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Resource:Alizadehlab: MeeboChip and HeeboChip Open Source Project

Name: Resource:Alizadehlab: MeeboChip and HeeboChip Open Source Project
Description:

This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress.
Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology.
Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).
Sponsors: This resource is supported by Stanford, UCSF, Stowers-Institute, Rockefeller, and Basel University.

Keywords: Mouse, Exonic, Evidence, Oligonucleotide, Chip, Human, Array, Genomic, Annoation, Sequence, Transcriptome, Annotation, Dataset, mRNA, EST, Systematic, Transcript, Exon, Locus, Biology,
Other Name(s): MeeboChip and HeeboChip
Resource Type(s): database (nlx_res_20090405)
Resource: Resource
URL: http://alizadehlab.stanford.edu/
*Id: nif-0000-30030
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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Contributors

Aarnaud, Akash, Ccdbuser, Nifbot2



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Facts about Resource:Alizadehlab: MeeboChip and HeeboChip Open Source ProjectRDF feed
CurationStatusuncurated  +
DefiningCitationhttp://alizadehlab.stanford.edu/  +
Definition

This is an open-source Mouse Exoni
This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress.
Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology.
Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).
Sponsors: This resource is supported by Stanford, UCSF, Stowers-Institute, Rockefeller, and Basel University.

Keywords: Mouse, Exonic, Evidence, Oligonucleotide, Chip, Human, Array, Genomic, Annoation, Sequence, Transcriptome, Annotation, Dataset, mRNA, EST, Systematic, Transcript, Exon, Locus, Biology,
c, Transcript, Exon, Locus, Biology,
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase (nlx res 20090405)  +
Idnif-0000-30030  +
LabelResource:Alizadehlab: MeeboChip and HeeboChip Open Source Project  +
ModifiedDate19 October 2010  +
SuperCategoryResource  +
SynonymMeeboChip and HeeboChip  +