Results 61 to 70 of about 928,240 (334)

Genomic location analysis by ChIP‐Seq [PDF]

Journal of Cellular Biochemistry, 2009
AbstractThe interaction of a multitude of transcription factors and other chromatin proteins with the genome can influence gene expression and subsequently cell differentiation and function. Thus systematic identification of binding targets of transcription factors is key to unraveling gene regulation networks.
Artem, Barski, Keji, Zhao
openaire   +2 more sources

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

BMC Bioinformatics, 2018
Background Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcript, is introduced to prepare ...
Dejian Zhao, Deyou Zheng
doaj   +1 more source

diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. [PDF]

PLoS ONE, 2013
ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs.
Li Shen, Ning-Yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J Nestler   +5 more
doaj   +1 more source

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions. [PDF]

, 2015
BackgroundCTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation.ResultsHere we show that these two ...
Boukaba, Abdelhalim, Espinoza, Celso A, Kang, Sungyun, Kosaka-Suzuki, Natsuki, Lobanenkov, Victor V, Loukinov, Dmitri, Méndez-Catalá, Claudia Fabiola, Nagarajan, Vijayaraj, Pugacheva, Elena M, Rasko, John EJ, Ren, Bing, Rivero-Hinojosa, Samuel, Robinson, Susan, Strunnikov, Alexander V, Suzuki, Teruhiko, Ye, Zhen   +15 more
core   +3 more sources

LSD1-mediated enhancer silencing attenuates retinoic acid signalling during pancreatic endocrine cell development. [PDF]

, 2020
Developmental progression depends on temporally defined changes in gene expression mediated by transient exposure of lineage intermediates to signals in the progenitor niche.
Benner, Christopher W, Geusz, Ryan J, Harrington, Austin R, Jhala, Ulupi S, Matta, Ileana, Patel, Nisha A, Rosenfeld, Michael G, Sander, Maike, Shih, Hung-Ping, Vinckier, Nicholas K, Wang, Allen, Wang, Jianxun, Wang, Jinzhao, Wetton, Nichole, Wortham, Matthew   +14 more
core   +2 more sources

ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates

bioRxiv, 2020
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the primary protocol for detecting genome-wide DNA-protein interactions, and therefore a key tool for understanding transcriptional regulation.
Rhys Newell, Richard Pienaar, Brad Balderson, M. Piper, Alexandra Essebier, M. Bodén   +5 more
semanticscholar   +1 more source

Computational methodology for ChIP‐seq analysis [PDF]

Quantitative Biology, 2013
Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP‐seq) is a powerful technology to identify the genome‐wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChIP‐seq to unravel the transcriptional and epigenetic regulatory mechanisms,
Hyunjin, Shin, Tao, Liu, Xikun, Duan, Yong, Zhang, X Shirley, Liu   +4 more
openaire   +2 more sources

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

Nucleic Acids Res., 2017
With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as ...
Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, B. Ballester   +4 more
semanticscholar   +1 more source

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis [PDF]

, 2016
BACKGROUND: There has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized ...
Mark Bieda, Nathan Cormier, Tyler Kolisnik   +2 more
core   +1 more source

Diversity and complexity in neural organoids

FEBS Letters, EarlyView.
Neural organoid research aims to expand genetic diversity on one side and increase tissue complexity on the other. Chimeroids integrate multiple donor genomes within single organoids. Self‐organising multi‐identity organoids, exogenous cell seeding, or enforced assembly of region‐specific organoids contribute to tissue complexity.
Ilaria Chiaradia, Madeline A. Lancaster
wiley   +1 more source