Cassavabase-PhenoApp sample tracking

•

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solgenomics

Plant tissue sampling & tracking workflow using cassavabase and PhenoApp Coordinate

Science

Sampling for genotyping
using cassavabase and
Coordinate App
Workshopand
Guillaume Bauchet
ISTRC Workshop 2018
CIAT Colombia

@nextgencassavanextgencassava.org • cassavabase.org
Coordinate App
& Barcodes

@nextgencassavanextgencassava.org • cassavabase.org

-1- Design trial
and
-2- Generate barcodes

@nextgencassavanextgencassava.org • cassavabase.org
-1- Design trial: “Manage” -> “Field Trials”
https://solgenomics.github.io/sgn/03_managing_breeding_data/03_07.html#adding-trials
-2- Generate barcodes and label design
https://solgenomics.github.io/sgn/03_managing_breeding_data/03_11.html
https://solgenomics.github.io/sgn/03_managing_breeding_data/03_12.html

@nextgencassavanextgencassava.org • cassavabase.org
On trial page
-1- go to barcode section
-2- select “plots barcode”
-3- Ensure Fieldbook option is selected (Wont work otherwise)

-3- Collect samples
with PhenoApp Coordinate

-Step 1- Create a template for “NextGen” including
the
Required blank wells for DarSeq (G11 and G12)
=> Once created, the template can be used for all
plates (grid) to be sampled for genotyping at
DartSeq
-Step 2- Create a grid and do tissue sampling
=> For each 96 well plate you need to sample, use
the “NextGen” template created in Step 1

@nextgencassavanextgencassava.org • cassavabase.org
1 2 3 4
5 6 7 8
-Step1- Create
template
Set blanks

@nextgencassavanextgencassava.org • cassavabase.org
9 10 11 12
13 14-Step 2- Create Grid
-b create a grid:
Now you have the “NextGen” template
with well G12 and H12 set as blanks as
required by DartSeq genotyping
(confusingly Intertek requires H11 and
H12 but we can stick to G12 and H12).
You can now create a grid for sample
collection. Here the grid is named “NR-
NG-C2a-cass-0001”
Disable random blank

@nextgencassavanextgencassava.org • cassavabase.org
PLot1:
PLot2:
Scan
Scanning-Sampling procedure
-1- Scan
-2- Sample
-1- Scan
-2- Sample
Etc….

@nextgencassavanextgencassava.org • cassavabase.org
15 16 17 18
19 20 21 22
Export samples

@nextgencassavanextgencassava.org • cassavabase.org
Select the file and export it to your laptop

@nextgencassavanextgencassava.org • cassavabase.org
Export .csv file example:

@nextgencassavanextgencassava.org • cassavabase.org
https://cassavabase.org/breeders/genotyping/

@nextgencassavanextgencassava.org • cassavabase.org
“Add genotyping trial”

@nextgencassavanextgencassava.org • cassavabase.org
Fill in plate
information

@nextgencassavanextgencassava.org • cassavabase.org
Intertek export excel file format
DartSeq export excel file format
Exporting formats:

@nextgencassavanextgencassava.org • cassavabase.org
Intertek: Submit the Intertek export excel file format send excel file by email
DartSeq: Submit the DartSeq export excel file format from cassavabase at
https://ordering.diversityarrays.com/cgi-bin/order/login.pl

@nextgencassavanextgencassava.org • cassavabase.org
Thank you!
ftp://ftp.cassavabase.org/intertek/
All documentation available here:

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Cassavabase-PhenoApp sample tracking

1. Sampling for genotyping using cassavabase and Coordinate App Workshopand Guillaume Bauchet ISTRC Workshop 2018 CIAT Colombia

3. @nextgencassavanextgencassava.org • cassavabase.org Coordinate App & Barcodes

4. @nextgencassavanextgencassava.org • cassavabase.org

5. -1- Design trial and -2- Generate barcodes

6. @nextgencassavanextgencassava.org • cassavabase.org -1- Design trial: “Manage” -> “Field Trials” https://solgenomics.github.io/sgn/03_managing_breeding_data/03_07.html#adding-trials -2- Generate barcodes and label design https://solgenomics.github.io/sgn/03_managing_breeding_data/03_11.html https://solgenomics.github.io/sgn/03_managing_breeding_data/03_12.html

7. @nextgencassavanextgencassava.org • cassavabase.org On trial page -1- go to barcode section -2- select “plots barcode” -3- Ensure Fieldbook option is selected (Wont work otherwise)

8. -3- Collect samples with PhenoApp Coordinate

9. -Step 1- Create a template for “NextGen” including the Required blank wells for DarSeq (G11 and G12) => Once created, the template can be used for all plates (grid) to be sampled for genotyping at DartSeq -Step 2- Create a grid and do tissue sampling => For each 96 well plate you need to sample, use the “NextGen” template created in Step 1

10. @nextgencassavanextgencassava.org • cassavabase.org 1 2 3 4 5 6 7 8 -Step1- Create template Set blanks

11. @nextgencassavanextgencassava.org • cassavabase.org 9 10 11 12 13 14-Step 2- Create Grid -b create a grid: Now you have the “NextGen” template with well G12 and H12 set as blanks as required by DartSeq genotyping (confusingly Intertek requires H11 and H12 but we can stick to G12 and H12). You can now create a grid for sample collection. Here the grid is named “NR- NG-C2a-cass-0001” Disable random blank

12. @nextgencassavanextgencassava.org • cassavabase.org PLot1: PLot2: Scan Scanning-Sampling procedure -1- Scan -2- Sample -1- Scan -2- Sample Etc….

13. @nextgencassavanextgencassava.org • cassavabase.org 15 16 17 18 19 20 21 22 Export samples

14. @nextgencassavanextgencassava.org • cassavabase.org Select the file and export it to your laptop

15. @nextgencassavanextgencassava.org • cassavabase.org Export .csv file example:

16. -4- Upload template to Cassavabase

17. @nextgencassavanextgencassava.org • cassavabase.org https://cassavabase.org/breeders/genotyping/

18. @nextgencassavanextgencassava.org • cassavabase.org “Add genotyping trial”

19. @nextgencassavanextgencassava.org • cassavabase.org Fill in plate information

20. @nextgencassavanextgencassava.org • cassavabase.org

21. @nextgencassavanextgencassava.org • cassavabase.org

22. @nextgencassavanextgencassava.org • cassavabase.org Intertek export excel file format DartSeq export excel file format Exporting formats:

23. -5- Submit genotyping order

24. @nextgencassavanextgencassava.org • cassavabase.org Intertek: Submit the Intertek export excel file format send excel file by email DartSeq: Submit the DartSeq export excel file format from cassavabase at https://ordering.diversityarrays.com/cgi-bin/order/login.pl

25. @nextgencassavanextgencassava.org • cassavabase.org Thank you! ftp://ftp.cassavabase.org/intertek/ All documentation available here:

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