PROJECT ID: PRJNA564810

Data source SRA: PRJNA564810
Description The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge, we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap, we produced an Atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single-cell transcriptome Atlas encompasses transcriptional profiles from 44,102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single-cell resolution. Furthermore, we highlight the power of this analysis to assign new cell-type or developmental stage-specific expression information to many genes, including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic (mutant) or functional analysis, to launch an effort to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time.
Key word Connexin; gap junction; single cell RNA-seq; zebrafish
Publication Lukowicz-Bedford, Rachel M., Dylan R. Farnsworth, and Adam C. Miller. "Connexinplexity: The spatial and temporal expression of connexin genes during vertebrate organogenesis." bioRxiv (2021).
Abstract Animal development requires coordinated communication between cells. The Connexin family of proteins is a major contributor to intercellular communication in vertebrates by forming gap junction channels that facilitate the movement of ions, small molecules, and metabolites between cells. Additionally, individual hemichannels can provide a conduit to the extracellular space for paracrine and autocrine signaling. Connexin-mediated communication is widely used in epithelial, neural, and vascular development and homeostasis, and most tissues likely use this form of communication. In fact, Connexin disruptions are of major clinical significance contributing to disorders developing from all major germ layers. Despite the fact that Connexins serve as an essential mode of cellular communication, the temporal and cell-type specific expression patterns of connexin genes remain unknown in vertebrates. A major challenge is the large and complex connexin gene family. To overcome this barrier, we determined the expression of all connexins in zebrafish using single-cell RNA-sequencing of entire animals across several stages of organogenesis. Our analysis of expression patterns has revealed that few connexins are broadly expressed, but rather, most are expressed in tissue- or cell-type-specific patterns. Additionally, most tissues possess a unique combinatorial signature of connexin expression with dynamic temporal changes across the organism, tissue, and cell. Our analysis has identified new patterns for well-known connexins and assigned spatial and temporal expression to genes with no-existing information. We provide a field guide relating zebrafish and human connexin genes as a critical step towards understanding how Connexins contribute to cellular communication and development throughout vertebrate organogenesis.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. PRJNA564810 (5dpf) Danio rerio embryo baseline 5dpf, a single-cell transcriptome atlas for zebrafish development SRA: SRR10095964
2. PRJNA564810 (2dpf) Danio rerio embryo baseline 2dpf, a single-cell transcriptome atlas for zebrafish development SRA: SRR10095966
3. PRJNA564810 (1dpf) Danio rerio embryo baseline 1dpf, a single-cell transcriptome atlas for zebrafish development SRA: SRR10095968

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Cranial neural crest ENSDARG00000044935 (hpdb) marker DOI:10.1093/g3journal/jkac062
1 Cranial neural crest ENSDARG00000045979 (zgc:153704) marker DOI:10.1093/g3journal/jkac062
