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| Status |
Public on Oct 31, 2018 |
| Title |
miRTrace quality control of small RNA-Seq data prepared from low-input, degraded and contamianted HEK-293T RNA samples |
| Organisms |
Drosophila melanogaster; Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
miRTrace is a tool for quality control and tracing taxonomic origins of microRNA sequencing data. It operates in two modes: Trace mode, in which the software reports the composition of clade-specific miRNAs; and QC mode, in which it performed an all-round quality control. To validate the QC mode of the software, we subjected the in-house control samples from HEK-293T cells to various treatments, such as cross-species contamiantion with Drosophila S2 RNAs, sample dilution and RNase A digestion. These samples were processed using QC mode of miRTrace. We demonstrate that miRTrace accurately identities poor-quality samples and to some extent even the causes of the compromised quality.
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| Overall design |
miRTrace quality control profiles of standard HEK-293T and Drosophila S2 samples (with 1000 ng total RNA as input) and compromised HEK-293T samples that are contaminated with S2 RNAs in ratio 10:1, 100:1 and 1000:1, diluted to 50 ng and degraded with RNase A enzyme.
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| Contributor(s) |
Kang W, Eldfjell Y, Fromm B, Estivill X, Biryukova I, Friedländer MR |
| Citation(s) |
30514392 |
| |
| Submission date |
Aug 12, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Marc Riemer Friedländer |
| E-mail(s) |
[email protected]
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| Organization name |
Stockholm University / SciLifeLab
|
| Department |
Department of Molecular Biosciences, The Wenner-Gren Institute
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| Lab |
Lab Friedländer
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| Street address |
Svante Arrhenius väg 20C
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| City |
Stockholm |
| ZIP/Postal code |
10691 |
| Country |
Sweden |
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| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
| GPL22339 |
Illumina NextSeq 500 (Drosophila melanogaster; Homo sapiens) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA485638 |
| SRA |
SRP157338 |
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