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Circle-Seq for extrachromosomal circular DNA in PLC-PRF-5 cells after treatment with 25OHD

ABSTRACT: Circle-Seq for extrachromosomal circular DNA in PLC-PRF-5 cells after treatment with 25OHD

PROVIDER: PRJNA914289 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22829026_1.fastq.gz	Fastqsanger.gz
	SRR22829026_2.fastq.gz	Fastqsanger.gz
	SRR22829027_1.fastq.gz	Fastqsanger.gz
	SRR22829027_2.fastq.gz	Fastqsanger.gz
	SRR22829028_1.fastq.gz	Fastqsanger.gz

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Circle-Seq for extrachromosomal circular DNA in PLC-PRF-5 cells after treatment with 25OHD

Project description:It has been verified that extrachromosomal circular DNA (ecDNA) has important clinical significance, and the formation process of ecDNA, its immunogenicity, and its other functions have also been described. However, the balancing mechanism by which cells respond to ecDNA, i.e., how ecDNA degrades within cells, is unclear. Here, by using Circle-Seq method conducted on PLC-PRF-5 HCC Cells, ecDNA was purified and the samples were used for DNA Library Preparation and Next Generation Paired-End Sequencing using Illumina MiSeq Technology, We found that some ecDNAs disappeared after VD treatment compared with the DMSO group, and these disappearing ecDNA were related to EMT, proliferation, cell cycle, focal adhesion and other malignant behaviors. Moreover, Circle-seq peaks narrowed after VD treatment, and the coverage over the whole gene was significantly reduced, suggesting that ecDNA after VD treatment carried smaller DNA fragments, which may cause them not to function as a whole gene. Importantly, we demonstrate that VD can cause a continuous and steady decrease in ecDNA in HCC cells.

2023-02-01 | GSE221428 | GEO

PLC/PRF/5 cells ChIP on CHIP

Project description:PLC/PRF/5 cells were harvested for chromatin immunoprecipitation followed by CHIP analysis performed on Aligent platform.

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RRBS of PCK1 knockout in PLC/PRF/5

Project description:RRBS analysis of Parental and PCK1 knockout groups of PLC/PRF/5 cells.

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Effect of knock-down of circular RNA circUCK2 on gene expression in PLC/PRF/5 cell

Project description:CircRNAs have emerged as crucial contributors to cancer progression. Nonetheless, the expression regulation, biological functions, and underlying mechanisms of circRNAs in mediating hepatocellular caicinoma(HCC) progression remain insuffuciently elucidated. Here we uncovered a novol circular RNA, circUCK2, which is highly expressed in HCC tissues and associated with recurrence-free survival in HCC patients. Knockdown of circUCK2 inhibits proliferation and metastasis of HCC cell lines.To investigate the function of circUCK2-silence in HCCs, we performed gene expression profiling analysis using data obtained from RNA-seq of PLC/PRF/5 cells.

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Expression data from hepatitis E virus inoculated PLC/PRF/5 cells

Project description:Hepatitis E virus (HEV) is an important causative pathogen of acute hepatitis. Because of the absence of an in vitro culture system for HEV, research has been greatly impeded. And interaction between HEV and host cells was mainly studied by tansfection/transinfection system, such as Adeno virus transinfection system. We developed an in vitro culture system for HEV in PLC/PRF/5 cells. With this in vitro culture system, we studied the gene expression profile change by HEV infection. Using a microarray assay, we analysed genes of PLC/PRF/5 cells, whose transcription level could be changed by HEV infection. Five flasks of PLC/PRF/5 cells inoculated with HEV were used as test sample, and five flasks inoculated with serum-free DMEM/199 medium were used as control samples. Both test and control flasks were cultured under the same conditions. Sixty days after inoculation, the test and control flasks was resolved with Trizol and analysed with Affymetrix HG-U133 Plus 2 array.

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RNAi knock down of Hepatitis B viral gene expression in human HepG2.2.15 or PLC/PRF/5 cells

Project description:Gene expression profiling comparisons of HepG2.2.15 or PLC/PRF/5 cells either mock (M) transfected or transfected with 0.2 microM S2 RNA or Scrambled (SCR) siRNA were carried out in duplicate 48 hours after transfection. The experiments were carried out in duplicate (a and b). The following combinations of RNA were used on 2 slides each: 1. 2.2.15 cells: mock transfection (reference) versus S2 treatment (test) 2. 2.2.15 cells: mock transfection (reference) versus Scr treatment (test) 3. 2.2.15 cells: Scr treatment (reference) versus S2 treatment (test) 4. PLC/PRF/5 cells: mock transfection (reference) versus S2 treatment (test) 5. PLC/PRF/5 cells: mock transfection (reference) versus Scr treatment (test) 6. PLC/PRF/5 cells: Scr treatment (reference) versus S2 treatment (test)

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Project description:Purpose: to analyze gene expression in XL413 treated liver cancer cells. Methods: PLC/PRF/5 cells are treated with XL413 (10uM) for 96 hours .For RNA sequencing, the library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). Gene set enrichment analysis was performed using gene set enrichment analysis software.

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Extrachromosomal circular SUZ12 amplicon dictates retinoblastoma progression through reprogramming H3K27 methylation [eccDNA-seq]

Project description:Extrachromosomal circular DNA (eccDNA) is double-stranded circular DNA that is derived from but independent of chromosomal DNA. Owing to its nonchromosomal inheritance, eccDNA facilitates the amplification of oncogenes and expedites the process of genome evolution in tumor. However, the role of eccDNA in RB remains enigmatic. We combined Circle-Seq and RNA-Seq to identified crucial extrachromosomal circular oncogene amplicons. Herein, we revealed that extrachromosomal circular SUZ12 amplicon regulates H3K27me3 modification during the oncogenic progression of retinoblastoma. Conclusively, our study initially delineated an integrated picture of the eccDNA landscape in retinoblastoma and unveiled a novel SUZ12-containing eccDNA/H3K27me3 oncogenic mechanism where eccDNA dictates retinoblastoma progression through regulating transcription levels of linear DNA.

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Expression data from hepatitis E virus inoculated PLC/PRF/5 cells

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CDC7 inhibition in PLC/PRF/5 cells

Project description:CDC7 inhibition in PLC/PRF/5 cells

| PRJNA761976 | ENA