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:3
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Epic Link:
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Sprint:Summer 3 2023 June 12, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21, Fall 6, Fall 7, Spring 1, Spring 2
Description
Prepare the sequence data from the 3 separate sequencing runs.
Rename the sequencing files to match the single letter coding format like we use in the Muday time course.
Create a Biosample Spreadsheet.
Create an SRA spread sheet.
Figure out what aspects of this project that require different entries compared to the Muday and Johnson projects.
Attachments
Issue Links
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- Closed
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Activity
For this submission, we will put:
USA:University of Arizona, Tucson, AZ
On the cluster, in the time series experiment, there are 126 sequence files. Since they are paired, there are 63 experiments.
3 of those are Heinz ovary.
15 experiments of Heinz
15 experiments of Nag
15 experiments of Mal
15 experiments of Tamaulipas
total = 63
The Md5 sums can be seen in the google drive here and the expt names:
https://drive.google.com/drive/folders/1TxUDhJHr9mrXOVysrcceS9YGyTXFHRmo?usp=drive_link
Naming convention for this data
We have tissue types in addition to:
- genotype
- temperature
- time point in hours
- tissue type (unpolinated, pistil, self, ovary)
- replicate
T.37.3hr.pist.Rep1_R2.fastq.gz
Or
T.37.3.p.1_R2.fastq.gz
In Ravi's run experiment (tam only), they had self versus pistil as the labels.
I suspect this is supposed to be self versus unpollinated.
I have reached out to Kelsey to get clarification.
Will adjust once I know.
This is what the file names will be :
T.25.0hr.p.1_R1.fastq.gz T.25.0hr.p.1_R2.fastq.gz
T.25.0hr.u.2_R1.fastq.gz T.25.0hr.u.2_R2.fastq.gz
T.25.3hr.p.1_R1.fastq.gz T.25.3hr.p.1_R2.fastq.gz
T.25.3hr.u.2_R1.fastq.gz T.25.3hr.u.2_R2.fastq.gz
T.37.3hr.p.1_R1.fastq.gz T.37.3hr.p.1_R2.fastq.gz
T.37.3hr.u.2_R1.fastq.gz T.37.3hr.u.2_R2.fastq.gz
T.25.8hr.p.1_R1.fastq.gz T.25.8hr.p.1_R2.fastq.gz
T.25.8hr.u.2_R1.fastq.gz T.25.8hr.u.2_R2.fastq.gz
T.37.8hr.p.1_R1.fastq.gz T.37.8hr.p.1_R2.fastq.gz
T.37.8hr.u.2_R1.fastq.gz T.37.8hr.u.2_R2.fastq.gz
H.25C.0hr.U.1_R1.fastq.gz H.25C.0hr.U.1_R2.fastq.gz
H.25C.3hr.U.1_R1.fastq.gz H.25C.3hr.U.1_R2.fastq.gz
H.37C.3hr.U.1_R1.fastq.gz H.37C.3hr.U.1_R2.fastq.gz
H.25C.8hr.U.1_R1.fastq.gz H.25C.8hr.U.1_R2.fastq.gz
H.37C.8hr.U.1_R1.fastq.gz H.37C.8hr.U.1_R2.fastq.gz
H.25C.0hr.U.2_R1.fastq.gz H.25C.0hr.U.2_R2.fastq.gz
