Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-30583 - Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa

Status
Released on 15 January 2014, last updated on 2 June 2014
Organism
Oryza sativa Japonica Group
Samples (20)
Array (1)
Protocols (13)
Description
High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5´and 3´adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. The libraries containing unique barcodes were combined and subjected to pyrosequencing (454 Life SciencesTM, Roche) [Expression profiling by array] Leaves from rice plants were harvested at two time points after the onset of treatment (30' and 2h) with elicitors of Magnaporthe oryzae 18.1 and used for RNA extraction and hybridization on Affymetrix microarrays. Mock inoculations were performed with sterile water for control experiments. Three biological replicates were analyzed. Each sample represented a pool of approximately 150 rice plants. [High throughput sequencing] 8 samples examined: leaves and roots, treated or not with elicitors at two different time points, 30' and 2h (2x2x2)
Experiment types
transcription profiling by array, RNA-seq of non coding RNA 
Contacts
Ana B Moreno, Blanca San Segundo, Cedric Notredame, Christelle Siré, César Llave, Livia Donaire, Matthias Zytnicki, Sonia Campo
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Links