Agarose

Manufactured by Meridian Bioscience

Sourced in United Kingdom, Australia, United States

Agarose is a polysaccharide derived from seaweed. It is a commonly used gel matrix in various laboratory techniques, such as gel electrophoresis, for the separation and analysis of biomolecules like DNA, RNA, and proteins. Agarose forms a porous, stable gel structure that allows the migration and separation of these molecules based on their size and charge.

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Lab products found in correlation

4 6 diamidino 2 phenylindole (dapi), by Thermo Fisher Scientific (3 mentions) 100 bp dna ladder, by Thermo Fisher Scientific (1 mentions) Cleanup kit, by Qiagen (1 mentions) Gotaq green master mix, by Promega (1 mentions) Normal horse serum, by Thermo Fisher Scientific (1 mentions) Glycerol gelatin, by Merck Group (1 mentions) Bovine serum albumin (bsa), by Avantor (1 mentions) Ethidium bromide, by Merck Group (1 mentions) Sterile 0.9 nacl, by Fresenius (1 mentions) Dnase rnase free distilled water, by Thermo Fisher Scientific (1 mentions) N per neuronal protein extraction reagent, by Thermo Fisher Scientific (1 mentions) Rnalater, by Merck Group (1 mentions) Supersignal west pico chemiluminescent substrate, by Thermo Fisher Scientific (1 mentions) Adenosine triphosphate (atp), by Merck Group (1 mentions) Foetal bovine serum (fbs), by Lonza (1 mentions) Sodium dodecyl sulfate (sds), by Merck Group (1 mentions) Complete protease inhibitor cocktail, by Roche (1 mentions) Vt1000, by Leica (1 mentions) Hoechst 33258, by Merck Group (1 mentions) Dp74 camera, by Olympus (1 mentions)

Spelling variants of this product

Agarose gel (6 citations) Normal melting point (NMP) agarose (4 citations) Molecular grade agarose (4 citations) 10% agarose solution (2 citations)

10 protocols using agarose

DNA Amplification and Electrophoresis Protocol

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The following were used for DNA amplification: Taq DNA polymerase 5U (Promega); an LMP1-EBV gene primer pair with a sequence from 168373–168174 (Phu Sa biochemical company); buffer (Taq buffer with KCl and MgCl₂) (Promega); dNTP (dATP, dCTP, dGTP, and dTTP) (Promega); and sterile, distilled water.
The chemical electrophoresis amplification products included the following: agarose (Bioline company); 1 × TBE electrophoresis buffer (Tris base: 10.8 g, boric acid: 5.5 g/L, and 0.5M EDTA: 4 mL); loading buffer (3 mL glycerol (30%), 20 mg bromophenol blue (0.25%), 200 mM Tris, 20 mM Na2EDTA, and 10 mL distilled water stored at 4 °C); 10 mg/mL safe view (Bioline); and 100 bp DNA Ladder (Fermentas company).

Trinh C.T., Tran D.N., Nguyen L.T., Tran N.T., Nguyen M.T., Nguyen V.T., Vu N.T., Dang K.D., Van Vo K., Chau H.C., Phan P.T, & Truc Phuong M.H. (2023). LMP1-EBV Gene Deletion Mutations and HLA Genotypes of Nasopharyngeal Cancer Patients in Vietnam. Pathophysiology, 30(1), 1-12.

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RAPD PCR Amplification and Sequencing

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RAPD PCR was done using DNA Primer P1 (CCGCAGCCAA [16 (link)]) at a concentration of 100 pmol µl⁻¹, with 10 µl GoTaq® Green Mastermix (Promega, UK) and 8 µl SDW and added to a 200 µl PCR microtube. Pae 2250 was used as a control alongside a negative control containing only SDW. Reaction conditions were followed as described by Gutierrez, Martin-Platero [17 (link)]: four cycles at 94 °C for 45 s, 30 °C for 120 s and 72 °C for 60 s; 26 cycles at 94 °C for 5 s, 36 °C for 30 s and 72 °C for 30 s (the extension step increased by 1 s for every new cycle); a final step of 10 min at 75 °C followed by 4 °C for ∞. DNA amplicons were electrophoresed through a 1% (w/v) agarose (Bioline, UK) gel and bands excised from the gel and purified with a QIAGEN clean-up kit (QIAGEN, UK) to be cloned for sequencing. DNA fragments were cloned using the TOPO One-shot system according to manufacturer’s instructions (Invitrogen, ThermoFisher Scientific, UK).

