Dataset DOI: 10.5061/dryad.gf1vhhn26

Description of the data and file structure

Experiments measure the amplification of pathogen DNA using a fluorescent reporter, either in tube, in porous media, or in porous media microfluidic devices. Data are archived in a .zip file, and are organized in folders by figure and subfigure (e.g. Figure 4A, Figure 4B, etc). Data for supplemental figures and tables is also included in this archive. Each file within the archive is described below.

• Folder: Figure 2
• Folder: Figure 2B
• Folder: 1a Clamshell 032923 – This folder contains .jpg images taken through a filter-modified cell phone camera to show fluorescence generated during the course of DNA amplification. Each image file is named with the date and time it was taken.
• Folder: 1b Clamshell 042823 – This folder contains .jpg images taken through a filter-modified cell phone camera to show fluorescence generated during the course of DNA amplification. Each image file is named with the date and time it was taken.
• Folder: 2a Clamshell 032223 – This folder contains .jpg images taken through a filter-modified cell phone camera to show fluorescence generated during the course of DNA amplification. Each image file is named with the date and time it was taken.
• Folder: 2b Clamshell 050223 – This folder contains .jpg images taken through a filter-modified cell phone camera to show fluorescence generated during the course of DNA amplification. Each image file is named with the date and time it was taken.
• Folder: 3a Clamshell 032223 – This folder contains .jpg images taken through a filter-modified cell phone camera to show fluorescence generated during the course of DNA amplification. Each image file is named with the date and time it was taken.
• Folder: 3b Clamshell 052523 – This folder contains .jpg images taken through a filter-modified cell phone camera to show fluorescence generated during the course of DNA amplification. Each image file is named with the date and time it was taken.
• Folder: Figure 2C
• Folder: Swab 1A
• File: LAMP NG CT swab 1a 032923-analysis – This is a .csv file that lists the fluorescent intensity measurements (arbitrary units) taken from the photographs in Folder 1a Clamshell 032923 (described above). Column A lists the time points in minutes after the LAMP reaction was started. Columns B – G list intensity in relative fluorescence units (RFU) in the green color channel from each of the six pads in the test device. Cells I3-I62 list time points in minutes again. Cells J2:O2 list the background fluorescence intensity values (RFU) for each of the six pads (see methods and references for details for how these background values were calculated). Cells J3:O63 list background subtracted fluorescence intensity values (RFU). These are replicates of the data shown in Figure 2C, and are not explicitly shown in the figure.
• Folder: Swab 1B
• File: LAMP NG CT Swab 1b 042823 - analysis – This is a .csv file that lists the fluorescent intensity measurements (arbitrary units) measurements taken from the photographs in Folder 1b Clamshell 042823 (described above). Column A lists the time points in minutes after the LAMP reaction was started. Columns B – G list intensity in relative fluorescence units (RFU) in the green color channel from each of the six pads in the test device. Cells I3-I62 list time points in minutes again. Cells J2:O2 list the background fluorescence intensity values (RFU) for each of the six pads (see methods and references for details for how these background values were calculated). Cells J3:O63 list background subtracted fluorescence intensity values (RFU), which were used to create the graph shown in Figure 2C.
• Folder: Swab 2A
• File: LAMP NG CT Swab 2a 032223 - analysis – This is a .csv file that lists the fluorescent intensity measurements (arbitrary units) measurements taken from the photographs in Folder 2a Clamshell 032223 (described above). Column A lists the time points in minutes after the LAMP reaction was started. Columns B – G list intensity in relative fluorescence units (RFU) in the green color channel from each of the six pads in the test device. Cells I3-I62 list time points in minutes again. Cells J2:O2 list the background fluorescence intensity values (RFU) for each of the six pads (see methods and references for details for how these background values were calculated). Cells J3:O63 list background subtracted fluorescence intensity values (RFU). These are replicates of the data shown in Figure 2C, and are not explicitly shown in the figure.
• Folder: Swab 2B
• File: LAMP NG CT Swab 2b 050223 - analysis – This is a .csv file that lists the fluorescent intensity measurements (arbitrary units) measurements taken from the photographs in 2b Clamshell 050223 (described above). Column A lists the time points in minutes after the LAMP reaction was started. Columns B – G list intensity in relative fluorescence units (RFU) in the green color channel from each of the six pads in the test device. Cells I3-I62 list time points in minutes again. Cells J2:O2 list the background fluorescence intensity values (RFU) for each of the six pads (see methods and references for details for how these background values were calculated). Cells J3:O63 list background subtracted fluorescence intensity values (RFU). These are replicates of the data shown in Figure 2C, and are not explicitly shown in the figure.
