Results 1 to 10 of about 186,580 (246)

Establishing an optimized ATAC-seq protocol for the maize

Frontiers in Plant Science
The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin
Jo-Wei Allison Hsieh, Rita Jui-Hsien Lu, Pao-Yang Chen   +2 more
exaly   +5 more sources

Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

Frontiers in Medicine, 2020
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is associated with significant progress in biological research and has attracted increasing attention.
Xianwen Zhang, Guodong Sun, Kebing Chen   +2 more
exaly   +3 more sources

Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

Nature Communications
Cis-regulatory elements (CREs) are pivotal in orchestrating gene expression throughout diverse biological systems. Accurate identification and in-depth characterization of functional CREs are crucial for decoding gene regulation networks during cellular ...
Ruitu Lyu, Yun Gao, Tong Wu, Chang Ye, Pingluan Wang, Chuan He   +5 more
doaj   +2 more sources

A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis [PDF]

Nature Communications
The rapid advancement of transposase-accessible chromatin using sequencing (ATAC-seq) technology, particularly with the emergence of single-cell ATAC-seq (scATAC-seq), accelerates the studies of gene regulation.
Qiuchen Meng, Xinze Wu, Wenchang Chen, Yubo Zhao, Chen Li, Zheng Wei, Xiaocheng Zeng, Jiaqi Li, Xi Xi, Sijie Chen, Catherine Zhang, Shengquan Chen, Jiaqi Li, Xiaowo Wang, Rui Jiang, Lei Wei, Xuegong Zhang   +16 more
doaj   +2 more sources

STAT3 Facilitates Super Enhancer Formation to Promote Fibroblast-To-Myofibroblast Differentiation by the Analysis of ATAC-Seq, RNA-Seq and ChIP-Seq. [PDF]

J Cell Mol Med
A cellular characteristic of IPF is the transformation of fibrosis into myofibroblasts. This study identifies several transcription factors—STAT3, FOXP1, JUNB, ATF3, FosL2, BATF, Fra2 and AP‐1—that play crucial roles in promoting pulmonary fibrogenesis ...
Wang Y, Zhao Y, Cao G, Jiang M, Yuan X, Li H, Song X, Zhang J, Lv C, Zhang S.   +9 more
europepmc   +2 more sources

GNNMF: a multi-view graph neural network for ATAC-seq motif finding

BMC Genomics
Background The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) utilizes the Transposase Tn5 to probe open chromatic, which simultaneously reveals multiple transcription factor binding sites (TFBSs) compared to traditional ...
Shuangquan Zhang, Xiaotian Wu, Zhichao Lian, Chunman Zuo, Yan Wang   +4 more
doaj   +2 more sources

Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq

Cell Reports, 2017
Identification of tissue-specific and developmentally active enhancers provides insights into mechanisms that control gene expression during embryogenesis.
Aurélie Quillien, Jianhong Ou, Lihua Julie Zhu   +2 more
exaly   +3 more sources

MMGAT: a graph attention network framework for ATAC-seq motifs finding

BMC Bioinformatics
Background Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene regulation.
Xiaotian Wu, Wenju Hou, Ziqi Zhao, Lan Huang, Nan Sheng, Qixing Yang, Shuangquan Zhang, Yan Wang   +7 more
doaj   +2 more sources

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

Nature Communications, 2021
Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity.
Rongxin Fang, Sebastian Preissl, Y. Li, Xiaomeng Hou, J. Lucero, Xinxin Wang, Amir Motamedi, A. Shiau, Xinzhu Zhou, Fangming Xie, E. Mukamel, Kai Zhang, Yanxiao Zhang, M. Behrens, J. Ecker, B. Ren   +15 more
semanticscholar   +1 more source

ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

Nucleic Acids Res., 2022
ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape.
Zhaonan Zou, Tazro Ohta, F. Miura, Shinya Oki   +3 more
semanticscholar   +1 more source