This codebook.txt file was generated on 2018-04-30 by Fernando Leite
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GENERAL INFORMATION
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1. Title of Dataset 
A Cell Proliferation and Inflammatory Signature is Induced by Lawsonia intracellularis Infection in Swine

2. File Information:
	A. Filename: Sample Information.txt
   	Short description: Contains sample IDs, the time point of the study and treatment group
   
	B. Filename: BAMfiles.zip
	Short description: BAM file of each sample

2. Author Information
  Principal Investigator Contact Information
        Name: Richard E. Isaacson
           Institution: University of Minnesota
           Address: 1971 Commonwealth Ave. St. Paul, Minnesota 55108
           Email: isaac015@umn.edu

  Associate or Co-investigator Contact Information
        Name: Fernando L. Leite
           Institution:University of Minnesota
           Address: 1971 Commonwealth Ave. St. Paul, Minnesota 55108
           Email: lopes029@umn.edu

3. Date of data collection: Jan 2017

4. Geographic location of data collection: Rice, MN USA

5. Information about funding sources that supported the collection of the data:
This work was funded by a USDA Multistate Health Formula Fund and Zinpro Corporation.

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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data:
N/A

2. Links to publications that cite or use the data:
Not yet published

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? No.

6. Recommended citation for the data:
Leite, Fernando, L; Abrahante, Juan, E.; Vasquez, Erika; Vannucci, Fabio; Gebhart, Connie, J.; Nathan, Winkelman; Mueller, Adam; Jerry, Torrinson; Rambo, Zachary; Isaacson, Richard, E.. (). A Cell Proliferation and Inflammatory Signature is Induced by Lawsonia intracellularis Infection in Swine. Retrieved from the University of Minnesota Digital Conservancy, http://hdl.handle.net/:75143.

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DATA & FILE OVERVIEW
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1. File List
   A. Filename: Sample Information.txt      
      Short description: Contains information regarding each sample        
       
   B. Filename: BAMfiles.zip
      Short description: Contains the BAM file of each sample.       

2. Relationship between files: Sample Information.txt contains information regarding the samples in file BAMfiles which are the BAM files of each sample.     
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: 
Intestinal scrapping was performed with a microscope slide to collect intestinal mucosa always on the same location on all pigs adjacent to the ileal cecal junction and Peyer's patch. The sample was immediately placed in RNAlater (ThermoFisher) and total RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen). RNA quantity and quality were assessed using RiboGreen RNA and Agilent Analysis system, respectively.

2. Methods for processing the data: 
Samples that passed quality metrics were used to create a cDNA library for sequencing using Illumina Library Creation. Samples from each pig were individually sequenced using the Illumina HiSeq 2500 sequencer using 50 base paired-end reads,20 million reads per sample were obtained. The Illumina sequence files were processed using a pipeline developed by the University of Minnesota Informatics Institute. Briefly, FastQ files were trimmed via trimmomatic and mapping was performed via TopHAT (v2.0.13) using bowtie (v2.2.4.0). The Sus Scrofa 3.0 (susScr3) genome was used and gene annotation was performed using Ensembl from the same genome build. 

3. People involved with sample collection, processing, analysis and/or submission:
Fernando Leite, Erika Vasquez, Fabio Vannucci, Juan Abrahante, Richard Isaacson, University of Minnesota Genomics Institute.

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DATA-SPECIFIC INFORMATION
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1. Number of variables:
Treatment (infected or non-infected); Timepoint (14,21,28 days post infection)

2. Number of cases/rows: 
There are a total of 35 samples.

3. Missing data codes: 
        In: intestinal sample         
        I: same as In

4. Variable List: N/A
	Each BAM file is named with the Sample ID followed by either In or I, they are all intestinal samples.