Project description:<p>This integrated multi-omics resource delineates the molecular and phenotypic trajectories underlying male morphotype differentiation (Blue Claw [BC], Orange Claw [OC], Small Male [SM]) in <em>macrobrachium rosenbergii</em> during determinative developmental stages (100, 110, and 120 days post-stocking). The dataset comprises paired testicular transcriptomic profiles, hemolymph serum metabolomes, and quantitative morphological trait data (15 key metrics), thereby establishing a holistic framework capturing concurrent gene expression dynamics, metabolic flux alterations, and phenotypic manifestations throughout morphotype specification. The synergistic integration of these multidimensional layers enables mechanistic dissection of regulatory networks governing crustacean growth polymorphism, facilitates identification of heritable biomarkers associated with commercially advantageous morphotypes, and provides foundational insights into arthropod phenotypic plasticity.</p>
2025-08-22 | MTBLS12876 | MetaboLights
Project description:Elucidating microRNA regulatory networks using transcriptional, post-transcriptional and histone modification measurements
Project description:Advances in cellular reprogramming and stem cell differentiation now enable ex vivo studies of human neuronal differentiation. However, it remains challenging to elucidate the underlying regulatory programs because differentiation protocols are laborious and often result in low neuron yields. Here, we overexpressed two murine Neurogenin transcription factors in human induced pluripotent stem cells, and obtained neurons with bipolar morphology in four days at greater than 90% purity. The high purity enabled mRNA and microRNA expression profiling during neurogenesis, thus revealing the genetic programs involved in the transition from stem cell to neuron. These profiles were then analyzed to identify the regulatory networks underlying the differentiation of the neurons. Paired end RNA sequencing of iPS cells (PGP1) at 0, 1, 3, and 4 days post- doxycycline induction of murine NGN1 and NGN2. This was done using an Illumina HiSeq, and reads were aligned to hg19
Project description:Identification of nuclear CSF-1R, H3K4me1 and H3K4me3 localization on chromatin in human primary monocytes and modification of this localization during monocyte differentiation into macrophage induced by 100ng/mL CSF-1 during 6 hours (1 donor) or 72h (3 donors). Identification of EGR1 chromatin localization in human primary monocytes (3 donors) Comparison of nuclear CSF-1R chromatin localization in monocytes from 1 healthy donor and 2 chronic myelomonocytic leukemia patients.
Project description:Early stem cell differentiation programmes are tightly controlled by coordinated pre- and post-transcriptional regulatory networks. In this study, we investigate and characterise miRNA networks responsible for the post-translational gene regulation in early differentiation in both female and male mouse embryonic stem cells. We obtained miRNA-Seq and RNA-Seq profiles of male and female cells from day 0 (D0; 2i) to days 4, 10, 20 and 30. Interestingly, we observed a significant difference in gene expression profiles between females and males, both in terms of identity of regulated genes and of temporal characteristics. Similarly, we observed differences between miRNA species playing significant regulatory roles in female and male cells.
Project description:The seamless transition through stages of pluripotency relies on a delicate balance between transcription factor networks and epigenetic silencing mechanisms that ensure proper regulation of the developmental program, critical for normal development. Here, we uncover the pivotal role of the transgene activation suppressor (TASOR), a component of the human silencing hub (HUSH) complex, in sustaining cell viability during the transition from naive to primed pluripotency, despite its rapid downregulation during this transition. Loss of TASOR in naive cells triggers replication stress, disrupts H3K9me3 heterochromatin formation, and compromise the transcriptional and post-transcriptional silencing of LINE-1 (L1) transposable elements (TEs), with these effects become more pronounced in primed cells. Remarkably, the survival of Tasor-knockout cells during naive to primed transition can be restored through the inhibition of cysteine-aspartic acid protease (Caspase) or deletion of mitochondrial antiviral signaling protein (MAVS). This suggests that unscheduled L1 expression activates an innate immune response, leading to programmed cell death, specifically in cells exiting naïve pluripotency. Additionally, we propose that HUSH-promoted H3K9me3 in naïve PSCs sets the stage for ensuing DNA methylation in primed cells, establishing long-term silencing during differentiation. Our findings shed insights on the crucial impact of epigenetic programs established in early developmental stages on subsequent phases, underscoring their significance in the developmental process.
