|
| Status |
Public on Sep 16, 2016 |
| Title |
p19syn_nb.mock.p19ip-ip |
| Sample type |
SRA |
| |
|
| Source name |
p19syn_nb.mock.p19ip-ip
|
| Organism |
Nicotiana benthamiana |
| Characteristics |
plant genotype: transgenic p19syn
infection with virus: mock
ip antibody: p19 (homemade by immunizing with purified protein)
tissue: young leaf
|
| Treatment protocol |
Young leafs of 5-6 week old plants were inoculated as described. Samples were taken 7 days post inoculation, from upper leafs.
|
| Growth protocol |
plants were grown under constant 21 °C, 16h light - 8h dark
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immunoprecipitation RNA was extracted with phenol-chloroform (as described in the material and methods). RNA was fractioned purified by isolating from a 8% denaturing poliacrylamide gel.
Standard Illumina TruSeq Small RNA Library Preparation Kit
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Nicotiana benthamiana
smallRNA-seq
|
| Data processing |
adapter removeal (UEA smallRNA workbanch 3.0)
out filtration of low complexety reads and reads under 14 nt (UEA smallRNA workbanch 3.0)
alignmant to genomes (PatMaN 1.2.2)
normalization, 5' end analysis and visualization programs have been uploaded to: https://github.com/kontral/Burgyan_Lab to ensure reproducibility and transparency.
Genome_build: Niben v1.0.1 and ViralProj15066 (NC_003532.1)
Supplementary_files_format_and_content: Processed data files were uploaded as data matrixes. These matrixes contain a short header followed by the data itself. Header lines alway begin with a '#'. The first column contains the sequences, second column contains total read counts, the third contains normalized read counts. Columns are TAB delimited.
|
| |
|
| Submission date |
Jan 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gábor Nyíri |
| E-mail(s) |
[email protected]
|
| Organization name |
HUN-REN Institute of Experimental Medicine
|
| Department |
-
|
| Lab |
Cerebral Cortex Research Group
|
| Street address |
Szigony st 43.
|
| City |
Budapest |
| ZIP/Postal code |
H-1083 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL21356 |
| Series (1) |
| GSE77070 |
Distinct effects of p19 RNA silencing suppressor on small RNA mediated pathways in plants |
|
| Relations |
| BioSample |
SAMN04432443 |
| SRA |
SRX1540534 |
