REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-collagen XII, KR33	Veit et al.2	RRID: AB_2801624
Goat anti-rabbit IgG(H+L), Cy3	Jackson ImmunoResearch	Cat# 111-165-144; RRID: AB_2338006
Chemicals, peptides, and recombinant proteins
Bovine Serum Albumin	SERVA	Cat# 11924
Collagenase II	Worthington Biochemicals	Cat# LS004176 Lot# 41K21578 ACT 265U/mg
DAPI	Sigma-Aldrich	Cat# 32670
DMEM/F12	Thermo Fisher Scientific	Cat# 11320033
Ethylenediaminetetraacetic acid (EDTA)	Carl Roth	Cat# 8043.2
Fetal Bovine Serum	Biochrom	Cat# S0115
Hyaluronidase	Sigma-Aldrich	Cat# H3506
Iodine-potassium iodide solution	Sigma-Aldrich	Cat# L6146
10% Neutral-buffered formalin (NBF)	Sigma- Aldrich	Cat# HT501128
Mowiol 4-88	Calbiochem	Cat# 475904
Normal Goat Serum	Abcam	Cat# ab7481
Paraformaldehyde	VWR	Cat# 28794.295
Sodium acetate trihydrate	Merck	Cat# 1.06267.1000
Sodium monobasic phosphate dihydrate	VWR	Cat# 28011.291
Triton X-100	Sigma-Aldrich	Cat# T9284
Tween20	Sigma-Aldrich	Cat# P7949
Wheat Germ Agglutinin, Alexa 488 conjugated	Invitrogen	Cat# W11261
Deposited data
Single cell RNA-seq data	this study	GEO: GSE234964
Experimental models: Organisms/strains
Mouse C57BL6N/129JS2/SvPasCrl, Col12a1 KO	Izu et al.9	N/A
Software and algorithms
3D Gaussian filter algorithm	Bouxsein et al.33	https://www.scanco.ch/sw.html
Cell Ranger V7.0.0	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
CTVox	Bruker microCT	https://www.bruker.com/en/products-and-solutions/preclinical-imaging/micro-ct/3d-suite-software.html
Funrich V3.1	Pathan et al.34	http://www.funrich.org/
Graphpad 8.0	Graphpad	https://www.graphpad.com/
Grid/Collection stitching tool	Preibisch et al.35	https://imagej.net/plugins/image-stitching
ImageJ, Fuji Distribution	ImageJ	https://imagej.net/ij/index.html
Loupe Browser V6.2	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
NRecon	Bruker microCT	https://www.bruker.com/en/products-and-solutions/preclinical-imaging/micro-ct/3d-suite-software.html
Myosoft	Encarnacion-Rivera et al.11	https://bio.tools/myosoft