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| Status |
Public on Aug 18, 2013 |
| Title |
MicroRNA sequencing and Novel HPV miRNA discovery in HPV cell lines and human tissue samples |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Human papillomaviruses (HPV) preferentially infect keratinocytes of mucous membranes or skin and cause numerous benign and malignant lesions at different anatomical locations. A number of DNA viruses encode their own miRNAs as well. To date, no studies have been able to validate viral miRNAs in papillomavirus infected cells using standard sequencing or next generation sequencing techniques. We sequenced small RNA (sRNA) libraries of two HPV 16 immortalized cell lines, HPK IA and HPK II, and ten formalin fixed paraffin embedded (FFPE) tissue samples from HPV infected cervical epithelium by SOLiD 4 technology. We used the miRSeqNovel software, to predict novel miRNAs and their likely pre-miRNAs. We further validated (qRT-PCR, northern blotting and in situ hybridization) the candidate miRNAs in a number of tissue samples from HPV associated cervical disease and also in HPV 16 positive cell lines CaSki and SiHa. Altogether nine candidate microRNAs were identified. The expression of four out of five studied miRNAs was confirmed in human tissue or human epithelial cell lines harboring HPV 16.
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| Overall design |
Small RNA (sRNA) libraries of two HPV 16 immortalized cell lines, HPK IA and HPK II, and ten formalin fixed paraffin embedded (FFPE) tissue samples from HPV infected cervical epithelium, were made according to SOLiD sequencing instructions.
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| Contributor(s) |
Qian K, Pietilä T, Rönty M, Michon F, Frilander M, Ritari J, Tarkkanen J, Thesleff I, Paulín L, Auvinen P, Auvinen E |
| Citation(s) |
23936163 |
| Submission date |
Nov 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kui Qian |
| E-mail(s) |
kui.qian@helsinki.fi
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| Organization name |
University of Helsinki
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| Lab |
DNA Sequencing and Genomics Laboratory
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| Street address |
Viikinkaari 4
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| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
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| Platforms (1) |
| GPL13393 |
AB SOLiD 4 System (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA181288 |
| SRA |
SRP017235 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE42380_RAW.tar |
33.3 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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