PROJECT ID: GSE128350

Data source GEO: GSE128350
Description The behavior of (stem) cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment, we applied a genome-wide RNA tomography sequencing approach in zebrafish, chicken, mouse and human embryos. The resulting anterior-posterior and/or dorsal-ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment, where the first hematopoietic stem cells are generated during embryonic development. By performing inter-species comparative analyses, we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo, paving the way for improved (stem) cell production in vitro and clinical cell therapy.
Key word endothelial-cells; blood development; yolk-sac; origin; generation; emergence; pathway; region; niche; gata2
Publication Yvernogeau L, Klaus A, Maas J, Morin-Poulard I et al. Multispecies RNA tomography reveals regulators of hematopoietic stem cell birth in the embryonic aorta. Blood 2020 Aug 13;136(7):831-844. PMID: 32457985
Abstract The defined location of a stem cell within a niche regulates its fate, behavior, and molecular identity via a complex extrinsic regulation that is far from being fully elucidated. To explore the molecular characteristics and key components of the aortic microenvironment, where the first hematopoietic stem cells are generated during development, we performed genome-wide RNA tomography sequencing on zebrafish, chicken, mouse, and human embryos. The resulting anterior-posterior and dorsal-ventral transcriptional maps provided a powerful resource for exploring genes and regulatory pathways active in the aortic microenvironment. By performing interspecies comparative RNA sequencing analyses and functional assays, we explored the complexity of the aortic microenvironment landscape and the fine-tuning of various factors interacting to control hematopoietic stem cell generation, both in time and space in vivo, including the ligand-receptor couple ADM-RAMP2 and SVEP1. Understanding the regulatory function of the local environment will pave the way for improved stem cell production in vitro and clinical cell therapy.


Dataset Information

Dataset ID Tissue / Organ Technique Experiment type Sample description Source dataset ID
1. GSE128350 (1.67dpf whole embryo replicate1) embryo Tomo-seq baseline late embryo, 1.67dpf, whole embryo, untreatment GEO: GSM3672145
2. GSE128350 (1.17dpf whole embryo replicate1) embryo Tomo-seq baseline late embryo, 1.17dpf, whole embryo, untreatment GEO: GSM3672146
3. GSE128350 (1.17dpf whole embryo replicate2) embryo Tomo-seq baseline late embryo, 1.17dpf, whole embryo, untreatment GEO: GSM3672147
4. GSE128350 (1.17dpf trunk) embryo Tomo-seq baseline late embryo, 1.17dpf, trunk, untreatment GEO: GSM3672148
5. GSE128350 (1.67dpf trunk) embryo Tomo-seq baseline late embryo, 1.67dpf, trunk, untreatment GEO: GSM3672149
6. GSE128350 (1.67dpf whole embryo replicate2) embryo Tomo-seq baseline late embryo, 1.67dpf, whole embryo, untreatment GEO: GSM3672157
7. GSE128350 (1.17dpf whole embryo replicate3) embryo Tomo-seq baseline late embryo, 1.17dpf, whole embryo, untreatment GEO: GSM3672158