Project description:To further understand the biological properties of hair cells of the mammalian cochlea, we examined the transcriptome of adult inner and outer hair cells. Morphologically distinct inner and outer hair cells were isolated from the organ of Corti from adult CBA/J mice. One thousand inner and outer hair cells were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of two biological replicates of IHCs and three biological replicates of OHCs, each with two technical repeats, was performed. The resulting sequenced reads were mapped. Comparisons between inner and outer hair cells allow identification of enriched genes, as well as differentially expressed genes that result in cellular specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult mouse inner and outer hair cells.

2018-08-02 | GSE111348 | GEO

Mouse preimplantation imprinting [WGBS]

Project description:Mouse preimplantation imprinting [WGBS]

| PRJNA638354 | ENA

ROS control in human iPS cells reveals early events in spontaneous carcinogenesis

Project description:We developed a system to control the intracellular level of reactive oxygen species (ROS) in human iPS cells. By introducing a specific substitution (I69E) into the SDHC protein, a component of the mitochondrial respiratory chain complex, the intracellular ROS level considerably increased. This caused an abnormal development of iPS cells, and these abnormalities were reverted by the overproduction of mitochondria-targeted catalase. When ROS-overproducing iPS cells (ChiPSC12-M cells) were used for subcutaneous inoculation on the backs of nude mice, the mice exhibited tumor formation. The expression of tumor-related FOXC1 transcription factor increased as early as 4 h after the the development of ROS-overproducing iPS cells was initiated. An RNA-seq analysis revealed that 27 transcript clusters among the more than 20,000 transcrips that were examined were highly expressed at 4 h after the initiation of tumor development in ChiPSC12-M cells. Some of these overexpressed transcripts might make networks to activate protooncogenes for spontaneous carcinogenesis.

2021-12-01 | GSE123428 | GEO

RiboTag translatome analysis of outer hair cell postnatal development

Project description:In order to determine the regulators of outer hair cell postnatal maturation, we utilized the RiboTag mouse model to perform a detailed transcriptomic analysis of outer hair cells at five postnatal developmental time points: P8, P14, P28, 6 weeks (6wk) and 10 weeks (10wk). This analysis resulted in consistent enrichment of outer hair cell expressed genes in the immunoprecipitated RNA compared to whole cochlear input RNA from each time point. Using transcription factor binding motif prediction on a set of defined outer hair cell enriched genes, we further use this dataset to identify the helios transcription factor as a regulator of the postnatal outer hair cell transcriptome.

2018-11-28 | GSE116703 | GEO

Preimplantation mouse embryo proteome during 8C to 16C division

Project description:Preimplantation stages of mouse embryo development involve temporal and spatial specification and segregation of three late blastocyst cell lineages; trophectoderm (TE), primitive endoderm (PrE) and epiblast (EPI). Spatial separation of the outer TE lineage from the two inner-cell-mass (ICM) lineages (PrE and EPI) starts with the 8- to 16-cell transition and concludes following transit through the 16- to 32-cell stages. This results in a nascent early blastocyst ICM derived from descendants of primary founding inner cells and a secondarily contributed population; of which subsequent relative EPI versus PrE potencies are subject to debate. We showed that generation of primary but not the secondary ICM populations is highly dependent on temporally discreet activation of the mammalian target of rapamycin (mTOR – specifically mTORC1) around 8-cell stage M-phase entry. Moreover, that this role is mediated via the regulated function of the 7-methylguanosine- (7mG) cap binding initiation complex (EIF4F) and potentiating the translation of a subset of key but otherwise intransigent mRNAs containing 5’ UTR terminal oligopyrimidine (TOP-) sequence motifs. To find out translation of which mRNAs is regulated by mTOR during 8- to 16-cell transition, we analysed proteomes of control and mTOR-inhibited embryos during this time window.

2023-08-18 | PXD039423 | Pride

Asymmetric cancer cell division regulated by AKT, Reactive Oxygen Species (ROS) high versus ROS low mRNA

Project description:Human tumors often contain slowly proliferating cancer cells that resist treatment but we do not know precisely how these cells arise. We show that rapidly proliferating cancer cells can divide asymmetrically to produce slowly proliferating “G0-like” progeny that are enriched following chemotherapy in breast cancer patients. Asymmetric cancer cell division results from asymmetric suppression of AKT/PKB kinase signaling in one daughter cell during telophase of mitosis. Moreover, inhibition of AKT signaling with small molecule drugs can induce asymmetric cancer cell division and the production of slow proliferators. Cancer cells therefore appear to continuously flux between symmetric and asymmetric division depending on the precise state of their AKT signaling network. This model may have significant implications for understanding how tumors grow, evade treatment, and recur. 3 replicates each of MCF7 Reactive Oxygen Species (ROS) high, HCT116 ROS high, MCF7 ROS low, and HCT116 ROS low.

2011-07-14 | E-GEOD-30465 | biostudies-arrayexpress

Transcriptome of mouse preimplantation development

Project description:Transcriptome of mouse preimplantation development

| PRJNA291206 | ENA