GEO DataSets

(Submitter supplied) Here, we reported transcriptome-wide m6A modification maps within single-base resolution using m6A-SAC-seq in rice and Arabidopsis. Our analysis uncovered a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL27860

32 Samples

Download data: TSV, TXT

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

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL13834 GPL27860

75 Samples

Download data: BIGWIG, BW, COV

(Submitter supplied) To investigate the effect of the OsINO80, we analysed differentially expressed genes of osino80 mutant compared to WT. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and osino80 mutant.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27860

6 Samples

Download data: BW, TXT

(Submitter supplied) To investigate the effect of the OsINO80, we analysed OsINO80 binding regions and analysed genome-wide H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 in the mutant and WT by ChIP-seq.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27860 GPL13834

61 Samples

Download data: BIGWIG

(Submitter supplied) To investigate the effect of the OsINO80, we analysed DNA methylation of osino80 mutant compared to WT.

Organism:

Oryza sativa Japonica Group

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27860

8 Samples

Download data: COV

(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:

Oryza sativa; Pyricularia oryzae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33328 GPL32309

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) Nitrogen (N) and phosphorus (P) are two primary components of fertilizers for crop production. Coordinated acquisition and utilization of N and P are crucial for plants to achieve nutrient balance and optimal growth in a changing rhizospheric nutrient environment. However, little is known about how N and P signaling pathways are integrated. We performed transcriptomic analyses and physiological experiments to explore gene expression profiles and physiological homeostasis in the response of rice (Oryza sativa) to N and P deficiency. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

9 Samples

Download data: TXT

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

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL27860

21 Samples

Download data

(Submitter supplied) I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences, which can be formed under various pH conditions. DNA methylation exhibits complex impacts on iM formation in vitro. However, how DNA methylation differentially affects pH dependent iM formation on a genome wide scale is completely uncharacterized in both humans and plants. To this end, we conducted iM-IP-seq under pH 5.5 and 7.0 conditions using CK and hyper/hypomethylated DNA in combination with BS-seq in rice. more...

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27860

17 Samples

Download data: NARROWPEAK

(Submitter supplied) I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences, which can be formed under various pH conditions. DNA methylation exhibits complex impacts on iM formation in vitro. However, how DNA methylation differentially affects pH dependent iM formation on a genome wide scale is completely uncharacterized in both humans and plants. To this end, we conducted iM-IP-seq under pH 5.5 and 7.0 conditions using CK and hyper/hypomethylated DNA in combination with BS-seq in rice. more...

Organism:

Oryza sativa Japonica Group

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27860

4 Samples

Download data: TXT

(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