Project description:This SuperSeries is composed of the following subset Series: GSE30897: Nucleosome occupancy in yeast BY4741and a strain lacking MSN2 and MSN4 responding to 20 min treatment with 0.4mM H2O2 GSE30898: Msn2p occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min) GSE30899: Gene expression dynamics in yeast BY4741 and a strain lacking MSN2 and MSN4 responding to 0.4mM H2O2 over time (0-60min) GSE30900: Nucleosome occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min) Refer to individual Series
Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide to reveal new relationships between regulators of stress-dependent gene expression. Nucleosome occupancy was measured by MNase-Seq in response to .4mM H2O2 in the S288c yeast derivative BY4741. A single replicate was performed for the time-course experiment with time points at 0, 4, 12, 20, 40 and 60 minutes after treatment.
Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide. and reveal new relationships between regulators of stress-dependent gene expression in yeast. Msn2p occupancy was measured in response to 0.4mM H2O2 in the S288c derivative BY4741 with an integrated myc-tagged Msn2p. A single replicate of the time course was performed with time points at 0, 4, 12, 20, 40 and 60 minutes after treatment.
Project description:BY4741 (S288c haploid) cells have different gene expression in response to 0.4mM H2O2 when pretreated with 0.7M NaCl compared to cells that are not pretreated with NaCl (mock cells). BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of mock cells to 0.4mM H2O2 was assessed every 10 mins for 40 mins. To study the effects of NaCl treatement on H2O2 response, BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of cells was measured in response to 0.7M NaCl over the course of 60 min every 15 mins. The cells were then removed from stress and grown in stress free media for four hours (T240). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 40 minutes. To see if the handling of cells had an affect on gene expression, BY4741 cells were grown for exponentially for 3 doublings (t0), received a mock YPD treatment for 60 mins, grown for 4 hours (T240) and then collected to asses genomic expression. Duplicates were done for at 30 and 45 minutes for the NaCl timecourse, triplicate were done for 0, 10 and 20 minutes in H2O2 timecourse and duplicates were done for 30 and 40 minutes in the H2O2 timecourse.
Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide and reveal new relationships between regulators of stress-dependent gene expression in yeast. Nucleosome occupancy was measured in the S288c derivative BY4741 and a strain lacking MSN2 and MSN4. Nucleosomes were isolated from unstressed yeast and yeast treated for 20 min with 0.4mM H2O2. Nucleosomal samples were compared in a 2-color, competitive hybridization to sheared genomic DNA.
Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide and reveal new relationships between regulators of stress-dependent gene expression in yeast. Gene expression was measured in response to 0.4mM H2O2 in the S288c derivative BY4741 in wild-type cells and cells lacking MSN2 and MSN4. A single replicate of a time course spanning from 4 to 60 minutes after treatment in each cell type. An additional 3 repliactes were collected from cells 30 minutes after treatment.
Project description:We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0, 5, 15 and 30 min after the addition of 10 mM H2O2.
