Gel doc xr imager

Manufactured by Bio-Rad

Sourced in United States

The Gel Doc XR+ imager is a laboratory instrument designed for the detection and analysis of nucleic acids and proteins separated by gel electrophoresis. It captures high-quality digital images of gels and blots and provides tools for quantitative analysis of band intensity and molecular weight.

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Lab products found in correlation

Gelred, by Biotium (3 mentions) Ultrapure agarose gel, by Thermo Fisher Scientific (3 mentions) Gelred, by Bio-Rad (3 mentions) Dneasy blood and tissue kit, by Qiagen (3 mentions) Generuler 1 kb plus dna ladder, by Thermo Fisher Scientific (2 mentions) Rneasy plus mini kit, by Qiagen (2 mentions) Rnase free dnase set, by Qiagen (2 mentions) Tris glycine gel, by Thermo Fisher Scientific (2 mentions) X ray film, by Kodak (2 mentions) C1000 thermal cycler, by Bio-Rad (2 mentions) Nucleospin gel, by Macherey-Nagel (2 mentions) Odyssey blocking buffer, by LI COR (2 mentions) Mini protean tgx stain free gel, by Bio-Rad (2 mentions) Odyssey imaging system, by LI COR (2 mentions) Trans blot turbo system, by Bio-Rad (2 mentions) Trans blot turbo kit, by Bio-Rad (2 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Evagreen, by Jena Biosciences (2 mentions) Mastercycler nexus, by Eppendorf (2 mentions) Any kd mini protean tgx gel, by Bio-Rad (1 mentions)

Close spelling variants of this product

Gel Doc XR (575 citations) Gel Doc (337 citations) Gel imager (150 citations) Gel Doc Imager (94 citations) Molecular Imager Gel DocTM XR+ (19 citations) Molecular Imager® Gel DocTM XR+ System (14 citations) Gel DocTM XR+ imager (8 citations) Molecular Imager® Gel DocTM XR + System with Image LabTM Software (3 citations)

66 protocols using gel doc xr imager

Polyacrylamide Gel Electrophoresis of Oligos and LNPs

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Oligos and protein-oligo conjugates were run on a pre-cast 4–20% polyacrylamide-TBE gel (Bio-Rad, Hercules, CA, USA) for 1 h at 100 V. The gel was then stained for 30 min with SYBR Gold (Invitrogen) and visualized with a Bio-Rad GelDoc XR+ imager.
LNPs formulated with nAv or nAv-oligo conjugates were run on a pre-cast Any kD mini-Protean TGX gel (Bio-Rad) for 30 min at 100 V. The gel was stained for 1 h with Bio-Safe Coomassie Stain (Bio-Rad), destained overnight, and visualized using a Bio-Rad GelDoc XR+ imager. The entrapment efficiency was determined as: (S_free − S_LNP)/S_free, where S_free is the total signal per lane for the free protein or conjugate and S_LNP that for the LNP-encapsulated protein or conjugate.

Eltoukhy A.A., Chen D., Veiseh O., Pelet J., Dong Y, & Anderson D.G. (2014). Nucleic Acid-Mediated Intracellular Protein Delivery by Lipid-like Nanoparticles. Biomaterials, 35(24), 6454-6461.

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Evaluating IFN-stimulated Gene Expression

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Total RNA was isolated from PBMCs and BLCLs and reverse transcribed using the High-Capacity cDNA Reverse Transcription Kit (ThermoFisher Scientific) and gene expression was analyzed by qPCR using a TaqMan Fast Universal PCR Master Mix and specific TaqMan probes (IRF7: Hs01014809_g1; IFIT1: Hs03027069_s1; ISG15: Hs01921425_s1; STAT2: Hs01013116_g1; IFNα2: Hs00265051_s1; GAPDH: Hs02786624_g1); USP18 (Hs07289021_m1) (ThermoFisher Scientific) in accordance with the manufacturer’s instruction. Relative quantifications using GADPH as endogenous control were evaluated with the comparative CT method (ΔΔCT).
Cell extracts for immunoblotting were prepared by incubating PBMCs or BLCLs in RIPA lysis buffer (Sigma-Aldrich, San Luis, MO, USA) with Protease and Phosphatase Inhibitor Cocktail (ThermoFisher Scientific) in accordance with the manufacturer’s instruction. Western blot was performed on 4–20% precast polyacrylamide gel and proteins were transferred onto a nitrocellulose membrane (Bio-rad, CA, USA). Antibodies used were STAT2 (Cell signaling, MA, USA) and β-actin (Merck Life Science, Darmstadt, Germany). Signal was detected in a Gel Doc XR + Imager (Bio-Rad).

López-Nevado M., Sevilla J., Almendro-Vázquez P., Gil-Etayo F.J., Garcinuño S., Serrano-Hernández A., Paz-Artal E., González-Granado L.I, & Allende L.M. (2023). Inborn Error of STAT2-Dependent IFN-I Immunity in a Patient Presented with Hemophagocytic Lymphohistiocytosis and Multisystem Inflammatory Syndrome in Children. Journal of Clinical Immunology.

