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Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons [gpDRG]

ABSTRACT: Sensory neurons of the dorsal root ganglion (DRG) play a crucial role in maintaining tissue homeostasis by sensing and initiating responses to stimuli. While most preclinical studies of DRGs are conducted in rodents, much less is known about the mechanisms of sensory perception in primates. We generated a transcriptome atlas for mouse, guinea pig, cynomolgus monkey, and human DRGs using a framework that implements a common laboratory workflow (i.e sequencing technologies, laboratory protocols, and sample archival methods) and multiple data-integration approaches to generate accurate cross-species mappings of sensory neuron subtypes.

ORGANISM(S): Cavia porcellus

PROVIDER: GSE201546 | GEO | 2022/12/21

REPOSITORIES: GEO

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Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons [mouseDRG]

Project description:Sensory neurons of the dorsal root ganglion (DRG) play a crucial role in maintaining tissue homeostasis by sensing and initiating responses to stimuli. While most preclinical studies of DRGs are conducted in rodents, much less is known about the mechanisms of sensory perception in primates. We generated a transcriptome atlas for mouse, guinea pig, cynomolgus monkey, and human DRGs using a framework that implements a common laboratory workflow (i.e sequencing technologies, laboratory protocols, and sample archival methods) and multiple data-integration approaches to generate accurate cross-species mappings of sensory neuron subtypes.

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Transcription profiling of mouse dorsal root ganglion

Project description:The molecular identity of touch sensation is still largely unknown. We choose an extrem and very specific example, touch sensation of pennis glan, to study this problem. It's known from previous retro-grade labeling result that only one DRG in rat innervate the pennis glan, which makes it idea for microarry analysis. To clone the mechanosensory receptor specifically or highly expressed in the primary sensory neurons innervating pennis glan. There is a specific mechanosensory receptor in the primary sensory neurons innervating pennis glan. 1. Retrograde labeling the innervating nerve by DiI; 2. Dissect DRGs, dissociate neurons and pick up the fluorescent cells. 3. Pool around 20 positive cells and 50 control cells (big diameter neuron and small to medium diameter neuron respectively), purify total RNA. 4. Two rounds of amplification; 5. Affymetrix analysis

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A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys [RNA-seq]

Project description:Non-human primates (NHP) are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium of cell types from the cynomolgus monkey Macaca fascicularis (denoted as ‘Monkey Atlas’) using both single-cell chromatin accessibility (scATAC-seq) and RNA sequencing (scRNA-seq) data at the organism-wide level. The integrated cell map enables in-depth dissection and comparison of molecular dynamics, cell-type composition and cellular heterogeneity across multiple tissues and organs. Using single-cell transcriptomic data, we inferred pseudotime cell trajectories and cell-cell communications to uncover key molecular signatures underlying their cellular processes. Furthermore, we identified various cell-specific cis-regulatory elements and constructed organ-specific gene regulatory networks at the single-cell level. Finally, we performed a comparative analysis of single-cell landscapes among mouse, cynomolgus monkey and human, and we showed that cynomolgus monkey has significantly higher degree of cell-type similarity to human than mouse. Taken together, our study provides a valuable resource for NHP cell biology.

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Dorsal root ganglion (katz-affy-mouse-210210)

Project description:The molecular identity of touch sensation is still largely unknown. We choose an extrem and very specific example, touch sensation of pennis glan, to study this problem. It's known from previous retro-grade labeling result that only one DRG in rat innervate the pennis glan, which makes it idea for microarry analysis. To clone the mechanosensory receptor specifically or highly expressed in the primary sensory neurons innervating pennis glan. There is a specific mechanosensory receptor in the primary sensory neurons innervating pennis glan. 1. Retrograde labeling the innervating nerve by DiI 2. Dissect DRGs, dissociate neurons and pick up the fluorescent cells. 3. Pool around 20 positive cells and 50 control cells (big diameter neuron and small to medium diameter neuron respectively), purify total RNA. 4. Two rounds of amplification 5. Affymetrix analysis Keywords: dorsal root ganglion, touch sensatiion

2008-04-19 | GSE11207 | GEO

LC-MS/MS identification of BMAL1 interaction proteins

Project description:Advances in circadian research revealed an intricate relationship between aging and circadian rhythms. However, whether and how the circadian machinery contribute to stem cell aging, especially in primates, remains poorly understood. In this study, we investigated the role of BMAL1, the only non-redundant circadian clock component, during aging in mesenchymal progenitor cells (MPCs). We observed an accelerated aging phenotype in both BMAL1 deficient human and cynomolgus monkey MPCs. Notably, this phenotype is mainly attributed to a transcriptional-independent role of BMAL1 in stabilizing the heterochromatin and thus preventing LINE1 activation. In senescent MPCs from human and cynomolgus monkeys, dampened LINE1 binding capacity of BMAL1 and synergistically activated LINE1 transcripts were observed. Furthermore, similar de-stabilized heterochromatin and aberrant LINE1s transcription was observed in the skin and muscle tissues from BMAL1-deficient cynomolgus monkey. Altogether, these findings uncover a noncanonical role of BMAL1 in stabilizing heterochromatin to inactivate LINE1 that drives aging in primates.

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Genome-wide copy number variation profiling in Cynomolgus monkeys using customized NimbleGen CGH microarrays

Project description:Cynomolgus monkeys are well-established translational models for biomedical research and drug testing. Cynomolgus monkeys are outbred species and exhibit substantial levels of genetic variation which can affect the outcome and interpretation of biomedical studies. Copy number variations (CNVs) are a significant source of genetic diversity and a comprehensive understanding of the genomic impact of CNVs on phenotypic traits is limited. A custom 4.2 million probes comparative genomic hybridization (CGH) array (Design-ID: 120405_Cynomolgus5_CGH_UX1) has been designed on the basis of the Cynomolgus monkey genome (Ebeling et al. (2011) Genome Research; PMID: 21862625) to assess genome-wide copy number variation among Cynomolgus monkeys. Using Cynomolgus monkey specific NimbleGen CGH Microarrays we profiled the genomes of 21 Cynomolgus monkeys. Germline DNA from 21 Cynomolgus monkeys with different origin was tested against a Cynomolgus monkey reference. Cynomolus monkey samples were derived from breeding centers located in the Philippines (3 females and 3 males), in Vietnam (2 males and 2 females), in China for animals from Mainland Southeast Asia (3 females), or in Mauritius (4 females and 4 males). Furthermore genome-wide expression profiles were analyzed in 5 vitally important tissue samples (heart, kidney, liver, lung, spleen) from the same animals using a custom Cynomolgus monkey specific NimbleGen gene expression microarray (design ID: 120419_Cynomolgus_v5_TH_exp_HX12) to associate CNV genotypes with expression changes of proximal genes using a cis expression quantitative trait loci (cis-eQTL) mapping approach. Expression data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession numbers GSE76560. The array CGH results analyzed in this study are further described in Gschwind A.R. et al. (2016) "Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis". under submission

2016-02-24 | GSE76707 | GEO

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