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Sample GSM8060090 Query DataSets for GSM8060090
Status Public on Feb 07, 2024
Title HSVd-infected tomato seedlings 1
Sample type SRA
 
Source name stem apex
Organism Solanum lycopersicum
Characteristics cultivar: Ailsa Craig
tissue: stem apex
cell line: none
treatment: HSVd-infected
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (v4.2) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description HSVd-infected tomato
Data processing Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: ftp://ftp.ensemblgenomes.org/pub/release-54/plants/fasta/solanum_lycopersicum/dna/
Supplementary files format and content: excel,expression profiles
 
Submission date Feb 02, 2024
Last update date Feb 07, 2024
Contact name Tang wenkun
E-mail(s) twk1300344374@126.com
Organization name Guizhou University
Street address Xibei Street
City guiyang
ZIP/Postal code 550025
Country China
 
Platform ID GPL19694
Series (1)
GSE254910 Exogenous Melatonin RegulatesAlternaria brassicaeReproduction and Pathogenicity in a Dose-Dependent Manner [miRNA]
Relations
BioSample SAMN39748133
SRA SRX23507657

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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