Results 81 to 90 of about 176,761 (289)

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

Nrsn1–Smarcc1 Coupling Regulates Neural Stem Cell Differentiation and Chronic‐phase Recovery After Ischemic Stroke

Advanced Science, EarlyView.
In the post‐stroke brain, Foxa2 induces the transcriptional upregulation of Nrsn1 in NSCs. Nrsn1 functionally couples with Smarcc1, modulating its nuclear availability and protein abundance, thereby influencing Smarcc1‐associated regulatory programs linked to neuronal lineage commitment. Through this coupling, Nrsn1 promotes the differentiation of NSCs
Ruolin Zhang, Chang Liu, Yuneng Zhou, Kaichen Zhao, Muyang Li, Bingcheng Cai, Ying Wang, Zhiyuan Yuan, Zhaoxin Liu, Zilong Yuan, Yao Xiao, Peiyang Zhou, Ke Shui, Wendai Bao, Min Zhang, Jun Qin, Jun Chen, Xin Yang, Zhiqiang Dong   +18 more
wiley   +1 more source

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   +1 more source

Practical NicE-seq workflow for chromatin accessibility analysis in plants

Molecules and Cells
: Open chromatin profiling identifies regulatory DNA regions that are accessible to transcription factors and other proteins, offering insights into gene regulation.
Zein Eddin Bader, Nassem Albakri, Dae-Jin Yun, Young Hun Song, Junghoon Park   +4 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 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

ATAC-seq analysis in Clk^DN photoreceptors.

, 2022
A. Bar plot showing the genomic distribution of accessible peaks identified in ATAC-seq data from the indicated genotypes and ages. Promoter annotation was based on -/+ 2 kb around transcription start sites. B.
Vikki M. Weake (9268870), Kimaya Bakhle (12024874), Juan Jauregui-Lozano (12024868), Makayla M. Marlin (12024877), Sarah C. Stanhope (12024871), Hana Hall (605802)   +5 more
core   +1 more source

Transient Sleep Deprivation Induces Persistent Auditory Neuropathy via ROS‐Initiated Neuroinflammation and BK Channel Suppression

Advanced Science, EarlyView.
Sleep disturbance severity closely tracks hearing loss in a clinical cohort, yet the mechanistic link remains unclear. Acute sleep deprivation is shown to trigger transient cochlear oxidative stress that switches into a self‐sustaining neuroinflammatory state, suppressing BK channels and causing irreversible synaptopathy.
Dan Chen, Ying Ma, Lixuan Huang, Xin Chen, Fanliang Kong, Zhenzhou Qian, Mingyue Guan, Xinlin Wang, Yanyan Yang, Shasha Zhang, Peng Li, Renjie Chai   +11 more
wiley   +1 more source

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   +1 more source

ATAC-Seq Nott 19 Microglia 128 resolution bigWig

, 2023
BigWig file containing the -log10 p-value score after peak calling for the multi-sample, multi-replicate isolated microglia data from Nott et al., 2019. The data has been processed using the ATAC-Seq ENCODE protocol to obtain the bigWig file.
Alan Murphy (14408475)
core   +1 more source