| 1. |
- Ericsson, Olle, et al.
(författare)
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A dual-tag microarray platform for high-performance nucleic acid and protein analyses
- 2008
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 36:8, s. e45-
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Tidskriftsartikel (refereegranskat)abstract
- DNA microarrays serve to monitor a wide range of molecular events, but emerging applications like measurements of weakly expressed genes or of proteins and their interaction patterns will require enhanced performance to improve specificity of detection and dynamic range. To further extend the utility of DNA microarray-based approaches we present a high-performance tag microarray procedure that enables probe-based analysis of as little as 100 target cDNA molecules, and with a linear dynamic range close to 10(5). Furthermore, the protocol radically decreases the risk of cross-hybridization on microarrays compared to current approaches, and it also allows for quantification by single-molecule analysis and real-time on-chip monitoring of rolling-circle amplification. We provide proof of concept for microarray-based measurement of both mRNA molecules and of proteins, converted to tag DNA sequences by padlock and proximity probe ligation, respectively.
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| 2. |
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| 3. |
- Göransson, Jenny, 1978-, et al.
(författare)
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A single molecule array for digital targeted molecular analyses
- 2009
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Ingår i: Nucleic Acids Research. - England : Oxford University Press. - 0305-1048 .- 1362-4962. ; 37:1, s. e7-
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Tidskriftsartikel (refereegranskat)abstract
- We present a new random array format together with a decoding scheme for targeted multiplex digital molecular analyses. DNA samples are analyzed using multiplex sets of padlock or selector probes that create circular DNA molecules upon target recognition. The circularized DNA molecules are amplified through rolling-circle amplification (RCA) to generate amplified single molecules (ASMs). A random array is generated by immobilizing all ASMs on a microscopy glass slide. The ASMs are identified and counted through serial hybridizations of small sets of tag probes, according to a combinatorial decoding scheme. We show that random array format permits at least 10 iterations of hybridization, imaging and dehybridization, a process required for the combinatorial decoding scheme. We further investigated the quantitative dynamic range and precision of the random array format. Finally, as a demonstration, the decoding scheme was applied for multiplex quantitative analysis of genomic loci in samples having verified copy-number variations. Of 31 analyzed loci, all but one were correctly identified and responded according to the known copy-number variations. The decoding strategy is generic in that the target can be any biomolecule which has been encoded into a DNA circle via a molecular probing reaction.
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| 4. |
- Pinidiyaarachchi, Amalka, et al.
(författare)
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Digital image processing for multiplexing of single molecule detection
- 2005
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Ingår i: Medicinteknikdagarna.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Using padlock and proximity probing techniques, individual molecular identification events are converted to long DNA molecules, carrying repeated sequence motifs used for identification of the detected molecules. We show that identification events can be amplified using rolling circle replication, and randomly attached to a surface for repeated access by identification probes. Repeated hybridization with detection probes carrying fluorescing nano-crystals (quantum dots) of varying spectral properties opens the possibility to search for large numbers of different identification events simultaneously. Methods for digital image processing of the resulting multi-spectral data include spatial as well as spectral data clustering. Spatial data processing includes registration of images from repeated hybridization events as well as delineation of clustered reporter events. Spectral data processing and analysis includes classification of spectral data into groups of either pre-defined or unknown patterns representing different molecular identification events.
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