Infant gut microbiota coverage by different culture media
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PROVIDER: PRJEB91169 | ENA |
REPOSITORIES: ENA
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Project description:In the field of in vitro embryo production it is generally thought that the culture media are not as good as the oviductal fluid, resulting in detrimental changes of embryonic gene expression. Yet in vitro embryo culture (IVC) is one of the pillars of the assisted reproductive technologies. Therefore, unintended effects on gene expression may impact on the health of ART babies (PMID 27554442). Granted, human ART has many more components than just the culture media, but, the practice of embryo culture superimposes with the phase of life when cellular totipotency is present - that's why embryo culture media receive special attention. Discerning what culture media do is difficult because several confounders are present, including but not limited to oocyte heterogeneity, sperm heterogeneity as well as time of fertilization. We propose to take advantage of experimentally produced parthenogenetic embryos, and thereby remove two confounders (sperm variability, time of fertilization), in order to assess the effects of specific culture media of embryonic gene expression, in the mouse model of human reproduction. After synchronous parthenogenetic activation of MII oocytes, pronuclear oocytes were cultured in parallel in ART medium vs KSOM(aa) medium. Resultant blastocysts were compared and contrasted for gene expression among the parthenotes, as well as against zygotic blastocysts.
2022-02-01 | GSE111112 | GEO
Project description:Culture Media Silage Microbiome Targeted loci environmental
| PRJNA606030 | ENA
Project description:Following fertilization in mammals, it is generally accepted that totipotent cells are exclusive to the zygote and to each of the two blastomeres originating from the first mitotic division. We counter that this classic view needs to be revised, because we have presented compelling evidence the sister blastomeres are both totipotent in only a subset of 2-cell stage mouse embryos (PMID 28811525). Building on our previous findings, we here ask the question if the differences between sister blastomeres can be modulated experimentally. To this end, we separate the sister blastomeres, yielding monozygotic twins. We culture these twins in two different media (GM501 vs. Sage 1 step), to see if the mRNA ratios of twin blastocysts lie more far apart from each other when culture took place in different media as compared to culture in the same medium (GSE90674). Transcriptome analysis followed by intra-pair mRNA ratio analysis revealed differences between the blastocysts of the same monozygotic pair. Some of the differences were sensitive to the choice of culture conditions, while other differences were insensitive.
2021-12-31 | GSE110735 | GEO
Project description:Metabolomics of Vibrio diabolicus grown in different culture media. Data dependent and independent acquisition (DDA and DIA) was used in positive and negative ionization mode.
2024-05-20 | MSV000094810 | MassIVE
Project description:Mouse zygotes are suspected to mount adaptive responses (e.g. physiology, metabolism, gene expression) to the environment, which can be the natural environment of the female genital tract or the artificial environment of a culture medium. The jury is still out when it comes to the possible long-term effects of culture media on embryo development. In 2016 the ESHRE took a stance about this subject, saying that the environment the early embryo is exposed to can cause reprogramming of embryonic, fetal and postnatal development, with negative consequences for the conceptus (Sunde et al., Hum Reprod. 31(10):2174-82, 2016). Of course, in order to possibly measure these long-term effects, the embryo has to develop to term. On the one hand, the impact of prior adaptive responses on postimplantation development is contingent on the presence of sufficient cells in the epiblast compartment of the blastocyst-stage embryo. In mice the viable epiblast number is considered to have a minimum at 4 (Morris et al., Cell Rep. 2(4):756-65, 2012) and a maximum at 8 (Soriano and Jaenisch, Cell 46(1):19-29, 1986). On the other hand, regular embryos have reserve capacities and lie well above the minimum level, whereby detrimental effects of culture conditions are probably underestimated. In plain words, there are embryos that might have suffered from in vitro culture, but they make it because they already secured the minimum epiblast number. We reasoned that these effects may be exposed if the embryos had half the number of total cells, thereby bringing them closer to the critical minimum epiblast threshold. These half embryos live on the knife’s edge: if they make it above the threshold, then they can survive, otherwise they fail. Therefore, if any adaptation during embryo culture were to occur, it could either raise the half embryos above the critical threshold or deliver the final blow. This would give us the opportunity to work with a clear dichotomy and to measure clear responses in terms of development vs. no development. We used the model system of mouse half-embryo system to assess the adaptive responses to culture media in terms of gene expression. After in vivo zygote production and short culture in KSOM(aa) medium to complete the first cell cycle, 2-cell embryos were split, and the individual blastomeres were cultured in KSOM(aa), GM501 or SAGE 1step medium. Resultant blastocysts were compared and contrasted with each other. Transcriptome analysis revealed differences of gene expression due to culture media.
