Sandberg Lab

Ludwig Institute for Cancer Research & Department of Cell and Molecular Biology, Karolinska Institutet

welcome to sandberg lab

We are studying global aspects of gene regulation by combining genome-wide experimental and computational techniques to better understand stem cell characteristics and differentiation processes. 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 (e.g. transcriptional and post-transcriptional) using next-generation sequencing techniques. In particular, we are interested in gene expression regulation of differentiation and cell fates during mouse early embryonic development, using single-cell RNA sequencing methods.

We are located at the Ludwig Institute for Cancer Research, Stockholm branch and the Department of Cell and Molecular Biology at Karolinska Institutet.

Funded Postdoc Position Available in Bioinformatics (see Positions)!


Daniel Ramsköld's thesis awarded best PhD thesis at Karolinska Institutet 2014

Daniel Ramsköld recieved his Phd in June 2014 and was recently awarded the Dimitris N. Chorafas prize for his contributions to medical research. Read more...Congrats Daniel! [Oct 2014]

Transposase technology published

To allow for flexible and innovative moleular biology and deep sequencing, we have just realized our protocols for Tn5 production and use. It works even down to sub-picograms of input DNA! Read more. [Jul 2014]

Independent allelic transcription generates fluctuations in the single-cell transcriptome

Using the single-cell rna-sequencing methods developed within our lab, we have studied allelic transcription in individual cells form mouse preimplantation embryos. We discovered that many genes (~20%) had only RNA from one of the parental alleles at any given time of analyses, likely a consequence of pulsing allelic transcription. We desribe these allelic expression patterns in our study published in Science. [Jan 2014]

Single-cell transcriptomics 2.0

Our lab has developed an improved single-cell RNA-seq method (smart-seq2)! It more sensitive, automation-friendly, has lower bias, see our recent publication in Nature methods for details. For comprehensive details on smart-seq2 library preparations, please see our Nature Protocol. [Sep 2013]

A reference transcriptome and inferred proteome of the red spotted newt

Together with Andras Simon's lab we have generated a comprehensive reference transcriptome for the red spotted newt. Our study is now out in Experimental Cell Research, and the reference transcriptome, proteome and annotations are available here. [Mar 2013]

MULTo: comprehensive uniqueness files for NGS

Tired of generating uniqueness files for different read lengths. Download and use our uniqueness files that cover read lengths from 20-255 in one single file. This resource was recently published in PLoS ONE. [Jan 2013]

Single-cell RNA-Sequencing of circulating tumor cells using Smart-Seq

Our study describing Smart-Seq for analyses of gene expression in individual cells is now out in Nature Biotechnology. [publications] [Jul 2012]

Sequentially Acting Sox Transcription Factors in Neural Lineage Development

We have worked together with Jonas Muhrs lab on the genome-wide mapping of Sox transcription factors at different developmental stages in neural development. Interestingly, we found that factors pre-bind regions that will be first activated at subsequent developmental stage, often by another Sox factor. This study has now been published in Genes & Development. [Nov 2011]

CTCF promotes RNA pol II pausing and pre-mRNA splicing

We have been working together with Shalini Oberdoerffers lab on the effects of DNA-binding protein CTCF on pre-mRNA splicing. This work is now out in Nature (AOP, Oct 2nd) [Oct 2011]

Future Research Leader Grant (FFL4)

The sandberg lab received a long-term grant from the Swedish Foundation for Strategic Research so that our research areas will continue to expand during the coming years [Dec 2010]

Move to Ludwig Institute

We have moved the lab to Ludwig Institute for Cancer Research, Stockholm branch. New contact address is Nobels väg 3. [Jun 2010]

An Abundance of Ubiquitously Expressed Genes Revealed by RNA-Seq

Using RNA-sequencing data from human and mouse tissues we explored general features of tissue transcriptomes. This work was done in collaboration with Burge lab (MIT) and is now out in PLoS Comp Biol. [Dec 2009]

ERC Starting Grant

The sandberg lab received a highly competitive Starting Grant from the European Research Council, therefore the lab will be expanding over the next few years. [Sep 2009]

RNA-seq of human tissue transcriptomes

Alternative mRNA regulation across human tissues and cell lines was investigated by illumina/solexa mRNA sequencing. This was a collaboration with Burge lab (MIT) and Schroth and co-workers at Illumina, Hayward. This work is now out in Nature. [Oct 2008]

3'UTR shortening in proliferation cells paper published

The study on dynamical regulation of 3' untranslated regions is now published in Science (see publications). [Jun 2008]

Poster Award, Systems Biology Meeting at CSHL

The poster ("Widespread evasion of post-transcriptional regulation associated with proliferation." by Sandberg*, Neilson*, Sarma,Sharp and Burge) won the only Poster Price at the Systems Biology: Global Regulation of Gene Expression meeting in Cold Spring Harbor, NY, USA March 27-30, 2008. The poster presented the study of 3'UTR dynamics in activated immune cells and in proliferation. [Mar 2008]

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