GEO DataSets

(Submitter supplied) Cellular senescence is a program of irreversible cell cycle arrest that normal cells undergo in response to progressive shortening of telomeres, changes in telomeric structure, oncogene activation or oxidative stress. The underlying signalling pathways, potentially of major clinicopathological relevance, are unknown. A major stumbling block to studying senescence has been the absence of suitable model systems because of the asynchrony of this process in heterogeneous cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

48 Samples

Download data: CEL

(Submitter supplied) We sequenced mRNA from HCT116 p21-/- cells treated with Nutlin-3a, doxorubicin, or DMSO for 24 h.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6244 GPL9115

24 Samples

Download data: BAM, CEL

(Submitter supplied) To identify genomic regions bound by B-Myb and LIN9 (a subunit of the MuvB complex), we performed ChIP-Sequencing (ChIP-Seq) using chromatin from proliferating HeLa cells in which we can detect a robust association between B-Myb and subunits of the MuvB complex. This analysis allowed us identify late cell cycle or G2/M expressed genes as specific targets of the B-Myb-MuvB complex.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

6 Samples

Download data: BAM, PDF

(Submitter supplied) Periodic expression of cell cycle genes highlights the importance of precise temporal control of transcription in regulating cell cycle events. We used HeLa cells enriched for different phases of the cell cycle to identify genes that are expressed in a periodic fashion in specific cell cycle phases. These data were generated for comparison with ChIP-Sequencing data obtained for two subunits of the B-Myb-MuvB complex, B-Myb and LIN9, in HeLa cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

18 Samples

Download data: CEL

(Submitter supplied) A549 cells with FOXM1 or LIN54 sgRNA knockout, which confers resistance to the CHK1 inhibitor prexasertib, were generated. These cells and control (empty vector) cells were synchronized in S phase, released for 1 hour and treated with 100 nM prexasertib or DMSO (vehicle) for 2 hours. RNA-seq profiling was performed to identify drug-induced perturbations in gene expression in these cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) Studying DNA damage-induced senescence, we observed a similar phenotype upon CDK4/6 inhibition in breast cancer cells. We used RNA sequencing to investigate the gene expression profile of MCF7 cells upon CDK4/6 inhibition five days after exposure.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BW

(Submitter supplied) Transcriptomic gene expression analysis of MCF7 cells stimulated for 120 h with benzoapyrene, ionizing radiation or nothing

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TSV

(Submitter supplied) YAP, a major downstream effector of the Hippo signaling pathway, is an important regulator of cell proliferation. Previous studies have shown that YAP cooperates with the two transcription factors E2F and MYC to mediate G1 to S transition by regulating early cell cycle gene expression. On the other hand, the ability of YAP to regulate G2/M gene expression is dependent on the Myb-MuvB (MMB) complex, consisting of the evolutionary MuvB core complex of five proteins and the facultative subunit B-MYB, a transcription factor. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

22 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) YAP/TAZ, downstream effectors of the Hippo pathway, are important regulators of proliferation. Here we show that the ability of YAP to activate mitotic gene expression is dependent on the Myb-MuvB (MMB) complex, a master regulator of genes expressed in the G2/M phase of the cell cycle. By carrying out genome-wide expression and binding analyses, we found that YAP promotes binding of the MMB subunit B-MYB to the promoters of mitotic target genes. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL19057 GPL18573

33 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) The mammalian Retinoblastoma (RB) family including pRB, p107, and p130 represses E2F target genes through mechanisms that are not fully understood. In D. melanogaster, RB-dependent repression is mediated in part by the multisubunit protein complex Drosophila RBF, E2F, and Myb (dREAM) that contains homologs of the C. elegans synthetic multivulva class B (synMuvB) gene products. Using an integrated approach combining proteomics, genomics, and bioinformatic analyses, we identified a p130 complex termed DP, RB-like, E2F, and MuvB (DREAM) that contains mammalian homologs of synMuvB proteins LIN-9, LIN-37, LIN-52, LIN-54, and LIN-53/RBBP4. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3364

Platform:

