Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Emergence and patterning dynamics of mouse definitive endoderm

ABSTRACT: The segregation of definitive endoderm (DE) from bi-potent mesendoderm progenitors leads to the formation of two distinct germ layers. Dissecting DE commitment and onset has been challenging as it occurs within a narrow spatio-temporal window in the embryo. Here we employ a novel dual Bra/Sox17 reporter cell line to study DE onset dynamics. We find Sox17 expression initiates in a few isolated cells in vivo within a temporally restricted window. Using 2D and 3D in vitro models, we show that DE cells emerge from mesendoderm progenitors at a temporally regular, but spatially stochastic pattern, which is subsequently arranged by self-sorting of Sox17+ cells. A subpopulation of Bra-high cells commits to a Sox17+ fate independent of external Wnt signal. Self-sorting coincides with up-regulation of E-cadherin but is not necessary for DE differentiation or proliferation. Our in vivo and in vitro results highlight basic rules governing DE onset and patterning through the commonalities and differences between these systems.

ORGANISM(S): Mus musculus

PROVIDER: GSE189224 | GEO | 2021/12/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

BRACHYURY orchestrates distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells

Project description:The transcription factor BRACHYURY (T, BRA) is one of the first markers of gastrulation and lineage specification in mammals. Despite its wide use and importance in stem cell and developmental biology, its genomic targets are largely unknown. Here, we used differentiated human embryonic stem cells to study the role of BRA in Bmp4-induced mesoderm and Activin-induced endoderm progenitors by ChIP-seq. We show that BRA has distinct genome-wide binding landscapes in these two populations. Our data illuminate the function of BRA in the context of human embryonic development and show that the regulatory role of BRA is context-dependent. ChIP-seq of BRACHYURY (T, BRA) in two cell types: endoderm and mesoderm progenitors derived from human embryonic stem cells after 36 hours of growth in chemically-defined media (described in Bernardo et al., Cell Stem Cell, 2011, 9:144-155). Input DNA samples are included as a control.

2015-05-18 | E-GEOD-60606 | biostudies-arrayexpress

BRACHYURY orchestrates distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells

2015-05-18 | GSE60606 | GEO

Single-cell transcriptomic analysis of Sox17-expressing lineages reveals dynamic developmental trajectories and distinct gene regulatory networks during embryogenesis

Project description:As Sox17 plays a critical role in the development of multiple cell types during early embryogenesis, we utilized a dual-color lineage-tracing strategy in combination with single-cell RNA sequencing (scRNAseq) to capture and analyze Sox17-expressing lineages. GFP production from Sox17GFPCre allele marks cells that currently express Sox17 or short-term progeny of Sox17 expressing progenitors. TdTomato production from R26LSL.TdTomato reporter allele in the presence of Sox17GFPCre marks long-term progeny of Sox17-expressing progenitors. In brief, GFP and Tdtomato positive cells were isolated from E9.5 embryos of specific genotypes to generate two separate scRNAseq datasets, referred to in the manuscript as the GFP and TdTomato datasets, respectively.

2023-07-20 | E-MTAB-12719 | biostudies-arrayexpress

Layered ontogeny and in situ perinatal priming of tissue ILC2s

Project description:The perinatal period is a critical window for the distribution of innate tissue-resident immune cells to developing organs. Despite epidemiologic evidence implicating early life environment in risk for allergy, temporally controlled lineage-tracing of ILC2s during this period has not been done. Using complementary fate-mapping approaches and fluorescent reporters of ILC2 activation, we demonstrate that ILC2s appear in multiple organs during late gestation similar to tissue macrophages, but unlike the latter, a majority of peripheral ILC2 pools are generated de novo during a postnatal window. This period was accompanied by systemic ILC2 priming and acquisition of tissue-specific expression profiles. Although perinatal ILC2s are variably replaced with age, the dramatic increases in tissue ILC2s following helminth infection are mediated through local expansion independent of de novo generation by BM hematopoiesis. We provide the first comprehensive temporally controlled fate-mapping of an innate lymphocyte subset with notable nuances as compared to tissue macrophage ontogeny

2019-04-15 | GSE126924 | GEO

Transcription profiling by array of human embryonic stem cells over-expression SOX7 and SOX17