H.25C.3hr.U.2_R1.fastq.gz H.25C.3hr.U.2_R2.fastq.gz
H.37C.3hr.U.2_R1.fastq.gz H.37C.3hr.U.2_R2.fastq.gz
H.25C.8hr.U.2_R1.fastq.gz H.25C.8hr.U.2_R2.fastq.gz
H.37C.8hr.U.2_R1.fastq.gz H.37C.8hr.U.2_R2.fastq.gz
H.25C.0hr.U.3_R1.fastq.gz H.25C.0hr.U.3_R2.fastq.gz
H.25C.3hr.U.3_R1.fastq.gz H.25C.3hr.U.3_R2.fastq.gz
H.37C.3hr.U.3_R1.fastq.gz H.37C.3hr.U.3_R2.fastq.gz
H.25C.8hr.U.3_R1.fastq.gz H.25C.8hr.U.3_R2.fastq.gz
H.37C.8hr.U.3_R1.fastq.gz H.37C.8hr.U.3_R2.fastq.gz
M.25C.0hr.U.1_R1.fastq.gz M.25C.0hr.U.1_R2.fastq.gz
M.25C.3hr.U.1_R1.fastq.gz M.25C.3hr.U.1_R2.fastq.gz
M.37C.3hr.U.1_R1.fastq.gz M.37C.3hr.U.1_R2.fastq.gz
M.25C.8hr.U.1_R1.fastq.gz M.25C.8hr.U.1_R2.fastq.gz
M.37C.8hr.U.1_R1.fastq.gz M.37C.8hr.U.1_R2.fastq.gz
M.25C.0hr.U.2_R1.fastq.gz M.25C.0hr.U.2_R2.fastq.gz
M.25C.3hr.U.2_R1.fastq.gz M.25C.3hr.U.2_R2.fastq.gz
M.37C.3hr.U.2_R1.fastq.gz M.37C.3hr.U.2_R2.fastq.gz
M.25C.8hr.U.2_R1.fastq.gz M.25C.8hr.U.2_R2.fastq.gz
M.37C.8hr.U.2_R1.fastq.gz M.37C.8hr.U.2_R2.fastq.gz
M.25C.0hr.U.3_R1.fastq.gz M.25C.0hr.U.3_R2.fastq.gz
M.25C.3hr.U.3_R1.fastq.gz M.25C.3hr.U.3_R2.fastq.gz
M.37C.3hr.U.3_R1.fastq.gz M.37C.3hr.U.3_R2.fastq.gz
M.25C.8hr.U.3_R1.fastq.gz M.25C.8hr.U.3_R2.fastq.gz
M.37C.8hr.U.3_R1.fastq.gz M.37C.8hr.U.3_R2.fastq.gz
N.25C.0hr.U.1_R1.fastq.gz N.25C.0hr.U.1_R2.fastq.gz
N.25C.3hr.U.1_R1.fastq.gz N.25C.3hr.U.1_R2.fastq.gz
N.37C.3hr.U.1_R1.fastq.gz N.37C.3hr.U.1_R2.fastq.gz
N.25C.8hr.U.1_R1.fastq.gz N.25C.8hr.U.1_R2.fastq.gz
N.37C.8hr.U.1_R1.fastq.gz N.37C.8hr.U.1_R2.fastq.gz
N.25C.0hr.U.2_R1.fastq.gz N.25C.0hr.U.2_R2.fastq.gz
N.25C.3hr.U.2_R1.fastq.gz N.25C.3hr.U.2_R2.fastq.gz
N.37C.3hr.U.2_R1.fastq.gz N.37C.3hr.U.2_R2.fastq.gz
N.25C.8hr.U.2_R1.fastq.gz N.25C.8hr.U.2_R2.fastq.gz
N.37C.8hr.U.2_R1.fastq.gz N.37C.8hr.U.2_R2.fastq.gz
N.25C.0hr.U.3_R1.fastq.gz N.25C.0hr.U.3_R2.fastq.gz
N.25C.3hr.U.3_R1.fastq.gz N.25C.3hr.U.3_R2.fastq.gz
N.37C.3hr.U.3_R1.fastq.gz N.37C.3hr.U.3_R2.fastq.gz
N.25C.8hr.U.3_R1.fastq.gz N.25C.8hr.U.3_R2.fastq.gz
N.37C.8hr.U.3_R1.fastq.gz N.37C.8hr.U.3_R2.fastq.gz
T.25C.0hr.U.1_R1.fastq.gz T.25C.0hr.U.1_R2.fastq.gz
T.25C.3hr.U.1_R1.fastq.gz T.25C.3hr.U.1_R2.fastq.gz
T.37C.3hr.U.1_R1.fastq.gz T.37C.3hr.U.1_R2.fastq.gz
T.25C.8hr.U.1_R1.fastq.gz T.25C.8hr.U.1_R2.fastq.gz
T.37C.8hr.U.1_R1.fastq.gz T.37C.8hr.U.1_R2.fastq.gz
T.25C.0hr.U.2_R1.fastq.gz T.25C.0hr.U.2_R2.fastq.gz
T.25C.3hr.U.2_R1.fastq.gz T.25C.3hr.U.2_R2.fastq.gz
T.37C.3hr.U.2_R1.fastq.gz T.37C.3hr.U.2_R2.fastq.gz
T.25C.8hr.U.2_R1.fastq.gz T.25C.8hr.U.2_R2.fastq.gz
T.37C.8hr.U.2_R1.fastq.gz T.37C.8hr.U.2_R2.fastq.gz
Still more to from the last sequencing dataset.
