Reads were aligned to the GRCh38 (version 90) for genome annotation, demultiplexing, barcode filtering, and gene quantification. hiPSC chondrogenesis, as well as dynamic transcriptome profiles orchestrating chondrocyte proliferation and differentiation. and and were upregulated in unique hiPSC lines, both the hypertrophic chondrocyte marker collagen type X alpha 1 chain (and at later time points (Fig.?2B). Gene KW-2478 ontology (GO) enrichment analysis of the genes using R package KW-2478 GAGE was performed13. Significantly upregulated GO terms in Biological Process highlighted skeletal system and cartilage development (Supplementary Fig.?2A). GAGE analysis also exposed that 134 out of the 205 genes defined by cartilage development (GO:0051216) were significantly increased. Interestingly, in addition to upregulated and as a hub gene of neurogenesis while was highly associated with melanocyte development. scRNA-seq data of d14 pellets (with a total of 2148 cells and 3784 genes) was used for this computation. Sequencing of mixed-species ensured a low cell multiplet rate (2.7%) (Supplementary Fig.?3A). To verify the reproducibility of the differentiation, two batches of d28 samples were collected from self-employed experiments for scRNA-seq. Canonical correlation analysis (CCA) was used to align cells from the two batches15 (Supplementary Fig.?3B). The cells in the same cluster from different batches exhibited a high correlation in their gene manifestation (Spearmans rank coefficient (Fig.?3C). Additional neural cell markers such as and were also enriched with this branch (Supplementary Fig.?3E). The off-target cell differentiation toward neurogenic lineage confirmed our findings of improved in the bulk RNA-seq data. To explore unique cell populations at each stage, scRNA-seq data were subjected to unsupervised clustering and visualized using t-distributed stochastic neighbor embedding (tSNE) plots (Fig.?3D). By comparing DEGs with signature genes of KW-2478 cell types in the literature and GO term analyses, we annotated broad cell populations by combining clusters expressing related marker genes. For example, 2 of 7 clusters recognized in the chondroprogenitor (Cp) stage not only had high manifestation levels of and but were also enriched in several markers resembling neural crest cells including and forkhead package D3 (are known markers for mesenchyme (Supplementary Fig.?3G)18. Related major cell populations were also observed in d1 and d3 pellets, and?it appeared the percentage of chondrogenic?cells increased in d7 while there was a decreased percentage of neural crest cells?over time (Supplementary Fig.?3H, I). Of notice, a cluster with high manifestation of melanocyte-inducing TF (was strongly associated with several TFs regulating neural differentiation. We also observed that was associated KW-2478 with both and ETS variant 1 (and labeling?(green) but more homogenous distribution (reddish) in the pellets. Level pub?=?200?m. The experiment was performed twice with related results. RNA fluorescence in situ hybridization (RNA-FISH) labeling of WNTs and within d28 pellets indicated that although some labeling could be detected in the center of the pellets, most WNTs were located in the perichondral coating, consistent to the inhomogeneous cell populations observed via IHC staining. Furthermore, C59-treated pellets showed a more homogenous distribution of RNA-FISH labeling vs. TGF-3-treated pellets (Fig.?4E and Supplementary Fig.?5). scRNA-seq confirms WNT inhibition enhances chondrogenesis To determine how WNT inhibition modified cell populations in chondrogenesis and to determine chondrocyte subpopulations, pellets treated with C59 were analyzed using scRNA-seq with a total of 14,683 cells from your stage of hiPSC, Cp as well as d7, d14, d28, and d42 C59-treated pellets (Fig.?5A, B). We found the C59-treated pellets comprised two major cell populations: mesenchyme and chondrocytes. Mesenchyme exhibited high manifestation of actin (manifestation, higher levels of and manifestation, and an earlier decrease in manifestation as compared to pellets treated with TGF-3 only (Supplementary Fig.?6A). Open in a separate windowpane Fig. 5 scRNA-seq of pellets with WNT inhibition shows Hyal1 improved chondrogenesis.A scRNA-seq was performed within the pellets with WNT inhibition. B Chondrocytes and mesenchymal cells were two major populations in C59-treated pellets. Cells that approved quality?control were?utilized for tSNE plots; hiPSC: 4798 cells,?Cp: 1888 cells, d7: 1682 cells, d14: 3076 cells, d28: 1756 cells, and d42: 1483 cells. C Differentiation trajectory of C59-treated pellets. scRNA-seq data with a total of 14,683?cells from your stage of hiPSC, Cp as well while d7, d14, d28, and d42 C59-treated pellets were used to reconstruct the differentiation trajectory. D C59-treated.