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Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets [P0NeuronData]

ABSTRACT: Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets [P0NeuronData]

PROVIDER: PRJNA720221 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14160725_1.fastq.gz	Fastqsanger.gz
	SRR14160725_2.fastq.gz	Fastqsanger.gz
	SRR14160726_1.fastq.gz	Fastqsanger.gz
	SRR14160726_2.fastq.gz	Fastqsanger.gz
	SRR14160727_1.fastq.gz	Fastqsanger.gz

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Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets [P0NeuronData]

Project description:We uncovered orderly genetic tiers that sequentially divide groups of neurons by their motor- sensory, local-long range, and excitatory-inhibitory features. The genetic signatures defining neuronal projections were tied to neuronal birthdate and conserved across cardinal classes. The intersection of cardinal class with projection markers provides a unifying taxonomic solution for systematically identifying distinct functional subsets. In order to minimize technical and biological variabilities, timed-matings were set up to obtain both Vglut2:Cre; tdTomato and Vgat:Cre ;tdTomato neonates at postnatal day 0 on the experiment day. Sex of the animals were visually inspected and verified by genotyping (40). Lumbar segments were dissected from Vglut2; tdTomato (2 female and 1 male) and Vgat; tdTomato (2 female and 1 male) in aCSF. Cell dissociation was conducted using Papain following the manufacturer’s instruction (Worthington Biochemical) with 5% Trehalose, 50uM APV, and 800uM KA added during the dissociation process (41). Via FACS (FACSDIVA, BD), 30,000 Vglut2; tdTomato cells and 30,000 Vgat;tdTomato cells were sequentially collected into 500ul of FACS buffer (DMEM w/o Phenol Red; 1mM EDTA; 25mM Hepes pH7.0; 5% FBS). Cell suspension was centrifuged at 300 rcf for 2 minutes, and supernatant was removed leaving 60 ul of FACS buffer and cell pellet. The cells were resuspended, and 33.4 ul of the resuspended cells (~30,000 cells) were loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.

2021-04-27 | GSE171605 | GEO

Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets.

Project description:Motor and sensory functions of the spinal cord are mediated by populations of cardinal neurons arising from separate progenitor lineages. However, each cardinal class is composed of multiple neuronal types with distinct molecular, anatomical, and physiological features, and there is not a unifying logic that systematically accounts for this diversity. We reasoned that the expansion of new neuronal types occurred in a stepwise manner analogous to animal speciation, and we explored this by defining transcriptomic relationships using a top-down approach. We uncovered orderly genetic tiers that sequentially divide groups of neurons by their motor-sensory, local-long range, and excitatory-inhibitory features. The genetic signatures defining neuronal projections were tied to neuronal birth date and conserved across cardinal classes. Thus, the intersection of cardinal class with projection markers provides a unifying taxonomic solution for systematically identifying distinct functional subsets.

| S-EPMC8612134 | biostudies-literature

High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling [scRNA-seq]

Project description:Deciphering patterns of connectivity between neurons in the mammalian brain is a critical step toward understanding brain function. Conventional imaging based neuroanatomical tracing methods identify area-to-area or sparse neuron-to-neuron connectivity patterns, but with extremely limited throughput. Recently developed barcode-based connectomics methods can efficiently map large numbers of single-neuron projections, but linking these data to single-cell transcriptomics remains a challenge. Here, we established a retro-AAV barcode-based multiplexed tracing method called MERGE-seq (Multiplexed projection neuRons retroGrade barcodE sequencing), which is capable of simultaneously characterizing the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets (AI, DMS, BLA, MD and LH). We found that projection-defined vmPFC neurons are molecularly heterogeneous, which are composed of different neuronal subtypes. We further identified transcriptional signatures of various dedicated and bifurcated vmPFC neurons, and verified Pou3f1 as the marker gene of neurons sending collateral axons to DMS and LH. Finally, we fitted our single-neuron connectome/transcriptome data into a machine learning-based model and revealed groups of genes that were predictive of certain projection pattern. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.

2024-02-25 | GSE210172 | GEO

High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling [bulk RNA-seq]

2024-02-25 | GSE210173 | GEO

Temporal controls over interareal cortical projection neuron fate diversity (connectID)

Project description:Temporal controls over interareal cortical projection neuron fate diversity (connectID)

| PRJNA656719 | ENA

Temporal controls over interareal cortical projection neuron fate diversity (MAPseq)

Project description:Temporal controls over interareal cortical projection neuron fate diversity (MAPseq)

| PRJNA486447 | ENA

Temporal controls over interareal cortical projection neuron fate diversity (retrobeads)

Project description:Temporal controls over interareal cortical projection neuron fate diversity (retrobeads)

| PRJNA480667 | ENA

Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-cell RNA Sequencing

Project description:How a neuronal cell type is defined and how this relates to its transcriptome are still open questions. The Drosophila olfactory projection neurons (PNs) are among the bestcharacterized neuronal types: Different PN classes target dendrites to distinct olfactory glomeruli and PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA-sequencing, we comprehensively characterized the transcriptomes of 40 PN classes and unequivocally identified transcriptomes for 6 classes. We found a new lineage-specific transcription factor that instructs PN dendrite targeting. Transcriptomes of closely-related PN classes exhibit the largest difference during circuit assembly, but become indistinguishable in adults, suggesting that neuronal subtype diversity peaks during development. Genes encoding transcription factors and cell-surface molecules are the most differentially expressed, indicating their central roles in specifying neuronal identity. Finally, we show that PNs use highly redundant combinatorial molecular codes to distinguish subtypes, enabling robust specification of cell identity and circuit assembly.

2017-10-21 | GSE100058 | GEO

Projection neuron subtypes establish microglia sub-states and regulate neuroimmune interactions

Project description:Projection neuron subtypes establish microglia sub-states and regulate neuroimmune interactions

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Transcriptomic (RNA-seq) analysis of wild-type and Nolz1-/- (Zfp503) mutant striatal tissue reveals altered expression of several genes involved in striatal projection neuron specification.

Project description:Midbrain dopaminergic (DA) axons make long longitudinal projections towards target areas in the forebrain, including the striatum. After demonstrating a striatal specific requirement of transcriptional regulator Nolz1 (Zfp503) in regulating DA axon guidance and innervation, we performed RNA-seq analysis on both wild-type and Nolz1-/- mutant striatal tissue. The gene expression analysis revealed a requirement of Nolz1 in regulating striatal projection neuron specification. The RNA-seq results reveal several secreted factors that underlie the observed guidance defects and resulted in the identification of proteins that can restore DA axonal outgrowth.

2020-05-12 | E-MTAB-8240 | biostudies-arrayexpress

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