Results 21 to 30 of about 186,580 (246)

scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing

Genome Biology
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs.
Xuan Zhang, Alexandre P. Marand, Haidong Yan, Robert J. Schmitz   +3 more
doaj   +2 more sources

Successful ATAC-Seq From Snap-Frozen Equine Tissues [PDF]

Frontiers in Genetics, 2021
An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues.
Sichong Peng, Rebecca Bellone, Rebecca Bellone, Jessica L. Petersen, Theodore S. Kalbfleisch, Carrie J. Finno   +5 more
doaj   +5 more sources

A Biophysical Model for ATAC-seq Data Analysis

bioRxiv
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) can be used to identify open chromatin regions, providing complementary information to RNA-seq which measures gene expression by sequencing.
Catherine Felce, Gennady Gorin, L. Pachter   +2 more
semanticscholar   +2 more sources

A simple ATAC-seq protocol for population epigenetics [PDF]

Wellcome Open Research, 2021
We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues.
Augusto, Ronaldo de Carvalho, REY, Olivier, Cosseau, Céline, Chaparro, Cristian, Vidal-Dupiol, Jeremie, Allienne, Jean-François, Duval, David, Pinaud, Silvain, Tönges, Sina, Andriantsoa, Ranja, Luquet, Émilien, Aubret, Fabien, Dia Sow, Mamadou, David, Patrice, Thomson, Vicki, Joly, Dominique, Lima, Mariana Gomes, Federico, Déborah, Danchin, Etienne, Minoda, Aki, Grunau, Christoph   +20 more
openaire   +5 more sources

Unsupervised contrastive peak caller for ATAC-seq

Genome Research, 2023
The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing.
Ha T.H. Vu, Yudi Zhang, Geetu Tuteja, Karin Dorman   +3 more
openaire   +3 more sources

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

PLoS Computational Biology, 2023
Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular ...
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi   +14 more
doaj   +1 more source

Computational Analyses and Challenges of Single-cell ATAC-seq. [PDF]

Genomics Proteomics Bioinformatics
Abstract Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) has emerged as a powerful technique to study cell-specific epigenetic landscapes and to provide a multidimensional portrait of gene regulation. However, low genomic coverage per cell results in intrinsic data sparsity and missing-data issues,
Wang C, Zhou J, Zhang H, Zhuang Z, Bai G, Tang M, Liu S, Liu T.   +7 more
europepmc   +3 more sources

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples [PDF]

PeerJ, 2017
Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers.
Zeeshan Ahmed, Duygu Ucar
doaj   +2 more sources

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

Nature Communications, 2020
While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread ...
Mette Bentsen, Philipp Goymann, H. Schultheis, Kathrin Klee, Anastasiia Petrova, R. Wiegandt, A. Fust, J. Preussner, C. Kuenne, Thomas Braun, Johnny Kim, M. Looso   +11 more
semanticscholar   +1 more source

Modeling fragment counts improves single-cell ATAC-seq analysis

bioRxiv, 2023
This paper proposes quantitative modeling of single-cell ATAC-seq data, which improves various downstream analyses. Single-cell ATAC sequencing coverage in regulatory regions is typically binarized as an indicator of open chromatin.
Laura D. Martens, David S. Fischer, Vicente A. Yépez, F. Theis, J. Gagneur   +4 more
semanticscholar   +1 more source