Additional file 2 of A transcriptomic examination of encased rotifer embryos reveals the developmental trajectory leading to long-term dormancy; are they “animal seeds”?

Additional file 2: Tables S1. Embryonic developmental stages in AMs and REs, based on observations of time-lapse photographs. S2 Table. The temporal mean normalized gene counts (DeSeq2-VSD log-scale normalization) during the development of AMs (1–14 h post-extrusion) and REs (1–192 h post-extrusion). S3 Table. Cluster analyses (mean normalized transcript abundance values). S4 Table. (A) Cluster analysis of maternal gene transcripts (1-2 h after extrusion) with differential abundance between AMs and REs, and (B) the corresponding enriched KEGG pathways. S5 Table. (A, C) Cluster analyses of transcripts with differential abundance between early development (1–12 h post-extrusion) and very late development in each egg type. S6 Table. (A)The temporal transcript abundance patterns of transcripts encoding for dormancy hallmark proteins during the very late in RE development (24–192 h post extrusion).  (B) The temporal transcript abundance patterns of genes in the KEGG longevity regulating pathway (worm) in AMs (1–14 h post-extrusion) and REs (1–192 h post-extrusion). S7 Table. (A) The temporal transcript abundance patterns of genes associated with the following signaling pathways: Wnt, TGFβ, Notch, Hippo, FoxO, PI3-AKT, Insulin signaling, JAK-STAT, MAPK, AMPK, mTOR, and Hedgehog. S8 Table. The temporal transcript abundance patterns of genes encoding for transcription factors in AMs and REs. S9 Table. The temporal transcript abundance patterns of homeobox genes in AMs and REs. S10 Table. The temporal transcript abundance patterns of genes encoding for nuclear receptors in AMs and REs. S11 Table. The temporal transcript abundance patterns of (A) genes associated with lipid droplets and genes involved in KEGG lipid metabolic pathways. S12 Table. The temporal transcript abundance patterns of genes involved in the (A) phototransduction, (B) circadian rhythm, and (C) circadian entrainment KEGG pathways in AMs and REs. S13 Table. List of opsin-associated genes in AMs and REs.