Transcriptomics,Multiomics

Dataset Information

2

Catharanthus Transcriptome and Gene Expression


ABSTRACT: In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples. We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the Catharanthus transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.

OTHER RELATED OMICS DATASETS IN: PRJNA246273

ORGANISM(S): Catharanthus Roseus

TISSUE(S): Flower, Root, Leaf

SUBMITTER: Ghangal Rajesh   Mukesh Jain  Sinha Alok  Sharma Raghvendra  Verma Mohit  Jain Mukesh 

PROVIDER: E-GEOD-57326 | ArrayExpress | 2014-07-29

SECONDARY ACCESSION(S): GSE57326SRP041695PRJNA246273

REPOSITORIES: GEO, ArrayExpress, ENA

Dataset's files

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E-GEOD-57326.idf.txt Idf
E-GEOD-57326.processed.1.zip Processed
E-GEOD-57326.sdrf.txt Txt
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Publications

Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling.

Verma Mohit M   Ghangal Rajesh R   Sharma Raghvendra R   Sinha Alok K AK   Jain Mukesh M  

PloS one 20140729 7


The medicinal plant, Catharanthus roseus, accumulates wide range of terpenoid indole alkaloids, which are well documented therapeutic agents. In this study, deep transcriptome sequencing of C. roseus was carried out to identify the pathways and enzymes (genes) involved in biosynthesis of these compounds. About 343 million reads were generated from different tissues (leaf, flower and root) of C. roseus using Illumina platform. Optimization of de novo assembly involving a two-step process resulted  ...[more]

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