---
identifier: CDCFrontier.gnm3.ann1.expr.ICC4958.Singh_Garg_2013

provenance: "The files in this directory derive from supplementary data from Singh et al., A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnology 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: "Chickpea Transcriptome Atlas - I"

scientific_name: Cicer arietinum

taxid: 3827

scientific_name_abbrev: cicar

genotype:
  - ICC4958 (desi variety)

expression_unit: TPM
  
description: "In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues. Overall design: We collected different tissue samples used in this study and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to 34760 chickpea transcripts and reads per kilobase per million (RPKM) was calculated for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes preferentially expression during various stages of flower development as compared to vegetative stages and those with speciifc expression were identified."

original_file_creation_date: "2015-11-27"

local_file_creation_date: "2025-03-06"

dataset_release_date: "2015-07-22"

publication_doi: 10.1111/pbi.12059

publication_title: "A global view of transcriptome dynamics during flower development in chickpea by deep sequencing"

bioproject: PRJNA182724

geoseries: GSE42679

sraproject: SRP017394

data_curators: Andrew Farmer, Evan Lavelle

public_access_level: public

license: open

keywords: chickpea, flower, germinating 

citation: "Singh, V.K., Garg, R. and Jain, M. (2013), A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol J, 11: 691-701"

contributors: "Vikash K Singh, Rohini Garg, Mukesh Jain"