---
identifier: IT97K-499-35.gnm1.ann1.expr.Yao_Jiang_2016 

provenance: "The files in this directory derive from supplementary data from Yao et al., The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms. The Plant Journal. The files here are held as part of the SoyBase, LegumeInfo, and LegumeFederation projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the SoyBase, LegumeInfo, and Legume Federation project(s). If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files (noted below under Transformations where applicable), then please also cite the respective database project(s) related to this directory."


synopsis: Black-eyed pea gene expression atlas (IT97K-499-35) 

scientific_name: Vigna unguiculata
  
taxid: 3917

scientific_name_abbrev: pissa

genotype:
  - IT97K-499-35

expression_unit: TPM

description: "The black-eyed pea reference genotype has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem, flower, pod and seed), with a developmental time series for pods and seeds. From these various organs, 27 cDNA libraries were generated and sequenced, resulting in more than one billion reads. Following filtering, these reads were de novo assembled into 36 529 transcript sequences that were annotated and quantified across the different tissues. A set of 24,866 unique transcript sequences, called Unigenes, was identified. All the information related to transcript identification, annotation and quantification were stored into a gene expression atlas webserver (http://vugea.noble.org), providing a user-friendly interface and necessary tools to analyse transcript expression in black-eyed pea organs and to compare data with other legume species. Using this gene expression atlas, we inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, we found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation."

original_file_creation_date: "2017-11-01"

local_file_creation_date: "2024-10-09"

dataset_release_date: "2017-06-07"

publication_doi: 10.1111/tpj.13279

publication_title: "The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms" 

bioproject: PRJNA389300

data_curators: Andrew Farmer, Evan Lavelle

public_access_level: public

license: open

keywords: cowpea, black-eyed pea, pod, seed, leaf

citation: "Yao et al., The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms. The Plant Journal. 2016 October;88(2):318-327."

contributors: "Yao, Shaolun; Jiang, Chuan; Huang, Ziyue; Torres-Jerez, Ivone; Chang, Junil; Zhang, Heng; Udvardi, Michael; Liu, Renyi; Verdier, Jerome"