Mini-metagenomics
Microbial sequencing

Yu, F.B.
Quake Lab, Stanford University

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PUBLISHED ON: APRIL 19, 2017 | REV A
SUPPORTED IFCS: Open App™ IFC
NUMBER OF IFC RUNS: 40

Overview

This protocol enables the lysis and whole genome amplification of bacterial cells isolated from standard lab conditions as well as from environmental samples. This protocol can be used to generate amplified genomic DNA from small groups of 5–10 cells, producing mini-metagenomes. The cell wash step is removed from the standard cell capture protocol. Instead, well suspended bacterial cells are loaded into the C1™ IFC chambers via random Poisson distribution. Lysis is performed using Epicenter Ready-Lyse™, and MDA based amplification is performed using the Qiagen Repli-g Single Cell Kit.

Protocol: Mini-metagenomics | Duration (H:M): 2:00

Tested Primary Cells or Cell Lines

Cell Name

Cell Type

Source

Microbial Sample Environmental Microbial Communities

Performance

During mini-metagenomic applications, 5–10 cells are randomly loaded into each chamber or capture site. This protocol performs MDA for 5 hours and can generate 10–200 ng of DNA at the output in 3.5 µL harvest reagent.


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