genomes we'll be representing in IGB.
5. There's one R. varieornatus study in the mastersheet with only an ENA ID listed. There's no SRP number associated with that project, but I was able to find those samples in the Run Selector which I will link here. Do we want to include that in the SRA folder, too?

Moving this back to To-Do so that some or all of the above suggestions can be incorporated.

Thank you for the suggestions. These will be done later. Moving to DONE.