Indentifying the binding site of FL1 on DNA in blue light condition
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1082336 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28168529_1.fastq.gz | Fastqsanger.gz | |||
| SRR28168529_2.fastq.gz | Fastqsanger.gz | |||
| SRR28168530_1.fastq.gz | Fastqsanger.gz | |||
| SRR28168530_2.fastq.gz | Fastqsanger.gz | |||
| SRR28168531_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:FLs can regulate the transcription of a series of downstream genes. Therefore, this sequencing was devised to verify whether FL1 can associate with the chromatin of these downstream genes.
2025-05-19 | GSE260609 | GEO
Project description:This sequencing was designed to identify the downstream genes that were regulated by CRY2 in darkness and blue light or regulated by FL1/FL3 in darkness.
2025-05-19 | GSE260607 | GEO
Project description:A tuberization inhibitor has long been postulated, but not yet found. We found that blue light inhibits tuberization in Norland, a day-neutral variety of Solanum tuberosum L. Tissue-cultured plants formed tubers within 8 weeks under continuous darkness, and white, red, or far-red light. Preliminary experiments indicated that a one- or two-day exposure to blue light after 3-4 weeks of dark treatment will inhibit tuber formation in ‘Norland’ plants. Using this system and expression profiling, we may be able to identify candidate tuberization inhibitors. 'Norland' plants (subcultured from existing cultures and grown for two weeks under continuous 100 umol/m2-s white fluorescent light) were placed in tuber-inducing media containing 6% sucrose, vitamins, MS salts, and kinetin (2.5 mg/L). Tubes containing plants were wrapped in two layers of aluminum foil. After 3 weeks and 2 days, half of the tubes were exposed to 6-7 umol/m2-s blue light. The other half of the tubes were left in darkness (controls). After 2 days, all plants were harvested and frozen in liquid nitrogen. Plants exposed to blue light were harvested under blue light. Control plants were harvested under < 2 umol/m2-s light conditions. All plant transfers were done at 1700 (5 PM) to avoid possible complications due to circadian effects. Experiments were performed four times, from subculture to harvest. RNA was extracted from stem and leaf tissue of plants using the Qiagen RNeasy Plant Mini kit. Extracted RNA was then converted to dsDNA using the Invitrogen protocol and reagents for double stranded cDNA synthesis. The resulting dsDNA was in vitro transcribed into amplified RNA using the Ambion procedure and reagents for in vitro transcription. cDNA was purified using Qiagen MinElute columns and protocol. Amplified RNA was purified using Ambion columns or Qiagen RNeasy columns and the Ambion protocol, and quantified using RiboGreen dye fluorometry. Keywords: Direct comparison
2008-02-13 | GSE10491 | GEO
Project description:Purpose: The goal of this study was to characterize the transcript levels of genes in Drosophila photoreceptor neurons in response to blue light. Using transcriptome profiling of isolated photoreceptor nuclei, we analyzed the changes in gene expression that occur in response to 3h of blue light exposure at 1 or 6 days post-eclosion. We identified sets of genes with both up-regulated and down-regulated expression in response to blue light at either age.
2018-06-20 | GSE106820 | GEO
Project description:We investigated light dependent gene expression changes in the marine ochrophyte Nannochloropsis oceanica CCMP1779. These algae have several putative blue light photoreceptors but appear to lack red light photoreceptors. To study early light signaling in N. oceanica and avoid as much as possible secondary downstream events, we quantified gene expression changes in dark-adapted cells after a short blue or red light pulse. More genes were differentially expressed under blue than under red light. In addition, fold change in expression was smaller for the red light-treated samples. For example, the median fold change of induced genes was 3 for blue light and 2.5 for red light. Moreover, hierarchical cluster analysis showed that gene expression after red light treatment was more similar to the dark control than after blue light treatment.
2022-01-05 | GSE164714 | GEO
Project description:FelixGarza2017 - Blue Light Treatment of
Psoriasis (simplified)
This model is described in the article:
A Dynamic Model for
Prediction of Psoriasis Management by Blue Light
Irradiation.
Félix Garza ZC, Liebmann J,
Born M, Hilbers PA, van Riel NA.
Front Physiol 2017; 8: 28
Abstract:
Clinical investigations prove that blue light irradiation
reduces the severity of psoriasis vulgaris. Nevertheless, the
mechanisms involved in the management of this condition remain
poorly defined. Despite the encouraging results of the clinical
studies, no clear guidelines are specified in the literature
for the irradiation scheme regime of blue light-based therapy
for psoriasis. We investigated the underlying mechanism of blue
light irradiation of psoriatic skin, and tested the hypothesis
that regulation of proliferation is a key process. We
implemented a mechanistic model of cellular epidermal dynamics
to analyze whether a temporary decrease of keratinocytes
hyper-proliferation can explain the outcome of phototherapy
with blue light. Our results suggest that the main effect of
blue light on keratinocytes impacts the proliferative cells.
