Massachusetts Institute of Technology

Harvard College

The Broad Institute, Inc.

Children's Medical Center Corporation

Jason Daniel Buenrostro

Aviv Regev

Edward Stuart Boyden

Fei Chen

Shahar Alon

Vijay G Sankaran

Andrew C Payne

Sai Ma

Leif S Ludwig

Jacob C Ulirsch

Paul Reginato

Christoph Muus

Caleb A Lareau

Embodiments disclosed herein provide methods of using somatic mutations in mitochondrial genomes to retrospectively infer cell lineages in native contexts and to serve as genetic barcodes to measure clonal dynamics in complex cellular populations. Further, somatic mutations in mitochondrial DNA (mtDNA) are tracked by single cell genomic approaches for simultaneous analysis of single cell lineage and state. Applicants further show that mitochondrial mutations can be readily detected with contemporary single cell transcriptomic and epigenomic technologies to concomitantly capture gene expression profiles and chromatin accessibility, respectively.

Lineage tracing using mitochondrial genome mutations and single cell genomics

Provided herein include methods and compositions for analyzing nucleic acid in individual cells. In some embodiments, the methods herein include generating, within individual cells, fragmented cellular genomic DNA and cDNA copies of cellular RNA molecules, barcoding the fragmented genomic DNA and the cDNA within each cell such that the genomic DNA and the cDNA from the same cell receive the same unique barcode sequence, isolating the barcoded genomic DNA and cDNA, and characterizing one or more features of the individual cells based, at least in part, on sequencing of the isolated barcoded genomic DNA and the cDNA.

Methods and compositions for analyzing nucleic acids

The present invention provides methods for analyzing polynucleotides such as genomic DNA. In some embodiments, the disclosure provides a method for preparing and amplifying a genomic DNA library in situ in a fixed biological sample. The method comprises treating a fixed biological sample with an insertional enzyme complex to produce tagged fragments of genomic DNA. The method further comprises circularizing the tagged fragments of genomic DNA. The method further comprises amplifying the tagged fragments of genomic DNA.

In situ ATAC sequencing

Growing community of inventors

Cambridge, MA, United States of America

Jason Daniel Buenrostro