GSE118851
In vivo imaging and deep learning tools expose two distinct E2F cell cycle transcriptional relays (in preparation)
Purpose: We used next-generation sequencing (NGS) to identify genes which oscillate during cell cycle in embryos in mRNA level Methods: Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) bi-transgenic mice (mKO2-hCDT1;mAG-hGEM) mRNA profiles of Embryo day 10.5, 11.5 and 13.5 were generated for deep sequencing. The reads were aligned using STAR program and . qRT–PCR validation was performed using SYBR Green assays Results: Genes consistently expressed >2 log fold higher (with an adjusted P-value < 0.05) in DR, YE, or GR samples than in BR samples, were denoted 'proliferation-related'. Of these 258 proliferation-related genes, 86 were previously reported as periodically expressed during the cell cycle. The majority of genes whose expression was enriched in BR samples (267 genes) were related to cell differentiation and non-proliferative processes, and were thus classified as 'quiescent-related' . In agreement with measurements made in cell culture systems, E2f1-3a and E2f7-8 mRNA levels increased in cycling cells when compared to cells in G0, with maximum levels observed in S and G2, albeit the increased expression of E2f7-8 was more pronounced. The mRNA levels of E2f3b, E2f4, E2f5 and E2f6 remained relatively unchanged among the various cell cycle fractions Conclusions: Our research use NGS to deeply study the cell-cyle related gene expression in vivo. The data analysis work flows reported here provides gene expression information regarding to different cell cycle phase and embryo age. Overall design: Examine the gene expression for different cell cycle phases (BR,DR,YE,GE) using FUCCI wild type 10.5, 11.5 and 13.5 embryos (E10.5,E11.5 and E13.5)