California Institute of Technology

Massachusetts Institute of Technology

The Broad Institute, Inc.

Harvard College

Mitchell Guttman

Eric Lander

Mario R Blanco

Rustem F Ismagilov

Eric S Lander

Chun-Kan Chen

Sofia A Quinodoz

Alexander A Shishkin

Christine F Surka

Matthew S Curtis

David A Selck

Elena Stamenova

Devdoot Majumdar

Colleen A McHugh

Mary Arrastia

Ward Walkup, Iv

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.

Detection of molecular associations

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.

Methods and systems for performing single cell analysis of molecules and molecular complexes

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. 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.

Massively multiplexed RNA sequencing

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.

Reactivation of x chromosome genes

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.

HDAC inhibitor compositions for reactivation of the X chromosome

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

High-throughput identification of intermolecular interactions

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.

Methods for identifying macromolecule interactions

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.

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West Hollywood, CA, United States of America

Mitchell Guttman