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Items: 1 to 20 of 44606

1.

Enterochromaffin cells act as intestinal signal integration hubs for microbial metabolites

(Submitter supplied) The intestinal epithelium senses and responds to the myriad of signals from gut microbiota, but it remains unclear how these signals are integrated to drive physiological responses. In this work, we found that enterochromaffin (EC) cells in the gut serve as signal integration hubs for microbial metabolites. EC cells coordinate responses to combinations of microbial metabolites, resulting in complex alterations in serotonin signaling that drive changes in GI physiology. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
18 Samples
Download data: BED
Series
Accession:
GSE286305
ID:
200286305
2.

Dynamic investigation of hypoxia-induced L-lactylation

(Submitter supplied) The recently identified histone modification lysine lactylation can be stimulated by L-lactate and glycolysis. Although the chemical group added upon lysine lactylation was originally proposed to be the L-enantiomer of lactate (KL-la), two isomeric modifications, lysine D-lactylation (KD-la), and N-ε-(carboxyethyl) lysine (Kce), also exist in cells, with their precursors being metabolites of glycolysis. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
8 Samples
Download data: BW
Series
Accession:
GSE285693
ID:
200285693
3.

Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21103 GPL17021 GPL24247
96 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE267053
ID:
200267053
4.

Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells [ChIP-seq]

(Submitter supplied) Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it remains uncertain whether disordered epigenetic mechanisms can be fully corrected. Disruption of DNA methyltransferase 1 (DNMT1), responsible for DNA methylation maintenance, has particularly devastating biological consequences. Therefore, here we explored if rescuing DNMT1 activity is sufficient to reverse the effects of its loss utilizing mouse embryonic stem cells. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
33 Samples
Download data: BED, BW
Series
Accession:
GSE266929
ID:
200266929
5.

Genomic profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Msh3 knockout mice [ATACSeq]

(Submitter supplied) Striatum was isolated from 12-month-old Msh3-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Genomic analysis (ATACseq) was performed on 4 genotypes: WT, Msh3-/-, Het (Q140) KI, and Het (Q140) KI X Msh3-/-, 6 replicates per genotype.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
24 Samples
Download data: TXT
Series
Accession:
GSE235279
ID:
200235279
6.

Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

(Submitter supplied) Metazoan gene transcription by RNA polymerase (Pol) II is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region, but whether this can contribute to transcription regulation in cells remains unclear. Here, we extend our previous multi-omics analysis to quantify changes in transcription kinetics during a human cell type transition event. We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL21697
44 Samples
Download data: BW, TXT
Series
Accession:
GSE235181
ID:
200235181
7.

Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties [MNase-Seq]

(Submitter supplied) Probing the rice genome for novel histone coding genes revealed a genera specific, histone H4 variant with several variations in N-terminal tail sequence motifs, expressing in a tissue-specific manner. Genetic perturbation of the H4 variant in rice led to defects in growth and fertility. Probing the chromatin binding sites of the H4 variant with a custom antibody revealed its binding at specific genes and its knockout led to mis-expression of stress-associated genes. more...
Organism:
synthetic construct
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26526
3 Samples
Download data: BW
Series
Accession:
GSE229602
ID:
200229602
8.

Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties [ChIP-Seq]

(Submitter supplied) Probing the rice genome for novel histone coding genes revealed a genera specific, histone H4 variant with several variations in N-terminal tail sequence motifs, expressing in a tissue-specific manner. Genetic perturbation of the H4 variant in rice led to defects in growth and fertility. Probing the chromatin binding sites of the H4 variant with a custom antibody revealed its binding at specific genes and its knockout led to mis-expression of stress-associated genes. more...
Organism:
Oryza sativa
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19290 GPL27660
21 Samples
Download data: BW
Series
Accession:
GSE229599
ID:
200229599
9.

Phosphine-Nitrogen-Phosphine chelated CoCl2 (Co68) is a novel therapeutic agent for pancreatic cancer [ATAC-seq]

(Submitter supplied) Pancreatic cancer is projected to become the second leading cause of cancer-related deaths globally by 2030, yet effective therapeutic options remain limited. Within the pancreatic cancer tumor microenvironment (TME), tumor-associated macrophages (TAMs) secrete interleukin-1 beta (IL-1β), promoting cancer progression while suppressing type I interferons (IFN-I), which is critical for effective tumor treatment. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18480
4 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE288553
ID:
200288553
10.

Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties

(Submitter supplied) Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the occurrence, mechanism of action and functional significance of several variants of core histones are well known except that of histone H4. Here we show that a novel variant of H4 (H4.V), expressing tissue-specifically among members of Oryza genera, mediates specific epigenetic changes contributing majorly to salt tolerance. more...
Organism:
Oryza sativa; synthetic construct
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL26526 GPL19290 GPL27660
40 Samples
Download data: BW, TSV
Series
Accession:
GSE229604
ID:
200229604
11.

