This readme.txt file was generated on 2017-11-11 by Katie Wilson

GENERAL INFORMATION

1. Title of Dataset: Vaccination Against Lawsonia intracellularis Decreases Shedding of Salmonella enterica serovar Typhimurium in Co-Infected Pigs and Alters the Gut Microbiome
2. File Information:
   A. Filename: MappingFileSubmission.txt
   B. Short description: Mapping file with sample descriptions
   C. Filename: FastqCoinfectionMicrobione.tar.gz
   D. Short description: Fastq files detailing gene sequencing
   E. If data set includes multiple files related to one another, include relationship here: 

3. Principal Investigator Contact Information
   A. Name: Richard E Isaacson
   B. Institution: University of Minnesota
   C. Address: 1971 Commonwealth Ave. St. Paul, Minnesota 55108
   D. Email: isaac015@umn.edu

4. Associate or Co-investigator Contact Information
   A. Name: Fernando Lopes Leivas Leite
   B. Institution: University of Minnesota
   C. Address: 1971 Commonwealth Ave. St. Paul, Minnesota 55108
   D. Email: lopes029@umn.edu

6. Date of data collection (single date, range, approximate date): 2016-02-10 to 2015-04-06

7. Geographic location of data collection (where was data collected?): St Paul, Minnesota USA
8. Date files were created: 2016-05-25
9. Are there multiple versions of the dataset? no

10. Information about funding sources that supported the collection of the data: Sponsorship: USDA-AFRI grant 1005423


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
Fecal samples were collected from pigs, DNA was extracted using the MOBIO PowerSoil kit and the V1-V3 region of the 16SrRNA gene was amplified following a dual indexing approach with KAPA HiFidelity Hot Start Polymerase. Sequencing was performed using the Illumina MiSeq with paired end 300 base pair reads at the University of Minnesota Genomics Center. 

2. Methods for processing the data: 

3. Instrument-specific information needed to interpret the data:
Sequences were generated in Illumina MiSeq sequencer with paired end 300 base pair reads.

4. Standards and calibration information, if appropriate: 

5. Environmental/experimental conditions: 

6. Describe any quality-assurance procedures performed on the data: 
These are raw fastq files from the sequencer.
7. Codes or symbols used to note or characterize low quality/questionable outliers that people should be aware of
   A. Code/symbol: 
   B. Definition: 
   C. Code/symbol:
   D. Definition: 

8. People involved with sample collection, processing, analysis and/or submission:
Fernando Leite, Tonya Ward, Trevor Gould, Richard Isaacson, University of Minnesota Genomics Institute.

DATA-SPECIFIC INFORMATION
1. Parameters and/or variables used in the data set
   A. Group Names: There are 5 groups total in this dataset 
1) challenged with S. Typhimurium alone = Sal
2) challenged with both S. Typhimurium and L. intracellularis = Sal Law
3) challenged with S. Typhimurium and vaccinated against L. intracellularis = Sal Vac
4) challenged with both S. Typhimurium and L. intracellularis and vaccinated against L. intracellularis =Sal Law Vac 
5) non-infected control = Control

2. Column headings for data
#SampleID
Description: Name of each sample  
filenames
Description: Name of each fastq file
SampleID2
Description: Summary of sample name 
BarcodeSequence
Description: Data are already demultiplexed, barcode added to facilitate work in Qiime
LinkerPrimerSequence
Description: Sequence of linker primer
fastqR1
Description: Name of fastq read 1 file
fastqR2
Description: Name of fastq read 2 file
Group
Description: Treatment group of study
Week
Definition: Week of study in which sample was collected
Zero values signify: Control blank samples which were not collected fecal samples
Dpi
Definition: Days post infection with Salmonella enterica serovar Typhimurium
Zero values signify: The day of infection with Salmonella enterica serovar Typhimurium
Code
Description: Designation of week and initials of each treatment
Zero values signify: Control blank samples which were not collected fecal samples


SHARING/ACCESS INFORMATION 

1. Licenses/restrictions placed on the data:

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

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

4. Links/relationships to ancillary data sets:

5. Was data derived from another source?
   A. List source(s): N/A

6. Recommended citation for the data:
Isaacson, Richard E; Gebhart, Connie J; Ward, Tonya; Singer, Randall S; Leite, Fernando L L. (2017). Vaccination Against Lawsonia intracellularis Decreases Shedding of Salmonella enterica serovar Typhimurium in Co-Infected Pigs and Alters the Gut Microbiome. Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/190879.


Credits: Template provided by the University of Minnesota Libraries, http://lib.umn.edu/datamanagement