GEO DataSets

(Submitter supplied) Castor is an important industrial raw material. Drought leads to delayed development and reduced yield of castor plants. However, the molecular mechanism of the response of castor plants to drought stress has not been determined. In this study, physiological, biochemical, and RNA-seq analyses were conducted on castor roots under PEG-6000 stress for 3, 7, and 4 d (11 d) of rehydration. The activities of GR, APX, SOD, and CAT in the roots of the castor plants under PEG-6000 stress increased at 3 d and decreased at 7 d, while the activity of POD continued to increase. more...

Organism:

Ricinus communis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27533

18 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are small non-coding RNAs between 18-23nts in size which regulate the translation and stability of target mRNAs. miRNAs are present in dietary plants and are conventionally thought to be degraded during the gastrointestinal digestion process. Recent reports suggest that a few dietary microRNAs may exhibit resistance to this process, enter systemic circulation and exert biological effects on animal physiology, currently known as cross-kingdom regulation. more...

Organism:

Glycine max; Allium sativum; Curcuma longa; Emblica officinalis

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

8 Samples

Download data: XLSX

(Submitter supplied) The goal of this study was to produce a reference transcriptome for the nickel hyperaccumulator Leucocroton havanensis endemic from Cuba and use this transcriptome as a reference to identify genes responding to the presence or the absence of nickel in both roots and shoots of this species

Organism:

Leucocroton havanensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25206

4 Samples

Download data: CSV, FASTA

(Submitter supplied) Light plays a key role in plant growth, development and response to adversity. Plants perceive different wavelengths of light in the environment through various photoreceptors and regulate plant growth and development through light signaling. However, there are fewer studies on the effects of different light qualities on the growth and development of tree species at high altitude. In the study, the effects of blue and green light treatments on the growth and development of Populus cuttings were investigated. more...

Organism:

Populus qamdoensis; Populus schneideri

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34572 GPL34573

18 Samples

Download data: TXT

(Submitter supplied) For the RNA-seq experiments, two-week-old seedlings were cutting and harvested the basal ends of stem cuttings (0.5 cm). Samples were collected from two biological replicates (40 cuttings each).

Organism:

Populus ussuriensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25374

2 Samples

Download data: TXT

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

Organism:

Manihot esculenta

Type:

Expression profiling by high throughput sequencing

4 related Platforms

26 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) The gene expression profiling analysis from WT and cold treated samples of cassava that were used with other multi-omics data to build gene model annotation of Cassava.

Organism:

Manihot esculenta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28909

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) The start site analysis of transcripts from WT and cold treated samples of cassava that were used with other multi-omics data to build gene model annotation of Cassava.

Organism:

Manihot esculenta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33130

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Quant-Seq (3'-end sequencing technique) of mRNAs to identify the 3'-ends of transcripts to analyse the 3'-UTR that were used with other multi-omics data to build gene model annotation of Cassava.

Organism:

Manihot esculenta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21635

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Full length long read transcript sequences were used as guides along with other multi-omics data to build gene model annotation of Cassava.

Organism:

Manihot esculenta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33129

2 Samples

Download data: BED

(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:

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

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:

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

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

154 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) The plant cell wall serves as a critical interface between the plant and its environment, offering protection against various stresses and contributing to biomass production. Hemicellulose is one of the major components of the cell wall, and understanding the transcriptional regulation of its production is essential to fully understanding cell wall formation. This study explores the regulatory mechanisms underlying one of the genes involved in hemicellulose biosynthesis, PtrPARVUS2. more...

Organism:

Populus tremula x Populus alba

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34368

7 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) For the RNA-seq experiments there week-old seedlings were cutting and subsequently transfer to 1/2 MS medium with or without 6% PEG6000 for 7 d and harvested roots. Samples were collected from there biological replicates (12 seedings each).

Organism:

Populus ussuriensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25374

12 Samples

Download data: TXT

(Submitter supplied) Frost is a major abiotic stress limiting plant growth and development. Climate change models predict an increase in the magnitude and frequency of late-frost events, which, together with an observed loss of soil insulation, will significantly damage roots. To withstand freezing stress, plants have evolved an adaptative process known as cold acclimation. While this process is well documented, it is known that the plant response to multiple stresses is unique and cannot be deduced from the response to each stress taken separately. more...

Organism:

Salix viminalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32869

12 Samples

Download data: FA, TXT

(Submitter supplied) The length of internodes is critical in determining the height of the castor plant (Ricinus communis L.), and is closely associated with internode elongation. However, the exact mechanisms underlying internode elongation, particularly in the main stem of the castor plant, remain uncertain. To investigate further, we conducted a study using the dwarf castor variety 071113, comparing it with the homologous high-stalk Zhuansihao as a control. more...

Organism:

Ricinus communis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33754

6 Samples

Download data: XLSX

(Submitter supplied) ChIP-seq was carried out with H3K4me3 antibody using Stem differentiating xylem from wild-type plants under drought conditions

Organism:

Populus trichocarpa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26322

12 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Illumina technology was used to generate mRNA profiles of stem apex of Populus yunnanensis with cutting and inverted cutting. Total RNA was extracted separately from each plant and pooled to three biological replicates per condition. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

Organism:

Populus yunnanensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33986

12 Samples

Download data: FA, TXT

(Submitter supplied) We reported the small RNA profiles of disease free and SLCMV infected leaves of susceptible and tolerant genotypes of cassava. The sRNA data generated through high throughput small RNA sequencing revealed critical regulatory role of host and pathogen derived small RNAs during SLCMV infection.

Organism:

Manihot esculenta

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21982

3 Samples

Download data: FA

(Submitter supplied) Illumina technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering. Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France). more...

Organism:

Populus trichocarpa; Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30192 GPL30193

60 Samples

Download data: TXT