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Pfge agarose gel

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PFGE agarose gel is a laboratory product used for pulsed-field gel electrophoresis (PFGE), a technique for separating large DNA molecules. The gel provides a porous medium for the migration and separation of DNA fragments during the PFGE process.

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Lab products found in correlation

Chef dr 2 system, by Bio-Rad (6 mentions) Alui and mboi, by New England Biolabs (4 mentions) Typhoon 9400 phosphoimager, by GE Healthcare (4 mentions) Amershan typhoon, by GE Healthcare (2 mentions) Molecular analyst fingerprinting software, by Bio-Rad (1 mentions) Storage phosphor screen, by GE Healthcare (1 mentions) Storm 860, by GE Healthcare (1 mentions) Imagequant, by GE Healthcare (1 mentions) Typhoon 9400 phospholmager, by GE Healthcare (1 mentions)

Close spelling variants of this product

PFGE grade agarose gel PFGE agarose Agarose gel Agarose

7 protocols using pfge agarose gel

1

PFGE Analysis of S. Enteritidis Isolates

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In order to determine their clonal relationship, 13 isolates of S. Enteritidis from stool samples and one from water were analysed by pulsed-field gel electrophoresis (PFGE). These 13 stool isolates were chosen for PFGE analysis as representative samples, according to epidemiological interviews. The plugs were prepared according to the protocol described by Ribot et al. [16 (link)] and afterwards restricted with XbaI for 3 h at 37 °C. Salmonella Braenderup H9812 strain was used as a size standard. Electrophoresis was performed using 1.4% certified PFGE agarose gel (Bio-Rad, Germany) in CHEF DRII/III (Bio-Rad, Germany), according to the conditions described in the PulseNet PFGE protocol for Salmonella issued by the US Centers for Disease Control and Prevention. Obtained fingerprinting patterns were analysed by Molecular Analyst Fingerprinting software (Bio-Rad, Germany). Dice similarity coefficients were calculated using pairwise comparison, with optimization and a position tolerance of 1.5%. The dendrogram was created using the unweighted pair group method with arithmetic averages.
Kovačić A., Huljev Ž, & Sušić E. (2017). Ground water as the source of an outbreak of Salmonella Enteritidis. Journal of Epidemiology and Global Health, 7(3), 181-184.
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2

Telomere Length Measurement by TRF Analysis

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Telomere gels were performed using telomere restriction fragment (TRF) analysis. Genomic DNA was digested using AluI and MboI (NEB). 4–10 μg of DNA was run on a 1% PFGE agarose gel (Bio-Rad) in 0.5× TBE buffer using the CHEF-DRII system (Bio-Rad) at 6 V cm−1; initial switch time 5 s, final switch time 5 s, for 16 h at 14 °C. The gel was then dried for 4 h at 50 °C, denatured in a 0.5 N NaOH 1.5 M NaCl solution, and neutralized. Gel was hybridized with 32P-labelled (CCCTAA)6 oligonucleotides in Church buffer overnight at 42 °C. The next day, the membrane was washed four times in 4× SSC buffer, exposed onto a storage phosphor screen (GE Healthcare) and scanned using STORM 860 with ImageQuant (Molecular Dynamics). Telomere length was determined using TeloTool software35 (link).
Dilley R.L., Verma P., Cho N.W., Winters H.D., Wondisford A.R, & Greenberg R.A. (2016). Break-induced telomere synthesis underlies alternative telomere maintenance. Nature, 539(7627), 54-58.
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3

Telomere Length Analysis by Gel Electrophoresis

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Telomere gels were performed using telomere restriction fragment (TRF) analysis. Genomic DNA was digested using AluI and MboI (NEB). 5 μg of DNA was run on a 1% PFGE agarose gel (Bio-Rad) in 0.5 × TBE buffer using the CHEF-DRII system (Bio-Rad) at 6V cm−1; initial switch time 1 s, final switch time 6 s, for 17hrs at 14°C. The gel was then dried for 2hrs at 60°C, denatured in a 0.5N NaOH 1.5M NaCl solution, and neutralized. The gel was hybridized with 32P-labeled (TTAGGG)4 oligonucleotides in Church buffer overnight at 55°C. The next day, the membrane was washed three times in 2 × SSC buffer and once in 2x SSC 0.5% SDS, exposed onto a storage phosphor screen and scanned using Amershan™ Typhoon (GE Healthcare). Telomere length was determined using TeloTool software. To detect TTAGGG and TCAGGG variants from genomic DNA using a Dot Blot system, 2 μg of AluI and MboI (NEB) digested genomic DNA was diluted to 100 μL with 2 × SSC, heated at 95°C for 5mins, cooled on ice and dot-blotted onto a 2 × SSC-soaked nylon membrane. DNA was UV cross-linked onto the membrane and hybridized with P32 end-labeled oligos (CCCTAA)4 or (TCAGGG)4 products. An Alu probe was used as a loading control. Blots were denatured, neutralized, washed, exposed to PhosphoImager screens, scanned using a Typhoon 9400 PhosphoImager (GE Healthcare) and quantified with ImageJ.
Barroso-González J., García-Expósito L., Galaviz P., Lee Lynskey M., Allen J.A., Hoang S., Watkins S.C., Pickett H.A, & O’Sullivan R.J. (2021). Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell reports, 37(10), 110088.
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4

