Andru Tomoiu

Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences

Sara Clohisey, Nick Parkinson, Bo Wang, Nicolas Bertin et autres

Infection with influenza A virus (IAV) infection is responsible for an estimated 500,000 deaths and up to 5 million cases of severe respiratory illness each year. In this study, we looked at human primary immune cells (macrophages) infected with IAV. Our method …

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Comprehensive characterisation of molecular host-pathogen interactions in influenza A virus-infected human macrophages

Sara Clohisey, Nick Parkinson, Bo Wang, Nicolas Bertin et autres

Abstract Macrophages in the lung detect and respond to influenza A virus (IAV), determining the nature of the immune response. Using terminal depth 5’-RNA sequencing (CAGE) we quantify transcriptional activity of both host and pathogen over a 24-hour timecourse of IAV infection …

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FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno et autres

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting …

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genomic coordinates of the human CAGE peaks

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

bed file of the human CAGE peaks

expression table of the human CAGE peaks

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

CAGE peak based expression table (RLE normalized) for human samples

genomic coordinates of the mouse CAGE peaks

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

bed file of the mouse CAGE peaks

sample information of the human samples

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

Sample information (SDRF file) for human, including their details and details of their RNA extractions

assay information of the mouse tissue samples for HeliScopeCAGE (low quantity ver.)

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

a tab delimited flat file (SDRF file) describing the experimental details for mouse tissue samples for the low quantity version of the HeliScopeCAGE protocol

DRA000991

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

List of DRA (http://trace.ddbj.nig.ac.jp/dra/index_e.html) accession numbers of the FANTOM5 samples, sequences and genomic coordinations. Files are in tab-delimited format, which includes * Library ID * FFID * BioSamples accession number * DRA experiment accession number * DRA run accession numbers * DRA …

assay information of the human primary cell samples for HeliScopeCAGE

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

a tab delimited flat file (SDRF file) describing the experimental details for human primary cell samples for the standard protocol of the HeliScopeCAGE protocol

assay information of the human tissue samples for HeliScopeCAGE

Hans Clevers, Albert S.B. Edge, Marc van de Wetering, Michael Detmar et autres

a tab delimited flat file (SDRF file) describing the experimental details for human tissue samples for the standard protocol of the HeliScopeCAGE protocol

assay information of the human cell line samples for HeliScopeCAGE (low quantity ver.)

Hans Clevers, Albert Edge, Marc van de Wetering, Michael Detmar et autres

a tab delimited flat file (SDRF file) describing the experimental details for human cell line samples for the low quantity version of the HeliScopeCAGE protocol