http://www.cnr.it/ontology/cnr/individuo/prodotto/ID274249
A platform independent RNA-Seq protocol for the detection of transcriptome complexity (Articolo in rivista)
- Type
- Label
- A platform independent RNA-Seq protocol for the detection of transcriptome complexity (Articolo in rivista) (literal)
- Anno
- 2013-01-01T00:00:00+01:00 (literal)
- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
- 10.1186/1471-2164-14-855 (literal)
- Alternative label
Claudia Calabrese1+, Marina Mangiulli2+, Caterina Manzari2, Anna Maria Paluscio3, Mariano Francesco Caratozzolo3, Flaviana Marzano3, Ivana Kurelac1, Anna Maria D'Erchia2, Domenica D'Elia3, Flavio Licciulli3, Sabino Liuni3, Ernesto Picardi2, Marcella Attimonelli2, Giuseppe Gasparre1, Anna Maria Porcelli4, Graziano Pesole25, Elisabetta Sbisà3 and Apollonia Tullo3* (2013)
A platform independent RNA-Seq protocol for the detection of transcriptome complexity
in BMC genomics
(literal)
- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
- Claudia Calabrese1+, Marina Mangiulli2+, Caterina Manzari2, Anna Maria Paluscio3, Mariano Francesco Caratozzolo3, Flaviana Marzano3, Ivana Kurelac1, Anna Maria D'Erchia2, Domenica D'Elia3, Flavio Licciulli3, Sabino Liuni3, Ernesto Picardi2, Marcella Attimonelli2, Giuseppe Gasparre1, Anna Maria Porcelli4, Graziano Pesole25, Elisabetta Sbisà3 and Apollonia Tullo3* (literal)
- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#url
- http://www.biomedcentral.com/1471-2164/14/855 (literal)
- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
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- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
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- PubMed (literal)
- ISI Web of Science (WOS) (literal)
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- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
- 1 Dip. Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, via Massarenti 9, 40138, Bologna, Italy
2 Dip. Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari, via E. Orabona 4, 70126, Bari, Italy
3 Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy
4 Dip. Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
5 Istituto di Biomembrane e Bioenergetica (IBBE), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy (literal)
- Titolo
- A platform independent RNA-Seq protocol for the detection of transcriptome complexity (literal)
- Abstract
- Background
Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein coding genes and their splice variants. Indeed, most transcripts are the result of antisense, overlapping and non-coding RNA expression. In this frame, one of the key aims of high throughput transcriptome sequencing is the detection of all RNA species present in the cell and the first crucial step for RNA-seq users is represented by the choice of the strategy for cDNA library construction. The protocols developed so far provide the utilization of the entire library for a single sequencing run with a specific platform.
Results
We set up a unique protocol to generate and amplify a strand-specific cDNA library representative of all RNA species that may be implemented with all major platforms currently available on the market (Roche 454, Illumina, ABI/SOLiD). Our method is reproducible, fast, easy-to-perform and even allows to start from low input total RNA. Furthermore, we provide a suitable bioinformatics tool for the analysis of the sequences produced following this protocol.
Conclusion
We tested the efficiency of our strategy, showing that our method is platform-independent, thus allowing the simultaneous analysis of the same sample with different NGS technologies, and providing an accurate quantitative and qualitative portrait of complex whole transcriptomes. (literal)
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