Patent application number | Description | Published |
20090062138 | Array-based method for performing SNP analysis - An array-based method for performing SNP analysis is provided. In certain embodiments, the method may comprise: a) contacting a labeled genomic sample with an array comprising a first SNP-detecting oligonucleotide and a second SNP-detecting oligonucleotide that differ from each other by a single nucleotide, under hybridization conditions that provide binding equilibrium; and b) evaluating a SNP of said labeled genomic sample by comparing: i. binding of the labeled genomic sample to the first SNP-detecting oligonucleotide and ii. binding of the labeled genomic sample to said second SNP-detecting oligonucleotide. | 03-05-2009 |
20100081131 | IDENTIFICATION OF MICROBES USING OLIGONUCLEOTIDE BASED IN SITU HYBRIDIZATION - A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting a sample comprising a microbe with a set of at least two labeled oligonucleotides under in situ hybridization conditions to produce a contacted sample, where the labeled oligonucleotides i. hybridize to different RNA molecules of the microbe at sites that are unique to the microbe, ii. provide a predetermined optically detectable signature that identifies the microbe when the labeled oligonucleotides are hybridized to the different RNA molecules of the microbe, and iii. do not hybridize to ribosomal RNA of the microbe; b) reading the contacted sample to detect hybridization of the labeled oligonucleotides; and c) determining the identity of the microbe on the basis of the predetermined optically detectable signal, where the predetermined optically detectable signal indicates the identity of the microbe in the sample. | 04-01-2010 |
20100081576 | METHOD FOR GENOME ANALYSIS - A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting under primer extension conditions a genomic sample comprising a test genome with a set of at least ten sequence-specific primers that are complementary to sites in only one strand of a reference chromosomal region, to produce primer extension products, and b) analyzing the primer extension products to identify a chromosomal rearrangement in the test genome. | 04-01-2010 |
20100129879 | GENOME PARTITIONING USING A NICKING ENDONUCLEASE - A method for partitioning a genome is provided. In certain embodiments, the method comprises: a) nicking a region of the genome using a sequence-specific nicking endonuclease to produce a nicked double-stranded genomic region; b) hybridizing the nicked double-stranded genomic region with an oligonucleotide comprising: i. an affinity tag; and ii. a nucleotide sequence that is complementary to the nucleotide sequence that is immediately adjacent to the nick site, to produce a duplex in which a terminal nucleotide of the oligonucleotide lies immediately adjacent to said a nucleotide of the nick site; c) ligating the terminal nucleotide of the oligonucleotide to the nucleotide of the nick site to produce a ligation product; and d) separating the ligation product from unligated products using the affinity tag. Compositions and kits for practicing the method are provided. | 05-27-2010 |
20100137154 | GENOME ANALYSIS USING A METHYLTRANSFERASE - A method of genome analysis is provided. In certain embodiments, the method may comprise: labeling the test genome using a first site-specific methyltransferase to produce a labeled test genome comprising a label; and analyzing the labeled test genome to determine if the test genome comprises a sequence alteration relative to a reference sequence. In certain embodiments, the method may comprise: evaluating binding of the labeled test genome to an array of probes, or observing a pattern of labeling along the labeled test genome. | 06-03-2010 |
20100221708 | METHOD FOR CHROMOSOME ENUMERATION - A method of sample analysis is provided. The method comprises: a) contacting a genomic sample comprising a plurality of intact chromosomes, i.e., metaphase or interphase chromosomes, with a first set of labeled oligonucleotide probes under in situ hybridization conditions to produce a contacted sample comprising labeled chromosomes, where i. each of the labeled oligonucleotide probes is complementary to a non-repetitive, unique sequence in a region that flanks the centromere of a single chromosome of the plurality of chromosomes; and ii. hybridization of the labeled oligonucleotide probes to the chromosomes produces a distinct labeling pattern for each hybridized chromosome, thereby allowing each of the labeled chromosomes to be distinguished from one another; b) imaging the hybridized chromosomes to provide an image showing the labeling pattern for each labeled chromosome; and c) enumerating a labeled chromosome based on the labeling pattern of said labeled chromosome. A composition and kits for performing the method are also provided. | 09-02-2010 |
20120115237 | ISOLATION OF RNA-PROTEIN COMPLEXES USING CROSS-LINKING REAGENTS AND OLIGONUCLEOTIDES - Provided herein is a method of sample analysis. In certain embodiments, the method comprises: a) cross-linking protein of a cell using a first compound to produce a first cross-linked product comprising cross-linked protein, and RNA; b) contacting the first cross-linked product and a second compound under conditions by which an oligonucleotide portion of the second compound hybridizes to the RNA; c) activating a reaction the first and second compound, thereby covalently crosslinking the oligonucleotide to the cross-linked protein to produce a second cross-linked product; d) isolating the second cross-linked product using an affinity tag; and e) analyzing the isolated second cross-linked product. Compounds for performing the method are also provided. | 05-10-2012 |
20120208707 | LIGATION METHOD EMPLOYING RTCB - A method of processing an RNA sample is provided. In certain embodiments, the method may comprise: a) obtaining a fragmented RNA sample comprising: i. RNA fragments of long RNA molecules; and ii. unfragmented short RNA; and b) contacting said fragmented RNA sample with a first adaptor in the presence of a RtcB ligase, thereby producing a ligated RNA sample comprising adaptor-ligated fragments of long RNA. A kit for performing the method is also provided. | 08-16-2012 |
20130123129 | USE OF DNAZYMES FOR ANALYSIS OF AN RNA SAMPLE - Provided herein is method comprising: contacting an initial RNA sample containing a population of different RNA molecules with a divalent cation and a set of DNAzymes that are designed to cleave multiple target RNAs in the initial sample, thereby producing a product RNA sample that comprises: a) uncleaved RNA molecules and b) cleaved RNA fragments that contain a 2′,3′-cyclic-phosphate and a 5′ hydroxyl as the result of DNAzyme cleavage. | 05-16-2013 |
20140356867 | NUCLEIC ACID ENRICHMENT USING CAS9 - A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided. | 12-04-2014 |
20140357523 | METHOD FOR FRAGMENTING GENOMIC DNA USING CAS9 - A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided. | 12-04-2014 |