Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1.5
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Epic Link:
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Sprint:Spring 9
Description
This task is to check the 2 SRA datasets that are related to Rasha's upcoming papers.
Email from Mark:
We're working on a paper that will draw on three data sets and we want to make sure we have the SRA submissions all set.
1. Heinz, Tam, Nag pollen tubes
@ 30', 60', and 120'
@ 28 and 34
This experiment was performed by Rasha
2. Mature Pollen
28c and 37c for one hour
Heinz, Tam, Nag, and Malintka
This experiment was performed by Michelle Medina
Do we have a stand alone SRA entries for these experiments? I just want to check to make sure so that we can cite it properly.
The third data set is proteomics data
Heinz, Tam, Nag pollen tubes
@ 30' and 120'
@ 28 and 34
Mature Pollen - no treatment (dry pollen)
This experiment was performed by Rasha. Do you have any advice on a repository for these proteomics data?
We need to
- Check the pollen tube data
- Check the mature Pollen data
- Make a table that is a subset of the data they used.
- Explore if there is an NCBi proteomics data solution.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Email I sent to Mark:
Part 1:Bioproject PRJNA980666
54 samples: 4 varieties * 3 time points * 2 conditions *3 replicates
Part 2 Mature Pollen:I think this is the original study from 2020 correct?24 experiments: 4 varieties * 2 conditions * 3 replicatesBioproject: PRJNA611819https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA611819
Part 3:ProteomicsThis cannot go into NCBI like the other datasets.There is a org that is dedicated to public repos for proteomic data, https://www.proteomexchange.org/
This seems to be the front runner.
The Proteome exchange has 3 venues for data uploading:he GUI based PX Submission Tool can be downloaded to start data upload.PeptideAtlas - PASSEL SRM/MRM data can be submitted to PASSEL.MassIVEShotgun proteomics data can be submitted to MassIVE.
As to which is best suited, I do not know!
Will wait for response from them before closing this ticket.
We might be submitting proteome data! (which we do not have).
Comment from Mark:
I'm going to ask our proteomics person whether he recommends a specific repository and will let you know what he says.
Best,
Mark
I will close this ticket and in the event they need help with Proteomics data managing, we can open a new ticket.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Part 1:
Bioproject PRJNA980666
54 samples: 4 varieties * 3 time points * 2 conditions *3 replicates
Part 2 Mature Pollen:
I think this is the original study from 2020 correct?
24 experiments: 4 varieties * 2 conditions * 3 replicates
Bioproject: PRJNA611819
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA611819