4.8 Article

scChIX-seq infers dynamic relationships between histone modifications in single cells

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

scChIX-seq infers dynamic relationships between histone modifications in single cells

Jake Yeung et al.

Summary: scChIX-seq is a novel experimental and computational framework that allows mapping of multiple histone marks in single cells. This method enables systematic analysis of the interplay between histone modifications in individual cells.

NATURE BIOTECHNOLOGY (2023)

Article Biotechnology & Applied Microbiology

Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag

Michael P. Meers et al.

Summary: This article describes a scalable barcoding method that can measure multiple chromatin-associated proteins in single cells. The method allows for simultaneous profiling of multiple histone modifications and can be used to analyze cell types, developmental trajectories, and associations between histone marks.

NATURE BIOTECHNOLOGY (2023)

Article Biotechnology & Applied Microbiology

CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells

Derek H. Janssens et al.

Summary: CUT&Tag is a method for chromatin profiling in small samples and single cells, which allows high-resolution mapping of both active and repressive regulomes. It provides a complete profiling strategy suitable for high-throughput single-cell platforms.

GENOME BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Simultaneous profiling of multiple chromatin proteins in the same cells

Sneha Gopalan et al.

Summary: Multi-CUT&Tag allows simultaneous mapping of multiple proteins in the same cells using antibody-specific barcodes, revealing co-localization sites of histone marks and RNA Polymerase II, active and repressed genes, and candidate cis-regulatory elements. This technology aids in identifying distinct cell types and characterizing their chromatin architecture.

MOLECULAR CELL (2021)

Article Genetics & Heredity

Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia

Derek H. Janssens et al.

Summary: This study maps fusion-specific targets of KMT2A oncofusion proteins across the genome, revealing aberrant chromatin regulation induced by these fusion proteins and cell-to-cell heterogeneity at these sites, which can predict sensitivity to therapeutic agents. Automated and single-cell CUT&Tag profiling characterizes the effects of KMT2A fusion proteins on chromatin in human primary leukemia samples, identifying oncogenic networks and fusion-specific therapeutic vulnerabilities.

NATURE GENETICS (2021)

Article Biochemistry & Molecular Biology

Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing

Wai Lim Ku et al.

Summary: iscChIC-seq is a multiplex indexing method for single-cell analysis, capable of rapidly analyzing histone modifications in a large number of single cells. It successfully distinguishes different cell types within white blood cells and has the potential for broad applications.

GENOME RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression

Steven J. Wu et al.

Summary: In this study, we successfully adapted the CUT&Tag method to single-cell platforms for profiling chromatin landscapes at single-cell level. The analysis of H3K27me3 using scCUT&Tag distinguished cell types and allowed generation of cell-type-specific PcG landscapes.

NATURE BIOTECHNOLOGY (2021)

Article Biotechnology & Applied Microbiology

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

Marek Bartosovic et al.

Summary: An improved method for single-cell analysis of histone modifications was applied to the mouse brain, combining CUT&Tag technology with droplet-based single-cell library preparation to produce high-quality data. The results provided unique insights into epigenomic landscapes in the central nervous system at single-cell resolution, highlighting the potential of this method for studying chromatin modifications and transcription factor occupancy.

NATURE BIOTECHNOLOGY (2021)

Article Hematology

Regulation of RNA polymerase II activity is essential for terminal erythroid maturation

Zachary C. Murphy et al.

Summary: The terminal maturation of human erythroblasts involves significant changes in histone marks associated with active transcription elongation, rather than heterochromatin accumulation. Regulation of RNA polymerase II activity and gene expression at the transcriptional level play a critical role in controlling the maturation process of erythroblasts.

BLOOD (2021)

Article Biotechnology & Applied Microbiology

simATAC: a single-cell ATAC-seq simulation framework

Zeinab Navidi et al.

