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Chemidox xrs system

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The ChemiDox XRS system is a high-performance imaging system designed for the detection and analysis of chemiluminescent and fluorescent signals. The system features a cooled CCD camera, motorized filter wheel, and versatile imaging capabilities, making it suitable for a wide range of applications in molecular biology and life science research.

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Lab products found in correlation

Quantity one image software, by Bio-Rad (2 mentions) Sodium chloride (nacl), by Merck Group (2 mentions) Sodium dodecyl sulfate (sds), by Avantor (2 mentions) Sodium deoxycholate, by Merck Group (2 mentions) Mastercycler pro, by Eppendorf (1 mentions) Onetaq 2x master mix with standard buffer, by New England Biolabs (1 mentions) Purelink dnase, by Thermo Fisher Scientific (1 mentions) High capacity cdna reverse transcription kit, by Thermo Fisher Scientific (1 mentions) Purelink rna mini kit, by Thermo Fisher Scientific (1 mentions) Lipofectamine 3000 transfection reagent, by Thermo Fisher Scientific (1 mentions) Claudin 2, by Abcam (1 mentions) Pdvf membrane, by Merck Group (1 mentions) β actin, by Merck Group (1 mentions) Epiquik nuclear extraction kit, by Epigentek (1 mentions) Ripa lysis buffer, by Thermo Fisher Scientific (1 mentions) Ecl western blotting substrate, by Thermo Fisher Scientific (1 mentions) Bolt lds sample buffer, by Thermo Fisher Scientific (1 mentions) Bca protein assay kit, by Thermo Fisher Scientific (1 mentions) α sma, by Abcam (1 mentions) Laemmli sample buffer, by Bio-Rad (1 mentions)

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ChemiDox XRS (32 citations) ChemiDox XRS imaging system (13 citations) Molecular Imager ChemiDox XRS+ Imaging System (11 citations) ChemiDox (6 citations) ChemiDox XRS Chemiluminescence imaging system (6 citations)

10 protocols using chemidox xrs system

1

Evaluating mRNA Encapsulation by LNPs

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The mRNA encapsulation/complexation ability of LNPs was assayed by an agarose retardation assay. A total of 300 ng of eGFP-encoding mRNA (5moU) (eGFP mRNA, 996 nucleotides, catalog no. L-7201, TriLink Biotechnologies, San Diego, California) was encapsulated or complexed with LNP, Lipo, and CNE, and electrophoresis was performed using 2% (w/v) agarose gels stained with Golden View for 20 min at 110 V. Images were then acquired using a Bio-Rad ChemiDoxXRS system.
Shi Y., Huang J., Liu Y., Liu J., Guo X., Li J., Gong L., Zhou X., Cheng G., Qiu Y., You J, & Lou Y. (2022). Structural and biochemical characteristics of mRNA nanoparticles determine anti–SARS-CoV-2 humoral and cellular immune responses. Science Advances, 8(47), eabo1827.
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2

Splicing Reporter Assay in HEK293T Cells

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Minigene constructs were designed in silico, synthesized by GenScript and sub-cloned into a vector with the GFP splicing control. HEK 293T TDP-43 knockout cells and the parent HEK 293T cells were seeded into standard P12 tissue culture plates (at 1.6 × 105 cells per well), allowed to adhere overnight, and transfected with the indicated splicing reporter constructs (400 ng per well) using Lipofectamine 3000 transfection reagent (Invitrogen). Each reporter comprised one of the splicing modules (shown in Fig. 4d), which is expressed from a bidirectional promoter. Twenty-four hours after transfection, RNA was extracted from these cells using PureLink RNA Mini Kit (Life Technologies) according to the manufacturer’s protocol, with on-column PureLink DNase (Invitrogen) treatment. The RNA was reverse transcribed into cDNA using the High Capacity cDNA Reverse Transcription Kit (Invitrogen) according to the manufacturers’ instructions. PCRs were performed using OneTaq 2X Master Mix with Standard Buffer (NEB) with the following cycling parameters: denaturation: 94 °C for 30 s; 30 cycles: 94 °C for 20 s, 54 °C for 30 s, 68 °C for 30 s; final extension: 68 °C for 5 min on a Mastercycler Pro (Eppendorf) thermocycler PCR machine. PCR products were separated by electrophoresis on a 1.5% TAE gel and imaged ChemiDox XRS+ System (Bio-Rad). See Supplementary Table 6 for primers.
Ma X.R., Prudencio M., Koike Y., Vatsavayai S.C., Kim G., Harbinski F., Briner A., Rodriguez C.M., Guo C., Akiyama T., Schmidt H.B., Cummings B.B., Wyatt D.W., Kurylo K., Miller G., Mekhoubad S., Sallee N., Mekonnen G., Ganser L., Rubien J.D., Jansen-West K., Cook C.N., Pickles S., Oskarsson B., Graff-Radford N.R., Boeve B.F., Knopman D.S., Petersen R.C., Dickson D.W., Shorter J., Myong S., Green E.M., Seeley W.W., Petrucelli L, & Gitler A.D. (2022). TDP-43 represses cryptic exon inclusion in the FTD–ALS gene UNC13A. Nature, 603(7899), 124-130.
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3

