Rickard Sandberg's Group

We are studying global aspects of gene regulation by combining genome-wide experimental and computational techniques to deepen our understanding of the molecular nature of cell identities in development and disease.

In particular, we develop and use unbiased, quantitative single-cell transcriptomics to monitor cell identities at single-cell resolution during early mouse development and in cancer cells. We aim towards a better understanding of the molecular regulation of gene expression programs by the combined study of gene regulation acting on different levels (for example transcriptional and post-transcriptional) using next-generation sequencing techniques.

Currently, we are interested in generating a single-cell resolution map of an in vivo differentiation process and to this end we are using single-cell transcriptome analyses to analyze individual cells within the developing preimplantation embryos. When a mouse embryo develops into a blastocyst (after approximately 4 days) it contains roughly 60 cells, including the pluripotent inner cell mass while the remaining cells are trophectoderm progenitors. We would like to determine how and when the first signs of cellular differentiation occur, and to map out the key regulatory pathways involved in determining pluripotency in vivo.

We are also developing functional genomics tools that will help us to better identify gene regulatory interactions, for example those between promoters and distal enhancers and working on how to better integrate diverse sets of next-generation sequencing data.

Group Members

Rickard Sandberg

Group leader and Professor

Gerardus Johannes Hendriks

Postdoctoral researcher

Per Ah Johnsson

Postdoctoral researcher

Lisa Anna Jung

Postdoctoral researcher

Anton Larsson

PhD student

Daniel Ramsköld

Senior lab manager

Christoph Ziegenhain

Postdoctoral researcher

Members of the Eukaryotic Single-cell Genomics facility, SciLifeLab

Samaneh Masoumi

Research engineer

Helena Parra Acero

Research engineer

Mathilda Eriksson

Research engineer

Henrik Gezelius

Research engineer

Anastasios Glaros

Research engineer

Selected Publications

Genomic encoding of transcriptional burst kinetics.
Larsson AJM, Johnsson P, Hagemann-Jensen M, Hartmanis L, Faridani OR, Reinius B, et al
Nature 2019 01;565(7738):251-254

Computational correction of index switching in multiplexed sequencing libraries.
Larsson AJM, Stanley G, Sinha R, Weissman IL, Sandberg R
Nat. Methods 2018 04;15(5):305-307

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.
Segerstolpe Å, Palasantza A, Eliasson P, Andersson EM, Andréasson AC, Sun X, et al
Cell Metab. 2016 10;24(4):593-607

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.
Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula SP, Codeluppi S, et al
Cell 2016 Sep;167(1):285

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects.
Picelli S, Björklund A, Reinius B, Sagasser S, Winberg G, Sandberg R
Genome Res. 2014 Dec;24(12):2033-40

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Deng Q, Ramsköld D, Reinius B, Sandberg R
Science 2014 Jan;343(6167):193-6