***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 7 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***
Isolated PBMCs and MLN cells were stained with a DC or T lymphocyte/NK cell antibody panel (see Table 2 manuscript). 
Flow cytometry data analysis was performed by using FlowJo software (Version 10).
Examples of the gating strategies can be found in the 'Supplementary Materials' of the manuscript; Figure S3 (DCs) and Figure S4 (T lymphocytes and NK cells).

***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 8', four subfolders can be found namely:

1. Raw_data:
You can find here two folders (MLN and PBMCs) each containing 6 excel files which includes the raw data results from MLN and PBMCs at different time points. 
Values generated are percentages (frequency of the parent population) or 'mean fluorescent intensity' values (also referred to in the headings as 'Median'). 
The Excel files are generated and exported by using Flowjo.

2. Unprocessed_Figure:
This folder contains a PDF file with the figure as generated by GraphPad Prism. 
This PDF file is imported in Adobe Illustrator for adjustments.  

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 (csv) files used for the R code to generate graphs and for statistical analysis. 
This folder contains two subfolders named 'Flowcytometry_MLN' and 'Flowcytometry_PBMC' containing 25 Excel and 41 files (csv), respectively. 
When data was not normally distrubuted, log-transformed data was used to perform statistical analysis and is indicated in the Excel file names (includes 'LOG').


