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Dual RNA-Seq specifications

Information


Unique identifier OMICS_12986
Name Dual RNA-Seq
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Jan-Willem Veening

Publication for Dual RNA-Seq

Dual RNA-Seq citations

 (19)
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Gene expression differs in susceptible and resistant amphibians exposed to Batrachochytrium dendrobatidis

2018
R Soc Open Sci
PMCID: 5830717
PMID: 29515828
DOI: 10.1098/rsos.170910
call_split See protocol

[…] e some previous gene expression studies examining amphibian responses to Bd infection have sought to exclude potential Bd-derived sequences from analysis [], others have explicitly called for such a ‘dual RNA-seq’ approach to study host–pathogen interactions in the amphibian–Bd system []. Following these recommendations, we sought to characterize any Bd-derived sequence that might be present in sa […]

library_books

Genome Wide Identification of Cyclic Nucleotide Gated Ion Channel Gene Family in Wheat and Functional Analyses of TaCNGC14 and TaCNGC16

2018
Front Plant Sci
PMCID: 5786745
PMID: 29403523
DOI: 10.3389/fpls.2018.00018

[…] The transcript level of all TaCNGC genes were performed by unpublished time series dual RNA-Seq data in our lab. We sequenced two groups of wheat-rust interaction combination, named NIL_R vs. CYR32 and NIL_S vs. CYR32 and selected the time point at 0, 18, 24, 48, 96, and 168 hpi. Th […]

call_split

A Laboratory Methodology for Dual RNA Sequencing of Bacteria and their Host Cells In Vitro

2017
Front Microbiol
PMCID: 5613115
PMID: 28983295
DOI: 10.3389/fmicb.2017.01830
call_split See protocol

[…] The latter stages of a dual RNA-Seq experiment are the key statistical and bioinformatic analyses that underlie the inference of biological knowledge. The difficulties of dealing with both prokaryotic and eukaryotic transcr […]

call_split

Streptococcus pneumoniae in the heart subvert the host response through biofilm mediated resident macrophage killing

2017
PLoS Pathog
PMCID: 5589263
PMID: 28841717
DOI: 10.1371/journal.ppat.1006582
call_split See protocol

[…] d with AMPure XT beads (Beckman Coulter Genomics, Danvers, MA). In order to achieve sufficient levels of RNA sequencing for bacterial transcripts in the presence of an abundance of mouse transcripts (dual RNA-seq), libraries were loaded on 150nt paired-end runs of the Illumina HiSeq4000 sequencing platform as follows: half of a channel for each of the BIP and HIP libraries, a quarter of a channel […]

library_books

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection

2017
mSystems
PMCID: 5566787
PMID: 28845460
DOI: 10.1128/mSystems.00057-17

[…] Mass spectrometry and dual RNA-seq data were imported into Matlab (MathWorks) for quantitative and statistical analysis. For differential analysis, human samples with spiked bacteria at a ratio of 0, 5, 10, or 20 bacteria […]

library_books

Pseudogymnoascus destructans transcriptome changes during white nose syndrome infections

2017
PMCID: 5810475
PMID: 28614673
DOI: 10.1080/21505594.2017.1342910

[…] We determined how parasitism affects the expression patterns of P. destructans genes by comparing expression levels between the fungus in culture and during host infection. We used dual RNA-Seq data and an approach that simultaneously mapped the reads to both host and pathogen transcriptomes followed by the removal of reads that mapped to host transcripts. This approach allowed […]

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Dual RNA-Seq institution(s)
Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, Netherlands; Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
Dual RNA-Seq funding source(s)
EMBO Young Investigator Program; Grant (864.12.001), Netherlands Organization for Scientific Research; Earth and Life Sciences (NWO-ALW); ERC Starting Grant 337399-PneumoCell

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