Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

[1]  K. Itoh,et al.  Non-coding RNA derived from the region adjacent to the human HO-1 E2 enhancer selectively regulates HO-1 gene induction by modulating Pol II binding , 2014, Nucleic acids research.

[2]  Tae-Kyung Kim,et al.  Enhancer RNA facilitates NELF release from immediate early genes. , 2014, Molecular cell.

[3]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[4]  G. Daley,et al.  Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. , 2014, Molecular cell.

[5]  Luca Pinello,et al.  Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions , 2013, Epigenetics.

[6]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[7]  R. Shiekhattar,et al.  Activating RNAs associate with Mediator to enhance chromatin architecture and transcription , 2013, Nature.

[8]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[9]  Marc D. Perry,et al.  ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.

[10]  Vijay K. Tiwari,et al.  DNA-binding factors shape the mouse methylome at distal regulatory regions , 2011, Nature.

[11]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[12]  P. Scacheri,et al.  Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. , 2011, Genome research.

[13]  M. Gut,et al.  Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters , 2011, Nature Structural &Molecular Biology.

[14]  C. Glass,et al.  Reprogramming Transcription via Distinct Classes of Enhancers Functionally Defined by eRNA , 2011, Nature.

[15]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[16]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[17]  T. Derrien,et al.  Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.

[18]  S. Orkin,et al.  Differential Roles of Sall4 Isoforms in Embryonic Stem Cell Pluripotency , 2010, Molecular and Cellular Biology.

[19]  J. Ragoussis,et al.  A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers , 2010, PLoS biology.

[20]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[21]  Jonghwan Kim,et al.  Use of in vivo biotinylation to study protein–protein and protein–DNA interactions in mouse embryonic stem cells , 2009, Nature Protocols.

[22]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[23]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[24]  A. Visel,et al.  ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.

[25]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[26]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[27]  R. Myers,et al.  An Integrated Software System for Analyzing Chip-chip and Chip-seq Data (supplementary Information) , 2008 .

[28]  K. Bomsztyk,et al.  Protocol for the fast chromatin immunoprecipitation (ChIP) method , 2006, Nature Protocols.

[29]  C. Lottaz,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .