{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["James Griffiths"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16924"],"description":["Single-cell RNA sequencing was performed on murine oral tissue to characterise immune responses during Candida albicans infection. Control and IL-1RAcP knockout mice were analysed across a time course comprising naïve (uninfected), day 1, and day 2 post-infection samples. The dataset captures genotype-dependent differences in epithelial and immune cell populations and their transcriptional responses to infection. This study enables analysis of cell-type composition, activation states, and gene expression dynamics across infection and between genotypes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on an Illumina platform according to standard 10x Genomics recommendations, generating paired-end reads (Read 1: cell barcode and UMI; Read 2: transcript sequence) along with index reads.","Library Construction - Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium platform (Single Cell 3′ Gene Expression, v3/v3.1 chemistry) according to the manufacturer’s instructions. Briefly, single cells were encapsulated into droplets with barcoded gel beads to generate Gel Bead-in-Emulsions (GEMs), followed by reverse transcription, cDNA amplification, and library construction.","Sample Collection - Mice were infected with Candida albicans as described in the main manuscript. At the indicated timepoints (naive, day 1, day 2 post-infection), tissues (tongue) were harvested, mechanically and enzymatically dissociated into single-cell suspensions, and filtered through a 40 µm cell strainer. Cell viability was assessed  prior to downstream processing.","Nucleic Acid Extraction - Single-cell suspensions were processed directly for library preparation. Cells were counted and viability confirmed (>85%) prior to loading onto the Chromium platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["James Griffiths"],"additional_accession":[]},"is_claimable":false,"name":"scRNA-seq of control and IL-1RAcP knockout across Candida infection timecourse","description":"Single-cell RNA sequencing was performed on murine oral tissue to characterise immune responses during Candida albicans infection. Control and IL-1RAcP knockout mice were analysed across a time course comprising naïve (uninfected), day 1, and day 2 post-infection samples. The dataset captures genotype-dependent differences in epithelial and immune cell populations and their transcriptional responses to infection. This study enables analysis of cell-type composition, activation states, and gene expression dynamics across infection and between genotypes.","dates":{"release":"2026-06-16T00:00:00Z","modification":"2026-06-16T01:00:36.908Z","creation":"2026-04-17T09:27:50.898Z"},"accession":"E-MTAB-16924","cross_references":{"ENA":["ERP192288"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}