E-GEOD-57052 - High-throughput sequencing of small RNAs in Petunia

Status
Released on 24 April 2014, last updated on 3 June 2014
Organism
Petunia x hybrida
Samples (1)
Protocols (2)
Description
Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Petunia x hybrida tissues (including leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves and flowers (see Series GSE13764) of Petunia x hybrida. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Ana Dorantes-Acosta and Richard A. Jorgensen for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
Experiment type
RNA-seq of non coding RNA 
Contacts
Blake C Meyers, Emanuele De Paoli, Monica Accerbi, Pamela J Green
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-57052.idf.txt
Sample and data relationshipE-GEOD-57052.sdrf.txt
Processed data (2)E-GEOD-57052.processed.1.zip, E-GEOD-57052.processed.2.zip
Links