Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink by Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros

“…Summary: Analyzing host-microbe interactions is essential for understanding how microbiota changes disrupt host homeostasis. …”
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Protocol for automated graph-based clustering of single-cell RNA-seq data with application in mouse intestinal stem cells by Alexander L.E. Wang, Luca Zanella, Yosuke Ochiai, Leonardo Golinelli, Andrea Califano, Ermanno Malagola, Alessandro Vasciaveo

“…Summary: We present a protocol for isolating highly purified crypt epithelial cells from the mouse intestine for single-cell RNA sequencing (scRNA-seq). …”
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Profiling low-mRNA content cells in complex human tissues using BD Rhapsody single-cell analysis by Alexandra Scheiber, Manuel Trebo, Annabella Pittl, Isabel Heidegger, Theresa Hautz, Rupert Oberhuber, Zlatko Trajanoski, Florian Augustin, Sieghart Sopper, Dominik Wolf, Andreas Pircher, Stefan Salcher

“…Summary: The successful recovery of immune cells, particularly those with low mRNA content, by single-cell RNA sequencing (scRNA-seq) remains a significant challenge. …”
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Protocol for modeling blood flow recovery and angiogenesis in response to hindlimb ischemia by Sheila Sharma, Julia Pierce, Celia A. Butler, Olivya Caballero, Chris Mantsounga, Alan R. Morrison

“…Summary: Here, we present a protocol that models peripheral artery disease using the surgical induction of hindlimb ischemia (HLI) in mice. …”
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Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm by Yanqiang Li, Jiayi Chen, Yunxia Wang, Dean Li, Jiahan Li, Yang Yi, Lili Zhang, Qi Cao, Kaifu Chen

“…Summary: 2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. …”
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Protocol for identifying immune mediators during Leishmania infection in mice using metabolomic analysis by Thalia Pacheco-Fernandez, Laura Klenow, Nazli Azodi, Hannah Markle, Matthew Bernier, Greta Volpedo, Timur Oljuskin, Parna Bhattacharya, Shinjiro Hamano, Greg Matlashewski, Hira L. Nakhasi, Abhay R. Satoskar, Sreenivas Gannavaram

“…Summary: Here, we present a protocol for identifying immune mediators during Leishmania infection in mice using metabolomic analysis. …”
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Protocol for the purification of the plastid-encoded RNA polymerase from transplastomic tobacco plants by Xiao-Xian Wu, Fan Li, Chuxia Zhu, Shu-Yi Sun, Wen-Hui Mu, Stephanie Ruf, Ralph Bock, Yu Zhang, Fei Zhou

“…Summary: The plastid-encoded RNA polymerase (PEP) plays an essential role in the transcription of the chloroplast genome. …”
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Protocol on utilizing murine gastric cancer organoids for modeling subcutaneous, orthotopic primary, and liver metastatic disease in mice by Joshua Konecnik, Ryan N. O’Keefe, Kiruthiga Raghunathan, Saumya P. Jacob, Megan O’Brien, Anne Huber, Purva Trivedi, Christine Dijkstra, Amr H. Allam, Michael Buchert, Matthias Ernst, Moritz F. Eissmann

“…Summary: Tumor initiation, growth, and spread are influenced by cancer cell intrinsic and tissue microenvironment factors of the organ the tumor resides in. …”
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Protocols for the application of human embryonic stem cell-derived neurons for aging modeling and gene manipulation by Hui Zhang, Shuhui Sun, Juan Carlos Izpisua Belmonte, Guang-Hui Liu, Si Wang, Weiqi Zhang, Jing Qu

“…Summary: In vitro models of neuronal aging and gene manipulation in human neurons (hNeurons) are valuable tools for investigating human brain aging and diseases. …”
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Protocol for generation and utilization of patient-derived organoids from multimodal specimen by Sumin Kang, Mi Rim Lee, Wonyoung Choi, Sun-Young Kong, Yun-Hee Kim

“…Summary: Patient-derived organoids (PDOs) are robust preclinical models for precision oncology. …”
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Protocol for high-power, brain-focused microwave fixation to define rodent metabolism by Alex R. Cantrell, Tara R. Hawkinson, Jelena A. Juras, Madison B. Webb, Terrymar Medina, Roberto A. Ribas, James Collins, Amelia A. Bunnell, Lyndsay E.A. Young, Kia H. Markussen, Douglas A. Andres, Joanna R. Long, Craig W. Vander Kooi, Bret N. Smith, Ramon C. Sun, Matthew S. Gentry

