E-MTAB-10119
RNA-Seq of anterior cruciate ligament and knee joint synovium in dogs that are affected with cruciate rupture compared to matched controls.
The intent of the experiment was to identify genes that were differentially expressed between dogs affected with anterior cruciate ligament (ACL) rupture and breed-matched controls. Anterior cruciate ligament and knee synovial tissue biopsies were collected from 4 ACL rupture affected cases and 4 unaffected control dogs. Cases and controls were matched as closely as possible based on breed, sex, neutered status, age, and weight. Medications that the dogs were taking at the time of sample collection were also considered. We prioritized sample size and quality above all other variables, therefore, two matched pairs of Golden Retrievers were chosen with two matched pairs of Labrador Retrievers for this analysis. Tissues from cases were collected during knee stabilization surgery. Tissues from unaffected control dogs were collected from dogs undergoing pelvic limb amputation or euthanasia for reasons unrelated to this study. Illumina TruSeq RNA libraries were constructed and 150bp paired-end sequencing was performed using the Illumina Hi-Seq 2500 platform.  Table 1. Breed, sex, age, and weight of matched case and control pairs chosen for RNA sequencing analysis Cases Matched Controls Breed Sex Age (yr) Weight (kg) Breed Sex Age (yr) Weight (kg) GR1 CM 8.8 30.5  GR2 CM 14.9 N/A GR3 CM 5.6 44.0  GR4 CM 3.9 34.0 LR1          CM 9.7 36.0  LR2  CM 12.7 28.5 LR3  CM 13.3 36.0  LR4  CM 13.5 35.0 GR = Golden Retriever. LR = Labrador Retriever. CM= castrated male. Weight at the time of death was not available for one dog.
The intent of the experiment was to identify genes that were differentially expressed between dogs affected with anterior cruciate ligament (ACL) rupture and breed-matched controls. Anterior cruciate ligament and knee synovial tissue biopsies were collected from 4 ACL rupture affected cases and 4 unaffected control dogs. Cases and controls were matched as closely as possible based on breed, sex, neutered status, age, and weight. Medications that the dogs were taking at the time of sample collection were also considered. We prioritized sample size and quality above all other variables, therefore, two matched pairs of Golden Retrievers were chosen with two matched pairs of Labrador Retrievers for this analysis. Tissues from cases were collected during knee stabilization surgery. Tissues from unaffected control dogs were collected from dogs undergoing pelvic limb amputation or euthanasia for reasons unrelated to this study. Illumina TruSeq RNA libraries were constructed and 150bp paired-end sequencing was performed using the Illumina Hi-Seq 2500 platform.  Table 1. Breed, sex, age, and weight of matched case and control pairs chosen for RNA sequencing analysis Cases Matched Controls Breed Sex Age (yr) Weight (kg) Breed Sex Age (yr) Weight (kg) GR1 CM 8.8 30.5  GR2 CM 14.9 N/A GR3 CM 5.6 44.0  GR4 CM 3.9 34.0 LR1          CM 9.7 36.0  LR2  CM 12.7 28.5 LR3  CM 13.3 36.0  LR4  CM 13.5 35.0 GR = Golden Retriever. LR = Labrador Retriever. CM= castrated male. Weight at the time of death was not available for one dog.