Heart Cell Atlas Heart HCA Sample Track Settings
 
Heart cell RNA binned by biosample from https://heartcellatlas.org

Track collection: Heart single cell RNA data from https://heartcellatlas.com

+  Description
+  All tracks in this collection (9)

Display mode:      Duplicate track

Label: Name or ID of item    Alternative name for item   

Log10(x+1) transform:    View limits maximum: UMI/cell (range 0-10000)

Categories:  
 H0015 LA new
 H0015 LV
 H0015 RA
 H0015 RV
 H0015 apex
 H0015 septum
 H0020 LA new
 H0020 LV
 H0020 RA
 H0020 RV
 H0020 apex
 H0020 septum
 H0025 LA
 H0025 LV
 H0025 RA
 H0025 RV
 H0025 apex
 H0025 septum
 H0026 LA
 H0026 LV V3
 H0026 RA
 H0026 RV
 H0026 apex
 H0026 septum2
 H0035 LA
 H0035 LV
 H0035 RA
 H0035 RV
 H0035 apex
 H0035 septum
 H0037 Apex
 H0037 LA corr
 H0037 LV
 H0037 RA corr
 H0037 RV
 H0037 septum
 HCAHeart7606896
 HCAHeart7656534
 HCAHeart7656535
 HCAHeart7656536
 HCAHeart7656537
 HCAHeart7656538
 HCAHeart7656539
 HCAHeart7664652
 HCAHeart7664653
 HCAHeart7664654
 HCAHeart7698015
 HCAHeart7698016
 HCAHeart7698017
 HCAHeart7702873
 HCAHeart7702874
 HCAHeart7702875
 HCAHeart7702876
 HCAHeart7702877
 HCAHeart7702878
 HCAHeart7702879
 HCAHeart7702880
 HCAHeart7702881
 HCAHeart7702882
 HCAHeart7728604
 HCAHeart7728605
 HCAHeart7728606
 HCAHeart7728607
 HCAHeart7728608
 HCAHeart7728609
 HCAHeart7745966
 HCAHeart7745967
 HCAHeart7745968
 HCAHeart7745969
 HCAHeart7745970
 HCAHeart7751845
 HCAHeart7757636
 HCAHeart7757637
 HCAHeart7757638
 HCAHeart7757639
 HCAHeart7829976
 HCAHeart7829977
 HCAHeart7829978
 HCAHeart7829979
 HCAHeart7833852
 HCAHeart7833853
 HCAHeart7833854
 HCAHeart7833855
 HCAHeart7835148
 HCAHeart7835149
 HCAHeart7836681
 HCAHeart7836682
 HCAHeart7836683
 HCAHeart7836684
 HCAHeart7843999
 HCAHeart7844000
 HCAHeart7844001
 HCAHeart7844002
 HCAHeart7844003
 HCAHeart7844004
 HCAHeart7850539
 HCAHeart7850540
 HCAHeart7850541
 HCAHeart7850542
 HCAHeart7850543
 HCAHeart7850544
 HCAHeart7850545
 HCAHeart7850546
 HCAHeart7850547
 HCAHeart7850548
 HCAHeart7850549
 HCAHeart7850551
 HCAHeart7880860
 HCAHeart7880861
 HCAHeart7880862
 HCAHeart7880863
 HCAHeart7888922
 HCAHeart7888923
 HCAHeart7888924
 HCAHeart7888925
 HCAHeart7888926
 HCAHeart7888927
 HCAHeart7888928
 HCAHeart7888929
 HCAHeart7905327
 HCAHeart7905328
 HCAHeart7905329
 HCAHeart7905330
 HCAHeart7905331
 HCAHeart7905332
 HCAHeart7964513
 HCAHeart7985086
 HCAHeart7985087
 HCAHeart7985088
 HCAHeart7985089
 HCAHeart8102858
 HCAHeart8102859
 HCAHeart8102860
 HCAHeart8102861
 HCAHeart8102862
 HCAHeart8102863
 HCAHeart8102864
 HCAHeart8102865
 HCAHeart8102866
 HCAHeart8102867
 HCAHeart8102868
 HCAHeart8287123
 HCAHeart8287124
 HCAHeart8287125
 HCAHeart8287126
 HCAHeart8287127
 HCAHeart8287128
View table schema
Data last updated at UCSC: 2022-05-12 02:27:52

Description

This track displays data from Cells of the adult human heart. Single-cell and single-nucleus RNA sequencing (RNA-seq) was used to profile transcriptomes from six regions of the heart: the interventricular septum (SP), apex (AX), left ventricle (LV), right ventricle (RV), left atrium (LA), and right atrium (RA). A total of 11 cardiac cell types were identified along with their marker genes after uniform manifold approximation and projection (UMAP) embedding of 487,106 cells. Note that the RNA-seq data is generated using Tag-sequencing (Tag-seq) and does not cover all exons.

This track collection contains nine bar chart tracks of RNA expression in the human heart where cells are grouped by cell type (Heart HCA Cells), age (Heart HCA Age), donor (Heart HCA Donor), region of the heart (Heart HCA Region), sample (Heart HCA Sample), sex (Heart HCA Sex), source (Heart HCA Source), cell state (Heart HCA State), and 10x chemistry version (Heart HCA Version). The default track displayed is Heart HCA Cells.

Display Conventions

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

Color Cell classification
neural
adipose
fibroblast
immune
muscle
lymphoid
epithelial
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 Heart HCA 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.

Method

Healthy heart tissues were obtained from 14 UK and North American transplant organ donors ages 40-75. Tissues were taken from deceased donors after circulatory death (DCD) and after brain death (DBD). To minimize transcriptional degradation, heart tissues were stored and transported on ice until freezing or tissue dissociation. Single nuclei were isolated from flash-frozen tissue using mechanical homogenization with a glass Dounce tissue grinder. Fresh heart tissues were enzymatically dissociated and automatically digested using gentleMACS Octo Dissociator. Next, Hoechst-positive single nuclei were FACS sorted prior to library preparation. In parallel, Cell suspensions from fresh heart tissue were enriched for CD45+ cells using MACS LS columns. Libraries of single cell and single nuclei were prepared using 10x Genomics 3' v2 or v3. 3' gene expression libraries were sequenced on an Illumina HiSeq4000 and NextSeq500. In total 45,870 cells, 78,023 CD45+ enriched cells, and 363,213 nuclei were profiled for 11 major cell types of the heart.

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 Monika Litviňuková, Carlos Talavera-Ló, 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 Gerardo Perez. The UCSC work was paid for by the Chan Zuckerberg Initiative.

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.

References

Litviňuková M, Talavera-López C, Maatz H, Reichart D, Worth CL, Lindberg EL, Kanda M, Polanski K, Heinig M, Lee M et al. Cells of the adult human heart. Nature. 2020 Dec;588(7838):466-472. PMID: 32971526; PMC: PMC7681775