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Links from GEO DataSets

Items: 20

1.

Gene expression in unfertilized eggs and the MBT stage of zebrafish embryos

(Submitter supplied) Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL9998
7 Samples
Download data: TXT
Series
Accession:
GSE20137
ID:
200020137
2.

Marking of the genome by H3K4 methylation prior to embryonic gene activation

(Submitter supplied) Early zebrafish embryo development proceeds first from a maternally transcribed and stored mRNAs, and zygotic gene activation (ZGA) is initiated at the mid-blastula transition (MBT; 1000-cell stage), 3.3 h post-fertilization. Very little is known on how the zygotic genome is programmed for transcriptional activation at the MBT. To start addressing this issue, we have mapped by ChIP-chip genome-wide promoter histone methylation (H3K4me3, H3K9me3, H3K27me3, H3K36me3) and RNA Pol II profiles before ZGA (256-cell stage; 2.5 hpf), during ZGA (MBT; 3.5 hpf)) and after ZGA (Post-MBT; 5.3 hpf) . more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10835
25 Samples
Download data: PAIR
Series
Accession:
GSE27314
ID:
200027314
3.

Chromatin signature of embryonic pluripotency is established during zygotic genome activation [Danio rerio]

(Submitter supplied) [PROJECT] After fertilization the embryonic genome is inactive until transcription is initiated during the maternal-zygotic transition (MZT). This universal process coincides with the formation of pluripotent cells, which in mammals can be used to generate embryonic stem (ES) cells. To study the changes in chromatin structure that accompany zygotic genome activation and pluripotency, we mapped the genomic locations of histone H3 modifications before and after MZT in zebrafish embryos. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL9970
12 Samples
Download data: PAIR, WIG
Series
Accession:
GSE20023
ID:
200020023
4.

H3K4me3 and H3K27me3 modification profiling in early zebrafish embryo

(Submitter supplied) Multicellular organism requires concise gene regulation during ontogeny and epigenetic modifications, such as DNA methylation and histone modification, facilitate the concise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described but knowledge of how histone modifications are passed on to zygote from gametes are limited and conservations of histone modifications are not clear.We profiled H3K4me3/H3K27me3 modifications in gametes and early embryos in zebrafish and find out that patterns in gene promoter regions have been largely set to either bivalent or active states in gametes and then passed on to zygote. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL23085
29 Samples
Download data
Series
Accession:
GSE110663
ID:
200110663
5.

The S-adenosyl-homosteine hydrolase inhibitor DZNeP unspecifically affects histone methylation patterns in embryos and results in developmental aberrations

(Submitter supplied) 3-deazaneplanocin A (DZNeP) is a promising cancer drug affecting the methylation status of histone lysine residues. To investigate the specificity and mode of action of DZNeP, zebrafish embryos displaying high histone methyltransferase activity were cultured with DZNeP and histone methylation (H3K4me3, H3K9me3, H3K27me3) was mapped by ChIP-chip genome-wide promoter at post-MBT stage (5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10835
6 Samples
Download data: PAIR
Series
Accession:
GSE53209
ID:
200053209
6.

The genomic landscape of histone modifications in human T cells.

(Submitter supplied) To understand the molecular basis that supports the dynamic gene expression programs unique to T cells, we investigated the genomic landscape of activating histone modifications, including histone H3 K9/K14 diacetylation (H3K9acK14ac), H3 K4 trimethylation (H3K4me3), and the repressive histone modification H3 K27 trimethylation (H3K27me3) in primary human T cells. We show that H3K9acK14ac and H3K4me3 are associated with active genes required for T cell function and development, whereas H3K27me3 is associated with silent genes that are involved in development in other cell types. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL4812
2 Samples
Download data
Series
Accession:
GSE6981
ID:
200006981
7.

Genome-wide identification of putative cis-regulatory elements through epigenetic profiling in zebrafish

(Submitter supplied) In this study, we have applied ChIP-Seq to identify putative regulatory elements throughout the zebrafish genome. For this purpose we identified sequences within the zebrafish genome that associate with H3K4me1 and H3K4me3, which are epigenetic modifications known to be associated with active cis-regulatory elements in other species.
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10164
6 Samples
Download data: BED, WIG
Series
Accession:
GSE20600
ID:
200020600
8.

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
9.

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
10.

Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

(Submitter supplied) In mature human sperm, genes of importance for embryo development (i.e. transcription factors) lack DNA methylation and bear nucleosomes with distinctive histone modifications, suggesting the specialized packaging of these developmental genes in the germline. Here, we explored the tractable zebrafish model and found conceptual conservation as well as several new features. Biochemical and mass spectrometric approaches reveal the zebrafish sperm genome packaged in nucleosomes and histone variants (and not protamine), and we find linker histones high and H4K16ac absent - key factors which may contribute to genome condensation. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array; Expression profiling by array
Platforms:
GPL6600 GPL7302 GPL6601
38 Samples
Download data: TXT
Series
Accession:
GSE26609
ID:
200026609
11.

Zebrafish promoter microarrays identify actively transcribed embryonic genes

(Submitter supplied) We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody directed against tri-methylated lysine 4 of Histone H3, we demonstrate the feasibility of this method in zebrafish. This approach will allow investigators to determine the genomic binding locations of DNA interacting proteins during development and expedite the assembly of the genetic networks that regulate embryogenesis. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL3766 GPL3767
6 Samples
Download data
Series
Accession:
GSE4863
ID:
200004863
12.

