title: 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
design: A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar
library_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.
attributes.tag: Experimental Factor: Clipper
attributes.value: genotype
attributes.tag: Experimental Factor: Control
attributes.value: compound
attributes.tag: Experimental Factor: 0
attributes.value: dose
attributes.tag: Experimental Factor: Root elongation zone
attributes.value: organism part