PROJECT ID: PRJNA415636

Data source SRA: PRJNA415636
Description A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many different cell types. Single-cell RNA-sequencing (scRNA-seq) has become a widely-used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However, a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here, we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses, LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences) can be used as a systematic approach for identifying the lineage origin of novel cell types, or of known cell types under different conditions.
Key word single cells; stem-cells; zebrafish embryo; expression; dynamics; progenitors; tracking; design; model
Publication Spanjaard B, Hu B, Mitic N, Olivares-Chauvet P et al. Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol 2018 Jun;36(5):469-473. PMID: 29644996
Abstract A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ(1). However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. PRJNA415636 (pancreas, liver) Danio rerio hepatopancreas baseline adult, Zebrabow M, pancreas and liver SRA: SRR6211488
2. PRJNA415636 (heart, blood) Danio rerio heart, blood baseline adult, Zebrabow M, heart and blood SRA: SRR6211492
3. PRJNA415636 (brain) Danio rerio brain baseline adult, Zebrabow M, brain SRA: SRR6811819
4. PRJNA415636 (primary pancreatic islet) Danio rerio primary pancreatic islet baseline adult, Zebrabow M, primary pancreatic islet SRA: SRR6811821

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Pancreas endocrine cells ENSDARG00000014190 (sst2) marker DOI:10.1038/nbt.4124
1 Pancreas endocrine cells ENSDARG00000044566 (fabp6) marker DOI:10.1038/nbt.4124
1 Pancreas endocrine cells ENSDARG00000039490 (pitpnaa) marker DOI:10.1038/nbt.4124
1 Pancreas endocrine cells ENSDARG00000033161 (sst1.2) marker DOI:10.1038/nbt.4124
1 Pancreas endocrine cells ENSDARG00000054616 (cldni) marker DOI:10.1038/nbt.4124
2 Bi-hormonal endocrine cells ENSDARG00000035350 (ins) marker DOI:10.1038/nbt.4124
2 Bi-hormonal endocrine cells ENSDARG00000079296 (gcga) marker DOI:10.1038/nbt.4124
2 Bi-hormonal endocrine cells ENSDARG00000040907 (gcgb) marker DOI:10.1038/nbt.4124
2 Bi-hormonal endocrine cells ENSDARG00000040799 (sst1.1) marker DOI:10.1038/nbt.4124
3 Pancreas endocrine cells ENSDARG00000036505 (syt4) marker DOI:10.1038/nbt.4124
3 Pancreas endocrine cells ENSDARG00000094836 (si:ch211-195b15.8) marker DOI:10.1038/nbt.4124
3 Pancreas endocrine cells ENSDARG00000079462 (si:ch211-131k2.3) marker DOI:10.1038/nbt.4124
4 Smooth muscle cells ENSDARG00000002701 (rasl12) marker DOI:10.1038/nbt.4124
4 Smooth muscle cells ENSDARG00000044365 (angptl3) marker DOI:10.1038/nbt.4124
4 Smooth muscle cells ENSDARG00000056795 (serpine1) marker DOI:10.1038/nbt.4124
4 Smooth muscle cells ENSDARG00000062592 (myl10) marker DOI:10.1038/nbt.4124
6 Smooth muscle cells ENSDARG00000045180 (acta2) marker DOI:10.1038/nbt.4124
7 Pancreas duct epithelial cells ENSDARG00000038153 (lgals2b) marker DOI:10.1038/nbt.4124
7 Pancreas duct epithelial cells ENSDARG00000077982 (elf3) marker DOI:10.1038/nbt.4124
7 Pancreas duct epithelial cells ENSDARG00000006207 (gpx1b) marker DOI:10.1038/nbt.4124
8 Pancreas endocrine cells ENSDARG00000010946 (cbsb) marker DOI:10.1038/nbt.4124
9 Monocytes ENSDARG00000009087 (cd74a) marker DOI:10.1038/nbt.4124
10 Pancreas endocrine cells ENSDARG00000053130 (pcp4a) marker DOI:10.1038/nbt.4124
11 Endothelium ENSDARG00000045141 (aqp8a.1) marker DOI:10.1038/nbt.4124
12 Pancreas exocrine cells ENSDARG00000077880 (si:ch211-255i20.3) marker DOI:10.1038/nbt.4124
12 Pancreas exocrine cells ENSDARG00000012539 (dnase1) marker DOI:10.1038/nbt.4124
12 Pancreas exocrine cells ENSDARG00000010146 (cpa2) marker DOI:10.1038/nbt.4124

