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Omics score: 1000

Single GAM datasets collected with one nuclear profile each (samples failing QC)

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000 (Mus musculus)

ORGANISM(S): Mus Musculus

SUBMITTER: Robert A Beagrie

PROVIDER: GSE166377 | GEO | 2022-06-13

REPOSITORIES: GEO

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Multiplex GAM datasets collected with an average of three nuclear profiles each (samples failing QC)

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

Multiplex GAM datasets collected with an average of three nuclear profiles each

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.

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Single GAM datasets collected with one nuclear profile each (samples failing QC)

Project description:Single GAM datasets collected with one nuclear profile each (samples failing QC)

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Single (1 NP) GAM datasets collected from mouse ES cells

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 each containing a single nuclear profiles from mouse embryonic stem (mES) cells.

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Multiplex GAM datasets collected with an average of three nuclear profiles each (samples failing QC)

Project description:Multiplex GAM datasets collected with an average of three nuclear profiles each (samples failing QC)

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Multiplex GAM datasets collected with an average of three nuclear profiles each

Project description:Multiplex GAM datasets collected with an average of three nuclear profiles each

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Single and Multiplex GAM datasets from mouse ES cells

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."

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Project description:Single (1 NP) GAM datasets collected from mouse ES cells

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The Gam protein of bacteriophage Mu is an orthologue of eukaryotic Ku.

Project description:Mu bacteriophage inserts its DNA into the genome of host bacteria and is used as a model for DNA transposition events in other systems. The eukaryotic Ku protein has key roles in DNA repair and in certain transposition events. Here we show that the Gam protein of phage Mu is conserved in bacteria, has sequence homology with both subunits of Ku, and has the potential to adopt a similar architecture to the core DNA-binding region of Ku. Through biochemical studies, we demonstrate that Gam and the related protein of Haemophilus influenzae display DNA binding characteristics remarkably similar to those of human Ku. In addition, we show that Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae. These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved.

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Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.

Project description:Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled, framework against known 3D structures of polymer models of murine and human loci, which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed fluorescence in situ hybridization (FISH) single-molecule conformations. We find that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D structures whereas single-cell data reflect strong variability among single molecules. The minimal number of cells required in replicate experiments to return statistically similar contacts is different across the technologies, being lowest in SPRITE and highest in GAM under the same conditions. Noise-to-signal levels follow an inverse power law with detection efficiency and grow with genomic distance differently among the three methods, being lowest in GAM for genomic separations >1 Mb.

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