GEO DataSets

(Submitter supplied) Manipulation of immune cell functions, independently of direct infection of these cells, emerges as a key process in viral pathophysiology. Chronic infection by Human T-cell Leukemia Virus type 1 (HTLV-1) is associated with immune dysfunctions, including misdirected responses of dendritic cells (DCs). Here, we interrogate the ability of HTLV-1-infected T cells to indirectly manipulate human DC functions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: CSV

(Submitter supplied) Despite genome-wide association studies (GWAS) of late-onset Alzheimer’s disease (LOAD) have identified 75 genetic risk loci 2-7, the disease causal mechanism underlying most GWAS risk loci remains largely unknown. A major challenge is how to identify a putative causal disease variant among multiple risk variants at individual GWAS risk locus and functionally link the risk allele to LOAD-relevant cellular phenotypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

141 Samples

Download data: BW

(Submitter supplied) The current model of hematopoiesis only resolves the thymus around the production and establishment of the peripheral T cell pool. However, the role and in situ development of other immune subsets has been overlooked. We aim to demonstrate that during TL1A and IL-18 induced inflammation, the thymus is capable of producing other cell types such as neutrophils, monocytes, and macrophages and that these potentially have other functions aside from supporting T cell development as scavengers. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL21103

12 Samples

Download data: H5

(Submitter supplied) Studies in animal models have suggested a linkage between the inflammatory response to injury and subsequent nephron loss during the acute kidney injury (AKI) to chronic kidney disease (CKD) transition. Failure of normal repair during the CKD transition correlates with de novo expression of vascular cell adhesion protein-1 (VCAM-1) by a subset of injured proximal tubule cells. This study identified the role of VCAM-1 expression in promoting the failed repair state. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: TXT

(Submitter supplied) ScRNA-seq analysis of 11,450 cells from mouse muscle tissue sections following R848 injection identified 19 cell clusters, including four fibroblast, two endothelial cell, two macrophage, and two T cell subpopulations. To identify which cell populations were activated downstream of TLR7/8, interferon gene signature (IFN-GS) and NF-κB-gene signature (NF-κB-GS) scores were calculated and heat maps generated. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

23 Samples

Download data: H5AD, H5SEURAT

(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

15 Samples

Download data: TSV

(Submitter supplied) Epigenetic regulation drives the differentiation of T cells into phenotypically stable subsets including a dysfunctional state termed exhaustion, the presence of these epigenetically distinct T cells in tumors make them non-responsive to checkpoint blockade. Cancer immunotherapies restoring T cell function have transformed cancer treatment by preventing immune evasion of tumor cells allowed by T cell exhaustion. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

11 Samples

Download data: TSV, TXT

(Submitter supplied) Alcoholic liver disease (ALD) is a kind of liver disease that will result in liver cancer and some other high death rate liver disease. The study results show that riboflavin could protect the mouse against ALD. Then the study divides the C57BL/6 mice into the three groups including Control (C), Alcohol, Alcohol with riboflavin (AR) groups respectively. And the study makes the mouse stool samples 16S RNA sequencing (RNA-seq) to find the differential itestinal microbiota homeostasis among three groups futher and does the related analysis in riboflavin-treated alcoholic liver disease.

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

18 Samples

Download data: TXT

(Submitter supplied) The emerging recognition of heterogeneity among T regulatory cells (Treg) in peripheral tissues raises renewed questions of how Treg cells adapt to changing environments and diverse inflammatory settings. Herein, we addressed the consequences of a T helper 2 (Th2) type environment on the phenotype and function of Foxp3-expressing Treg cells. In vivo, both Treg cells and conventional T cells exhibited discrete transcriptional states corresponding to naïve and activated conditions influenced by shared microenvironmental cues affecting both cell types. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL13112 GPL21493

35 Samples

Download data: BED, BW, MTX, TSV

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

Organism:

Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21626 GPL16417

937 Samples

Download data: BED, BW, NARROWPEAK

(Submitter supplied) In this experiment, we sought to identify how genome organization change in WT versus PATZ1 KO cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

