{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE324nnn/GSE324753/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Mus musculus"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE324753"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Highly sensitive, sub-micron spatial host-microbiome transcriptomics in FFPE tissues via iterative hydrogel expansion","description":"Spatial transcriptomics (ST) of clinical formalin-fixed paraffin-embedded (FFPE) tissues is fundamentally limited by a trade-off between spatial resolution and transcriptomic sensitivity due to severe molecular crowding and RNA degradation. Here, Ex-spRandom is presented, a highly sensitive platform that integrates random-primed in situ cDNA synthesis with an interpenetrating polymer network (IPN)-based tissue expansion protocol. This physicochemical synergy physically decrowds the dense FFPE matrix, directly converting fragmented host and microbial RNAs into stably anchored cDNA. Consequently, Ex-spRandom translates macro-scale arrays into a sub-micron effective resolution of ~0.9 µm while achieving an unprecedented transcriptomic sensitivity exceeding 40,000 unique genes per sample. This platform successfully rescues non-coding regulatory transcripts and unmasks continuous neurodevelopmental trajectories in the dense embryonic eye. Furthermore, it enables the simultaneous, high-fidelity spatial mapping of host epithelial architectures alongside localized resident microbiomes in the colon. By breaking the resolution-sensitivity barrier without aggressive proteolysis, Ex-spRandom establishes a highly scalable framework for deciphering complex structural and functional microenvironments across vast archival clinical cohorts.","dates":{"publication":"2026/08/26"},"accession":"GSE324753","cross_references":{"GSM":["GSM9584942","GSM9584943","GSM9584940","GSM9584941","GSM9584946","GSM9584944","GSM9584945","GSM9584939","GSM9584938"],"GPL":["24247"],"GSE":["324753"],"taxon":["Mus musculus"],"PMID":["[42605963]"]}}