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Fluorescent Dyes

Fluorescent dyes are a class of chemical compounds that emit light when exposed to certain wavelengths of electromagnetic radiation.
These dyes are widely used in various scientific and medical applications, including flow cytometry, microscopy, and DNA sequencing.
They can be used to label and visualize specific biomolecules, such as proteins, nucleic acids, and lipids, allowing researchers to study their localization, interactions, and dynamics within cells and tissues.
Fluorescent dyes come in a variety of colors, each with unique excitation and emission spectra, enabling the simultaneous detection of multiple targets.
Proper selection and optimization of fluorescent dyes is crucial for enhancing the reproducibility and accuracy of fluorescent-based research.
PubCompare.ai, a leading AI platform, can assist researchers in this process by providing access to a comprehensive database of fluorescent dye protocols from literature, pre-prints, and patents, and offering AI-driven comparisons to identify the best dyes and protocols for their specific needs.
By leveraging PubCompare.ai's powerful tools, researchers can improve the quality and reliability of their fluorescent dye-based studies.

Most cited protocols related to «Fluorescent Dyes»

1
PacBio Sequencing by Synthesis Protocol
Genomic DNA was sheared to 8 kb using an ultrasonicator (Covaris Inc, Woburn, MA) and was converted into the proprietary SMRTbell™ library format using RS DNA Template Preparation Kit (Pacific Biosciences, Melon Park, CA). Briefly, sheared DNA was end repaired, and hairpin adapters were ligated using T4 DNA ligase. Incompletely formed SMRTbell templates were degraded with a combination of Exonuclease III and Exonuclease VII. The resulting DNA templates were purified using SPRI magnetic beads (AMPure, Agencourt Bioscience, Beverly, MA) and annealed to a two-fold molar excess of a sequencing primer that specifically bound to the single-stranded loop region of the hairpin adapters.
SMRTbell templates were subjected to standard SMRT sequencing using an engineered phi29 DNA polymerase on the PacBio RS system according to manufacturer's protocol. The PacBio RS system continuously monitors zero-mode waveguides (ZMWs) in sets of 75000 at a time. Within each ZMW a single DNA polymerase molecule is attached to the bottom surface such that it permanently resides within the detection volume where it can be watched as it performs sequencing by synthesis. Within each chamber, Phospholinked nucleotides, each type labeled with a different colored fluorophore, are then introduced into the reaction solution at high concentrations that promote enzyme speed, accuracy, and processivity. Pulse calling, utilized a threshold algorithm on the dye weighted intensities of fluorescence emissions, and read alignments, achieved using a Smith-Waterman algorithm. Reads were filtered after alignment to remove low quality sequences derived from doubly-loaded ZMWs.
English A.C., Richards S., Han Y., Wang M., Vee V., Qu J., Qin X., Muzny D.M., Reid J.G., Worley K.C, & Gibbs R.A. (2012). Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology. PLoS ONE, 7(11), e47768.
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Publication 2012
Anabolism DNA DNA-Directed DNA Polymerase DNA Library Enzymes exodeoxyribonuclease III Exonuclease Fluorescent Dyes Genome Melons Molar NCOR2 protein, human Nucleotides Oligonucleotide Primers Pulse Rate T4 DNA Ligase
2
Genome-wide Transcription Factor Binding and DNA Methylation Analysis

