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  1. IGB
  2. IGBF-3686

Resubmit ARE 120 Minute

        Details

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

          Description

          GOAL: Because the ARE 120 minute submission got suppressed by the NCBI, we are making a new submission with this dataset.

          Why did it get suppressed? When I combined this dataset with Marks, it was under the same Bioproject umbrella. Later, when I split the 2, they simply repressed this dataset, taking away the Bioproject.

          Information for submission is the same except now we are using the 1 letter code for IDs like we do in the other projects.

          A summary of the data can be found here, along with a new column depicting those codes.
          https://docs.google.com/spreadsheets/d/1LF-FaWDGAILx3mcSLBOcCzRopoqvD3kC/edit?usp=sharing&ouid=100714234126361751017&rtpof=true&sd=true

          V=VF36
          A=are
          F=OX3
          G=OX4

          1 Letter Code
          V.28.120.1
          A.28.120.1
          F.28.120.1
          G.28.120.1
          V.34.120.1
          A.34.120.1
          F.34.120.1
          G.34.120.1
          V.28.120.2
          A.28.120.2
          F.28.120.2
          G.28.120.2
          V.34.120.2
          A.34.120.2
          F.34.120.2
          G.34.120.2
          V.28.120.3
          A.28.120.3
          F.28.120.3
          G.28.120.3
          V.34.120.3
          A.34.120.3
          F.34.120.3
          G.34.120.3

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              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3688 Rerun nextflow with ARE 120 minute Muday data

              • Major - Major loss of function.
              • Closed

                Activity

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                Hide
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                robofjoy Robert Reid added a comment -

                FTP almost completed 46/48 files are uploaded.

                That is final step in submission.
                Upon submission, data could be ready within hours.

                I did an SRA submission Tuesday for a starfish and the data was available the next day.

                Show
                robofjoy Robert Reid added a comment - FTP almost completed 46/48 files are uploaded. That is final step in submission. Upon submission, data could be ready within hours. I did an SRA submission Tuesday for a starfish and the data was available the next day.
                Hide
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                robofjoy Robert Reid added a comment -

                BioSample accessions: SAMN40749348, SAMN40749349, SAMN40749350, SAMN40749351, SAMN40749352, SAMN40749353, SAMN40749354, SAMN40749355, SAMN40749356, SAMN40749357 ... (see attached file)
                Temporary SubmissionID: SUB14356512
                Release date: as soon as processing is complete

                A submission summary and the links by which your BioSample records will be accessible are appended and attached.

                Please reference BioSample accessions SAMN40749348, SAMN40749349, SAMN40749350, SAMN40749351, SAMN40749352, SAMN40749353, SAMN40749354, SAMN40749355, SAMN40749356, SAMN40749357 ... (see attached file) when making corresponding sequence data submissions.

                Send questions and update requests to biosamplehelp@ncbi.nlm.nih.gov; include the BioSample accessions SAMN40749348, SAMN40749349, SAMN40749350, SAMN40749351, SAMN40749352, SAMN40749353, SAMN40749354, SAMN40749355, SAMN40749356, SAMN40749357 ... (see attached file) in any correspondence.

                Regards,

                NCBI BioSample Submissions Staff
                Bethesda, Maryland USA
                ***********************************************************
                (301) 496-2475
                (301) 480-2918 (Fax)
                biosamplehelp@ncbi.nlm.nih.gov (for BioSample questions/replies)
                info@ncbi.nlm.nih.gov (for general questions regarding NCBI)
                ***********************************************************

