Transcription profiling of mouse jejunum tisuses from B6D2F1 animals transgeneic for Col13A1del
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Anne Tuomisto
PROVIDER: E-MEXP-1760 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed during early embryogenesis to establish full developmental potential. Previous studies have suggested that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes subsequent passive demethylation via DNA replication during cleavage. Active demethylation is known to depend on 5mC oxidation by Tet dioxygenases and excision of oxidized bases by thymine DNA glycosylase (TDG). Here we show that both maternal and paternal genomes undergo widespread active and passive demethylation in zygotes before the first mitotic division. Passive demethylation was blocked by the replication inhibitor aphidicolin, and active demethylation was abrogated by deletion of Tet3 in both pronuclei. At actively demethylated loci, 5mCs were processed to unmodified cytosines. Surprisingly, the demethylation process was unaffected by the deletion of TDG from the zygote, suggesting the existence of other demethylation mechanisms downstream of Tet3-mediated oxidation. The dataset includes RRBS anlysis of 2 MII oocyte samples, 3 WT female pronuclei samples PN3-4 stage, 2 Tet3 KO female pronuclei samples and 2 Aphidicolin treated female pronuclei samples. Also as male counterpart, a Sperm sample, 2 WT male pronuclei samples PN3-4 stage, 2 Tet3 KO male pronuclei samples and 2 Aphidicolin treated male pronuclei samples were included.
2014-09-11 | E-GEOD-56650 | biostudies-arrayexpress
Project description:Gene regulation at the maternal-embryonic transition in the pre-implantation mouse embryo is not well understood. We knock down Ccna2 to establish proof-of-concept that antisense morpholino oligonucleotides can be used to target specific genes. We applied this strategy to study Oct4 and discovered that Oct4 is required prior to blastocyst development. Specifically, gene expression is altered as early as the 2-cell stage in Oct4-knockdown embryos. Distinct subsets of genes are differentially expressed between Oct4 and Ccna2-knockdown embryos, and indicated differential functions. Further, a large panel of genes were confirmed to be differentially-expressed in Oct4-knockdown embryos by quantitative, real time RT-PCR. Keywords: gene knockdown 3-5 week old wild type F1 (C57BL6xDBA/2) females (Charles River) were superovulated by intraperitonial injections of 5 IU of pregnant mare’s serum gonadotropin (Sigma) followed by 5 IU of human chorionic gonadotropin (Sigma) 48 hours later, and mated overnight with wild type males. Mice were sacrificed by cervical dislocation 17 hours after hCG injection, and 1-cell embryos were released from oviducts. Cumulus cells were removed by hyaluronidase (Sigma) treatment and pipetting. Pre-implantation embryos at the two pronuclei stage were recovered, pooled from 3-6 females in M2 media (Chemicon International), followed by immediate cytoplasmic microinjection of gene-specific antisense morpholino oligonucleotides and culture in Human Tubal Fluid with 10% serum supplement (In-Vitro Fertilization, Inc.) microdrops under mineral oil (Sigma) in mixed gas (90% nitrogen, 5% oxygen, 5% carbon dioxide; Praxair) at 37°C, and cultured at ten embryos per 20 μL drop. Uninjected control embryos derived from the same embryo pool, and were placed in identical conditions in parallel, except that they were not injected.
2008-12-30 | E-GEOD-13981 | biostudies-arrayexpress
Project description:The oviducts play a critical role in gamete and embryo transport, as well as supporting fertilization and early embryo development. Progesterone receptor (PGR) is a transcription factor highly expressed in oviductal cells, while it’s activating ligand, progesterone (P4), surges to peak levels as ovulation approaches. P4 is known to regulate oviduct cilia beating and muscular contractions in vitro, but how PGR may mediate this in vivo is poorly understood. We used PGR-knockout (PRKO) mice to determine how PGR regulates oviductal function during the periovulatory period, in particular oviductal transport and embryo support. We used microarrays to identify putative PGR-regulated genes in the oviduct during the periovulatory period, a time when the oviduct is preparing to receive the newly-ovulated COC. The mutant strain used in this experiment were PRlacZ knock-in mice which originated from Assoc Prof John Lydon, Baylor College of Medicine, Houston TX, USA. The lacZ insertion results in disruption of transcription of both isoforms of PGR (Ismail et al, 2002, Mol Endocrinol 16:2475-2489), and therefore mice homozygous for the lacZ insertion are a phenocopy of the knockout strain described by Lydon et al. (1995, Genes Dev. 9:2266-2278) and are hereafter referred to as PRKO. Heterozygous mice (PR+/-) are a phenocopy of WT and have normal fertility (Ismail et al, 2002) and are therefore appropriate controls. Whole oviducts were collected from pre-pubertal PRKO and PR+/- mice 8 h after a standard protocol for hormonal induction of ovulation. Day 21-23 old mice were injected i.p. with 5IU of equine chorionic gonadotropin (eCG) to stimulate follicle growth, followed 44-47 h later by i.p. injection of 5 IU of human chorionic gonadotropin (hCG) to trigger ovulatory processes. Oviducts from 15 animals were collected per genotype, with oviducts from 3 animals pooled per sample for a total of n = 5 samples per genotype.
2014-06-16 | E-GEOD-51499 | biostudies-arrayexpress
Project description:With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during pre-implantation development. Recent studies have suggested that Tet3-mediated oxidation of 5-methylcytosine (5mC) and DNA replication-dependent dilution both contribute to global paternal DNA demethylation, but demethylation of the maternal genome occurs via replication. Here we present genome-scale DNA methylation maps for both the paternal and maternal genomes of Tet3-depleted and/or DNA replication-inhibited zygotes. In both genomes, we found that inhibition of DNA replication blocks DNA demethylation independently from Tet3 function, and that Tet3 facilitates DNA demethylation by coupling with DNA replication. For both, our data indicate that replication-dependent dilution is the major contributor to demethylation, but Tet3 plays an important role, particularly at certain loci. Our study therefore both defines the respective functions of Tet3 and DNA replication in paternal DNA demethylation and reveals an unexpected contribution of Tet3 to demethylation of the maternal genome. In this data set, we include RRBS data of manually isolated paternal and maternal pronuclei from both WT and Tet3 CKO zygotes with or without aphidicolin treatment
2014-10-21 | E-GEOD-61330 | biostudies-arrayexpress
Project description:We develop a single cell methylome analysis technique based on RRBS, which works robustly for mouse embryonic stem cells (mESCs), sperm, metaphase II oocytes, and zygotes. In total, 36 samples were analyzed, including 8 single mouse embryonic stem cells (mESCs), pooled-5, 10, 20 mESCs, bulk mESCs, 7 single sperms, 10 single pronuclei from 5 individual zygotes, 2 metaphase II oocytes, 2 the first polar bodies and 3 negative controls.
2013-08-31 | E-GEOD-47343 | biostudies-arrayexpress
Project description:Currently there is growing concern with respect to scenarios where people are likely to be presented with radiation exposure along with many kinds of other injuries such as trauma and infection. The potential for such scenarios was brought to reality with the events and aftermath of the Fukushima nuclear disaster in Japan. As such medical complications arising from such exposures would be poorly dealt with as no evidence-based guidelines exist for their rehabilitation or recovery. Our research intends to differentially characterize combined radiation and burn injuries and identify novel pathways and biomarkers. Such findings will lead to better medical practices in the diagnosis, care and rehabilitation of affected individuals. The study includes four groups of mice: 1) Control sham mice group (n=4), 2) Skin burn injury mice group (n=6), 3) Radiation injury mice group (n=6), 4) Combined radiation and burn injury mice group (n=6). We propose to characterize the effects of combined radiation and burn injuries using microRNA microarray analysis. Our primary aim is to identify novel molecular pathways and biomarkers specific to whole blood samples (serum) from mice exposed to combined radiation and burn injuries. B6D2F1/J female mice will be used. 30 days following combined radiation and burn injuries arterial blood will be harvested from euthanized mice. 200ul of serum from whole blood samples will be used for microRNA microarray experiments (Affymetrix).
2015-05-15 | E-GEOD-66739 | biostudies-arrayexpress
Project description:Sequencing of polyA RNA fraction from MT oocytes and 1cell embryos.
2017-05-21 | E-MTAB-4775 | biostudies-arrayexpress
Project description:Comparison of gene expression in wild type and Wt1 (Wilms tumor suppressor gene 1) heterozygous knockout mice. Background: in Wt1+/- mice (MF1 strain) litter sizes are significantly smaller than in wild type animals. In addition, we observe retarded embryonic development of pre-implantation embryos that are still within the oviduct. By gene expression analysis we want to elucidate the molecular basis for these phenomena. 3 wild type and 3 heterozygous RNA samples
2015-12-12 | E-GEOD-75924 | biostudies-arrayexpress
Project description:Estrogen receptor α (ERα) is a nuclear transcription factor crucial for the female reproductive function. We previously reported that mice lacking epithelial ERα in the epithelial cells of female reproductive tract (Wnt7aCre+;Esr1fl/fl, conditional knockout or cKO) were infertile, in part, due to an implantation defect. To determine if oviductal dysfunction also contributed to their infertility, we examined the fertilization rates and embryo development in vivo during the first few days of pregnancy. At 0.5 days post coitum (dpc), cKO females had significantly fewer zygotes than wild type control littermates (WT). At 1.5 dpc, cKO females had no 2-cell embryos at all; only dead oocytes or embryos and empty zona pellucidas were observed. These results indicate that lack of ERα in the oviductal epithelium resulted in alterations in the oviductal microenvironment that were detrimental to the embryos. Microarray analysis revealed dramatic differences in gene expression between cKO and WT oviducts collected at 0.5 dpc and significant but less dramatic differences at 1.5 dpc. These findings indicate that signaling via epithelial ERα is essential to generate an oviductal milieu supportive of fertilization and embryo development.and may have implications for infertility in women. The oviduct samples were collected from female reproductive tract epithelial ER α knockout (cKO) and wild type control littermates (WT) at days 1 and 2 of pregnancy (0.5 and 1.5 days post coitum). Each experimental group contains 4 replicates. Gene expression analysis was conducted by using Agilent Whole Mouse Genome 4�44 multiplex format oligo arrays (no. 014868; Agilent Technologies, Santa Clara, CA)
2015-12-08 | E-GEOD-37471 | biostudies-arrayexpress
Project description:In this study, we evaluated the PK/PD and explored the efficacy of a PDE4 inhibitor, CC-11050 in a murine model of Mtb infection. Infected mouse lungs with or without CC-11050 treatment was also used to interrogate genome-wide transcriptional changes. Standard aerosol infection of mice with MtbCDC1551, followed by enumeration of lung bacterial load, pathology and transcriptional changes were monitored upto 112 days post infection. Mice were infected with Mtb and treatment with CC11050 was started at 14 days post-infection. Uninfected mice were included as control. At 28 days post-infection, mice from all 3 groups (uninfected, Mtb-infected untreated or CC11050 treated) were euthanized and lung tissue was collected to isolate total RNA and used in microarray experiments. (N=4 per group)
2016-06-10 | E-GEOD-83188 | biostudies-arrayexpress