The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE213150 | GEO | 2023/04/28
REPOSITORIES: GEO
Similar Datasets
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.
2023-04-28 | GSE213151 | GEO
Project description:The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]
| PRJNA879346 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-04-24 | GSE213152 | GEO
Project description:Introduction: CUT&RUN (Cleavage Under Targets and Release Using Nuclease) followed by next-generation sequencing is a powerful method increasingly used in place of ChIP-seq to profile genome-wide protein-DNA interactions including those of transcription factors, histone modifications and chromatin remodelers. Although the choice of antibody is well known to affect data quality, we found that enrichment chemistry and protocol significantly affect data quality as well. Methods: In this study, we evaluated the performance of three commercially available CUT&RUN kits (Active Motif - ChIC/CUT&RUN Assay Kit, Cell Signaling Technology (CST) – CUT&RUN Assay Kit, EpiCypher - CUTANA™ ChIC/CUT&RUN Kit) on two target histone marks to represent sharp peaks (H3K4me3) and broad domains (H3K27me3). ATAC-seq data was integrated to assess the accuracy of peaks generated with each CUT&RUN kit.
2026-05-15 | GSE306141 | GEO
Project description:Introduction: CUT&RUN (Cleavage Under Targets and Release Using Nuclease) followed by next-generation sequencing is a powerful method increasingly used in place of ChIP-seq to profile genome-wide protein-DNA interactions including those of transcription factors, histone modifications and chromatin remodelers. Although the choice of antibody is well known to affect data quality, we found that enrichment chemistry and protocol significantly affect data quality as well. Methods: In this study, we evaluated the performance of three commercially available CUT&RUN kits (Active Motif - ChIC/CUT&RUN Assay Kit, Cell Signaling Technology (CST) – CUT&RUN Assay Kit, EpiCypher - CUTANA™ ChIC/CUT&RUN Kit) on two target histone marks to represent sharp peaks (H3K4me3) and broad domains (H3K27me3). We compared data quality from libraries generated with fresh and frozen cells as well as with cell numbers that represent the low and high ends of the recommended input. Results and Discussion: Our results show that all three chemistries generate high-quality libraries. Our data revealed that despite generating libraries with fewer H3K4me3 peaks than the EpiCypher and Active Motif workflows did, the CST protocol generated libraries with superior signal and higher accuracy. Compared with the H3K4me3 libraries, the H3K27me3 libraries presented a lower percentage of shared peaks across all libraries and lower reproducibility between technical replicates. Compared with the CST protocol, the Active Motif and EpiCypher protocols generated H3K27me3 libraries with higher peak numbers, and the EpiCypher chemistry scored highest in accuracy. Libraries from cryopreserved cells generated data of similar quality as libraries from fresh cells; libraries generated with 100,000 cells had higher concordance between technical replicates than did libraries made with 500,000 cells.
2026-05-15 | GSE306233 | GEO
Project description:Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has rapidly gained prominence as an effective approach for mapping protein-DNA interactions, especially histone modifications, offering substantial improvements over conventional chromatin immunoprecipitation sequencing (ChIP-seq). However, the effectiveness of this technique is contingent upon accurate peak identification, necessitating the use of optimal peak calling methods tailored to the unique characteristics of CUT&RUN data. Here, we benchmark four prominent peak calling tools - MACS2, SEACR, GoPeaks, and LanceOtron - evaluating their performance in identifying peaks from CUT&RUN datasets. Our analysis utilizes in-house data of three histone marks (H3K4me3, H3K27ac, and H3K27me3) from mouse brain tissue, as well as samples from the 4DNucleome database. We systematically assess these tools based on parameters such as the number of peaks called, peak length distribution, signal enrichment, and reproducibility across biological replicates. Our findings reveal substantial variability in peak calling efficacy, with each method demonstrating distinct strengths in sensitivity, precision, and applicability depending on the histone mark in question. These insights provide a comprehensive evaluation that will assist in selecting the most suitable peak caller for high-confidence identification of regions of interest in CUT&RUN experiments, ultimately enhancing the study of chromatin dynamics and transcriptional regulation.
2025-06-02 | GSE282809 | GEO
Project description:Taf4b-deficient male mice are initially sub-fertile and become infertile due to a depletion of the spermatogonial stem cell (SSC) reserve. During embryonic time points, significantly reduced numbers of germ cells have been observed in the Taf4b-deficient male gonad and previous research has shown that Taf4b mRNA expression peaks at E15.5. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates cell cycle and SSC gene programs. However, the direct targets of TAF4b have not been thoroughly explored. Therefore, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in E16.5 mouse prospermatogonia.
2023-10-04 | GSE188701 | GEO
Project description:We used single-nucleus multiomic sequencing (snRNA-seq + snATAC-seq) to analyze the dynamic transcriptional regulation in mouse substantia nigra cell types across aging.
2025-12-03 | GSE267831 | GEO
Project description:Endosperm is an essential seed tissue with a unique epigenetic landscape. During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. Profiling the endosperm epigenetic landscape on a genome-wide scale is challenging due to its small size, mode of development, and close association with maternal tissue. Here, we applied a low input chromatin profiling method, CUT&RUN (cleavage under targets and release using nuclease), to profile parental-specific chromatin modifications using low numbers of Arabidopsis endosperm nuclei. We demonstrate that CUT&RUN generates genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility using around 20,000 endosperm nuclei purified by flow cytometry and fluorescence-activated cell sorting. H3K27me3 peaks identified by CUT&RUN and previous ChIP (chromatin immunoprecipitation) approaches were largely overlapping, with some distinctions in heterochromatin. The versatility and simplicity of CUT&RUN makes it a viable alternative to ChIP, which requires greater amounts of starting material, and will enable the study of tissue or even cell-type specific epigenomes in Arabidopsis and other plant species.
2019-02-22 | GSE123602 | GEO
Project description:While comparative genetic analysis has been performed between distinct regions of the embryonic forebrain, a comprehensive characterization of differential epigenomic organization has not been performed. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a ‘ground truth’ epigenomic landscape at this critical stage of neurogenesis.
2022-07-01 | GSE201400 | GEO