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---
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title: "Rabbit early life coprophagia effect on the ileum transcriptome"
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description: |
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  R-scripts used to analyse the data presented in the article   
  "Coprophagia early in life tunes immune system gene expression in ileum after weaning in rabbit", Cauquil L., Beaumont M., Schmaltz-Panneau B., Liaubet L., Lippi Y., Bluy L., Poli M., Gress L., Lencina C. , Duranthon V., Combes S.
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author:
  - name: Laurent Cauquil 
  - affiliation: INRAE GenPhySE
date: "`r Sys.Date()`"
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site: distill::distill_website
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)

# Learn more about creating websites with Distill at:
# https://rstudio.github.io/distill/website.html

# Learn more about publishing to GitHub Pages at:
# https://rstudio.github.io/distill/publish_website.html#github-pages

```

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**Background and aims**  

Coprophagia  in suckling rabbits is observed in the first 14  days after birth. This behavior stimulates the maturation of the microbiota and strongly reduces mortality after weaning (Combes et al., 2014; doi: 10.2527/jas.2013-6394). In the current study, we hypothesized that this beneficial effect of coprophagia is immune-mediated at the gut level. We present here the R-script used to analyse the ileal transcriptome using a rabbit 60K microarray platform at day 35 and 49 in rabbits with different coprophagia beahavior in early life.

**Experimental design encompassed three groups**  
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- the **NF** group: ingestion of maternal feces in the nest was prevented (No access to Feces)
- the **FF** group: pup feces ingestion was enhanced removing the maternal feces from the nest and replacing them with feces from unrelated does  (coprophagia)
- the **FFab** group: pup feces ingestion was enhanced removing the maternal feces from the nest and replacing them with feces from unrelated antibiotic treated does (coprophagia with antibiotic feces).
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