RNA as in. Two passages of the 5538, 7711 and 0029 fibroblasts were similarly treated to extract and amplify RNA. In situ Hybridization Whole-mount in situ hybridization. The isolated embryonic discs that were dissected from AI, IVP, or SCNT conceptuses were fixed in 4% paraformaldehyde, stored, and hybridised with a Brachyury-DIG-labelled riboprobe as in. The hybridized embryos were mounted in mowiol and photographed with a Coolsnap camera. The embryo staging was as in. In situ hybridization on tissue sections. Extra-embryonic tissue sections from AI, IVP, and SCNT conceptuses at Day 18 were hybridized as described in, using DIG-labelled 
riboprobes. Sense and antisense riboprobes were also prepared as in, using specific primers adapted to i) the plasmid of each cDNA library to generate a cDNA template prior to in vitro transcription and ii) the orientation of each cDNA to synthesise the proper sense and antisense probes. Of the ESTs of interest that were initially annotated, 4 gave either no DNA template or no riboprobe, 5 gave similar results with the sense and antisense probes, 2 gave distinct signals with the sense and anti-sense probes, 18 gave weak signals, 4 gave fuzzy signals and were thus left over. Finally, 22 cDNA fragments that were i) isolated from the 10 K cDNA libraries, ii) successfully transcribed in vitro, and iii) provided clear sense/antisense signals, were considered. Among them, 8 were ubiquitous whereas 14 displayed restricted cellular locations. Two controls were used: the c93/ SSLP1 or SOLD1 and Pou5f1/Oct-4 cDNA . Slides were scanned with a Nanozoomer and exported as.tif images. Bovine 10 K Array This array was partly developed in the laboratory. It contains 7800 cDNA inserts from term placenta and 2400 cDNA inserts from extra-embryonic tissues of bovine embryos as well as young foetuses. The corresponding libraries are indexed in Unigene as Lib. 3743, 17188, 15992. Internal controls were also included in the array. Finally, 10,214 unique cDNA were spotted onto Nylon NC membranes with a 363 pattern at the CRB GADIE. Array Hybridisation, Image Acquisition, and Quantification Array hybridisation was as described in. Briefly, 500 ng of amplified RNA were labelled with dATP by RT and hybridised to each membrane. Membranes were then exposed to phosphorscreens for 7 days. The hybridisation signals were quantified with the Imagene 5.5 software on the ICE platform. The hybridisation with the extra-embryonic tissues gave rise to the GSE34944 data set in the Gene Omnibus database. The hybridisations with the 5538, 7711 and 0029 fibroblasts gave rise to a data set with only one biological replicate and thus were not deposited in the GEO database. Scanning Electron Microscopy A piece of each EE tissue was rinsed with phosphate-buffered saline and fixed in SU11274 chemical information pubmed ID:http://www.ncbi.nlm.nih.gov/pubmed/22189542 2.5% glutaraldehyde for 30 min at room temperature. After having been washed repeatedly with distilled water, samples were dehydrated in an ascending series of ethanol and dried at the critical point using carbon dioxide as the transitional fluid. Dried samples were then coated with a conductive layer of carbon. Observations and photographs were made using a Hitachi S4500 scanning electron microscope set at 8 or 10 kV. Gene Expression Data Analysis Supporting Information Acknowledgments The authors gratefully acknowledge Y Lavergne1,2 and S Peron1,2 for IVP and cell culture, T Meylheuc for the training on the SEM of the microscopy platform MIMA2, P Bardou for the submissi