Droplet-based single-cell RNA-sequencing of mouse and naked mole-rat spleen and circulating immune cells, in natural conditions, following lipopolysaccharide (LPS) challenge, and saline control

Experiment ID:SRP201320
Technology:scRNA-Seq
Description:Single-cell RNA-sequencing was performed in the mouse and naked mole-rat immune systems in order to map and compare their immune cell repertoirs and their cell-specific gene-expression responses to LPS challenge Overall design: Single-cell RNA-sequencing was obtained from: 1. 4 adult mouse and 4 adult naked mole-rat spleens in duplicate; 2. 4 adult mouse and 3 adult naked mole-rat circulating immune cells; 3. 2 adult mouse and 2 adult naked mole-rat spleens following LPS challenege in duplicate; 4. 2 adult mouse and 2 adult naked mole-rat spleens following saline administration in duplicate; 5. 2 adult mouse and 2 adult naked mole-rat circulating immune cells following LPS challenege in duplicate; 4. 2 adult mouse and 2 adult naked mole-rat circulating immune cells following saline administration in duplicate;
Cell count:131,944
DOI:10.1371/journal.pbio.3000528
Source:SRP201320  SRA
Download:
scRNA-Seq droplet-based processed expression values per cell population in Heterocephalus glaberscRNA-Seq droplet-based H5AD data per cell in Heterocephalus glaberscRNA-Seq droplet-based processed expression values per cell population in Mus musculusscRNA-Seq droplet-based H5AD data per cell in Mus musculusBulk RNA-Seq processed expression values in Heterocephalus glaberBulk RNA-Seq processed expression values in Mus musculus

List of assays

Show

entries

Showing 1 to 20 of 594 entries

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
SRX6060792CL:0000236 B cellB-cellUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299072424784516026.5Browse results
SRX6060792CL:0000548 animal cellMultipletUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired1292896739035529902161914812590.5Browse results
SRX6060792CL:0000898 naive T cellNaive-T-cellUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired1292896739035529901778661111416496.5Browse results
SRX6060792CL:0000775 neutrophilNeutrophil.1UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired129289673903552990163950498415955.5Browse results
SRX6060792CL:0000775 neutrophilNeutrophil.2UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired1292896739035529907381522313252.5Browse results
SRX6060792CL:0000775 neutrophilNeutrophil.3UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired129289673903552990172648412101Browse results
SRX6060792CL:0000786 plasma cellPlasma-cellUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299016859737014288Browse results
SRX6060792CL:0000874 splenic red pulp macrophageRed-pulp-macrophageUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299016091631314219.5Browse results
SRX6060792CL:0000451 dendritic cellTimeless-high-dendritic-cellUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299013144541314543.5Browse results
SRX6060792CL:0000548 animal cellUnassigned.1UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299018603449314666.5Browse results
SRX6060792CL:0000548 animal cellUnassigned.2UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired1292896739035529908514730613943.5Browse results
SRX6060792CL:0000625 CD8-positive, alpha-beta T cellCD8-T-cellUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299026656452215077Browse results
SRX6060792CL:0000548 animal cellUnassigned.3UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired1292896739035529902644315212774Browse results
SRX6060792CL:0000548 animal cellUnassigned.4UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299052375011542Browse results
SRX6060792CL:0000764 erythroid lineage cellErythroid-cell.1UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299057517228513157.5Browse results
SRX6060792CL:0000764 erythroid lineage cellErythroid-cell.2UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired1292896739035529903157628132515843.5Browse results
SRX6060792CL:0000764 erythroid lineage cellErythroid-cell.3UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299019910441814173.5Browse results
SRX6060792CL:0000775 neutrophilLtf-high-neutrophilUBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired12928967390355299059961858214738Browse results
SRX6060792CL:0000871 splenic macrophageMacrophage.1UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired129289673903552990102644099216160Browse results
SRX6060792CL:0000871 splenic macrophageMacrophage.2UBERON:0002106 spleenspleenUBERON:0000113 post-juvenile23-25 months oldfemaleNANANAHeterocephalus glaberNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired1292896739035529909331936514141Browse results

Showing 1 to 20 of 594 entries