                Accession Sample Name SPUID Organism Tax ID Cultivar
                SAMN40749348 V.28.120.1 V.28.120.1 Solanum lycopersicum 4081 VF-36
                SAMN40749349 A.28.120.1 A.28.120.1 Solanum lycopersicum 4081 anthocyanin reduced (are)
                SAMN40749350 F.28.120.1 F.28.120.1 Solanum lycopersicum 4081 F3H-OX3
                SAMN40749351 G.28.120.1 G.28.120.1 Solanum lycopersicum 4081 F3H-OX4
                SAMN40749352 V.34.120.1 V.34.120.1 Solanum lycopersicum 4081 VF-36
                SAMN40749353 A.34.120.1 A.34.120.1 Solanum lycopersicum 4081 anthocyanin reduced (are)
                SAMN40749354 F.34.120.1 F.34.120.1 Solanum lycopersicum 4081 F3H-OX3
                SAMN40749355 G.34.120.1 G.34.120.1 Solanum lycopersicum 4081 F3H-OX4
                SAMN40749356 V.28.120.2 V.28.120.2 Solanum lycopersicum 4081 VF-36
                SAMN40749357 A.28.120.2 A.28.120.2 Solanum lycopersicum 4081 anthocyanin reduced (are)
                SAMN40749358 F.28.120.2 F.28.120.2 Solanum lycopersicum 4081 F3H-OX3
                SAMN40749359 G.28.120.2 G.28.120.2 Solanum lycopersicum 4081 F3H-OX4
                SAMN40749360 V.34.120.2 V.34.120.2 Solanum lycopersicum 4081 VF-36
                SAMN40749361 A.34.120.2 A.34.120.2 Solanum lycopersicum 4081 anthocyanin reduced (are)
                SAMN40749362 F.34.120.2 F.34.120.2 Solanum lycopersicum 4081 F3H-OX3
                SAMN40749363 G.34.120.2 G.34.120.2 Solanum lycopersicum 4081 F3H-OX4
                SAMN40749364 V.28.120.3 V.28.120.3 Solanum lycopersicum 4081 VF-36
                SAMN40749365 A.28.120.3 A.28.120.3 Solanum lycopersicum 4081 anthocyanin reduced (are)
                SAMN40749366 F.28.120.3 F.28.120.3 Solanum lycopersicum 4081 F3H-OX3
                SAMN40749367 G.28.120.3 G.28.120.3 Solanum lycopersicum 4081 F3H-OX4
                SAMN40749368 V.34.120.3 V.34.120.3 Solanum lycopersicum 4081 VF-36
                SAMN40749369 A.34.120.3 A.34.120.3 Solanum lycopersicum 4081 anthocyanin reduced (are)
                SAMN40749370 F.34.120.3 F.34.120.3 Solanum lycopersicum 4081 F3H-OX3
                SAMN40749371 G.34.120.3 G.34.120.3 Solanum lycopersicum 4081 F3H-OX4

                https://www.ncbi.nlm.nih.gov/biosample/40749348
                https://www.ncbi.nlm.nih.gov/biosample/40749349
                https://www.ncbi.nlm.nih.gov/biosample/40749350
                https://www.ncbi.nlm.nih.gov/biosample/40749351
                https://www.ncbi.nlm.nih.gov/biosample/40749352
                https://www.ncbi.nlm.nih.gov/biosample/40749353
                https://www.ncbi.nlm.nih.gov/biosample/40749354
                https://www.ncbi.nlm.nih.gov/biosample/40749355
                https://www.ncbi.nlm.nih.gov/biosample/40749356
                https://www.ncbi.nlm.nih.gov/biosample/40749357
                https://www.ncbi.nlm.nih.gov/biosample/40749358
                https://www.ncbi.nlm.nih.gov/biosample/40749359
                https://www.ncbi.nlm.nih.gov/biosample/40749360
                https://www.ncbi.nlm.nih.gov/biosample/40749361
                https://www.ncbi.nlm.nih.gov/biosample/40749362
                https://www.ncbi.nlm.nih.gov/biosample/40749363
                https://www.ncbi.nlm.nih.gov/biosample/40749364
                https://www.ncbi.nlm.nih.gov/biosample/40749365
                https://www.ncbi.nlm.nih.gov/biosample/40749366
                https://www.ncbi.nlm.nih.gov/biosample/40749367
                https://www.ncbi.nlm.nih.gov/biosample/40749368
                https://www.ncbi.nlm.nih.gov/biosample/40749369
                https://www.ncbi.nlm.nih.gov/biosample/40749370
                https://www.ncbi.nlm.nih.gov/biosample/40749371

