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RNA-seq analysis of several immortalized B cell lines (Namalwa, Daudi, Ramos, Raji, Toledo, ARH-77): Project 6 of Open Targets - Epigenomes of Cell Lines

ABSTRACT: RNA-seq analysis of several immortalized B cell lines (Namalwa, Daudi, Ramos, Raji, Toledo, ARH-77): Project 6 of Open Targets - Epigenomes of Cell Lines

PROVIDER: PRJEB27198 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2618740_1.fastq.gz	Fastqsanger.gz
	ERR2618740_2.fastq.gz	Fastqsanger.gz
	ERR2618741_1.fastq.gz	Fastqsanger.gz
	ERR2618741_2.fastq.gz	Fastqsanger.gz
	ERR2618742_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of several immortalized B cell lines (Namalwa, Daudi, Ramos, Raji, Toledo, ARH-77): Project 6 of Open Targets - Epigenomes of Cell Lines

Project description:The aim of this experiment was to characterize the gene expression of several immortalized B cell lines (Namalwa, Daudi, Ramos, Raji, Toledo, ARH-77). Two independent cultures were carried out for each of the cell lines. Cell lines were grown using supplier recommended culture methods and harvested sub-confluence in exponential growth phase. This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalised cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.

2018-06-11 | E-MTAB-6867 | biostudies-arrayexpress

Effect of KEAP1 knockout and CDDO-2P-Im Treatment in ARH-77 Cells

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E-MTAB-6867

Project description:RNA-seq analysis of several immortalized B cell lines (Namalwa, Daudi, Ramos, Raji, Toledo, ARH-77): Project 6 of Open Targets - Epigenomes of Cell Lines

2019-05-15 | E-MTAB-6867 | ExpressionAtlas

Quantitative proteomics of non hodgkin's

Project description:Abstract: ArtinM, a D-mannose-binding lectin from Artocarpus heterophyllus induces the activation of a Mast cell, neutrophils, macrophages, and CD4+ and CD8+ T cells, via carbohydrate recognition. we previously reported, that ArtinM is able to induce IL-17 and IL-12p40 production in murine B cells. Here, we further investigated the effects of ArtinM on murine B lymphocytes and Raji and Daudi cells, both human cell lines derived from non-Hodgkin lymphoma. We showed that ArtinM did not induce cell proliferation and low levels of IL-2, IFN-γ, and IL-12 were produced by murine B cells. However, high concentrations of ArtinM induced apoptosis of murine B cells. Then, evaluated the cytotoxic effect of ArtinM lectin against Raji and Daudi cells. we observed the ArtinM ability to reduce cell growth and cell viability, with a more pronounced cytotoxic effect on Raji cells. In addition, we observed the absence of DNA fragmentation, a strong indication of the exclusion of the apoptosis cascade via mitochondrial pathway, and the possible involvement of PTK, kinases of Src family, and CD45 phosphatase activity under Lck molecule in the cytotoxic effect of ArtinM in the Raji and Daudi cells. Thus, the present work demonstrates the limitations of the immunomodulatory effect of ArtinM under murine B cells, and provides insights in the investigative field in the non-Hodgkin lymphoma treatment, via carbohydrate recognition.

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Next generation sequencing analysis of transcriptomes at different timepoints after CBL0137 treatment in SU-DHL-4, Raji and Jeko cell lines

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Effect of bryostatin-1 on gene expression profile of Raji cells

Project description:To investigate bryostain's effect on Raji , we performed a whole-transcriptome RNA sequencing experiment for Raji cells treated with Bryostatin and established differntial expression profile comparing to raji treated with DMSO.

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Determine genes differentially expressed between Raji cells and a subline which is resistant to APTO-253 (Raji/253R)

Project description:To obtain further insight into the resistance mechanism, RNA-seq analysis was carried out on 3 independent samples of both the sensitive Raji and resistant Raji/253R cells. A gene-level differential expression analysis was performed by removing all genes with less than 50 reads across all 6 samples as genes with only low level expression can cause irregularities in differential expression analysis. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction. Among the 13,791 evaluable genes there were 1,012 that were significantly up-regulated in the Raji/253R cells and 704 genes that were significantly down regulated relative to the parental sensitive Raji cells. The ATP-binding cassette sub-family member ABCG2 was the most up-regulated gene with more than a thousand-fold increase in transcript level. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction.

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