Tight Junction Protein Expression Analysis

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In this part, we applied the methods described in previous articles [19 (link)]. In brief, the total tissue proteins were collected for the determination of ZO-1, occludin, claudin-1, and claudin-2. By the way, equal amounts of total protein extracted from the ileal mucosa were respectively fractionated on 8%, 10%, and 12% sodium dodecyl sulfate- polyacrylamide gel electrophoresis (SDS-PAGE) gel and then transferred to polyvinylidene difluoride (PDVF) membrane (Millipore, Bedford, MA). Furthermore, after the membrane was blocked, the membranes were incubated with antibodies specific for ZO-1 (1:1000, Invitrogen), occludin (1:1000, Invitrogen), claudin-1 (1:1000, Invitrogen), claudin-2 (1:1000, Abcam), and β-actin (1:5000, Sigma) overnight at 4 °C. After washing with Tris-buffered saline Tween-20 (TBST), membranes were incubated with appropriate peroxidase-conjugated secondary antibodies (KPL, America) at room temperature for 60 min. The chemiluminescence signal was captured using a ChemiDox XRS system (Bio-Rad). The densities of the bands were quantified with Quantity One Image software (Bio-Rad).
Feng Y., Huang Y., Wang Y., Wang P, & Wang F. (2019). Severe burn injury alters intestinal microbiota composition and impairs intestinal barrier in mice. Burns & Trauma, 7, 20.
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4

CHD4 Chromatin Remodeling Assay

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A restriction enzyme accessibility assay was used to measure the remodeling activities 21 (link). Each reaction took place in the presence of 20 mM Tris-HCl pH 7.5, 1 mM MgCl2, 1 mM DTT, 0.1 mg/mL BSA, 1 mM ATP, and 5 U HhaI. Wild-type or mutant CHD4 was added to 12 nM nucleosomes at final concentrations of 12 nM, 6 nM, and 3 nM to initiate the reaction. Mixtures were incubated at 37°C for 60 minutes and quenched by the addition of 2 μL of proteinase K buffer (167 mM EDTA, 1.7% SDS, and 6.7 mg/mL proteinase K), then incubated at 50°C for 15 minutes for deproteination to take place. Samples were analyzed by 6% native polyacrylamide gel electrophoresis. DNA fragments were visualized on a ChemiDox XRS system (BIO-RAD) and were quantitated using Image Lab software. Three individual experiments from two biological replicates (n = 6) were conducted for each mutant.
Weiss K., Lazar H.P., Kurolap A., Martinez A., Paperna T., Cohen L., Smeland M.F., Wallen S., Heide S., Keren B., Terhal P., Irving M., Takaku M., Roberts J.D., Petrovich R.M., Vergano S.A., Kenney A., Hove H., DeChene E., Quinonez S.C., Colin E., Ziegler A., Rumple M., Jain M., Monteil D., Roeder E.R., Nugent K., van Haeringen A., Gambello M., Santani A., Medne L., Krock B., Skraban C.M., Zackai E.H., Dubbs H.A., Smol T., Ghoumid J., Parker M.J., Wright M., Turnpenny P., Clayton-Smith J., Metcalfe K., Kurumizaka H., Gelb B.D., Feldman H.B., Campeau P.M., Muenke M., Wade P.A, & Lachlan K. (2019). The CHD4-Related Syndrome: A Comprehensive Investigation of the Clinical Spectrum, Genotype-Phenotype Correlations and Molecular Basis. Genetics in medicine : official journal of the American College of Medical Genetics, 22(2), 389-397.
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5

