543f461e-53a0-4721-b015-7c16ad9036bf - samples
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ABSTRACT:
PROVIDER: EGAD00001008744 | EGA |
REPOSITORIES: EGA
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Project description:Primary Mediastinal large B-cell lymphoma (PMBL) is a rare form of non-Hodgkin lymphoma (NHL) representing 2% of mature B-cell NHL in patients less than 18 years of age.We compared the gene expression profiling between fully humanized anti-CD20 targeted monoclonal antibody recognizing a unique CD20 type II epitope, obinutuzumab and IgG or PBS treated Karpas Primary Mediastinal B-cell lymphoma (PMBL) cell line. -
2016-12-01 | GSE75605 | GEO
Project description:Lung cancers are a heterogeneous group of diseases with respect to biology and clinical behavior. Currently, diagnosis and classification are based on histological morphology and immunohistological methods for discrimination between two main histologic groups: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) which account for 20% and 80% of lung carcinomas, respectively. NSCLCs, which are divided into the three major subtypes adenocarcinoma, squamous cell carcinoma and dedifferentiated large cell carcinoma, show different characteristics such as the expression of certain keratins or production of mucin and lack of neuroedocrine differentiation. The molecular pathogenesis of lung cancer involves the accumulation of genetic und epigenetic alterations including the activation of proto-oncogenes and inactivation of tumor suppressor genes which are different for lung cancer subgroups. The development of microarray technologies opened up the possibility to quantify the expression of a large number of genes simultaneously in a given sample. There are several recent reports on expression profiling on lung cancers but the analysis interpretation of the results might be difficult because of the heterogeneity of cellular components. The methods used for sample selection and processing can have a strong influence on the expression values obtained through microarray profiling. Laser capture microdissection (LCM) provides higher specificity in the selection of target cells compared to traditional bulk tissue selection methods, but at an increased processing cost. Here we describe the use of an expression microarray study on NSCLC samples and surrounding tissue, comparing macroscopic lung tumor and tissue samples (“grind and bind”), versus tumor and alveolar compartment cells laser capture microdissected (LCM) from the same macroscopic lung samples. In this study, an initial set of 30 pairs of macroscopic tumor and non-tumor samples (10 pairs squamous-cell carcinoma, 18 pairs adenocarcinoma, 2 pairs adeno-squamous carcinoma) and 2 unpaired samples was selected for bulk/macro sampling. Of these 30 pairs and 2 unpaired samples, 17 pairs and 9 unpaired samples were reanalyzed using laser capture microdissection (LCM) for sampling the cells (7 pairs squamous and 1 unpaired sample, 9 pairs adenocarcinomas and 7 unpaired samples, 1 pair adeno-squamous carcinoma and 1 unpaired sample). For macroscopic samples, 50 to 80 µg of tissue was used to isolate total RNA. Gene expression profile was determined using Affymetrix Human Genome Gene 1.0 ST genechip. For the LCM samples, from representative slides histologically confirmed and mapped by a pathologist, approximately 1000 cells/sample were collected by LCM. cDNA was amplified using Nugen WT-Ovation One-Direct amplification system. In order to validate Nugen amplification bias of WT-Ovation One-Direct amplification system, the total RNA samples of 10 pairs of macroscopic tumor and non-tumor samples were amplified with this amplification system, and their cDNA was used to microarray.
2011-08-26 | GSE31552 | GEO
Project description:MicroRNAs expression profile was acquired in 99 frozen tissues corresponding to 14 Burkitt's lymphoma, 17 diffuse large B-cell lymphoma, 29 follicular lymphoma, 19 mantle cell lymphoma, 8 primary mediastinal B-cell lymphoma and 12 lymph nodes. Additionally, we performed microRNA expression profile of 14 Burkitts' lymphoma cell lines, 2 mantle cell lymphoma cell lines, 5 acute lymphoblastic leukemia cell preparations, 5 samples of mononucleosis cells, 4 Epstein Barr virus infected lymphoblastoid cell lines (EBV), 27 purified samples of B cells at different stage of development (13 GC-CD23-/CD39-, 11 GC-CD5- and 3 GC-CD5+), 4 peripheral blood CD19+ B cells, 4 purified samples of T cells (2 CD4+ and 2 CD8+) and 2 samples of bone marrow CD34+ cells. The data were used to discriminate among diverse pathological and nonpathological samples and to identify microRNAs expression differences between pathological samples and their nonpathological counterparts.
2017-08-20 | E-MTAB-6035 | biostudies-arrayexpress
Project description:This study contains total RNA sequencing data from plasma of 65 different human donors: 30 diffuse large B-cell lymphoma patients, 13 primary mediastinal large B-cell lymphoma patients and 22 cancer-free controls.
| EGAS00001007127 | EGA
Project description:Diffuse large B-cell lymphoma (DLBCL) is currently divided into three main molecular subtypes, defined by gene expression profiling (GEP): Germinal Center B-cell like (GCB), Activated B-Cell like (ABC), and Primary Mediastinal B-cell Lymphoma (PMBL). DLBCL subtypes were determined according to patients' gene expression profiles.
2017-01-30 | GSE87371 | GEO
Project description:Cell lines of mediastinal lymphomas, one each of primary mediastinal (thymic) large B cell lymphoma (PMBL), classic Hodgkin lymphoma (CHL), B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and CHL, and T-cell lymphoma were treated with rituximab (RmAb), brentuximab vedotin (BV), ibrutinib (IBR), prednisone (PRED) or untreated (UT) for 48 hours. Flow cytometry for PD-L1 protein was performed, and differential expression (DE) analysis of mRNA and miRNA performed by RNAseq. B-cell lines exhibited 2- fold increase in PD-L1 protein (p<.05) with RmAb compared to UT. Others showed no effect of RmAb, however, the T-cell line showed 2-fold increase on treatment with BV (P<.05). DE performed by limma showed no genomic level changes. ANOVA analysis of PMBL treated with RmAb, however, showed physiologic level DE involving >3000 genes involving multiple pathways associated with cell death and survival, protein degradation, mRNA translation, mRNA degradation, immunologic functions, and PD-1/PD-L1 immunotherapy. In the B cell lines, DE of CD274 (PD-L1) was decreased or not significant. MiRNA DE showed upregulation of 7 miRNAs, including miR-155-5p.
2022-06-14 | GSE206130 | GEO
Project description:Dataset contains total RNA sequencing data from plasma of 65 different human donors: 30 diffuse large B-cell lymphoma (DLBCL) and 13 primary mediastinal large B-cell lymphoma (PMBCL) patients, and 22 cancer-free controls. Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.
| EGAD00001010259 | EGA
Project description:This submission contains raw 10x Genomics Visium HD Spatial Gene Expression FASTQ files from three FFPE mucosa-associated lymphoid tissue lymphoma samples analyzed in the O2 marginal zone lymphoma study. Processed Space Ranger and downstream spatial transcriptomics files will be added before final GEO release. Submitter contact email: lcxujiadai@163.com.
2026-07-15 | GSE337521 | GEO
Project description:Primary mediastinal large B-cell lymphoma is hallmarked by large-scale copy-neutral loss of heterozygosity
| PRJEB50976 | ENA
Project description:Primary mediastinal large B-cell lymphoma is hallmarked by large-scale copy-neutral loss of heterozygosity
| PRJNA763590 | ENA