Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4293390_1.fastq.gz | Fastqsanger.gz | |||
| SRR4293390_2.fastq.gz | Fastqsanger.gz | |||
| SRR4293391_1.fastq.gz | Fastqsanger.gz | |||
| SRR4293391_2.fastq.gz | Fastqsanger.gz | |||
| SRR4293392_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans. Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.
2023-06-27 | GSE229536 | GEO
Project description:Dimethyl sulfate (DMS) is a methylating reagent that has long been used to detect footprints of DNA-bound proteins in vitro as well as in vivo. Here we describe DMS-seq for in vivo genome-wide mapping of protein-DNA interactions. DMS-seq exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation, thereby simplifying the process to detect binding sites of transcription factors. Furthermore, we found that DMS preferentially attacks nucleosome centers in vivo, evidencing for DMS-seq as a first method that locates them without using genetically-modified histones and is hence applicable to any eukaryote. DMS-seq should be a simple and unique method in epigenomics.
2017-09-18 | GSE92973 | GEO
Project description:Dimethylsulfide is a volatile organic sulfur compound that provides the largest input of biogenic sulfur from the oceans to the atmosphere, and thence back to land, constituting an important link in the global sulfur cycle. Microorganisms degrading DMS affect fluxes of DMS in the environment, but the underlying metabolic pathways are still poorly understood. Methylophaga thiooxydans is a marine methylotrophic bacterium capable of growth on DMS as sole source of carbon and energy. Using proteomics and transcriptomics we identified genes expressed during growth on dimethylsulfide and methanol to refine our knowledge of the metabolic pathways that are involved in DMS and methanol degradation in this strain. Amongst the most highly expressed genes on DMS were the two methanethiol oxidases driving the oxidation of this reactive and toxic intermediate of DMS metabolism. Growth on DMS also increased expression of the enzymes of the tetrahydrofolate linked pathway of formaldehyde oxidation, in addition to the tetrahydromethanopterin linked pathway. Key enzymes of the inorganic sulfur oxidation pathway included flavocytochrome c sulfide dehydrogenase, sulfide quinone oxidoreductase, and persulfide dioxygenases. A sulP permease was also expressed during growth on DMS. Other enzymes of organic and inorganic sulfur metabolism previously detected in cell extracts of Methylophaga have not been characterised at the genetic level yet; their expression level and regulation could not be analysed. A pan-genome analysis of six available Methylophaga genomes suggests that only two of the six investigated bacteria have the metabolic potential to utilize methanethiol, the degradation product of DMS. These results mirror phenotypic analyses and demonstrate that DMS-utilization and subsequent C1 and sulfur oxidation are not conserved across the entire genus.
2019-11-12 | PXD011992 | Pride
Project description:Double minutes (DMs), a major form of gene amplification, commonly carry oncogenes or chemoresistance-related genes that are associated with the occurrence, development and prognosis of tumors. Thus, probing molecular structures of DMs allows us to further understand molecular mechanisms underlying tumorigenesis. In this study, we identified four amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716. These amplification regions localized in two populations of DMs. Through a combined analysis on the results of array CGH, high throughput sequencing, multiplex-fluorescence in situ hybridization and chromosome walking results, we constructed molecular structures of the two populations of DMs at nucleotide resolution.
2018-12-31 | GSE110070 | GEO
Project description:Double minutes (DMs), a major form of gene amplification, commonly carry oncogenes or chemoresistance-related genes that are associated with the occurrence, development and prognosis of tumors. Thus, probing molecular structures of DMs allows us to further understand molecular mechanisms underlying tumorigenesis. In this study, we identified four amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716. These amplification regions localized in two populations of DMs. Through a combined analysis on the results of array CGH, high throughput sequencing, multiplex-fluorescence in situ hybridization and chromosome walking results, we constructed molecular structures of the two populations of DMs at nucleotide resolution.
