Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar

ABSTRACT: Paired-end RNA-Seq libraries were constructed for three root sections of the roots of barley cv. Clipper, and landrace Sahara, grown under control and salt-treated (100 mM NaCl) conditions on agar plates in quadruplicate. Experiments were conducted in a temperature-controlled growth cabinet at 17 C in the dark. After three days of germination, seminal roots were dissected according to the following steps: A 1.5 mm long section marked Zone 1 (meristematic zone) was taken from the root tip. A second section (Zone 2) was dissected from the elongation zone up to a third section, Zone 3 (maturation zone), which was excised at the point of visible root hair elongation up to 34 of the entire root. Four biological replicates were generated for each sample in four separate experiments totaling 48 samples. All RNA-seq libraries were constructed and paired-end sequenced (100 bp) on an Illumina HiSeq 2000 system at the Australian Genome Research Facility (Melbourne, Australia).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Hordeum vulgare

SUBMITTER: Andrew Cassin

PROVIDER: E-MTAB-4634 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure.

Hill Camilla Beate CB Cassin Andrew A Keeble-Gagnère Gabriel G Doblin Monika S MS Bacic Antony A Roessner Ute U

Scientific reports 20160816

Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create two de novo assemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known ...[more]

PMID: 27527578

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Dataset Information

A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar

Publications

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure.

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