Schema for Pancreas Cells - Pancreas cells binned by cell type from Baron et al 2016
  Database: hg38    Primary Table: pancreasBaronCellType Data last updated: 2022-05-12
Big Bed File: /gbdb/hg38/bbi/pancreasBaron/cell_type.bb
Item Count: 17,530
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
expCount11Number of categories
expScores0.00294575,0,0.000739534,0.00436678,0.00330237,0.0121987,0.00441826,0,0.0196171,0,0Comma separated list of category values

Sample Rows
 
chromchromStartchromEndnamescorestrandname2expCountexpScores
chr1166070019166166969FAM78B0-ENSG00000188859.6110.00294575,0,0.000739534,0.00436678,0.00330237,0.0121987,0.00441826,0,0.0196171,0,0
chr1166840088166854473POGK0+ENSG00000143157.11110.125715,0.11138,0.147329,0.147465,0.153026,0.21713,0.149129,0.200992,0.167543,0.0791994,0.199778
chr1166856509166876327TADA10-ENSG00000152382.5110.00873062,0.0345259,0.036794,0.0560543,0.051717,0.0298634,0.0203714,0.0517947,0.0537865,0,0.0301154
chr1166908190166975324ILDR20-ENSG00000143195.12110,0,0.0132652,0.0296336,0.0363553,0.00101646,0,0.145123,0.0700727,0,0.00461776
chr1166989108167022214MAEL0+ENSG00000143194.12110,0,0.0022208,0.00780348,0,0,0,0,0.00347066,0,0
chr1167220828167427345POU2F10+ENSG00000143190.22110.0758377,0.105638,0.131809,0.136122,0.126534,0.166092,0.134251,0.307621,0.20473,0.169805,0.137495
chr1167430639167518538CD2470-ENSG00000198821.10110.000958977,0.00993091,0.00166998,0.00137302,0.00351872,0,0.0121795,0,0.00595345,0.0715432,0
chr1167541012167553767CREG10-ENSG00000143162.8110.0560399,0.219207,0.0554708,0.0874304,0.0589492,0.0867952,0.202865,0.21383,0.0723463,0.590663,0.143836
chr1167630092167706249RCSD10+ENSG00000198771.10110.00426746,0.0291232,0,0.000820261,0,0.00137613,0.0724858,0,0,0.107518,0.039282
chr1167721949167791919MPZL10+ENSG00000197965.11110.410773,1.33061,0.279367,0.219024,0.227675,0.646694,0.954774,0.460511,0.35699,0.349209,0.596231

Pancreas Cells (pancreasBaronCellType) Track Description
 

Description

This track shows data from A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Pancreas tissue was analyzed using droplet-based single-cell RNA-sequencing (scRNA-seq) and subsequent clustering distinguished 14 pancreas-resident cell types based on their identified marker genes found in Baron et al., 2016.

There are four bar chart tracks in this track collection with pancreas cells grouped by either batch (Pancreas Batch), cell type (Pancreas Cells), detailed cell type (Pancreas Details) and donor (Pancreas Donor). The default track displayed is pancreas cells grouped by cell type.

Display Conventions

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

Color Cell classification
secretory
endothelial
epithelial
fibroblast

Cells that fall into multiple classes will be colored by blending the colors associated with those classes. The colors will be purest in the Pancreas 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.

Method

Human islets were obtained from two female cadaveric donors ages 51 (human2) and 59 (human4) and two male cadaveric donors ages 17 (human1) and 38 (human3). The samples collected from human 1-3 were non-diabetic and human 4 had type 2 diabetes mellitus. Using single-cell RNA-sequencing ~10,000 human pancreatic cells were isolated and sequenced. For each donor, several separate batches of ~800 cells were prepared and sequenced to obtain an average of about 100,000 reads per cell. Cells were barcoded using the inDrop platform which follows the CEL-Seq protocol for library construction. Paired end sequencing was done on the Illumina Hiseq 2500. After filtering out cells with limited numbers of detected genes, the dataset contained 8,629 cells from the four donors.

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 Mayaan Baron, Adrian Veres, Samuel L. Wolock, Aubrey L. Faust, 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 Jairo Navarro. The UCSC work was paid for by the Chan Zuckerberg Initiative.

References

Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM et al. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell Syst. 2016 Oct 26;3(4):346-360.e4. PMID: 27667365; PMC: PMC5228327