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Genome-wide DNA methylation analysis using MethylCap-seq in canine diffuse large B-cell (cDLBCL) cell lines

ABSTRACT: Genome-wide DNA methylation analysis using MethylCap-seq in canine diffuse large B-cell (cDLBCL) cell lines

PROVIDER: PRJNA630576 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11697805_1.fastq.gz	Fastqsanger.gz
	SRR11697805_2.fastq.gz	Fastqsanger.gz
	SRR11697806_1.fastq.gz	Fastqsanger.gz
	SRR11697806_2.fastq.gz	Fastqsanger.gz
	SRR11697807.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome-wide DNA methylation analysis using MethylCap-seq in canine diffuse large B-cell (cDLBCL) cell lines

Project description:MethylCap-seq was performed to characterize the genome-wide DNA methylation in CLBL-1 8.0, a doxorubicin-resistant cDLBCL cell line, and CLBL-1 as control, and aimed to investigate underlying mechanisms of doxorubicin resistance in cDLBCL. Strong difference in methylation pattern of both promoter and gene-body regions was detected between CLBL-1 8.0 and CLBL-1. Methylated peaks with fold-change greater than 4 and a P value of less than 0.01 were defined as differentially methylated regions (DMRs); there were a total of 20289 hypermethylated and 38362 hypomethylated DMRs detected. Among these, 1339 hypermethylated and 4861 hypomethylated DMRs were in promoter regions, while 12855 hypermethylated and 18904 hypomethylated DMRs were in gene-body regions. There were 6.6% hypermethylated DMRs located on the promoter regions. A high percentage (63.4%) of hypermethylated DMRs were distributed within the gene body, and 7.8%, 5.1% and 23.8% hypermethylated DMRs were found to be clustered in upstream, downstream, and intergenic regions, respectively.

2020-10-22 | GSE149925 | GEO

Array comparative genomic hybridization of canine diffuse large B-cell lymphoma (cDLBCL)

Project description:Array comparative genomic hybridization of canine diffuse large B-cell lymphoma (cDLBCL)

| PRJNA450597 | ENA

Genome-wide RNA-seq analysis in canine diffuse large B-cell (cDLBCL) cell lines

Project description:Genome-wide RNA-seq analysis in canine diffuse large B-cell (cDLBCL) cell lines

| PRJNA628596 | ENA

Gene expression analysis in canine diffuse large B cell lymphoma (DLBCL)

Project description:We performed a veterinary clinical oncology trial in client-owned dogs to determine if immune modulating drugs could be combined in rational approaches to treat spontaneous canine diffuse large B cell lymphoma (DLBCL).

2023-08-29 | GSE213088 | GEO

Genome-wide RNA-seq analysis in canine diffuse large B-cell (cDLBCL) cell lines

Project description:To analyze the biological relevance of methylation changes, gene expression from both CLBL-1 and CLBL-1 8.0, a doxorubicin-resistanct cDLBCL cell line, were examined. In total, we obtained 24.8 M and 23.7 M sequence reads for CLBL-1 and CLBL-1 8.0, respectively. After filtering out low-quality bases and reads from the datasets prior to read mapping, 19.8 M reads for CLBL-1 and 19.1 M reads for CLBL-1 8.0 were mapped to canine genome. The criteria that transcripts per million (TPM) >5 in one of sample and the log2 fold-change ≥ 0.67 or ≤ -0.67 were applied to identified differentially expressed genes. Upregulated and downregulated genes were 1127 and 602, respectively.

2020-10-22 | GSE149384 | GEO

Genome-wide DNA methylation analysis using MethylCap-seq in canine high-grade B-cell lymphoma

Project description:In the present study, MethylCap-seq was used to characterize the genome-wide DNA methylation patterns in canine high-grade B-cell lymphoma (cHGBL). Canine methylated DNA fragments were captured and the MEDIUM-HIGH and LOW fraction of methylated DNA was obtained based on variation in CpG methylation density. In the MEDIUM-HIGH and LOW fraction, 2,144 and 1,987 cHGBL-specific hypermethylated genes, respectively, were identified. Functional analysis highlighted pathways strongly related to oncogenesis. The relevant signaling pathways associated with neuronal system were also revealed. In addition, 14 genes were hypermethylated in all the cHGBL cases but not in the healthy dogs. These genes might be potential signatures for tracing cHGBL. Further, the distinct methylation pattern of cHGBL showed a concordance with the clinical outcome, suggesting that aberrant epigenetic changes may influence tumor behavior. In summary, our study characterized genome-wide DNA methylation patterns using MethylCap-seq in cHGBL; the findings suggest that specific DNA hypermethylation holds promise for dissecting tumorigenesis and uncovering biomarkers for monitoring the progression of cHGBL.

