Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations

Experiment ID:SRP149989
Technology:scRNA-Seq
Description:Overall design: Primary liver samples from 5 patients were used for single cell RNA sequencing by 10X Genomics
Cell count:8,444
DOI:10.1038/s41467-018-06318-7
Source:SRP149989  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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Showing 1 to 20 of 78 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
SRX4180079CL:0000798 gamma-delta T cellgamma-delta_T_Cells_2UBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091409832350622026Browse results
SRX4180079CL:0019022 endothelial cell of pericentral hepatic sinusoidCentral_venous_LSECsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired4632369173620409140644865138524887Browse results
SRX4180079CL:0009094 endothelial cell of hepatic portal veinPortal_endothelial_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091409193070922091.5Browse results
SRX4180079CL:0000182 hepatocyteHepatocyte_5UBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091402415184192524467.5Browse results
SRX4180079CL:0000798 gamma-delta T cellgamma-delta_T_Cells_1UBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired463236917362040914014770444822482Browse results
SRX4180079CL:0000738 leukocyteNK-like_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired463236917362040914026809665823295Browse results
SRX4180079CL:0000863 inflammatory macrophageInflammatory_MacrophageUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired4632369173620409140997364139824711Browse results
SRX4180079CL:0000789 alpha-beta T cellalpha-beta_T_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired4632369173620409140752367102424586Browse results
SRX4180079CL:0000235 macrophageNon-inflammatory_MacrophageUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired463236917362040914053691991723621Browse results
SRX4180079CL:1000488 cholangiocyteCholangiocytesUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091406484537021602.5Browse results
SRX4180079CL:0000182 hepatocyteHepatocyte_2UBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired463236917362040914091138418452Browse results
SRX4180079CL:0000764 erythroid lineage cellErythroid_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired4632369173620409140105804517843Browse results
SRX4180079CL:0000786 plasma cellPlasma_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired463236917362040914010255237220736Browse results
SRX4180079CL:0000632 hepatic stellate cellHepatic_Stellate_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091405566332921333.5Browse results
SRX4180079CL:0000785 mature B cellMature_B_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091402158318019343.5Browse results
SRX4180079CL:0000182 hepatocyteHepatocyte_6UBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091401996314919052.5Browse results
SRX4180079CL:0019021 endothelial cell of periportal hepatic sinusoidPeriportal_LSECsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired46323691736204091409685247622178.5Browse results
SRX4180080CL:0009094 endothelial cell of hepatic portal veinPortal_endothelial_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired53731670427033562401408913219387Browse results
SRX4180080CL:0000785 mature B cellMature_B_CellsUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired53731670427033562401579515518886.5Browse results
SRX4180080CL:0000863 inflammatory macrophageInflammatory_MacrophageUBERON:0001117 caudate lobe of livercaudate liver lobeUBERON:0000104 life cycleNANANANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0paired53731670427033562407545534521532.5Browse results

Showing 1 to 20 of 78 entries