Back to Search
Start Over
Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears
- Source :
- Journal of Orthopaedic Research.
- Publication Year :
- 2017
- Publisher :
- Wiley, 2017.
-
Abstract
- 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. There was a higher correlation between the PCR data and the RNA-seq as well as the microarrays data. These findings demonstrate that RNA-seq has advantages over microarrays for transcriptome profiling of ligament tissues when available and affordable. This article is protected by copyright. All rights reserved
- Subjects :
- 0301 basic medicine
Concordance
Anterior cruciate ligament
genetic processes
RNA
RNA-Seq
Computational biology
Biology
Bioinformatics
Transcriptome
03 medical and health sciences
030104 developmental biology
medicine.anatomical_structure
Gene expression
medicine
natural sciences
Orthopedics and Sports Medicine
DNA microarray
Gene
Subjects
Details
- ISSN :
- 07360266
- Database :
- OpenAIRE
- Journal :
- Journal of Orthopaedic Research
- Accession number :
- edsair.doi...........aa4663d6c8ecd224fd9fc16b04fdc05c