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  1. IGB
  2. IGBF-3423

Splitting BioProject PRJNA980666 into 2

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1
        • Epic Link:
        • Sprint:
          Fall 1 - Sep 5, Summer 8 2023 Aug 21, Fall 2 2023 Sep 17, Fall 3 2023 Oct 2, Fall 4 2023 Oct 16

          Description

          To make IGB-3406 and IGB-3347 less confusing,
          we need to separate these 2 studies, that are currently contained under the same bioProject ID:

          PRJNA980666

          Rob will email the SRA and make the request.

          The end goal is to have 2 Bioprojects (or 2 SRP study numbers).
          And have new updated titles and abstracts that better reflect what is happening in these studies.

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              Activity

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              robofjoy Robert Reid added a comment -

              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

              Show
              robofjoy Robert Reid added a comment - 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
              Hide
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              robofjoy Robert Reid added a comment -

              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.

              Show
              robofjoy Robert Reid added a comment - 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.
              Hide
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              robofjoy Robert Reid added a comment - - edited

              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

              Show
              robofjoy Robert Reid added a comment - - edited 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
              Hide
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              robofjoy Robert Reid added a comment -

              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!

              Show
              robofjoy Robert Reid added a comment - 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!
              Hide
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              robofjoy Robert Reid added a comment -

              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.

              Show
              robofjoy Robert Reid added a comment - 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.
              Hide
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              robofjoy Robert Reid added a comment -

              Next step.

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

              Show
              robofjoy Robert Reid added a comment - Next step. Get the Time Series SRA samples moved from their original Bioproject to this new BioProject which is currently empty.
              Hide
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              robofjoy Robert Reid added a comment -

              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

              Show
              robofjoy Robert Reid added a comment - 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
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              robofjoy Robert Reid added a comment -

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

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

              Show
              robofjoy Robert Reid added a comment - The next task will be to confirm that these SRA accessions are all in order and good. New task to come...............
              Hide
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              robofjoy Robert Reid added a comment -

              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.

              Show
              robofjoy Robert Reid added a comment - 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.
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              robofjoy Robert Reid added a comment -

              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!

              Show
              robofjoy Robert Reid added a comment - 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!
              Hide
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              robofjoy Robert Reid added a comment -

              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

              Show
              robofjoy Robert Reid added a comment - 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

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                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
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                    Updated:
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