Results 21 to 30 of about 45,113 (260)

Analysis and Visualization of Spatial Transcriptomic Data [PDF]

Frontiers in Genetics, 2022
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of spatial information.
Boxiang Liu, Yanjun Li, Liang Zhang
openaire   +4 more sources

A unified pipeline for FISH spatial transcriptomics [PDF]

Cell Genomics, 2023
Abstract In recent years, high-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and the effects it may have on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write
Cecilia Cisar, Nicholas Keener, Mathew Ruffalo, Benedict Paten   +3 more
openaire   +3 more sources

Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning

Nature Communications, 2022
Multi-view graph approaches could enhance the analysis of tissue heterogeneity in spatial transcriptomics. Here, the authors develop the Spatial Transcriptomics data analysis by Multiple View Collaborative-learning - stMVC - framework, and apply it to ...
Chunman Zuo, Yijian Zhang, Chen Cao, Jinwang Feng, Mingqi Jiao, Luonan Chen   +5 more
doaj   +1 more source

WEST is an ensemble method for spatial transcriptomics analysis

Cell Reports: Methods
Summary: Spatial transcriptomics is a groundbreaking technology, enabling simultaneous profiling of gene expression and spatial orientation within biological tissues.
Jiazhang Cai, Huimin Cheng, Shushan Wu, Wenxuan Zhong, Guo-Cheng Yuan, Ping Ma   +5 more
doaj   +1 more source

MUSTANG: Multi-sample spatial transcriptomics data analysis with cross-sample transcriptional similarity guidance

Patterns
Summary: Spatially resolved transcriptomics has revolutionized genome-scale transcriptomic profiling by providing high-resolution characterization of transcriptional patterns.
Seyednami Niyakan, Jianting Sheng, Yuliang Cao, Xiang Zhang, Zhan Xu, Ling Wu, Stephen T.C. Wong, Xiaoning Qian   +7 more
doaj   +1 more source

A Meta-Review of Spatial Transcriptomics Analysis Software

Cells
Spatial transcriptomics combines gene expression data with spatial coordinates to allow for the discovery of detailed RNA localization, study development, investigating the tumor microenvironment, and creating a tissue atlas.
Jessica Gillespie, Maciej Pietrzak, Min-Ae Song, Dongjun Chung   +3 more
doaj   +1 more source

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues

BMC Genomics, 2020
Background Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on the distribution, heterogeneity and
Emelie Berglund, Sami Saarenpää, Anders Jemt, Joel Gruselius, Ludvig Larsson, Ludvig Bergenstråhle, Joakim Lundeberg, Stefania Giacomello   +7 more
doaj   +1 more source

Sampling and ranking spatial transcriptomics data embeddings to identify tissue architecture

Frontiers in Genetics, 2022
Spatial transcriptomics is an emerging technology widely applied to the analyses of tissue architecture and corresponding biological functions. Substantial computational methods have been developed for analyzing spatial transcriptomics data.
Yu Lin, Yu Lin, Yan Wang, Yan Wang, Yanchun Liang, Yanchun Liang, Yang Yu, Jingyi Li, Qin Ma, Fei He, Dong Xu   +10 more
doaj   +1 more source

Advances in spatial transcriptomics and its applications in cancer research

Molecular Cancer
Malignant tumors have increasing morbidity and high mortality, and their occurrence and development is a complicate process. The development of sequencing technologies enabled us to gain a better understanding of the underlying genetic and molecular ...
Yang Jin, Yuanli Zuo, Gang Li, Wenrong Liu, Yitong Pan, Ting Fan, Xin Fu, Xiaojun Yao, Yong Peng   +8 more
doaj   +1 more source

Transferrin receptor 1‐mediated iron uptake supports thermogenic activation in human cervical‐derived adipocytes

FEBS Letters, EarlyView.
In this study, we found that human cervical‐derived adipocytes maintain intracellular iron level by regulating the expression of iron transport‐related proteins during adrenergic stimulation. Melanotransferrin is predicted to interact with transferrin receptor 1 based on in silico analysis.
Rahaf Alrifai, Mizuki Seo, Gyath Karadsheh, Fachrur Rizal Mahendra, Máté Á Demény, Ferenc Győry, János András Mótyán, László Fésüs, Endre Kristóf, Rini Arianti   +9 more
wiley   +1 more source