2022-06-20 | GSE155211 | GEO

miRNome Expression Analysis in Canine Diffuse Large B-Cell Lymphoma

Project description:miRNome Expression Analysis in Canine Diffuse Large B-Cell Lymphoma

| PRJNA1005657 | ENA

Gene expression analysis in canine diffuse large B cell lymphoma (DLBCL)

Project description:Gene expression analysis in canine diffuse large B cell lymphoma (DLBCL)

| PRJNA879076 | ENA

miRNome Expression Analysis in Canine Diffuse Large B-Cell Lymphoma

Project description:Introduction: Lymphoma is a common canine cancer with translational relevance to human disease. Diffuse large B-cell lymphoma (DLBCL) is the most frequent subtype, contributing to almost fifty percent of clinically recognized lymphoma cases. Identifying new biomarkers capable of early diagnosis and monitoring DLBCL is crucial for enhancing remission rates. This research seeks to advance our knowledge of the molecular biology of DLBCL by analyzing the expression of microRNAs, which regulate gene expression by negatively impacting gene expression via targeted RNA degradation or translational re-pression. The stability and accessibility of microRNAs make them appropriate biomarkers for the diagnosis, prognosis, and monitoring of diseases. Methods: We extracted and sequenced microRNAs from ten fresh-frozen lymph node tissue samples (six DLBCL and four non-neoplastic). Results: Small RNA sequencing data analysis revealed 35 differently expressed miRNAs (DEMs) compared to controls. RT-qPCR confirmed that 23/35 DEMs in DLBCL were significantly upregulated (n = 14) or downregulated (n = 9). Statistical significance was determined by comparing each miRNA's average expression fold-change (2-Cq) between the DLCBL and healthy groups by applying the unpaired parametric Welch's 2-sample t-test and false discovery rate (FDR). The predicted target genes of the DEMs were mainly enriched in the PI3K-Akt-MAPK pathway. Discussion: Our data point to the potential value of miRNA signatures as diagnostic biomarkers and serve as a guideline for subsequent experimental studies to determine the targets and functions of these altered miRNAs in canine DLBCL.

2023-08-30 | GSE240893 | GEO

Comparative Transcriptional Analysis of Canine and Human Diffuse Large B cell Lymphoma (DLBCL). Molecular Signatures of NF-κB Pathway Activation and Sub-Classification of Canine DLBCL.

Project description:In this study, we present the first comparison of global transcriptional changes taking place in canine lymphoma and human diffuse large B-cell lymphoma (DLBCL), with particular reference to the nuclear factor-kappaB (NF-κB) pathway. Microarray data generated from lymph nodes diagnosed with canine DLBCL and healthy lymph nodes were used for differential expression analysis, co-expression analysis and pathway analysis, and compared with analysis of publicly available microarray data from human healthy and DLBCL lymph nodes. The comparisons between species at gene level were performed by mapping the probesets in canine microarrays to orthologous genes in humans and vice versa. A considerable number of differentially expressed genes between canine lymphoma and healthy lymph node samples were also found differentially expressed between human DLBCL and healthy lymph node samples. Principal component analysis (PCA) using a literature derived 120 NF-κB target gene set mapped to 199 orthologous canine array probesets and 259 human array probesets clearly separated the healthy and cancer samples in both canine and human datasets. The analysis demonstrated that for both human and canine DLBCL there is activation of the NF-κB/p65 canonical pathway rather than the alternative pathway. This has therapeutic implications for the use of specific pathway inhibitors for the treatment of DLBCL for both species and also indicates that naturally occurring canine lymphoma could be used as a model to study therapeutic strategies for human lymphoma. The model was further validated by the identification of molecular signatures that could sub-classify canine DLBCL into activated B-cell-like (ABC) or germinal centre B-cell-like (GCB) types equivalent to human subtypes.

2013-09-26 | GSE30881 | GEO

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