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| Status |
Public on Apr 15, 2013 |
| Title |
Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (3-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson’s r=0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.
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| Overall design |
we analyzed eight matched frozen and FFPE tissues of different histologies for which detailed processing and storage information.
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| Contributor(s) |
Meng W, McElroy JP, Volinia S, Palatini J, Warner S, Ayers LW, Palanichamy K, Chakravarti A, Lautenschlaeger T |
| Citation(s) |
23696889 |
| Submission date |
Apr 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
wei meng |
| E-mail(s) |
wei.meng@osumc.edu
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| Organization name |
The Ohio State University
|
| Department |
Radiation Oncology
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| Street address |
400 W12 street
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
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| Platforms (1) |
| GPL13393 |
AB SOLiD 4 System (Homo sapiens) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA196169 |
| SRA |
SRP020495 |
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