Understanding gene regulation networks in multicellular organisms is crucial to decipher many complex physiological processes ranging from development to aging. One technique to characterize gene expression with tissue-specificity in whole organisms is single-molecule fluorescence in situ hybridization (smFISH). However, this protocol requires lengthy incubation times, and it is challenging to achieve multiplexed smFISH in a whole organism. Multiplexing techniques can yield transcriptome-level information, but they require sequential probing of different genes. The inefficient macromolecule exchange through diffusion-dominant transport across dense tissues is the major bottleneck. In this work, we address this challenge by developing a microfluidic/electrokinetic hybrid platform to enable multicycle smFISH in an intact model organism, Caenorhabditis elegans. We integrate an ion concentration polarization based ion pump with a microfluidic array to rapidly deliver and remove gene-specific probes and stripping reagents on demand in individual animals. Using our platform, we can achieve rapid smFISH, an order of magnitude faster than traditional smFISH protocols. We also demonstrate the capability to perform multicycle smFISH on the same individual samples, which is impossible to do off-chip. Our method hence provides a powerful tool to study individual-specific, spatially resolvable, and large-scale gene expression in whole organisms.
Skip Nav Destination
Rapid and multi-cycle smFISH enabled by microfluidic ion concentration polarization for in-situ profiling of tissue-specific gene expression in whole C. elegans
,
,
CHORUS
Article navigation
November 2019
Research Article|
November 01 2019
Rapid and multi-cycle smFISH enabled by microfluidic ion concentration polarization for in-situ profiling of tissue-specific gene expression in whole C. elegans
Available to Purchase
Special Collection:
Festschrift for Professor Hsueh-Chia Chang
Gongchen Sun
;
Gongchen Sun
a)
1
School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
, Atlanta, Georgia
30332, USA
Search for other works by this author on:
Jason Wan
;
Jason Wan
a)
2
Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University
, Atlanta, Georgia 30332, USA
Search for other works by this author on:
Hang Lu
Hang Lu
b)
1
School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
, Atlanta, Georgia
30332, USA
b)Author to whom correspondence should be addressed: [email protected]
Search for other works by this author on:
Gongchen Sun
1,a)
Jason Wan
2,a)
Hang Lu
1,b)
1
School of Chemical & Biomolecular Engineering, Georgia Institute of Technology
, Atlanta, Georgia
30332, USA
2
Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University
, Atlanta, Georgia 30332, USA
a)
Contributions: G. Sun and J. Wan contributed equally to this work.
b)Author to whom correspondence should be addressed: [email protected]
Note: This article is part of the special topic, Festschrift for Professor Hsueh-Chia Chang.
Biomicrofluidics 13, 064101 (2019)
Article history
Received:
August 16 2019
Accepted:
October 15 2019
Citation
Gongchen Sun, Jason Wan, Hang Lu; Rapid and multi-cycle smFISH enabled by microfluidic ion concentration polarization for in-situ profiling of tissue-specific gene expression in whole C. elegans. Biomicrofluidics 1 November 2019; 13 (6): 064101. https://doi.org/10.1063/1.5124827
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Citing articles via
Cognitive dynamics of drug-mediated zebrafish under sound stimuli in a microfluidic environment
Prashant Kishor Sharma, Dineshkumar Loganathan, et al.
Droplet acoustofluidics: Recent progress and challenges
Mushtaq Ali, Woohyuk Kim, et al.
Related Content
Dynamic range in the C. elegans brain network
Chaos (January 2016)
Characterizations of kinetic power and propulsion of the nematode Caenorhabditis elegans based on a micro-particle image velocimetry system
Biomicrofluidics (April 2014)
UGT-29 protein expression and localization during bacterial infection in Caenorhabditis elegans
AIP Conf. Proc. (September 2014)
An automated microfluidic system for screening Caenorhabditis elegans behaviors using electrotaxis
Biomicrofluidics (February 2016)