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Cardiomyocytes ENSDARG00000099870 (tnni4a) marker DOI:10.1038/nbt.4124
1 Cardiomyocytes ENSDARG00000019096 (myl7) marker DOI:10.1038/nbt.4124
1 Cardiomyocytes ENSDARG00000001950 (ak1) marker DOI:10.1038/nbt.4124
2 Erythroid cells ENSDARG00000097011 (hbaa1) marker DOI:10.1038/nbt.4124
2 Erythroid cells ENSDARG00000069735 (hbaa2) marker DOI:10.1038/nbt.4124
2 Erythroid cells ENSDARG00000077504 (si:ch211-103n10.5) marker DOI:10.1038/nbt.4124
3 Endocardial cells ENSDARG00000070266 (spock3) marker DOI:10.1038/nbt.4124
3 Endocardial cells ENSDARG00000045141 (aqp8a.1) marker DOI:10.1038/nbt.4124
4 Endocardial cells ENSDARG00000045141 (aqp8a.1) marker DOI:10.1038/nbt.4124
4 Endocardial cells ENSDARG00000070266 (spock3) marker DOI:10.1038/nbt.4124
5 Endocardial cells ENSDARG00000070266 (spock3) marker DOI:10.1038/nbt.4124
6 Fibroblasts ENSDARG00000006526 (fn1b) marker DOI:10.1038/nbt.4124
6 Fibroblasts ENSDARG00000088116 (gstm.3) marker DOI:10.1038/nbt.4124
7 T cells ENSDARG00000094002 (ccl34b.4) marker DOI:10.1038/nbt.4124
8 Cardiomyocytes ENSDARG00000090637 (myh6) marker DOI:10.1038/nbt.4124
8 Cardiomyocytes ENSDARG00000037539 (tnnc1b) marker DOI:10.1038/nbt.4124
8 Cardiomyocytes ENSDARG00000041257 (smtnl1) marker DOI:10.1038/nbt.4124
9 Macrophages ENSDARG00000070542 (mafbb) marker DOI:10.1038/nbt.4124
10 Apelin expressing cells ENSDARG00000053279 (apln) marker DOI:10.1038/nbt.4124
10 Apelin expressing cells ENSDARG00000039222 (mpl) marker DOI:10.1038/nbt.4124
10 Apelin expressing cells ENSDARG00000058557 (il11b) marker DOI:10.1038/nbt.4124
11 Smooth muscle cells ENSDARG00000055053 (itih1) marker DOI:10.1038/nbt.4124
11 Smooth muscle cells ENSDARG00000039273 (fbln5) marker DOI:10.1038/nbt.4124
11 Smooth muscle cells ENSDARG00000089187 (wfdc2) marker DOI:10.1038/nbt.4124
12 Fibroblasts ENSDARG00000027582 (angptl7) marker DOI:10.1038/nbt.4124
12 Fibroblasts ENSDARG00000068275 (ptx3a) marker DOI:10.1038/nbt.4124
12 Fibroblasts ENSDARG00000104340 (rspo1) marker DOI:10.1038/nbt.4124
12 Fibroblasts ENSDARG00000086189 (mgp) marker DOI:10.1038/nbt.4124
13 B cells ENSDARG00000074014 (zgc:194275) marker DOI:10.1038/nbt.4124
13 B cells -- (zgc:153659.1) marker DOI:10.1038/nbt.4124
13 B cells ENSDARG00000093272 (igic1s1) marker DOI:10.1038/nbt.4124
13 B cells ENSDARG00000057633 (cxcr4a) marker DOI:10.1038/nbt.4124
14 Granule cells ENSDARG00000057789 (lyz) marker DOI:10.1038/nbt.4124
14 Granule cells ENSDARG00000033227 (lect2l) marker DOI:10.1038/nbt.4124
14 Granule cells ENSDARG00000101479 (BX908782.2) marker DOI:10.1038/nbt.4124
14 Granule cells ENSDARG00000010423 (npsn) marker DOI:10.1038/nbt.4124
14 Granule cells ENSDARG00000093124 (scpp8) marker DOI:10.1038/nbt.4124

