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The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

ABSTRACT: The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

PROVIDER: PRJNA879346 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21530802_1.fastq.gz	Fastqsanger.gz
	SRR21530802_2.fastq.gz	Fastqsanger.gz
	SRR21530803_1.fastq.gz	Fastqsanger.gz
	SRR21530803_2.fastq.gz	Fastqsanger.gz
	SRR21530804_1.fastq.gz	Fastqsanger.gz

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The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

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The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses

Project description:The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses

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The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [multi-omics]

Project description:We performed single nucleus RNA sequencing (snRNA-seq) and assay for transposase-accessible chromatin with sequencing (snATAC-seq) to map the epigenetic and gene expression signatures of human kidney organoids during the organoid differentiation time course.

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The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [multi-omics]

Project description:The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [multi-omics]

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Cleavage under targets and release using nuclease (CUT&RUN) sequencing for HNF4A in human adult kidney and kidney organoid-derived proximal tubular cells

Project description:We performed CUT&RUN sequencing to characterize HNF4A binding sites in human adult kidney and kidney organoid-derived proximal tubular cells.

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Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [single-nucleus CUT&RUN]

Project description:Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [single-nucleus CUT&RUN]

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Single nucleus RNA-seq, ATAC-seq, and multiomic sequencing of adult human kidney

Project description:In this study, we generated a single nucleus multiomic (snRNA-seq and snATAC-seq) dataset of adult human kidney. We developed a bioinformatic tool to analyze this dataset by identifying key cis-regulatory elements and transcription factors associated with specific cell types and states. We applied this tool to identify transcription factors implicated in proximal tubule cell injury and failed repair states. We demonstrate this tool can be applied to single cell multiomic datasets to derive insight into cell type- and state-specific gene regulatory networks.

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Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [single-nucleus CUT&RUN]

Project description:Single-cell RNA sequencing (scRNA-seq) has proven to be an invaluable tool for the study of tumor evolution. However, interrogating regulatory epigenetic alterations during cancer progression at the resolution of single-cells has remained a major challenge due to the lack of sensitivity of current assays. Here, we developed the highly-sensitive single-nucleus CUT&RUN (snCUT&RUN) assay to profile histone modifications in primary, metastatic, and cisplatin-resistant head and neck squamous cell carcinoma (HNSCC) patient-derived cell lines. We find that the epigenome can employ diverse modes to contribute towards cancer progression. Notably, we demonstrate that gene expression changes during cancer progression are co-modulated by alterations in both copy number and chromatin activity to drive epigenetic rewiring of cell-states. Furthermore, intratumor epigenetic heterogeneity may predispose sub-clonal populations within the primary tumor to acquire malignant characteristics. In conclusion, snCUT&RUN serves as a valuable addition to existing toolkit of single-cell assays to dissect the function of the epigenome during cancer progression.

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Project description:COVID-19 is a systemic disease involving multiple organs. Human pluripotent stem cells (hPSCs) derived organoids/cells provide insight into cellular tropism and host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here, we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different MOIs for airway organoids (AWOs), alveolar organoids (ALOs) and cardiomyocytes (CMs), and identified several genes, including CIART, that are generally implicated in controlling SARS-CoV-2 infection. AWOs, ALOs, and CMs derived from isogenic CIART-/- hPSCs were significantly resistant to SARS-CoV-2 infection, independent of viral entry. Single-cell RNA-seq further validated the decreased levels of SARS-CoV-2 infection in multi-ciliated cells of AWOs. CUT&RUN, ATAC-seq and RNA-seq analyses found that CIART controls SARS-CoV-2 infection at least in part through regulating NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition revealed that the Retinoid X Receptor (RXR) pathway regulates SARS-CoV-2 infection downstream of CIART/NR4A1. The multi-organoid platform provides potential therapeutic targets for protection against COVID-19 across organ systems.

2022-12-07 | GSE202966 | GEO

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