Organism:

Mus musculus

Type:

Other

Platform:

GPL34328

4 Samples

Download data: HIC, TXT

(Submitter supplied) The mechanisms controlling trophoblast proliferation and differentiation during embryo implantation are fundamentally important in defining a successful pregnancy, yet poorly understood. Human trophoblast stem cells (TSC) and BMP4/A83-01/PD17034-treated pluripotent stem cell derived trophoblast cells (BAP) are two widely employed, contemporary models to study trophoblast development and function but how faithfully they mimic the identity of early stage trophoblast cells has not been fully examined. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

41 Samples

Download data: TXT

(Submitter supplied) In this experiment, we sought to analyze how transcriptome of WT and PATZ1 knock-out (KO) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: TXT

(Submitter supplied) Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. Here, by relocating different promoter-reporter constructs into >1,000 alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape, in which the native Sox2 gene occupies an optimal position for its activation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

1 Sample

Download data: BED, BW, NARROWPEAK

(Submitter supplied) Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. Here, by relocating different promoter-reporter constructs into >1,000 alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape, in which the native Sox2 gene occupies an optimal position for its activation. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL16417 GPL21626

936 Samples

Download data: TXT

(Submitter supplied) Ethanol’s anxiolytic actions contribute to increased consumption and the development of Alcohol Use Disorder (AUD). Our laboratory previously identified genetic loci contributing to the anxiolytic-like properties of ethanol in BXD recombinant inbred mice, derived from C57BL/6J (B6) and DBA/2J (D2) progenitor strains. That work identified Ninein (Nin) as a candidate gene underlying ethanol’s acute anxiolytic-like properties in BXD mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

10 Samples

Download data: CSV

(Submitter supplied) Convergent microbial biocatalysis has emerged as a promising approach for the conversion of lignin side-streams into value-added chemicals in recent decades. However, the current knowledge of metabolic pathways directing the bioconversion of lignin-related aromatics is still limited to a few microbial species and unavailable for some of these compounds. Thus, the aim of this study was to identify the genes involved in the bioconversion of aromatic compounds in Xanthomonas citri subsp. more...

Organism:

Xanthomonas citri subsp. citri 306

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34065

38 Samples

Download data: XLSX

(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:

GPL19057

46 Samples

Download data: BW

(Submitter supplied) Cumulative stress and adverse experiences precipitate changes in overall health, disrupting homeostasis and increasing disease. Stress is a known driver of allostatic changes, allowing for cellular adaptation in the face of environmental challenges. However, the molecular mechanisms regulating allostasis and long-term changes in intra- and intercellular signaling important for health are not clear. In males, chronic stress produces lasting changes in epididymal epithelial cell (EEC) intercellular signaling and extracellular vesicle (EV) composition important for sperm maturation. Here we used this system to assess the mechanisms regulating allostasis and the role of EVs to impact downstream target cell physiology and function. We found that prior corticosterone treatment decreased EEC energy requirements and altered mitochondrial ultrastructure, with changes in the cellular set point involving the mitochondrial complex I. CUT&RUN sequencing and gene co-expression network analysis separately identified significant epigenetic and transcriptomic reprogramming important for mitochondrial function. We found this new EEC allostatic state regulated EV intercellular communication with sperm, where EVs isolated from stress EECs increased sperm mitochondrial respiration, ultimately increasing sperm motility. These data support a signaling pathway by which a new cellular allostatic setpoint can be communicated to other cells, affecting their function.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

18 Samples

Download data: BW

(Submitter supplied) Polymeric elastomers are extensively employed to fabricate implants intended for prolonged implantation. However, implantation of the elastomers can induce strong immune rejection reaction known as foreign body response (FBR), resulting in the rejection of foreign implants and thereby diminishing their in vivo efficacy. Herein, we present a group of immunocompatible elastomers, termed easy-to-synthesize vinyl-based anti-FBR dense elastomers (EVADE), synthesized via a straightforward and scalable method. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: XLS