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MICROBIOLOGY
STAINS & KITS

Featuring highly dead-cell selective BactoView™ Dead Stains for gram-positive or gram-negative bacteria.
Our broad catalog of stains for labeling live and dead bacteria as well as endospores. Available in various colors and localizations.
Browse our selection of bright WGA CF® Dye Conjugates and kits for one-step labeling of gram-positive bacteria.
Explore our library of fluorescent stains and kits for live/dead discrimination in yeast.
View our list of cellular stains validated for labeling yeast vacuoles, cell walls, bud scars, cytoplasm, and more.
A sensitive and rapid PCR-based method for analyzing microbial viability without time-consuming culturing.

At Biotium, our specialty is creating fluorescent dyes that simplify and improve your scientific experiments. For Microbiology, we offer a wide range of fluorescent dyes and assays kits to stain bacteria, yeast and fungi, including dyes to assess cell viability and bacterial gram stain type. We have also developed a complete toolkit of reagents for viability PCR, a revolutionary method for determining microbial viability using qPCR.

Also visit our Cellular Stains Table for a comprehensive list of cellular stains with their ability to stain various cell types.

BACTERIAL VIABILITY STAINS

BactoView™  Dead Stains

BactoView™ Dead Stains are unique DNA binding dyes designed for highly-selective dead cell staining for microscopy or flow cytometry analysis. Unlike traditional vital nucleic acid dyes like propidium iodide or ethidium homodimer that are excluded from gram-negative bacteria but are taken up by live gram-positive bacteria, BactoView™ Dead Stains are excluded from both gram-positive and gram-negative strains for highly selective live/dead discrimination.

  • Highly Selective: Bright staining of dead cells with minimal background
  • Compatible: Works with gram-positive and gram-negative strains
  • Easy: Requires a single 30-minute staining step, no wash required
  • Color Choice: Available in 7 colors from green to near-IR

BactoView™  Viability Kits

BactoView™  Viability Kits are designed for convenient two-color staining of both live and dead bacteria. Each kit contains a BactoView™ Dead Stain for staining dead cells, and a BactoView™ Viability Green Counterstain for labeling both live and dead bacteria with green fluorescence. The kits are compatible with both gram-positive or gram-negative bacteria strains and are available with a red or far-red  BactoView™ Dead Stain.

  • Two-Color Staining: Labels both live and dead bacteria
  • Compatible: Works with gram-positive and gram-negative strains
  • Easy: Requires a single 30-minute staining step, no wash required
  • Two Kit Options: Choose from either a red or far-red BactoView™ Dead Stain

BactoView™ Dead Stains Offer Improved Dead Cell Selectivity for Gram-Positive Bacteria

BactoView™ Dead is less permeant to live gram-positive bacteria than other dead cell stains like EthD-III. S. epidermids cultures were left untreated or heat killed, then stained with 5 uM Ethidium Homodimer III (EthD-III) or 1X BactoView™ Dead 570/585. Cells were stained in medium for microscopy or PBS for flow cytometry. EthD-III stains many live S. epidermidis cells, resulting in poor live/dead discrimination, while BactoView™ Dead allows clear discrimination between live and dead cell populations. Gray peaks: Unstained cells; Blue peaks: stained live cells; Red peaks: stained heat-killed cells.

Obtain Robust Visualization of Live & Dead Cells with BactoView™ Viability Kits

Live or heat-killed cultures of B. subtilis stained with the BactoView™ Viability Green/Red kit and imaged by confocal microscopy. Dead cells are stained red with BactoView™ Dead 570/585, all cells are stained green with BactoView™ Green Viability Counterstain. Co-stained cells appear yellow in the merged images.

