GSE136183
Transcriptomic network of Tulipa gesneriana during petal senescence
Purpose: We aimed to dissect transcriptomic responses of Tulipa gesneriana during petal senescence and characterize function of senescence related genes. Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis between each two different stages was performed using the DESeq R package (1.18.0). Results:In total, 15 samples with three biological replicates per stage combination were used for RNA sequencing analysis. At least 6 G clean bases were generated for each sample. Comparative analysis identified genes involved in flower development and/or fllower senescence. Overall design: In this study, five stages of a flower including buds, partial blooming, full blooming, early senescence and late senescence are collected individually. The whole flowers with different developmental stages were then used in RNA sequencing.