ArticleRNA (New York, N.Y.)2009
Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAs.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 31 citations in OpenAlex.
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- Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells.Scientific reports · 2023Article
- Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment.RNA biology · 2021Article
- Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.Scientific reports · 2021Article
- Heterogeneous glutamatergic receptor mRNA expression across phrenic motor neurons in rats.Journal of neurochemistry · 2020Article
- Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network.Nucleic acids research · 2019Article
- Experimental Considerations for Single-Cell RNA Sequencing Approaches.Frontiers in cell and developmental biology · 2018Review
- Differential gene expression in disease: a comparison between high-throughput studies and the literature.BMC medical genomics · 2017Article
- Nuclear Compartmentalization Contributes to Stage-Specific Gene Expression Control inFrontiers in cell and developmental biology · 2017Article
- Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons.Nature protocols · 2016Article
- Influence of RNA extraction methods and library selection schemes on RNA-seq data.BMC genomics · 2014Article
- A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA.Molecular and cellular biology · 2014Article
- RNA-sequencing from single nuclei.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.BMC genomics · 2012Article
- SMAD4-dependent polysome RNA recruitment in human pancreatic cancer cells.Molecular carcinogenesis · 2012Article
- Obesity is mediated by differential aryl hydrocarbon receptor signaling in mice fed a Western diet.Environmental health perspectives · 2012Article
- Implication of the miR-184 and miR-204 competitive RNA network in control of mouse secondary cataract.Molecular medicine (Cambridge, Mass.) · 2012Article
- Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming.RNA (New York, N.Y.) · 2012Article
- Imaging mRNA Expression in Live Cells via PNA·DNA Strand Displacement-Activated Probes.Journal of nucleic acids · 2012Article
- Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR.RNA (New York, N.Y.) · 2012Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
With no known exceptions, every published microarray study to determine differential mRNA levels in eukaryotes used RNA extracted from whole cells. It is assumed that the use of whole cell RNA in microarray gene expression analysis provides a legitimate profile of steady-state mRNA. Standard labeling methods and the prevailing dogma that mRNA resides almost exclusively in the cytoplasm has led to the long-standing belief that the nuclear RNA contribution is negligible. We report that unadulterated cytoplasmic RNA uncovers differentially expressed mRNAs that otherwise would not have been detected when using whole cell RNA and that the inclusion of nuclear RNA has a large impact on whole cell gene expression microarray results by distorting the mRNA profile to the extent that a substantial number of false positives are generated. We conclude that to produce a valid profile of the steady-state mRNA population, the nuclear component must be excluded, and to arrive at a more realistic view of a cell's gene expression profile, the nuclear and cytoplasmic RNA fractions should be analyzed separately.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.