Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Jonathan Fiorentino

PROVIDER: E-MTAB-9645 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Early mouse embryo development

Project description:Expression profiling of mouse embryos at E2.5, E3.5, E4.25, E4.5, E5.5 E6.0 to identify genes regulated during development of the ICM (inner cell mass), TE (Trophectoderm) and PrE (Primative endoderm) Keywords: development dupicate analysis of time points

2010-05-25 | E-GEOD-8339 | biostudies-arrayexpress

Single-cell RNA-seq reveal lineage formation and X-chromosome dosage compensation in human preimplantation embryos

Project description:Single-cell RNA-seq of 1,529 cells obtained from 88 human preimplantation embryos ranging from embryonic day 3 to 7.

2016-04-06 | E-MTAB-3929 | biostudies-arrayexpress

Visceral Endoderm differentiation mediated by Hnf1B and is required for epiblast survival

Project description:E5.0 entails an intermediate state for primitive endoderm (PE) to visceral endoderm (VE) differentiation: a process required for proper embryonic development. Hnf1b is essential for primitive to visceral endoderm differentiation from E4.5 to E5.5. To understand development at E5.0 and pinpoint the role Hnf1b in proper embryonic development, embryos were harvest at E5.0 and single cells from three WT embryos and 3 Hnf1b KO embryos were isolated, dissociated, and scRNA sequenced using smartseq2. For experiments on WT embryos, CD1 females were crossed with CD1 or homozygous E-cadherin-GFP males. Hnf1b -/+22 line was derived through IVF of oocytes of Black6 mice with EMMA strain EM:07827(B6.129P2(D2)-Hnf1btm1Sce/Orl) Sperm, that was bought from the EMMA institution in Orleans.

2024-11-19 | E-MTAB-11140 | biostudies-arrayexpress

Single cell RNA-Seq of wild type and caspase inhibitor treated mouse embryos at the stage E6.5

Project description:We investigated the features of cells eliminated during early mouse embryogenesis by means of Single Cell RNA-Sequencing (RNA-Seq). To enrich for apoptotic cells, we treated a number of embryos with caspase inhibitor, and then collected and sequenced single-cells isolated from them.

2020-01-17 | E-MTAB-8640 | biostudies-arrayexpress

Time course analysis of human colorectal cancer organoid treatment with Sacituzumab Govitecan (SG) or untargeted control IgG1-SN-38

Project description:Human colorectal cancer organoids were treated with the TROP2-targeting antibody-drug conjugate Sacituzumab Govitecan (SG) or non-targeting control IgG1-SN-38. Samples were harvested at different time points under treatment {0h, 3h, 6h, 9h, 12h} as well as after drug washout at 12 h on the following time points {12h + 12h, 12h + 36h, 12h + 60h}. Samples were subjected to single-cell RNA-seq using sample hashtag multiplexing.

2026-04-01 | E-MTAB-16843 | biostudies-arrayexpress

Single-cell RNA-sequencing of colorectal cancer PDOX tumors treated with vehicle or the TROP2-targeting antibody-drug conjugate Sacituzumab Govitecan

Project description:Patient-derived colorectal cancer organoids were injected into mice to grow into subcutaneous tumors. Starting at 100 mm3, tumors were treated with Trodelvy (Sacituzumab Govitecan (SG)) or vehicle twice per week for 28 days before samples were harvested and subjected to single-cell RNA-sequencing of the tumor cells.

2026-04-29 | E-MTAB-16433 | biostudies-arrayexpress

Single-cell RNA-sequencing of PDOX colorectal tumors

Project description:Patient-derived colorectal cancer organoids were injected into mice to grow into subcutaneous tumors. Tumors were profiled through multiplexed single-cell RNA-sequencing.

2026-04-01 | E-MTAB-16585 | biostudies-arrayexpress

Regulation of extraembryonic endoderm stem cell differentiation by Nodal and EGF-CFC signaling

Project description:The signaling pathway for Nodal, a ligand of the transforming growth factor-beta (TGF-beta) superfamily, plays a central role in regulating the maintenance and/or differentiation of stem cell types that can be derived from the peri-implantation mouse embryo. Extraembryonic endoderm stem (XEN) cells are derived from the primitive endoderm of the blastocyst, which normally gives rise to the parietal and the visceral endoderm in vivo, but XEN cells do not contribute efficiently to the visceral endoderm in chimeric embryos. We have found that treatment of XEN cells with Nodal and/or Cripto, an EGF-CFC co-receptor for Nodal, results in up-regulation of markers for visceral endoderm as well as anterior visceral endoderm (AVE). Re-introduction of treated XEN cells into chimeric embryos by blastocyst injection or morula aggregation results in contribution to visceral endoderm and AVE. In culture, XEN cells do not express Cripto, but do express the related EGF-CFC co-receptor Cryptic and require Cryptic for Nodal signaling. Notably, the response to Nodal can be blocked by treatment with the ALK4/ALK5/ALK7 inhibitor SB431542, but Cripto treatment is unaffected, suggesting that its activity is independent of type I activin receptors. Gene set enrichment analysis of genome-wide expression signatures generated from XEN cells under these treatment conditions confirms the differing responses of Nodal- and Cripto-treated XEN cells to SB431542. Our findings define distinct pathways for Nodal and Cripto in the differentiation of visceral endoderm and AVE from XEN cells, and provide new insights into the specification of these cell types in vivo. Murine Xen-eyfg cell line treated with Alk4 inhibitor SB431542, Nodal and Cripto recombinant proteins.

2011-11-29 | E-GEOD-23675 | biostudies-arrayexpress

Single-cell RNA-sequencing of primary colorectal cancer tumor tissue and liver metastasis

Project description:Primary tumor or liver metastasis biopsies were obtained from colorectal cancer patients and processed for multiplexed single-cell RNA-sequencing.

2026-04-01 | E-MTAB-16583 | 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