GEO DataSets

(Submitter supplied) Pseudomonas syringae is an important plant pathogen that infects a wide variety of crops. The mgo (mangotoxin-generating operon) gene cluster produces an extracellular signaling molecule, leudiazen, and is highly conserved in Pseudomonas syringae strains. Here, we genetically removed mgo in Pseudomonas syringae pv. syringae (Pss) UMAF0158 to interrogate its impacts on bacterial infection. Loss of mgo not only alleviated the chlorosis symptom caused by Pss UMAF0158 infection, but also reduced bacterial population in tomato leaflets. more...

Organism:

Pseudomonas syringae pv. syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34164

6 Samples

Download data: TXT

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) The occurrence of Tomato chlorosis virus (ToCV) disease seriously damages tomato growth and yield, and there is no effective way to control ToCV transmission. So far, no studies have reported exploring the interaction between ToCV and tomato at the single cellular level. In this study, single cell RNA sequence was performed on a total of 26720 individual cells from healthy and ToCV-infected tomato leaves. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

4 Samples

Download data: MTX, TSV

(Submitter supplied) Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short- and long-term adjustments. more...

Organism:

Chlamydomonas reinhardtii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15922

18 Samples

Download data: TSV

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL26208

44 Samples

Download data: BW, TXT

(Submitter supplied) Transcriptome-wide association studies (TWAS) to pinpoint enhanced expression of genes involved in DNA repair attributed to viral resistance of atxr5 atxr6.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

20 Samples

Download data: TXT

(Submitter supplied) We identified RAD51 and RPA1A as partners of virus-encoded Rep protein. The two DNA repair proteins showed increased binding to heterochromatic regions and defense-related genes in atxr5 atxr6 vs wild-type plants. Consequently, the proteins had reduced binding to viral DNA in the mutant, thus hampering viral amplification. Additionally, RAD51 recruitment to the host genome arose via BRCA1, HOP2, and CYCB1;1, and this recruitment was essential for viral resistance in atxr5 atxr6. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

24 Samples

Download data: BW

(Submitter supplied) The mechanisms of acclimating to a nitrogen-fluctuating environment are necessary for the survival of aquatic cyanobacteria in their natural habitats, but our understanding is still far from complete. Here, the synthesis of phycobiliprotein is confirmed to be much earlier than that of photosystem components during recovery from nitrogen chlorosis and an unknown protein Ssr1698 is discovered to be involved in this synthetic process. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31267

6 Samples

Download data: TXT

(Submitter supplied) Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. V. vinifera scions are generally grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25542

60 Samples

Download data: TXT

(Submitter supplied) The mechanism underlying thrombocytosis in patients with iron deficiency anemia remains unknown. We present findings that support the hypothesis that low iron biases the commitment of Megakaryocytic-Erythroid Progenitors (MEP) toward the megakaryocytic (Mk) lineage in mice. In MEP of Transmembrane serine protease 6 knockout (Tmprss6-/-) mice, which exhibit iron deficiency microcytic anemia concomitant with thrombocytosis, we observed a megakaryocytic (Mk) bias, decreased labile iron, and decreased proliferation relative to wild-type (WT) MEP. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: TXT

(Submitter supplied) To determine whether circRNAs are involved in multiple myeloma (MM), we analyzed the expression profile of circRNAs and mRNAs in MM.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL21825

10 Samples

Download data: TXT

(Submitter supplied) Translational control of gene expression, including recruitment of ribosome to mRNA, is particularly important for stress responses. Translating Ribosome Affinity Purification (TRAP)-based RNA-sequencing offers a tool to study ribosome-associated mRNAs, which better proxies protein levels via the levels of transcripts to be translated into proteins. Magnesium (Mg) greatly inhibits plant growth and affects crop productivity. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

32 Samples

Download data: TXT

(Submitter supplied) Transcript and metabolite profiling were performed in leaf segments (sheath, base, middle, tip) of six rice cultivars with different sensitivity to high night temperatures (HNT). On the phenotypic level, leaves of HNT-sensitive rice cultivars showed clear stress symptoms by chlorosis and necrosis while almost no leaf phenotype different from the control was observed for the tolerant varieties. The aim of this study was to identify molecular key-player for HNT-sensitivity causing leaf senescence.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28757

48 Samples

Download data: TXT

(Submitter supplied) Rice stripe virus (RSV) causes the general chlorosis symptom and influences expression of numberous chloropalst-related genes at transcriotional level in Nicotiana benthamiana plants, but the mechanism are not well understood. Small RNAs (sRNAs), including virus-derived siRNA (vsiRNA) play roles in modulating genes expression post-transcriptionally. This present work presents multi-omics analysis of the transcriptome, sRNAome and degradome in RSV-infected N.benthamiana plants. more...

Organism:

Tenuivirus oryzaclavatae; Nicotiana benthamiana

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL30026 GPL30025

13 Samples

Download data: TXT

(Submitter supplied) Mitochondrial respiration and gene expression related to mitochondrial function were measured from the peripheral blood of infection and sepsis patients as well as healthy controls

Organism:

Homo sapiens

Type:

Other

Platform:

GPL29783

39 Samples

Download data: TXT

(Submitter supplied) Plant hormones and small secretory peptides often function as environmental stress mediators. Some recent reports indicate that small secretory peptides, such as CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE), also function as mediators of environmental stimuli. CLE2 is induced in roots by light depriviation. Plants without functional CLE2 showed a chlorosis phenotype when grown under shade. Here, we identified specific genes downstream of CLE2 in roots and shoots with transformed Arabidopsis plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17416

12 Samples

Download data: CEL, CHP

(Submitter supplied) Purpose: The goal of this study was to probe for the effects of iron-deficiency anemia on the cardiac transciprtome using RNA-seq Methods: C57B6 mice were weaned onto a control or iron-deficient diet for 6 weeks. Hearts were removed and total mRNA was submitted for RNA-seq. Sequencing data was aligned using STAR and differetial gene expression analysis conducted in R using EdgeR and DESeq2. qRT–PCR validation for genes of interest was performed using TaqMan and SYBR Green assays. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

20 Samples

Download data: TXT

(Submitter supplied) Millet is a dangerous weed in Hungary. Lack of seed dormancy helps it to spread easily and be present at maize, wheat and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study we detected the presence of several viruses in millet using DAS ELISA. Because serological methods can only detect the presence of the investigated particular pathogens, we suspected that other, previously unknown viruses can also be present in this weed. more...

Organism:

Panicum miliaceum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL28341

2 Samples

Download data: TXT

(Submitter supplied) Iron (Fe) is an essential micronutrient for the survival and proliferation of plants. Plants have evolved complex mechanisms to maintain Fe homeostasis in response of Fe deficiency conditions. To explore the mechanisms of Populus tomentosa response to Fe deficiency, we evaluated the physiological, biochemical and transcriptome differences of P. tomentosa between Fe-sufficient and Fe-deficient conditions. more...

Organism:

Populus tomentosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25314

12 Samples

Download data: TXT