[~RobertReid] request more space in "projects" (backed-up) directory on Research Computing cluster.
The last sequencing set names:
M.25C.0hr.S.1.R1.fastq.gz M.25C.0hr.S.1.R2.fastq.gz
M.25C.3hr.S.1.R1.fastq.gz M.25C.3hr.S.1.R2.fastq.gz
M.25C.8hr.S.1.R1.fastq.gz M.25C.8hr.S.1.R2.fastq.gz
M.37C.3hr.S.1.R1.fastq.gz M.37C.3hr.S.1.R2.fastq.gz
M.37C.8hr.S.1.R1.fastq.gz M.37C.8hr.S.1.R2.fastq.gz
M.25C.0hr.S.2.R1.fastq.gz M.25C.0hr.S.2.R2.fastq.gz
M.25C.3hr.S.2.R1.fastq.gz M.25C.3hr.S.2.R2.fastq.gz
M.25C.8hr.S.2.R1.fastq.gz M.25C.8hr.S.2.R2.fastq.gz
M.37C.3hr.S.2.R1.fastq.gz M.37C.3hr.S.2.R2.fastq.gz
M.37C.8hr.S.2.R1.fastq.gz M.37C.8hr.S.2.R2.fastq.gz
M.25C.0hr.S.3.R1.fastq.gz M.25C.0hr.S.3.R2.fastq.gz
M.25C.3hr.S.3.R1.fastq.gz M.25C.3hr.S.3.R2.fastq.gz
M.25C.8hr.S.3.R1.fastq.gz M.25C.8hr.S.3.R2.fastq.gz
M.37C.3hr.S.3.R1.fastq.gz M.37C.3hr.S.3.R2.fastq.gz
M.37C.8hr.S.3.R1.fastq.gz M.37C.8hr.S.3.R2.fastq.gz
N.25C.0hr.S.1.R1.fastq.gz N.25C.0hr.S.1.R2.fastq.gz
N.25C.3hr.S.1.R1.fastq.gz N.25C.3hr.S.1.R2.fastq.gz
N.25C.8hr.S.1.R1.fastq.gz N.25C.8hr.S.1.R2.fastq.gz
N.37C.3hr.S.1.R1.fastq.gz N.37C.3hr.S.1.R2.fastq.gz
N.37C.8hr.S.1.R1.fastq.gz N.37C.8hr.S.1.R2.fastq.gz
N.25C.0hr.S.2.R1.fastq.gz N.25C.0hr.S.2.R2.fastq.gz
N.25C.3hr.S.2.R1.fastq.gz N.25C.3hr.S.2.R2.fastq.gz
N.25C.8hr.S.2.R1.fastq.gz N.25C.8hr.S.2.R2.fastq.gz
N.37C.3hr.S.2.R1.fastq.gz N.37C.3hr.S.2.R2.fastq.gz
N.37C.8hr.S.2.R1.fastq.gz N.37C.8hr.S.2.R2.fastq.gz
N.25C.0hr.S.3.R1.fastq.gz N.25C.0hr.S.3.R2.fastq.gz
N.25C.3hr.S.3.R1.fastq.gz N.25C.3hr.S.3.R2.fastq.gz
N.25C.8hr.S.3.R1.fastq.gz N.25C.8hr.S.3.R2.fastq.gz
N.37C.3hr.S.3.R1.fastq.gz N.37C.3hr.S.3.R2.fastq.gz
N.37C.8hr.S.3.R1.fastq.gz N.37C.8hr.S.3.R2.fastq.gz
H.25C.0hr.S.1.R1.fastq.gz H.25C.0hr.S.1.R2.fastq.gz
H.25C.3hr.S.1.R1.fastq.gz H.25C.3hr.S.1.R2.fastq.gz
H.25C.8hr.S.1.R1.fastq.gz H.25C.8hr.S.1.R2.fastq.gz
H.37C.3hr.S.1.R1.fastq.gz H.37C.3hr.S.1.R2.fastq.gz
H.37C.8hr.S.1.R1.fastq.gz H.37C.8hr.S.1.R2.fastq.gz