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Organ RNA Isolation Protocol

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Mice were euthanized and organs were prepared by macrodissection and were quick‐frozen in liquid nitrogen and stored in −70 °C until processing, which was carried out typically within a month. RNA isolation was carried out as quickly as possible using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The organs were kept in liquid nitrogen, and approximately 20 mg of samples was excised. Before homogenization, samples were kept on ice. Mini beadbeater 96 (Biospec Products, Bartlesville, OK, USA) was used for homogenization with 0.9–2.0 mm RNase‐free stainless‐steel beads (Next Advance, Averill Park, NY, USA) for 1 min. DNase treatment was carried out with RNase‐Free DNase Set (Qiagen) according to the manufacturer’s instructions. RNA was eluted in 50 µL of RNase‐free water (Ambion, Austin, TX, USA), and the concentration and purity were determined with NanoDrop ND‐1000 (Table S2). Samples were diluted to 24 ng·µL⁻¹ final concentration. The integrity and genomic DNA contamination of all RNA samples were tested using nondenaturing gel electrophoresis with 1% agarose gel in TBE buffer stained with ethidium bromide (Fig. S3). GeneRuler 1kb plus DNA ladder (Thermo Scientific, Waltham, MA, USA) was loaded as marker. Gel Doc XR+ Imager (Bio‐Rad) was used for imaging.

Rácz G.A., Nagy N., Gál Z., Pintér T., Hiripi L, & Vértessy B.G. (2019). Evaluation of critical design parameters for RT‐qPCR‐based analysis of multiple dUTPase isoform genes in mice. FEBS Open Bio, 9(6), 1153-1170.

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Visualizing DNA Nanostructure Assembly

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The assembly of DNA nanostructures was confirmed by 12% polyacrylamide gel electrophoresis (PAGE) under 100 V for 1 h. An oligonucleotide concentration of 150 nM was loaded into each lane. The gels were stained by Sybr^® Gold and visualized by Gel Doc XR + imager (Bio-Rad, Hercules, CA, USA).

Shiu S.C., Fraser L.A., Ding Y, & Tanner J.A. (2018). Aptamer Display on Diverse DNA Polyhedron Supports. Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry, 23(7), 1695.

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SDS-PAGE and Western Blotting of HSV-1

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Herpes simplex virus 1 in Laemmli buffer with 200 mM dithiothreitol was boiled for 5 min. Proteins was resolved by SDS–PAGE on Tris-glycine gels (Thermo Fisher Scientific). For protein staining, the gels were fixed and stained with 0.025% Coomassie brilliant blue (J. T. Baker Chemical Co., Phillipsburg, NJ, United States), 40% methanol (Baker Chemical), and 10% glacial acetic acid (Baker Chemical), followed by destaining with 30% methanol and 7% glacial acetic acid (Delboy et al., 2010 (link)). The gel was dried and imaged with a Gel Doc XR imager (Bio-Rad, Hercules, CA, United States). For Western blotting, following transfer to nitrocellulose, membranes were blocked and incubated with HR50, a rabbit polyclonal antibody to HSV-1 strain F. Per the manufacturer, HR50 recognizes HSV-1 late structural proteins, such as the viral envelope glycoproteins. After incubation with horseradish peroxidase-conjugated secondary antibodies, enhanced chemiluminescent substrate (Pierce) was added, and membranes were exposed to X-ray film (Kodak).

Wudiri G.A., Schneider S.M, & Nicola A.V. (2017). Herpes Simplex Virus 1 Envelope Cholesterol Facilitates Membrane Fusion. Frontiers in Microbiology, 8, 2383.

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Evaluating Cu(II)-Peptide DNA Damage

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In vitro DNA damage brought about by the Cu^II–peptide complexes were assessed by agarose gel electrophoresis. Reaction mixtures contained 10 μm base pair pUC19, 100 nm Cu^II–ATCUN–AMP with 1 mm H₂O₂ and 1 mm sodium ascorbate in 20 mm HEPES, 100 mm NaCl, at pH 7.40. Reaction was incubated at room temperature and quenched by adding 3X loading dye containing 1 mm EDTA at two time points—30 min and 2 h. Then, a 15 μL aliquot was loaded on a 1 % agarose gel containing ethidium bromide (EtBr) and run at 80 V for 90 min. Gels were imaged using a Bio-Rad GelDoc XR+ Imager, and bands were quantified using the accompanying Image Lab 5.0 software. A correction factor or 1.47 was applied to the intensity of the supercoiled form to account for its decreased ability to intercalate EtBr.^{[25 (link)]} Normalized DNA cleavage activity was calculated using the initial and final amounts of supercoiled DNA according to the formula: [(initial–final)/initial] × 100. Quantified supercoiled DNS is shown as mean ± standard deviation of three independent measurements.

Libardo M.D., Cervantes J.L., Salazar J.C, & Angeles-Boza A.M. (2014). Improved Bioactivity of Antimicrobial Peptides by Addition of Amino-Terminal Copper and Nickel (ATCUN) Binding Motifs. ChemMedChem, 9(8), 1892-1901.

