DOI: 10.57760/sciencedb.16793
title: RNA-Seq data of R. agastum and R. irroratum
title: RNA-Seq data of R. agastum and R. irroratum

description: R. agastum and R. irroratum from experimental field at National Forest Garden of GuiZhou province were employed in this paper. Flower samples during the four developmental stages (S1-S4) were sheared and harvested. According to instructions of RNA pure Plant Kit (CWBIO, China), total RNA was extracted from flowers of R. agastum and R. irroratum. RNA concentration and integrity was identified through Nanodrop spectrophotometer (Life Technologies, USA) and bioanalyzer 2100 (Agilent, USA) respectively. cDNA libraries preparation were finished via Biomarker Technology (Beijing, China) and then subjected to sequence using Illumina HiSeq X™ Ten platform. The high-quality clean reads/data were generated by removing the low-quality, adapter- and N-base reads, and assembled basing on the genome of Rhododendron delavayi assessed by Rhododendron plant Genome Database (RPGD, http://bioinfor.kib.ac.cn/RPGD/index.html). Function of the assembled unigene was annotated against the following database: KEGG (Kyoto Encyclopedia of Genes and Genomes); PFAM (protein family); Nt (non-redundant nucleotide sequences, NCBI); Swiss-Prot (a protein sequence database); Nr (non-redundant protein sequences, NCBI); KO (Kyoto Encyclopedia of Genes and Genomes Ortholog database); GO (Gene Ontology); and COG (Clusters of Orthologous Groups of proteins). To normalize the gene expression level, FPKM (Fragments Per Kilobase of transcriptome per Million mapped reads) method was selected. Differential expression analysis of two groups (Ra and Ri) was conducted using DESeq2 package with the screening parameters: fold change ≥2 and FDR (false discovery rate) &lt; 0.01 to identify the genes expressed significantly different. Meanwhile, GO and KEGG enrichment analysis were applied for analyzing the biological function of DEGs through using TopGO and KOBAS.
description: R. agastum and R. irroratum from experimental field at National Forest Garden of GuiZhou province were employed in this paper. Flower samples during the four developmental stages (S1-S4) were sheared and harvested. According to instructions of RNA pure Plant Kit (CWBIO, China), total RNA was extracted from flowers of R. agastum and R. irroratum. RNA concentration and integrity was identified through Nanodrop spectrophotometer (Life Technologies, USA) and bioanalyzer 2100 (Agilent, USA) respectively. cDNA libraries preparation were finished via Biomarker Technology (Beijing, China) and then subjected to sequence using Illumina HiSeq X™ Ten platform. The high-quality clean reads/data were generated by removing the low-quality, adapter- and N-base reads, and assembled basing on the genome of Rhododendron delavayi assessed by Rhododendron plant Genome Database (RPGD, http://bioinfor.kib.ac.cn/RPGD/index.html). Function of the assembled unigene was annotated against the following database: KEGG (Kyoto Encyclopedia of Genes and Genomes); PFAM (protein family); Nt (non-redundant nucleotide sequences, NCBI); Swiss-Prot (a protein sequence database); Nr (non-redundant protein sequences, NCBI); KO (Kyoto Encyclopedia of Genes and Genomes Ortholog database); GO (Gene Ontology); and COG (Clusters of Orthologous Groups of proteins). To normalize the gene expression level, FPKM (Fragments Per Kilobase of transcriptome per Million mapped reads) method was selected. Differential expression analysis of two groups (Ra and Ri) was conducted using DESeq2 package with the screening parameters: fold change ≥2 and FDR (false discovery rate) &lt; 0.01 to identify the genes expressed significantly different. Meanwhile, GO and KEGG enrichment analysis were applied for analyzing the biological function of DEGs through using TopGO and KOBAS.