This SuperSeries is composed of the SubSeries listed below.
Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans.
No sample metadata fields
View SamplesAnalysis of the transcriptional response to viral infection in C.elegans.
Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans.
No sample metadata fields
View SamplesAttempt to identify small non-coding RNAs that change in levels as a result of viral infection of C.elegans Overall design: Small non-coding RNA (18-30nt) was extracted from animals either infected with Orsay virus or uninfected as indicated.
Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans.
Cell line, Subject
View SamplesThe transition in developmental control from maternal to zygotic gene products marks a critical step in early embryogenesis. Here, we use GRO-seq analysis to map the genome-wide RNA polymerase distribution during the Drosophila maternal to zygotic transition. This analysis unambiguously identifies the zygotic transcriptome, and provides insight into its mechanisms of regulation. Overall design: Two replicates of GRO-seq at each time point.
Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription.
Specimen part, Cell line, Subject, Time
View SamplesYeast cells were grown up in SD media containing all required amino acids. Each strain set was performed in triplicate. One set had no changes, the second set had 1mM methionine supplenting the media for the duration of growth and the third set was exposed to 0.5mM hydrogen peroxide for 15 minutes prior to harvesting
Gcn4 is required for the response to peroxide stress in the yeast Saccharomyces cerevisiae.
Compound
View SamplesGlobal restriction of protein synthesis is a hallmark of cellular stress. Using hydrogen peroxide, we monitor the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analysed.
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.
Sex, Compound
View SamplesWnt signaling in early eye development, specifically the lens placode shows expression of 12 out of 19 Wnt ligands. We these Wnt activities were suppressed using conditional deletion of Wntless, dramatic phenotypic changes in morphogensis occurred.
Wnt ligands from the embryonic surface ectoderm regulate 'bimetallic strip' optic cup morphogenesis in mouse.
Specimen part
View SamplesThe coupling between cell-cycle exit and onset of differentiation is a common feature throughout the developing nervous system, but the mechanisms that link these processes are mostly unknown. Although the transcription factor Pax6 was implicated in both proliferation and differentiation of multiple regions within the CNS, its contribution to the transition between these successive states remains elusive. To gain insight into the role of Pax6 during the transition from proliferating progenitors to differentiating precursors, we investigated cell-cycle and transcriptomic changes occurring in Pax6- retinal progenitor cells (RPCs). Our analyses revealed a unique cell-cycle phenotype of the Pax6-deficient RPCs, which included a reduced number of cells in the S phase, an increased number of cells exiting the cell cycle, and delayed differentiation kinetics of Pax6- precursors. These alterations were accompanied by co-expression of factors that promote (Ccnd1, Ccnd2, Ccnd3) and inhibit (P27kip1 and P27kip2) the cell cycle. Further characterization of the changes in transcription profile of the Pax6-deficient RPCs revealed abrogated expression of multiple factors which are known to be involved in regulating proliferation of RPCs, including the transcription factors Vsx2, Nr2e1, Plagl1 and Hedgehog signaling. These findings provide novel insight into the molecular mechanism mediating the pleiotropic activity of Pax6 in RPCs. The results further suggest that rather than conveying a linear effect on RPCs, such as promoting their proliferation and inhibiting their differentiation, Pax6 regulates multiple transcriptional networks which function simultaneously, thereby conferring the capacity to proliferate, assume multiple cell fates and execute the differentiation program into retinal lineages.
Pax6 is required for normal cell-cycle exit and the differentiation kinetics of retinal progenitor cells.
Specimen part
View SamplesWe used microarrays to determine the effect of prenatal nicotine exposure on gene expression profiles in the striatum of adolescent rats. We found a number of immediate early genes to be differentially expressed due to food-restriction.
Long-term effects of gestational nicotine exposure and food-restriction on gene expression in the striatum of adolescent rats.
Specimen part
View SamplesSingle-neuron transcriptome profiles of Dorsal Raphe neurons marked by a history of expression of Drd2::Cre and Pet1::Flpe (GFP+), as well as Dorsal Raphe neurons marked by a history of Pet1::Flpe expression only (mCherry+). Overall design: GFP and mCherry expressing neurons from triple transgenic Drd2::Cre;Pet1::Flpe;RC:FrePe mice were acutely dissociated, manually sorted, and single-neuron RNA-seq was performed (17 GFP+ cells, 8 mCherry+ cells).
Identification of Serotonergic Neuronal Modules that Affect Aggressive Behavior.
Specimen part, Subject
View Samples