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Homo sapiens

ABSTRACT: Ago HITS-CLIP in KSHV-infected primary effusion lymphoma (PEL) cell lines BCBL-1 and BC-3

PROVIDER: PRJNA176666 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR580352.fastq.gz	Fastqsanger.gz
	SRR580353.fastq.gz	Fastqsanger.gz
	SRR580354.fastq.gz	Fastqsanger.gz
	SRR580355.fastq.gz	Fastqsanger.gz
	SRR580356.fastq.gz	Fastqsanger.gz

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Ago HITS-CLIP in KSHV-infected primary effusion lymphoma (PEL) cell lines BCBL-1 and BC-3

Project description:We performed Ago HITS-CLIP to identify targets of viral and human miRNAs in latently KSHV-infected PEL cells Ago HITS-CLIP was performed in two latently infected PEL cell lines, BCBL-1 and BC-3; Argonaute-immunoprecipitation of UV cross-linked Ago-miRNA-mRNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina GAxII); we performed 3 biological replicates for each cell line, two technical (sequencing) replicates of BCBL-1 biological replicate 1

2012-10-05 | E-GEOD-41357 | biostudies-arrayexpress

Ago HITS-CLIP in KSHV-infected primary effusion lymphoma (PEL) cell lines BCBL-1 and BC-3

Project description:We performed Ago HITS-CLIP to identify targets of viral and human miRNAs in latently KSHV-infected PEL cells

2012-10-05 | GSE41357 | GEO

microRNA Targetome Analysis of Latently KSHV-infected Primary Effusion Lymphoma Cell lines Using PAR-CLIP

Project description:This SuperSeries is composed of the following subset Series: GSE31745: Primary effusion lymphoma cell lines BC-1 and BC-3 GSE31746: BJAB Cell Lines Transduced with lentiviral vector pNL-SIN-CMV-AcGFP expressing KSHV miRNAs miR-K1, miR-K12-11, or miR-K4-3p GSE32109: microRNA Targetome Analysis of Latently KSHV-infected Primary Effusion Lymphoma Cell lines Using PAR-CLIP [Illumina] Refer to individual Series

2011-11-16 | E-GEOD-32113 | biostudies-arrayexpress

mRNA Sequencing of BC-1 Cells

Project description:Kaposi’s sarcoma-associated herpesvirus (KSHV) causes the B cell malignancy primary effusion lymphoma (PEL). Here we performed mRNA sequencing to characterize the mRNA expression profile of the primary effusion lymhoma (PEL) cell line BC-1.

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Altered global gene profile in KSHV+ PEL cells exposure to dhC16-Cer

Project description:Primary effusion lymphoma (PEL) is a rare B-cell malignancy that originates from B cells latently infected with Kaposi’s sarcoma-associated herpesvirus (KSHV, also known as human herpesvirus-8, HHV8). Our previous data indicated that several exogenous ceramide and dh-ceramide species, such as C18-Cer and dhC16-Cer, also displayed effective anti-cancer activities for KSHV+ PEL in vitro and in vivo. However, the underlying mechanisms for exogenous ceramide “killing” PEL cells still require further investigation, which will be helpful to better understand PEL pathogenesis and identify more potential therapeutic targets. In the current study, we used Illumina microarray to determine the altered gene profile in KSHV+ PEL cell-line, BCBL-1 exposure to dhC16-Cer.

2017-06-10 | GSE90038 | GEO

CLIP-seq analysis of KSHV ORF57-associated RNAs

Project description:Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 is a viral RNA-binding protein essential for viral lytic gene expression. ORF57 binds to target RNA directly via interaction with cellular cofactors. To investigate the entire repertoire of ORF57-associated RNAs we performed UV cross-linking immunoprecipitatin (CLIP) experiment using an affinity-purified, highly specific anti-ORF57 antibody in KSHV-infected primariy effusion lymphoma BCBL-1 cells undegoing lytic virus replication.

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AGO-PAR-CLIP of DG75 and BCBL-1

Project description:AGO-PAR-CLIP was employed to identify microRNA binding sites in BCBL-1, a Kaposi's sarcoma-associated herpesvirus (KSHV) infected B-cell line and DG75, a KSHV negative B-cell line as a control. By using our novel computational method (PARma) and differential analysis of PAR-CLIP data, highly accurate target sites of KSHV microRNAs can be defined.

2013-06-27 | GSE43909 | GEO

Kinome profiling of Non-Hodgkin Lymphoma identifies Tyro3 as a therapeutic target in PEL

Project description:Non-Hodgkin lymphomas (NHL) make up the majority of lymphoma diagnoses and represent a very diverse set of malignancies. We sought to identify kinases uniquely upregulated in different NHL subtypes. Using Multiplexed Inhibitor Bead-mass spectrometry (MIB/MS), we found Tyro3 was uniquely upregulated and important for cell survival in primary effusion lymphoma (PEL), which is a viral lymphoma infected with Kaposi’s sarcoma-associated herpesvirus (KSHV).

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Serial time induction by TPA on BCBL-1 cells in the absence or presence of viral replication inhibitor cidofovir

Project description:BCBL-1 cells were induced with 20 ng/ml TPA either in the absence (U) or presence (+) of 100 µM cidofovir (CDV) treatment and collected at 0, 6, 8, 10, 12, 24, 36, 48, 72, 96 hours (h) post-TPA addition, and compared against untreated (U), uninduced latent BCBL-1 reference cells. Three biological repeats were performed. Keywords = Kaposi's sarcoma-associated herpesvirus Keywords = KSHV Keywords = human herpesvirus type 8 Keywords = HHV-8 Keywords = primary effusion lymphoma (PEL) cells Keywords = body-cavity based lymphoma-1 (BCBL-1) cells Keywords = lytic induction Keywords = 12-O-tetradecanoylphorbol-13-acetate (TPA) Keywords = viral replication inhibition Keywords = cidofovir (CDV) Keywords: time-course

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AGO-PAR-CLIP of DG75 and BCBL-1

2013-06-27 | E-GEOD-43909 | biostudies-arrayexpress