Genocea Biosciences, Inc.

Massachusetts Institute of Technology

Harvard College

Children's Medical Center Corporation

The General Hospital Corporation

The Broad Institute, Inc.

Honeycomb Biotechnologies, Inc.

The Chidlren's Medical Center Corporation

Todd Michael Gierahn

J Christopher Love

Jessica Baker Flechtner

Richard Malley

Viktor A Adalsteinsson

Denis Loginov

Alan Stockdale

Darren E Higgins

Alexander K Shalek

Travis K Hughes

Michael N Starnbach

Nadia R Roan

Marc H Wadsworth, Ii

Paul Blainey

Bradley Bernstein

Navpreet Ranu

Peter Van Galen

Volker Hovestadt

Ang A Tu

Marc Havens Wadsworth

Shaina Carroll

Jessica Fletchner

Described herein are systems, methods, and apparatus for automatically identifying and recovering individual cells of interest from a sample of biological matter, e.g., a biological fluid. Also described are methods of enriching a cell type of interest. These systems, methods, and apparatus allow for coordinated performance of two or more of the following, e.g., all with the same device, thereby enabling high throughput: cell enrichment, cell identification, and individual cell recovery for further analysis (e.g., sequencing) of individual recovered cells.

Systems, methods, and apparatus for in vitro single-cell identification and recovery

The present application provides a method of assembling a container for one or multiple parallel steps of biochemical analysis on one or more cells comprising performing molecular bonding of a porous membrane on an apical or basal surface of an array having a plurality of wells, wherein the molecular bonding substantially isolates each well from adjacent wells.

Semi-permeable arrays for analyzing biological systems and methods of using same

Modifications to both hardware and enzymatic reactions used in single cell analyses such as but not limited to Seq-well that enable significant increases in the yield of transcripts per cell, portability and ease of use, increased scalability of the assay, and linkage of transcript information to other measurements made in the picowell arrays are disclosed.

Single cell analyses

The present invention relates to methods of detecting region(s) of interest in a gene comprising a polyA tail. The region(s) of interest can include gene(s), region(s), mutation(s), deletion(s), insertion(s), indel(s), and/or translocation(s). The region(s) can be greater than or less than 1 kilobases from the polyA tail. Methods can include forming a library of single cell transcripts comprising the region(s) in close proximity to a cell barcode and a unique molecular identifier (UMI). Methods for distinguishing cells by genotype can include amplifying the transcripts using PCR methods and detecting the cell barcode and UMI using single cell sequencing methods. Transcripts can be enriched using tagged region-specific PCR primers. Cell barcodes can be brought into close proximity to the region(s) by circularizing the transcripts. Sequencing of the transcripts can include using primer binding sites added during PCR amplification and library indexes for multiplexed sequencing.

Single cell sequencing libraries of genomic transcript regions of interest in proximity to barcodes, and genotyping of said libraries

The present invention relates to the analysis of complex single cell sequencing libraries. Disclosed are methods for enrichment of library members based on the presence of cell-of origin barcodes to identify and concentrate DNA that is relevant to interesting cells or components that would be expensive or difficult to study otherwise. Also, disclosed are methods of capturing cDNA library molecules by use of CRISPR systems, hybridization or PCR. The present invention allows for identifying the properties of rare cells in single cell RNA-seq data and accurately profile them through clustering approaches. Further information on transcript abundances from subpopulations of single cells can be analyzed at a lower sequencing effort. The methods also allow for linking TCR alpha and beta chains at the single cell level.

Single cell cellular component enrichment from barcoded sequencing libraries

Disclosed herein are cellular cassettes for the storage, collection, and analysis of biological samples. The cellular cassette can enable easy sample collection and sealing of microwell arrays with semi-permeable membrane for stable storage and future processing of single cells. Also disclosed herein are systems and kits comprising one or more described cassettes. The described cassettes, systems, and kits can be used to create barcoded, single-cell sequencing libraries. Further described herein are methods of using the cassettes, systems, and kits.

Cellular cassettes for the collection, storage, and analysis of biological samples

is a major health concern, especially in very young, elderly, or immunocompromised patients. The present disclosure provides, inter alia, certain highly effective vaccines and pharmaceutical compositions in. The antigens may be used therapeutically or prophylactically.

Vaccines and compositions against

Methods and compositions for identifying antigens of human lymphocytes are provided herein.

Antigen screening system

Replicable libraries having discrete members in defined locations for screening for antigens to a pathogenic organism are provided. Also provided are methods for using such libraries as well as a specific antigen, CT788, which induces T-cell activation during ainfection.

Compositions for and methods of identifying antigens

is a major health concern, especially in very young, elderly, or immunocompromized patients. The present disclosure provides, inter alia, certain highly effective vaccines and pharmaceutical compositions in. The antigens may be used therapeutically or prophylactically.

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Growing community of inventors

Brookline, MA, United States of America

Todd Michael Gierahn