Spatial gene expression maps in vertebrate limbs display conserved and regenerative species-specific features within connective tissue - Seurat Objects

Seurat objects used in the following paper: Spatial gene expression maps in vertebrate limbs display conserved and regenerative species-specific features within connective tissue Conor L. McMann, Chanyoung Park, Jennifer K. Cloutier, Peter W. Reddien bioRxiv 2025.12.15.694399; doi: https://doi.org/10.64898/2025.12.15.694399 All Seurat objects are final objects used for analysis in paper. All objects are processed, meaning they have been subjected to CellBender and scDblFinder quality control, as well as filtered for minimum and maximum UMI and unique gene counts. See methods for details. "_AllCells" indicates that the object including the full atlas of cells from the designated samples. "_CTOnly" indicates that only the subclustered, annotated connective tissue cells from those samples are included. Metadata for each cell includes "orig.ident" (position of origin), "seurat_clusters" (the original Seurat cluster identity), and "celltype" (annotated cell type identity, either broad class for _AllCells files or designated CT subset in _CTOnly files). Seurat objects contain cells from the following positional hindlimb origins: proximal, medial, distal, dorsal, ventral, anterior, and posterior. Axolotl objects also include forelimb medial cells. The mouse NextGEM objects do not have forelimb cells. The mouse GEMX files include only forelimb medial and hindlimb medial cells, which were analyzed separately due to different chemistries generating difficult to combine datasets.