3,684 datasets

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 8 samples

Interleukin-6 (IL-6) is a pleiotropic cytokine that drives macrophage functions ranging from tissue homeostasis to inflammation, yet how STAT3 specifies these divergent outcomes remains unclear. By integrating transcriptomic and epigenomic profiling with selective STAT3 degradation, we show that STAT3 controls IL-6-induced epigenomic remodeling and restrains a latent STAT1-associated interferon pr

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 6 samples

People living with HIV (PLWH) on antiretroviral therapy (ART) accumulate primarily defective proviral sequences in genomes of often clonally expanded CD4+ HIV-1 target cells. The majority of viral-derived DNA is transcriptionally active and preferentially found at distinct genomic loci suggesting a selective process driven by integration site-specific crosstalk between viral and host sequences. Fo

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 10 samples

We identified 5 patients from two families with a defect in antibody production without a known inborn error of immunity.

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 4 samples

Interleukin-6 (IL-6) is a pleiotropic cytokine that drives macrophage functions ranging from tissue homeostasis to inflammation, yet how STAT3 specifies these divergent outcomes remains unclear. By integrating transcriptomic and epigenomic profiling with selective STAT3 degradation, we show that STAT3 controls IL-6-induced epigenomic remodeling and restrains a latent STAT1-associated interferon pr

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 12 samples

Memory follicular helper T cells (TFH) are essential for rapidly re-eliciting sufficient effector TFH cells in facilitating B cells to produce high-affinity neutralizing antibody against re-infection. However, the mechanism underlying memory TFH cell differentiation is largely unknown. Here, we show that a subset of antigen-specific CD4 effector cells highly expressing transcription factor Hhex (H

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 18 samples

Precise and rapid control over cellular protein levels is essential to dissect complex biological systems. Chemical genetic approaches such as dTAG, in which a target is fused to a degron tag (FKBP12F36V) and degraded upon small molecule-mediated recruitment of E3 ligases, have enabled rapid and tunable control over protein abundance. However, no analogous tool exists to precisely increase protein

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 7 samples

People living with HIV (PLWH) on antiretroviral therapy (ART) accumulate primarily defective proviral sequences in genomes of often clonally expanded CD4+ HIV-1 target cells. The majority of viral-derived DNA is transcriptionally active and preferentially found at distinct genomic loci suggesting a selective process driven by integration site-specific crosstalk between viral and host sequences. Fo

NCBI GEO2026 · RNA sequencing · 60 samples

This SuperSeries comprises transcriptomic and epigenomic datasets generated in human macrophages to investigate IL-6-STAT3 signaling. The datasets include RNA-seq under STAT3 degradation and JAK inhibition, IL-6 time-course RNA-seq, hMDM RNA-seq, ATAC-seq, and CUT&Tag profiling of H3K27ac, STAT3, and STAT1. Together, these data characterize IL-6-induced chromatin and transcriptional changes and th

NCBI GEO2026 · RNA sequencing · 50 samples

This SuperSeries is composed of the SubSeries listed below.

NCBI GEO2026 · RNA sequencing · 46 samples

Shortly after mitosis, a wave of hyper-transcription reactivates the genome, especially in mouse embryonic stem (ES) cells, where rapid reactivation is essential for self-renewal and pluripotency. While recent work has illuminated how specific groups of genes are reactivated, whether dedicated mechanisms enable the global, efficient and accurate post-mitotic reactivation of the genome remains unkn

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 2 samples

Glioblastoma (GBM) is the most aggressive primary malignant tumor of the adult central nervous system, with a median survival of less than 15 months despite surgery combined with radiochemotherapy. Super-enhancers (SEs) are large clusters of cis-regulatory elements densely marked by H3K27ac that drive high-level expression of key oncogenes. In this study, we systematically identified SE-regulated

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 8 samples

Interleukin-6 (IL-6) is a pleiotropic cytokine that drives macrophage functions ranging from tissue homeostasis to inflammation, yet how STAT3 specifies these divergent outcomes remains unclear. By integrating transcriptomic and epigenomic profiling with selective STAT3 degradation, we show that STAT3 controls IL-6-induced epigenomic remodeling and restrains a latent STAT1-associated interferon pr

