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Science!
100
This genetic condition makes animals grey and is never requested by the Canadian Angus Association.
What is Dilutor (DL)? The Dilutor gene dilutes Black to Grey and Dilutes Dark Red to Light Red or Yellow
100
Please refer to Oddities 100 handout. These tests do not belong on the following extraction layout.
What is Kinsella Breeding? Explanation: All sample submitted from Mike Vinsky (Kinsella or Huston Block) should be on 50K. This is because the PI in charge of the project would like everything on the same panel for comparison.
100
This function is used to create and edit extraction layouts in LIMS.
What is "Plate Config"? Explanation: Any assay can be searched for in plate config, which will pull assigned samples based on date and add them to a plate
100
This is the one day of the week a Day 1 Illumina protocol cannot be carried out.
What is Friday? Explanation: Illumina does not have natural pause points between Day 1 amplification and Day 2 fragmentation. Once amplification is started, the plate has to be incubated at 37 degrees for at least 16 hours followed by addition of FMS for fragmentation.
100
This solution is added to DNA samples extracted from red haired animals so that they can be successfully amplified in a PCR reaction.
What is Bovine Serum Albumin (BSA)? Explanation: BSA is believed to bind to contaminants in a PCR reaction.
200
A cross between Homozygous black animal and a wildtype red animal will always produce this coloured offspring.
What is a black animal?
200
Please refer to Oddities 200 handout. These tests do not belong on the following extraction layout.
What is Hereford RFI Trial on 50K? Explanation, Hereford RFI Trial can only go on the 130K or GGP-uHD panel because the Canadian Hereford Association requires DL,HY,IE on every animal and the 50K chip does not have these conditions on them.
200
Updating Code 50 and Code 100 samples must be done in this tab in LIMS.
What is the update stages tab?
200
This is the turn around time between receiving a sample and sending results for the Canadian Angus Association
What is 10 business days or 2 weeks? Explanation: Our regular TAT for most breeds and customers are 10 business days.
200
This component of the buffer ATL produces large amounts of bubbles when agitated.
What is SDS? Explanation: SDS is an anionic surfactant that is able to break up cell wall and cell membrane. It is also commonly used it laundry detergent and shampoo.
300
This genetic abnormality also known as curly calf syndrome is caused by a large 23kb deletion in Chromosome 16 of the Bovine genome.
What is Arthrogryposis Multiplex (AM)? Explanation: AM-affected calves are born dead with a twisted spine and extended and contracted limbs, and calving difficulties are common.
300
Please refer to Oddities 300 handout. This is missing from the following extraction layout.
What is interbull ID? Explanation: A missing interbull ID on a sample will prevent us from sending the results to the Canadian Simmental office resulting in delays.
300
The "Client Identifier" search in LIMS can find animals based on their Supplied ID, Tattoo, Tag, "Other ID" and Registration Number, but not this ID.
What is name?
300
This amount of water is required to dissolve 1 tablespoon (15g) of Alcanox to make a 1% solution.
What is 1.5L? Explanation: 1% solution = 1 w (g)/v (mL) x 100%
300
This strong smelling carcinogen used in difficult DNA extractions at Delta Genomics used to be an anesthetic in the early 20th century.
What is Chloroform?
400
This genetic abnormality is only almost exclusively requested by the Canadian Limousin Association.
What is Protoporphyria (PP)? Explanation: The CLA bylaws and rules require DNA tests for Parent verification and protoporphyria genotype on file for all AI sires. It is estimated that about eight percent of Limousin cattle are carriers of the defective gene.
400
DAILY DOUBLE Please refer to Oddities 400 handouts. This test is odd in the extraction layout.
What is SNP for Simmental Parentage? Explanation: The CSA only does GGP-LD or 50K for SNP testing. They will never request for just a SNP test.
400
This search function in LIMS makes it possible to search for a specific list of DGIDs, such as those found on an extraction layout.
What is the batch search? Explanation: A list of DGIDs can be copied out of Excel and pasted into this function, which will pull every instance of that DGID it can find and return these results.
400
This buffer is used to elute DNA from the magnetic beads in a DNA extraction protocol on the Biosprint.
What is AE?
400
This liquid used during the normalization of plates going on the Sequenom is also used to elute libraries off magnetic Ampure beads.
What is Nuclease Free water?
500
During the Shorthorn Advantage Program two Shorthorn conditions were included for a discounted price because they were available on the GGP-LD panel. This condition was not.
What is DS (digital sublaxation)? Explanation: DS is not part of the GGP-LD panel and has to be sent to Geneseek for a standalone test.
500
DAILY DOUBLE Please refer to Oddities 500 handout. This test request is incomplete from the DNA extraction layout
What is MBV on a GGP-LD test from Canadian Limousin Associaiton? Explanation: Every GGP-LD or 50K request from the the CLA require MBVs.
500
In order to update the information for a single sample, this tab in LIMS must be used.
What is "Create Single Job"? Explanation: Jobs can be added in the Create Multiple Jobs tab, however to update that information after it has been added to LIMS the Create Single Job tab must be used.
500
This is the day of the week that EnvigourHX genotyping has to be completed by.
What is Thursday? Explanation: The Envigour Breed composition algorithm requires about 48 hours to run. While running, it disrupts all server functions including LIMS usage. Therefore it needs to run overnight on the weekends to prevent disruptions to our regular workflow.
500
This compound is component of TE which chelates metals ions to prevent DNA degradation.
What is EDTA? Explanation: Metal ions are enzyme co-factors. EDTA competes with enzymes for the binding of metal ions. A reduction in metal ions will also reduce enzymatic activity of DNases therefore reducing DNA degradation.