|
| Status |
Public on Dec 20, 2017 |
| Title |
1 wk DMM-4 |
| Sample type |
RNA |
| |
|
| Source name |
Synovium (Anterior)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
gender: Male
stress: DMM
post surgery time point: 1 wk
|
| Treatment protocol |
Sixteen animals had bilateral DMM surgery. Briefly, under isoflurane anaesthesia, the medial menisco-tibial ligament was exposed by medial para-patellar arthrotomy and intrapatellar fat pad elevation, and transected with curved dissecting forceps by one surgeon (CBL). Joints were flushed with sterile saline prior to separate closure of the joint capsule, subcutaneous tissue (8/0 polyglactin 910 suture) and skin (cyanoacrylate). Bilateral sham-operations were performed in 16 age- and sex-matched mice, where all procedures were identical except the medial menisco-tibial ligament was visualised but not transected. Mice were randomly allocated to DMM/sham and harvest time
|
| Growth protocol |
Mice with DMM and sham surgery were co-housed 2-5 animals/30×20×18cm individually-ventilated-cage with filter lids, provided with sterilised bedding and environmental enrichment, maintained at 21-22°C with a 12-hour light/dark cycle, and received water and complete pelleted food ad libitum. Mice received no post-arthritis-induction medication and were allowed unrestricted cage exercise. Animals were sacrificed at 1 and 6 weeks after surgery.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The anterior synovial tissues (comprising the joint capsule plus synovial lining plus infrapatellar fat pad, excluding muscle) were isolated using a dissecting microscope.
|
| Label |
Cyanine 3-pCp
|
| Label protocol |
mRNA expression profiling was performed using SurePrint mouse mRNA expression V2 microarray technology (G4852B, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the low input quick amp WT labelling kit (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.
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| |
|
| Hybridization protocol |
mRNA expression profiling was performed using SurePrint mouse mRNA expression V2 microarray technology (G4852B, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the low input quick amp WT labelling kit (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.
|
| Scan protocol |
The arrays were scanned on a G2565CA microarray scanner and the features were extracted using Agilent Feature Extraction 12.0.07 software
|
| Description |
Bilateral surgeries performed. Knees taken from the same mouse for both histology and expression profiling.
|
| Data processing |
The raw microarray data was processed in statistical language R, using the limma package (limma_3.20.9) and background corrected with Normexp, normalized within arrays with cyclic loess. This synovial mRNA array data was normalised with mRNA array data from subchondral bone tissue from the same cohort of mice as part of a separate study (GSE101573). Only probes with 10% greater signal than the negative controls in at least 5 samples were maintained for differential expression analysis. Probes were summarised at the gene level and the data was adjusted for multiple testing using Benjamini-Hochberg method to control for false discovery rate.
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| |
|
| Submission date |
Jun 06, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
John Bateman |
| Organization name |
Murdoch Childrens Research Institute
|
| Department |
Skeletal Biology
|
| Lab |
John Bateman
|
| Street address |
Flemington Road
|
| City |
Melbourne |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21163 |
| Series (2) |
| GSE99731 |
Comprehensive Expression Analysis of microRNAs and mRNAs in Osteoarthritic Synovial Tissue from a Mouse Model of Early Post-Traumatic OA [mRNA] |
| GSE99738 |
Comprehensive Expression Analysis of microRNAs and mRNAs in Osteoarthritic Synovial Tissue from a Mouse Model of Early Post-Traumatic OA |
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