                Show
                robofjoy Robert Reid added a comment - BioSample accessions: SAMN40749348, SAMN40749349, SAMN40749350, SAMN40749351, SAMN40749352, SAMN40749353, SAMN40749354, SAMN40749355, SAMN40749356, SAMN40749357 ... (see attached file) Temporary SubmissionID: SUB14356512 Release date: as soon as processing is complete A submission summary and the links by which your BioSample records will be accessible are appended and attached. Please reference BioSample accessions SAMN40749348, SAMN40749349, SAMN40749350, SAMN40749351, SAMN40749352, SAMN40749353, SAMN40749354, SAMN40749355, SAMN40749356, SAMN40749357 ... (see attached file) when making corresponding sequence data submissions. Send questions and update requests to biosamplehelp@ncbi.nlm.nih.gov; include the BioSample accessions SAMN40749348, SAMN40749349, SAMN40749350, SAMN40749351, SAMN40749352, SAMN40749353, SAMN40749354, SAMN40749355, SAMN40749356, SAMN40749357 ... (see attached file) in any correspondence. Regards, NCBI BioSample Submissions Staff Bethesda, Maryland USA *********************************************************** (301) 496-2475 (301) 480-2918 (Fax) biosamplehelp@ncbi.nlm.nih.gov (for BioSample questions/replies) info@ncbi.nlm.nih.gov (for general questions regarding NCBI) *********************************************************** Accession Sample Name SPUID Organism Tax ID Cultivar SAMN40749348 V.28.120.1 V.28.120.1 Solanum lycopersicum 4081 VF-36 SAMN40749349 A.28.120.1 A.28.120.1 Solanum lycopersicum 4081 anthocyanin reduced (are) SAMN40749350 F.28.120.1 F.28.120.1 Solanum lycopersicum 4081 F3H-OX3 SAMN40749351 G.28.120.1 G.28.120.1 Solanum lycopersicum 4081 F3H-OX4 SAMN40749352 V.34.120.1 V.34.120.1 Solanum lycopersicum 4081 VF-36 SAMN40749353 A.34.120.1 A.34.120.1 Solanum lycopersicum 4081 anthocyanin reduced (are) SAMN40749354 F.34.120.1 F.34.120.1 Solanum lycopersicum 4081 F3H-OX3 SAMN40749355 G.34.120.1 G.34.120.1 Solanum lycopersicum 4081 F3H-OX4 SAMN40749356 V.28.120.2 V.28.120.2 Solanum lycopersicum 4081 VF-36 SAMN40749357 A.28.120.2 A.28.120.2 Solanum lycopersicum 4081 anthocyanin reduced (are) SAMN40749358 F.28.120.2 F.28.120.2 Solanum lycopersicum 4081 F3H-OX3 SAMN40749359 G.28.120.2 G.28.120.2 Solanum lycopersicum 4081 F3H-OX4 SAMN40749360 V.34.120.2 V.34.120.2 Solanum lycopersicum 4081 VF-36 SAMN40749361 A.34.120.2 A.34.120.2 Solanum lycopersicum 4081 anthocyanin reduced (are) SAMN40749362 F.34.120.2 F.34.120.2 Solanum lycopersicum 4081 F3H-OX3 SAMN40749363 G.34.120.2 G.34.120.2 Solanum lycopersicum 4081 F3H-OX4 SAMN40749364 V.28.120.3 V.28.120.3 Solanum lycopersicum 4081 VF-36 SAMN40749365 A.28.120.3 A.28.120.3 Solanum lycopersicum 4081 anthocyanin reduced (are) SAMN40749366 F.28.120.3 F.28.120.3 Solanum lycopersicum 4081 F3H-OX3 SAMN40749367 G.28.120.3 G.28.120.3 Solanum lycopersicum 4081 F3H-OX4 SAMN40749368 V.34.120.3 V.34.120.3 Solanum lycopersicum 4081 VF-36 SAMN40749369 A.34.120.3 A.34.120.3 Solanum lycopersicum 4081 anthocyanin reduced (are) SAMN40749370 F.34.120.3 F.34.120.3 Solanum lycopersicum 4081 F3H-OX3 SAMN40749371 G.34.120.3 G.34.120.3 Solanum lycopersicum 4081 F3H-OX4 https://www.ncbi.nlm.nih.gov/biosample/40749348 https://www.ncbi.nlm.nih.gov/biosample/40749349 https://www.ncbi.nlm.nih.gov/biosample/40749350 https://www.ncbi.nlm.nih.gov/biosample/40749351 https://www.ncbi.nlm.nih.gov/biosample/40749352 https://www.ncbi.nlm.nih.gov/biosample/40749353 https://www.ncbi.nlm.nih.gov/biosample/40749354 https://www.ncbi.nlm.nih.gov/biosample/40749355 https://www.ncbi.nlm.nih.gov/biosample/40749356 https://www.ncbi.nlm.nih.gov/biosample/40749357 https://www.ncbi.nlm.nih.gov/biosample/40749358 https://www.ncbi.nlm.nih.gov/biosample/40749359 https://www.ncbi.nlm.nih.gov/biosample/40749360 https://www.ncbi.nlm.nih.gov/biosample/40749361 https://www.ncbi.nlm.nih.gov/biosample/40749362 https://www.ncbi.nlm.nih.gov/biosample/40749363 https://www.ncbi.nlm.nih.gov/biosample/40749364 https://www.ncbi.nlm.nih.gov/biosample/40749365 https://www.ncbi.nlm.nih.gov/biosample/40749366 https://www.ncbi.nlm.nih.gov/biosample/40749367 https://www.ncbi.nlm.nih.gov/biosample/40749368 https://www.ncbi.nlm.nih.gov/biosample/40749369 https://www.ncbi.nlm.nih.gov/biosample/40749370 https://www.ncbi.nlm.nih.gov/biosample/40749371
                Hide
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                robofjoy Robert Reid added a comment -

                Now we wait.........

                Show
                robofjoy Robert Reid added a comment - Now we wait.........
                Hide
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                robofjoy Robert Reid added a comment -

                Dear Robert Reid,

                This is an automatic acknowledgment that your submission:

                SubmissionID: SUB14356512
                BioProject ID: PRJNA1096260
                Title:

                has been successfully registered with the BioProject database. After review by the database staff, your project information will be accessible with the following link, usually within a few days of the
                release date that you set (or the release of linked data, whichever is first):

                http://www.ncbi.nlm.nih.gov/bioproject/1096260

                Please use the BioProject ID PRJNA1096260 with your correspondence and your data submissions.

                Show
                robofjoy Robert Reid added a comment - Dear Robert Reid, This is an automatic acknowledgment that your submission: SubmissionID: SUB14356512 BioProject ID: PRJNA1096260 Title: has been successfully registered with the BioProject database. After review by the database staff, your project information will be accessible with the following link, usually within a few days of the release date that you set (or the release of linked data, whichever is first): http://www.ncbi.nlm.nih.gov/bioproject/1096260 Please use the BioProject ID PRJNA1096260 with your correspondence and your data submissions.
                Hide
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                robofjoy Robert Reid added a comment -

                It's never easy.
                Error thrown in the BioProject due to the existence of the suppressed SRR runs in their system.

                I have sent a message to the SRA to remove the original SRR runs
                that were a part of
                PRJNA611819 .

                These are the suppressed SRR:

                SRR18087909
                SRR18087910
                SRR18087911
                SRR18087912
                SRR18087913
                SRR18087914
                SRR18087915
                SRR18087916
                SRR18087917
                SRR18087918
                SRR18087919
                SRR18087902
                SRR18087903
                SRR18087904
                SRR18087905
                SRR18087906
                SRR18087907
                SRR18087908
                SRR18087901
                SRR18087897
                SRR18087898
                SRR18087899
                SRR18087900
                SRR18087896

                I hope or a quick turn around time, they have been responsive.
                Rob

                Show
                robofjoy Robert Reid added a comment - It's never easy. Error thrown in the BioProject due to the existence of the suppressed SRR runs in their system. I have sent a message to the SRA to remove the original SRR runs that were a part of PRJNA611819 . These are the suppressed SRR: SRR18087909 SRR18087910 SRR18087911 SRR18087912 SRR18087913 SRR18087914 SRR18087915 SRR18087916 SRR18087917 SRR18087918 SRR18087919 SRR18087902 SRR18087903 SRR18087904 SRR18087905 SRR18087906 SRR18087907 SRR18087908 SRR18087901 SRR18087897 SRR18087898 SRR18087899 SRR18087900 SRR18087896 I hope or a quick turn around time, they have been responsive. Rob
                Hide
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                robofjoy Robert Reid added a comment -

                Got a response. The submission is being pushed forward. Data is being moved from cold storage on their end.

