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    Results: 20

    1.

    A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network.

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array; Methylation profiling by array
    Platforms:
    GPL6244 GPL13534
    53 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE45461
    ID:
    200045461
    2.

    Expression data from early human B-cell development

    (Submitter supplied) A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res. 2012 Dec;40(22):11339-51. We examined DNA methylation and RNA expression status during early B-cell development by sorting multiple replicates of four separate stages of pre-B cells derived from normal human fetal bone marrow and applied high-dimension DNA methylation scanning and expression arrays. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL6244
    31 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE45460
    ID:
    200045460
    3.

    DNA Methylation data from early human B-cell development

    (Submitter supplied) A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res. 2012 Dec;40(22):11339-51. We examined DNA methylation and RNA expression status during early B-cell development by sorting multiple replicates of four separate stages of pre-B cells derived from normal human fetal bone marrow and applied high-dimension DNA methylation scanning and expression arrays. more...
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by array
    Platform:
    GPL13534
    22 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE45459
    ID:
    200045459
    4.

    Expression data from Hodgkin lymphoma cell lines L-428 and L-1236: L-428 and L-1236 cells were transduced with tGFP-EBF1 or as control tGFP-only.

    (Submitter supplied) The transcription factor network in Hodgkin lymphoma (HL) represents a unique composition of proteins found in no other hematopoietic cell. An aberrant downregulation of the B cell transcription factor EBF1 is observed in the B cell-derived Hodgkin and Reed/Sternberg (HRS) tumor cells. Herein, we elucidated the consequences of the down regulation of this factor in HL. To obtain a more comprehensive overview of EBF1 regulated genes in cHL cell lines, we performed a gene chip analysis comparing gene expression in tGFP-EBF1-transduced L-1236 and L-428 cells compared to samples transduced with vectors encoding only tGFP.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL6244
    12 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE41493
    ID:
    200041493
    5.

    Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Mus musculus
    Type:
    Expression profiling by array; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platforms:
    GPL6887 GPL9185
    28 Samples
    Download data:
    GEO (BEDGRAPH)
    Series
    Accession:
    GSE25689
    ID:
    200025689
    6.

    Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (MAP-Seq and ChIP-Seq data)

    (Submitter supplied) Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, about 50% of all CGIs are remote from annotated promoters, but nevertheless often have promoter-like features. To document the role of CGI methylation in cell differentiation, we analysed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. more...
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
    Platform:
    GPL9185
    10 Samples
    Download data:
    GEO (BEDGRAPH), SRA SRP004771
    Series
    Accession:
    GSE25688
    ID:
    200025688
    7.

    Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (gene expression data)

    (Submitter supplied) Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, about 50% of all CGIs are remote from annotated promoters, but nevertheless often have promoter-like features. To document the role of CGI methylation in cell differentiation, we analysed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Platform:
    GPL6887
    18 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE25578
    ID:
    200025578
    8.

    Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development

    (Submitter supplied) To further our understanding of the role of DNA methylation in development, Methylated DNA Immunoprecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis. Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). more...
    Organism:
    Mus musculus
    Type:
    Methylation profiling by genome tiling array
    Platform:
    GPL7060
    26 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE21415
    ID:
    200021415
    9.

    Genome-Wide DNA Methylation Profiles in Hematopoietic Stem and Progenitor Cells Reveal Over-Representation of ETS Transcription Factor Binding Sites

    (Submitter supplied) DNA methylation is an essential epigenetic mark that is required for normal development. Knockout of the DNA methyltransferase enzymes in the mouse hematopoietic compartment reveals that methylation is critical for hematopoietic differentiation. To better understand the role of DNA methylation in hematopoiesis, we characterized genome-wide DNA methylation in primary mouse hematopoietic stem cells (HSC), common myeloid progenitors (CMP), and erythroblasts (ERY). more...
    Organism:
    Mus musculus
    Type:
    Methylation profiling by high throughput sequencing
    Platform:
    GPL9185
    6 Samples
    Download data:
    GEO (BED), SRA SRP013455
    Series
    Accession:
    GSE38354
    ID:
    200038354
    10.

