|
| Status |
Public on Jan 15, 2014 |
| Title |
Endogenous small RNAs from rice, control ROOTS (30') |
| Sample type |
SRA |
| |
|
| Source name |
Control Roots
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
age: 15-days old plants
cultivar: Nipponbare
|
| Treatment protocol |
Elicitor treatment of rice leaves was performed by spraying the rice plants with 100 mL of a Magnaporthe oryzae 18.1 suspension (300 µg elicitor/mL) of sterile water containing 0.02% Tween-20 (v/v)
Elicitor treatment of rice roots was performed by covering the roots covered 30mL of a Magnaporthe oryzae 18.1 suspension (300 µg elicitor/mL) of sterile water containing 0.02% Tween-20 (v/v) and another piece of sterile paper
|
| Growth protocol |
Leaf tissues were collected from 15 day-old Nipponbare rice plants that had been grown at 28º±2ºC using a 16-h/8-h light/dark cycle
Root tissues were collected from rice seedings that had been grown in square-plates (24cmx24cm) containing ½ MS agar medium for 8 days, grown at 28º±2ºC using a 16-h/8-h light/dark cycle. During this period, rice roots were allowed to grow over a piece of sterile paper placed over the agar medium.
Elicitors from the Magnaporthe oryzae strain 18.1 were prepared as previously described (Casacuberta JM, Raventos D, Puigdomenech P and Segundo BS. (1992). Expression of the Gene Encoding the PR-Like Protein PRms in Germinating Maize Embryos. Mol Gen Genet 234(1): 97-104.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissues using TRIzol reagent according to manufacturerâs instructions (Invitrogen). 300 µg of total RNA were used for construction of small RNA libraries as described (Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. 2007. Genome-Wide Profiling and Analysis of Arabidopsis siRNAs. PLoS Biol 5(3): e57.; Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C. 2009. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology 392(2): 203-214.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
454 GS FLX |
| |
|
| Description |
Total Endogenous small RNAs from rice, control leaves (30')
library strategy: Barcode
|
| Data processing |
Small RNA sequences were parsed from FASTA formatted files containing reads from 454 sequencing and assigned to each one of the 8 specific libraries (leaf and root tissues, treated or not with elicitors for 30 min or 2h) through identification of the small RNA/adapter boundaries and barcode analysis. The adapter sequences in the 454 sequencing reads were removed and the remaining sequences were collected and mapped to the rice genome (Oryza sativa, version 5.0 - http://www.tigr.org/tdb/e2k1/osa1/pseudomolecules/info.shtml) using BLASTn. The unique RNA sequences that perfectly matched the genome were subjected to subsequent analysis.
|
| |
|
| Submission date |
Jul 15, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Sonia Campo |
| E-mail(s) |
scampo@cragenomica.es
|
| Organization name |
Center for Research in Agricultural Genomics (CRAG)
|
| Street address |
Parc de Recerca UAB Edifici CRAG, Campus UAB
|
| City |
Bellaterra (Cerdanyola del Vallés) |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13925 |
| Series (1) |
| GSE30583 |
Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa |
|
| Relations |
| SRA |
SRX084592 |
| BioSample |
SAMN00672597 |
