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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 01, 2024 |
| Title |
Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain [Mouse snATAC-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The dorsal horn of the spinal cord transforms incoming somatosensory information and transmits it supraspinally to generate sensory perception, including pain and itch. Recent research using mouse Cre-driver lines has implicated specific populations of dorsal horn neurons in the transmission of different types of pain. In parallel, human genome-wide association studies (GWAS) have identified dozens of loci confidently associated with the genetic predisposition to chronic pain. The ability to connect controlled experiments in rodent models with human genetic studies could provide a platform for translational research, but the cell type heterogeneity of the dorsal horn and the complex genetic architecture of chronic pain have created challenges in bridging that gap. Here, we apply a variety of single cell genomic technologies and a comparative genomic analysis to identify conserved dorsal horn neuron subtypes whose open chromatin regions show enrichment for genetic variants associated with human chronic pain phenotypes. To achieve this, we first use single nucleus RNA-Seq and fluorescence in situ hybridization in Rhesus macaque to create a more detailed map of primate dorsal horn neuron subtypes. These were integrated with publicly available human and mouse single nucleus RNA-Seq datasets to create a multi-modal cross species atlas. Then, for the mouse dorsal horn, we combined single nucleus RNA-Seq, spatial transcriptomics, and single nucleus ATAC-Seq to infer spatial and epigenomic profiles of conserved dorsal horn neuron subtypes. Finally, we compared our conserved cell-type open chromatin resource to chronic pain GWAS and found that open chromatin regions of specific dorsal horn neuron subtypes showed enrichment for a variety of human chronic pain phenotypes. Our results provide a foundation to further explore how conserved dorsal horn neuron subtypes influence the transmission of pain signals.
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| Overall design |
Spinal cord dissections from healthy adult (n=20 F/M mice), were taken to generate single nucleus suspensions for snATAC-seq.
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| Contributor(s) |
Leone MJ, Arokiaraj CM, Seal RP, Pfenning AR |
| Citation(s) |
39453813 |
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| Submission date |
Jan 23, 2024 |
| Last update date |
Nov 03, 2024 |
| Contact name |
Michael Leone |
| E-mail(s) |
mjleone45@gmail.com
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| Organization name |
Carnegie Mellon University
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| Street address |
4315 Tesla St
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| City |
Pittsburgh |
| ZIP/Postal code |
15217 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (12)
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| GSM8030982 |
Replicate 4, mouse mixed pool, snATAC |
| GSM8030983 |
Replicate 5, mouse mixed pool, snATAC |
| GSM8030984 |
Replicate 6, mouse mixed pool, snATAC |
| GSM8030985 |
Replicate 7, mouse mixed pool, snATAC |
| GSM8030986 |
Replicate 8, mouse mixed pool, snATAC |
| GSM8030987 |
Replicate 9, mouse mixed pool, snATAC |
| GSM8030988 |
Replicate 10, mouse mixed pool, snATAC |
| GSM8030989 |
Replicate 11, mouse mixed pool, snATAC |
| GSM8030990 |
Replicate 12, mouse mixed pool, snATAC |
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| This SubSeries is part of SuperSeries: |
| GSE253954 |
Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain. |
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| Relations |
| BioProject |
PRJNA1067989 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE253952_Mouse_DorsalHorn_scATAC.tar.gz |
43.5 Gb |
(ftp)(http) |
TAR |
| GSE253952_Mouse_scATAC_DorsalHorn_neuron2_wDeviations.tar.gz |
17.8 Gb |
(ftp)(http) |
TAR |
| GSE253952_Readme.txt |
458 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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