Equipment

10x Genomics Chromium X platform

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.

On-Chip Multiplexing

The GEM-X on-chip multiplexing (OCM) assay provides a scalable microfluidic platform for multiplex up to 8 samples (two sets of up to 4 samples each) to assess single cell 3′ or 5′ gene expression by profiling 500-5,000 individual cells per sample.

Single Cell Gen Expression Fixed RNA (FLEX) v1

FLEX allows access to full transcriptome from formaldehyde fixed samples. This is a great solution for multiplexing sample with different time points, facilitating sample handling logistics.

Single Cell Gen Expression Fixed RNA (FLEX) v2

Full transcriptome analysis is possible with this probe plate-based approach. It is possible to tag up to 384 individual samples.

Request a quote via info@lgtc.nl

Waters (BD) Rhapsody

A robust, high-throughput microwell based single-cell partitioning system for reliability in single-cell workflows

Technology

The BD Rhapsody™ Single-Cell Analysis System allows high-throughput capture of multiomic information from single cells using a Simple cartridge workflow and a multitier barcoding system. The resulting captured information can be used to generate various  types of nextgeneration sequencing (NGS) libraries. NGS libraries are sequenced and analyzed to provide high-dimensional resolution of single cells.

Applications

• Analyze the whole transcriptome or a targeted set of genes
• Profile cell surface and intracellular markers without panel optimization
• Unravel the TCR repertoire, covering α-, β-, γ- and δ-chains
• Couple single cell ATAC and whole transcriptome analysis

10X Genomics Xenium

The LGTC has recently invested in 2 platforms for spatial transcriptomics from 10x Genomics:

• 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.
• 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.

10X Genomics Xenium

Technology

Both FFPE or fresh frozen sections can be analyzed 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

The LGTC has recently invested in 2 platforms for spatial transcriptomics from 10x Genomics:

• 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.
• 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.

10X Genomics Visium CytAssist

Technology

The LGTC offers the Visium HD workflow on the CytAssist platform. This workflow is compatible with either human, mouse or rat FFPE sections. The input for this workflow is either a 6.5 x 6.5 mm or 11 mm x 11 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.

Element AVITI24

Single-cell and spatial co-detection of RNA, protein, and cell morphology at subcellular resolution with no library prep and next-day results.

With Teton CytoProfiling you can generate multiomic data including expression of RNA, proteins, phospho-proteins, and cell morphology in up to 2 million adherent cells or 10 million cells in suspension. There are pre-designed panels and possibilities to create your own panel.

You can target up to:

• RNA: 350 targets
• Protein: 138 targets
• Morphology: 6 markers

For more information, please contact us at info@lgtc.nl.

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

Pacific Biosciences Revio

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).

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

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.

Applications

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

Element AVITI24

The AVITI24 offers high-quality next generation sequencing (NGS) with multiple read lengths and output options. The AVITI24 is able to generate more than 3 billion reads per run with the use of their avidite base chemistry (ABC) combined with Cloudbreak Freestyle technology. One of the advantages of Cloudbreak Freestyle is its compatibility with a diverse range of library types.

ABC sequencing uses Rolling circle amplification (RCA) to avoid index hopping and other PCR-induced errors to increase the quality.

• > 90% Q30 with 2 x 150 and 2 x 75 cycles
• > 85% Q30 with 2 x 300 cycles

For more information, please contact us, info@lgtc.nl

Illumina MiSeq

MiSeq System is a benchtop sequencing system capable of performing a broad range of sequencing applications. The Miseq enables lower-output 300bp paired-end runs on single lane flow cells.

For more information, please contact us at info@lgtc.nl.

Agilent Femto Pulse system

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

Sage Science Blue Pippin

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

Luna FX7 Automated cell counter

The LUNA cell counter performs up to 8 counts in one go