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Title: Identification of the 3' end of the pig miRNA by the RAKE technology [platform 2: 9003179]      
dateReleased:
03-31-2014
description:
We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful. 90K microarray was hybridized with a pool of small RNAs from 20 different tissues (superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node). Same experiment was replicated four times to grant the reliability of the identified 3’ end of miRNAs and microarray slides were scanned three times at low, medium and high PMT to improve microarray dynamic range.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-28138
refinement:
raw
alternateIdentifiers:
28138
keywords:
functional genomics
dateModified:
06-02-2014
availability:
available
types:
gene expression
name:
Sus scrofa
ID:
A-GEOD-13320
name:
CRIBI Tiling array for the identification of 3' end of pig miRNAs (platform 2)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28138/E-GEOD-28138.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-28138/E-GEOD-28138.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=GSE28138
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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