Single-cell RNA-sequencing data from developing embryonic human finger joints

A single cell atlas of developing human embryonic proximal and distal interphalangeal finger joints. This deposition holds the raw 10x single-cell sequencing data in FASTQ format and processed data in anndata format. All of the anndata objects contain normalised counts in the .X slot and gene names in the anndata.var. They hold the cluster assignments for the related figure(s) and are ready for use with cellxgene. The six anndata objects are described below: (1) anndata_allQCed_cells_SF2.h5ad. This is the primary object which additionally holds the raw counts for all cells in the .layers['counts'] slot and the Ensembl gene IDs in the .var table. It is recommended to use this object for data analysis. The object contains the data shown in Extended Data Fig. S2a. Integration with scVI was performed with default parameters with regression of % mito and cell cycle phases (both S and G2M). The following parameters were used for the analysis: nearest neighbour graph (NNG): nSCVI_comp=30, k=15; UMAP: min.dist 0.1; Clustering: Leiden, resolution 2. No cell types were removed. (2) anndata_Fig1.h5ad. This object contains cells understood to form the joint tissue as shown in Fig. 1. Integration with scVI was performed with regression of % mito content and cell cycle phases (both S and G2M). The following parameters were used for the analysis: NNG: nSCVI_comp=30, k=20; UMAP:min.dist 0.5; Clustering: Leiden, resolution 2. The following cell types were removed: keratinocytes, myocyte-related cells, erythrocytes, cluster with high mito content, NRK+IRF+ cluster. (3) anndata_stromal1_SF3.h5ad. The object contains all the stromal cells as shown in Extended Data Fig. 3a (stromal cells 1). Integration with scVI was performed with regression of % mito content and cell cycle phases (both S and G2M) . The following parameters were used for the analysis: NNG: nSCVI_comp=30, k=15; UMAP:min.dist 0; Clustering: Leiden, resolution 1.2. The following cell types were removed: myeloid cells, endothelial cells, pericytes, lymphatic endothelial cells, glial cells. (4) anndata_stromal2_Fig2_SF4.h5ad. The object contains the stromal cells as shown in Extended Data Fig. 4a, Fig. 2a (stromal cells 2). Integration with scVI was performed with regression of cell cycle gene expression . The following parameters were used for the analysis: NNG: k=30, UMAP: min dist 0.1, Leiden clustering resolution 1 (with further manual curation). The following cell types were removed from the 'stromal 1' subset: Skin precursors (TWIST2+), tenocytes, MSX1+ cells, low quality cells. (5) anndata_STFs_Fig3a.h5ad. The object contains the soft-tissue fibroblasts as shown in Fig.3a. Integration with scVI was performed with regression of cell cycle phases (both S and G2M). The following parameters were used for the analysis: NNG: k=20, Leiden clustering resolution 0.5. The following cell types were removed from the 'stromal 2' subset: Cartilage and CZSC. (6) anndata_CZSC_chondro_Fig3b.h5ad. The object contains the cartilage cells shown in Fig. 3b. Integration with scVI was performed with regression of cell cycle phases (both S and G2M). The following parameters were used for the analysis: NNG: k=20, Leiden clustering resolution 0.5 . The following cell types were removed from the 'stromal 2' subset: soft-tissue fibroblasts. The following columns are present in the .obs of the anndata objects: \"sample_id\": sample identifier; \"alias\": the sample name; \"subject_id\": Anonymized subject identifier \"sex\": Biological sex; \"post_conception_week\": Post conception week that sample was derived from; \"joint_development_stage\": 'early' corresponds to 8-9 post conception weeks and 'late' corresponds to 12-14 weeks post conception; \"joint\": DIP = distal interphalangeal joint, PIP = proximal interphalangeal joint; \"group\": Categories: 'PIP_early', 'DIP_early', 'PIP_late', 'DIP_late'; \"cluster_id\" and \"cluster\": Cluster assignments for all single cells in the object. \"cluster_id\" corresponds to numeric cluster (details in Table above), while \"cluster\" is a given name used for the respective Figure.; \"pct_mitochondrial\": percentage mitochondrial reads; \"S_score\": Cell cycle S phase score; \"G2M_score\": cell cycle G2M phase score.