README File: 

Title: Programmable Design of Isothermal Nucleic Acid Diagnostic Assays through Abstraction-based Models.

Authors: Gaolian Xu, Yunfei Guo, Julien Reboud, Hao Yang, Hongchen Gu, Chunhai Fan, Xiaohua Qian, and 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.  

Note 1: Files with the extensions .ab1 are sequencing results and can be read with software Chromas (http://technelysium.com.au/wp/chromas/ v2.6.6 accessed 6th February 2022) or 4peaks (https://nucleobytes.com/4peaks/index.html v1.8, accessed 6th February 2022)

Note 2: The aggregated patient data is provided in the publication (Supplementary Information Table S4). Individual patient data is available from corresponding authors Professor Jonathan Cooper (Jon.Cooper@glasgow.ac.uk) and Dr. Gaolian Xu (gaolian.xu@sjtu.edu.cn), upon motivated request. 

Figure 1: 
	“Figure 1.xlsx” contains the data associated with Figure 1b and Figure 1d as two separate sheets: 
	In Figure 1b, rows 2-6 contain the aggregated results used to plot the figure: the first column contains the concentrations of target for the reaction. The second column is the average Tt value for a length of primer of 40 nucleotides, with the standard deviation as a error in the next column. This is repeated for lengths of 50 and 60 nucleotides in the next columns. 
Rows following row 9 present the raw data, including replicates. The first column is the time (in min) whilst other columns contain the fluorescence intensity for each sample. Samples are indicated in the top row (e.g. 40-1000-1 is 40 nucleotides, target concentration of 1000 copies/reaction and replicate #1). 
	In Figure 1d is presented the raw image of the gel with markers. 
	“Figure 1c.ab1” contains the trace of the sequencing results presented in Figure 1c. 

Figure 3: 
	“Figure 3.xlsx” contains the data associated with Figure 3d-g as four separate sheets
	In figure 3d is presented the raw image of the gel with markers.
	Figure 3e provides the fluorescence reading for each sample as separate columns. The first column is Time (in min). Each sample is identified by the target concentration (in fM) in the first row. 
	Figure 3e-inset provides the average of Tt for each sample and the standard deviation as an error, whilst the raw data for all samples is provided below (rows 11 onwards) with the first column being time (in min) and each subsequent column a separate sample replicate (e.g. “2pM-1” is replicate #1 for a concentration of 2pM). 
	Figure 3f presents the raw image of the gel with markers.
	Figure 3g contains the raw data of fluorescence intensity for all replicates (identified by a suffix “-1” for example). The first column is Time (in min). 
	“Figure 3c.ab1” contains the trace of the sequencing results presented in Figure 3c.

Figure 4: “Figure 4b.xlsx” presents the raw image of the gel with markers. 

Figure 5: 
	“Figure 5.xlsx” contains the data associated with Figure 5b-d as three separate sheets
	Figure 5b presents the raw data of fluorescence intensity for each sample. The first column is time (in min) and samples are identified by the concentration of target. Data starts at row 3 
	Figure 5c presents the aggregated data on the top (rows 1-10) where the first column is the sample (as per figure legend), second column is concentration (cells/reaction), whilst the next column is the average Tt value, followed by standard deviation. After row 13 is provided the raw data where the first column is time and the next columns are the samples (e.g. 5A+4A+3A-1000-1 is the first replicate for the concentration of 1000 copies, for primer 5A+4A+3A). 
	Figure 5d presents the raw image of the gel with markers.

Figure S1: 
      “Figure S.xlsx” provides the raw data of melting curve, i.e. the derivative of the fluorescence intensity with temperature. The first three rows present the denomination of the columns. Data starts at row 4. The first column is temperature (in degree C). The second column is the derivative of fluorescence intensity for the sample with both hairpins (H1 and H2) at a concentration of 50nM. The sample denomination as in the figure is provided in row 3 (#1 for H1&H2). 
      Columns from K onwards provides the data used in the inset of the figure for three samples. 

Figure S2: 
      “Figure S2.xlsx” provides the raw data of melting curve for both Figures S2a-b, i.e. the derivative of the fluorescence intensity with temperature. The first two rows present the denomination of the columns. Data starts at row 3. The first column is temperature (in degree C). The other columns are different oligo sequences, as provided in the manuscript.

Figure S3: 
	“Figure S3b.ab1” contains the trace of the sequencing results presented in Figure S3b.

Figure S4:
	“Figure S4c.xlsx” presents the raw image of the gel with markers.
	“Figure S4d.ab1” contains the trace of the sequencing results presented in Figure S4d.

Figure S6:
	“Figure S6.xlsx” presents the raw image of the gel with markers.

Figure S7:
      “Figure S7c.xlsx” presents the raw image of the gel with markers.

Figure S8: 
	“Figure S8b.ab1” and “Figure S8c.ab1” contain the trace of the sequencing results presented in Figure S8b and S8c respectively.

Figure S9
	“Figure S9b.ab1” and “Figure S9c.ab1” contain the trace of the sequencing results presented in Figure S9b and S9c respectively.

Figure S10: 
	“Figure S10.xlsx” contains the data associated with Figure S10a-c as three separate sheets
	Figure S10a presents the aggregated data on the top (rows 1-6). Data starts at row 3. The first column (B) is the target concentration. The second column is average Tt for the mechanism presented in Figure 5, with the standard deviation next. The following columns are for LAMP and the mechanism of Figure 3. The raw data of fluorescence intensity for each sample is presented below (after row 8). Data starts at row 10. The first column is time (in min), followed by the fluorescence intensity for each sample (e.g. “4000-1” is replicate #1 of the sample at 4000 cells). Row 8 provides the mechanism involved.  
	Sheets Figure S10b and Figure S10c provide the raw gel image with annotation.