James S.L., Rabiey M., Neuman B.W., Percival G, & Jackson R.W. (2020). Isolation, Characterisation and Experimental Evolution of Phage that Infect the Horse Chestnut Tree Pathogen, Pseudomonas syringae pv. aesculi. Current Microbiology, 77(8), 1438-1447.

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Neuronal Protein Extraction and Analysis

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BBG, ethidium bromide, ATP, paraformaldehyde (PFA), RNAlater and glycerol gelatin were from Sigma-Aldrich (St. Louis, MO, USA). Sterile 0.9% NaCl was from Fresenius Kabi (Bad Homburg, Germany). Agarose was from Bioline (Alexandria, Australia). Ammonium-chloride-potassium (ACK) lysing buffer, N-PER™ neuronal protein extraction reagent, 100 × Halt™ protease inhibitor single-use cocktail, normal horse serum (NHS), DNase/RNase-free distilled water and SuperSignal West Pico Chemiluminescent Substrate were from ThermoFisher Scientific (Waltham, MA, USA). Foetal bovine serum (FBS) was from Lonza (Basel, Switzerland). Tissue-Tek^® optimal cutting temperature (OCT) compound was from Sakura (Flemingweg, Netherlands) and 22 mm glass coverslips were from Menzel Glaser (Braunschweig, Germany). Diploma full-cream milk powder was from Fonterra (Mount Waverley, Australia). Bovine serum albumin (BSA) and all other reagent grade chemicals and salts were from Amresco (Solon, OH, USA). The antibodies used are listed in Table 1.

Bartlett R., Sluyter V., Watson D., Sluyter R, & Yerbury J.J. (2017). P2X7 antagonism using Brilliant Blue G reduces body weight loss and prolongs survival in female SOD1G93A amyotrophic lateral sclerosis mice. PeerJ, 5, e3064.

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Mutant Huntingtin Protein Analysis

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Crude tissue homogenates were prepared using a dounce homogeniser in 1% Triton X-100 plus complete protease inhibitor cocktail (Roche). Homogenates were centrifuged (4000×g) at 4 °C for 10 minutes, and electrophoresis was performed on a gel containing 1.8% agarose (Bioline) and 0.1% SDS (Sigma) dissolved in 375 mM Tris–HCl (pH 8.8). A total of 25 μg of protein was loaded per well. The AGERA gel was run at 100 V in Tris–glycine SDS running buffer and transferred in Tris–glycine transfer buffer at 15 V at 4 °C. Immunoblotting was performed using the mouse monoclonal MW8 antibody (1/1000, DSHB) against mutant huntingtin protein.

Huefner A., Kuan W.L., Mason S.L., Mahajan S, & Barker R.A. (2019). Serum Raman spectroscopy as a diagnostic tool in patients with Huntington's disease †Electronic supplementary information (ESI) available. See DOI: 10.1039/c9sc03711j. Chemical Science, 11(2), 525-533.

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Tracing Cortical Connections Using DiI

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Brains from Gad65‐GFP positive animals aged P2 or P7 were sectioned on a vibrating microtome (VT1000S; Leica, Germany) to 600 μm coronally. Small crystals of the carbocyanine dye DiI (1,1′‐didodecyl‐3,3,3′,3′‐tetra‐methylindocarbocyanine perchlorate; Invitrogen, Paisley, UK) were placed under visual guidance into the upper cortical layers, the internal capsule or the white matter/corpus callosum into the thick slices. Slices were incubated at 37 °C for 5–10 weeks (Molnár, Blakey, Bystron, & Carney, 2006). Following the incubation, the thick slices were re‐embedded in 5% agarose (Bioline, London, UK) and re‐sectioned to 70 μm on a vibrating microtome, counterstained with bisbenzimide (2.5 μg/100 mL, Hoechst33258; Sigma, Gillingham, UK) or DAPI (Invitrogen) and mounted using 0.1 M PB.

