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Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (Dnase-Seq)

ABSTRACT: DHS enahncers to identify novel pathways in OB differentiation

ORGANISM(S): Homo sapiens

PROVIDER: GSE75231 | GEO | 2016/02/20

SECONDARY ACCESSION(S): PRJNA302853

REPOSITORIES: GEO

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Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (Dnase-Seq)

Project description:DHS enahncers to identify novel pathways in OB differentiation We examined DHS identified enhancers and promoters during OB differentiation

2016-02-20 | E-GEOD-75231 | biostudies-arrayexpress

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (microarray)

Project description:DHS enahncers identify novel pathways in OB differentiation We examined gene expression and compared to DHS on promoters and enhancers during OB differentiation

2016-02-20 | E-GEOD-75230 | biostudies-arrayexpress

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (microarray)

Project description:DHS enahncers identify novel pathways in OB differentiation

2016-02-20 | GSE75230 | GEO

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation.

Project description: Not available

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Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-20 | E-GEOD-75232 | biostudies-arrayexpress

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-02-20 | GSE75232 | GEO

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

Project description:DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional regulatory elements and the state of chromatin in mammalian cells1, 2, 3. Conventional DNase sequencing (DNase-seq) for genome-wide DHSs profiling is limited by the requirement of millions of cells4, 5. Here we report an ultrasensitive strategy, called single-cell DNase sequencing (scDNase-seq) for detection of genome-wide DHSs in single cells. We show that DHS patterns at the single-cell level are highly reproducible among individual cells. Among different single cells, highly expressed gene promoters and enhancers associated with multiple active histone modifications display constitutive DHS whereas chromatin regions with fewer histone modifications exhibit high variation of DHS. Furthermore, the single-cell DHSs predict enhancers that regulate cell-specific gene expression programs and the cell-to-cell variations of DHS are predictive of gene expression. Finally, we apply scDNase-seq to pools of tumour cells and pools of normal cells, dissected from formalin-fixed paraffin-embedded tissue slides from patients with thyroid cancer, and detect thousands of tumour-specific DHSs. Many of these DHSs are associated with promoters and enhancers critically involved in cancer development. Analysis of the DHS sequences uncovers one mutation (chr18: 52417839G>C) in the tumour cells of a patient with follicular thyroid carcinoma, which affects the binding of the tumour suppressor protein p53 and correlates with decreased expression of its target gene TXNL1. In conclusion, scDNase-seq can reliably detect DHSs in single cells, greatly extending the range of applications of DHS analysis both for basic and for translational research, and may provide critical information for personalized medicine. Exploring the landscape of chromatin accessibility in single cells and clinical samples

2015-11-25 | E-GEOD-61844 | biostudies-arrayexpress

Genes differentially expressed during early osteoblast (OB) differentiation

Project description:RNA-seq analysis was performed to identify early OB-regulating genes in C3H10T1/2 MSCs.

2021-03-20 | GSE169224 | GEO

Signaling and transcriptional regulation in osteoblast commitment and differentiation.

Project description: Not available

| S-EPMC3571113 | biostudies-literature

DNase IM-bM-^@M-^Shypersensitive exons colocalize with promoters and distal regulatory elements

Project description:Native-ChIP was performed to determine whether cross-linked ChIP-Seq enrichments observed at DHS exons result from co-precipitation with proximal promoter. Native ChIP-Seq was performed on H3K4me3 and H3K27me3 histone modifications in human cells

2013-06-01 | E-GEOD-46945 | biostudies-arrayexpress

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