Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human fetal yolk sac scRNA-seq data (sample ID: F158 for Haniffa Lab; 16099 for HDBR)

ABSTRACT: Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas. The embryo was dissected into 12 coronal sections, yolk sac, and yolk sac stalk. Live single cells sorted, with cell suspension then undergoing 10x chromium 5 prime scRNA-seq. This accession contains the yolk sac and yolk sac stalk data from this embryo. A matched accession contains the coronal section data. Lane "WS_wEMB12142156" (from yolk sac) was excluded from downstream analysis due to low fraction reads in cells post-CellRanger QC. Termination procedure for this embryo was medical. The F158_[features...barcodes...matrix].[tsv...mtx].gz files attached to this accession represent raw count data from all the 10x lanes in this accession combined, and as output from CellRanger filtered matrices (CellRanger version 6.0.1 using human reference genome GRCh38-2020-A). One set of count matrices relates to the yolk sac data, and one set of count matrices relates to the yolk sac stalk data.

INSTRUMENT(S): 10x Genomics Chromium Controller, Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Simone Webb

PROVIDER: E-MTAB-11673 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Cynomolgus monkey embryo model captures gastrulation and early pregnancy

Project description:Here, we constructed monkey blastoids resembling blastocysts in morphology and transcriptomics using naïve ESCs and optimized protocol. The synthetic blastoids could develop to embryonic disk stage with the structure of yolk sac, chorionic cavity, amnion cavity, primitive streak, connecting stalk along the rostral–caudal axis by in-vitro prolonged culture (IVC). Primordial germ cells, gastrulating cells, visceral endoderm/yolk-sac endoderm, three germ layers and haemato-endothelial progenitors were identified in the monkey blastoid IVC embryo by single-cell transcriptomics or immunostaining. Besides, pregnancies with early gestation sacs were achieved by transferring monkey blastoids to surrogates. Our results revealed the in-vitro gastrulation and in-vivo early pregnancy of primate synthetic embryos, providing a powerful system to dissect primate embryonic development with less ethical concerns and restrict access.

2023-04-06 | GSE218375 | GEO

Comparison of gene expression pattern between Wild-type and Hypb knockout embryo yolk sacs

Project description:This study aimed at exploring the physiological function of mammalian HYPB by means of knockout mouse model. Homogenous disruption of mouse Hypb gene leads to embryonic lethality at E10.5-E11.5. Severe vascular defects were observed in the Hypb-/- embryos, yolk sac and placenta.In the mutant embryo and yolk sac, disorganized and abnormally dilated capillaries cannot be remodeled into large blood vessels or intricate networks. Thus, our results suggest that the mammalian HYPB HMT plays an important role in embryonic vascularization. Keywords: knockout, mouse embryo development, angiogenesis, yolk sac, E9.0, E10.5

2009-12-28 | GSE10113 | GEO

Genome-wide gene expression analysis of Cirh1a heterozygote state on early embryo in mice

Project description:CIRHIN is a transcription co-factor, shows postive effect on Hiv-1 LTR enhancer element(NF-κB site); and Cirh1a null is preimplantation lethal, but highly expressed in the early mice embryo (E6.0-E12.5). We hypothesis that Cirh1a's effect on gene transcription of early embryo can be detected with Cirh1a down regulated in Cirh1a+/- state. Result shows that Cirh1a+/- has significant effect on early mice embryo gene transcription, Differentially expressed genes (DEGs) detected are mainly involved in cell proliferation/differenciation, cell cycle progress, embryo development and multi-orgnaogenesis. Littermate embryos (E8.5) were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR. Littermate embryos (E9.5) were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR. Liver buds from littermate embryos (E11.5) were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR. Liver buds from littermate embryos were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR.

2014-01-01 | E-GEOD-51104 | biostudies-arrayexpress

Self-organized yolk sac-like organoids allow for scalable generation of multipotent hematopoietic progenitor cells from human induced pluripotent stem cells

Project description:The human definitive yolk sac is an important organ supporting the early developing embryo through nutrient supply and by facilitating the establishment of the embryonic circulatory system. However, the molecular and cellular biology of the human yolk sac remains largely obscure due to the lack of suitable in vitro models. Here, we show that human induced pluripotent stem cells (hiPSCs) co-cultured with various types of stromal cells as spheroids self-organize into yolk sac-like organoids without the addition of exogenous factors. Yolk sac-like organoids recapitulated a yolk sac specific cellular complement and structures as well as the functional ability to generate definitive hematopoietic progenitor cells (HPCs). Furthermore, sequential hemato-vascular ontogenesis could be observed during organoid formation. Notably, our organoid system can be performed in a scalable, autologous, and xeno-free condition, thereby providing an important model of human definitive yolk sac development and allows for efficient bulk generation of hiPSC-derived HPCs.

2021-05-05 | GSE157140 | GEO

Gene expression profiling of rudhira null embryo and yolk sac at 9.5 dpc

Project description:Rudhira is essential for mouse developmental angiogenesis and tissue morphogenesis. Embryos lacking endothelial rudhira die at mid-gestation with vascular patterning defects. Rudhira mutant yolk sac endothelial cells show slow and random migration. So to identify key signaling pathways perturbed in the absence of rudhira, we undertook whole transcriptome based analysis of gene expression in rudhira null yolk sac and embryo. Transcriptome analysis shows that key mediators of angiogenesis, cell adhesion, migration and extracellular matrix degradation as well as several components of the TGFÎ² pathway are perturbed in rudhira null mutant yolk sacs at 9.5 dpc. We used two embryo samples ( 2E- wild type; 5E- rudhira mutant). Repetition was done on each sample. We used 4 yolk sac samples (3Y,4Y- wild type; 7Y,8Y-rudhira mutant) for the analysis. Repetition was done on each sample.

