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. 2017 Dec 12:4:170186.
doi: 10.1038/sdata.2017.186.

Gene expression profiling in the intestinal mucosa of obese rats administered probiotic bacteria

Julio Plaza-Díaz  1   2   3 , Cándido Robles-Sánchez  1   2   3 , Francisco Abadía-Molina  4 , María José Sáez-Lara  2   5 , Laura María Vilchez-Padial  2 , Ángel Gil  1   2   3   6 , Carolina Gómez-Llorente  1   2   3   6 , Luis Fontana  1   2   3
Affiliations

Gene expression profiling in the intestinal mucosa of obese rats administered probiotic bacteria

Julio Plaza-Díaz et al. Sci Data. .

Abstract

We investigated whether the administration of Lactobacillus paracasei CNCM I-4034, Bifidobacterium breve CNCM I-4035 and Lactobacillus rhamnosus CNCM I-4036 modulate the expression of genes in the intestinal mucosa of obese Zucker rats. Forty-eight Zucker-Leprfa/fa and 16 Zucker lean Lepr+/fa rats were used. Eight Zucker lean Lepr+/fa and 8 Zucker-Leprfa/fa rats were euthanized as a reference. The remaining 40 Zucker-Leprfa/fa rats were then assigned to receive 1010 colony forming units (CFU) of one of the three probiotic strains, a mixture of L. paracasei CNCM I-4034 and B. breve CNCM I-4035, or a placebo by oral administration for 30 days. An additional group of 8 Zucker lean Lepr+/fa rats received the placebo for 30 days. Over 27,000 rat genes were studied using a DNA array. Four animals per group were used. Total RNA was extracted from intestinal mucosa and cDNA was synthesized, fragmented and labeled. Labeled cDNA was hybridized using GeneChip kits, and the latter were scanned. Intensity values of each probe were processed and normalized to obtain an individual value for each set of probes.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Workflow scheme.
The number of rats from which high quality RNA was obtained is shown for each condition tested. Abbreviations: ZL, Zucker lean Lepr+/fa rats; ZO, Zucker Leprfa/fa rats.
Figure 2
Figure 2. Microarray results obtained with the Rat Gene 1.1 ST Array Plate (Affymetrix®).
These results were uploaded to the Gene Expression Omnibus (GEO) platform as ‘GSE73848 Expression data from intestinal mucosa of Zucker rats.’ n=4 rats per group.
Figure 3
Figure 3. Fragmentation of cDNAs.
(a) Bioanalyzer. (b) gel-shift assay.
Figure 4
Figure 4. Quality control assessment for microarrays of the RNA samples from intestinal mucosa.
(a) Hybridization controls. (b) Labeling controls with transcripts from Bacillus subtilis.
Figure 5
Figure 5. Relative log expression signal graph.
This reference array is made from the median of all the arrays for each probe set. It is assumed that most of the expression values do not change with respect to the median and, accordingly, are around 0.
See this image and copyright information in PMC

Dataset use reported in

  • doi: 10.1038/s41598-017-02203-3

References

Data Citations

    1. 2016. Gene Expression Omnibus. GSE73848

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