Qiaolin Deng's group

Gene regulation in early fate specification after implantation

Our lab is mainly interested in understanding the early cell fate specification after implantation, with focusing on neural plate patterning and primordial germ cells.

After implantation, the cluster of mouse epiblast cells undergoes rapid proliferation and expansion that in turn, forms a cup-shaped single-layer epithelium known as the post-implantation epiblast at E5.0-5.5. Epiblast cells are pluripotent and in turn give rise to all types of cells in the body. Gastrulation commences at embryonic day (E) 6 in mice, which is a fundamental morphogenetic process that generates three germ layers including naïve ectoderm, mesoderm and endoderm. Our first goal is to understand the cell composition in the seeming homogenous epiblast before gatstrulation starts. Following up the gastrulating, we are interested in how the naïve ectoderm is patterning into two major territories i.e neural plate and ectodermis with neural crest progenitors segregating two domains.

During the gastrulating, primordial germ cells are spared from other somatic cells and undergo reprogramming and migration to form a small tight cluster at the base of allantois at E7.5. BMP signaling is crucial during this specification but little is known why so few cells in proximal epiblast respond to the signaling and selected out from the surrounding somatic cells. We are interested in characterizing this early fate specification by single-cell RNA sequencing and lineage tracing methods.



Research in our lab is funded by:
Swedish Research Council (VR)
Swedish Association for Medical Research (SSMF)
Karolinska Institutet
Jeanssons Stiftelser


Available Postions

Applications for postdoc scholarship, in areas of
Stem cell biology & developmental biology
Master project students are also welcome


Group Members

Qiaolin Deng PhD, assistant professor
Shangli Chen Postdoc
Julio Aguila Benitez   Postdoc
Marlene Yilmaz PhD Student
Yu Pei   Biomedicine master project student


Geng Chen

Mathias  Ahlqvist


Selected publications

Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation.
Chen G, Schell J, Benitez J, Petropoulos S, Yilmaz M, Reinius B, et al
Genome Res. 2016 Oct;26(10):1342-1354

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling.
Nichterwitz S, Chen G, Aguila Benitez J, Yilmaz M, Storvall H, Cao M, et al
Nat Commun 2016 Jul;7():12139

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.
Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula S, Codeluppi S, et al
Cell 2016 May;165(4):1012-26

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

Identification of intrinsic determinants of midbrain dopamine neurons.
Andersson E, Tryggvason U, Deng Q, Friling S, Alekseenko Z, Robert B, et al
Cell 2006 Jan;124(2):393-405

Developmental BiologyGene regulationStem Cell Biology