Universität Basel Universität Zürich Swiss Institute of Bioinformatics ETH Zurich École Polytechnique Fédérale de Lausanne  Friedrich Miescher Institute for Biomedical Research

Cell Plasticity

Systems Biology of Cell Differentiation

The developmental process that forms a living organism from a fertilized egg cell is still a miracle. While the DNA blueprint is the same in every cell, the program that determines its fate resides in layers of controls on top of the DNA sequence. These determine the expression of genes within the DNA blueprint, and yield hundreds of cell types with unique expression profiles from a single fertilized egg.





Published Data

  Publication   Link to Data
Genome Res. 2013;23(1):60-73. doi:10.1101/gr.142661.112. Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jørgensen H, Stadler MB, van Nimwegen E, Schübeler D. Link
  • Expression data from REST knock-out versus REST wild type cells during in vitro neurogenesis. GEO data.
  • Dataset comprises of 15 ChIP-seq samples using chromatin from embryonic stem (ES) and neuronal progentor (NP) of wildtype and RESTko cells, which was immunoprecipitated, using antibodies against REST, H3K27me3, or Suz12. GEO data
Mol Syst Biol. 2012;8:593. doi:10.1038/msb.2012.23. Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D. Link
  • Strand specific expression profiling by high throughput sequencing. GEO data
  • H3K36me3 ChIP followed by deep sequencing // time-series of mRNA measurement on Affymetrix microarray platform following actinomycinD treatment. MmES Samples: mRNA measurement on Affymetrix microarray platform following thioU labeling and separation of fractions according to labeled (newly synthetised) and unlabeled (pre-existing) RNA. GEO data
Genes Dev. 2012;26(9):920-32. doi:10.1101/gad.188094.112. Polycomb function during oogenesis is required for mouse embryonic development. Posfai E, Kunzmann R, Brochard V, Salvaing J, Cabuy E, Roloff TC, Liu Z, Tardat M, van Lohuizen M, Vidal M, Beaujean N, Peters AH.
  • Expression profiling by array: 3 biological replicates of each of the 4 genotypes (Ring1+/+Rnf2F/F (control), Ring1-/-Rnf2F/F (Ring1 mutant), Ring1+/+Rnf2F/FZp3-cre (Rnf2 mutant) and Ring1-/-Rnf2F/FZp3-cre (Ring1/Rnf2 double mutant)). Each sample contains 50 GV oocytes. GEO data
  • Expression profiling by array: 3 biological replicates (except alpha-amanitin treated maternal Ring1/Rnf2 double mutant, where only 2 replicates were analyzed) of each genotype and treatment group were analyzed. Each sample contains 40 late 2-cell embryos. GEO data
Proc Natl Acad Sci U S A. 2012;109(16):E934-43. doi: 10.1073/pnas.1119798109. Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state. Tiwari VK, Burger L, Nikoletopoulou V, Deogracias R, Thakurela S, Wirbelauer C, Kaut J, Terranova R, Hoerner L, Mielke C, Boege F, Murr R, Peters AH, Barde YA, Schübeler D.
  • Gene expression in the Top2β knocnout ES, NP and TN stages of stem cell differention to the corresponidng wild type cells. In vitro derived neurons and cortical glutamatergic neurons were either treated with DMSO or ICRF-193 and were compared to reveal differentially expressed genes. GEO data
  • Chromatin IP was performed with Top2β antibodies in WT neurons and hybridized to custom designed tiling array. GEO data
  • Our Dataset comprises 5 ChIP-seq samples using chromatin from ES, NP and TN cells which was immunoprecipitated, using antibodies against H3K27me3, H3K4me2, RNA Pol II, JNK1/3 and NF-YA. From the same cells we generated biological replicates of RNA-seq data. GEO data
  • Gene expression in the SP600125 treated neurons was compared to the DMSO treated neurons. a to e suffixes indicate biological replicates. Batch indicates different batches of the drug SP600125. GEO data
Nature. 2011;480(7378):490-5. doi: 10.1038/nature10716. DNA-binding factors shape the mouse methylome at distal regulatory regions. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D.
  • RNA_sequencing of mouse embryonic stem (ES) cells and derived neuronal progenitors (NP). GEO Data
  • Strand specific expression profiling by high throughput sequencing. GEO Data
  • Pax6 ChIP-chip in mouse NP cells. GEO Data
  • CTCF ChIP sequencing in mouse ES and Dnmt1/3a/3b triple knock-out ES (TKO) cells. H3K4me1, H3K4me2 and H3K27me3 ChIP sequencing in mouse SE cells. GEO Data
  • Whole genome shotgun bisulfite sequencing of mouse embryonic stem (ES) cells and derived neuronal progenitors (NP). GEO Data


E-mail: sybit(at)sympa.systemsx.ch | Wiki: SyBIT Wiki
Copyright © 2012,SyBIT - SystemsX.ch Biology IT.

E-mail: sybit(at)sympa.systemsx.ch
Wiki: SyBIT Wiki
Copyright © 2012,SyBIT - SystemsX.ch Biology IT.