|
| Status |
Public on May 12, 2020 |
| Title |
Control-E-L35-A_FPKM |
| Sample type |
SRA |
| |
|
| Source name |
grape berry
|
| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Cabernet Sauvignon
Stage: E-L 35
treatment: Control
|
| Treatment protocol |
The 1000 mg/L ABA, 800 mg/L ABA and 100 mg/L NAA solutions containing 0.05% Tween 20 were applied at seven weeks after flowering (berry still hard and green, E-L 33 stage), with 0.05% Tween solution as the control. The spray of these solutions was performed at sunset to avoid the rapid evaporation of the solutions. After the first spray solution was absorbed, the second application were conducted ten hours later at the same day. A randomized block design was considered for this study, and each treatment or control was replicated in three plots of 50 vines. Each berry sample replicate included 500 berries collected from 50 vines. Sampling was performed at four E-L stages (E-L 34, E-L 35, E-L 36 and E-L 38) according to modified E-L system. Then, the samples were kept in dry ice and immediately transferred to laboratory. Before the extraction, samples were washed with distilled water to remove the unabsorbed ABA and NAA residues on berry surface.
|
| Growth protocol |
Clusters of Vitis vinifera L. cv. Cabernet Sauvignon grapevines cultivated in Shanxi Academy of Agricultural Sciences Pomology Institute, Shanxi, China in 2015 were used for the study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three biological replicates for each sample were performed. A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNA was extracted from the frozen deseeded berries (whole pericarp) using a SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, CA, USA). RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference grapevine genome V2 using Bowtie. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using FPKM method.
Genome_build: http://genomes.cribi.unipd.it/DATA/V2/V2.1/
Supplementary_files_format_and_content: Results include length, excepted_count and FPKM and the description of gene for each sample were shown in xlsx table files.
|
| |
|
| Submission date |
May 11, 2020 |
| Last update date |
May 13, 2020 |
| Contact name |
Lei He |
| E-mail(s) |
helei@cau.edu.cn
|
| Phone |
18518638514
|
| Organization name |
China Agricultural University
|
| Street address |
No. 17 Tsinghua east road
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL25271 |
| Series (1) |
| GSE150343 |
Integrated omics analysis reveals the norisoprenoid responses in Vitis vinifera L. cv. Cabernet Sauvignon berries to abscisic acid and synthetic auxin |
|
| Relations |
| BioSample |
SAMN14891997 |
| SRA |
SRX8326484 |
