Equipment

10x Genomics Chromium X platform

The Leiden Genome Technology Center acquired the 10x Genomics Chromium X platform in January 2022.

The market leader for single-cell studies, the Chromium controller series is an advanced microfluidics platform that can process up to 16 samples at once, generating up to 1 million barcoded single-cells per run. More information about the technology can be found on 10xgenomics.com.

Single-cell 3’ solution
High-throughput single-cell expression measurements that enable the discovery of gene expression dynamics and molecular profiling of individual cell types

Single cell V(D)J solution
A comprehensive, scalable tool for profiling full-length paired V(D)J transcripts from hundreds to millions of lymphocytes.  This new solution enables the assembly of full-length V(D)J sequences on a cell-by-cell basis, providing high-resolution insights into the adaptive immune system.

Single cell ATAC-seq solution
Reveal the epigenomic landscape and analyse chromatin accessibility cell-by-cell to decipher gene regulatory mechanisms.

Single cell multiome solution
Explore combined gene expression and chromatin accessibility data from the same cell to uncover gene regulatory programs

Request a quote via info@lgtc.nl

Spatial transcriptomics

The LGTC has recently invested in 2 platforms for spatial transcriptomics from 10x Genomics: the Xenium in situ platform and the Visium CytAssist platform.

10X Genomics Xenium

Xenium

The Xenium is an in situ spatial transcriptomics platform with subcellular resolution from 10x Genomics. This technology can map thousands of RNA targets within the same tissue section. These targets are defined by probe panels, which are pre-designed by 10x Genomics or can be custom ordered.

Technology

Both FFPE or fresh frozen sections can be analysed using the Xenium platform. After sample preparation, the Xenium workflow begins with probe panel hybridization. The Xenium platform uses padlock probes with gene-specific barcodes which undergo enzymatic amplification. Then, on the instrument, fluorophore-labelled oligo probes bind to these tags, and through successive imaging rounds an optical signature is generated for precise gene identification in situ. The onboard analysis software ensures that the data is viewable immediately after the run. The data can be processed with many third-party downstream analysis tools. For more information check the 10X Genomics website https://www.10xgenomics.com/xenium/.

10X Genomics Visium CytAssist

Visium CytAssist

The Visium CytAssist is a compact instrument designed to simplify the Visium workflow by facilitating the transfer of transcriptomic probes from standard glass slides to Visium slides. This enables whole transcriptome spatial profiling insights across your entire tissue section.

Technology

The LGTC offers the Visium HD workflow on the CytAssist platform. This workflow is compatible with either human or mouse FFPE sections. The input for this workflow is a 6.5 x 6.5 mm area of interest within the tissue section. The Visium HD technology uses pairs of probe sets covering the whole transcriptome. These probe pairs will hybridize to their complementary target RNA within the tissue section. After adding ligase, the hybridized probes will form a ligation product which will be released from the tissue slides and captured by the Visium HD slide using the CytAssist platform. The Visium HD slides contains a lawn of barcoded oligos spaced in a 2µm x 2µm grid. The captured spatial gene expression libraries are then sequenced using Illumina technology. For more information, please check the 10X Genomics website https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression. 

Dolomite Bio Nadia

The Nadia Instrument is a fully automated system to encapsulate samples. This microfluidic droplet-based platform can be used for single-cell capture. It’s possible to encapsulate up to 8 samples, in parallel, in under 20 mins. Over 50,000 single cells can be captured per cartridge in a run. More information about the technology can be found on dolomite-bio.com.

Applications

• Single-cell RNA-Seq
• Single-nucleus RNA-Seq
• Encapsulation of cells in agarose

Formulatrix MANTIS Liquid Handler

The MANTIS dispenses any reagent efficiently and reproducibly regardless of volume, viscosity, temperature, or concentration. It accurately dispenses a range of volumes from 0.1ul – 200ul in formats from 6-well to 1536-well plates. Different wells can receive different volumes and different reagents, which allows for a variety of applications including reaction miniaturization, plate dispensing, and plate normalization. More information about the technology can be found on formulatrix.com.

Applications

• Assay Development and Design of Experiment
• Next-Generation Sequencing – Library Preparation
• Polymerase Chain-reaction Workflows – Real-time and Digital
• Enzyme-Linked Immunosorbent Assays
• Cell Culture and Bead-Based Assays

PacBio Revio

The LGTC installed the PacBio Revio platform in March 2024. The Revio platform offers affordable, high-throughput, highly accurate long read sequencing.

Technology

The Revio is an upgrade of the Sequel II platform. The high-density Single Molecule Real Time (SMRT) cells contain 25 million zero-mode waveguides (ZMWs) capable of sequencing 90Gb+ per SMRT cell.

Each time a nucleotide is incorporated within a ZMW, it is held in place by the polymerase and a fluorescent signal is detected in real time. The incorporated nucleotides are identified by four different fluorescent labels corresponding to A, T, G, and C. The collection of data consists of the recording of a movie of light pulses (pulse data) which is then translated into bases (base data). More information about the technology can be found on https://www.pacb.com.

Applications

• De novo assembly of small and large genomes with 99.95% accuracy (Q33)
• Sequence full-length transcriptomes or targeted transcripts
• High accuracy variant calling for all variant types
• Target regions not currently accessible by other technologies
• Detect genomic variation in complex populations on all size scales
• Detect epigenetic modification including polymerase kinetics

Oxford Nanopore PromethION 24

The LGTC installed the PromethION 24 in January 2023. The PromethION 24 offers flexible and affordable on-demand sequencing.

Technology

The PromethION is a single molecule sequencing platform with real-time base calling. The technology utilizes nanopores for sequencing and up to 24 flow cells can be run at a time. The sequencing yield will depend on the sample and library type but one flow cell can generate more than 100 Gb of data. Please check https://nanoporetech.com/ for more information.

Applications

• Targeted sequencing with adaptive sampling
• Direct RNA sequencing
• Whole genome sequencing
• Native methylation detection
• Single-cell full-length transcriptome sequencing

Femto Pulse | Agilent Femto Pulse system

Pulsed-field capillary electrophoresis system for QC of high molecular weight DNA and RNA samples.

Blue Pippin

DNA size selection using a pulsed-field gel (100bp-50kb).

Sage HLS HMW Library system

Extract up to 2MB of DNA directly from cells.