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Series GSE134350 Query DataSets for GSE134350
Status Public on Jul 17, 2019
Title Single cell RNA‐seq in the sea urchin embryo show marked cell‐type specificity in the Delta/Notch pathway
Organism Strongylocentrotus purpuratus
Experiment type Expression profiling by high throughput sequencing
Summary Overall, we conclude that single cell RNA‐seq analysis in this embryo is revealing of the cell types present during development, of the changes in the gene regulatory network resulting from inhibition of various signaling pathways, and of the selectivity of these pathways in influencing developmental trajectories.
 
Overall design Adult S. purpuratus were obtained from South Coast Bio‐Marine info@scbiomarine.com and were spawned using 0.5 M KCl injections intracoelomically. DAPT (Tocris) was added at fertilization to 8 μM, a concentration previously determined to effectively perturb Delta/Notch signaling without affecting overall development (Materna & Davidson, 2012). C59 (Cellagen) was added at 0.5 μM at fertilization as previously described (Cui et al., 2014). Embryos were cultured and, at appropriate developmental stages, were dissociated into single cells as described (McClay, 2004). We started with 50 ml cultures containing 0.25% of embryos (125 ul of embryos in 50 ml). The full volume was dissociated into single cells. We obtained 12 million single cells from which 5,000 were used for the DropSeq.The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v2 chemistry and cells were loaded on a GemCode Single Cell Instrument (10× Genomics, Pleasanton, CA).
 
Contributor(s) Foster S, Wessel G
Citation(s) 31199038
Submission date Jul 16, 2019
Last update date Oct 16, 2019
Contact name Gary Wessel
Organization name Brown University
Department Molecular Biology, Cell Biology & Biochemistry
Street address 185 Meeting St
City Providence
State/province RI
ZIP/Postal code 02912
Country USA
 
Platforms (1)
GPL20965 Illumina HiSeq 2500 (Strongylocentrotus purpuratus)
Samples (3)
GSM3943022 DMSO1
GSM3943023 DAPT1
GSM3943024 W1
Relations
BioProject PRJNA554833
SRA SRP214801

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

Supplementary file Size Download File type/resource
GSE134350_RAW.tar 7.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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