Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions

Roman Stocker, Kang Soo Lee, Fátima C. Pereira, Márton Palatinszky, Lars Behrendt, Uria Alcolombri, David Berry, Michael Wagner

Published: 2020-12-10 DOI: 10.1038/s41596-020-00427-8

Optofluidic Raman-activated cell sorting

Supplementary information

Supplementary Video 1 Raman-activated cell sorting (RACS) procedures . The movie is composed of four sections: (i) visualization of flow in the microfluidic device; (ii) system calibration; (iii) case 1, the process for a captured and selected cell (sorted); and (iv) case 2, the process for a captured and rejected cell (not sorted). In section (i), the two separate flow streams do not interfere with each other–the sample flow traverses the analysis region and exits into the waste outlet by default, whereas the flow carries a cell released at the ‘release location’ (blue box) through the collection outlet. Section (ii) shows the Raman measurement of the working fluid (in the absence of a cell) to be used to calculate the P C values (eqn. (1) in the main text) during the RACS. For sections (iii) and (iv), the left and right panels represent the CCD image (obtained by the lower microscope) and the corresponding operation of the RACS software, respectively. The details of the sorting procedures are described in the lower panel of the movie.

41596_2020_427_MOESM4_ESM.zip

Supplementary Data 1 Computer-aided design (CAD) diagrams for the microfluidic sorter . The CAD file is provided as a separate supplement, “Supplementary_Data_1.dxf”. Users with access to a cleanroom facility can prepare the device from scratch (i.e., fabrication from a master mold using this photomask design and creation of the PDMS microfluidic device), whereas those who do not have expertise in microfabrication can ask commercial manufacturers to fabricate the master mold and then fabricate the PDMS microfluidic device in their laboratory.

Supplementary Data 2

Statistical source data for Supplementary Fig. 2

Supplementary Data 3

Statistical source data for Supplementary Fig. 3cd

41596_2020_427_MOESM7_ESM.zip

Supplementary Software 1 MATLAB GUI platform and corresponding script code to operate the RACS . ‘fig’ and ‘m’ files are bound together and thus should be identically named. See ‘README.pdf’ file that accompanies in the same zip file for system requirements and instructions to run this code.

41596_2020_427_MOESM8_ESM.zip

Supplementary Software 2 MATLAB GUI platform and corresponding script code to operate the RACS based on a machine-learning ( **K ** -means clustering) algorithm . ‘fig’ and ‘m’ files are bound together and thus should be identically named. See ‘README.pdf’ file that accompanies in the same zip file for system requirements and instructions to run this code.

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Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question “who does what?” in complex microbial communities when coupled with fluorescence insitu hybridization or do
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
References
ACKNOWLEDGMENTS

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Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions

Supplementary information

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