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Series GSE188341 Query DataSets for GSE188341
Status Public on Apr 27, 2023
Title Atlas of lymphangiogenesis [scRNA-Seq]
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary During development, lymphatic vasculature forms as a second and distinct network that derives from embryonic blood vessels. Transdifferentiation of venous endothelial cells into specified lymphatic endothelial cells (LECs) is the first step in this process. Transdifferentiation and specification of LEC fate requires Prox1, but how Prox1 regulates transdifferentiation and differentiation is not fully understood. We present a single cell transcriptomic atlas of lymphangiogenesis spanning four key developmental stages that reveals new markers and functional regulators of lymphatic development. We extend this to comprehensively profile single cell transcriptomic and chromatin changes controlled by Prox1 using zygotic prox1a mutants, which form lymphatics that then dedifferentiate. Combining this with single cell analysis of Prox1-null, double prox1a/prox1b maternal zygotic mutants, we reveal in depth the role of Prox1 in control of LEC fate specification and differentiation. This resource reveals dual and progressive functions for Prox1, blocking blood vascular and hematopoietic fate while simultaneously up-regulating a small number of early acting genes that include tspan18a/b and lgals3a/b which are essential for lymphangiogenesis. This embryonic developmental resource will serve as a baseline to better understand both developmental and pathological lymphangiogenesis in the future. [Citations in sample metadata correspond to reference numbers in the associated publication.]
 
Overall design Single cell RNA profiles of endothelial cells from wild type developing zebrafish across 4 stages of development (40hpf, 3dpf, 4dpf, 5dpf), Zprox-/- mutant and matched WT siblings at 4dpf, and MZprox-/- mutant and matched WT siblings at 40hpf. All code associated with this data and publication are publicly available under an open source software license at: https://atlassian.petermac.org.au/bitbucket/users/tyrone.chen/repos/hogan_lab/browse/2022_Grimm_Mason_et_al_PROX1_NatCellBiol/
 
Contributor(s) Grimm L, Mason E, Bower NI, Okuda K, Chen T, Yu O, Dudczig S, Paterson S, Senabouth A, Powell J, Smith KA, Harvey N, Koltowska K, Hogan BM
Citation(s) 36912146
Submission date Nov 06, 2021
Last update date Apr 27, 2023
Contact name Tyrone Chen
E-mail(s) tyrone.chen@monash.edu
Organization name Monash University
Department School of Biological Sciences
Lab Computational Biology Lab
Street address 18 Innovation Walk
City Melbourne
State/province VIC
ZIP/Postal code 3800
Country Australia
 
Platforms (1)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (9)
GSM5677992 20043: WT_40hpf scRNA-seq
GSM5677993 20044: WT_3dpf scRNA-seq
GSM5677994 20045: WT_5dpf scRNA-seq
This SubSeries is part of SuperSeries:
GSE188342 Atlas of lymphangiogenesis
Relations
BioProject PRJNA778401
SRA SRP344884

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
GSE188341_processed_rna.tar.gz 223.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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