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ERX1437572: Illumina HiSeq 2000 paired end sequencing; A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar
4 ILLUMINA (Illumina HiSeq 2000) runs: 32.4M spots, 6.5G bases, 4.3Gb downloads

Design: A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar
Submitted by: MU (Murdoch University)
Study: A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar
show Abstracthide 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 3/4 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).
Sample: S100_Z1-4
SAMEA3935086 • ERS1122220 • All experiments • All runs
Organism: Hordeum vulgare
Library:
Name: S100_Z1-4
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: Uniformly sized seeds were selected, surface-sterilised, and grown under control (nutrient medium without additional NaCl) and salt-treated (nutrient medium supplemented with 100 mM NaCl) conditions as described in (Shelden et al. 2013). After three days of germination, seminal roots were dissected, collected into 1.5 mL tubes, immediately snap-frozen in liquid nitrogen, and then stored at -80°C. Samples were dissected in the following steps: A 1.5 mm long section marked Zone 1 (meristematic zone) was taken from the root tip. The second section (Zone 2) was dissected from the elongation zone up to the third section, Zone 3 (maturation zone), which was excised at the point of visible root hair elongation up to 3/4 of the entire root. Total RNA was isolated from 50 mg root tissue using the Qiagen RNeasy kit following the manufacturer’s protocol. The RNA was analyzed for quality and concentration using a DeNovix DS-11 spectrophotometer (Wilmington, DE, USA) and an Agilent Technologies 2100 Bioanalyzer. Libraries were amplified through 13 cycles of PCR using Illumina guidelines. The Illumina TruSeq RNA Sample preparation kit v2 (Illumina Inc.) was used according to the manufacturer’s protocol. Poly(A) enrichment was used.
Spot descriptor:
forward101  reverse

Experiment attributes: (show all 4 attributes...) (hide...)
Experimental Factor: Sahara: genotype
Experimental Factor: NaCl: compound
Experimental Factor: 100: dose
Experimental Factor: Root meristematic zone: organism part
Runs: 4 runs, 32.4M spots, 6.5G bases, 4.3Gb
Run# of Spots# of BasesSizePublished
ERR13664198,136,9721.6G1.1Gb2017-01-07
ERR13664208,067,0321.6G1.1Gb2017-01-07
ERR13664218,067,8201.6G1.1Gb2017-01-07
ERR13664228,087,8601.6G1.1Gb2017-01-07

ID:
3585498

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