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ABSTRACT: RNA-Seq of Gloriosa superba Rothschildiana Petal

PROVIDER: PRJNA1000228 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR25473879_1.fastq.gz	Fastqsanger.gz
	SRR25473879_2.fastq.gz	Fastqsanger.gz
	SRR25473880_1.fastq.gz	Fastqsanger.gz
	SRR25473880_2.fastq.gz	Fastqsanger.gz
	SRR25473881_1.fastq.gz	Fastqsanger.gz

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Project description:Purpose: The goal of this study is to evaluate transcriptional regulation of the accumulation of phenols and anthocyanins in young leaves of subtropical forest tree species by using NGS-derived RNA-seq. Methods: Leaf mRNA profiles of subtropical tree Schima superba and Cryptocarya concinna grown under contasting light were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. FPKM produced by RSEM are provided. Results: Assemblies of the sequence data yielded 61,618 and 64,413 unigenes for Schima superba and Cryptocarya concinna,respectively. Overall,75.14% and 66.46% of the unigenes were annotated in the protein database Nonredundant protein (Nr), Nonredundant nucleotide (Nt), Swiss-Prot、Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG) and Gene Ontology (GO) for S. superba and C concinna,respectively.A total of 3896, 3488 and 266 genes were differentially expressed in full light-exposed young leaf (FLY), low light-exposed young leaf (LYL) and low light-exposed mature leaf (LML) relative to low light-exposed mature leaf (FML) of S. superba, respectively, and 2097, 2047 and 211 genes were differentially expressed in the corresponding leaves of C. concinna. Conclusions: Our study represents the first detailed analysis of transcriptomes in young and mature leaves of dorminant trees from a subtropical forest in China, with biologic replicates, generated by RNA-seq technology. Photosynthesis-related genes and phenol pathways-related genes were extensively down- and up-regulated in young versus mature leaves of the two species.

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Project description:To test Pbodies (anibodies screened from PETAL) for more applications, we performed ChIP-seq with selected Pbodies. ChIP-seq assays in HepG2 for Pbodies against SMRC1, SATB1 and NFIC were carried out.

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