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| Status |
Public on Mar 31, 2014 |
| Title |
Identification of the 5' end of the pig miRNA by the RAKE technology |
| Organism |
Sus scrofa |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
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.
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| Overall design |
12K 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 three times to grant the reliability of the identified 5’ end of miRNAs and microarray slides were scanned three times at low, medium and high PMT to improve microarray dynamic range.
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| Contributor(s) |
Cagnin S, Sales G, Martini P, Gandaglia A, Naso F, Brugiolo M, De Pitta’ C, Gerosa G, Spina M, Romualdi C, Lanfranchi G |
| Citation(s) |
24699212 |
| Submission date |
Mar 23, 2011 |
| Last update date |
Jun 30, 2014 |
| Contact name |
Gerolamo Lanfranchi |
| E-mail(s) |
stefano.cagnin@unipd.it
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| Phone |
+39-0498276219
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| Organization name |
University of Padova
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| Department |
CRIBI - Biotechnology Center and Biology Department
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| Lab |
Functional Genomics Lab
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| Street address |
Via U. Bassi, 58/B
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| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
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| Platforms (1) |
| GPL13321 |
CRIBI Tiling array for the identification of 5' end of pig miRNAs |
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| Samples (9)
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| This SubSeries is part of SuperSeries: |
| GSE28637 |
Discovering, evolution, biogenesis, expression and target prediction of porcine micro-RNAs: new regulatory gene expression network in different tissues. |
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| Relations |
| BioProject |
PRJNA143155 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE28139_RAW.tar |
4.0 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data not applicable for this record |
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