RNA sequencing
For RNA-seq analyses, Col-0, parp1-2 , parp2-1 ,parp3-1 , parp1-2x2-1x3-1,srt1-4 hete,srt2-1 and srt1-4hete
x srt2-1 mutant seedlings were grown for two weeks in the conditions
used for the other experiments. Three independent biological replicate
seedlings were collected at ZT6 and ZT18 representing the day and night
samples.
RNA was extracted using the same method as for the qRT-PCR. RNAseq
libraries were generated using the Illumina TruSeq RNA Prep Kit v2
(Illumina, San Diego, CA) and sequenced by BGI-Hongkong (Hong Kong,
China) on an Illumina Hiseq 4000 with 100 base pair paired-end reads.
The sequencing data were provided demultiplexed, pre-filtered and with
the adaptor sequences trimmed off. Quality Checks (QC) on the data were
performed using the fastQC software v0.11.4
(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).