Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq

(2018) Michael J Guertin et al.   NUCLEIC ACIDS RESEARCH

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies

(2018) Rohan N. Shah et al.   MOLECULAR CELL

Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing

(2016) James R. Davie et al.   Biochemistry and Cell Biology

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

Enhancer priming by H3K4 methyltransferase MLL4 controls cell fate transition

(2016) Chaochen Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape

(2016) C. Lu et al.   SCIENCE

FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3

(2016) Kamila M. Jozwik et al.   Cell Reports

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition

(2016) Brian Egan et al.   PLoS One

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide

(2015) Adrian T. Grzybowski et al.   MOLECULAR CELL

An Interactive Database for the Assessment of Histone Antibody Specificity

(2015) Scott B. Rothbart et al.   MOLECULAR CELL

LSD1-Mediated Demethylation of H3K4me2 Is Required for the Transition from Late Progenitor to Differentiated Mouse Rod Photoreceptor

(2015) Evgenya Y. Popova et al.   MOLECULAR NEUROBIOLOGY

Reproducibility crisis: Blame it on the antibodies

(2015) Monya Baker   NATURE

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally

(2015) K. Siklenka et al.   SCIENCE

Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders

(2015) Christina N Vallianatos et al.   Epigenomics

Chromatin dynamics: H3K4 methylation and H3 variant replacement during development and in cancer

(2014) Moonmoon Deb et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

(2014) N. Bonhoure et al.   GENOME RESEARCH

H3K4me2 reliably defines transcription factor binding regions in different cells

(2014) Ying Wang et al.   GENOMICS

Histone methylation and V(D)J recombination

(2014) Noriko Shimazaki et al.   INTERNATIONAL JOURNAL OF HEMATOLOGY

A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers

(2014) Jemmie Cheng et al.   MOLECULAR CELL

Regulation of histone H3K4 methylation in brain development and disease

(2014) E. Shen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Recombinant antibodies to histone post-translational modifications

(2013) Takamitsu Hattori et al.   NATURE METHODS

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

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A quantitative atlas of histone modification signatures from human cancer cells

(2013) Gary LeRoy et al.   Epigenetics & Chromatin

Macrohistone Variants Preserve Cell Identity by Preventing the Gain of H3K4me2 during Reprogramming to Pluripotency

(2013) María J. Barrero et al.   Cell Reports

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

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

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Broad Ranges of Affinity and Specificity of Anti-Histone Antibodies Revealed by a Quantitative Peptide Immunoprecipitation Assay

(2012) Shingo Nishikori et al.   JOURNAL OF MOLECULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays

(2011) Ina Bock et al.   Epigenetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Influence of Combinatorial Histone Modifications on Antibody and Effector Protein Recognition

(2010) Stephen M. Fuchs et al.   CURRENT BIOLOGY

Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore

(2010) Jan H Bergmann et al.   EMBO JOURNAL

Human LSD2/KDM1b/AOF1 Regulates Gene Transcription by Modulating Intragenic H3K4me2 Methylation

(2010) Rui Fang et al.   MOLECULAR CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

An assessment of histone-modification antibody quality

(2010) Thea A Egelhofer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Where Does Mediator Bind In Vivo?

(2009) Xiaochun Fan et al.   PLoS One

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

(2009) Leonid Teytelman et al.   PLoS One

Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia

(2008) M. G. Guenther et al.   GENES & DEVELOPMENT

Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography

(2008) Marjorie Brand et al.   Nature Protocols