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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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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

SP140 ChIP-seq for Daudi and Ramos cell lines

Project description:Study of the effect of SP140 deletion on the distribution of H3K27me3 in two independent Burkitt''s Lymphoma cell lines (DAUDI and Ramos).

2024-11-21 | GSE229801 | GEO

SP140 ChIP-seq for Daudi and Ramos cell lines

Project description:SP140 ChIP-seq for Daudi and Ramos cell lines

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

Project description:ARH-77 cells were genetically editted with CRISPR-Cas9 to knock out KEAP1 and treated with various doses of CDDO-2P-Im or DMSO.

2023-04-20 | GSE229914 | GEO

Homo sapiens strain:ARH-77

Project description:Homo sapiens strain:ARH-77 Epigenomics

| PRJNA1110570 | ENA

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

Next Generation Sequencing Facilitates Quantitative Analysis of Ramos and Rituximab-resistant Ramos cell Transcriptomes

Project description:The goal of this study is to screen the differential genes between Ramos and Rituximab-resistant Ramos cells, then analyze the significant pathways.

2019-02-13 | GSE112592 | GEO

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.

2023-03-11 | PXD029399 | Pride

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

Project description:To understand the mechanisms of CBL0137 in B-NHL therapy, gene expression changes of SU-DHL-4, Raji and Jeko cell lines after CBL0137 treatment were analyzed by RNA-seq

2023-02-07 | GSE208679 | GEO

Expression profile of MCF7, CCD18 and Ramos human cell lines

Project description:To uncover the chromosome 16 associated proteome and to take advantage of the generated knowledge to make progress in human biology in health and disease, a consortium of 15 groups was organized in four working groups: SRM and protein sequencing, antibody and peptide standard, clinical healthcare and biobanking and bioinformatics. According to a preliminary in silico study integrating knowledge from Ensembl, UniProt and GPM, Ramos B lymphocyte cells, MCF-7 epitelial cells and CCD18 fibroblast were selected as it is theoretically expected that any chromosome 16 protein coding gene is expressed in at least one of them. To define in detail the transcriptome of the above mentioned cell lines Affymetrix microarray based analyses were performed. Upon hybridization in Human ST 1.0 arrays, raw data were processed with RMA algorithm for background correction and normalization. Chromosome 16 gene expression pattern was then defined in each cell line and comparative analysis was done with R package statistics. Biological functions involving chromosome 16 genes were analysed with GO and functional networks were studied with Ingenuity Pathway Analysis. Expressed genes were compared with data from shotgun proteomic experiments to find the degree of correlation mRNA-protein. Expression of genes coding for proteins with weak or none MS evidence is shown. The integration of this information in decision-making process of the mass spectrometry group is discussed. Expression profiles of MCF7, CCD18 and Ramos human cell lines.

2013-05-31 | E-GEOD-40168 | biostudies-arrayexpress

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