{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Affymetrix U219"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000472"],"sample_count":["219"],"description":["EGA dataset EGAD00010000472"],"repository":["EGA"],"title":["Title not provided"],"pubmed_abstract":["Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes-most of which are not differentially expressed-exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences."],"pubmed_title":["Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia."],"pubmed_authors":["Ferreira Pedro G PG, Jares Pedro P, Rico Daniel D, Gómez-López Gonzalo G, Martínez-Trillos Alejandra A, Villamor Neus N, Ecker Simone S, González-Pérez Abel A, Knowles David G DG, Monlong Jean J, Johnson Rory R, Quesada Victor V, Djebali Sarah S, Papasaikas Panagiotis P, López-Guerra Mónica M, Colomer Dolors D, Royo Cristina C, Cazorla Maite M, Pinyol Magda M, Clot Guillem G, Aymerich Marta M, Rozman Maria M, Kulis Marta M, Tamborero David D, Gouin Anaïs A, Blanc Julie J, Gut Marta M, Gut Ivo I, Puente Xose S XS, Pisano David G DG, Martin-Subero José Ignacio JI, López-Bigas Nuria N, López-Guillermo Armando A, Valencia Alfonso A, López-Otín Carlos C, Campo Elías E, Guigó Roderic R"],"name_synonyms":["leukemia, CLL, Cll, small lymphocytic lymphoma, c15, B-cell chronic lymphocytic leukemia, DmelCG7937, CG7937., Chronic Lymphocytic Leukemia, chronic LYMPHOCYTIC, lymphoplasmacytic leukaemia, 311, lymphoplasmacytic leukemia, adult chronic leukaemia, chronic, B-cell chronic lymphocytic leukaemia, Ect5, cll, CML, Hox11-311, 93Bal, B-cell chronic lymphoid leukemia, adult chronic leukemia, microarray, chronic lymphocytic leukaemia, chronic lymphatic leukemia, lymphocytic, chronic lymphatic leukaemia, chronic lymphatic"],"pubmed_title_synonyms":["Lymphoplasmacytoid Lymphomas, CLL Lymphoplasmacytoid Lymphomas, CLL, Chronic B-Cell Leukemia, Chronic B-Cell, RNA Sequence Determination, Lymphocytic Leukemia, Transcriptome Profile, Sequence Determination, RNA Sequence, B-Lymphocytic Leukemias, chronic LYMPHOCYTIC, Chronic B-Lymphocytic, Gene Expression Profile, Gene, B-Cell, Lymphatic Leukemia, Profiles, B-cell chronic lymphocytic leukaemia, B Cell, Small, B-cell chronic lymphoid leukemia, Chronic B-Cell Leukemias, Well-Differentiated Lymphocytic, Lymphoplasmacytoid Lymphoma, Analysis, Well Differentiated, Chronic Lymphocytic Leukemias, Lymphomas, chronic lymphatic, Low-Grade, Lymphocytic, Leukemia, B-cell chronic lymphocytic leukemia, Analyses, Malignancy, Determination, Small-Cell Lymphomas, Profile, CLL Lymphoplasmacytoid Lymphoma, Plasmacytoid, Small Lymphocytic Lymphoma, Well-Differentiated Lymphocytic Lymphoma, Small-Cell Lymphoma, B-Lymphocytic Leukemia, B Cell., Sequence Determinations, Signatures, Sequencing, Diffuse, Lymphoblastic Leukemias, Chronic Lymphatic Leukemias, RNA Sequence Analyses, Disrupted In B Cell Malignancy, Expression Signature, Transcriptomes, RNA Sequencing, Chronic, Diffuse Well Differentiated Lymphocytic Lymphoma, Malignancies, Chronic B-Lymphocytic Leukemias, chronic lymphatic leukaemia, Chronic Lymphocytic, Diffuse Well-Differentiated Lymphocytic