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Sytox blue

Manufactured by Thermo Fisher Scientific
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Sytox Blue is a nucleic acid stain that selectively binds to DNA and RNA. It is commonly used in flow cytometry and fluorescence microscopy applications to identify and quantify cell populations.

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Lab products found in correlation

Facsaria, by BD (17 mentions) Facsdiva software, by BD (15 mentions) Lsrfortessa, by BD (13 mentions) Lsrii flow cytometer, by BD (12 mentions) Diva software, by BD (11 mentions) Lsrii system, by BD (11 mentions) Lsr 2, by BD (10 mentions) Sytox green, by Thermo Fisher Scientific (9 mentions) Facscanto 2, by BD (8 mentions) Facsaria 3, by BD (8 mentions) Sytoxblue, by BD (8 mentions) Propidium iodide, by Thermo Fisher Scientific (8 mentions) Mitotracker green, by Thermo Fisher Scientific (7 mentions) Facsaria fusion, by BD (7 mentions) Cd45 apc, by BD (6 mentions) Calcein am, by Thermo Fisher Scientific (6 mentions) Tryple express, by Thermo Fisher Scientific (6 mentions) Facsaria 2, by BD (6 mentions) Facsdiva, by BD (5 mentions) Sytox orange, by Thermo Fisher Scientific (5 mentions)

Close spelling variants of this product

SYTOX Blue Dead Cell Stain (108 citations) SYTOX Blue nucleic acid stain (23 citations) Sytox Blue Stain (9 citations) Sytox Blue viability dye (8 citations) SYTOX blue dye (7 citations) Pacific Blue™ Annexin V/SYTOX™ AADvanced™ Apoptosis Kit (5 citations) SYTOX Blue dead stain (4 citations) SYTOX Blue Dead Cell Stain for flow cytometry (3 citations) Sytox blue live/dead stain (3 citations) Sytox® blue viability marker (2 citations)

353 protocols using sytox blue

1

Quantifying Innate Immune Cells in Neonates

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Single cell suspensions were stained with anti-Ly6G APC (Becton-Dickinson (BD) (Franklin Lakes, NJ), anti-CD11b-PECy7 (BD, Franklin Lakes, NJ), and anti-F4/80-APC (Ebioscience, San Diego, CA). Sytox Blue (Invitrogen, Carlsbad, CA) was used for cell viability analysis. Samples were acquired and analyzed on an LSR II flow cytometer (BD) and analyzed via FACSDiva™ (BD) software. At least 1 × 104 live cells (Sytox Blue−; Invitrogen, Carlsbad, CA) were collected for analysis. The absolute numbers of innate immune effector cells were determined by multiplying the percentage of neutrophils (CD11b+, Ly6G+) and macrophages)(CD11b+, Ly6G−, F4/80+) within the total sample population by the total sample cell number. In neonates, these were divided by the total number of mice in the pooled sample. Absolute numbers represent total macrophages or neutrophils per mouse.
Gentile L.F., Nacionales D.C., Lopez M.C., Vanzant E., Cuenca A., Cuenca A.G., Ungaro R., Szpila B.E., Larson S., Joseph A., Moore F., Leeuwenburgh C., Baker H.V., Moldawer L.L, & Efron P.A. (2014). Protective Immunity and Defects in the Neonatal and Elderly Immune Response to Sepsis. Journal of immunology (Baltimore, Md. : 1950), 192(7), 3156-3165.
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2

