Hip OA Functional Genomics - EGA European Genome-Phenome Archive

Study ID	Alternative Stable ID	Type
EGAS00001002483		Transcriptome Analysis

Study ID

Alternative Stable ID

Type

EGAS00001002483

Transcriptome Analysis

Study Description

The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of hip 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
EGAD00001003354	From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset ... (Show More) From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). 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	27
EGAD00010001291	Methylation profiling of hip osteoarthritis patients who have undergone total joint replacement Methylation profiling of hip osteoarthritis patients who have undergone total joint replacement	Illumina HumanMethylation450K	27
EGAD00010001292	Genotyping of hip osteoarthritis patients who have undergone total joint replacement Genotyping of hip osteoarthritis patients who have undergone total joint replacement	Illumina InfiniumCoreExome-24v1-1_A	9

Dataset ID

Description

Technology

Samples

EGAD00001003354

From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset ... (Show More)

Illumina HiSeq 2500

EGAD00010001291

Methylation profiling of hip osteoarthritis patients who have undergone total joint replacement

Illumina HumanMethylation450K

EGAD00010001292

Genotyping of hip osteoarthritis patients who have undergone total joint replacement

Illumina InfiniumCoreExome-24v1-1_A

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.