|
Status |
Public on Sep 19, 2022 |
Title |
Papaya, 1B, Ripe, bio rep 2 |
Sample type |
SRA |
|
|
Source name |
fruit
|
Organism |
Carica papaya |
Characteristics |
tissue: fruit cultivar: 1B phenotype: bitter flavour and musty 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.
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|
|
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.
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|
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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 |
SAMN30869712 |
SRA |
SRX17591870 |