ChIP–chip dataset. A number of assays have been recently developed that use immunopercipitation-based enrichment of cellular DNA for the purpose of identifying binding or other chemical events and the genomic locations at which they occur. Location analysis, also known as ChIP–chip, is a technique that enables the mapping of transcription binding events to genomic locations at which they occur [1 (link),54 ]. The output of the assay is a fluorescence dye ratio at each spot of the array. If spots are taken to represent genomic regions, then we can regard the ratio and p-value associated with each spot as an indication of TF binding in the corresponding genomic region. We applied DRIM to S. cerevisiae genome-wide location data reported in Harbison et al. [25 (link)] and Lee et al. [28 (link)]. The first consists of the genomic occupancy of 203 putative TFs in rich media conditions (YPD). In addition, the genomic occupancy of 84 of these TFs was measured in at least one other condition (OC). In each of the experiments, the genomic sequences were ranked according to the TF binding p-value. Surprisingly, we observed that 69 of the 203 ranked sequence lists of YPD had significantly longer sequences at the top of the list (first 300 sequences) compared with the rest of the list with t-test p-value ≤ 10−3. We observed a similar phenomenon in 76 of the 148 ranked sequence lists of OC experiments (see Figure S1). In other words, for some TFs, longer sequences are biased toward stronger binding signals. This observation is unexpected since, although longer probes hybridize more labeled material than shorter probes, the increase should be proportional in both channels. This type of length bias may cause spurious results under our model assumptions and hence the final dataset, termed “Harbison filtered dataset,” refers to the remaining 207 experiments (135 YPD, and 72 OC) of 162 unique TFs that did not have length bias (Table S1).
An additional ChIP–chip dataset was constructed using the data reported in Lee et al. [28 (link)] containing 113 experiments in rich media. The data is partially exclusive to the data of Harbison et al. [25 (link)]. The same filtering procedure was performed, resulting in a set of 65 experiments, termed “Lee filtered dataset.”
Methylated CpG dataset. Using a technique similar to ChIP–chip, termed methyl-DNA immunoprecipitation (mDIP), enables the measurement of methylated CpG island patterns [2 (link),55 (link)]. The third dataset contains the CpG island methylation patterns of four different human cancer cell lines (Caco-2, Polyp, Carcinoma, PC3) where several replicate experiments were done for each of the cell lines. In each of these experiments, the CpG methylation signal was measured in ∼13,000 gene promoters as reported in [2 (link)].
Eden E., Lipson D., Yogev S, & Yakhini Z. (2007). Discovering Motifs in Ranked Lists of DNA Sequences. PLoS Computational Biology, 3(3), e39.
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Publication 2007
Biological Assay Carcinoma Cell Lines Cells ChIP-Chip CpG Islands DNA Replication Exanthema Fluorescent Dyes Genome Homo sapiens Immunoprecipitation Malignant Neoplasms Methylation Polyps Promoter, Genetic Transcription, Genetic
3
Automated Comet Assay Image Analysis

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Publication 2014
1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidine)quinolinium, tetraiodide Cells Comet Assay DAPI DNA Damage EDNRB protein, human Fluorescent Dyes Gold Head Light Propidium Iodide Silver Nitrate SYBR Green I Tail
4
Immunofluorescent Analysis of Ocular Proteins

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Publication 2021
Actins Animals Antibodies Biopharmaceuticals Capsule Catabolism Cataract Cells DNA Replication Epithelium Epitopes Eye Fibrosis Fluorescent Antibody Technique Fluorescent Dyes Freezing Gene Expression Genes Homo sapiens Immunoglobulins Institutional Animal Care and Use Committees Lens, Crystalline Mice, Inbred C57BL Microscopy, Confocal Mus Operative Surgical Procedures Protein Denaturation Proteins RNA-Seq Smooth Muscles Tissues Training Programs Vision Western Blotting
5
Immunophenotypic Analysis of Cell Viability
After cells were counted, and 2x106 cells per sample were stained with Aqua Live/Dead viability dye (Life Technologies) according the manufacturer’s instructions. Cells were then incubated in blocking solution containing 5% normal mouse serum, 5% normal rat serum, and 1% FcBlock (eBiosciences, San Diego, CA) in PBS and then stained with a standard panel of immunophenotyping antibodies (See S2 Table for a list of antibodies, clones, fluorochromes, manufacturers, and concentrations) for 30 minutes at room temperature. After staining, cells were washed and fixed with 0.4% paraformaldehyde in PBS. Data was acquired with a BD LSRII flow cytometer using BD FACSDiva software (BD Bioscience). Compensation was performed on the BD LSRII flow cytometer at the beginning of each experiment. Data were analyzed using Flowjo v10. Cell sorting for cytospins was performed on a BD Aria II. The collected cells were stained with a Jenner-Giemsa Stain Kit (ENG Scientific Inc, Clifton, NJ) and examined by light microscopy.
Yu Y.R., O’Koren E.G., Hotten D.F., Kan M.J., Kopin D., Nelson E.R., Que L, & Gunn M.D. (2016). A Protocol for the Comprehensive Flow Cytometric Analysis of Immune Cells in Normal and Inflamed Murine Non-Lymphoid Tissues. PLoS ONE, 11(3), e0150606.
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Publication 2016
Antibodies Cells Clone Cells Fluorescent Dyes Light Microscopy Mus NRG1 protein, human paraform Serum Stain, Giemsa Stains

Most recents protocols related to «Fluorescent Dyes»

