Research

The Facility Core of the School of Life Sciences was founded in 2009. In 2012, the facility core began managing the national protein sciences infrastructure—Beijing Base, also known as the Phenix Facility Center. The core’s mission is to support the research needs of all principal investigators within the school. It encompasses several specialized platforms, including Electron Microscopy, Optical Imaging, Flow Cytometry, Protein, Mass Spectrometry, and Isotopes.

The Electron Microscopy Platform offers a comprehensive range of technical services, advice, training, and access to facilities for academic clients requiring electron microscopy to address specific research questions. The platform covers a wide spectrum of EM techniques including: Transmission Election Microscopy (TEM) sample preparation, including embedding in various resin and ultrathin sectioning; Scanning Election Microscopy (SEM) sample preparation, such as chemical dehydration, critical point drying, and sputter coating; Cryo-sample preparation for both TEM and SEM, including high-pressure freezing, freeze substitution, cryo-ultramicrotomy, plunge freezing, and freeze fracture; Immunoelectron microscopy using pre-embedding, post-embedding, or Tokuyasu methods; Negative staining of purified macromolecular complexes, bacteria, viruses, liposomes, nanoparticles, or viral like particles (VLP); Advanced microscopy techniques, such as FIB-SEM, correlative LM/EM (CLEM), and Volume EM (vEM). Facility Staff are available to help users to define optimal experimental conditions for their research. The platform is equipped with four transmission electron microscopes including: FEI Tecnai G2 Spirit BioTWIN (Gatan Orius 832 CCD camera); FEI Tecnai G2 20 Twin (EMSIS XAROSA CMOS camera); JEOL JEM-1400Flash (HC) (EMSIS XAROSA/ PHURONA CMOS camera); JEOL JEM-F200 (Gatan Oneview CMOS camera). Additionally, the platform includes one scanning electron microscope (FEI Quanta FEG 450) and one DualBeam FIB SEM (FEI Helios NanoLab G3 UC).

The Optical Imaging Platform provides bioimaging services, spinning from single-molecule imaging to whole-animal or plant models, and tissue imaging using optical microscopes. These include confocal, super-resolution, live-cell, high-content, spatial biology, and biomechanical related microscopes. Laser Scanning Confocal Microscopy (Nikon A1Rsi+, Nikon AXR invert, Nikon AXR upright, Zeiss LSM710 and LSM980 with Airy Scan2) for multi-channel fluorescence imaging with 3D structure and FRAP/FRET/FLIM/FCS analysis. Spinning Disk Confocal Microscopy (Andor Dragonfly, Nikon Live SR, Evident SpinSR) for live-cell imaging with high optical and time resolution. Super-Resolution Microscopy includes structured illumination microscopes (SIM) and stimulated emission microscopes (STED). SIM (GE DeltaVision OMX SR, His-SIM, Polar SIM) with 2D-SIM, 3D-SIM, and TIRF-SIM achieving resolutions down to 100 nm with superfast imaging. Leica STED 3X with a lateral resolution of 50 nm, is more appropriate for fixed samples. High content screening system using PerkinElmer Operetta CLS, achieve automating 96-well plates scanning and analysis for high-throughput screening. Automatic Slide Scanners (Zeiss Axio Scan Z1, Evident VS200, Akoya PhenoCycler-Fusion2.0) capture high-quality virtual slide images through automated high-speed scanning and tiling process for H&E or immunohistochemical or immunofluorescent stained tissue sections. Akoya Phenocycler-Fusion combines automated fluidics with high-speed imaging to generate high-resolution images of multiple biomarkers on tissue sections, thus providing an up to 100-plex spatial phenotyping assay. 10x Genomics Xenium in Situ platform characterizes up to 5,000 genes in tissues with ultra-precise single-cell spatial imaging, which allows in situ spatial transcriptomics analysis to deeply characterize cell types, pathways, cell-cell interactions. Atomic force microscope (AFM) obtains high-resolution topographic information and mechanical properties (such as Young's modulus and adhesion force) of the sample surface by detecting the interaction force between the probe and the sample surface, while it can maintain the physiological state of biological samples and perform in-situ detection directly in a solution environment. Fluidic force microscope (FluidFM) combines AFM and microfluidic systems, which can perform micromanipulation by using a hollow probe cantilever on biological samples in a solution environment, such as single-cell injection/extraction, single-cell sorting, and single-cell adhesion force measurement.

