Cassavabase-PhenoApp sample tracking

Oct 20, 20180 likes334 views

This document provides instructions for sampling cassava plants for genotyping using the Cassavabase database and Coordinate mobile app. It describes how to: 1. Design a field trial and generate barcodes in Cassavabase 2. Use the Coordinate app to collect samples according to the trial template and export the sample data 3. Upload the template and sample data to Cassavabase 4. Submit the genotyping order to the service provider The goal is to efficiently collect samples from the field trial and prepare the data for genotyping.

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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This comprehensive assignment explores the pivotal role of DNA profiling and Short Tandem Repeat (STR) analysis in forensic science and genetic studies. The document begins by laying the molecular foundations of DNA, discussing its double helix structure, the significance of genetic variation, and how forensic science exploits these variations for human identification. The historical journey of DNA fingerprinting is thoroughly examined, highlighting the revolutionary contributions of Dr. Alec Jeffreys, who first introduced the concept of using repetitive DNA regions for identification. Real-world forensic breakthroughs, such as the Colin Pitchfork case, illustrate the life-saving potential of this technology. A detailed breakdown of traditional and modern DNA typing methods follows, including RFLP, VNTRs, AFLP, and especially PCR-based STR analysis, now considered the gold standard in forensic labs worldwide. The principles behind STR marker types, CODIS loci, Y-chromosome STRs, and the capillary electrophoresis (CZE) method are thoroughly explained. The steps of DNA profiling—from sample collection and amplification to allele detection using electropherograms (EPGs)—are presented in a clear and systematic manner. Beyond crime-solving, the document explores the diverse applications of STR typing: Monitoring cell line authenticity Detecting genetic chimerism Tracking bone marrow transplant engraftment Studying population genetics Investigating evolutionary history Identifying lost individuals in mass disasters Ethical considerations and potential misuse of DNA data are acknowledged, emphasizing the need for careful policy and regulation. Whether you're a biotechnology student, a forensic professional, or a researcher, this document offers an in-depth look at how DNA and STRs transform science, law, and society.

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Poultry require at least 38 dietary nutrients inappropriate concentrations for a balanced diet. A nutritional deficiency may be due to a nutrient being omitted from the diet, adverse interaction between nutrients in otherwise apparently well-fortified diets, or the overriding effect of specific anti-nutritional factors. Major components of foods are – Protein, Fats, Carbohydrates, Minerals, Vitamins Vitamins are A- Fat soluble vitamins: A, D, E, and K ; B - Water soluble vitamins: Thiamin (B1), Riboflavin (B2), Nicotinic acid (niacin), Pantothenic acid (B5), Biotin, folic acid, pyriodxin and cholin. Causes: Low levels of vitamin A in the feed. oxidation of vitamin A in the feed, errors in mixing and inter current disease, e.g. coccidiosis , worm infestation Clinical signs: Lacrimation (ocular discharge), White cheesy exudates under the eyelids (conjunctivitis). Sticky of eyelids and (xerophthalmia). Keratoconjunctivitis. Watery discharge from the nostrils. Sinusitis. Gasping and sneezing. Lack of yellow pigments, Respiratory sings due to affection of epithelium of the respiratory tract. Lesions: Pseudo diphtheritic membrane in digestive and respiratory system (Keratinized epithelia). Nutritional roup: respiratory sings due to affection of epithelium of the respiratory tract. Pustule like nodules in the upper digestive tract (buccal cavity, pharynx, esophagus). The urate deposits may be found on other visceral organs Treatment: Administer 3-5 times the recommended levels of vitamin A @ 10000 IU/ KG ration either through water or feed. Lesions: Pseudo diphtheritic membrane in digestive and respiratory system (Keratinized epithelia). Nutritional roup: respiratory sings due to affection of epithelium of the respiratory tract. Pustule like nodules in the upper digestive tract (buccal cavity, pharynx, esophagus). The urate deposits may be found on other visceral organs Treatment: Administer 3-5 times the recommended levels of vitamin A @ 10000 IU/ KG ration either through water or feed. Lesions: Pseudo diphtheritic membrane in digestive and respiratory system (Keratinized epithelia). Nutritional roup: respiratory sings due to affection of epithelium of the respiratory tract. Pustule like nodules in the upper digestive tract (buccal cavity, pharynx, esophagus). The urate deposits may be found on other visceral organs Treatment: Administer 3-5 times the recommended levels of vitamin A @ 10000 IU/ KG ration either through water or feed.

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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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