Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution

Experiment ID:SRP131661
Technology:scRNA-Seq
Description:We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication. Overall design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
Cell count:54,837
DOI:10.1038/s41586-018-0590-4
Source:SRP131661  SRA
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scRNA-Seq droplet-based processed expression values per cell population in Mus musculusscRNA-Seq droplet-based H5AD data per cell in Mus musculus

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Showing 1 to 20 of 186 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
SRX3791763CL:0002187 basal cell of epidermisbasal cell of epidermisUBERON:0001723 tonguetongueMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single271485896197830995027781920591627571.5Browse results
SRX3791763CL:0000312 keratinocytekeratinocyteUBERON:0001723 tonguetongueMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single271485896197830995026113272567727012.5Browse results
SRX3791763CL:0002371 somatic cellunknownUBERON:0001723 tonguetongueMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single271485896197830995014885143822064Browse results
SRX3791764CL:0000312 keratinocytekeratinocyteUBERON:0001723 tonguetongueMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single315339439230317303015342379475626723.5Browse results
SRX3791764CL:0002187 basal cell of epidermisbasal cell of epidermisUBERON:0001723 tonguetongueMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single315339439230317303028482591633427777Browse results
SRX3791764CL:0002371 somatic cellunknownUBERON:0001723 tonguetongueMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single315339439230317303011589543221927.5Browse results
SRX3791765CL:0000182 hepatocytehepatocyteUBERON:0002107 liverliverMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single35172182528374868504093053184724483.5Browse results
SRX3791765CL:0000115 endothelial cellendothelial cellUBERON:0002107 liverliverMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single35172182528374868501669513720240.5Browse results
SRX3791766CL:0008019 mesenchymal cellmesenchymal cellUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single2728026691932943840709984127024484Browse results
SRX3791766CL:1001319 bladder cellbladder cellUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single27280266919329438401015085210924606.5Browse results
SRX3791766CL:0000115 endothelial cellendothelial cellUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single27280266919329438403451425520026Browse results
SRX3791766CL:1000486 basal cell of urotheliumbasal cell of urotheliumUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single272802669193294384020930971622511Browse results
SRX3791766CL:0000738 leukocyteleukocyteUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single27280266919329438402477520920451.5Browse results
SRX3791767CL:1001319 bladder cellbladder cellUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single248674713173443894013069390506026883Browse results
SRX3791767CL:0008019 mesenchymal cellmesenchymal cellUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single24867471317344389406669796323326471.5Browse results
SRX3791767CL:1000486 basal cell of urotheliumbasal cell of urotheliumUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single24867471317344389403690661295125514Browse results
SRX3791767CL:0000115 endothelial cellendothelial cellUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single248674713173443894044240288523835.5Browse results
SRX3791767CL:0000738 leukocyteleukocyteUBERON:0001255 urinary bladderbladderMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single248674713173443894018557159323432.5Browse results
SRX3791768CL:0000738 leukocyteleukocyteUBERON:0000082 adult mammalian kidneykidneyMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single296457069250022863012149056722742Browse results
SRX3791768CL:0000666 fenestrated cellfenestrated cellUBERON:0000082 adult mammalian kidneykidneyMmusDv:0000063 3-month-old stage (mouse)3 monthsmaleC57BL/6JNANAMus musculusNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0single2964570692500228630507547132724432Browse results

Showing 1 to 20 of 186 entries