Resources and Equipment
Sample Analysis & Preparation
| Location | Equipment Name | Use | Equipment Description |
|---|---|---|---|
| CEMRC, Wright lab | Baker SterilGard III Advance | Biosafety cabinet | Biosafety cabinet: An enclosed, ventilated laboratory workspace for safely working with materials contaminated with (or potentially contaminated with) pathogens requiring a defined biosafety level (BSL1 or BSL2). |
| CEMRC, Wright lab | Labnet 311DS | Incubator | Shaking and stationary incubators for culturing prokaryotes or maintaining reagents at a specified temperature. |
| CEMRC, Wright lab | VWR 2375T CO2 Incubator | CO2 incubator | CO2 incubator for culturing of cells that require specified atmospheric conditions. |
| MCCET, Wright lab | CellBox travel incubator | CO2 incubator (transportable) | Portable CO2 incubator for live cell transport. |
| CEMRC | PELCO easiGlow | Grid Preparation | EM grid cleaning: Plasma-cleaner used under regular vacuum conditions to alter grid hydrophobicity. |
| MCCET, CEMRC | EMS Glo-Qube | Grid Preparation | EM grid cleaning: Plasma-cleaner that can be used under regular vacuum conditions or with the addition of amylamine to alter grid hydrophobicity. |
| MCCET | Leica ACE600 with platinum/gold sputter head | Grid Preparation | EM grid modification: Plasma-cleaner used under regular vacuum conditions; carbon evaporation of additional carbon layer to EM grids or other substrates |
| CEMRC | Leica ACE600 | Grid Preparation | EM grid modification: Plasma-cleaner used under regular vacuum conditions; carbon evaporation of additional carbon layer to EM grids or other substrates |
| MCCET | Leica EM-GP 2 | Grid Plunge Freezing | Automated environmentally controlled EM grid plunge freezer used to freeze macromolecules, viruses, and cells. Used at 4-50ºC, 0-100% humidity, and with single-sided blotting. |
| Wright Lab | Leica EM-GP | Grid Plunge Freezing | Automated environmentally controlled EM grid plunge freezer used to freeze macromolecules, viruses, and cells. Used at 4-50ºC, 0-100% humidity, and with single-sided blotting. |
| MCCET, CEMRC, Wright lab | ThermoFisher Scientific Vitrobot Mark IV | Grid Plunge Freezing | Automated environmentally controlled EM grid plunge freezer used to freeze macromolecules, viruses, and cells. Used at 4-50ºC, 0-100% humidity, and with double-sided blotting. |
| Wright lab | Gatan CP3 with gentle-blot blotting | Grid Plunge Freezing | Semi-automated environmentally controlled EM grid plunge freezer used to freeze macromolecules, viruses, and cells. Used at 4-50ºC, 0-100% humidity, and with double- and single-sided blotting. |
| Wright lab | Manual plunge freezer | Grid Plunge Freezing | A semi-automated EM grid plunge freezer used to freeze macromolecules, viruses, and cells. Used at locations where the global environment is controlled. Single-sided manual blotting. Can be transported to different locations for grid preparation. |
| MCCET | Leica EM ICE | High-pressure freezing | Automated high-pressure freezer used to cryo-preserve tissue blocks, viruses, cells, and macromolecules for downstream processing by cryo-FIB milling/cryo-ultramicrotomy or freeze-substitution and conventional ultramicrotomy. |
| MCCET | Leica AFS2 | Freeze substitution | Automated system to transition cryo-preserved materials into resin blocks for downstream conventional ultramicrotomy. |
| MCCET | CryoSol-World Vitrojet | Jet freezing | Automated sample vitrification on EM grids: Combines an embedded glow discharger, pin printing technology, and jet vitrification. |
| MCCET, CEMRC, Wright lab | Sub-Angstrom Puck Storage System | Cryo-sample storage | Aluminum puck and dewar system for storing cryo-preserved samples. |
| MCCET, CEMRC, Wright lab | Dry shipper | Dry shipper | Dewar and storage case for shipping cryo-preserved samples. |
Sample Thinning
| Location | Equipment Name | Use | Equipment Description |
|---|---|---|---|
| MCCET | Leica EM UC7 Ultramicrotome | Conventional and Cryo-ultramicrotomy | The ultramicrotome is used for cutting specimens into extremely thin slices, called ultra-thin sections, with a diamond knife. The sections (plastic or vitreous ice) can be studied and documented at different magnifications in a TEM. |
| MCCET | Aquilos 2 with iFLM | Cryo-FIB-SEM for lamella, slice-and-view & lamella liftout | Aquilos 2 Cryo-FIB-SEM with dedicated cryo-stage cooling, a loading and transfer system, field-emission SEM column. Integrated fluorescence (iFLM) imaging for correlative fluorescence light microscopy. |
| CEMRC | Aquilos 2 | Cryo-FIB-SEM for lamella, slice-and-view & lamella liftout | Aquilos 2 Cryo-FIB-SEM with dedicated cryo-stage cooling, a loading and transfer system, field-emission SEM column. |
Light Microscopy (LM)
| Location | Equipment Name | Use | Equipment Description |
|---|---|---|---|
| MCCET | Leica S9 | Stereomicroscope | For the inspection and manipulation of samples. Has a long working distance of 122mm and up to 55x magnification. |
