LAB

MALDI-TOF

Mass spectrometry of ionized

proteins

MALDI-TOF

Microbial or yeast identification

SDS-PAGE

Size-based protein separation

SDS-PAGE

Checking of protein purity from plasmid protein expression, molecular weight estimation of expressed protein

Western Blot

Antibody-based protein detection

Western Blot

Protein identification, detection of protein markers for certain diseases or infections

Conventional PCR and AGE

Detection of target genes, presence or absence only no quantification

Conventional PCR and AGE

Extract DNA -> run PCR -> Mix PCR amplicon with loading dye -> Load in agarose gel (some gels have incorporated dye like GelRed or SYBR safe) -> Run electrophoresis -> if conventional dye, stain with ethidium bromide -> Visualize with a UV transilluminator

PCR

Amplify specific targeted gene

AGE

separate DNA fragment and visualize with respect to a DNA ladder marker

Quantitative PCR (qPCR)

Amplify specific gene target with real-time quantification using reporter fluorescent dyes that bind in the amplified DNA

Quantitative PCR (qPCR)

Presence or absence of a certain gene with quantification of bacterial/viral load based on the Threshold cycle (Ct)

Quantitative PCR (qPCR)

Extract DNA -> mix extracted DNA with qPCR mastermix -> run qPCR -> Analyze threshold cycle curves

PFGE

Separate large DNA fragments using restriction enzymes

PFGE

Strain typing

PFGE

Embed bacterial suspension in agarose plugs -> Lysis and Digestion of bacterial cells -> Run PFGE -> Staining of agarose gel -> Visualize with a UV transilluminator

GeneXpert

Same principle as automated real-time PCR using sputum samples for detection of Mycobacterium in sample and rifampicin resistance

GeneXpert

Clinical diagnostics

GeneXpert

Sputum liquefaction and inactivation -> loading in cartridge -> automated workflow from lysis and quantitative PCR

DNA Microarray

Hybridization principle where single stranded DNA bind to complementary probes with fluorescent dye.

DNA Microarray

Identification of microbial strain, or assessment of gene upregulation or deregulation

DNA Microarray

Extract DNA -> fluorescent dye labeling-> hybridization in chip or slide -> washing to remove non-sepcific binding -> Scan -> Analyze

Whole Genome Sequencing

Sequencing of the entire genome of a microbe

Whole Genome Sequencing

Microbial identification, comparison of strains

Whole Genome Sequencing

Extract DNA-> Check purity and that DNA concentration is enough using NanoDrop and Qubit fluorometer-> Library Preparation -> Run sequence -> Analyze

Metagenomic Sequencing

Sequence all present microbial communities in a sample

Metagenomic Sequencing

Microbiome

Metagenomic Sequencing

Extract DNA-> Check purity and that DNA concentration is enough using NanoDrop and Qubit fluorometer-> Library Preparation -> Run sequence -> Analyze