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ShRNA screens for mediators of anti-proliferative effects of p53 in SJSA cell line

ABSTRACT: To identify genes required for anti-proliferative function of p53 we performed genome-wide and p53TARGET screens in SJSA cells treated with Nutlin.

ORGANISM(S): Homo sapiens

PROVIDER: GSE86220 | GEO | 2017/08/22

SECONDARY ACCESSION(S): PRJNA340953

REPOSITORIES: GEO

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p53 ChIP-seq in Nutlin-treated HCT116, MCF7, and SJSA cell lines

Project description:To identify genomic loci occupied by p53, we performed p53 ChIP-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

2017-08-22 | GSE86164 | GEO

12hr 5-FU treatment vs. DMSO in SJSA cells (from 'A kinase independent role for CDK19 in p53 response')

Project description:The human Mediator complex regulates RNA Polymerase II transcription genomewide. A general factor that regulates Mediator function is the four-subunit Mediator kinase module, which contains either CDK8 or CDK19. Whereas CDK8 has been linked to specific signaling cascades and oncogenesis, the cellular roles of its paralog, CDK19, are poorly studied. To define cellular roles for CDK19, we used osteosarcoma cells (SJSA) that naturally lack endogenous CDK8 protein. Although stable CDK19 knockdown was tolerated in SJSA cells, it caused reduced proliferation vs. control shRNA cells. Global gene expression analyses (RNA-Seq) suggested that defects in cholesterol biosynthesis contributed to reduced proliferation in CDK19 knockdown cells (vs. shCTRL). Notably, proliferation defects were rescued with transient expression of wild-type or kinase-dead CDK19. Using RNA-Seq and other assays, we established a general role for CDK19 in the transcriptional response to 5-fluorouracil (5-FU), an inducer of genotoxic and metabolic stress. These experiments also implicated CDK19 in activation of p53 target genes during 5-FU treatment. To further probe a potential role for CDK19 in the p53 response, SJSA cells (shCDK19 vs. shCTRL) were treated with the p53 activator Nutlin-3. Remarkably, CDK19 was required for SJSA cells to return to a proliferative state following Nutlin-3 treatment, and this effect was kinase-independent. These results implicate CDK19 as a regulator of p53 stress responses and suggest a manifestation of CDK19 knockdown—potentially reduced levels of cholesterol metabolites—blocks cellular resistance to Nutlin-3.

2017-05-09 | GSE89807 | GEO

GRO-seq from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin

Project description:To identify loci with transcriptionally engaged RNA polymerase, we performed GRO-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

2017-08-22 | GSE86165 | GEO

Total RNA-seq from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin

Project description:To determine effects of p53 activation on steady-state mRNA levels, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116 (p53+/+ and p53 -/-), breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

2017-08-22 | GSE86221 | GEO

RNAseq from polysomal RNA harvested from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin

Project description:To determine effects of p53 activation on levels of RNA associated with polysomes, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.

2017-08-22 | GSE86219 | GEO

Datasets for the effects of RUNX2 silencing on transcriptomic and metabolomic profiles in SJSA-1 osteosarcoma cells

Project description:Osteosarcoma is the most common primary malignant bone tumor with a high risk of metastasis and recurrence. Metabolic reprogramming is a hallmark of osteosarcoma and other cancers and is associated with genetic and epigenetic alterations. RUNX2 is an important transcription factor for osteoblastic differentiation, and aberrant expression of the gene contributes to the development and progression of osteosarcoma. To identify the effects of RUNX2 silencing on transcriptomic and metabolomic profiles in osteosarcomas, we generated SJSA-1 osteosarcoma cells stably expressing RUNX2 shRNA and SJSA-1 cells stably expressing scramble shRNA and analyzed transcriptome and metabolome profiles in the two cell types using Illumina NovaSeq 6000 and ultrahigh-performance liquid chromatography coupled with time-of-flight mass spectrometry, respectively. The datasets can be used by researchers to identify novel targets of RUNX2 and elucidate the role and underlying mechanism of RUNX2 in osteosarcoma pathogenesis and metabolic reprogramming.

2023-06-25 | GSE158976 | GEO

shRNA profiling of human breast carcinoma cells expressing over 300 shRNA constructs using barcode tiling arrays - screens 2 and 3

Project description:RNAi screens via pooled short hairpin RNAs (shRNAs) have recently become a powerful tool for the identification of essential genes in mammalian cells. We synthesized DNA microarrays with six overlapping 25 nt long tiling probes complementary to each unique 60 nt molecular barcode sequence associated with every shRNA expression construct.. In this part of the study pooled shRNAs were transduced into MDA-MB-231 breast carcinoma cell lines and their inhibitory effects four weeks post transduction were analyzed via microarray hybridization.

2009-12-08 | E-MEXP-2477 | biostudies-arrayexpress

Optimized PCR conditions and increased shRNA fold representation improve reproducibility of pooled shRNA screens.

Project description: Not available

| S-EPMC3411659 | biostudies-literature

Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

Project description:Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

| PRJNA608420 | ENA

Human BJ fibroblasts containing control vs. BRD7 shRNA

Project description:Transcriptional profiling of human BJ fibroblasts comparing control FF shRNA expressing cells vs. BRD7 shRNA expressing cells under two conditions, either untreated or treated with 8uM nutln-3a for 8 hours. This experiment was done using two independent shRNAs targeting BRD7. Nutlin-3a was used to stabilize p53 and induce its transcriptional activity. Two-condition experiment, FF shRNA cells vs. BRD7 shRNAs cells in two experimental conditions, either untreated or treated with nutlin-3a.

2010-07-01 | E-GEOD-22607 | biostudies-arrayexpress

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