• Folder: Swab 3A
• File: LAMP NG CT Swab 3a 032223 - analysis – This is a .csv file that lists the fluorescent intensity measurements (arbitrary units) measurements taken from the photographs in Folder 3a Clamshell 032223 (described above). Column A lists the time points in minutes after the LAMP reaction was started. Columns B – G list intensity in relative fluorescence units (RFU) in the green color channel from each of the six pads in the test device. Cells I3-I62 list time points in minutes again. Cells J2:O2 list the background fluorescence intensity values (RFU) for each of the six pads (see methods and references for details for how these background values were calculated). Cells J3:O62 list background subtracted fluorescence intensity values (RFU). These are replicates of the data shown in Figure 2C, and are not explicitly shown in the figure.
• Folder: Swab 3B
• File: LAMP NG CT Swab 3b 052523 – analysis – This is a .csv file that lists the fluorescent intensity measurements (arbitrary units) measurements taken from the photographs in Folder 3b Clamshell 052523 (described above). Column A lists the time points in minutes after the LAMP reaction was started. Columns B – G list intensity in relative fluorescence units (RFU) in the green color channel from each of the six pads in the test device. Cells I3-I62 list time points in minutes again. Cells J2:O2 list the background fluorescence intensity values (RFU) for each of the six pads (see methods and references for details for how these background values were calculated). Cells J3:O62 list background subtracted fluorescence intensity values (RFU). These are replicates of the data shown in Figure 2C, and are not explicitly shown in the figure.
• Folder: Figure 2D
• File: Swab 1A_2023-03-21 14-39-29_CT013064 - raw data – This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as measured by a BioRad CFX optical qPCR machine. Column B lists plate read cycles; plate reads were taken at 0.5 minute intervals. Columns C-P show background subtracted RFUs for the labeled plate wells at each cycle timepoint. Columns R-X and Z-AF are copies of data from columns to their left, relabeled according to the correct condition. These are replicates of the data shown in Figure 2D, but are not explicitly shown in the figure.
• File: Swab 1B 20230428_114611_CT013064_LAMP_120_30S - raw data– This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as measured by a BioRad CFX optical qPCR machine. Column B lists plate read cycles; plate reads were taken at 0.5 minute intervals. Columns C-R show RFUs (not background subtracted) for the labeled plate wells at each cycle timepoint. Columns U-AB and AD-AK are copies of data from columns to their left, relabeled according to the correct condition. These are replicates of the data shown in Figure 2D, but are not explicitly shown in the figure.
• File: Swab 2A_2023-03-22 11-08-10_CT013064 - raw data – This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as measured by a BioRad CFX optical qPCR machine. Column B lists plate read cycles; plate reads were taken at 0.5 minute intervals. Columns C-P show background subtracted RFUs for the labeled plate wells at each cycle timepoint. Columns R-X and Z-AF are copies of data from columns to their left, relabeled according to the correct condition. These are the data shown in Figure 2D.
• File: Swab 2B_2023-05-02 11-43-17_CT013064 - raw data – This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as measured by a BioRad CFX optical qPCR machine. Column B lists plate read cycles; plate reads were taken at 0.5 minute intervals. Columns C-R show background subtracted RFUs for the labeled plate wells at each cycle timepoint. Columns V-AC and AF-AM are copies of data from columns to their left, relabeled according to the correct condition. These are replicates of the data shown in Figure 2D, but are not explicitly shown in the figure.
• File: Swab 3A_2023-03-22 15-59-28_CT013064 - raw data – This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as measured by a BioRad CFX optical qPCR machine. Column B lists plate read cycles; plate reads were taken at 0.5 minute intervals. Columns C-P show background subtracted RFUs for the labeled plate wells at each cycle timepoint. Columns S-Y and AF-AG are copies of data from columns to their left, relabeled according to the correct condition. These are replicates of the data shown in Figure 2D, but are not explicitly shown in the figure.
