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Links from GEO DataSets

Items: 20

1.

ChIP-seq analysis of histone modifications and RNA polymerase II at 4 stages of directed cardiac differentiation of mouse embryonic stem cells

(Submitter supplied) We interrogated the genome-wide occupancy of histone modifications and RNA polymerase II at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of histone modifications during differentiation that are coordinated with stage-specific gene expression including a novel preactivation chromatin pattern found at genes associated with cardiac function. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
54 Samples
Download data: TXT, WIG
Series
Accession:
GSE47949
ID:
200047949
2.

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13112 GPL11002
62 Samples
Download data: BW, TXT, WIG
Series
Accession:
GSE47950
ID:
200047950
3.

RNA-seq analysis of global RNA levels at 4 stages of directed cardiac differentiation of mouse embryonic stem cells

(Submitter supplied) We interrogated the transcriptome using RNA-seq at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of mRNAs and long non-coding RNAs (lncRNAs) and identified groups of genes with similar expression patterns during differentiation.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11002
8 Samples
Download data: BW, TXT
Series
Accession:
GSE47948
ID:
200047948
4.

Cardiac transcription factors in HL-1 cells: gene expression and genome binding profiling

(Submitter supplied) [1] Gene expression profiling in Gata4, Mef2a knockdown in HL-1 cells. HL-1 cells infected with adenovirus expressing either control siRNA or Gata4, and Gata4 & Mef2a siRNA. [2] Genome-wide maps of cardiac transcription factors binding region in HL-1 cells. We performed bio-ChIP-seq using streptavidin beads immunoprecipitation of biotinylated 5 cardiac transcription factors (fbio) and P300 antibody ChIP-seq. more...
Organism:
Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9185 GPL6246
17 Samples
Download data: CEL, GFF, TXT
5.

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

(Submitter supplied) In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. more...
Organism:
Mus musculus
Type:
Other; Expression profiling by high throughput sequencing
Platforms:
GPL9318 GPL11002 GPL9250
8 Samples
Download data: MAP, TXT, XLS
6.

Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation [ChIP-exo]

(Submitter supplied) We investigated the genome-wide occupancy changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells of chromatin regulators and histone modifications.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
4 Samples
Download data: BW
Series
Accession:
GSE63976
ID:
200063976
7.

Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL13112
38 Samples
Download data: BED, BW
Series
Accession:
GSE45448
ID:
200045448
8.

Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation [ChIP-Seq]

(Submitter supplied) We investigated the genome-wide occupancy changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells of chromatin regulators and histone modifications.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
28 Samples
Download data: BED, BW
Series
Accession:
GSE45447
ID:
200045447
9.

Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation [RNA-Seq]

(Submitter supplied) We investigated the global gene expression changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
6 Samples
Download data: BW
Series
Accession:
GSE45446
ID:
200045446
10.

Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation

(Submitter supplied) The 3D organization of the genome is important for regulation of diverse nuclear processes ranging from transcription to DNA replication. Knowledge of the higher order chromatin structure is critical for understanding mechanisms of gene regulation by long-range control elements such as enhancers and insulators. We describe high resolution, genome-wide dynamic chromatin interaction maps in human embryonic stem cells (hESC) as they differentiate into four distinct embryonic cell lineages. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL11154 GPL16791
27 Samples
Download data: BEDGRAPH, VCF, XLS
11.

Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by array
4 related Platforms
27 Samples
Download data: BED, CEL
Series
Accession:
GSE70677
ID:
200070677
12.

Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [Retroviral scanning (MLV-Seq)]

(Submitter supplied) The rapidly expanding information on the structural and functional characteristics of the human genome allows the development of genome-wide approaches to investigate the molecular circuitry wiring the genetic and epigenetic programs of clinically relevant stem/progenitor cells. Here, we define the transcriptional and epigenetic profile of human hematopoietic stem/progenitor cells (HSPC) and their committed, early myeloid and erythroid progeny. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL9186
3 Samples
Download data: BED
13.

Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [ChIP-Seq]

(Submitter supplied) The rapidly expanding information on the structural and functional characteristics of the human genome allows the development of genome-wide approaches to investigate the molecular circuitry wiring the genetic and epigenetic programs of clinically relevant stem/progenitor cells. Here, we define the transcriptional and epigenetic profile of human hematopoietic stem/progenitor cells (HSPC) and their committed, early myeloid and erythroid progeny. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL10999 GPL11154
12 Samples
Download data: BED
Series
Accession:
GSE70675
ID:
200070675
14.

Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [RNA-seq (CAGE)]

(Submitter supplied) The rapidly expanding information on the structural and functional characteristics of the human genome allows the development of genome-wide approaches to investigate the molecular circuitry wiring the genetic and epigenetic programs of clinically relevant stem/progenitor cells. Here, we define the transcriptional and epigenetic profile of human hematopoietic stem/progenitor cells (HSPC) and their committed, early myeloid and erythroid progeny. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL10999
3 Samples
Download data: TXT
Series
Accession:
GSE70674
ID:
200070674
15.

Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [Microarray]

(Submitter supplied) The rapidly expanding information on the structural and functional characteristics of the human genome allows the development of genome-wide approaches to investigate the molecular circuitry wiring the genetic and epigenetic programs of clinically relevant stem/progenitor cells. Here, we define the transcriptional and epigenetic profile of human hematopoietic stem/progenitor cells (HSPC) and their committed, early myeloid and erythroid progeny. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL19633
9 Samples
Download data: CEL
Series
Accession:
GSE64888
ID:
200064888
16.

ChIP-chip for histone modifications in hESCs and differentiated hESCs

(Submitter supplied) The objective of this study was to identify how histone modifications are differentially marked at promoter and enhancer elements in hESCs before and after differentiation to understand the regulatory mechanisms that defined pluripotency and early differentiation.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by genome tiling array
29 related Platforms
94 Samples
Download data: CEL, GFF, PAIR
Series
Accession:
GSE30434
ID:
200030434
17.

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL570
31 Samples
Download data: BEDGRAPH, CEL, CHP
Series
Accession:
GSE75232
ID:
200075232
18.

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (Dnase-Seq)

(Submitter supplied) DHS enahncers to identify novel pathways in OB differentiation
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
10 Samples
Download data: BEDGRAPH, CSV
Series
Accession:
GSE75231
ID:
200075231
19.

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (microarray)

(Submitter supplied) DHS enahncers identify novel pathways in OB differentiation
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
21 Samples
Download data: CEL, CHP
Series
Accession:
GSE75230
ID:
200075230
20.

Gene expression profiles of mouse ESC cardiomyocyte-specific differentiation

(Submitter supplied) The differentiation to cardiomyocytes is a prerequisite and an important part of heart development. A good understanding of the complicated cardiomyocyte differentiation process benefits cardiogenesis study. Embryonic stem cells (ESCs), cell lines with infinite ability to proliferate and to be differentiated into all cell types of the adult body, are important research tools for investigation of differentiation and meanwhile good models for developmental research. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6096
8 Samples
Download data: CEL, TXT
Series
Accession:
GSE58300
ID:
200058300
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