BactoView™ Dead Stains & Viability Kits

Product Name Ex/Em (nm) Detection Channel Size (500X in DMSO) Catalog No.
BactoView™ Dead 500/515 497/515 FITC 20 uL 40107-T
100 uL 40107
BactoView™ Dead 560/570 559/570 Rhodamine, PI, PE 20 uL 40108-T
100 uL 40108
BactoView™ Dead 570/585 572/583 Rhodamine, PI, PE 20 uL 40109-T
100 uL 40109
BactoView™ Dead 600/615 603/613 Texas Red® or PE-Texas Red® 20 uL 40110-T
100 uL 40110
BactoView™ Dead 655/670 653/671 Cy®5, APC 20 uL 40111-T
100 uL 40111
BactoView™ Dead 690/710 683/707 Cy®5.5 20 uL 40112-T
100 uL 40112
BactoView™ Dead 760/780 759/780 Cy®7, APC-Cy®7 20 uL 40113-T
100 uL 40113
BactoView™ Viability Kit (Green/Red) Green (498/522)/Red (572/583) FITC (Green)/Rhodamine, PI, PE (Red) 1 kit 32019
BactoView™ Viability Kit (Green/Far-Red) Green (498/522)/Far-Red (653/671) FITC (Green)/Cy®5, APC (Far-Red) 1 kit 32020
Texas Red is a registered trademark of Thermo Fisher Scientific; Cy Dye is a registered trademark of Cytiva.

Other Bacterial Viability Stains & Kits

Product Name Features
Live-or-Dye™ Fixable Viability Staining Kits •   Fixable dead cell stains
•   Available in 8 fluorescent colors
•   Useful for flow cytometry or microscopy
Live-or-Dye NucFix™ Red Staining Kit •   Fixable, DNA-binding dead cell stain
•   Works in gram-negative bacteria only
•   Stains dead cells red
RedDot™2 Far-Red DNA Dye •   Nuclear-specific dead cell stain
•   Stains dead cells with far-red fluorescence
Viability/Cytotoxicity Assay Kit •   Suitable for gram-negative bacteria only
•   Green fluorescent DMAO stains DNA in all bacteria
•   EthD-III stains gram-negative dead cells red
Bacterial Viability and Gram Stain Kit •   CF®488A WGA stains gram-positive cells green
•   EthDIII stains gram-negative dead cells red
•   DAPI stains alll cells blue
5-Cyano-2,3-ditolyl tetrazolium chloride (CTC) •   Substrate for measuring bacterial respiratory activity
•   Healthy cells reduce CTC into an insoluble red fluorescent formazan product

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LIVE BACTERIAL STAINS

Bright Staining of All Bacteria in Your Sample

Need to visualize all bacteria in your sample regardless of species or metabolic state? BactoView™ Live stains are unique cell-permeant, fluorogenic DNA-binding dyes designed for bright staining of live and dead, gram-positive and gram-negative bacteria. The dyes are suitable for both microscopy or flow cytometry and are available in green or red fluorescence.

  • Fluorescently label all bacteria in your sample
  • Stains live and dead, gram-positive and gram-negative cells
  • Suitable for microscopy or flow cytometry
  • Available in green or red fluorescence
Live B. subtilis stained with BactoView™ Live Green, imaged by confocal microscopy.
Heat-killed B. subtilis stained with BactoView™ Live Green, imaged by confocal microscopy.
Live E. coli stained with BactoView™ Live Red, imaged by confocal microscopy.
Heat-killed E. coli stained with BactoView™ Live Red, imaged by confocal microscopy.

BactoView™ Live Dyes

Product Name Ex/Em (nm) (with DNA) Detection Channel Size (500X
in DMSO)
Catalog No.
BactoView™ Live Green 500/520 FITC 20 uL 40102-T
100 uL 40102
BactoView™ Live Red 572/675 Cy®3 (microscopy)
PE-Cy®5 (flow cytometry)
20 uL 40101-T
100 uL 40101
Cy Dye is a registered trademark of Cytiva.

Optimized Staining of Endospores

BactoSpore™ stains were develop to tackle the challenge of endospore detection by offering bright staining of endospores as well as live and dead gram-positive and gram-negative bacteria. In B. subtilis, the dyes stain both vegetative cells and endospores and have been validated for detection by fluorescence microscopy and flow cytometry.

 

  • Optimized for staining endospores, unlike other bacterial detection reagents
  • Validated for microscopy or flow cytometry
  • BactoSpore™ 485/500 for membrane staining in the FITC channel
  • BactoSpore™ 488/540 for nucleic acid staining in the FITC or PE channel

BactoSpore™ 485/500 Membrane Stain

BactoSpore™ 485/500 Membrane Stain labels gram-negative bacteria, gram-positive bacteria, and endospores. E. coli or B. subtilis vegetative cultures were grown in tryptic soy broth (TSB) overnight. B. subtilis were induced to form endospores by growing cultures in Difco sporulation medium (DSM) for 7 days. Cultures were washed in PBS and stained with 1X BactoSpore™ 485/500 Membrane Stain in PBS for 30 minutes at room temperature, then imaged by confocal microscopy in the FITC channel. Scale bars: 10 um.

