Comment[ArrayExpressAccession]	E-GEOD-42679
MAGE-TAB Version	1.1			
Public Release Date	2014-01-09
Investigation Title	Chickpea Transcriptome Atlas - I			
Comment[Submitted Name]	Chickpea Transcriptome Atlas - I
Experiment 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. 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.			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	Jain	Singh	Garg	Jain
Person First Name	Mukesh	Vikash	Rohini	Mukesh
Person Mid Initials		K		
Person Email	mjain@nipgr.ac.in			
Person Affiliation	National Institute of Plant Genome Research (NIPGR)			
Person Phone	91-11-26735182			
Person Address	National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, New Delhi, India			
Person Roles	submitter			
Protocol Name	P-GSE42679-3	P-GSE42679-2	P-GSE42679-1	
Protocol Description	Illumina 1.3 pipeline used for basecalling Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3 Reads per kilobase per million (RPKM) value was calculated for all the genes in each tissue sample Genome_build: Chickpea transcriptome v1.0 (http://www.nipgr.res.in/ctdb.html) Supplementary_files_format_and_content: tab delimited text files include RPKM values for each sample	Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol	Seedlings were grown in a culture room and mature plants were grown in field	
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol	
Experimental Factor Name	DEVELOPMENTAL STAGE	ORGANISM PART		
Experimental Factor Type	developmental stage	organism part		
Publication Title	A global view of transcriptome dynamics during flower development in chickpea by deep sequencing.			
Publication Author List	Singh VK, Garg R, Jain M			
PubMed ID	23551980			
Publication DOI	10.1111/pbi.12059			
Comment[SecondaryAccession]	GSE42679			
Comment[GEOReleaseDate]	2014-01-09			
Comment[ArrayExpressSubmissionDate]	2012-12-03			
Comment[GEOLastUpdateDate]	2014-01-09			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[SecondaryAccession]	SRP017394			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR627762-SRR627772			
SDRF File	E-GEOD-42679.sdrf.txt