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Links from GEO DataSets

Items: 20

1.

Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [ChIP-Seq]

(Submitter supplied) Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9115
13 Samples
Download data: BED, TXT
Series
Accession:
GSE39538
ID:
200039538
2.

Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [RNA-Seq]

(Submitter supplied) Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9115
1 Sample
Download data: BED, RPKM
3.

Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis

(Submitter supplied) Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9115
14 Samples
Download data: BED, RPKM, TXT
Series
Accession:
GSE39229
ID:
200039229
4.

Chromatin Signatures in Multipotent Human HSCs Indicate the Fate of Bivalent Genes during Differentiation

(Submitter supplied) Histone modifications have been implicated in stem cell maintenance and differentiation. We have analyzed genome-wide changes in gene expression and histone modifications during differentiation of multipotent human primary hematopoietic stem cells/progenitor cells (HSCs/HPCs) into erythrocyte precursors. Our data indicate that H3K4me1, H3K9me1, and H3K27me1 associate with enhancers of differentiation genes prior to their activation and correlate with basal expression, suggesting that these monomethylations are involved in the maintenance of activation potential required for differentiation. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL9052 GPL570
24 Samples
Download data: BED, CEL, CHP, TXT
5.

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

(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:
GPL19832 GPL10999
20 Samples
Download data: CEL, WIG
Series
Accession:
GSE71031
ID:
200071031
6.

H3K4me3 and H3K27me3 ChIP-seq profiling in MCF7 cell lines under hypoxia and reoxygenation

(Submitter supplied) Purpose: Study hypoxia and reoxygenation induced changes in genome-wide H3K4me3 and H3K27me3 occupancy Methods: Using the MCF7 breast epithelial adenocarcinoma cell line as a model, we studied epigenomic reprogramming as a function of fluctuating oxygen tension. To this end, we combined chromatin-immunoprecipitation and deep-sequencing analysis to identify H3K4me3-marks and H3K27me3-marks in MCF7 cells subjected to changes in oxygenation (i.e. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10999
8 Samples
Download data: WIG
Series
Accession:
GSE71030
ID:
200071030
7.

Gene expression profiling in MCF7 cell lines under hypoxia and reoxygenation

(Submitter supplied) Purpose: Study hypoxia and reoxygenation induced changes in genome-wide gene expression Methods: Using the MCF7 breast epithelial adenocarcinoma cell line as a model, we studied epigenomic reprogramming as a function of fluctuating oxygen tension. To this end, we performed a transcriptomics analysis in MCF7 cells subjected to changes in oxygenation (i.e. acute hypoxia, chronic hypoxia, reoxygenation). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL19832
12 Samples
Download data: CEL
Series
Accession:
GSE70805
ID:
200070805
8.

Hierarchical chromatin regulation during blood formation uncovered by single-cell sortChIC

(Submitter supplied) Post-translational histone modifications modulate chromatin packing to regulate gene expression. How chromatin states, both at euchromatic and at heterochromatic regions, underlie cell fate decisions in single cells is relatively unexplored. We develop sort assisted single-cell chromatin immunocleavage (sortChIC) and apply it to map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in hematopoietic stem and progenitor cells (HSPCs), and mature blood cells in the mouse bone marrow. more...
Organism:
Homo sapiens; Mus musculus
Type:
Other
Platforms:
GPL18573 GPL19057
106 Samples
Download data: BAM, CSV, TXT
Series
Accession:
GSE164779
ID:
200164779
9.

Geminin regulates self-renewal and fate commitment decisions in fetal hematopoietic stem cells.

(Submitter supplied) Conditional deletion of Geminin from the entire hematopoietic compartment using Vav1:iCre mice led to defective hematopoiesis/dyserythropoiesis in E15.5 mouse embryos. The present data set includes data from lineage-negative cells isolated from homogenized livers that were dissected from E15.5.dpc embryos. The two conditions compared were wild-type versus Geminin-KO Lin- cells. The cells were collected from littermates.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
6 Samples
Download data: CEL
Series
Accession:
GSE53056
ID:
200053056
10.

H2AZ extended acidic patch is necessary for formation specialized chromatin states in ESCs

(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
9 Samples
Download data: BED, BIGWIG
Series
Accession:
GSE40065
ID:
200040065
11.

