Project description:We will perform RNAseq to evaluate the effects of the loss of a list of TSGs on the transcriptome.
This dataset contains all the data available for this study on 2017-08-10.
Project description:Early embryo loss is an important factor affecting the reproductive capacity of cattle. Recent studies have revealed that during the process of the embryonic genome activation (EGA), epigenetic modification, such as, histone lactylation modification remodeling is crucial for early embryonic development. However, the effect and mechanism of histone lactylation modification on bovine early embryo development remain unknown. In this study, we found that histone lactylation, including pan Kla, H3K9la, and H3K18la were mainly located in nuclear, and were significantly decreased from 8-cell to morula stage as well as increased from morula to blastocyst stage in bovine IVF embryos. Decreased or increased levels of histone lactylation by GSKA or NaLa supplementation inhibited bovine early embryo development and blastocyst lineage differentiation. Furthermore, combined with scRNA-Seq data and EU straining revealed that reduction of histone lactylation levels altered expression of genes associated with DNA transcription and RNA polymerase activity, thereby impairing the process of EGA. Importantly, NMN rescued the inhibitory effects of GSKA supplementation in bovine EGA and early embryonic development. Altogether, these results indicated that histone lactylation maintains bovine early embryo development via regulating EGA process. These findings provide theoretical references for addressing early embryo loss and thereby enhancing the reproductive capacity of cattle.
Project description:This study aimed to perform microarray analysis of the peripheral blood mononuclear cell (PBMC) transcriptome to evaluate differential lncRNA expression in women with luminal A breast cancer
Project description:Bariatric surgical techniques are known to cause weight loss and diabetes remission to varying degrees in severly obese patients. However, the mechanisms involved in the restoration of beta-cell function remain to be uncovered. In this study, the leptin-deficient ob/ob mouse was used as a model to investigate the effect of EGA bariactric surgery on pancreatic islet miRNA expression.
Project description:Calcium dynamics drive metabolic regulation of epigenetic reprogramming at fertilization and alter EGA resulting in long term effects in offspring.
Project description:Embryonic genome activation (EGA), a pivotal transcriptional event during preimplantation development, is accompanied by post-transcriptional regulation of maternal mRNAs. Disentangling the transcriptional output of the newly activated embryonic genome from concomitant post-transcriptional processing is important for decoding EGA dynamics.Here, using optimized low-input SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing) in mouse embryos, we delineates the temporal hierarchy of EGA nascent transcription during mouse preimplantation embryogenesis and uncovers a mechanistic link between EGA and the first lineage specification, providing new insights into the regulatory architecture of early mammalian development.
Project description:Currently, the novel brominated flame retardant, 1,2,5,6-tetrabromocyclooctane (TBCO), is considered as a potential replacement for hexabromocyclododecane (HBCD). As such, use of TBCO could increase significantly in the near future. Therefore, this study investigated the toxicity of TBCO in order to assess its potential toxicological risks to aquatic organisms. Embryos of Japanese medaka (Oryzias latipes) were exposed to 10, 100 and 1,000 μg/L TBCO, and molecular responses were characterized by use of transcriptomics (RNAseq) and proteomics in embryos exposed to 100 μg/L TBCO that were collected on the day of hatch. TBCO was accumulated in embryos by 0.43-1.3×104 30 fold and the rate of accumulation was 1.7-1.8 day-131 . Number of days to hatch and success of hatching of embryos exposed to the two greatest concentrations of TBCO were impaired. Consistent with effects on hatching, proteins that were less abundant were enriched in pathways of embryo development and hatching. Responses of the transcriptome and proteome to TBCO also were used to predict adverse effects of TBCO. Functionally grouped gene ontology terms indicated that TBCO might impair contraction of cardiac muscle and vision, and these effects were confirmed by use of targeted bioassays designed to evaluate cardiac and visual performance. Results of this study provided a comprehensive understanding of effects of TBCO on medaka at early-life stages. Also, the study illustrated the power of “omics” approaches to explain and predict phenotypic responses to the exposure with chemicals.
Project description:To evaluate the impact of the RNA purification method on extracellular RNA (exRNA) sequencing, 8 different RNA purification kits were compared by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma. Minimum and maximum plasma input volumes recommended by the manufacturers were tested in triplicate. Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.
Project description:In this study we have used ChIPseq analysis to perform comprehensive mapping of the binding profile of the cAMP receptor protein (CRPMt) of M. tuberculosis combined with RNAseq studies to further investigate the transcriptional response following crp gene deletion and under alternative growth conditions.
