Genomics :

Equipment

The facility is equipped with a broad range of Illumina short-read sequencing platforms, which allows generation of high throughput of data generation and provides the necessary flexibility to accommodate sequencing needs of researchers at the Crick. These instruments are operated by facility staff only unless otherwise stated.

• NovaSeq X Plus
• NovaSeq 6000
• NextSeq 500 - available for general Crick use, training provided.
• MiSeq (x2)

We also utilize Oxford Nanopore Technologies instruments for long-read sequencing and direct RNA sequencing.

• PromethION 24
• P2 Solo
• MinION & MinION Mk1C - available for general Crick use, training provided.
• Flongle

We use the 10X Chromium and Chromium X platforms for the isolation of single cells and their processing for sequencing. These instruments are usually operated by our expert facility staff, but training is also offered for Crick staff to run their own experiments.

We use the CellenONE platform for isolation of single cells in 96- and 384-well plates. This can also be provided by the Flow Cytometry STP via FACS.

For single cell QC, we use the Luna FX7 cell counter (Logos Biosystems), the EVE cell counter (NanoEnTek), and Leica microscope.

We own an STP Mosquito and have access to a Labcyte Echo ultrasonic liquid dispenser in the High Throughput Screening STP for miniaturisation.
 

We aim to automate as many processes as possible for QC and library preparation. The use of robotics increases throughput and robustness of the data generated. We work with the following equipment - these instruments are operated by facility staff only unless otherwise stated.

• Beckman Coulter Biomek i7
• STP mosquito and firefly - available for general Crick use, training provided.
• Hamilton STAR x3 - One integrated into the Automata LINQ platform.
   

Spatial genomics aims to assay the genomic information of single cells within their native tissue environment. This is a fast-moving frontier and the Genomics STP are actively carrying out development projects in this area. We have established workflows for the following platforms:

• Nanostring GeoMx
• Nanostring CosMx
• 10X Visium
• 10X Xenium
   

The facility is equipped with the following instruments that are used for QC and library preparation. These instruments are operated by facility staff only unless otherwise stated.

• Nanostring nCounter
• Agilent 4200 Tapestation - available for general Crick use, training provided.
• Agilent 2100 Bioanalyser
• Covaris LE220-plus ultrasonicator - available for general Crick use, training provided.
• Eco qPCRmax
• Promega GloMax-Multi Detection System

The Genomics Equipment Park contains a wide range of equipment, all of which are available for general Crick use with training provided, unless otherwise stated. These include:

• Real-Time PCR quantitation – thermal cycling systems (96 well and 384 well format) designed to detect fluorescence during the thermal cycling of PCR. By plotting the increase in fluorescence versus the cycle number, the system produces amplification plots that provide a more complete picture of the PCR reaction. 
• PHERASTARPlus micro-plate reader – multi-detection HTS micro-plate reader with Simultaneous Dual Emission in all modes. The reader is able to perform all leading non-isotopic detection technologies including:
• Fluorescence Intensity, Fluorescence Polarization, Time-Resolved Fluorescence, TR-FRET, Luminescence and Absorbance UV/Vis. 
• PerkinElmer EnVision Multilabel Reader – the instrument features modular label-specific optical mirror modules, high energy flash lamps, high-speed detectors and can accept micro-plates from 98 to 1536 wells. EnVision can handle kinetic measurements for enzyme assays and scanning of the well area for cellular assays. Detection options include Fluorescence Intensity, Fluorescence Polarisation, Time-Resolved Fluorescence, Luminescence and Absorbance. 
• Agilent 2100 Bioanalyzer – the instrument detects biomolecules by laser-induced fluorescence. During chip preparation, a dye concentrate is mixed with the gel. With the help of the priming station, the channels of the chip are filled with the gel-dye mix. During the chip run, the dye intercalates directly with DNA or RNA. Operated by facility staff. 
• DNA/RNA extraction – automated sample preparation using QIAGEN spin-column kits. Source material: cell (lysates), genomic and plasmid DNA. Operated by facility staff only.
• Typhoon 9500 Imager – the system provides several imaging modes such a fluorescence, filmless autoradiography, and digitization of colorimetric stained gels, providing quantitative measurements of western blots, multiplex fluorescence and radio-isotopic labels. 
• ImageQuant Amersham 800 – a digital (CCD) imaging system for sensitive, quantitative imaging of gels and blots without film, by chemiluminescence and fluorescence. The high sensitivity and wide dynamic range is designed to capture the signals from ECL western blotting reagents. A wide range of visible fluorescent dyes can also be imaged via Red, Green and Blue epi-illumination. 
• Li-Cor Odyssey Infrared Imager – the imaging system offers a different way to analyse blots and gels. Odyssey is uniquely equipped with two infrared channels for direct fluorescence detection enabling simultaneous probing of two separate targets on the same gel, e.g. Western blot (see below). 
• Ensight Plate Reader - Fluorescence, luminescence, absorbance plate reader for measuring samples in flat-bottomed multi-well plates (usually 96 or 384).
• Lunatic Plate Reader - An absorbance based reader with dedicated 16 well strips and 96 well plates with microfluidic channels. Load 2ul of sample into the wells.
• Droplet Digital PCR - A system for direct quantification of sample DNA and RNA. Using the auto droplet generator (ADG) your qPCR sample mix is randomly distributed among about 20,000 oil droplets. End point PCR is performed in each droplet (dedicated heat sealer and PCR instrument). On the QX200 droplet reader the numbers of positive and negative droplets are counted to give precise quantification of target sequences in a sample.
• Jess Automated Western - Western Blot protein detection and quantitation. The separation takes place in a capillary, samples and reagents are loaded into a prefilled plate.
• Precision Nanosystems Ignite and Spark instruments - Used for lipid nanoparticle (LNP) generation. This is done by controlled microfluidic mixing of two phases, using syringes fixed to a specialised cartridge.
• Malvern Panalytical Nanosight LM10 viewer and microscope - A laser based light scattering system for the characterisation of nanoparticles.