Prism 9.0.1 for macos

Manufactured by GraphPad

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GraphPad Prism 9.0.1 for macOS is a scientific data analysis and graphing software. It provides tools for data analysis, curve fitting, and graph creation. The software is designed for use on macOS operating systems.

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Lab products found in correlation

Instantblue coomassie stain, by Abcam (1 mentions) Nupage bis tris gel, by Thermo Fisher Scientific (1 mentions) Ti2 e, by Nikon (1 mentions) Prestoblue, by Thermo Fisher Scientific (1 mentions) Synergy h1 plate reader, by Agilent Technologies (1 mentions) Synergy h1, by Agilent Technologies (1 mentions) One glo buffer, by Promega (1 mentions)

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Prism 9 (24382 citations) Prism 9 for macOS (91 citations) Prism for MacOS (29 citations) GraphPad 9.0 Prism (7 citations) Prism Graphpad 9.1.0 for MacOs (2 citations) Prism 9.1.1 for MacOS (2 citations)

7 protocols using prism 9.0.1 for macos

Opioid Dose Equivalence Calculation

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Descriptive statistics were used with continuous variables reported as medians, interquartile ranges (IQRs) and ranges. To compare the doses ingested for differing opioids, an oral morphine equivalent dose (OME) was calculated using the table synthesised by Nielsen et al.
⁹ (link) with multiplication factors of the following: parenteral buprenorphine × 75, sublingual buprenorphine × 38.8, codeine × 0.1, oral dextropropoxyphene × 0.1, parenteral fentanyl × 0.2, transdermal fentanyl × 2.7, oral hydromorphone × 5, parenteral morphine × 3, oral oxycodone × 1.5, parenteral pethidine × 0.4, oral tapentadol × 0.4 and oral tramadol × 0.4. Dose equivalents for heroin and methadone were not performed. All analyses were performed in GraphPad Prism 9.0.1 for Mac OS (GraphPad Software, San Diego, CA, USA).

Isoardi K.Z, & Isbister G.K. (2023). Opioid poisoning in Newcastle over the last three decades: From heroin to prescription opioids. Emergency Medicine Australasia, 35(6), 946-952.

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Particle Size Analysis of Biomolecules

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All sizing and polydispersity measurements were carried out on an Uncle by Unchained Labs (USA) at 25°C in triplicate. Samples were adjusted to the indicated concentrations in 150 mM KCl and 20 mM of the following buffers based on pH: HEPES, pH 7.2; Tris–HCl, pH 8.2; CAPS, pH 10.2. Samples were analyzed both before and after a centrifugation step at 20,000 rcf for 10 min as indicated. Data were exported, further tabulated, graphed, and analyzed using GraphPad Prism 9.0.1 for macOS (GraphPad Software, San Diego, CA, https://www.graphpad.com).

Basalla J.L., Mak C.A., Byrne J.A., Ghalmi M., Hoang Y, & Vecchiarelli A.G. (2023). Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB. eLife, 12, e81362.

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Centrifugation-Based Quantification of McdB Condensation

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Centrifugation was used to quantify the degree to which McdB and its variants condensed under certain conditions, as previously described (Alberti et al., 2019 (link)). Briefly, 100 µl of sample was incubated at the conditions specified for 30 min, and then centrifuged at 16,000 rcf for 2 min. The supernatant was removed and the pellet resuspended in an equal volume of McdB solubilization buffer [300 mM KCl, 20 mM CAPS, pH 10.2]; McdB does not condense at pH 10.2. Samples were then diluted into 4× Laemmli SDS–PAGE sample buffer. Pellet and supernatant fractions were visualized on a 4–12% Bis-Tris NuPAGE gel (Invitrogen) by staining with InstantBlue Coomassie Stain (Abcam) for 1 hr and then destaining in water for 14–16 hr. The intensities of the bands were quantified using Fiji v 1.0 and resultant data graphed using GraphPad Prism 9.0.1 for macOS (GraphPad Software, San Diego, CA, https://www.graphpad.com).

