ArticleRoyal Society open science2015
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.
Article in Royal Society open science, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach.Scientific reports · 2018Pooled it
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- A measure of agreement across numerous conditions: assessing when changes in network structures are tissue-specific.BMC genomics · 2019Article
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- Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2018Article
- Orthogonal Comparison of Molecular Signatures of Kidney Transplants With Subclinical and Clinical Acute Rejection: Equivalent Performance Is Agnostic to Both Technology and Platform.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2017Article
- Androgen receptor-deficient islet β-cells exhibit alteration in genetic markers of insulin secretion and inflammation. A transcriptome analysis in the male mouse.Journal of diabetes and its complications · 2017Article
- Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.Briefings in bioinformatics · 2017Article
- RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles.Scientific reports · 2017Article
- Analysis of Drosophila p8 and p52 mutants reveals distinct roles for the maintenance of TFIIH stability and male germ cell differentiation.Open biology · 2016Article
- Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome.Human molecular genetics · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA microarrays and RNA sequencing (RNA-seq) are major technologies for performing high-throughput analysis of transcript abundance. Recently, concerns have been raised regarding the concordance of data derived from the two techniques. Using cDNA libraries derived from normal human foreskin fibroblasts, we measured changes in transcript abundance as cells transitioned from proliferative growth to quiescence using both DNA microarrays and RNA-seq. The internal reproducibility of the RNA-seq data was greater than that of the microarray data. Correlations between the RNA-seq data and the individual microarrays were low, but correlations between the RNA-seq values and the geometric mean of the microarray values were moderate. The two technologies had good agreement when considering probes with the largest (both positive and negative) fold change (FC) values. An independent technique, quantitative reverse-transcription PCR (qRT-PCR), was used to measure the FC of 76 genes between proliferative and quiescent samples, and a higher correlation was observed between the qRT-PCR data and the RNA-seq data than between the qRT-PCR data and the microarray data.
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