[IGBF-3498] Review SRA Submissions - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
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Story Points:
2
Epic Link:
Support NSF pollen grant
Sprint:
Fall 6, Fall 7, Spring 1, Spring 2, Spring 3, Spring 4, Spring 9

Description

Review the SRA submissions made for Ravi, Johnson, and Muday lab. For this ticket:

Collect all SRP names associated with the labs and submissions
Review the SRP on NCBI and ensure it is associated with the correct lab
Review details of the experiment including the descriptions and who the data belongs to
Ensure names and contacts are added to each experiment
Review the data and ensure all is accounted for

Attachments

Issue Links

relates to

IGBF-3544 Re-run mature pollen and seedling pipeline with SL4 using data newly submitted to SRA

Closed

IGBF-3545 Re-run nextflow Mark pollen tube data for SL4 and SL5 with data dowloaded from SRA

Closed

IGBF-3253 Submit Muday time course data to SRA

Closed

IGBF-3254 Submit Johnson lab mature pollen and tomato seedling data to SRA

Closed

IGBF-3365 Prepping data and entries for SRA for Ravi / Kelsey data

Closed

IGBF-3406 Re-run Nextflow Muday time course data with SL5 data downloaded from SRA

Closed

IGBF-3424 Re-run mature pollen and seedling pipeline with SL5 using data newly submitted to SRA

Closed

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Molly Davis added a comment - 29/Nov/23 2:04 PM - edited

SRP Experiments:

mark-2022-timeseries = SRP441343

Name = Johnson, Mark
Contact email = mark_johnson_1@brown.edu
University name = Brown University
Lab link: https://www.brown.edu/Departments/Molecular_Biology/pgl/index.html

mark-2020-pollentube = SRP252265

Name = Johnson, Mark
Contact email = mark_johnson_1@brown.edu
University name = Brown University
Lab link: https://www.brown.edu/Departments/Molecular_Biology/pgl/index.html

muday-2022-timeseries = SRP460750

Name = Gloria K. Muday
Contact email = muday@wfu.edu
University name = Wake Forest University
Lab link: https://muday.sites.wfu.edu/

seedlingPollen = SRP438952

Name = Johnson, Mark
Contact email = mark_johnson_1@brown.edu
University name = Brown University
Lab link: https://www.brown.edu/Departments/Molecular_Biology/pgl/index.html

30-681594536 = SRP486761

Name = Palanivelu, Ravishankar
Contact email = rpalaniv@arizona.edu
University name = University of Arizona, School of Plant Sciences
Lab link: http://ag.arizona.edu/research/ravilab

30-804059537 = SRP487154

Name = Palanivelu, Ravishankar
Contact email = rpalaniv@arizona.edu
University name = University of Arizona, School of Plant Sciences
Lab link: http://ag.arizona.edu/research/ravilab

30-605730043 = SRP482647

Name = Palanivelu, Ravishankar
Contact email = rpalaniv@arizona.edu
University name = University of Arizona, School of Plant Sciences
Lab link: http://ag.arizona.edu/research/ravilab

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Molly Davis added a comment - 29/Nov/23 2:04 PM - edited SRP Experiments : mark-2022-timeseries = SRP441343 Name = Johnson, Mark Contact email = mark_johnson_1@brown.edu University name = Brown University Lab link: https://www.brown.edu/Departments/Molecular_Biology/pgl/index.html mark-2020-pollentube = SRP252265 Name = Johnson, Mark Contact email = mark_johnson_1@brown.edu University name = Brown University Lab link: https://www.brown.edu/Departments/Molecular_Biology/pgl/index.html muday-2022-timeseries = SRP460750 Name = Gloria K. Muday Contact email = muday@wfu.edu University name = Wake Forest University Lab link: https://muday.sites.wfu.edu/ seedlingPollen = SRP438952 Name = Johnson, Mark Contact email = mark_johnson_1@brown.edu University name = Brown University Lab link: https://www.brown.edu/Departments/Molecular_Biology/pgl/index.html 30-681594536 = SRP486761 Name = Palanivelu, Ravishankar Contact email = rpalaniv@arizona.edu University name = University of Arizona, School of Plant Sciences Lab link: http://ag.arizona.edu/research/ravilab 30-804059537 = SRP487154 Name = Palanivelu, Ravishankar Contact email = rpalaniv@arizona.edu University name = University of Arizona, School of Plant Sciences Lab link: http://ag.arizona.edu/research/ravilab 30-605730043 = SRP482647 Name = Palanivelu, Ravishankar Contact email = rpalaniv@arizona.edu University name = University of Arizona, School of Plant Sciences Lab link: http://ag.arizona.edu/research/ravilab

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Robert Reid added a comment - 22/Feb/24 9:17 AM

The Bioproject updated, all good!

I think this is all good.

Molly,
Just add the lab websites in the comments above to the summary and then done.

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Robert Reid added a comment - 22/Feb/24 9:17 AM The Bioproject updated, all good! I think this is all good. Molly, Just add the lab websites in the comments above to the summary and then done.

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Molly Davis added a comment - 26/Feb/24 10:17 AM

Next Step: Create a document with all the information above and share with tomato group.

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Molly Davis added a comment - 26/Feb/24 10:17 AM Next Step : Create a document with all the information above and share with tomato group.

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Robert Reid added a comment - 27/Feb/24 9:54 AM

I have created the Doc in the shared GTTR Google Drive.

It is in the top layer of experiments.

https://docs.google.com/document/d/1pob8hHpQwQ6KMeHcVsHQ9AERclpv83MJThqoSDm_vFY/edit?usp=drive_link

I think we can move this to done?

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Robert Reid added a comment - 27/Feb/24 9:54 AM I have created the Doc in the shared GTTR Google Drive. It is in the top layer of experiments. https://docs.google.com/document/d/1pob8hHpQwQ6KMeHcVsHQ9AERclpv83MJThqoSDm_vFY/edit?usp=drive_link I think we can move this to done?

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Robert Reid added a comment - 27/Feb/24 9:55 AM

I guess next step, is we send email out to the entire group with the info so that they know where to access it also.

I can send. Let's discuss!

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Robert Reid added a comment - 27/Feb/24 9:55 AM I guess next step, is we send email out to the entire group with the info so that they know where to access it also. I can send. Let's discuss!

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Molly Davis added a comment - 27/Feb/24 2:13 PM - edited

I went ahead and added the NCBI link to the information as well so the data is easily found. Next step is to email tomato group.

Dr. Reid would you like to send the email out then move this ticket to done?

Robert Reid

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Molly Davis added a comment - 27/Feb/24 2:13 PM - edited I went ahead and added the NCBI link to the information as well so the data is easily found. Next step is to email tomato group. Dr. Reid would you like to send the email out then move this ticket to done? Robert Reid

People

Assignee:

Molly Davis

Reporter:

Molly Davis

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Dates

Created:

15/Nov/23 2:45 PM

Updated:

10/May/24 10:35 AM

Resolved:

10/May/24 10:35 AM