Abstract: In some embodiments, methods of detecting an association between a query protein and a target moiety are described. In some embodiments, compositions are described. In some embodiments, kits are described.

Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.

Abstract: Disclosed herein include methods, compositions, and kits suitable for use in generating barcoded detection particles. Each barcoded detection particle can comprise a particle associated with an antigen-binding protein and a plurality of barcoding oligonucleotides. The plurality of barcoding oligonucleotides can comprise a first ligand. The particle can comprise a second ligand. The plurality of barcoding oligonucleotides can be associated with the particle via a multivalent binding agent comprising two or more binding moieties capable of binding the first ligand and/or the second ligand. There are provided, in some embodiments, methods for detecting interactions between nucleic acid molecules and proteins of interest. Methods for detecting interactions between ribonucleic acid molecules and RNA-binding proteins (RBPs) are also provided herein.

Abstract: In some embodiments, methods of detecting an association between a query protein and a target moiety are described. In some embodiments, compositions are described. In some embodiments, kits are described.

Abstract: The present disclosure relates generally to compositions of synthetic bifunctional molecules comprising a first domain that specifically binds to a target ribonucleic acid sequence and a second domain that specifically binds to a target protein, and uses thereof.

Abstract: The present disclosure relates generally to compositions of synthetic bifunctional molecules comprising a first domain that specifically binds to a target ribonucleic acid and a second domain that specifically binds to a target protein, and uses thereof.

Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.

Abstract: The disclosed invention is related to a universal strand-specific protocol for the sequencing preparation of all classes of RNA. The protocol allows for sequencing for dozens to more than thousands of samples simultaneously. Specifically, the disclosed invention is a method for parallel sequencing target RNA from samples from multiple sources while maintaining source identification.

Abstract: Disclosed is a method for detecting spatial proximity relationships between RNA and DNA molecules in a cell. The method includes: providing a sample of RNA and DNA wherein the RNA and DNA have ends capable ofjoining to other DNA and RNA, respectively; joining at least one end of the fragmented RNA to the end of at least one fragmented DNA, to create at least one joined RNA-DNA hybrid molecule, wherein the join encodes the information about the proximity of the RNA and DNA in the cell; reverse transcribing the at least one joined rRNA-DNA hybrid molecule to create least one target join DNA molecule that retains the information of the join, and determining the sequence of the target join thereby detecting spatial proximity relationships between RNA and DNA molecules in a cell.

Abstract: Methods of prohibiting Xist-dependent silencing of X chromosome genes include targeting the required Xist silencing complex components including SHARP, SMRT, HDAC3, SAF-A, LBR, and the respective binding sites of SHARP, LBR, and SAF-A on Xist, thereby prohibiting Xist repression, allowing for reactivation of the silenced X chromosome genes.

Abstract: A reactivation composition for activating or re-activating expression of a silenced X chromosome gene in a cell includes a non-cytotoxic histone deacetylase (HDAC) inhibitor. The reactivation composition includes the non-cytotoxic HDAC inhibitor and may further include a DNA methylation inhibitor. A method of activating or re-activating expression of a silenced X chromosome gene in a cell includes administering a reactivation composition including a non-cytotoxic HDAC inhibitor. The method of activating or re-activating expression of a silenced X chromosome gene may further includes administering a reactivation composition that includes a non-cytotoxic HDAC inhibitor and an inhibitor of DNA methylation.

Abstract: Methods of detecting an interaction between a macromolecule and an interaction partner are described. Kits are also described.

Abstract: A method for identifying interactions of DNA, RNA, and/or protein molecules in a cell includes distributing a cell lysate or fraction thereof into a plurality of lysate suspensions, adding a unique nucleotide tag to each lysate suspension to tag each DNA, RNA, and/or protein, pooling the tagged suspensions, and repeating the tagging, pooling, and sorting (distributing) as desired to decrease the probability that non-interacting molecules will receive all of the same nucleotide tags.

Abstract: The disclosed invention is related to a universal strand-specific protocol for the sequencing preparation of all classes of RNA. The protocol allows for sequencing for dozens to more than thousands of samples simultaneously. Specifically, the disclosed invention is a method for parallel sequencing target RNA from samples from multiple sources while maintaining source identification.

Abstract: A reactivation composition for activating or re-activating expression of a silenced X chromosome gene in a cell includes a non-cytotoxic histone deacetylase (HDAC) inhibitor. The reactivation composition includes the non-cytotoxic HDAC inhibitor and may further include a DNA methylation inhibitor. A method of activating or re-activating expression of a silenced X chromosome gene in a cell includes administering a reactivation composition including a non-cytotoxic HDAC inhibitor. The method of activating or re-activating expression of a silenced X chromosome gene may further includes administering a reactivation composition that includes a non-cytotoxic HDAC inhibitor and an inhibitor of DNA methylation.

Abstract: A method for parallel sequencing target RNA from samples from multiple sources while maintaining source identification is provided. The method includes providing samples of RNA comprising target RNA from two or more sources; labeling, at the 3? end, the RNA from the two or more sources with a first nucleic acid adaptor that comprises a nucleic acid sequence that differentiates between the RNA from the two or more sources; reverse transcribing the two or more sources to create a single stranded DNA comprising the nucleic acid sequence that differentiates between the RNA from the two or more sources; amplifying the single stranded DNA to create DNA amplification products that comprise the nucleic acid sequence that differentiates between the RNA from the two or more sources; sequencing the DNA amplification products thereby parallel sequencing target RNA from samples from multiple sources while maintaining source identification.

Abstract: Methods of detecting an interaction between a macromolecule and an interaction partner are described. Kits are also described.

Abstract: In some embodiments, methods of detecting an association between a query protein and a target moiety are described. In some embodiments, compositions are described. In some embodiments, kits are described.

Abstract: A method for identifying interactions of DNA, RNA, and/or protein molecules in a cell includes distributing a cell lysate or fraction thereof into a plurality of lysate suspensions, adding a unique nucleotide tag to each lysate suspension to tag each DNA, RNA, and/or protein, pooling the tagged suspensions, and repeating the tagging, pooling, and sorting (distributing) as desired to decrease the probability that non-interacting molecules will receive all of the same nucleotide tags.

Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.