2015-12-31 | E-GEOD-69204 | biostudies-arrayexpress

The migratory pathways of the cells that form the endocardium, dorsal aortae, and head vasculature in the mouse embryo

Project description:Background Vasculogenesis in amniotes is often viewed as two spatially and temporally distinct processes, occurring in the yolk sac and in the embryo. However, the spatial origins of the cells that form the primary intra-embryonic vasculature remain uncertain. In particular, do they obtain their haemato-endothelial cell fate in situ, or do they migrate from elsewhere? Recently developed imaging techniques, together with new Tal1 and existing Flk1 reporter mouse lines, have allowed us to investigate this question directly, by visualising cell trajectories live and in three dimensions. Results We describe the pathways that cells follow to form the primary embryonic circulatory system in the mouse embryo. In particular, we show that Tal1-positive cells migrate from within the yolk sac, at its distal border, to contribute to the endocardium, dorsal aortae and head vasculature. Other Tal1 positive cells, similarly activated within the yolk sac, contribute to the yolk sac vasculature. Using single-cell transcriptomics and our imaging, we identify VEGF and Apela as potential chemo-attractants that may regulate the migration into the embryo. The dorsal aortae and head vasculature are known sites of secondary haematopoiesis; given the common origins that we observe, we investigate whether this is also the case for the endocardium. We discover cells budding from the wall of the endocardium with high Tal1 expression and diminished Flk1 expression, indicative of an endothelial to haematopoietic transition. Conclusions In contrast to the view that the yolk sac and embryonic circulatory systems form by two separate processes, our results indicate that Tal1-positive cells from the yolk sac contribute to both vascular systems. It may be that initial Tal1 activation in these cells is through a common mechanism.

2021-03-23 | GSE165402 | GEO

Investigation of the physiological functions of PRDM6

Project description:PRDM6 belongs to the PRDM family of transcriptional repressors that all contain a PR domain and Zinc finger domains. Prdm6 has transcriptional repressor activity. Prdm6 may regulate factors that are involved in the differentiation / proliferation of smooth muscle cells, promoting proliferation. PRDM6 knockouts are embryonic lethal around 12.0 dpc knockout embryos eventually develop edema: cardiovascular defect vascularization defect in the yolk sac: dysorganized angiogenesis Keywords: cDNA array, yolk sac, murine embryo E10.5

2008-04-01 | GSE9065 | GEO

Erythro-myeloid progenitors contribute endothelial cells to developing blood vessels

Project description:The earliest blood vessels in the mammalian embryo are formed when endothelial cells (ECs) differentiate from angioblasts and coalesce into tubular networks. Thereafter, the en-dothelium is thought to expand solely by proliferation of pre-existing ECs. Here we show that the earliest precursors of erythrocytes, megakaryocytes and macrophages, the yolk sac-derived erythro-myeloid progenitors (EMPs), provide a complementary source of ECs that are recruited into pre-existing vasculature. Whereas a first wave of yolk sac-resident EMPs contributes ECs to the yolk sac endothelium, a second wave of EMPs colonises the embryo and contributes ECs to intraembryonic endothelium in multiple organs, where they persist into adulthood. By demonstrating that EMPs constitute a hitherto unrecognised source of ECs, we reveal that embryonic blood vascular endothelium expands in a dual mechanism that involves both the proliferation of pre-existing ECs and the incorporation of ECs derived from hematopoietic precursors.

2018-08-02 | GSE117978 | GEO

Gene expression analysis of inducible ES cells overexpressing Etv2 (induced for 12 hours at day 3 of differentiation)

Project description:During embryogenesis, the endothelial and the hematopoietic lineages first appear during gastrulation in the blood island of the yolk sac. We have previously reported that an Ets variant gene 2 (Etv2/ER71) mutant embryo lacks hematopoietic and endothelial lineages, however, the precise roles of Etv2 in yolk sac development remains unclear. We carried out a transcriptome analysis using an ES cell line that can inducibly express Etv2. Cells were induced for 12 hours at day 3 of differentiation.

2012-07-04 | GSE37658 | GEO

Gene expression profiling of rudhira null embryo and yolk sac at 9.5 dpc

Project description:Rudhira is essential for mouse developmental angiogenesis and tissue morphogenesis. Embryos lacking endothelial rudhira die at mid-gestation with vascular patterning defects. Rudhira mutant yolk sac endothelial cells show slow and random migration. So to identify key signaling pathways perturbed in the absence of rudhira, we undertook whole transcriptome based analysis of gene expression in rudhira null yolk sac and embryo. Transcriptome analysis shows that key mediators of angiogenesis, cell adhesion, migration and extracellular matrix degradation as well as several components of the TGFβ pathway are perturbed in rudhira null mutant yolk sacs at 9.5 dpc.

2015-12-31 | GSE69204 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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