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Transcriptome analysis in B16F10 and 4T1 cell lines with decitabine treatment [RNA-seq]

ABSTRACT: Transcriptome analysis in B16F10 and 4T1 cell lines with decitabine treatment [RNA-seq]

PROVIDER: PRJNA873589 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21201200_1.fastq.gz	Fastqsanger.gz
	SRR21201200_2.fastq.gz	Fastqsanger.gz
	SRR21201201_1.fastq.gz	Fastqsanger.gz
	SRR21201201_2.fastq.gz	Fastqsanger.gz
	SRR21201202_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis in B16F10 and 4T1 cell lines with decitabine treatment [RNA-seq]

Project description:The goal of RNA-seq is to identify the differential expressed genes in the B16F10 and 4T1 cells after Decitabine treatment. Three biological replicates were assigned for each group and in total 12 groups were prepared for RNA-seq libraries with 300 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped over 60 million reads per sample to mouse genome (mm10) with RSEM workflow. P-values of differential expression were adjusted for multiple-hypothesis testing using False Discovery Rate (FDR) method.

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Project description:The goal of ATAC-seq is to identify the open chromatin regions in the B16 and 4T1 cells after Decitabine treatment. Three biological replicates were assigned for each group and in total 12 groups were prepared for ATAC-seq libraries. We mapped about 30-100 million reads per sample to M.musculus (mm10) with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed M.Musculus have dispartate chromatin accessibility after Decitabine treatment

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Genomewide methylation analysis of B16F10 and 4T1 after Decitabine treatment with Reduced Representative Bisulfite Sequencing [RRBS]

Project description:Genomewide methylation analysis of B16F10 and 4T1 after Decitabine treatment with Reduced Representative Bisulfite Sequencing [RRBS]

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Chromatin accessibility in B16 and 4T1 cell lines with decitabine treatment [ATAC-seq]

Project description:Chromatin accessibility in B16 and 4T1 cell lines with decitabine treatment [ATAC-seq]

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Genomewide methylation analysis of B16F10 and 4T1 after Decitabine treatment with Reduced Representative Bisulfite Sequencing [RRBS]

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Project description:Treatment of cancer cells with anti-cancer drugs often fails to achieve complete remission. Yet, such drug treatments may induce alteration in the tumor’s gene expression patterns, including those of Cancer/Testis Antigens (CTA). The degradation products of such antigens can be presented as HLA peptides on the surface of the tumor cells and be developed into anti-cancer immunotherapeutics. For example, the DNA methyl transferase inhibitor, 5-aza-2'-deoxycytidine (Decitabine) has limited anti-tumor efficacy, yet it induces the expression of many genes, including CTAs that are normally silenced in the healthy adult tissues. In this study, the presentation of many new HLA peptides derived from CTAs and induced by Decitabine was demonstrated in three human Glioblastoma cell lines. Such presentation of CTA-derived HLA peptides can be exploited for development of new treatment modalities, combining drug treatment with anti-CTA targeted immunotherapy. The Decitabine-induced HLA peptidomes include many CTAs that are not normally detected in healthy tissues or in cancer cells, unless treated with the drug. In addition, the study included large-scale analyses of the simultaneous effects of Decitabine on the transcriptomes, proteomes and HLA peptidomes of the human Glioblastoma cells. It demonstrates the poor correlations between these three levels of gene expression, both in their total levels and in their response to the drug.

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Project description:Methylation status of breast cancer cell lines 4T1, D2A1, D2.0R and 4T1 cell lines treated with the demethylating agent decitabine were assess using methylarray to identify whether the baseline degree of genomic DNA methylation is correlating with the cell line's metastatic potential.

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