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.

More detailed information is available on the lab web site

Group Members

Leonard HartmanisGraduate Student
Gert-Jan HendriksPostdoc
Per Ah JohnssonPostdoc
Anton LarssonPhD student, Graduate Student
Mtakai NgaraPhD student, Graduate Student
Athanasia PalasantzaGraduate Student
Rickard SandbergSenior researcher, Professor
Gosta WinbergSenior researcher
Christoph ZiegenhainAssociated, Postdoc

Selected Publications

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

Entering the era of single-cell transcriptomics in biology and medicine.
Sandberg R
Nat. Methods 2014 Jan;11(1):22-4

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

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.
Picelli S, Björklund , Faridani O, Sagasser S, Winberg G, Sandberg R
Nat. Methods 2013 Nov;10(11):1096-8

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.
Ramsköld D, Luo S, Wang Y, Li R, Deng Q, Faridani O, et al
Nat. Biotechnol. 2012 Aug;30(8):777-82

Developmental BiologyGene regulationStem Cell Biology