|
| Status |
Public on Jul 22, 2015 |
| Title |
2011G1 |
| Sample type |
SRA |
| |
|
| Source name |
grape berry
|
| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Muscat Blanc a Petits Grains
developmental stage: E-L31
origin: Gaotai region of Gansu province
|
| Growth protocol |
The vines used for grape sampling were cultivated in 2001 (in gaotai region) and 2006 (in changli rigion), respectively. The grapevines in both regions were planted from cutting stems and trained on a vertical shoot positioning (VSP), arranged in north-south oriented rows spaced 2.0 m apart, with a distance of approximately 1.0 m between two plants in each row. The management of the vineyards was in accordance with the local wine grape production technical rules.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 50 berries were randomly selected from a 1000-berry biological replicate for RNA extraction. Total RNAs for RNA-seq analysis and real-time polymerase chain reaction (PCR) experiments were extracted from frozen deseeded berries using a plant RNA isolation kit (Sigma RT-250, St. Louis, MO, USA), and further incubated with DNase I (Promega, USA) according to the manufacturer’s instructions. RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
The Gene Expression Sample Prep Kit (IlluminaInc; San Diego, CA, USA) was used for sequence tag preparation according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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
Clean reads were mapped to reference sequences using CLC software. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using RPKM method (Reads Per kb per Million reads). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Vitis vinifera NCBI RefSeq mRNAs
Supplementary_files_format_and_content: Results include the coverage of each gene, RPKM values, toatal number of reads that aligned to gene, and the description of gene for each sample
|
| |
|
| Submission date |
Jul 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Qiu-hong Pan |
| E-mail(s) |
[email protected]
|
| Organization name |
China Agriculture University
|
| Department |
College of Food Science and Nutritional Engineering
|
| Lab |
Centre for Viticulture and Enology
|
| Street address |
Tsinghua East Road No.17,Haidian district
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL18740 |
| Series (1) |
| GSE71146 |
Using the combined analysis of transcripts and metabolites to propose key genes for differential terpene accumulation across two regions |
|
| Relations |
| BioSample |
SAMN03892112 |
| SRA |
SRX1113879 |
