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Series GSE112294 Query DataSets for GSE112294
Status Public on Apr 26, 2018
Title Systematic mapping of cell state trajectories, cell lineage, and perturbations in the zebrafish embryo using single cell transcriptomics
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease. Here, we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell state landscape that describes axis patterning, germ layer formation, and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (“TracerSeq”) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin-deficient embryos. We provide web-based resources for further analysis of the single-cell data.
Overall design Single-cell mRNA sequencing of zebrafish embryonic cells. Samples1-7: Single cell libraries from untreated embryos (4-24 hours post-fertilization). Samples8-12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1-cell stage. Samples13-18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1-cell stage.
Contributor(s) Wagner DE, Weinreb C, Collins ZM, Megason SG, Klein AM
Citation(s) 29700229
Submission date Mar 23, 2018
Last update date May 04, 2020
Contact name Daniel E Wagner
Phone 8023099497
Organization name Harvard Medical School
Department Systems Biology
Street address 200 Longwood Ave, Harvard Medical School, Systems Biology, Warren Alpert 536
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (18)
GSM3067189 Zebrafish Embryos, 4hpf
GSM3067190 Zebrafish Embryos, 6hpf
GSM3067191 Zebrafish Embryos, 8hpf
BioProject PRJNA445487
SRA SRP136369

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE112294_ClusterNames.csv.gz 1.7 Kb (ftp)(http) CSV
GSE112294_LibraryName_SRR_readme.txt 2.1 Kb (ftp)(http) TXT
GSE112294_RAW.tar 1.6 Gb (http)(custom) TAR (of CSV, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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