Results 121 to 130 of about 186,580 (246)

stMixer for Scalable Mosaic Integration and Label Transfer in Spatial Histology and Multi‐Omics

Advanced Science, EarlyView.
stMixer is an unsupervised framework for scalable integration and label transfer across spatial histology and multi‐slide multi‐omics data with incomplete modality overlap. It combines self‐looped cross‐attention, multimodal metric learning, and graph‐guided cluster voting to align heterogeneous sections, correct batch effects, and propagate ...
Qixing Yang, Yan Wang, Luonan Chen, Chunman Zuo   +3 more
wiley   +1 more source

Integrative ATAC-seq and RNA-seq analysis of myogenic differentiation of ovine skeletal muscle satellite cell.

Genomics
Skeletal muscle satellite cells (SMSCs) play an important role in regulating muscle growth and regeneration. Chromatin accessibility allows physical interactions that synergistically regulate gene expression through enhancers, promoters, insulators, and ...
Yingxiao Su, Siqi He, Qian Chen, Hechun Zhang, Chang Huang, Qianjun Zhao, Y. Pu, Xiao-hong He, Lin Jiang, Yuehui Ma, Qianjun Zhao   +10 more
semanticscholar   +1 more source

Accurately Deciphering Tissue Heterogeneity From Spatial Multi‐Modal and Multi‐Omics With STransformer

Advanced Science, EarlyView.
STransformer is a unified deep learning framework designed to seamlessly accommodate a comprehensive landscape of spatial data. By simultaneously capturing short‐range cellular interactions and tissue‐wide semantic patterns, it extracts robust representations to accurately dissect complex tissue heterogeneity.
Xingyi Li, Jialuo Xu, Gaoyuan Du, Xiangting Jia, Dongmin Zhao, Chunyan Zhou, Kexin Xiao, Jia Gu, Junnan Zhu, Xuequn Shang   +9 more
wiley   +1 more source

Integrative analysis based on ATAC-seq and RNA-seq reveals a novel oncogene PRPF3 in hepatocellular carcinoma

Clinical Epigenetics
Assay of Transposase Accessible Chromatin Sequencing (ATAC-seq) is a high-throughput sequencing technique that detects open chromatin regions across the genome.
Yi Bai, Xiyue Deng, Dapeng Chen, Shuangqing Han, Zijie Lin, Zhongmin Li, W. Tong, Jinming Li, Tianze Wang, Xiangyu Liu, Zirong Liu, Zilin Cui, Yamin Zhang   +12 more
semanticscholar   +1 more source

Cholesterol‐Mediated Metabolic‐mechanotransductive Crosstalk Orchestrates Castration Resistance in Prostate Cancer

Advanced Science, EarlyView.
Full androgen deprivation (FAD) induces paracrine cholesterol in prostate cancer that drives the polarization of cancer‐associated fibroblasts (CAFs) and subsequent elevated matrix stiffness. Matrix stiffness in turn potentiates tumor cell survival under FAD pressure via dual mechanotransductive activation of the IRE1α‐XBP1s stress‐response axis ...
Shaojie Liu, Chao Xu, Jun Jiang, Limin He, Yike Zhou, Zhengxuan Li, Yu Li, Keying Zhang, Fa Yang, Tong Lu, Hongtao Song, Hai Zhu, Zhihao Hu, Xiaolong Zhao, Kai Gan, Hongji Li, Bo Yang, Rui Zhang, Weihong Wen, Donghui Han, Weijun Qin   +20 more
wiley   +1 more source

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9

Scientific Reports, 2017
ATAC-seq is a high-throughput sequencing technique that identifies open chromatin. Depending on the cell type, ATAC-seq samples may contain ~20–80% of mitochondrial sequencing reads. As the regions of open chromatin of interest are usually located in the
Lindsey Montefiori, Liana Hernandez, Zijie Zhang, Yoav Gilad, Carole Ober, Gregory Crawford, Marcelo Nobrega, Noboru Jo Sakabe   +7 more
doaj   +1 more source

NAD+ Metabolism Licenses Zygotic Genome Activation via PARP7‐Mediated ADP‐Ribosylation of UHRF1 in Mouse Early Embryos

Advanced Science, EarlyView.
This study uncovers a metabolic‐epigenetic axis licensing zygotic genome activation (ZGA) in mouse embryos. A developmental decline in NAD+ levels activates PARP7, which mono‐ADP‐ribosylates and stabilizes UHRF1. This modification promotes the establishment of permissive histone acetylation marks, thereby facilitating timely ZGA.
Guangyi Cao, Ziqi Zhang, Anqi Chen, Yanbo Liu, Yuling Lin, Lina Yu, Ruixin Shi, Aolei Guo, Yan Mao, Ganggui Lou, Chaojun Li, Luhong Wen, Guijun Yan, Haixiang Sun   +13 more
wiley   +1 more source

ATAC-seq protocol v1

ATAC-seq protocol for ESC-DE differentiation
Renhe Luo, Michael Beer, Danwei Huangfu
openaire   +1 more source

Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

eLife
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement represents a ...
Aurélie Anne-Gaëlle Gabriel, Julien Racle, Maryline Falquet, Camilla Jandus, David Gfeller   +4 more
doaj   +1 more source

Integrative Omics Analysis Reveals the Regulation of Hypoxia Tolerance in Large Yellow Croaker (Larimichthys crocea) via the Lipoic Acid Synthase (lias) Gene

Advanced Science, EarlyView.
Lipoic acid synthase (lias) can regulate α‐KG levels through lipoylation, thereby negatively regulating HIF‐1α protein levels via PHD under hypoixa. The Hap2 allele of lias exhibits lower expression levels than Hap1, leading to the accumulation of more HIF‐1α protein and thereby enhancing hypoxia tolerance. ABSTRACT Hypoxia stress seriously affects the
Jie Ding, Songpeng Jia, Ran Meng, Xuelei Wang, Xiongfei Wu, Weiliang Shen, Yibo Zhang, Junquan Zhu   +7 more
wiley   +1 more source