E-GEOD-6682 - Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

Status
Released on 1 February 2007, last updated on 3 June 2014
Organism
Arabidopsis thaliana
Samples (14)
Protocols (8)
Description
To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.
Experiment type
RNA-seq of non coding RNA 
Contacts
James C Carrington <carrington@cgrb.oregonstate.edu>, Christopher M Sullivan, Elisabeth J Chapman, Jason S Cumbie, Kristin D Kasschau, Noah Fahlgren
Citations
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. , Europe PMC 17299599
Genome-wide profiling and analysis of Arabidopsis siRNAs. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. , Europe PMC 17298187
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-6682.idf.txt
Sample and data relationshipE-GEOD-6682.sdrf.txt
Processed data (1)E-GEOD-6682.processed.1.zip
Links