Knee_OA_Functional_Genomics - EGA European Genome-Phenome Archive

Study ID	Alternative Stable ID	Type
EGAS00001001899		Transcriptome Analysis

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.

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. 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 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 Array methylation profiling of knee osteoarthritis patients who have undergone total joint replacement	Illumina HumanMethylation450K	68

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

EGAD00010001285

Genotyping of knee osteoarthritis patients who have undergone total joint replacement

Illumina InfiniumCoreExome-24v1-1_A

EGAD00010001287

Array methylation profiling of knee osteoarthritis patients who have undergone total joint replacement

Illumina HumanMethylation450K

Study

Study Description

Study Datasets 3 datasets.

Who archives the data?

Publications

Citations

The European Genome-phenome Archive (EGA) is part of the ELIXIR infrastructure.