Results 111 to 120 of about 186,580 (246)

A rapid and robust method for single cell chromatin accessibility profiling

Nature Communications, 2018
ATAC-seq is widely used to identify regulatory regions in the genome. Here the authors develop a simple and robust plate-based single-cell ATAC-seq method that works in fresh and cryopreserved cells.
Xi Chen, Ricardo J. Miragaia, Kedar Nath Natarajan, Sarah A. Teichmann   +3 more
doaj   +1 more source

Combining Spatial Multi‐Omics Data to Decipher Spatial Domains and Elucidate Cell Heterogeneity Based on Self‐Supervised Graph Learning

Advanced Science, EarlyView.
A self‐supervised multi‐view graph fusion framework integrates spatial multi‐omics, excelling in domain identification and denoising. It reconstructs spatial pseudo‐expression, jointly analyzes multi‐omics data, infers RNA velocity, predicts spatial omics features from single‐cell multi‐omics, and detects spatially dark genes and transcription factors,
Yuejing Lu, Rui Qiao, Ying Li, Junhong Li, Nuoya Yue, Jing Ge, Jiao Wang, Luonan Chen, Peiluan Li   +8 more
wiley   +1 more source

Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data

Genomics, Proteomics & Bioinformatics
Efficient and reliable profiling methods are essential to study epigenetics. Tn5, one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency, is widely adopted in different genomic and epigenomic protocols for ...
Siyuan Cheng, Benpeng Miao, Tiandao Li, Guoyan Zhao, Bo Zhang   +4 more
semanticscholar   +1 more source

Master Regulator SMC1A, Stabilized by N6‐Methyladenosine Reader IGF2BP1, Promotes HCC Progression Through Facilitating Enhancer–Promoter Interaction of Nestin

Advanced Science, EarlyView.
IGF2BP1‐mediated m6A stabilization sustains SMC1A expression, enabling cohesin‐associated chromatin regulation of Nestin in hepatocellular carcinoma. This work reveals an epitranscriptomic‐chromatin‐cytoskeletal regulatory axis linked to malignant phenotypes and identifies SMC1A as a biologically relevant vulnerability in HCC.
Zhenxiang Peng, Diguang Wen, Lu Zeng, Lin Lv, Shengtao Liao, Wenguang Zhang, Zhechuan Mei, Chuanfei Li   +7 more
wiley   +1 more source

txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

Genome Biology
We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction.
Hao Zhang, Ryan M. Mulqueen, N. Iannuzo, Dominique O. Farrera, F. Polverino, James J. Galligan, Julie G. Ledford, Andrew C. Adey, Darren A. Cusanovich   +8 more
semanticscholar   +1 more source

PlantGFM: A Genomic Foundation Model for Discovery and Creation of Plant Genes

Advanced Science, EarlyView.
A plant genomic foundation model pre‐trained on 12 species enables both accurate gene prediction and de novo gene design. Through AI‐human knowledge screening, seven designed sequences showed transcriptional activity in plants, with two expressing stable proteins—demonstrating the first DNA‐RNA‐protein expression of LLM‐generated genes in plants and ...
Changhao Li, Qizhe Zhang, Hanchen Chen, Kepeng Lin, Chengfang Luo, Mengying Yang, Wei Xu, Fan Yao, Jianbing Yan, Qing‐Yong Yang, Xuehai Hu   +10 more
wiley   +1 more source

Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq

, 2023
AbstractOpen or accessible chromatin typifies euchromatic regions and helps define cell type-specific transcription programs. DNA replication massively disorders chromatin composition and structure, and how accessible regions are affected by and recover from this disruption has been unclear.
Stewart-Morgan, Kathleen R., Groth, Anja
openaire   +4 more sources

Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls

Nature Communications
Amyotrophic Lateral Sclerosis (ALS), like many other neurodegenerative diseases, is highly heritable, but with only a small fraction of cases explained by monogenic disease alleles.
Stanislav Tsitkov, Kelsey Valentine, Velina Kozareva, Aneesh Donde, Aaron Frank, Susan Lei, Michael J. Ryan G. Jie Zhuoxing Loren Lindsay Erick Daniel Workman Lim Wu Wu Ornelas Panther Galvez Perez Mee, Michael J. Workman, Ryan G. Lim, Jie Wu, Zhuoxing Wu, L. Ornelas, Lindsay Panther, Erick Galvez, Daniel Perez, Imara Meepe, Viviana Valencia, Emilda Gomez, Chunyan Liu, Ruby Moran, L. Pinedo, Richie Ho, J. Kaye, T. Thompson, Dillon Shear, Robert H. Baloh, M. Banuelos, Veronica Garcia, Ronald Holewenski, Oleg A. Karpov, Danica-Mae Manalo, B. Mandefro, Andrea D. Matlock, Rakhi Pandey, N. Sundararaman, H. Trost, V. Vaibhav, Vidya Venkatraman, O. Wang, Jonathan D. Glass, Arish Jamil, Naufa Amirani, Leandro Lima, Krishna Raja, W. Robinson, Reuben Thomas, Edward Vertudes, S. Wyman, Carla Agurto, Guillermo A. Cecchi, Raquel Norel, Omar Ahmad, E. Baxi, Aianna Cerezo, Alyssa N. Coyne, Lindsey Hayes, John Krakauer, Nicholas Maragakis, E. Mosmiller, Promit Roy, S. Zeiler, Miriam Adam, Noura Albistami, T. Ehrenberger, Nhan Huynh, Connie New, A. LeNail, Jonathan Li, N. Patel-Murray, Yogindra Raghav, Divya Ramamoorthy, Egun Im, K. Sachs, Brook T. Wassie, James D. Berry, M. Cudkowicz, Alanna Farrar, Sara Thrower, Sarah Luppino, Lindsay Pothier, Alexander V Sherman, E. Sinani, P. Vigneswaran, Hong Yu, J. Beavers, Mary Bellard, E. Bruce, S. Ajroud-Driss, Deniz Alibazoglu, Ben Joslin, Matthew B. Harms, S. Heintzman, Stephen J. Kolb, Carolyn Prina, D. Heitzman, Todd Morgan, Ricardo Miramontes, Jennifer T. Stocksdale, Keona Q. Wang, Jennifer Jockel-Balsarotti, Elizabeth Karanja, Jesse Markway, M. McCallum, Timothy M. Miller, J. Roggenbuck, Jennifer E Van Eyk, Steve Finkbeiner, Jeffrey D. Rothstein, Leslie M. Thompson, D. Sareen, Clive N. Svendsen, Ernest Fraenkel   +111 more
semanticscholar   +1 more source

Targeting KDM3B Elicits Anti‐tumor Immunity by Alleviating SHP1–mediated STING Suppression in Triple–Negative Breast Cancer

Advanced Science, EarlyView.
P3FI–90 treatment targets KDM3B, reshapes the epigenetic landscape, and suppresses SHP1 expression, thereby activating STING–TBK1–IRF3–type I IFN signaling pathway. Consequently, CD8+ T cells are recruited to the tumor site and activated to produce IFN–γ and GZMB, leading to the killing of TNBC cells.
Xiaolong Wang, Wenhao Li, Yifei Wang, Ning Zhang, Bing Chen, Wenjing Zhao, Lijuan Wang, Dan Luo, Qifeng Yang   +8 more
wiley   +1 more source

IGN: Invariable gene set-based normalization for chromatin accessibility profile data analysis

Computational and Structural Biotechnology Journal
Chromatin accessibility profiles generated using ATAC-seq or DNase-seq carry functional information of the regulatory genome that controls gene expression.
Shengen Shawn Hu, Hai-Hui Xue, Chongzhi Zang   +2 more
doaj   +1 more source