{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tangra Draia-Nicolau"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16260"],"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":["Nucleic Acid Extraction - Tissue samples for those datasets underwent enzymatic digestion with pronase (Streptomyces griseus, 1 mg/mL) for 25 minutes at room temperature. Cells were dissociated and triturated into a single-cell suspension using three glass Pasteur pipettes of decreasing diameters in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). For P30 datasets, enzymatic digestion and cell dissociation followed the Worthington Papain Dissociation System manufacturer's instructions  Enzymatic digestion was processed by using pronase (Septomyces Argeus at 1 mg/mL) during 25 min at room temperature (RT) for P0 to P8 datasets. Cells were dissociated and triturated into single cell suspension in a solution consisted of ACSF, 1% FCS and DNAse (1µl/10mL). Trituration was carried out by using 3 glass pasteur pipets prepared at 3 different diameters. For P30 datasets, we used the Worthington Papain Dissociation System to carry out the enzymatic digestion and the cell dissociation following the manufacturer instructions.","Library Construction - Single-cell suspensions were loaded onto a Chromium Next GEM Chip G using the Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics), following the manufacturer's protocol. Individual cells or nuclei were encapsulated into Gel Beads-in-Emulsion (GEMs), where barcoding and reverse transcription (GEM-RT) occurred to generate barcoded full-length cDNA.  After GEM-RT incubation, emulsions were broken, and the barcoded cDNA was recovered and amplified via PCR with SPRIselect bead-based cleanups. The amplified cDNA was enzymatically fragmented, followed by end repair, A-tailing, adaptor ligation, and sample index PCR to construct final 3' gene expression sequencing libraries.  Constructed libraries were sequenced on an Illumina HiSeq 4000 platform. The final libraries incorporate Illumina P5 and P7 adapters, with Read 1 capturing the 10x barcode and UMI sequences and Read 2 sequencing the cDNA fragment for gene expression analysis.","Sequencing - Libraries were sequenced on an Illumina HiSeq 4000 platform using 10x Genomics v3 chemistry. Sequencing reads were aligned to the mouse pre-mRNA reference transcriptome (mm10) using the 10x Genomics CellRanger pipeline (versions 3.1.0 or 6.1.1) with default parameters.","Sample Collection - Animals: Mice (Mus musculus) were group-housed (2–5 mice per cage) with same-sex littermates under a 12-hour light-dark cycle, with ad libitum access to food and water. Animals were bred and maintained on a mixed SVeV-129/C57BL/6N genetic 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). Single-Cell Isolation: Mice brains were dissected in ice-cold, carbogen-bubbled (95% O₂, 5% CO₂) artificial cerebrospinal fluid (ACSF). The ACSF composition was: 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 kynurenic acid (0.567 g/L). Brains were sliced into 300 µm coronal sections (P0 and P2 mice) or 500 µm coronal sections (P5, P8, and P30 mice) using a vibratome (Leica). The somatosensory cortex was dissected under a binocular microscope. Single-Nuclei Isolation: The somatosensory cortex was dissected as described for single-cell isolation. Dissected cortices were immediately transferred into 500 µL of Hibernate™-E Medium (#A12476-01) and flash-frozen for 3 minutes in isopentane pre-cooled to -80°C. Samples were stored at -80°C for long-term preservation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["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.","10X v3"],"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":["Inferring Ligand-Receptor Interactions between neuronal subtypes during mouse cortical development"],"pubmed_authors":["Lucas Silvagnoli","Ludovic Telley","Tangra Draia-Nicolau","Léa Corbières","Annousha Govidan","Antoine De Chevigny","Rémi Mathieu, Léa Corbières,Tangra Draia-Nicolau,Annousha Govindan, Vianney Bensa,Emilie Pallesi-Pocachard, Lucas Silvagnoli, Alfonso Represa, Carlos Cardoso, Ludovic Telley,  Antoine de Chevigny","Carlos Cardoso","Rémi Mathieu","Alfonso Represa","Vianney Bensa","Emilie Pallesi-Pocachard"],"additional_accession":[]},"is_claimable":false,"name":"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":"2026-01-30T00:00:00Z","modification":"2026-01-31T02:02:06.489Z","creation":"2026-01-19T13:41:03.65Z"},"accession":"E-MTAB-16260","cross_references":{"ENA":["ERP187866"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.09.02.610245"]}}