Project description:High-throughput systems for gene expression profiling have been developed and matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised regarding data comparability and agreement across technologies. Within an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing). The DNA microarray platforms generally provided highly correlated data, while moderate correlations between microarrays and MPSS were obtained. Disagreements between the two types of technologies can be attributed to limitations inherent to both technologies. The variation found between pooled biological replicates underlines the importance of exercising caution in identification of differential expression, especially for the purposes of biomarker discovery. Based on different principles, hybridization-based and sequencing-based technologies should be considered complementary to each other, rather than competitive, and currently, both provide indispensable tools for transcriptome profiling. Keywords: biological replicates
Project description:This sample is part of a study that compares small sample amplification technologies. The analysis looks at differential gene expression when compared to one round of T7 amplification. A tumor cell line was used in comparison to a human reference RNA in this study. Keywords = amplification Keywords = small sample Keywords = Affymetrix Keywords: other
Project description:Next-generation sequencing has emerged as a promising platform for whole genome transcriptome profiling. The microarray technology has in contrast a long track record, but may suffer from issues related to background fluorescence and non-specific hybridization. The two technologies have been compared for eukaryotic transcriptomes in various studies. However, for prokaryotes information on comparative performance of the two technologies is sparse. We thus compared the two technologies for Streptococcus thermophilus. With just single experiments there was a strong correlation between the technologies.
Project description:Next-generation sequencing has emerged as a promising platform for whole genome transcriptome profiling. The microarray technology has in contrast a long track record, but may suffer from issues related to background fluorescence and non-specific hybridization. The two technologies have been compared for eukaryotic transcriptomes in various studies. However, for prokaryotes information on comparative performance of the two technologies is sparse. We thus compared the two technologies for Streptococcus thermophilus. With just single experiments there was a strong correlation between the technologies.
Project description:This SuperSeries is composed of the following subset Series: GSE34461: Comparing two transcriptome technologies - sequencing match microarrays [Array] GSE34477: Comparing two transcriptome technologies - sequencing match microarrays [RNA-Seq] Refer to individual Series
Project description:Next-generation sequencing has emerged as a promising platform for whole genome transcriptome profiling. The microarray technology has in contrast a long track record, but may suffer from issues related to background fluorescence and non-specific hybridization. The two technologies have been compared for eukaryotic transcriptomes in various studies. However, for prokaryotes information on comparative performance of the two technologies is sparse. We thus compared the two technologies for Streptococcus thermophilus. With just single experiments there was a strong correlation between the technologies. We compared our in house spotted DNA microarray platform with the same RNA samples sequenced externally. The aim was to, without replicate arrays or sequencing, to determine if the two technologies correlate well.
Project description:The aim of this project was to elucidate the microRNA profile of platelets and of platelet-derived microparticles isolated from clinical platelet concentrates treated or not with pathogen reduction technologies.
