GEO DataSets

(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) Understanding the complex interactions between plants and herbivores is essential for improving crop resistance. To deep into the role of cyanogenesis in plant defence, we investigated the response of the cyanogenic Phaseolus lunatus (lima bean) and the non-cyanogenic Phaseolus vulgaris (common bean) to Tetranychus urticae infestation. Despite spider mite infesting both legumes, severity of leaf damage was reduced in lima bean. more...

Organism:

Phaseolus lunatus; Phaseolus vulgaris

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34090 GPL18673

12 Samples

Download data: TXT

(Submitter supplied) The nuclei of Glycine max from different tissues were collected. The samples were: soybean seed mid-maturation stage (10mm), seed late cotyledon stage (5mm), seed early cotyledon stage (3mm), seed heart stage (1mm), soybean green pods without seeds (stage), soybean flower bud (early flowering stage), soybean shoot apical meristem (stage), soybean trifoliate leaf (R5 stage), and soybean true leave (stage). more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

18 Samples

Download data: MTX, TSV

(Submitter supplied) The nuclei of Glycine max root seedlings (6 days-old) and nodules (28 days-old) were isolated and the library consstruction was performed applying 10x Genomics tecnology.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

5 Samples

Download data: MTX, TSV

(Submitter supplied) Cis-regulatory elements (CREs) precisely control the spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression and chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) binding motifs controlling cell-type specification and maintenance. more...

Organism:

Glycine max

Type:

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

Platform:

GPL28801

59 Samples

Download data: CSV, JPG, JSON, PNG, RDS, 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) The establishment of symbiotic interactions between leguminous plants and rhizobia requires complex cellular programming activated by Rhizobium Nod factors (NFs) as well as type III effector (T3E)-mediated symbiotic signaling. However, the mechanisms by which different signals jointly affect symbiosis are still unclear. Here we describe the mechanisms mediating the cross talk between the Sinorhizobium fredii T3E Nodulation Outer Protein L (NopL) effector and NF signaling in soybean. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

12 Samples

Download data: CSV

(Submitter supplied) In monocarpic plants, after the production of a certain number of fruits/seeds, the activity of the Shoot Apical Meristem (SAM) and of the meristems of the secondary axes stop in a coordinated way, leading to the cessation of flower production. This phenomenon has been called Proliferative Arrest (PA). It can be assumed as a general phenomenon in monocarpic plants, as it has been described in different species of this economically important group of plants. more...

Organism:

Pisum sativum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32857

16 Samples

Download data: TSV

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

Organism:

Phaseolus vulgaris; Xanthomonas citri pv. fuscans

Type:

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

Platform:

GPL33255

17 Samples

Download data: SF

(Submitter supplied) In cereal crop plants, sexual development and reproduction are key steps in producing seeds. However, genes responsible for reproductive function and development are largely unknown in soybean. Here, the soybean flower development was divided into three stages, namely the early stage(E), before pollination (BP) and post-pollination (PP). The flowers were hand-dissected into six tissues under the stereomicroscope, including anther (An), filament (Fi), stigma (St), style and ovary (SO), petal (Pe) and sepal (Se). more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21998

57 Samples

Download data: TXT

(Submitter supplied) Phosphorus (P) and iron (Fe) deficiency are major limiting factors for plant productivity worldwide. White lupin (Lupinus albus L.) has become a model plant for understanding plant adaptations to P and Fe deficiency, because of its ability to form cluster roots, bottle-brush-like root structures that play an important role in the uptake of P and Fe from soil. However, little is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. more...

Organism:

Lupinus albus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34521

12 Samples

Download data: CSV

(Submitter supplied) To investigate the effect of overepxression of wild-type and kinase deactivated GmMKK2 on soybean trangenic hairy root gene expression

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

18 Samples

Download data: XLSX

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

Organism:

Glycine max

Type:

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

Platform:

GPL28801

28 Samples

Download data: BW, TXT

(Submitter supplied) Flowering time is a critical trait to determine regional adaptation and yield of crops including soybean. Evening Complex (EC) components soybean LUX1, LUX2, and ELF3a are critical for flowering and adaptation to lower latitudes. However, the mechanisms of EC in regulating flowering time remain largely unclear in soybean. Here, we identified GmJMJ19 and GmJMJ20 gene paralogs encoding JmjC-domain containing proteins, which co-express and interact with GmLUX2. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

4 Samples

Download data: TXT

(Submitter supplied) Flowering time is a critical trait to determine regional adaptation and yield of crops including soybean. Evening Complex (EC) components soybean LUX1, LUX2, and ELF3a are critical for flowering and adaptation to lower latitudes. However, the mechanisms of EC in regulating flowering time remain largely unclear in soybean. Here, we identified GmJMJ19 and GmJMJ20 gene paralogs encoding JmjC-domain containing proteins, which co-express and interact with GmLUX2. more...

Organism:

Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28801

4 Samples

Download data: BW

(Submitter supplied) Flowering time is a critical trait to determine regional adaptation and yield of crops including soybean. Evening Complex (EC) components soybean LUX1, LUX2, and ELF3a are critical for flowering and adaptation to lower latitudes. However, the mechanisms of EC in regulating flowering time remain largely unclear in soybean. Here, we identified GmJMJ19 and GmJMJ20 gene paralogs encoding JmjC-domain containing proteins, which co-express and interact with GmLUX2. more...

Organism:

Glycine max

Type:

Other

Platform:

GPL28801

20 Samples

Download data: BW

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

Organism:

Arabidopsis thaliana; Glycine max

Type:

Other

Platforms:

GPL21309 GPL17970

19 Samples

Download data: TSV

(Submitter supplied) Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. more...

Organism:

Glycine max; Arabidopsis thaliana

Type:

Other

Platforms:

GPL21309 GPL17970

11 Samples

Download data: TSV

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

Organism:

Brassica napus; Glycine max; Dianthus caryophyllus; Arabidopsis thaliana; Solanum lycopersicum; Citrus sinensis; Zea mays; Populus; Solanum tuberosum; Oryza sativa; Saccharum officinarum

Type:

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

11 related Platforms

160 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. more...

Organism:

Arabidopsis thaliana; Brassica napus; Solanum tuberosum; Saccharum officinarum; Glycine max; Dianthus caryophyllus; Solanum lycopersicum; Zea mays; Citrus sinensis; Populus; Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

152 Samples

Download data: BROADPEAK, NARROWPEAK