RNA-Sequencing of virus species infecting sweetpotato - SRA

SRX18549908: RNA-Sequencing of virus species infecting sweetpotato
1 ILLUMINA (Illumina HiSeq X) run: 51.6M spots, 15.5G bases, 4.8Gb downloads

Design: Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit(Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (AgilentTechnologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agarose gel. 1 g totalRNA with RIN value above 7 was used for following library preparation.Next generation sequencing library preparations were constructed according to the manufacturersprotocol (NEBNext Ultra RNA Library Prep Kit for Illumina). The poly(A) mRNA isolation wasperformed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) or Ribo-Zero rRNA removalKit (illumina). The mRNA fragmentation and priming was performed using NEBNext First Strand SynthesisReaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript IIReverse Transcriptase and the second-strand cDNA was synthesized using Second Strand SynthesisEnzyme Mix. The purified double-stranded cDNA (by AxyPrep Mag PCR Clean-up (Axygen)) was thentreated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed bya T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performedusing AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert sizeof 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers,with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up usingAxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies,Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrumentaccording to manufacturers instructions (Illumina, San Diego, CA, USA). Sequencing was carried outusing a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by theHiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (illumina) on the HiSeq instrument.

Submitted by: Plant Virology Section

Study: Complete genome sequence of viruses species associated with sweetpotato virus disease in Thailand

PRJNA910466 • SRP412187 • All experiments • All runs

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Sweetpotato virus disease is an important disease and caused seriously yield losses in sweetpotato production. To identify the causal viruses by RT-PCR were time-consuming to get full-length nucleotide sequences of viruses. This research aims to use next-generation sequencing by Illumina 150PE platform, to elucidate the complete genome of virus species infecting sweetpotato in Thailand.

Sample:

SAMN32123875 • SRS16016354 • All experiments • All runs

Organism: Sweet potato chlorotic stunt virus

Library:

Name: SP-LEB3155_L1_1

Instrument: Illumina HiSeq X

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: RT-PCR

Layout: PAIRED

Runs: 1 run, 51.6M spots, 15.5G bases, 4.8Gb

Run	# of Spots	# of Bases	Size	Published
SRR22586910	51,608,744	15.5G	4.8Gb	2022-12-09

ID:: 25606999

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