Massachusetts Institute of Technology

Harvard College

The Broad Institute, Inc.

Dana-farber-cancer Institute Inc.

Anindita Basu

Aviv Regev

David A Weitz

Christopher B Ford

Hongkun Park

Alexander K Shalek

Steven Andrew McCarroll

Evan Macosko

Naomi Habib

Feng Zhang

Orit Rozenblatt-Rosen

Yinqing Li

Matthias Heidenreich

Asaf Rotem

Kevin Struhl

Lukasz Swiech

Eugene Drokhlyansky

Inbal Avraham-Davidi

Inbal Avraham Davidi

Evan Zane Macosko

Techniques Nuc-seq, Div-Seq, and Dronc-Seq are allow for unbiased analysis of any complex tissue. Nuc-Seq, a scalable single nucleus RNA-Seq method, can sensitively identify closely related cell types, including within the adult hippocampus. Div-seq combines Nuc-Seq with EdU-mediated labeling of proliferating cells, allowing tracking of transcriptional dynamics of newborn neurons in an adult neurogenic region in the hippocampus. Dronc-Seq uses a microfluidic device to co-encapsulate individual nuclei in reverse emulsion aqueous droplets in an oil medium together with one uniquely barcoded mRNA-capture bead.

Methods for determining spatial and temporal gene expression dynamics during adult neurogenesis in single cells

Transcriptomes of individual neurons provide rich information about cell types and dynamic states. However, it is difficult to capture rare dynamic processes, such as adult neurogenesis, because isolation from dense adult tissue is challenging, and markers for each phase are limited. Here, Applicants developed Nuc-seq, Div-Seq, and Dronc-Seq. Div-seq combines Nuc-Seq, a scalable single nucleus RNA-Seq method, with EdU-mediated labeling of proliferating cells. Nuc-Seq can sensitively identify closely related cell types within the adult hippocampus. Div-Seq can track transcriptional dynamics of newborn neurons in an adult neurogenic region in the hippocampus. Dronc-Seq uses a microfluidic device to co-encapsulate individual nuclei in reverse emulsion aqueous droplets in an oil medium together with one uniquely barcoded mRNA-capture bead. Finally, Applicants found rare adult newborn GABAergic neurons in the spinal cord, a non-canonical neurogenic region. Taken together, Nuc-Seq, Div-Seq and Dronc-Seq allow for unbiased analysis of any complex tissue.

Methods for determining spatial and temporal gene expression dynamics in single cells

The present invention generally relates to a controlled fluidic device to develop spatially complex environments to enhance the rate of evolution in cell populations. The method further provides an enhanced understanding in the emergence, for example, drug resistance during cancer chemotherapy.

High-throughput dynamic reagent delivery system

The present invention generally relates to a combination of molecular barcoding and emulsion-based microfluidics to isolate, lyse, barcode, and prepare nucleic acids from individual cells in a high-throughput manner.

Droplet-based method and apparatus for composite single-cell nucleic acid analysis

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Cambridge, MA, United States of America

Anindita Basu