1
Quantifying IL-2 Effects on T Cell Activation
Not available on PMC !

Example 7

Impact of IL-2 signalling on Teff responses is characterised in a T cell activation assay, in which intracellular granzyme B (GrB) upregulation and proliferation are examined. Previously frozen primary human Pan T cells (Stemcell Technologies) are labelled with eFluor450 cell proliferation dye (Invitrogen) according to manufacturer's recommendation, and added to 96-U-bottom well plates at 1×105 cells/well in RPMI 1640 (Life Technologies) containing 10% FBS (Sigma), 2 mM L-Glutamine (Life Technologies) and 10,000 U/ml Pen-Strep (Sigma). The cells are then treated with 10 μg/ml anti-CD25 antibodies or control antibodies followed by Human T-Activator CD3/CD28 (20:1 cell to bead ratio; Gibco) and incubated for 72 hrs in a 37° C., 5% CO2 humidified incubator. To assess T cell activation, cells are stained with the eBioscience Fixable Viability Dye efluor780 (Invitrogen), followed by fluorochrome labelled antibodies for surface T cell markers (CD3-PerCP-Cy5.5 clone UCHT1 Biolegend, CD4-BV510 clone SK3 BD Bioscience, CD8-Alexa Fluor 700 clone RPA-T8 Invitrogen, CD45RA-PE-Cy7 clone HI100 Invitrogen, CD25-BUV737 clone 2A3 BD Bioscience) and then fixed and permeabilized with the eBioscience™ Foxp3/Transcription Factor Staining Buffer Set (Invitrogen) before staining for intracellular GrB and intranuclear FoxP3 (Granzyme B-PE clone GB11 BD Bioscience, FoxP3-APC clone 236A/E7). Samples are acquired on the Fortessa LSR X20 Flow Cytometer (BD Bioscience) and analysed using the BD FACSDIVA software. Doublets are excluded using FCS-H versus FCS-A, and lymphocytes defined using SSC-A versus FCS-A parameters. CD4+ and CD8+ T cell subsets gated from the live CD3+ lymphocytes are assessed using a GrB-PE-A versus proliferation eFluor450-A plot. Results are presented as percentage of proliferating GrB positive cells from the whole CD4+ T cell population. Graphs and statistical analysis is performed using GraphPad Prism v7. (results not shown)

US11873341B2. Anti-CD25 for tumour specific cell depletion (2024-01-16). Tusk Therapeutics Ltd. [GB], Cancer Research Technology Limited [GB]. Inventors: Anne Goubier [GB], Beatriz Goyenechea Corzo [GB], Josephine Salimu [GB], Kevin Moulder [GB], Pascal Merchiers [GB], Sergio Quezada [GB].
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Patent 2024
Anti-Antibodies Antibodies Biological Assay Buffers CD4 Positive T Lymphocytes Cell Proliferation Cells Clone Cells CY5.5 cyanine dye Eragrostis Fluorescent Dyes Freezing Glutamine GZMB protein, human Homo sapiens IL2RA protein, human Lymphocyte prisma Protoplasm Stem Cells Streptococcal Infections T-Lymphocyte T-Lymphocyte Subsets Transcriptional Activation Transcription Factor
2
Binding Affinity of CD40-CEA Bispecific Antibodies
Not available on PMC !

Example 6

Aim and Background

The aim of this study was to assess the binding of the CD40-CEA RUBY™ bispecific antibodies to CEACAM5 expressed on cells and evaluate potential cross-reactivity to CEACAM1. In this study both CEACAM5 transfected cells and human tumor cells with endogenous CEACAM5 expression were used.

Materials and Methods

The human CEACAM5 and CEACAM1 genes were cloned into pcDNA3.1, and the vector was subsequently stably transfected into CHO cells. The tumor cell line MKN45, expressing high levels of CEACAM5, LS174T expressing intermediate levels of CEACAM5, and HT29 and LOVO expressing low levels of CEACAM5 (Table 16), CHO-CEACAM5, CHO-CEACAM1 and to CHO wt cells were incubated with titrated concentrations of CD40-CEA bispecific antibodies. Binding of the antibodies was detected using fluorochrome-conjugated anti-human IgG and analyzed using flow cytometry.

