Cell Reports Methods最新文献_第10页

Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing. 利用量子计算对二倍体和多倍体基因组进行单倍型解析组装。

IF 3.8

Cell Reports Methods Pub Date : 2024-04-01 DOI: 10.1016/j.crmeth.2024.100754

Yibo Chen, Jun-Han Huang, Yuhui Sun, Yong Zhang, Yuxiang Li, Xun Xu

引用次数: 0

Global O-glycoproteome enrichment and analysis enabled by a combinatorial enzymatic workflow. 利用组合酶工作流程进行全球 O 型糖蛋白组富集和分析。

IF 3.8

Cell Reports Methods Pub Date : 2024-04-01 DOI: 10.1016/j.crmeth.2024.100744

Taewook Kang, R. Budhraja, Jinyong Kim, Neha Joshi, Kishore Garapati, Akhilesh Pandey

引用次数: 0

Methodological advances enabled by the construction of a synthetic yeast genome. 构建合成酵母基因组带来的方法学进步。

IF 3.8

Cell Reports Methods Pub Date : 2024-04-01 DOI: 10.1016/j.crmeth.2024.100761

Daniel Schindler, Roy S.K. Walker, Yizhi Cai

引用次数: 0

Epigenomic tomography for probing spatially defined chromatin state in the brain. 表观基因组层析成像技术用于探测大脑中空间定义的染色质状态。

IF 3.8

Cell Reports Methods Pub Date : 2024-03-25 Epub Date: 2024-03-19 DOI: 10.1016/j.crmeth.2024.100738

Zhengzhi Liu, Chengyu Deng, Zirui Zhou, Ya Xiao, Shan Jiang, Bohan Zhu, Lynette B Naler, Xiaoting Jia, Danfeng Daphne Yao, Chang Lu

{"title":"Epigenomic tomography for probing spatially defined chromatin state in the brain.","authors":"Zhengzhi Liu, Chengyu Deng, Zirui Zhou, Ya Xiao, Shan Jiang, Bohan Zhu, Lynette B Naler, Xiaoting Jia, Danfeng Daphne Yao, Chang Lu","doi":"10.1016/j.crmeth.2024.100738","DOIUrl":"10.1016/j.crmeth.2024.100738","url":null,"abstract":"Spatially resolved epigenomic profiling is critical for understanding biology in the mammalian brain. Single-cell spatial epigenomic assays were developed recently for this purpose, but they remain costly and labor intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here, we demonstrate an approach, epigenomic tomography, that maps spatial epigenomes of mouse brain at the scale of centimeters. We individually profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness. Tri-methylation of histone 3 at lysine 27 (H3K27me3) or acetylation of histone 3 at lysine 27 (H3K27ac) features across these slices were grouped into clusters based on their spatial variation patterns to form epigenomic brain maps. As a proof of principle, our approach reveals striking dynamics in the frontal cortex due to kainic-acid-induced seizure, linked with transmembrane ion transporters, exocytosis of synaptic vesicles, and secretion of neurotransmitters. Epigenomic tomography provides a powerful and cost-effective tool for characterizing brain disorders based on the spatial epigenome.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10985265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140176809","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

Pooled CRISPR screening of high-content cellular phenotypes using ghost cytometry. 利用幽灵细胞计数法对高含量细胞表型进行联合 CRISPR 筛选。

IF 3.8

Cell Reports Methods Pub Date : 2024-03-25 DOI: 10.1016/j.crmeth.2024.100737

Asako Tsubouchi, Yuri An, Yoko Kawamura, Yuichi Yanagihashi, Hirofumi Nakayama, Yuri Murata, Kazuki Teranishi, Soh Ishiguro, Hiroyuki Aburatani, Nozomu Yachie, Sadao Ota

{"title":"Pooled CRISPR screening of high-content cellular phenotypes using ghost cytometry.","authors":"Asako Tsubouchi, Yuri An, Yoko Kawamura, Yuichi Yanagihashi, Hirofumi Nakayama, Yuri Murata, Kazuki Teranishi, Soh Ishiguro, Hiroyuki Aburatani, Nozomu Yachie, Sadao Ota","doi":"10.1016/j.crmeth.2024.100737","DOIUrl":"10.1016/j.crmeth.2024.100737","url":null,"abstract":"Recent advancements in image-based pooled CRISPR screening have facilitated the mapping of diverse genotype-phenotype associations within mammalian cells. However, the rapid enrichment of cells based on morphological information continues to pose a challenge, constraining the capacity for large-scale gene perturbation screening across diverse high-content cellular phenotypes. In this study, we demonstrate the applicability of multimodal ghost cytometry-based cell sorting, including both fluorescent and label-free high-content phenotypes, for rapid pooled CRISPR screening within vast cell populations. Using the high-content cell sorter operating in fluorescence mode, we successfully executed kinase-specific CRISPR screening targeting genes influencing the nuclear translocation of RelA. Furthermore, using the multiparametric, label-free mode, we performed large-scale screening to identify genes involved in macrophage polarization. Notably, the label-free platform can enrich target phenotypes without requiring invasive staining, preserving untouched cells for downstream assays and expanding the potential for screening cellular phenotypes even when suitable markers are absent.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10985231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294778","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

Live-cell biosensors based on the fluorescence lifetime of environment-sensing dyes. 基于环境感应染料荧光寿命的活细胞生物传感器。

IF 3.8

Cell Reports Methods Pub Date : 2024-03-25 Epub Date: 2024-03-18 DOI: 10.1016/j.crmeth.2024.100734

