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

Experiment ID:SRP372346
Technology:scRNA-Seq
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. Overall design: Fresh or frozen DRG tissues from mouse, guinea pig, cynomologus monkey and human were collected and nuclei were isolated with FACS or density-gradient centrifugation and analyzed with snRNA-seq.
DOI:10.1038/s41467-023-36014-0
Source:SRP372346 SRA
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scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiens

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX15003464CL:0000516 perineuronal satellite cellSatellite gliaUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired353470231200894759014310749864029080.5Browse results
SRX15003464CL:0000235 macrophageMacrophageUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35347023120089475901193455459826625.5Browse results
SRX15003464CL:0000218 myelinating Schwann cellMyelinating Schwann cellUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3534702312008947590261107319724753.5Browse results
SRX15003464CL:0000057 fibroblastFibroblastUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35347023120089475901324944458026977Browse results
SRX15003464CL:0000115 endothelial cellEndothelialUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3534702312008947590306120324825079.5Browse results
SRX15003464CL:1001451 sensory neuron of dorsal root ganglionDRG NeuronUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired353470231200894759050286161822043.5Browse results
SRX15003464CL:0000183 contractile cellPericyte/Smooth muscleUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired353470231200894759036762142821342Browse results
SRX15003464CL:0000542 lymphocyteLymphocyteUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35347023120089475901355067219865Browse results
SRX15003464CL:0000136 fat cellAdipocyteUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3534702312008947590288613518249Browse results
SRX15003465CL:0000516 perineuronal satellite cellSatellite gliaUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired30879133115220123601047487405226229Browse results
SRX15003465CL:0000235 macrophageMacrophageUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired308791331152201236062166162721801Browse results
SRX15003465CL:0000218 myelinating Schwann cellMyelinating Schwann cellUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired30879133115220123601127157319165.5Browse results
SRX15003465CL:0000057 fibroblastFibroblastUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired308791331152201236067771172721758Browse results
SRX15003465CL:0000115 endothelial cellEndothelialUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired30879133115220123601550679919675.5Browse results
SRX15003465CL:1001451 sensory neuron of dorsal root ganglionDRG NeuronUBERON:0003943 fourth lumbar dorsal root ganglionDorsal Root Ganglion, Lumbar 4UBERON:0000104 life cycleundisclosedfemaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3087913311522012360862545218870.5Browse results
SRX15003466CL:0000516 perineuronal satellite cellSatellite gliaUBERON:0002850 seventh thoracic dorsal root ganglionDorsal Root Ganglion, Thoracic 7HsapDv:0000125 31-year-old stage (human)31 yearsmaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired36184669820487723008322135765928863Browse results
SRX15003466CL:0000057 fibroblastFibroblastUBERON:0002850 seventh thoracic dorsal root ganglionDorsal Root Ganglion, Thoracic 7HsapDv:0000125 31-year-old stage (human)31 yearsmaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired36184669820487723001202295473527116Browse results
SRX15003466CL:0000235 macrophageMacrophageUBERON:0002850 seventh thoracic dorsal root ganglionDorsal Root Ganglion, Thoracic 7HsapDv:0000125 31-year-old stage (human)31 yearsmaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired36184669820487723001255239474127129.5Browse results
SRX15003466CL:1001451 sensory neuron of dorsal root ganglionDRG NeuronUBERON:0002850 seventh thoracic dorsal root ganglionDorsal Root Ganglion, Thoracic 7HsapDv:0000125 31-year-old stage (human)31 yearsmaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3618466982048772300229744332325065.5Browse results
SRX15003466CL:0000183 contractile cellPericyte/Smooth muscleUBERON:0002850 seventh thoracic dorsal root ganglionDorsal Root Ganglion, Thoracic 7HsapDv:0000125 31-year-old stage (human)31 yearsmaleNANANAHomo sapiensNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired361846698204877230055813166622178.5Browse results

Showing 1 to 20 of 150 entries

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