Summary: Researchers have developed a robust and systematic approach named simATAC, an R package that generates scATAC-seq count matrices resembling real datasets, to assess analytical pipelines. It deploys statistical models derived from analyzing real scATAC-seq cell groups for benchmarking in silico scATAC-seq samples with known cell labels.

GENOME BIOLOGY (2021)

Article Biochemical Research Methods

Efficient low-cost chromatin profiling with CUT&Tag

Hatice S. Kaya-Okur et al.

NATURE PROTOCOLS (2020)

Article Multidisciplinary Sciences

The single-cell transcriptional landscape of mammalian organogenesis

Junyue Cao et al.

NATURE (2019)

Article Biochemical Research Methods

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

Wai Lim Ku et al.

NATURE METHODS (2019)

Article Multidisciplinary Sciences

CUT&Tag for efficient epigenomic profiling of small samples and single cells

Hatice S. Kaya-Okur et al.

NATURE COMMUNICATIONS (2019)

Article Cell Biology

Profiling chromatin states using single-cell itChIP-seq

Shanshan Ai et al.

NATURE CELL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

Qianhao Wang et al.

MOLECULAR CELL (2019)

Article Cell Biology

A chromatin integration labelling method enables epigenomic profiling with lower input

Akihito Harada et al.

NATURE CELL BIOLOGY (2019)

Article Anatomy & Morphology

Zebrafish Rfx4 controls dorsal and ventral midline formation in the neural tube

Irina Sedykh et al.

DEVELOPMENTAL DYNAMICS (2018)

Article Biochemical Research Methods

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

Peter J. Skene et al.

NATURE PROTOCOLS (2018)

Review Immunology

Expression and Function of Tetraspanins and Their Interacting Partners in B Cells

Fagui Zou et al.

FRONTIERS IN IMMUNOLOGY (2018)

Article Multidisciplinary Sciences

RNA velocity of single cells

Gioele La Manno et al.

NATURE (2018)

Article Cell & Tissue Engineering

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

Dominic Grun et al.

CELL STEM CELL (2016)

Article Multidisciplinary Sciences

Integrative analysis of 111 reference human epigenomes

Anshul Kundaje et al.

NATURE (2015)

Article Biotechnology & Applied Microbiology

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

Assaf Rotem et al.

NATURE BIOTECHNOLOGY (2015)

Article Statistics & Probability

topicmodels: AnRPackage for Fitting Topic Models

Bettina Grün et al.

Journal of Statistical Software (2015)

Article Multidisciplinary Sciences

A comparative encyclopedia of DNA elements in the mouse genome

Feng Yue et al.

NATURE (2014)

Article Multidisciplinary Sciences

Transcriptional divergence and conservation of human and mouse erythropoiesis

Novalia Pishesha et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Chromatin state dynamics during blood formation

David Lara-Astiaso et al.

SCIENCE (2014)

Article Biochemistry & Molecular Biology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Stephen G. Landt et al.

GENOME RESEARCH (2012)

Article Genetics & Heredity

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

Eric M. Mendenhall et al.

PLOS GENETICS (2010)

Article Multidisciplinary Sciences

Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors

Jun K. Takeuchi et al.

NATURE (2009)

Article Developmental Biology

Analysis of mouse Cdh6 gene regulation by transgenesis of modified bacterial artificial chromosomes

Takayashi Inoue et al.

DEVELOPMENTAL BIOLOGY (2008)

Article Developmental Biology

Loss of both GATA4 and GATA6 blocks cardiac myocyte differentiation and results in acardia in mice

Roong Zhao et al.

DEVELOPMENTAL BIOLOGY (2008)

Review Immunology

SLP76 and SLP65: complex regulation of signalling in lymphocytes and beyond

GA Koretzky et al.

NATURE REVIEWS IMMUNOLOGY (2006)

Article Immunology

Epigenetic ontogeny of the Igk locus during B cell development

M Goldmit et al.

NATURE IMMUNOLOGY (2005)