GEO DataSets

(Submitter supplied) To investigate the effect of genotype on soybean transcriptomic response to different soybean cyst nematode races

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

18 Samples

Download data: XLSX

(Submitter supplied) To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.08G227700 in early maturation embryos using ChIP-seq.

Organism:

Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28801

4 Samples

Download data: NARROWPEAK

(Submitter supplied) To understand the molecular events underlying seed desiccation and germination, we performed transcriptome analysis of soybean (Glycine max) embryos at three seed developmental stages (early, mid and late desiccation), mature dry seeds, and three germination stages (3, 16 and 27 hour-after-imbibition).

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28801 GPL26488

46 Samples

Download data: TXT

(Submitter supplied) To understand the processes governing soybean seed development, we profiled the mRNA transcriptome and chromatin accessibility of cotyledon-stage seeds at the single-nucleus level.

Organism:

Glycine max

Type:

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

Platform:

GPL28801

2 Samples

Download data: BED, H5, MTX, TSV

(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 soja; Glycine max

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34481 GPL28801

12 Samples

Download data: TXT

(Submitter supplied) Nodulation Outer Protein P (NopP) and NopI of the type 3 secretion system (T3SS) of the rhizobium determine host specificity. Sinorhizobium fredii CCBAU25509 (R2) and CCBAU45436 (R4) have different NopP and NopI variants, affecting their respective symbiotic compatibilities with the cultivated soybean C08 and the wild soybean W05. Swapping the NopP variants between R2 and R4 has been shown to switch their compatibility with C08 with the rj2/Rfg1 genotype. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

45 Samples

Download data: TSV

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

Organism:

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

Type:

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

11 related Platforms

162 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:

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

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

154 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) ThisresearchonOceanobacilluspicturaeprovidesnewinsightsintomitigatingCdstressinsoybeanplants,reducingsoilCdcontent,andpromotingsoybeanseedlingrootgrowth.Italsoidentifiesnovelgenesandmicrobialspeciesrelevanttothemicrobialreductionofsoilheavymetalpollutionandtheresponsemechanismsofsoybeanplantstoheavymetals.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

12 Samples

Download data: TXT

(Submitter supplied) Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL28801

16 Samples

Download data: TXT

(Submitter supplied) Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21998 GPL28801

64 Samples

Download data: TXT