Schema for Ileum Donor - Ileum cells binned by organ donor from Wang et al 2020
  Database: hg38    Primary Table: ileumWangDonor Data last updated: 2022-05-12
Big Bed File: /gbdb/hg38/bbi/ileumWang/donor.bb
Item Count: 18,372
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
expCount2Number of categories
expScores0.00204412,0.00122496Comma separated list of category values

Sample Rows
 
chromchromStartchromEndnamescorestrandname2expCountexpScores
chr1166070019166166969FAM78B0-ENSG00000188859.620.00204412,0.00122496
chr1166475771166490039RP11-276E17.20-ENSG00000234142.120.000214773,0.000495675
chr1166840088166854473POGK0+ENSG00000143157.1120.0443169,0.0357959
chr1166856509166876327TADA10-ENSG00000152382.520.0229857,0.0208771
chr1167052835167090631GPA330-ENSG00000143167.1120.586487,0.670775
chr1167219830167220512RP11-277B15.30-ENSG00000272205.120.00812599,0.00350561
chr1167220828167427345POU2F10+ENSG00000143190.2120.0316558,0.0215235
chr1167430639167518538CD2470-ENSG00000198821.1020,0.00132467
chr1167541012167553767CREG10-ENSG00000143162.720.15099,0.167684
chr1167721949167791919MPZL10+ENSG00000197965.1120.217353,0.157031

Ileum Donor (ileumWangDonor) Track Description
 

Description

This track shows data from Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. Droplet-based single-cell RNA sequencing (scRNA-seq) was used to survey gene expression profiles of the epithelium in the human ileum, colon, and rectum. A total of 7 cell clusters were identified: enterocytes (EC), goblet cells (G), paneth-like cells (PLC), enteroendocrine cells (EEC), progenitor cells (PRO), transient-amplifying cells (TA) and stem cells (SC).

This track collection contains two bar chart tracks of RNA expression in ileum cells where cells are grouped by cell type (Ileum Cells) or donor (Ileum Donor). The default track displayed is Ileum Cells.

Display Conventions

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

Color Cell classification
epithelial
secretory
stem cell

Cells that fall into multiple classes will be colored by blending the colors associated with those classes. Note that the Ileum Donor track is colored by donor for improved clarity.

Method

Using single-cell RNA sequencing, RNA profiles of intestinal epithelial cells were obtained for 6,167 cells from two human ileum samples. Tissue samples belonged to a male donor age 60 with Neuroendocrine Carcinoma (Ileum-1) and a female donor age 67 with Adenocarcinoma (Ileum-2). The healthy intestinal mucous membranes used for each sample were cut away from the tumor border in surgically removed ileum tissue. Additionally, the intestinal tissues were washed in Hank's balanced salt solution (HBSS) to remove mucus, blood cells, and muscle tissue. The sample was enriched for epithelial cells through centrifugation before being dissociated with Tryple to obtain single-cell suspensions. RNA-seq libraries were prepared using 10x Genomics 3' v2 kit and sequenced on an Illumina Hiseq X Ten PE150.

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 Yalong Wang, Wanlu Song, 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 Luis Nassar. The UCSC work was paid for by the Chan Zuckerberg Initiative.

References

Wang Y, Song W, Wang J, Wang T, Xiong X, Qi Z, Fu W, Yang X, Chen YG. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J Exp Med. 2020 Feb 3;217(2). PMID: 31753849; PMC: PMC7041720