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| Status |
Public on Sep 08, 2009 |
| Title |
Quantification of synthetic miRNAs |
| Platform organisms |
Homo sapiens; Mus musculus; Rattus norvegicus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Murid gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus hominis; Betapolyomavirus macacae |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification.
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| Overall design |
Two artificial samples (sample A and sample B) were constructed by mixing different amounts of 744 synthetic RNAs.
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| Contributor(s) |
Willenbrock H, Salomon J, Søkilde R, Hansen TN, Barken KB, Nielsen FC, Møller S, Litman T |
| Citation(s) |
19745027 |
| Submission date |
Jan 22, 2009 |
| Last update date |
Feb 21, 2019 |
| Contact name |
Hanni Willenbrock |
| E-mail(s) |
hanni@cbs.dtu.dk
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| Phone |
+45 45 66 09 85
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| Organization name |
DTU
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| Department |
Center for Biological Sequence Analysis
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| Street address |
Kemikalievej, bygning 208
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| City |
Kgs. Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
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| Platforms (3) |
| GPL7722 |
miRCURY LNA microRNA Array, v.10.0 - hsa, mmu & rno |
| GPL7731 |
Agilent-019118 Human miRNA Microarray 2.0 G4470B (Feature Number version) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (18)
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| GSM364514 |
Illumina sequenced synthetic miRNA sample A |
| GSM364515 |
Illumina sequenced synthetic miRNA sample B |
| GSM364523 |
Illumina sequenced synthetic miRNA sample A with barcode 1 |
| GSM364526 |
Illumina sequenced synthetic miRNA sample A with barcode 2 |
| GSM364527 |
Illumina sequenced synthetic miRNA sample A with barcode 3 |
| GSM364528 |
Illumina sequenced synthetic miRNA sample A with barcode 4 |
| GSM364529 |
Illumina sequenced synthetic miRNA sample B with barcode 1 |
| GSM364532 |
Illumina sequenced synthetic miRNA sample B with barcode 2 |
| GSM364533 |
Illumina sequenced synthetic miRNA sample B with barcode 3 |
| GSM364536 |
Illumina sequenced synthetic miRNA sample B with barcode 4 |
| GSM368462 |
Exiqon synthetic miRNA sample A #1 |
| GSM368463 |
Exiqon synthetic miRNA sample A #2 |
| GSM368473 |
Exiqon synthetic miRNA sample B #1 |
| GSM368474 |
Exiqon synthetic miRNA sample B #2 |
| GSM370546 |
Agilent synthetic miRNA sample A #1 |
| GSM370547 |
Agilent synthetic miRNA sample A #2 |
| GSM370548 |
Agilent synthetic miRNA sample B #1 |
| GSM370549 |
Agilent synthetic miRNA sample B #2 |
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| Relations |
| BioProject |
PRJNA111655 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE14511_RAW.tar |
486.3 Mb |
(http)(custom) |
TAR (of TXT, ZIP) |
| Raw data provided as supplementary file |
| Processed data included within Sample table |
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