README File: 

Title: Rapid Veterinary Diagnosis of Bovine Reproductive Infectious Dis-eases from Semen using Paper-Origami DNA Microfluidics

Authors: Zhugen Yang, Gaolian Xu, Julien Reboud, Atif Syed, Gurpreet Kaur, John McGiven, Nongthombam Boby, Praveen K Gupta, Pallab Chaudhuri, Jonathan M. Cooper
 

This readme file aims to provide a guide to use the data associated with this publication, available here in the following folders : 

1. data of figure 1
  1.1 photo of paper device without folding
  1.2 photo of plastic devices 
  1.3 photo of paper device for extraction
  1.4 photo of paper device for elution
  1.5 image of detection internal control
  1.6 image of detection Leptos
  1.7 image of detection leptos and Brucella
  1.8 image of detection of leptos, Burcella and BoHV

2. data for figure 2 
Note : rule for file naming. 
1-1, first measurement for the first (highest) concentration (here 25 pg/μl), 
2-1, second measurement (replicate) for the first concentration, [...], 
1-2, first measurement for the second concentration (second highest), etc...
 
Each set of images is stored in a folder as follows:
   2.1 leptos genomic DNA spiked into semen
   2.2 Brucella genomic DNA spiked into semen
   2.3 BoHV genomic DNA spiked into semen
   
2.4 extracted data from image for LOD of 3 spiked genomic DNA: each sheet corresponds to one organism (e.g. 'LOD of leptos' uses pictures from the folder 2.1)
Column A describes DNA concentration spiked into semen (C1 is highest for the organism)
Column B: PC is positive control, S is sample under study, NC is negative control. 
Columns C-E represent different measurements of pixel values, minimum, maximum and mean of intensity within the ROI. 
This is then done again for the replicates, and the overall structure is replicated for the different organisms. 

3. data of Figure 3, 
file naming rule identical to the one used in 2. above. 

   3.1 photos of detection of sensitivity of paper device by spiking 3 organisms
   3.2 extracted data: 
Column A - concentrations from highest to lowest. 
Column B - organism (PC, positive control, NC negative control). 
Columns C-E - same as 2.4 above.   


ESI

5. raw data of PCR for DNA recovery calculation (Figure S3). 
Sheet 1. 
column A - wells in a 96 well plate
column B - cycle number
Column 3-7 - fluorescence intensity (a.u.) for the different diameters of paper spot. 

Sheet 2. Calculations of DNA recovery
Column A: concentration of DNA
Columns B, C, D Threshold time of PCR curve of three replicates; 
column E mean value of three Ct value, 
Column F standard deviation
column H: the size of spot in Figure S3 (b), 
column I, DNA recovery calculated according to the calibration curve (each measurement with at least three independent replicates), using data from Sheet1 (raw data)

column (K) different concentration of DNA, column (L): DNA recovery determined with the calibration curve. (each measurement with at least three independent replicates)



6. Figure S3: Realtime LAMP detection of genomic DNA
   6.1 data for leptos
   6.2 data for Brucella
   6.3 data for BoHV

7. data for figure S5
   3.1 semen samples (without spiked organims)
1-12 are 12 different semen samples. 
   3.2 spiking with E.coli
   3.3 spiking with 3 organisms
   3.4 extracted data - presented in the same format as in 2.4