BactoSpore™ 488/540 Nucleic Acid Stain

BactoSpore™ 488/540 Nucleic Acid Stain labels gram-negative bacteria, gram-positive bacteria, and endospores. E. coli or B. subtilis vegetative cultures were grown in tryptic soy broth (TSB) overnight. B. subtilis were induced to form endospores by growing cultures in Difco sporulation medium (DSM) for 7 days. Cultures were washed in PBS and stained with 1X BactoSpore™ 488/540 Nucleic Acid Stain in PBS for 30 minutes at room temperature, then imaged by confocal microscopy in the FITC channel. Scale bars: 10 um.

BactoSpore™ Bacterial Stains

Product Name Ex/Em (nm) Detection Channel Size Catalog No.
BactoSpore™ 485/500 Membrane Stain,
500X in EtOH
484/504 FITC 20 uL 40119-T
100 uL 40119
BactoSpore™ 488/540 Nucleic Acid Stain,
500X in DMSO
488/536 (with DNA) FITC or PE Channel 20 uL 40120-T
100 uL 40120

Other Available Dyes for Staining All Bacteria

Product Name

Features

RedDot™1 Far-Red DNA Dye • Nucleic acid binding dye
• Far-red fluorescence
• Useful for fluorescence microscopy
DMAO, 2 mM in DMSO • Green nucleic acid binding dye
• Useful for fluorescence microscopy or flow cytometry
Hoechst 33342, 10 mg/mL in H2O • Blue nucleic acid binding dye
• Useful for fluorescence microscopy or flow cytometry
Thiazole Orange • Nucleic acid binding dye
• Green fluorescence
• Useful for fluorescence microscopy or flow cytometry
CellBrite® Fix Membrane Stains • Fixable membrane dyes
• Green, red and far-red options
• Useful for fluorescence microscopy
SynaptoGreen™ C4 • Green fluorescent membrane dye
• Useful for fluorescence microscopy
SynaptoRed™ C2 • Red fluorescent membrane dye
• Useful for fluorescence microscopy

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BACTERIAL GRAM STAINS

A traditional colorimetric gram staining protocol is laborious, requiring up to 5 different solutions to stain cells, including toxic alcohol and acetone to decolorize the sample, and precise timing. In contrast, Wheat Germ Agglutinin (WGA) has been shown to bind specifically to N-acetylglucosamine in the peptidoglycan layer of the cell wall of gram-positive bacteria, and can be labeled with a number of different fluorescent dyes for one-step fluorescent cell labeling. Our WGA conjugates feature bright and photostable CF® Dyes for rapid and sensitive staining of gram-positive bacteria. The WGA conjugates are available in 13 color options as well as combination kits that include counterstains for viability analysis or all bacteria.

Product Name Features
Wheat Germ Agglutinin (WGA) CF® Dye conjugates •   Fast and sensitive gram stains
•   Available in 13 colors
Live Bacterial Gram Stain Kit •   CF®594 WGA stains gram-positive cells red
•   DAPI stains all cells blue
Bacterial Viability and Gram Stain Kit •   CF®488A WGA stains gram-positive cells green
•   EthD-III stains dead cells red
•   DAPI stains all cells blue
Microbiology Stain - E. coli and Salmonella co-culture stained with DAPI and CF633-WGA
A co-culture of E. coli and Staphylococcus epidermidis stained with DAPI (blue) and CF®633 WGA (red). Spherically-shaped gram-positive Staphylococcus  stain with WGA, while rod-shaped gram-negative E. coli do not stain. DAPI stains all cells blue.
E. coli and Staphylococcus stained with CF594-WGA and DAPI
Co-culture of E. coli and Staphylococcus epidermidis stained with CF®594 WGA  and DAPI. Gram-positive Staphylococcus show blue DAPI staining and red cell surface staining with WGA, while gram-negative E. coli show only DAPI staining.
Heat-killed Pseudomonas and Micrococcus stained with the Bacterial Viability and Gram Stain Kit
Heat-killed Pseudomonas and Micrococcus stained with the Bacterial Viability and Gram Stain Kit. CF®488A WGA stains gram-positive Micrococcus green, EthDIII stains dead cells red, and DAPI stains all cells blue.

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YEAST VIABILITY STAINS

Browse our selection of fluorescent dyes and kits validated for yeast viability analysis cells, including dyes for live/dead discrimination, combination staining kits, and organelle stains. Also learn about Viability PCR for rapid and sensitive assessment of viable yeast by qPCR.

Product Name Features
Live-or-Dye™ Fixable Viability Staining Kits •   Fixable dead cell stains
•   Choice of 8 fluorescent colors
Propidium Iodide •   Red dead cell stain
•   Not fixable
Ethidium Homodimer III (EthD-III) •   Far-red dead cell stain
•   Not fixable
RedDot™2 Far-Red Nuclear Stain •   Far-red, nuclear dead cell stain
•   Not fixable
NucSpot® 470 •   Green, nuclear dead cell stain
•   Not fixable
ViaVac™ Red/Green •   Yeast-specific vitality dye
•   stains the vacuole red in metabolically active cells
Yeast Live-or-Dye™ Fixable Live/Dead Staining Kit •   Thiazole Orange stains all cells green
•   Live-or-Dye™ 568/583 stains dead cells red
•   Fixable staining
Yeast Viability Staining Kit •   CF® Dye-labeled Concanavalin A (ConA) to label the cell walls of all cells
•   Live-or-Dye™ viability dye to label dead cells
•   Choose blue/green, green/red, or red/far-red color combinations
Yeast Vitality Staining Kit •   Calcofluor White labels all cell walls blue
•   ViaVac™ Red/Green stains the vacuole red in metabolically active cells
S. cerevisiae stained with the Yeast Vitality Staining Kit: Calcofluor White stains all cell walls blue and ViaVac™ stains the vacuoles of metabolically active cells red and the cytoplasm of all cells green (not shown).
S. cerevisiae stained with the Yeast Live-or-Dye™ Fixable Live/Dead Staining Kit: Thiazole Orange to stain all cells (green) and Live-or-Dye™ 568/583 to stain dead cells (red, appears yellow in overlay).
Yeast Viability Staining Kit
S. cerevisiae stained with the Yeast Viability Staining Kit: CF®640R ConA stains cell walls of all cells with far-red fluorescence (pseudocolored blue in image), while Live-or-Dye™ 568/583 stains dead cells red.

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YEAST ORGANELLE STAINS

A number of our organelle and cellular stains can be used to stain yeast cells. Browse our selection of stains below validated for labeling yeast vacuoles, cell walls, bud scars, cytoplasm, and more.

Product Name Features
MitoView™ Dyes •   Mitochondrial dyes in five colors:
•   MitoView™ 633 is mitochondrial membrane potential-dependent
LysoView™ 540 & 633 •   Label vacuoles in live yeast cells
•   2 LysoView dyes stain the yeast vacuole LysoView™ 540 & LysoView™ 633
LipidSpot™ 488 •   Label vacuoles in live yeast cells
•   Stains intracellular membrane structures
Calcofluor White •   Blue fluorescent chitin stain stains cell walls
•   Strongly stains bud scars
CellBrite™ Fix •   Stains the cell membrane
•   Available in 3 dye colors
•   Staining is fixable
MemBrite™ Fix •   Stains the cell periphery
•   Available in 8 dye colors
•   Staining is fixable
CF® Dye Concanavalin A (Con A) Conjugates •   Con A lectin binds to a-mannopyranosyl and a-glucopyranosy in the cell wall of yeast and fungi
•   Available in 10 colors
CF® Dye Wheat Germ Agglutinin (WGA) Conjugates •   WGA lectin binds sialic acid and N-acetylglucosamine
•   Strongly labels bud scars
•   Available in 13 colors
Thiazole Orange •   Green nucleic acid binding dye
•   Can be used as an all-cell yeast stain
•   Staining in yeast is both nuclear and cytoplasmic in unfixed cells and cytoplasmic after fixation
NucSpot® 470 Nuclear Stain •   Green nucleic acid binding dye
•   Stains the nucleus of dead or fixed and permeabilized yeast
ViaFluor® CFSE •   Can be used as an all-cell cytoplasmic stain in yeast
Phalloidin conjugates •   Phalloidin stains F-actin cables and patches in fixed and permeabilized yeast
•   Available in 20 colors and biotin
S. cerevisiae stained with CF®488A WGA (green) to stain bud scars and CF®594 ConA (red) to stain the cell wall.
S. cerevisiae stained with LysoView™ 633 to visualize the vacuoles. Imaged on a Zeiss confocal microscope.
S. cerevisiae stained separately with MemBrite® Fix 488/515, 568/580, and 640/660, then combined and imaged by confocal microscopy.
Mitochondrial staining of S. cerevisiae with MitoView™ 633. Imaged on a Zeiss confocal microscope.
Fixed and permeabilized S. cerevisiae stained with CF®568-conjugated phalloidin
Heat-killed S. cerevisiae stained with NucSpot®470 Nuclear Stain.

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VIABILITY PCR WITH PMA & PMAXX™

Biotium is the inventor of the original viability PCR dye, PMA, and the new and improved viability PCR dye PMAxx™. We have also developed a large range of products and kits for viability PCR. To learn more about this technology and all of the associated products, please visit the Viability PCR Technology Page.


Introduction to viability PCR (v-PCR)

Viability PCR is a powerful technology for the sensitive and rapid detection of viable microorganisms. Unlike time-consuming culturing methods, qPCR is a fast and sensitive method of detection. However, normal qPCR does not distinguish between live and dead cells. With v-PCR using PMAxx™ or PMA, you get the speed, sensitivity and specificity of PCR, plus quantifiable viability. And because no culturing is required, you can even detect viable but not culturable (VBNC) bacteria.The v-PCR technology can be applied not only to bacteria but to other organisms like yeast, viruses, eukaryotes, and archaea.

How does v-PCR work?

The infographic below shows the basic mechanism of v-PCR. PMAxx™ and PMA are photoreactive dyes with high affinity for DNA. The dyes intercalate into dsDNA and form a covalent linkage upon exposure to intense visible light. The reaction inhibits PCR amplification of modified DNA templates by a combination of removal of modified DNA during purification and inhibition of template amplification by DNA polymerases. Because the dyes are cell membrane-impermeable, when a sample containing both live and dead bacteria is treated with dye, only dead bacteria with compromised cell membranes are susceptible to DNA modification. In a qPCR reaction, dead cell DNA will show delayed amplification and higher Ct than live cells.

Viability PCR dyes like PMAxx™ or PMA are membrane-impermeant, which makes them dead cell specific. Once inside of a dead cell, they bind to DNA. Exposure to intense visible light renders the dyes reactive, and causes them to covalently attach to the DNA. This DNA modification prevents amplification in subsequent PCR reactions.

PMA & PMAxx™ Dyes for Viability PCR

PMA is the original dye developed at Biotium for v-PCR. It has been validated in a wide variety of bacterial strains, as well as yeast and viruses (see PMA References). However, while PMA is generally effective at differentiating between live and dead bacteria by qPCR, it does not completely eliminate PCR products from dead cell DNA. This could potentially give false positive results.

PMAxx™ was designed by Biotium scientists to be a superior alternative to PMA. PMAxx™ is much more effective at eliminating PCR amplification of dead cell DNA, and therefore provides the best discrimination between live and dead bacteria.

Download the PMA™ and PMAxx™ flyer to learn more.

Live or dead bacteria treated with either PMA or PMAxx™ prior to qPCR. Dead bacteria treated with either PMA or PMAxx™ show delays in amplification compared to either live cells, or untreated dead cells. Bacteria treated with PMAxx™ show a larger delay than those treated with PMA. Therefore PMAxx™ is better able to differentiate live vs dead bacteria by viability PCR.

