Schema for Muscle Sample - Muscle RNA binned by biosample from De Micheli et al 2020
  Database: hg38    Primary Table: muscleDeMicheliSample Data last updated: 2022-05-12
Big Bed File: /gbdb/hg38/bbi/muscleDeMicheli/sample.bb
Item Count: 23,498
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
expCount10Number of categories
expScores0.0123023,0.0221354,0,0.00825309,0.0147574,0.0361029,0.0124294,0.0100177,0.0075979,0.00727763Comma separated list of category values

Sample Rows
 
chromchromStartchromEndnamescorestrandname2expCountexpScores
chr1166070019166166969FAM78B0-ENSG00000188859.6100.0123023,0.0221354,0,0.00825309,0.0147574,0.0361029,0.0124294,0.0100177,0.0075979,0.00727763
chr1166334883166335762RP11-479J7.20+ENSG00000229588.1100,0.00520833,0,0,0,0.00181339,0,0.000883913,0.00233781,0.00242588
chr1166840088166854473POGK0+ENSG00000143157.11100.100176,0.0950521,0.0956522,0.0371389,0.0757879,0.119189,0.0644068,0.0388922,0.0642899,0.058221
chr1166856509166876327TADA10-ENSG00000152382.5100.0228471,0.0104167,0.0173913,0.0178817,0.02001,0.0308276,0.0135593,0.0094284,0.012858,0.0137466
chr1166908190166975324ILDR20-ENSG00000143195.12100.00351494,0.00130208,0,0,0.0050025,0.00824266,0,0.00265174,0.00116891,0.0132075
chr1166989108167022214MAEL0+ENSG00000143194.12100,0.00520833,0,0.00412655,0.00275138,0.00642928,0.00338983,0.00206246,0,0.00458221
chr1167094339167128608DUSP270+ENSG00000198842.9100,0.00651042,0,0.00412655,0.00825413,0.00939664,0,0.00441956,0,0.00943396
chr1167175916167195789LINC013630-ENSG00000231605.5100.00527241,0.00390625,0,0,0,0,0.00338983,0,0.0169492,0
chr1167219830167220512RP11-277B15.30-ENSG00000272205.1100,0.00260417,0,0,0.00125063,0.00214309,0.00451977,0.000883913,0,0.00296496
chr1167220828167427345POU2F10+ENSG00000143190.21100.126538,0.173177,0.0695652,0.0563961,0.15983,0.170129,0.151412,0.0494991,0.0397428,0.0504043

Muscle Sample (muscleDeMicheliSample) Track Description
 

Description

This track displays data from A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. Muscle tissue was analyzed using single-cell RNA-sequencing (scRNA-seq) and subsequent clustering distinguished 16 muscle-resident cell types based on their identified marker genes found in De Micheli et al., 2020. Muscle samples were from surgically discarded tissue taken from a wide variety of anatomical sites.

This track collection contains two bar chart tracks of RNA expression in the human muscle where cells are grouped by cell type (Muscle Cells) or biosample (Muscle Sample). The default track displayed is Muscle Cells.

Display Conventions

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

Color Cell classification
stem cell
adipose
fibroblast
immune
muscle
endothelial

Cells that fall into multiple classes will be colored by blending the colors associated with those classes. The colors will be purest in the Muscle Cells subtrack, where the bars represent relatively pure cell types. They can give an overview of the cell composition within other categories in other subtracks as well. Note that the Muscle Sample subtrack is colored based on colors provided from Figure 1 from De Micheli et al., 2020.

Relevant Figures From De Micheli et al. 2020

Details on sex, age, anatomical site, and single-cell transcriptomes after quality control (QC) filtering from 10 donors. Colors represent areas from which samples were taken from.

Muscle Sample Donors
De Micheli et al. Skelet Muscle. 2020. / CC BY 4.0


Cell type proportions across the 10 donors and grouped by leg (donors 02, 07, 08), trunk (donors 01, 05, 06, 09, 10), and face (donors 03, 04).

Cell Type Proportions
De Micheli et al. Skelet Muscle. 2020. / CC BY 4.0

Method

Muscle samples were taken from 10 healthy donors of ages ranging from 41-81 years old from different sections of the face (F), trunk (T), and leg (L). Excessive fat and connective tissue were removed from the muscle samples prior to enzymatic dissociation. Next, libraries were prepared using the 10x Genomics 3' v2 or v3 library kit and sequenced on the Illumina NextSeq 500. This resulted in libraries with 200-250 million reads which were processed using Cell Ranger version 3.1. In total, over 22,000 RNA transcriptomic profiles were generated from all of the samples after quality control filtering. The single cell transcriptomes from all 10 datasets were integrated using a scRNA-seq integration method called Scanorama as described in the reference below.

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 Andrea De Micheli of the Cosgrove Laboratory at Cornell University 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 Luis Nassar. The UCSC work was paid for by the Chan Zuckerberg Initiative.

References

De Micheli AJ, Spector JA, Elemento O, Cosgrove BD. A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. Skelet Muscle. 2020 Jul 6;10(1):19. PMID: 32624006; PMC: PMC7336639