Intestinal Tight Junction Regulation

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Inflammatory cytokines and TJ protein expression were detected by western blotting. The distal ileum mucosa was collected and protein was extracted by RIPA lysis buffer with a cocktail of protease inhibitors. After the supernatant was obtained by centrifugation, protein was quantified using a standard BCA protein assay. Equal amounts of protein (25 μg) were fractionated on 8 and 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis gels and then transferred to polyvinylidene difluoride membranes. After the nonspecific sites were blocked with 5% skimmed milk, the membranes were incubated with Abs specific for TNF-α, IL-17A, TGF-β, ZO-1, occludin or β-actin at 4°C overnight. Subsequently, the membranes were incubated with the corresponding horseradish peroxidase-labeled secondary Abs at room temperature for 1 h. The chemiluminescence signal was obtained using a ChemiDox XRS system (Bio-Rad, USA). The densities of the bands were quantified with Quantity One Image software (Bio-Rad, USA).
Song Y., Li Y., Hu W., Li F., Sheng H., Huang C., Gou X., Hou J., Zheng J, & Xiao Y. (2024). Luminol-conjugated cyclodextrin biological nanoparticles for the treatment of severe burn-induced intestinal barrier disruption. Burns & Trauma, 12, tkad054.
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6

Protein Extraction and Western Blot Analysis

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We extracted the proteins from total cell lysates using RIPA lysis buffer (Thermo Scientific, Rockford, IL, USA), and nuclear proteins with EpiQuik Nuclear Extraction Kit (Epigentek, Farmingdale, NY, USA). The protein concentrations were determined with a BCA protein assay kit (Thermo Scientific). We used Bolt LDS sample buffer (Thermo Scientific) or sodium dodecyl sulfate sample buffer (2% sodium dodecyl sulfate, 62.5 mM Tris-base (pH 6.8), 10% glycerol, 5% β-mercaptoethanol and 0.005% bromophenol blue) to denature the proteins before sample loading for gel electrophoresis and membrane transferring as described previously.55 (link), 56 The signals were detected with ECL Western Blotting substrate (Thermo Scientific) with a ChemiDox XRS system (Bio-Rad Laboratories, Inc., Hercules, CA, USA).
As described previously,55 (link), 56 for immunofluorescence, we seeded 2 × 104 cells per well into 24-well plates. After 48-h culture, the cells were washed and processed to overnight primary antibody incubation at 4 °C. The fluorochrome-conjugated secondary antibody was incubated the next day in dark for 1 h at room temperature. DAPI staining was conducted to visualize the nuclei.
Yu T., Wang C., Yang J., Guo Y., Wu Y, & Li X. (2017). Metformin inhibits SUV39H1-mediated migration of prostate cancer cells. Oncogenesis, 6(5), e324-.
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7

Western Blot Analysis of Protein Expression

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Total protein from RAEC was isolated using Laemmli sample buffer (Bio-Rad; Kukoyi et al., 2019 (link)). Because we cannot measure the amount of protein after adding Laemmli buffer, equal volumes of samples were separated on a 4%–20% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel and transferred to PVDF membranes. After blocking with 5% non-fat dry milk/Tris-buffered saline with 0.1% Tween 20 (blocking buffer, pH 7.4) for 1 h, the membranes were incubated with antibodies for ZO-1 (Invitrogen, 1:1000), alpha-smooth muscle actin (α-SMA; Abcam, 1:5000), collagen type 1A1 (col1A1; Santa Cruz Biotechnology, 1:200), GAPDH (Sigma-Aldrich, 1:50,000) at 4°C overnight. We chose GAPDH as the housekeeping gene in our experiments because it has the least variation within our experimental conditions compared β-actin and because β-actin has similar molecular weight to α-SMA. The membranes were incubated for 1 h at room temperature with an appropriate horseradish peroxidase-conjugated secondary antibody prior to adding the Clarity Western ECL substrate (Bio-Rad). The immunoreactive bands were captured with a ChemiDox XRS system (Bio-Rad). The relative densitometry of the protein of interest was normalized to the densitometry of the GAPDH band from the same membrane.
Sueblinvong V., Fan X., Hart C., Molina S., Koval M, & Guidot D.M. (2023). Ethanol-exposed lung fibroblasts cause airway epithelial barrier dysfunction. Alcohol, clinical & experimental research, 47(10), 1839-1849.
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8

