{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Draia-Nicolau Tangra Ondina"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16355"],"description":["The cerebral cortex comprises diverse excitatory and inhibitory neuron subtypes, each with distinct laminar positions and connectivity patterns. Yet, the molecular logic underlying their precise wiring remains poorly understood. To identify ligand–receptor (LR) interactions involved in cortical circuit assembly, we tracked gene expression dynamics across major neuronal populations at 17 developmental stages using single-cell transcriptomics. This generated a comprehensive atlas of LR-mediated communication between excitatory and inhibitory neuron subtypes, capturing known and novel interactions. Notably, we identify neogenin-1 as the principal receptor for Cbln4 during the perinatal period, mediating synapse formation between somatostatin-expressing interneurons and glutamatergic neurons. We also identify cadherin superfamily members as candidate regulators of perisomatic inhibition onto deep and superficial excitatory neurons by parvalbumin-expressing basket cells, with opposing effects on synapse formation. These findings suggest a context-dependent role for cadherins in synaptic specificity and underscore the power of single-cell transcriptomics for decoding molecular mechanisms of cortical wiring."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Nuclei suspensions were prepared according to 10x Genomics recommendations. GEM generation and barcoding were performed using the Chromium Next GEM Single Cell 3' Reagent Kits, following the manufacturer’s protocol. Single-nucleus suspensions were loaded onto a Chromium Next GEM Chip G, and GEMs were generated using the Chromium Controller. After GEM-RT incubation, cDNA was recovered, cleaned up, and amplified using SPRIselect bead-based purification. The amplified cDNA underwent fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR to construct the final 3' gene expression libraries.","Sample Collection - Mice (Mus musculus) were group-housed (2–5 mice per cage) with same-sex littermates on a 12-hour light-dark cycle, with ad libitum access to food and water. They were bred and maintained on a mixed SVeV-129/C57BL/6N background. All animal experiments were conducted in accordance with European Communities Council Directives and approved by French ethical committees (Comité d’Éthique pour l’expérimentation animale no. 14; permission number: 62-12112012, Apafis #21683-2019073011285386v4). For sample collection, mice brains were dissected while submerged in ice-cold, carbogen-bubbled (95% O₂, 5% CO₂) artificial cerebrospinal fluid (ACSF). The ACSF composition was as follows: NaCl (7.32 g/L), KCl (0.26 g/L), NaH₂PO₄·H₂O (0.165 g/L), CaCl₂·2H₂O (0.438 g/L), MgCl₂·6H₂O (0.264 g/L), D(+)-Glucose (1.98 g/L), NaHCO₃ (2.1 g/L), and acid kynurenic (0.567 g/L). The somatosensory cortex was dissected under a binocular loop.","Nucleic Acid Extraction - For single-nucleus isolation, the dissected somatosensory cortex was immediately transferred into 500 µL of Hibernate™-E Medium (#A12476-01) and frozen for 3 minutes in isopentane pre-cooled to -80°C. Samples were stored at -80°C for long-term preservation. After conservation, the medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. The tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times with a wide-bore tip and incubated for an additional 10 minutes on ice. After lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times with a regular-bore tip. The suspension was filtered through a 30 µm cell strainer to remove debris, transferred to a 1.5 mL tube, and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis.","Sequencing - The constructed libraries (10x v3) were sequenced on an Illumina HiSeq 4000 platform. Sequencing reads were aligned to the mouse pre-mRNA reference transcriptome (mm10) using the 10x Genomics CellRanger pipeline (version 3.1.0 or 6.1.1) with default parameters."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Chromium Next GEM Chip G","Illumina HiSeq 4000","Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis."],"pubmed_abstract":["The cerebral cortex hosts a diverse array of excitatory glutamatergic and inhibitory GABAergic neuron types, each characterized by distinct positional and synaptic connectivity patterns. However, the molecular mechanisms orchestrating this precise organization remain largely unknown. To identify ligand-receptor (LR) pairs regulating interactions and connectivity among cortical neurons during embryonic and postnatal development, we analyzed the transcriptional dynamics of all genes across major cortical neuron subtypes at 17 developmental time points using single-cell transcriptomics. From these data, we constructed a comprehensive bioinformatic atlas that inferred significant LR-mediated interactions between glutamatergic and GABAergic neurons throughout cortical maturation. This atlas not only corroborated known interactions but also enabled the discovery of novel regulators, identifying two cadherin superfamily members as key mediators of perisomatic inhibition in deep and superficial layer excitatory neurons by parvalbumin-expressing basket cells. These findings underscore the power of large-scale transcriptional profiling to unravel fundamental molecular mechanisms driving cortical circuit assembly."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["Uncovering the Molecular Logic of Cortical Wiring between Neuronal subtypes Across Development Through Ligand–Receptor Inference"],"pubmed_authors":["Lucas Silvagnoli","Rémi Mathieu, Tangra Draia-Nicolau,Léa Corbières,Annousha Govindan, Vianney Bensa,Emilie Pallesi-Pocachard, Lucas Silvagnoli, Alfonso Represa, Carlos Cardoso, Ludovic Telley,  Antoine de Chevigny","Ludovic Telley","Draia-Nicolau Tangra Ondina","Léa Corbières","Annousha Govidan","Antoine De Chevigny","Rémi Mathieu","Alfonso Represa","Vianney Bensa","Emilie Pallesi-Pocachard"],"additional_accession":[]},"is_claimable":false,"name":"Single-nucleus data for Uncovering the Molecular Logic of Cortical Wiring between Neuronal subtypes Across Development Through Ligand–Receptor Inference","description":"The cerebral cortex comprises diverse excitatory and inhibitory neuron subtypes, each with distinct laminar positions and connectivity patterns. Yet, the molecular logic underlying their precise wiring remains poorly understood. To identify ligand–receptor (LR) interactions involved in cortical circuit assembly, we tracked gene expression dynamics across major neuronal populations at 17 developmental stages using single-cell transcriptomics. This generated a comprehensive atlas of LR-mediated communication between excitatory and inhibitory neuron subtypes, capturing known and novel interactions. Notably, we identify neogenin-1 as the principal receptor for Cbln4 during the perinatal period, mediating synapse formation between somatostatin-expressing interneurons and glutamatergic neurons. We also identify cadherin superfamily members as candidate regulators of perisomatic inhibition onto deep and superficial excitatory neurons by parvalbumin-expressing basket cells, with opposing effects on synapse formation. These findings suggest a context-dependent role for cadherins in synaptic specificity and underscore the power of single-cell transcriptomics for decoding molecular mechanisms of cortical wiring.","dates":{"release":"2025-12-14T00:00:00Z","modification":"2025-12-14T02:02:16.922Z","creation":"2025-12-04T11:51:06.574Z"},"accession":"E-MTAB-16355","cross_references":{"ENA":["ERP186153"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.09.02.610245"]}}