﻿***Title of the dataset / Data underlying the publication: ‘Effects of E. coli Nissle 1917 on the Porcine Gut Microbiota and Immune System in Early Life’***

***Creators***
Mirelle Geervliet 1,†, Hugo de Vries 2,3,†, Christine A. Jansen 1,4, Victor P.M.G. Rutten 4,5, Hubèrt van Hees 6, Caifang Wen 3, 
Kerstin Skovgaard 7, Giacomo Antonello 8, Huub F.J. Savelkoul 1, Hauke Smidt 3, Edwin Tijhaar 1,†, and Jerry M. Wells2,†,*

1	Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, The Netherlands; mirelle.geervliet@wur.nl; huub.savelkoul@wur.nl; edwin.tijhaar@wur.nl; christine.jansen@wur.nl 
2	Host-Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands; jerry.wells@wur.nl
3	Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands; hugo.devries@wur.nl; caifang.wen@wur.nl; hauke.smidt@wur.nl 
4	Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; v.rutten@uu.nl 
5	Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa; v.rutten@uu.nl 
6	Research and Development, Trouw Nutrition, Amersfoort, The Netherlands; hubert.van.hees@trouwnutrition.com
7       Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; kesk@dtu.dk
8       Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy; giacomo.antonello@unitn.it

* Correspondence: jerry.wells@wur.nl

† These authors have contributed equally to this work and share first or last authorship.

***Related publication***
Title: Effects of E. coli Nissle 1917 on the Porcine Gut Microbiota and Immune System in Early Life
DOI: 10.3389/fcimb.2022.842437
Received: December 23th, 2021; Accepted: February 1st, 2022; Published: 2022

***General Introduction***
This README file corresponds to the data corresponding to Figure 5 of the manuscript.
This dataset contains data collected during an in vivo experiment with pigs at the Wageningen University as part of the PhD Thesis Projects of Mirelle Geervliet and Hugo de Vries (first authors of the manuscript). 
This research project was made possible by The Netherlands Organisation for Scientific Research and Vereniging Diervoeders Nederland (VDN).

***Purpose of analysis***
To assess differences in gene expression of mucosal scrapings of different gut segments between the treatment groups.

***Methodological information***
For a detailed description of how Fluidigm data was generated, please see the Materials & Methods section of the manuscript.

***Data specific information***
In the Figure 5 folder, two subfoldors can be found, namely:

1. Unprocessed_Figure:
This folder contains a PDF file with the figures as generated by R. 
This PDF file was used to create final Figure 5. 

2. Final_Figure:
This folder contains the final figure as presented in the manuscript. 
The final figure is prepared in Adoble Illustrator. 

Raw_data:
Fluidigm datafiles can be found in the folder named "Fluidigm_data"

R script: 
R script can be found under the following folder: Data_analyses_in_R_Studio
This folder also contains the processed data files used in R-Studio, in the subfolder 'input_data'. These datafiles contain fold gene expression and p-value columns for either ileum or colon.