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Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in negative control and miR-1290 knockdown HCT116 cells

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in negative control and miR-1290 knockdown HCT116 cells

PROVIDER: PRJNA675837 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13018802_1.fastq.gz	Fastqsanger.gz
	SRR13018802_2.fastq.gz	Fastqsanger.gz
	SRR13018803_1.fastq.gz	Fastqsanger.gz
	SRR13018803_2.fastq.gz	Fastqsanger.gz
	SRR13018804_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in negative control and miR-1290 knockdown HCT116 cells

Project description:Colorectal cancer (CRC) ranks third in incidence and second in mortality among cancers worldwide. Emerging researches showed that microRNAs (miRNAs) play an important role in CRC progression. Here, we aimed to investigate the expression and regulatory mechanism of miR-1290 in CRC. miR-1290 is significantly overexpressed in CRC primary tissues and metastatic tissues compared to that in normal tissues, and up-regulated miR-1290 is correlated with poor overall survival (OS) of CRC patients. Functional experiments showed that miR-1290 can promote the proliferation, migration, invasion and inhibit apoptosis of CRC cells. Mechanistically, miR-1290 directly targets KLF9 and promotes the malignancy progression of CRC cells through regulating MMP9 and p53 expression, subsequently. In addition, high H3K4me3 levels in miR-1290 promoter region activate its transcription in CRC. In summary, our study demonstrated the expression and regulatory mechanism of miR-1290 in CRC which supports the notion that therapeutic targeting of miR-1290 may be a promising treatment approach for CRC patients.

2020-11-11 | GSE161186 | GEO

Exosomal miR-1290 and miR-375 as prognostic markers in castrate resistant prostate cancer

Project description:Extracellular microRNAs (miRNAs) embedded in circulating exosomes may serves as prognostic biomarkers in cancer. This study was performed to identify and evaluate plasma exosomal miRNAs for prognostication in castration resistant prostate cancer (CRPC). RNA sequencing was performed to identify candidate exosomal miRNAs associated with overall survival in a screening cohort of 23 CRPC patients. Candidate miRNAs were further evaluated for prognosis using qRT-PCR in a follow-up cohort of 100 patients. Cox regression and Kaplan–Meier survival curve analysis were used to evaluate prognostic value of miRNA candidates with and without incorporation of clinical prognostic factors (age, Gleason score and time from androgen deprivation therapy to clinical progression). In the screening cohort, we obtained ~6.80 million mappable RNA reads per patient. Of those with normalized read counts ? 5, 43% were mapped to miRNAs for a total of 375 known and 57 novel miRNAs. Cox regression analysis identified an association of miR-1290, -1246, and -375 with overall survival (FDR<0.1). Of those, higher levels of miR-1290 and -375 were verified to be significantly associated with poor overall survival (p<0.004) in the follow-up cohort. The miR-1290/-375-based prediction model showed better performance with time-dependent area under the curve (AUC) =72% compared to clinical variable-based model with AUC=65%. Plasma exosomal miR-1290 and miR-375 are promising prognostic biomarkers for CRPC patients. Prospective validation is needed for further development of these candidate miRNAs.

2014-12-30 | GSE58410 | GEO

Coemansia sp. RSA 1290 isolate:RSA 1290

Project description:Coemansia sp. RSA 1290 Resequencing genome sequencing

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

| PRJNA787124 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection，Tumor tissue were isolated from infected recipients，and Total RNA was collected. Besides,about 5x106 cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing. Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor has a very positive significance for the pathological process of colorectal cancer，especially for cell adhension

2022-12-15 | GSE190435 | GEO

Tumor-initiating cell-specific miR-1246 and miR-1290 converge to promote non-small cell lung cancer progression [Illumina]

Project description:The tumor-initiating cell (TIC) model accounts for the phenotypic and functional heterogeneity among cancer cells found within human cancers. MicroRNAs (miRNAs) are key regulatory molecules frequently aberrantly expressed in tumors, and may play important roles in contributing towards tumor heterogeneity and TIC behavior. More recent efforts have focused on miRNAs for diagnosis and as targets for novel therapies. In this study, we identified the miRNAs, miR-1246 and miR-1290, which are crucial for the function of TICs, thereby driving cancer progression in human non-small cell lung cancer (NSCLC). These miRNAs are restricted to patient-derived tumorspheres and CD166+ primary tumor cells, both enriched for TICs. Loss of either miRNA impacted the tumorigenic potential of TICs and their ability to metastasize. Interestingly, longitudinal analyses of serum miR-1246 and miR-1290 levels correlated circulating levels of either miRNA to the clinical response seen in lung cancer patients to epidermal growth factor receptor (EGFR) tyrosine kinase inhibition, chemotherapy and radiotherapy. Functionally, direct inhibition of miR-1246 or miR-1290 with locked nucleic acid (LNA) administered systemically, could arrest the growth of established patient-derived tumors xenografted in immunocompromised mice, thus indicating these miRNAs are clinically useful as biomarkers for tracking disease progression and as therapeutic targets.

2015-11-30 | GSE69630 | GEO

Tumor-initiating cell-specific miR-1246 and miR-1290 converge to promote non-small cell lung cancer progression [Agilent]

2015-11-30 | GSE69574 | GEO

Pseudomonas putida strain:1290

Project description:Pseudomonas putida strain:1290 Genome sequencing

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Next-generation sequencing facilitates quantitative analysis of miRNAs of cetuximab-resistant colorectal cancer (HCT116-R) cells

Project description:Total RNAs were isolated from three groups, including A group (0×10^9/mL PA-MSHA-treated HCT116 cells), B group (0.3×10^9/mL PA-MSHA-treated HCT116 cells) and C group (0.4×10^9/mL PA-MSHA-treated HCT116 cells). MiRNA sequencing was performed to assess differential expression using next-generation sequencing. The data showed that most miRNAs levels were different in A, B and C groups. Importantly, miR-7-5p was greatly increased in a dose-dependent manner.

2021-08-13 | GSE181843 | GEO

Exosomal circRNA-MANBA mediates sorafenib resistance of hepatocellular carcinoma via miR-1290/CD109/p-STAT3 (Ser727) axis

Project description:Circular RNAs (circRNAs) are increasingly gaining importance and attention due to their diverse potential functions. Our study aims to explore the novel mechanisms by which exosome-contained circRNAs promote sorafenib resistance in hepatocellular carcinoma (HCC). Here we report that a circular RNA, circRNA-MANBA (a circular RNA upregulated in exosomes derived from sorafenib-resistant HCC cells), plays a significant role in sorafenib resistance in HCC. We identified that circRNA-MANBA is increased in sorafenib-resistant HCC cells, their exosomes, and tumor samples from sorafenib-treated HCC patients. Depletion of circRNA-MANBA substantially increases the cell-killing ability of sorafenib. Co-culture experiments revealed that exosomes from sorafenib-resistant HCC cells carrying large amounts of circRNA-MANBA could transmit drug resistant capacity to parental cells. Further studies revealed that circRNA-MANBA acted as ‘miRNAs sponge’ to absorb miR-1290, which prevented miR-1290 interaction with CD109 and thus upregulated STAT3 phosphorylation subsequently. Using different HCC mouse models, we demonstrated that silencing circRNA-MANBA by injection of siRNA could substantially overcome sorafenib resistance. Our study provides a proof-of-concept demonstration for a potential strategy to overcome sorafenib resistance in HCC patients by targeting circRNA-MANBA.

2023-11-07 | GSE213242 | GEO

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