GEO DataSets

(Submitter supplied) The maintenance of protein homeostasis is an essential characteristic of life. Transcription factor NRF1 (NFE2L1) has been reported to be activated by proteasome dysfunction, although the genome-wide target genes are poorly understood. Using ChIP-seq analysis, we found a potential association between NRF1 and autophagy. Our findings highlight the new activation mechanism of autophagy through gene regulation under proteasome dysfunction.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

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(Submitter supplied) We executed ChIPseq for SOX2 a different mouse strain E14TG2a.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

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(Submitter supplied) We executed CUT&RUN-seq for SOX2, ESRRB, and EZH2 upon the mitotic depletion of SMARCE1 in mouse ES cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

20 Samples

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(Submitter supplied) We executed CUT&RUN-seq for SOX2 a different mouse strain E14TG2a

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

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(Submitter supplied) We executed CUT&RUN-seq for SMARCE1 and SOX2 in BRG1 inhibitor BRM014 treated ,in MD or MD mutatnt mouse embryonic stem cells at 90 min from mitotic release.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

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(Submitter supplied) We conduct ATAC-seq in SMARCE1 MD/MD(R42A) after mitotic release 90 min in either DMSO treated or BRG1 inhibitor BRM014 treated conditions

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

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(Submitter supplied) We performed ChIP-seq for H3K4me3, H3K27ac, H3K4me1, H3K27me3, H3K36me3, H3K9me3, and H4K20me3 to characterize chromatin states and investigated SOX2 deposition in asynchronous and mitotic cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

86 Samples

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(Submitter supplied) We executed CUT&RUN-seq for SWI/SNF components ARID1A, BRD9, SMARCA4, SMARCB1, SMARCE1, as well as ESRRB, SOX2, and EZH2 in asynchronous and mitotic cells and reported that, in asynchronous cells, ARID1A localized primarily at enhancer regions and EZH2 preferentially deposited at bivalent promoters and silent enhancer domains. The remaining factors were enriched at both TSS/promoters and to varying degrees at active enhancers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

104 Samples

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(Submitter supplied) In order to determine how NAT10 regulates NFE2L3 to promote the progression of ccRCC, since NFE2L3 is a transcription factor, we performed CHP-seq detection for NFE2L3, as well as RNA-seq detection for 786-O cells with stable NFE2L3 knocking and control 786-O cells. The results of RNA-seq showed that 312 transcripts in the NFE2L3 knockdown group were down-regulated, and 3 114 transcripts in the previous ccRCC tissue were up-regulated. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29480

2 Samples

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(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; Other

Platform:

GPL24247

137 Samples

Download data: BW

(Submitter supplied) Modifications of histones are intricately linked with the regulation of gene expression, with demonstrated roles in various physiological processes and disease pathogenesis. Methylation of histone H3 lysine 4 (H3K4), implemented by the COMPASS family, is enriched at promoters and associated cis-regulatory elements, with H3K4 trimethylation (H3K4me3) considered a hallmark of active gene promoters. However, the relative roles of deposition and removal of H3K4 methylation, as well as the extent to which these events contribute to transcriptional regulation have so far remained unclear. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

127 Samples

Download data: BW

(Submitter supplied) A large number of lncRNAs has been found aberrant expression in breast cancer and paly functional role in tumor progression. However, the role of small peptide hidden in lncRNA are largely unexplored. In this study, we applied the CRISPR/Cas9 screen and ribosome profiling to systematically discover nocanonical open reading frame encoded in long noncoding RNAs (lncRNAs) and explored their critical roles in ER+ breast cancer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

31 Samples

Download data: CSV, NARROWPEAK, TSV, TXT

(Submitter supplied) For cells to initiate and sustain a differentiated state, it is necessary that a “memory” of this state is transmitted through mitosis to the daughter cells. Mammalian SWItch/ Sucrose Non- Fermentable (SWI/SNF) complexes, also called Brg1/ Brg- associated factors (BAF), control cell identity by modulating chromatin architecture to regulate gene expression, but whether they participate in cell fate memory is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

394 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

62 Samples

Download data: BW

(Submitter supplied) We determined that glucocorticoid treatment (prednisolone) affects oncogenic signaling in aggressive B-cell lymphomas. We sought to identify genes directly controlled and bound by NR3C1.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

21 Samples

Download data: WIG

(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:

GPL30173

83 Samples

Download data: WIG

(Submitter supplied) Gliomas are among the most invasive and chemo-resistant cancers, making them challenging to treat. Chronic inflammation is one of the key drivers of glioma progression as it promotes the aberrant activation of inflammatory pathways such as NF-κB signalling which drives cancer cell invasion, angiogenesis and tissue remodelling. NF-κB factors typically dimerize with its own family members, but emerging evidence of their promiscuous interactions with other oncogenic factors have been reported to activate the transcription of new target genes and function. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL11154

35 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) Numerous models of synthetic embryos have recently been established to simulate mammalian development. Two main strategies have been developed to build mouse or human embryo-like structures (ELS): by assembling embryonic and extraembryonic stem cells or by challenging embryonic stem cells (ESCs) with a pulse of WNT agonist. However, both models did not fully recapitulate early organogenesis, particularly the emergence of brain derivatives. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing

4 related Platforms

256 Samples

Download data: BW, TXT

(Submitter supplied) Epigenetic alterations are a key hallmark of aging but have not been extensively explored in tissues. Here, using naturally aged murine liver as a model and extending study to other quiescent tissues, we find that aging is driven by temporal chromatin alterations that promote a refractory cellular state and compromise cellular identity. Using an integrated multi-omics approach and the first direct visualization of aged chromatin, we find that old cells show global H3K27me3-driven broad heterochromatinization and transcription suppression. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL30172

160 Samples

Download data: BW