| MCCET | Leica M165 | Stereomicroscope | For the inspection and manipulation of samples. Magnification up to 120x; equipped with fluorescent illumination. Equipped with a polarizing filter for improved inspection of protein and other crystals. |
| MCCET | Leica DMi8 Widefield Florescence Microscope | Widefield microscope | Inverted widefield fluorescent microscope equipped with 10x-63x objectives. Leica DFC9000 Camera. Eight channel fluorescence with Leica LED8 light source. Precision motorized ITK stage. Leica LASX acquisition and processing software. |
| Wright lab | Leica DMi8 Widefield Florescence Microscope | Widefield microscope | Inverted widefield fluorescent microscope equipped with 4x-100x objectives. Hamamatsu Orca Flash 4.0 camera. Märzhäuser Wetzlar motorized stage. Mercury lamp. Tokai Hit stage top incubator for extended live cell imaging. Leica LASX acquisition and processing software. |
| MCCET | Alveole Labs PRIMO 2 Micropatterning System (mounted on the DMi8 microscope) | Grid micropatterning | Alveole Labs PRIMO system is a maskless substrate micropatterning system. It is used to support directed cell positioning and adhesion to EM grids or other substrates to mimic in vivo phenotypes. |
| Wright lab | Alveole Labs PRIMO 2 Micropatterning System (mounted on the DMi8 microscope) | Grid micropatterning | Alveole Labs PRIMO system is a maskless substrate micropatterning system. It is used to support directed cell positioning and adhesion to EM grids or other substrates to mimic in vivo phenotypes. |
| MCCET | Leica Stellaris 5 Cryo-Confocal Microscope | Cryo-confocal microscope | Confocal and widefield light microscope equipped with Leica cryo-stage. 50X/0.9 NA objective capable of super-resolution imaging with Leica Lightning. White light laser for fully tunable excitation wavelengths. TauGating and TauContrast allow separation of signal using fluorescence lifetime. Leica LASX and Coral Cryo acquisition and processing software. |
| Wright Lab | Leica Thunder Cryo-CLEM | Widefield Cryo-CLEM | Leica Cryo-CLEM System with cryo-CLEM stage and transfer shuttle, Leica DM6 FS automated wide-field upright microscope and motorized stage; filter systems for DAPI, GFP, Texas Red (mCherry), YFP, CFP, Cy3, and Cy5. Software for automation and image processing. |
Cryo-TEM (collection)
| Location | Equipment Name | Use | Equipment Description |
|---|---|---|---|
| MCCET | Titan Krios G4i Cryo-TEM | Cryo-TEM 300kV | Cryo-TEM for sample screening, imaging, and tomography data collection. 300 kV TEM with cold-FEG, Volta phase plates, Panther STEM detectors, Falcon 4i direct electron detector, SelectrisX energy filter + Falcon 4i direct electron detector, CETA-D CMOS detector. Software: Velox, EPU, EPU-D, MAPS, Tomo5, SerialEM, and CorRelator. |
| CEMRC | Titan Krios G3i Cryo-TEM | Cryo-TEM 300kV | Cryo-TEM for sample screening, imaging, and tomography data collection. 300 kV TEM with Schottky-FEG, Volta phase plates, STEM detectors, Falcon 3C direct electron detector, Gatan BioQuantum energy filter + K3 direct electron detector, CETA-D CMOS detector. Software: Velox, EPU, EPU-D, MAPS, Tomo5, SerialEM, and CorRelator. |
| CEMRC | Talos Arctica Cryo-TEM | Cryo-TEM 200 kV | Cryo-TEM for sample screening, imaging, and tomography data collection. 200 kV TEM with Schottky-FEG, Volta phase plates, Falcon 3C direct electron detector, Gatan BioQuantum energy filter + K3 direct electron detector, CETA CMOS detector. Software: Velox, EPU, MAPS, Tomo5, SerialEM, and CorRelator. |
| CEMRC | Talos L120C TEM | TEM 120 kV | TEM for sample screening and imaging. 120 kV TEM with LaB6, CETA CMOS detector. Software: Velox, SerialEM, and CorRelator. |
Computation
| Location | Equipment Name | Use | Equipment Description |
|---|---|---|---|
| MCCET, CEMRC | Petabyte-Scale Ceph Centralized Storage. | Large scale storage for facility instruments. Temporary storage turnover, archival storage, and active processing use-cases are supported. | 2.8 PB Ceph Storage Cluster, with additional 300 TB nVME storage intended for active processing work integrated with a computational cluster. |
| MCCET, CEMRC | Facility GPU Preprocessing Servers | Preprocessing pipelines for micrographs from instruments. Staff computation. | 8 preprocessing servers for initial data mirroring and pre-processing pipelines (frame alignment, CTF estimation, data QC). Fiber-optic network to facility instruments, bonded 10Gbit networking to data storage. |
| MCCET, CEMRC | SLURM GPU Cluster | Cluster with 10 GPU-accelerated nodes directly integrated with Ceph storage | SLURM cluster with GPU acceleration with 2 GPU nodes for machine learning tasks. |
| MCCET, CEMRC | Remote access for sessions. | Remote session support. | Support for instrument control, offline instance of SerialEM, and CorRelator. |
| MCCET, CEMRC | Globus | Secure file transfer service. | Robust transfers and collaborative data sharing for data collection and processing. |