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Sample GSM761762 Query DataSets for GSM761762
Status Public on Jan 15, 2014
Title Endogenous small RNAs from rice, elicitor-treated LEAVES (2h)
Sample type SRA
 
Source name Elicitor Leaves
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 manufacturer’s 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, elicitor leaves (2h)
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 SRX084591
BioSample SAMN00672596

Data table header descriptions
SEQUENCE read
COUNT read count
READ_ID

Data table
SEQUENCE COUNT READ_ID
AGCCGATTGTAGGTTATATAGCGA 1 seq_29824
AGAAACCACGGGTTGTAGAGTGT 3 seq_59774
CAACGAGAGCACCAAACATGGAAGGTGGTGTGATGTGA 1 seq_29828
GTAAGTTATGGCTAACAATTTGAT 1 seq_89534
AAAGTTTAGTAGCATCGATTGTGA 1 seq_89535
ACGTCGTCATATATTCACCATGGC 1 seq_59776
AATAAGACGAGTGATTAAACAGTG 1 seq_12
ATTCAGCAAGCCACGCAGCAAA 1 seq_89541
TGGCGATGATGATA 1 seq_29835
GGGGATGTAGCTCAAATGGTAGA 3 seq_29837
CGGGAGATGCCCAGCTTGAGAAT 1 seq_59784
AAAGATTTGAATAAGATGAATGGT 1 seq_89549
GATGACATGCAAACAACGAGAGGA 1 seq_29839
AGCTTTCATAGGTCATAGACTGCC 1 seq_29843
TACATCATCTTGCTGATTGGACCA 1 seq_29845
GCAAGTTGGAGCCCGTTTTGGTC 1 seq_29846
TGTGCATACTCCCTA 1 seq_89553
AAAAAAAAAAGCCTGTCGGGACCCGAAAGATGGT 1 seq_29850
TAGACGACCAGGCTACTCAAA 4 seq_29851
AGAACAGAAATCTCGTGTGGAA 1 seq_40

Total number of rows: 20527

Table truncated, full table size 720 Kbytes.




Supplementary file Size Download File type/resource
GSM761762_4._LeafElicitor2h.fasta.gz 235.9 Kb (ftp)(http) FASTA
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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