Cell Death and DNA Quantification Assay

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Cells were trypsinized and stained with SytoxBlue (Invitrogen, Carlsbad, CA, USA) to distinguish the dead cells. Vybrant DyeCycle Ruby stain (Invitrogen) was applied to quantify DNA in living cells for 30 minutes in 37°C. Stained cells were analyzed by flow cytometry (LSRFortessa, BD Biosciences, Franklin Lakes, NJ, USA) using filter1 (Em: 680 nm) for signal acquisition, and analysis was done by using Flowjo (v9) software (Tree Star Inc, Ashland, OR, USA). After 48 hours of treatment, cells were trypsinized and stained with Annexin V-APC (Invitrogen) and SytoxBlue (Invitrogen) for 15 minutes before being analyzed by flow cytometry (LSRFortessa, BD Biosciences) using filter1 (Em: 680 nm) and filter2 (Em: 480 nm) for Annexin V and SytoxBlue staining, respectively. Data analysis was done by using Flowjo (v9) software (Tree Star).
Fu X., Creighton C.J., Biswal N.C., Kumar V., Shea M., Herrera S., Contreras A., Gutierrez C., Wang T., Nanda S., Giuliano M., Morrison G., Nardone A., Karlin K.L., Westbrook T.F., Heiser L.M., Anur P., Spellman P., Guichard S.M., Smith P.D., Davies B.R., Klinowska T., Lee A.V., Mills G.B., Rimawi M.F., Hilsenbeck S.G., Gray J.W., Joshi A., Osborne C.K, & Schiff R. (2014). Overcoming endocrine resistance due to reduced PTEN levels in estrogen receptor-positive breast cancer by co-targeting mammalian target of rapamycin, protein kinase B, or mitogen-activated protein kinase kinase. Breast Cancer Research : BCR, 16, 430.
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3

Isolation of mT3-2D-GFP and KP1 Cancer Cells

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For the RNA-seq experiments, six mT3–2D-GFP WT and 5 SCID tumors were processed into single-cell suspensions as described above. The cells were stained with Helix NP Blue (Biolegend, #425305) and live GFP+ cells were isolated using a BD FACSAria IIu fluorescence-activated cell sorting (FACS) cytometer. Sorted cells were then snap frozen in liquid nitrogen. For sorting mT3–2D-GFP/Luc malignant cells from the tumors, Sytox Blue (Thermofisher Scientific, #34857) staining was used, and live GFP+ cells were isolated via FACS. To sort KP1 cells, tumors were processed into single-cell suspensions as stated. Cells were then stained with Sytox Blue (Thermofisher Scientific, #34857), CD45 (clone 30-F11; BioLegend #103115), and CD44 (clone IM7; BioLegend #103047), and Live CD44+CD45− cells were selected.
Ajina R., Malchiodi Z.X., Fitzgerald A.A., Zuo A., Wang S., Moussa M., Cooper C.J., Shen Y., Johnson Q.R., Parks J.M., Smith J.C., Catalfamo M., Fertig E.J., Jablonski S.A, & Weiner L.M. (2021). Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance. Cancer immunology research, 9(4), 386-400.
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4

Bacterial Growth Curve Measurement

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P. aeruginosa strains were inoculated into test tubes (16 mm diameter) containing 2 mL CA-MHB and grown at 37°C, shaking at 250 rpm. After 4–5 h of growth, inocula were diluted 100-fold into 2 mL BSM in test tubes. After overnight growth (16 h), cells were diluted to an optical density at 600 nm (OD600) of 0.001–0.005 in a 250 mL baffled Erlenmeyer flask with 25 mL BSM and cultured at 37°C. OD600 readings were measured hourly on a Biotek multimode plate reader for 12 h and again at 16 and 28 h. For E. coli growth curves, cells were inoculated in LB and diluted 200-fold into Gutnick-glucose media for overnight growth. After overnight growth (16 h), E. coli was diluted to OD600 <0.01 in flasks of 25 mL Gutnick-glucose media. For growth curves with SytoxBlue (ThermoFisher S11348), SytoxBlue dye was added to media for a final concentration of 2.5 µM.
Hare P.J., Gonzalez J.R., Quelle R.M., Wu Y.I, & Mok W.W. (2023). Metabolic and transcriptional activities underlie stationary-phase Pseudomonas aeruginosa sensitivity to Levofloxacin. Microbiology Spectrum, 12(1), e03567-23.
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5

