Epu automated acquisition software

Manufactured by Thermo Fisher Scientific

EPU automated acquisition software is a tool used for controlling and automating the data collection process for cryo-electron microscopy (cryo-EM) experiments. It provides a user-friendly interface for setting up and executing acquisition workflows, allowing researchers to efficiently capture high-quality image data for structural biology studies.

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Lab products found in correlation

Titan krios microscope, by Thermo Fisher Scientific (5 mentions) K3 direct electron detector, by Ametek (4 mentions) Vitrobot mark 4, by Thermo Fisher Scientific (4 mentions) Titan krios g4, by Thermo Fisher Scientific (3 mentions) Pelco easiglow glow discharge unit, by Ted Pella (3 mentions) Falcon 3 direct electron detector, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

EPU software (267 citations) EPU Automated Data Acquisition Software for Single Particle Analysis (9 citations) EPU acquisition software (3 citations)

9 protocols using epu automated acquisition software

Cryo-EM Data Acquisition Protocol

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A total of 7,355 raw movies were acquired using a 300 keV Titan Krios microscope (FEI) equipped with a K3 direct electron detector (Gatan) operated in electron counting mode using the EPU automated acquisition software (ThermoFisher) with “Faster Acquisition” mode (AFIS) enabled. A slit width of 20 eV was used for the BioQuantum energy filter. Data were collected at a pixel size of 0.86 Å/pixel using a defocus range of -2.1 to -3.5 μm. Movies were dose-fractionated into 39 fractions over a 4 s exposure resulting in a total dose of 47.4 e^-/Å².

Jones M.L., Aria V., Baris Y, & Yeeles J.T. (2023). How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Molecular Cell, 83(16), 2911-2924.e16.

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Cryo-EM Structural Analysis of SARS-CoV-2 S Protein

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For cryo-EM, 2.25 mg/mL S protein was vitrified on Quantifoil R1.2/1.3 Cu mesh 300 holey carbon grids after a glow discharge of 15 s at 10 mA. For S protein-hACE2 complex (1:1.2 S protein trimer: hACE2 molar ratio) and S protein-mACE2 complex (1:2.1 S protein trimer: mACE2 molar ratio), 2.25 mg/mL mixtures were vitrified on Quantifoil R1.2/1.3 Cu mesh 200 holey carbon grids, coated with 25 nm gold on each side, after a glow discharge of 20 s at 15 mA. All grids were glow discharged using a Pelco easiGlow glow discharge unit (Ted Pella) before 1.8 μL of protein suspension was applied to the surface of the grid at a temperature of 10 °C and a humidity level of >98%. Grids were subsequently blotted (12 s, blot force −10) and plunge frozen into liquid ethane using a Vitrobot Mark IV (ThermoFisher Scientific) plunge freezing device. Grids were imaged using a 300 kV Titan Krios G4 transmission electron microscope (TEM) (Thermo Fisher Scientific) equipped with a Falcon4 direct electron detector in electron event registration (EER) mode. Movies were collected at 155,000× magnification (calibrated pixel size of 0.5 Å per physical pixel) over a defocus range of −0.5 μm to −2 μm with a total dose of 40 e⁻/Å² using EPU automated acquisition software (ThermoFisher Scientific).

Mannar D., Saville J.W., Poloni C., Zhu X., Bezeruk A., Tidey K., Ahmed S., Tuttle K.S., Vahdatihassani F., Cholak S., Cook L., Steiner T.S, & Subramaniam S. (2024). Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein. Nature Communications, 15, 1854.

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Cryo-EM Imaging of Raw Movies

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A total of 6,718 raw movies were acquired using a 300 keV Titan Krios microscope (FEI) equipped with a Falcon III direct electron detector (Thermo) operated in linear mode using the EPU automated acquisition software (ThermoFisher). Data were collected at a pixel size of 1.07 Å/pixel using a defocus range of -0.9 to -3.5 μm. Movies were dose-fractionated into 39 fractions over a 1 s exposure resulting in a total dose of 88.5 e^-/Å².

Jones M.L., Aria V., Baris Y, & Yeeles J.T. (2023). How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Molecular Cell, 83(16), 2911-2924.e16.

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Cryo-EM Data Acquisition Protocol

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A total of 10,825 raw micrographs were acquired in a single dataset using a 300 keV Titan Krios microscope (FEI) equipped with a K3 direct electron detector (Gatan) operated in electron counting mode using the EPU automated acquisition software (ThermoFisher) with “Faster Acquisition” mode (AFIS) enabled. A slit width of 20 eV was used for the BioQuantum energy filter. Data were collected in super-resolution mode and with a binning-factor of 2 yielding an effective pixel size of 1.09 Å/pixel (nominal magnification of 81,000 X), using a defocus range of -1.0 to -2.5 μm and dose-fractionating into 41 fractions per micrograph. An exposure time of 1.7 s achieved a dose of 40.1 e-/Å2 per micrograph.

Xia Y., Sonneville R., Jenkyn-Bedford M., Ji L., Alabert C., Hong Y., Yeeles J.T, & Labib K.P. (2023). DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in C. elegans. Science (New York, N.Y.), 381(6664), eadi4932.

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Cryo-EM Data Acquisition Protocol

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A total of 12,819 raw movies were acquired using a 300 keV Titan Krios microscope (FEI) equipped with a K3 direct electron detector (Gatan) operated in electron counting mode using the EPU automated acquisition software (ThermoFisher) with “Faster Acquisition” mode (AFIS) enabled. A slit width of 20 eV was used for the BioQuantum energy filter. Data were collected in super-resolution mode bin 2 at an effective pixel size of 0.86 Å/pixel over a defocus range of -1.8 to -3.5 μm. Movies were dose-fractionated into 39 fractions over a 4 s exposure, resulting in a total dose of 39.2 e^-/Å².

Jones M.L., Aria V., Baris Y, & Yeeles J.T. (2023). How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Molecular Cell, 83(16), 2911-2924.e16.

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Cryo-EM Imaging of Lipid-Polymer Hybrids

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Neat lipid, block copolymer and their hybrid samples for cryogenic transmission electron microscopy were prepared on a lacey carbon-coated 200 mesh grid (Electron Microscopy Sciences) using a Vitrobot Mark IV (Thermo Fisher Scientific). Briefly, 3.5 μL of sample was applied to the glow-discharged surface of the grid at a chamber temperature of 25 °C with a relative humidity level of 100 %, and then vitrified in liquid ethane. Before vitrification samples were blotted for 5 s with a blot force of 1. All Cryo-EM grids were imaged using a 200 keV Glacios (Thermo Fisher Scientific) TEM equipped with a Falcon4 direct electron detector. Images were collected at 120kX magnification (physical pixel size 1.3 Å) with a total dose of 6.9 e⁻/Å² and a defocus of −5 μm using EPU automated acquisition software (Thermo Fisher).

, & Johnston M. (2000). Unrest in the West. CMAJ: Canadian Medical Association Journal, 163(12), 1583.

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Cryo-EM Data Acquisition Protocol

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SARS-CoV-2 S Trimer Beta Mutant Cryo-EM

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For cryo-EM, SARS-CoV-2 S trimer Beta mutant were deposited on grids at a final concentration of 2 mg/mL. Complexes were prepared by incubating S trimer Beta mutant with VH F6 at a molar ratio of 1:10. Grids were cleaned with H2/O2 gas mixture for 15 s in PELCO easiGlow glow discharge unit (Ted Pella) and 1.8 μL of protein suspension was applied to the surface of the grid. Using a Vitrobot Mark IV (Thermo Fisher Scientific), the sample was applied to either Quantifoil Holey Carbon R1.2/1.3 copper 300 mesh grids or UltrAuFoil Holey Gold 300 mesh grids at a chamber temperature of 10°C with a relative humidity level of 100%, and then vitrified in liquid ethane after blotting for 12 s with a blot force of −10. All cryo-EM grids were screened using a 200-kV Glacios (Thermo Fisher Scientific) TEM equipped with a Falcon4 direct electron detector and data were collection on a 300-kV Titan Krios G4 (Thermo Fisher Scientific) TEM equipped with a Falcon4 direct electron detector in electron event registration (EER) mode. Movies were collected at 155,000× magnification (physical pixel size 0.5 Å) over a defocus range of −3 μm to −0.5 μm with a total dose of 40 e – /Å2 using EPU automated acquisition software (Thermo Fisher).

Chen C., Saville J.W., Marti M.M., Schäfer A., Cheng M.H., Mannar D., Zhu X., Berezuk A.M., Banerjee A., Sobolewski M.D., Kim A., Treat B.R., Da Silva Castanha P.M., Enick N., McCormick K.D., Liu X., Adams C., Hines M.G., Sun Z., Chen W., Jacobs J.L., Barratt-Boyes S.M., Mellors J.W., Baric R.S., Bahar I., Dimitrov D.S., Subramaniam S., Martinez D.R, & Li W. (2022). Potent and broad neutralization of SARS-CoV-2 variants of concern (VOCs) including omicron sub-lineages BA.1 and BA.2 by biparatopic human VH domains. iScience, 25(8), 104798.

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Cryo-EM Analysis of SARS-CoV-2 S Trimer Beta Mutant

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For cryo-EM, SARS-CoV-2 S trimer Beta mutant were deposited on grids at a final concentration of 2 mg/ml. Complexes were prepared by incubating S trimer Beta mutant with V_H F6 at a molar ratio of 1:10. Grids were cleaned with H2/O2 gas mixture for 15 s in PELCO easiGlow glow discharge unit (Ted Pella) and 1.8 μl of protein suspension was applied to the surface of the grid. Using a Vitrobot Mark IV (Thermo Fisher Scientific), the sample was applied to either Quantifoil Holey Carbon R1.2/1.3 copper 300 mesh grids or UltrAuFoil Holey Gold 300 mesh grids at a chamber temperature of 10°C with a relative humidity level of 100%, and then vitrified in liquid ethane after blotting for 12 s with a blot force of −10. All cryo-EM grids were screened using a 200-kV Glacios (Thermo Fisher Scientific) TEM equipped with a Falcon4 direct electron detector and data were collection on a 300-kV Titan Krios G4 (Thermo Fisher Scientific) TEM equipped with a Falcon4 direct electron detector in electron event registration (EER) mode. Movies were collected at 155,000× magnification (physical pixel size 0.5 Å) over a defocus range of −3 μm to −0.5 μm with a total dose of 40 e – /Å2 using EPU automated acquisition software (Thermo Fisher).

Chen C., Saville J.W., Marti M.M., Schäfer A., Cheng M.H., Mannar D., Zhu X., Berezuk A.M., Banerjee A., Sobolewski M.D., Kim A., Treat B.R., Da Silva Castanha P.M., Enick N., McCormick K.D., Liu X., Adams C., Hines M.G., Sun Z., Chen W., Jacobs J.L., Barratt-Boyes S.M., Mellors J.W., Baric R.S., Bahar I., Dimitrov D.S., Subramaniam S., Martinez D.R, & Li W. (2022). Potent Neutralization of Omicron and other SARS-CoV-2 Variants of Concern by Biparatopic Human VH Domains. bioRxiv.

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