Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq

An IntronicFlk1Enhancer Directs Arterial-Specific Expression via RBPJ-Mediated Venous RepressionHighlights

(2016) Philipp W. Becker et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation

(2016) Lauren Waldron et al.   DEVELOPMENTAL CELL

Genome-wide compendium and functional assessment of in vivo heart enhancers

(2016) Diane E. Dickel et al.   Nature Communications

Coronary risk in relation to genetic variation in MEOX2 and TCF15 in a Flemish population

(2015) Wen-Yi Yang et al.   BMC GENETICS

Meox2/Tcf15 Heterodimers Program the Heart Capillary Endothelium for Cardiac Fatty Acid Uptake

(2015) G. Coppiello et al.   CIRCULATION

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

A microfluidic device for epigenomic profiling using 100 cells

(2015) Zhenning Cao et al.   NATURE METHODS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

(2015) Nergiz Dogan et al.   Epigenetics & Chromatin

Novel regulators of endothelial barrier function

(2014) Dolly Mehta et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

An arterial-specific enhancer of the human endothelin converting enzyme 1 (ECE1) gene is synergistically activated by Sox17, FoxC2, and Etv2

(2014) Ashley S. Robinson et al.   DEVELOPMENTAL BIOLOGY

Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis

(2014) Margaret Buckingham et al.   DEVELOPMENTAL CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease

(2014) Aibin He et al.   Nature Communications

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

(2014) William C. Gasper et al.   Scientific Reports

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

ETS Factors Regulate Vegf-Dependent Arterial Specification

(2013) Joshua D. Wythe et al.   DEVELOPMENTAL CELL

Molecular Signatures of Tissue-Specific Microvascular Endothelial Cell Heterogeneity in Organ Maintenance and Regeneration

(2013) Daniel J. Nolan et al.   DEVELOPMENTAL CELL

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity

(2013) B. Zhang et al.   GENOME RESEARCH

Analysis of Dll4 regulation reveals a combinatorial role for Sox and Notch in arterial development

(2013) N. Sacilotto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification

(2013) P. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Accumulation of the Inner Nuclear Envelope Protein Sun1 Is Pathogenic in Progeric and Dystrophic Laminopathies

(2012) Chia-Yen Chen et al.   CELL

PRC2 directly methylates GATA4 and represses its transcriptional activity

(2012) A. He et al.   GENES & DEVELOPMENT

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies

(2012) E. H. Bresnick et al.   NUCLEIC ACIDS RESEARCH

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Ets1 and Ets2 are required for endothelial cell survival during embryonic angiogenesis

(2009) G. Wei et al.   BLOOD

DLL1-mediated Notch activation regulates endothelial identity in mouse fetal arteries

(2009) I. Sorensen et al.   BLOOD

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

TFCat: the curated catalog of mouse and human transcription factors

(2009) Debra L Fulton et al.   GENOME BIOLOGY

Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors

(2008) Sarah De Val et al.   CELL

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL

Quantitative Control of Adaptive Cardiac Hypertrophy by Acetyltransferase p300

(2008) Jian Qin Wei et al.   CIRCULATION

Reassessment of Isl1 and Nkx2-5 cardiac fate maps using a Gata4-based reporter of Cre activity

(2008) Qing Ma et al.   DEVELOPMENTAL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY