Skip to main content

Developmental Biology and Reproductive Medicine

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

Following implantation, the cluster of mouse epiblast cells undergoes rapid proliferation and expansion to form a cup-shaped single-layer epithelium. The pluripotency of the epiblast cells gradually becomes restricted with time and gastrulation commences, which is a fundamental morphogenetic process that generates three germ layers including naïve ectoderm, mesoderm and endoderm. Our goal is to understand how this dynamic process is regulated at transcriptional level.

During the gastrulating, primordial germ cells are spared from other somatic cells and form a small tight cluster at the base of allantois. BMP signaling is crucial during this specification but little is known why so only very few epiblast cells respond to the signaling. We are also interested in how the migration of primordial germ cells are coordinated and how stray primordial germ cells are eliminated. Moreover, we are also interested in the transgenerational inheritance due to the impact of maternal diet and physiological/pathological condition.

In order to answer all these questions, we combine both the molecular and genetic analysis of mouse models with state-of-the-art technologies including single-cell sequencing and CRISPR/Cas9 screening. We also employ embryonic stem cell culture as a tool to reconstitute developmental process in vitro.

Qiaolin Deng's research group

Group members

Qiaolin Deng – Group Leader, PhD, Assistant Professor

Shangli Chen – Postdoc

Han-pin Pui – Postdoc

Yu Pei – Research Assistant


Geng Chen – Postdoc

Julia Aguila-Benitez – Postdoc

Marlene Yilmaz – Student

Mathias Ahlqvist – Student

Available positions

Postdoctoral positions in areas of Stem cell biology & developmental biology, CRISPR/Cas9 screen, Bioinformatics. Master project students are also welcome.


  1. Single cell analysis of early embryo development
  2. Mechanisms of primordial germ cell migration
  3. Effects of maternal diet and hormones on primordial germ cell development

Research Support

  • Swedish Research Council (VR)
  • Swedish Association for Medical Research (SSMF)
  • Karolinska Institutet
  • Jeanssons Stiftelser
  • Åke Wiberg Stiftelser



Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.
Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PPL, et al
Cell Rep 2019 Mar;26(10):2593-2607.e3

Single-cell RNA sequencing: Technical advancements and biological applications.
Hedlund E, Deng Q
Mol. Aspects Med. 2018 02;59():36-46

Revealing allele-specific gene expression by single-cell transcriptomics.
Benitez JA, Cheng S, Deng Q
Int. J. Biochem. Cell Biol. 2017 09;90():155-160

Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation.
Chen G, Schell JP, Benitez JA, Petropoulos S, Yilmaz M, Reinius B, et al
Genome Res. 2016 10;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 07;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 SP, 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


Qiaolin Deng

Senior researcher
08-524 839 33
C3 Department of Physiology and Pharmacology