GEO DataSets

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

Organism:

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

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; Citrus sinensis; Populus; Oryza sativa; Dianthus caryophyllus; Solanum lycopersicum; Zea mays; Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

152 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) The goals of this study were to compare the transcriptome of two rice genotypes under salt stress by RNA-Seq. We performed differential gene expression analysis by comparing samples of same genotypes in control and stress conditions and different genotypes in the same condition.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

10 Samples

Download data: TXT

(Submitter supplied) At the transition from vegetative to reproductive growth in rice, a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem (SAM) to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27660

8 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) To investigate the underlying mechanisms that which genes involving in M. oryzae peroxisome dynamics in response to oxidative stress.

Organism:

Pyricularia oryzae; Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32309 GPL33328

6 Samples

Download data: XLS

(Submitter supplied) We examined the transcriptional data in rice leaves of TOP6A3 overexpressed line (TOP6A3-OE1) with WT (K3) plants under normal growth.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

4 Samples

Download data: XLSX

(Submitter supplied) RNA internal modifications play critical role in development of multicellular organisms and their response to environmental cues. Using nanopore direct RNA sequencing (DRS), we constructed a large in vitro epitranscriptome (IVET) resource from plant cDNA library labeled with m6A, m1A and m5C respectively. Furthermore, after transfer learning, the pre-trained model was used to detect additional RNA internal modification such as m1A, hm5C, m7G and Ψ modification. more...

Organism:

Oryza sativa; synthetic construct

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25738 GPL33241

8 Samples

Download data: FA, TXT

(Submitter supplied) Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. The combination of constitutive and acquired traits governs drought tolerance, which is crucial for maintaining crop productivity under drought. Drought affects protein synthesis, to uncover the translational landscape with response to drought stress in rice, polysome bound mRNA sequencing at anthesis stage in resistant APO and sensitive IR64 genotypes were performed. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

12 Samples

Download data: TSV

(Submitter supplied) Precise regulation of cell proliferation and differentiation is a key factor for diversity in morphology during organogenesis. Rice palea comprises two distinct regions, the marginal region of palea (MRP) and the body of palea (BOP), which exhibit heterogeneity in cellular composition and behavior. This study reveals that REP1 promotes epidermal cell proliferation and differentiation in the BOP, forming hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27029

4 Samples

Download data: TXT

(Submitter supplied) We report raw bulk RNA sequencing data of rice root sections from Meristem, Elongation and Maturation zones

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21087

30 Samples

Download data: COUNTS, XLSX

(Submitter supplied) We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

14 Samples

Download data: PDF, RDS

(Submitter supplied) Flowering of rice is triggered by transcriptional reprogramming at the shoot apical meristem (SAM) mediated by florigenic proteins produced in leaves in response to changes in the photoperiod. Florigens are more rapidly expressed under short day (SD) and include the HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) Phosphatidyl Ethanolamine Binding Proteins (PEBP). Hd3a and RFT1 are largely redundant at converting the SAM into an inflorescence, but whether they activate the same target genes and convey all photoperiodic information that modifies gene expression at the SAM is currently unclear. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

18 Samples

Download data: CSV

(Submitter supplied) Polyploidization is one of the effective ways to improve plant height and yield of rice (Oryza sativa L.). However, the molecular mechanism of regulation is not yet fully understood. Here, we investigated the agronomic traits of diploid (Balilla-2x) and tetraploid (Balilla-4x) of japonica rice variety Balilla. Compared with Balilla-2x, Balilla-4x exhibited significantly increased plant height, spike length and yield per plant. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: XLSX

(Submitter supplied) Stomata play a fundamental role modulating the exchange of gases between plants and the atmosphere. These microscopic structures form in high numbers on the leaf epidermis and are also present on flowers. Although leaf stomata are well-studied, little attention has been paid to the development or function of floral stomata. To characterise gene expression during the stomatal development in IR64 florets, as well as to identify potential gene expression differences in florets of transgenic plants with a reduction in stomatal density, a RNA-sequencing was carried out using floret samples from different developmental stages of IR64 (control) and transgenic plants overexpressing the gene OsEPF1. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

36 Samples

Download data: CSV

(Submitter supplied) We provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23013

6 Samples

Download data: BW, TXT

(Submitter supplied) The experiment tested organ-specific responses of rice (Oryza sativa ssp. japonica) to cold stress with a special focus on phytohormonal regulation. Cold stress (5°C, 24 h) was applies on the whole plants, leaves or roots. The results showed distinct responses when cold stress was applied on leaves, relating to photosynthesis and sugar synthesis as well as specific changes in phytohormones. On the other hand, stress applied to roots was more similar to the stress on the whole plant indicating roots to be more important in cold stress responses. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

46 Samples

Download data: SF

(Submitter supplied) Temperature-sensitive male sterility is one of the core components for hybrid rice breeding based on two-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) caused temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in ago1d mutant remain to be determined. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

12 Samples

Download data: XLSX

(Submitter supplied) In order to study the effects of GRP3 and GRP162 on rice resistance to high temperature stress, we knocked out these two genes.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

12 Samples

Download data: TXT

(Submitter supplied) In order to investigate the roles of ScOYE3, an old yellow enzyme gene from Saccharomyces cerevisiae, in detoxification and phytoremediation of 2-Nitroaniline (2-NA) in rice, we employed the RNA-seq approach to identify differentially expressed genes in 2-NA-treated wild-type (ZH11) rice plants and transgenic (OE1) rice plants overexpressing ScOYE3. Processing of RNA samples on the Illumina HiSeq 4000 system yielded more than 50 million reads, each 100bp in length, encompassing 6.28Gb of sequence data for each sample which was then mapped to the reference genome. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

8 Samples

Download data: XLS, XLSX

(Submitter supplied) Transcriptomic analyses (RNA-seq) on RNA isolated from rice embryo at 3 h, 6 h, and 12 h pot-imbibition was performed to identify changes in gene expression in response to CSA.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

18 Samples

Download data: TXT