Product Name Catalog No. Features
PMAxx™, 20 mM in H2O 40069 •    Next-generation v-PCR dye
•    Gives the best live/dead discrimination
PMA Dye 40013 •    Original v-PCR dye developed at Biotium
•    Validated in hundreds of publications and a wide variety of organisms
PMA Dye, 20 mM in H2O 40019

Other Viability PCR Reagents

Viability PCR Starter Kits

The customizable Viability PCR Starter Kits contain the materials that you need for selective detection of viable cells using either PMA or PMAxx™ viability dye and qPCR. You also have the choice of selecting a kit with or without the Enhancer for Gram Negative Bacteria (not to be used with other cell types). The user will need to supply their own primers to amplify their species of interest .

Product Name Catalog No. Viability Dye Target Cell Type
Viability PCR Starter Kit with PMA 31075 PMA Any cells
Viability PCR Starter Kit with PMAxx™ 31075-X PMAxx™ Any cells
Viability PCR Starter Kit with PMA and Enhancer 31076 PMA Gram-negative bacteria
Viability PCR Starter Kit with PMAxx™ and Enhancer 31076-X PMAxx™ Gram-negative bacteria

Strain-Specific Viability PCR Kits

Strain-specific v-PCR kits are designed for selective detection of viable bacteria from a specific strain using PMAxx or PMA dye and real-time PCR. The kits contain PMA dye OR PMAxx™ dye, Forget-Me-Not™ EvaGreen® qPCR Master Mix, and validated PCR primers for detection of selected strains of bacteria.

Strain-Specific Bacterial Viability PCR Kits

Bacteria Strain Gene name Kit with PMA (catalog #) Kit with PMAxx™ (catalog #)
Salmonella enterica invA 31033 31033-X
Mycobacterium tuberculosis groEL2 31034 N/A
Staphylococcus aureus nuc 31035 N/A
MRSA mecA 31036 N/A
E. coli O157:H7 Z3276 31037 31037-X
E. coli uidA 31050 31050-X
Listeria monocytogenes hly 31051 31051-X
Legionella pneumophila mip 31053 N/A

PMA Enhancer for Gram-Negative Bacteria

PMA Enhancer for Gram Negative Bacteria was designed to improve discrimination between live and dead gram-negative bacteria during viability PCR. PMA Enhancer is provided as a 5X solution, and is added to a sample before the addition of viability dye.

Product Name Catalog No. Features
PMA Enhancer for Gram Negative Bacteria, 5X Solution 31038 •    Improves live/dead discrimination in gram-negative strains

Photoactivation Device

The PMA-Lite™ 2.0 LED Photolysis Device allows for time- and temperature-controlled light treatment of PMAxx- or PMA-treated samples in microcentrifuge tubes.

Product Name Catalog No. Features
PMA-Lite™ 2.0 LED Photolysis Device E90006 •    Photoactivation device, holds 18 microcentrifuge tubes

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Cy Dye is a registered trademark of Cytiva.

Bacterial Viability and Gram Stain Kit

From: $261 Sizes: 200 assaysCatalog #: 32001

Concanavalin A (Con A) CF® Dye Conjugates

From: $189 Sizes: 5 x 1 mgCatalog #:
29015
, 29016, 29017, 29018, 29019, 29020, 29058, 29074, 29075, - 29080View allHide

PMAxx™ Dye, 20 mM in H2O

From: $159 Sizes: 100 uLCatalog #: 40069

Viability/Cytotoxicity Assay Kit for Bacteria Live & Dead Cells

From: $345 Sizes: 1000 assaysCatalog #: 30027

Yeast Live-or-Dye™ Fixable Live/Dead Staining Kit

From: $439 Sizes: 1,000 assaysCatalog #: 31064

Yeast Vitality Staining Kit

From: $261 Sizes: 1,000 assaysCatalog #: 31062

Wheat Germ Agglutinin (WGA) Conjugates

From: $84 Sizes: 1 mg, 5 x 1 mgCatalog #:
29021
, 29022, 29023, 29024, 29025, 29026, 29027, 29028, 29029, 29059, 29064, 29073, 29021-1, 29022-1, 29023-1, 29024-1, 29025-1, 29026-1, 29027-1, 29028-1, 29029-1, 29059-1, 29064-1, 29077-1, 29077, 29076-1, - 29076View allHide

Live Bacterial Gram Stain Kit

From: $158 Sizes: 200 assays, 800 assaysCatalog #:
32000
, - 32000-1View allHide