    Genome-scale DNA methylation profiling of TEL/AML positive childhood acute lymphoblastic leukaemia

    (Submitter supplied) DNA methylation profiling of 48 samples to determine a DNA methylation signature specific to leukaemic bone marrow samples. Matching Leukaemia bone marrow and day 28 remission bone marrow or post induction follow up (follow up up to 2 years post induction) genomic DNA were extracted from archived microscope smear slides from 11 children diagnosed with TEL/AML positive Acute Lymphoblastic Leukaemia (ALL). more...
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by array
    Platform:
    GPL8490
    48 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE29189
    ID:
    200029189
    11.

    A global network of transcription factors, involving E2A, EBF1 and FOXO1, that orchestrates the B cell fate

    (Submitter supplied) It is now established that the transcription factors E2A, EBF1 and Foxo 1 play critical roles in B cell development. Here we show that E2A and EBF1 bound regulatory elements present in the Foxo1 locus. E2A and EBF1 as well as E2A and Foxo1, in turn, were wired together by a vast spectrum of cis-regulatory codes. These associations were dynamic during developmental progression. Occupancy by the E2A isoform, E47, directly elevated the abundance as well as the pattern of histone H3K4 monomethylation across putative enhancer regions. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
    Platforms:
    GPL7202 GPL9250 GPL9185
    30 Samples
    Download data:
    GEO (BED, FA, TXT), SRA SRP002585
    Series
    Accession:
    GSE21978
    ID:
    200021978
    12.

    methylatedDNA_peripheralBlood

    (Submitter supplied) The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters Keywords: DNA methylation, Methylated CpG island amplification coupled with promoter arrays, normal tissue
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array
    4 related Platforms
    4 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE8810
    ID:
    200008810
    13.

    B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array; Methylation profiling by genome tiling array
    Platforms:
    GPL10671 GPL10191
    68 Samples
    Download data:
    GEO (PAIR)
    Series
    Accession:
    GSE24919
    ID:
    200024919
    14.

    B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [DNA methylation profiling]

    (Submitter supplied) DNA methylation profiling of human B cell populations representing a developmental series before and after immune activation. The B cells are derived from inflamed tonsils. The B cells were already activated in vivo in patients, therefore there was no need to stimulate the B cells after isolation. Gene expression profiling was also performed from the same samples.
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array
    Platform:
    GPL10671
    32 Samples
    Download data:
    GEO (PAIR)
    Series
    Accession:
    GSE24918
    ID:
    200024918
    15.

    B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [gene expression profiling]

    (Submitter supplied) DNA methylation profiling of human B cell populations representing a developmental series before and after immune activation. The B cells are derived from inflamed tonsils. The B cells were already activated in vivo in patients, therefore there was no need to stimulate the B cells after isolation. Gene expression profiling was also performed from the same samples.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL10191
    36 Samples
    Download data:
    GEO (PAIR)
    Series
    Accession:
    GSE24863
    ID:
    200024863
    16.

    Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing

    (Submitter supplied) We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from CLL patient and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1764 gene promoters were identified as being differentially methylated between the two groups. more...
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by high throughput sequencing
    Platform:
    GPL10999
    17 Samples
    Download data:
    GEO (BED), SRA SRP008815
    Series
    Accession:
    GSE32698
    ID:
    200032698
    17.

    Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation

    (Submitter supplied) The study investigated the changes in DNA-methylation and gene expression during granulopoiesis. To this end CMP, GMP, PMC and PMN cell populations were isolated by FACS from bone marrow from healthy donors and analysed by CAGE as well as expression and DNA microarrays.
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by genome tiling array
    Platform:
    GPL13534
    12 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE50797
    ID:
    200050797
    18.

    Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation [expression]

    (Submitter supplied) The study investigated the changes in DNA-methylation and gene expression during granulopoiesis. To this end CMP, GMP, PMC and PMN cell populations were isolated by FACS from bonemarrow from healty donors and analysed by CAGE as well as expression and DNA microarrays
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL10904
    20 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE49883
    ID:
    200049883
    19.

    High-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers

    (Submitter supplied) Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. more...
    Organism:
    Homo sapiens
    Type:
    Methylation profiling by high throughput sequencing
    Platform:
    GPL9052
    17 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE29071
    ID:
    200029071
    20.

    Illumina gene expression beadchips of human ES cell lines

    (Submitter supplied) Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL5060
    15 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE29070
    ID:
    200029070

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