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Homo sapiens

ABSTRACT: Ribosome profiling and RNA sequencing of MCF10A-ER-Src and fibroblast cell transformation

PROVIDER: PRJNA275305 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1802130.fastq.gz	Fastqsanger.gz
	SRR1802140.fastq.gz	Fastqsanger.gz
	SRR1802150.fastq.gz	Fastqsanger.gz
	SRR1802131.fastq.gz	Fastqsanger.gz
	SRR1802141.fastq.gz	Fastqsanger.gz

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Project description:DNase-seq during MCF10A-ER-Src cell transformation

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Ribosome profiling and RNA sequencing of MCF10A-ER-Src and fibroblast cell transformation

Project description:We applied ribosome profiling and RNA sequencing to examine gene expression regulation during oncogenic cell transformation. One model involves normal mammary epithelial cells (MCF10A) containing ER-Src. Treatment of such cells with tamoxifen rapidly induces Src, thereby making it possible to kinetically follow the transition between normal and transformed cells. The other model consists of three isogenic cell lines derived from primary fibroblasts in a serial manner (Hahn et al., 1999). EH cell is immortalized by overexpression of telomerase (hTERT), and exhibits normal fibroblast morphology. EL cell expresses hTERT along with both large and small T antigens of Simian virus 40, and it displays an altered morphology but is not transformed. ELR cell expresses hTERT, T antigens, and an oncogenic derivative of Ras (H-RasV12).

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RNA-seq during MCF10A-ER-Src cell transformation and upon factor knockdowns

Project description:We performed RNA-seq to examine RNA expression profiles during MCF10A-ER-Src cell transformation and upon knockdowns of transcription factors

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Project description:RNA-seq during MCF10A-ER-Src cell transformation and upon factor knockdowns

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STAT3 knockdown during transformation

Project description:siSTAT3 knockdown of a tamoxifen initiated, transformation inducible, breast cancer model system (MCF10A-ER-Src), with associated controls of EtOH and siNEG treatments. A description of MCF10A-ER-Src cells can be found here: www.encodeproject.org

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Project description:ChIP-seq for histone modifications during MCF10A-ER-Src cell transformation

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DNase-seq during MCF10A-ER-Src cell transformation

Project description:We performed DNase-seq to study the dynamic genome-wide chromatin accessibility during MCF10A-ER-Src cell transformation.

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ChIP-seq for histone modifications during MCF10A-ER-Src cell transformation

Project description:We performed ChIP-seq for histone modifications to map chromatin status and dynamics during MCF10A-ER-Src cell transformation.

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Nutrient deprivation elicits a transcriptional and translational inflammatory response coupled to decreased protein synthesis

Project description:Purpose: The goal of this study is to examine gene expression regulation at the transcriptional and translational levels in response to various forms of nutrient deprivation, and whether there are differences between isogenic transformed and non-transformed cells. Mehods: We apply high-throughput sequencing of ribosome footprints (ribosome profiling) and poly(A) RNA (RNA sequencing) in an isogenic pair of transformed (tamoxifen-treated) and non-transformed (ethanol control) MCF10A-ER-Src cells subjected to the metabolic stresses that differentially affect global protein synthesis (Figure 1): deprivation of glutamine (for 30min and 4 hours), glucose (4hours), cysteine/cystine (4hours) or leucine/isoleucine/valine (brach-chain aminoacids - BCAA) (4hours). The same experiments were also performed in transformed ER-Src MCF10A treated with torin1 (500nM) for 4 hours. Results: Genome-wide translational profiling of glutamine deprived ER-Src MCF10A cells (for 30 minutes) shows increased translation of uORFs-containing mRNAs and down-regulation of ribosomal protein mRNAs, which is followed by increased translation and transcription of cytokine and inflammatory mRNAs (after 4 hours of glutamine deprivation). The transcription and translation of inflammatory and cytokine mRNAs is also stimulated in response to 4 hours deprivation of glucose, cysteine/cystine and BCAA, with the extent of stimulation correlating with the i) decrease in global protein synthesis and ii) down-regulation of all translationally-repressed mRNAs or ribosomal protein mRNAs. Conclusions: Pro-inflammatory gene expression is associated with translational repression in response to short-term nutrient deprivation.

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Homo sapiens

Project description:Ribosome profiling and RNA sequencing of MCF10A cells treated with TGFb

| PRJNA256319 | ENA