The landscape of enhancer transcription in prostate cancer [ATAC-Seq]

(Submitter supplied) Current genome-wide detection of chromatin accessibility uses the assay for transposase-accessible chromatin (ATAC-seq). To a provide panoramic view of the chromatin accessibility landscape in prostate cancer and normal prostate, we performed ATAC-seq in 20 pairs of prostate cancer tissues and matched adjacent tissues. Assay of transposase accessible chromatin with high-throughput sequencing (ATAC-seq) for 20 pairs of prostate cancer tissues and matched adjacent tissues.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
40 Samples
Download data: BW
Series
Accession:
GSE221108
ID:
200221108
12.

Vanguard is a glucose deprivation-responsive long non-coding RNA essential for chromatin remodeling-reliant DNA repair

(Submitter supplied) Glucose metabolism contributes to DNA damage response (DDR) pathways by regulating chromatin remodeling, double-strand break (DSB) repair, and redox homeostasis, although the underlying mechanisms are not fully established. Here, we reveal a previously uncharacterized long noncoding RNA we call Vanguard which acts to promote HMGB1-dependent DNA repair in association with changes in global chromatin accessibility. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL23227
2 Samples
Download data: BED, TXT
Series
Accession:
GSE197519
ID:
200197519
13.

CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation II

(Submitter supplied) Although the chromatin regulator CTCF is enriched at genes escaping from X-chromosome inactivation (XCI), molecular mechanisms remain elusive. We examined CTCF and epigenetic features at escape genes on the inactive X (Xi) in mouse F1 hybrid cells and tissues. We found that escape genes are located inside topologically insulated domains limited by convergent arrays of CTCF binding sites, suggesting loop formation. more...
Organism:
Mus musculus; Mus spretus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL33375
12 Samples
Download data: BW
Series
Accession:
GSE288844
ID:
200288844
14.

SND1-SMARCA5 interaction strengthened by PIM promoted the proliferation, metastasis and chemoresistance of ESCC

(Submitter supplied) Chromatin remodeling plays a pivotal role in the progression of esophageal squamous cell carcinoma (ESCC), yet the precise mechanisms remain poorly understood. Here, we elucidate the critical function of staphylococcal nuclease and tudor domain-containing 1 (SND1) in modulating chromatin dynamics, thereby driving ESCC progression in both in vitro and in vivo models. Our data revealed that SND1 was markedly overexpressed in ESCC cell lines. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
2 Samples
Download data: BIGWIG
Series
Accession:
GSE281371
ID:
200281371
15.

SUV39H1 inhibition by Chaetocin targets stemness and oncogenic networks and synergizes with ONC201 against Diffuse intrinsic pontine gliomas

(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
Platforms:
GPL16791 GPL24676
12 Samples
Download data: BW
Series
Accession:
GSE225029
ID:
200225029
16.

SUV39H1 inhibition by Chaetocin targets stemness and oncogenic networks and synergizes with ONC201 against Diffuse intrinsic pontine gliomas [CUT&RUN]

(Submitter supplied) To identify potential direct targets of SUV39H1, we performed Cut&Run-seq for H3K9me3 and SUV39H1 genomic occupancy
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: BW
Series
Accession:
GSE225028
ID:
200225028
17.

The landscape of enhancer transcription in prostate cancer

(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:
GPL24676
80 Samples
Download data: BW
Series
Accession:
GSE221109
ID:
200221109
18.

Foxp1 developing neocortex

(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
Platform:
GPL24247
40 Samples
Download data
Series
Accession:
GSE267673
ID:
200267673
19.

Foxp1 developing neocortex (snRNA-Seq)

(Submitter supplied) The transcription factor Foxp1 is expressed in the neocortex with restricted patterns across development. We used single nuclei-RNA sequencing (snRNA-Seq) to determine the cell-type roles of Foxp1 in control and Foxp1 conditional knock-out animals generated by crossing to Emx1.Cre hemizygous mice. Samples were collected at embyonic day (E)13.5, E16.5, and post-natal day (P)0.5.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL24247
24 Samples
Download data: MTX, TSV
Series
Accession:
GSE267671
ID:
200267671
20.

Foxp1 developing neocortex (scATAC-Seq)

(Submitter supplied) The transcription factor Foxp1 is expressed in the neocortex with restricted patterns across development. We used single nuclei-ATAC sequencing (snATAC-Seq) to determine the cell-type roles of Foxp1 in control and Foxp1 conditional knock-out animals generated by crossing to Emx1.Cre hemizygous mice. Samples were collected at embyonic day (E)13.5, E16.5, and post-natal day (P)0.5.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
16 Samples
Download data: MTX, TSV
Series
Accession:
GSE267670
ID:
200267670
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