Datasets	Category	Treg source	Type	TotalDEGs	CS up	/DEGs%	CS down	/DEGs%
GSE50096	Lymphoid	Skeletal muscle injured 2w spleen	Array	308	48	15.58	14	4.55
GSE50096	Lymphoid	Skeletal muscle injured 4d spleen	Array	313	47	15.02	12	3.83
E-MTAB-7961	Non-lymphoid	Fibrosis kidney	RNA-seq	2440	179	7.34	71	2.91
E-MTAB-7961	Non-lymphoid	Regeneration kidney	RNA-seq	2608	265	10.16	86	3.30
GSE50096	Non-lymphoid	Skeletal muscle injured 2w muscle	Array	539	74	13.73	27	5.01
GSE50096	Non-lymphoid	Skeletal muscle injured 4d muscle	Array	465	49	10.54	39	8.39

CS, canonical secretome; DEG, differentially expressed gene.

IPA analysis was performed to identify upregulated canonical secretome pathways in benign disease tissues (cut off: p < 0.05 and |Z-score| >= 2). In the benign disease Treg groups, a total of 24 activated pathways were enriched ( Supplementary Table 5 ). Most of the canonical secretome pathways were specific in E-MTAB-7961 kidney regeneration Treg, including Hepatic Fibrosis Signaling Pathway, PDGF Signaling, VEGF Signaling, and VEGF Family Ligand-Receptor Interactions, which functions were related to the tissue repair. IL-6 Signaling was specifically enriched in GSE50096 muscle injury 4D Treg, which was Treg in the muscle during the acute reaction phase after muscle injury.