Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3190

Create sample sheet with categorical classifications per sample

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          We need a computer-readable document (e.g., ".csv" or ".xlsx Excel document) that records attributes of the "SRR" sample names:

          • SRP accession (SRA project)
          • SRR accession
          • Genotype
          • Plant Part (tissue type)
          • Treatment (type of control or temperature of treatment or ...)
          • Duration of treatment, e.g., time point
          • Some type of code to signal replicate samples, e.g., "a" for one group, "b" for another

            Attachments

              Activity

              Ascending order - Click to sort in descending order
              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
              Field Original Value New Value
              Epic Link IGBF-2993 [ 21429 ]
              ann.loraine Ann Loraine made changes -
              Description We need a computer-readable document (e.g., ".csv" or ".xlsx Excel document) that records attributes of the "SRR" sample names:

              * SRP accession (SRA project)
              * SRR accession
              * Genotype
              * Plant Part (tissue type)
              * Treatment (type of control or temperature of treatment or ...)
              * Duration of treatment, e.g., time point
              * Some type of code for replicate samples, e.g., "a" for one group, "b" for another               		We need a computer-readable document (e.g., ".csv" or ".xlsx Excel document) that records attributes of the "SRR" sample names:

              * SRP accession (SRA project)
              * SRR accession
              * Genotype
              * Plant Part (tissue type)
              * Treatment (type of control or temperature of treatment or ...)
              * Duration of treatment, e.g., time point
              * Some type of code to signal replicate samples, e.g., "a" for one group, "b" for another
              ann.loraine Ann Loraine made changes -
              Sprint Fall 3 2022 Sep 26 [ 155 ] Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 155, 156 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              Hide
              Permalink
              Mdavis4290 Molly Davis added a comment - - edited

              Sample Sheet on google drive:
              https://docs.google.com/spreadsheets/d/1eXPF44kgVUMsqLr4wxZ33RpBIHXjXTbJwWXOUIPp8_Y/edit?usp=sharing

              Link to where data was collected to make sample sheet:

              SRP328042: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=1&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa

              SRP252265: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=2&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa

              Drought time (4 days) was determined by reading the research paper:
              https://www.mdpi.com/2073-4409/10/7/1809/htm

              Show
              Mdavis4290 Molly Davis added a comment - - edited Sample Sheet on google drive: https://docs.google.com/spreadsheets/d/1eXPF44kgVUMsqLr4wxZ33RpBIHXjXTbJwWXOUIPp8_Y/edit?usp=sharing Link to where data was collected to make sample sheet: SRP328042: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=1&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa SRP252265: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=2&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa Drought time (4 days) was determined by reading the research paper: https://www.mdpi.com/2073-4409/10/7/1809/htm
              Mdavis4290 Molly Davis made changes -
              Comment [ The drought stress study was largely focused on stress during certain development stages. I went ahead and put the stage of development under the {color:red}'Time'{color} column and also read the research paper which said the drought stress was for {color:red}4 days{color}.

              Paper: https://www.mdpi.com/2073-4409/10/7/1809/htm
              ]
              Mdavis4290 Molly Davis made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              Mdavis4290 Molly Davis made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              Hide
              Permalink
              Mdavis4290 Molly Davis added a comment - - edited

              Updated and uploaded sample sheet .csv and .xlsx file to cluster.

              Commands:
              rsync /Users/mollydavis333/Desktop/sample_sheet.csv mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing

              rsync /Users/mollydavis333/Desktop/sample_sheet.xlsx mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing

              Directory:
              /nobackup/tomato_genome/alt_splicing

              Show
              Mdavis4290 Molly Davis added a comment - - edited Updated and uploaded sample sheet .csv and .xlsx file to cluster. Commands: rsync /Users/mollydavis333/Desktop/sample_sheet.csv mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing rsync /Users/mollydavis333/Desktop/sample_sheet.xlsx mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing Directory: /nobackup/tomato_genome/alt_splicing
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
              nfreese Nowlan Freese made changes -
              Sprint Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 155, 156 ] Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24 [ 155, 156, 157 ]
              nfreese Nowlan Freese made changes -
              Rank Ranked higher
              Hide
              Permalink
              ann.loraine Ann Loraine added a comment - - edited

              Added above Excel spreadsheet above to the repository.
              Moved to Done.

              Show
              ann.loraine Ann Loraine added a comment - - edited Added above Excel spreadsheet above to the repository. Moved to Done.
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              ann.loraine Ann Loraine made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              ann.loraine Ann Loraine made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              ann.loraine Ann Loraine made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                People

                • Assignee:
                  Mdavis4290 Molly Davis
                  Reporter:
                  ann.loraine Ann Loraine
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  2 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: