Rob has the raw sequences both on cluster and locally on a backup at the following location:
/Volumes/Promise Pegasus/oat/tomato/johnson-jan22/30-614759823/00_fastq
(This location is easiest for the FTP transfer to NCBI)

Total files = 96.
Total R1 files = 48
Total R2 files = 48

Md5sum results are here also and are needed for the FTP transfer.

Biosample TSV table: Can be found here in the GTTR group experiments folder:
https://docs.google.com/spreadsheets/d/1WDfAbXmA-sdGSx4TF1-56FtXNS_G0CeOFPz5xoRFGR0/edit?usp=sharing

Updated the biosample sheet so the sample name is now this format:

M.28.MP.3

First value: H,M,N,T. (Heinz, Malintka, Nagcarlang, Tamaulipas)

2nd value: Temperature of treatment, 28 or 37 C

3rd value: MP = mature pollen, Se = seedling

4rth value: Replicate #. 1,2 or 3

Updated Bioproject to be a new ID.

Need a title for Experiment.

The original title for the first SRA's was : " Genomic analysis of heat stress tolerance during tomato pollination "
(PRJNA611819)

This title matches our NSF grant title.

I suggest we present to the group some title suggestions for each of the SRA expts to be submitted.

Idea 1:
Heat stress tolerance during tomato pollination: Mature pollen and seedlings

To chat with everyone, I started to Google slide deck to capture some of the things to talk about related to SRA submissions.

This is located on the team Google drive at this location:

https://docs.google.com/presentation/d/1lTM-mCmL9_yLaeEkGvxhYN4oIFvp7vUEfyA35lOz2Zk/edit?usp=sharing

Making a few title name suggestions in this file.

Stepped through more of the SRA steps, looking for where we might get stuck. We can go back and make changes at any step in the process.

Biosample .tsv was acceptable.
The SRA template sheet was also acceptable. That can be found here:

https://docs.google.com/spreadsheets/d/1bkaDGUYMnyTLi-akT9Upu05-W6xs3mpj/edit?usp=sharing&ouid=100714234126361751017&rtpof=true&sd=true

I still need to confirm 3-4 columns on this sheet.

For FTP upload, I have started uploading the raw sequences in their original format and naming convention. Uploading has been successful. I have not had gone through the SRA checking process yet however. This step can sometimes be smooth or very nasty!
I have had sequences rejected due to 2 sequences matching an adapter (out of 100 million )!

Data is uploaded to the NCBI site via FTP.
Data will be erased on May 24 if it is still in submission.

1. I need to review the SRA sheet.
2. And then we* will need to review all the steps.
3. And then it should be ready for submission.

• This would be good to review with entire group.
  Started a Google slide deck that we can eventually present to group.

https://docs.google.com/presentation/d/1lTM-mCmL9_yLaeEkGvxhYN4oIFvp7vUEfyA35lOz2Zk/edit?usp=sharing

Here, we can do the SRA web page summary where we show where each column in the Biosample and SRA excel sheets, become lines that the world can see after being published. And join the pieces together! (This should be an todo / item / action).

Also, the google slide deck above could be the next thing we present / talk about in the tomato group when our turn comes around!!

To review:

• Look at the spreadsheet
• Check for mismatches between files names and sample names
• Check that all columns have data in them
• Check that descriptions and samples names are unique within a row

Request:

• Once the data is imported to SRA, please record the BioProject and BioSample numbers for each sample.
• This should be added to the samples spreadsheet for the data set. (New ticket.)

SRA table:
Design Description Column.

Mark's group provided a description.

SRA Description - pollen grain and seedling experiments

Pollen Grain
For each biological replicate pollen from each cultivar was collected in a single 0.5ml conical tube. 300ul of tomato liquid pollen growth medium (tPGM) was added to the tube and mixed to break clumps. 150ul was immediately transferred to a new tube and 300ul tPGM added to both the new and old tubes. Both tubes were then moved to a water bath at 28C. After 3 hours of incubation, 1 tube was moved to 37C (S), the other left at 28C (C), and both incubated for an additional 3 hours. After incubation pollen tubes were collected by centrifugation and stored at -80C. Paired end RNA-Seq libraries were created with the NEBNext Ultra RNA Library Prep Poly A kit per the manufacturer’s protocol.

Seedling
For each biological replicate pollen from each cultivar was collected in a single 0.5ml conical tube. 300ul of tomato liquid pollen growth medium (tPGM) was added to the tube and mixed to break clumps. 150ul was immediately transferred to a new tube and 300ul tPGM added to both the new and old tubes. Both tubes were then moved to a water bath at 28C. After 3 hours of incubation, 1 tube was moved to 37C (S), the other left at 28C (C), and both incubated for an additional 3 hours. After incubation pollen tubes were collected by centrifugation and stored at -80C. Paired end RNA-Seq libraries were created with the NEBNext Ultra RNA Library Prep Poly A kit per the manufacturer’s protocol.

This is in experiments in Google Drive (https://docs.google.com/document/d/1S8YoZ3hM0jPUwXKxTn_f1Fjhne1c81fJmWztnG1GEys/edit?usp=sharing).

Updated the SRA submit sheet with this column.

Library Selection column

This column is a Pull down menu with only a small selection of options. For RNA-Seq, we choose "PolyA" .
This will be true for all RNA-Seq experiments.

Easy peasy.

Started a Google Slide Deck:

https://docs.google.com/presentation/d/1lTM-mCmL9_yLaeEkGvxhYN4oIFvp7vUEfyA35lOz2Zk/edit?usp=sharing

This is the start of an overview of the Biosamples / SRA process.

Also in here is the starting attempt to show how the spreadsheets translate to the actual NCBI biosample pages after completion.

For review,

Take a look at the Biosample sheet in the google docs.

https://docs.google.com/spreadsheets/d/1WDfAbXmA-sdGSx4TF1-56FtXNS_G0CeOFPz5xoRFGR0/edit?usp=sharing

For the SRA sheet, this needs a set of eyes as well!
https://docs.google.com/spreadsheets/d/1bkaDGUYMnyTLi-akT9Upu05-W6xs3mpj/edit?usp=sharing&ouid=100714234126361751017&rtpof=true&sd=true

Also, take a peak at the slide deck. This component is still a work in progress.

For each row in the tables, we need to make sure that the ID matches the details.

See note above about how the IDs are made. They hold almost all the info needed to learn about the sample.
We just need to make sure:
the temps are right,
the genotype is correct. (TMNH)
the replicate # is correct.
The tissue type is correct. (MP or se) (mature pollen, seedling)

Review:

Mark_MaturePollenSeedling_SRA_metadata

• Row 10: ID says 28C but title says 37C
• Row 13: ID says 37C title says 28C
• Row 22: ID says 28C title says 37C
• Row 25: ID says 37C title says 28C
• Row 34: ID says 28C title says 37C
• Row 37: ID says 37C title says 28C
• Row 46: ID says 28C title says 37C
• Row 49: ID says 37C title says 28C

SRA_BiosampleForm-Mark_MaturePollenSeedling

• Rows seem to match across.

Good catch!
I made that mistake early on. Corrected it in Biosample but forgot to correct it in the SRA sheet.

Made the changes now.

I compared the SRA data I submitted for Mark Johnson's lab in ~2020 to the current form to see if it lined up.

Biosample - The only difference is that I included the duration of the treatment in the treatment column (Incubated at 37°C for 3 hours). I'm not familiar with these new samples so I'm not sure if that is relevant. I did not include age in my submission, but that might have been because the sequencing was from pollen tubes.

Metadata - Everything looks good to me. We had to go back and forth with GeneWiz in 2020 to figure out the instrument model (HiSeq 4000). I would be surprised if they were still using a HiSeq now, though I'm not sure when these samples were sequenced. I would think GeneWiz would be using something like a NovaSeq 6000 now, which is an option in the dropdown.

Recommend we update / check into the sequencing machine value as the current value may not be correct.

I am first looking through Google Drive as there are Azenta quotes etc., available there.

Does not give instrument. Nor do any of the reports after sequencing is completed.
Most likely we will need to reach out to Azenta to find which instrument was used.

I am first looking through Google Drive as there are Azenta quotes etc., available there.

Found one:
Google Drive Azenta Quote

Does not give instrument. Nor do any of the reports after sequencing is completed.
Most likely we will need to reach out to Azenta to find which instrument was used.

Rob: Investigating whether we can identify the instrument using the fastq read name.
Nowlan: Used the tracking number from the original quote to ask vender what the instrument was. Vender was able to look it up right away and provide an answer.

Azenta contact info:
NGS Study Managers
United States: 1+877-436-3949 x 1 | ngs@azenta.com

Will probably need this soon.

Had a chance to chat with Gloria and mark about one of the columns in the Biosample spreadsheet.

Under the time column, we tentatively had 50-80 days.
We decided that this information is mostly irrelevant/not entire true. The neighboring column stating that we are in the "flowering" stage is way more important and encompasses the time period nicely.

So time column is now blank in the Biosamples.

I heard back from Azenta. We can go with the Hiseq 4000 for the instrument column on the SRA tabbed sheet.

Here is the response:
Hi Rob,

Thank you for reaching out!

All Dr. Johnson’s experiments to date were run on a HiSeq 4000 or equivalent.

For this particular experiment (30-614759823), your samples were sequenced on a HiSeq 4000.

Please let us know if you have any questions.

Best,

Dafne

Dafne Alves Winders, Ph.D.

Assistant Manager | Next Generation Sequencing

115 Corporate Blvd.

South Plainfield, NJ 07080

We have a BioProject ID:

Dear Robert Reid,

This is an automatic acknowledgment that your submission:

SubmissionID: SUB13087168
BioProject ID: PRJNA975110
Title:

has been successfully registered with the BioProject database.

BIOSAMPLES

Dear Robert Reid,

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

BioSample accessions: SAMN35305410, SAMN35305411, SAMN35305412, SAMN35305413, SAMN35305414, SAMN35305415, SAMN35305416, SAMN35305417, SAMN35305418, SAMN35305419 ... (see attached file)
Temporary SubmissionID: SUB13087168
Release date: 2024-07-01, or with the release of linked data, whichever is first

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

Please reference BioSample accessions SAMN35305410, SAMN35305411, SAMN35305412, SAMN35305413, SAMN35305414, SAMN35305415, SAMN35305416, SAMN35305417, SAMN35305418, SAMN35305419 ... (see attached file) when making corresponding sequence data submissions.

Send questions and update requests to biosamplehelp@ncbi.nlm.nih.gov; include the BioSample accessions SAMN35305410, SAMN35305411, SAMN35305412, SAMN35305413, SAMN35305414, SAMN35305415, SAMN35305416, SAMN35305417, SAMN35305418, SAMN35305419 ... (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
SAMN35305410 H.28.MP.1 H.28.MP.1 Solanum lycopersicum 4081 Heinz
SAMN35305411 H.28.MP.2 H.28.MP.2 Solanum lycopersicum 4081 Heinz
SAMN35305412 H.28.MP.3 H.28.MP.3 Solanum lycopersicum 4081 Heinz
SAMN35305413 H.37.MP.1 H.37.MP.1 Solanum lycopersicum 4081 Heinz
SAMN35305414 H.37.MP.2 H.37.MP.2 Solanum lycopersicum 4081 Heinz
SAMN35305415 H.37.MP.3 H.37.MP.3 Solanum lycopersicum 4081 Heinz
SAMN35305416 M.28.MP.1 M.28.MP.1 Solanum lycopersicum 4081 Malintka
SAMN35305417 M.28.MP.2 M.28.MP.2 Solanum lycopersicum 4081 Malintka
SAMN35305418 M.28.MP.3 M.28.MP.3 Solanum lycopersicum 4081 Malintka
SAMN35305419 M.37.MP.1 M.37.MP.1 Solanum lycopersicum 4081 Malintka
SAMN35305420 M.37.MP.2 M.37.MP.2 Solanum lycopersicum 4081 Malintka
SAMN35305421 M.37.MP.3 M.37.MP.3 Solanum lycopersicum 4081 Malintka
SAMN35305422 N.28.MP.1 N.28.MP.1 Solanum lycopersicum 4081 Nagcarlang
SAMN35305423 N.28.MP.2 N.28.MP.2 Solanum lycopersicum 4081 Nagcarlang
SAMN35305424 N.28.MP.3 N.28.MP.3 Solanum lycopersicum 4081 Nagcarlang
SAMN35305425 N.37.MP.1 N.37.MP.1 Solanum lycopersicum 4081 Nagcarlang
SAMN35305426 N.37.MP.2 N.37.MP.2 Solanum lycopersicum 4081 Nagcarlang
SAMN35305427 N.37.MP.3 N.37.MP.3 Solanum lycopersicum 4081 Nagcarlang
SAMN35305428 T.28.MP.1 T.28.MP.1 Solanum lycopersicum 4081 Tamaulipas
SAMN35305429 T.28.MP.2 T.28.MP.2 Solanum lycopersicum 4081 Tamaulipas
SAMN35305430 T.28.MP.3 T.28.MP.3 Solanum lycopersicum 4081 Tamaulipas
SAMN35305431 T.37.MP.1 T.37.MP.1 Solanum lycopersicum 4081 Tamaulipas
SAMN35305432 T.37.MP.2 T.37.MP.2 Solanum lycopersicum 4081 Tamaulipas
SAMN35305433 T.37.MP.3 T.37.MP.3 Solanum lycopersicum 4081 Tamaulipas
SAMN35305434 H.28.Se.1 H.28.Se.1 Solanum lycopersicum 4081 Heinz
SAMN35305435 H.28.Se.2 H.28.Se.2 Solanum lycopersicum 4081 Heinz
SAMN35305436 H.28.Se.3 H.28.Se.3 Solanum lycopersicum 4081 Heinz
SAMN35305437 H.37.Se.1 H.37.Se.1 Solanum lycopersicum 4081 Heinz
SAMN35305438 H.37.Se.2 H.37.Se.2 Solanum lycopersicum 4081 Heinz
SAMN35305439 H.37.Se.3 H.37.Se.3 Solanum lycopersicum 4081 Heinz
SAMN35305440 M.28.Se.1 M.28.Se.1 Solanum lycopersicum 4081 Malintka
SAMN35305441 M.28.Se.2 M.28.Se.2 Solanum lycopersicum 4081 Malintka
SAMN35305442 M.28.Se.3 M.28.Se.3 Solanum lycopersicum 4081 Malintka
SAMN35305443 M.37.Se.1 M.37.Se.1 Solanum lycopersicum 4081 Malintka
SAMN35305444 M.37.Se.2 M.37.Se.2 Solanum lycopersicum 4081 Malintka
SAMN35305445 M.37.Se.3 M.37.Se.3 Solanum lycopersicum 4081 Malintka
SAMN35305446 N.28.Se.1 N.28.Se.1 Solanum lycopersicum 4081 Nagcarlang
SAMN35305447 N.28.Se.2 N.28.Se.2 Solanum lycopersicum 4081 Nagcarlang
SAMN35305448 N.28.Se.3 N.28.Se.3 Solanum lycopersicum 4081 Nagcarlang
SAMN35305449 N.37.Se.1 N.37.Se.1 Solanum lycopersicum 4081 Nagcarlang
SAMN35305450 N.37.Se.2 N.37.Se.2 Solanum lycopersicum 4081 Nagcarlang
SAMN35305451 N.37.Se.3 N.37.Se.3 Solanum lycopersicum 4081 Nagcarlang
SAMN35305452 T.28.Se.1 T.28.Se.1 Solanum lycopersicum 4081 Tamaulipas
SAMN35305453 T.28.Se.2 T.28.Se.2 Solanum lycopersicum 4081 Tamaulipas
SAMN35305454 T.28.Se.3 T.28.Se.3 Solanum lycopersicum 4081 Tamaulipas
SAMN35305455 T.37.Se.1 T.37.Se.1 Solanum lycopersicum 4081 Tamaulipas
SAMN35305456 T.37.Se.2 T.37.Se.2 Solanum lycopersicum 4081 Tamaulipas
SAMN35305457 T.37.Se.3 T.37.Se.3 Solanum lycopersicum 4081 Tamaulipas

