PMID- 31788681 OWN - NLM STAT- MEDLINE VI - 20 IP - 2 TI - smFISH in chips: a microfluidic-based pipeline to quantify in situ gene expression in whole organisms. PG - 266-273 LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Lab Chip JT - Lab on a chip JID - 101128948 IS - 1473-0189 (Electronic) LID - 10.1039/c9lc00896a [doi] FAU - Wan, Jason AU - Wan J AUID- ORCID: 0000-0002-4434-9357 AD - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. hang.lu@gatech.edu and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. FAU - Sun, Gongchen AU - Sun G AUID- ORCID: 0000-0002-7973-0422 AD - School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. FAU - Dicent, Jocelyn AU - Dicent J AD - School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. FAU - Patel, Dhaval S AU - Patel DS AUID- ORCID: 0000-0002-1110-0125 AD - School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. FAU - Lu, Hang AU - Lu H AUID- ORCID: 0000-0002-6881-660X AD - Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. hang.lu@gatech.edu and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. IS - 1473-0189 (Linking) RN - 0 (Caenorhabditis elegans Proteins) RN - 0 (DAF-7 protein, C elegans) RN - 0 (Transforming Growth Factor beta) RN - 0 (gpa-3 protein, C elegans) RN - EC 3.6.5.1 (GTP-Binding Protein alpha Subunits, Gi-Go) SB - IM MH - Animals MH - Caenorhabditis elegans MH - Caenorhabditis elegans Proteins/*genetics MH - GTP-Binding Protein alpha Subunits, Gi-Go/*genetics MH - Gene Expression MH - *In Situ Hybridization, Fluorescence MH - *Lab-On-A-Chip Devices MH - Tissue Culture Techniques MH - Transforming Growth Factor beta/*genetics PMC - PMC8146400 DCOM- 20210201 LR - 20231111 DP - 20200121 DEP - 20191202 AB - Gene expression and genetic regulatory networks in multi-cellular organisms control complex physiological processes ranging from cellular differentiation to development to aging. Traditional methods to investigate gene expression relationships rely on using bulk, pooled-population assays (e.g. RNA-sequencing and RT-PCR) to compare gene expression levels in hypo- or hyper-morphic mutant animals (e.g. gain-of-function or knockout). This approach is limited, especially in complex gene networks, as these genetic mutations may affect the expressions of related genes in unforseen ways. In contrast, we developed a microfluidic-based pipeline to discover gene relationships in a single genetic background. The microfluidic device provides efficient reagent exchange and the ability to track individual animals. By automating a robust microfluidic reagent exchange strategy, we adapted and validated single molecule fluorescent in situ hybridization (smFISH) on-chip and combined this technology with live-imaging of fluorescent transcriptional reporters. Together, this multi-level information enabled us to quantify a gene expression relationship with single-animal resolution. While this microfluidic-based pipeline is optimized for live-imaging and smFISH C. elegans studies, the strategy is highly-adaptable to other biological models as well as combining other live and end-point biological assays, such as behavior-based toxicology screening and immunohistochemistry.