Results 81 to 90 of about 186,580 (246)

ATAC-Seq Data for Genome-Wide Profiling of Transcription Factor Binding Sites in the Rice False Smut Fungus Ustilaginoidea virens

Molecular Plant-Microbe Interactions, 2021
Identification of transcription factor binding sites is one of the most important steps in understanding the function of transcription factors and regulatory networks in organisms. The assay for transposase accessible chromatin sequencing (ATAC-seq) is a
Xiaoyang Chen, Hao Liu, Xiaolin Chen, Junbin Huang, Tom Hsiang, Lu Zheng   +5 more
doaj   +1 more source

Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types

Nature Communications
Prioritizing disease-critical cell types by integrating genome-wide association studies (GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) have characterized cell types at ...
Samuel S. Kim, B. Truong, K. Jagadeesh, K. Dey, Amber Z Shen, Soumya Raychaudhuri, M. Kellis, Alkes L. Price   +7 more
semanticscholar   +1 more source

3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species

Advanced Science, EarlyView.
ABSTRACT Three‐dimensional (3D) chromatin architecture plays a fundamental role in eukaryotic gene regulations, its functional significance in perennial fruit trees remains poorly characterized despite extensive applications in crop genomics. Here, we developed high‐resolution (∼5 kb) Hi‐C maps of Pyrus and compared 3D genomic architecture of three ...
Yueyuan Liu, Chenhui Han, Cheng Xue, Manyi Sun, Bobo Song, Yongsong Xue, Guangyan Yang, Shaozhuo Xu, Wei Wei, Jiaming Li, Runze Wang, Jun Wu   +11 more
wiley   +1 more source

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Nature Communications, 2020
Most currently available statistical tools for the analysis of ATAC-seq data were repurposed from tools developed for other functional genomics data (e.g. ChIP-seq).
Mariano I. Gabitto, Anders Rasmussen, Orly Wapinski, Kathryn Allaway, Nicholas Carriero, Gordon J. Fishell, Richard Bonneau   +6 more
doaj   +1 more source

Deep learning-based enhancement of epigenomics data with AtacWorks

Nature Communications, 2021
ATAC-seq measures chromatin accessibility as a proxy for the activity of DNA regulatory regions across the genome. Here the authors present AtacWorks, a deep learning tool to denoise and identify accessible chromatin regions from low cell count, low ...
Avantika Lal, Zachary D. Chiang, Nikolai Yakovenko, Fabiana M. Duarte, Johnny Israeli, Jason D. Buenrostro   +5 more
doaj   +1 more source

A Toolkit for Targeted Neuromodulation of Striatal Direct Pathway Neurons Rescues Parkinsonian Motor Deficits in Mice

Advanced Science, EarlyView.
An adeno‐associated virus (AAV) toolkit enables selective anatomical and functional targeting of striatal D1‐MSNs through retrograde transduction. Enhanced capsids and engineered enhancers drive robust transgene expression across murine and primate models.
Zexuan Hong, Yujing Zhang, Junjiao Zhang, Hanhe Liu, Qiwei Liu, Yanglei Li, Lixin Yang, Lixia Li, Zhongjie Liu, Zhen Yuan, Zhonghua Lu, Yefei Chen, Yuantao Li, Yuwu Jiang, Taian Liu   +14 more
wiley   +1 more source

sci-ATAC-seq HTAN v1 [PDF]

, 2019
Single-cell combinatorial indexing ATAC-seq (Sci-ATAC-seq) workflow fro human cells/tissue. This protocol is the up-to-date Adey Lab protocol that incorporates the use of Pitstop2
Andrew Adey, Andrew Fields, Casey Th, Ryan Mulqueen, Sarah Vitak, Eleonora Juarez   +5 more
openaire   +1 more source

Detect accessible chromatin using ATAC-sequencing, from principle to applications

Hereditas, 2019
Background Chromatin accessibility is crucial for gene expression regulation in specific cells and in multiple biological processes. Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is an effective way to reveal ...
Yuanyuan Sun, Nan Miao, Tao Sun
doaj   +1 more source

A simple and robust method for simultaneous dual-omics profiling with limited numbers of cells

Cell Reports: Methods, 2021
Summary: Deciphering epigenetic regulation of gene expression requires measuring the epigenome and transcriptome jointly. Single-cell multi-omics technologies have been developed for concurrent profiling of chromatin accessibility and gene expression ...
Ruifang Li, Sara A. Grimm, Paul A. Wade
doaj   +1 more source

Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit

Frontiers in Plant Science, 2023
Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared ‘JF308’ (a normal tomato cultivar) and ‘YS006’ (a storable tomato cultivar) to determine ...
Susu Guo, Yanhai Ji, Yanyan Zheng, C. Watkins, Lili Ma, Qing Wang, Hao Liang, C. Bai, A. Fu, Ling Li, Demei Meng, Ming-chi Liu, Jinhua Zuo   +12 more
semanticscholar   +1 more source