Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA-seq of in vitro cultured human embryos

ABSTRACT: Human embryogenesis is characterised by a series of coordinated cell fate specification events. Upon implantation on day 7, the three cell lineages forming the human blastocyst undergo major morphogenetic and transcriptomic changes. Using single-cell RNA sequencing, we reconstruct the molecular events driving post-implantation development of the human embryo at day 9 and 11. Our study provides the first molecular map of gene expression patterns in early post-implantation human embryos, unveiling how signalling interactions between embryonic and extra-embryonic tissues drive human embryogenesis.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Tim Coorens

PROVIDER: E-MTAB-8060 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.

Molè Matteo A MA Coorens Tim H H THH Shahbazi Marta N MN Weberling Antonia A Weatherbee Bailey A T BAT Gantner Carlos W CW Sancho-Serra Carmen C Richardson Lucy L Drinkwater Abbie A Syed Najma N Engley Stephanie S Snell Philip P Christie Leila L Elder Kay K Campbell Alison A Fishel Simon S Behjati Sam S Vento-Tormo Roser R Zernicka-Goetz Magdalena M

Nature communications 20210617 1

Following implantation, the human embryo undergoes major morphogenetic transformations that establish the future body plan. While the molecular events underpinning this process are established in mice, they remain unknown in humans. Here we characterise key events of human embryo morphogenesis, in the period between implantation and gastrulation, using single-cell analyses and functional studies. First, the embryonic epiblast cells transition through different pluripotent states and act as a sou ...[more]

PMID: 34140473

Similar Datasets

In vitro modelling of the human embryo implantation niche

Project description:Single-cell RNA-sequencing (10X) data from a three-dimensional cell-engineered system for human implantation that closely recapitulates the cytoarchitecture and physiology of the receptive human endometrium

2024-07-17 | E-MTAB-13629 | biostudies-arrayexpress

Single-cell RNA-Seq of VE-enriched cell populations from E5.5 and E6.25 wild type mouse embryos

Project description:We investigated the transcriptomic features of the Visceral Endoderm during early post-implantation mouse embryonic development by means of Single Cell RNA-Sequencing (RNA-Seq). To enrich for Visceral Endoderm cells, we labelled the outer cells of the embryo with a fluorescent membrane-labelling dye, before single-cell dissociation and FACS to select the labelled population.

2021-09-07 | E-MTAB-9645 | biostudies-arrayexpress

A developmental coordinate of the spectrum of pluripotency among mice, monkeys, and humans

Project description:The epiblast (EPI) is the origin of all somatic and germ cells in mammals, and of the spectrum of pluripotent stem cells (PSCs) in vitro. To explore the ontogeny of human/primate pluripotency, we performed comprehensive single-cell RNA sequencing for pre- and post-implantation EPI development in cynomolgus monkeys. Here we show that after specification in the blastocysts [embryonic day (E)7], cyEPI undergoes major transcriptome changes upon implantation. Thereafter, cyEPI, while generating gastrulating cells (~E13), maintains its transcriptome relatively stably over a week, retaining a unique set of pluripotency genes while acquiring properties for âneuron differentiation.â h/cyPSCs show the highest similarity to post-implantation late cyEPI (~E17), which, despite co-existing with gastrulating cells, bears characteristics of pre-gastrulating mouse EPI (E5.5) and epiblast-like cells (EpiLCs) in vitro. These findings not only reveal divergence/coherence of EPI development, but also identify a developmental coordinate of the spectrum of pluripotency among key species, providing a basis for better regulation of human pluripotency in vitro. Single cell transcriptome analysis of cynomolgus monkey embryo E6-17 and mouse embryo E4.5 - E6.5 as well as of cynomogus monkey embryonic stem cells (ESCs) and mouse ESC, epiblast like cells (EpiLCs), using SC3-seq technology.

2016-08-24 | E-GEOD-74767 | biostudies-arrayexpress

Global gene expression profiles in Oct4-knockdown and Ccna2-knockdown mouse embryos.

Project description:Gene regulation at the maternal-embryonic transition in the pre-implantation mouse embryo is not well understood. We knock down Ccna2 to establish proof-of-concept that antisense morpholino oligonucleotides can be used to target specific genes. We applied this strategy to study Oct4 and discovered that Oct4 is required prior to blastocyst development. Specifically, gene expression is altered as early as the 2-cell stage in Oct4-knockdown embryos. Distinct subsets of genes are differentially expressed between Oct4 and Ccna2-knockdown embryos, and indicated differential functions. Further, a large panel of genes were confirmed to be differentially-expressed in Oct4-knockdown embryos by quantitative, real time RT-PCR. Keywords: gene knockdown 3-5 week old wild type F1 (C57BL6xDBA/2) females (Charles River) were superovulated by intraperitonial injections of 5 IU of pregnant mare’s serum gonadotropin (Sigma) followed by 5 IU of human chorionic gonadotropin (Sigma) 48 hours later, and mated overnight with wild type males. Mice were sacrificed by cervical dislocation 17 hours after hCG injection, and 1-cell embryos were released from oviducts. Cumulus cells were removed by hyaluronidase (Sigma) treatment and pipetting. Pre-implantation embryos at the two pronuclei stage were recovered, pooled from 3-6 females in M2 media (Chemicon International), followed by immediate cytoplasmic microinjection of gene-specific antisense morpholino oligonucleotides and culture in Human Tubal Fluid with 10% serum supplement (In-Vitro Fertilization, Inc.) microdrops under mineral oil (Sigma) in mixed gas (90% nitrogen, 5% oxygen, 5% carbon dioxide; Praxair) at 37°C, and cultured at ten embryos per 20 μL drop. Uninjected control embryos derived from the same embryo pool, and were placed in identical conditions in parallel, except that they were not injected.

