{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Clarisse Ganier"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17297"],"description":["Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by recurrent painful abscesses and tunnels in flexural sites. The mechanisms driving HS pathogenesis, particularly the interactions between epithelial, stromal and immune cell populations, remain incompletely understood. To characterise the cellular and molecular landscape of HS, we analyzed lesional skin from severe HS patients using single-cell RNA-sequencing and spatial transcriptomics, with a focus on fibroblast-keratinocyte interactions. We identified a migratory S100+ pathogenic keratinocyte state enriched within HS lesions and observed spatially distinct fibroblast populations associated with different tissue compartments. COL6A5+ papillary fibroblasts showed spatial association with undifferentiated "],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Optimal permeabilization time for 10um skin sections was 20minutes. cDNA libraries were quality controlled using the Agilent Bioanalyser.","Library Construction - The cDNA libraries were sequenced on the Illumina HiSeq 4000 system, targeting 300 million reads per section with parameters 28cy R1, 8cy i7 index, 0cy i5 index, 91cy read 2.","Sample Collection - Fresh frozen OCT-embedded skin biopsies were cryosectioned as 10 μm sections, placed onto SuperFrost Plus glass slides (Thermo Fisher Scientific, Waltham, MA, USA) and stored for less than a week at -80˚C prior to high sensitivity library preparation. Optimal RNA integrity on the skin sections was assessed by RNAscope using three housekeeping genes with high (UBC) and medium (PPIB) expressors (Supplementary figure 3B). We also validated the integrity of the Visium library after sequencing: all samples presented good RNA quality (Supplementary figure 3C). However, we excluded 2 of the 32 10X Visium samples from further analysis due to poor tissue attachment to the slide.  Visium spatial gene expression slides and reagents were used according to manufacturer instructions ","Sequencing - For each frozen sample, FASTQ files were manually aligned with corresponding H&E images and then analyzed with Space Ranger version 1.3.0 which uses the STAR genome aligner version v.2.5.1b and the human reference genome : Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome) [star] and Homo_sapiens (GRCh38_15_plus_hs38d1 + ensembl_90_transcriptome) [star]."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Standard Space Ranger output for 10x including gene matrices; barcodes etc"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Xinyi Du-Harpur","Clarisse Ganier"],"additional_accession":[]},"is_claimable":false,"name":"Pathogenic Keratinocyte States and Fibroblast Niches Define the Tissue Microenvironment in Severe Hidradenitis Suppurativa - Visium","description":"Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by recurrent painful abscesses and tunnels in flexural sites. The mechanisms driving HS pathogenesis, particularly the interactions between epithelial, stromal and immune cell populations, remain incompletely understood. To characterise the cellular and molecular landscape of HS, we analyzed lesional skin from severe HS patients using single-cell RNA-sequencing and spatial transcriptomics, with a focus on fibroblast-keratinocyte interactions. We identified a migratory S100+ pathogenic keratinocyte state enriched within HS lesions and observed spatially distinct fibroblast populations associated with different tissue compartments. COL6A5+ papillary fibroblasts showed spatial association with undifferentiated ","dates":{"release":"2026-07-19T00:00:00Z","modification":"2026-07-19T01:00:43.201Z","creation":"2026-07-09T10:49:31.304Z"},"accession":"E-MTAB-17297","cross_references":{"ENA":["ERP200974"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}