PROJECT ID: GSE176129

Data source GEO: GSE176129
Description We performed single cell and bulk RNA-seq analyses on pdgfrb-positive cells to identify candidate pericyte-expressed genes. For bulk RNA-seq, we used wild type pdgfrb-positive samples from Series GSE152759 (GEO ID: GSM4625924, GSM4625925, GSM4625926) for comparison to mutant pdgfrb-positive cells in this Series. These cells had originally been isolated in parallel.
Key word pericyte; vascular development; pdgfrb; zebrafish;smooth-muscle-cells; neural-crest; pdgf-b; brain; deficient; markers; receptor; beta
Publication Shih YH, Portman D, Idrizi F, Grosse A et al. Integrated molecular analysis identifies a conserved pericyte gene signature in zebrafish. Development 2021 Dec 1;148(23). PMID: 34751773
Abstract Pericytes reside in capillary beds where they share a basement membrane with endothelial cells and regulate their function. However, little is known about embryonic pericyte development, in part, due to lack of specific molecular markers and genetic tools. Here, we applied single cell RNA-sequencing (scRNA-seq) of platelet derived growth factor beta (pdgfrb)-positive cells to molecularly characterize pericytes in zebrafish larvae. scRNA-seq revealed zebrafish cells expressing mouse pericyte gene orthologs, and comparison with bulk RNA-seq from wild-type and pdgfrb mutant larvae further refined a pericyte gene set. Subsequent integration with mouse pericyte scRNA-seq profiles revealed a core set of conserved pericyte genes. Using transgenic reporter lines, we validated pericyte expression of two genes identified in our analysis: NDUFA4 mitochondrial complex associated like 2a (ndufa412a), and potassium voltage-gated channel, lsk-related family, member 4 (kcne4). Both reporter lines exhibited pericyte expression in multiple anatomical locations, and kcne4 was also detected in a subset of vascular smooth muscle cells. Thus, our integrated molecular analysis revealed a molecular profile for zebrafish pericytes and allowed us to develop new tools to observe these cells in vivo.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE176129 (pdgfrb-positive) Danio rerio whole body baseline 5dpf, FACS-isolated pdgfrb-positive cells GEO: GSM5356650

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
2 Neuron ENSDARG00000014420 (elavl3) marker DOI:10.7554/eLife.44431
7 Epidermal cells ENSDARG00000088514 (and1) marker DOI:10.7554/eLife.44431
8 Chondrocranium cells ENSDARG00000052470 (igfbp2a) marker DOI:10.7554/eLife.44431
9 Epidermal cells ENSDARG00000088514 (and1) marker DOI:10.7554/eLife.44431
10 Chondrocranium cells ENSDARG00000015947 (matn4) marker DOI:10.7554/eLife.44431
11 Smooth muscle cells ENSDARG00000045180 (acta2) marker DOI:10.7554/eLife.44431
12 Smooth muscle cells ENSDARG00000045180 (acta2) marker DOI:10.7554/eLife.44431
13 Proliferating cells ENSDARG00000024488 (top2a) marker DOI:10.7554/eLife.44431
14 Epidermal cells ENSDARG00000092947 (cyt1) marker DOI:10.7554/eLife.44431
15 Ph arch mesench cells ENSDARG00000011956 (dlx4a) marker DOI:10.7554/eLife.44431
16 Chondrocytes ENSDARG00000052437 (mia) marker DOI:10.7554/eLife.44431
17 Brain ventricular zone cells ENSDARG00000015349 (mfge8a) marker DOI:10.7554/eLife.44431
21 Epidermal cells ENSDARG00000088514 (and1) marker DOI:10.7554/eLife.4443
22 Smooth muscle cells ENSDARG00000045180 (acta2) marker DOI:10.7554/eLife.44431
23 Neuron ENSDARG00000014420 (elavl3) marker DOI:10.7554/eLife.44431
24 Skeletal muscle cells ENSDARG00000007344 (tcap) marker DOI:10.7554/eLife.44431
25 Epidermal cells ENSDARG00000092947 (cyt1) marker DOI:10.7554/eLife.4443
28 Pronephros ENSDARG00000040469 (enpp6) marker DOI:10.7554/eLife.44431
29 Epidermal cells ENSDARG00000088514 (and1) marker DOI:10.7554/eLife.44431
29 Epidermal cells ENSDARG00000092947 (cyt1) marker DOI:10.7554/eLife.44431
31 Neutrophils ENSDARG00000057789 (lyz) marker DOI:10.7554/eLife.44431
32 Neuromast cells ENSDARG00000069503 (cldnh) marker DOI:10.7554/eLife.44431
33 Xanthophores ENSDARG00000071475 (aox5) marker DOI:10.7554/eLife.44431
34 Ph arch mesench cells ENSDARG00000011956 (dlx4a) marker DOI:10.7554/eLife.44431
35 Chondrocranium cells ENSDARG00000052470 (igfbp2a) marker DOI:10.7554/eLife.44431
36 Periderm cells ENSDARG00000043128 (cldne) marker DOI:10.7554/eLife.44431
37 Hepatocytes ENSDARG00000037191 (ttr) marker DOI:10.7554/eLife.44431
38 Skeletal muscle cells ENSDARG00000007344 (tcap) marker DOI:10.7554/eLife.44431
40 Oligodendrocytes ENSDARG00000036186 (mbpa) marker DOI:10.7554/eLife.44431
41 Cleithrum cells ENSDARG00000054753 (col10a1a) marker DOI:10.7554/eLife.44431
42 Macrophages ENSDARG00000056874 (lygl1) marker DOI:10.7554/eLife.44431
43 Pancreas cells ENSDARG00000030915 (cpa1) marker DOI:10.7554/eLife.44431
43 Pancreas cells ENSDARG00000043722 (cpa4) marker DOI:10.7554/eLife.44431
43 Pancreas cells ENSDARG00000021339 (cpa5) marker DOI:10.7554/eLife.44431
44 Erythroid cells ENSDARG00000089475 (hbae1.1) marker DOI:10.7554/eLife.44431
45 Melanophores ENSDARG00000003732 (mitfa) marker DOI:10.7554/eLife.44431