Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Embryonic and adolescent forelimbs, brains, whole embryos, Aha-enrichment forelimbs, Mus musculus (wild-type, C57BlJ6/J; OIM, B6C3Fe a/a-Col1a2oim/J), proteomic dataset

ABSTRACT: Embryonic day (E)12.5 whole murine embryos, E11.5 - E14.5 whole murine embryos, E11.5 - E14.5, post-natal day (P)3 and P35 murine forelimbs, E14.5 brains, and COL1A2-mutant and COL1A2-WT forelimbs were fractionated and specific fractions were analyzed via LC-MS/MS. Aha-enrichment experiments consisted of in vivo protein labeling with azidohomoalanine (Aha) followed by tissue fractionation of the forelimbs and enrichment of labeled ECM proteins from the final IN pellet ('enriched'). 'Unenriched samples', or the background from which newly synthesized proteins were enriched from, were also analyzed via LC-MS/MS.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Sarah Calve

PROVIDER: MSV000085556 | MassIVE | Fri Jun 05 13:20:00 BST 2020

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide prediction of human embryos

Project description:BACKGROUND: Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (<36 h) required for fresh embryo transfer. Here, we describe and validate a method for inferring the inherited whole genome sequence of an embryo for preimplantation genetic diagnosis (PGD). METHODS: We combine haplotype-resolved, parental genome sequencing with rapid embryo genotyping to predict the whole genome sequence of a day-5 human embryo in a couple at risk of transmitting alpha-thalassemia. RESULTS: Inheritance was predicted at approximately 3 million paternally and/or maternally heterozygous sites with greater than 99% accuracy. Furthermore, we successfully phase and predict the transmission of an HBA1/HBA2 deletion from each parent. CONCLUSIONS: Our results suggest that preimplantation whole genome prediction may facilitate the comprehensive diagnosis of diseases with a known genetic basis in embryos.

| EGAS00001001020 | EGA

MicroRNA expression patterns in mouse tissues and staged embryos

Project description:RNA from seven adult mouse tissues, four staged whole mouse embryos, ES cells, 3 day and 28 day embryoid bodies was profiled against the microRNA microarray. A custom microarray platform for analysis of microRNA gene expression; Nature Methods 1, 47 - 53 (2004) Keywords = microRNA Keywords = miRNA Keywords: other

2004-09-02 | GSE1635 | GEO

Zebrafish early embryos isolated nuclei and whole blastomeres LC-MSMS

Project description:Nuclear pore complex (NPC) structure and maturity changed during early development before MBT in zebrafish embryos. Aiming to further confirm the difference of NPCs among different stages during MZT, we first isolated nuclei from 32-cell and 512-cell stage embryos as most zygotic genes have not been transcribed at these two stages yet. The lysates from identical number (about 12,500 nuclei per stage) isolated nuclei were then trypsin-digested and fractionated, followed by high-resolution LC-MS/MS analysis on the Q-Exactive HF-X mass spectrometers using a label-free assay. Whole blastomeres from 32-cell and 512-cell were also prepared with yolk removal to serve as total protein profile control, and the same amount lysates were analyzed by high-resolution LC-MS/MS with TMT labelled. Each sample for MS analysis had two repeats. Correlation analysis revealed that the abundance ratio from isolated Nuclei and whole deyolking balstomeres did not correlate well, but samples in Nuclei or Whole blastomeres were well correlated. This result indicates the convincible sample preparation as well as the variability in nuclei composition in early developmental period before MBT.

2023-08-25 | PXD017896 | Pride

Vitrification of embryos modifies foetal placenta proteome. LCMSMS

Project description:Very limited information about the post-implantatory effects of vitrification has been published till now. In a previous study, we observed that vitrification procedure introduced transcriptomic and proteomic modifications in the rabbit foetal placenta at the middle of gestation. In addition, a reduction in maternal placenta and foetal weight was also detected. In order to know if these alterations were temporary or not, the aim of the current study was to analyse the proteomic profile of rabbit foetal placenta at two different times of gestation: Day 14 and Day 24. We performed a comparative 2D-DIGE analysis and found that placentas from vitrified embryos expressed eleven different proteins at Day 14 and thirteen at Day 24. The alteration of serum albumin, isocitrate dehydrogenase 1 [NADP+] and phosphoglycerate mutase 1 were maintained both Day 14 and Day 24. Our results demonstrate that vitrification is not neutral, and induce a substantial alteration of placental protein expression, even at the end of gestation. But, apart from short-term effects observed on embryos, could vitrification entail long-term consequences in those foetuses that are going to be born? Further studies will determine if alterations observed could be the set point of future modifications to manifest into adulthood

