Schema for Liver Cells - Liver cells binned by cell type from MacParland et al 2018
  Database: hg38    Primary Table: liverMacParlandCellType Data last updated: 2022-05-12
Big Bed File: /gbdb/hg38/bbi/liverMacParland/cell_type.bb
Item Count: 21,830
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166070019Start position in chromosome
chromEnd166166969End position in chromosome
nameFAM78BName or ID of item
score0Score from 0-1000, typically derived from total of median value from all categories
strand-+ or - for strand. Use . if not applicable
name2ENSG00000188859.6Alternative name for item
expCount15Number of categories
expScores0,0.0185517,0,0.00581212,0.00145601,0.00355526,0,0,0,0.00115727,0.00285666,0,0,0,0.000512527Comma separated list of category values

Sample Rows
 
chromchromStartchromEndnamescorestrandname2expCountexpScores
chr1166070019166166969FAM78B0-ENSG00000188859.6150,0.0185517,0,0.00581212,0.00145601,0.00355526,0,0,0,0.00115727,0.00285666,0,0,0,0.000512527
chr1166840088166854473POGK0+ENSG00000143157.11150.0321949,0.026282,0,0.0420756,0.0494343,0.0391281,0.0534917,0.034612,0.0777287,0.0688692,0.0701099,0.0301428,0.0327476,0.012355 ...
chr1166856509166876327TADA10-ENSG00000152382.5150.0297702,0.0056624,0,0.0723119,0.0150332,0.00888165,0.0129677,0.0227566,0.0136119,0.0186984,0.0124901,0,0.00989965,0.0336596,0. ...
chr1166908190166975324ILDR20-ENSG00000143195.12150,0,0,0.00557235,0,0.00196342,0,0.00442162,0,0,0,0,0.000745151,0.00519668,0.00094675
chr1166989108167022214MAEL0+ENSG00000143194.12150,0,0,0.000242393,0,0,0,0.00454672,0,0,0,0,0,0,0
chr1167052835167090631GPA330-ENSG00000143167.11150,0,0,0,0.00184817,0,0,0.00306957,0.0207987,0,0,0,0.00448159,0.0132911,0
chr1167219830167220512RP11-277B15.30-ENSG00000272205.1150,0,0,0.000482002,0.00337389,0.00079904,0.00581115,0.00163773,0.00459167,0.00299476,0,0,0,0.0112549,0.0185047
chr1167220828167427345POU2F10+ENSG00000143190.21150.0886465,0.0367161,0.0543756,0.0459495,0.0763802,0.0456112,0.0369166,0.0562613,0.259123,0.140432,0.0487832,0,0.0568918,0.062511 ...
chr1167430639167518538CD2470-ENSG00000198821.10150.0340237,0.00470194,0.083916,0.00551861,0.0240335,0.0146182,0.0210328,1.30176,0.0194209,0.0519084,0.00814469,0,0.527688,1.72924 ...
chr1167457741167459891RP11-104L21.30-ENSG00000273160.1150,0,0,5.82647e-05,0.00237615,0.00105325,0.00125669,0.0852495,0,0,0,0,0.0250452,0.0880009,0.0156522

Liver Cells (liverMacParlandCellType) Track Description
 

Description

This track shows data from Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Liver tissue was analyzed using droplet-based single-cell RNA-sequencing (scRNA-seq) and subsequent clustering distinguished 20 hepatic cell populations based on their identified marker genes found in MacParland et al., 2018.

There are three bar chart tracks in this track collection with liver cells grouped by either broad cell type (Liver Broad), specific cell type (Liver Cells) and donor (Liver Donor). The default track displayed is Liver Cells.

Display Conventions

The cell types are colored by which class they belong to according to the following table.

Color Cell classification
immune
endothelial
fibroblast
epithelial
stem cell
hepatocyte

Cells that fall into multiple classes will be colored by blending the colors associated with those classes. The colors will be purest in the Liver Cells subtrack, where the bars represent relatively pure cell types. They can give an overview of the cell composition within other categories in other subtracks as well.

Relevant Figures From MacParland et al., 2018

Map of the human liver and its associated cell types. The liver is constructed of hepatic lobules which are composed of a portal triad (hepatic artery, the portal vein and the bile duct), hepatocytes aligned between a capillary network, and a central vein.

Human Liver Map MacParland et al. Nat Commun. 2018. / CC BY 4.0

Method

Fresh liver samples were taken from 5 neurologically deceased donors (NDD) deemed acceptable for liver transplantation. The caudate lobe of the liver was surgically separated and flushed with HTK solution to leave only tissue resident cells that were used to prepare a cell suspension for scRNA-seq analysis. Samples were prepared using 10x Genomics 3' v2 library kit and sequenced on the Illumina HiSeq 2500. A total of 8,444 transcriptional profiles were obtained for organ specific and non-organ specific cells from healthy hepatic tissue.

The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell Browser. The UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed were used to transform these into a bar chart format bigBed file that can be visualized. The coloring was done by defining colors for the broad level cell classes and then using another UCSC utility, hcaColorCells, to interpolate the colors across all cell types. The UCSC utilities can be found on our download server.

Data Access

The raw bar chart data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credit

Thanks to Sonya MacParland and to the many authors who worked on producing and publishing this data set. The data were integrated into the UCSC Genome Browser by Jim Kent and Brittney Wick then reviewed by Daniel Schmelter. The UCSC work was paid for by the Chan Zuckerberg Initiative.

References

MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. 2018 Oct 22;9(1):4383. PMID: 30348985; PMC: PMC6197289