(A) Experimental protocol. Briefly, [CD11c-DTR > C57BL/6] BM chimeras were treated as indicated with DTx. 2 × 106 CD117- CD11b+ CD115+ Ly6C+ GFPint BM monocytes isolated from Cx3cr1GFP/+ mice were injected intravenously. Macrophages were sorted from the colon and ileum at days 4, 8 and 12 post-transfer. Experiment was repeated three times, total 3–4 samples from each tissue at each time point. (B) Graft-derived macrophages were sorted at days 4, 8 and 12 post transfer based on CD45.1 and CX3CR1 (GFP) expression. GFP+ cells also express CD64, CD11b and variable levels of CD11c, and lacked Ly6C expression. (C) Principal component analysis (PCA) of transcriptomes of BM monocytes and grafted cells from colon and ileum at 4, 8 and 12 days post-transfer. Analysis performed in MATLAB. (D) Expression heat map of 4213 genes that show at least four fold change across all samples in the dataset, divided to seven clusters by the unbiased K-means algorithm in MATLAB. (Supplementary file 1, data sets 1,2, 5–11). (E) Representative genes from heat map in (D). (F–H) Double volcano plots of genes that change from monocytes to day 4, day 4 to day 8 and day 8 to day 12 in the colon (green dots) and ileum (blue dots). Blue and green squares indicate genes that are significantly (Student's T-test, p-value<0.05) changed between the different time points. Numbers within blue and green squares represent the number of genes in the square, namely genes that significantly change. Arrows indicate up –or down-regulation.