GEO DataSets

(Submitter supplied) Various species of rhizobium establish compatible symbiotic relationships with soybean (Glycine max) leading to the formation of nitrogen-fixing nodules in roots. The formation of functional nodules is mediated through complex developmental and transcriptional reprogramming that involves the activity of thousands of plant genes. However, host transcriptome responses that determine the outcome of the symbiotic interactions leading to the formation of functional or non-functional nodules remain unexplored. more...

Organism:

Glycine max; Glycine soja

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34481 GPL28801

12 Samples

Download data: TXT

(Submitter supplied) The luminal surface of the endothelium is exposed to dynamic blood flow patterns that are known to affect endothelial cell phenotype. In this study, human aortic endothelial cells (HAECs) were exposed to unidirectional laminar flow (20 dynes/cm2) or disturbed flow (±4 dynes/cm2, 2 Hz) for 48 hrs and then subjected to RNA sequencing. The sequencing data was used to analyze changes in endothelial cell gene expression and pathways associated with lipid metabolism.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

6 Samples

Download data: TXT

(Submitter supplied) Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacts human health beyond acute infection. Myalgia and fatigue represent two of the most prevalent symptoms in post-COVID-19 syndrome. To determine the mechanisms underlying prolonged muscle symptoms, we characterized longitudinal histopathological and transcriptional changes of skeletal muscle after acute respiratory SARS-CoV-2 infection in a COVID-19 hamster model and compared them with respiratory influenza A virus (IAV) infection. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33389

21 Samples

Download data: TXT

(Submitter supplied) Comprehensive profiling of hormone-dependent breast cancer (HDBC) has identified hundreds of protein-coding alterations contributing to cancer initiation, but only a handful have been linked to endocrine therapy resistance, potentially contributing to 40% of relapses. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ integrative functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. more...

Organism:

Homo sapiens; mixed DNA library

Type:

Other

Platforms:

GPL16791 GPL32000 GPL20301

68 Samples

Download data: FA, TXT

(Submitter supplied) Effective weed management tools are crucial for maintaining the profitable production of snap bean (Phaseolus vulgaris [L.]). Preemergence herbicides help the crop to gain a size advantage over the weeds, but the few preemergence herbicides registered in snap bean have poor waterhemp (Amaranthus tuberculatus) control, a major pest in snap bean production. Waterhemp and other difficult-to-control weeds can be managed by flumioxazin, an herbicide that inhibits protoporphyrinogen oxidase (PPO). more...

Organism:

Phaseolus vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29011

46 Samples

Download data: TXT

(Submitter supplied) Purpose: Parasites of the genus Eimeria, and the closely related human pathogen Cyclospora cayetanensis, cause enteric disease in livestock and people worldwide. These coccidian parasites must undergo maturation (sporulation) before becoming infectious. Understanding oocyst maturation would benefit attempts to reduce the harm they cause to veterinary and human health. No animal model exists to study C. more...

Organism:

Eimeria acervulina

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30280

19 Samples

Download data: XLSX

(Submitter supplied) DNA methylation was profiled in a genome-wide manner by Enzymatic Methyl-seq (EM-seq) in fetal brain of both sexes at three gestation days 45, 60 and 90. The analysis showed nearly 3-fold fewer differentially methylated sites (DMSs) between GD90 and GD60 (n=54) compared to that between GD60 and GD45 (n=150). Comparative analysis of the methylation data with the RNA-seq data previously generated from the same gestation times showed an opposition pattern where more number of differentially expressed genes (DEGs) were observed between GD90 and GD60 compared to GD60 and GD45.

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26351

12 Samples

Download data: COV

(Submitter supplied) Endothelial cells (ECs) in the descending aorta are exposed to high laminar shear stress, which supports an anti-inflammatory phenotype. High laminar shear stress also supports flow-aligned cell elongation and front-rear polarity, but whether these are required for the anti-inflammatory phenotype is unclear. Here, we show that Caveolin-1-rich microdomains polarize to the downstream end of ECs exposed to continuous high laminar flow. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) A critical problem facing all U. S. aquaculture is loss due to disease. In the past year alone, diseases accounted for 90% of all losses of trout intended for sale, greatly impacting the livelihood of our farmers. Previously, we focused on sustainable aquaculture efforts by evaluating the effects of dietary replacement (marine-based to plant-based protein sources) on rainbow trout. Through this effort, we developed a rainbow trout strain that thrives on an all plant-protein formulated diet (PSel/UI strain). more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24430

270 Samples

Download data: TXT

(Submitter supplied) Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) and a phaR mutant, both cultured under microoxic conditions (0.5% O2) in Götz minimal medium supplemented with mannitol. Keywords: microoxia, polyhydroxybutyrate, protein-DNA interaction, proteomics, Rhizobia, transcriptomics

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium diazoefficiens

Type:

Expression profiling by array

Platform:

GPL3401

6 Samples

Download data: CEL, CHP

(Submitter supplied) To investigate the effect that biological nitrogen fixation will have on plant responses to nitrogen dose at elevated CO2, alfalfa (Medicago sativa) lines were grown at three nitrogen doses and ambient or elevated CO2. Four lines were used in the study, two lines that can form nodules capable of fixing nitrogen (effective lines) and two lines that can not form nodules capable of nitrogen fixation (ineffective lines). more...