“…Summary: Analysis of metabolites provides key insights into brain physiology and function. …”
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E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data by Hua Yu, Yunjie Liu, Zhouming Zhang, Guanglei Xie, Jingyu Liu, Yijia Liu, Siyue He, Zhiwei Peng, Lu Lu, Fei Li, Xi Wang

“…Summary: Here, we present a computational framework, E3RC, for exploring enhancer RNA (eRNA) expression and regulation using conventional RNA sequencing (RNA-seq) data. …”
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Financial and Non-Financial Information Seeking: The Role of Managing Anger and Fear in Investment Strategies and Decision-making by Vahid Oskou, Sahar Yousefizadeh, Fatemeh Asnad

“…The sampling method was purposeful and non-probability, with participants selected from among available investors. The scenario execution method involved the following steps: In the first stage, participants were asked to make investment decisions between two different companies. …”
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Protocol to quantify bacterial burden in time-kill assays using colony-forming units and most probable number readouts for Mycobacterium tuberculosis by Marie Sylvianne Rabodoarivelo, Eik Hoffmann, Cyril Gaudin, Diana Angélica Aguilar-Ayala, Jordana Galizia, Lindsay Sonnenkalb, Michael Dal Molin, Laura Cioetto-Mazzabò, Giulia Degiacomi, Deborah Recchia, Jan Rybniker, Riccardo Manganelli, Maria Rosalia Pasca, Santiago Ramón-García, Ainhoa Lucía

“…Summary: Here, we present a protocol to perform a time-kill assay (TKA) to quantify bacterial burden at multiple time points using colony-forming units and most probable number readouts simultaneously. …”
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Protocol for affinity enrichment of polyclonal autoantibodies from human plasma by Aws Aljnabi, Kelly A. Hagadorn, Louisa E. Neumann, Mary E. Peterson, Bethany Scott, Kazutoyo Miura, Aissata Ongoiba, Safiatou Doumbo, Didier Doumtabe, Shanping Li, Kassoum Kayentao, Boubacar Traore, Silvia Bolland, Peter D. Crompton, Christine S. Hopp

“…Summary: Autoantibodies (AAbs) contribute to various immune-mediated diseases and are valuable biomarkers for diagnosis, classification, and disease activity. …”
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A simplified, one step technique for disinfection of non-hardened rainbow trout eggs with tosylchloramide (Chloramine T) and peroxide (Wofasteril) compounds and the effects on bact... by Franz Lahnsteiner, Anna Dünser

“…The process involves two highly time-sensitive steps, requiring precise execution, as any errors can lead to fertilization failure or ineffective disinfection. …”
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Protocol for the generation and immunostaining of thick murine lung tissue slices by Ali Khadim, Mahtab Shahriari Felordi, Hawlader Sabbir Hasan, Georgios Kiliaris, Mahsa Zabihi, Hannah Hofmann, Elie El Agha

“…Summary: Precision-cut lung slices (PCLSs) largely preserve the native structural and cellular complexity of the lung, enabling detailed spatial analysis of resident cell populations. …”
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Protocol to visualize three distinct neuronal ensembles encoding different events in the mouse brain using genetic and viral approaches by Sylvie L. Lesuis, Asim J. Rashid, Annelies Hoorn, Sungmo Park, Andrew J. Mocle, Angelica M. Torelli, Antonietta DeCristofaro, Paul W. Frankland, Matthew N. Hill, Sheena A. Josselyn

“…Summary: Activity tagging of neuronal ensembles has become an important tool in neuroscience. …”
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Protocol for the generation of HLF+ HOXA+ human hematopoietic progenitor cells from pluripotent stem cells by Sherry Li Zheng, Jonas L. Fowler, Julie Y. Chen, Christopher Li, Elaine Lin, Alana T. Nguyen, Angela Chen, George Q. Daley, Lay Teng Ang, Kyle M. Loh

“…Summary: Hematopoietic stem cells (HSCs) generate blood and immune cells. …”
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Strawberry Pest Management Strategic Plan (PMSP) by Mark A. Mossler, Olaf Norman Nesheim

“…The generalized results of the meeting are presented in the executive summary, while specific actions are broken out in the summary at the end of the report. …”
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