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Quantitative PCR Analysis of Signaling Proteins

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cDNA synthesis and PCR were performed as described before.^{30 (link)} The following primer sets were ordered from Eurogentec (Maastricht, The Netherlands): PRKCZ foreward 5′-GGGGGACATCTTCATCA-3′, reverse 5′-CTCGGGAAAACATGAATG-3′ PRKMZ (encoding PKMζ) forward 5′-GGCCTTCCGTTAAATA-3′, reverse 5′-ATTCGGCTTTCTTCTCCT-3′ and Ribosomal Protein S20 (RPS20) forward 5′-AAGGGCTGAGGATTTTTG-3′, reverse 5′-CGTTGCGGCTTGTTAG-3′. RPS20 expression was used as a control for cDNA input.
PCR was run at the following temperatures: 2 min 50 °C, 10 min 95 °C, 40 × (15 s 95 °C and 1 min 60 °C). PCR products with 0.1% Orange G (Merck) and 3% Ficoll (Pharmacia, Stockholm, Sweden) were run on a 1% agarose (Roche Applied Science, Almere, The Netherlands) gel containing 1:30 000 GelRed (Biotium, Hayward, CA, USA). Gels were scanned with a Gel Doc XR imager and Quantity One v4.6.3 software (Bio-Rad Laboratories, Hercules, CA, USA).

Hartsink-Segers S.A., Beaudoin J.J., Luijendijk M.W., Exalto C., Pieters R, & Den Boer M.L. (2014). PKCζ and PKMζ are overexpressed in TCF3-rearranged paediatric acute lymphoblastic leukaemia and are associated with increased thiopurine sensitivity. Leukemia, 29(2), 304-311.

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Fission Yeast Growth Temperature Assay

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S. pombe cells were cultured for 24 h on a rotary wheel in YE5S liquid medium at 25 °C, diluted 1:100, and cultured an additional 16 h at 25 °C. Equal numbers of cells were taken from cultures in exponential growth phase (OD₅₉₅ < 0.6) and serial diluted 10-fold four times. 5uL aliquots from each dilution were spotted onto YE5S agar plates and incubated at 25 °C, 30 °C or 36 °C for 36–72 h. Plates were imaged with transmitted light by a GelDoc XR imager (BioRad, Hercules, CA).

Kwon L., Magee E.M., Crayton A, & Goss J.W. (2019). Fission yeast type 2 node proteins Blt1p and Gef2p cooperate to ensure timely completion of cytokinesis. BMC Molecular and Cell Biology, 20, 1.

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Detecting Protein S-Glutathionylation by Western Blot

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To determine the relative levels of Pr-SSG, western blot analysis was employed. After adding the reducing agent, dithiothreitol (DTT), Pr-SSG reactive target bands disappear. Parallel experiments without DTT treatment were also studied. Hippocampal and cortical tissues were homogenized with 2 μl/mg in detergent-free RAB buffer, containing 100 mM 2-(N-morpholino) ethanesulphonic acid (MES; pH 7.0), 1 mM EGTA, 0.5 mM MgSO₄, 750 mM NaCl, 20 mM NaF, 1 mM Na₃VO₄, 1 mM PMSF, and protease and phosphatase inhibitor cocktail EDTA-free for measuring Pr-SSG levels. 10 μg of protein of each samples was loaded and then separated on a 10–20% gradient gel. S-glutathionylated proteins were detected with an anti-GSH monoclonal antibody (1:5000), and Enhanced Chemiluminescence (ECL) detection was performed using the Gel Doc XR+ Imager (Bio-Rad Laboratories Inc., Hercules, CA). A polyclonal anti-β-actin antibody (1:1000) was used as a loading control. All samples were normalized using β-actin levels.

Zhang C., Kuo C.C., Moghadam S.H., Monte L., Rice K.C, & Rissman R.A. (2015). Corticotropin-Releasing Factor Receptor-1 Antagonism Reduces Oxidative Damage in an Alzheimer’s Disease Transgenic Mouse Model. Journal of Alzheimer's disease : JAD, 45(2), 639-650.

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Thermal Stability of Cbx4 Chromodomain

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For measuring thermal stability, 40 µM Cbx4.wt or Cbx4.VD protein sample in PBS pH 7.4 in a final volume of 30 μL was incubated at 25, 40, 50, 70, or 90 °C for 3 min and then cooled to 10 °C at 3 °C/s in a Bio-Rad C1000 Thermal Cycler. Samples were then spun at 17,000×g at 4 °C for 30 min to remove aggregates, and the supernatant was analyzed by SDS-PAGE. Gels were stained with Coomassie blue and band intensities were quantified by densitometry using a Gel Doc XR imager and Image Lab 3.0 software (Bio-Rad). Percent soluble chromodomain was calculated as ×100 (band intensity at the indicated temperature/ band intensity of samples heated at 25 °C).

Veggiani G., Villaseñor R., Martyn G.D., Tang J.Q., Krone M.W., Gu J., Chen C., Waters M.L., Pearce K.H., Baubec T, & Sidhu S.S. (2022). High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression. Nature Communications, 13, 6975.

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