GEO DataSets

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11002 GPL13112

4 Samples

Download data: BW

(Submitter supplied) 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. In order determine transcriptional effects dependent on MSK1/2 kinase activity, H89 inhibitor was used in the study.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

14 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11002 GPL13112 GPL4134

56 Samples

Download data: BW, TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) 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:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11002 GPL13112

22 Samples

Download data: BW

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

12 Samples

Download data: TXT

(Submitter supplied) We report a synthetic chromatin kinase, by fusing nuclease-null CRISPR/Cas9 to a hyperactive, truncated variant of the human MSK1 histone kinase (dCas9-dMSK1). To investigate the role of MSK1 on transcriptional regulation, we explore the different transcriptome between wildtype and MSK1 knockout HEK 293T cell lines by RNA-seq. To test the efficacy of dCas9-dMSK1 at thousands of human promoters in high-throughput and to evaluate if histone phosphorylation could uncover novel mediators of pathological gene expression, we performed a CRISPRa screening assay in A375 cells using the genome wild gRNA library. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15520 GPL21290

31 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL6887

14 Samples

Download data

(Submitter supplied) ChIP-Seq analysis revealed that suberoylanilidehydroxamic acid (SAHA) increases genome-wide H4 acetylation in differentially regulated genes, except for the 500 bp upstream of transcription start sites (TSS).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) Suberoylanilidehydroxamic acid (SAHA) significantly increased the expression levels of 127 transcripts and suppressed expression of 130 genes by more than 2-fold within 3 standard deviations of the mean in differentiating MC3T3 sc4 osteoblasts

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) MAP kinases are integral to the mechanisms by which cells respond to a wide variety of environmental stresses. In Caenorhabditis elegans, the KGB-1 JNK signaling pathway regulates the response to heavy metal stress. The deletion mutants of this cascade show hypersensitivity to heavy metals like copper or cadmium. However, factors that function downstream of KGB-1 pathway are not well characterized. To understand how the KGB-1 pathway modulates gene activity and to define the physiological processes in which the heavy metal stress response may be involved, we used microarray to examine gene expression changes in wild-type and kgb-1 mutant animals subjected to heavy metal stress.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS4568

Platform:

GPL200

4 Samples

Download data: CEL, CHP

Analysis of kgb-1 mutants incubated with 1mM copper sulfate for 1hr. The conserved KGB-1 JNK mitogen-activated protein kinase pathway regulates the response to heavy metal stress. Results provide insight into molecular mechanisms underlying the heavy metal stress response.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, count, 2 genotype/variation, 2 stress sets

Platform:

GPL200

Series:

GSE42703

4 Samples

Download data: CEL, CHP

(Submitter supplied) Cardiac hypertrophy is characterized by an increase in heart size and profound gene expression changes. Pharmacological histone deacetylase (HDAC) inhibitors attenuate pathological cardiac remodeling and hypertrophic gene expression. Published literature has linked enzymes that mediates histone acetylation to pathogenesis, however, the role of histone acetylation to define hypertrophic gene regulatory events are not well understood. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

4 Samples

Download data: BED, TXT

(Submitter supplied) We report on the identification of nitric-oxide regulated H3K9/14ac sites in Arabidopsis. For this purpose liquid grown Arabidopsis seedlings were treated with the natural NO-donor S-nitrosoglutathione (GSNO), GSNO in combination with the NO-scavenger cPTIO, GSH (control) or TSA (positive control). Material was crosslinked and harvested 3h and 16h after onset of the treatments. Then, quantitative analysis of the H3K9/14ac patterns across these treatment was performed using DiffBind. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

40 Samples

Download data: BED, CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL198 GPL9062

12 Samples

Download data: CEL, TAR, XLS

(Submitter supplied) These ChIP-seq data files are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Keywords: stress response, histone modification

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: TAR, XLS

(Submitter supplied) These microarrays are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels (via ChIP-seq) in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Water deficit stress causes a large number of genes to change their transcript levels, which provided a large set of genes to examine for corresponding chromatine changes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) RNA-seq (at parturition: L1) as well as STAT5A and H3K4me3 ChIP-seq with wild-type mammary gland tissues (at day 6 of pregnancy: p6, day 13 of pregnancy: p13, and L1).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL13112

11 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:

GPL7107 GPL1322

21 Samples

Download data: CEL, PAIR

(Submitter supplied) Profiling of changes in steady state RNA levels upon RNAi-mediated knockdown of the chromosomal kinase JIL-1 in Drosophila S2 cells.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

10 Samples

Download data: CEL