|
| Status |
Public on Feb 24, 2020 |
| Title |
90_MR small RNA |
| Sample type |
SRA |
| |
|
| Source name |
samples derived from rootstock nursery
|
| Organism |
Vitis vinifera |
| Characteristics |
cultivar: 5C, Gerorgikon, Berlandieri, Fercal
locale: Mogyorósi Raposka
tissue: pooled RNA from leaf, shoot tip, tendril
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
variety: 5C, Gerorgikon, Berlandieri, Fercal
|
| Data processing |
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary_files_format_and_content: trimmed redundant list, each read with its number of repeats
|
| |
|
| Submission date |
May 10, 2019 |
| Last update date |
Feb 25, 2020 |
| Contact name |
Éva Várallyay |
| E-mail(s) |
varallyay.eva@abc.naik.hu
|
| Organization name |
National Agricultural Research and Innovation Centre
|
| Department |
Agricultural Biotechnology Institute
|
| Lab |
Diagnostics
|
| Street address |
4 Szent-Györgyi Albert Street
|
| City |
Gödöllő |
| ZIP/Postal code |
2100 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL18740 |
| Series (1) |
| GSE130994 |
small RNA NGS based diagnostic survey of Hungarian grapevine rootstock plantations |
|
| Relations |
| BioSample |
SAMN11618374 |
| SRA |
SRX5817240 |