Boon J., Clarke E., Kessaris N., Goffinet A., Molnár Z, & Hoerder‐Suabedissen A. (2019). Long‐range projections from sparse populations of GABAergic neurons in murine subplate. The Journal of Comparative Neurology, 527(10), 1610-1620.

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Microcolony Growth and Viability Assay

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Microcolony growth and viability was assessed at 50, 78 and 162 days of incubation (Fig. 2A). To confirm growth of microcolonies, ¼ PCM from one TCI replicate was abstracted using a sterile razor blade and secured to a microscope slide with 0.1% agarose (Bioline, Narellan, Australia). The PCM portion was treated with 1 drop (~ 25µL) of Vectashield mounting medium (Vector Laboratories, Burlingame, CA, USA), and a 1:1 ratio of Ultrapure™ water and the LIVE/DEAD^® BacLight™ Bacterial Viability stain (Invitrogen, Carlsbad, CA, USA) (Ferrari et al. 2005 (link)), and incubated at 4 °C in the dark for 30 min. PCM portions were then observed via epi-fluorescent microscopy using an Olympus BX51 microscope with DP74 camera (Olympus, North Ryde, Australia) and filters appropriate for excitation/emission maxima of 480/500 nm for SYTO 9 and 490/635 nm for propidium iodide (PI). When stained with the SYTO 9 and PI nucleic acid stains, live intact cells fluoresce green, while damaged and dead cells fluoresce red.

Benaud N., Chelliah D.S., Wong S.Y, & Ferrari B.C. (2022). Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica. Extremophiles, 26(2), 24.

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Synthesis and Characterization of Lanthanide-Based Compounds

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All chemicals were ready for use without additional purification. Calcium chloride dihydrate (CaCl₂·2H₂O, 99.5%), yttrium (III) chloride heptahydrate (YCl₃·6H₂O, 99.99%), neodymium (III) chloride hexahydrate (NdCl₃·6H₂O, 99.9%), gadolinium (III) chloride hexahydrate (GdCl₃·6H₂O, 99.9%), ammonium fluoride (NH₄F, ≥98.0%), potassium citrate tribasic monohydrate (HOC(COOK)(CH₂COOK)₂·H₂O, ≥99.0%), and ethylenediaminetetraacetic acid (EDTA) were purchased from Sigma-Aldrich (St. Louis, MO, USA); 4′,6-diamidino-2-phenylindole (DAPI), Dulbecco’s modified eagle’s medium (DMEM), MHC II-PE, CD86-FITC, and fetal calf serum (FCS, Gibco Laboratories, Brooklyn, NY, USA) were purchased from Thermo Fisher Scientific (Waltham, MA, USA); CellTiter 96 AQueous MTS reagent powder was purchased from Promega (Madison, WI, USA); lipopolysaccharide (LPS) was purchased from PeproTech (Cranbury, NJ, USA); agarose was purchased from Bioline (London, UK); phalloidin-iFluor 488 Reagent was purchased from Abcam (Cambridge, UK); CD40-APC was purchased from Biolegend (San Diego, CA, USA). All experimental water was deionized (DI) water.

Yu Z., He Y., Schomann T., Wu K., Hao Y., Suidgeest E., Zhang H., Eich C, & Cruz L.J. (2022). Achieving Effective Multimodal Imaging with Rare-Earth Ion-Doped CaF2 Nanoparticles. Pharmaceutics, 14(4), 840.

