|
| Status |
Public on Dec 31, 2019 |
| Title |
C-R-1 |
| Sample type |
SRA |
| |
|
| Source name |
Solanum lycopersicum roots inoculated with pUC9
|
| Organism |
Solanum lycopersicum |
| Characteristics |
organ: roots
infecious variants: pUC9-control
|
| Treatment protocol |
Two μg of purified plasmids containing monomeric full-length cDNAs of PSTVd-M (GenBank nr X76844) or PSTVd-S23 (GenBank nr X76846) and empty pUC9 plasmid as a control were mechanically inoculated into tomato leaves. Whole roots were collected at 17 days post inoculation.
|
| Growth protocol |
Inoculated tomato plants were maintained in a greenhouse at 28-30ºC for 16 h and at 25ºC for 8 h in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plant Mini Kit according to manufacturer’s instruction (Qiagen). Contaminating DNA was removed from the extracted RNA using TURBO DNase-free TM Kit (Ambion).
ERCC RNA Spike-In Mix 1 (Thermo Fisher) was added as internal control to each sample. Ribosomal RNA was removed using Ribo-Zero Plant rRNA Removal Kit (Illumina). Libraries were prepared with Ion Total RNA-Seq Kit v2 and Ion Xpress RNA-Seq Barcode 1-16 Kit according to user guide. Sequencing template was generated with Ion PI™ Template OT2 200 Kit v3 on Ion OneTouch™ 2 System. Sequencing was performed on Ion PI™ chip v2 and Ion Proton™ sequencer using Ion PI™ Sequencing 200 Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Gene expression data from pUC9 inoculated roots
|
| Data processing |
Base calling and adapter trimming was performed automatically by Torrent Suite software.
Residual rRNA and ERCC reads were identified and filtered out using bbsplit and filterbyname scripts from BBTools suite (Brian Bushnell).
Reads were aligned to genome using TMAP 5.0.13. with soft clipping from both ends and returning all the mappings with the best score. Other settings were set according to Torrent Suite defaults. Unaligned reads were aligned with BBMap (Brian Bushnell).
Quantitation to ITAG3.2 transcripts and differential expression analysis was performed in Partek Flow (Partek Inc.) using Partek GSA algorithm.
Genome_build: ITAG3
Supplementary_files_format_and_content: gene read counts - Table with raw read counts derived from Partek E/M Quantification Algorithm. Genes are in rows, samlples - in columns
Supplementary_files_format_and_content: differential expression table - table containing results of GSA differential gene expression analysis. For each comparison (Contrast), values of p-value, q-value,FDR, ratio and fold change are presented in column for each gene (in rows)
|
| |
|
| Submission date |
Jan 17, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Aneta Więsyk |
| E-mail(s) |
anetaw@ibb.waw.pl
|
| Organization name |
Institute of Biochemistry and Biophysics, PAS
|
| Street address |
Pawinskiego 5a
|
| City |
Warszawa |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platform ID |
GPL26062 |
| Series (1) |
| GSE125228 |
Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection. [roots RNA-seq] |
|
| Relations |
| BioSample |
SAMN10762495 |
| SRA |
SRX5257296 |
