Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA671638 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.
2022-02-10 | GSE165217 | GEO
Project description:We recently introduced CUT&Tag, an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei, and then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds DNA sequencing adapters (“tagmentation”) for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses exposure artifacts to ensure high-fidelity mapping of the antibody-targeted protein and improves signal-to-noise over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube from cells to amplified libraries, providing low-cost high-resolution genome-wide chromatin maps. By simplifying library preparation, CUT&Tag requires less than a day at the bench from live cells to sequencing-ready barcoded libraries. Because of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for ~$25 per sample, enabling routine genome-wide profiling of chromatin proteins and modifications that requires no special skills or equipment.
2020-07-15 | GSE145187 | GEO
Project description:Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing precipitation-based methods. The efficiency of the method enabled chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution high-throughput single-cell chromatin profiling. We describe a pipeline for single-cell indexed CUT&Tag (sciCUT&Tag) that uses SNPs to facilitate doublet-cell removal and minimize batch effects. We illustrate the optimized protocol by analysis of mouse and human cell lines, as well as human peripheral blood mononuclear cells. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.
2023-07-13 | GSE224579 | GEO
Project description:Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed transposase-tethering chromatin profiling strategy for small samples and single cells. Previously, we showed that activation of tethered Tn5 transposase under low-salt conditions using antibodies that target promoters and enhancers produces high-resolution genome-wide chromatin accessibility maps. Here we show that low-salt CUT&Tag using a mixture of an antibody to the initiation form of RNA Polymerase II (Pol2 Serine-5 phosphate) and an antibody to repressive Polycomb domains (H3K27me3) followed by computational signal deconvolution produces efficient high-resolution maps of both the active and repressive regulomes. We have extended this CUT&Tag2for1 method to single cells using a novel deconvolution approach, thus producing high-quality multifactorial single-cell chromatin maps with a workflow that is identical to that for standard single-cell CUT&Tag. The ability to seamlessly map both the active and repressive regulatory elements in single cells provides a complete regulome profiling strategy suitable for high-throughput single-cell platforms.
2022-02-14 | GSE183032 | GEO
Project description:Targeted epigenomic profiling methods CUT&RUN and CUT&Tag were used to examine TASOR genome binding and TASOR-regulated H3K9me3 deposition on chromatin.
2020-08-05 | GSE155693 | GEO
Project description:Methods derived from CUT&RUN and CUT&Tag enable genome-wide mapping of the localization of proteins on chromatin from as few as one cell. These and other mapping approaches focus on one protein at a time, preventing direct measurements of co-localization of different chromatin proteins in the same cells and requiring prioritization of targets where samples are limiting. Here we describe multi-CUT&Tag, an adaptation of CUT&Tag that overcomes these hurdles by using antibody-specific barcodes to simultaneously map multiple proteins in the same cells. Highly specific multi-CUT&Tag maps of histone marks and RNA Polymerase II uncovered sites of co-localization in the same cells, active and repressed genes, and candidate cis-regulatory elements. Single-cell multi-CUT&Tag profiling facilitated identification of distinct cell types from a mixed population and inference of cell type-specific gene expression. In sum, multi-CUT&Tag increases the “per cell” information content of epigenomic maps, facilitating direct analysis of the interplay of different proteins on chromatin.
2021-09-06 | GSE171554 | GEO
Project description:Here we describe successful implementation of CUT&Tag for profiling protein-DNA interactions in zebrafish embryos. We optimized CUT&Tag protocol to generate high resolution maps of enrichment for the histone variant H2A.Z during zebrafish development. We were able to establish dynamics of H2A.Z genomic patterning from shield stage to 24hpf embryos. Our work demonstrates the power of combining CUT&Tag with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.
2022-02-15 | GSE178559 | GEO
Project description:Genome-wide profiling of chromatin modifications by Cleavage Under Targets and Tagmentation (CUT&Tag) assay in Lu134A, a SCLC-A cell line.
2022-07-17 | GSE185083 | GEO
Project description:Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag
| PRJNA738523 | ENA
Project description:Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag
| PRJNA739658 | ENA