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Nitrosation of Amino Acids Protocol

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Unless otherwise stated, all materials, reagents and chemicals were purchased from Sigma-Aldrich (Gillingham, UK). Agarose, molecular grade crystalline powder was purchased from Bioline, UK, gel red nucleic acid stain from Biotium, UK and sodium hydroxide from Fisher Scientific, UK. SH-SY5Y, a human neuroblastoma cell line, was obtained from the Professor Doig (University of Manchester) at passage 10 and were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% (v/v) foetal bovine serum (FBS), 1% (w/v) glutamine, 10mL/L of solution containing 10,000 U penicillin-G and 10 mg streptomycin/ml, and in a humidified incubator with gas mixture 95% air/5% CO2 (v/v) at 37°C. Cells were subcultured every 3-4 days when they had reached approximately 80% confluency and were discarded after passage 20. The plasmid nicking assay used a pUC8-based plasmid (pchAT 3319 bp) that was extracted from exponentially growing E. coli (strain DH5alpha). Amino acids were Nnitrosated by incubation with sodium nitrite (1M) at 37 o C for 1 hr in sodium citrate buffer (pH2.1) either simultaneously with [25] or immediately before the subsequent experimental procedure [24] .

Potjewyd G., Day P.J., Shangula S., Margison G.P, & Povey A.C. (2017). L-β-N-methylamino-l-alanine (BMAA) nitrosation generates a cytotoxic DNA damaging alkylating agent: An unexplored mechanism for neurodegenerative disease. Neurotoxicology, 59.

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Sanger Sequencing of PCR Amplicons

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All PCR amplicons were resolved on 2% agarose (Bioline, Memphis, USA) gels stained with GelRed® Nucleic Acid Gel Stain (Biotium, California, USA) and visualized on an ultraviolet transilluminator (Wagtech International, Thatcham, UK) for fragment size determination. The amplicons were sized against a 50 bp DNA molecular ladder (Bioline, Memphis, USA). PCR products were purified from agarose gels using QIAquick® PCR purification kit (Hilden, Germany) according to manufacturer's instructions prior to sequencing. The PCR amplicons were commercially Sanger sequenced at Inqaba Biotechnical Industries (Pty) Ltd (Pretoria, South Africa).

Ndekezi C., Nkamwesiga J., Ochwo S., Kimuda M.P., Mwiine F.N., Tweyongyere R., Amanyire W, & Muhanguzi D. (2019). Identification of Ixodid Tick-Specific Aquaporin-1 Potential Anti-tick Vaccine Epitopes: An in-silico Analysis. Frontiers in Bioengineering and Biotechnology, 7, 236.

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Multiplex PCR for Listeria Identification

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The multiplex PCR was performed through the use of primers described by D’Agostino et al. (2004) [19 (link)] and Doumith et al. (2004) [20 (link)] (Table S1—Supplementary File). The 25 µL PCR reaction consisted of 2.5 µL bacterial DNA, 12.5 µL of 2× QIAGEN Multiplex PCR Master Mix (Qiagen, Hilden, Germany), and 10 µL of primers mix formed by 0.4 µM (forward and reverse primers) for lmo1118, 0.4 µM for lmo0737, orf 2819 and orf 2110, 0.1 µM for prs and 0.2 µM for prfA. The multiplex PCR comprised a step for pre-denaturation and polymerase activation at 95 °C for 5 min, a step of 40 amplification cycles (denaturation at 95 °C for 20 s, hybridization at 54 °C for 40 s, and elongation at 72 °C for 90 s) followed by a final step at 72 °C for 7 min for elongation. The electrophoresis gel was prepared from 2% agarose (Bioline, London, UK) in TAE (Bioline, UK). Electrophoresis was performed for 1 h and 30 min at 100 V, using 10 µL of DNA ladder (Promega, Southampton, UK) and 10 µL of amplicons, all of them mixed with 2 µL of 6x dual-action nontoxic fluorescent nucleic acid stain and loading dye (RedSafe, Bioline, UK). The expected bands for each gene identification are detailed in Table S1 (Supplementary File).

Duma M.N., Ciupescu L.M., Dan S.D., Crisan-Reget O.L, & Tabaran A. (2024). Virulence and Antimicrobial Resistance of Listeria monocytogenes Isolated from Ready-to-Eat Food Products in Romania. Microorganisms, 12(5), 954.

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