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Immunology and Infection
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JoVE Journal Immunology and Infection
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Article DOI: 10.3791/62324-v • 14:58 min • March 5th, 2022
March 5th, 2022 •
1,2, 3, 2,3, 3, 2,3, 2,3,4
1Laboratory of Pathology of Infectious Diseases, Department of Pathology, Medical School, University of São Paulo, 2Scientific Platform Pasteur USP, 3Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, 4Hospital Israelita Albert Einstein

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Summary
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The protocol presented here describes a complete pipeline to analyze RNA-sequencing transcriptome data from raw reads to functional analysis, including quality control and preprocessing steps to advanced statistical analytical approaches.

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High-throughput Transcriptome Analysis Host-pathogen Interactions Quality Control Low-quality Reads Adapter Sequences Sequencing Annotations Reference Genomes Genes Statistical Analysis Co-expression Analysis Differentially Expressed Genes Co-expression Modules Molecular Degree Of Perturbation Analysis Functional Analysis Biological Functions Tools Linux System Docker Container Blood Samples RNA Sequencing Chikungunya Virus Docker Installation
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