GSM2218737: T24_1; Andrographis paniculata; RNA-Seq - SRA

SRX1880252: GSM2218737: T24_1; Andrographis paniculata; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 22M spots, 6.6G bases, 2.6Gb downloads

Submitted by: NCBI (GEO)

Study: Time-serialized expression profile of MeJA induced Andrographis paniculata leaves

PRJNA326960 • SRP077300 • All experiments • All runs

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To shed light on the biosynthesis mechanisms of these diterpenes, we performed the first high-throughput RNA-seq for A. paniculata leaves with time-serialized MeJA treatments. The transcriptomic approach not only defined a comprehensive transcriptome (comprised of 20,629 highly expressed genes), but also profiled time-serialized gene expression patterns with 4,463 up-regulated genes and 6,517 down-regulated genes responding to MeJA induction. These up-regulated genes significantly enriched in biological processes like stress responses, metabolic pathways, and secondary metabolites biosynthesis, especially terpene/terpenoid metabolic process. Consistent with the gradual accumulation of andrographolide, the expression of most genes involved in MEP pathway showed progressive increase. In the hypothetical terpenoid metabolism pathway, ApCPS2, which was putatively involved in andrographolide synthesis, dramatically increased its expression. Among other co-regulated genes, 154 genes encode cytochrome P450s (CYP450s); 42 genes were predicted as UDP glycosyltransferases (UGTs); and 363 genes belong to transcription factors. Overall design: Strand-specific paired-end mRNA-seq data were generated in MeJA treated leaf samples including 0 hours past induction (hpi), 12 hpi, 24 hpi and 48 hpi with three biological replicates each to ensure the veracity.

Sample: T24_1

SAMN05296543 • SRS1527234 • All experiments • All runs

Organism: Andrographis paniculata

Library:

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: Total RNAs from leaves induced for 0, 12, 24 and 48 hours with three biological replicates were extracted using Trizol (Invitrogen, 15596-018) according to the manufacturer’s instructions. Highly purified and intact mRNAs were enriched from total RNAs using Dynabeads® mRNA purification kit (Ambion, 61006). RNAs were fragmented into ~ 300 nt fragments by 1 min incubation at 94℃ in fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl, pH 7.0). The fragmentation reaction was stopped with 50 mM EDTA, followed by standard ethanol precipitation and collected for sequencing and expression validation. For the strand-specific RNA-seq, fragmented RNAs were re-suspended in H2O and used for library generation with mRNA sequencing kit (Illumina Inc. San Diego, CA). Sequencing was carried out on Illumina HiSeq 4000 sequencer (Illumina Inc. San Diego, CA) according to the manufacturer’s instructions and 150 nt paired-end sequencing reads were generated.

Experiment attributes:

GEO Accession: GSM2218737

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 22M spots, 6.6G bases, 2.6Gb

Run	# of Spots	# of Bases	Size	Published
SRR3722540	22,036,420	6.6G	2.6Gb	2019-01-01

ID:: 2686961

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