Genome-wide Promoter Mapping of Histone H3 Lysine 4 and Lysine 27 Methylation in Preimplantation Embryos

(Submitter supplied) First lineage specification in the mammalian blastocyst embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to the embryo proper and extraembryonic tissues. We show histone methylation asymmetry on promoters in the first two developmental lineages, and highlight epigenetic skewing associated with derivation of embryonic stem (ES) cells.
Organism:
Mus musculus
Type:
Methylation profiling by genome tiling array
Platform:
GPL8943
16 Samples
Download data: PAIR
Series
Accession:
GSE17387
ID:
200017387
13.

UTX_CHIP_FIBROBLASTS

(Submitter supplied) The recent discovery of a large number of histone demethylases suggests a central role for these enzymes in regulating histone methylation dynamics. Histone H3K27 trimethylation (H3K27me3) has been linked to Polycomb Group (PcG) protein-mediated suppression of Hox genes and animal body patterning, X-inactivation and possibly maintenance of embryonic stem (ES) cell identity. An imbalance of H3K27 methylation due to over-expression of the methylase EZH2 has been implicated in metastatic prostate and aggressive breast cancers. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL5790
2 Samples
Download data: GFF, PAIR, TIFF
Series
Accession:
GSE8855
ID:
200008855
14.

Identification of histone codes and crosstalk in fission yeast

(Submitter supplied) Aims: To map histone modifications with unprecedented resolution both globally and locus-specifically, and to link modification patterns to gene expression. Materials & methods: Using correlations between quantitative mass spectrometry and chromatin immunoprecipitation/microarray analyses, we have mapped histone post-translational modifications in fission yeast (Schizosaccharomyces pombe). Results: Acetylations at lysine 9, 18 and 27 of histone H3 give the best positive correlations with gene expression in this organism. more...
Organism:
Saccharomyces cerevisiae; Schizosaccharomyces pombe
Type:
Expression profiling by array; Genome binding/occupancy profiling by array
Platforms:
GPL2529 GPL11381
41 Samples
Download data: CEL, TXT
Series
Accession:
GSE11511
ID:
200011511
15.

Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach

(Submitter supplied) DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect of tissue origins or clinically and aetiologically distinct subtypes. In this study, we adapted our liquid hybridization capture-based bisulfite sequencing approach on the targeted sequencing of promoter methylomes. We detected ten cell lines originated from different tissue origins and demonstrated a similar potentiality of promoter methylomes as classifiers for cancer cell lines from different tissue origins in comparison with gene expression profiles. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL11154
12 Samples
Download data: BED, TXT
Series
Accession:
GSE44866
ID:
200044866
16.

Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells

(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; Methylation profiling by high throughput sequencing
Platform:
GPL11154
16 Samples
Download data: BED, TXT, WIG
Series
Accession:
GSE43096
ID:
200043096
17.

Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells (ChIP-BS)

(Submitter supplied) The model describing that aberrant CpG island (CGI) methylation leads to transcription repression of tumor suppressor genes and thereby is implicated in tumor progression has been established in many cancers. However, recent studies indicated aberrantly hypermethylated genes in multiple cancers are already repressed in pre-cancerous tissues despite their promoters are hypomethylated. Here, we hypothesized that the occurrence of CGI promoter hypermethylation in cancers are associated with Polycomb-repressive complex and the associated H3K27me3 mark in pre-cancerous tissues. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
13 Samples
Download data: BED, TXT, WIG
Series
Accession:
GSE43094
ID:
200043094
18.

Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells (RNA-seq)

(Submitter supplied) Aberrant DNA hypermethylation of CpG island (CGI) promoters are associated with transcriptional repression of many tumor suppressor genes and lead to tumor progression in many cancers. Most recently, one research group observed that aberrantly hypermethylated genes in multiple cancers are already repressed, but their promoters are maintained in a hypomethylated state in pre-cancerous tissues.Their studies didn't provide a clue to explain by what mechanisms those genes were repressed in pre-cancerous tissues. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
3 Samples
Download data: BED, TXT
Series
Accession:
GSE43093
ID:
200043093
19.

Unique Broad Histone Lysine 4 Methylation Domains in Mouse Oocytes and Dynamic Regulation during Maternal to Zygotic Transition

(Submitter supplied) The maternal to zygotic transition (MZT) involves the transfer of genome regulation from the oocyte to the embryo and is essential for the formation of totipotent embryos. However, regulatory mechanisms are still poorly understood despite recent progress in mapping the dynamics in RNA transcripts and DNA methylation1-9. Previous studies suggest that dynamic histone modifications may play important roles in MZT10-12, however direct measurements of chromatin states has been hindered by technical difficulties in profiling histone modifications from small quantities of cells. more...
Organism:
Homo sapiens; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL17021 GPL16791
65 Samples
Download data: BW, TXT
Series
Accession:
GSE72784
ID:
200072784
20.

Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...
Organism:
Eucalyptus grandis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20030
5 Samples
Download data: BEDGRAPH
Series
Accession:
GSE67873
ID:
200067873
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