Results and Conclusions

The data demonstrate that all tested CD40-CEACAM5 RUBYs bind to CEACAM5 expressed on CHO-CEACAM5 (FIG. 6A-FIG. 6E), and MKN45 (high expressing) (FIG. 8A-FIG. 8C) and LS174T (intermediate expressing) human tumor cells (FIG. 8D-FIG. 8F). Low or no binding was observed to the CEACAM5 low expressing tumor cells, the LOVO cells (FIG. 8G-FIG. 8I). In addition, a low cross-reactivity to CEACAM1 or stickiness to CHO wt cells was observed with some of the CD40-CEA bispecific antibodies at very high concentrations (FIG. 7). In conclusion, all the CD40-CEA RUBY™ bispecific antibodies bind to CEACAM5 and with low or no binding to CEACAM1.

TABLE 16
Summary of CEA expression levels on CEACAM5 transfected
CHO cells and CEA expressing human tumor cells.
Tumor cell line and CEA
transfected CHO cellsReceptors/cell
HT2911 300
LOVO 5 500
LS174T51 500
MKN45353 000 
CHO-CEACAM5125 000 

US11873348B2. Peptides (2024-01-16). ALLIGATOR BIOSCIENCE AB [SE]. Inventors: Peter Ellmark [SE], Karin Hagerbrand [SE], Laura Varas [SE], Mattias Levin [SE], Anna Säll [SE], Laura von Schantz [SE].
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Patent 2024
anti-IgG Antibodies Antibodies, Bispecific biliary glycoprotein I CEACAM5 protein, human Cell Line, Tumor Cells CHO Cells Cloning Vectors Cross Reactions Flow Cytometry Fluorescent Dyes Genes Homo sapiens HT29 Cells Neoplasms
3
Anti-PD-L1 Antibodies Modulate Lymphocyte Proliferation
Not available on PMC !

Example 3

This example provides a showing of the effect of disclosed anti-PD-L1 antibodies on lymphocyte proliferation. Anti-PD-L1 antibodies were assayed for their ability to modulate the response of lymphocytes to stimulation. The anti-PD-L1 antibodies H1, H6 and H10 were added at 10 μg/ml to cultures of peripheral blood mononuclear cells labeled with the fluorescent dye carboxyfluorescein (CFSE) and stimulated with anti-CD3 (1 ng/ml). After three days of culture, the cells were assayed for proliferative activity by flow cytometry using a FACS Aria (Becton Dickinson, San Jose, CA). The results, shown in FIG. 3, show that the anti-PD-L1 antibodies inhibited lymphocyte proliferation.

US11878058B2. Antigen binding proteins that bind PD-L1 (2024-01-23). Sorrento Therapeutics, Inc. [US]. Inventors: Heyue Zhou [US], Randy Gastwirt [US], Barbara A. Swanson [US], John Dixon Gray [US], Gunnar F. Kaufmann [US].
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Patent 2024
Anti-Antibodies Antigens Binding Proteins carboxyfluorescein CD274 protein, human Cells Flow Cytometry Fluorescent Dyes Lymphocyte Muromonab-CD3 NRG1 protein, human PBMC Peripheral Blood Mononuclear Cells
4
Mitochondrial Membrane Potential Measurement
Not available on PMC !

Example 4

The measurement of mitochondrial membrane potential (MMP) with JC-9 was performed with two independent fluorescence channels (green and red fluorescence signals), as changes in MMP cause aggregation of the dye, with different fluorescence emission by the aggregated versus non-aggregated dye molecules. As shown in FIG. 6A, both red and green fluorescence initially increase in response to increasing valinomycin concentration, with a peak green fluorescence at˜0.05 μM valinomycin. At higher valinomycin concentrations, red fluorescence increases, with the red/green fluorescence ratio increasing. A unique aspect of this assay is that it correlates changes in MMP (JC-9) and cell death (SYTOXRED™) with the phases of the cell cycle (G1, S, and G2M).

An identical study to the one described before was conducted with exposing HL60 cells exposed to 1.23 μM idarubicin, an analog of daunorubicin which inserts into DNA and prevents it from unwinding during DNA replication and arrests cell division. As shown in FIG. 6B, the red fluorescence of JC-9 dye is significantly higher in cells treated with idarubicin than untreated control cells (first two data points on the left indicate control cells).

US11867690B2. Identification of functional cell states (2024-01-09). ASEDASCIENCES AG [CH]. Inventors: Bartlomiej Rajwa [US], Vincent T Shankey [US].
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Patent 2024
Biological Assay Cardiac Arrest Cell Cycle Cell Death Cells Daunorubicin Division, Cell DNA Replication Fluorescence Fluorescent Dyes HL-60 Cells Idarubicin Membrane Potential, Mitochondrial Valinomycin
5
High-Throughput Compound Toxicity Screening
Not available on PMC !

