Schema for Colon Cells - Colon cells binned by cell type from Wang et al 2020
Database: hg38 Primary Table: colonWangCellType Data last updated: 2022-05-12|
Big Bed File: /gbdb/hg38/bbi/colonWang/cell_type.bb
Item Count: 18,583
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
|chrom||chr1||Reference sequence chromosome or scaffold|
|chromStart||166070019||Start position in chromosome|
|chromEnd||166166969||End position in chromosome|
|name||FAM78B||Name or ID of item|
|score||0||Score from 0-1000, typically derived from total of median value from all categories|
|strand||-||+ or - for strand. Use . if not applicable|
|name2||ENSG00000188859.6||Alternative name for item|
|expCount||7||Number of categories|
|expScores||0,0.00348887,0.00313029,0,0.00642377,0.0166279,0||Comma separated list of category values|
Colon Cells (colonWangCellType) Track 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 colon
cells where cells are grouped by cell type
(Colon Cells) or donor
(Colon Donor). The default track
displayed is Colon Cells.
The cell types are colored by which class they belong to according to the following table.
Cells that fall into multiple classes will be colored by blending the colors associated
with those classes. Note that the Colon Donor track
is colored by donor for improved clarity.
Using scRNA-seq, RNA profiles of intestinal epithelial cells were obtained for
4,472 cells from two human colon samples. Tissue samples belonged to a male
donor age 54 (Colon-1) and a female donor age 67 (Colon-2) both diagnosed with
Adenocarcinoma. The healthy intestinal mucous membranes used for each sample
were cut away from the tumor border in surgically removed ascending colon 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.
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
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.
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
J Exp Med. 2020 Feb 3;217(2).
PMID: 31753849; PMC: PMC7041720