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| Status |
Public on Mar 30, 2018 |
| Title |
Whole-organism clone-tracing using single-cell sequencing |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We present ScarTrace, a single-cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast, we find that cells in the eyes, brain, and caudal tail fin arise from many embryonic progenitors, which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types.
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| Overall design |
Single cell sequencing data from cells isolated from zebrafish organs (whole kidney marrow, forebrain, hindbrain, left eye, right eye, left midbrain, right midbrain, and regenerated fin). For each cell, we provide libraries with transcritpome and with clonal information, respectively.
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| Contributor(s) |
Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A |
| Citation(s) |
29590089 |
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| Submission date |
Aug 23, 2017 |
| Last update date |
Jan 18, 2021 |
| Contact name |
Anna Alemany |
| E-mail(s) |
a.alemany@hubrecht.eu
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| Phone |
+31638680750
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| Organization name |
Hubrecht Institue
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| Lab |
AVO
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (56)
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| Relations |
| BioProject |
PRJNA399711 |
| SRA |
SRP116018 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE102990_P1_scarclones.txt.gz |
36.6 Kb |
(ftp)(http) |
TXT |
| GSE102990_P2_scarclones.txt.gz |
18.4 Kb |
(ftp)(http) |
TXT |
| GSE102990_R1_R2_R4_wkm_transcriptome.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE102990_R1_R2_wkm_tsne.txt.gz |
59.0 Kb |
(ftp)(http) |
TXT |
| GSE102990_R1_R3_head_transcriptome.txt.gz |
4.7 Mb |
(ftp)(http) |
TXT |
| GSE102990_R1_R3_head_v2.tsv.gz |
54.7 Kb |
(ftp)(http) |
TSV |
| GSE102990_R1_head_tsne.txt.gz |
48.0 Kb |
(ftp)(http) |
TXT |
| GSE102990_R1_scarclones.txt.gz |
105.5 Kb |
(ftp)(http) |
TXT |
| GSE102990_R2_scarclones.txt.gz |
48.1 Kb |
(ftp)(http) |
TXT |
| GSE102990_R3_head_tsne.txt.gz |
28.5 Kb |
(ftp)(http) |
TXT |
| GSE102990_R3_scarclones.txt.gz |
51.7 Kb |
(ftp)(http) |
TXT |
| GSE102990_R4_R5_fin_transcriptome.txt.gz |
13.2 Mb |
(ftp)(http) |
TXT |
| GSE102990_R4_R5_fin_tsne.txt.gz |
103.3 Kb |
(ftp)(http) |
TXT |
| GSE102990_R4_scarclones.txt.gz |
77.9 Kb |
(ftp)(http) |
TXT |
| GSE102990_R4_wkm_tsne.txt.gz |
23.4 Kb |
(ftp)(http) |
TXT |
| GSE102990_R5_scarclones.txt.gz |
33.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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