Belcour2020 - Chondrus crispus Genome-Scale Metabolic Network model, version 1.3
Ontology highlight
ABSTRACT: This is the first version of a Genome-Scale Metabolic Network model of the red alga Chondrus crispus, published in a paper by Belcour et al., iScience 2020 (https://doi.org/10.1016/j.isci.2020.100849)
Project description:In order to evaluate the molecular effects of Roundup at a concentration at which no morphological effects were identified, RNA extracted from Roundup-treated A. nidulans cultures were subjected to a global gene expression profiling using a custom agilent microarray (8 × 15 K format), for which the reproducibility, specificity and sensitivity was described previously (Delomenie et al., Curr Genet 2016 Nov;62(4):897-910. PMID: 27038308). This data is published in Mesnage R, Oestreicher N, Poirier F, Nicolas V, Boursier C, Vélot C. (2020) Transcriptome profiling of the fungus Aspergillus nidulans exposed to a commercial glyphosate-based herbicide under conditions of apparent herbicide tolerance. Environmental Research. Available online 7 January 2020, 109116. https://doi.org/10.1016/j.envres.2020.109116
Project description:This study characterizes the transcriptomic alterations of Tuber melanosporum during fruiting body development. Stage III, IV, V and VI were analyzed. For images and description of stages see Zarivi et al.2015 (https://doi.org/10.1016/j.phytochem.2015.02.024)
Project description:We find that the 'high-confidence oscillating' genes initiate oscillations similarly as after release from L1 dauer. We performed high-throughput RNA sequencing on worms that were synchronously released from the dauer stage by refeeding on OP50. In particular, we investigate oscillatory gene expression as described in Hendriks et al., 2014 (doi: 10.1016/j.molcel.2013.12.013) and observe the re-initiation of oscillatory gene expression from stable expression with a time delay upon dauer exit. Experimental observation of the transitions between non-oscillatory and oscillatory states during the first 5 hours after dauer exit reveals that the oscillatory gene expression is arrested in a specific oscillator phase, similar to the observation we make in animals released from L1 arrest (see Meeuse et al., 2020, doi: https://doi.org/10.1101/755421).
Project description:Oligophrenin1 X-linked Intelectual disability (ID) gene is mutated in ID patients with cerebellar hypoplasia. It encodes OPHN1 protein which has been shown to interact with Rev-erb alpha, a negative regulator of the circadian clock in cells (https://doi.org/10.1038/nn.2911) In this study, we searched fo gene expression differences in hippocampi from adult mouse ophn1 KO and controls during 24 hours. Three replicates were collected evey 6 hours for both genotype. Data from controls were analyzed and reported in http://dx.doi.org/10.1016/j.neuroscience.2015.08.066.
Project description:This SuperSeries is composed of the SubSeries listed below. The main processed data are organized in the following two Figshare links: Seurat objects: https://doi.org/10.6084/m9.figshare.23290004 ReDeeM-V output: https://doi.org/10.6084/m9.figshare.24418966.v1
2023-11-18 | GSE219015 | GEO
Project description:Long-read sequencing and hybrid assemblies related to the NORM collection described in Gladstone et al. 2020 https://doi.org/10.1016/S2666-5247(21)00031-8
Project description:Components of the transcription machinery can undergo liquid-liquid phase separation, but the functional importance of phase-separated condensates in transcriptional control is not well understood. Here we report that disease-causing mutations in several transcription factors (TFs) alter the phase separation capacity of those TFs. We first demonstrate that the Hoxd13 TF, and its intrinsically disordered N-terminus form phase-separated condensates. Expansions of a polyalanine repeat, which cause hereditary synpolydactyly in humans, facilitate phase separation of Hoxd13, and alter the transcriptional program of several cell types in a cell-specific manner in vivo. Disease-associated expansions of aminoacid repeats in intrinsically disordered regions of other TFs were similarly found to alter phase separation. These results suggest that aberrant phase separation of transcriptional regulators may underlie a spectrum of human pathologies. The paper is available at https://doi.org/10.1016/j.cell.2020.04.018
2020-05-07 | GSE128818 | GEO
Project description:Long-read sequencing and hybrid assemblies related to the NORM collection described in Gladstone et al. 2020 https://doi.org/10.1016/S2666-5247(21)00031-8. Part 2