SICOF - our offer

Our services

Smart-seq2

Developed in 2014 by the Sandberg lab at KI, the Smart-seq2 chemistry paved the way for single cell RNA sequencing. By using the SMART technique of template switch, full-length sequencing of the transcriptome became possible on a single cell level, enabling detection of thousands of genes per cell (2500-6000 depending on cell type).

Smart-seq2 is currently being phased out for Smart-seq3, while we continue to offer Smart-seq2 as a service for existing projects.

Smart-seq3

The Smart-seq3 chemistry is an evolution of Smart-seq2, offering increased depth (3500-9000 genes/cell, depending on cell type) while also introducing UMI based gene counting for more accurate gene expression counts. The full-length information is also preserved, and less starting material is required.

SmartBulk RNA-seq in single cell format via Smart-seq3 and Smart-seq2 chemistry​

We use SMART chemistry to study bulk cells/organisms in a high-throughput manner. Cells or small tissues are lysed in a 384 well plate and the lysates are then processed as single cells, but with adjustment for the higher starting material.

Right now, this method is optimized for sets of 384 samples, but SICOF is working on methods to scale this down to study smaller sample numbers.

Small RNA-seq

Small RNA-seq is another adaptation of the SMART chemistry, focusing on the study of the small RNAs in a single cell. This is mostly miRNA’s but may also include tRNA’s and snoRNA’s. Abundant ribosomal RNAs are masked so that they don’t overwhelm the sequencing data.

10x genomics-based droplet sequencing

In 2015, the single cell field was revolutionized by the introduction of droplet sequencing, which encapsulates cells and reagents into small droplets for library preparation. This dramatically increased the throughput of single cell sequencing while reducing the cost per cell. This approach is commercialized by several companies, and we offer the entire portfolio of single cell solutions from 10x Genomics.

Spatial transcriptomics

This technology aims to preserve anatomical information while studying single cells. We have acquired the CytAssist instrument and are starting to offer Visium spatial gene expression analysis in fixed tissues as a collaborative service with BEA, LCI, and FENO for tissue processing, along with NGI for sequencing. This service has started autumn 2024 and we are still in the process of evaluating pricing and sample logistics.

Additionally, we will offer Visium HD spatial gene expression services upon customer request.

Small molecule screening

Using the acoustic dispensing of the LabCyte Echo, we offer the possibility to do compound screening for our users. Each of these assays are custom designed and availability depends on our capacity to assist you.

Contact us for more information on pricing/availability.

Quality Control 

Good single cell data starts with high quality cells. We therefore focus a lot on Quality Control (QC) before proceeding with single cell sequencing. We house several instruments for QC, such as three Bioanalyzers, a Fragment Analyzer and a LUNA FL cell counter. We use these instruments to assess your cells and/or cDNA quality prior to single cell sequencing.

Liquid handling 

We use several robots which we can also use for custom high throughput liquid handling outside of our single cell pipeline, depending on feasibility and time of the SICOF staff. One example includes the dispensing of molecule libraries using the acoustic tip-free Echo dispenser.

Services under development

Note! These services are under implementation.

Their availability as a service is dependent on the workload of SICOF and therefore, implementation takes an undefined length of time. In case of a strong desire of the single cell user base for a technology to be implemented, we will prioritize its implementation.

Single cell fractionations

This technology uses Smart-seq3 on the cytoplasm for mRNA transcriptional profiling and preserves the nucleus for different analysis; whole genome sequencing (DNTR-Seq) or chromatin analysis (ATAC-Smart3)

Parse Biosciences Evercode

We are exploring the possibility of implementing Evercode, the commercial implementation of Sci-Seq as a single cell sequencing solution. Contact us if you have any projects that would benefit from Evercode!