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Neuron ENSDARG00000015537 (gad2) marker DOI:10.1038/nbt.4124
2 Neuron ENSDARG00000027740 (adcyap1b) marker DOI:10.1038/nbt.4124
3 Radial glia ENSDARG00000010710 (msi1) marker DOI:10.1038/nbt.4124
4 Microglia ENSDARG00000098012 (itgae.1) marker DOI:10.1038/nbt.4124
4 Microglia ENSDARG00000090890 (cmklr1) marker DOI:10.1038/nbt.4124
5 Oligodendrocytes ENSDARG00000040946 (olig2) marker DOI:10.1038/nbt.4124
5 Oligodendrocytes ENSDARG00000036670 (aplnrb) marker DOI:10.1038/nbt.4124
5 Oligodendrocytes ENSDARG00000089477 (si:ch211-132g1.3) marker DOI:10.1038/nbt.4124
5 Oligodendrocytes ENSDARG00000029239 (syt9b) marker DOI:10.1038/nbt.4124
6 Lymphocyte cells ENSDARG00000055186 (ccr9a) marker DOI:10.1038/nbt.4124
7 Radial glia ENSDARG00000087556 (pacrg) marker DOI:10.1038/nbt.4124
8 Radial glia ENSDARG00000053831 (vtnb) marker DOI:10.1038/nbt.4124
9 Endothelium ENSDARG00000102100 (mrc1a) marker DOI:10.1038/nbt.4124

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Pancreas endocrine cells ENSDARG00000054616 (cldni) marker DOI:10.1038/nbt.4124
1 Pancreas endocrine cells ENSDARG00000044566 (fabp6) marker DOI:10.1038/nbt.4124
2 Pancreas endocrine cells ENSDARG00000078768 (abhd15a) marker DOI:10.1038/nbt.4124
3 Smooth muscle cells ENSDARG00000038123 (myl9a) marker DOI:10.1038/nbt.4124
4 Pancreas exocrine cells ENSDARG00000073742 (prss59.2) marker DOI:10.1038/nbt.4124
4 Pancreas exocrine cells ENSDARG00000079274 (prss59.1) marker DOI:10.1038/nbt.4124
4 Pancreas exocrine cells ENSDARG00000090428 (ctrb1) marker DOI:10.1038/nbt.4124
4 Pancreas exocrine cells ENSDARG00000056765 (ela2l) marker DOI:10.1038/nbt.4124
5 Pancreas endocrine cells ENSDARG00000017739 (ak5l) marker DOI:10.1038/nbt.4124
6 Endothelium ENSDARG00000045141 (aqp8a.1) marker DOI:10.1038/nbt.4124
6 Endothelium ENSDARG00000019371 (flt1) marker DOI:10.1038/nbt.4124
7 Pancreas duct epithelial cells ENSDARG00000014047 (cldn7b) marker DOI:10.1038/nbt.4124
7 Pancreas duct epithelial cells ENSDARG00000055647 (ftr82) marker DOI:10.1038/nbt.4124
7 Pancreas duct epithelial cells ENSDARG00000077982 (elf3) marker DOI:10.1038/nbt.4124
8 Pancreas exocrine cells ENSDARG00000009443 (zgc:92137) marker DOI:10.1038/nbt.4124
8 Pancreas exocrine cells ENSDARG00000018263 (pdia2) marker DOI:10.1038/nbt.4124
8 Pancreas exocrine cells ENSDARG00000010146 (cpa2) marker DOI:10.1038/nbt.4124
8 Pancreas exocrine cells ENSDARG00000044204 (endou) marker DOI:10.1038/nbt.4124
9 Pancreas endocrine cells ENSDARG00000093677 (si:ch211-56a11.2) marker DOI:10.1038/nbt.4124
10 Smooth muscle cells ENSDARG00000002701 (rasl12) marker DOI:10.1038/nbt.4124
12 Peripheral Neurons ENSDARG00000034588 (scn4ab) marker DOI:10.1038/nbt.4124
13 T cells ENSDARG00000090728 (tnfrsf9b) marker DOI:10.1038/nbt.4124
14 Pancreas duct epithelial cells ENSDARG00000006137 (star) marker DOI:10.1038/nbt.4124
15 Pancreas endocrine cells ENSDARG00000054794 (plcxd3) marker DOI:10.1038/nbt.4124
18 Macrophages ENSDARG00000059294 (marco) marker DOI:10.1038/nbt.4124