|
| Status |
Public on Jun 03, 2014 |
| Title |
Seed 9WAF |
| Sample type |
SRA |
| |
|
| Source name |
Seed 9WAF
|
| Organism |
Vitis vinifera |
| Characteristics |
index sequence: GCCC
total tag counts: 329399
developmental stage: 9 weeks after flowering
tissue: seed
light regime: light exposure
|
| Treatment protocol |
Three treatments on the clusters of the same vines were performed: light exposure (control), shading with light-proof boxes from flowering onward (shade), shading during 2 weeks (14 days) from the onset of the treatment and then light exposed (shade/light exposure). Berry samples from the grape clusters of the three treatments were collected 3 days after removal of light-proof boxes (17 days after flowering)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with a previously described procedure (Reid et al. BMC Plant Biology 6:27). Quality control was performed with the Agilent 2100 Bioanalyzer.
Ds-cDNA was synthesized using biotinylated dT primer. After digestion of cDNA with anchoring enzymes NlaIII, digested fragments were associated streptavidin magnetic beads. Adapters were ligated to cDNA ends on the beads and adapter-cDNA was digested with EcoP15I. Released fragments after enzyme digestion were ligated to adapter encoding barcode. Obtained fragments were once amplified PCR and applied to sequence analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 9
|
| Data processing |
Tags were extracted from sequence data of multiplexed samples, which were analyzed by Illumina Genome Analyzer II. Sequence reads were sorted by index seqence into separate files. From each read in each file, 26-bp sequence upstream anchoring enzyme site (CATG) was extracted. Extracted 26-bp sequences (tags) were counted. Non singleton tags were extracted in each sample and used for transcript profiling. These process was done by script written in Perl.
Supplementary_files_format_and_content: Tab-delimited text files include tag sequences and tag counts per million total tags for each Sample.
|
| |
|
| Submission date |
Feb 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kazuya Koyama |
| E-mail(s) |
koyama@nrib.go.jp
|
| Phone |
+81-82-420-0812
|
| Organization name |
National Research Institute of Brewing
|
| Department |
Fundamental Reesearch Division
|
| Street address |
3-7-1, Kagamiyama
|
| City |
Higashi-Hiroshima |
| State/province |
Hiroshima |
| ZIP/Postal code |
739-0046 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14639 |
| Series (2) |
| GSE55473 |
High-throughput SuperSAGE for transcript profiling in berry tissues of Vitis vinifera L. under different light regimes |
| GSE55474 |
Functional characterization of a new grapevine MYB transcription factor and regulation of proanthocyanidin biosynthesis in grapes |
|
| Relations |
| BioSample |
SAMN02666827 |
| SRA |
SRX478599 |
