IPSC ATAC-seq open chromatin
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21856 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air-liquid interface (HBE-ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. Here we perform open chromatin mapping by ATAC-seq and transcriptomics by RNA-seq in parallel, to define the functional genomics of key stages of the definitive endoderm (DE) to HBE-ALI differentiation. Within open chromatin peaks the overrepresented motifs include the architectural protein CTCF at all stages, while motifs for the FOXA and GATA pioneer factors families are only seen at early stages, and those regulating key airway epithelial functions such as EHF are limited to later stages. The RNA seq data illustrate dynamic pathways during the DE to HBE-ALI differentiation and also the marked functional divergence of different iPSC lines at the ALI stages of differentiation. Moreover, a comparison of iPSC-derived and lung donor-derived HBE cultures reveals substantial differences in these culture models.
2021-01-06 | GSE136857 | GEO
Project description:We aim to profile the dynamic changes of chromatin accessibility (openness) to transcription factors during cortical neuron differentiation from human iPSCs. We used ATAC-seq to map open chromatins in iPSCs, neural stem cells (NSCs) at day 27 and day 33 of neural induction (designated as iN-d30 for simplicity), and neurons at day 41 (iN-d41). We found that there were robust dynamic changes of open chromatins that are corresponding to cell stage-specific gene function both at genome-wide level and at individual loci of interest to neurodevelopment and psychiatric disorders, with NSC (iN-d30) gaining most (89%) of the neuron specific open chromatin peaks. Open chromatin peaks shared by different cell stages were overrepresented in core promoters, while the peaks specific to each cell stage or showing dynamic change of openness were enriched in introns and intergenic sequences. The dynamic change of open chromatins is orchestrated by specific sets of transcription factors (TFs) in each cell stage, providing epigenomic support the central role of NEUROD1 and NEUROG2 in cortical neuron differentiation.
2017-07-27 | GSE70823 | GEO
Project description:Mapping open chromatin in mouse nephron progenitor cells
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Project description:Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell type-specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell type-specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell type-specific chromatin accessibility.
2017-12-23 | GSE108458 | GEO
Project description:Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell type-specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell type-specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell type-specific chromatin accessibility.
2017-12-23 | GSE108459 | GEO
Project description:Current in-vitro islet differentiation protocols suffer from heterogeneity and low efficiency. Induced-pluripotent stem cells (iPSCs) derived from pancreatic beta-cells (BiPSCs) preferentially differentiate towards endocrine pancreas-like cells versus those from fibroblasts (FiPSCs). We interrogated genome-wide open chromatin in BiPSCs and FiPSCs via ATAC-seq, and identified ~8.3k significant, differential open chromatin sites (DOCS) between the two iPSC subtypes (FDR<0.05). DOCS where chromatin was more accessible in BiPSCs (Bi-DOCS) were significantly enriched for known regulators of endodermal development, including bivalent and weak enhancers, and FOXA2 binding sites (FDR<0.05). Bi-DOCS were associated with genes related to pancreas development and beta-cell function, including transcription factors mutated in monogenic diabetes (PDX1, NKX2-2, HNF1A; FDR<0.05). Moreover, Bi-DOCS correlated with enhanced gene expression in BiPSC-derived definitive endoderm and pancreatic progenitor cells. Bi-DOCS therefore highlight genes and pathways governing islet-lineage commitment, which can be exploited for differentiation protocol optimisation, diabetes disease modelling, and therapeutic purposes.
| EGAS00001002591 | EGA
Project description:The goal of this study is to characterize interactions between accessible chromatin sites within a diverse collection of human iPSCs. Here, we generated 150 bulk ATAC-seq libraries for iPSCs from the iPSCORE collection. We identified sites of open chromatin and calculated the pairwise correlation between sites to characterize functional coordination of epigenetic modifications.
2024-01-04 | GSE203377 | GEO
Project description:The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air-liquid interface (HBE-ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. Here we perform open chromatin mapping by ATAC-seq and transcriptomics by RNA-seq in parallel, to define the functional genomics of key stages of the iPSC to HBE-ALI differentiation. Within open chromatin peaks the overrepresented motifs include the architectural protein CTCF at all stages, while motifs for the FOXA and GATA pioneer factors families are only seen at early stages, and those regulating key airway epithelial functions, such as EHF, are limited to later stages. The RNA-seq data illustrate dynamic pathways during the iPSC to HBE-ALI differentiation, and also the marked functional divergence of different iPSC lines at the ALI stages of differentiation. Moreover, a comparison of iPSC-derived and lung donor-derived HBE-ALI cultures reveals substantial differences between these models.
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Project description:We performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) using 88 tissue samples to profile open chromatin regions in the cattle genome.
2023-08-24 | E-MTAB-11825 | biostudies-arrayexpress
Project description:Here, we used Omni-ATAC-seq to identify open chromatin regions in human peripheral blood-derived MCs and tonsillar MCs
2019-03-17 | GSE125888 | GEO