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US 2003/0157529 A1Published application
Methods for determining transcriptional activity
AssigneeAffymetrix, Inc.
InventorThomas R. Gingeras
Life of this patent
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Abstract
In some embodiments of the invention, methods are provided to interrogate the transcriptional activity. The methods employ hybridization of a large number of oligonucleotide probes with nucleic acid derived from RNAs in a cellular compartment.
Claims64
A method of determining genomic transcriptional activity comprising:
- obtaining a polyA+ RNA sample from a cellular compartment;
- hybridizing the polyA+ RNA or nucleic acids derived from the RNA with an oligonucleotide probe array, wherein the oligonucleotide probe array contains at least 10,000 perfect match (PM) probes, wherein each of the perfect match probes targets a different transcript sequence from a region of a genome;
- and
- determining that a genomic sequence is transcribed if the probe against the genomic sequence is hybridized with a target.
1 more element
A method for comparing the transcriptional activity of two biological samples comprising:
- obtaining a first polyA+ RNA sample from a cellular compartment of a first sample;
- obtaining a second polyA+ RNA sample from a cellular compartment of a second sample;
- hybridizing the first and second polyA+ RNA or nucleic acids derived from the first and second polyA+ RNA with an oligonucleotide probe array wherein the oligonucleotide probe array contains at least 10,000 perfect match (PM) probes, wherein each of the perfect match probes targets a different transcript sequence from a region of a genome;
- and
- determining, for each of the first and second sample, that a genomic sequence is transcribed if the probe against the genomic sequence is hybridized with a target;
- and
- comparing the transcribed sequences between the first and second sample.
4 more elements
An oligonucleotide probe array for interrogating the transcriptional activity comprising:
- a substrate;
- at least 100,000 different oligonucleotide probes immobilized on the substrate, wherein each probe targets transcripts from a genome.
Dependencies are inferred from the claim text.