https://www.ncbi.nlm.nih.gov/biosample/35305410
https://www.ncbi.nlm.nih.gov/biosample/35305411
https://www.ncbi.nlm.nih.gov/biosample/35305412
https://www.ncbi.nlm.nih.gov/biosample/35305413
https://www.ncbi.nlm.nih.gov/biosample/35305414
https://www.ncbi.nlm.nih.gov/biosample/35305415
https://www.ncbi.nlm.nih.gov/biosample/35305416
https://www.ncbi.nlm.nih.gov/biosample/35305417
https://www.ncbi.nlm.nih.gov/biosample/35305418
https://www.ncbi.nlm.nih.gov/biosample/35305419
https://www.ncbi.nlm.nih.gov/biosample/35305420
https://www.ncbi.nlm.nih.gov/biosample/35305421
https://www.ncbi.nlm.nih.gov/biosample/35305422
https://www.ncbi.nlm.nih.gov/biosample/35305423
https://www.ncbi.nlm.nih.gov/biosample/35305424
https://www.ncbi.nlm.nih.gov/biosample/35305425
https://www.ncbi.nlm.nih.gov/biosample/35305426
https://www.ncbi.nlm.nih.gov/biosample/35305427
https://www.ncbi.nlm.nih.gov/biosample/35305428
https://www.ncbi.nlm.nih.gov/biosample/35305429
https://www.ncbi.nlm.nih.gov/biosample/35305430
https://www.ncbi.nlm.nih.gov/biosample/35305431
https://www.ncbi.nlm.nih.gov/biosample/35305432
https://www.ncbi.nlm.nih.gov/biosample/35305433
https://www.ncbi.nlm.nih.gov/biosample/35305434
https://www.ncbi.nlm.nih.gov/biosample/35305435
https://www.ncbi.nlm.nih.gov/biosample/35305436
https://www.ncbi.nlm.nih.gov/biosample/35305437
https://www.ncbi.nlm.nih.gov/biosample/35305438
https://www.ncbi.nlm.nih.gov/biosample/35305439
https://www.ncbi.nlm.nih.gov/biosample/35305440
https://www.ncbi.nlm.nih.gov/biosample/35305441
https://www.ncbi.nlm.nih.gov/biosample/35305442
https://www.ncbi.nlm.nih.gov/biosample/35305443
https://www.ncbi.nlm.nih.gov/biosample/35305444
https://www.ncbi.nlm.nih.gov/biosample/35305445
https://www.ncbi.nlm.nih.gov/biosample/35305446
https://www.ncbi.nlm.nih.gov/biosample/35305447
https://www.ncbi.nlm.nih.gov/biosample/35305448
https://www.ncbi.nlm.nih.gov/biosample/35305449
https://www.ncbi.nlm.nih.gov/biosample/35305450
https://www.ncbi.nlm.nih.gov/biosample/35305451
https://www.ncbi.nlm.nih.gov/biosample/35305452
https://www.ncbi.nlm.nih.gov/biosample/35305453
https://www.ncbi.nlm.nih.gov/biosample/35305454
https://www.ncbi.nlm.nih.gov/biosample/35305455
https://www.ncbi.nlm.nih.gov/biosample/35305456
https://www.ncbi.nlm.nih.gov/biosample/35305457

Dear Robert Reid,

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 PRJNA975110 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: PRJNA975110
Temporary Submission ID: SUB13087168
Release date: 2024-07-01

Your SRA records will be accessible with the following link after the indicated release date:
https://www.ncbi.nlm.nih.gov/sra/PRJNA975110

Object IDs and corresponding URLs:

