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Stress-induced signaling to the nucleosome in serum deprived mouse fibroblasts.

ABSTRACT: We have employed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to analyze changes in chromatin architecture as well as the occupancy of two RNA Polymerase II (RNAPII) isoforms, initiation-competent (RNAPIIS5ph) as well as elongation-competent (RNAPIIS2ph) upon stress induction. We used resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin to induce the p38/MAP kinase pathway.

ORGANISM(S): Mus musculus

PROVIDER: GSE55774 | GEO | 2014/08/12

SECONDARY ACCESSION(S): PRJNA240993

REPOSITORIES: GEO

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Stress-induced signaling to the nucleosome in serum deprived mouse fibroblasts.

Project description:We have employed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to analyze changes in chromatin architecture as well as the occupancy of two RNA Polymerase II (RNAPII) isoforms, initiation-competent (RNAPIIS5ph) as well as elongation-competent (RNAPIIS2ph) upon stress induction. We used resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin to induce the p38/MAP kinase pathway. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1 h (in duplicates). Untreated, serum-starved cells were used as a control. Isolated chromatin was subjected to immunoprecipitation with the following antibodies: a-H3S28ph, a-H3K9ac, a-H3K4me3, a-RNAPIIS5ph and a-RNAPIIS2ph. Resulting DNA was sequenced using Illumina platforms.

2014-08-12 | E-GEOD-55774 | biostudies-arrayexpress

Transcriptional response to stress in serum deprived mouse fibroblasts [RNA-Seq]

2014-08-12 | GSE55776 | GEO

Transcriptional response to stress in serum deprived mouse fibroblasts [RNA-Seq]

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin to induce the p38/MAP kinase pathway. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1 h (in duplicates). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using strand-specific RNA-seq was performed.

2014-08-12 | E-GEOD-55776 | biostudies-arrayexpress

Transcriptional response to stress in serum deprived mouse fibroblasts

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Transcriptional response to stress in serum deprived mouse fibroblasts in the presence of MSK1/2 inhibitor.

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Transcriptional response to stress in serum deprived mouse fibroblasts

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in mouse Swiss 3T3 fibroblasts, where we induced p38/MAP kinase pathway using anisomycin. Serum starved (72 h) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1, 3, and 6 h (in triplicates). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using mouse Agilent expression array (4x44k) was performed.

2014-08-12 | E-GEOD-55554 | biostudies-arrayexpress

Transcriptional response to stress in serum deprived mouse fibroblasts in the presence of MSK1/2 inhibitor.

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin for 3 or 6 hours to induce the p38/MAP kinase pathway.Â In order determine transcriptional effects dependent on MSK1/2 kinase activity, H89 inhibitor was used in the study. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 3 h or 6h (in duplicates) either with or without 15-min pre-treatment with MSK1/2 inhibitor H89 (10 uM). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using strand-specific RNA-seq was performed.

2014-08-12 | E-GEOD-58746 | biostudies-arrayexpress

Promoter proximal pausing in response to stress in serum deprived mouse fibroblasts.

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Promoter proximal pausing in response to stress in serum deprived mouse fibroblasts.

Project description:We have employed short-capped RNA sequencing (sc-RNA-seq) in order to identify genes whose expression is regulated by promoter proximal pausing of RNA Polymerase II (RNAPI) in response to stress stimulation. We used serum-deprived mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin to induce the p38/MAP kinase pathway. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1 h (in duplicates). Untreated, serum-starved cells were used as a control. We isolated nuclear RNA, performed size fractionation followed by isolation of short-capped RNAs (scRNA). scRNAs were subsequently converted into DNA library and sequenced.

2014-08-12 | E-GEOD-55775 | biostudies-arrayexpress

Expression data from anisomycin- and imiquimod-induced dermatitis

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