{"id":422,"date":"2023-10-11T16:32:18","date_gmt":"2023-10-11T23:32:18","guid":{"rendered":"https:\/\/dornsife.usc.edu\/fuhrmanlab\/?page_id=422"},"modified":"2023-12-11T16:53:05","modified_gmt":"2023-12-12T00:53:05","slug":"methods","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/fuhrmanlab\/methods\/","title":{"rendered":"Methods"},"content":{"rendered":"\n\n\n  \n              \n    \n    \n        \n    \n    \n        \n    \n    \n        \n    \n    \n        \n    \n    \n        \n    \n  \n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--interactive-content-pane \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--interactive-content-pane\"\n    \n      >\n\n    \n<div class=\"inner-wrapper\">\n  <div class=\"left\">\n              \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Current Methods and Protocols\n      <\/h2>\n\n\n<\/div>\n      \n    <div class=\"pagination-wrapper\">\n      <ul class=\"interactive-content-pane-pagination\"><\/ul>\n    <\/div>\n  <\/div>\n\n  <div class=\"right\">\n          <div class=\"swiper\">\n        <div class=\"swiper-wrapper\">\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                515F-926R 16S and 18S rRNA Gene Sequencing Protocol V.2 \n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>*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.<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/fuhrman-lab-515f-926r-16s-and-18s-rrna-gene-sequen-j8nlkpd1g5r7\/v2\n  target=\"_blank\"  aria-label=\"Read more about Fuhrman Lab 515F-926R 16S and 18S rRNA Gene Sequencing Protocol V.2 on protocols.io\"  \n>\n    Fuhrman Lab 515F-926R 16S and 18S rRNA Gene Sequencing Protocol V.2 on protocols.io \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/default-fuhrman-lab-pipeline-for-exact-amplicon-se-vi9e4h6\n  target=\"_blank\"  aria-label=\"Read more about Default Fuhrman Lab Pipeline for Exact Amplicon Sequence Variant (eASV) Calling from SSU rRNA Amplicons Derived From 515Y\/926R Primers\"  \n>\n    Default Fuhrman Lab Pipeline for Exact Amplicon Sequence Variant (eASV) Calling from SSU rRNA Amplicons Derived From 515Y\/926R Primers \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                Filtering for cell collection\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>Author: SangHoon Lee<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/Filtering-for-Cell-Collection-n92ldywxl5br\/v1\n  target=\"_blank\"  aria-label=\"Read more about Filtering for Cell Collection on protocols.io\"  \n>\n    Filtering for Cell Collection on protocols.io \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                Filtering and extracting for virus fractions\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>0.22um to 0.02um fractionation of whole seawater to isolate viruses<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/file\/n8fzc84w.docx\n  target=\"_blank\"  aria-label=\"Read more about 0.02um Anotop filter extraction\"  \n>\n    0.02um Anotop filter extraction \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                Bacterial heterotrophic production\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>Author: Jed Fuhrman<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/Protocol-for-Bacterial-Heterotrophic-Production-dm6gprypvzpn\/v1\n  target=\"_blank\"  aria-label=\"Read more about Bacterial Heterotrophic Production on protocols.io\"  \n>\n    Bacterial Heterotrophic Production on protocols.io \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                SYBR Green I counts of viruses and bacteria\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>Authors: Anand Patel and Rachel Noble<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/virus-and-bacteria-counts-by-epifluorescence-micro-5jyl8mddg2wp\/v2\n  target=\"_blank\"  aria-label=\"Read more about SYBR Green Epifluorescence in protocols.io\"  \n>\n    SYBR Green Epifluorescence in protocols.io \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                SPOT DNA Extraction from 142mm Durapore 0.22\u00b5m Filters\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>Authors: Rohan Sachdeva and Cheryl Chow<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/SPOT-DNA-Extraction-from-142mm-Durapore-0-22-m-Fil-36wgq5m5gk57\/v1\n  target=\"_blank\"  aria-label=\"Read more about 0.22um Durapore DNA extraction on protocols.io\"  \n>\n    0.22um Durapore DNA extraction on protocols.io \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                  <\/div>\n      <\/div>\n      <\/div>\n  \n<\/div>\n\n\n\n  <div class=\"background-images\">\n          <div class=\"swiper swiper-background-images\">\n        <div class=\"swiper-wrapper\">\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                  <\/div>\n      <\/div>\n      <\/div>\n\n\n\n  <\/div><\/div>\n\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--spacer \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--spacer\"\n    \n      >\n\n    \n\n  <\/div><\/div>\n\n\n\n\n\n  \n        \n    \n    \n        \n    \n    \n        \n    \n  \n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--interactive-content-pane \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--interactive-content-pane\"\n    \n      >\n\n    \n<div class=\"inner-wrapper\">\n  <div class=\"left\">\n              \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Archive Methods and Protocols\n      <\/h2>\n\n\n<\/div>\n      \n    <div class=\"pagination-wrapper\">\n      <ul class=\"interactive-content-pane-pagination\"><\/ul>\n    <\/div>\n  <\/div>\n\n  <div class=\"right\">\n          <div class=\"swiper\">\n        <div class=\"swiper-wrapper\">\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                 Molecular fingerprinting (ARISA)\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>Automated rRNA Intergenic Spacer Analysis (<em>ARISA<\/em>)<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/docs.google.com\/document\/d\/1Si8x3bax_7sfEx749LQSwEt0spaYNgCd\/edit?usp=sharing&#038;ouid=106819345238875844679&#038;rtpof=true&#038;sd=true\n  target=\"_blank\"  aria-label=\"Read more about 2011 ARISA protocol\"  \n>\n    2011 ARISA protocol \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                Pulsed Field Gel Electrophoresis\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>Author: John Griffith<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/Protocol-for-Pulsed-Field-Gel-Electrophoresis-n2bvjy25vk5w\/v1\n  target=\"_blank\"  aria-label=\"Read more about PFGE on protocols.io\"  \n>\n    PFGE on protocols.io \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                      <div class=\"swiper-slide\">\n              <h3 class=\"pane-title\">\n                Cytoscape Tutorial\n              <\/h3>\n                                  \n<div class=\"f--field f--description\">\n\n    \n  <p>Authors: Cheryl Chow and Jacob Cram<\/p>\n\n\n\n<\/div>\n                          \n  \n                              <ul>\n                                            <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/dornsife.usc.edu\/fuhrmanlab\/wp-content\/uploads\/sites\/207\/2023\/09\/Cytoscape_Tutorial_in_progress_-_STAMPS.pdf\n  target=\"_blank\"  aria-label=\"Read more about Cytoscape Tutorial\"  \n>\n    Cytoscape Tutorial \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n                        <\/li>\n                                    <\/ul>\n                          <\/div>\n                  <\/div>\n      <\/div>\n      <\/div>\n  \n<\/div>\n\n\n\n  <div class=\"background-images\">\n          <div class=\"swiper swiper-background-images\">\n        <div class=\"swiper-wrapper\">\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                      <div class=\"swiper-slide\">\n                          <\/div>\n\n                  <\/div>\n      <\/div>\n      <\/div>\n\n\n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":623,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-content-detail.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-422","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ 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