Extended Data Fig. 9: Haemogenic potential of BM ECs and transcriptome characterisation of the YFP⁺ and YFP⁻ LSK cells.

a, representative flow cytometry profile showing the gates used to isolate the CD144⁺CD45⁻ and the CD144⁻CD45⁺ populations. Image representative of 7 mice. b-e, representative pictures of the CD144⁻CD45⁺ (b) and CD144⁺CD45⁻ (c, d) cells from 8-day old mouse bone marrow in culture in the endothelial/haematopoietic medium. A high number of floating cells are present in the CD144⁻CD45⁺ cells fraction (b). Flat adherent cells (in c) and round, floating, haematopoietic-like cells (arrows in c and d) are present in the CD144⁺CD45⁻ cell fraction after 4 days of culture. Image representative of 3 experiments. Bar = 10µm. e, f, representative FACS analysis of the CD45⁺ populations generated after 4 days of culture from the CD144⁻CD45⁺ (e) and the CD144⁺CD45⁻ (f) cell populations. Image representative of 3 experiments. g, PCA with the entire set of mRNAs (30,922 genes) as variables and the basic set of YFP⁺ (green) and YFP⁻ (red) LSK cells as observations. The two types of transcriptomes were strongly separated (3 biological replicates per population). h, Major GO categories given by DAVID for the gene sets up-regulated in YFP⁺ (green) and YFP⁻ (red) LSK cells. i, Hierarchical clustering obtained with the 23 samples (3 biological replicates per population except for HC BM and LSK CD150⁺ BM where quadruplicates were used) as observations and the gene set of 2056 DEGs (986 up, 1070 down) as variables was generated from the PCA displayed in Fig. 6a, bottom panel. Branch organisation reflects the association between the different samples displayed on the PCA. Scale Bars: 50µm in b, c, d.