ABSTRACT: 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
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: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:This study explores whether HuD could bind to and regulate the expression circRNAs from genes associated with neuronal development and synaptic plasticity circRNAs bound to HuD were isolated from the striatum of HuD-OE mice by RNA immunoprecipitation (RIP) as described in Bolognani et al, 2010 (https://doi.org/10.1093/nar/gkp863) using Dynabeads® (Thermo Fisher Scientific) coated with mouse monoclonal anti-myc tag antibody (9B11; Cell Signalling Technology Inc.) specifically recognizing myc-tagged HuD transgenic protein expressed in HuD-OE as described before (Bolognani et al., 2010; Zimmerman et al., 2020). Controls for RIP assays were performed using either non-immune IgG and HuD-OE tissue or the myc-tag antibody and wild type (WT) tissue.
Project description:E10.5 whole brain were isolated from WT and Piezo1-KO mice (C57BL/6J strain backgound) described in Ranade et al 2014. https://doi.org/10.1073/pnas.1409233111
Project description:Placenta derived Okae et al. human trophoblast stem cells cultured in Okae et al. conditions (ttps://doi.org/10.1016/j.stem.2017.11.004). In addition, we sequenced SHEF6 primed human pluripotent stem cells as a control. Individual cells were manually isolated with a mouth pipette and subjected to single-cell full-lengths transcriptome profiling using a modified version of Smart-Seq2.
Project description:Lineage tracing of individual cells during directed differentiation human iPSC into alveolospheres was performed using a lentiviral barcode labeling system (Weinreb et al., 2020) as described in Hurley et al., 2020.
Project description:Methylation microarray profiling (Illumina Human Methylation 450k and EPIC platforms) of 60 adult glioblastomas. Tumours were subtyped using the approach from Sturm et al. (https://doi.org/10.1016/j.ccr.2012.08.024): 12 IDH, 18 MES, 12 RTK I, 18 RTK II. DNA was prepared, assayed on the microarrays, and raw data computationally processed as described in Capper et al., "DNA methylation-based classification of central nervous system tumours": https://www.nature.com/articles/nature26000
Project description: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)
