GEO DataSets

(Submitter supplied) The phytochromes (PHYs) are a family of photoreceptors which absorb light of red and far-red wavelengths to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in wheat and performed replicated RNA-seq studies to analyze and compare the regulons of each phytochrome under long day photoperiods.

Organism:

Triticum turgidum subsp. durum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19107

32 Samples

Download data: FA, TXT

(Submitter supplied) The phytochromes (PHYs) are a family of photoreceptors which absorb red and far-red light to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in tetraploid wheat and performed RNA-seq studies to analyze and compare the regulons of each phytochrome under short day photoperiods.

Organism:

Triticum turgidum subsp. durum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27807

12 Samples

Download data: TXT

(Submitter supplied) The present study quantifies the transcriptomes of wild-type and transgenic Ubi::OsYHB rice seedlings (in the genetic background of Oryza sativa ssp. japonica CV Nipponbare) grown in the dark or under continous red light (Rc, at 50 µmol m-2 s-1) conditions.

Organism:

Oryza sativa; Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL2025

8 Samples

Download data: CEL

(Submitter supplied) Two aspects of light are very important for plant development: the length of the light phase or photoperiod and the quality of incoming light. Photoperiod detection allows plants to anticipate the arrival of the next season, whereas light quality, mainly the red to far-red ratio (R:FR), is an early signal of competition by neighbouring plants. phyB represses flowering by antagonising CO at the transcriptional and post-translational levels. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) Daylength is a key indicator of seasonal information that determines major patterns of behavior in plants and animals. Photoperiodism has been described in plants for about 100 years, but the underlying molecular mechanisms of daylength perception and signal transduction in many systems are not well understood. In trees, photoperiod perception plays a major role in growth cessation during the autumn as well as activating the resumption of shoot growth in the spring, both processes controlled by FLOWERING LOCUS T2 (FT2) expression levels and critical for the survival of perennial plants over winter. more...

Organism:

Brachypodium distachyon

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23254

149 Samples

Download data: BW, TXT

(Submitter supplied) Daylength is an important seasonal cue, and genetic variation in the regulation of photoperiodism has been selected for in adapting wheat and barley to northern latitudes. Despite the importance of this trait, the mechanism by which monocot plants sense photoperiod is not known. We find in Brachypodium distachyon that photoperiodism is mediated by phytochromeC (phyC), a chromophore that acts as a molecular timer and measures the length of the night. more...

Organism:

Brachypodium distachyon

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23254 GPL29167

11 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) This study is the first research that provides valuable insight into the complex regulation networks underlying phytochrome-mediated anther development in plant. Furthermore, the results also provide new clues for cultivating new male sterile lines in hybrid rice breeding.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

12 Samples

Download data: XLSX

(Submitter supplied) Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

22 Samples

Download data: CEL

(Submitter supplied) Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21179

12 Samples

Download data: TXT, XLSX

(Submitter supplied) To investigate the molecular and physiological functions of SWAP1 in light signaling. We show that SWAP1 modulates global gene expression and alternative splicing both under dark and red light treated conditions

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

36 Samples

Download data: XLSX

(Submitter supplied) The maintained vegetative phase (mvp) mutant has a non-flowering phenotype caused by deletions including, but not limited to, the genes CYS, PHYC and VRN1. However the impact of these deletions on flowering genes and global gene expression is still unknown. In this study, we showed that these deletions caused the up-regulation of several pathogenesis related (PR) and jasmonate responsive genes using microarray analysis. more...

Organism:

Triticum aestivum; Triticum monococcum

Type:

Expression profiling by array

Platform:

GPL3802

6 Samples

Download data: CEL

(Submitter supplied) Etiolated seedling response to one hour of continuous red light. Four-day-old dark-grown wild-type RLD and phyA101, phyB1 and phyAphyB mutant seedlings were transferred to Rc (680 nm, 8 mol m-2 s-1) for 1 h or retained in darkness as controls. Three different biological replicates of each treatment were grown separately and extracted, processed, and analyzed independently.RNA was extracted and subjected to expression analysis by using the Affymetrix ATH1 microarray containing approximately 22,000 Arabidopsis genes .

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

24 Samples

Download data

(Submitter supplied) Plants of Solanum tuberosum ssp andigena, which tuberize only under SD conditions, were grown in growth chambers under non-inductive LD conditions and half of the plants were transferred to inductive SD conditions for 1 or 15 days, whilst the rest of the plants were kept as controls in LD. Transgenic potato plants with reduced phyB levels, which tuberize irrespective of photoperiod, were also grown in LD conditions. more...

Organism:

Solanum tuberosum; Nicotiana sylvestris; Solanum tuberosum subsp. andigenum; Nicotiana tabacum

Type:

Expression profiling by array

Platform:

GPL1901

28 Samples

Download data: GPR

(Submitter supplied) Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su & Lagarias 2007 Plant Cell 19, 2124-2139). In the present study, comparative transcript profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

15 Samples

Download data: CEL, CHP

(Submitter supplied) Phytochrome B (phyB), one member of phytochrome family in rice, plays important roles in regulating a range of developmental processes, and stress responses. However, little information about the mechanism involved in phyB-mediated light signaling pathway has been reported in rice. Another, it has been well-known that microRNAs (miRNAs) perform important roles in plant development and stress responses. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19290

4 Samples

Download data: TXT

(Submitter supplied) The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15302

4 Samples

Download data: TXT

(Submitter supplied) Molecular mechanisms of flowering in Adonis amurensis

Organism:

Adonis amurensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26179

6 Samples

Download data: FA, XLS

(Submitter supplied) phytochrome B (phyB) acts as the red light photoreceptor and negatively regulates the growth-promoting factor PHYTOCHROME INTERACTING 4 (PIF4) through a direct physical interaction, which in turn changes the expression of a large number of genes. phyB-PIF4 module regulates a variety of biological and developmental processes in plants. In this study, we demonstrate that B-BOX PROTEIN 11 (BBX11) physically interacts with both phyB and PIF4. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: TXT

(Submitter supplied) To analyse the regulation of transcripts in grain embryo and endosperm during development, we performed RNA-Seq for wheat from 14 and 25 day post anthesis (DPA). And long-read sequencing for mixed whole grains from 14 and 25 DPA was employed to obtain full-length transcripts. A series of differentially expressed genes and tissues-specific genes of embryo and endosperm were identified. Moreover, 4351, 4641, 4516 and 4453 genes with A, B and D homoeoloci were detected in the four tissues. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23509

12 Samples

Download data: TXT, XLSX

(Submitter supplied) Photoperiod regulated flowering is a well understood developmental pathway in the intensively studied Brassicaceae species Arabidopsis thaliana and in the monocot rice, but less so in other angiosperm groups. One such group, the temperate legumes in the Fabaceae family which are important both agriculturally and ecologically, accelerate their flowering in response to long-day photoperiods (LD), but lack functional homologues of key regulatory genes present in A. more...

Organism:

Medicago truncatula

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17491

18 Samples

Download data: CSV