2018-12-31 | GSE110069 | GEO
Project description:Trimethylated H3K4 (H3K4me3), which is often found surrounding the transcriptional start site of active genes, is strongly enriched in the promoter regions of Myc-targeted genes. Succinate, which inhibits JmjC domain-containing histone demethylases (JHDMs), can induce H3K4me3 level of the promoter regions. It's interesting to ask whether Myc can mediate H3K4me3 by regulating cellular succinate level. Here, We used ChIP-seq to study Myc modulates H3K4me3 by altering succinate levels, dimethyl succinate (DMS), a membrane-permeable succinate analog, was introduced to treat CA46 cells with high or depleted Myc expression. And we also performed RNA-seq assays in Myc expressed or depleted CA46 cells with or without DMS treatment.
2020-03-18 | GSE141227 | GEO
Project description:Fourth-generation EGFR tyrosine kinase are in development to overcome common resistance mutations. We performed deep mutational scanning (DMS) of the EGFR kinase domain in the context of L858R by introducing a saturation library of ~17,000 variants into Ba/F3 cells. DMS library-expressing cells were exposed to osimertinib or BLU-945 to identify escape mutations. L718X mutations were enriched across all conditions. BLU-945 specific mutations included K714R, K716T, L718V, T725M, K728E, K754E/N, N771S/T, T783I, Q791L/K, G863S, S895N, K929I, and M971L. A secondary DMS screen combining osimertinib and BLU-945 exclusively enriched for L718X mutations. Clinically, L718X mutations emerged in two patients treated with BLU-945. One patient with baseline EGFR L858R and L718Q mutations experienced early progression. Another with baseline EGFR L858R, T790M, and C797S acquired an L718V mutation at progression. This study demonstrate how comprehensive resistance profiling of targeted therapies can predict clinically relevant mutations and guide rational combinations to delay or prevent resistance.
2025-08-11 | GSE305057 | GEO
Project description:Myoferlin is a transmembrane protein, encoded by the MYOF gene, initially identified in myoblasts for its crucial role in membrane biology via its C2 domain. MYOF was overexpressed in PDAC and functional studies have revealed myoferlin's critical involvement in mitochondrial adaptation, metatstasis and ferroptosis.
2025-08-28 | GSE306771 | GEO
Project description:Cardiac myosin-binding protein C (cMyBP-C) is a thick filament–associated protein that influences actin–myosin interactions. cMyBP-C alters myofilament structure and contractile properties in a protein kinase A (PKA) phosphorylation–dependent manner. To determine the effects of cMyBP-C and its phosphorylation on the microsecond rotational dynamics of actin filaments, we attached a phosphorescent probe to F-actin at Cys-374 and performed transient phosphorescence anisotropy (TPA) experiments. Binding of cMyBP-C N-terminal domains (C0-C2) to labeled F-actin reduced rotational flexibility by 20–25º, indicated by increased final anisotropy of the TPA decay. The effects of C0-C2 on actin TPA were highly cooperative (n ~ 8), suggesting that the cMyBP-C N terminus impacts the rotational dynamics of actin spanning seven monomers (i.e. the length of tropomyosin). PKA-mediated phosphorylation of C0-C2 eliminated the cooperative effects on actin flexibility and modestly increased actin rotational rates. Effects of Ser-to-Asp phosphomimetic substitutions in the M-domain of C0-C2 on actin dynamics only partially recapitulated the phosphorylation effects. C0-C1 (lacking M-domain/C2) similarly exhibited reduced cooperativity, but not as reduced as by phosphorylated C0-C2. These results suggest an important regulatory role of the M-domain in cMyBP-C effects on actin structural dynamics. In contrast, phosphomimetic substitution of the glycogen synthase kinase (GSK3beta) site in the Pro/Ala-rich linker of C0-C2 did not significantly affect the TPA results. We conclude that cMyBP-C binding and PKA-mediated phosphorylation can modulate actin dynamics. We propose that these N-terminal cMyBP-C–induced changes in actin dynamics help explain the functional effects of cMyBP-C phosphorylation on actin–myosin interactions.
2019-09-26 | PXD015391 | Pride
Project description:Cohesin subunits, the Nipped-B cohesin loader, the MED1 and MED30 subunits of the Mediator complex, and the Fs(1)h BET domain protein were mapped by ChIP-seq in ML-DmBG3-c2 cells and their effects on each other's association with promoters, enhancers, Polycomb Response Elements, and DNA replication origins were measured. DNA replication in early S phase was measured by ChIP-seq and correlated with functional element occupancy by cohesin.
2019-02-20 | GSE118484 | GEO