H.25C.0hr.S.2.R1.fastq.gz H.25C.0hr.S.2.R2.fastq.gz
H.25C.3hr.S.2.R1.fastq.gz H.25C.3hr.S.2.R2.fastq.gz
H.25C.8hr.S.2.R1.fastq.gz H.25C.8hr.S.2.R2.fastq.gz
H.37C.3hr.S.2.R1.fastq.gz H.37C.3hr.S.2.R2.fastq.gz
H.37C.8hr.S.2.R1.fastq.gz H.37C.8hr.S.2.R2.fastq.gz
H.25C.0hr.S.3.R1.fastq.gz H.25C.0hr.S.3.R2.fastq.gz
H.25C.3hr.S.3.R1.fastq.gz H.25C.3hr.S.3.R2.fastq.gz
H.25C.8hr.S.3.R1.fastq.gz H.25C.8hr.S.3.R2.fastq.gz
H.37C.3hr.S.3.R1.fastq.gz H.37C.3hr.S.3.R2.fastq.gz
H.37C.8hr.S.3.R1.fastq.gz H.37C.8hr.S.3.R2.fastq.gz
T.25C.0hr.S.1.R1.fastq.gz T.25C.0hr.S.1.R2.fastq.gz
T.25C.3hr.S.1.R1.fastq.gz T.25C.3hr.S.1.R2.fastq.gz
T.25C.8hr.S.1.R1.fastq.gz T.25C.8hr.S.1.R2.fastq.gz
T.37C.3hr.S.1.R1.fastq.gz T.37C.3hr.S.1.R2.fastq.gz
T.37C.8hr.S.1.R1.fastq.gz T.37C.8hr.S.1.R2.fastq.gz
T.25C.0hr.S.2.R1.fastq.gz T.25C.0hr.S.2.R2.fastq.gz
T.25C.3hr.S.2.R1.fastq.gz T.25C.3hr.S.2.R2.fastq.gz
T.25C.8hr.S.2.R1.fastq.gz T.25C.8hr.S.2.R2.fastq.gz
T.37C.3hr.S.2.R1.fastq.gz T.37C.3hr.S.2.R2.fastq.gz
T.37C.8hr.S.2.R1.fastq.gz T.37C.8hr.S.2.R2.fastq.gz
T.25C.0hr.S.3.R1.fastq.gz T.25C.0hr.S.3.R2.fastq.gz
T.25C.3hr.S.3.R1.fastq.gz T.25C.3hr.S.3.R2.fastq.gz
T.25C.8hr.S.3.R1.fastq.gz T.25C.8hr.S.3.R2.fastq.gz
T.37C.3hr.S.3.R1.fastq.gz T.37C.3hr.S.3.R2.fastq.gz
T.37C.8hr.S.3.R1.fastq.gz T.37C.8hr.S.3.R2.fastq.gz
H.25C.0hr.O.1.R1.fastq.gz H.25C.0hr.O.1.R2.fastq.gz
H.25C.0hr.O.2.R1.fastq.gz H.25C.0hr.O.2.R2.fastq.gz
H.25C.0hr.O.3.R1.fastq.gz H.25C.0hr.O.3.R2.fastq.gz
Request has been made to the URC to up the space.
If they are restricted on space I have offered to steal allocated space from the banana_genome allotment.
Should be a quick response, pending vacations of key people.
Kelsey's sample sheet is now complete with the "new" coded file names.
https://docs.google.com/spreadsheets/d/1WwPzifPzbACmgS3uR_V92cYIGN3qS1yWPGHBu7DY_-I/edit?usp=sharing
This sheet will need a review as well!
Specifically,
Columns G and H need to match the description in Column B.
