Project description:Human tissue based proteomics projects are challenging due to low abundance of proteins and tissue specificity of protein expression. In this study, we aimed to develop a cell-based approach to profile the male specific region of the Y chromosome (MSY) proteins. First, we profiled the expression of 23 Y chromosome genes and 15 of their X-linked homologues during neural cell differentiation from NT2 cells at three different developmental stages using qRT-PCR, western blotting and immunofluorescent (IF) techniques. The expression level of 12 Y-linked genes significantly increased over neural differentiation. Including RBMY1, EIF1AY, DDX3Y1, HSFY1, BPY2, PCDH11Y, UTY, RPS4Y1, USP9Y, SRY, PRY, and ZFY. Subsequently, DDX3Y was selected as a candidate for knockdown as it was significantly expressed in neural progenitor cells and it is known to be expressed in a gender specific manner and play a role in spermatogenesis. A siRNA-mediated DDX3Y knockdown in neural progenitor cells impaired cell cycle progression and increased apoptosis, consequently interrupting differentiation. Label-free quantitative shotgun proteomics based on a spectral counting approach was then used to characterize the proteomic profile of the cells after DDX3Y knockdown. Among 920 reproducibly identified proteins detected, 74 proteins were differentially expressed following DDX3Y siRNA treatment compared to mock treated cells. Functional grouping indicated these proteins were associated with cell cycle, cell-to-cell signaling, apoptosis and other important networks such as RNA processing and transcription regulation. Disease-based analysis confirmed DDX3Y involvement primarily in neurological and RNA metabolism disorders. Our results confirm that MSY genes are expressed in male neuronal cells, and demonstrate that Y linked DDX3 (DDX3Y) could play a multifunctional role in neural cell development in a sexually dimorphic manner.

2019-06-10 | MSV000083949 | MassIVE

Differentially Expressed Genes upon Knockdown of ZRANB1 or EZH2 in LM2 Cells

Project description:Differentially Expressed Genes upon Knockdown of ZRANB1 or EZH2 in LM2 Cells

| PRJNA414117 | ENA

Homo sapiens

Project description:Identification of differentially expressed genes in LBH589-treated cells

| PRJNA153461 | ENA

Differentially expressed genes in H2AX knockdown cells undergoing apoptosis

Project description:H2AX has been characterized as a novel tumor suppressor protein. Difficiency of H2AX will result in apoptotic inhibition of cancer cells. However, how H2AX epigenetically regulates apoptosis of cancer cells is still unclear. To reveal the genes expression regulated by H2AX and involved in apoptosis, the microarray profiling analysis was employed to identify differentially expressed genes in H2AX knockdown lung cancer cells and control ones after apoptotic induction. H2AX was knockdown by miRNA interfering system in human lung cancer originated cell A549 and the stable cell line named P1, while the control stable cell line named C. Genes with greater than 1.2-fold change and P-value ï¼0.05 were identified as differentially expressed genes between C and P1 cells both with apoptosis induction. The two groups including control (C) and H2AX knockdown lung cancer cells (P1) were harvested 48 h after VP-16 treatment. Three independent experiments were performed for each group.

2013-01-16 | E-GEOD-43498 | biostudies-arrayexpress

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