Difference between revisions of "Poland Lab Wiki"

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== General Lab Information ==
 
== General Lab Information ==
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[[Lab Procedures]]
  
 
[[Reading List]]
 
[[Reading List]]
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[[Travel Instructions]]
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== Projects==
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[[NSF BREAD]]
  
 
== Genotyping Procedures ==
 
== Genotyping Procedures ==
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Lab protocols
 
Lab protocols
  
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NGS Ordering
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[[Media:GBS_NGS_Service_Order_Quebec.pdf|NGS Ordering]]
  
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GBS Data Management
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[[GBS Data Management]]
  
 
== High-Throughput Phenotyping Procedures ==
 
== High-Throughput Phenotyping Procedures ==
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[[UAS Phenotyping and Aerial Image Acquisition Procedures]]
 
[[UAS Phenotyping and Aerial Image Acquisition Procedures]]
  
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UAS Field Data Collection Schedule
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[[UAS Phenotyping and Aerial Image Acquisition Procedure for DJI]]
  
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[[UAS Data Management Procedures]]
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[[Media:UAV_Data_Upload_SOP_v1.3.pdf|UAS Data Management Procedures]]
  
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UAS HTP Data Analysis
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[[UAS HTP Data Analysis]]
  
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Land-based HTP Data Acquisition
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[[Media:CAMERAS_README.txt|Cameras README]]
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Land-based HTP Data Collection Schedule
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Land-based HTP Data Management
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Land-based HTP Data Analysis
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== Research Methods ==
 
== Research Methods ==
  
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=== Genomic Selection ===
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[[Genomic Selection]]
  
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[[Media:GSquality_sbattenfield_033016.pdf|Genomic selection for quality PowerPoint]]
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[[Meta-GWAS]]
  
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[[Media:GS CV script.docx|Genomic selection example code]]
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== Database ==
  
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=== Meta-GWAS ===
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[[Connecting to the Database]]
  
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[[Media:MetaGWAS sbattenfield 033016.pdf|Meta-GWAS Methodology]]
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[[Media:Wheatgenetics_Quick_Start_Guide_ML_20171016.pdf|Wheatgenetics Database Quick Start Guide]]
  
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== Database ==
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[[Media:DatabaseQueryFromR.pdf|Connecting to the Database with R]]
  
 
[[Genotyping Database]]
 
[[Genotyping Database]]
  
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=== Genotyping Database ===
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[[Land-based High-Throughput Phenotyping Database]]
  
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The genotyping database stores information related to DNA libraries. The core set of tables related to genotyping are:
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[[UAV High-Throughput Phenotyping Database]]
  
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* The gbs table stores information about DNA libraries, DNA sequencing orders and DNA Sequence files.
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[[Manual Phenotyping Database]]
  
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* The dna table stores information about DNA plates and the samples contained in each well on a plate.
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[[Seed and Plant Database]]
  
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* The dnaQuant table stores DNA quantification values fluorescence values for each well on a plate.
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[[CIMMYT Wheat Breeding Database]]
  
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* The barcodes table stores information about the barcode sequences used for each plexing scheme for each well on a plate.
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[[Media:CIMMYT_Automation_File_Interfaces.pdf|CIMMYT Database Import File Interface Specifications]]
  
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In addition to the core tables, the following tables provide details on the tissue and plant DNA sources:
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== Scripts ==
  
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* The tissue table stores information about the tissue used to prepare a DNA sample.
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[[Tassel 5 GBS v2 Pipeline sample script for calling SNPs using reference genome]]
  
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* The plant table stores information about the plant that the tissue was extracted from.
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== Equipment ==
  
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The figure below illustrates the table definitions and the key relationships used to formulate queries related to genomic analysis. (PK indicates the primary key for each table.)
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The links below provide access to the user manuals for the Toshiba Stake Printer and the Zebra Label Printer.  
  
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If you encounter problems while using the printers please refer to the Troubleshooting section in the relevant user manual.
  
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[[File:Gbs.png]]
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[[Media:B-SX5T-R_Owners-Manual_EN.pdf|Toshiba Stake Printer User Manual]]
  
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[[Media:zt200series_userguide.pdf|Zebra Printer User Manual]]
  
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== Guides ==
  
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== Example Queries ==
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[[ How to Submit GBS Data to the NCBI Sequence Read Archive (SRA) ]]
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=== Key Query ===
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The query below shows an example of how to obtain the information used to construct a key file that is required as input to TASSEL.
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SELECT gbs.flowcell,
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    gbs.lane,
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    barcodes.barcode,
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    dna.sample_name,
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    plant.plant_name,
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    dna.plate_id,
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    substring(dna.well_A01,1,1),
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    substring(dna.well_A01,2,2),
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    dna.well_A01,
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    dna.notes,
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    gbs.plexing,
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    gbs.project,
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    gbs.enzyme,
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    dna.sample_id,
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    dna.tissue_id,
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    dna.external_id,
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    dna.dna_person,
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    dna.line_num,
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    gbs.gbs_name,
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    dna.plate_name,
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    dna.well_01A,
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    gbs.gbs_id,
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    barcodes.`set`
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FROM dna LEFT JOIN gbs ON gbs.dna_id = dna.plate_id
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      LEFT JOIN plant ON dna.tissue_id = plant.plant_id
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      INNER JOIN barcodes ON dna.well_A01 = barcodes.well_A01 AND gbs.plexing LIKE barcodes.`set`
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WHERE gbs.project LIKE "%My_Project%" ORDER BY gbs.gbs_id, dna.well_01A ASC
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== Equipment ==
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For instructions on how to use the Toshiba Stake Printer and the Zebra Label printer see the links to the user manuals below. If you encounter any problems while using the printers, refer to the Troubleshooting sections in each manual.
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[[Media:B-SX5T-R_Owners-Manual_EN.pdf|Toshiba Stake Printer User Manual]]
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[[Media:zt200series_userguide.pdf|Zebra Printer User Manual]]
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Latest revision as of 20:04, 13 May 2020

Welcome to the Poland Lab Wiki!

General Lab Information

Lab Procedures

Reading List

Travel Instructions

Projects

NSF BREAD

Genotyping Procedures

Lab protocols

NGS Ordering

GBS Data Management

High-Throughput Phenotyping Procedures

UAS Phenotyping and Aerial Image Acquisition Procedures

UAS Phenotyping and Aerial Image Acquisition Procedure for DJI

UAS Data Management Procedures

UAS HTP Data Analysis

Cameras README

Research Methods

Genomic Selection

Meta-GWAS

Database

Connecting to the Database

Wheatgenetics Database Quick Start Guide

Connecting to the Database with R

Genotyping Database

Land-based High-Throughput Phenotyping Database

UAV High-Throughput Phenotyping Database

Manual Phenotyping Database

Seed and Plant Database

CIMMYT Wheat Breeding Database

CIMMYT Database Import File Interface Specifications

Scripts

Tassel 5 GBS v2 Pipeline sample script for calling SNPs using reference genome

Equipment

The links below provide access to the user manuals for the Toshiba Stake Printer and the Zebra Label Printer.

If you encounter problems while using the printers please refer to the Troubleshooting section in the relevant user manual.

Toshiba Stake Printer User Manual

Zebra Printer User Manual

Guides

How to Submit GBS Data to the NCBI Sequence Read Archive (SRA)

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