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:   

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: 2018-09-12 08:07:43

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