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Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma

ABSTRACT: Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma

PROVIDER: PRJNA492494 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7890120_1.fastq.gz	Fastqsanger.gz
	SRR7890120_2.fastq.gz	Fastqsanger.gz
	SRR7890130_1.fastq.gz	Fastqsanger.gz
	SRR7890130_2.fastq.gz	Fastqsanger.gz
	SRR7890140_1.fastq.gz	Fastqsanger.gz

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Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [RNA-Seq]

Project description:Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [RNA-Seq]

| PRJNA492497 | ENA

Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [ChIP-Seq]

Project description:Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [ChIP-Seq]

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Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [Primary RNA-Seq]

Project description:Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [Primary RNA-Seq]

| PRJNA492493 | ENA

Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [THE1B RACE-Seq]

Project description:Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [THE1B RACE-Seq]

| PRJNA492490 | ENA

Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [RNA-Seq]

Project description:Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported that a member of the THE1B class of LTR elements in classical Hodgkin Lymphoma (cHL) acted as a promoter for the growth factor receptor gene CSF1R and that expression of this gene is required for tumor survival. However, to which extent and how such elements participate in globally shaping the unique cHL gene expression program is unknown. To address this question we mapped the genome-wide activation of THE1-LTRs in cHL cells using a targeted next generation sequencing approach (RACE-Seq). Integration of these data with global gene expression data from cHL and control B cell lines showed a unique pattern of LTR activation impacting on gene expression, including genes associated with the cHL phenotype. We also show that global LTR activation is induced by strong inflammatory stimuli. Together these results demonstrate that LTR activation provides an additional layer of gene deregulation in classical Hodgkin lymphoma and highlight the potential impact of genome-wide LTR activation in other inflammatory diseases.

2018-12-13 | GSE120330 | GEO

Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [ChIP-Seq]

2018-12-13 | GSE120538 | GEO

Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [THE1B RACE-Seq]

2018-12-13 | GSE120329 | GEO

Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [Primary RNA-Seq]

2018-12-13 | GSE120328 | GEO

miRNA expression in classical Hodgkin lymphoma diseased nodes

Project description:To determine differential expression of miRNA in classical Hodgkin lymphoma diseased nodes compared to non-malignant lymph nodes, we used agilent microarray release 16 and quantile normalisation using Genespring GX software to quantify and compare miRNA expression.. Total RNA was extracted from 8 non-malignant lymph node and 14 classical Hodgkin lymphoma diseased node (6 mixed cellularity and 8 nodular sclerosing) formalin-fixed paraffin-embedded tissue samples

2013-03-19 | E-GEOD-45264 | biostudies-arrayexpress

Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma.

Project description:Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported in classical Hodgkin Lymphoma (cHL) that a member of the THE1B class of LTR elements acted as a promoter for the proto-oncogene and growth factor receptor gene CSF1R and that expression of this gene is required for cHL tumour survival. However, to which extent and how such elements participate in globally shaping the unique cHL gene expression programme is unknown. To address this question we mapped the genome-wide activation of THE1-LTRs in cHL cells using a targeted next generation sequencing approach (RACE-Seq). Integration of these data with global gene expression data from cHL and control B cell lines showed a unique pattern of LTR activation impacting on gene expression, including genes associated with the cHL phenotype. We also show that global LTR activation is induced by strong inflammatory stimuli. Together these results demonstrate that LTR activation provides an additional layer of gene deregulation in classical Hodgkin lymphoma and highlight the potential impact of genome-wide LTR activation in other inflammatory diseases.

| S-EPMC6558280 | biostudies-literature

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