2015-08-11 | PXD001836 | Pride

Genome-wide profiling the epigenetic landscape of histone variant TH2B in murine oocytes and pre-implantation embryos [ChIP-seq]

Project description:The testis-specific histone variant of H2B, TH2B, is enriched in the oocytes, sperm and early embryos, with levels decreasing as the embryos differentiate into pre-gastrula stages. However, the involvement of TH2B in epigenetic reprogramming in the preimplantation embryos is largely unknown. The current study mapped the genome-wide epigenetics of TH2B in MII oocytes and early embryos using ultra-low-input ChIP-seq (ULI-ChIP). We demonstrate that TH2B deposition varies greatly between gametes; however, following fertilization, TH2B from gametes is swiftly redistributed in 2-cell embryos. A considerable enrichment of TH2B at the transcription start site (TSS) was identified in sperm chromatin compared to that in oocytes. We also found some overlap between the dynamics of the sperm and the 2 cell, which contain genes related to transcription regulation. Additionally, TH2B was enriched at zygotic genome activation (ZGA) genes. H2A.Z and TH2B were associated, as was discovered in the presence of H2AK119ub1. The correct execution of ZGA and other developmental programs, such as timing the expression or repression of particular genes, may involve TH2B along with H2A.Z, and H2AK119ub1, the latter two regulating the aforementioned processes. Also, early embryos had H3K9me3 deposited at TH2B-bound loci, which is a sign of heterochromatin and functions in regulating retrotransposons. In our study, we found that TH2B was enriched in LTRs. Thus, TH2B chromatin in gametes and preimplantation embryos has distinctive properties, as highlighted by our study, and they also present fresh opportunities to investigate the epigenetic dynamics in murine preimplantation embryos.

2024-08-31 | GSE243322 | GEO

Vitrification of embryos modifies foetal placenta proteome. MALDI TOF/TOF

2015-07-17 | PXD001840 | Pride

Proteomic analysis of fractionated E13.5 Pax3-KO and WT murine forelimbs

Project description:Forelimbs were dissected from embryonic day (E) 13.5 Pax3-knockout and wild-type murine embryos (n=3 per genotype), homogenized, and proteins were fractionated into 5 samples (C, N, M, CS, and IN fractions). C, N, M, CS, and IN fractions for Pax3-KO (KO) and wild-type (WT) were analyzed by LC-MS/MS.

2021-12-27 | MSV000088620 | MassIVE

Metabolomics of murine embryos cultured in a microfluidic device and comparison with traditional microdrops culture

Project description:Global untargeted metabolomics study to analyse culture media extracted from an innovative microfluidic device or traditional microdrops in presence or absence of murine embryos to investigate PDMS-release of biomolecules and embryo metabolic activity.

2020-08-29 | ST001494 | MetabolomicsWorkbench

Regional expression of X. tropicalis transcription factors in early gastrula embryos

Project description:Purpose: We wished to obtain spatial expression profiles of transcription factor gene expression and expression of other genes. Methods: Embryos were dissected and RNA-seq was performed to determine expression levels of genes. Comparisons between explanted regions permits determination of spatial enrichment of gene expression. mRNA-seq performed on 5 dissected regions of NF stage 10.5 X. tropicalis embryos and stage-matched sibling whole embryos. Experiment performed in duplicate.

2016-08-22 | E-GEOD-81458 | biostudies-arrayexpress

5CAPture-seq: a method for enriching full-length cDNA and identifying 5′ capped nucleotides

Project description:Current transcriptomic methods for mapping 5′-ends of eukaryotic RNA employ only 5′-end enriched samples. The absence of a matched unenriched control limits the ability to distinguish genuine 5′ ends from incomplete cDNAs. We developed a transcriptomic method based on sequencing of cDNA enriched for full-length fragments and an unenriched control. From the mapped sequence reads, enrichment scores are calculated for all transcribed nucleotides and a statistical model of the enrichment constructed. We tested the method in the human malaria parasite Plasmodium falciparum. Data were obtained from ring, trophozoite and schizont stages of the parasite intra-erythrocytic development cycle. Two groups of 5′ capped nucleotides were assigned by unsupervised clustering. The first group contains sites located mostly outside of annotated protein-coding exons in regions of high local nucleosomal occupancy, but low occupancies of ribosome and elongating RNA polymerase II. The majority of sites in the second group are intra-exonic and show different patterns, most notably a peak of ribosome occupancy centered on the 5′ end position and a biased representation among codons possibly prone to ribosome stalling. Our method can be used to annotate 5′ capped nucleotides, including intra-exonic nucleotides that can be distinguished from incomplete cDNA artifacts.

2021-08-02 | GSE103036 | 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