GEO DataSets

(Submitter supplied) Background. Plasma donor-derived cell-free DNA (dd-cfDNA) is used to screen for rejection in heart transplants. We launched the Trifecta-Heart (ClinicalTrials.gov #NCT04707872), an investigator-initiated, prospective trial, to examine the correlations between genome-wide molecular changes in endomyocardial biopsies (EMBs) and plasma dd-cfDNA. The present report analyzes the correlation of plasma dd-cfDNA with the gene expression in EMBs from 4 vanguard centers and compared these correlations with those in 604 kidney transplant biopsies in the Trifecta-Kidney study (ClinicalTrials.gov #NCT04239703). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

137 Samples

Download data: CEL

(Submitter supplied) A majority of genes code for non-protein-coding RNA (ncRNA). Only a handful of ncRNA have characterised molecular functions, including key epigenetic roles in development and human disease. In human skeletal muscle reliance on suboptimal sequencing-based data has obfuscated characterization of ncRNAs. Herein, using more comprehensive RNA profiling and data-driven quantitative network methods we study regulation of ncRNAs during skeletal muscle hypertrophy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL34649

274 Samples

Download data: CEL, XLSX

(Submitter supplied) As the climate changes due to global warming, the frequency of appearance of marine-derived toxins increases. In particular, the need to investigate marine-derived toxins for which toxicity has not yet been identified is emerging. Blood vessels are passageways through which compounds entering the body move to various organs and are the sites first exposed to compounds. Therefore, it is important to know the effects of compounds on blood vessels when they enter the body. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) This study explored how the omega-6 to omega-3 fatty acid ratio in low-fish oil aquafeeds influences Atlantic salmon's antiviral and antibacterial immune responses. Atlantic salmon were fed aquafeeds rich in soy oil (high in omega-6) or linseed oil (high in omega-3) for 12 weeks and then challenged with bacterial (formalin-killed Aeromonas salmonicida; Asal) or viral-like (polyriboinosinic polyribocytidylic acid; pIC) antigens. more...

Organism:

Salmo salar

Type:

Expression profiling by RT-PCR

Platform:

GPL33997

116 Samples

Download data: TXT

(Submitter supplied) Early diagnosis of sepsis and discrimination from SIRS is crucial for clinicians to provide appropriate care, management and treatment to critically ill patients. Here, we describe identification of transcriptional mRNA biomarkers able to identify severe systemic inflammation and differentiate Sepsis from SIRS, in adult patients within a multi-center clinical study. All patients were recruited in Intensive Care Units (ICUs) from multiple UK hospitals including 59 patients with abdominal sepsis, 84 patients with pulmonary sepsis, 42 SIRS patients with Out-of-Hospital Cardiac Arrest (OOHCA), at four time points including 30 healthy control donors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

447 Samples

Download data: TXT

(Submitter supplied) Early multiple sclerosis lesions feature relative preservation of oligodendrocyte cell bodies with dying back retraction of their myelinating processes. Cell loss occurs with disease progression. Putative injury mediators include metabolic stress (low glucose/nutrient), pro-inflammatory mediators (interferon γ and tumor necrosis factor a), and excitotoxins (glutamate). Our objective was to compare the impact of these disease relevant mediators on the injury responses of human mature oligodendrocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

35 Samples

Download data: XLSX

(Submitter supplied) New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL24973

8 Samples

Download data: CSV

(Submitter supplied) New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24106

8 Samples

Download data: CSV

(Submitter supplied) Several studies have reported that functionally related genes exhibit similar codon usage, which has been shown to impact protein production by the control of mRNA decay or translation. However, codon-mediated control and their relationship to growth conditions have been intensely debated and remain unclear. Here, we investigate the post-transcriptional gene expression control mechanisms employed in cells in proliferation or quiescence. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) Signals are relayed from receptor tyrosine kinases (RTKs) at the cell surface to effector systems in the cytoplasm and nucleus, and coordination of this process is important for the execution of migratory phenotypes, such as cell scattering and invasion. The endosomal system influences how RTK signalling is coded, but the ways in which it transmits these signals to the nucleus to influence gene expression are not yet clear. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) While the acquisition of cellular plasticity in adult stem cells is essential for rapid restoration after tissue injury, little is known about the underlying molecular mechanisms governing this process. Here, we reveal that Notch signaling is a pivotal determinant conferring cross-compartment differentiation plasticity of airway secretory cells. Temporal Notch inhibition in secretory cells is required for alveolar differentiation upon injury, which is mediated by IL-1β-dependent modulation of Jag1/2 expression in ciliated cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