Flow Cytometry Analysis and Sorting

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For flow cytometry analysis and sorting, cells were washed in FACS buffer (1% FBS in PBS) before antibody staining. For the CLL patient derived PBMC staining a FITC-conjugated CD19 antibody (HIB19, 302206, Biolegend) was used at 1:50 dilution. For live/ dead cell discrimination Sytox Blue was used according to the manufacturer’s instructions (Thermo Fisher, S34857). FACS analysis was conducted on a BD Bioscience Fortessa flow cytometer at the Whitehead Institute Flow Cytometry core. Data was analyzed using FlowJo software v10.4.2. Cell sorting was conducted using the Sony SH800 sorter with a 100 μm chip at the Broad Institute Flow Cytometry Facility. Sytox Blue (ThermoFisher) was used for live/ dead cell discrimination.
Lareau C.A., Ludwig L.S., Muus C., Gohil S.H., Zhao T., Chiang Z., Pelka K., Verboon J.M., Luo W., Christian E., Rosebrock D., Getz G., Boland G.M., Chen F., Buenrostro J.D., Hacohen N., Wu C.J., Aryee M.J., Regev A, & Sankaran V.G. (2020). Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature biotechnology, 39(4), 451-461.
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6

Flow Cytometry Analysis and Sorting

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For flow cytometry analysis and sorting, cells were washed in FACS buffer (1% FBS in PBS) before antibody staining. For the CLL patient derived PBMC staining a FITC-conjugated CD19 antibody (HIB19, 302206, Biolegend) was used at 1:50 dilution. For live/ dead cell discrimination Sytox Blue was used according to the manufacturer’s instructions (Thermo Fisher, S34857). FACS analysis was conducted on a BD Bioscience Fortessa flow cytometer at the Whitehead Institute Flow Cytometry core. Data was analyzed using FlowJo software v10.4.2. Cell sorting was conducted using the Sony SH800 sorter with a 100 μm chip at the Broad Institute Flow Cytometry Facility. Sytox Blue (ThermoFisher) was used for live/ dead cell discrimination.
Lareau C.A., Ludwig L.S., Muus C., Gohil S.H., Zhao T., Chiang Z., Pelka K., Verboon J.M., Luo W., Christian E., Rosebrock D., Getz G., Boland G.M., Chen F., Buenrostro J.D., Hacohen N., Wu C.J., Aryee M.J., Regev A, & Sankaran V.G. (2020). Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature biotechnology, 39(4), 451-461.
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7

Phenotypic Profiling of AML and HSC

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Compounds were purchased from Tocris Bioscience, Cedarlane or Sigma-Aldrich. Primary AML cells or CD34+ enriched human cord blood cells were plated as described above. Candidate molecules or dimethyl sulfoxide (DMSO; Fisher Scientific) were added to the cells at specified concentrations and incubated for 6 days for 8227 AML cells and 4 days for primary AML and cord blood samples. Cells were analyzed by flow cytometry. Briefly, for AML cells, phenotype and viability were assessed using CD34-APC or APC-Cy7 (581), CD38-PE (HB-7), CD15-FITC (HI98), SYTOX Blue (Life Technologies) and when necessary CD33-APC (WM53) and CD14-AlexaFluor 700 (HCD14). HSC phenotype and viability were assessed using CD34-APC-Cy7, CD33-APC, CD38-PE, CD19-PerCP-Cy5.5 (HIB19), CD15-FITC and SYTOX Blue (Life Technologies). All antibodies were purchased from Biolegend. Flow cytometry was performed using a LSRFortessa fitted with a high-throughput sampler (BD Biosciences).
Laverdière I., Boileau M., Neumann A.L., Frison H., Mitchell A., Ng S.W., Wang J.C., Minden M.D, & Eppert K. (2018). Leukemic stem cell signatures identify novel therapeutics targeting acute myeloid leukemia. Blood Cancer Journal, 8(6), 52.
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8