• File: Swab 3A_2023-03-22 15-59-28_CT013064 - raw data – This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as measured by a BioRad CFX optical qPCR machine. Column B lists plate read cycles; plate reads were taken at 0.5 minute intervals. Columns C-P show background subtracted RFUs for the labeled plate wells at each cycle timepoint. Columns S-Y and AF-AG are copies of data from columns to their left, relabeled according to the correct condition. These are replicates of the data shown in Figure 2D, but are not explicitly shown in the figure.
• File: Swab 3B_2023-05-25 11-56-11_CT013064 - raw data– This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as measured by a BioRad CFX optical qPCR machine. Column B lists plate read cycles; plate reads were taken at 0.5 minute intervals. Columns C-P show background subtracted RFUs for the labeled plate wells at each cycle timepoint. Columns S-Y and AF-AG are copies of data from columns to their left, relabeled according to the correct condition. These are replicates of the data shown in Figure 2D, but are not explicitly shown in the figure.
• Folder: Figure 3
• File: Figure 3A photo – This is an unedited .jpg image file showing PCR tubes containing LAMP reagents (including hydroxynapthol blue) rehydrated by clinical swab samples.
• File: Figure 3B - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device shown in figure 3A. Column A lists time points in minutes. Columns B-E list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• Folder: Figure 4
• File: Figure 4AB – This is a .pdf file which shows more time point photographs than the published 4A figure, as well as a larger copy of the graph shown in figure 4B.
• File: Figure 4B - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device shown in figure 4A. Column A lists time points in minutes. Columns B-G list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• File: Figure 4CD – This is a .pdf file which shows more time point photographs than the published 4C figure, as well as a larger copy of the graph shown in figure 4D.
• File: Figure 4D - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device shown in figure 4C. Column A lists time points in minutes. Columns B-G list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• Folder: Figure 5
• File: Figure 5AD - This is a .pdf file which shows more time point photographs than the published 5A figure, as well as a larger copy of the graph shown in figure 5D. It also shows a graph of amplification zone thermal profile. Time is shown on the x-axis in minutes and temperature is shown on the y-axis in degrees C.
• File: Figure 5B - This is a .pdf file which shows more time point photographs than the published 5B figure, as well as a larger copy of the graph shown in figure 5D. It also shows a graph of amplification zone thermal profile. Time is shown on the x-axis in minutes and temperature is shown on the y-axis in degrees C.
• File: Figure 5C - This is a .pdf file which shows more time point photographs than the published 5C figure, as well as a larger copy of the graph shown in figure 5D.
• File: Figure 5D – This is a .csv file lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device shown in figure 5A.
• File: Figure 5E – This is a .csv file lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device shown in figure 5B.
• File: Figure 5F – This is a .csv file lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device shown in figure 5C.
• Folder: Figure 6
• Folder: Figure 6A
• Folder: NG CT Vaginal Sample NG10 031324 photos
• Files: 63 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NG11 031424 photos
• Files: 61 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NG12 032224 photos
• Files: 62 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NG13 032724 photos
• Files: 61 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NG14 032824 photos
• Files: 62 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• File: Figure 6A – CT - This is a .csv file that lists background subtracted fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Column A lists time points in minutes. Columns B-F list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• File: Figure 6A – NG - This is a .csv file that lists background subtracted fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Column A lists time points in minutes. Columns B-F list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• File: Figure 6A – NG - This is a .csv file that lists background subtracted fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Column A lists time points in minutes. Columns B-F list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NG10 031324 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NG10 031324 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NG11 031424 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NG11 031424 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NG12 032224 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NG12 032224 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NG13 032724 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NG13 032724 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NG14 032824 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NG14 032824 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• Folder: Figure 6B
