The transcriptome profiling analysis of intestines and kidneys in conventionally raised (CV) and germ-free (GF) wild type zebrafish embryos

To investigate how the zebrafish embryos respond to the absence of the microbiota, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32,948 cDNAs of the zebrafish genome assembly were annotated after reads mapping for further analysis. For the 5 dpf intestinal tissue samples, 948 genes (4% of the total number of genes) were differentially expressed, 371 genes were up-regulated and 577 genes were down-regulated in the GF group . For the 7 dpf kidney tissue samples, 697 genes (3% of the total number of genes) were differentially expressed, 341 genes were up-regulated and 356 genes were down-regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos (both in intestines at 5 dpf and in kidneys at 7 dpf). To investigate how the transcriptome changes in the chd8-/- zebrafish embryos, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively. Intestinal mRNA profiles of conventionally raised(CV) and germ-free(GF) embryos at 5 dpf,and renal (the location of their hematopoietic tissue) mRNA profiles of CV and GF embryos at 7 dpf. Analysis of mRNA profiles of intestines at 5 dpf and renal (the location of their hematopoietic tissue) at 7 dpf in chd8-/- embryos, and comparing the data with those from the wildtype embryos.