These microarray data confirmed the altered expression of hundreds of genes in SSc-ILD that we reported previously [6], such as chemokine C-C motif ligand 18 (CCL18), several collagens (types I and III), macrophage activation markers (for example, CD163 and MS4A4A), secreted phosphoprotein 1/osteopontin (SPP1), and others (Additional file 2: Table S2). Here, SPP1 is linked to interstitial lung disease.