• Folder: NG CT Vaginal Sample NG CT Vaginal Sample CT11 051024 photos
• Files: 61 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample CT12 050724 photos
• Files: 60 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample CT13 052124 photos
• Files: 61 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample CT14 052224 photos
• Files: 60 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample CT15 052424 photos
• Files: 61 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• File: Figure 6B – CT - This is a .csv file that lists background subtracted fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Column A lists time points in minutes. Columns B-F list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• File: Figure 6B – NG - This is a .csv file that lists background subtracted fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Column A lists time points in minutes. Columns B-F list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample CT11 051024 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample CT11 051024 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample CT12 050724 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample CT12 050724 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample CT13 052124 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample CT12 050724 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample CT13 052124 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample CT13 052124 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample CT14 052324 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample CT14 052324 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample CT15 052424 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample CT15 052424 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• Folder: Figure 6C
• Folder: NG CT Vaginal Sample NEG10 040524 photos
• Files: 85 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NEG11 040924 photos
• Files: 65 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NEG12 041224 photos
• Files: 67 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NEG13 041624 photos
• Files: 61 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• Folder: NG CT Vaginal Sample NEG14 041924 photos
• Files: 90 .jpg files named by time stamp in a year-month-day_hour-minute-second format (e.g. 2024-03-13_15-30-23). Each photo shows a filtered (see methods) top view of the diagnostic device, focused on the two amplification membranes.
• File: Figure 6C – CT - This is a .csv file that lists background subtracted fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Column A lists time points in minutes. Columns B-F list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• File: Figure 6C – NG - This is a .csv file that lists background subtracted fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Column A lists time points in minutes. Columns B-F list background subtracted fluorescence (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NEG10 040524 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NEG10 040524 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NEG11 040924 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NEG11 040924 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NEG12 041224 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NEG12 041224 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NEG13 041624 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NEG13 041624 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• File: NG CT Vaginal Sample NEG14 041924 - photo analysis - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Columns A and E list time points in minutes. Columns B-C list fluorescence intensities (RFU) for each of the listed conditions at the listed time points. Columns F-G list background subtracted fluorescence intensities (RFU) for each of the listed conditions at the listed time points.
• File: NG CT Vaginal Sample NEG14 041924 - raw data - This is a .csv file that lists fluorescence intensity data in relative fluorescence units (RFU) as taken from photographs of the device found in the above-listed folders. Fluorescence data is broken into red (columns B-F) and green (columns G-K) color channels. Columns L-P show the difference in fluorescence intensity between the red and green color channels. Column Q shows the file name of the photo used to measure fluorescence intensity.
• Folder: Figure S1
• File: Figure S1 – This is a .csv file that shows LAMP liftoff times in minutes. Column A shows replicate numbers. Columns B – E show liftoff times for the listed conditions.
• Folder: Figure S2
• File: CT LAMP_2023-11-17 10-17-42_CT013064 - Quantification Amplification Results – This is a .csv file that shows LAMP amplification results as measured by Bio-Rad qPCR machine (see methods). Column A lists cycle numbers. Columns B – Y list fluorescence intensity (RFU) for each cycle. Column AB lists a time (in minutes) for each cycle. Columns AC – AK, AM – AU, AW – BB, and BD – BK are copies of columns B – Y labeled by experimental condition.