1 Cranial neural crest ENSDARG00000071095 (abi3bpb) marker DOI:10.1093/g3journal/jkac062
2 Neuron ENSDARG00000018259 (atp1a3a) marker DOI:10.1093/g3journal/jkac062
3 Neuron ENSDARG00000003469 (neurod4) marker DOI:10.1093/g3journal/jkac062
4 Periderm cells ENSDARG00000040534 (epcam) marker DOI:10.1093/g3journal/jkac062
4 Periderm cells ENSDARG00000016691 (cd9b) marker DOI:10.1093/g3journal/jkac062
4 Periderm cells ENSDARG00000055514 (icn2) marker DOI:10.1093/g3journal/jkac062
6 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
7 Neuron ENSDARG00000003469 (neurod4) marker DOI:10.1093/g3journal/jkac062
8 Hematopoietic cells ENSDARG00000045142 (hbae5) marker DOI:10.1093/g3journal/jkac062
8 Hematopoietic cells ENSDARG00000092945 (si:ch211-250g4.3) marker DOI:10.1093/g3journal/jkac062
8 Hematopoietic cells ENSDARG00000029019 (epb41b) marker DOI:10.1093/g3journal/jkac062
9 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1093/g3journal/jkac062
10 Neuroblast ENSDARG00000041799 (cx43) marker DOI:10.1093/g3journal/jkac062
10 Neuroblast ENSDARG00000102340 (ptn) marker DOI:10.1093/g3journal/jkac062
10 Neuroblast ENSDARG00000091579 (si:ch211-66e2.5) marker DOI:10.1093/g3journal/jkac062
11 Neuron ENSDARG00000070107 (six7) marker DOI:10.1093/g3journal/jkac062
11 Neuron ENSDARG00000075295 (tulp1a) marker DOI:10.1093/g3journal/jkac062
11 Neuron ENSDARG00000010680 (gngt2a) marker DOI:10.1093/g3journal/jkac062
12 Skeletal muscle cells ENSDARG00000007344 (tcap) marker DOI:10.1093/g3journal/jkac062
12 Skeletal muscle cells ENSDARG00000020574 (atp2a1) marker DOI:10.1093/g3journal/jkac062
13 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1093/g3journal/jkac062
14 Multipotent cells ENSDARG00000055186 (ccr9a) marker DOI:10.1093/g3journal/jkac062
15 Enteric smooth muscle ENSDARG00000045180 (acta2) marker DOI:10.1093/g3journal/jkac062
15 Enteric smooth muscle ENSDARG00000045408 (tagln) marker DOI:10.1093/g3journal/jkac062
16 Photoreceptor cells ENSDARG00000029898 (cnga1a) marker DOI:10.1093/g3journal/jkac062
16 Photoreceptor cells ENSDARG00000070666 (rhol) marker DOI:10.1093/g3journal/jkac062
16 Photoreceptor cells ENSDARG00000058803 (grk1a) marker DOI:10.1093/g3journal/jkac062
17 Intesinal epithelial cells ENSDARG00000016081 (cldn15la) marker DOI:10.1093/g3journal/jkac062
17 Intesinal epithelial cells ENSDARG00000101979 (eps8l3a) marker DOI:10.1093/g3journal/jkac062
17 Intesinal epithelial cells ENSDARG00000112049 (cldn15a) marker DOI:10.1093/g3journal/jkac062
18 Iridophore ENSDARG00000060345 (apoda.1) marker DOI:10.1093/g3journal/jkac062
18 Iridophore ENSDARG00000075629 (si:dkey-197i20.6) marker DOI:10.1093/g3journal/jkac062
18 Iridophore ENSDARG00000062688 (gpnmb) marker DOI:10.1093/g3journal/jkac062
18 Iridophore ENSDARG00000055172 (si:ch211-256m1.8) marker DOI:10.1093/g3journal/jkac062
18 Iridophore ENSDARG00000091792 (akap12a) marker DOI:10.1093/g3journal/jkac062
19 Hepatocytes ENSDARG00000016771 (tfa) marker DOI:10.1093/g3journal/jkac062
19 Hepatocytes ENSDARG00000087143 (serpina7) marker DOI:10.1093/g3journal/jkac062
19 Hepatocytes ENSDARG00000015866 (apoa2) marker DOI:10.1093/g3journal/jkac062
20 Hepatocytes ENSDARG00000016771 (tfa) marker DOI:10.1093/g3journal/jkac062
20 Hepatocytes ENSDARG00000087143 (serpina7) marker DOI:10.1093/g3journal/jkac062
20 Hepatocytes ENSDARG00000015866 (apoa2) marker DOI:10.1093/g3journal/jkac062
21 Endothelium ENSDARG00000105215 (kdrl) marker DOI:10.1093/g3journal/jkac062
21 Endothelium ENSDARG00000060263 (pecam1) marker DOI:10.1093/g3journal/jkac062
