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Transcriptomics analysis of NOP16-regulated genes in MDA-MB231 cells [RNA-seq]

ABSTRACT: Transcriptomics analysis of NOP16-regulated genes in MDA-MB231 cells [RNA-seq]

PROVIDER: PRJNA791661 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17311931_1.fastq.gz	Fastqsanger.gz
	SRR17311931_2.fastq.gz	Fastqsanger.gz
	SRR17311932_1.fastq.gz	Fastqsanger.gz
	SRR17311932_2.fastq.gz	Fastqsanger.gz
	SRR17311933_1.fastq.gz	Fastqsanger.gz

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Transcriptomics analysis of NOP16-regulated genes in MDA-MB231 cells [RNA-seq]

Project description:The goal of RNA-seq is to identify the global transcriptional alteration by NOP16 overexpression or deletion in triple negative breast cancer cell line MDA-MB231 cells. Three (or Two) biological replicates were assigned for each group and in total 6 groups were prepared for these RNA seq libraries. We mapped about 20 million reads per sample to hg38 human reference genome, and counted and normalized each reads number and identified the differentially expressed genes.

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Identification of Fra-1 and/or Fra-2 regulated genes in MDA-MB231 cells

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Expression data from knockdown of G9a in MDA-MB231 cells

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RAI2 overexpression in MDA-MB231

Project description:MDA-MB231 cells were transfected with control vector, RAI2-overexpression vector, or vector with RAI2-4A, which has a mutated interaction domain w.r.t. CtBP/CtBP2 Three replicates each of control condition, RAI2 overexpression or RAI2-4A overexpression.

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Intensity-based absolute quantification (iBAQ) of proteins in MDA-MB231

Project description:To determine the absolute copy number of proteins in MDA-MB231 breast cancer cells, we employed IBAQ mediated absolute quantification of proteins based on (Schwanhäusser et al., Nature, 2011), with some modifications. Maqquant calculated iBAQ values were calibrated using spike-in standards, and used to calculate copy numbers for each identified protein within the dataset. Copy numbers for a total of 3,584 proteins were calculated in MDA-MB231 cells.

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Project description:To define and compare the interactomes of the RNA binding protein HNRNPC in poorly vs. efficiently metastatic breast adenocarcinoma cells, we carried out immunoprecipitation of endogenous HNRNPC from parental MDA-MB231 cells vs. its highly metastatic isogenic derivate, the MDA-MB231-LM2 cells. We used a non-specific MOUSE IgG IP from each line as control. Each IP was performed in triplicate, and analysed by LC-MS/MS, on a Thermo Q-Exactive-plus instrument.

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Project description:TDP43 and SRSF3 has been reported to be RNA-binding proteins; however their roles in breast cancer progression has not been examined previously. Here, we performed RNA-seq on MDA-MB231 cells stably expressed sh-control, shTDP43, shSRSF3 or sh-TDP43 and sh-SRSF3 using lentivirus in duplicates. In addition, MDA-MB231 cells with stable expression of flag-TDP43 or flag-SRSF3 were also generated by using lentivirus. RIP-seq was also applied to identify binding RNA against Flag antibodies.

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