Difference between revisions of "Poland Lab Wiki"
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=== 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.) | ||
| + | |||
| + | |||
| + | [[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!
Contents
General Lab Information
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
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.)
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.
