***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 S14 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 investigate if EcN influences the local (MLN) or systemic (PBMCs) cell response. 

***Methodological information***
PBMCs and MLN cells were stimulated ex vivo with ConA or left unstimulated for 24 hours. 
After 24 hours cell supernatant was collected and stored until measurement.
TNFa and IL-10 levels were measured using ELISA's. 

***Data specific information***

R script can be found under the following folder: Data_analyses_in_R_Studio.
This folder also contains the data files used in the subfolder 'input_data'. This includes the metadata file.

In folder 'Figure S14', four subfolders can be found namely:

1. Raw_data:

You can find here six Excel files which includes the raw data results from MLN and PBMCs at different time points. 
Every excel file consists of two sheets, one with TNFa results and one with IL-10 results. 
The values in these files are the cytokine responses in pg/mL (calculated by Luminex system using the standard curves).

2. Unprocessed_Figure:
This folder contains a PDF file with the figures as generated by GraphPad Prism. 
This PDF file is imported and adjusted in Adobe Illustrator. 

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

4. Excel_File_R
Contains all Excel files used for the R code to generate graphs and for statistical analysis. 
This file contains two subfolders named 'Restimulation_MLN' and 'Restimulation_PBMC' containing both 22 Excel (csv) files. 
When the name of the Excel file end with '_LOG' it means that data was log-transformed.