Lymphoma, Low Grade, Sequence Analyses, leukemia, B-Cell Chronic Lymphocytic Leukemia, RNA, Transcriptome, RNA Sequence Determinations, B Cell Malignancy, Small Cell, Expression Profiles, Chronic Lymphocytic Leukemia, Chronic B-Lymphocytic Leukemia, lymphoplasmacytic leukaemia, B-Cell Malignancy, Low-Grade B-Cell Malignancies, Chronic Lymphoblastic Leukemia, lymphoplasmacytic leukemia, Leukemias, chronic, B-Cell Leukemia, Determinations, Gene Expression, Well-Differentiated, Chronic Lymphatic, Small Cell Lymphoma, Expression Signatures, Gene Expression Signatures, Lymphocytic Leukemias, B-Cell Malignancies, B Lymphocytic Leukemia, B Cell Chronic Lymphocytic Leukemia, chronic lymphatic leukemia, Gene Expression Signature, B Cell Leukemia, lymphocytic, Expression Profile, Low-Grade B-Cell, Transcriptome Profiles, Lymphoblastic Leukemia, Chronic Lymphatic Leukemia, small lymphocytic lymphoma, Lymphatic Leukemias, Lymphocytic Lymphomas, Well-Differentiated Lymphocytic Lymphomas, B-Cell Leukemias, Disrupted In B-Cell Malignancy, Lymphoblastic, Chronic Lymphoblastic, Small Lymphocytic, Chronic Lymphoblastic Leukemias, Low-Grade B-Cell Malignancy, Small-Cell, Lymphocytic Lymphoma, Gene Expression Profiles, Lymphoplasmacytoid, CLL Lymphoplasmacytoid, RNA Sequence Analysis, Lymphoma, chronic lymphocytic leukaemia, Signature, Small Lymphocytic Lymphomas"],"description_synonyms":["leukemia, CLL, Cll, small lymphocytic lymphoma, c15, B-cell chronic lymphocytic leukemia, DmelCG7937, Chronic Lymphocytic Leukemia, chronic LYMPHOCYTIC, lymphoplasmacytic leukaemia, 311, lymphoplasmacytic leukemia, adult chronic leukaemia, chronic, B-cell chronic lymphocytic leukaemia, Ect5, cll, CML, Hox11-311, 93Bal, microarray., B-cell chronic lymphoid leukemia, adult chronic leukemia, chronic lymphocytic leukaemia, chronic lymphatic leukemia, lymphocytic, chronic lymphatic leukaemia, chronic lymphatic, CG7937"],"pubmed_abstract_synonyms":["B Cells, Materials, Node, RNA Sequence Determination, determination, Bursa-Dependent Lymphocytes, Sequence Determination, Globulin, RNA Sequence, Immune Globulin, B cell, ribosomal RNA, Long Term, element, diseases, Processed Genes, spliceosome, Multicatalytic Endopeptidase Complex, BCR, diseases and disorders, CG40494, Whole Transcriptome, Transcriptome Sequencing, Analysis, Effect, chronic lymphatic, BCR1, Lymph, average, Pseudogene, treatment, human disease, thymus nucleic acid, Gene Expressions, B-cell chronic lymphocytic leukemia, Genomes, Analyses, Determination, Macropain, beta-Tubulin Pseudogenes, Multivariate Analyses, Complete Exome Sequencing, Whole Transcriptome Sequencing, beta-Tubulin, Lymph., Sequence Determinations, Proteasome Endopeptidase, 20S Proteasome, adult chronic leukaemia, AI853148, geographical area, Immune, B lymphocyte, disease management, adult chronic leukemia, Therapies, 26S proteasome, Homo sapiens disease, Pseudogenes, Double-Stranded DNA, deoxyribonucleic acids, chronic lymphatic leukaemia, DNAn, B Lymphocyte, spliceosome complex, Long-Term Effects, protein-coding, single-organism behavior, Therapy, Proteinase, Endopeptidase Complex, Process, B