alexa Whole Transcriptome Analysis with Ion Torrent Platform on Challenging Tissues: Formalin-Fixed, Paraffin-Embedded Tissues and Laser Capture Microdissected Samples
ISSN 2469-9853

Journal of Next Generation Sequencing & Applications
Open Access

Like us on:
OMICS International organises 3000+ Global Conferenceseries Events every year across USA, Europe & Asia with support from 1000 more scientific Societies and Publishes 700+ Open Access Journals which contains over 50000 eminent personalities, reputed scientists as editorial board members.

Open Access Journals gaining more Readers and Citations

700 Journals and 15,000,000 Readers Each Journal is getting 25,000+ Readers

This Readership is 10 times more when compared to other Subscription Journals (Source: Google Analytics)

Research Article

Whole Transcriptome Analysis with Ion Torrent Platform on Challenging Tissues: Formalin-Fixed, Paraffin-Embedded Tissues and Laser Capture Microdissected Samples

Francesca Lessi1*, Paolo Aretini1, Sara Franceschi1, Marco La Ferla1, Samuele Negro2, Generoso Bevilacqua1 and Chiara Maria Mazzanti1

1Genomic Section, Pisa Science Foundation ONLUS, Via Panfilo Castaldi, 2, 56121, Pisa (PI), Italy

2Department of Biomedical Sciences, University of Padova, Italy

*Corresponding Author:
Francesca Lessi
Staff Scientist, Genomic Section
Pisa Science Foundation ONLUS
Via Panfilo Castaldi, 2, 56121, Pisa (PI), Italy
Tel: +39050974061
Fax: +390509656178
E-mail: [email protected]

Received date: June 09, 2016; Accepted date: October 14, 2016; Published date: October 16, 2016

Citation: Lessi F, Aretini P, Franceschi S, La Ferla M, Negro S, et al. (2016) Whole Transcriptome Analysis with Ion Torrent Platform on Challenging Tissues: Formalin-Fixed, Paraffin-Embedded Tissues and Laser Capture Microdissected Samples. Next Generat Sequenc & Applic 3:136. doi: 10.4172/2469-9853.1000136

Copyright: © 2016 Lessi F, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.



Background: The advent of the NGS revolutionized cancer research by making it possible to study the complexity of cancer using high throughput sequencing methodologies. The current trends are to adapt highthroughput sequencing technologies to the level of small cell populations and even individual cells. In our laboratory, we developed some different methods that would allow us to work optimally with very low amount of material, based on the technique of the SMARTer technology and on the Ion Torrent protocols that we modified carefully, applied to Ion Proton system.

Materials and methods: We collected 12 formalin-fixed, paraffin-embedded tissues and 20 laser capture microdissected formalin-fixed, paraffin-embedded samples derived from brain and breast cancer and 13 laser capture microdissected fresh frozen samples derived from mouse brain cells.

Results: We developed high performance methods to analyse the whole transcriptomes of our samples, obtaining a very high number of reads (78,186,377 usable reads), perfectly comparable with samples with a large amount of RNA such as samples obtained from cells or fresh tissues.

Conclusions: We have found that the combination of SMARTer technology and Ion TargetSeq Exome Enrichment kit, in addition to some improvements to their conventional protocols, provides excellent results with challenging samples.


Share This Page

Additional Info

Loading Please wait..
Peer Reviewed Journals
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

Agri, Food, Aqua and Veterinary Science Journals

Dr. Krish

[email protected]

1-702-714-7001 Extn: 9040

Clinical and Biochemistry Journals

Datta A

[email protected]

1-702-714-7001Extn: 9037

Business & Management Journals


[email protected]

1-702-714-7001Extn: 9042

Chemical Engineering and Chemistry Journals

Gabriel Shaw

[email protected]

1-702-714-7001 Extn: 9040

Earth & Environmental Sciences

Katie Wilson

[email protected]

1-702-714-7001Extn: 9042

Engineering Journals

James Franklin

[email protected]

1-702-714-7001Extn: 9042

General Science and Health care Journals

Andrea Jason

[email protected]

1-702-714-7001Extn: 9043

Genetics and Molecular Biology Journals

Anna Melissa

[email protected]

1-702-714-7001 Extn: 9006

Immunology & Microbiology Journals

David Gorantl

[email protected]

1-702-714-7001Extn: 9014

Informatics Journals

Stephanie Skinner

[email protected]

1-702-714-7001Extn: 9039

Material Sciences Journals

Rachle Green

[email protected]

1-702-714-7001Extn: 9039

Mathematics and Physics Journals

Jim Willison

[email protected]

1-702-714-7001 Extn: 9042

Medical Journals

Nimmi Anna

[email protected]

1-702-714-7001 Extn: 9038

Neuroscience & Psychology Journals

Nathan T

[email protected]

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

John Behannon

[email protected]

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

[email protected]

1-702-714-7001 Extn: 9042

© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version