|
| Status |
Public on Sep 28, 2018 |
| Title |
PARE Library from leaves of mock - inoculated plants |
| Sample type |
SRA |
| |
|
| Source name |
mock-inoculated
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: cv. Money maker
infected with: mock-inoculated
tissue: leaves
molecule subtype: 3'-poly-adenylated, RNA 5'-uncapped
|
| Treatment protocol |
Geminiviruses were infected by agroinfiltration following the procedure previously described by Miozzi et al., 2013-Virus research.
|
| Growth protocol |
Samples were collected from plants grown in greenhouse under controlled conditions of light (16 h light- 8 h dark) and temperature (20-22 °C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tri-Reagent (Sigma-Aldrich)
TrueSeq sRNA Illumina kit's instructions for sRNAseq and German et al., 2008 (Nature protocol) for PARE libraries
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PARE2
|
| Data processing |
FastX tool kit (http://hannonlab.cshl.edu/fastx_toolkit/) was used for elaboration of row data
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.Then converted to FASTA
Fasta files form sRNA datasets mock-inoculated and virus-infected were filtered for 16-26nt long sequences
Fasta files from PARE datasets mock-inoculated and virus-infected were filtered for 20-21nt long sequences
sRNAs and PARE libraries from same plant tissues either from virus-infected or mock-inoculated plants were used as input in the PAREsnp software (http://srna-workbench.cmp.uea.ac.uk) in order to identify miRNA-mediated cleaved transcripts. The output is contained in two different files denoted as outputPARETomatoMock#2.xltx and outputPARETomatoTYLCS#2.xltx
Supplementary_files_format_and_content: tab-delimited text files for each sample containing the filtered 16-26nt long sRNAs or 20-21nt long 5'-remnants of RNAs.The outputs of PARE analysis is in the XlS format and contain the 5'RNA remnants from sample PARE1 or PARE2 explained by each sRNA from sample sRNA1 or sRNA2, respectively.
|
| |
|
| Submission date |
Jan 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Vitantonio Pantaleo |
| E-mail(s) |
vitantonio.pantaleo@cnr.it
|
| Phone |
00390805442935
|
| Organization name |
Institute for Sustainable Plant Protection
|
| Lab |
Research Unit of Bari (ex IVV-CNR)
|
| Street address |
Via Amendola 165/a
|
| City |
Bari |
| ZIP/Postal code |
70126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE93648 |
Gene family Diversification in conserved miRNAs target sites in Tomato revealed as layers of interaction with a nuclear-replicating virus. |
|
| Relations |
| BioSample |
SAMN06233914 |
| SRA |
SRX2495274 |
