Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 13
Release date: Nov 9 2012
Last update date: Dec 21 2017
Access: Public
Diseases: Anemia, Hypochromic, Tobacco Use Disorder
Dataset link Digital gene expression (DGE) of CMV-infected tobacco leaves

Experimental Protocol


Tobacco leaves were inoculated by CMV-infected leaf homogenate and healthy leaf homogenate, respectivley. Six time points with different symptom stage were selected, and one virus-infect sample and one mock-inoculated sample were collected at each time. In order to average out variation of different plants, five leaves from five different plants were mixed to prepare every RNA sample. Twelve individual tag libraries of samples (six infected samples and six mock-inoculated samples) were constructed in parallel. For the gene expression analysis, the twelve samples were grouped into six groups, and each group contained a virus-infected sample and a mock-inoculated sample collected at the same time. In each group, the DGE data of virus-infected sample were compared to that of mock-inoculated sample to obtain the gene expression variations. Illumina sequencing of transcripts from virus-infected and mock-inoculated samples to get gene information for tobacco leaves in different symptom stages. In order to get more gene information, the systemically infected leaves and mock-inoculated leaves were harvested at six time points and five leaves from five different plants were collected at each time point. The RNA-Seq analysis provided gene information for mock-inoculated and virus-infected tobacco leaves in different symptom stages.

Repositories


GEO

GSE30162

ArrayExpress

E-GEOD-30162

ENA

SRP007356

BioProject

PRJNA143809

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Contact


Jie Lu