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Agarose

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Agarose is a polysaccharide derived from red seaweed. It is commonly used as a gel matrix in various laboratory techniques, such as electrophoresis and chromatography, to separate and analyze biological molecules like DNA, RNA, and proteins.

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Lab products found in correlation

Peptone, by BD (3 mentions) Bovine serum albumin (bsa), by Merck Group (2 mentions) Ethylene glycol, by Thermo Fisher Scientific (2 mentions) Phenylboronic acid, by Thermo Fisher Scientific (2 mentions) Psyllim fiber, by BD (2 mentions) 2 2 dimethoxypropane, by Thermo Fisher Scientific (2 mentions) Taqman primer, by Thermo Fisher Scientific (2 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) Supersignal west pico chemiluminescent substrate, by Thermo Fisher Scientific (2 mentions) Dulbecco modified eagle medium (dmem), by Thermo Fisher Scientific (2 mentions) Mz16f, by Leica (1 mentions) Table centrifuge, by Eppendorf (1 mentions) Xad 16 adsorber resin, by Merck Group (1 mentions) Recombinant ifn γ, by Thermo Fisher Scientific (1 mentions) Penicillin streptomycin, by Thermo Fisher Scientific (1 mentions) Rpmi 1640, by Thermo Fisher Scientific (1 mentions) Sodium pyruvate, by Thermo Fisher Scientific (1 mentions) Dextran fluorescein, by Thermo Fisher Scientific (1 mentions) Texas red dextran, by Thermo Fisher Scientific (1 mentions) Phenol red free rpmi 1640, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

Glutathione-agarose beads (11 citations) 0.8% agarose gel (2 citations) Low-melting agarose (2 citations) Low-melting-temperature agarose (2 citations) Type I Agarose (2 citations)

18 protocols using agarose

1

Spheroid-Based Anchorage-Independent Assay

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Cell suspensions (5 × 103 cells) from disaggregated pancreatic cancer spheroids suspended in CSM were prepared at 1.5 mL/well with 0.3% agarose (Becton Dickinson) in the presence or absence of edelfosine, and overlaid onto each well of a six-well plate containing a solidified bottom layer of 0.6% agarose in the medium (2 mL/well). Once the top layer solidified, 1 mL of CSM was placed on top of the cell layer, and the plates were incubated for 3 weeks, and the colonies were counted using a stereo microscope Leica MZ16F (Wetzlar, Germany). The colony size was evaluated by measuring the colony perimeter using the ImageJ software (NIH, Bethesda, MD, USA). Vehicle-treated control cells were run in parallel. The results are expressed as the mean arbitrary units ± SD from three independent experiments in two replicates.
Gajate C., Gayet O., Fraunhoffer N.A., Iovanna J., Dusetti N, & Mollinedo F. (2021). Induction of Apoptosis in Human Pancreatic Cancer Stem Cells by the Endoplasmic Reticulum-Targeted Alkylphospholipid Analog Edelfosine and Potentiation by Autophagy Inhibition. Cancers, 13(23), 6124.
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2

Myxobacteria Cultivation in Enriched Media

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All myxobacterial cultures were grown in 300 mL shake flasks containing 50 mL of VY/2, VY, PYGS, or CyHv3 medium (Tables S1–S4) for both Corallococcus sp. MCy9049 and Myxococcaceae sp. MCy9003. Following inoculation with 1 mL pre-culture the medium was supplemented with 2% of sterile XAD-16 adsorber resin (Sigma Aldrich, Taufkirchen, Germany) suspension in water to bind metabolites from the culture medium. Small scale cultures were grown for 10–12 days until the fermentation medium had cleared up except for the myxobacterial biofilm clumps and XAD-16 resin particles. After fermentation the cultures were pelleted in a 50 mL tubes at 6000 rcf for 10 min using a table centrifuge (Eppendorf) and stored at −20 °C until further use. The myxobacterial strains were kept in agar culture for storage for timespans of a few days. The agar media used in this case were VY/2 agar, prepared by adding 14 g/L agarose (BD) to VY/2 medium before autoclaving.
Panter F., Popoff A., Garcia R., Krug D, & Müller R. (2022). Myxobacteria of the Cystobacterineae Suborder Are Producers of New Vitamin K2 Derived Myxoquinones. Microorganisms, 10(3), 534.
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3

