MRNA expression changes after SAM CRISPRa activator (MCP-p65AD-HSF1AD) expression in the primary effusion lymphoma cell line BC-3
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PROVIDER: PRJNA1277346 | ENA |
REPOSITORIES: ENA
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Project description:CRISPR-based transcriptional activation (CRISPRa) has extensive research and clinical potential. In our related work, we showed that commonly used CRISPRa systems can exhibit pronounced cytotoxicity. Here, we investigated mRNA expression changes after the inducible expression of a fusion protein that is commonly used for CRISPRa, including the activation domains (ADs) of the transcription factors p65 and HSF1, components of the synergistic activation mediator (SAM) CRISPRa system.
2025-07-30 | GSE299931 | GEO
Project description:Microarray analysis of primary effusion lymphoma cell lines BC-1 and BC-3
2011-11-16 | GSE31745 | GEO
Project description:Microarray analysis of primary effusion lymphoma cell lines BC-1 and BC-3 Total RNA from BC-1 and BC-3 cell lines was processed for analysis in one replicate on Human Gene 1.0 ST arrays to obtain data on whether genes are expressed and to compare to existing microarray data.
2011-11-16 | E-GEOD-31745 | biostudies-arrayexpress
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.
2022-08-10 | GSE210446 | GEO
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
Project description:Halomonas sp. BC strain:BC Genome sequencing
| PRJNA259513 | ENA
Project description:Primary effusion lymphomas (PELs) are specifically associated with KSHV/HHV-8 infection, and most frequently occur in HIV-positive individuals as lymphomatous effusions in the serous cavities without a detectable solid tumor mass. Most PELs have concomitant EBV infection, suggesting that EBV is an important pathogenetic co-factor, although other as yet unidentified cofactors, such as cellular genetic alterations, are also likely to play a role. Lymphomatous effusions that lack KSHV also occur; these are frequently EBV-associated in the setting of HIV infection. Here we used gene expression profile analysis to determine the viral impact on cellular gene expression and the pathogenesis of these lymphomatous effusions. We used the Affymetrix HG-U133A microarray to analyze the gene expression profile of these effusion lymphomas (three virologic groups: KSHV-positive EBV-positive PELs, KSHV-positive EBV-negative PELs and KSHV-negative EBV-positive lymphomatous effusions). Nine cell lines derived from patients with lymphomatous effusions (three from each virologic group and each cell line was done in duplicates.) and three PEL patient samples were used in the study. Our results suggest that KSHV-positive PELs are very different from KSHV-negative lymphomatous effusions, and the genes that are differentially expressed include apoptosis regulators, cell cycle regulators, transcriptional factors and signal transduction regulators. KSHV clearly plays a dominant role in the phenotype of PEL. Within the KSHV-positive PELs, two subgroups can be identified, which were correlated with their EBV viral status. Among these genes (45 gene probes), four were regulators of the MAP kinase pathway that were up-regulated in the KSHV-positive, EBV-negative PELs, suggesting that in the absence of EBV, events that lead to the activation of the MAP kinase pathway may act as a cofactor for the development of PEL. Next we determined whether we could predict the viral status of the three primary patient cases of PEL based on the 45 gene probes that were differentially expressed in KSHV-positive cell lines according to EBV status (pt. 1: KSHV-positive, EBV-positive; Pt. 2: KSHV-positive, low proportion of EBV-positive; pt. 3: KSHV-positive EBV-negative), and we could.<br><br>Samples:<br>KSHV-positive EBV-positive cell lines: BC-1, BC-2, BC-5 <br>KSHV-positive EBV-negative cell lines: BC-3, BCBL-1, PEL-5 <br>KSHV-negative EBV-positive cell lines: IBL4, SM1, BCKN-1 <br>Patient 1: KSHV-positive, EBV-positive <br>Patient 2: KSHV-positive, EBV-positive (low number of positive cells) <br>Patient 3: KSHV-positive, EBV-negative.
2007-08-25 | E-GEOD-2149 | biostudies-arrayexpress
Project description:Transcriptome comparison of CRISPRa induced human pluripotent stem cell lines, control iPSC line induced with Sendai viral vectors, H9 embryonic stem cell line and human foreskin fibroblasts.
2018-06-07 | E-MTAB-6185 | biostudies-arrayexpress
Project description:The Kaposi's sarcoma-associated herpesviruses causes several cancers including Kaposi's sarcoma and primary effusion lymphoma (PEL). Our work reveals that the cellular transcription factors interferon regulatory factor 4 (IRF4) and basic leucine zipper ATF-like transcription factor (BATF), as well as the viral interferon regulatory factor 3 (vIRF3) are critical oncogenic dependencies specific to PEL cell lines. To understand the functions of these transcription factors, we performed ChIP-Seq on these proteins in BC-3 PEL cell line. Our results reveal that these oncogenic factors may cooperate to regulate the expression of the same mRNAs.
2020-08-13 | GSE132777 | GEO