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Propidium iodide dye

Manufactured by Thermo Fisher Scientific
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Propidium iodide is a fluorescent dye that intercalates with DNA. It is commonly used in flow cytometry to stain and measure DNA content in cells.

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11 protocols using propidium iodide dye

1

Visualizing Cytoskeletal Actin Microfilaments

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The immunofluorescent microscopy of cytoskeletal actin microfilaments was provided using an inverted confocal microscopy system (Leica, TCS SP5). Treated (stimulated) and non‐treated cells fixed by 4% methanol‐free formaldehyde (Sigma‐Aldrich, Pro. No. 489417, Merck, Pro. No. 1‐27‐3228) solution and gently washed three times with phosphate‐buffered saline (PBS, Gibco, Pro. No. 70011‐044). The fixed cells were permeabilized using 0.2% Triton‐X100 (Sigma‐Aldrich, Pro. No. T8787) in PBS for 20 min and then gently washed three times with PBS. Blocking was provided using 1% bovine serum albumin (BSA, Sigma‐Aldrich, Pro. No. A5611) diluted with PBS in the incubator (37℃, 5% CO2, RH ~95%) for 1 h. In the next step, BSA was aspirated, and actin dye Alexa Fluor® 488 Phalloidin (Invitrogen, Cat. No. A12379) was added to the cells and maintained for 45 min in an incubator (37℃, 5% CO2, RH ~95%). Propidium iodide dye (PI, Invitrogen, Cat. No. P3566) was used to stain the cell nucleus. In the final step, inverted confocal microscopy (Zeiss, LSM 800) at 1000× magnification was used to obtain the cell images.
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2

Quantifying Cellular Proliferation and Cell Cycle Dynamics

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NPC proliferation assay was performed using the Click-it EdU Alexa Fluor 488 imaging kit (Invitrogen) in biological triplicates. EdU was added at a concentration of 10 µM in media incubated for an hour at 37 °C. Subsequently, cells were fixed and immunocytochemistry performed using the EdU detection cocktail and DAPI. The ratio of EDU positive to DAPI positive nuclei gave the percentage of cells in the proliferative phase.
Cell cycle assays were performed in LCLs fixed in 70% ethanol and subsequently incubated with Propidium Iodide dye (Invitrogen) at 15 ug/ml and RNase A (Invitrogen) at 40 ug/ml at 37 °C for 30 min. Flow cytometry was performed as described earlier. FlowJo software was used for the analysis. Appropriate gates were applied on scatter plot using parameters required to remove debris and clumps from analysis while including only singlet cells. A histogram plot was generated for the gated singlet cells. The histogram plot was analyzed to estimate the percentage of cells in different phases of cell-cycle (Supplementary Figure 1D, E).
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3

Fluorescence Microscopy of YFP-Expressing Roots

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Detection of YFP was achieved using a YFP filter (excitation, 488 nm; emission, 505–550 nm) and a Karl Zeiss Lsm880 or a Nikon Eclipse TE-2000 Model-E2 confocal microscope. Roots were mounted in propidium iodide dye (Invitrogen) and the imaging settings were 488 nm excitation and >585 nm emission.
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4

Iron Quantification in Cell Lysates

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Namalwa and Raji B cells were lysed in 1 mL RIPA buffer, and iron concentration in lysates was determined using the QuantiChromTM Iron Assay Kit (Bioassay Systems, Hayward, CA, United States). The number of live/dead cells was determined by flow cytometry using propidium iodide dye (Invitrogen).
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5

Immunoblotting and Cell Viability Assays

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The antibodies used in this experiment, including primary (Bak, Bax, Bcl-2, PARP, cleaved caspase 3, cleaved caspase 9, E-cadherin, N-cadherin, DVL-2, DVL-3, c-Myc, Cyclin B1, β-catenin, Histone 3 and β-actin) and secondary (secondary anti-mouse, secondary anti-mouse) antibodies, and anti-rabbit IgG (R) Alexa Fluor® 488 molecular probe and Anti-mouse IgG (R) Alexa Fluor® 488 molecular probe were purchased from Cell Signaling Technology (Danvers, MA, USA). Propidium iodide (PI) dye was purchased Life Technologies (Eugene, Oregon, USA). Fluoroshield mounting medium, containing 4',6-diamidino-2-phenylindole dihydrochloride (DAPI), was purchased from Abcam (Cambridge, MA, USA). Crystal violet dye was purchased from Sigma-Aldrich (St. Louis, MO, USA). Dulbecco's Modified Eagle Medium (DMEM) was purchased from GE Healthcare Life Sciences and HyClone Laboratories (Logan, Utah, USA). Green cytotox, Annexin red and caspase 3/7 IncuCyte reagents were purchased from Essen BioScience (Ann Arbor, MI 48108, USA). The 6.5 mm diameter inserts, with 8.0 μM pore size polycarbonate membrane for 24 well plates, were purchased from Corning Incorporated (One Riverfront Plaza Corning, NY 14831, USA). Growth-factor-reduced matrigel was purchased from BD Biosciences (Ontario, Canada).
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6

