Fig. 1

A Gross anatomy of riboflavin-deficient (A) and riboflavin-rescued (B) chick embryos on embryonic day 15 (e15). The riboflavin-deficient (Rf-) embryos present with extensive hemorrhage of skin, liver and heart, retarded development of the eye, feathers, beak and cranium, and excessive lipid deposition in the liver. On the other hand, the riboflavin-rescued (Rf+) embryos show normal development of the head, feathers and liver, which typically shows yellowing due to storage and utilization of yolk lipids. Gross anatomy of Rf + and Rf- embryos at e15 was documented using a Leica M420 macroscope (Buffalo Grove, IL) fitted with a cold light source and the Spot Insight 4 imaging system. The photomicrographs were taken at a magnification of 10X. B Venn diagram of differentially-expressed (DE) and “Analysis Ready” (AR) genes mapped to the Ingenuity Knowledge Base using Ingenuity® Pathway Analysis (IPA) software. Statistical analysis showed no DE (FDR ≤ 0.05) genes between the Rf + and Rf- embryos on e9 and e11. Of the 395 DE genes identified in the liver at e13, only 221 DE genes (or 56%) were considered by IPA as “Analysis Ready” (AR), which reflects incomplete annotation of the Roslin chicken oligo printed on this array. Likewise, 1467 DE genes were identified from statistical analysis on e15; and of these genes, only 929 (or 63%) were mapped to the Ingenuity® Knowledge Base (i.e., AR-DE genes). While only 162 AR-DE genes were commonly shared between riboflavin treatment groups across e13 and e15