|
| Status |
Public on Sep 16, 2016 |
| Title |
p19syn_nb.cym19s.mRNA |
| Sample type |
SRA |
| |
|
| Source name |
p19syn_nb.cym19s.mRNA
|
| Organism |
Nicotiana benthamiana |
| Characteristics |
genotype/variation: transgenic p19syn
tissue: Cym19stop
infection with virus: young leaf
|
| Treatment protocol |
Young leafs of 5-6 week old plants were inoculated. Samples were taken 7 days post inoculation, from upper (non inoculated) leafs.
|
| Growth protocol |
plants were grown under constant 21 °C, 16h light - 8h dark
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with phenol-chlorophorm (as described in the material and methods). RNA was fractionated by isolating from a 8% denaturing poliacrylamide gel run.
RNA-seq: RNA was extracted with phenol-chlorophorm (as described in the material and methods). RNA was polyA fractionated prior library prep.
Illumina TruSeq Small RNA Library Preparation Kit and Illumina TruSeq Stranded mRNA library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
processed data file: nbv5.datamatrix.txt
|
| Data processing |
adapter removeal (UEA smallRNA workbanch 3.0)
Filtration of low complexety reads and reads under 14 nt (UEA smallRNA workbanch 3.0)
alignmant to genomes (PatMaN 1.2.2)
reads were normalized to 1 million total reads passing quality control
Genome_build: Niben v1.0.1. and NC_003532.1
Supplementary_files_format_and_content: Processed data files were uploaded as data matrixes. These matrixes contain a short header followd by the data itself. Headder lines alway begin with a '#'. The first column contains the sequences, second column contains total read counts, the third contains normalised read counts. Column are TAB separsted.
Quality control was done by fastQC 0.10.1
Trim_galore 0.4.1 and FASTX Toolkit 0.0.13 were used to remove adaptor sequences, low quality bases, reads under 20 nt and unpaired reads.
Bowtie2 was used to align reads to the transcriptome
reads were normalized to 1 million total reads passing quality control
Genome_build: Nbv5
Supplementary_files_format_and_content: Processed data were uploaded as a data matrix. The matrix contains a short header followed by the data itself. Header lines always begin with a '#'. The first column contains the transcriptome IDs, second contains wt uninfected read counts from Baksa et al 2015 doi: 10.1186/s12864-015-2209-6, the third contains read counts from sample p19syn_nb.cym19s.mRNA, the fourth column contains read counts from sample wt_nb.cym19s.mRNA, the fifth contains read counts from sample p19syn_nb.mock.mRNA. Column are TAB separated.
|
| |
|
| Submission date |
Aug 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Levente Kontra |
| E-mail(s) |
[email protected]
|
| Organization name |
HUNREN
|
| Department |
institute of experimental medicine
|
| Lab |
Translational Behavioural Neuroscience 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 |
SAMN05504544 |
| SRA |
SRX1994483 |