                Show
                robofjoy Robert Reid added a comment - Got a response. The submission is being pushed forward. Data is being moved from cold storage on their end.
                Hide
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                robofjoy Robert Reid added a comment -

                SRA complete !!

                This is an automatic acknowledgment that your recent submission to the SRA database has been successfully processed and will be released on the date specified.

                Please reference PRJNA1096260 in your publication. This BioProject accession number is provided instead of SRP and should be used in your publication as it will allow better searching in Entrez.

                Accession to cite for these SRA data: PRJNA1096260
                Temporary Submission ID: SUB14356512
                Release date: 2024-04-06

                Your SRA records will be accessible with the following link after the indicated release date:
                https://www.ncbi.nlm.nih.gov/sra/PRJNA1096260

                Send questions and update requests to sra@ncbi.nlm.nih.gov; include the citation accession PRJNA1096260 in any correspondence.

                Regards,

                NCBI SRA Submissions Staff
                Bethesda, Maryland USA

                Show
                robofjoy Robert Reid added a comment - SRA complete !! This is an automatic acknowledgment that your recent submission to the SRA database has been successfully processed and will be released on the date specified. Please reference PRJNA1096260 in your publication. This BioProject accession number is provided instead of SRP and should be used in your publication as it will allow better searching in Entrez. Accession to cite for these SRA data: PRJNA1096260 Temporary Submission ID: SUB14356512 Release date: 2024-04-06 Your SRA records will be accessible with the following link after the indicated release date: https://www.ncbi.nlm.nih.gov/sra/PRJNA1096260 Send questions and update requests to sra@ncbi.nlm.nih.gov; include the citation accession PRJNA1096260 in any correspondence. Regards, NCBI SRA Submissions Staff Bethesda, Maryland USA
                Hide
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                robofjoy Robert Reid added a comment -

                To review:

                Take a peak at the SRA above and check out the 24 samples for logical completeness.

                In the first comment above there is the SRA excel sheet. It would be good to compare this sheet to the SRA samples posted in the comment above.

                Show
                robofjoy Robert Reid added a comment - To review: Take a peak at the SRA above and check out the 24 samples for logical completeness. In the first comment above there is the SRA excel sheet. It would be good to compare this sheet to the SRA samples posted in the comment above.
                Hide
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                Mdavis4290 Molly Davis added a comment - - edited

                Review:

                I took the SRA meta data excel sheet Dr. Reid made and compared it to the SRA Runinfo.csv file from NCBI and compared both. It seems all of the sample names match their library names.The runs also seem correct on NCBI. I would say this submission was successful and it fixed the problem with combining experiments onto the same bio project. To confirm, the next step would be to pull the data from SRA and run it through the nextflow pipeline then compare the original data to the SRA submission data. Moving this ticket to testing for Dr. Reid to close if ready and then I will create the next step tickets!

                SRP499796

                Show
                Mdavis4290 Molly Davis added a comment - - edited Review : I took the SRA meta data excel sheet Dr. Reid made and compared it to the SRA Runinfo.csv file from NCBI and compared both. It seems all of the sample names match their library names.The runs also seem correct on NCBI. I would say this submission was successful and it fixed the problem with combining experiments onto the same bio project. To confirm, the next step would be to pull the data from SRA and run it through the nextflow pipeline then compare the original data to the SRA submission data. Moving this ticket to testing for Dr. Reid to close if ready and then I will create the next step tickets! SRP499796
                Hide
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                robofjoy Robert Reid added a comment -

                All done.

                Show
                robofjoy Robert Reid added a comment - All done.

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    • Created:
                      Updated:
                      Resolved: