Transcriptome Analysis of Nipponbare Rice

Ribosomal RNA was depleted as per the instructions provided in the Epicenter Ribo-Zero Gold Kit (Illumina, San Diego, USA). The cDNA libraries were created following fragmentation of the poly(A)−/(A) + RNA fractions, reverse-transcription. Paired-end sequencing was conducted on an Illumina HiSeq 4000 (LC-Bio, China). The reads with adaptor contamination, low quality and undetermined bases were removed, followed by quality verification using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie 2 [60 (link)] and TopHat2 [61 (link)] to map reads to the genome of Nipponbare rice Reference Genome (IRGSP build 5.0). The mapped reads of each sample were assembled using StringTie [62 (link)]. After the final transcriptome was generated, Ballgown [63 (link)] was used to estimate the expression levels of all transcripts. The raw data was available at NCBI Gene Expression Omnibus (GEO) repository with Accession Number GSE142323.