Results 91 to 100 of about 5,931 (188)

Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq [PDF]

, 2016
© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities.
Chang, Yiming K, Havranek, James J, Hu, Caizhen, Jauch, Ralf, Joyce, Adam, Srivastava, Yogesh, Stormo, Gary D, Yang, Xiaoxiao, Zuo, Zheng   +8 more
core   +3 more sources

Interaction of TFAP2A with the Ku70/80 complex is crucial for HIF‐dependent activation of hypoxia‐inducible genes

The FEBS Journal, Volume 292, Issue 16, Page 4333-4352, August 2025.
Under normoxic conditions, the SUMOylated fraction of TFAP2A cannot interact with the Ku70/Ku80 complex, nor it can bind to chromatin. The unSUMOylated fraction pre‐occupies the chromatin of a subset of hypoxia‐induced genes together with the Ku70/Ku80 complex for basal euchromatin formation. Under hypoxic conditions, the SUMOylation equilibrium shifts
Amalia Kanoura, Antonis Giakountis, Chrysa Filippopoulou, Angeliki Karagiota, George Stamatakis, Martina Samiotaki, George Panayotou, George Simos, Georgia Chachami   +8 more
wiley   +1 more source

Paracrine cross-talk between skeletal muscle and macrophages in exercise by PGC-1α-controlled BNP [PDF]

, 2017
Activation of resident and infiltrating immune cells is a central event in training adaptation and other contexts of skeletal muscle repair and regeneration.
Beer, Markus, Eisele, Petra S., Furrer, Regula, Handschin, Christoph, Schmidt, Alexander   +4 more
core   +1 more source

ChIPseq libraries preparation v1

ChIP-seq was performed to analyze H3K27ac and H3K27me3 in CTRL and EZH2KO UN-KC6141 cells. Cells were crosslinked, lysed, and sonicated. Chromatin was immunoprecipitated using specific antibodies and Protein G Dynabeads. Libraries were prepared on beads using the NEBNext Ultra II kit, PCR-amplified, size-selected (200–500 bp), and sequenced on HiSeq ...
Laura Antonucci, Isidoro Cobo, Christopher K. Glass, Michael Karin   +3 more
openaire   +1 more source

Systematic Evaluation of Factors Influencing ChIP-Seq Fidelity [PDF]

, 2012
We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments.
A Barski, A Mortazavi, A Valouev, AP Boyle, AR Quinlan, Barbara J Wold, DA Nix, DS Johnson, DS Johnson, E Larschan, EG Wilbanks, G Benson, G Robertson, H Ji, Housheng Hansen He, I Kozarewa, J Rozowsky, Jason D Lieb, JC Dohm, Jennifer Zieba, Joanna O Mieczkowska, JW Ho, Kevin P White, L Teytelman, Matthew Slattery, N Negre, N Negre, Nicolas Negre, NU Rashid, P Kolasinska-Zwierz, Peter J Bickel, PV Kharchenko, PV Kharchenko, Q Li, Qunhua Li, R Jothi, Richard M Myers, RM Myers, S Pepke, S Roy, SE Celniker, Tae-Kyung Kim, Tao Liu, TD Laajala, TS Mikkelsen, WE Johnson, X Feng, X Shirley Liu, Y Zhang, Y Zhang, Yijun Ruan, Yiwen Chen, Yong Zhang   +52 more
core   +4 more sources

Identifying differential transcription factor binding in ChIP-seq

Frontiers in Genetics, 2015
ChIP seq is a widely used assay to measure genome-wide protein binding. The decrease in costs associated with sequencing has led to a rise in the number of studies that investigate protein binding across treatment conditions or cell lines. In addition to
Dai-Ying eWu, Danielle eBittencourt, Michael R Stallcup, Kimberly D. Siegmund   +3 more
doaj   +1 more source

Tbr1 instructs laminar patterning of retinal ganglion cell dendrites. [PDF]

, 2018
Visual information is delivered to the brain by >40 types of retinal ganglion cells (RGCs). Diversity in this representation arises within the inner plexiform layer (IPL), where dendrites of each RGC type are restricted to specific sublaminae ...
Chen, Bin, Krishnaswamy, Arjun, Laboulaye, Mallory A, Liu, Jinyue, Pandey, Shristi, Reggiani, Jasmine DS, Rubenstein, John LR, Sanes, Joshua R   +7 more
core   +1 more source

ChIPseq analysis using deepTools and MACS

, 2016
Slides for this  training session  at the  2016 Galaxy Community Conference (GCC2016) . Did my IP work? Where is my signal? How well do my replicates correlate? What might my peaks even look like? Where are my peaks (or signal) in
openaire   +1 more source

Telomere Position Effect‐Over Long Distances Acts as a Genome‐Wide Epigenetic Regulator Through a Common Alu Element

Aging Cell, Volume 24, Issue 6, June 2025.
Proposed TPE‐OLD model. TPE‐OLD genes are defined by a progressive modulation of gene expression following telomere attrition. In our study, focusing on the molecular mechanism of TPE‐OLD, we found that the TPE‐OLD loop requires a cis‐signature corresponding to a newly evolved Alu repeats (AluY). The Alu repeat can be either in an intergenic region, as
Raphaël Chevalier, Victor Murcia Pienkowski, Nicolas Jullien, Leslie Caron, Pascal Verdier Pinard, Frédérique Magdinier, Jérôme D. Robin   +6 more
wiley   +1 more source

In silico pooling of ChIP-seq control experiments.

PLoS ONE, 2014
As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation.
Guannan Sun, Rajini Srinivasan, Camila Lopez-Anido, Holly A Hung, John Svaren, Sündüz Keleş   +5 more
doaj   +1 more source