Characterization of Immune Cell Populations

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We purchased the following tissue culture reagents from Life Technologies (Carlsbad, CA): RPMI 1640, Phenol Red-free RPMI 1640, Dulbecco’s Modified Eagle Medium, fetal calf serum, GlutaMAX, sodium pyruvate, Non-essential amino acids, penicillin/ streptomycin, Hank’s buffered saline solution (HBSS), nigericin, valinomycin, fluorescein dextran (average molecular weight 3,000 Daltons), Texas Red dextran (average molecular weight 3,000 Daltons) and SYTOX red. Recombinant IFN-γ, TNF-α and M-CSF were purchased from Peprotech, Inc (Rocky Hill, NJ). Recombinant IL-4 as well as APC-cy7 conjugated anti-CD11c (clone N418), perCP-cy5.5 conjugated anti-CD45 (clone 30F11) and PE-cy7 conjugated anti-Gr-1 (clone RB6-8C5) were from Biolegend (San Diego, CA). Sabouraud Dextrose broth and agarose were purchased from BD biosciences (San Jose, CA). Normal mouse serum was from Innovative Research (Novi, MI). Fluconazole was purchased from Sigma-Aldrich Corporation (St. Louis, MO). Uvitex-2B was purchased from Polyscience, Inc (Warrington, PA). Glass bottom culture dishes (catalog # P35G-1.5-14-C) were from Mat-tek Corporation (Ashland, MA). Dextran doubly-conjugated with fluorescein plus sulfarhodamine 101 (average molecular weight approximately 10,000 Daltons) was a custom product purchased from TdB Consultancy (Uppsala, Sweden).
Davis M.J., Eastman A.J., Qiu Y., Gregorka B., Kozel T.R., Osterholzer J.J., Curtis J.L., Swanson J.A, & Olszewski M.A. (2015). Cryptococcus neoformans-induced macrophage lysosome damage crucially contributes to fungal virulence. Journal of immunology (Baltimore, Md. : 1950), 194(5), 2219-2231.
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4

Sterilization and Preparation of Plant Seeds

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Seed sterilisation solution (see REAGENT SETUP)

Sodium hypochloride (Applichem-Panreac, cat. no. 213322.1214)

Tween-20 (Applichem-Panreac, cat no. A1389,0500)

70 and 100 % ethanol (Applichem-Panreac, cat. no. A3678,1000)

Murashige and Skoog (MS) medium (Duchefa, cat. No. M0245.0050)

Sucrose (Applichem-Panreac, cat. no. A3935,5000)

Agarose (BD, cat. no. 214010)

Sterile deionised water

Hydroponic medium (see REAGENT SETUP)

Carboxyfluorescein diacetate (CFDA) (Sigma-Aldrich, cat. no. 21879-100MG-F)

Dimethylsulfoxide (Applichem-Panreac, cat. no. A1584,0500)

Einheitserde Classic (Einheitserdewerk Uetersen).

Ostendorp A., Pahlow S., Deke J., Thieß M, & Kehr J. (2016). Protocol: optimisation of a grafting protocol for oilseed rape (Brassica napus) for studying long-distance signalling. Plant Methods, 12, 22.
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5

Preparation of Manganese Chloride Solutions

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Manganese chloride (MnCl2), cholesterol and bovine serum albumin (BSA) were purchased from Sigma (St. Louis, MO, USA). Agar, peptone and Agarose were purchased from BD (Franklin Lakes, NJ, USA). VU0026921 was synthetized at Vanderbilt University, Nashville, TN, USA. VU0063088 was purchased from Vitas-M Laboratory (Champaign, IL, USA). Small molecules stock solutions were prepared in DMSO at 10 mM and were kept at −20°C. All other reagents were of analytical grade.
Peres T.V., Horning K.J., Bornhorst J., Schwerdtle T., Bowman A.B, & Aschner M. (2018). Small molecule modifiers of in vitro manganese transport alter toxicity in vivo. Biological trace element research, 188(1), 127-134.
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6

Thrombolytic Nanoparticle Formulation

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tPA was purchased from Merck (USA). SDS, thrombin from human plasma, plasminogen from human plasma, and the protease substrate H-d-isoleucyl-l-prolyl-l-arginine-p-nitroaniline (S-2288) were purchased from Sigma-Aldrich (USA). Mesoporous silica nanoparticles (SiO2) were purchased from Shanghai So-Fe Biomedical (China). Fe3O4 nanoparticles were purchased from Alfa Aesar (USA). Fibrinogen from human plasma was purchased from Shanghai Yuan Yu Bio-Tech Co. Ltd. (China). Agarose was purchased from BD (USA). All the other chemicals and solvents were purchased from Sigma-Aldrich.
Wang S., Guo X., Xiu W., Liu Y., Ren L., Xiao H., Yang F., Gao Y., Xu C, & Wang L. (2020). Accelerating thrombolysis using a precision and clot-penetrating drug delivery strategy by nanoparticle-shelled microbubbles. Science Advances, 6(31), eaaz8204.
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7

