strain: C57BL/6 tissue: ileum gender: male days of conventionalized: 0 age at start of experiment: 10 wks
Treatment protocol
After 2 weeks of acclimatization and diet adaptation, a subset of GF mice were randomly assigned to sacrifice by oral anesthesia using isoflurane (t=d0, GF). The remaining GF mice were conventionalized by oral gavage with 0.5ml of mixed fecal suspension derived from 0.2g of freshly obtained fecal material of conventionally raised mice (C57 BL/6) diluted 100-folds in Brain Heart infusion (BHI) broth. Conventionalized mice were sacrificed at days (d) d1, d2, d4, d8, d16 and d30 after conventionalization. Small intestine (SI; jejunum, and ileum), and large intestine (LI; colon) from each mouse were removed. The 2 segments of the SI and the entire colon were then divided into 2-cm segments that were immediately stored in RNA-later at room temperature for 1 hour prior to subsequent storage at -80°C for RNA isolation.
Growth protocol
Germ free (GF) mice (male, C57 BL/6) were purchased from the Centre de Recherché, Institute National de la Recherche Agronomique (Jouy-en-Josas, France). Mice were maintained under sterile conditions. Mice had ad libitum access to sterilized water and were maintained on a commercial laboratory chow diet (UAR 1016C Laboratory Chow, UAR, Villemoisson sur Orge, France) that was sterilized by gamma irradiation (45KGy).
Extracted molecule
total RNA
Extraction protocol
Total mouse RNA was obtained from a 2-cm segment of jejunum, ileum and colon by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA), followed by DNAse treatment and column purification using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.
Label
biotin
Label protocol
The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.
Hybridization protocol
The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 144 arrays that were used in this experiment were provided as 1x 96 array plate and 3x 24 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
Scan protocol
Arrays were scanned on an Affymetrix GeneTitan instrument.
Data processing
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0). The SI samples were normalzed together, separately from the colon samples.
