Tabula Muris Splice Sites Track Settings
 
Tabula Muris single cell RNA-Seq splice sites

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

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+  All tracks in this collection (3)

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 acinar cell Sp  pancreatic acinar cell Splice Junctions (182 cells)    Schema 
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 adipocyte Sp  mesenchymal stem cell of adipose Splice Junctions (2107 cells)    Schema 
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 astrocyte Sp  astrocyte Splice Junctions (432 cells)    Schema 
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 B cell Sp  B cell Splice Junctions (2029 cells)    Schema 
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 basal cell Sp  basal cell Splice Junctions (1340 cells)    Schema 
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 basophil Sp  basophil Splice Junctions (25 cells)    Schema 
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 Bergmann glial Sp  Bergmann glial cell Splice Junctions (40 cells)    Schema 
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 bladder cell Sp  bladder cell Splice Junctions (695 cells)    Schema 
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 blood cell Sp  blood cell Splice Junctions (206 cells)    Schema 
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 brain pericyte Sp  brain pericyte Splice Junctions (156 cells)    Schema 
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 Brush cell Sp  Brush cell of epithelium proper of large intestine Splice Junctions (63 cells)    Schema 
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 cardiac muscle Sp  cardiac muscle cell Splice Junctions (133 cells)    Schema 
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 CFU-GM Sp  granulocyte monocyte progenitor cell Splice Junctions (134 cells)    Schema 
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 cilliated cell Sp  ciliated columnar cell of tracheobronchial tree Splice Junctions (25 cells)    Schema 
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 class monocyte Sp  classical monocyte Splice Junctions (90 cells)    Schema 
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 collecting duc Sp  kidney collecting duct epithelial cell Splice Junctions (121 cells)    Schema 
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 comm lymph prg Sp  common lymphoid progenitor Splice Junctions (156 cells)    Schema 
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 DN1 pro-T cell Sp  DN1 thymic pro-T cell Splice Junctions (32 cells)    Schema 
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 EC-HS Sp  endothelial cell of hepatic sinusoid Splice Junctions (182 cells)    Schema 
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 endocardial Sp  endocardial cell Splice Junctions (165 cells)    Schema 
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 endothelial Sp  endothelial cell Splice Junctions (3319 cells)    Schema 
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 enterocyte Sp  enterocyte of epithelium of large intestine Splice Junctions (964 cells)    Schema 
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 enteroendocr Sp  enteroendocrine cell Splice Junctions (59 cells)    Schema 
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 epiderm basal Sp  basal cell of epidermis Splice Junctions (1648 cells)    Schema 
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 epidermal cell Sp  epidermal cell Splice Junctions (276 cells)    Schema 
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 epithelial Sp  epithelial cell Splice Junctions (201 cells)    Schema 
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 erythrocyte Sp  erythrocyte Splice Junctions (91 cells)    Schema 
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 fibroblast Sp  fibroblast Splice Junctions (2189 cells)    Schema 
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 globet cell Sp  large intestine goblet cell Splice Junctions (833 cells)    Schema 
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 granulocyte Sp  granulocyte Splice Junctions (761 cells)    Schema 
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 hepatocyte Sp  hepatocyte Splice Junctions (391 cells)    Schema 
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 HPC Sp  hematopoietic precursor cell Splice Junctions (265 cells)    Schema 
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 immat T cell Sp  immature T cell Splice Junctions (1337 cells)    Schema 
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 immature B Sp  immature B cell Splice Junctions (344 cells)    Schema 
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 immature NK Sp  immature natural killer cell Splice Junctions (36 cells)    Schema 
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 immature NKT Sp  immature NK T cell Splice Junctions (37 cells)    Schema 
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 keratinocyte Sp  keratinocyte Splice Junctions (330 cells)    Schema 
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 keratinocyteSC Sp  keratinocyte stem cell Splice Junctions (1404 cells)    Schema 
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 keratinocyteSC Sp  stem cell of epidermis Splice Junctions (53 cells)    Schema 
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 Kupffer cell Sp  Kupffer cell Splice Junctions (61 cells)    Schema 
