Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human joint tissue using multiple biopsies taken from the same knee

ABSTRACT: Analysis of intra- and inter variation using multiple biopsies taken from the same knee. The biopsies were obtained from thirteen different patients; seven by orthopedic surgery and six by rheumatic arthroscopy. Orthopedic samples (patients 1-7 Three synovial tissue specimens were obtained from random sites of the synovium for each patient. Biopsy III of patient 7 was not used due to bad RNA quality. For patients 1-3 each biopsy was divided into three parts (1/3 of a biopsy is denoted subbiopsy). In total this resulted in 39 specimens from the orthopedic patients (nine biopsies from patients 1-3 and three biopsies from each of patients 4-7). For patient 1-3, pt1 b1.BA means patient 1 biopsy 1 subbiopsy B Technical replicate A. For patient 4-7, pt4 b1A means patient 4 biopsy 1 technical replicate A. Arthroscopic samples (patients 8-13) Arthroscopic biopsies were taken at the site of inflammation close to cartilage (cc) or not close to cartilage (ncc), defined as less or more than 1.5 cm away from cartilage, respectively. Multiple biopsies were taken from two sites in patients 8, 11, 12, 13 and from four sites in patients 9 and 10. pt12_ncc_1A means patient 12 not close to cartilage biopsy 1 technical replicate.

ORGANISM(S): Homo sapiens

SUBMITTER: Johan Lindberg

PROVIDER: E-MEXP-367 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:The purpose of this experiment was to do investigatge the transcriptional effect of anti-TNF treatment in patients suffering from rheumatoid arthritis. Two series of hybridizations were performed. Each hybridization was done with a technical replicate (the same amount of RNA taken from the same amplified RNA aliquot labeled in two separate reactions and hybridized onto two separate arrays). In the first series of hybridizations RNA exptracted from biopsies taken before treatment was hybridized in a common reference design to enable comparisons between patients. In the second series RNA from biopsies taken after and before treatment were hybridized on the same chip in a direct design to enable investigation of the effect of treatment. 10 patients (8 females and 2 males, median age 54, range 25-69) meeting the American College of Rheumatology (ACR) criteria for RA were recruited for this study. All patients received infliximab (an antibody directed against TNF-alpha) infusions 3mg/kg at week 0 and than after 2 weeks and 6 weeks. Five of these patients were receiving prednisolon and all ten patients were treated with methotrexate to a maximum of 20 mg per week. Synovial biopsies were obtained during arthroscopy from all patients before and after a median of 9 weeks of treatment (with one exception, patient 7 where the second biopsy was obtained during open surgery). Biopsies were taken at the site of inflammation close to cartilage (cc) or not close to cartilage (ncc), defined as less or more than 1.5 cm away from cartilage, respectively. One biopsy was taken before and after treatment from patient 5, 7, 9 and 10. Multiple biopsies were retrieved before and/or after treatment from patient 1, 2, 3, 4, 6 and 7. Due to small amounts of RNA available for patient 9 it was only used in the second series of hybridizations. The average biopsy weight was 22 mg. The ethical committee at the Karolinska Hospital approved all experiments on human cells and tissues. Informed consent was obtained from all study subjects.

Dataset Information

Transcription profiling of human joint tissue using multiple biopsies taken from the same knee

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets