|
| Status |
Public on Jul 29, 2009 |
| Title |
Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNA replicates (Illumina) |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libraries from a biological sample as well as an equimolar pool of synthetic miRNAs and analyzed the results using capillary dideoxy sequencing and next-generation sequencing platforms (Roche/454, AB/SOLiD and Illumina/Solexa). Whereas different sequencing platforms provided highly similar results, large differences in DGE profiles were observed depending on the library preparation method used. Nevertheless, our results indicate that the preferential nature of the library preparation methods is systematic and highly reproducible and we show that DGE is well suited for the quantification of relative expression differences between samples.
Keywords: Transcriptome analysis
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| |
|
| Overall design |
Examination library method on preparation of equimolar pool of miRNAs, three replicates, sequenced on Illumina GA II
|
| |
|
| Contributor(s) |
de Wit E, Linsen S, Cuppen E |
| Citation(s) |
19564845 |
| Submission date |
Jun 01, 2009 |
| Last update date |
Dec 03, 2018 |
| Contact name |
Elzo de Wit |
| Phone |
+31 30 2121 800
|
| Organization name |
Hubrecht Institute
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
|
| Samples (3) |
| GSM410826 |
synthetic_miRNAs_modban_amplified_rep1 |
| GSM410827 |
synthetic_miRNAs_modban_amplified_rep2 |
| GSM410828 |
synthetic_miRNAs_modban_amplified_rep3 |
|
| This SubSeries is part of SuperSeries: |
| GSE16374 |
Limitations and possibilities of small RNA digital gene expression profiling |
|
| Relations |
| BioProject |
PRJNA122865 |
