Pluto Bioinformatics

GSE118851: In vivo imaging and deep learning tools expose two distinct E2F cell cycle transcriptional relays (in preparation)

Bulk RNA sequencing

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 . qRTPCR 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. SOURCE: Daokum Sun ( - Medical University of South Carolina

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