|
| Status |
Public on Dec 31, 2019 |
| Title |
S-49-2 |
| Sample type |
RNA |
| |
|
| Source name |
Solanum lycopersicum roots inoculated with PSTVd-S23 at 49 dpi
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: roots
treatment: inoculated with PSTVd-S23 at 49 dpi
cultivar: Rutgers
|
| Treatment protocol |
Tomato seedlings with true leaves were mechanically inoculated with purified plasmids (2 μg/plant) containing monomeric full-length cDNAs of PSTVd-M (GenBank nr X76844) or PSTVd-S23 (GenBank nr X76846) and empty pUC9 plasmid as a control. Tomato roots were collected at 17, 24 and 49 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).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNAs were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cDNA were hybridized on GeneChip Tomato Gene 1.0 ST Array in the Affymetrix according to standard Affymetrix protocol. scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Scan protocol |
The chips were scanned using the Affymetrix GeneAtlas Scanner.
|
| Description |
roots at 49 dpi, biological rep2
Gene expression data from PSTVd-S23 inoculated roots at 49 dpi
|
| Data processing |
The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.
|
| |
|
| Submission date |
Mar 12, 2018 |
| 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 |
GPL4741 |
| Series (1) |
| GSE111736 |
Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection. |
|