Brian P Mehl, Pothiappan Vairaprakash, Li Li, Elizabeth Hinde, Christopher J MacNevin, Chia-Wen Hsu, Enrico Gratton, Bei Liu, Klaus M Hahn

引用次数: 0

SOX17/ETV2 improves the direct reprogramming of adult fibroblasts to endothelial cells. SOX17/ETV2 可改善成纤维细胞向内皮细胞的直接重编程。

IF 3.8

Cell Reports Methods Pub Date : 2024-03-25 Epub Date: 2024-03-18 DOI: 10.1016/j.crmeth.2024.100732

Alexander Grath, Guohao Dai

引用次数: 0

An autologous ex vivo model for exploring patient-specific responses to viro-immunotherapy in glioblastoma. 探索胶质母细胞瘤患者对病毒免疫疗法特异性反应的自体体外模型。

IF 3.8

Cell Reports Methods Pub Date : 2024-03-25 Epub Date: 2024-03-01 DOI: 10.1016/j.crmeth.2024.100716

Eftychia Stavrakaki, Wouter B L van den Bossche, Lisette B Vogelezang, Cristina Teodosio, Dana M Mustafa, Jacques J M van Dongen, Clemens M F Dirven, Rutger K Balvers, Martine L Lamfers

{"title":"An autologous ex vivo model for exploring patient-specific responses to viro-immunotherapy in glioblastoma.","authors":"Eftychia Stavrakaki, Wouter B L van den Bossche, Lisette B Vogelezang, Cristina Teodosio, Dana M Mustafa, Jacques J M van Dongen, Clemens M F Dirven, Rutger K Balvers, Martine L Lamfers","doi":"10.1016/j.crmeth.2024.100716","DOIUrl":"10.1016/j.crmeth.2024.100716","url":null,"abstract":"Oncolytic virus (OV) clinical trials have demonstrated remarkable efficacy in subsets of patients with glioblastoma (GBM). However, the lack of tools to predict this response hinders the advancement of a more personalized application of OV therapy. In this study, we characterize an ex vivo co-culture system designed to examine the immune response to OV infection of patient-derived GBM neurospheres in the presence of autologous peripheral blood mononuclear cells (PBMCs). Co-culture conditions were optimized to retain viability and functionality of both tumor cells and PBMCs, effectively recapitulating the well-recognized immunosuppressive effects of GBM. Following OV infection, we observed elevated secretion of pro-inflammatory cytokines and chemokines, including interferon γ, tumor necrosis factor α, CXCL9, and CXCL10, and marked changes in immune cell activation markers. Importantly, OV treatment induced unique patient-specific immune responses. In summary, our co-culture platform presents an avenue for personalized screening of viro-immunotherapies in GBM, offering promise as a potential tool for future patient stratification in OV therapy.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10985229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140022731","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

A multi-omics systems vaccinology resource to develop and test computational models of immunity. 多组学系统疫苗学资源，用于开发和测试免疫计算模型。

IF 3.8

Cell Reports Methods Pub Date : 2024-03-25 Epub Date: 2024-03-14 DOI: 10.1016/j.crmeth.2024.100731

Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Lisa Willemsen, Mari Kojima, Brendan Ha, Jason A Greenbaum, James A Overton, Hector Guzman-Orozco, Somayeh Nili, Shelby Orfield, Jeremy P Gygi, Ricardo da Silva Antunes, Alessandro Sette, Barry Grant, Lars Rønn Olsen, Anna Konstorum, Leying Guan, Ferhat Ay, Steven H Kleinstein, Bjoern Peters

{"title":"A multi-omics systems vaccinology resource to develop and test computational models of immunity.","authors":"Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Lisa Willemsen, Mari Kojima, Brendan Ha, Jason A Greenbaum, James A Overton, Hector Guzman-Orozco, Somayeh Nili, Shelby Orfield, Jeremy P Gygi, Ricardo da Silva Antunes, Alessandro Sette, Barry Grant, Lars Rønn Olsen, Anna Konstorum, Leying Guan, Ferhat Ay, Steven H Kleinstein, Bjoern Peters","doi":"10.1016/j.crmeth.2024.100731","DOIUrl":"10.1016/j.crmeth.2024.100731","url":null,"abstract":"Systems vaccinology studies have identified factors affecting individual vaccine responses, but comparing these findings is challenging due to varying study designs. To address this lack of reproducibility, we established a community resource for comparing Bordetella pertussis booster responses and to host annual contests for predicting patients' vaccination outcomes. We report here on our experiences with the \"dry-run\" prediction contest. We found that, among 20+ models adopted from the literature, the most successful model predicting vaccination outcome was based on age alone. This confirms our concerns about the reproducibility of conclusions between different vaccinology studies. Further, we found that, for newly trained models, handling of baseline information on the target variables was crucial. Overall, multiple co-inertia analysis gave the best results of the tested modeling approaches. Our goal is to engage community in these prediction challenges by making data and models available and opening a public contest in August 2024.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10985234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140137318","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

GAUSS-EM, guided accumulation of ultrathin serial sections with a static magnetic field for volume electron microscopy. GAUSS-EM，利用静态磁场引导积聚超薄连续切片，用于体视电子显微镜。

IF 3.8

Cell Reports Methods Pub Date : 2024-03-25 Epub Date: 2024-03-06 DOI: 10.1016/j.crmeth.2024.100720

Kara A Fulton, Paul V Watkins, Kevin L Briggman

引用次数: 0