Abstract: The present disclosure discloses a method for detecting single strand breaks (SSBs) in DNA based on the following steps. First, DNA of interest is fragmented with a method that generates 3? ends that cannot be tailed. Second, the available 3? ends of the fragmented DNA corresponding to the pre-existing breaks are tailed. Third, SSBs are captured and their positions are identified genome-wide based on the following steps: (1) the tailed fragments are linearly amplified using a chimeric 5?-DNA-RNA-3? primer; (2) the products of primer extension are tailed at the 3? ends; (3) the desired products are amplified by PCR with oligonucleotides containing Illumina® adaptor sequences complementary to both tails and subjected to next-generation sequencing (NGS); 4) finally, positions of SSBs are revealed through the analysis of sequencing results.

Abstract: The present disclosure discloses a method for detecting single strand breaks (SSBs) in DNA based on the following steps. First, DNA of interest is fragmented with a method that generates 3? ends that cannot be tailed. Second, the available 3? ends of the fragmented DNA corresponding to the pre-existing breaks are tailed. Third, SSBs are captured and their positions are identified genome-wide based on the following steps: (1) the tailed fragments are linearly amplified using a chimeric 5?-DNA-RNA-3? primer; (2) the products of primer extension are tailed at the 3? ends; (3) the desired products are amplified by PCR with oligonucleotides containing Illumina adaptor sequences complementary to both tails and subjected to next-generation sequencing (NGS); 4) finally, positions of SSBs are revealed through the analysis of sequencing results.

Abstract: A method, flow cell and/or device for increasing the recovery of a limiting analyte in a sample, e.g., for single molecule analysis is disclosed. Methods for preparing a nucleic acid sample from a single cell and capturing nucleic acids on a surface configured for use in or with single molecule analysis are also provided.

Abstract: In some embodiments of the invention, methods are provided to interrogate the transcriptional activity relating to RNAs of small molecular weight. The methods employ hybridization of a large number of oligonucleotide probes with nucleic acid derived from RNAs of small molecular weight.

Abstract: In one aspect of the invention, high density arrays are used with 5? and 3? RACE (rapid amplification of cDNA ends) or RAGE (rapid amplification of Genomic DNA) in tandem to detect and characterize transcripts or genomic structures.

Abstract: The present invention provides a novel bi-directional promoter. The present invention further provides methods of producing proteins of interest and methods of controlling gene expression using the bi-directional promoter. The present invention also provides methods of expressing one or more proteins of interest from a novel bi-directional promoter of the present invention. The present invention thus provides improved methods of regulating gene expression in plants or other organisms and expressing one or more proteins concurrently in a variety of cell types.

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.

Abstract: In one aspect of the invention, high density arrays are used with 5? and 3? RACE (rapid amplification of cDNA ends) or RAGE (rapid amplification of Genomic DNA) in tandem to detect and characterize transcripts or genomic structures.

Abstract: In some embodiments of the invention, methods are provided to profile transcriptionally active sites of the genome. The methods employ hybridization of a large number of oligonucleotide probes to nucleic acid derivatives of cytosolic RNAs derived from cell lines that respond to an exogenous stimulation.

Abstract: In some embodiments of the invention, methods are provided to interrogate the transcriptional activity relating to RNAs of small molecular weight. The methods employ hybridization of a large number of oligonucleotide probes with nucleic acid derived from RNAs of small molecular weight.

Abstract: The present invention provides a novel bi-directional promoter. The present invention further provides methods of producing proteins of interest and methods of controlling gene expression using the bi-directional promoter. The present invention also provides methods of expressing one or more proteins of interest from a novel bi-directional promoter of the present invention. The present invention thus provides improved methods of regulating gene expression in plants or other organisms and expressing one or more proteins concurrently in a variety of cell types.