Organism:

Medicago sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30915

86 Samples

Download data: TXT

(Submitter supplied) The objective of this study is to evaluate ASO biodistribution and pharmacodynamic response following intravenous delivery of conjugated OTV, which utilizes transferrin-receptor binding to deliver ASO, vs. intrathecal delivery of naked ASO in cynomolgus monkeys, the current gold standard for ASO delivery. Three groups were included for comparison: 1) Negative control cohort = Four biweekly intravenous doses of saline (n=3); 2) IT cohort = Single intrathecal dose of 4mg MALAT1 ASO (n=3); 3)  OTV multi dose cohort = Four biweekly intravenous doses of 30mpk OTV:MALAT1 (n=3). more...

Organism:

Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28212

9 Samples

Download data: CSV, H5, MTX, TSV

(Submitter supplied) Erythromycin (ERY) is a commonly used antibiotic that can be found in wastewater effluents globally. Due to the mechanisms by which they kill and prevent bacterial growth, antibiotics can have significant unwanted impacts on the fish gut microbiome. The overall objective of this project was to assess the effects of erythromycin and an antibiotic mixture on fish gut microbiomes. The project was split into two experiments to assess gut microbiome in response to exposure with ERY alone or in mixture with other common antibiotics. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29994

18 Samples

Download data: CSV

(Submitter supplied) Intraspecific phenotypic variation markedly influences the damage that parasites inflict on their hosts. Such is the case for strains of Eimeria maxima, a costly enteric parasite of poultry, where strain APU-1 exhibits greater pathogenicity than APU-2. Here, we examined how these strains differ as oocysts mature to the fully-sporulated stage. We performed mi-croscopy and RNA-Sequencing on oocysts at regular intervals (6-12 hours) during sporulation. more...

Organism:

Eimeria maxima

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33915

42 Samples

Download data: XLSX

(Submitter supplied) Nosema is a diverse fungal genus of microsporidian unicellular, obligate symbionts of insects and other arthropods. We performed a comparative genomic analysis of N. muscidifuracis, a Nosema species infecting parasitoid wasp genus Muscidifurax, with six other genome-sequenced Nosema species. A sequence motif containing at least three consecutive Cs was significantly enriched immediately upstream of the start codon in all seven Nosema genomes. more...

Organism:

Muscidifurax zaraptor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33950

12 Samples

Download data: TXT

(Submitter supplied) Identify the change in transcriptomic and epigenetic profiles within the sorghum root system of the cultivar BTx623 in response to limiting phosphorus conditions. This data is from the 2022 publication "Sorghum root epigenetic landscape during limiting phosphorus conditions".

Organism:

Sorghum bicolor

Type:

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

Platforms:

GPL21615 GPL20818

34 Samples

Download data: BW, CSV, TSV

(Submitter supplied) Sunflowers are famous for their ability to track the sun throughout the day, and then reorient at night to face east the following morning. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism we used RNA sequencing to compare the transcriptional profiles of sunflower stems during heliotropism, and blue light-induced phototropism.

Organism:

Helianthus annuus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29971

180 Samples

Download data: CSV

(Submitter supplied) A cocktail of five bioinformatically and experimentally prioritized recombinant proteins was used immunize pigs and test for active antibody responses.

Organism:

Sus scrofa; Ascaris suum

Type:

Protein profiling by protein array

Platform:

GPL33467

111 Samples

Download data: TXT, XLSX

(Submitter supplied) Enzymatic browning on the cut edge of lettuce significantly limits its quality and shelf life. To characterize its molecular mechanisms, we performed comparative transcriptome analysis of three Romaine lettuce cultivars, Parris Island Cos (PC) with low browning potential, Tall Guzmaine (TG) with high degree of browning and Clemente (CL), a medium degree of browning cultivar derived from TG x PC. Before cutting, the phenylpropanoid and oxidative stress genes, such as PAL1, MYB1 and PPO were up-regulated in PC as compared to TG, while the expressions of genes involved in auxin, cytokinin hormone signalings and defense, such as ARF, AHP and PTI in PC were higher than TG. more...

Organism:

Lactuca sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22142

18 Samples

Download data: TXT

(Submitter supplied) Twelve clinically healthy backgrounded cattle (n=6 vaccinated, n=6 non-vaccinated), over four time points (median age in days: 107, 114, 183, 230) were selected for whole blood (Tempus Blood RNA Tubes) mRNA sequencing via NovaSeq 6000 S4 workflow. Sequenced raw reads (~35M/sample) were analyzed for the influence of time (immunological development) and vaccination with a commercial modified live viral multivalent vaccine on host gene expression.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

48 Samples

Download data: TXT