Multiplex GAM datasets collected with an average of three nuclear profiles each (samples failing QC)
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PROVIDER: PRJNA700652 | ENA |
REPOSITORIES: ENA
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Project description:Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. We developed multiplex-GAM, a faster and more affordable version of Genome Architecture Mapping (GAM), a ligation-free technique to map chromatin contacts genome-wide. We applied multiplex-GAM to Mouse ES cells. Overall design: This series contains multiplex-GAM samples containing an average of three nuclear profiles from mouse embryonic stem (mES) cells that failed our QC checks.
2022-06-13 | GSE166379 | GEO
Project description:Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. We applied the original GAM protocol to Mouse ES cells to generate a deeper dataset for comparison to Hi-C. Overall design: This series contains GAM samples with a single nuclear profile from mouse embryonic stem (mES) cells that failed our QC checks.
2022-06-13 | GSE166377 | GEO
Project description:Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. We developed multiplex-GAM, a faster and more affordable version of Genome Architecture Mapping (GAM), a ligation-free technique to map chromatin contacts genome-wide. We applied multiplex-GAM to Mouse ES cells. Overall design: This series contains multiplex-GAM samples each containing an average of three nuclear profiles from mouse embryonic stem (mES) cells.
2022-06-13 | GSE166380 | GEO
Project description:Single GAM datasets collected with one nuclear profile each (samples failing QC)
| PRJNA700650 | ENA
Project description:Multiplex GAM datasets collected with an average of three nuclear profiles each
| PRJNA700651 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below. Overall design: Refer to individual Series Processed data files included at the foot of this record: gam_contact_matrices_40kb.tar.gz - "GAM normalised linkage (Dprime) matrices at 40kb resolution." slice_interaction_matrices_40kb.tar.gz - "SLICE prominent interaction matrices (thresholded at p<=0.05) at 40kb resolution."
2022-06-13 | GSE166381 | GEO
Project description:With respect to molecular switches, initializing the quadricyclane (QC) to norbornadiene (NBD) back-reaction by light is highly desirable. Our previous publication provided a unique solution for this purpose by utilizing covalently bound C<sub>60</sub> . In this work, the fundamental processes within these hybrids has been investigated. Variation of the linker unit connecting the NBD/QC moiety with the fullerene core is used as a tool to tune the properties of the resulting hybrids. Utilizing the Prato reaction, two unprecedented NBD/QC - fullerene hybrids having a long-rigid and a short-rigid linker were synthesized. Molecular dynamics simulations revealed that this results in an average QC-C<sub>60</sub> distance of up to 14.2 Å. By comparing the NBD-QC switching of these derivatives with the already established one having a flexible linker, valuable mechanistic insights were gained. Most importantly, spatial convergence of the QC moiety and the fullerene core is inevitable for an efficient back-reaction.
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Project description:24 hours following transfection with either a control mix, a construct overexpressing GAM or siRNAs directed against GAM (siGAM), THP-1 cells were challenged with LPS 100 ng/ml. RNAs were analyzed after 6 hours of LPS challenge
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Project description:<h4>Background</h4>In recent years more than 20 assemblers have been proposed to tackle the hard task of assembling NGS data. A common heuristic when assembling a genome is to use several assemblers and then select the best assembly according to some criteria. However, recent results clearly show that some assemblers lead to better statistics than others on specific regions but are outperformed on other regions or on different evaluation measures. To limit these problems we developed GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus (called blocks) are identified through reads' alignments and stored in a weighted graph. The merging phase is carried out with the help of this weighted graph that allows an optimal resolution of local problematic regions.<h4>Results</h4>GAM-NGS has been tested on six different datasets and compared to other assembly reconciliation tools. The availability of a reference sequence for three of them allowed us to show how GAM-NGS is a tool able to output an improved reliable set of sequences. GAM-NGS is also a very efficient tool able to merge assemblies using substantially less computational resources than comparable tools. In order to achieve such goals, GAM-NGS avoids global alignment between contigs, making its strategy unique among other assembly reconciliation tools.<h4>Conclusions</h4>The difficulty to obtain correct and reliable assemblies using a single assembler is forcing the introduction of new algorithms able to enhance de novo assemblies. GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best tool. In this context we propose a tool that improves assemblies (and, as a by-product, perhaps even assemblers) by merging them and selecting the generating that is most likely to be correct.
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Project description:The Gam protein of transposable phage Mu is an ortholog of eukaryotic and bacterial Ku proteins, which carry out nonhomologous DNA end joining (NHEJ) with the help of dedicated ATP-dependent ligases. Many bacteria carry Gam homologs associated with either complete or defective Mu-like prophages, but the role of Gam in the life cycle of Mu or in bacteria is unknown. Here, we show that MuGam is part of a two-component bacterial NHEJ DNA repair system. Ensemble and single-molecule experiments reveal that MuGam binds to DNA ends, slows the progress of RecBCD exonuclease, promotes binding of NAD+-dependent Escherichia coli ligase A, and stimulates ligation. In vivo, Gam equally promotes both precise and imprecise joining of restriction enzyme-digested linear plasmid DNA, as well as of a double-strand break (DSB) at an engineered I-SceI site in the chromosome. Cell survival after the induced DSB is specific to the stationary phase. In long-term growth competition experiments, particularly upon treatment with a clastogen, the presence of gam in a Mu lysogen confers a distinct fitness advantage. We also show that the role of Gam in the life of phage Mu is related not to transposition but to protection of genomic Mu copies from RecBCD when viral DNA packaging begins. Taken together, our data show that MuGam provides bacteria with an NHEJ system and suggest that the resulting fitness advantage is a reason that bacteria continue to retain the gam gene in the absence of an intact prophage.
| S-EPMC6294893 | BioStudies