Details

Autor(en) / Beteiligte

• Ciobanu, Doina
• Chan, Sandy
• Ahrendt, Steven
• Quandt, C. Alisha
• Benny, Gerald L.
• Smith, Matthew E.
• James, Timothy Y.
• Cheng, Jan-Fang

Titel

Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis

Ist Teil von

• STAR protocols, 2022-03, Vol.3 (1), p.100968-100968, Article 100968

Ort / Verlag

United States: Elsevier Inc

Erscheinungsjahr

2022

Quelle

MEDLINE

Beschreibungen/Notizen

• 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). [Display omitted] •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 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.