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Items: 1 to 20 of 8389

1.

Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain

(Submitter supplied) ChIP-seq and RNA-seq datasets newly generated for this manuscript are included in the SubSeries listed below. For previously published datasets, see accession no. GSE21172 and additional links provided in references 16, 18, 20. For references 16, 18: https://zlab.umassmed.edu/zlab/publications/ShulhaPLOSGen2013.html https://zlab.umassmed.edu/zlab/publications/ShulhaAGP2011.html For reference 20, sequences are accessible through: http://www.umassmed.edu/zlab/publications/
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL9115 GPL11154
18 Samples
Download data:
GEO (BED, TXT)
Series
Accession:
GSE71238
ID:
200071238
2.

localization of Scc2 between wild type and scc4-m35 cells in S-phase

(Submitter supplied) Wild-type (AM15307) and scc4-m35 (AM15311) cells carrying SCC2-3FLAG were fixed for 2 hr, 15 min following an a-factor arrest. Samples were harvested, anti-HA ChIP was performed and both input and IP samples were sequenced for both strains.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13821
4 Samples
Download data:
GEO (BEDGRAPH), SRA SRP061275
Series
Accession:
GSE70316
ID:
200070316
3.

Distinct Function for ASCL1 and NEUROD1 in Pulmonary Neuroendocrine Tumors

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL10999 GPL13112 GPL9520
15 Samples
Download data:
GEO (BEDGRAPH)
Series
Accession:
GSE69398
ID:
200069398
4.

Distinct Function for ASCL1 and NEUROD1 in Pulmonary Neuroendocrine Tumors (ChIP-seq)

(Submitter supplied) Small cell lung carcinoma (SCLC) and large cell neuroendocrine carcinoma (LCNEC) are high-grade pulmonary neuroendocrine tumors. The neural basic helix-loop-helix (bHLH) transcription factors ASCL1 and NEUROD1 have been shown to play crucial roles in promoting the malignant behavior and survival of human SCLC cell lines. In this study, we find ASCL1 and NEUROD1 identify distinct neuroendocrine tumors, bind distinct genomic loci, and regulate mostly distinct genes. more...
Organism:
Mus musculus; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL10999 GPL13112
9 Samples
Download data:
GEO (BEDGRAPH), SRA SRP058872
Series
Accession:
GSE69394
ID:
200069394
5.

Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain [ChIP-Seq]

(Submitter supplied) Trimethylated histone H3-lysine 4 is primarily distributed in the form of sharp peaks, extending in neuronal chromatin on average only across 500-1500 base pairs mostly in close proximity to annotated transcription start sites. To explore whether H3K4me3 peaks could also extend across much broader domains, we undertook a detailed analysis of broadest domain cell-type specific H3K4me3 peaks in ChIP-seq datasets from sorted neuronal and non-neuronal nuclei in human, non-human primate and mouse prefrontal cortex (PFC), and blood for comparison. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9115
6 Samples
Download data:
GEO (BED), SRA SRP063599
Series
Accession:
GSE72929
ID:
200072929
6.

Retrotransposon derepression leads to activation of the unfolded protein response and apoptosis in pro B cells

(Submitter supplied) The establishment of distinct transcription programs during development is controlled by transcription factor networks acting in specific chromatin environments. The H3K9me3-specific histone methyltransferase Setdb1 impacts on transcriptional regulation by repressing both developmental genes and retrotransposons. How impaired retrotransposon silencing may lead to developmental phenotypes is currently unclear. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
7 Samples
Download data:
GEO (BEDGRAPH, FPKM_TRACKING), SRA SRP069730
Series
Accession:
GSE77636
ID:
200077636
7.

Synergistic model of chromatin predicts Dnase-I accessibility

(Submitter supplied) Enhancers and promoters commonly occur in accessible chromatin characterized by depleted nucleosome contact; however, it is unclear how chromatin accessibility is governed. We show that a logic of cis-acting DNA sequence features can predict the majority of chromatin accessibility at high spatial resolution. We develop a new type of high-dimensional machine learning model, the Cooperative Chromatin Model (CCM), that is capable of predicting a large fraction of genome-widepromoters chromatin accessibility at basepair-resolution in a range of human and mouse cell types from DNA sequence alone. more...
Organism:
Homo sapiens; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL11154 GPL13112 GPL16417
8 Samples
Download data:
GEO (TAR, TSV, TXT), SRA SRP073108
Series
Accession:
GSE80105
ID:
200080105
8.

EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis [ChIP-seq]

(Submitter supplied) The EZH2 histone methyltransferase mediates the humoral immune response and drives lymphomagenesis through de novo formation of bivalent chromatin domains at critical germinal center (GC) B cell promoters. Herein we show that the actions EZH2 in driving GC formation and lymphoma precursor lesions are dependent on the presence of the BCL6 transcriptional repressor, both of which are in turn dependent on the presence of non-canonical PRC1-BCOR complex. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
2 Samples
Download data:
GEO (TXT), SRA SRP075486
Series
Accession:
GSE81623
ID:
200081623
9.

EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis

(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
Platform:
GPL11154
20 Samples
Download data:
GEO (TXT)
Series
Accession:
GSE81705
ID:
200081705
10.

The Nuclear Receptor Rev-erb alpha Regulates Adipose Tissue-Specific FGF21 Signaling

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9250 GPL6246
10 Samples
Download data:
GEO (BW, CEL)
Series
Accession:
GSE79166
ID:
200079166
11.

