Tabula Muris Cell expression Track Settings
 
Single Cell RNA-Seq Gene Expression from Tabula Muris

Track collection: Single Cell FACS RNA-Seq of 44,779 cells from Tabula Muris

+  Description
+  All tracks in this collection (3)

Display mode:      Duplicate track

Label: Gene name    Gene identifier   

Log10(x+1) transform:    View limits maximum: TPM (range 0-10000)

Categories:  
 B cell
 Bergmann glial cell
 Brush cell of epithelium proper of large intestine
 DN1 thymic pro-T cell
 Kupffer cell
 Slamf1-negative multipotent progenitor cell
 Slamf1-positive multipotent progenitor cell
 T cell
 astrocyte
 basal cell
 basal cell of epidermis
 basophil
 bladder cell
 bladder urothelial cell
 blood cell
 brain pericyte
 cardiac muscle cell
 ciliated columnar cell of tracheobronchial tree
 classical monocyte
 common lymphoid progenitor
 endocardial cell
 endothelial cell
 endothelial cell of hepatic sinusoid
 enterocyte of epithelium of large intestine
 enteroendocrine cell
 epidermal cell
 epithelial cell
 epithelial cell of large intestine
 epithelial cell of lung
 epithelial cell of proximal tubule
 erythrocyte
 fibroblast
 granulocyte
 granulocyte monocyte progenitor cell
 granulocytopoietic cell
 hematopoietic precursor cell
 hepatocyte
 immature B cell
 immature NK T cell
 immature T cell
 immature natural killer cell
 keratinocyte
 keratinocyte stem cell
 kidney collecting duct epithelial cell
 large intestine goblet cell
 late pro-B cell
 leukocyte
 luminal epithelial cell of mammary gland
 lung endothelial cell
 lymphocyte
 macrophage
 mature natural killer cell
 megakaryocyte-erythroid progenitor cell
 mesenchymal cell
 mesenchymal stem cell
 mesenchymal stem cell of adipose
 microglial cell
 monocyte
 myeloid cell
 myofibroblast cell
 naive B cell
 natural killer cell
 neuron
 oligodendrocyte
 oligodendrocyte precursor cell
 pancreatic A cell
 pancreatic D cell
 pancreatic PP cell
 pancreatic acinar cell
 pancreatic ductal cell
 pancreatic stellate cell
 pre-natural killer cell
 precursor B cell
 professional antigen presenting cell
 regulatory T cell
 skeletal muscle satellite cell
 skeletal muscle satellite stem cell
 smooth muscle cell
 stem cell of epidermis
 stromal cell
 type B pancreatic cell
View table schema
Data last updated at UCSC: 2018-09-12 17:07:43

Description

Tabula Muris is a compendium of single cell transcriptome data from the model organism Mus musculus, containing nearly 100,000 cells from 20 organs and tissues. The data allow for direct and controlled comparison of gene expression in cell types shared between tissues, such as immune cells from distinct anatomical locations.

This track shows the results from FACS sorted cells sequenced with the SmartSeq2 protocol, as it has much higher transcript coverage. The sequencing data comprises more than 2TB and was summarized into a track at UCSC.

Display Conventions and Configuration

As indicated by the "..." after its name, this is a 'super track', a container for subtracks. There are three different subtracks:

Cell type expression:
A rectangle on the genome, at the location of a gene, filled with a bar graph that indicates the gene's expression by single cell cluster. The term "cluster" refers to a cluster of single cells, which usually represents a cell or tissue type. The height of the bar graph on the genome is the median expression level and a click-through on the bar chart displays a boxplot of expression level quartiles with outliers, per cluster. On the boxplot, the number of cells from each experiment is shown.
Coverage:
Bar graphs indicate the number of reads at this base pair. You may want to switch on auto-scaling of the y-axis. For configuration options, see the graph tracks configuration help page. These tracks are shown in "dense" by default, set any of the tracks to "full" to see the detailed coverage plot.
Splice Junctions:
Thick rectangles show exons around a splice site, connected by a line that indicates the intron. These gaps are shown and are annotated with the number of reads, in the 'score' field. You can use the 'score' filter on the track configuration page to show only introns with a certain number of supporting reads. The maximum number of reads that are shown is 1,000, even if more reads support an intron. These tracks are shown in dense by default, set this track to "pack" to see. Then click the splice junctions to see their score.

Methods

BAM files were provided by the data submitters, one (single end) or two files (paired end) per cell. The BAM alignments were used as submitted. They were merged with "samtools merge" into a single BAM file per cluster. The readgroup (RG) BAM tag indicates the original cell.

From the resulting merged BAM file, coverage was obtained using "wiggletools coverage" a tool written by Daniel Zerbino and the result was converted with the UCSC tool "wigToBigWig".

Also on the merged BAM file, the software IntronProspector was run with default settings. It retains reads with a gap longer than 70 bp and shorter than 500 kbp and merges them into annotated splice junctions.

Data Access

The merged BAM files, coverage bigWig files and splice junctions in bigBed format can be downloaded from the /gbdb fileserver.

Since the splice junction .bigBed files have their scores capped at 1000, the original IntronProspector .bed files are available in the same track hub directory. You can also find there *.calls.tsv files with more details about each junction, e.g. the number of uniquely mapping reads.

Credits

WiggleTools was written by Daniel Zerbino, IntronProspector was written by Mark Diekhans, track hubs were written to a large extent by Brian Raney and colleages at the UCSC Genome Browser. Track creation was done by Max Haeussler and tested by Jairo Navarro.

References

Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P. WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. Bioinformatics. 2014 Apr 1;30(7):1008-9. PMID: 24363377; PMC: PMC3967112

Mark Diekhans, IntronProspector GitHub Repository. Github 2018

The Tabula Muris Consortium, Stephen R. Quake, Tony Wyss-Coray, Spyros Darmanis: Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris. bioRxiv preprint March 2018, accepted paper in Nature 2018 (562) p.367-372