Agilent Technologies, Inc.

Hewlett-packard Company

Other

Alverix, Inc.

Nicholas Michael Sampas

Zohar H Yakhini

Glenda Choate Delenstarr

Paul K Wolber

Kristin Briana Bernick

Andreas N Dorsel

Brian Jon Peter

Victor Lim

Adrienne Mccampbell

Herbert F Cattell

Kyle J Schleifer

Cynthia Y Enderwick

Jeffrey Robert Sampson

David A King

Carol T Schembri

Joel Myerson

Bo U Curry

Peter G Webb

Robert A Ach

John W Sadler

Scott D Connell

David Taussig

Anna M Tsalenko

Rene P Helbing

Julie Elizabeth Fouquet

John Frederick Corson

Daniel H Lange

Rick P Trebino

Richard Paul Tella

Steven M Lefkowitz

Leslie Anne Leonard

Robert Lloyd Kincaid

Eric K Gustafson

Amir Ben-Dor

Alexander S Belyaev

Bahram Arezi

Paige Anderson

Nazumi Alice Yama-Dang

Leslie B Overman

Kevin J Luebke

Alicia Scheffer-Wong

Peter Tsang

Doron Lipson

Kyle Schleifer

Jeffery R Sampson

The present disclosure is directed to an improved method for distinguishing tissue from an embedding medium, such as paraffin in a formalin-fixed paraffin-embedded sample. The method involves the use of fluorescence of naturally-occurring species in tissue to determine the location of the tissue in the embedded sample. An embedded sample is generally excited by light of a selected wavelength, and the fluorescence emission at an emitted wavelength is used to locate the boundary or location of the tissue in the embedded sample.

Preparation of tissue sections using fluorescence-based detection

The present disclosure relates to a method of assembling long nucleic acids by enzymatically ligating oligonucleotide molecules hybridized to an indexed splint oligonucleotide molecules. Also disclosed are oligonucleotide structures comprising an indexed splint oligonucleotide useful in performing the disclosed method.

Assembly of long nucleic acids by ligation using indexed splint oligos

Described herein is an adapter comprising a population of first oligonucleotides, a second oligonucleotide and a third oligonucleotide, wherein the first oligonucleotides, the second oligonucleotide and the third oligonucleotide are hybridized together to produce a complex that comprises: (i) a first end comprising a transposase recognition sequence, (ii) a central single-stranded region of variable sequence and (iii) a second end comprising sequences that are non-complementary. A method, as well as a kit for practicing the method, are also provided.

Use of transposase and Y adapters to fragment and tag DNA

A method for making an asymmetrically-tagged sequencing library is provided. In some embodiments, the method may comprise: obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, hybridizing a tailed first primer to the 3' sequence tag of the library and extending the same to produce primer extension products, and amplifying the primer extension products using a pair of tailed primers to produce asymmetrically-tagged library.

Method for making an asymmetrically-tagged sequencing library

Provided herein, among other things, are compositions for improving signal-to-noise in hybridization to oligonucleotide arrays. In some embodiments, the composition may comprise a population of indexing oligonucleotides of formula X-Y, where the sequences of region X hybridize to an array and the sequences of region Y hybridize to distinct sites within a genomic region, transcript, set of transcripts, or complement of the same. Use of these oligonucleotides increases signal, reduces background and smoothens array hybridization analyses. Methods and kits that employ the compositions are also provided.

Composition and method for improving signal-to-noise in hybridization to oligonucleotide arrays

Provided herein, among other things, is a method for producing a ligation product on a support. In some embodiments, the method may comprise hybridizing a first double-stranded oligonucleotides and a second double-stranded oligonucleotide to a substrate comprising surface-tethered oligonucleotides and ligating the distal ends of the first and second double-stranded oligonucleotides together, thereby producing a first ligation product that is tethered to the support at both ends.

On-array ligation assembly

Provided is an emulsion comprising: (a) droplets that contain a single polymeric compound or a pre-defined mixture thereof, and (b) an immiscible liquid, wherein: (i) each of the droplets comprises multiple molecules of the compound(s) contained therein; and the droplets do not contain monomeric precursors for the polymeric compound. A method for making the emulsion is also provided.

Creating and harvesting surface-bound emulsion

Systems and methods for displaying gene- and/or protein-related data with respect to chromosome maps at locations identifying relevant positioning of the genes with which the gene- and/or protein related data are associated. Multiple experiments may be plotted onto the display adjacent one or more chromosome maps. Automatic extraction of genomic location, based on accession numbers or other unique identifiers and cross connection with expression data is provided. Statistical assessments of correlations between expression and genome localization may be performed. Zooming capabilities, thumbnail/fullview toggling, browsability and linked data may be included as features of the visualization systems described.

Visualizing expression data on chromosomal graphic schemes

The present disclosure provides methods for barcoding a plurality of DNA samples using a microarray of barcode-containing transposase complexes. In some embodiments, the DNA samples and transposase complexes are present in aqueous droplets on the surfaces of opposing substrates, which allows a single DNA sample droplet to be combined with a single transposase-complex droplet. The barcoded DNA in the combined droplets can be used for any number of purposes, including as templates for amplification and sequencing.

Methods for on-array fragmentation and barcoding of DNA samples

A method for analyzing a sequence comprising a SNP site is provide. In general terms, the method comprises: a) contacting a first DNA sample with a first restriction enzyme to provide DNA fragments, wherein: i) the first restriction enzyme cleaves the sequence only if a first allele of a SNP is present at the SNP site; b) end-labeling the DNA fragments to produce an end-labeled sample; c) hybridizing the end-labeled sample to an array comprising a probe sequence; and d) comparing the amount of hybridization between the digested sample and the probe sequence to a reference signal.

Analysis of single nucleotide polymorphisms using end labeling

A sample probe includes a tip including a distal end for penetrating a cellular membrane, an opening located at or proximal to the distal end, and tip microchannels extending through the tip and communicating with the opening; and a body adjoining the tip and including body microchannels, wherein at least one of the body microchannels communicates with at least one of the tip microchannels. A method for sampling intracellular material includes inserting a probe tip through a cellular membrane; aspirating intracellular material from the cell, through an opening of the tip, and into a first microchannel of the tip; flowing isolator fluid from a second microchannel of the tip into the first microchannel to form a plug of intracellular material; and aspirating the plug and the isolator fluid through the first microchannel.

Sample probes and methods for sampling intracellular material

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San Jose, CA, United States of America

Nicholas Michael Sampas