This readme.txt file was generated on <202000801> by ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data for: Diffusion of Knots along DNA Confined in Nanochannels 2. Author Information Principal Investigator Contact Information Name:Zixue Ma Institution:University of Minnesota Address:Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Email:ma000052@umn.edu Associate or Co-investigator Contact Information Name: Kevin D. Dorfman Institution: University of Minnesota Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Email: dorfman@umn.edu ORCID ID: 0000-0003-0065-5157 3. Date of data collection: 2019-08-22 to 2019-12-23 4. Geographic location of data collection: N/A 5. Information about funding sources that supported the collection of the data: NIH (R01-HG006851) and NSF (CBET-2016879) -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data:CC0 1.0 Universal 2. Links to publications that cite or use the data: Ma, Zixue, & Dorfman, Kevin D. (2020). Diffusion of Knots along DNA Confined in Nanochannels. Macromolecules, 53(15), 6461-6468. https://doi.org/10.1021/acs.macromol.0c00561 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? If yes, list source(s): 6. Recommended citation for the data: Ma, Zixue; Dorfman, Kevin D. (2020). Data for: Diffusion of Knots along DNA Confined in Nanochannels. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/5nqr-b219. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Image_Analysis.zip Short description: This file contains all the MATLAB codes to process the knot diffusion data. Knot_Analysis_v2.m is used to analyze knot diffusion along DNA chain and generate knot positions and MSD data. MATLAB codes in choose_DNA_molecules folder are used to process DNA images to generate DNA intensity data. Extension_Analysis.m is used to analyze DNA extension. B. Filename: Videos.zip Short description: This file contains all the DNA image data. C. Filename: Figure_Data.zip Short description: This file contains all the figures, data and MATLAB code used to generated those figures. 2. Relationship between files: MATLAB codes in Image_Analysis.zip are used to process DNA images in Videos.zip. 3. Additional related data collected that was not included in the current data package: No 4. Are there multiple versions of the dataset? no -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: The nanofluidic device was designed based on the knot factory concept. The images of the DNA were recorded by an EMCCD camera (Photometrics, Cascade II:512). To obtain data for knot diffusion, the DNA with knots were imaged at 5 fps with a 200 ms exposure time for 8 min in a quiescent fluid. After each experiment, which consists of multiple loading and compression cycles, the device was cleaned and dried to be reused for the next experiment. Additional information can be found in the associated publication. 2. Methods for processing the data: The videos were processed using a customwritten MATLAB script that outputs the time evolution of each DNA molecule’s intensity profile. Additional information can be found in the associated publication. 3. Instrument- or software-specific information needed to interpret the data: Matlab 4. Standards and calibration information, if appropriate: Please see the main text of the paper for additional information. 5. Environmental/experimental conditions: Please see the main text of the paper for additional information. 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: Kevin D. Dorfman ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Image_Analysis ----------------------------------------- Instructions on how to run image analysis codes Software: MATLAB Part A: Process DNA images to generate DNA intensity data and DNA extension Step 1: Change the directory that MATLAB uses to find DNA image data and MATLAB codes in DNAAnalyze_one.m, DNANanoStretch.m, ExtensionFluct21_one.m, and Extension_Analysis.m under the Image_Analysis folder. Step 2: Open DNANanoStretch.m Change the DNA image file name (line 23 and 29 in the code) and the number of frames of the DNA images (line 212 in the code). Select DNA by creating first a large box and then a small box around the analyzed DNA molecule. Run the code. Step 3: Open Extension_Analysis.m Change the DNA image file name (line 27). Change the number of frames (line 28, 30 and 31). Run the code. Part B: Analyze knot diffusion along a DNA molecule confined in a nanochannel Step 1: Open Knot_Analysis_v2.m and change the directory that MATLAB uses to find the DNA intensity, edge and extension data. Step 2: Change the DNA image file name (line 21). Run the code.