Data from 'Sustainability in the laboratory: evaluating the reuseability of microtiter plates for PCR and fragment detection'

This repository contains the data for the manuscript: Sustainability in the laboratory: evaluating the reuseability of microtiter plates for PCR and fragment detection.

The script can be found here: https://github.com/AneLivB/SGP

Files: 

R15*_R*.csv

The processed data used for the script. All other files of the same name format contain the same elements!

Columns: Rack_location, ID, all loci

Rack_location: the location on the microwell plate the individual had in the wet lab

ID: individual identification tag of the animal the DNA sample stems from

_a and _b denotes the first and second allele of all loci

Mismatches

A dataframe created by the script and later used to calcualte per treatment single-locus genotype error rates.

Columns: Rack.1, Rack.2, Treatment, No..of.mistyped.alleles, No..of.mistyped.reactions, No..of.reactions, Allelic.error.rate, Genotype.error.rate

Rack.1: One of three racks (R154, R155, R156) from the standard protocol

Rack.2: One of three racks (R154, R155, R156) from one of the other treatments (e.g. R154_R2, R154_R3, R154_R4)

Treatment: One of three treatments (Internal control, Reused detection plate, Reused PCR plate)

No..of.mistyped.alleles: Number of mismatched alleles within one treatment group, within a DNA plate

No..of.mistyped.reactions: Number of mismatched single-locus genotypes within one treatment group, within a DNA plate

No..of.reactions: Number of single-locus genotypes within one treatment group, within a DNA plate

Allelic.error.rate: Error rate per allele

Genotype.error.rate: Error rate per single-locus genotypes

model.mismatch.2.Rdata

RData file containing the model output.

Manuscript abstract: 

Single-use plastics (SUPs) are indispensable in laboratory research, but their disposal contributes substantially to environmental pollution. Consequently, reusing common SUP items such as microtiter plates represents a promising strategy for improving laboratory sustainability. However, the key challenge lies in determining whether SUP reuse can be implemented without sacrificing data quality. To investigate this, we conducted a simple experiment to assess the impact of reusing microtiter plates on microsatellite genotyping accuracy. Plates previously used for PCR and fragment detection were cleaned using an environmentally friendly method and then reused. Our results indicate that, while reusing PCR plates significantly increases genotyping error rates due to residual DNA contamination, detection plates can be reused without compromising data quality. Our approach offers laboratories a practical and sustainable option for reducing SUP waste and costs while maintaining research integrity.