Time to check file integrity via MD5:
/projects/tomato_genome/rnaseq/renamed_Ravi_Combined
The new file
for f in *gz; do echo $f; md5sum $f >> md5sums-here.txt; done
The old files
while read p; do echo $p; md5sum $p >> md5sum-originals.txt; done < originalSequenceLocations.txt
Check if same
From MD5sums, take the md5 output alone, sort using the sort command and compare to previous files using diff.
*awk '
{ print $1 }' md5sums-here.txt | sort> tmpnowawk '{ print $1 }
' md5sum-originals.txt | sort > tmpold
head tmpnow*
00b21a195a1db617e503e6074bd90568
017bb5802c3f4c7c42f2782b8ad42c4c
04441f5f3a00c0618759a5c3b2c74ee7
074f1ac7fbf9ee7d581f02f4eefc63d1
07a124da5b970d1f7f58bff3b861f3fa
09c676eee09ba63cfbbf30de4706b6bc
0b925de9537cb78436f1cd725e38ceca
0d08de2482ea6e4932f2df1b4d21d108
0d97238f02c7ad9a4bd1068bcfcd302c
10b5af522dfdd1e27ed5ec358dbe0839
head tmpold
00b21a195a1db617e503e6074bd90568
017bb5802c3f4c7c42f2782b8ad42c4c
04441f5f3a00c0618759a5c3b2c74ee7
074f1ac7fbf9ee7d581f02f4eefc63d1
07a124da5b970d1f7f58bff3b861f3fa
09c676eee09ba63cfbbf30de4706b6bc
0b925de9537cb78436f1cd725e38ceca
0d08de2482ea6e4932f2df1b4d21d108
0d97238f02c7ad9a4bd1068bcfcd302c
10b5af522dfdd1e27ed5ec358dbe0839
diff tmpnow2 tmpold2
No results. Yay. File contents are the same.
No reply from Kelsey. So I reached out to her again with a simpler question.
All all samples pistil with the exception of the 3 ovary samples? (That would be enough info)
If my tissue assumptions are correct then the Biosample spreadsheet is ready for review.
The SRA sheet still needs attention so I am not moving for review just yet.
R
"That nomenclature seems okay to me. And yes, you are correct! Everything is pistil (just stigma/style) that are either unpollinated or self-pollinated except for the 3 ovary samples. Those 3 samples are only the ovary and do not include other parts of the pistil."
Kelsey
I need to review everything here since time has passed. But I believe everything is in place.
Once I do this, I'll move to review for Molly /Nowlan.
The 2 spreadsheets check out as correct.
Need to check FTP upload status, does the data still exist in proper location? Will find out.
FTP upload to NCBI underway.
4 failed FTP files to the NCBI server.
These are now in the queue again.
FTP all good at NCBI. The data is in place.
I have sent a request to NCBI bioproject for a slight name change to the title:
PRJNA980666RNA-Seq of Solanum lycopersicum pollen tube under acute heat stress: A time seriesOrganization: UNC Charlotte Tomato
Could I get the title changed to:
RNA-Seq of Solanum lycopersicum reproductive tissues under acute heat stress: A time series
This will reflect all of Mark's, Gloria's and Ravi's data with this change.
Now we wait to hear back from them.
This is ready for review!
2 tables need reviewing. The Biosample table and SRA table like before.
The Biosample Table can be found here:
https://docs.google.com/spreadsheets/d/1QMHA4uqwReI_Fr49kXCvYZWqTysQaHCq/edit?usp=sharing&ouid=100714234126361751017&rtpof=true&sd=true
The SRA table can be found here:
https://docs.google.com/spreadsheets/d/1qvZzKeLc3S28ceE03_uuzOXn6vaE2oM8/edit?usp=sharing&ouid=100714234126361751017&rtpof=true&sd=true
Need to look for any inconsistencies, omissions, etc!!!!
Review
Biosample Table:
- Row 64, Column description, there is some text missing.
- Row 79 and below I think is actually 2023 data and the first 10 rows are 2021? I am unsure if all the sample were collected in 2022?
SRA Table:
- I see no issues when scanning over the file!
Review
Biosample Table:
- Double-check the sample_name. My understanding was that the sample_name should also be the same in the SRA metadata table. They are currently using two different naming conventions.
- Double-check the last three rows. The tissues are from ovary, but the column description includes:
Self-Pollinated Pistils Ovary unpol
SRA Table:
- No issues.
