A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes

被引：0
|
作者：
Roi Avraham
Nathan Haseley
Amy Fan
Zohar Bloom-Ackermann
Jonathan Livny
Deborah T Hung
机构：
[1] Broad Institute of MIT and Harvard,Department of Medicine
[2] Brigham and Women's Hospital,Department of Molecular Biology
[3] Harvard Medical School,Department of Microbiology and Immunobiology
[4] Massachusetts General Hospital,undefined
[5] Center for Computational and Integrative Biology,undefined
[6] Massachusetts General Hospital,undefined
[7] Harvard Medical School,undefined
[8] Present address: Department of Biological Regulation,undefined
[9] Weizmann Institute of Science,undefined
[10] Rehovot,undefined
[11] Israel.,undefined
来源：
Nature Protocols | 2016年 / 11卷
关键词：
D O I：
暂无
中图分类号：
学科分类号：
摘要：
This protocol enables simultaneous analysis of host and bacterial transcripts by RNA-seq. It includes procedures for efficient host and bacterial cell lysis, barcoding of samples and analysis of both mammalian and microbial reads from mixed host–pathogen RNA-seq data.
引用
收藏
页码：1477 / 1491
页数：14
相关论文
共 50 条
  • [41] Novel RNA Extraction Method for Dual RNA-seq Analysis of Pathogen and Host in the Early Stages of Yersinia pestis Pulmonary Infection
    Israeli, Ofir
    Cohen-Gihon, Inbar
    Aftalion, Moshe
    Gur, David
    Vagima, Yaron
    Zauberman, Ayelet
    Levy, Yinon
    Zvi, Anat
    Chitlaru, Theodor
    Mamroud, Emanuelle
    Tidhar, Avital
    MICROORGANISMS, 2021, 9 (10)
  • [42] Rna-Seq Analysis Of Human Neutrophil Transcriptomes Regulated By Nicotinamide Phosphoribosyltransferase With Or Without LPS
    Heruth, D. P.
    Bi, L. G.
    Zhang, L. Q.
    Xiong, M.
    Ye, S. Q.
    AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 2017, 195
  • [43] Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen
    Mika-Gospodorz, Bozena
    Giengkam, Suparat
    Westermann, Alexander J.
    Wongsantichon, Jantana
    Kion-Crosby, Willow
    Chuenklin, Suthida
    Wang, Loo Chien
    Sunyakumthorn, Piyanate
    Sobota, Radoslaw M.
    Subbian, Selvakumar
    Vogel, Jorg
    Barquist, Lars
    Salje, Jeanne
    NATURE COMMUNICATIONS, 2020, 11 (01)
  • [44] Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
    Francisco Avila Cobos
    Mohammad Javad Najaf Panah
    Jessica Epps
    Xiaochen Long
    Tsz-Kwong Man
    Hua-Sheng Chiu
    Elad Chomsky
    Evgeny Kiner
    Michael J. Krueger
    Diego di Bernardo
    Luis Voloch
    Jan Molenaar
    Sander R. van Hooff
    Frank Westermann
    Selina Jansky
    Michele L. Redell
    Pieter Mestdagh
    Pavel Sumazin
    Genome Biology, 24
  • [45] Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen
    Bozena Mika-Gospodorz
    Suparat Giengkam
    Alexander J. Westermann
    Jantana Wongsantichon
    Willow Kion-Crosby
    Suthida Chuenklin
    Loo Chien Wang
    Piyanate Sunyakumthorn
    Radoslaw M. Sobota
    Selvakumar Subbian
    Jörg Vogel
    Lars Barquist
    Jeanne Salje
    Nature Communications, 11
  • [46] Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins
    Jase Gehring
    Jong Hwee Park
    Sisi Chen
    Matthew Thomson
    Lior Pachter
    Nature Biotechnology, 2020, 38 : 35 - 38
  • [47] Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins
    Gehring, Jase
    Park, Jong Hwee
    Chen, Sisi
    Thomson, Matthew
    Pachter, Lior
    NATURE BIOTECHNOLOGY, 2020, 38 (01) : 35 - +
  • [48] Simultaneous profiling of Arabidopsis thaliana and Vibrio vulnificus MO6-24/O transcriptomes by dual RNA-seq analysis
    Park, Yong-Soon
    Park, Jong-Seok
    Lee, Soohyun
    Jung, Sung-Hee
    Kim, Seon-Kyu
    Ryu, Choong-Min
    COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2021, 19 : 2084 - 2096
  • [49] Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
    Cobos, Francisco Avila
    Panah, Mohammad Javad Najaf
    Epps, Jessica
    Long, Xiaochen
    Man, Tsz-Kwong
    Chiu, Hua-Sheng
    Chomsky, Elad
    Kiner, Evgeny
    Krueger, Michael J.
    di Bernardo, Diego
    Voloch, Luis
    Molenaar, Jan
    van Hooff, Sander R.
    Westermann, Frank
    Jansky, Selina
    Redell, Michele L.
    Mestdagh, Pieter
    Sumazin, Pavel
    GENOME BIOLOGY, 2023, 24 (01)
  • [50] Dual RNA-Seq of H5N1 Avian Influenza Virus and Host Cell Transcriptomes Reveals Novel Insights Into Host-Pathogen Cross Talk
    Wang, Qiao
    Wang, Zixuan
    Zhang, Jin
    Zhang, Qi
    Zheng, Maiqing
    Wen, Jie
    Zhao, Guiping
    Li, Qinghe
    FRONTIERS IN MICROBIOLOGY, 2022, 13
12345