To globally assess whether HFI feeding affects the transcriptome oscillation of ELGs, we first performed a transcriptional time course experiment cycle every 3 hours over an LD using the ELGs of NC-fed and HFI-fed mice (
Fig. 2A). Totals of 24,341 and 24,538 genes were measured from the ELGs of the NC-fed and HFI-fed mice, respectively (
Figs. 2B,
2C). To determine the differences in all the transcriptomes between the two groups' ELGs, we compared the transcripts expressed in both groups. Venn diagram plotting revealed that the overlap between the total transcripts in the NC-fed group and HFI-fed group accounted for 94.54% (23,758) of the total transcripts (24,938) from both groups together; HFI-fed ELGs lost 581 genes but induced the expression of 779 new genes that were not measured in NC-fed ELGs (
Fig. 2D). To further understand the differences between the two groups, we divided all the transcripts from each group's ELGs into three categories: rhythmic, not-rhythmic, and low-expressed (FPKM < 0.001) (
Figs. 2B,
2C). To identify rhythmic transcripts over an LD cycle, we used a JTK_CYCLE approach (a 24-hour oscillation period and
P < 0.05 cutoff) to process all the transcripts from both groups. The data showed that of the 24,341 transcripts in the ELGs of NC-fed mice, approximately 3.11% (757) exhibited rhythmic expression, 67.02% (16,313) exhibited not-rhythmic expression, and 29.87% (7271) were low-expressed (
Fig. 2B).
Supplementary Table S1 lists all information about oscillating gene transcripts identified by RNA-Seq and JTK_CYCLE in NC-fed ELGs. However, of the 24,538 transcripts in the ELGs of HFI-fed mice, approximately 7.14% (1752) exhibited rhythmic expression, 71.31% (17,499) exhibited not-rhythmic expression, and 21.55% (5287) were low-expressed (
Fig. 2C).
Supplementary Table S2 presents all the information about oscillating gene transcripts identified using RNA-Seq and JTK_CYCLE in HFI-fed ELGs. These data suggest that short-term HFI feeding altered the composition of the ELG transcriptome.