They show that the decrease in the keratinocytes proliferative
capacity is sufficient to induce a transient decrease in the
severity of psoriasis. To study the impact of the therapeutic
regime on the efficacy of psoriasis treatment, we performed
simulations for different combinations of the treatment
parameters, i.e., length of treatment, fluence (also referred
to as dose), and intensity. These simulations indicate that
high efficacy is achieved by regimes with long duration and
high fluence levels, regardless of the chosen intensity. Our
modeling approach constitutes a framework for testing diverse
hypotheses on the underlying mechanism of blue light-based
phototherapy, and for designing effective strategies for the
treatment of psoriasis.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000695.
To cite BioModels Database, please use:
Chelliah V et al. BioModels: ten-year
anniversary. Nucl. Acids Res. 2015, 43(Database
issue):D542-8.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000695 | BioModels
Project description:Cryptochromes are blue-light receptors in plants and animals. Homodimers are the physiologically active form of plant cryptochromes that mediates blue light regulation of gene expression and photomorphogenesis, but how light regulates the photoreceptor activation and inactivation remains unclear. We identified an Arabidopsis protein BIC1 (Blue-light Inhibitor of Cryptochromes 1) that inhibits all photoreactions of plant cryptochrome 2 (CRY2) examined, allowing direct tests of the photoactivation and inactivation mechanisms of CRY2. We found that blue light stimulates homodimerization of CRY2, whereas BIC1 binds to CRY2 to suppress CRY2 dimerization and the interaction of CRY2 with its signaling partners. We further show that cryptochromes and phytochromes mediate light induction of BIC1 transcription, evoking the negative feedback circuitry to control homeostasis of the active cryptochromes under the broad spectra of solar radiation in nature.
2016-12-02 | GSE80350 | GEO
Project description:Saccharina japonica is one of the most important marine economic crops worldwide. Blue light usually plays a significant role in the lives of Saccharina that may be beneficial to the culture system. Here we applied high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of Saccharina japonica with blue light and dark exposure respectively. Comparative analysis of gene expression was conducted to understand the underlying molecular mechanisms. RNA-seq analysis yielded 70,497 non-redundant unigenes. 25,924 unigenes of them had good comparability with known gene sequences in existing species. Based on the values of RPKM, 11,660 differentially expressed unigenes were detected in expression profiles between blue light and dark exposed samples. Our results provide clues to potential genes identification in the species and lay the foundation for future functional genomics study. mRNA expression of Saccharina japonica with 2 different treatment (sample exposed to Dark condition, and sample exposed to blue light respectively) was determined by method of RNA-Seq
2012-10-02 | E-GEOD-33853 | biostudies-arrayexpress
Project description:The growth orientation of the Marchantia polymorpha thallus – a system of dorsiventralized, indeterminate axes – is modulated by light. We show that red and blue light act antagonistically to control thallus flatness, with red light signalling promoting epinasty and blue light signalling promoting hyponasty. We found that loss-of-function mutations in the blue light receptor MpPHOT led to epinasty, while loss-of-function mutations in the red light receptor MpPHY resulted in hyponasty. We hypothesize that these antagonistic activities of blue and red light signalling are balanced in white light, resulting in the development of flat thalli. Using time-resolved transcriptomics, we identified genes that were rapidly induced upon light exposure. Among these genes were all six members of the M. polymorpha BBX gene family. Mutants harbouring loss-of-function mutations in two of the six MpBBX transcription factors developed defective thalli. Mpbbx1 loss-of-function mutants formed hyponastic thalli, while Mpbbx5 loss-of-function mutants developed epinastic thalli. Double mutants Mpbbx1 Mpbbx5 grew flat, supporting the hypothesis that they function antagonistically. Together, these data indicate that phototropin-mediated blue light and phytochrome-mediated red light signalling antagonistically modulate thallus flatness, and that BBX transcription factors also act antagonistically to regulate thallus flatness.
2026-01-21 | GSE316508 | GEO
Project description:We identified 737 differentially expressed genes, including 430 upregulated genes and 307 downregulated genes, by calculating the gene FPKM in each sample and conducting differential gene analysis. Gene ontology analysis and KEGG pathway enrichment analysis suggested that blue light influenced visual perception, sensory perception of light stimulus, phototransduction, and JAK-STAT signaling pathways. Differential lncRNA, circRNA and miRNA analysis suggested that blue light exposure affected pathways for retinal cone cell development and phototransduction, among others.
2020-08-24 | GSE149549 | GEO