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(Database)
(Genotyping Database)
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=== Genotyping Database ===
 
=== Genotyping Database ===
  
[[HTP Database]]
+
The genotyping database stores information related to DNA libraries. The core set of tables related to genotyping are:
  
[[HTP Database Table Structure]]
+
* The gbs table stores information about DNA libraries, DNA sequencing orders and DNA Sequence files.
  
[[Seed and Plant Database]]
+
* The dna table stores information about DNA plates and the samples contained in each well on a plate.
 +
 
 +
* The dnaQuant table stores DNA quantification values fluorescence values for each well on a plate.
 +
 
 +
* The barcodes table stores information about the barcode sequences used for each plexing scheme for each well on a plate.
 +
 
 +
In addition to the core tables, the following tables provide details on the tissue and plant DNA sources:
 +
 
 +
* The tissue table stores information about the tissue used to prepare a DNA sample.
 +
 
 +
* The plant table stores information about the plant that the tissue was extracted from.
 +
 
 +
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.)
 +
 
 +
 
 +
[[File:Gbs.png]]
 +
 
 +
 
 +
 
 +
== Example Queries ==
 +
 
 +
=== Key Query ===
 +
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.
 +
SELECT gbs.flowcell,
 +
    gbs.lane,
 +
    barcodes.barcode,
 +
    dna.sample_name,
 +
    plant.plant_name,
 +
    dna.plate_id,
 +
    substring(dna.well_A01,1,1),
 +
    substring(dna.well_A01,2,2),
 +
    dna.well_A01,
 +
    dna.notes,
 +
    gbs.plexing,
 +
    gbs.project,
 +
    gbs.enzyme,
 +
    dna.sample_id,
 +
    dna.tissue_id,
 +
    dna.external_id,
 +
    dna.dna_person,
 +
    dna.line_num,
 +
    gbs.gbs_name,
 +
    dna.plate_name,
 +
    dna.well_01A,
 +
    gbs.gbs_id,
 +
    barcodes.`set`
 +
FROM dna LEFT JOIN gbs ON gbs.dna_id = dna.plate_id
 +
      LEFT JOIN plant ON dna.tissue_id = plant.plant_id
 +
      INNER JOIN barcodes ON dna.well_A01 = barcodes.well_A01 AND gbs.plexing LIKE barcodes.`set`
 +
WHERE gbs.project LIKE "%My_Project%" ORDER BY gbs.gbs_id, dna.well_01A ASC
  
 
== Equipment ==
 
== Equipment ==

Revision as of 16:05, 12 May 2016

Welcome to the Poland Lab Wiki!

General Lab Information

Reading List

Genotyping Procedures

Lab protocols

NGS Ordering

GBS Data Management

High-Throughput Phenotyping Procedures

UAS Phenotyping and Aerial Image Acquisition Procedures

UAS Field Data Collection Schedule

UAS Data Management Procedures

UAS HTP Data Analysis

Land-based HTP Data Acquisition

Land-based HTP Data Collection Schedule

Land-based HTP Data Management

Land-based HTP Data Analysis

Research Methods

Genomic Selection

Genomic selection for quality PowerPoint

Genomic selection example code

Meta-GWAS

Meta-GWAS Methodology

Database

Genotyping Database

Genotyping Database

The genotyping database stores information related to DNA libraries. The core set of tables related to genotyping are:

  • The gbs table stores information about DNA libraries, DNA sequencing orders and DNA Sequence files.
  • The dna table stores information about DNA plates and the samples contained in each well on a plate.
  • The dnaQuant table stores DNA quantification values fluorescence values for each well on a plate.
  • The barcodes table stores information about the barcode sequences used for each plexing scheme for each well on a plate.

In addition to the core tables, the following tables provide details on the tissue and plant DNA sources:

  • The tissue table stores information about the tissue used to prepare a DNA sample.
  • The plant table stores information about the plant that the tissue was extracted from.

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.)


Gbs.png


Example Queries

Key Query

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.

SELECT gbs.flowcell,
    gbs.lane,
    barcodes.barcode,
    dna.sample_name,
    plant.plant_name,
    dna.plate_id,
    substring(dna.well_A01,1,1),
    substring(dna.well_A01,2,2),
    dna.well_A01,
    dna.notes,
    gbs.plexing,
    gbs.project,
    gbs.enzyme,
    dna.sample_id,
    dna.tissue_id,
    dna.external_id,
    dna.dna_person,
    dna.line_num,
    gbs.gbs_name,
    dna.plate_name,
    dna.well_01A,
    gbs.gbs_id,
    barcodes.`set`
FROM dna LEFT JOIN gbs ON gbs.dna_id = dna.plate_id
     LEFT JOIN plant ON dna.tissue_id = plant.plant_id
     INNER JOIN barcodes ON dna.well_A01 = barcodes.well_A01 AND gbs.plexing LIKE barcodes.`set` 
WHERE gbs.project LIKE "%My_Project%" ORDER BY gbs.gbs_id, dna.well_01A ASC

Equipment

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.

Toshiba Stake Printer User Manual

Zebra Printer User Manual