TITLE: Preparation of DNA Samples for Copy Number Analysis by iDNA Technologies
AUTHORS: Lynn Doran

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Preparation of extracted genomic DNA for copy number analysis by </span><a href="https://www.idnagenetics.com/idna_location.php" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">iDNA Genetics.</span></a></div></div>

[STEPS]
?. [Quote Preparation]
Email iDNA Technologies for a quote.  Include the number of samples to be tested, which genes you want copy number analysis on, and which species the samples are from. Include one sample with a known copy number of 1 as an internal reference standard for each assay (gene).
Minimum of 24 samples is required for analysis.  Contact other members of the lab and transformation facility if you do not have the minimum to see if they will be sending samples soon.As of 4/9/2021, iDNA Technologies contacts are peter.isaac@idnagenetics.com, michala.woodvine@idnagenetics.com, and gelli.christodoulou@idnagenetics.com.
?. [Quote Preparation]
When you've received the quote, enter it into the appropriate lab group's Quartzy account.
?. [Sample Preparation]
Ensure DNA samples are suspended in an acceptable buffer.  Acceptable buffers include EA elution buffer from the Qiagen DNeasy Plant Kit, molecular grade water, or TE (10mM TrisHCl pH8.0,  0.1mM EDTA).
Do not use TE with >0.1 mM EDTA.  Too high of a salt concentration can interfere with analysis.If DNA is in the wrong buffer, perform an ethanol precipitation and wash and resuspend in an acceptable buffer.
?. [Quote Preparation]
Enter the following information:Vendor: i-Dna BiotechnologyCatalog #: xxxxxxxxxUnit size: 1Qty: 1Unit Price: From quote (convert from British pound to US dollar before entering)Upload File: Attach quote from iDNAGrant ID: Appropriate CFOP for project
?. [Sample Preparation]
Ensure that DNA volume and concentration exceeds  30 ul of 4-20 ng/ul (species and gene dependent).
Fluorometric analysis (Qubit or Picogreen e.g.) is preferred.  However, if nanodrop is used recommended concentration is >70 ng/ul due to RNA and carbohydrates causing artificially high calculations of DNA in nanodrop readings.
?. [Sample Preparation]
Label a non-skirted 96 well PCR plate with your name, date, gene, and species.
?. [Sample Preparation]
Pipette 30 ul of each sample into a unique well.
?. [Sample Preparation]
Fill out the iDNA 96-well template and sample submission form. Fill columns first, before rows.  For example if you only have 10 samples, fill A1-8, and B 1-2.
For required assay (gene), commonly used assays for RIPE include the following:VPZ_Bar is called BarPatF3 in iDNA Technologies assay listAP3_Bar is called JICBar in iDNA Technologies assay listA mix of genes may be possible for certain combinations.For  genes other than these, email the gene oglio sequence to the iDNA team to determine the best assay for your needs.
?. [Sample Preparation]
Seal the 96 well plate.
?. [Sample Preparation]
Heat seal a foil over the 96 well plate using the PCR Plate Sealer at  for.
180 °C
?. [Sample Preparation]
Place the 96 well plate in a 10 ul tip box insert and place a second 10 ul tip box insert on top.  Tightly parafilm all together.
?. [Sample Preparation]
Alternatively, seal the 96 well plate using 8 well strip caps.
?. [Sample Preparation]
Place a folded paper towel in the bottom of a microtube freezer box. Place the reinforced, parafilmed 96 well plate in the box on the paper towel.  Add additional paper towels around the edges and over the top.
?. [Sample Preparation]
Tape the freezer box closed.
?. [Sample Preparation]
Place the microcentrifuge tube freezer box inside a slightly larger, standard cardboard box for shipment.
DNA is stable at room temperature.  No ice or cold packs are needed for shipment.
?. [Shipping Document Preparation]
Prepare the shipping documents.
?. [Sample Preparation]
Weigh the complete package.  Record the weight.
?. [Shipping Document Preparation]
Give the package and shipping documents to IGB Shipping Department to review.
?. [Shipping Document Preparation]
Forward shipping tracking information from IGB Shipping Department on to iDNA Genetics.