Current Methods and Protocols

    515F-926R 16S and 18S rRNA Gene Sequencing Protocol V.2

    *NOTE: THE COMBINATORIAL BARCODING AND INDEXING STRATEGY HERE IS SUITABLE FOR MISEQ AND HISEQ2500, BUT DUE TO HIGHER INCIDENCE OF INDEX HOPPING WITH NOVASEQ AND OTHER NEW PLATFORMS WITH PATTERNED FLOWCELLS, IT IS HIGHLY RECOMMENDED TO CHANGE TO UNIQUE DUAL INDEXING (UDI). This allows informatic removal of spurious forward-reverse combinations, resembling cross-contamination between samples (up to a few percent of sequences in our experience). We recommend replacing the forward and reverse barcodes/indices with unique 10 nt index combinations.

    Filtering for cell collection

    Author: SangHoon Lee

    Filtering and extracting for virus fractions

    0.22um to 0.02um fractionation of whole seawater to isolate viruses

    Bacterial heterotrophic production

    Author: Jed Fuhrman

    SYBR Green I counts of viruses and bacteria

    Authors: Anand Patel and Rachel Noble

    SPOT DNA Extraction from 142mm Durapore 0.22µm Filters

    Authors: Rohan Sachdeva and Cheryl Chow

    Archive Methods and Protocols

      Molecular fingerprinting (ARISA)

      Automated rRNA Intergenic Spacer Analysis (ARISA)

      Pulsed Field Gel Electrophoresis

      Author: John Griffith

      Cytoscape Tutorial

      Authors: Cheryl Chow and Jacob Cram