STAR Protocols
Volume 3, Issue 1, 18 March 2022, 100968
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Protocol
Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis

https://doi.org/10.1016/j.xpro.2021.100968Get rights and content
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Highlights

  • We describe EME sample-collection, single-cell isolation, lysis, genome amplification

  • These protocols are suitable for mining single-cell EME genomes

  • These protocols are directed towards recovery of high-quality genomes

  • The genomes are suitable for species-specific de novo genome assembly

Summary

We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline.

For complete details on the use and execution of this protocol, please refer to Ciobanu et al. (2021).

Subject areas

Sequence analysis
Cell isolation
Single Cell
Flow Cytometry/Mass Cytometry
Genomics
Sequencing
Microbiology
Molecular Biology
Environmental sciences

Data and code availability

This study did not generate/analyze new [datasets/code]. All the datasets are given in the associated study Ciobanu et al. (2021) “A Single-cell Genomics Pipeline for Environmental Microbial Eukaryotes” ISCI_102290.

Cited by (0)

6

These authors contributed equally

7

Present address: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA

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Lead contact

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Technical contact