The development of human induced pluripotent stem cell (iPSC)–based regenerative therapies is challenged by the lack of specific cell markers to isolate differentiated cell types and improve differentiation protocols. This issue is particularly critical for notochordal-like cells and chondrocytes, which are crucial in treating back pain and osteoarthritis, respectively. Both cell types produce abundant proteoglycan aggrecan (ACAN), crucial for the extracellular matrix. We generated two human iPSC lines containing an ACAN-2A-mScarlet reporter. The reporter cell lines were validated using CRISPR-mediated transactivation and functionally validated during notochord and cartilage differentiation. The ability to isolate differentiated cell populations producing ACAN enables their enrichment even in the absence of specific cell markers and allows for comprehensive studies and protocol refinement. ACAN’s prevalence in various tissues (e.g., cardiac and cerebral) underscores the reporter’s versatility as a valuable tool for tracking matrix protein production in diverse cell types, benefiting developmental biology, matrix pathophysiology, and regenerative medicine. Overall design: ACAN-2A-mScarlet human iPSC reporter lines were used to investigate the efficiency of chondrogenic and notochordal differentiation. Cells were collected in the end of the differentiation and the mScarlet postive and negative cells were sorted by flowcytometry. Bulk RNA seqeuncing via CEL-seq2 was performed to characterize the different transcriptome of the mScarlet positive and negative cells.