Introduction

The Single Cell Unit (SCU) aims to provide scientific services to the Josep Carreras Institute community as well as external users. It is equipped with cutting-edge technology used for basic and translational genomic and transcriptomic studies at single cell resolution.

Single Cell Technology has emerged, in the past decade, as one of the most important techniques in the biomedical field, able to resolve highly complex biological systems and capture the full heterogeneity of a sample. It allows us to identify cell populations that are impossible to isolate with less resolutive technologies previously used, such us bulk sequencing.

The appreciation of cellular heterogeneity is improving our understanding of complex diseases and empowering the development of new drugs.

The SCU has currently Chromium Controller and Chromium X devices (10X Genomics), for single cell analysis, at the transcriptomic level, and a Tapestri Platform device (Mission Bio), for single cell analysis at the genomic and immunophenotypic level.

Both Chromium Controller and Tapestri instruments are based in the microfluidic droplet technology, which allows the encapsulation of hundreds to thousands of individual cells in just a few minutes.

This system enables the encapsulation of individual cells or nuclei together with other reagents in solution, allowing the cell barcoding and library construction inside these tiny droplets. Libraries generated from these cells will then be sequenced and analyzed with specific bioinformatic tools.

Since 2022 the SCU is the First Center of Excellence for Tapestri Platform in Europe and is also one of the Certified Service Providers from 10X Genomics Technology.

The IJC and Mission Bio have signed a collaboration agreement that will advance the application of single-cell DNA sequencing to investigate disease progression, therapeutic resistance and measurable residual disease (MRD) in blood cancers, as well as in its new breast cancer research program.

Services

Scientific and technological support in the field of single cell: from the project’s planning and experimental design stage to the execution phase, processing of samples and the delivery of the sequencing data.

Single Cell Transcriptomics (Chromium from 10X Genomics): With single-cell RNA sequencing, the focus is on identifying single-cell gene expression differences to study cell types and states in a context-specific manner, thereby revealing among other things tissue-specific cellular heterogeneity, novel therapeutic biomarkers and targets, and characterize complex cellular responses to treatment and intervention.

• Single-cell RNA-seq 3’

• Single-cell RNA-seq 3’ + Feature Barcoding (for Cell Surface Protein and CRISPER screening detection)

• Single-cell Immune profiling (scRNA-seq 5’ + TCR/BCR)

• Single-cell Immune profiling (scRNA-seq 5’ + TCR/BCR) + Feature Barcoding (for Cell Surface Protein, CRISPER and Barcode Enabled Antigen Mapping-BEAM screening detection)

• Single-cell ATAC-seq

• Single-cell Multiome (ATAC + scRNA-seq 3’)

• Single-cell Gene Expression Flex (for fresh, frozen & FFPE samples)

• Single-cell Gene Expression v4 – GEM-X technology

• Single-cell Immune Profiling v3 – GEM-X technology

Single Cell Genomics (Tapestri from Mission Bio)

This is the only platform capable of simultaneously providing both genotype information, such us single nucleotide mutations, indels and copy number variations alone or together with phenotype data from the same cell, dissecting the architecture of tumors with unprecedented resolution. This technique allows the identification of true mutation co-ocurrence in clonal populations and detect rare subclones down to 0.1%.

Mission Bio offers the possibility of using pre-designed or custom DNA and protein panels, to determine the source of resistance, response or relapse of different hematologic malignancies as well as solid tumors such as breast cancer and gliobastoma.

• Single-cell targeted DNA-seq (mutation analysis and or CNV analysis)

• Single-cell DNA-seq + cell-surface protein-seq

PBMCs/BBMCs Nuclei Extraction: for scATAC and scMultiome RNA transcriptomics protocols.

QC Viability Tests: this option is specifically useful for novel single cell users who need support in sample preparation and don’t know how to evaluate the quality and quantity of their cellular suspensions.

Dead Cell Removal Step: in case cellular suspensions brought by the user have less than 70% of viability.

Customized Single-cell protocols