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Protocol for differentiation of human embryonic stem cells into surface epithelium and functional keratinocytes. 人胚胎干细胞向表面上皮细胞和功能性角化细胞分化的方法。
IF 1.3
STAR Protocols Pub Date : 2025-06-27 DOI: 10.1016/j.xpro.2025.103919
Jiafeng Liu, Huaxing Huang, Hong Ouyang
{"title":"Protocol for differentiation of human embryonic stem cells into surface epithelium and functional keratinocytes.","authors":"Jiafeng Liu, Huaxing Huang, Hong Ouyang","doi":"10.1016/j.xpro.2025.103919","DOIUrl":"10.1016/j.xpro.2025.103919","url":null,"abstract":"<p><p>The normal development and function of the epidermis and other ectodermal appendages depend on the proper formation of the surface epithelium (SE). Here, we present a protocol to differentiate human embryonic stem cells (hESCs) into SE and subsequently into epidermal keratinocyte progenitors. We then detail procedures for the passage and expansion of keratinocyte progenitors, followed by 2D validation of terminal differentiation and 3D assessment of stratification potential. This protocol represents a promising advancement for stem cell-based regenerative medicine. For complete details on the use and execution of this protocol, please refer to Liu et al.<sup>1</sup> and Huang et al.<sup>2</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 3","pages":"103919"},"PeriodicalIF":1.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144529965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol to quantify energy landscape of high-dimensional oscillatory systems using diffusion decomposition. 协议量化高维振荡系统的能量景观使用扩散分解。
IF 1.3
STAR Protocols Pub Date : 2025-06-27 DOI: 10.1016/j.xpro.2025.103922
Shirui Bian, Ruisong Zhou, Wei Lin, Chunhe Li
{"title":"Protocol to quantify energy landscape of high-dimensional oscillatory systems using diffusion decomposition.","authors":"Shirui Bian, Ruisong Zhou, Wei Lin, Chunhe Li","doi":"10.1016/j.xpro.2025.103922","DOIUrl":"10.1016/j.xpro.2025.103922","url":null,"abstract":"<p><p>Here, we present a numerical framework to quantify the energy landscape of high-dimensional stochastic oscillatory systems, based on the diffusion decomposition of Gaussian approximation (DDGA). We describe steps for downloading codes, setting the oscillatory dynamics, and calculating the one-dimensional pre-solution along the limit cycle and the covariance matrix on normal planes. We then detail procedures for quantifying the global landscape through the DDGA. For complete details on the use and execution of this protocol, please refer to Bian et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 3","pages":"103922"},"PeriodicalIF":1.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144529968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for patterning competency assay in regenerative axolotl limb cells using the competency accessory limb model. 利用能力副肢模型在再生蝾螈肢体细胞中进行模式能力测定的方案。
IF 1.3
STAR Protocols Pub Date : 2025-06-27 DOI: 10.1016/j.xpro.2025.103920
Michael J Raymond, Catherine D McCusker
{"title":"Protocol for patterning competency assay in regenerative axolotl limb cells using the competency accessory limb model.","authors":"Michael J Raymond, Catherine D McCusker","doi":"10.1016/j.xpro.2025.103920","DOIUrl":"10.1016/j.xpro.2025.103920","url":null,"abstract":"<p><p>A key question in limb regeneration is how axolotl limb cells become competent to specific types of regeneration signals. Here, we present the competency accessory limb model (CALM), a regenerative assay that assesses whether limb cells have achieved the ability to respond to patterning signals. We describe the steps for positioning a wound, deviating the nerve into a limb wound site, and injecting retinoic acid. We also detail the harvest and analyses in both anterior and posterior CALMs. For complete details on the use and execution of this protocol, please refer to Raymond et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 3","pages":"103920"},"PeriodicalIF":1.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12266493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144529967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol to study DNA strand breaks during development and apoptosis using in situ nick translation in Drosophila. 利用原位缺口翻译研究果蝇发育和凋亡过程中DNA链断裂的方案。
IF 1.3
STAR Protocols Pub Date : 2025-06-26 DOI: 10.1016/j.xpro.2025.103921
Deepak Maurya, Bama Charan Mondal