RUN:32258521: https://www.ncbi.nlm.nih.gov/sra/RUN:32258521
RUN:32258520: https://www.ncbi.nlm.nih.gov/sra/RUN:32258520
RUN:32258519: https://www.ncbi.nlm.nih.gov/sra/RUN:32258519
RUN:32258518: https://www.ncbi.nlm.nih.gov/sra/RUN:32258518
RUN:32258517: https://www.ncbi.nlm.nih.gov/sra/RUN:32258517
RUN:32258516: https://www.ncbi.nlm.nih.gov/sra/RUN:32258516
RUN:32258515: https://www.ncbi.nlm.nih.gov/sra/RUN:32258515
RUN:32258514: https://www.ncbi.nlm.nih.gov/sra/RUN:32258514
RUN:32258513: https://www.ncbi.nlm.nih.gov/sra/RUN:32258513
RUN:32258512: https://www.ncbi.nlm.nih.gov/sra/RUN:32258512
RUN:32258511: https://www.ncbi.nlm.nih.gov/sra/RUN:32258511
RUN:32258510: https://www.ncbi.nlm.nih.gov/sra/RUN:32258510
RUN:32258509: https://www.ncbi.nlm.nih.gov/sra/RUN:32258509
RUN:32258508: https://www.ncbi.nlm.nih.gov/sra/RUN:32258508
RUN:32258507: https://www.ncbi.nlm.nih.gov/sra/RUN:32258507
RUN:32258506: https://www.ncbi.nlm.nih.gov/sra/RUN:32258506
RUN:32258505: https://www.ncbi.nlm.nih.gov/sra/RUN:32258505
RUN:32258504: https://www.ncbi.nlm.nih.gov/sra/RUN:32258504
RUN:32258503: https://www.ncbi.nlm.nih.gov/sra/RUN:32258503
RUN:32258502: https://www.ncbi.nlm.nih.gov/sra/RUN:32258502
RUN:32258501: https://www.ncbi.nlm.nih.gov/sra/RUN:32258501
RUN:32258500: https://www.ncbi.nlm.nih.gov/sra/RUN:32258500
RUN:32258499: https://www.ncbi.nlm.nih.gov/sra/RUN:32258499
RUN:32258498: https://www.ncbi.nlm.nih.gov/sra/RUN:32258498
RUN:32258497: https://www.ncbi.nlm.nih.gov/sra/RUN:32258497
RUN:32258496: https://www.ncbi.nlm.nih.gov/sra/RUN:32258496
RUN:32258495: https://www.ncbi.nlm.nih.gov/sra/RUN:32258495
RUN:32258494: https://www.ncbi.nlm.nih.gov/sra/RUN:32258494
RUN:32258493: https://www.ncbi.nlm.nih.gov/sra/RUN:32258493
RUN:32258492: https://www.ncbi.nlm.nih.gov/sra/RUN:32258492
RUN:32258491: https://www.ncbi.nlm.nih.gov/sra/RUN:32258491
RUN:32258490: https://www.ncbi.nlm.nih.gov/sra/RUN:32258490
RUN:32258489: https://www.ncbi.nlm.nih.gov/sra/RUN:32258489
RUN:32258488: https://www.ncbi.nlm.nih.gov/sra/RUN:32258488
RUN:32258487: https://www.ncbi.nlm.nih.gov/sra/RUN:32258487
RUN:32258486: https://www.ncbi.nlm.nih.gov/sra/RUN:32258486
RUN:32258485: https://www.ncbi.nlm.nih.gov/sra/RUN:32258485
RUN:32258484: https://www.ncbi.nlm.nih.gov/sra/RUN:32258484
RUN:32258483: https://www.ncbi.nlm.nih.gov/sra/RUN:32258483
RUN:32258482: https://www.ncbi.nlm.nih.gov/sra/RUN:32258482
RUN:32258481: https://www.ncbi.nlm.nih.gov/sra/RUN:32258481
RUN:32258480: https://www.ncbi.nlm.nih.gov/sra/RUN:32258480
RUN:32258479: https://www.ncbi.nlm.nih.gov/sra/RUN:32258479
RUN:32258478: https://www.ncbi.nlm.nih.gov/sra/RUN:32258478
RUN:32258477: https://www.ncbi.nlm.nih.gov/sra/RUN:32258477
RUN:32258476: https://www.ncbi.nlm.nih.gov/sra/RUN:32258476
RUN:32258475: https://www.ncbi.nlm.nih.gov/sra/RUN:32258475
RUN:32258474: https://www.ncbi.nlm.nih.gov/sra/RUN:32258474

Dear Robert Reid,

This is an automatic acknowledgment that your submission:

SubmissionID: SUB13087168
BioProject ID: PRJNA975110
Title:

has been updated, eg by the linkage of one or more BioSamples. The locus_tag prefixes for
each linked BioSample are included in the locustagprefix.txt file that can accessed
from this BioProject in the submission portal:

https://submit.ncbi.nlm.nih.gov/subs/bioproject/SUB13087168/overview

In addition, you can view the locustagprefix.txt files for all of your BioProjects from the BioProject submission page,

https://submit.ncbi.nlm.nih.gov/subs/bioproject/.

Please use the BioProject ID PRJNA975110 with your correspondence and your data submissions.

Send questions to bioprojecthelp@ncbi.nlm.nih.gov, and include the BioProject ID and organism name.

I searched for "PRJNA975110" using the SRA interface but nothing was found.

attn: [~RobertReid]

We need to get a spreadsheet that maps our sample codes onto their corresponding SRR accessions.

It needs the following columns:

• SRR value
• Sample code

Let's keep track of this new work using this same ticket. Re-opening the ticket pending this final last bit of work!

I was able to log into the SRA and get a spreadsheet with sample submission information that maps SRR accessions onto our sample codes. Attaching it here.

For the next steps, we should create a new repository for this particular dataset.

Changed the release date to "immediately".

NCBI response:

Your data will be released after we process this date change from 2024-07-01 to 2023-05-30.
This may take a few hours but most requests will be processed sooner.