|
| Status |
Public on Jun 11, 2024 |
| Title |
Red_Flesh_Mesocarp_RepB_R201 |
| Sample type |
SRA |
| |
|
| Source name |
Treatment 2
|
| Organism |
Malus domestica |
| Characteristics |
tissue: Red-Flesh Mesocarp
cultivar: cv. 'R201'
treatment: None
|
| Treatment protocol |
Distinction between red-flesh and white-flesh mesocarps from same fruits
|
| Growth protocol |
This analysis included three semi-biological replicates of RF and WF mesocarps (fruits from different trees) from red-flesh cultivar, cv. 'R201' (plantation year : 2013). The transition stage between fully red fruits and heterogeneously pigmented fruits was targeted during fruit development (84 Days After Full Bloom - DAFB).\\
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fruit mesocarp according to the method detailed by Celton et al., 2014
Library construction and Pair Ends 100bp reads sequencing were completed by BGI using Illumina technology, and the quality was checked using FastQC. The library construction method and sequencing process are carried out according to the following steps : 1) Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; (2) mRNA molecules were fragmented into small pieces; (3) The fragmented mRNA was synthesized into first strand cDNA using random primers; (4) The second strand cDNA was synthesized with dUTP instead of dTTP; (5) The synthesized cDNA was subjected to end-repair and 3'adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; (6) Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; (7) Library quality control; (8) Library circularization; (9) The library was amplified to make DNA nanoball (DNB); (10) Sequencing on DNBSEQ (DNBSEQ Technology) platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
AnaDIff (10.5281/ZENODO.6477918)
Assembly: GDDH13 v1.1
Supplementary files format and content: .sf count files
|
| |
|
| Submission date |
Jun 06, 2024 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Jean-Marc Celton |
| E-mail(s) |
jean-marc.celton@inrae.fr
|
| Organization name |
IRHS
|
| Street address |
42 ue Georges Morel
|
| City |
Beuacouzé |
| ZIP/Postal code |
49070 |
| Country |
France |
| |
|
| Platform ID |
GPL34567 |
| Series (1) |
| GSE269214 |
Transcriptomic analysis between Red-Flesh and White-Flesh Mesocarps in Red-Flesh apple at 84 Days After Full Bloom (DAFB) |
|
| Relations |
| BioSample |
SAMN41706319 |
| SRA |
SRX24821611 |