Development of Perfluoropentane Contrast Agent

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Perfluoropentane (99%, Exfluor Research Corporation, Texas, USA) was used as the US contrast agent. Monostearoyl-2-hydroxy-sn-glycero-3-phosphocholine (MSPC), 1,2-dipalmitoylsn-glycero-3-phosphocholine (DPPC), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy (PolyEthylene glycol)2000] (DSPEPEG2000) were obtained from Corden Pharma Corporation (Colorado, USA). Dox was obtained from LC laboratory (MA, USA). Agarose and psyllim fiber were purchased from BDH (Pennsylvania, USA) and Konsyl Pharmaceuticals, (Maryland, USA), respectively. Graphite was purchased from Alpha Aesar, Ward Hill, MA. Acetonitrile (HPLC grade) was obtained from Pharmco-AAPER (Connecticut, USA). Ethylene glycol (99%, spectrophotometric grade), phenylboronic acid (98%), and 2,2-dimethoxypropane (98%) were purchased from Alpha Aesar (Massachusetts, USA). C26 cells were kindly provided by the National Cancer Institute. PC3 prostate and A549 lung cancer cells were kindly provided by Dr. Elankumaran Subbiah (Virginia Tech), and Dr. Lin Lin (Oklahoma State University).
Maples D., Mclean K., Sahoo K., Newhardt R., Venkatesan P., Wood B, & Ranjan A. (2015). Synthesis and characterization of ultrasound imageable heat-sensitive liposomes for HIFU therapy. International journal of hyperthermia : the official journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group, 31(6), 674-685.
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8

Evaluate p48/p42 Fragments on Cancer Cells

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U251 and breast cancer cells were transfected with GFP-tagged p48, p42, fragments 183–394 a.a, 280–394 a.a, or GFP-mock vector (2 × 103 cells per 12 well plate) and incubated in a humidified incubator at 37 °C with 5% CO2. For the proliferation assay, viable cells were counted on a disposal hemocytometer (In CYTO, DHC-N01-5) at 0, 24, 48, 72, and 96 h30 (link)31 (link). Invasion assays were performed using a Matrigel invasion assay Kit (BD Bioscience, Inc.). Invasive cells were fixed with 4% paraformaldehyde and stained with 1% Crystal violet32 (link). For the colony-forming assay, cells were seeded on 6-well plates in 0.35% agarose (supplemented with complete medium; BD Bioscience) and cultured for 4 weeks. The cells were fixed with 4% paraformaldehyde, stained with crystal violet, and the colonies were counted.
Hwang I., Kim C.K., Ko H.R., Park K.W., Cho S.W, & Ahn J.Y. (2016). C-terminal domain of p42 Ebp1 is essential for down regulation of p85 subunit of PI3K, inhibiting tumor growth. Scientific Reports, 6, 30626.
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9

Establishing Experimental Conditions

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Reagents such as lead (II) acetate trihydrate [Pb(CH3COO)2], cholesterol, albumin and polymerase chain reaction (PCR) primers were purchased from Sigma (St. Louis, MO, USA). TaqMan primers used for real-time quantitative reverse transcription PCR (qRT-PCR) analysis were obtained from Life Technologies (Carlsbad, CA, USA). Agar, peptone and Agarose were purchased from BD (Franklin Lakes, NJ, USA). Trizol and SuperSignal West Pico chemiluminescent substrate were purchased from Thermo Fisher Scientific (Waltham, MA, USA). All other reagents used were of analytical grade.
Akinyemi A.J., Miah M.R., Ijomone O.M., Tsatsakis A., Soares F.A., Tinkov A.A., Skalny A.V., Venkataramani V, & Aschner M. (2019). Lead (Pb) exposure induces dopaminergic neurotoxicity in Caenorhabditis elegans: Involvement of the dopamine transporter. Toxicology Reports, 6, 833-840.
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10

Formulation and Characterization of Doxorubicin-Loaded Nanoparticles

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PFP (99%, Exfluor Research Corporation, TX, USA) was used as the US contrast agent. Monostearoyl-2-hydroxy-sn-glycero-3-phosphocholine (MSPC), 1,2-dipalmitoylsn-glycero-3-phosphocholine (DPPC), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy (polyEthylene glycol)2000] (DSPE-mPEG2000) were obtained from Corden Pharma Corporation (CO, USA). Dox was obtained from LC laboratory (MA, USA). Agarose and psyllim fiber were purchased from BDH (PA, USA) and Konsyl Pharmaceuticals, (MD, USA), respectively. Graphite was purchased from Alpha Aesar (Ward Hill, MA, USA). Acetonitrile (HPLC grade) was obtained from Pharmco-AAPER (CT, USA). Ethylene glycol (99%, spectrophotometric grade), phenylboronic acid (98%), and 2,2-dimethoxypropane (98%) were purchased from Alpha Aesar. The PD-10 column was obtained from GE Healthcare Life Sciences (Buckinghamshire, UK). C26 cells were kindly provided by the National Cancer Institute.
Ektate K., Kapoor A., Maples D., Tuysuzoglu A., VanOsdol J., Ramasami S, & Ranjan A. (2016). Motion Compensated Ultrasound Imaging Allows Thermometry and Image Guided Drug Delivery Monitoring from Echogenic Liposomes. Theranostics, 6(11), 1963-1974.
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