Fetal Gene Atlas Fetal RT Group #1 Track Settings
Fetal Gene Atlas binned by RT group from Cao et al 2020 (duplicate #1)

Track collection: Fetal Gene Atlas from Cao et al 2020

+  Description
+  All tracks in this collection (9)

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Label: Name or ID of item    Alternative name for item   

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

 Adrenal H26350
 Adrenal H26547
 Adrenal H27098
 Adrenal H27471
 Adrenal H27472
 Adrenal H27474
 Adrenal H27552
 Cerebellum H27471
 Cerebellum H27472
 Cerebellum H27474
 Cerebellum H27477
 Cerebellum H27634
 Cerebrum H27058
 Cerebrum H27098
 Cerebrum H27423
 Cerebrum H27431
 Cerebrum H27432
 Cerebrum H27464
 Cerebrum H27471
 Cerebrum H27474
 Eye H27458
 Eye H27472
 Eye H27552
 Eye H27620
 Eye H27634
 Heart H26547
 Heart H27098
 Heart H27295
 Heart H27423
 Heart H27431
 Heart H27464
 Heart H27471
 Heart H27472
 Heart H27473
 Intestine H27771
 Intestine H27772
 Intestine H27798
 Intestine H27799
 Intestine H27876
 Intestine H27909
 Intestine H27913
 Intestine H27915
 Intestine H27948
 Kidney H27771
 Kidney H27772
 Kidney H27798
 Kidney H27870
 Kidney H27876
 Kidney H27909
 Kidney H27913
 Kidney H27915
 Kidney H27948
 Liver H27058
 Liver H27098
 Liver H27423
 Liver H27431
 Liver H27464
 Liver H27471
 Liver H27472
 Liver H27473
 Liver H27474
 Lung H26350
 Lung H26547
 Lung H27058
 Lung H27098
 Lung H27423
 Lung H27431
 Lung H27464
 Lung H27471
 Lung H27472
 Lung H27474
 Lung H27477
 Muscle H27098
 Muscle H27431
 Muscle H27471
 Muscle H27472
 Muscle H27473
 Muscle H27474
 Muscle H27477
 Muscle H27634
 Pancreas H27870
 Pancreas H27876
 Pancreas H27948
 Placenta H26350
 Placenta H26547
 Placenta H27058
 Placenta H27098
 Placenta H27423
 Placenta H27431
 Placenta H27464
 Placenta H27471
 Placenta H27472
 Placenta H27473
 Placenta H27474
 Spleen H26350
 Spleen H26547
 Spleen H27431
 Spleen H27464
 Spleen H27471
 Spleen H27472
 Spleen H27552
 Spleen H27634
 Stomach H27870
 Stomach H27876
 Stomach H27909
 Stomach H27948
 Thymus H26547
 Thymus H27423
 Thymus H27431
 Thymus H27471
 Thymus H27552
 Thymus H27634
Data schema/format description and download
Data last updated at UCSC: 2021-01-11 04:16:34


This group of tracks shows data from A human cell atlas of fetal gene expression. This is a collection of single cell and single nucleus combinatorial indexing-based RNA-seq data covering 4 million cells from 15 organs obtained during mid-gestation. The cells were sequenced in a highly multiplexed fashion and then clustered with annotations as described in Cao et al., 2020.

The Fetal Cells subtrack contains the data organized by cell type, with RNA signals from all cells of a given type pooled and averaged into one bar for each cell type. The Fetal Lineage subtrack shows similar data, but with the cell types subdivided more finely and by organ. Additional bar chart subtracks pool the cell by other characteristics such as by sex (Fetal Sex), assay (FetalAssay), donor (Fetal Donor ID), experiment (Fetal Exp), organ (Fetal Organ), and reverse transcription group (Fetal RT Group).

Please see descartes.brotmanbaty.org for further interactive displays and additional data.

Display Conventions and Configuration

The cell types are colored by which class they belong to according to the following table. The coloring algorithm allows cells that show some blended characteristics to show blended colors so there will be some color variation within a class. The colors will be purest in the Fetal 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.

Color Cell classification


Three-level single-cell combinatorial indexing (sci-RNAseq3) as described in Cao et al., 2020 was used on 121 samples from 28 fetuses estimated 72 to 129 days post-conception. This included samples from 15 organs. and resulted in RNA profiles for 4 million cells. The samples were flash-frozen for majority of the experiments and then nuclei extracted for sequencing. Samples from tissues from the kidney and digestive system were fixed after disassociation to deactivate endogenous RNases and proteases.

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.


Thanks 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 Jairo Navarro. The UCSC work was paid for by the Chan Zuckerberg Initiative.


Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F et al. A human cell atlas of fetal gene expression. Science. 2020 Nov 13;370(6518). PMID: 33184181; PMC: PMC7780123

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019 Feb;566(7745):496-502. PMID: 30787437; PMC: PMC6434952