title: NextSeq 500 paired end sequencing; Transcriptomics of Arabidopsis thaliana nrpd1-3 and nrpd1-3 plant 2L under control or heat stress
design: Transcriptomics of Arabidopsis thaliana nrpd1-3 and nrpd1-3 plant 2L under control or heat stress
library_construction_protocol: Arabidopsis thaliana seeds were surfaced sterilized and sown in petri dishes with agarified (0.8% Bacto Agar) 0.5x MS medium, containing 1% sucrose and 0.05% MES at pH 5.7. After stratification for 3 days at 4°C, plants were grown in a CU-22L growth chamber (Percival) under 21°C and a 12/12 h (day/night) light cycle. For the heat treatment, a pre-chilling step was performed to increase the relative activation of ONSEN. Seedlings were first placed at 4°C for 24 h on a chilling platform built-in within the growth chamber (controlled by an external mini-chiller), but with the chamber temperature set to 6°C. This chilling pre-treatment was followed by 24 h with the chamber set to 37°C for the stressed plants; control plants were moved to 21°C. Pools of seedlings were harvested for RNA extraction. Total RNA was isolated using the the Plant-RNAeasy kit (Invitrogen), following provider's instructions. Strand-specific libraries were prepared with 2 µg of RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina); following provider's instructions.
attributes.tag: Experimental Factor: environmental stress
attributes.value: warm/hot temperature regiment
attributes.tag: Experimental Factor: genotype
attributes.value: nrpd1-3 with novel insertions of ONSEN/Copia78 LTR retrotransposon