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TranscriptomicsStereo-sequencing: 3D Transcriptome of the mouse embryo at gastrulation
To glean an appreciation of the holistic genetic activity in the gastrulating mouse embryo, we performed a genome-wide spatial transcriptome analysis (Stereo-seq), using a low-cell number sequencing protocol on laser microdissected samples of epiblast cells with retained positional address. The 3D t...
ORGANISM(S): Mus musculus 
2016-03-24 | E-GEOD-65924 | biostudies-arrayexpress
ProteomicsPerturbations of hepatic proteome behind the onset of metabolic disorders in mouse offspring developed following assisted reproductive technologies
Background: Assisted Reproductive Technologies (ART) - treatments to allow parenthood to couples facing fertility issues- have allowed the birth of > 5 million babies worldwide. Notwithstanding most of ART children are healthy at birth, several studies reported that ART may affect early-life experie...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2020-05-14 | MSV000085413 | MassIVE
GenomicsEpigenetic regulation and transcriptional repression by Tet1 in the early post-implantation mouse embryo: ChIP seq
The mammalian TET dioxygenases contribute to global waves of DNA demethylation in the zygote and in primordial germ cells, but their involvement during de novo DNA methylation at peri/post-implantation development is unknown. Here, we show novel physiological functions of Tet1 in the pre-primitive s...
ORGANISM(S): Mus musculus 
2017-05-15 | E-MTAB-5562 | biostudies-arrayexpress
GenomicsA unique regulatory phase of DNA methylation in the early mammalian embryo
DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of global cytosine methylation at fertilization, followed by passive depletion that reaches a minimum at the blastocyst stage. However, this model is based on limit...
ORGANISM(S): Mus musculus 
2012-03-28 | E-GEOD-34864 | biostudies-arrayexpress
TranscriptomicsCharacterization of the Imprinting Signature of Mouse Embryo Fibroblasts by RNA Deep Sequencing
Mouse embryo fibroblasts (MEFs) closely resemble mouse embryos and are convenient sources for biochemical studies when cell number may be limiting from mouse embryos. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we characterized them using strand- and allel...
ORGANISM(S): Mus musculus 
2013-11-18 | E-GEOD-49538 | biostudies-arrayexpress
GenomicsEpigenetic regulation and transcriptional repression by Tet1 in the early post-implantation mouse embryo: Methylation data.
The mammalian TET dioxygenases contribute to global waves of DNA demethylation in the zygote and in primordial germ cells, but their involvement during de novo DNA methylation at peri/post-implantation development is unknown. Here, we show novel physiological functions of Tet1 in the pre-primitive s...
ORGANISM(S): Mus musculus 
2017-05-15 | E-MTAB-4581 | biostudies-arrayexpress
MetabolomicsMetabolic reaction network-based recursive metabolite annotation for untargeted metabolomics (Aging mouse liver negative mode)

Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard...

2019-03-26 | MTBLS606 | MetaboLights
Proteomics,Multiomicsembryo_proteome
We collected over 8000 mouse embryos of each developmental stage (zygote, 2-cell, 4-cell, 8-cell, morula, blastocyst) and performed tandem mass tag (TMT)-based quantitative mass spectrometry and identified nearly 5000 proteins for each stage. In-depth analysis indicates that protein expression profi...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2015-12-10 | MSV000079417 | MassIVE
MetabolomicsMetabolic reaction network-based recursive metabolite annotation for untargeted metabolomics (Aging mouse liver positive mode)

Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard...

2019-03-26 | MTBLS601 | MetaboLights
ProteomicsTranscription complexes in the embryo
In this study, we characterized the composition of TFIID and SAGA complexes in the mouse embryo and analyzed the effect of the depletion of a shared subunit TAF10 during development
ORGANISM(S): Mus musculus (Mouse) 
2017-09-22 | PXD004688 | Pride
Embryo Saga Transcription Tfiid Paraxial mesoderm Somitogenesis 
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