Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts

Trost, Brett; Moir, Catherine A.; Gillespie, Zoe E.; Kusalik, Anthony; Mitchell, Jennifer A.; Eskiw, Christopher H.

doi:10.1098/rsos.150402

Cited by 22 publications

(21 citation statements)

References 38 publications

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“…We also compared our data with the transcriptome of bag of marbles ( bam ) mutant testes, in which the transition from spermatogonial to primary spermatocyte is abolished and testes are enriched with over-proliferating spermatogonial cells [30]. Although these studies have been performed using different platforms, it is acceptable to compare the log 2 -fold change data obtained by RNA-seq with the geometric mean of the log 2 -fold change obtained by microarrays [43]. Therefore, the comparisons between these analyses were only at the level of what genes were upregulated or downregulated compared with the wild-type based on the significant log 2 -fold change values obtained from the GEO datasets for each mutant [19,28,29].…”

Section: Resultsmentioning

confidence: 99%

Analysis ofDrosophila p8andp52mutants reveals distinct roles for the maintenance of TFIIH stability and male germ cell differentiation

Cruz‐Becerra¹,

Juárez²,

Valadéz-Graham³

et al. 2016

Open Biol.

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Eukaryotic gene expression is activated by factors that interact within complex machinery to initiate transcription. An important component of this machinery is the DNA repair/transcription factor TFIIH. Mutations in TFIIH result in three human syndromes: xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Transcription and DNA repair defects have been linked to some clinical features of these syndromes. However, how mutations in TFIIH affect specific developmental programmes, allowing organisms to develop with particular phenotypes, is not well understood. Here, we show that mutations in the p52 and p8 subunits of TFIIH have a moderate effect on the gene expression programme in the Drosophila testis, causing germ cell differentiation arrest in meiosis, but no Polycomb enrichment at the promoter of the affected differentiation genes, supporting recent data that disagree with the current Polycomb-mediated repression model for regulating gene expression in the testis. Moreover, we found that TFIIH stability is not compromised in p8 subunit-depleted testes that show transcriptional defects, highlighting the role of p8 in transcription. Therefore, this study reveals how defects in TFIIH affect a specific cell differentiation programme and contributes to understanding the specific syndrome manifestations in TFIIH-afflicted patients.

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Section: Resultsmentioning

confidence: 99%

Analysis ofDrosophila p8andp52mutants reveals distinct roles for the maintenance of TFIIH stability and male germ cell differentiation

Cruz‐Becerra¹,

Juárez²,

Valadéz-Graham³

et al. 2016

Open Biol.

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“…Previous profiling strategies of Mecp2 mice employed microarray and more recently, sequencing-based technologies (66,69). Because strong evidence provided by multiple studies including those led by the Sequencing Quality Control/Microarray Quality Control consortium suggests that there is good concordance across gene expression platforms (83–87), such as array versus sequencing-based approaches, we chose to compare our data to the complete list of genes altered in Mecp2 mice from both array and RNA-seq studies. The ‘union’ of genes expression data, i.e.…”

Section: Discussionmentioning

confidence: 99%

Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome

et al. 2016

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Mouse models of the transcriptional modulator Methyl-CpG-Binding Protein 2 (MeCP2) have advanced our understanding of Rett syndrome (RTT). RTT is a ‘prototypical’ neurodevelopmental disorder with many clinical features overlapping with other intellectual and developmental disabilities (IDD). Therapeutic interventions for RTT may therefore have broader applications. However, the reliance on the laboratory mouse to identify viable therapies for the human condition may present challenges in translating findings from the bench to the clinic. In addition, the need to identify outcome measures in well-chosen animal models is critical for preclinical trials. Here, we report that a novel Mecp2 rat model displays high face validity for modelling psychomotor regression of a learned skill, a deficit that has not been shown in Mecp2 mice. Juvenile play, a behavioural feature that is uniquely present in rats and not mice, is also impaired in female Mecp2 rats. Finally, we demonstrate that evaluating the molecular consequences of the loss of MeCP2 in both mouse and rat may result in higher predictive validity with respect to transcriptional changes in the human RTT brain. These data underscore the similarities and differences caused by the loss of MeCP2 among divergent rodent species which may have important implications for the treatment of individuals with disease-causing MECP2 mutations. Taken together, these findings demonstrate that the Mecp2 rat model is a complementary tool with unique features for the study of RTT and highlight the potential benefit of cross-species analyses in identifying potential disease-relevant preclinical outcome measures.

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“…8,9 Using the microarray approach, we have recently identified a number of gene transcripts that showed repressed expression with time-from-injury in human anterior cruciate ligament (ACL) tears using the 24-sample microarrays dataset. 10 We observed that the most significant differences in expression of gene transcripts exist between acute (<3 month from injury) and chronic (>12 months from injury) groups with little differences between acute and intermediate (3)(4)(5)(6)(7)(8)(9)(10)(11)(12) months from injury) and chronic and intermediate groups. The differentially expressed gene transcripts were enriched for numerous biological processes that were consistent with the initial repair activity in the injured ligament to heal.…”

mentioning

confidence: 85%

“…To the best of our knowledge, no study has compared RNA-seq and microarrays transcriptome profiles in any area of musculoskeletal research. Studies performed on other tissues have focused on the concordance between RNA-seq and microarrays 8; 11; 12 . Our study focused on both the consistencies, as well as differences, between these technologies and further investigated the reasons for any observed discrepancies.…”

Section: Introductionmentioning

confidence: 99%

Advantages of RNA‐seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears

Farooq

Tycksen

Sandell

et al. 2017

Journal Orthopaedic Research

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Microarrays and RNA-seq are at the forefront of high throughput transcriptome analyses. Since these methodologies are based on different principles, there are concerns about the concordance of data between the two techniques. The concordance of RNA-seq and microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed in clinically derived ligament tissues. To demonstrate the concordance between RNA-seq and microarrays and to assess potential benefits of RNA-seq over microarrays, we assessed differences in transcript expression in anterior cruciate ligament (ACL) tissues based on time-from-injury. ACL remnants were collected from patients with an ACL tear at the time of ACL reconstruction. RNA prepared from torn ACL remnants was subjected to Agilent microarrays (N = 24) and RNA-seq (N = 8). The correlation of biological replicates in RNA-seq and microarrays data was similar (0.98 vs. 0.97), demonstrating that each platform has high internal reproducibility. 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 microarrays values were moderate. The cross-platform concordance for differentially expressed transcripts or enriched pathways was linearly correlated (r = 0.64). RNA-Seq was superior in detecting low abundance transcripts and differentiating biologically critical isoforms. Additional independent validation of transcript expression was undertaken using microfluidic PCR for selected genes. PCR data showed 100% concordance (in expression pattern) with RNA-seq and microarrays data. These findings demonstrate that RNA-seq has advantages over microarrays for transcriptome profiling of ligament tissues when available and affordable. Furthermore, these findings are likely transferable to other musculoskeletal tissues where tissue collection is challenging and cells are in low abundance. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:484-497, 2018.

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Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts

Cited by 22 publications

References 38 publications

Analysis ofDrosophila p8andp52mutants reveals distinct roles for the maintenance of TFIIH stability and male germ cell differentiation

Analysis ofDrosophila p8andp52mutants reveals distinct roles for the maintenance of TFIIH stability and male germ cell differentiation

Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome

Advantages of RNA‐seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears

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