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| Status |
Public on Mar 20, 2018 |
| Title |
Genome-wide profiling of mature piRNAs in human Neuroblastoma (NB) cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
To elucidate potential role of piRNAs in Neuroblastoma (NB), we performed the genome wide profiling in two human NB cell lines, IMR-32 and SH-SY-5Y by adopting high-throughput RNA sequencing (RNA-Seq) and unveil their possible functions in neoplastic pathways. The RNA sequencing results revealed both known and novel piRNAs in both the cell lines. We observed a total 630 annotated mature piRNAs, distributed across chromosomes and mitochondria which were mapped to various genomic locations such as introns, protein coding regions, repeats, pseudogenes, ncRNAs etc. This is the first study reporting the extensive catalogue of human NB piRNAs which will provide a useful resource to dissect complex neoplastic events that are possibly mediated by piRNAs in neuroblastoma. Moreover, these piRNAs could be used as probable small RNA biomarkers for the Neuroblastoma.
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| Overall design |
1 µg of total RNA isolated from above two cell lines was used as the starting material for library preparation as prescribed by Illumina Truseq small RNA library protocol. The small RNA libraries (size range 16 nts - 40 nts) were sequenced on Illumina NextSeq 500. Upon de-multiplexing, reads are obtained and then analyzed after QC to predict both known and novel piRNAs.
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| Contributor(s) |
Roy J, Mallick B |
| Citation(s) |
29516567 |
| Submission date |
Jul 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dr. Bibekanand Mallick |
| E-mail(s) |
vivek.iitian@gmail.com
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| Organization name |
National Institute of Technology
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| Department |
Department of Life Science
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| Lab |
RNAi & Functional Genomics Lab.
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| Street address |
NIT Rourkela
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| City |
Rourkela |
| State/province |
Odisha |
| ZIP/Postal code |
769008 |
| Country |
India |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA327500 |
| SRA |
SRP077720 |
