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Status |
Public on Jul 11, 2023 |
Title |
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [I] |
Organisms |
Caenorhabditis elegans; Homo sapiens; Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach that is highly accurate at only a small fraction of the cost. We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and C.elegans. Our new approach, controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ∼ 5%.
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Overall design |
Comparative allele-specific expression analysis of RNA-seq data with foreign RNA spike-ins (mixes of human, mouse and C.elegans).
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Contributor(s) |
Gupta S, Mendelevich A, Gimelbrant A |
Citation(s) |
37387154 |
Submission date |
Mar 22, 2023 |
Last update date |
Jul 11, 2023 |
Contact name |
Asia Mendelevich |
Organization name |
Altius
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Street address |
2211 Elliott Ave
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98121 |
Country |
USA |
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Platforms (6)
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GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
GPL25526 |
Illumina NovaSeq 6000 (Homo sapiens; Mus musculus) |
GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
GPL33277 |
Illumina NovaSeq 6000 (Caenorhabditis elegans; Mus musculus) |
GPL33278 |
Illumina NovaSeq 6000 (Caenorhabditis elegans; Homo sapiens) |
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Samples (39)
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This SubSeries is part of SuperSeries: |
GSE228009 |
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale |
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Relations |
BioProject |
PRJNA947650 |