H2AZ extended acidic patch is necessary for formation specialized chromatin states in ESCs [RNA-Seq]

(Submitter supplied) The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
6 Samples
Download data: TXT
Series
Accession:
GSE40064
ID:
200040064
12.

H2AZ extended acidic patch is necessary for formation specialized chromatin states in ESCs [ChIP-Seq]

(Submitter supplied) The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11002
3 Samples
Download data: BED, BIGWIG
Series
Accession:
GSE40063
ID:
200040063
13.

Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells

(Submitter supplied) Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells. Mouse embryonic stem cells (E14) were guided differentiated into mesoendoderm lineages by activin-A induction. cells in three time points (day0, day4 and day6) were collected. The genome-wide studies on three cell types were summerized as following: cytosine methylation data were generated using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq); DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms
36 Samples
Download data: BAM, BED, GTF, TXT
Series
Accession:
GSE38596
ID:
200038596
14.

Distinct features in establishing H3K4me3 and H3K27me3 in pre-implantation embryos

(Submitter supplied) Histone modifications play critical roles in regulating developmental genes expression during embryo development in mammals1,2. However, genome-wide analysis of histone modifications in pre-implantation embryos has been impeded by technical difficulties and the scarcity of required materials. Here, by using a small-scale chromatin immunoprecipitation sequencing (ChIP-seq) method3, for the first time, we mapped the genome-wide profile of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3), associated with gene activation and repression respectively, in mouse pre-implantation embryos. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
67 Samples
Download data: BW
Series
Accession:
GSE73952
ID:
200073952
15.

Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming.

(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; Methylation profiling by high throughput sequencing
Platform:
GPL13112
191 Samples
Download data: BW, FPKM_TRACKING, TXT
Series
Accession:
GSE70608
ID:
200070608
16.

Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency

(Submitter supplied) Around implantation, the epiblast transits from naïve to primed pluripotency, before giving rise to the three germ layers. How chromatin is reconfigured during this developmental window remains poorly understood. We performed a genome-wide investigation of chromatin landscapes during this period. We find that enhancers in ectoderm are already pre-accessible in embryonic day 6.5 (E6.5) Epi when cells enter a primed pluripotent state. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other
Platforms:
GPL21273 GPL17021
104 Samples
Download data: BED, HIC, TXT
Series
Accession:
GSE125318
ID:
200125318
17.

Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL1261 GPL9485
83 Samples
Download data: CEL, GFF, PAIR
Series
Accession:
GSE18737
ID:
200018737
18.

miniChIP-chip of murine hematopoietic stem cells and progeny with H3K4me3, H3K79me2, H3K9/14ac, H3K27me3, H3K9me3, PolII

(Submitter supplied) This study describes the changes in epigenetic chromatin modifications during murine hematopoietic stem cell differentiation in vivo using a modified miniChIP-chip technology. We have addressed issues including bivalent (H3K4me3/H3K27me3) modifications, lineage priming hypothesis, and stem cell chromatin properties in our study described in Weishaupt et al., 2009 (Blood)
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL9485
71 Samples
Download data: GFF, PAIR
Series
Accession:
GSE18734
ID:
200018734
19.

Analysis of murine hematopoieitic stem cells, multipotent progenitors, PreMegE progenitors and mature CD4+ T cells

(Submitter supplied) An investigation of the global gene expression signatures of murine hematopoietic stem cell differentiation during steady state hematopoiesis. This data compliments the miniChIP-chip data obtained from the same cell types as described in Weishaupt et al., 2009 (Blood).
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
12 Samples
Download data: CEL
Series
Accession:
GSE18669
ID:
200018669
20.

Unique cell cycle-dependent variations in the pluripotent epigenetic landscape define novel cohorts of temporal expressed bivalent genes during hESCs differentiation

(Submitter supplied) By mapping the genomic enrichments  of H3K4me3 and H3K27me3 modifications in pure populations of hESCs during the G2, mitotic and G1 phases of the cell cycle, we characterize cell cycle-dependent variations in the epigenetic landscape of bivalent genes, altering the current view of mitotic inheritance in pluripotent cells. We identified novel classes of bivalent domains that are highly enriched with H3K4me3 during mitosis, depleted during G1 only, and ubiquitously bivalent. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL15433 GPL9115
24 Samples
Download data: BW, TXT
Series
Accession:
GSE55502
ID:
200055502
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