Single Cell Unit

Introduction

SERVICES & APPLICATIONS

The Single Cell Unit is equipped with state-of-the-art instruments for single-cell isolation and library preparation. We are a scientific and technological support unit for high level research projects in the Single Cell Genomics field and we will assist researchers from the experimental design to the data analysis.

10x Genomics Chromium™ System (10x genomics)

The unit is equipped with a Chromium Controller instrument. This technology is based on microfluidics and allows the generation in parallel of single cell or nuclei partitions with identifying barcodes and the preparation of sequencing libraries. 

- Single cell transcriptome 3' gene expression
- Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin)
- Chromium Single Cell Multiome ATAC + Gene Expression 

Spatial Transcriptomics - Visium (10x genomics)

10x Genomics has developed a workflow for sequencing mRNA without the loss of spatial information. The Visium Spatial Gene Expression Solution allows for whole transcriptome and targeted analysis of mRNA using high-throughput sequencing, and subsequently maps a transcript’s expression pattern in tissue sections using high-resolution microscope imaging.

Tapestri Platform (Mission Bio)

The Tapestri Platform is designed for targeted single-cell sequencing. The platform is designed to produce targeted scDNA sequencing libraries alone or in a multi-omics solution which combines targeted single-cell DNA and protein analysis. Mission Bio offers the possibility of using pre-designed or custom DNA and protein panels.

-Tapestri Single-Cell targeted DNA Sequencing

-Tapestri Single-Cell targeted DNA + Protein Sequencing 

Data Analysis

Single-cell and spatial genomics enable the comprehensive characterization of cells in their identity and function. However, single cell data are noisy and present several computational and analytical challenges, which require the application of tools specifically designed for their analysis. The unit will provide support for the bioinformatic analysis of data from individual cells.

OUR MISSION

The mission of the Single Cell Unit is to facilitate academic research by offering services based on cutting-edge single-cell and spatial genomics technologies. 

Single-cell genomics represent a powerful tool for the analysis of complex tissues and have significantly advanced our knowledge in basic and clinical sciences. The Single Cell Unit will provide support to the scientific community through the most advanced technology for single-cell analysis. 

The unit belongs to the scientific and technical services (SCT) of the Josep Carreras Leukemia Research Institute and represents one of the new strategic research lines of our institution.

HOW DO WE SUPPORT YOU?

-We provide scientific and technological support for high level research projects in the Single Cell Sequencing field according to international standard procedures.

-We give scientific advice to researchers, from the planning and optimization of new experiments to their execution and bioinformatic analysis. 

- We contribute to the promotion of innovation in health technologies and the transfer of the knowledge generated to the NHS. 

SINGLE CELL UNIT TEAM

The team involves dedicated technicians with extended expertise in genomics:

Single-cell technologies and analyses in hematopoiesis and hematological malignancies. Campillo-Marcos, Ignacio, Damiana Alvarez-Errico, Regina A. Alandes, Elisabetta Mereu, and Manel Esteller (2021). Experimental Hematology. 98, 1-13 (2021). 

The Single Cell Unit has the support of Dr. Elisabetta Mereu, Principal Investigator of the Cellular Systems Genomics Lab at the Josep Carreras Leukemia Research Institute. She assists the Single Cell Unit in the design of new experiments and data analysis.  

She has a PhD in Statistical Genetics and more than four years of experience in the analysis of single cell genomics data. As part of the Human Cell Atlas (HCA) consortium, she has extensively worked on the systematic comparison of single-cell RNA-seq protocols and currently on its extension to integrate other data types, such as single-cell epigenomics (scATAC-seq) and spatial transcriptomics. She works in international consortia, such as the Human Pancreas Atlas as well as in other national and international research projects, including the profiling of glioblastomas and colorectal tumors. Her work on healthy and diseased tissues allowed her to build a deep understanding of cell-type structure and plasticity.

GRANTS, PROJECTS & COLLABORATIONS

"Cell Atlas of COVID-19 patients with pre-existing Autoimmunity and Immunodeficiency conditions"
Principal Investigator: Esteban Ballestar

"Single-cell transcriptomics for the analysis of differential neural subtypes in a human cell model of Rett syndrome"
Principal Investigator: Sonia Guil

"Single cell analysis of clonal heterogeneity in myelodysplastic syndromes treated with hypomethylating agents" 
Principal Investigator: Manel Esteller 

PUBLICATIONS

1. Reynolds, G. et al. Developmental cell programs are co-opted in inflammatory skin disease. Science (80-. ).6500, (2021).
2. Fawkner-Corbett, D. et al. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 1–17 (2021) doi:10.1016/j.cell.2020.12.016.
3. Guilhamon, P. et al. Single-cell chromatin accessibility profiling of glioblastoma identifies an Invasive cancer stem cell population associated with lower survival. Elife 10, 1–20 (2021).
4. Mereu, E. et al. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Nat. Biotechnol.38, 747–755 (2020).
5. Zavidij, O. et al. Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma. Nat. Cancer 1, 493–506 (2020).
6. Moncada, R. et al. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma (2020). Nat. Biotechnology.
7. Ji, A. L. et al. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell 1–18 (2020) doi:10.1016/j.cell.2020.05.039.

Contact

IJC Building

Ctra. de Can Ruti

Cami de les Escoles s/n 08916 Badalona Barcelona, Spain
(+34) 93 557 28 00 (Mon-Thu 7.00-17.30, Fri 7.00-15.00)

FOR ENQUIRIES AND QUOTES:

singlecellunit@carrerasresearch.org

 

   

Documents and prices

For detailed information about our fees, please contact singlecellunit@carrerasresearch.org before sending any samples. 

Services

10x Genomics Chromium™ System (10x genomics)

The unit is equipped with a Chromium Controller instrument. This technology is based on microfluidics and allows the generation in parallel of single cell or nuclei partitions with identifying barcodes and the preparation of sequencing libraries. 

- Single cell transcriptome 3' gene expression

- Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin)

- Chromium Single Cell Multiome ATAC + Gene Expression 

 

Spatial Transcriptomics - Visium (10x genomics)

10x Genomics has developed a workflow for sequencing mRNA without the loss of spatial information. The Visium Spatial Gene Expression Solution allows for whole transcriptome and targeted analysis of mRNA using high-throughput sequencing, and subsequently maps a transcript’s expression pattern in tissue sections using high-resolution microscope imaging.

Tapestri Platform (Mission Bio)

The Tapestri Platform is designed for targeted single-cell sequencing. The platform is designed to produce targeted scDNA sequencing libraries alone or in a multi-omics solution which combines targeted single-cell DNA and protein analysis. Mission Bio offers the possibility of using pre-designed or custom DNA and protein panels.

-Tapestri Single-Cell targeted DNA Sequencing

-Tapestri Single-Cell targeted DNA + Protein Sequencing 

 

Data Analysis

Single-cell and spatial genomics enable the comprehensive characterization of cells in their identity and function. However, single cell data are noisy and present several computational and analytical challenges, which require the application of tools specifically designed for their analysis. The unit will provide support for the bioinformatic analysis of data from individual cells.