Ontology highlight
ABSTRACT:
PROVIDER: PRJNA596543 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:NIH-3T3 cells were infected with wildtype MCMV at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at the indicated times of infection as described in Rutkowski et al., Nature Communications 2015.
2020-08-07 | GSE102375 | GEO
Project description:Feng et al 2019 - Microarray Raw Data
| PRJNA562147 | ENA
Project description:We previously reported a polyvinyl alcohol-based mouse hematopoietic stem cell (HSC) culture protocol that efficiently expanded transplantable HSCs for at least a month ex vivo (Wilkinson et al., Nature 2019). Here, we investigated the molecular consequences of oxygen concentration on 28-day ex vivo HSC cultures using bulk RNA-seq
2023-02-07 | GSE207740 | GEO
Project description:We previously reported a polyvinyl alcohol-based mouse hematopoietic stem cell (HSC) culture protocol that efficiently expanded transplantable HSCs for at least a month ex vivo (Wilkinson et al., Nature 2019). Here, we investigated the molecular consequences of oxygen concentration on 28-day ex vivo HSC cultures using single cell RNA-seq
2023-02-07 | GSE207742 | GEO
Project description:Key regulators of septum formation between the left and right ventricle in mammals, including the transcription factors TXB5 and PITX2, feature loss-of-function phenotypes that affect development of the two-chambered zebrafish heart, suggesting uncharacterized primordial functions of these septation regulators prior to the evolution of any physical boundaries between heart chambers. Data is as published in Mosimann & Panakova et al (Nature Communications, 2015)
2015-07-14 | GSE70750 | GEO
Project description:yeast-GEM: The consensus genome-scale metabolic model of Saccharomyces cerevisiae. Further curations of this model will be tracked in the GitHub repository:https://github.com/SysBioChalmers/yeast-GEM For you use yeast-GEM, please cite the yeast8 paper: Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). https://doi.org/10.1038/s41467-019-11581-3. The FROG analysis was performed with the yeastGEM_rich_medium.mat, which is a rich medium setup.
2023-11-22 | BIOMD0000001063 | BioModels
Project description:Fastq files for the 16S rDNA amplicon library of 714 fecal samples of 20 time series (as described in Vandeputte et al. 2021, Nature Communications)
| EGAD00001008275 | EGA
Project description:While DNA methylation is an important gene regulatory mechanism in mammals (Razin and Riggs 1980; Moore, Le, and Fan 2013), its function in arthropods remains poorly understood. Studies in eusocial insects have argued for its role in caste development by regulating gene expression and splicing (Elango et al. 2009; Lyko et al. 2010; Bonasio et al. 2012; Flores et al. 2012; Foret et al. 2012; Li-Byarlay et al. 2013; Marshall, Lonsdale, and Mallon 2019; Shi et al. 2013)(Alvarado et al. 2015; Kucharski et al. 2008). However, such findings are not always consistent across studies, and have therefore remained controversial (Arsenault, Hunt, and Rehan 2018; Cardoso-Junior et al. 2021; Harris et al. 2019; Herb et al. 2012; Libbrecht et al. 2016; Oldroyd and Yagound 2021b; Patalano et al. 2015). Here we use CRISPR/Cas9 to mutate the maintenance DNA methyltransferase DNMT1 in the clonal raider ant, Ooceraea biroi. Mutants have greatly reduced DNA methylation but no obvious developmental phenotypes, demonstrating that, unlike mammals (Brown and Robertson 2007; En Li, Bestor, and Jaenisch 1992; Jackson-Grusby et al. 2001; Panning and Jaenisch 1996), ants can undergo normal development without DNMT1 or DNA methylation. Additionally, we find no evidence of DNA methylation regulating caste development. However, mutants are sterile, while in wildtypes, DNMT1 is localized to the ovaries and maternally provisioned into nascent oocytes. This supports the idea that DNMT1 plays a crucial but unknown role in the insect germline (Amukamara et al. 2020; Arsala et al. 2021; Bewick et al. 2019; Schulz et al. 2018; Ventós-Alfonso et al. 2020; Washington et al. 2020).
2023-03-23 | GSE182212 | GEO
Project description:Genomic DNA from 191 asy1/+ Col x Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Lawrence et al, 2019 Current Biology). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3 (Bethesda); Yelina et al, 2015 Genes & Dev; Lawrence et al, 2019 Current Biology).
2020-05-18 | E-MTAB-8725 | biostudies-arrayexpress
Project description:In recent years, several small molecule cytotoxic drugs have been identified as potential inhibitors of ribosome biogenesis (Drygin et al., 2011; Peltonen et al., 2014a; Peltonen et al., 2014b). CX-5461 is one such drug that has also demonstrated anticancer potential for a wide range of malignancies (Bywater et al., 2012; Cornelison et al., 2017; Devlin et al., 2015; Drygin et al., 2011; Hald et al., 2019; Hein et al., 2017; Ismael et al., 2019; Lawrence et al., 2018; Lee et al., 2017; Negi and Brown, 2015; Taylor et al., 2019; Xu et al., 2017; Yan et al., 2017) (Haddach et al., 2012), and is presently under phase I trials for the treatment of both hematological cancers and solid tumours (Group, 2016; Khot et al., 2019). CX-5461 was initially characterized as an inhibitor of RNA Polymerase I (RPI/PolR1/PolI) that is responsible for the synthesis of the major ribosomal RNAs and the initial step in ribosome biogenesis (Drygin et al., 2011). Since RPI and its corresponding core transcription factors are dedicated to this task alone, they present ideal molecular targets by which to modulate ribosome biogenesis. However, the specificity of CX-5461 has been questioned and it has been suggested that this drug may also act by stabilizing DNA G-quadruplexes or by “poisoning” topoisomerase II (Topo II). Thus, the primary target of this drug and its mode of action are still in doubt. Here we used Deconvolution-ChIP-Seq in NIH3T3 and HEK293T cells treated for different times with CX-5461. The data show that the primary target of CX5461 is the initiation of ribosomal RNA gene (rDNA) transcription. CX-5461 blocks transcription initiation in vitro and in vivo by arresting RNA polymerase I (RPI/Pol1) within the preinitiation complex. In contrast to previous suggestions, CX-5461 does not effect recruitment of the TBP-TAF complex SL1 to the rDNA promoter, the recruitment of the initiation competent RPI-Rrn3 complex or ongoing transcription elongation, arguing against a role for G-quadruplex stabilization or topoisomerase II poisoning. Inhibition of transcription by CX-5461 is not reversible, the RPI-Rrn3 complex remains arrested in the preinitiation complex even after drug removal. This leads to nucleolar stress, extensive DNA damage and cell senescence. Our data show that the cytotoxicity of CX-5461 is the downstream result of the highly specific inhibition of rDNA transcription. The observation that this inhibition is irreversible will be important for the future design of chemotherapeutic strategies and the avoidance of drug resistance.
2021-04-07 | E-MTAB-9242 | biostudies-arrayexpress