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使用基于 RNA-seq 的方法解码转录活跃的微生物在 SARS-CoV-2 阳性患者中的作用的方案。

Protocol to decode the role of transcriptionally active microbes in SARS-CoV-2-positive patients using an RNA-seq-based approach.

机构信息

Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.

Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Indraprastha Institute of Information Technology (IIIT), New Delhi 110020, India.

出版信息

STAR Protoc. 2024 Jun 21;5(2):103071. doi: 10.1016/j.xpro.2024.103071. Epub 2024 May 19.

DOI:10.1016/j.xpro.2024.103071
PMID:38768029
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11111823/
Abstract

The elucidation of the role of microorganisms in human infections has been hindered by difficulties using conventional culture-based techniques. Here, we present a protocol for the investigation of transcriptionally active microbes (TAMs) using an RNA sequencing (RNA-seq)-based approach. We describe the steps for RNA isolation, viral genome sequencing, RNA-seq library preparation, and metatranscriptomic and transcriptomic analysis. This protocol permits a comprehensive evaluation of TAMs' contributions to the differential severity of infectious diseases, with a particular focus on diseases such as COVID-19. For complete details on the use and execution of this protocol, please refer to Devi et al..

摘要

阐明微生物在人体感染中的作用一直受到传统基于培养的技术的困难的阻碍。在这里，我们提出了一种使用基于 RNA 测序（RNA-seq）的方法研究转录活性微生物（TAMs）的方案。我们描述了 RNA 分离、病毒基因组测序、RNA-seq 文库制备以及宏转录组学和转录组学分析的步骤。该方案允许全面评估 TAMs 对传染病严重程度差异的贡献，特别关注 COVID-19 等疾病。有关此方案的使用和执行的完整详细信息，请参阅 Devi 等人的研究。

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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/accdc65e3b96/fx5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/b7525c3150cb/fx6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/f25069d97578/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/c6760203eee1/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/23efc4a4cc01/fx7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/0dd9adb79a85/fx8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/9291c5d5346d/fx9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/228619dccc16/fx10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/0f5e3c755bfc/fx11.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9e81/11111823/9d042aaf631a/fx13.jpg

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