Lymphocytes, lymphatic system, Exome, Longterm Effect, RNA-seq, Lymphocyte B-Cell, Double-Stranded, lymphoplasmacytic leukemia, Acceptance Processes, Determinations, (Deoxyribonucleotide)n+m, D22S662, Acceptance Process, Ingensin, Diseases, Genetic Materials, atomo, chronic lymphatic leukemia, lymphocytic, atome, desoxyribose nucleic acid, Genetic Material, activation, AI561783, proteasome, Complete Transcriptome, Element, positional polypeptide feature, atoms, Heterogeneity, whole genome, Treatments, CG17960, disease, immunoglobulin, Patient, B-Lymphocyte, Material, ds DNA, Nodes, Whole Exome Sequencing, Spliceosome, chronic lymphocytic leukaemia, Cistron, Globulins, DNA, Transcriptome Sequencings, Dmel_CG00000, CLL, Cll, other disease, Bursa-Dependent, nuclear mRNA cis splicing, DNS, Immunoglobulin, (Deoxyribonucleotide)n, Complete Exome, region or site annotation, Effects, Processes, 5133400C09Rik, chronic LYMPHOCYTIC, B-Cell, Gene, high weight, Lymphocyte B-Cells, B-cell chronic lymphocytic leukaemia, Deoxyribonucleic acids, Processed, cll, CML, antibody, Multicatalytic Proteinase, CG17617, Deoxyribonucleic Acid, B-cell chronic lymphoid leukemia, Genetic heterogeneity, heavy, disease or disorder, Whole Transcriptome Shotgun Sequencing, rhoGAP1A, DmelCG40494, WES, positional, B-cell, Complete, Exome Sequencings, Genetic, Longterm, beta-Tubulin Pseudogene, D22S11, Bursa Dependent Lymphocytes, Complex, Double Stranded, PHL, Deoxyribonucleic acid, Long-Term, EG:23E12.5, Expressions, Sequencing, EG:23E12.2, Ect5, non-neoplastic, via U2-type spliceosome, Whole Exome, Multicatalytic Endopeptidase, RNA Sequence Analyses, Multicatalytic, Clients, Whole, Macroxyproteinase, disorder, RNA Sequencing, Long-Term Effect, Expression, (Deoxyribonucleotide)m, elements, Behaviors, atom, Lymphocyte, CG7937, Sequence Analyses, leukemia, ALL, RNA, Complete Exome Sequencings, RNA Sequence Determinations, DNAn+1, disorders, Chronic Lymphocytic Leukemia, lymphoplasmacytic leukaemia, 311, medical condition, Cistrons, Client, Immune Globulins, chronic, Cell, Multivariate, Proteasome, Exome Sequencing, 93Bal, Long Term Effects, chemical analysis, CG40453, sequence, condition, atomus, ds-DNA, membrane bound ribosome, Processed Gene, nodus lymphaticus, free ribosome, opsonin activity, Acceptance, small lymphocytic lymphoma, Ribosome, c15, Genes, Complete Transcriptome Sequencing, Bursa-Dependent Lymphocyte, Exhibit, Lymph Node, Prosome, DmelCG7937, Lymphocytes, Bursa-Equivalent Lymphocyte, 20S, primary structure of sequence macromolecule, Longterm Effects, B-Cells, Lymph node, Hox11-311, Therapeutic, RNA Sequence Analysis, B cell receptor activity, Desoxyribonukleinsaeure, Treatment, lymph gland, assay, mKIAA3017, B-lymphocyte, variable, multicatalytic endopeptidase, beta Tubulin Pseudogene, proteasome endopeptidase complex"],"additional_accession":[]},"is_claimable":false,"name":"U219-array-CLL-00001000374 - samples","description":"CLL Expression Array","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAD00010000472","cross_references":{"TAXONOMY":["9606"],"pubmed":["24265505"],"EGA":["EGAC00001000010","EGAS00001000374"]}}