• File: NG LAMP_2023-11-17 13-42-37_CT013064 - Quantification Amplification Results – This is a .csv file that shows LAMP amplification results as measured by Bio-Rad qPCR machine (see methods). Column A lists cycle numbers. Columns B – Y list fluorescence intensity (RFU) for each cycle. Column AA lists a time (in minutes) for each cycle. Columns AB – AQ, AS – AZ, BB – BF, BH – BL, BO – BT and BV are copies of columns B – Y labeled by experimental condition.
• Figure S2A – This is a .pdf file that shows photographs of six-pads devices labeled with times after amplification was started. These photographs are excerpts of the full data set that was used to generate the graph shown in the lower left. These amplification data are found in the other files in this folder (Figure S2B)
• File: Figure S2B – This is a .csv file that shows background subtracted LAMP amplification results as measured from a series of photographs (excerpts shown in File: Figure S2A). Column A lists time in minutes. Columns B-G list background subtracted fluorescence intensity (RFU) for each timepoint. The condition for each column is listed in row 2.
• Folder: Figure S3
• File: Figure S3 – This is a .csv file that shows background subtracted LAMP amplification results as measured by Bio-Rad qPCR machine (see methods). Column A lists time in minutes. Columns B-F list background subtracted fluorescence intensity (RFU) for each timepoint. The condition for each column is listed in row 2.
• Folder: Figure S4
• File: Figure S4 – This is a .csv file that shows background subtracted LAMP amplification results as measured by Bio-Rad qPCR machine (see methods). Column A lists time in minutes. Columns B-S list background subtracted fluorescence intensity (RFU) for each timepoint. The condition for each column is listed in row 2.
• Folder: Figure S5
• This is a .csv file that shows background subtracted LAMP amplification results as measured from a series of photographs of QMA pads in six-pad devices. Column A lists time in minutes. Columns B-K list background subtracted fluorescence intensity (RFU) for each timepoint. The condition for each column is listed in row 2.
• Folder: Table S4
• File: CT positive clinical sample qPCR results – This is a .csv file that shows qPCR results as measured by Bio-Rad qPCR machine (see methods). Rows 1-19 contain header information. Rows 1-17 include information provided by BioRad CFX Maestro software about the PCR run. Row 18 states the C. trachomatis fg plasmid mass to copy number discovered in a separate experiment, and the date that experiment was run. Row 19 lists the units of the starting quantity of CT DNA. Row 20 lists the headers for the data in the rows below. Column A lists the well number of each sample. Column B lists the fluorophore used (FAM in all cases). Column C is labeled “Target”, which does not contain any data. In all cases, the target was the CT cryptic plasmid. Column D lists Content. Std-# indicates that sample was a standard of known quantity. Unk indicates that sample was of unknown DNA quantity. NTC indicates that sample did not contain any CT DNA (no template control). Column E lists sample names. Cq lists calculated cycle at which fluorescence crossed the threshold value. This same data is reorganized in columns J—Q. Column J lists sample name again (reorganized from column E). Column K lists starting DNA content again (reorganized from column G). Column L calculates total fg DNA content per 24 µl amplification pad by multiplying the value in column K by 24. Column M is blank. Column N converts fg DNA to CT plasmid copy number by multiplying the value in column K by 25.1. Column O lists CT plasmid copy number per 24 µl amplification pad, calculated by multiplying the value in column N by 24. Column P lists sample name again (duplicated from column J). Column Q lists CT plasmids per ml of sample, calculated by multiplication by 41.7 (1000/24).

Files and variables

File: Heiniger_et_al_2025_data_v2.zip

Description: A compressed file consisting of a hierarchical archive of file folders containing data files. Data are organized in folders by figure and subfigure (e.g. Figure 4A, Figure 4B, etc). Data for supplemental figures and tables is also included in this archive. Data are stored as .csv spreadsheets or photographs taken by a filter-modified cell phone camera. Units of measurement are time (in minutes or cycle number) or relative fluorescence units. qPCR values are reported in copies per microliter or copies per sample.

Code/software

Photographs - any software that can read HEIC or .jpg files (e.g. windows photo app, Mac Preview, or ImageJ); photos are also archived as .pdf files, which can be opened by Adobe Acrobat or similar

qPCR and fluorescence image quantification data are provided as .csv files (read by Excel, Google sheets, or similar)