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Fluorescence Recovery After Photobleaching Assay

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All FRAP measurements were performed using the indicated protein concentration with the addition of 1:1000 mNG-McdB based on molarity. All fluorescence imaging was performed using a Nikon Ti2-E motorized inverted microscope controlled by NIS Elements software with a SOLA 365 LED light source, a ×100 objective lens (Oil CFI60 Plan Apochromat Lambda Series for DIC), and a Photometrics Prime 95B Back-illuminated sCMOS camera. mNG signal was acquired using a ‘GFP’ filter set [excitation, 470/40 nm (450–490 nm); emission, 525/50 nm (500–550 nm); dichroic mirror, 495 nm]. Bleaching was conducted with a 405-nm laser at 40% power (20 mW) with a 200-μs dwell time. Recovery was monitored with a time-lapse video with 5-s intervals for 20 min. Image analysis was done in Fiji v 1.0. Intensities from bleached regions of interest were background subtracted and normalized using an unbleached condensate to account for any full field of view photobleaching. The values for each condensate were then normalized such that a value of 1 was set to the pre-bleach intensity and a value of 0 was set to the intensity immediately post-bleaching. Data were exported, further tabulated, graphed, and analyzed using GraphPad Prism 9.0.1 for macOS (GraphPad Software, San Diego, CA, https://www.graphpad.com).

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Quantitative Analysis of Carboxysome Localization

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Image analysis including cell segmentation, quantification of cell length, foci number, intensity and spacing were performed using Fiji plugin MicrobeJ 5.13I (Ducret et al., 2016) . Cell perimeter detection and segmentation were done using the rod-shaped descriptor with default threshold settings. Carboxysome detection was performed using the smoothed foci function with tolerance of 50 and Z-score of 30. Data were exported, further tabulated, graphed and analyzed using GraphPad Prism 9.0.1 for macOS, GraphPad Software, San Diego, California USA, www.graphpad.com. Bacterial Two-Hybrid N -terminal T18 and T25 fusions of McdA, all McdA mutant variants, and McdB were constructed using the plasmids pKT25 and pUT18C. Plasmids were sequence-verified and co-transformed into E. coli BTH101 in both pairwise combinations (Karimova et al., 1998) . Several colonies of T18/T25 cotransformants were cultured in LB medium with 100 mg/ml ampicillin, 50 mg/ml kanamycin and 0.5 mM IPTG overnight at 30 C with 225 rpm shaking. Overnight cultures were spotted on indicator LB Xgal plates supplemented with 100 mg/ml ampicillin, 50 mg/ml kanamycin and 0.5 mM IPTG. Plates were incubated in the dark at 30˚C up to 48 hours before imaging.

Hakim P., & Vecchiarelli A.G. (2021). Dissection of the ATPase active site of McdA reveals the sequential steps essential for carboxysome distribution.

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Cell Viability Assay with PrestoBlue

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HEp-2 or primary HAE cells were seeded at 50% confluence in 96-well plates and incubated with threefold serial dilution of compound with positive and negative controls as described above. After 48-hour incubation at 37°C, cells were incubated with PrestoBlue (Thermo Fisher Scientific, catalog no. A-13262) for 1 hour at 37°C and fluorescence was measured with an H1 synergy plate reader (BioTek). CC₅₀ and 95% CIs after normalized nonlinear regression and variable slope were determined using Prism 9.0.1 for MacOS (GraphPad).

Sourimant J., Lieber C.M., Yoon J.J., Toots M., Govindarajan M., Udumula V., Sakamoto K., Natchus M.G., Patti J., Vernachio J, & Plemper R.K. (2022). Orally efficacious lead of the AVG inhibitor series targeting a dynamic interface in the respiratory syncytial virus polymerase. Science Advances, 8(25), eabo2236.

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Luciferase-based Dose-Response Assay for RSV

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Compound stocks were prepared in dimethyl sulfoxide (DMSO) and, upon dilution in cell culture medium, reached in all wells a final DMSO concentration of 0.1%. For luciferase-based dose-response assays, HEp-2 or primary HAE cells were seeded a day before to reach 50% confluence in 96-well white plates. Threefold serial dilutions of compounds were prepared in triplicate using an automated Nimbus liquid handler (Hamilton) and transferred to the cells. Immediately after addition of compound, cells were infected with recRSV-fireSMASh. Each plate contained four wells each of positive and negative control (medium containing 100 μM cycloheximide or vehicle, respectively). Luciferase activities were determined at 48 hours after transfection using One-GLO buffer (Promega, catalog no. E6130) and a Synergy H1 (BioTek) plate reader. Normalized luciferase activities were analyzed with the following formula: % inhibition = (Signal_sample – Signal_min)/(Signal_max – Signal_min) × 100, and dose-response curves were further analyzed by normalized nonlinear regression with variable slope to determine EC₅₀ and 95% confidence intervals (CIs) with Prism 9.0.1 for MacOS (GraphPad).

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