2019-07-10 | GSE120905 | GEO
Project description:seawater metagenome isolate:algae culture media Genome sequencing
| PRJNA611913 | ENA
Project description:Spent culture media was collected on day 5 after in vitro fertilization from 5 human blastocysts that were subsequently transferred or frozen. Corresponding blank culture media from the same lot were cultured alongside the embryos and used as negative controls along with PBS. The samples were prepared for total RNA sequencing using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) and for small RNA sequencing using the QIAseq RNA Library Prep kit (Qiagen). Prepared libraries were sequenced as 100 bp paired end on an Illumina HiSeq 4000 sequencer for total RNA and Illumina NextSeq500 sequencer for small RNA. We found that total RNA mapped only 3% of the reads to gene regions in spent culture media and control and only 2% in PBS samples mapped to gene regions. For the small RNA analysis, human annotated miRNAs constituted from 0.1% to 1.4% of the mapped reads and 40% of small RNA reads mapped to the human genome. tiRNAs derived from 5 different mature tiRNA were differentially expressed when comparing conditioned to unconditioned media. We conclude, that in spite of applying state-of-the-art sensitive detection methods no miRNAs were found to be reliably present in the spent culture medium. In contrast, tiRNA fragments appear to be overexpressed in cultured IVF media samples.
2020-09-07 | GSE142380 | GEO
Project description:Cancer cell culture models frequently rely on fetal bovine serum as a source of protein and lipid factors that support cell survival and proliferation; however, serum-containing media imperfectly mimics the in vivo cancer environment. Recent studies suggest that typical serum-containing cell culture conditions can mask cancer dependencies, for example on cholesterol biosynthesis enzymes, that exist in vivo and emerge when cells are cultured in media that provides more realistic levels of lipids. Here we describe a high-throughput screen that identified fenretinide and ivermectin as small molecules whose cytotoxicity is greatly enhanced in lipid-restricted media formulations. Mechanism of action studies indicate that the ivermectin-induced cell death involves oxidative stress, while fenretinide likely targets DEGS1, a lipid desaturase necessary for ceramide synthesis, to induce cell death. Notably, both fenretinide and ivermectin have previously demonstrated in vivo anticancer efficacy despite their low cytotoxicity under typical cell culture conditions. These studies reveal ceramide synthesis as a targetable vulnerability of cancer cells cultured under lipid-restricted conditions and suggest a general screening strategy for identifying additional cancer dependencies masked by culture conditions unrepresentative of the in vivo environment.
2024-11-14 | GSE247900 | GEO
Project description:Abstract The therapeutic properties of extracellular vesicles (EVs) derived from stem cells and stem-like cells make them promising cell-free alternative to regenerative medicine. However, clinical translation of this technology relies heavily on the ability to manufacture EVs in a scalable, reproducible, cGMP-compliant manner. The choice of cell culture media is a critical component for EV manufacturing. In this study, we used human amniotic epithelial cells (hAECs) as a cell model system to explore the effect of chemically defined serum-free media on EV production. Here we showed that different culture media and different cell culture supplements have variable effects on EV production including culture parameters, EV yield, and EV biogenesis. Cell viability and proliferation rate are not reliable quality indicators of EV manufacturing. The levels of common EV tetraspanins and epitope makers can be impacted by different culture media formulations even when culture parameters are maintained, and EV yield are comparable. This study has uncovered some critical aspects regarding EV production culture media that need to be considered in clinical-grade scalable EV manufacturing.
2021-12-20 | PXD024733 | Pride
Project description:Infant gut microbiota Raw sequence reads
| PRJNA780309 | ENA