Gerat news!

We can simply generate a 2nd BioProject. And then point the Muday files to this new BioProject!
See email below.

Yes, you can register a new BioProject here:
https://submit.ncbi.nlm.nih.gov/subs/bioproject/

Once the new BioProject is registered you can link this BioProject to the appropriate Run from submission portal's manage data view:
https://dataview.ncbi.nlm.nih.gov/object/PRJNA980666?limit=200

You can also edit the PRJNA980666 study title from this page if necessary.
Best,
Rick Lapoint
SRA Curator

Next, we need to decide what title and abstract we want for this BioProject.

I'll start the process and and we will know exactly what fields we need to enter.

Here is a summary of the fields we can enter when creating a NEW bioproject:

Tab Project Type:
Project data type
Sample scope

Target
Organism name
Strain
Breed
Cultivar
Isolate name
Label

Description (A brief description to elaborate on the label)

General Info
When data can be released
Title
Public description. (A paragraph of study goals and relevance)
Relevance (drop down menu = agriculture, environmental, evolution) - must pick one
Is your project part of a larger initiative which is already registered with NCBI? (NO, yes is uncommon)

External links
Description. URL

Select your grants
Consortium name
Consortium URL

Going to capture all of the major details for each Bioproject in the existing Google slide deck:

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

Here I am laying out exactly what pieces are seen on a typical Bioproject page. (see slide #16)

In this slide deck, it will become a quick way to look up all of the SRA info pieces for every experiment!

A new Bioproject exists !

PRJNA1017816

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1017816

Title is: Solanum lycopersicum RNA-Seq: Flavonols improve thermotolerance in tomato pollen during germination and tube elongation

Abstract:
Temperatures above the optimum can result in lower crop yields with substantial reductions in reproductive success. Temperature stress increases the levels of reactive oxygen species (ROS) in pollen of Solanum lycopersicum (tomato) resulting in impaired pollen performance. Plants have multiple mechanisms to maintain ROS homeostasis including the synthesis of antioxidants, including flavonol metabolites. The tomato mutant, anthocyanin reduced (are) has a defect in the gene encoding flavanone 3 hydroxylase (F3H), which results in the reduced synthesis of flavonols. We examined pollen production, viability, germination, and pollen tube elongation in the are mutant and found significant reductions in each of these parameters relative to the VF36 parental line, all of which were accentuated by heat stress. Genetic complementation with a F3H transgene and chemical complementation with exogenous flavonols reversed the effect of elevated temperature on pollen germination in are to levels similar to the parental line, VF36. Transformation of the VF36 line with a F3H transgene was able to prevent the impaired pollen performance at elevated temperatures. Consistent with flavonol modulated ROS defining pollen performance, the ROS levels in these tomato lines are inversely proportional to flavonol levels and inhibitors of ROS synthesis improved pollen performance. RNA-Seq was performed with pollen grains during germination and tube extension in are, VF36, and VF36 transformed with the F3H transgene at optimal and stress temperatures. This analysis revealed a robust set of genes whose transcript abundance increased at elevated temperature, with the greatest number of differentially expressed transcripts found in are. These results demonstrated that heat-induced ROS limit reproductive success, and flavonols protect pollen from heat-induced ROS and the resulting reproductive impairments. We identified changes in transcripts whose expression are inversely correlated with reproductive success providing insight into genetic targets for future development of plants with enhanced tolerance to the temperature stress associated with climate change.

Next step.

Get the Time Series SRA samples moved from their original Bioproject to this new BioProject which is currently empty.

All samples moved !!

There are 72 samples.
Here are all the SRA IDs. This will be needed for the next ticket!

SRR25478240
SRR25478241
SRR25478242
SRR25478243
SRR25478244
SRR25478245
SRR25478246
SRR25478247
SRR25478248
SRR25478249
SRR25478250
SRR25478251
SRR25478252
SRR25478253
SRR25478254
SRR25478255
SRR25478256
SRR25478257
SRR25478258
SRR25478259
SRR25478260
SRR25478261
SRR25478262
SRR25478263
SRR25478264
SRR25478265
SRR25478266
SRR25478267
SRR25478268
SRR25478269
SRR25478270
SRR25478271
SRR25478272
SRR25478273
SRR25478274
SRR25478275
SRR25478276
SRR25478277
SRR25478278
SRR25478279
SRR25478280
SRR25478281
SRR25478282
SRR25478283
SRR25478284
SRR25478285
SRR25478286
SRR25478287
SRR25478288
SRR25478289
SRR25478290
SRR25478291
SRR25478292
SRR25478293
SRR25478294
SRR25478295
SRR25478296
SRR25478297
SRR25478298
SRR25478299
SRR25478300
SRR25478301
SRR25478302
SRR25478303
SRR25478304
SRR25478305
SRR25478306
SRR25478307
SRR25478308
SRR25478309
SRR25478310
SRR25478311

The next task will be to confirm that these SRA accessions are all in order and good.

New task to come...............

Updating the Mark Johnson BioProject to more accurately reflect the dataset contained therein.

My draft version:

TITLE:
TOMATO PISTIL TUBES DURING GERMINATION AND TUBE ELONGATION UNDER ACUTE HEAT STRESS OVER A SHORT TIME COURSE

Other details can be found in the Google Doc:
https://docs.google.com/document/d/1_nkCRl62umA_LAB_yrzPuko-9GSXV8BHKkWEvKY0KA0/edit?usp=sharing

Will send to Mark and his people for edits and improvements. This gives them something to start with.
I'll update the Bioproject once I get feedback from them.

Having not heard back from the Johnson lab, I will reach out again.

And in the meantime, I will go ahead and make the changes I proposed above to Mark's Bioproject so that we can move this task along!

I am calling this closed. a new title and abstract are now in place.

https://dataview.ncbi.nlm.nih.gov/object/PRJNA980666

I can make future edits as needed, in the event I hear back from mark.

R