2008-12-30 | E-GEOD-13981 | biostudies-arrayexpress

Transcription profiling by array of human ovary cell cultures stimulated with embryo-conditioned media

Project description:Stimulation of ovary cell cultures with embryo-conditioned media

2014-07-01 | E-TABM-1064 | biostudies-arrayexpress

Transcription profiling of embryonic kidneys from wild type and Hoxa11, Hoxd11 compound null mice throughout development to characterize Hoxa11/Hoxd11 mutant kidney development

Project description:Complete (whole) embryonic kidneys were dissected from wild type and Hoxa11, Hoxd11 compound null embryos throughout development. Targets from two biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430A and MOE430B arrays. Comparisons between normal and mutant and comparisons of development samples identified global patterns of gene regulation in kidney development Experiment Overall Design: Embryonic metanephric kidney samples throughout development were analyzed based on normalization to adult kidney samples. In addition, Hoxa11, Hoxd11 compound null embronic kidneys were normalized to wild type embryonic controls. All developmental and adult stages were represented in biological (seperate embryo/animal replicate).<br><br>Normalized data files were not included because there appears to be a mismatch between the composite sequence identifiers in some of them and the array design selected.

2008-10-15 | E-GEOD-3808 | biostudies-arrayexpress

Drosophila melanogaster proteome dynamics during embryogenesis - 1

Project description:In this study we use a combination of proteomics Label-Free quantification methods to monitor protein expression changes over a time course of more than 20 hours of embryo development in Drosophila melanogaster.

2016-04-11 | PXD003178 | Pride

Preimplantation mouse embryo proteome during 8C to 16C division

Project description:Preimplantation stages of mouse embryo development involve temporal and spatial specification and segregation of three late blastocyst cell lineages; trophectoderm (TE), primitive endoderm (PrE) and epiblast (EPI). Spatial separation of the outer TE lineage from the two inner-cell-mass (ICM) lineages (PrE and EPI) starts with the 8- to 16-cell transition and concludes following transit through the 16- to 32-cell stages. This results in a nascent early blastocyst ICM derived from descendants of primary founding inner cells and a secondarily contributed population; of which subsequent relative EPI versus PrE potencies are subject to debate. We showed that generation of primary but not the secondary ICM populations is highly dependent on temporally discreet activation of the mammalian target of rapamycin (mTOR – specifically mTORC1) around 8-cell stage M-phase entry. Moreover, that this role is mediated via the regulated function of the 7-methylguanosine- (7mG) cap binding initiation complex (EIF4F) and potentiating the translation of a subset of key but otherwise intransigent mRNAs containing 5’ UTR terminal oligopyrimidine (TOP-) sequence motifs. To find out translation of which mRNAs is regulated by mTOR during 8- to 16-cell transition, we analysed proteomes of control and mTOR-inhibited embryos during this time window.

2023-08-18 | PXD039423 | Pride

Protein interactors of MEG-1 in C. elegans embryos

Project description:In animals with germ plasm, specification of the germline involves “germ granules”, cytoplasmic condensates that enrich maternal transcripts in the germline founder cells. In C. elegans embryos, P granules enrich maternal transcripts, but surprisingly P granules are not essential for germ cell fate specification. Here we have described a second condensate in the C. elegans germ plasm. Like canonical P-bodies found in somatic cells, “germline P-bodies” contain regulators of mRNA decapping and deadenylation and, in addition, the intrinsically-disordered proteins MEG-1 and MEG-2 and the TIS11-family RNA-binding protein POS-1. Embryos lacking meg-1 and meg-2 do not stabilize P-body components, miss-regulate POS-1 targets, miss-specify the germline founder cell, and do not develop a germline. Our findings suggest that specification of the germ line involves at least two distinct condensates that independently enrich and regulate maternal mRNAs in the germline founder cells.

2022-10-05 | PXD036610 | Pride

Uncoupling X chromosome number from sex determination separates contribution of sex and X dose to sex-biased gene expression in C. elegans

Project description:The difference in X chromosome copy number creates a potential difference in X chromosomal gene expression between males and females. In many animals, dosage compensation mechanisms equalize X chromosome expression between sexes. Yet, X chromosome is also enriched for sex-biased genes due to differences in the evolutionary history of the X and autosomes. The manner in which dosage compensation and sex-biased gene expression exist on the X chromosome remains an open question. Most studies compare gene expression between two sexes, which combines expression differences due to X chromosome number (dose) and sex. Here, we uncoupled the effects of sex and X dose in C. elegans and determined how each process affects expression of the X chromosome compared to autosomes. We found that in the soma, sex-biased expression on the X chromosome is almost entirely due to sex because the dosage compensation complex (DCC) effectively compensates for the X dose difference between sexes. In the germline where the DCC is not present, X chromosome copy number contributes to hermaphrodite-biased gene expression. These results suggest that X dose contributes to sex-biased gene expression based on the level of dosage compensation in different tissues and developmental stages. RNA-Seq profiles of C. elegans XO hermaphrodite and XX male L3 larvae and adults

2016-04-06 | E-GEOD-77794 | biostudies-arrayexpress

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