Capture sequencing analysis of Miwi2-asEGFP transgene
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Mus musculus
SUBMITTER: Daisuke Itou
PROVIDER: E-MTAB-3257 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Small RNAs were subjected to deep sequence using Illumina Hiseq.
2015-03-18 | E-MTAB-3248 | biostudies-arrayexpress
Project description:The septins are a conserved family of GTP-binding proteins that, in the baker's yeast, assemble into a highly ordered array of filaments at the mother bud neck. These filaments undergo dramatic structural rearrangements during the cell cycle which are mechanistically not yet understood. We aimed at identifying key components that are involved in the transitions of the septins. Combining cell synchronization and quantitative affinity-purification mass-spectrometry (AP-MS), we identified interaction partners of the septins at three distinct stages of the cell cycle. A total of 83 interaction partners of the septins were assigned. We detected DNA-interacting/nuclear proteins and proteins involved in ribosome biogenesis and protein synthesis predominantly present in G1 arrested cells without an assembled septin structure. In addition, two distinct sets of regulatory proteins that are specific for cells at S-phase with a stable septin collar or at mitosis with split septin rings were identified. Complementary methods such as the SPLIFF method allowed us to more exactly define the spatial and temporal characteristics of selected candidate proteins of the AP-MS screen.
2016-01-28 | PXD002561 | Pride
Project description:Undifferentiated spermatogonia were sorted from Miwi2Tom/FL; ERT-Cre/+ (Miwi2-iKO) and Miwi2Tom/+; ERT-Cre/+ (Miwi2-CTL) mice injected with tamoxifen two weeks after last tamoxifen injection to understand an impact of acute Miwi2 deletion on spermatogenic homeostasis.
2018-03-21 | E-MTAB-6612 | biostudies-arrayexpress
Project description:Despite advances in molecular pathogenesis, pancreatic cancer remains a major unsolved health problem. It is a rapidly invasive, metastatic tumor that is resistant to standard therapies. The phosphatidylinositol-3-kinase (PI3K)/Akt and mammalian target of rapamycin (mTOR) signaling pathways are frequently dysregulated in pancreatic cancer. Gemcitabine (Gem) is the mainstay treatment for metastatic pancreatic cancer. P276 is a novel CDK inhibitor that induces G2/M arrest and inhibits tumor growth in vivo models. Here, we determined that P276 sensitizes pancreatic cancer cells to Gem induced apoptosis, a mechanism mediated through inhibition of Akt-mTOR signaling. In vitro, the combination of P276 and Gem resulted in a dose- and time-dependent inhibition of proliferation and colony formation of pancreatic cancer cells but not with normal pancreatic ductal cells. This combination also induced apoptosis, as seen by activated caspase 3 and increased Bax/Bcl2 ratio. Gene profiling studies demonstrated that this combination down regulated Akt-mTOR signaling pathway, which was confirmed by western blot analyses. There was also a down regulation of vascular endothelial growth factor (VEGF) and interleukin-8 expression suggesting effects on angiogenesis pathway. In vivo, intraperitoneal administration of the P276-Gem combination significantly suppressed the growth of pancreatic cancer tumor xenografts. There was a reduction in CD31 positive blood vessels, and reduced VEGF expression, again suggesting an effect on angiogenesis. Taken together, these data suggest that P276-Gem combination is a novel potent therapeutic agent that can target the Akt-mTOR signaling pathway to inhibit both tumor growth and angiogenesis. Case control dual channel design
2012-03-23 | E-GEOD-36703 | biostudies-arrayexpress
Project description:Streptococcus agalactiae, also known as Group B streptococcus, emerged in the 1960s as a leading cause of septicemia and meningitis in neonates. It is also an increasing cause of infections in adults with underlying diseases. To characterize regulatory elements in this species we performed a genome-wide transcription start site (TSS) profiling and whole-transcript sequencing. TSS were identified by using a differential RNA-seq strategy, based on selective Tobacco Acid Pyrophosphatase (TAP) treatment and adapter ligation, which differentiates primary transcripts and processed RNAs. The accuracy and sensitivity of TSS identification were increased by combining differential RNA-seq analyses under eight conditions corresponding to variations in growth conditions and genetic backgrounds. Whole-transcript sequencing used a two-step adaptor ligation-based directional RNA-seq protocol and was performed under two experimental conditions with triplicate experiments to assess variations in gene expression in response to an acid stress
2015-04-21 | E-MTAB-3200 | biostudies-arrayexpress
Project description:Piwi proteins and piRNAs have conserved functions in transposonM- silencing. The murine Piwi proteins Mili and Miwi2 direct epigeneticM- LINE1 (L1) and intracisternal A particle (IAP) transposon silencingM- during genome reprogramming in the embryonic male germline. PiwiM- proteins are proposed to be piRNA-guided endonucleases that initiateM- secondary piRNA biogenesis . However the actual contribution of theirM- endonuclease activities to piRNA biogenesis and transposon silencingM- remain unknown. To investigate the role of Piwi-catalyzedM- endonucleolytic activity, we engineered point mutations in the mouseM- that substitute the second D to an A in the catalytic triad (DDH) ofM- Mili and Miwi2, generating the MiliDAH and Miwi2DAH alleles,M- M- respectively. Analysis of Mili-bound piRNAs from homozygous MiliDAHM- fetal gonadocytes revealed the failure of transposon piRNA amplification resulting in the stark reduction of piRNA bound withinM- Miwi2 ribonuclear particles (RNPs). We find that Mili-mediated piRNA amplification is selectively required for L1 but not IAP silencing.M- The defective piRNA pathway in MiliDAH mice results in spermatogenic failure and sterility. Surprisingly, homozygous Miwi2DAH mice areM- fertile, transposon silencing is established normally and no defectsM- in secondary piRNA biogenesis are observed. In addition, the hallmarks of piRNA amplification are observed in Miwi2-deficient gonadocytes. WeM- conclude that cycles of intra-Mili secondary piRNA biogenesis fuelM- piRNA amplification that is selectively required for L1 silencing.M-
