Microbial Sequencing

Feiqiao Brian Yu
Quake Lab, Stanford University

(...) Published on Rev A

  • supported ifcs:
    Open App IFC
  • number of ifc runs:


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's Ready-Lyse, and MDA based amplification is performed using the Qiagen Repli-g sc kit.

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Protocol: Mini-metagenomicsDuration (H:M): 2:00

Random Capture

Qiagen Lysis MDA

view protocol worksheet

Tested Primary Cells or Cell Lines

Cell Name Cell Type Source
Microbial Sample Environmental Microbial Communities


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 uL harvest reagent.

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