title: Illumina HiSeq 2500 paired end sequencing; FAIRE-seq of the first leaf of two maize lines of contrasting cold-sensitivity.
design: FAIRE-seq of the first leaf of two maize lines of contrasting cold-sensitivity.
library_construction_protocol: Samples were taken at three growth stages: coleoptile (VE); seedling with the tip of the second leaf visible (called here “VE/V1 stage”); seedling with the first leaf fully developed (V1, ligular region present). Each sample consisted of pooled material from at least three plants (coleoptile for VE, first leaf for VE/V1 and V1 stages). Plants were grown from kernels in a growth chamber under 14h/10h photoperiod, light irradiance of 500 μmol quanta m−2 s−1 during the light phase, and 70% air relative humidity. Day/night temperature 14°C/10°C from the start of the experiment. Nucleosome-free DNA was extracted according to the FAIRE procedure. Briefly, leaf samples were fixed with formaldehyde solution, crosslinked chromatin was sonicated (to 200-800 bp range), isolated with Phenol-Chlorophorm-Isoamyl alcohol method and cleaned with DNA Clean & Concentrator-5 (Zymo Research, USA). Standard Protocol Illumina ChIP-Seq TruSeq