Supplementary Materials

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

Sadia Saeed, Jessica Quintin, Hindrik H. D. Kerstens, Nagesha A. Rao, Ali Aghajanirefah, Filomena Matarese, Shih-Chin Cheng, Jacqueline Ratter, Kim Berentsen, Martijn A. van der Ent, Nilofar Sharifi, Eva M. Janssen-Megens, Menno Ter Huurne, Amit Mandoli, Tom van Schaik, Aylwin Ng, Frances Burden, Kate Downes, Mattia Frontini, Vinod Kumar, Evangelos J. Giamarellos-Bourboulis, Willem H. Ouwehand, Jos W. M. van der Meer, Leo A. B. Joosten, Cisca Wijmenga, Joost H. A. Martens, Ramnik J. Xavier, Colin Logie, Mihai G. Netea, Hendrik G. Stunnenberg

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S9
  • References
Table S1
List of genes that are differentially expressed during monocyte (Mo) to macrophages (Mf) differentiation (Fig. 1J).
Table S2
Extended list of gene ontology terms associated with differentially expressed genes during monocyte (Mo) to macrophage (Mf) differentiation (Fig 1J) and genes assigned to the expression modules M1-6 (Fig. 3B).
Table S3
List of genomic loci associated with each epigenomic clusters (Fig. 2A-B, Fig S2A-B).
Table S4
List of genes that fit into differential expression models and that are assigned to expression modules (Fig. 3A).
Table S5
List of the 1581 human DNA sequence-specific transcription factors used in this study (Fig. 4A).
Table S6
List of transcription factor motifs that are enriched in dynamic distal regulatory elements (ACe, Fig. 4D).