21 Endothelium ENSDARG00000030125 (sox7) marker DOI:10.1093/g3journal/jkac062
21 Endothelium ENSDARG00000103533 (clec14a) marker DOI:10.1093/g3journal/jkac062
21 Endothelium ENSDARG00000036616 (gpr182) marker DOI:10.1093/g3journal/jkac062
22 Oligodendrocytes ENSDARG00000036186 (mbpa) marker DOI:10.1093/g3journal/jkac062
23 Enteric smooth muscle ENSDARG00000045180 (acta2) marker DOI:10.1093/g3journal/jkac062
23 Enteric smooth muscle ENSDARG00000045408 (tagln) marker DOI:10.1093/g3journal/jkac062
24 Epidermal cells ENSDARG00000088514 (and1) marker DOI:10.1093/g3journal/jkac062
25 Lens ENSDARG00000037402 (lim2.3) marker DOI:10.1093/g3journal/jkac062
25 Lens ENSDARG00000102129 (crygn1) marker DOI:10.1093/g3journal/jkac062
25 Lens ENSDARG00000014803 (cryba1l2) marker DOI:10.1093/g3journal/jkac062
25 Lens ENSDARG00000068507 (crybb1) marker DOI:10.1093/g3journal/jkac062
26 Monocytes ENSDARG00000090873 (ccl34a.4) marker DOI:10.1093/g3journal/jkac062
26 Monocytes ENSDARG00000103466 (ccl35.1) marker DOI:10.1093/g3journal/jkac062
26 Monocytes ENSDARG00000059294 (marco) marker DOI:10.1093/g3journal/jkac062
27 Leukocytes ENSDARG00000087909 (il4) marker DOI:10.1093/g3journal/jkac062
27 Leukocytes ENSDARG00000093248 (si:dkey-238m4.4) marker DOI:10.1093/g3journal/jkac062
27 Leukocytes ENSDARG00000105530 (si:dkey-19b23.14) marker DOI:10.1093/g3journal/jkac062
27 Leukocytes ENSDARG00000007534 (itln1) marker DOI:10.1093/g3journal/jkac062
27 Leukocytes ENSDARG00000036940 (ctss1) marker DOI:10.1093/g3journal/jkac062
28 Pancreatic epsilon cells ENSDARG00000044204 (endou) marker DOI:10.1093/g3journal/jkac062
28 Pancreatic epsilon cells ENSDARG00000090899 (sycn.3) marker DOI:10.1093/g3journal/jkac062
28 Pancreatic epsilon cells ENSDARG00000024503 (c6ast3) marker DOI:10.1093/g3journal/jkac062
29 Epiphysis ENSDARG00000045153 (slc16a8) marker DOI:10.1093/g3journal/jkac062
29 Epiphysis ENSDARG00000078618 (inpp5kb) marker DOI:10.1093/g3journal/jkac062
29 Epiphysis ENSDARG00000087059 (selenou1b) marker DOI:10.1093/g3journal/jkac062
29 Epiphysis ENSDARG00000028862 (rdh20) marker DOI:10.1093/g3journal/jkac062

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neuron ENSDARG00000027740 (adcyap1b) marker DOI:10.1093/g3journal/jkac062
1 Neuron ENSDARG00000056092 (si:dkey-12h9.6) marker DOI:10.1093/g3journal/jkac062
1 Neuron ENSDARG00000018259 (atp1a3a) marker DOI:10.1093/g3journal/jkac062
1 Neuron ENSDARG00000014018 (lhx1a) marker DOI:10.1093/g3journal/jkac062
2 Neuroblast ENSDARG00000010770 (sox19a) marker DOI:10.1093/g3journal/jkac062
3 Neuroblast ENSDARG00000010770 (sox19a) marker DOI:10.1093/g3journal/jkac062
4 Neuron ENSDARG00000068168 (hes2.2) marker DOI:10.1093/g3journal/jkac062
4 Neuron ENSDARG00000069552 (atoh7) marker DOI:10.1093/g3journal/jkac062
4 Neuron ENSDARG00000010385 (sept4a) marker DOI:10.1093/g3journal/jkac062
4 Neuron ENSDARG00000014059 (cldn5b) marker DOI:10.1093/g3journal/jkac062
5 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
6 Cranial neural crest ENSDARG00000105223 (pmp22a) marker DOI:10.1093/g3journal/jkac062
6 Cranial neural crest ENSDARG00000007407 (barx1) marker DOI:10.1093/g3journal/jkac062
6 Cranial neural crest ENSDARG00000011956 (dlx4a) marker DOI:10.1093/g3journal/jkac062
6 Cranial neural crest ENSDARG00000038056 (fgfbp2b) marker DOI:10.1093/g3journal/jkac062
6 Cranial neural crest ENSDARG00000059073 (gsc) marker DOI:10.1093/g3journal/jkac062
7 Neuron ENSDARG00000025495 (nhlh2) marker DOI:10.1093/g3journal/jkac062