GPL570

4 Samples

Download data: CEL, CHP

(Submitter supplied) This experiment is a part of global location analysis of the human DREAM complex including subunits: E2F4, RBL2/p130, LIN9 and LIN54. Specifically, the regions in Human Promoter Array 1.0R (GPL5082) bound by: E2F4 in G0-arrested T98G cells E2F4 in S-phase synchronized T98G cells LIN54 in G0-arrested T98G cells LIN54 in S-phase synchronized T98G cells LIN9 in G0-arrested T98G cells LIN9 in S-phase synchronized T98G cells p130 in G0-arrested T98G cells p130 in S-phase synchronized T98G cells were compared with input chromatin. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5082

30 Samples

Download data: BAR, CEL, TXT

Analysis of T98G cells in asynchronously growing state, after 72 hr of serum starvation to induce G0, or after serum restimulation to enter cell cycle. Results provide insight into mammalian cell-cycle gene regulation and mechanisms underlying repression of cell cycle dependent genes in quiescence.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 growth protocol sets

Platform:

GPL570

Series:

GSE8537

4 Samples

Download data: CEL, CHP

(Submitter supplied) The DREAM complex represses cell-cycle gene transcription in quiescence. To investigate the role of the DREAM component Lin37, we created Lin37 knockout cells by CRISPR/Cas9-nickase. pRTS episomal vectors expressing luciferase or Lin37 were introduced in two independent knockout clones (411-27 and 632-2) to create Lin37 knockout and rescue cells. To exit the cell cycle and to enter quiescence, cells were serum starved for 60h. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16173

10 Samples

Download data: TXT

(Submitter supplied) The Retinoblastoma-like pocket proteins p130 and p107 act as gatekeepers of the cell cycle through their activity within the DREAM (Dp/Rb-like/E2F/MuvB) transcriptional repressor complex. The goal of this study was to address how the pocket protein contributes to DREAM complex assembly and function on chromatin by utilizing a protein null mutant of the only C. elegans pocket protein LIN-35. We performed ChIP-seq of C. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL22765 GPL13657 GPL9269

46 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The nuclear factor kB (NF-kB) subunits RelA, RelB, c-Rel, p50 and p52 are each critical for B-cell development and function. To systematically characterize their responses to canonical and non-canonical NF-kB pathways activity, we performed ChIP-seq analysis in lymphoblastoid B-cells. We found a surprisingly complex NF-kB binding landscape, which did not readily reflect the two NF-kB pathway paradigm. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: TDF

(Submitter supplied) Cellular senescence wreaks defects in the aging organism. In this study, we co-treated two chemicals: rho-associated protein kinase (ROCK) inhibitor (Y-27632) and ataxia telangiectasia mutated (ATM) inhibitor (KU-60019) to overcome senescence more efficaciously, these two chemicals are already revealed to have senomorphic effects, suppressing senescent phenotypes. We find out that cocktail treatment synergistically alleviates diverse senescent phenotypes in senescent human dermal fibroblast cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

39 Samples

Download data: TXT

(Submitter supplied) YAP, the key protein effector of the Hippo pathway, is a transcriptional co-activator that controls the expression of cell cycle genes, promotes cell growth and proliferation and regulates organ size. YAP modulates gene transcription by binding to distal enhancers, but the mechanisms of gene regulation by YAP-bound enhancers remain poorly understood. Here we show that constitutive active YAP5SA leads to widespread changes in chromatin accessibility in untransformed MCF10A cells. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL30173

30 Samples

Download data: BIGWIG, TXT

(Submitter supplied) CRISPR-Cas9 genome-wide screens were performed in retinal pigment epithelial cells (RPE1) with either wild-type TP53 gene, or a TP53-null background. Results show wild-type TP53 has minimal impact on the efficiency of CRISPR dropout screens.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL18573

25 Samples

Download data: TXT

(Submitter supplied) Cellular senescence is a dynamic tumor suppression mechanism that limits the proliferation of impaired cells, by executing a stable cell cycle arrest. Understanding the molecular pathways and regulatory circuits that are involved in the process of senescence is presently incomplete. In this study, we determined the changes in gene expression during the establishment of replicative senescence, by comparing the expression profiles of young and senescent human umbilical vein endothelial cells (HUVECs). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

12 Samples

Download data: CEL, TXT