Disclosed herein are compositions, methods and kits useful for epigenetic analysis based on the use of transposons that are targeted to specific regions of chromatin based on DNA-DNA interactions, protein-protein interactions, RNA-RNA interactions, and nucleic acid-protein interactions.

Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template ribonucleic acid (RNA), a template switch oligonucleotide including a 3 hybridization domain and a sequencing platform adapter construct, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template RNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.

Methods of labeling or barcoding molecules within one or more portions of a plurality of cells are provided. Kits and systems for labeling or barcoding molecules within one or more portions of a plurality of cells are also provided. The methods, kits, and systems may utilize photo-controlled adapter sequences, nucleic acids tags, and/or linkers.

There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, on device assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments.

The present disclosure provides ultrahigh-throughput single cell genomic sequencing methods, referred to herein as SiC-seq, which methods include encapsulating single cells in molten gel droplets to facilitate bulk cell lysis and purification of genomic DNA in microgels. Systems and devices for practicing the subject methods are also provided.

A method for searching for a compound having a interaction with a target molecule includes growing a base fragment molecule and obtaining a grown molecule by performing molecular dynamics calculation using a reactive force field and bonding an atom to the base fragment molecule at a binding site of the target molecule.

The present disclosure relates to multifunctional molecules, including molecules according to formula (I-A) [(B1).sub.M-L.sub.1].sub.O-G, and (I) [(B.sub.1).sub.M-L.sub.1].sub.O-G-[(L.sub.2-(B.sub.2).sub.K].sub.P wherein B.sub.1, M, L.sub.1, O, G, L.sub.2, B.sub.2, K, and P are defined herein, wherein each positional building block B1 is identified by from 1 to 5 coding regions in G, and from about 10% to 100% of the positional building blocks B.sub.1 at position M and/or B.sub.2 at position K, based on a total number of positional building blocks, are identified by a combination of from 2 to 5 independent coding regions. Methods of making such multifunctional molecules, and methods of serially enriching an oligonucleotide encoded library, are also disclosed. The present disclosure also relates to methods of preparing and using such multifunctional molecules to identify encoded molecules capable of binding target molecules.

Methods for generating a sequencing library from a sample comprising a plurality of single-stranded DNA molecules are provided, along with methods of using the generated sequencing library for detecting cancer, determining cancer stage, monitoring cancer progression, and/or determining a cancer classification from a test sample obtained from a subject.

Methods and systems for sample preparation techniques that allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells are provided. The methods and systems generally operate by forming or providing partitions (e.g., droplets) including a single biological particle and a single bead comprising a barcoded oligonucleotide. The preparation of barcoded next-generation sequencing libraries prepared from a single cell is facilitated by the transposon-mediated transposition and fragmentation of a target nucleic acid sequence. The methods and systems may be configured to allow the implementation of single-operation or multi-operation chemical and/or biochemical processing within the partitions.

The invention relates to a method for synthesising templated molecules attached to the templated which directed the synthesis thereof. The method involves a template, a scaffold functional entity and a functional entity attached to a building block, which, in turn, is attached the template. The scaffold functional entity and the functional entity of the building block are both provided with complementary dimerization domains allowing the functional entities to come into close proximity when the complementary domains interact with to each other. The method may be used for generating libraries of templated molecules which may be selected for biological activity.