The gene expression profile data of RA synovium were downloaded from the Gene Expression Omnibus (GEO, access number: GSE1919) database.15 Briefly, synovial tissue samples were collected from eight RA patients undergoing synovectomy or arthroplasty, and from 15 normal subjects who died from fatal accidents, and were matched for age and gender. All donors were Caucasians living in Berlin, Germany. Total ribonucleic acid (RNA) was isolated from the synovium using RNeasy spin columns (Qiagen, Hilden, Germany). The isolated total RNA was labelled and hybridised to Affymetrix Human Genome U95A Array (containing 12 600 oligonucleotide probes) following standard protocol. Global normalisation of raw signal intensities was performed by GeneChip software (MAS 5.0, Affymetrix). Data analysis was conducted using DMT 3.0 software (Affymetrix). A detailed description of study subjects, experimental procedures and analysis approaches can be found in the previous study.4 (link)
Genechip software mas 5
Manufactured by Thermo Fisher Scientific
The GeneChip software (MAS 5.0) is a suite of analysis tools developed by Thermo Fisher Scientific for use with their GeneChip arrays. The software provides the core functionality to process and analyze data generated from GeneChip experiments.
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Lab products found in correlation
3 protocols using genechip software mas 5
1
Profiling Gene Expression in Rheumatoid Arthritis Synovium
2
Microarray Analysis of Light Submergence Response
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Microarray analysis was performed as described previously [76 (link)]. Wild-type (Col-0; 4-week-old) plants were light submergence-treated and rosettes were harvested at 0 and 48 h after treatment. Each sample included three biological replicates, and each replicate collected from three independent plants. Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instructions. Labeling, hybridization, scanning, and detection on the ATH1 Arabidopsis chips (Affymetrix), as well as raw data collection using the Affymetrix Gene Chip software MAS 5.0 were carried out as previously described [76 (link)]. The data were deposited on the Gene Expression Omnibus (GEO) database under accession number GSE59719. In addition, Affymetrix CEL files of short-term anoxia (6 h) in GSE2133 [77 (link)], hypoxia (2 and 9 h) in GSE9719 [78 (link)], dark submergence treatment in GSE24077 [36 (link)] were also applied for analysis together with light submergence (48 h) data. The genes involved in lipid biosynthesis and metabolism were identified according to the pathways described in Li-Beisson et al. [7 (link)] and Nakamura et al. [79 (link)]. GeneSpring 12.6 was used to identify differential expression genes with the criterion of 1.5-fold or more change and P < 0.05 cutoffs for the subsequent analysis. R language was used for all calculations and plots.
3
Affymetrix GeneChip cRNA Hybridization
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Double-strained cDNA from RNA was used as a template for isolation and preparation of cRNA. Isolation and hybridization of cRNA and scanning of the arrays were performed according to protocols specified by the manufacturer. Hybridization was done using three sets of human U133A GeneChips (Affymetrix, CA, USA). The arrays were scanned using the GeneArray scanner (Affymetrix). Image analysis was performed with GeneChip software (MAS 5.0; Affymetrix).
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