2011-10-28 | E-MTAB-730 | biostudies-arrayexpress
Project description:Medicinal plants have shown great promise as a source of novel drug compounds for the treatment of inflammatory disorders. In our search for new entities with anti-inflammatory potential, the extracts of the whole plant of Saussurea heteromalla (family-Asteraceae), collected from Himalayas, were evaluated in the high throughput screen for TNF-α and IL-6 inhibitors. The plant has been found as a new source of chlorojanerin, a guaianolide type of sesquiterpene lactone. This is the first report on the potent anti-inflammatory activity of the compound. Chlorojanerin was shown to be significantly effective in inhibiting TNF-α and IL-6 production in LPS induced THP-1 cells (TNF-α, IC50 = 3µM and IL-6, IC50 = 0.8µM). The compound also blocked TNF-α and IL-6 production from LPS induced human monocytes and synovial cells from RA patients. Chlorojanerin also inhibited the binding of NF-κB in a GFP reporter assay system. Transcriptional profiling of the LPS stimulated THP-1 cells revealed that chlorojanerin exerted its anti-inflammatory effect by inhibiting the expression of genes involved in activating the transcription factor – NF-κB. Real time analysis of these genes validated the effect of chlorojanerin on the classical downstream targets of NF-κB. Thus, this study clearly delineated 8 targets specific for the effect of chlorojanerin on NF-κB induced signaling at the mRNA level. This work is a step towards the isolation and characterization of lead anti-inflammatory agents from the extract of Saussurea heteromalla, which can be developed into better therapeutic molecules targeted towards some specific inflammatory diseases. Single dye labelling with Cy3 for all treatment RNA samples. Treatments included unstimulated, LPS stimulated, Chlorjanerin treatment and dexamethasone treatment.
2011-12-14 | E-GEOD-34180 | biostudies-arrayexpress
Project description:The PIWI-piRNA pathway serves as a critical defense mechanism through which the genome of the male germline is protected from invasion by transposable elements (TEs). MIWI2/PIWIL4, a member of the murine PIWI subclade of the Argonaute family, has been shown to be expressed in primordial germ cells (PGCs) and prospermatogonia in fetal and prepubertal testes. Global inactivation of Miwi2 leads to male sterility due to an early meiotic arrest, which correlates with retrotransposon desuppression. However, it remains unclear whether MIWI2 functions beyond the PGC stage and whether MIWI2 has a role beyond TE suppression during male germ line development. Through conditional inactivation of Miwi2, we demonstrate herein that MIWI2 function is restricted to a narrow time window during male PGC reprograming and that Miwi2 is dispensable for postnatal male germline development and testicular function in mice. Moreover, persistent activation of LINE1 and IAP retrotransposons caused by Miwi2 inactivation is compatible with mitotic cell cycle progression of spermatogonia during the first wave of spermatogenesis, but can cause zygotene to pachytene arrest in early meiosis due to multiple defects including enhanced DNA double-strand breaks, aberrant histone modifications and altered mRNA transcriptome. Our data not only validate those from global Miwi2 KO studies, but also suggest that MIWI2 and MIWI2-associated piRNAs have functions beyond TE suppression.
| S-EPMC3978311 | biostudies-literature
Project description:We are submitting two small RNA libraries derived from ovarian tissue of mutant and heterozygous for the Kumo/Qin gene, required for the piRNA production in germline cells. In absence of Kumo/Qin, piRNA production is reduced and transposons are derepressed. Analysis of piRNA production in Kumo/Qin mutants
2011-12-31 | E-GEOD-34728 | biostudies-arrayexpress
Project description:The homeobox gene HOXA10 plays a key role in endometrial differentiation during embryogenesis and is abundantly expressed in the adult endometrium and decidual cells. In the adult endometrium the expression of HOXA10 is regulated by estrogen and progesterone and the levels are highest in the decidualized cells. We have shown that HOXA10 is required in the endometrial cells to maintain the decidual cell phenotype. In this study we aimed to determine the molecular mechanisms by which HOXA10 maintains the decidual phenotype and the other roles it might have in decidual physiology. In vitro decidualized human endometrial stromal cells were knocked down for HOXA10 using siRNA and gene expression profiles of the scrambled and HOXA10 siRNA transfected cells were compared at 24, 48 and 72 h post transfection. Several genes having multiple functions were found to be differentially expressed. We postulate that HOXA10 is required by the decidual cells to support immune cell differentiation, trophoblast invasion and cellular remodeling. In vitro decidualized priamry cultures of human endometrial strmal cells transfected with a siRNA againts HOXA10 or a scrambled siRNA. Cells harvested at 24, 48 and 72 h post transfection. Dual channel hybridization with dye swap design in biological replicates
2012-02-14 | E-GEOD-35801 | biostudies-arrayexpress