Massachusetts Institute of Technology

The Broad Institute, Inc.

University of California

Harvard College

The Brigham and Women's Hospital, Inc.

Other

The Board Institute, Inc.

Jellert Gaublomme

Aviv Regev

Vijay K Kuchroo

Hongkun Park

Alexander K Shalek

Nir Yosef

Chao Wang

Orit Rozenblatt-Rosen

Youjin Lee

Eric Lander

Le Cong

Ana Carrizosa Anderson

Jonathan S Weissman

Thomas W Norman

Brian Cleary

Atray Dixit

Oren Parnas

Bo Li

Brittany Adamson

Nicole C Joller

Chuan Wu

Kathryn Geiger-Schuller

James Kaminski

Pratiksha Thakore

The application relates to methods and systems for proteomics and spatial mapping of biomolecules using a next generation sequencing readout to decipher biomolecular and cellular interaction networks. Specifically, disclosed are antenna networks generated by conjugating DNA antennas to proteins. The antennas carry a unique antenna identifier (UAI) sequence that can provide spatial location of the network, as well as biomolecules by transfer of the UAI to reporter oligonucleotides associated with other antennas and biomolecules. The methods and systems are also applicable to single cells.

Proteomics and spatial patterning using antenna networks

This invention relates generally to compositions and methods for identifying the regulatory network that modulates, controls or otherwise influences T cell balance, for example, Th17 cell differentiation, maintenance and/or function, as well compositions and methods for exploiting the regulatory network that modulates, controls or otherwise influences T cell balance in a variety of therapeutic and/or diagnostic indications. This invention also relates generally to identifying and exploiting target genes and/or target gene products that modulate, control or otherwise influence T cell balance in a variety of therapeutic and/or diagnostic indications.

T cell balance gene expression, compositions of matters and methods of use thereof

The present invention provides methods and tools for analyzing genetic interactions. The subject matter disclosed herein is generally directed to single cell genomics and proteomics. In one embodiment provided is a method of cell and nuclei hashing using sample barcodes. In another embodiment are method of performing genomewide CRISPR perturbation screens.

Methods and compositions for multiplexing single cell and single nuclei sequencing

The present invention provides tools and methods for the systematic analysis of genetic interactions, including higher order interactions. The present invention provides tools and methods for combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.

Assays for massively combinatorial perturbation profiling and cellular circuit reconstruction

The present invention relates to methods for high multiplex protein or cellular constituent analysis in single cells or single isolated aggregations of cellular constituents. The methods provide for embedding cells or isolated aggregations of cellular constituents in a hydrogel mesh and labeling of cellular constituents with labeling ligands linked to a nucleic acid tag. Cellular constituents can be determined using sequencing methods.

Multiplex analysis of single cell constituents

The application relates to proteome analysis in single cells. Specifically, disclosed are high throughput methods of detecting proteins in single cells using barcoding, aptamers and single cell sequencing. Solid supports used in recording the cell-of-origin of target proteins and target proteins expressed in the cell-of-origin are disclosed. Additionally, methods of detecting proteins and mRNA in single cells are disclosed. Additionally, methods of detecting protein interactions are disclosed. Additionally, methods of detecting post translationally modified proteins in single cells are disclosed. The application also relates to solid supports or beads and methods of producing said solid supports or beads for use in the described methods.

Single-cell proteomic assay using aptamers

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Cambridge, MA, United States of America

Jellert Gaublomme