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Developing an ultra-high throughput droplet microfluidic workflow for genetic circuit characterization

Award Number: F31HG013052
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS
PERIOD OF PERFORMANCE START DATE: 06/01/2023
PERIOD OF PERFORMANCE END DATE: 05/31/2025

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Developing an ultra-high throughput droplet microfluidic workflow for genetic circuit characterization - PROJECT SUMMARY Existing single cell sequencing technologies provide an unprecedented understanding of the unique genomic and transcriptomic differences that underlie heterogeneous biological samples. These differences are key to understand disease pathologies in clinical samples and fundamental mechanisms in basic biological applications. Recent attention has been directed towards the development of multiomic technologies that better capture the differences in paired datasets such as genome and transcriptome or transcriptome and epigenome. Currently however, there is no single cell technology that can profile sequence information with the corresponding phenotypic behavior of the cell. The purpose of this project is to develop a novel sequencing platform to address this technology gap. To demonstrate the utility of this platform, I will then apply it to rapidly characterize a tunable genetic oscillator. To accomplish this goal, I propose the following 2 specific aims. In Aim 1, I will develop FAB-seq (Fluorescence Annotated Barcoding and Sequencing). I will first demonstrate a novel dual barcoding approach that co-delivers optical and DNA barcodes to create single cell maps between microscopy image data and sequence data. I will also show that FAB-seq can be used to perform targeted sequencing according to an arbitrary phenotype. Then, I will leverage additional injected DNA barcodes to enhance the total barcode space of FAB-seq. In Aim 2, I will then demonstrate that FAB-seq can be used to rapidly characterize a tunable genetic oscillator. First, I will demonstrate that FAB-seq can detect oscillatory phenotypes from a circuit library containing oscillatory and non-oscillatory genetic circuits. Then I will show that when the oscillatory behavior of the circuit is perturbed, FAB-seq can map individual oscillation dynamics to the corresponding single cell transcriptome. The long-term goal of this project is to develop a platform technology that can map single cell microscopy data to single cell sequencing data at ultra-high throughput. I envision FAB-seq to be a transformative tool in addressing questions at the frontier of the genomics field.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2024 ( Subtotal = $48,974 )
2024	2024	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	77 MASSACHUSETTS AVE	CAMBRIDGE	MA	02139	MIDDLESEX	USA	Human Genome Research	000	2	5/23/2024	NON-COMPETING CONTINUATION	$48,974
														Subtotal = $48,974

Issue Date FY: 2023 ( Subtotal = $47,694 )
2023	2023	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	77 MASSACHUSETTS AVE	CAMBRIDGE	MA	02139	MIDDLESEX	USA	Human Genome Research	000	1	3/29/2023	NEW	$47,694
2023	2023	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	77 MASSACHUSETTS AVE	CAMBRIDGE	MA	02139	MIDDLESEX	USA	Human Genome Research	001	1	3/29/2023	NEW	$0
														Subtotal = $47,694

Grand Total All Awards = $96,668

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Developing an ultra-high throughput droplet microfluidic workflow for genetic circuit characterization

Award Number: F31HG013052

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS

PERIOD OF PERFORMANCE START DATE: 06/01/2023

PERIOD OF PERFORMANCE END DATE: 05/31/2025

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