IlEgiCons
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB83477 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14075527_1.fastq.gz | Fastqsanger.gz | |||
| ERR14075527_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Egira conspicillaris (silver cloud), genomic and transcriptomic data
| PRJEB83476 | ENA
Project description:The advent of single cell (Sc) genomics has challenged the dogma of haematopoiesis as a tree-like structure of stepwise lineage commitment through distinct and increasingly restricted progenitor populations. Instead, analysis of ScRNA-seq has proposed that the earliest events in human hematopoietic stem cell (HSC) differentiation are characterized by only subtle molecular changes, with hematopoietic stem and progenitor cells (HSPCs) existing as a continuum of low-primed cell-states that gradually transition into a specific lineage (CLOUD-HSPCs). Here, we combine ScRNA-seq, ScATAC-seq and cell surface proteomics to dissect the heterogeneity of CLOUD-HSPCs at different stages of human life. Within CLOUD-HSPCs, pseudotime ordering of both mRNA and chromatin data revealed a bifurcation of megakaryocyte/erythroid and lympho/myeloid trajectories immediately downstream a subpopulation with an HSC-specific enhancer signature. Importantly, both HSCs and lineage-restricted progenitor populations could be prospectively isolated based on correlation of their molecular signatures with CD35 and CD11A expression, respectively. Moreover, we describe the changes that occur in this heterogeneity as hematopoiesis develops from neonatal to aged bone marrow, including an increase of HSCs and depletion of lympho-myeloid biased MPPs. Thus, this study dissects the heterogeneity of human CLOUD-HSPCs revealing distinct HSPC-states of relevance in homeostatic settings such as ageing.
2023-09-27 | GSE173075 | GEO
Project description:We applied high throughput sequencing technology to identify microRNA genes in bighead carp and silver carp. We identified 167 conserved miRNAs in bighead carp and 166 in silver carp. By two computational stragegies, we obtained 39 novel miRNAs in bighead carp and 54 in silver carp, for which, no homologs were found in other species. Several miRNA* sequences were found in our dataset as well, some particular ones might have gene regulation function. Gain and loss of family members were observed in several miRNA families, which partially reflected the fate of miRNA gene duplicates.
2010-09-01 | GSE22232 | GEO
Project description:Silver-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering method. Briefly, genetic diversity in reference strain, CEN.PK.113-7D, was increased by ethyl methane sulfonate (EMS)-mutagenesis. The mutant population was passaged several times in gradually increasing silver stress. Several mutant individuals were selected from the final population. Among selected mutant individuals, one of them was much more resistant to silver stress than the reference strain, called as 2E. Whole-genome transcriptomic analysis was performed to identify the silver resistance mechanisms in the silver-resistant mutant strain.
2020-01-09 | GSE143335 | GEO
Project description:Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24h of exposure, but with a recovery at 48h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24h, but not at 48h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. mRNA profiles of whole zebrafish embryos at 24 and 48 hours post-fertilisation (hpf) exposed to silver in nano, bulk and ionic forms were generated by deep sequencing using HT-SuperSAGE (Illumina GA2).
2013-06-17 | E-GEOD-38125 | biostudies-arrayexpress
Project description:Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24h of exposure, but with a recovery at 48h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24h, but not at 48h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.
2013-06-17 | GSE38125 | GEO
Project description:Background: The uncontrolled and widespread use of (nano)silver compounds has led to the increased release of these compounds into the environment, raising concerns about their negative impact on ecosystems. Concomitantly, silver resistance determinants are widely spread among environmental and clinically relevant bacteria although the underlying mechanisms are not yet fully understood. Results: In this study, we show that Cupriavidus metallidurans is able to adapt to toxic silver concentrations and explicate the genetic circuit responsible for this adaptation. None of the known silver resistant determinants present in C. metallidurans are involved in the adapted response. Instead, increased silver resistance is achieved by the concerted action of a two-component system AgrR-AgrS, previously not associated with metal resistance, and two intrinsically disordered proteins PrsQ1 and PrsQ2. Both belong to an unique group of small, uncharacterized, extracellular proteins restricted to the genera Cupriavidus and Ralstonia. This system seems to be much more efficient as it gives C. metallidurans the ability to withstand much higher silver concentrations. The latter could be facilitated by the accumulation of silver ions and the formation of silver nanoparticles. Conclusions: Detailed knowledge and exploitation of this protein family could result in novel routes for metal nanoparticle formation and metal processing relevant for biotechnical and biomedical applications.
2018-12-31 | GSE107669 | GEO
Project description:Comparison of brain gene expression between silver foxes selected for tame behavior and non-selected silver fox.
2005-12-31 | E-MEXP-451 | biostudies-arrayexpress
Project description:We assessed the whole genome response of C. elegans exposed for 48 hours from L1 to the pristine silver nanomterials, artifically aged silver nanomatierls, and AgNO3.
2015-08-22 | GSE70509 | GEO