Nucleosome remodeling by CHD3 proteins

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Remodeling activities were measured with a restriction enzyme accessibility assay as previously described27 (link). 12.5 nM nucleosomes (347 bp) were incubated with the indicated amounts of CHD3 proteins at 37 °C for 60 min in the remodeling buffer (20 mM Tris–HCl pH 7.5, 1 mM DTT, 1 mM MgCl2, 1 mM ATP, 0.1 mg/ml BSA, and 5 U HhaI). The reactions were stopped by adding 2 µL of proteinase K buffer containing 6.7 mg/ml proteinase K, 167 mM EDTA, and 1.7% SDS. After incubation at 50 °C for 10 min, the DNAs were analyzed by 6% native polyacrylamide gel electrophoresis. The separated DNA fragments were visualized with UV light on the ChemiDox XRS system (BIO-RAD). The band intensities were quantified by ImageJ.
Snijders Blok L., Rousseau J., Twist J., Ehresmann S., Takaku M., Venselaar H., Rodan L.H., Nowak C.B., Douglas J., Swoboda K.J., Steeves M.A., Sahai I., Stumpel C.T., Stegmann A.P., Wheeler P., Willing M., Fiala E., Kochhar A., Gibson W.T., Cohen A.S., Agbahovbe R., Innes A.M., Au P.Y., Rankin J., Anderson I.J., Skinner S.A., Louie R.J., Warren H.E., Afenjar A., Keren B., Nava C., Buratti J., Isapof A., Rodriguez D., Lewandowski R., Propst J., van Essen T., Choi M., Lee S., Chae J.H., Price S., Schnur R.E., Douglas G., Wentzensen I.M., Zweier C., Reis A., Bialer M.G., Moore C., Koopmans M., Brilstra E.H., Monroe G.R., van Gassen K.L., van Binsbergen E., Newbury-Ecob R., Bownass L., Bader I., Mayr J.A., Wortmann S.B., Jakielski K.J., Strand E.A., Kloth K., Bierhals T., Roberts J.D., Petrovich R.M., Machida S., Kurumizaka H., Lelieveld S., Pfundt R., Jansen S., Deriziotis P., Faivre L., Thevenon J., Assoum M., Shriberg L., Kleefstra T., Brunner H.G., Wade P.A., Fisher S.E, & Campeau P.M. (2018). CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language. Nature Communications, 9, 4619.
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9

Western Blotting Protein Extraction and Analysis

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This experiment was conducted as described by Fathi et al. with some modifications [25 (link)]. Total proteins were extracted with a lysis buffer consisting of 150 mM NaCl (Merck, NJ, USA), 1.0% Triton X-100, 1% sodium deoxycholate (Merck), 0.1% SDS (Amresco) and 50 mM Tris–Cl pH 8.0 (Merck), followed by centrifugation at 14,000 rpm for 10 min at 4 °C. Extracted proteins (20 μg) were denatured and resolved in 10% SDS-PAGE gels. The separated protein bands were then transferred onto PVDF membrane. These blots were incubated with the primary antibodies at 4 °C overnight, followed by incubation with secondary antibodies at room temperature for 1 h. After subsequent incubation with ECL solution (Genenorth, Beijing, China), chemiluminescence signal on the blots were captured using the ChemiDox XRS + system (Bio-Rad, Hercules, CA). The primary antibodies used in this study are listed in Additional file 11: Table S6.
Zhang Y., Qiu F., Ye T., Lee S.H., Xu J., Jia L., Zeng R., Wang X., Hu X., Yan X., Li H., Lu Y., Wang X., Jiang R, & Xu W. (2022). Epiregulin increases stemness-associated genes expression and promotes chemoresistance of non-small cell lung cancer via ERK signaling. Stem Cell Research & Therapy, 13, 197.
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10

Protein Extraction and Western Blot Analysis

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Total proteins were extracted with a lysis buffer consisting of 150 mM NaCl (Merck, NJ, USA), 1.0% Triton X-100, 1% sodium deoxycholate (Merck), 0.1% SDS (Amresco) and 50 mM Tris-Cl pH 8.0 (Merck), followed by centrifugation at 14,000 rpm for 10 minutes at 4°C. Extracted proteins (20 µg) were denatured and resolved in 10% SDS-PAGE gels. The separated protein bands were then transferred onto PVDF membrane. These blots were incubated with the primary antibodies at 4°C overnight, followed by incubation with secondary antibodies at room temperature for 1 hour. After subsequent incubation with ECL solution (Genenorth, Beijing, China), chemiluminescence signal on the blots were captured using the ChemiDox XRS+ system (Bio-Rad, Hercules, CA). The primary antibodies used in this study were listed in the Table S6.
Wei X., Zhang Y., Qiu F., Ye T., Lee S.H., Xu J., Jia L., Zeng R., Wang X., Hu X., Yan X., Li H., Lu Y., & Jiang R. (2022). EREG increases stemness associated genes expression and promotes Chemoresistance of non-small cell lung cancer via ERK signaling.
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