Effects of sample treatments on genome recovery via single-cell genomics

Journal Article · Fri Jun 13 00:00:00 EDT 2014 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2014.92· OSTI ID:1241191

Clingenpeel, Scott ^[1]; Schwientek, Patrick ^[1]; Hugenholtz, Philip ^[2]; Woyke, Tanja ^[1]

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1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
2. Univ. of Queensland, Brisbane (Australia)

It is known that single-cell genomics is a powerful tool for accessing genetic information from uncultivated microorganisms. Methods of handling samples before single-cell genomic amplification may affect the quality of the genomes obtained. Using three bacterial strains we demonstrate that, compared to cryopreservation, lower-quality single-cell genomes are recovered when the sample is preserved in ethanol or if the sample undergoes fluorescence in situ hybridization, while sample preservation in paraformaldehyde renders it completely unsuitable for sequencing.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC); Australian Research Council
• DOE Contract Number: AC02-05CH11231; LE120100025; DP120103498
• OSTI ID: 1241191
• Report Number(s): LBNL-7046E
• Journal Information: The ISME Journal, Vol. 8, Issue 12; ISSN 1751-7362
• Publisher: Nature Publishing Group
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
single-cell genomics
sample preservation
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