Comment[GEAAccession]	E-GEAD-692
MAGE-TAB Version	1.1
Investigation Title	The mechanism of joint homeostasis in the coupling of articular cartilage and synovium
Experiment Description	The temporomandibular joint (TMJ) is mainly composed of the articular condyle, articular disc and synovium tissues. Excessive mechanical stress, inflammation or dislocation of the TMJ disc causes degenerative changes that affect TMJ disorder. By performing single-cell RNA sequencing analysis and spatial transcriptomics Xenium of TMJ disc and synovium tissues, we investigate the mechanism of TMJ homeostasis in the coupling of articular cartilage and synovium.
Experimental Design	cell component comparison design	disease state design	injury design	pathogenicity design	secreted protein identification design	all pairs
Experimental Factor Name	disease
Experimental Factor Type	disease
Person Last Name	Yano	Sequence
Person First Name	Fumiko	Kashiwa
Person Affiliation	Showa University	
Person Roles	submitter	submitter
Public Release Date	2026-06-01
Protocol Name	P-GEAD-2229	P-GEAD-2230	P-GEAD-2231	P-GEAD-2232	P-GEAD-2233	P-GEAD-2234
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	Mouse bone and cartilage tissues of temporomandibular joint (FFPE block) Freshly collected  temporomandibular joint from adult C57bl/6 mice 1. Tissue fixation: 4% PFA at 4°C  O/N (18-24h) fixation 2. Decalcification:  1xPBS wash (3x), Decalcification with 10% EDTA (PH 8.0) for 3 weeks  4°C 3.Dehydration: 1xPBS wash (3x), Dehydration with  70% EtOH 15min 4. Processing default O/N protocol  Embed in paraffin in plane ideal for sectioning hard tissues  5. Sectioning  Ensure to clean the workstation, microtome, tools, and blades with RNase Decontamination Solution before sectioning to minimize introducing exogenous RNases. Utilize a clean, new blade for sectioning  5 µm section thickness has been validated for FFPE samples going into Xenium In Situ Gene Expression	according to the manufacturer's protocol.	Gene panel : KEPGAC_mMulti_100g_gene_panel	according to the manufacturer's protocol.	Fluorescent probe hybridization and imaging were conducted using the Xenium Analyzer (10x Genomics).	On board analysis was perfomed by the xenium-1.7.1.0
SDRF File	E-GEAD-692.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-2
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB17873
Comment[Last Update Date]	2026-06-01