Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9218086_1.fastq.gz | Fastqsanger.gz | |||
| SRR9218086_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping
2007-01-24 | GSE5773 | GEO
Project description:To investiage the ability of positve inotropism from myocardial Rad reduction we induced Rad knockout after onset of pressure overload to reverse or compensate progression of heart failure
2024-09-01 | GSE220640 | GEO
Project description:One of the most recognizable physiological phenomena is the adrenergic-induced fight-or-flight increase in heart rate and cardiac contraction. For the β-adenergic agonist-induced enhancement of calcium influx and transients, and contractility in the heart, we identify the dual requirement of a subpopulation of Rad-bound calcium channels under basal conditions and PKA phosphorylation of Rad. In mice expressing a non-phosphorylatable Rad mutant, basal cardiac contractility is reduced and adrenergic-augmentation of the calcium current and contractility are disabled. Expression of mutant calcium channel β-subunits that cannot bind the mutant Rad restored contractility, revealing a highly specific therapeutic approach to mimic the contractility imparted by adrenergic agonists. Our findings place Rad and its modulation of calcium channels at the nexus of adrenergic modulation of cardiac responses.
2022-03-20 | GSE198903 | GEO
Project description:Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. The effector protein of retron 78, ptuAB, specifically degraded tRNATyr leading abortive infection, but phage countervailed this defense by supplying tRNATyr. Rad inhibited retron function by degrading noncoding RNA, the precursor of msDNA. In summary, we demonstrated that viruses encode at least two independent strategies for overcoming bacterial defense systems: anti-defense, such as Rad, and defense canceler, like tRNA.
2024-10-10 | GSE256078 | GEO
Project description:Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. The effector protein of retron 78, ptuAB, specifically degraded tRNATyr leading abortive infection, but phage countervailed this defense by supplying tRNATyr. Rad inhibited retron function by degrading noncoding RNA, the precursor of msDNA. In summary, we demonstrated that viruses encode at least two independent strategies for overcoming bacterial defense systems: anti-defense, such as Rad, and defense canceler, like tRNA.
2024-10-10 | GSE256077 | GEO
Project description:Fight-or-flight responses involve β-adrenergic-induced increases in heart rate and contractile force. Despite decades of investigations, predominantly focusing on ryanodine receptor and phospholamban phosphorylation, the molecular mechanisms underlying the sympathetic nervous system control of cardiac contractility remain controversial and incompletely elucidated. Here, we identify the calcium-channel inhibitor Rad as a critical component. In cardiomyocytes isolated from knock-in mice expressing Rad with alanine-substitutions of the four PKA-phosphorylated serine residues (4SA-Rad), calcium currents cannot be increased by adrenergic agonists or phosphatase inhibitor. In these mice, basal cardiac contractility, exercise capacity and heart rate are reduced, and the augmentation of contractile force by adrenergic agonists is severely blunted. Expression of mutant calcium-channel β-subunits that cannot bind Rad is sufficient to restore calcium influx and cardiac contractility in 4SA-Rad mice to levels induced by adrenergic agonists in wild-type mice, revealing a potential therapeutic approach to enhance cardiac contractility while bypassing stimulation of adrenergic receptors.
2022-09-26 | PXD033492 | Pride
Project description:Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) provides an accurate way to depict the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. Here, we develop and validate Cellformer, a novel deep learning method, that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enhances the bulk ATAC-seq resolution and allows an efficient cell type specific open chromatin profiling on large size cohorts at a low cost. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms and putative mediators involved in resilient to Alzheimer’s disease (RAD), an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer’s disease (AD). Cell type-resolved chromatin profiling unveils cell type specific pathways and nominates potential epigenetic mediators underlying RAD that may illuminate therapeutic opportunities to limit the cognitive impact of this highly prevalent yet incurable disease. Cellformer has been made freely and publicly available to advance analysis of high-throughput bulk ATAC-seq in future investigations.
2023-07-20 | GSE226529 | GEO
Project description:Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. The effector protein of retron 78, ptuAB, specifically degraded tRNATyr leading abortive infection, but phage countervailed this defense by supplying tRNATyr. Rad inhibited retron function by degrading noncoding RNA, the precursor of msDNA. In summary, we demonstrated that viruses encode at least two independent strategies for overcoming bacterial defense systems: anti-defense, such as Rad, and defense canceler, like tRNA.
2025-06-01 | GSE259275 | GEO
Project description:We hypothesised that induction of a torpor-like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis, a torpor-like state was induced in zebrafish using melatonin treatment and cold temperatures, and radiation exposure was administered twice over the course of 10 days. The protective effects of induced-torpor were assessed via RNA sequencing of mRNA extracted from the liver. A systems-level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation (28.5-rad), temperature+melatonin (18.5-mel), temperature+radiation (18.5-rad), and temperature+melatonin+radiation (18.5-mel-rad) groups compared with a control group (28.5-Ctrl). The results revealed that the torpor group experiences a reduction in metabolic genes, and increased pro-survival, antiapoptotic and DNA repair genes. The radiation group had changes to lipid metabolism and absorptions, a wound healing response and an immune response. While the induced torpor group showed a response to stress including changes to metabolism and perturbation of the circadian rhythm, it also maintained the pro-survival, anti-apoptotic and DNA repair genes seen in the torpor group suggesting a conferred radio-protective effect.
2023-01-25 | GSE200212 | GEO
Project description:Single cell RNA-seq was conducted on embryonic brains from wild-type CD1 mice at embryonic day 15.5 following The Illumina® Bio-Rad® SureCell Single-Cell RNA Sequencing workflow. Four cell captures and sequencing runs were conducted with four to eight fetal brains used for each collection. For each brain, the cerebral cortex was dissected and collected (although ventral forebrain structures, especially the gonglionic eminence may be mixed in due to difficulty in dissection).
2020-07-01 | GSE143949 | GEO