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 12 samples

Alterations in histone acetylation are frequently detected in various cancers and upon neurological deseases. The histone acetylation is known to disrupt both intra- and inter-nucleosomal interactions. However, its influence on the higher order chromatin organization has been studied to a lesser extent. In this study, we changed global levels of histone acetylation in Drosophila S2 cells by treatm

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 8 samples

Interleukin-6 (IL-6) is a pleiotropic cytokine that drives macrophage functions ranging from tissue homeostasis to inflammation, yet how STAT3 specifies these divergent outcomes remains unclear. By integrating transcriptomic and epigenomic profiling with selective STAT3 degradation, we show that STAT3 controls IL-6-induced epigenomic remodeling and restrains a latent STAT1-associated interferon pr

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 4 samples

Memory follicular helper T cells (TFH) are essential for rapidly re-eliciting sufficient effector TFH cells in facilitating B cells to produce high-affinity neutralizing antibody against re-infection. However, the mechanism underlying memory TFH cell differentiation is largely unknown. Here, we show that a subset of antigen-specific CD4 effector cells highly expressing transcription factor Hhex (H

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 4 samples

Mammalian enhancers are regulatory sequences that modulate gene expression. Deep learning models have predicted individual enhancer activity but have not yet predicted activity of enhancer pairs, which have high potential to activate expression. However, direct observation of paired enhancers on single chromatin molecules has been challenging. Here we use single chromatin molecule foot printing an

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 2 samples

Transforming the malignant characteristics of cancer cells instead of killing them is one potential strategy to overcome limitations associated with cancer therapies intended to induce cancer cell apoptosis. A systems approach could identify mechanisms to drive the reversion of cancer cells into normal-like cells. Here, we identify the transition state between normal and cancer cells in colon and

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 8 samples

HU proteins belong to nucleoid-associated proteins that contribute to the compaction and organization of bacterial genomes. Although HU proteins are generally considered to bind preferentially to distorted DNA structures rather than specific DNA sequence motifs, their binding properties may vary depending on environmental conditions. Here, using ChIP-seq, we identified the DNA-binding motif of the

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 4 samples

Reverting cancer cells into a normal-like state offers a therapeutic alternative to eliminating malignant cells. This raises questions about the existence and possible identification of a molecular switch that governs such reversion. We analyzed single-cell transcriptomes from patient-derived paired colon organoids, integrating copy number alterations to delineate a transition state between normal

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 13 samples

Mammalian enhancers are regulatory sequences that modulate gene expression. Deep learning models have predicted individual enhancer activity but have not yet predicted activity of enhancer pairs, which have high potential to activate expression. However, direct observation of paired enhancers on single chromatin molecules has been challenging. Here we use single chromatin molecule foot printing an

NCBI GEO2026 · RNA sequencing · 72 samples

This SuperSeries is composed of the SubSeries listed below.

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 64 samples

Mammalian enhancers are regulatory sequences that modulate gene expression. Deep learning models have predicted individual enhancer activity but have not yet predicted activity of enhancer pairs, which have high potential to activate expression. However, direct observation of paired enhancers on single chromatin molecules has been challenging. Here we use single chromatin molecule foot printing an

NCBI GEO2026 · RNA sequencing · 25 samples

Astrocytes play a pivotal role in maintaining brain homeostasis. In response to injury or disease, functional changes in astrocytes can be detrimental to neural repair and contribute to the progression of neuroinflammatory conditions. While studies have characterized the gene expression programs activated in astrocytes during neuroinflammation, the gene regulatory mechanisms underlying proinflamma

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 18 samples

The epigenetically silent heterochromatin is replicated at a specific window during the cell cycle; however, the mechanisms governing the completion of heterochromatin replication remain elusive. Here, through mass spectrometry to analyze factors enriched in P53-binding Protein 1 (53BP1) condensates, we report that 53BP1 is intricately involved in complexes governing both DNA replication and epige

NCBI GEO2026 · Genome binding/occupancy profiling by high throughput sequencing · 8 samples

Quiescence is a conserved program of endurance and readiness in non-cycling cells that is fundamental to the longevity of eukaryotic lineages, from clonal microbial populations to human regenerative tissues. While this G₀ state is universally associated with a compact chromatin organization, the active safeguards that preserve this structural template—and their necessity for future division compet