Example 8

Cells were treated with troglitazone, followed by incubation with the various fluorescence dyes (CALCEIN AM, MBBR, MITOSOX™ and CYTOSOX™). For each non-control well, the quadratic chi-distance distance to positive and negative control templates (for each fluorescence channel) was calculated and normalized with the scaling factor. The normalized data are reorganized into tensors, and the distance from positive and negative control templates are calculated. The similarities of the trioglitazone tensor to another compound tensor can be computed using known techniques by comparing the fiber columns of the tensors using dynamic time warping distance (see, Giorgino et al. “Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package.” Journal of Statistical Software, 31(7), 1-24, 2009). Dissimilarities or distances to all other compounds can be calculated this way.

Results are shown in FIG. 12.

US11867690B2. Identification of functional cell states (2024-01-09). ASEDASCIENCES AG [CH]. Inventors: Bartlomiej Rajwa [US], Vincent T Shankey [US].
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Patent 2024
Cells Fibrosis Fluorescence Fluorescent Dyes fluorexon MitoSOX monobromobimane Troglitazone

Top products related to «Fluorescent Dyes»

1
Facscanto 2 by BD
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The FACSCanto II is a flow cytometer instrument designed for multi-parameter analysis of single cells. It features a solid-state diode laser and up to four fluorescence detectors for simultaneous measurement of multiple cellular parameters.
2
Facscalibur by BD
Sourced in United States, Germany, United Kingdom, China, Canada, Japan, Italy, France, Belgium, Switzerland, Singapore, Uruguay, Australia, Spain, Poland, India, Austria, Denmark, Netherlands, Jersey, Finland, Sweden
The FACSCalibur is a flow cytometry system designed for multi-parameter analysis of cells and other particles. It features a blue (488 nm) and a red (635 nm) laser for excitation of fluorescent dyes. The instrument is capable of detecting forward scatter, side scatter, and up to four fluorescent parameters simultaneously.
3
Lsrfortessa by BD
Sourced in United States, United Kingdom, Germany, France, Canada, Australia, Belgium, China, Uruguay, Japan, Sweden, Switzerland, Cameroon
The LSRFortessa is a flow cytometer designed for multiparameter analysis of cells and other particles. It features a compact design and offers a range of configurations to meet various research needs. The LSRFortessa provides high-resolution data acquisition and analysis capabilities.
4
Facsdiva software by BD
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FACSDiva software is a user-friendly flow cytometry analysis and data management platform. It provides intuitive tools for data acquisition, analysis, and reporting. The software enables researchers to efficiently process and interpret flow cytometry data.
5
Facscalibur flow cytometer by BD
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The FACSCalibur flow cytometer is a compact and versatile instrument designed for multiparameter analysis of cells and particles. It employs laser-based technology to rapidly measure and analyze the physical and fluorescent characteristics of cells or other particles as they flow in a fluid stream. The FACSCalibur can detect and quantify a wide range of cellular properties, making it a valuable tool for various applications in biology, immunology, and clinical research.
6
Lsrii flow cytometer by BD
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The BD LSRII flow cytometer is a multi-parameter instrument designed for advanced flow cytometry applications. It features a modular design that allows for customization to meet specific research needs. The LSRII utilizes laser excitation and sensitive detectors to analyze the physical and fluorescent properties of individual cells or particles passing through a fluid stream.
7
Trizol reagent by Thermo Fisher Scientific
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
8
Facscanto 2 flow cytometer by BD
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The FACSCanto II is a flow cytometer manufactured by BD. It is a versatile instrument designed for multicolor flow cytometric analysis. The FACSCanto II can detect and analyze various properties of cells or particles suspended in a fluid as they flow through the system.
9
4 6 diamidino 2 phenylindole (dapi) by Merck Group
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DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
10
4 6 diamidino 2 phenylindole (dapi) by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, Japan, China, Canada, Italy, Australia, France, Switzerland, Spain, Belgium, Denmark, Panama, Poland, Singapore, Austria, Morocco, Netherlands, Sweden, Argentina, India, Finland, Pakistan, Cameroon, New Zealand
DAPI is a fluorescent dye used in microscopy and flow cytometry to stain cell nuclei. It binds strongly to the minor groove of double-stranded DNA, emitting blue fluorescence when excited by ultraviolet light.

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