{"title":"Protocol to study DNA strand breaks during development and apoptosis using in situ nick translation in Drosophila.","authors":"Deepak Maurya, Bama Charan Mondal","doi":"10.1016/j.xpro.2025.103921","DOIUrl":"10.1016/j.xpro.2025.103921","url":null,"abstract":"<p><p>Cellular stress causes DNA strand breaks that are typically repaired to maintain homeostasis and regulate cell fate. However, unrepaired DNA breaks can be lethal, leading to cell death. Here, we present a protocol to study DNA strand breaks in Drosophila during development and apoptosis using in situ nick translation. We describe the steps for labeling DNA strand breaks using digoxigenin (DIG)-labeled nucleotide (DIG-11-dUTP) and visualizing them with anti-DIG immunostaining. We then detail procedures for mounting, imaging, and analysis. For complete details on the use and execution of this protocol, please refer to Maurya et al.<sup>1</sup> and Rigby et al.<sup>2</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 3","pages":"103921"},"PeriodicalIF":1.3,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144529969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for measuring force in skinned diaphragm muscle fibers of myopathic SEPN1 knockout mice following chronic tauroursodeoxycholic acid treatment. 慢性牛磺酸去氧胆酸治疗后，肌病SEPN1基因敲除小鼠皮肤膈肌纤维力测量方案。
IF 1.3
STAR Protocols Pub Date : 2025-06-26 DOI: 10.1016/j.xpro.2025.103918
Leonardo Nogara, Serena Germani, Cosimo De Napoli, Bert Blaauw, Ester Zito
{"title":"Protocol for measuring force in skinned diaphragm muscle fibers of myopathic SEPN1 knockout mice following chronic tauroursodeoxycholic acid treatment.","authors":"Leonardo Nogara, Serena Germani, Cosimo De Napoli, Bert Blaauw, Ester Zito","doi":"10.1016/j.xpro.2025.103918","DOIUrl":"10.1016/j.xpro.2025.103918","url":null,"abstract":"<p><p>Selenoprotein N1 (SEPN1) is a type II endoplasmic reticulum (ER) glycoprotein. Loss-of-function mutations in the gene encoding for SEPN1 give rise to myopathy. Here, we present a protocol for evaluating the contractility of diaphragmatic muscle fibers of SEPN1 knockout mice following chronic treatment with tauroursodeoxycholic acid (TUDCA). We describe steps for genotyping SEPN1 knockout mice, TUDCA in vivo treatment, diaphragm dissection, and chemical permeabilization. We then detail procedures for single muscle fiber isolation and tension measurement. For complete details on the use and execution of this protocol, please refer to Germani et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 3","pages":"103918"},"PeriodicalIF":1.3,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12266584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for phase-amplitude coupling analysis in local field potentials from macaque monkeys to investigate neural oscillation dynamics. 研究猕猴神经振荡动力学的局部场电位相幅耦合分析方案。
IF 1.3
STAR Protocols Pub Date : 2025-06-23 DOI: 10.1016/j.xpro.2025.103877
Mohammad Aliramezani, Ashkan Farrokhi, Christos Constantinidis, Mohammad Reza Daliri
{"title":"Protocol for phase-amplitude coupling analysis in local field potentials from macaque monkeys to investigate neural oscillation dynamics.","authors":"Mohammad Aliramezani, Ashkan Farrokhi, Christos Constantinidis, Mohammad Reza Daliri","doi":"10.1016/j.xpro.2025.103877","DOIUrl":"10.1016/j.xpro.2025.103877","url":null,"abstract":"<p><p>Phase-amplitude coupling (PAC) is a critical neural mechanism that reflects the coordination between oscillatory brain activity across different frequency bands. Here, we present a protocol for analyzing PAC in macaque monkeys. We describe steps for preprocessing local field potential (LFP), performing time-frequency decomposition, and computing PAC between distinct frequency bands. We then detail procedures for normalizing the results using surrogate data. This protocol can be applied to various experimental conditions to explore neural synchronization and its role in cognitive processes. For complete details on the use and execution of this protocol, please refer to Aliramezani et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 3","pages":"103877"},"PeriodicalIF":1.3,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12226356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk. 小体积早产儿乳汁中噬菌体与脂质体相互关系的研究方案。
IF 1.3
STAR Protocols Pub Date : 2025-06-21 DOI: 10.1016/j.xpro.2025.103917
Wen C Yew, Gregory R Young, William Cheung, Andrew Nelson, Janet E Berrington, Darren L Smith
