Study

Knee OA Functional Genomics

Study ID Alternative Stable ID Type
EGAS00001001899 Transcriptome Analysis

Study Description

The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of knee osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

Study Datasets 3 datasets.

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Dataset ID Description Technology Samples
EGAD00001003355
From 17 patients undergoing knee joint replacement surgery for osteoarthritis, we collected 4 samples each: intact cartilage, degraded cartilage, synovium, and meniscus. We also collected blood for DNA analysis. Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09.
Illumina HiSeq 2500 72
EGAD00010001285
Genotyping of knee osteoarthritis patients who have undergone total joint replacement
Illumina InfiniumCoreExome-24v1-1_A 17
EGAD00010001287
Array methylation profiling of knee osteoarthritis patients who have undergone total joint replacement
Illumina HumanMethylation450K 68

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