The Flow Cytometry Platform provides advanced equipment and services for phenotyping and isolating specific populations of cells or nanoparticles. The platform is equipped with 10+ flow cytometers, including spectral and conventional models, cell sorters, and small particle analyzers. Analytical flow cytometers (BD FACSVerse-3L, BD LSRFortessa-5L, full spectrum cell analyzer BD FACSymphony A5 SE-5L, Beckman Coulter CytoFlex LX -6L, full spectrum cell analyzer CyTek Aurora-5L, Apogee MicroPLUS Flow Cytometer-2L) can achieve basic to advanced multiparameter fluorescence analysis. Cell sorters (Beckman Coulter MoFlo XDP-4L, Beckman Coulter MoFlo Astrios EQ-5L, BD FACSAria III-4L, BD FACSAria SORP-5L, BD FACSAria Fusion-6L, Sony MA900-4L and full spectrum cell sorter BD FACSymphony S6 SE-5L) are enable to harvest purified samples such as cells, subcellular organelles, or bacteria through optimizing the sorting conditions. Cell transfection and tissue dissociation instruments (Bio-Rad Gene Pulser Xcell Electroporation System, Lonza 4D-Nucleofector, DeMeng Biotec Microchannel Cell Transfection instrument, Miltenyi Biotec gentleMACS Tissue Dissociators with Heaters) assist in processing of samples. Skilled staff provide expertise in multi-dimensional flow cytometry, cell sorting, project consultation, and collaboration. They offer professional training in experimental design, sample preparation, and the operation of analytical or sorting cytometers. Additionally, offline software such as FlowJo, SpectroFlo, Kluza, and ModFit is available to support comprehensive data analysis.

The Protein Platform offers professional research services, including protein purification, molecular interaction studies，next-generation sequencing, CRISPR-based high-throughput screening, etc. Key equipment and services include:

Sequencers: MGI-2000 and DNBSEQ-T7 for Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), Transcriptome analysis, DNA methylation profiling, Chromatin Immunoprecipitation Sequencing (ChIP-Seq), and targeted region sequencing. 10X Genomics Single-cell and Visium Platform: The platform leverages 10× Genomics technology for single-cell transcriptomics and immunomics library sequencing. Additionally, we offer Visium HD spatial transcriptome sequencing services, enabling precise in situ gene expression analysis. AKTA Purification Systems: A flexible and intuitive chromatography system designed for rapid purification of proteins, peptides, and nucleic acids ranging from microgram to gram quantities of the target product. Protein and Nucleic acid Characterization Service: Circular Dichroism Spectrometer for analyzing protein and nucleic acid conformation; NT8 Protein Crystallization and Imaging system for protein crystallization studies; Agilent 4150 Tapestation for RNA/DNA quality control; Real-time Quantitative PCR Detecting System for gene expression analysis; Agilent 1260 HPLC for biomolecule analysis; Ultrasonic Disruptor, Multimode Microplate Reader andAI600 Chemiluminescence Imager for sample preparation and analysis. Protein Interaction Analysis Service: Biacore T200 and ITC (Isothermal Titration Calorimeter) offers comprehensive analysis of protein interactions. PKU-EdiGene High-Throughput Screening Core (HTS core): The HTS Core, was founded in 2023, specializes in CRISPR-based high-throughput screening technology. To support functional genetics research, the platform provides genome-wide gene knockout sgRNA libraries for human and mouse models, including three levels of plasmid, viral, and cell-based CRISPR-Cas9 libraries. Additionally, we maintain a variety of arrayed libraries, such as the Open Reading Frame (ORF) library (human), shRNA libraries (human and mouse), and Sanger CRISPR libraries (human and mouse). The mass spectrometry platform was established in 2016, and specializes in mass spectrometry-based proteomics and small metabolite detection. The platform is equipped with four high-resolution liquid chromatography-mass spectrometry (LC-MS) instruments: Q Exactive Plus, Orbitrap Fusion Lumos, Orbitrap Exploris 480, and Orbitrap Astral for proteomics research. One liquid chromatograph (Agilent 1290) and one triple quadrupole mass spectrometer (Agilent 6495) are used for small metabolite detection. The mass spectrometry platform provides proteomics detection including protein identification, protein-protein interaction, identification and quantification of post-translational modifications of proteins, quantitative proteomics, single-cell proteomics and cross-linking mass spectrometry of proteins, etc. Proteomics has a wide range of applications in multiple fields, mainly including disease diagnosis, drug development, biomarker discovery, biological function research, etc.

The Isotope Platform is specially designed for safe handling of radioactive materials.  The platform is equipped with advanced instruments, including the Typhoon IP Image Analyzer, the Tri-Carb 3110TR Liquid Scintillation Counter, and Radiometric & Luminescence Detection systems, all of which are integral to high-precision scientific investigations. The Typhoon IP captures and displays stored information as digital images, enabling both qualitative and quantitative analysis of results in a digital format. The Tri-Carb 3110TR and Radiometric & Luminescence Detection systems provide high performance and flexibility for detecting radioactivity, making them essential tools for life science research.

Website Link：http://www.biocore.pku.edu.cn/genee/