{"title":"Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk.","authors":"Wen C Yew, Gregory R Young, William Cheung, Andrew Nelson, Janet E Berrington, Darren L Smith","doi":"10.1016/j.xpro.2025.103917","DOIUrl":"10.1016/j.xpro.2025.103917","url":null,"abstract":"<p><p>Bacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomics approaches, respectively. We describe steps for extracting phages and lipids in low-volume milk, characterizing phageome using an in-house bioinformatic pipeline, and statistical analysis to correlate the phageome and lipidome. Finally, we detail an in vitro assay to examine the associations between fatty acid chain length and phage morphotype. For complete details on the use and execution of this protocol, please refer to Yew et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 3","pages":"103917"},"PeriodicalIF":1.3,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12221710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144369235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for labeling and manipulating "home"-activated neurons in mice. 标记和操纵小鼠“家园”激活神经元的方案。
IF 1.3
STAR Protocols Pub Date : 2025-06-20 Epub Date: 2025-03-22 DOI: 10.1016/j.xpro.2025.103704
Xiaoya Su, Junyue He, Yunlong Liu, Keyu Liu, Bo Lei, Yi Zhong
{"title":"Protocol for labeling and manipulating \"home\"-activated neurons in mice.","authors":"Xiaoya Su, Junyue He, Yunlong Liu, Keyu Liu, Bo Lei, Yi Zhong","doi":"10.1016/j.xpro.2025.103704","DOIUrl":"10.1016/j.xpro.2025.103704","url":null,"abstract":"<p><p>Home-related cues, such as home bedding, influence affective behaviors in mice, including fear relief, anxiety reduction, and defensive aggression. Here, we present a protocol for labeling and manipulating \"home\"-activated neurons in the lateral hypothalamus (LH) using a Tet-Off inducible system. We describe steps for virus injection, postoperative recovery, and combining c-Fos-driven activity labeling with chemogenetics. This protocol integrates neuronal targeting with behavioral assays to provide insights into the functional role of \"home\"-activated neurons in home-driven behavioral adaptations. For complete details on the use and execution of this protocol, please refer to Su et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103704"},"PeriodicalIF":1.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143693608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for achieving enhanced snRNA-seq data quality using Quality Clustering. 使用质量聚类实现增强snRNA-seq数据质量的协议。
IF 1.3
STAR Protocols Pub Date : 2025-06-20 Epub Date: 2025-03-29 DOI: 10.1016/j.xpro.2025.103717
Paavo J Tavi, Johannes Ojanen, Pia Laitinen, Suvi Linna-Kuosmanen
{"title":"Protocol for achieving enhanced snRNA-seq data quality using Quality Clustering.","authors":"Paavo J Tavi, Johannes Ojanen, Pia Laitinen, Suvi Linna-Kuosmanen","doi":"10.1016/j.xpro.2025.103717","DOIUrl":"10.1016/j.xpro.2025.103717","url":null,"abstract":"<p><p>Single-nucleus RNA sequencing (snRNA-seq) data analysis presents a challenge in samples that have high levels of ambient RNA contamination. Quality Clustering (QClus) removes empty and highly contaminated droplets by utilizing multiple contamination metrics. Here, we present the steps for snRNA-seq data preprocessing using the QClus algorithm. First, we describe how to set up a computational environment. Next, we demonstrate how to use QClus to remove highly contaminated droplets, and finally, we show how to visualize and evaluate the results. For complete details on the use and execution of this protocol, please refer to Schmauch et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103717"},"PeriodicalIF":1.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11994394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for the isolation of mouse fibro/adipogenic progenitors using magnetic-activated cell sorting. 使用磁激活细胞分选分离小鼠纤维/脂肪祖细胞的方案。
IF 1.3
STAR Protocols Pub Date : 2025-06-20 Epub Date: 2025-04-08 DOI: 10.1016/j.xpro.2025.103741
Jinghui Gao, Yaochao Zheng, Aria Sikal, Elijah Sterling, Rachel Hankin, Yao Yao
{"title":"Protocol for the isolation of mouse fibro/adipogenic progenitors using magnetic-activated cell sorting.","authors":"Jinghui Gao, Yaochao Zheng, Aria Sikal, Elijah Sterling, Rachel Hankin, Yao Yao","doi":"10.1016/j.xpro.2025.103741","DOIUrl":"10.1016/j.xpro.2025.103741","url":null,"abstract":"<p><p>Fibro/adipogenic progenitors (FAPs) are mesenchymal progenitors that support muscle stem cell activation and modulate the extracellular matrix to facilitate muscle regeneration. Here, we present a protocol for the isolation of FAPs from mouse skeletal muscle. We describe steps for performing enzymatic digestion, mechanical dissociation, and magnetic-activated cell sorting (MACS). This protocol enables the isolation of FAPs with high yield and purity, facilitating research on muscle disorders and advancing muscle regeneration strategies.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103741"},"PeriodicalIF":1.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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