Fetal Gene Atlas Fetal Cells Track Settings
Fetal Gene Atlas binned by cell type from Cao et al 2020

Track collection: Fetal Gene Atlas from Cao et al 2020

+  Description
+  All tracks in this collection (8)

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)

color↓ organ and cell type count organ cell_class cell_type
mixed lymphatic endothelial cell 7305 mixed endothelial lymphatic endothelial cell
stomach parietal and chief cell 2322 stomach secretory parietal and chief cell
pancreas ductal cell 4829 pancreas secretory ductal cell
pancreas islet endocrine cell 4768 pancreas secretory islet endocrine cell
placenta extravillous trophoblast 1535 placenta trophoblast extravillous trophoblast
mixed neuroendocrine cell 1824 mixed secretory neuroendocrine cell
placenta IGFBP1+ DKK1+ cell 701 placenta other placenta IGFBP1+ DKK1+ cell
adrenal gland adrenocortical cell 328920 adrenal gland secretory adrenocortical cell
mixed erythroblast 46707 mixed immune erythroblast
mixed megakaryocyte 3498 mixed immune megakaryocyte
kidney metanephric cell 90876 kidney kidney specific metanephric cell
muscle satellite cell 5255 muscle precursor satellite cell
mixed smooth muscle cell 7344 mixed muscle smooth muscle cell
mixed vascular endothelial cell 75104 mixed endothelial vascular endothelial cell
eye corneal/conjunctival epithelial cell 104 eye epithelial corneal/conjunctival epithelial cell
mixed Schwann cell 1769 mixed glia Schwann cell
mixed ENS glial cell 3219 mixed glia enteric nervous system (ENS) glial cell
thymus thymic epithelial cell 259 thymus epithelial thymic epithelial cell
stomach goblet cell 3624 stomach secretory goblet cell
mixed ciliated epithelial cell 2886 mixed ciliated ciliated epithelial cell
intestine intestinal epithelial cell 24545 intestine epithelial intestinal epithelial cell
placenta PAEP+ MECOM+ cell 287 placenta other placenta PAEP+ MECOM+ cell
stomach PDE1C+ ACSM3+ cell 78 stomach other stomach PDE1C+ ACSM3+ cell
mixed squamous epithelial cell 2238 mixed epithelial squamous epithelial cell
pancreas acinar cell 11388 pancreas secretory acinar cell
stomach MUC13+ DMBT1+ cell 792 stomach other stomach MUC13+ DMBT1+ cell
placenta trophoblast giant cell 1137 placenta trophoblast trophoblast giant cell
mixed CSH1+ CSH2+ cell 109 mixed other mixed CSH1+ CSH2+ cell
placenta syncytiotrophoblast and vill... 14567 placenta trophoblast syncytiotrophoblast and villous cytot...
kidney mesangial cell 44177 kidney kidney specific mesangial cell
brain retinal pigment cell 704 brain other retinal pigment cell
heart endocardial cell 7398 heart endothelial endocardial cell
kidney ureteric bud cell 9138 kidney other ureteric bud cell
lung bronchiolar/alveolar epithelial ... 101249 lung epithelial bronchiolar/alveolar epithelial cell
spleen STC2+ TLX1+ cell 4487 spleen other spleen STC2+ TLX1+ cell
mixed stromal cell 152957 mixed other stromal cell
liver stellate cell 1743 liver fibroblast stellate cell
adrenal gland sympathoblasts 3805 adrenal gland other sympathoblasts
pancreas CCL19+ CCL21+ cell 206 pancreas other pancreas CCL19+ CCL21+ cell
adrenal gland chromaffin cell 21055 adrenal gland secretory chromaffin cell
liver hematopoietic stem cell 1096 liver stem cell hematopoietic stem cell
eye lens fibre cell 246 eye other lens fibre cell
brain astrocyte 318105 brain glia astrocyte
eye photoreceptor cell 12398 eye neural photoreceptor cell
heart cardiomyocyte 67610 heart muscle cardiomyocyte
liver hepatoblast 58447 liver hepatocyte hepatoblast
brain retinal progenitor/Muller glial... 14865 brain glia retinal progenitor/Muller glial cell
muscle skeletal muscle cell 13516 muscle muscle skeletal muscle cell
eye horizontal cell 2300 eye neural horizontal cell
heart CLC+ IL5RA+ cell 102 heart other heart CLC+ IL5RA+ cell
thymus thymocyte 7852 thymus other thymocyte
eye PDE11A+ FAM19A2+ cell 806 eye other eye PDE11A+ FAM19A2+ cell
brain oligodendrocyte 33748 brain glia oligodendrocyte
eye bipolar neuron 1207 eye neural bipolar neuron
mixed visceral neuron 610 mixed neural visceral neuron
adrenal gland SLC26A4+ PAEP+ cell 68 adrenal gland other adrenal gland SLC26A4+ PAEP+ cell
mixed AFP+ ALB+ cell 182 mixed other mixed AFP+ ALB+ cell
heart ELF3+ AGBL2+ cell 164 heart other heart ELF3+ AGBL2+ cell
mixed ENS neuron 2514 mixed neural enteric nervous system (ENS) neuron
mixed lymphoid cell 16873 mixed immune lymphoid cell
eye amacrine cell 7341 eye neural amacrine cell
brain unipolar brush cell 52646 brain neural unipolar brush cell
mixed mesothelial cell 2048 mixed epithelial mesothelial cell
brain microglial 8975 brain immune microglial cell
brain SLC24A4+ PEX5L+ cell 19722 brain other brain SLC24A4+ PEX5L+ cell
heart SATB2+ LRRC7+ cell 318 heart other heart SATB2+ LRRC7+ cell
brain Purkinje neuron 280377 brain neural Purkinje neuron
brain SKOR2+ NPSR1+ cell 15005 brain other brain SKOR2+ NPSR1+ cell
eye ganglion cell 10143 eye neural ganglion cell
thymus antigen presenting cell 465 thymus immune antigen presenting cell
brain inhibitory interneuron 129890 brain neural inhibitory interneuron
brain granule neuron 312675 brain neural granule neuron
brain excitatory neuron 1258818 brain neural excitatory neuron
brain limbic system neuron 45989 brain neural limbic system neuron
brain inhibitory neuron 350759 brain neural inhibitory neuron
mixed myeloid cell 18300 mixed immune myeloid cell
heart epicardial adipose cell 1891 heart adipose epicardial adipose cell
Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2021-01-11 04:16:11


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