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Series GSE52441 Query DataSets for GSE52441
Status Public on Dec 06, 2013
Title Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon
Organism Brachypodium distachyon
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using Parallel Analysis of RNA Ends (PARE) data is lacking in B. distachyon.
B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset to analyze small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner.
B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.

 
Overall design Examination of various tissues and stresses in Brachypodium by high throughput sequencing for small RNA profiling and PARE (Parallel Analysis of RNA Ends)
 
Contributor(s) Green PJ, Jeong D
Citation(s) 24367943
Submission date Nov 15, 2013
Last update date Mar 07, 2014
Contact name Dong-Hoon Jeong
E-mail jeong@dbi.udel.edu
Phone 3027383769
Organization name University of Delaware
Street address 15 Innovation Way
City NEWARK
State/province DE
ZIP/Postal code 19711
Country USA
 
Platforms (1)
GPL17338 Illumina Genome Analyzer IIx (Brachypodium distachyon)
Samples (19)
GSM1266839 BDI08 Root
GSM1266840 Seedling
GSM1266841 BDI04 Leaf 1
Relations
BioProject PRJNA229162
SRA SRP033203

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52441_RAW.tar 260.2 Mb (http)(custom) TAR (of TXT)
Processed data provided as supplementary file
Raw data are available in SRA

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