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Title: A microRNA expression atlas of grapevine based on small RNA library sequencing      
dateReleased:
05-01-2015
description:
Genetic and epigenetic regulations, mostly driven by small non-coding RNAs, play a crucial role to define genetic programming in plant biology and development. In this work, we focus on miRNAs, the most representative class of small RNAs, to present the first comprehensive miRNA expression atlas in Vitis vinifera L. Our atlas gives a clear picture of miRNA regulation and homeostasis in the whole plant during its lifecycle. We analyzed 68 small RNA libraries, which were prepared from a rich and diverse number of tissues (13) harvested on different developmental stages. We identified 110 known miRNAs and annotated 176 novel, some of which belonging to known families and others completely new. We found that very few miRNAs may be defined as tissue specific. However, interestingly, in the stamen 22 miRNAs were found highly specific. Most of the identified miRNAs show low expression levels, whereas, 32 miRNAs are present in all tissues and mainly highly expressed. Additionally, in each organ, the different developmental stages share 30—70% of miRNAs and their modulation leads the regulation of plant development. We also present a target prediction analysis and suggest a first functional description of hundreds of miRNAs. Our findings represent the most complete expression atlas for grapevine and any other woody species, paving the ground for future functional studies. Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation and Illumina Small RNA Sample Prep kit followed by high-throughput sequencing with Illumina HiSeq 2000 and GA IIx Illumina Sequencer platforms for 13 different organs/tissues of grapevine in different developmental stages, with two replicates each, comprising a total of 70 samples
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-59802
refinement:
raw
alternateIdentifiers:
59802
keywords:
functional genomics
dateModified:
05-10-2015
availability:
available
types:
gene expression
name:
Vitis vinifera
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-59802/E-GEOD-59802.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-59802/E-GEOD-59802.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59802
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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