This codebook.txt file was generated on 2018-01-16 by wilsonkm


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GENERAL INFORMATION
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1. Title of Dataset 
The effects of different feed additives on bird performance and the gastrointestinal microbiome of Salmonella-challenged broilers


2. Author Information


  Principal Investigator Contact Information
        Name: Timothy J Johnson
           Institution: University of Minnesota
           Address: 205C Veterinary Science Building,1971 Commonwealth Avenue, Saint Paul, MN 55108
           Email: tjj@umn.edu

 Associate or Co-investigator Contact Information
        Name: Nicholas Evans
           Institution: PMI Nutritional Additives
           Address: Shoreview, MN
           Email: evans436@umn.edu


 Associate or Co-investigator Contact Information
           Name: Peter Karnezos
           Institution: PMI Nutritional Additives
           Address: Shoreview, MN
           Email: TPKarnezos@landolakes.com


  Associate or Co-investigator Contact Information
           Name: Michael Sims
           Institution: Virginia Diversified Research Corp.
           Address: Blacksburg, VA
           Email: mdsims@comcast.net


  Associate or Co-investigator Contact Information
           Name: Bonnie P Youmans 
           Institution: University of Minnesota
           Address: Saint Paul, MN
           Email: byoumans@umn.edu


3. Date of data collection: 2016-2016

4. Geographic location of data collection: 
Minnesota, USA

5. Information about funding sources that supported the collection of the data:
Sponsorship: USDA-AFRI Grant nos. 2016-67015-24911


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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data: CC0 1.0 Universal


2. Links to publications that cite or use the data: Forthcoming


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:
 Johnson, Timothy J; Evans, Nicholas; Karnezos, Peter; Sims, Michael; Youmans, Bonnie P. (2018). The effects of different feed additives on bird performance and the gastrointestinal microbiome of Salmonella-challenged broilers. Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/192763. 

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DATA & FILE OVERVIEW
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1. File List

Please note: Files A-F, listed below, are tape archive folders that contain hundreds of .fastq.gz files in each folder. The filenames do not necessarily have meaning. VDRC was the location where the work was performed, Virginia Diversified Research Corp. The number following VDRC is a random unique number assigned to each sample. Everything following that (S#, L001, R#, 001, etc.) are sequencing designations by a sequencing facility. 

   A. Filename: chunk1.tar       
      Short description: Contains 424 .fastq.gz files.        
        
   B. Filename: chunk2.tar       
      Short description: Contains 394 .fastq.qz files.       
        
   C. Filename:  chunk3.tar      
      Short description: Contains 428 .fastq.qz files.  

   D. Filename: chunk4.tar       
      Short description: Contains 428 .fastq.qz files.  
        
   E. Filename: chunk5.tar       
      Short description: Contains 252 .fastq.qz files.  
        
   F. Filename:  chunk6.tar       
      Short description: Contains 232 .fastq.qz files.  

   G. Filename: Sample_metadata_file_DRUM.xlsx       
      Short description: Contains metadata pertaining to samples. Metadata is broken into two parts. The first part is a list of treatment acronyms and their definitions at the top of the sheet. The second part is a table containing a list of the samples, their treatment group, age of bird, sample type, and corresponding .tar file.       

2. Relationship between files:        
N/A



3. Additional related data collected that was not included in the current data package:
N/A


4. Are there multiple versions of the dataset? No


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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: 
Publication forthcoming.


2. Methods for processing the data: Samples were demultiplexed by the University of Minnesota Genomics Center. No other processing was performed.


3. Instrument- or software-specific information needed to interpret the data: DNA sequencing was performed using Illumina MiSeq 2X300bp PE runs.


4. Standards and calibration information, if appropriate:


5. Environmental/experimental conditions:


6. Describe any quality-assurance procedures performed on the data:


7. People involved with sample collection, processing, analysis and/or submission:

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DATA-SPECIFIC INFORMATION FOR: Sample_metadata_file_DRUM.xlsx 
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1. Number of variables: 5


2. Number of cases/rows: 1089 rows 


3. Missing data codes:
N/A


4. Variable List
            

    A. Name: Sample prefix
       Description: Sample prefix accompanying corresponding file. 
                    VDRC = Virginia Diversified Research Corp


    B. Name: Treatment Group
       Description: Type of treatment received by sample.
                    Value labels:
			NICON = non-infected control
			ICON = infected control
			VM20 = virginiamycin
			MCFA = medium-chained fatty acids
			MCFA+LA = medium-chained fatty acids + lactic acid
			Phyto = phytogenic blend

    C. Name: Age of Bird
       Description: Age of bird by day at time of euthanasia.
                    Value labels:
			D28 = Day 28
			D42 = Day 42
			D14 = Day 14

    D. Name: Sample Type
       Description: Type of sample.
                    Value labels: Litter, Ceca, Ileum


    E. Name: Tar File
       Description: This column denotes which tar file (Chunk1, Chunk2, etc.) columns A-D correspond.