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A topological atlas reveals layers of genome reorganization in colorectal cancer

ABSTRACT: A topological atlas reveals layers of genome reorganization in colorectal cancer

PROVIDER: PRJNA553150 | ENA |

REPOSITORIES: ENA

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A topological atlas reveals layers of genome reorganization in colorectal cancer

Project description:To understand how nuclear architecture is altered in cancer, we profiled genome topology along with DNA methylation, chromatin modifications and the DNA binding factors CTCF in primary colon tumors, normal colon and colon cancer cell lines.

2020-08-24 | GSE133928 | GEO

A Transcriptomic Atlas of Mouse Neocortical Layers

Project description:In the mammalian cortex, neurons and glia form a patterned structure across six layers whose complex cytoarchitectonic arrangement likely contributes greatly to cognitive abilities. We sequenced transcriptomes from layers 1-6b of the adult (P56) mouse primary somatosensory cortex, along with dorsal cortex and lateral cortex, to understand the transcriptional levels and functional repertoires of coding and noncoding loci for cells that constitute these layers. 5,835 protein-coding genes and 66 noncoding RNA loci are differentially expressed (patterned) across the layers, based on a machine-learning model (naive Bayes) approach. Layers 2-6b are each associated with specific functional and disease annotations that provide insights into their biological roles. This new resource greatly extends currently available resources, such as the Allen Mouse Brain Atlas and microarray data sets, by providing quantitative expression levels, by being genome-wide, by including novel loci, and by identifying alternatively spliced transcripts that are differentially expressed across layers.

2011-08-24 | GSE27243 | GEO

A single cell atlas of MMRd and MMRp colorectal cancer

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A single cell atlas of MMRd and MMRp colorectal cancer

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Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation

Project description:The 3D organization of the genome is important for regulation of diverse nuclear processes ranging from transcription to DNA replication. Knowledge of the higher order chromatin structure is critical for understanding mechanisms of gene regulation by long-range control elements such as enhancers and insulators. We describe high resolution, genome-wide dynamic chromatin interaction maps in human embryonic stem cells (hESC) as they differentiate into four distinct embryonic cell lineages. Extensive reorganization of higher-order chromatin structure occurs during hESC differentiation. In this process, topological domains remain largely intact but inter-domain association patterns change dramatically, coincident with widespread changes in chromatin state and gene expression. Moreover, using proximity ligation sequencing to generate chromosome span haplotypes, widespread allele biased gene activities are detected. The allelic gene expression patterns can be correlated to epigenetic state at distal enhancers, supporting the role of these elements in regulating gene expression over a distance. Two biological replicates of Hi-C experiment and one replicate of CTCF ChIP-Seq experiment in embryonic stem cells and 4 other differentiated cell-types from H1 cell line. Re-analysis of data from GSE16256 in an allele specific manner is linked as supplementary data.

2015-02-18 | E-GEOD-52457 | biostudies-arrayexpress

Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas

Project description:Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas

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Cohesin causes replicative DNA damage by trapping DNA topological stress

Project description:DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae we demonstrate that centromeric DNA and the rDNA array are especially vulnerable to DNA topological stress during replication. The activity of the SMC complexes cohesin and condensin are linked to both the generation and repair of DNA topological stress linked damage in these regions. At cohesin enriched centromeres cohesin activity causes the accumulation of DNA damage, RF rotation and precatenation, confirming that cohesin dependent DNA topological stress impacts on normal replication progression. In contrast, at the rDNA cohesin and condensin activity inhibit the repair of damage caused by DNA topological stress. We propose that as well as generally acting to ensure faithful genetic inheritance, SMCs can disrupt genome stability by trapping DNA topological stress.

2020-03-03 | GSE131558 | GEO

A transcriptomic atlas of mouse neocortical layers.

Project description: Not available

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Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin

Project description:Human skin provides both physical integrity and immunological protection from the external environment, using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combined advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantified 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe here the quantitative distribution of structural proteins, known and novel proteins specific to cellular subsets and those with specialized immunological funtions such as cytokines and chemokines. We anticipate this proteomic atlas of human skin will become an essential community resource for basic and translational research (www.skin.science).

2020-11-18 | PXD019909 | Pride

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