Schumer lab: DNA quantification and dilution

• We use a biotek plate reader in Bass Biology 216 to quantify DNA. Make sure you have trained with JJ Baczenas or someone who has used the biotek before using it. It belongs to the department.

• Prepare a plate for quantification. See DNA_Quantification_with_Bass216biotek.docx in the Protocols folder in Dropbox or email baczenas@stanford.edu for the protocol and all necessary reagents and consumables.

• Follow the instructions in the protocol above to use the machine.

• The automatic output of the biotek software won't calculate anything above the highest standard so it's often necessary to reanalyze the raw values

• Input formats, the directory for outputs, and an R script for calculate concentration can be found here /Swordtail Dropbox/Schumer_lab_resources/Extractions_and_library_preps/DNAquant_biotek

• Often the results of the script will not have the negatives as 0. As long as all the negatives are the same value we consider the negatives to be clear.

• copy the concentrations into the extraction grid you made for this plate.

• copy the concentrations into an Tn5 library template that can be found in /Swordtail Dropbox/Schumer_lab_resources/Extractions_and_library_preps/Library_Prep

• Dilute the gDNA as instructed to by the Tn5 library template