GEO DataSets

(Submitter supplied) During food trigger reintroductions, eosinophilia can recur in a patchy manner both endoscopically and histologically. We postulated that areas containing low eosinophils represented the early stage of EoE recurrence, while areas with >15 eos/HPF represented established active EoE. We identified ten patients with prior pan-esophageal EoE who experienced patchy eosinophilia during trigger food reintroduction. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

28 Samples

Download data: TXT

(Submitter supplied) Metformin reduces the incidence of breast cancer in patients with obesity and type 2 diabetes. However, our knowledge of the effects of metformin on breast cancer recurrence is limited. Within the randomized double-blind placebo-controlled phase II trial MetBreCS, we examined changes in breast tissue from breast cancer survivors with BMI >25 kg/m2 after treatment with metformin. To identify metformin-regulated signaling pathways, we integrated the transcriptomic, metabolomic and steroid hormone profiles using bivariate and functional analyses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

72 Samples

Download data: TXT

(Submitter supplied) Treatment with the toll-like receptor (TLR) 4 agonist monophosphoryl lipid A (MPLA) conditions innate immunocytes to respond robustly to subsequent infection, a phenotype termed innate immune memory. Our published studies show that metabolic reprogramming of macrophages is a prominent feature of the memory phenotype. We undertook studies to define the functional contributions of tricarboxylic acid (TCA) reprogramming to innate immune memory. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

26 Samples

Download data: TXT

(Submitter supplied) Filamentous fungi are promising organisms for lignin degradation and mineralization. However, novel lignin-degrading fungal species are underexplored. Here, we isolated a fungal strain of Curvularia clavata that can utilize lignosulfonate as the carbon source and exhibited a relative high laccase activity during growth on lignosulfonate. Comparative transcriptomic analysis of the WT strain grown on glucose and lignosulfonate indicates that lignosulfonate and/or its metabolites have a significant effect on the gene expression profiles of C. more...

Organism:

Curvularia clavata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34958

15 Samples

Download data: TXT

(Submitter supplied) In the KEAP1-NRF2 stress response system, KEAP1 acts as a sensor for oxidative and electrophilic stresses through formation of S-S bond and C-S bond, respectively. Of the many questions left related to the sensor activity, following three appear important; whether these KEAP1 sensor systems are operating in vivo, whether oxidative and electrophilic stresses are sensed by the similar or distinct systems, and how KEAP1 equips highly sensitive mechanisms detecting oxidative and electrophilic stresses in vivo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

16 Samples

Download data: TXT

(Submitter supplied) RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli. Here, employing high-throughput RNA sequencing, we explored the impact of Musashi expression on the transcriptomic and translatomic profiles of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

4 Samples

Download data: CSV, TXT

(Submitter supplied) RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli. Here, employing high-throughput RNA sequencing, we explored the impact of Musashi expression on the transcriptomic and translatomic profiles of E. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL25368

4 Samples

Download data: CSV, TXT

(Submitter supplied) we investigate the transcriptomic alterations induced by doxorubicin (DOX), a commonly used chemotherapeutic agent, in human colon cancer cells. Using single-cell RNA sequencing, we identified distinct cell populations and their transcriptional profiles following subtoxic dose DOX treatment, revealing cell clusters characterized by differential expression of genes involved in cell cycle regulation and interferon (IFN) signaling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34284 GPL24676

10 Samples

Download data: BW, MTX, TSV

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer without effective treatments. It is characterized by activating KRAS mutations and p53 alterations. However, how these mutations alter cell-intrinsic gene programs to influence the immune landscape of the tumor microenvironment (TME) remains poorly understood. Here, we demonstrate that p53R172H enhances tumor growth, establishes a suppressive TME by inducing immune evasion, and blunts the effectiveness of immune checkpoint inhibitors (ICIs). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

20 Samples

Download data: BEDGRAPH

(Submitter supplied) The signaling molecule cyclic di-GMP (cdG) controls the switch between bacterial motility and biofilm production, and fluctuations in cellular levels of cdG have been implicated in Vibrio cholerae pathogenesis. Intracellular concentrations of cdG are controlled by the interplay of diguanylate cyclase (DGC) enzymes, which synthesize cdG to promote biofilms, and phosphodiesterase (PDE) enzymes, which hydrolyse cdG to drive motility. more...

Organism:

Vibrio cholerae C6706

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34804

45 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) The signaling molecule cyclic di-GMP (cdG) controls the switch between bacterial motility and biofilm production, and fluctuations in cellular levels of cdG have been implicated in Vibrio cholerae pathogenesis. Intracellular concentrations of cdG are controlled by the interplay of diguanylate cyclase (DGC) enzymes, which synthesize cdG to promote biofilms, and phosphodiesterase (PDE) enzymes, which hydrolyse cdG to drive motility. more...

