Transcriptomics,Genomics

Dataset Information

166

Saffron Transcriptome and Gene Expression


ABSTRACT: In this study, we aim to present a global transcriptome analysis of medicinal/spice plant, Crocus sativus. We generated about 206 million high-quality reads from five tissues (corm, leaf, Tepal, stamen and stigma) 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. Overall design: 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 saffron transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.

INSTRUMENT(S): Illumina HiSeq 2000 (Crocus sativus)

SUBMITTER: Mukesh Jain 

PROVIDER: GSE65103 | GEO | 2016-03-04

SECONDARY ACCESSION(S): PRJNA273002

REPOSITORIES: GEO

altmetric image

Publications

De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis.

Jain Mukesh M   Srivastava Prabhakar Lal PL   Verma Mohit M   Ghangal Rajesh R   Garg Rohini R  

Scientific Reports 20160303


Saffron (Crocus sativus L.) is commonly known as world's most expensive spice with rich source of apocarotenoids and possesses magnificent medicinal properties. To understand the molecular basis of apocarotenoid biosynthesis/accumulation, we performed transcriptome sequencing from five different tissues/organs of C. sativus using Illumina platform. After comprehensive optimization of de novo transcriptome assembly, a total of 105, 269 unique transcripts (average length of 1047 bp and N50 length  ...[more]

Similar Datasets

2012-06-01 | E-GEOD-22079 | ArrayExpress
| GSE87120 | GEO
2018-10-31 | E-MTAB-5071 | ExpressionAtlas
2016-05-11 | E-MTAB-5071 | ArrayExpress
2012-06-01 | GSE22079 | GEO
2011-09-01 | E-GEOD-26514 | ArrayExpress
| GSE91187 | GEO
2011-07-09 | E-MTAB-4128 | ArrayExpress
| GSE26514 | GEO
2019-05-15 | E-MTAB-4128 | ExpressionAtlas