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Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Caenorhabditis elegans Mus musculus Homo sapiens

PROVIDER: GSE228009 | GEO | 2023/07/11

REPOSITORIES: GEO

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Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale.

Project description:MotivationAnalysis 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 which is highly accurate at only a small fraction of the cost.ResultsWe 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 Caenorhabditis 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%.Availability and implementationAnalysis pipeline for this approach is available at GitHub as R package controlFreq (github.com/gimelbrantlab/controlFreq).

| S-EPMC10311301 | biostudies-literature

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [III]

Project description: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%.

2023-07-11 | GSE228004 | GEO

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [II]

2023-07-11 | GSE228003 | GEO

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [I]

2023-07-11 | GSE228002 | GEO

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale

Project description:Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale

| PRJNA947657 | ENA

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [II]

Project description:Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [II]

| PRJNA947649 | ENA

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [I]

Project description:Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [I]

| PRJNA947650 | ENA

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [III]

Project description:Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [III]

| PRJNA947651 | ENA

Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-03-19 | GSE147203 | GEO

DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing.

Project description:The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine lab processes and results. This challenge will only increase with expanding global production of sequences by diverse research groups for epidemiological and clinical interpretation. We present an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through a sequencing workflow. Applying this approach to the ARTIC Consortium's amplicon design, we define a series of best practices for Illumina-based sequencing and provide a detailed characterization of approaches to increase sensitivity for low-viral load samples incorporating the SDSIs. We demonstrate the utility and efficiency of the SDSI method amidst a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases.

| S-EPMC7987014 | biostudies-literature

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