7 Neuron ENSDARG00000100821 (scrt1a) marker DOI:10.1093/g3journal/jkac062
7 Neuron ENSDARG00000091756 (insm1a) marker DOI:10.1093/g3journal/jkac062
7 Neuron ENSDARG00000102976 (uncx) marker DOI:10.1093/g3journal/jkac062
8 Neuron ENSDARG00000053364 (pax10) marker DOI:10.1093/g3journal/jkac062
8 Neuron ENSDARG00000031316 (six6b) marker DOI:10.1093/g3journal/jkac062
8 Neuron ENSDARG00000032705 (foxg1b) marker DOI:10.1093/g3journal/jkac062
8 Neuron ENSDARG00000004023 (isl1) marker DOI:10.1093/g3journal/jkac062
9 Hematopoietic cells ENSDARG00000096667 (hemgn) marker DOI:10.1093/g3journal/jkac062
9 Hematopoietic cells ENSDARG00000038643 (alas2) marker DOI:10.1093/g3journal/jkac062
9 Hematopoietic cells ENSDARG00000034852 (nt5c2l1) marker DOI:10.1093/g3journal/jkac062
9 Hematopoietic cells ENSDARG00000029019 (epb41b) marker DOI:10.1093/g3journal/jkac062
9 Hematopoietic cells ENSDARG00000044550 (hif1al2) marker DOI:10.1093/g3journal/jkac062
9 Hematopoietic cells ENSDARG00000013477 (gata1a) marker DOI:10.1093/g3journal/jkac062
10 Neuron ENSDARG00000011989 (crx) marker DOI:10.1093/g3journal/jkac062
10 Neuron ENSDARG00000043483 (otx5) marker DOI:10.1093/g3journal/jkac062
10 Neuron ENSDARG00000037921 (gng13b) marker DOI:10.1093/g3journal/jkac062
10 Neuron ENSDARG00000010420 (ndrg1b) marker DOI:10.1093/g3journal/jkac062
11 Neuron ENSDARG00000015537 (gad2) marker DOI:10.1093/g3journal/jkac062
12 Somites ENSDARG00000009438 (myog) marker DOI:10.1093/g3journal/jkac062
12 Somites ENSDARG00000030110 (myod1) marker DOI:10.1093/g3journal/jkac062
12 Somites ENSDARG00000079071 (jam2b) marker DOI:10.1093/g3journal/jkac062
12 Somites ENSDARG00000058996 (jam2a) marker DOI:10.1093/g3journal/jkac062
12 Somites ENSDARG00000010478 (hsp90aa1.1) marker DOI:10.1093/g3journal/jkac062
13 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1093/g3journal/jkac062
14 Neuron ENSDARG00000101984 (pde6gb) marker DOI:10.1093/g3journal/jkac062
14 Neuron ENSDARG00000043483 (otx5) marker DOI:10.1093/g3journal/jkac062
14 Neuron ENSDARG00000011989 (crx) marker DOI:10.1093/g3journal/jkac062
14 Neuron ENSDARG00000010680 (gngt2a) marker DOI:10.1093/g3journal/jkac062
15 Epidermal cells ENSDARG00000040534 (epcam) marker DOI:10.1093/g3journal/jkac062
16 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1093/g3journal/jkac062
17 Skeletal muscle cells ENSDARG00000020574 (atp2a1) marker DOI:10.1093/g3journal/jkac062
18 Somites ENSDARG00000103443 (vwde) marker DOI:10.1093/g3journal/jkac062
18 Somites ENSDARG00000105380 (fgl1) marker DOI:10.1093/g3journal/jkac062
18 Somites ENSDARG00000007891 (meox1) marker DOI:10.1093/g3journal/jkac062
18 Somites ENSDARG00000020072 (thbs4b) marker DOI:10.1093/g3journal/jkac062
19 Cranial neural crest ENSDARG00000058005 (hgd) marker DOI:10.1093/g3journal/jkac062
19 Cranial neural crest ENSDARG00000044935 (hpdb) marker DOI:10.1093/g3journal/jkac062
19 Cranial neural crest ENSDARG00000011693 (ttc36) marker DOI:10.1093/g3journal/jkac062
20 Skeletal muscle cells ENSDARG00000011615 (mybpc3) marker DOI:10.1093/g3journal/jkac062
20 Skeletal muscle cells ENSDARG00000045822 (tnnt2e) marker DOI:10.1093/g3journal/jkac062
20 Skeletal muscle cells ENSDARG00000073766 (tnni1d) marker DOI:10.1093/g3journal/jkac062
20 Skeletal muscle cells ENSDARG00000005139 (hhatlb) marker DOI:10.1093/g3journal/jkac062
20 Skeletal muscle cells ENSDARG00000114031 (smyhc3) marker DOI:10.1093/g3journal/jkac062
21 Melanophores ENSDARG00000056151 (tyrp1b) marker DOI:10.1093/g3journal/jkac062
