|
| Status |
Public on Dec 20, 2017 |
| Title |
RG_YL-Repl1 |
| Sample type |
SRA |
| |
|
| Source name |
Young leaves
|
| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Red globe
tissue: Young leaves
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from young leaves and fruits peels were extracted using the RNeasy Plant Mini Kit according to manufacters’ instructions with slight modifications
Transcriptome library for sequencing was constructed according to the NEXTflex Rapid Directional mRNA-Seq Bundle library protocol outlined in “NEXTflexTM Rapid Directional mRNA-Seq Sample Preparation Guide” (Cat # 5138-10)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to grape transcriptome using TopHat (v2.1.1).
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Genome_build: grape transcriptome Genoscope 12X v2
Supplementary_files_format_and_content: Text delimited files including RPKM for each sample.
|
| |
|
| Submission date |
Dec 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
shivaprasad@ncbs.res.in
|
| Phone |
+91 80 2366 6511
|
| Organization name |
National Center for Biological Sciences
|
| Department |
Plant epigenetics
|
| Street address |
GKVK Campus, Bellary road
|
| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL24368 |
| Series (1) |
| GSE107905 |
A cluster of miRNAs regulate MYB repressors to promote anthocyanin accumulation in grapes (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN08160026 |
| SRA |
SRX3461228 |