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 L.I. epithelia Sp  epithelial cell of large intestine Splice Junctions (2019 cells)    Schema 
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 late pro-B Sp  late pro-B cell Splice Junctions (306 cells)    Schema 
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 leukocyte Sp  leukocyte Splice Junctions (683 cells)    Schema 
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 luminal cell Sp  luminal epithelial cell of mammary gland Splice Junctions (578 cells)    Schema 
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 lung endothelia S  lung endothelial cell Splice Junctions (693 cells)    Schema 
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 lung epithelia Sp  epithelial cell of lung Splice Junctions (113 cells)    Schema 
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 lymphocyte Sp  lymphocyte Splice Junctions (81 cells)    Schema 
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 macrophage Sp  macrophage Splice Junctions (395 cells)    Schema 
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 mature NK Sp  mature natural killer cell Splice Junctions (49 cells)    Schema 
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 MEP cell Sp  megakaryocyte-erythroid progenitor cell Splice Junctions (55 cells)    Schema 
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 mesenchymalSC Sp  mesenchymal stem cell Splice Junctions (499 cells)    Schema 
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 mesenchyme Sp  mesenchymal cell Splice Junctions (830 cells)    Schema 
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 microglia Sp  microglial cell Splice Junctions (4394 cells)    Schema 
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 monocyte Sp  monocyte Splice Junctions (331 cells)    Schema 
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 myeloid cell Sp  myeloid cell Splice Junctions (1208 cells)    Schema 
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 myofibroblast Sp  myofibroblast cell Splice Junctions (178 cells)    Schema 
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 naive B cell Sp  naive B cell Splice Junctions (692 cells)    Schema 
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 neuron Sp  neuron Splice Junctions (281 cells)    Schema 
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 NK cell Sp  natural killer cell Splice Junctions (171 cells)    Schema 
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 oligodendroc. Sp  oligodendrocyte Splice Junctions (1574 cells)    Schema 
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 OPC Sp  oligodendrocyte precursor cell Splice Junctions (203 cells)    Schema 
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 pancr B cell Sp  type B pancreatic cell Splice Junctions (449 cells)    Schema 
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 pancr D cell Sp  pancreatic D cell Splice Junctions (140 cells)    Schema 
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 pancr PPcell Sp  pancreatic PP cell Splice Junctions (73 cells)    Schema 
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 pancreatic A Sp  pancreatic A cell Splice Junctions (390 cells)    Schema 
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 pancreatic duc Sp  pancreatic ductal cell Splice Junctions (161 cells)    Schema 
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 pre-B cell Sp  precursor B cell Splice Junctions (517 cells)    Schema 
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 pre-granulocyt Sp  granulocytopoietic cell Splice Junctions (221 cells)    Schema 
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 pre-NK cell Sp  pre-natural killer cell Splice Junctions (22 cells)    Schema 
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 Pro APC Sp  professional antigen presenting cell Splice Junctions (59 cells)    Schema 
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 proximal tube Sp  epithelial cell of proximal tubule Splice Junctions (219 cells)    Schema 
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 satellite SC Sp  skeletal muscle satellite stem cell Splice Junctions (439 cells)    Schema 
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 satellite Sp  skeletal muscle satellite cell Splice Junctions (540 cells)    Schema 
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 Slamf1+ cell Sp  Slamf1-positive multipotent progenitor cell Splice Junctions (134 cells)    Schema 
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 Slamf1- cell Sp  Slamf1-negative multipotent progenitor cell Splice Junctions (713 cells)    Schema 
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 smooth muscle Sp  smooth muscle cell Splice Junctions (42 cells)    Schema 
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 stellate cell Sp  pancreatic stellate cell Splice Junctions (49 cells)    Schema 
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 stromal cell Sp  stromal cell Splice Junctions (863 cells)    Schema 
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 T cell Sp  T cell Splice Junctions (793 cells)    Schema 
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 T-reg Sp  regulatory T cell Splice Junctions (27 cells)    Schema 
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 urothelial Sp  bladder urothelial cell Splice Junctions (683 cells)    Schema 
    

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