Sources of variability and effect of experimental approach on expression profiling data interpretation

Background: We provide a systematic study of the sources of variability in expression profiling data using 56 RNAs isolated from human muscle biopsies (34 Affymetrix MuscleChip arrays), and 36 murine cell culture and tissue RNAs (42 Affymetrix U74Av2 arrays). Results: We studied muscle biopsies from 28 human subjects as well as murine myogenic cell cultures, muscle, and spleens. Human MuscleChip arrays (4,601 probe sets) and murine U74Av2 Affymetrix microarrays were used for expression profiling. RNAs were profiled both singly, and as mixed groups. Variables studied included tissue heterogeneity, cRNA probe production, patient diagnosis, and GeneChip hybridizations. We found that the greatest source of variability was often different regions of the same patient muscle biopsy, reflecting variation in cell type content even in a relatively homogeneous tissue such as muscle. Inter-patient variation was also very high (SNP noise). Experimental variation (RNA, cDNA, cRNA, or GeneChip) was ...

• Type: Journal
• Year: 2002
• Where: BMCBI
• Authors: Marina Bakay, Yi-Wen Chen, Rehannah H. A. Borup, Po Zhao, Kanneboyina Nagaraju, Eric P. Hoffman
• Keywords: BMCBI 2002, Cell Cultures, Human Muscle Biopsies, Muscle Biopsies