title: Illumina HiSeq 1500 paired end sequencing; Differential transcriptomic analysis reveals hidden light stress response in Streptomyces lividans TK24
design: Differential transcriptomic analysis reveals hidden light stress response in Streptomyces lividans TK24
library_name: S_lividans_TK24_Syscomp_light_Dark_strRNA-S2-LIGHT_p
library_construction_protocol: Main cultures were performed in 48 well MTP 48 B “FlowerPlates®” covered by a F GP 10 gas-permeable sealing foil (m2p labs GmbH, Baesweiler, Germany). Per well, 1000 µL medium was inoculated to an initial OD600 of 0.2. Cultivation conditions were 30 °C, ≥ 85 % relative humidi-ty, 900 rpm shaking frequency and 200 µmol/ (m^-2 x s^-1) illumination intensity. The light spectrum was approximated to typical Mid-European daylight (Morschett et al., 2017). Illuminated cultures were run in a Photo BioLector® prototype (Morschett et al., 2017). In both setups, biomass was monitored online by scattered light. Samples for transcriptomic analysis were taken during the late growth phase . Main cultures were performed in 48 well MTP 48 B “FlowerPlates®” covered by a F GP 10 gas-permeable sealing foil (m2p labs GmbH, Baesweiler, Germany). Per well, 1000 µL medium was inoculated to an initial OD600 of 0.2. Cultivation conditions were 30 °C, ≥ 85 % relative humidi-ty, 900 rpm shaking frequency and 0 µmol/ (m^-2 x s^-1) illumination intensity. Experiment without illumination were carried out in a commercial BioLector® (m2p labs GmbH, Bae-sweiler, Germany). In both setups, biomass was monitored online by scattered light. Samples for transcriptomic analysis were taken during the late growth phase . Briefly, S. lividans TK24 cells were harvested at late growth phase. Total RNA was isolated from two biological replicates using RNeasy Mini Kit along with a DNase Kit (both from Qiagen). Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer.  Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany).
attributes.tag: Experimental Factor: Photo BioLector (BL) prototype (Morschett et al., 2017) (light)
attributes.value: growth condition