5C). cXEN cell derivation. This approach highlights an important function for in cXEN cell derivation. Paracrine FGF signalling compensates for the loss of endogenous and (Soudais et al., 1995; Morrisey et al., 1998; Capo-Chichi et al., 2005), and the SOX factor (Shimoda et al., 2007; Niakan et al., 2010). However, the stochastic nature of EB differentiation complicates the dissection of molecular interactions involved in development. In addition, the ExEn cells created from EBs cannot be managed indefinitely in culture as stable cell lines. However, the overexpression of or is sufficient to drive the establishment of self-renewing XEN cells from mESCs (Fujikura et al., 2002; Shimosato et al., 2007). Nevertheless, it remains unclear whether self-renewing XEN cells can be derived directly from mESCs Vialinin A without requiring transgenic over-expression. The fibroblast growth factor (FGF) receptor Fgfr2 is usually enriched in PrE cells, and the ligand Fgf4 is usually expressed by epiblast progenitor cells within the ICM (Feldman et al., 1995; Arman et al., 1998; Guo et al., 2010). This complementary receptor-ligand expression suggests that epiblast-secreted Fgf4 may be functionally important for PrE development (Rappolee et al., 1994; Goldin and Papaioannou, 2003). It has recently been suggested that PrE formation requires non-cell-autonomous provision of Fgf4 by and has been noted in mESC cultures (Chambers et al., 2007; Toyooka et al., 2008; Kalmar et al., 2009; Lanner et al., 2010). A small proportion of cells in mESC cultures contain extra-embryonic lineage-associated genes (Synthesis Kit (Fermentas). qRT-PCR was performed using Quantace Sensimix on an Applied Biosystems 7500 machine (Life Technologies Corporation, CA, USA). Primer pairs were designed using Primer3 software or previously published (Molkentin et al., 1997; Fujikura et al., 2002; Niwa et al., 2005; Brown et al., 2010) and are outlined in supplementary material Table S4. Immunohistochemistry and Lox imaging Samples were fixed in 4% paraformaldehyde at 4C overnight, permeabilized with 0.5% Tween in 1 PBS for 20 minutes and blocked with 10% FBS diluted in 0.1% Tween in 1 PBS for 1 hour. Main antibodies were diluted at 1:500 in blocking answer and samples incubated at 4C rotating overnight. Samples were incubated for 1 hour at room heat in 1:300 dilution of secondary antibody (Molecular Vialinin A Probes), then washed and covered with 0.1% Tween in 1 PBS containing DAPI Vectashield mounting medium (Vector Lab). A list of the antibodies used can be found in supplementary material Table S5. Images were taken either on an Olympus 1X71 microscope with Cell^F software (Olympus Corporation, Tokyo, Japan), Zeiss Axiovert 200M microscope with AxioVision Rel 4.7 software (Carl Zeiss, Jena, Germany), or Zeiss LSM 700 confocal microscope and ZEN software. Cell numbers were counted manually using the ImageJ Cell Counter Plugin. Flow cytometry Cells were dissociated with 0.05% Trypsin and re-suspended in 500 l FACS buffer (1 PBS, 10% FCS) and 7AAD solution (BD Pharmingen, 5 l/106 cells) to exclude dead cells. Cells were labelled with stage-specific embryonic antigen 1 (SSEA1) primary antibody at a 1:500 dilution in FACS buffer and APC anti-mouse IgM (BD Pharmingen) secondary antibody at a 1:300 dilution, and incubated for 15 minutes on ice. After two washes in FACS buffer, cells were resuspended in 1-2 ml FACS buffer and analyzed on a Beckman Coulter CyAn ADP flow cytometer (Beckman Coulter, High Wycombe, UK). FlowJo software (Becton Dickinson, Oxford, UK) was used to generate dotplots. Microarray analysis Total RNA was isolated as above and DNase treated (Ambion). RNA quality was assessed on a Eukaryote Total RNA Nano Series II (Agilent Technologies, Santa Clara, CA, USA) then processed on an Vialinin A Agilent 2100 Bioanalyzer using the RNA electrophoresis program. All RNA samples were amplified using the Total Prep 96 RNA amplification kit (Ambion). Illumina expression microarray MouseWG-6_V2 (Illumina, CA, USA) was used and the data analyzed with Bioconductor packages. Data have been deposited with GEO and will be released six months after publication (Accession Number “type”:”entrez-geo”,”attrs”:”text”:”GSE38477″,”term_id”:”38477″GSE38477). RESULTS A low dose of retinoic acid and activin promotes differentiation of mES to XEN cells To quantify the proportion of XEN-like cells within mESC cultures in serum and LIF, we used a transgenic reporter cell line in which the gene encoding a green fluorescent protein has been introduced into the endogenous locus (mESCs have high to moderate expression of SSEA1 and were GFPlow (92.3%), whereas a small proportion (1.9%) of cells have moderate SSEA1 expression and were GFPhigh. We then.