3 protocols
AccessionType
normalization data transformation protocol
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads. The cleaned reads were mapped to Arabidopsis thaliana genome (TAIR10) using TOPHATv2.0.8 for RNA sequencing with default settings. The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis. HTSeq-count was used to preprocess the RNA-seq alignments and deseq was used to detect the differentially expressed genes. Genome_build: TAIR10 Supplementary_files_format_and_content: In RNA-seq, read counts for genes (TAIR10) was provided.
nucleic acid library construction protocol
none provided by theh submitter
growth protocol
Arabidopsis seedlings were first cultured on 1/2 MS medium at 22 ◦C with a 16-h light and 8-h dark photoperiod. Leaf explants from 12-day-old seedlings were cultured on B5 medium without carbohydrate under a photoperiod with 16 h light and 8 h dark