ArticleBMC biotechnology2016
Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.
Article in BMC biotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia.Nature communications · 2024Article
- Doxycycline post-exposure prophylaxis for sexually transmitted infections impacts the gut antimicrobial resistome.Research square · 2024Article
- Spatial proteomics of hippocampal subfield-specific pathology in Alzheimer's disease and primary age-related tauopathy.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Transcriptome-wide profiling of acute stress induced changes in ribosome occupancy level using external standards.PloS one · 2023Article
- Functional Synthetic Biology.Synthetic biology (Oxford, England) · 2023Review
- Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children.Nature communications · 2022Article
- Differential protein expression in the hippocampi of resilient individuals identified by digital spatial profiling.Acta neuropathologica communications · 2022Article
- Boosting the power of transcriptomics by developing an efficient gene expression profiling approach.Plant biotechnology journal · 2022Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundHighly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approaches included a modified Latin square design to provide a broad dynamic range of relative abundance with known differences between four complex pools of ERCC RNA transcripts spiked into a human liver total RNA background.
resultsERCC pools were analyzed on four different microarray platforms: Agilent 1- and 2-color, Illumina bead, and NIAID lab-made spotted microarrays; and two different second-generation sequencing platforms: the Life Technologies 5500xl and the Illumina HiSeq 2500. Individual ERCC controls were assessed for reproducible performance in signal response to concentration among the platforms. Most demonstrated linear behavior if they were not located near one of the extremes of the dynamic range. Performance issues with any individual ERCC transcript could be attributed to detection limitations, platform-specific target probe issues, or potential mixing errors. Collectively, these pools of spike-in RNA controls were evaluated for suitability as surrogates for endogenous transcripts to interrogate the performance of the RNA measurement process of each platform. The controls were useful for establishing the dynamic range of the assay, as well as delineating the useable region of that range where differential expression measurements, expressed as ratios, would be expected to be accurate.
conclusionsThe modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.
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