The Nuclear Receptor Rev-erb alpha Regulates Adipose Tissue-Specific FGF21 Signaling (ChIP-seq, eWAT)

(Submitter supplied) The goal of this study is to identify the cistrome of the transcriptional repressor Rev-erb alpha in epididymal white adipose tissue. Performing Rev-erb alpha ChIP-seq on epididymal white adipose tissue from wildtype mice at 5PM when Rev-erb alpha protein level peaks in wild type (WT) mice, we were able to globally determine the genomic regions undergoing Rev-erb alpha-dependent de-repression.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9250
2 Samples
Download data:
GEO (BW), SRA SRP071727
Series
Accession:
GSE79165
ID:
200079165
12.

Vicious circle of LSD1 and TGF β1 promotes EMT of gastric cancer

(Submitter supplied) Vicious circle of some key proteins is critical in the process of tumor development. Nevertheless, the mechanism of how the epigenetic modifiers are involved in was seldom reported and has not been clearly illustrated. We found the expression of lysine specific demethylase 1 (LSD1), the first identified histone lysine demethylase, is positively correlated with transforming growth factor beta 1 (TGF β1) in gastric cancer tissues and can be promoted by TGF β1 activated (p-EKR)-(NF-κB)-p300 signaling pathway, which resulted in the progression of epithelial-mesenchymal transition (EMT) in human gastric cancer cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data:
GEO (WIG), SRA SRP078908
Series
Accession:
GSE84487
ID:
200084487
13.

GAF regulates transcriptional pausing via nucleosomal remodeling

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9058
7 Samples
Download data:
GEO (TXT)
Series
Accession:
GSE70634
ID:
200070634
14.

GAF regulates transcriptional pausing via nucleosomal remodeling [MNase-seq]

(Submitter supplied) Promoter-proximal pausing of RNA polymerase II (RNA-Pol) is a rate-limiting step primed for rapid and synchronous induction of genes involved in critical physiological processes. Its underlying mechanisms are not fully understood. Using cytogenetic, genomic and genetic approaches, we provide evidence to support a direct role of a prevalent upstream GAGA binding factor (GAF) in transcriptional pausing of Hsp70 and many developmental regulators in Drosophila. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9058
2 Samples
Download data:
GEO (TXT), SRA SRP060515
Series
Accession:
GSE70633
ID:
200070633
15.

GAF regulates transcriptional pausing via nucleosomal remodeling [ChIP-seq]

(Submitter supplied) Promoter-proximal pausing of RNA polymerase II (RNA-Pol) is a rate-limiting step primed for rapid and synchronous induction of genes involved in critical physiological processes. Its underlying mechanisms are not fully understood. Using cytogenetic, genomic and genetic approaches, we provide evidence to support a direct role of a prevalent upstream GAGA binding factor (GAF) in transcriptional pausing of Hsp70 and many developmental regulators in Drosophila. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9058
5 Samples
Download data:
GEO (TXT), SRA SRP060522
Series
Accession:
GSE70632
ID:
200070632
16.

Chromatin Remodeling Inactivates Activity Genes and Regulates Neural Coding

(Submitter supplied) Activity-dependent transcription influences neuronal connectivity, but the roles and mechanisms of inactivation of activity-dependent genes have remained poorly understood. Genome-wide analyses in the mouse cerebellum revealed that the nucleosome remodeling and deacetylase (NuRD) complex deposits the histone variant H2A.z at promoters of activity-dependent genes, thereby triggering their inactivation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL13112
48 Samples
Download data:
GEO (BED, BIGWIG, TXT), SRA SRP076455
Series
Accession:
GSE83253
ID:
200083253
17.

Network-based, cross-cohort discovery of transcriptional mechanisms presiding over maintenance of high-risk neuroblastoma subtype state

(Submitter supplied) Network-based analysis of neuroblastoma samples from two large cohorts identified master regulator proteins controlling the transcriptional state of three high-risk molecular subtypes. In particular, a TEAD4-MYCN positive feedback loop emerged as the core regulatory motif of a small protein module presiding over implementation and stability of the subtype associated with MYCN amplification. Specifically, MYCN transcriptionally activates TEAD4, which in turn activates MYCN both transcriptionally and post-translationally. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL16791
11 Samples
Download data:
GEO (BED, TXT), SRA SRP078495
Series
Accession:
GSE84389
ID:
200084389
18.

Massive redeployment of PRC1 proteins suppresses tumor formation during Drosophila development

(Submitter supplied) Polycomb group proteins form two main complexes, PRC2 and PRC1, which generally coregulate their target genes. Here, we show that PRC1 components act as neoplastic tumor suppressors independently of PRC2 function. By mapping the distribution of PRC1 components and the histone H3K27me3 mark, we identify genes that acquire PRC1 and H3K27me3 in larvae, and a much larger set of genes bound by PRC1 in the absence of H3K27me3 in larval tissues. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13304
16 Samples
Download data:
GEO (BED, XLS), SRA SRP064869
Series
Accession:
GSE74080
ID:
200074080
19.

Chromatin targets of androgen receptor and coregulator PIAS1 in molecular apocrine breast cancer cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL9052 GPL10558
19 Samples
Download data:
GEO
Series
Accession:
GSE70163
ID:
200070163
20.

Chromatin targets of androgen receptor and PIAS1 in molecular apocrine breast cancer cells [ChIP-seq]

(Submitter supplied) The majority of breast cancer subtypes express androgen receptor (AR) in addition to estrogen receptor a (ERa). Depending on the breast cancer subtype androgen signaling has either stimulatory or inhibitory roles in breast cancer cell growth. We have mapped AR cistrome in ERa negative human molecular apocrine breast cancer MDA-MB453 cells and analyzed it in relation to the androgen-regulated transcriptome in the same cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9052
7 Samples
Download data:
GEO (BED), SRA SRP059781
Series
Accession:
GSE70161
ID:
200070161
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