GEO DataSets

(Submitter supplied) Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5’P mRNA degradation intermediates, we show that co-translational mRNA decay is common in C. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32241

12 Samples

Download data: TXT

(Submitter supplied) Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5’P mRNA degradation intermediates, we show that co-translational mRNA decay is common in C. more...

Organism:

Candida albicans

Type:

Other

Platform:

GPL32241

28 Samples

Download data: TXT

(Submitter supplied) Traumatic brain injuries (TBIs) represent a large global disease burden and can result in several short- and long-term deficits. Treatment for TBIs are limited, however stem cell therapies involving either transplantation of exogenous stem cells or stimulation of endogenous stem cells have been proposed. These approaches possess issues with survival and differentiation of stem/progenitor cells, which highlights the need to elucidate mechanisms necessary for complete regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

28 Samples

Download data: MTX, TSV

(Submitter supplied) Live fish transport often results in mass mortality, but the underlying mechanisms are not well known. Largemouth bass (LMB, Micropterus salmoides) juveniles were subjected to 4-hour transportation followed by 5 days of recovery. Mortality (33.61 ± 10.58 %) of the transported fish mainly occurred between 2 and 3 days of recovery. Except for the dead fish, the survivors demonstrating abnormal symptoms were considered more sensitive to the transport stress than the normal ones. more...

Organism:

Micropterus salmoides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34925

68 Samples

Download data: TXT

(Submitter supplied) Deciphering the dietary immunomodulatory effects of a feed additive rich in verbascoside and triterpenic compounds like ursolic (MPLE, NATAC Biotech SL, Spain) on the systemic immune response and disease resistance of Atlantic salmon (Salmo salar L.) smolts.

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL28080

6 Samples

Download data: TXT

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

Organism:

Nannochloropsis oceanica

Type:

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

Platforms:

GPL20272 GPL16324

14 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that Kbu and H3K9m2 histone modifications were present in N. oceanica IMET1. Moreover, both Kbu and H3K9m2 positively regulated gene expression.

Organism:

Nannochloropsis oceanica

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20272

8 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) To be consistent with ChIP-seq data in this study, transcription regulation of CCM was reaccessed. In this experiment, about 800M clean reads were obtained for each sample. Obtained clean reads in each sample were over 84%, which were then mapped to the N. oceanica IMET1 reference genome. Differential expression analysis between low CO2-treated (LC) and control (high CO2; 5% CO2; HC) samples was performed by edgeR. more...

Organism:

Nannochloropsis oceanica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16324

6 Samples

Download data: TXT

(Submitter supplied) Using a dedicated split-root approach, we identified miRNAs regulated systemically by nitrogen availability in both shoots and roots of the Medicago truncatula model legume, depending on the CRA2 pathway, highlighting the phosphate-related miR399.

Organism:

Medicago truncatula

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30272

24 Samples

Download data: TSV

(Submitter supplied) In our search for biomarkers of maldevelopment, we focused on chemically-induced perturbation of the retinoic acid signaling pathway (RA-SP), a major pathway implicated in a plethora of developmental processes. A genome-wide expression screening was was performed on zebrafish embryos treated with two teratogens, all-trans retinoic acid (ATRA) and valproic acid (VPA), and a negative control, folic acid (FA).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

32 Samples

Download data: TSV

(Submitter supplied) Plasmodium parasites cause malaria, a global health disease that is responsible for more than 200 million clinical cases and 600 000 deaths each year. Most deaths are caused by various complications, including malaria-associated acute respiratory distress syndrome (MA-ARDS). Despite the very rapid and efficient killing of parasites with antimalarial drugs, 15% of patients with complicated malaria succumb. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Expression dynamics for all genes significantly regulated after the transition from dark to light and vice versa.

Organism:

Sediminicoccus rosea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33854

25 Samples

Download data: TXT

(Submitter supplied) Rainbow trout (1000 fish) was exposed to the bacterial pathogen F. psychrophilum by simple bath challenge without any pre-treatment with hydrogen peroxide. Samples (fin clip for Affymetrix QTL analysis) were taken from 167 moribund fish during the course of infection. When mortality/morbidity ended (day 40) we euthanized a total of 197 specimens of the remaining fish and took samples for DNA (QTL analysis) and assigned the status: Survivor. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by RT-PCR

Platform:

GPL32679

270 Samples

Download data: XLSX

(Submitter supplied) Hybrid generations usually face either a heterosis advantage or a breakdown that can be expressed by the level of parasite infection in hybrid hosts. Hybrids are less infected by parasites than parental species (especially F1 generations) or more infected than parental species (especially post-F1 generations). We performed the experiment with blood-feeding gill parasite Paradiplozoon homoion (Monogenea) infecting leuciscid species, Abramis brama and Rutilus rutilus, their F1 generation, and two backcross generations. more...

Organism:

Rutilus rutilus x Abramis brama; Rutilus rutilus; Abramis brama

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33681 GPL33683 GPL33682

90 Samples

Download data: FASTA, GTF, TSV

(Submitter supplied) To get the different expression genes under the treatment.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28386

8 Samples

Download data: TXT

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

Organism:

Marchantia polymorpha; Cyanidioschyzon merolae strain 10D

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32971 GPL32970 GPL32972

26 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) To evaluate role of PRC2 on transcriptional regulation in Cyanidioschyzon merolae, we generated loss of function mutants of a Ez homolog in Cyanidioschyzon merolae by homologous recombination based mutagenesis. Then we performed comparative transcriptome analyses using data obtained from Cme(z) and WT.

Organism:

Cyanidioschyzon merolae strain 10D

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32972

6 Samples

Download data: GTF, TXT

(Submitter supplied) Production of sterile fishes through artificial retention of a third set of chromosomes (triploidy) is a sustainable alternative for aquaculture since it reduces pressure on wild populations. However, these fishes have reduced survival in stressful conditions and in response to pathogens. In this study, the impact of Vibrio anguillarum infection on diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) was investigated to identify if there was any significant regulation by microRNAs (miRNA) in immune responsive tissues. more...

Organism:

Oncorhynchus tshawytscha

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL32570

56 Samples

Download data: TAB

(Submitter supplied) This study assayed the gene expression changes in response to chilling stress in the shoots and roots of tomato seedlings. Both a pretreatment and a concurrent ambient control were sampled to contrast gene expression.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16345 GPL27957

27 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to compare the transcriptome (RNA-seq) modulations in the roots and shoots of Arabidopsis thaliana, as a plant model, exposed to two toxic concentrations of rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

18 Samples

Download data: TXT