This codebook.txt file was generated on 20180920 by wilsonkm

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GENERAL INFORMATION
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1. Title of Dataset 
 Measuring the wall depletion length of nanoconfined DNA (2018) 

2. Author Information

  Principal Investigator Contact Information
        Name: Aditya Bikram Bhandari
           Institution: University of Minnesota
           Email: bhand050@umn.edu

  Associate or Co-investigator Contact Information
           Name: Jeffrey G. Reifenberger
           Institution: Bionano Genomics, Inc.
           Address: 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA

  Associate or Co-investigator Contact Information
           Name: Hui-Min Chuang
           Institution: University of Minnesota

  Associate or Co-investigator Contact Information
           Name: Han Cao
           Institution: Bionano Genomics, Inc.
           Address: 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA

  Associate or Co-investigator Contact Information
        Name: Kevin D. Dorfman
           Institution: University of Minnesota
           Email: dorfman@umn.edu

3. Date of data collection: November - December 2017

4. Geographic location of data collection: San Diego, CA

5. Information about funding sources that supported the collection of the data:
Sponsorship: NIH R01-HG006851

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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data:
Depositor did not specify a license. Material may be reused with appropriate attribution.

2. Links to publications that cite or use the data:
Bhandari, A. B., Reifenberger, J. G., Chuang, H.-M., Cao, H., & Dorfman, K. D. (2018). Measuring the wall depletion length of nanoconfined DNA. The Journal of Chemical Physics, 149(10), 104901. https://doi.org/10.1063/1.5040458


3. Links to other publicly accessible locations of the data: N/A


4. Links/relationships to ancillary data sets: N/A


5. Was data derived from another source? N/A


6. Recommended citation for the data: 
Bhandari, A. B., Reifenberger, J. G., Chuang, H.-M., Cao, H., & Dorfman, K. D. (2018). Measuring the wall depletion length of nanoconfined DNA. The Journal of Chemical Physics, 149(10), 104901.

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DATA & FILE OVERVIEW
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1. File List
	A. Filename: archive.zip       
	Short description: Zipped folder containing three folders - figures, analyzed_data, and processed_images. More information about folder structure and files below.

        
	B. Filename: Readme.txt       
	Short description: Plain text document containing dataset metadata.           


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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: 
Irys Platform for genome mapping (BioNano Genomics): https://bionanogenomics.com/products/irys/


2. Instrument- or software-specific information needed to interpret the data: 
bnx files contain label information for each molecule after alignment
cmap files contain the reference genome data
xmap files contain unaligned molecule data
err files contain information about alignment results


3. People involved with sample collection, processing, analysis and/or submission: All of the authors : Aditya Bikram Bhandari, Jeffrey G. Reifenberger, Hui-Min Chuang, Han Cao, Kevin Dorfman.

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DATA-SPECIFIC INFORMATION FOR: figures folder
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1. Folder description: Codes and files to reproduce each of the figures in the manuscript.

2. Number of files: 35

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DATA-SPECIFIC INFORMATION FOR: processed_images folder
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1. Folder description: contains the files generated after image processing (.bnx, .xmap, .cmap files)


2. Number of files: 39

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DATA-SPECIFIC INFORMATION FOR: analyzed_data folder
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1. Folder description: contains data analyzed as nick pairs for varying cutoff lengths. Also contains analysis for Fig 6 and Fig 7.

2. Number of files: 9