{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Paul Pfluger"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16567"],"description":["Allan-Herndon-Dudley syndrome (AHDS) is a rare disorder caused by faulty thyroid hormone transport to the brain, leading to severe movement problems and intellectual disability. Our study in a murine model of the AHDS used snRNAseq to gain deep insights into individual cortical cells, aiming to unravel novel pathologies of the AHDS. Organism: Mus Musculus Tissue: cortical hemispheres and attached cerebral nuclei Groups: 3 x WT, 3x dKO (global, MCT8 & OATP1C1) Mouse Info: age at cortex extraction was 21 days, mice were on a pure C57BL/6J background. Animals were pooled from multiple litters to minimize litter effects. All mice were group-housed on a 12:12-h light-dark cycle at 23°C and fed standard chow diet ad libitum Technology: 10x Genomics"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - see Chromium Next GEM Automated Single Cell 3′ Reagent Kit v3.1 (Dual Index, 10× Genomics, #1000268) according to the manufacturer's instructions","Growth Protocol - After birth, mice were maintained on chow diet, at room temperature (approx 23dC), with a 12h-12h day-night-cycle.","Sequencing - Libraries underwent 150-bp paired-end sequencing of read 2 on a NovaSeq 6000 (Illumina)","Nucleic Acid Extraction - Immediately after sorting, GEM formation and library preparation was performed using the Chromium Next GEM Automated Single Cell 3′ Reagent Kit v3.1 (Dual Index, 10× Genomics, #1000268) according to the manufacturer's instructions.","Sample Collection - At the age of 21 days, immediately after cervical dislocation of 9 WT and 9 dKO (MCT8-OATP1C1-deficient, PMID: 36270613), brains were extracted and weighed. The cortex and all other brain areas were thoroughly dissected using anatomical references for guidance, weighed and then snap frozen in liquid nitrogen and stored at -80°C.For nuclear isolation, 9 WT and 9 dKO frozen cortical hemispheres were each transferred to a Dounce homogenizer containing 3 mL of freshly prepared ice-cold nuclei isolation buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tris pH 8.0, 0.4% IGEPAL 630, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1x phosphatase & protease inhibitor tablet, 0.4 units RNasin Plus RNase Inhibitor, 0.2 units SuperAsin RNase inhibitor).7 Homogenization was achie"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Gene-barcode count matrices were generated by mapping reads to the mouse reference genome GRCm39 (Ensembl release 109) using the CellRanger (v.6.1.2) following sequencing."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["<h4>Background</h4>  The Allan-Herndon-Dudley syndrome (AHDS) is a rare, X-linked human genetic disorder caused by mutations in the monocarboxylate transporter 8 (MCT8), essential for thyroid hormone (TH) transport across the blood-brain-barrier. The resulting central TH deprivation disrupts brain maturation and function, leading to intellectual disability and movement disorders. Cortical development, highly dependent on TH, is particularly affected and contributes significantly to AHDS pathologies. <h4>Methods</h4>  To elucidate disrupted cortical processes, we conducted single nucleus RNA sequencing in a mouse model engineered to mimic the central TH deficiency characteristic of human AHDS. This murine AHDS model features the concomitant deletion of both MCT8 and OATP1C1, a T4 transporte"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["Central T3 deprivation disturbs cortical cilia formation, oligodendrocyte lineage and neuronal cell-cell-communication in a MCT8/OATP1C1 deficient Allan-Herndon-Dudley Syndrome mouse model"],"pubmed_authors":["Anna Molenaar","Paul Pfluger","Anna Molenaar, Ekta Pathak, Miriam Bernecker, Noémi Mallet, Ruth Gutierrez-Aguilar, Cristina Mencias, Dominik Lutter, Meri De Angelis, Gandhari Maity, Peter Kühnen, Benedikt Obermayer, Robert Opitz, Sonja C. Schriever, Timo D. Müller, Paul T. Pfluger","Ekta Pathak"],"additional_accession":[]},"is_claimable":false,"name":"snRNA-seq of cortices from a MCT8-OATP1C1-deficient Allan-Herndon-Dudley Syndrome mouse model","description":"Allan-Herndon-Dudley syndrome (AHDS) is a rare disorder caused by faulty thyroid hormone transport to the brain, leading to severe movement problems and intellectual disability. Our study in a murine model of the AHDS used snRNAseq to gain deep insights into individual cortical cells, aiming to unravel novel pathologies of the AHDS. Organism: Mus Musculus Tissue: cortical hemispheres and attached cerebral nuclei Groups: 3 x WT, 3x dKO (global, MCT8 & OATP1C1) Mouse Info: age at cortex extraction was 21 days, mice were on a pure C57BL/6J background. Animals were pooled from multiple litters to minimize litter effects. All mice were group-housed on a 12:12-h light-dark cycle at 23°C and fed standard chow diet ad libitum Technology: 10x Genomics","dates":{"release":"2026-08-07T00:00:00Z","modification":"2026-08-07T17:55:04.531Z","creation":"2026-01-23T15:46:16.68Z"},"accession":"E-MTAB-16567","cross_references":{"ENA":["ERP188097"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0004184"],"doi":["10.64898/2025.12.23.696195"]}}