Cell Migration and Proliferation Assay

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Primary and secondary antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA). Propidium iodide (PI) dye was purchased from Life Technologies (Eugene, Oregon, USA). Dulbecco’s modified Eagle’s medium (DMEM) was purchased from GE Healthcare Life Sciences, HyClone Laboratories (Logan, UT, USA). The 0.25% trypsin + 2.2 mM ethylenediaminetraacetic acid (EDTA) and phosphate-buffered saline (PBS) were purchased from Mediatech, Inc. (Corning subsidiaries, Manassas, VA, USA). Crystal violet dye powder was purchased from Sigma-Aldrich (St. Louis, MO, USA). Corning® transwell inserts (24 mm Transwell with 8.0-μm pore polycarbonate membrane inserts, TC-treated, w/lid, sterile, 24/cs) were purchased from Sigma-Aldrich (St. Louis, MO, USA). The compound 3-(4,5dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide (MTT) was purchased from Calbiochem EMD Millipore (Billerica, MA, USA). Clarity™ and Clarity Max™ Western ECL blotting substrates were purchased from Bio-Rad Laboratories (Hercules, CA, USA).
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7

Live/Dead Cell Viability Assay

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hOLs viability was assessed by live staining using propidium iodide dye (PI; ThermoFisher Scientific). The average number of PI+ (dead cells) and total cell number (Hoechst) per condition was determined via Leica TSC SP8 confocal microscope and ImageJ. For apoptosis assay, cells were incubated in the presence of Cell Event Caspase 3/7 detection reagent (C10423, Invitrogen) for 1 h at 37 °C.
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8

Sperm Assay with Chemical Treatments

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All the chemicals were purchased from Sigma-Aldrich, UK, unless stated otherwise. The sperm preparation gradients (PureCeption 40% and 80%) and Quinn’s Advantage Sperm Washing Medium (SWM) were purchased from CooperSurgical, Inc., US. The allophycocyanin (APC)-conjugated Mouse Anti-Human CD46 (Clone E4.3) was purchased from BD Biosciences, Berkshire UK. The AlexaFluor 488 PNA and propidium iodide dye were purchased from ThermoFisher, UK. The progesterone (P4) and prostaglandin E1 (PGE1) were dissolved in DMSO. The final concentration of the DMSO in an experiment is maximally 0.02% v/v. The concentration of the compounds was 10 μM P4, 5 mM PGE1, 30 mM ammonium chloride (NH4Cl), 10 mM 17α-hydroxyprogesterone (P4OH) and 5 mM prostaglandin E2 (PGE2). The concentrations of the CatSper agonist are at EC100 values.
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9

Cell Labeling for Co-culture Experiments

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In the co-culture experiments, the iPS-MSCs-CD cells were labeled with copGFP
while HCC1806 cells were labeled with CellTracker Red (catalog number
C34552, Thermo Fisher Scientific, Waltham, MA, USA) as recommended by the
manufacturer. Very briefly, cells were washed with PBS and
10 μM dye was added to one million cells for
30 min. Afterwards, the unattached dye was removed by PBS washing and
centrifugation. For the detection of dead cells, propidium iodide dye
(catalog number P3566, Thermo Fisher Scientific) or trypan blue dye (catalog
number 15250061, Thermo Fisher Scientific) was used according to the
manufacturer’s instructions.
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10

Monocyte-Derived Dendritic Cell Expansion and Influenza-Specific T Cell Activation

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Monocyte-derived DCs (mo-DCs) were generated from purified CD14+ monocytes in the presence of IL-4 (25 ng/mL; R&D Systems) and GM-CSF (20 ng/mL; sagramostim [LEUKINE], Genzyme) and matured with LPS (25 ng/mL; MilliporeSigma) as previously described (26 (link)). For antigen-specific T cell stimulation, mature mo-DCs from HLA-A2+ donors were pulsed with 1 μg/mL HLA A2–restricted influenza matrix peptide (Flu-MP) (sequence GILGFVFTL, AnaSpec, catalog AS-28310) and cocultured with autologous T cells at a DC/T cell ratio of 1:20 in the presence of IL-2 (20 U/mL). After 1 week, T cells were restimulated with additional Flu-MP–loaded DCs in the presence of IL-2 (20 U/mL), IL-7 (5 U/mL), and IL-15 (5 U/mL). Flu-MP–specific T cells were identified by MHC tetramers (iTag Tetramer HLA-A2 Influenza-M1 [GILGFVFTL], MLB International) and sorted after 2 weeks of culturing (26 (link)). Fresh propidium iodide (PI) dye (10 μg) (Invitrogen, Thermo Fisher Scientific) was used in some experiments to monitor tumor cell lysis. For experiments relating to entry of antigen-specific T cells, antigen-loaded (or unpulsed) DCs were added to tumor colonies 4 hours prior to the addition of T cells. For some experiments, DCs were preincubated with 50 μg/mL α–MHC-1 (clone W6/32, BioLegend) or an isotype control for 1 hour at 37°C prior to peptide loading.
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