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Series GSE65469 Query DataSets for GSE65469
Status Public on Jan 30, 2015
Title RNA-seq and Microarray in Transcriptome Profiling of Anterior Cruciate Ligament Tears: Implications for Prognostic Biomarkers Discovery
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Injury to anterior cruciate ligament (ACL) is common in young individuals and a frequent cause of functional instability and early onset of osteoarthritis. The healing potential of an injured ACL is known to decay over time. The molecular origin of this healing deficiency largely remains elusive but plausibly involves gene transcripts associated with tissue healing. To explore this possibility, we set out to identify transcript expression differences in injured ACL remnants recovered at the time of surgical reconstruction, via microarray (n=24) and RNA-seq (n=8) technologies in transcriptome profiling. We found that time-from-injury was an important determinant of changes in gene expression signatures predominately resulting in repression of several biological processes as identified by gene ontology. The most interesting observation was a time-dependent decline in the gene transcripts as well as the biological processes common to both microarray and RNA-seq analyses. Compared to acute tears, in chronic several important biological processes were namely extracellular matrix organization, angiogenesis, cell adhesion, wound healing, mesenchyme transition, and response to hypoxia. Furthermore, the cross-platform concordance in terms of differentially expressed transcripts or enriched pathways was linearly correlated (r=0.64). Microfluidic digital PCR confirmed the expression of selected differentially expressed transcripts. These intriguing findings suggest an initial attempt of the injured ACL to repair, which drops with time. These findings have implications for efforts to repair the ACL and may be relevant for its reconstruction. These findings also emphasize the utility of differentially expressed transcripts as prognostic biomarkers in patients with ACL injury.
Overall design Examination of transcript expression differences by time-from-injury in anterior cruciate ligament
Contributor(s) Rai MF, Tycksen ED, Brophy RH, Sandell LJ
Citation(s) 28749036
Submission date Jan 30, 2015
Last update date Jul 09, 2019
Contact name Muhammad Farooq Rai
Organization name Washington University School of Medicine
Department Orthopaedic Surgery
Lab Linda Sandell
Street address 660 S. Euclid Ave.
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (8)
GSM1598127 P3-005A
GSM1598128 P3-007A
GSM1598129 P3-008A
BioProject PRJNA274125
SRA SRP052991

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Supplementary file Size Download File type/resource
GSE65469_RAW.tar 28.8 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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