Transformer and graph variational autoencoder to identify microenvironments: A deep learning protocol for spatial transcriptomics [0.03%]
基于深度学习的空间转录组数据分析微环境的变换器和图变分自动编码器模型
Karla Paniagua,Yufei Huang,Shou-Jiang Gao et al.
Karla Paniagua et al.
We present transformer and graph variational autoencoder to identify microenvironments (TG-ME), a computational framework that integrates transformer and graph variational autoencoders to dissect spatial niches using spatial transcriptomics...
Protocol for quantifying coccidian parasite mechanics and rupture force using advanced micromanipulation-based piercing [0.03%]
一种使用高级微操作穿刺技术量化球虫寄生虫力学和破裂力的协议
Jana El Husseiny,Pierre-Henri Puech,Aurélien Dumètre et al.
Jana El Husseiny et al.
Coccidian parasites can rely on their mechanical properties to infect their hosts. Here, we detail a microindentation-based technique for quantifying the wall mechanics of coccidian oocysts. We describe steps for micropipette fabrication, c...
Protocol for co-culture of primary neurons and organotypic hippocampal brain slices from mice [0.03%]
小鼠原代神经元和组织型海马脑切片共培养协议
Linlin Zhou,Qihui Wu
Linlin Zhou
Here, we present a protocol for establishing a co-culture system combining organotypic hippocampal slices with primary mouse neurons to model neuronal interactions. We describe steps for preparing hippocampal slices by whole-brain dissectio...
Protocol for screening anti-amyloidogenic compounds in cultured mammalian cells [0.03%]
在培养的哺乳动物细胞中筛选抗淀粉样蛋白生成化合物的方法
Emma Lacroix,Sandra Keerthisinghe,Evgenia A Momchilova et al.
Emma Lacroix et al.
A functional form of amyloid aggregate can be rapidly induced by various environmental stressors, yielding subnuclear structures called amyloid bodies (A-bodies). Here, we describe a cell-based high-throughput assay to identify anti-amyloid...
Protocol for in vitro phagocytosis assay for primary mouse microglia and human embryonic stem cell-derived microglia [0.03%]
小胶质细胞和人胚胎干细胞衍生的小胶质细胞的体外吞噬试验方案
Beika Zhu,Alicia L Thurber,Xianhua Piao
Beika Zhu
Microglia, the resident immune cells of the brain, maintain brain health by clearing detrimental debris, including amyloid-β (Aβ). Here, we present a protocol for assessing Aβ uptake by primary mouse microglia and human embryonic stem ce...
Protocol for developing a mouse model of gastric cancer following Helicobacter pylori eradication and chronic ethanol feeding [0.03%]
幽门螺旋杆菌根除联合慢性乙醇喂养的小鼠胃癌发生模型构建方案
Faisal Aziz,Zigang Dong
Faisal Aziz
Helicobacter pylori (H. pylori) infection drives gastric cancer through chronic inflammation. Here, we present a protocol for establishing a mouse model that induces persistent gastritis and tumorigenesis through chronic ethanol feeding aft...
Protocol to analyze changes in hippocampal neural stem cell quiescence from single-cell RNA sequencing data [0.03%]
单细胞RNA测序数据用于分析海马神经干细胞静息状态变化的流程图
Jessica Hart,Lachlan Harris
Jessica Hart
Here, we present a protocol to isolate mouse hippocampal neural stem cells from single-cell RNA sequencing datasets using a computational approach. We describe steps to analyze whether a perturbation affects quiescence depth. Specifically, ...
Protocol to establish rice root aphid colonies and experiments in greenhouse settings [0.03%]
在温室环境中建立水稻根蚜种群和进行实验的方法
Nuris M Acosta,Jonathan Lee-Rodriguez,Luis Canas
Nuris M Acosta
The rice root aphid (RRA) Rhopalosiphum rufiabdominalis (Sasaki) is a cosmopolitan species that attacks the root system of many plants grown in fields and greenhouses, including hydroponic production systems. Here, we present a protocol to ...
Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst [0.03%]
高密度多电极阵列神经生理数据增强分析的NiceSpike和SpikeNburst协议
Robert Wolff,Alessia Polito,Alessio Paolo Buccino et al.
Robert Wolff et al.
High-density multi-electrode arrays enable the recording of in vitro neuronal activity with exceptional spatial and temporal resolution. Here, we describe a protocol for analyzing these extensive datasets by using two complementary tools. T...
Protocol to investigate gene expression heterogeneity in cyanobacteria using mRNA CARD-FISH [0.03%]
使用mRNA CARD-FISH研究蓝藻基因表达异质性的方案
Anxhela Hania,Louison Dufour,Ondřej Prášil et al.
Anxhela Hania et al.
Here, we present a protocol for visualizing gene expression in the filamentous cyanobacterium Trichodesmium and the single-celled species Synechocystis and Cyanothece using the catalyzed reporter deposition fluorescence in situ hybridizatio...