3 Samples

Download data: MTX, TSV

(Submitter supplied) Purpose: To evaluate whether the single nucleotide polimorphsim rs41291957, located in the pri-miR-143/145, influences the primary RNA secondary structure. Methods: In vitro transcription and folding for the pri-miR-143/145 carrying the WT allele (G) or the mutated one (A) was carried out. The RNAs were then subjected to RNAseI treatement for 30 minutes and RNA seq performed on the digested nucleic acids. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

2 Samples

Download data: TXT

(Submitter supplied) Using RNA-sequencing and strategic bioinformatic analysis we investigated the down-stream effects of NR4A2 and NR4A3 in monocytes and dissected their common and distinct signalling roles.NR4A2 selective genes were most associated with antigen presentation, NR4A3 selective genes were most associated with interferon/viral reponse and NR4A2/3 co-regulated genes were most associated with clasical innate immure response signaling e.g. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

18 Samples

Download data: TXT

(Submitter supplied) Aneuploidy, the state in which an organism’s genome contains one or more missing or additional chromosomes, often causes widespread genotypic and phenotypic effects. Most often, aneuploidies are deleterious; the most common examples in humans being Down’s syndrome (Trisomy 21) and Turner’s syndrome (monosomy X). However, aneuploidy is surprisingly common in wild yeast populations. In recent years, there has been debate as to whether yeast contain an innate dosage compensation response on the whole-genome level, or if these natural isolates are robust to aneuploidy without such a mechanism. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

116 Samples

Download data: CSV, FPKM_TRACKING, TXT

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

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Non-coding RNA profiling by array

Platforms:

GPL19057 GPL27649

40 Samples

Download data: RCC

(Submitter supplied) H/ACA small nucleolar RNAs (snoRNAs) guide pseudouridylation as part of a small nucleolar ribonucleoprotein complex (snoRNP). Disruption of H/ACA snoRNA expression in stem cells impairs pluripotency, yet it remains unclear how H/ACA snoRNAs contribute to differentiation. To determine if H/ACA snoRNA expression is dynamic during differentiation, we comprehensively profiled H/ACA snoRNA expression in multiple murine cell types and during differentiation in three cellular models, including mouse embryonic stem cells and mouse myoblasts. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL27649

22 Samples

Download data: RCC

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL21103

30 Samples

Download data: TAB

(Submitter supplied) The scope of this project is to study, using state-of-the-art systems biology approaches integrating the changes in metabolomics, lipidomics and transcriptomics, changes in hepatocytes' metabolism occurring in liver regeneration. We focused on altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC) occurring in the liver following partial hepatectomy (PH) or carbon-tetrachloride (CCl4) injection.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: TAB

(Submitter supplied) The optimal dietary requirement of omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA), namely docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), for Atlantic salmon that promotes optimal growth and health warrants careful investigation. We used 44K microarrays to study the influence of increasing levels of dietary DHA + EPA (0, 1.0 and 1.4% of the diet, as formulated) in the presence of high linoleic acid (LA) on Atlantic salmon growth and liver transcriptome. more...

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL11299

24 Samples

Download data: TXT

(Submitter supplied) The female menopause, characterised by reduced estrogen associates with an increased risk of recurrent UTIs caused by uropathogenic Escherichia coli (UPEC). Clinically such infections can be countered by topical vaginal estrogen treatment and the aim of this study was to investigate, in vitro, the effects of topical estrogen treatment on vaginal epithelial responses following challenge with E.coli flagellin used to mimic UPEC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data: IDAT, TXT