|
| Status |
Public on Sep 19, 2022 |
| Title |
Papaya, RB1, Unripe, bio rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
fruit
|
| Organism |
Carica papaya |
| Characteristics |
tissue: fruit
cultivar: RB1
phenotype: sweet flavour and floral aroma
time: Unripe 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 |
SAMN30869714 |
| SRA |
SRX17591868 |