Telomere Length Analysis by Gel Electrophoresis

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Telomere gels were performed using telomere restriction fragment (TRF) analysis. Genomic DNA was digested using AluI and MboI (NEB). 5 μg of DNA was run on a 1% PFGE agarose gel (Bio-Rad) in 0.5 × TBE buffer using the CHEF-DRII system (Bio-Rad) at 6V cm−1; initial switch time 1 s, final switch time 6 s, for 17hrs at 14°C. The gel was then dried for 2hrs at 60°C, denatured in a 0.5N NaOH 1.5M NaCl solution, and neutralized. The gel was hybridized with 32P-labeled (TTAGGG)4 oligonucleotides in Church buffer overnight at 55°C. The next day, the membrane was washed three times in 2 × SSC buffer and once in 2x SSC 0.5% SDS, exposed onto a storage phosphor screen and scanned using Amershan™ Typhoon (GE Healthcare). Telomere length was determined using TeloTool software. To detect TTAGGG and TCAGGG variants from genomic DNA using a Dot Blot system, 2 μg of AluI and MboI (NEB) digested genomic DNA was diluted to 100 μL with 2 × SSC, heated at 95°C for 5mins, cooled on ice and dot-blotted onto a 2 × SSC-soaked nylon membrane. DNA was UV cross-linked onto the membrane and hybridized with P32 end-labeled oligos (CCCTAA)4 or (TCAGGG)4 products. An Alu probe was used as a loading control. Blots were denatured, neutralized, washed, exposed to PhosphoImager screens, scanned using a Typhoon 9400 PhosphoImager (GE Healthcare) and quantified with ImageJ.
Barroso-González J., García-Expósito L., Galaviz P., Lee Lynskey M., Allen J.A., Hoang S., Watkins S.C., Pickett H.A, & O’Sullivan R.J. (2021). Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell reports, 37(10), 110088.
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5

Telomere Length Analysis by TRF

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Telomere gels were performed using telomere restriction fragment (TRF) analysis. Genomic DNA was digested using AluI and MboI (NEB). Then, 4–10 μg of DNA was run on a 1% PFGE agarose gel (Bio-Rad) in 0.5× TBE buffer using the CHEF-DRII system (Bio-Rad) at 6 V cm−1; the initial switch time was 1 s, and the final switch time 6 s, for 17 h at 14 °C. The gel was then dried for 2 h at 60 °C, denatured in a 0.5 M NaOH/1.5 M NaCl solution, and neutralized. Gel was hybridized with 32P-labeled (TTAGGG)4 oligonucleotides in Church buffer overnight at 55 °C. The next day, the membrane was washed three times in 2× SSC buffer and once in 2× SSC 0.5% SDS, exposed onto a storage phosphor screen and scanned using Typhoon 9400 PhosphoImager (GE Healthcare). Telomere length was determined using TeloTool software.
Hoang S.M., Kaminski N., Bhargava R., Barroso-González J., Lynskey M.L., García-Expósito L., Roncaioli J.L., Wondisford A.R., Wallace C.T., Watkins S.C., James D.I., Waddell I.D., Ogilvie D., Smith K.M., da Veiga Leprevost F., Mellacharevu D., Nesvizhskii A.I., Li J., Ray-Gallet D., Sobol R.W., Almouzni G, & O’Sullivan R.J. (2020). Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nature structural & molecular biology, 27(12), 1152-1164.
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6

Telomere Length Determination Using TRF Analysis

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Telomere gels were performed using telomere restriction fragment (TRF) analysis. Genomic DNA was digested using AluI and MboI (NEB). Next, 4–10 μg of DNA was run on a 1% PFGE agarose gel (Bio-Rad) in 0.5× TBE buffer using the CHEF-DRII system (Bio-Rad) at 6 V cm−1; initial switch time 1 s, final switch time 6 s, for 17 h at 14 °C. The gel was then dried for 2 h at 60 °C, denatured in a 0.5 N NaOH 1.5 M NaCl solution and neutralized. The gel was hybridized with 32P-labeled (TTAGGG)4 oligonucleotides in Church buffer overnight at 55 °C. The next day, the membrane was washed three times in 2× SSC buffer and once in 2× SSC 0.5% SDS, exposed onto a storage phosphor screen and scanned using Typhoon 9400 PhosphoImager (GE Healthcare).
Wondisford A.R., Lee J., Lu R., Schuller M., Groslambert J., Bhargava R., Schamus-Haynes S., Cespedes L.C., Opresko P.L., Pickett H.A., Min J., Ahel I, & O’Sullivan R.J. (2024). Deregulated DNA ADP-ribosylation impairs telomere replication. Nature Structural & Molecular Biology, 31(5), 791-800.
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7

Telomere Length Analysis by TRF

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Telomere gels were performed using telomere restriction fragment (TRF) analysis. Genomic DNA was digested using AluI and MboI (NEB). 4-10 μg of DNA was run on a 1% PFGE agarose gel (Bio-Rad) in 0.5×TBE buffer using the CHEF-DRII system (Bio-Rad) at 6V cm-1; initial switch time 1 second, final switch time 6 seconds, for 17hrs at 14°C. The gel was then dried for 2hrs at 60°C, denatured in a 0.5 N NaOH 1.5 M NaCl solution, and neutralized. Gel was hybridized with 32P-labelled (TTAGGG)4 oligonucleotides in Church buffer overnight at 55°C. The next day, the membrane was washed three times in 2×SSC buffer and once in 2x SSC 0.5% SDS, exposed onto a storage phosphor screen and scanned using Typhoon 9400 Phospholmager (GE Healthcare). Telomere length was determined using TeloTool software.
Gonzalez J.B., Exposito L.G., Hoang S.M., Lynskey M.L., Roncaioli J.L., Ghosh A., Wallace C.T., Modesti M., Bernstein K.A., Sarkar S.N., Watkins S.C, & O’Sullivan R.J. (2019). RAD51AP1 is an essential mediator of Alternative Lengthening of Telomeres. Molecular cell, 76(1), 11-26.e7.
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