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Links from GEO DataSets

Items: 20

1.

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: TXT
Series
Accession:
GSE45459
ID:
200045459
2.

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: CEL
Series
Accession:
GSE45461
ID:
200045461
3.

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: CEL
Series
Accession:
GSE45460
ID:
200045460
4.

DNA methylation data from mouse hematopoietic progenitors

(Submitter supplied) Genome-wide DNA methylation was studied to determine the methylome map of lymphoid and myeoloid commitment from hematopoietic progenitors We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in FACs purified mouse hematopoietic progeniors
Organism:
Mus musculus
Type:
Methylation profiling by genome tiling array
Platforms:
GPL10680 GPL10683
35 Samples
Download data: XYS
Series
Accession:
GSE23110
ID:
200023110
5.

A comprehensive methylome map of lineage commitment from hematopoietic progenitors

(Submitter supplied) Epigenetic modifications must underlie lineage-specific differentiation since terminally differentiated cells express tissue-specific genes, but their DNA sequence is unchanged. Hematopoiesis provides a well-defined model of progressive differentiation in which to study the role of epigenetic modifications in cell fate decisions. Multi-potent progenitors (MPPs) can differentiate into all blood cell lineages, while downstream progenitors commit to either myeloerythroid or lymphoid lineages. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
26 Samples
Download data: CEL
Series
Accession:
GSE20244
ID:
200020244
6.

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: CEL
Series
Accession:
GSE41493
ID:
200041493
7.

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 GPL9185 GPL9250
30 Samples
Download data: BED, FA, TXT
8.

Two-Track Epigenetic Remodeling and Backtracking to Embryonic Stem Cell Bivalency in B-cell Acute Lymphoblastic Leukemias

(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; Methylation profiling by high throughput sequencing
Platforms:
GPL13534 GPL11154 GPL6244
310 Samples
Download data: CEL
Series
Accession:
GSE56602
ID:
200056602
9.

WGBS data of pediatric B-cell acute leukemias

(Submitter supplied) We investigated DNA methylomes of 227 pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. The current study identified a link between DNA methylome of B-cell acute lymphoblastic leukemias (B-ALLs) and embryonic stem cell (ESC) bivalency, through which tumor cells can mimic the pluripotency of ESCs.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11154
2 Samples
Download data: TXT
Series
Accession:
GSE56601
ID:
200056601
10.

Methylation data of pediatric B-cell acute leukemias

(Submitter supplied) We investigated DNA methylomes of 227 pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. The current study identified a link between DNA methylome of B-cell acute lymphoblastic leukemias (B-ALLs) and embryonic stem cell (ESC) bivalency, through which tumor cells can mimic the pluripotency of ESCs.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
227 Samples
Download data: TXT
Series
Accession:
GSE56600
ID:
200056600
11.

Expression data of pediatric B-cell acute leukemias

(Submitter supplied) We investigated DNA methylomes of 227 pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. The current study identified a link between DNA methylome of B-cell acute lymphoblastic leukemias (B-ALLs) and embryonic stem cell (ESC) bivalency, through which tumor cells can mimic the pluripotency of ESCs.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
81 Samples
Download data: CEL
Series
Accession:
GSE56599
ID:
200056599
12.

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: TXT
Series
Accession:
GSE21415
ID:
200021415
13.

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: BEDGRAPH
Series
Accession:
GSE25689
ID:
200025689
14.

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: BEDGRAPH
Series
Accession:
GSE25688
ID:
200025688
15.

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: TXT
Series
Accession:
GSE25578
ID:
200025578
16.

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: BED
Series
Accession:
GSE38354
ID:
200038354
17.

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: TXT
Series
Accession:
GSE29189
ID:
200029189
18.

Analysis of DNA methylation dynamics at Alu elements during human B cell activation

(Submitter supplied) Paired-end sequencing of methylated DNA fragments in B cell subsets revealed widespread loss of methylation at Alu elements upon B cell activation.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL10999
2 Samples
Download data: BEDGRAPH
Series
Accession:
GSE42386
ID:
200042386
19.

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: PAIR
Series
Accession:
GSE24919
ID:
200024919
20.

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: PAIR
Series
Accession:
GSE24918
ID:
200024918
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