Project description:This study aimed to understand the transcriptional networks regulating endoderm specification from HESC and therefore explored the phenotype of CA1 and CA2 HESC constitutively over-expressing SOX7 or SOX17. Cell lines were created using an inducible construct whereby clonal populations containing transgene integration are selected by Neomycin resistance without expressing of the gene of interest (NoCre controls). Transgene expression is induced via Cre-mediated recombination and selected for puromycin resistance (SOX O/E). The phenotype of the resulting cells suggests that SOX7 expressing HESC represent stable extraembryonic endoderm progenitors, while SOX17 expressing HESC represent early definitive endoderm progenitors. Both in vitro and in vivo SOX7 expressing HESC are restricted to the extraembryonic endoderm lineage, while SOX17 expressing HESC demonstrate mesendodermal specificity. In vitro, SOX17 expressing HESC efficiently produce mature definitive endoderm derivatives. The molecular phenotype of the resulting SOX7 and SOX17 expressing HESC was characterized by microarray analysis Experiment Overall Design: Total RNA was extracted from confluent monolayer cultures of SOX7 over-expressing HESC, SOX17 over-expressing HESC, and their respective control parental HESC lines (designated NoCre Sox7 and NoCre Sox17).

2008-10-20 | E-GEOD-10809 | biostudies-arrayexpress

Expression data from livers in wildtype and Sox17+/-mice at 17dpc

Project description:The onset of the liver inflamentation in the Sox17+/- embryos. The expression of Cxcl10, Cxcl2, Cxcl1 and stress-induced heat shock protein Hspa1a and Hspa1b were elevated in Sox17+/- livers at 17dpc, as compared with the wildtype livers. Total RNAs from liver tissues of wildtype and Sox17+/- mice at 17dpc were subjected to microarray analyses. Two biological replicates of each genotype were analyzed.

2013-01-09 | E-GEOD-33106 | biostudies-arrayexpress

Retrospective analysis of mesendoderm progenitors that give rise to cardiac microtissues, multilineage and gut organoids

Project description:Bulk RNA-sequencing of the mesendoderm progenitors before aggregation. Mesendoderm progenitors aggregates can lead to the formation of cardiac microtissues, multilineage and gut organoids in different batches. Despite batch-to-batch differences in spheroid phenotype, all spheroids (n>200) within a single batch derived from the same initial differentiation of progenitor cells manifested identical morphologies and cellularity.

2021-06-15 | GSE153071 | GEO

Expression data of human ES cells-derived CD34+CD43+CD45low cells (hemogenic endothelium-like cells) expanded upon overexpression of Sox17

Project description:Overexpression of transcription factor Sox17 in human ES cells-derived endothelial cells and hematopoietic cells enhances expansion of hemogenic endothelium-like cells. Human ES cells were differentiated for 6 days, 8 days or 12 days in EBs, then CD34+CD43-CD45- endothelial cells, CD34+CD43+CD45- pre-hematopoietic progenitor cells (HPCs) or CD34+CD43+CD45+ HPCs were isolated by fluorescence activated cell sorting (FACS) and subjected to a microarray analysis.M-cM-^@M-^@Some samples were plated onto OP9 cells after the isolation by FACS, and transduced with the 4OH-tamoxifen-inducible 1M-CM-^WFLAG-tagged Sox17-ERT retrovirus. The cells were cultured with 4OH-tamoxifen. CD34+CD43+CD45low hemogenic endothelium-like cells expanded by Sox17-ERT were collected by magnetic-activated cell sorting (MACS) and subjected to a ChIP-chip analysis.

2012-12-14 | E-GEOD-37348 | biostudies-arrayexpress

Direct Induction of hemogenic endothelial progenitors from hPSCs by defined factors revealed by single-cell transcriptome analysis

Project description:Transcription factors play critical roles in stem cell maintenance and differentiation. Using single cell RNA sequencing, we investigated transcription factors expressed in endothelial progenitors differentiated from human pluripotent stem cells (hPSCs) and identified upregulated differential expression of SOXF subgroup members SOX7, SOX17, and SOX18. To test whether overexpression of these factors increases differentiation efficiency, we established inducible hPSC lines and found only SOX17 improved differentiation of CD34+VEC+ cells. Temporal expression analysis of SOX17 and VEC revealed that SOX17 was turned on immediately before VEC, indicating SOX17 may be a causative factor in determining hemogenic endothelial differentiation. Upon Cas13d mediated repression of SOX17, differentiation was significantly abrogated. We found SOX17 forward programming is sufficient to generate more than 50% CD34+VEC+CD73- cells. Further differentiation of SOX17 forward programmed cells generated hematopoietic progenitors that emerged via an endothelial to hematopoietic transition and significantly upregulated definitive hematopoietic transcriptional programs. Our analyses reveal an uncharacterized function of SOX17 in directing hPSCs differentiation towards hematopoietic lineages.

2022-12-31 | GSE161408 | GEO

Expression data from livers in wildtype and Sox17+/-mice at 17dpc

2013-01-09 | GSE33106 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data