Great catches!
Row 64 has been corrected. It looks as though I tried to write linux commands in the wrong window, removing part of the text!
For the date collection, the first 10 rows were early 2022. The last set is late 2022. We did not receive the data until Feb of 2023 but this is referring to when the plants were alive. But excellent question!! I had to go verify!
The Biosample ids are now updated to reflect the SRA sample sheet using the 1 letter code described in the comments above.
I have changed the last 3 rows. It should unpollinated ovary. A unique sample that acts as a universal control in this dataset.
No pistils in these samples according to Kelsie.
Ann and I cleaned up the Cluster folder for /projects/tomato_genome.
For this dataset, it is actually 3 datasets that I have combined together for SRA purposes.
The question is, should we separate them into 3 individual SRA submissions?
Or send it as 1 big submission?
We can then separate and analyze the samples, pulling samples needed from the large SRA set.
I have made 3 separate metadata tables, 1 for each experiment.
I have made 3 biosample tables, 1 for each experiment.
I have sent an email out to Ravi and his group, suggesting meeting next week at the tech meeting.
Now we wait to see what they say.
Rob
They never said anything.
It's been a long while.
I will first review everything that we got and see where we are with this SRA submission.
- Need to check the data is ready to go
- Need to see if I started a submission or not.
- Check the status of the metatable that was created.
- Repeat this for all 3 datasets.
Reminder:
The meta data is all located on Google drive at this location:
https://drive.google.com/drive/folders/10-gf6u7fyzZijqvSN7vOzN5X-TmxEUa_?usp=drive_link
We have it set up as 3 separate submissions.
- Pilot Study -1
- Ravi 55 sample Run -2
- Kelsie Run -3
An SRA submission has been started.
First decision to be made. Do we do 3 submissions under one BioProject? Or 3 separate bioprojects?
I will dive in deeper and find an answer.
I am leaning to 3 Bioprojects.
To do so, the descriptions and titles need to be specific to make the NCBI Gods happy.
The data is ready to go.
The meta tables are complete.
I will go through them once more and then request review.
Upon testing the SRA submission suitability, the biosample template rows were not "unique enough" . Can't use sample name or desc to make each row unique. I added details to phenotype column and SRA now finds the excel sheets acceptable.
SRA has no issues with the SRA metatables I test uploaded.
Almost done......
NCBI SRA FTP location for SRA upload:
Establish an FTP connection using the credentials below:
Address: ftp-private.ncbi.nlm.nih.gov
Username: subftp
Password: HiomCukJophtEet3
The above credentials are temporary.
Starting the upload now.
Review time !!
I would like a person to review 6 sheets below.
We have reviewed these before so things should be logical and correct.
Just look for logical errors.
Biosamples
- https://docs.google.com/spreadsheets/d/1Vy2M7cW8ZE7u3R6y5080kF_U1LwTgt-H/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/14ZQt_FV2Eb66Ts8Yppbg_LKC3tQkROtO/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/1at78HnfhJepNWiSON5lRrxbRhjI7njSW/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
Meta Tables
- https://docs.google.com/spreadsheets/d/1t6P-mfkKjG0B9ywqGbaOXC5NqjUSfvnt/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/1d9rNnqbAMIF7RU_AdgvPsGVjLAw7yfBo/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/1AeWPrDwqtGVYjYIdOqXYRKZpf1C-fHrO/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
Review:
Biosamples
- Good
- Good
- Good
Meta Tables
- Good
- Good
- Good
Note: I saw no issues with the data. Moving to Ready for PR which equals submitting the data if ready to NCBI.
I'll need to once over this.
The data is in the FTP location.
I will likely click send to NCBI.
And then post the IDs we get.
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 PRJNA1071054 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: PRJNA1071054
Temporary Submission ID: SUB14180617
Release date: 2024-01-30
the SRA and Biosample sheets will reside in Google drive:
https://drive.google.com/drive/folders/10-gf6u7fyzZijqvSN7vOzN5X-TmxEUa_?usp=drive_link
The plan is for all of the samples run in Ravi's lab to be submitted at once. The sequences were run in 3 separate sequencing projects via Azenta. The first was a pilot test run.