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Series GSE233126 Query DataSets for GSE233126
Status Public on Oct 31, 2023
Title An interactive resource of molecular signalling in the developing human haematopoietic stem cell (HSC) niche [LCM-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The emergence of definitive human haematopoietic stem cells (HSCs) during Carnegie Stages (CS) 14-17 in the aorta-gonad-mesonephros (AGM) region is a complex and tightly regulated process. In a previous study we conducted spatial transcriptomic analysis of the human AGM region at the end of this period (CS16/17) and identified secreted factors involved in HSC development. Here, we extend our analysis to investigate the progression of dorso-ventral polarized signalling around the dorsal aorta over the entire period of HSC emergence. Our results reveal a dramatic increase in signalling complexity from the CS13 to CS14 transition, coinciding with the activation of endothelial-to-haematopoietic transition (EHT) in the ventral domain of the dorsal aorta. We further observe stage-specific changes in signalling complexity up to CS17. Signalling progression described here may underpin step-wise maturation of HSCs described in the mouse model. A data-rich bioinformatics resource presented here along with an interactive online interface enables in silico analysis of molecular interactions between spatially defined domains of the AGM region. This resource will be of particular interest for researchers studying mechanisms underlying human HSC development as well as those developing in vitro methods for the generation of clinically relevant HSCs from pluripotent stem cells.
 
Overall design Laser capture microdissection of spatial domains around the carnegie stage (CS) 13 and 14 dorsal aorta in the developing human embryo with RNA-Seq libraries prepared from each region. N = 2 for each embryo and 6 spatial domains were taken for each stage.
 
Contributor(s) Crosse EI, Medvinsky A, Binagui-Casas A, Gordon-Keylock S, Tamagno S, Oloffson D, Anderson RA
Citation(s) 37840454
Submission date May 22, 2023
Last update date Jan 03, 2024
Contact name Edie I Crosse
E-mail(s) ecrosse@fredhutch.org
Phone 2065914579
Organization name Fred Hutchinson Cancer Center
Street address 1100 Fairview Ave N
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (24)
GSM7401847 CS13_Ventral_Inner_Rep1 (VI_1)
GSM7401848 CS13_Dorsal_Inner_Rep1 (DI_1)
GSM7401849 CS13_Ventral_Outer_Rep1 (VO_1)
This SubSeries is part of SuperSeries:
GSE233132 An interactive resource of molecular signalling in the developing human haematopoietic stem cell (HSC) niche
Relations
BioProject PRJNA975088

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
GSE233126_CS13_gene_counts.csv.gz 814.8 Kb (ftp)(http) CSV
GSE233126_CS14_gene_counts.csv.gz 888.4 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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