Application of robotic technology to automated sequence fingerprint analysis by oligonucleotide hybridisation

Maier, Elmar; Meier‐Ewert, Sebastian; Ahmadi, Ali; Curtis, Jon; Lehrach, Hans

doi:10.1016/0168-1656(94)90035-3

Cited by 66 publications

(36 citation statements)

References 18 publications

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“…A cDNA-library from diseased synovium (day 7) was arrayed on high-density filters using a Q-bot picking and spotting robot device (Genetix, New Milton, U.K.) as previously described (17). On each filter, 9216 clones were arrayed in duplicate.…”

Section: Hybridization Of High-density Filter Arrays With Complex Ammentioning

confidence: 99%

Serum Amyloid A (apoSAA) Expression Is Up-Regulated in Rheumatoid Arthritis and Induces Transcription of Matrix Metalloproteinases

Vallon

Freuler

Desta-Tsedu

et al. 2001

The Journal of Immunology

143

117

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The acute-phase reactant rabbit serum amyloid A 3 (SAA3) was identified as the major difference product in Ag-induced arthritis in the rabbit, a model resembling in many aspects the clinical characteristics of rheumatoid arthritis (RA) in humans. In Ag-induced arthritis, up-regulated SAA3 transcription in vivo was detected in cells infiltrating into the inflamed joint, in the area where pannus formation starts and, most notably, also in chondrocytes. The proinflammatory cytokine IL-1β induced SAA3 transcription in primary rabbit chondrocytes in vitro. Furthermore, rSAA3 protein induced transcription of matrix metalloproteinases in rabbit chondrocytes in vitro. In the human experimental system, IL-1β induced transcription of acute-phase SAA (A-SSA; encoded by SAA1/SAA2) in primary chondrocytes. Similar to the rabbit system, recombinant human A-SAA protein was able to induce matrix metalloproteinases’ transcription in chondrocytes. Further, immunohistochemistry demonstrated that A-SAA was highly expressed in human RA synovium. A new finding of our study is that A-SSA expression was also detected in cartilage in osteoarthritis. Our data, together with previous findings of SAA expression in RA synovium, suggest that A-SAA may play a role in cartilage destruction in arthritis.

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Section: Hybridization Of High-density Filter Arrays With Complex Ammentioning

confidence: 99%

Serum Amyloid A (apoSAA) Expression Is Up-Regulated in Rheumatoid Arthritis and Induces Transcription of Matrix Metalloproteinases

Vallon

Freuler

Desta-Tsedu

et al. 2001

The Journal of Immunology

143

117

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“…Filter hybridizations using DIG-labeled PCR probes were performed as described [23]. Briefly, 15-100 µl probe and 2 µl each of oligonucleotide used for probe preparation as competitors (100 pmol/µl) were adjusted to 120 µl total volume using TE (pH 8.0).…”

Section: Filter Hybridizationsmentioning

confidence: 99%

“…However, its full potential could not be unleashed because identifying all different clones present in an enriched library would have required a major sequencing effort of cDNA inserts. Instead, we have employed robotic-based devices [21], as developed for automated library handling in genomics [22,23], for picking and high-density gridding of phage clones to rapidly catalogue redundant cDNA inserts. This efficient strategy enabled us to find rare clones in large, selectively enriched phage populations, and hence to define a vast variety of structurally different IgE-binding proteins form the mould Aspergillus fumigatus.…”

mentioning

confidence: 99%

Rapid Identification of Allergen-Encoding cDNA Clones by Phage Display and High-Density Arrays

Kodzius¹,

Rhyner²,

Konthur

et al. 2003

CCHTS

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Abstract:We describe a high-throughput, quantitative technology for fast identification of all different clones present in selectively enriched phage surface-displayed cDNA libraries. The strategy is based on a combination of phage display and high-density arrays. To demonstrate the utility of the method cDNAs of Aspergillus fumigatus cloned into phagemid pJuFo were expressed on the tip of filamentous M13 phage and affinityselected on solid phase-immobilized serum IgE from allergic patients. Enriched phagemid libraries were amplified in bacteria, plated and arrayed into 384-well microtitre plates by robotic colony picking. cDNA inserts were amplified by high-throughput PCR and gridded onto high-density filter membranes. Filters were iteratively probed with randomly-sequenced inserts until all clones were identified. Eighty-one different sequences encoding IgE-binding proteins likely to cover a large part of the allergen repertoire of the mould were found. This approach represents a widely applicable method for rapid high-throughput identification of all individual cDNAs present in selectively enriched libraries.

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“…By repeating this experiment with different probes (100-300), each clone is described by a characteristic vector of numerical valuessubsequently called a fingerprint. Detailed protocols of the procedure including possible quality checks have been published (Maier et al 1994;Schmitt et al 1999;Clark et al 1999).…”

mentioning

confidence: 99%

Large-Scale Clustering of cDNA-Fingerprinting Data

Herwig

Poustka²,

Müller³

et al. 1999

Genome Res.

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194

120

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Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements that is able to handle high-throughput data in the order of hundreds of thousands of data items measured on hundreds of variables. The practical motivation for our algorithm is oligonucleotide fingerprinting-a method for simultaneous determination of expression level for every active gene of a specific tissue-although the algorithm can be applied as well to other large-scale projects like EST clustering and qualitative clustering of DNA-chip data. As a pairwise similarity measure between two p-dimensional data points, x and y, we introduce mutual information that can be interpreted as the amount of information about x in y, and vice versa. We show that for our purposes this measure is superior to commonly used metric distances, for example, Euclidean distance. We also introduce a modified version of mutual information as a novel method for validating clustering results when the true clustering is known. The performance of our algorithm with respect to experimental noise is shown by extensive simulation studies. The algorithm is tested on a subset of 2029 cDNA clones coming from 15 different genes from a cDNA library derived from human dendritic cells. Furthermore, the clustering of these 2029 cDNA clones is demonstrated when the entire set of 76,032 cDNA clones is processed.

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Application of robotic technology to automated sequence fingerprint analysis by oligonucleotide hybridisation

Cited by 66 publications

References 18 publications

Serum Amyloid A (apoSAA) Expression Is Up-Regulated in Rheumatoid Arthritis and Induces Transcription of Matrix Metalloproteinases

Serum Amyloid A (apoSAA) Expression Is Up-Regulated in Rheumatoid Arthritis and Induces Transcription of Matrix Metalloproteinases

Rapid Identification of Allergen-Encoding cDNA Clones by Phage Display and High-Density Arrays

Large-Scale Clustering of cDNA-Fingerprinting Data

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