|
| Status |
Public on Jul 29, 2009 |
| Title |
Limitations and possibilities of small RNA digital gene expression profiling |
| Organisms |
Homo sapiens; Rattus norvegicus |
| 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.
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
Refer to individual Series
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| 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 (4)
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| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9138 |
AB SOLiD System 2.0 (Homo sapiens) |
| GPL9412 |
454 GS FLX (Rattus norvegicus) |
| GPL9413 |
AB SOLiD System 2.0 (Rattus norvegicus) |
|
| Samples (20)
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| This SuperSeries is composed of the following SubSeries:
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| GSE16369 |
Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (454) |
| GSE16370 |
Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (SOLiD) |
| GSE16371 |
Limitations and possibilities of small RNA digital gene expression profiling: spleen and liver comparison (SOLiD) |
| GSE16372 |
Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNAs replicates (SOLiD) |
| GSE16373 |
Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNA replicates (Illumina) |
|
| Relations |
| BioProject |
PRJNA115327 |
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