Mantle Cell Lymphoma Michael Wang Lab
Ontology highlight
ABSTRACT:
PROVIDER: EGAC00001001950 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 4 samples of primary cells from tonsil with cell surface markes CD20med/CD38high in young individuals (3 to 10 years old) are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of EGA data sets is EGAD00001001523. Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. The mapping of samples to these EGA accessions can be found in the 'Sample Data Relationship Format' file of this ArrayExpress record. Information on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu
2016-05-12 | E-MTAB-4754 | biostudies-arrayexpress
Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 29 samples of primary cells or cultured primary cells of different haemopoeitc lineages from cord blood are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of EGA data sets is EGAD00001001165. Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. The mapping of samples to these EGA accessions can be found in the 'Sample Data Relationship Format' file of this ArrayExpress record. Information on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu
2015-09-30 | E-MTAB-3819 | biostudies-arrayexpress
Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 74 samples of primary cells or cultured primary cells of different haemopoeitc lineages from cord blood, venous blood, bone marrow and thymus are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. There are 32 EGA data set accessions, which can be found under the Comment[EGA_DATA_SET] column in the 'Sample Data Relationship Format' (SDRF) file of this ArrayExpress record (http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3827/E-MTAB-3827.sdrf.txt). Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. Likewise, mapping of samples to these EGA accessions can be found in the SDRF file. Please note that the raw data files for 11 sequencing runs have yet been deposited at EGA, so they are marked with \\ot available\\ under the Comment[SUBMITTED_FILE_NAME] field in the SDRF file, and were included for the sake of completeness. Further iInformation on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu\
2015-09-30 | E-MTAB-3827 | biostudies-arrayexpress
Project description:Bortezomib (BZM) is the first proteasome inhibitor approved for relapsed Mantle Cell Lymphoma (MCL) with durable responses seen in 30%-50% of patients. The biological basis for differences in response to BZM is not completely understood. Our previous work demonstrated marked differences in methylation between primary MCL and normal B cells. We hypothesized that a subset of aberrantly methylated genes may be modulating BZM response in MCL patients. We examined genome-wide DNA methylation profiles in MCL patient treated with BZM using a NimbleGen array platform. DNA methylation analysis revealed a striking promoter hypomethylation in MCL patient samples following BZM treatment. Pathway analysis of differentially methylated genes identified molecular mechanisms of cancer as a top canonical pathway enriched among hypomethylated genes in BZM treated samples. Noxa, a pro-apoptotic Bcl-2 family member essential for the cytotoxicity of BZM, was significantly hypomethylated and induced following BZM treatment. Therapeutically, we could demethylate Noxa and induce anti-lymphoma activity using BZM and the DNA methytransferase inhibitor Decitabine (DAC) and their combination in vitro and in vivo in BZM resistant MCL cells. Noxa depletion by RNA interference protected MCL cells from death by these agents. These findings suggest a role for dynamic Noxa methylation for therapeutic benefit of BZM. Potent and synergistic cytotoxicity between BZM and DAC in vitro and in vivo supports a strategy for using epigenetic priming to overcome BZM resistance in relapsed MCL patients. Our data demonstrate that genomic methylation profiling can provide mechanistic insights to guide novel therapeutic approaches.
2017-02-09 | GSE58165 | GEO
Project description:Data Access Committee EGAC00001001119
| EGAC00001001119 | EGA
Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.
2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress
Project description: Not available
| S-EPMC7000480 | biostudies-literature
Project description: Not available
| S-EPMC7302387 | biostudies-literature
Project description: Not available
| S-EPMC9761215 | biostudies-literature
Project description:SILAC analysis of fludarabine resistance in human Mino cells.
2015-08-03 | PXD002034 | Pride