22 Optic vesicle ENSDARG00000001870 (atp1a1a.4) marker DOI:10.1093/g3journal/jkac062
23 Lens ENSDARG00000037402 (lim2.3) marker DOI:10.1093/g3journal/jkac062
24 Monocytes ENSDARG00000090873 (ccl34a.4) marker DOI:10.1093/g3journal/jkac062
25 Xanthophores ENSDARG00000093957 (si:dkey-251i10.2) marker DOI:10.1093/g3journal/jkac062
25 Xanthophores ENSDARG00000056028 (slc22a7a) marker DOI:10.1093/g3journal/jkac062
25 Xanthophores ENSDARG00000063288 (slc2a11b) marker DOI:10.1093/g3journal/jkac062
25 Xanthophores ENSDARG00000103789 (tmem130) marker DOI:10.1093/g3journal/jkac062
25 Xanthophores ENSDARG00000028257 (cyb561a3b) marker DOI:10.1093/g3journal/jkac062
26 Endothelium ENSDARG00000060263 (pecam1) marker DOI:10.1093/g3journal/jkac062
27 Cranial neural crest ENSDARG00000012422 (col11a2) marker DOI:10.1093/g3journal/jkac062
28 Erythroid cells ENSDARG00000045143 (hbbe2) marker DOI:10.1093/g3journal/jkac062

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neuroblast ENSDARG00000010770 (sox19a) marker DOI:10.1093/g3journal/jkac062
2 Neuroblast ENSDARG00000054879 (six3b) marker DOI:10.1093/g3journal/jkac062
3 Cranial neural crest ENSDARG00000039949 (fibina) marker DOI:10.1093/g3journal/jkac062
4 Neuron ENSDARG00000003469 (neurod4) marker DOI:10.1093/g3journal/jkac062
6 Hatching gland ENSDARG00000023656 (he1.1) marker DOI:10.1093/g3journal/jkac062
6 Hatching gland ENSDARG00000095072 (ctslb) marker DOI:10.1093/g3journal/jkac062
6 Hatching gland ENSDARG00000019122 (he1.2) marker DOI:10.1093/g3journal/jkac062
6 Hatching gland ENSDARG00000089750 (si:dkey-26g8.5) marker DOI:10.1093/g3journal/jkac062
6 Hatching gland ENSDARG00000094559 (zgc:174855) marker DOI:10.1093/g3journal/jkac062
7 Neuroblast ENSDARG00000058008 (six3a) marker DOI:10.1093/g3journal/jkac062
8 Neuron ENSDARG00000003469 (neurod4) marker DOI:10.1093/g3journal/jkac062
9 Neuron ENSDARG00000056092 (si:dkey-12h9.6) marker DOI:10.1093/g3journal/jkac062
10 Neuroblast ENSDARG00000076321 (col28a2a) marker DOI:10.1093/g3journal/jkac062
11 Somites ENSDARG00000103443 (vwde) marker DOI:10.1093/g3journal/jkac062
12 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1093/g3journal/jkac062
13 Neuron ENSDARG00000018259 (atp1a3a) marker DOI:10.1093/g3journal/jkac062
14 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1093/g3journal/jkac062
15 Skeletal muscle cells ENSDARG00000020574 (atp2a1) marker DOI:10.1093/g3journal/jkac062
16 Endothelium ENSDARG00000060263 (pecam1) marker DOI:10.1093/g3journal/jkac062
17 Neuron ENSDARG00000019566 (neurod1) marker DOI:10.1093/g3journal/jkac062
19 Skeletal muscle cells ENSDARG00000020574 (atp2a1) marker DOI:10.1093/g3journal/jkac062
20 Otic ENSDARG00000001870 (atp1a1a.4) marker DOI:10.1093/g3journal/jkac062
21 Hematopoietic cells ENSDARG00000045142 (hbae5) marker DOI:10.1093/g3journal/jkac062
22 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1093/g3journal/jkac062
23 Floor plate ENSDARG00000031483 (col9a1b) marker DOI:10.1093/g3journal/jkac062
24 Mucous secreting cells ENSDARG00000037790 (pvalb8) marker DOI:10.1093/g3journal/jkac062
25 Hatching gland ENSDARG00000019122 (he1.2) marker DOI:10.1093/g3journal/jkac062
26 Erythroid cells ENSDARG00000045143 (hbbe2) marker DOI:10.1093/g3journal/jkac062
27 Integument Ionocyte ENSDARG00000076833 (atp1b1b) marker DOI:10.1093/g3journal/jkac062
28 Monocytes ENSDARG00000090873 (ccl34a.4) marker DOI:10.1093/g3journal/jkac062
29 Lens ENSDARG00000014803 (cryba1l2) marker DOI:10.1093/g3journal/jkac062
30 Heart primordium ENSDARG00000079564 (myh7) marker DOI:10.1093/g3journal/jkac062