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
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Epic Link:
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Sprint:Spring 1 2023 Dec 26, Spring 2 2023 Jan 16, Spring 3 2023 Feb 1
Description
As was done previously (see https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/SRP252265_SRP328042_sample_sheet.xlsx) create a samples description sheet for SRP100604 and SRP268884.
Samples Link to Spreadsheet- https://docs.google.com/spreadsheets/d/1hg38PoQYAHUjx-H_40emgmpii3z2T1QNTcdSbX5LXBY/edit#gid=0
Links for Samples:
SRP100604- https://www.ncbi.nlm.nih.gov/sra?term=SRP100604
Paper- https://link.springer.com/article/10.1186/s12864-017-3869-1
SRP268884- https://www.ncbi.nlm.nih.gov/sra?term=SRP268884
Paper- https://link.springer.com/article/10.1007/s11103-021-01194-0
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Sprint | Spring 1 2023 Dec 26 [ 161 ] |
| Summary | Create sample description sheets for for SRP100604 and SRP268884 | Create sample description sheets for SRP100604 and SRP268884 |
| Description | As was done previously, create a samples description sheet for SRP100604 and SRP268884. |
As was done previously (see Also, please see |
| Description |
As was done previously (see Also, please see |
As was done previously (see https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/SRP252265_SRP328042_sample_sheet.xlsx) create a samples description sheet for SRP100604 and SRP268884.
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| Story Points | 0.5 | 1 |
| Description |
As was done previously (see https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/SRP252265_SRP328042_sample_sheet.xlsx) create a samples description sheet for SRP100604 and SRP268884.
|
As was done previously (see https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/SRP252265_SRP328042_sample_sheet.xlsx) create a samples description sheet for SRP100604 and SRP268884.
Samples Link to Spreadsheet- https://docs.google.com/spreadsheets/d/1hg38PoQYAHUjx-H_40emgmpii3z2T1QNTcdSbX5LXBY/edit#gid=0 *Links for Samples*: SRP100604- https://www.ncbi.nlm.nih.gov/sra?term=SRP100604 Paper- SRP268884- https://www.ncbi.nlm.nih.gov/sra?term=SRP268884 Paper- |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | SRP100604_SRP268884_sample_sheet.xlsx [ 17650 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Spring 1 2023 Dec 26 [ 161 ] | Spring 1 2023 Dec 26, Spring 2 2023 Jan 16 [ 161, 162 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Spring 1 2023 Dec 26, Spring 2 2023 Jan 16 [ 161, 162 ] | Spring 1 2023 Dec 26, Spring 2 2023 Jan 16, Spring 3 2023 Jan 30 [ 161, 162, 163 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Comment |
[ No need to enter values under "Color"
Change requests: * Delete all values in "Display Name" * Indicate cultivar and species in Genotype, e.g., JDE-9 S. lycopersicum * Double-check the genotypes. "JDE-13" looks like like it could be a replicate label, not a genotype. Genotype usually means something like a cultivar (e.g., "Moneymaker") or a transgenic line created by the investigator to test a hypothesis about gene function or a mutant line (e.g., ARE, a mutant of Ailsa Craig cultivar of Solanum lycopersicum, cultivated tomato) * Under category, use a single-letter code to indicate replicates as you did before. This is to ensure that downstream code can correctly perform statistical analysis, e.g., comparing groups * Add a new column "publication" that links to the PubMed article for the publication associated with the dataset. Review the SRA records. If the publication is not listed, google search. Usually searching for the "SRP" number finds the publication because authors include that in the paper as a condition for publicaiton. * Change Tissue Type "five-leaf stage" to indicate what the sample actual is. Five-leaf stage of what? An entire seeding, the above-ground part, what is it? Treatment: * Change "cooler temperatures" to "cool" * Change "elevated light conditions" to "high light" * Change "nitrogen deficiency" to "low N" * Change "warm temperatures" to "warm" * Change "drought stressed" to "dry" ] |
| Attachment | SRP100604_SRP268884_sample_sheet.xlsx [ 17677 ] |
| Attachment | SRP100604_SRP268884_sample_sheet.xlsx [ 17650 ] |
| Attachment | SRP100604_SRP268884_sample_sheet.csv [ 17685 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Attachment | V3_SRP100604_SRP268884_sample_sheet.xlsx [ 17697 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] | 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 ] |