Organism:

Vibrio cholerae C6706

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34804

91 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Paramyxoviruses (PMVs) exploit the host's translation machinery to enhance their replication. We found that the PMV matrix protein is crucial in this process, inhibiting host protein synthesis while boosting viral protein production. This occurs through interactions with the core exon-junction complex (cEJC), a key player in mRNA biogenesis. Disruption of this interaction using siRNA led to increased viral replication but did not affect other viruses like SARS-CoV-2. more...

Organism:

Homo sapiens; Human respirovirus 3

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL34775

21 Samples

Download data: XLSX

(Submitter supplied) Multiple studies suggest Dicer1 as a haploinsufficient tumor suppressor gene: while the loss of one allele promotes tumorigenesis, the complete loss of Dicer1 prevents tumor formation. To study the impact of Dicer1 partial or total loss in papillary thyroid carcinoma cells in vitro, we generated stable Dicer1 (+/-) cell lines by CRISPR-Cas9 from TPC1 cell line. No Dicer1 (-/-) cell lines could be generated. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: CSV

(Submitter supplied) Substance use disorders (SUDs) induce widespread molecular dysregulation in nucleus accumbens (NAc), a brain region pivotal for coordinating motivation and reward, which is linked to neural and behavioral disturbances promoting addiction. Despite the overlapping symptomatology of SUDs, different drug classes exert partly unique influences on neural circuits, cell types, physiology, and gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

75 Samples

Download data: TXT

(Submitter supplied) A hallmark of addiction is the ability of drugs of abuse to trigger relapse after periods of prolonged abstinence. Here, we describe a novel epigenetic mechanism whereby chronic cocaine exposure causes lasting chromatin and downstream transcriptional modifications in the nucleus accumbens (NAc), a critical brain region controlling motivation. We link prolonged withdrawal from cocaine to the depletion of the histone variant H2A.Z, coupled with increased genome accessibility and latent priming of gene transcription, in D1 dopamine receptor-expressing medium spiny neurons (D1 MSNs) that relate to aberrant gene expression upon drug relapse. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

26 Samples

Download data: TXT

(Submitter supplied) A hallmark of addiction is the ability of drugs of abuse to trigger relapse after periods of prolonged abstinence. Here, we describe a novel epigenetic mechanism whereby chronic cocaine exposure causes lasting chromatin and downstream transcriptional modifications in the nucleus accumbens (NAc), a critical brain region controlling motivation. We link prolonged withdrawal from cocaine to the depletion of the histone variant H2A.Z, coupled with increased genome accessibility and latent priming of gene transcription, in D1 dopamine receptor-expressing medium spiny neurons (D1 MSNs) that relate to aberrant gene expression upon drug relapse. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) This study investigates the impact of ionic strength on the gelation kinetics of collagen biomaterial inks and evaluates the efficiency of TGFβ-1 sequestration within these hydrogels, alongside their compatibility with bioprinting live chondrocyte and adipose-derived stem cell lines for cartilage tissue engineering. By adjusting sodium chloride and phosphate-buffered saline (PBS) concentrations, we demonstrate that reduced ionic strengths accelerate gelation, facilitating high-fidelity bioprinting while supporting high cell viability and post-printing proliferation of chondrocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: XLSX

(Submitter supplied) The life-threatening pathogen Leptospira interrogans navigates a dual existence: surviving in environmental reservoirs and infecting mammalian hosts. Leptospira biofilm formation is thought to be an important survival strategy in environmental contexts and may also contribute to the persistence of leptospirosis in maintenance hosts. Examining the correlation between biofilm formation and the virulence of pathogenic strains might improve our comprehension of the epidemiology of leptospirosis. more...

Organism:

Leptospira interrogans serovar Manilae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34667

8 Samples

Download data: TXT

(Submitter supplied) During early pregnancy, glucose is essential for the uterine epithelium and the developing embryo. In cows, studies have shown that progesterone increases the secretion of glucose into the uterine lumen. Nevertheless, how progesterone affects glucose metabolism in the uterine epithelium has been sparsely investigated. Therefore, our objective was to investigate how progesterone influences glucose metabolism in immortalized bovine uterine epithelial (BUTE) cells. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

8 Samples

Download data: TXT

(Submitter supplied) The effect of Runx1 expression in neonatal mouse ventricles was assessed with overexpression of Runx1 in cardiomyocytes using inducible Myh6-Cre.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

6 Samples

Download data: XLSX