E-GEOD-50032 - Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

Status
Released on 21 October 2013, last updated on 3 June 2014
Organism
Phytophthora sojae
Samples (1)
Protocols (2)
Description
Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level. Phytophthora sojae mycelium small RNAs were sequenced and aligned to the P. sojae genome for analysis. *Raw data files (fastq) are unavailable for this study.
Experiment type
RNA-seq of non coding RNA 
Contacts
James C Carrington <jcarrington@danforthcenter.org>, Caroline M Press, Christopher M Sullivan, Elisabeth J Chapman, J S Hoyer, Josh T Cuperus, Kerrigan B Gilbert, Kristin D Kasschau, Niklaus J Grünwald, Noah Fahlgren, Stephanie R Bollmann
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-50032.idf.txt
Sample and data relationshipE-GEOD-50032.sdrf.txt
Processed data (1)E-GEOD-50032.processed.1.zip
Links