Abstract: Provided herein is a method for imaging RNA transferred from a sample to a substrate. The method may include placing a sample comprising cells on a substrate, transferring RNA from the sample onto the substrate to produce an RNA blot in which the RNA is immobilized on the substrate, removing the sample from the substrate, hybridizing the RNA blot with a set of oligonucleotides that hybridize to different sites in the same RNA species, and reading the blot to obtain an image showing the binding pattern of the hybridized oligonucleotides.

Abstract: This invention relates to methods for capturing and encoding nucleic acid from a plurality of single cells. A plurality of solid supports is randomly placed into a plurality of compartments, such that the average number of solid supports per compartment, ?1, is less than 1, wherein each solid support carries (a) a unique identification sequence and (b) a capture moiety. A plurality of single cells is randomly placing into the plurality of compartments, such that the average number of cells per compartment, ?2, is less than 1. These random placement steps may be performed in any order. Nucleic acid is then released from each single cell and captured via the capture moiety, such that nucleic acid from each single cell is tagged with a unique identification sequence.

Abstract: Provided herein are systems and methods for pooling samples from separated sub-arrays in multi-well devices into collection wells of a multi-well sample collection device (e.g., allowing samples in a 100 well sub-array in a 9600-well chip to be pooled into a single collection well of a 96-well plate). In certain embodiments, the systems are composed of: i) a multi-well device, ii) an extraction device; and iii) an extraction device gasket. Also provided herein are dual barcoding (e.g., X-Y barcoding), pooling (e.g., dual pooling), RNA amplification methods (e.g., for single cell analysis), that may employ the extraction devices described herein.

Abstract: This invention relates to methods for capturing and encoding nucleic acid from a plurality of single cells. A plurality of solid supports is randomly placed into a plurality of compartments, such that the average number of solid supports per compartment, ?1, is less than 1, wherein each solid support carries (a) a unique identification sequence and (b) a capture moiety. A plurality of single cells is randomly placing into the plurality of compartments, such that the average number of cells per compartment, ?2, is less than 1. These random placement steps may be performed in any order. Nucleic acid is then released from each single cell and captured via the capture moiety, such that nucleic acid from each single cell is tagged with a unique identification sequence.

Abstract: The present invention provides a nucleic acid sequencing method. The method comprises enriching a nucleic acid sample for target nucleic acids, where the nucleic acid sample is enriched through at least a first round of hybridization selection and amplification, and a second round of hybridization selection and amplification. The enriched nucleic acids are in a form convenient for sequencing with the Cantaloupe sequencing technology, which employs shotgun sequencing by hybridization (SBH) of immobilized rolling circle amplicons.

Abstract: Nucleic acid sequencing, especially high-density fingerprinting, in which a panel of nucleic acid probes is annealed to nucleic acid containing a template for which sequence information is desired, with determination of the presence or absence of sequence complementary to each probe within the template, thus providing sequence information. A reference sequence at least partly related to the template is used.

Abstract: Nucleic acid sequencing-by-synthesis. Primed synthesis of a second strand complementary to a template strand in repeated sets of steps, each step comprising providing one or more of the possible nucleotide complementarity classes for incorporation into the synthesized strand, and each set of steps comprising providing all four possible nucleotide complementarity classes. Three of the four possible nucleotide complementarity classes may first be provided for incorporation into the synthesized strand, then separately the fourth nucleotide complementarity class alone.

Abstract: Identification of gene variants, and in particular identification of differences between sequence variants that occur in a population of nucleic acid molecules, especially identification or discovery of polyA site usage, or determination of polyA site usage in a nucleic acid sample, and gene variants arising from alternative polyA sites.

Abstract: Methods of manipulation of nucleic acid, in particular amplification by means of the polymerase chain reaction (PCR), including use of oligonucleotides and combinations and kits comprising such oligonucleotides, also methods comprising use of nested PCR, allowing for improved results in methods wherein large numbers of nucleic acid fragments are manipulated by means of PCR and electrophoresis. Oligonucleotides are provided for use a size standards in electrophoresis, and internal controls allowing for calculation of relative amounts of material present. Improved results can be achieved in methods of profiling mRNA transcribed in a system under investigation.

Abstract: A method for identifying mRNA molecules present in a sample, and also for quantifying the expression levels of the mRNA molecules. A profile of gene identities and/or expression levels is produced by generating two independent patterns characteristic of the population of mRNA molecules expressed in the sample and analysing these patterns using a combinatorial algorithm. Gene expression by different cell types or of the same cell types under different conditions may be compared. In this way, genes may be identified which play a role in determining various cellular processes and states, including susceptibility to external factors, development, and disease.