Quantifying Apoptosis in Tri-PyMT Cells

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To determine apoptosis of RFP+ and GFP+ cells, Tri-PyMT cells (Passage 10) were seeded on adherent 6-well plates (1×106 cells), and treated with 4-Hydroperoxy Cyclophosphamide (Santa Cruz) for 48 hours. After treatment, cells were trypsinized and stained with APC conjugated Annexin V (BD Biosciences) and SYTOX Blue (Invitrogen) for apoptotic cells labeling. The stained cells were analyzed in the LSRII flow cytometer to quantify the percentage of apoptotic, dead, and live RFP+ and GFP+ cells by FACS Diva software. To determine the viability of Tri-PyMT Control and +miR-200 cells treated with CTX, cells were plated in 96-well adherent black-walled plates (1×104 cells), and treated with 4-Hydroperoxy Cyclophosphamide for 48 hours. After treatment, cell viability was measured with the CellTiter-Glo® Luminescent Cell Viability Assay (Promega).
Fischer K.R., Durrans A., Lee S., Sheng J., Li F., Wong S., Choi H., El Rayes T., Ryu S., Troeger J., Schwabe R.F., Vahdat L.T., Altorki N.K., Mittal V, & Gao D. (2015). EMT is not required for lung metastasis but contributes to chemoresistance. Nature, 527(7579), 472-476.
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9

CCR7 Expression Analysis by Flow Cytometry

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300–19 cells were washed with PBS, incubated for 10 min at RT with monoclonal anti-mouse CD16/CD32 antibody (Fc block) and then stained for 20 min at 4°C with anti-human CCR7-APC in staining buffer (PBS + 0.5% FCS, pH 7.4). Unbound antibody was removed by two washing steps with staining buffer, and SYTOX Blue (Invitrogen; LuBio) was added as a dead cell indicator. All samples were filtered (50 μM Cup Filcons; BD Biosciences), measured with an LSRII flow cytometer using the FACSDiva 6 software, and analyzed with the FlowJo software (BD Biosciences).
Jørgensen A.S., Larsen O., Uetz-von Allmen E., Lückmann M., Legler D.F., Frimurer T.M., Veldkamp C.T., Hjortø G.M, & Rosenkilde M.M. (2019). Biased Signaling of CCL21 and CCL19 Does Not Rely on N-Terminal Differences, but Markedly on the Chemokine Core Domains and Extracellular Loop 2 of CCR7. Frontiers in Immunology, 10, 2156.
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10

Fluorescent Staining for Cell Analysis

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DRAQ5™ staining was undertaken using the manufacturer’s instruction (BioStatus Ltd., Loughborough, UK). Briefly, 1 × 105 cells were suspended in 1 ml of 5 µmol/l DRAQ5™ in 0·9 × PBS containing 2% FBS and kept in the dark for 15 min at room temperature. Cells were pelleted by centrifugation at 200 × g for 5 min at room temperature and analysed by flow cytometry without washing. Dead cells were excluded by incubation with TO-PRO®-1 iodide (Invitrogen, Eugene, OR, USA) in the case of both wild-type and Tg(gata1:dsRed) lines or SYTOX® Blue (Invitrogen) in the case of the Tg(myb:GFP) line. A filter of Per-Cp-Cy5 was set to detect the emitted fluorescent signal of DRAQ5™. Cells were sorted into RNAlater® (Life Technologies, Carlsbad, CA, USA) for gene expression analysis and into 0·9 × PBS containing 2% FBS for morphological analysis. Flow cytometry and cell sorting were performed using a BD FACSAria (BD Bioscience, San Jose, CA, USA).
Kulkeaw K., Inoue T., Ishitani T., Nakanishi Y., Zon L.I, & Sugiyama D. (2017). Purification of zebrafish erythrocytes as a means of identifying a novel regulator of haematopoiesis. British journal of haematology, 180(3), 420-431.
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