Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing of mouse embryonic day 3.5 blastocyst inner cell mass cells

ABSTRACT: Inner cell mass (ICM) cells of two independent E3.5 blastocysts were profiled by transcriptome sequencing to assess the expression of extracellular matrix components.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Paul Bertone

PROVIDER: E-MTAB-2555 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification.

Boroviak Thorsten T Loos Remco R Loos Remco R Bertone Paul P Smith Austin A Nichols Jennifer J

Nature cell biology 20140525 6

The precise relationship of embryonic stem cells (ESCs) to cells in the mouse embryo remains controversial. We present transcriptional and functional data to identify the embryonic counterpart of ESCs. Marker profiling shows that ESCs are distinct from early inner cell mass (ICM) and closely resemble pre-implantation epiblast. A characteristic feature of mouse ESCs is propagation without ERK signalling. Single-cell culture reveals that cell-autonomous capacity to thrive when the ERK pathway is i ...[more]

PMID: 24859004

Similar Datasets

RNA sequencing of marmoset embryonic development

Project description:Transcriptional profiling of common marmoset embryo stages spanning E5.0 to E7.0 was performed by RNA-seq.

2015-11-05 | E-MTAB-2959 | biostudies-arrayexpress

RNA sequencing of mouse embryonic development

Project description:Transcriptional profiling of mouse embryos spanning the 8-cell morula stage to E5.5 postimplantation epiblast was performed using lineage-specific RNA-seq.

2015-11-09 | E-MTAB-2958 | biostudies-arrayexpress

Single-cell RNA sequencing of marmoset embryonic development

Project description:Transcriptional profiling of common marmoset embryo stages spanning zygote to late preimplantation blastocyst was performed by single-cell RNA-seq.

2018-11-01 | E-MTAB-7078 | biostudies-arrayexpress

Programming and inheritance of parental DNA methylomes in mammals

Project description:The reprogramming of parental methylomes is essential for embryonic development. In mammals, paternal 5-methylcytosines (5mCs) have been proposed to be actively converted to oxidized bases. These paternal oxidized bases and maternal 5mCs are believed to be passively diluted by cell divisions. By generating single-base resolution, allele-specific DNA methylomes from mouse gametes, early embryos, and primordial germ cell (PGC), as well as single-base-resolution maps of oxidized cytosine bases for early embryos, we report the existence of 5hmC and 5fC in both maternal and paternal genomes and find that 5mC or its oxidized derivatives, at the majority of demethylated CpGs, are converted to unmodified cytosines independent of passive dilution from gametes to four-cell embryos. Therefore, we conclude that paternal methylome and at least a significant proportion of maternal methylome go through active demethylation during embryonic development. Additionally, all the known imprinting control regions (ICRs) were classified into germ-line or somatic ICRs. The cross of two mouse strains was performed using DBA/2J as the paternal strain and C57BL/6J as the maternal strain. The hybrid embryos were collected at 2-cell, 4-cell, ICM, E6.5, E7.5 stages. Female and male E13.5 PGC samples (B6; 129S4-Pou5f1tm2Jae/J) were collected from timed mating of C57BL/6J female mice. MethylC-Seq: oocytes (C57BL/6J), sperm (DBA/2J), 2-cell embryos, 4-cell embryos, ICM, E6.5 embryos, E7.5 embryos, E13.5 female PGCs and E13.5 male PGCs. TAB-Seq: 2-cell embryos. fCAB-Seq: 2-cell embryos. RNA-Seq: oocytes (C57BL/6J).

2014-05-12 | E-GEOD-56697 | biostudies-arrayexpress

Cut&Tag of mESCs in 2i, 30hr N2B27/DMSO/siNegative, 30hr N2B27MEK(i)/siNanog cells

Project description:Cut&Tag using antibodies against H3K27me3, H3K4me1, H3K4me3, HeK27ac, IgG Cells: mouses embryonic stem cells (mESCs), RGd2 Culture conditions: 2i, 30hr N2B27/DMSO/siNegative, 30hr N2B27MEK(i)/siNanog

2024-07-17 | E-MTAB-14031 | biostudies-arrayexpress

Identification of Oct4-dependent genes in vivo

Project description:Transcriptome analysis of Oct4 null and wild type preimplantation mouse embryos by RNA-sequencing N=3 embryos of two genotypes (+/+ or -/-) at each of three time points (E2.5, E3.75, E4.5) were sequenced.

2013-06-06 | E-GEOD-47089 | biostudies-arrayexpress

Cell-to-cell gene expression variability followed by reinforcement progressively segregates lineages in the early mouse embryo

Project description:Mammalian embryonic development begins with the specification and segregation of the two extra-embryonic lineages, trophectoderm and primitive endoderm, from the pluripotent embryonic lineage, the epiblast. To establish a map of epiblast (EPI) versus primitive endoderm (PrE) lineage segregation which occurs within the inner cell mass (ICM), we comprehensively characterised the gene expression profiles of individual inner cells during blastocyst development. Lineage represents the two embryonic cell lineages: the epiblast (EPI), and the primitive endoderm (PE), which are segregated within the inner cell mass(ICM) during blastocyst development.

2013-11-26 | E-MTAB-1681 | biostudies-arrayexpress

ATAC-seq on ESCs undergoing directed differentiation towards defined neural fates

Project description:We have used ATAC-seq to track cell state changes that occur during the differentiation of mouse embryonic stem cells to defined neural progenitor fates. We have performed ATAC-seq every 24 hours in cells en route to 3 distinct neural progenitors fates, anterior, hindbrain and spinal cord. This has allowed us to define how cells transition to a neural state, based on their enhancer usage. We identified regions distinct to different anterior-posterior neural progenitors, and validated their relevance by performing in vivo ATAC-seq on neural progenitors isolated from different axial levels of mouse embryos.

2018-08-27 | E-MTAB-6337 | biostudies-arrayexpress

The dynamic translatome of retinal ganglion cell axons during assembly and maintenance of the mouse visual system

Project description:Local mRNA translation mediates the adaptive responses of axons to extrinsic signals but direct evidence that it occurs in mammalian CNS axons in vivo is scant. We developed an axon-TRAP-RiboTag approach in mouse that allows deep-sequencing analysis of ribosome-bound mRNAs in the retinal ganglion cell axons of the developing and adult retinotectal projection in vivo. The embryonic-to-postnatal axonal translatome comprises an evolving subset of enriched genes with axon-specific roles suggesting distinct steps in axon wiring, such as elongation, pruning and synaptogenesis. Adult axons, remarkably, have a complex translatome with strong links to axon survival, neurotransmission and neurodegenerative disease. Translationally co-regulated mRNA subsets share common upstream regulators, and novel sequence elements generated by alternative splicing that promote axonal mRNA translation. Our results indicate that intricate regulation of compartment-specific mRNA translation in mammalian CNS axons supports the formation and maintenance of neural circuits in vivo. The profiling of ribosome-bound mRNAs in mouse retinal ganglion cell axons at 4 different developmental stages

2016-06-16 | E-GEOD-79352 | biostudies-arrayexpress

RBM15 CoIP in mouse Embryonic Stem cells

Project description:RBM15 interactome has been determined in mouse Embryonic Stem cells. The cells express inducible emGFP-PreScission-RBM15 alongside with inducible Xist RNA.

2020-02-07 | PXD017348 | Pride

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