Transcriptomic dataset reveals the molecular basis of genotypic variation in hexaploid wheat (T. aestivum L.) in response to Fe/Zn deficiency

Data in Brief
Om Prakash GuptaGyanendra Pratap Singh

Abstract

The datasets depicted in the paper are related to the original article entitled "Identifying transcripts associated with efficient transport and accumulation of Fe and Zn in hexaploid wheat (T. aestivum L.)" [1]. Four wheat genotypes i.e. Sonora 64, CRP 1660, Vinata, and DBW 17 were selected for RNA sequencing using Illumina HiSeq4000 platform. These genotypes were grown in Fe/Zn sufficient and deficient conditions in sand pot culture with intermittent administration of Hoagland solution. Pooled assembly was carried out for all of the four varieties subsequent to discarding low-quality reads, adaptor sequences and contamination resulting in approximately 315,904 clean transcripts of around 937 bp lengths and N50 of 1,294 bp. For the functional annotation of the identified transcripts databases like Pfam, KEGG pathway, Uniprot, PlnTFDB and wheat proteins were utilized. Differential expression calculation of transcripts was carried out by DESeq, an R package and real-time PCR study of 12 Fe/Zn metabolic pathway related transcripts was utilized for further revalidation of data. Elemental analysis of grain Fe and Zn was performed using Flame Atomic Absorption Spectrometry (FAAS). The RNA-seq data of all the four wheat genotypes was...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 29, 2007·Nucleic Acids Research·Yuki MoriyaMinoru Kanehisa
Oct 28, 2009·Nucleic Acids Research·Paulino Pérez-RodríguezBernd Mueller-Roeber
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
Apr 12, 2017·Bioinformatics·Sebastian BeierMartin Mascher

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Datasets Mentioned

BETA
PRJNA605909
SUB6961770

Methods Mentioned

BETA
RNA Seq
Assay
RNA-seq

Software Mentioned

FAAS
R
FastQC
PfamScan
MISA
BLAST
DESeq
Bowtie2
KAAS
Trinity

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