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Sample GSM6586149 Query DataSets for GSM6586149
Status Public on Sep 19, 2022
Title Papaya, RB1, Ripe, bio rep 3
Sample type SRA
 
Source name fruit
Organism Carica papaya
Characteristics tissue: fruit
cultivar: RB1
phenotype: sweet flavour and floral aroma
time: Ripe stage
Extracted molecule total RNA
Extraction protocol RNA was extracted from papaya flesh using NucleoZOL (Machery-Nagel Inc. USA) from approximately 50 mg of fruit flesh per sample according to the manufacturer’s instructions.
A total amount of 2 µg of the high-quality RNA per sample of ‘RB1’ and ‘1B’ were sequenced using an Illumina Sequencing platform. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The raw sequencing data was processed to remove adaptors, as well as low quality bases/reads using bbduk (from BBMap v38.34) followed with Trimmomatic (v0.40) and FastQC (v0.11.9)
Assembly: Trinity (v2.11.0) was then applied on the clean reads to de novo assemble the full transcriptome of ‘RB1’ and ‘1B’
Supplementary files format and content: Sample-related biases were identified through variance-stabilising transformation of the raw counts of reads and plotted into a between-sample distance matrix.
 
Submission date Sep 15, 2022
Last update date Sep 19, 2022
Contact name ziwei zhou
E-mail(s) ziwei.zhou2@griffithuni.edu.au
Organization name Griffith University
Street address 170 Kessels Rd, Nathan
City Brisbane
State/province QUEENSLAND
ZIP/Postal code 4111
Country Australia
 
Platform ID GPL32671
Series (1)
GSE213436 Identification and validation of key genes related to preferred flavour profiles in Australian commercial papaya (Carica papaya L.)
Relations
BioSample SAMN30869717
SRA SRX17591865

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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