Efficient low-cost chromatin profiling with CUT&Tag

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

(2019) Marlies E. Oomen et al.   GENOME RESEARCH

Profiling of Pluripotency Factors in Single Cells and Early Embryos

(2019) Sarah J. Hainer et al.   CELL

Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded

(2019) Michael P. Meers et al.   MOLECULAR CELL

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

(2019) Michael P. Meers et al.   Epigenetics & Chromatin

XL-DNase-seq: improved footprinting of dynamic transcription factors

(2019) Kyu-Seon Oh et al.   Epigenetics & Chromatin

Improved CUT&RUN chromatin profiling tools

(2019) Michael P Meers et al.   eLife

Profiling chromatin states using single-cell itChIP-seq

(2019) Shanshan Ai et al.   NATURE CELL BIOLOGY

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

(2019) Qianhao Wang et al.   MOLECULAR CELL

Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP

(2019) Tõnis Org et al.   PLoS One

Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)

(2019) Benjamin Carter et al.   Nature Communications

Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch

(2018) Nan Liu et al.   CELL

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

(2018) Peter J Skene et al.   Nature Protocols

Reprogramming human T cell function and specificity with non-viral genome targeting

(2018) Theodore L. Roth et al.   NATURE

A chromatin integration labelling method enables epigenomic profiling with lower input

(2018) Akihito Harada et al.   NATURE CELL BIOLOGY

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

(2018) Derek H. Janssens et al.   Epigenetics & Chromatin

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

A simple method for generating high-resolution maps of genome-wide protein binding

(2015) Peter J Skene et al.   eLife

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Impact of sequencing depth in ChIP-seq experiments

(2014) Youngsook L. Jung et al.   NUCLEIC ACIDS RESEARCH

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

(2012) S. G. Landt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS