title: Illumina HiSeq 2000 paired end sequencing; Gene expression profiling during adventitious root formation in carnation stem cuttings
design: Gene expression profiling during adventitious root formation in carnation stem cuttings
library_construction_protocol: Stem cuttings were pinched from several mother plants of the 2003 R 8 and 2101-02 MFR cultivars by skilled operators at noon on 2nd December 2013 (23 h). About 500 stem cuttings of each cultivar were wrapped in plastic bags after pinching and were sent refrigerated and in complete darkness to the laboratory (15 h).  Their basal regions were collected at 0, 6, 24 and 54 h after planting (hAP) in a walk-in growth chamber that was set at 22°C, 70% RH and under continuous fluorescent light with an average PPFD of 40 μmol m-2 s-1. Three biological replicates, each consisting of fifteen stem cutting bases (5 mm long), were collected per cultivar, treatment and time point, and were immediately frozen in liquid N2 After the treatment, the cuttings were individually planted in 70-well trays containing moistened perlite plugs. The stem cutting bases were submerged for 15 h in a 100 ml-water solution containing either mock or an auxin cocktail (1.5 uM indole-3-butyric acid and 1 uM α-naphtalene acetic acid.  For each sample, total RNA from 120 mg of powdered stem cutting base tissue that was kept at 65°C was extracted using Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer’s instructions The samples were prepared for sequencing using the TruSeq RNA Sample Preparation Kit v2 (Illumina, USA) following the manufacturer’s instructions. ERCC RNA Spike-In Controls (Life technologies, USA) were used to assess the sensitivity and dynamic range of the experiment.
attributes.tag: Experimental Factor: 2101-02 MFR
attributes.value: cultivar
attributes.tag: Experimental Factor: 0
attributes.value: time
attributes.tag: Experimental Factor: Control
attributes.value: stimulus