RNAseq analysis of wild type dark grown PSB-D cell cultures
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB10934 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1025437.fastq.gz | Fastqsanger.gz | |||
| ERR1025438.fastq.gz | Fastqsanger.gz | |||
| ERR1025439.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:RNA was isolated from wild-type dark grown PSB-D cell cultures in three biological repeats using the RNeasy Plant Mini Kit (Qiagen) and DNase I treated (Promega). A Trueseq RNA-Seq library (Illumina) was compiled and sequenced as 50-bp single read using Illumina HiSeq 2000.
2017-08-07 | E-MTAB-3915 | biostudies-arrayexpress
Project description:Genome-wide target genes of PPD2 were identified through ChIP-seq on Arabidopsis cell cultures. For ChIP-seq, PPD2 was fused to the GSyellow TAP tag and expressed from the 35S promoter. The p35S:PPD2-GSyellow construct was transformed into Arabidopsis thaliana PSB-D cell culture. ChIP was performed using anti-GFP antibody (abcam290).
2018-08-07 | E-MTAB-6513 | biostudies-arrayexpress
Project description:Arabidopsis bHLH transcription factor PIF1 has been shown function as a negative regulator of Chlorophyll biosynthesis. Pif1-2 mutant accumulate more protochlorophylide during prolonged dark growth condations, therefore the comparation between Wt and pif1-2 mutant will help us find the PIF1 target genes in Chlorophyll biosynthesis pathway at genome wide level under the dark grown conditions. We used microarrays to detail the global gene expression under the regulation of PIF1. Keywords: Genotype comparison
2008-05-30 | GSE11594 | GEO
Project description:Euglena gracilis is a flagellate photosynthetic microalga that, thanks to its metabolic adaptability, can grow under both autotrophic and heterotrophic conditions. We focused on the proteome of E. gracilis cultivated in Cramer-Myers medium in dark and light conditions. Cultures grown in the light showed a characteristic green coloration, while cultures incubated in the dark were bright, almost colorless, and had 60% fewer cells per volume. When cultured in the dark, microalga showed reduced concentration of chlorophylls (a, b, and total) and carotenoids compared to cells cultured in the light. Conversely, there was an increase in proline content in the dark compared to light cultivation. Phenol-extracted proteins were digested and purified using the SP3 protocol. We revealed 162 proteins, classified into 12 functional groups, which differentially accumulated in light- and dark-grown cells. The most represented categories in the case of dark cultivation were defense mechanisms, metabolism, and energy. Of note, in the category metabolism of lipids and sterols, we detected 4 proteins involved in the β-oxidation of fatty acids more abundant in the dark. Accumulation os stress- and detoxification-related proteins in microalgal cells cultivated in darkness supported interpretation of such condition as challenging stress factor. Euglena gracilis cultured in the dark is useful for basic research, applied biotechnology, and environmental protection.
2025-03-06 | PXD058143 | Pride
Project description:Dark grown Arabidopsis seedlings (Columbia gl1) were grown in the dark at 23°C for 4 days before adding 90 mM sucrose for 6h. Keywords: Response to nutrients; sugar sensing
2005-12-03 | GSE3704 | GEO
Project description:We investigated the transcriptional response of cand. Pelagibacter ubique cultures to light and dark when grown under carbon replete and deplete conditions. Results: During exponential phase, few genes were differentially transcribed between light:dark growth conditions. In stationary phase, a high proportion (9.7%) of coding sequences were found differentially expressed between treatments; 4.7% being up-regulated in the light (n=64) and 4.9% being up-regulated in the dark (n=67). Several components of the oxidative phosphorylation pathway were up-regulated in the dark, supporting physiological data showing higher respiration rates in darkness than in the light under starvation conditions. We also observed up-regulation of a proton translocating pyrophosphate synthase (SAR11_1040), which may be an additional energy production mechanism utilized by SAR11 cells in the dark. Finally, we noted the up-regulation of pili formation genes in the array data, consistent with the observation of pili in dark grown cells via electron microscopy.
2011-12-31 | GSE24134 | GEO
Project description:Transcriptome analysis of dark grown wild-type and lon1-1 mutant seedlings
| PRJNA1157344 | ENA
Project description:Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment. Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses
2005-09-04 | GSE2919 | GEO
Project description:Inhibition of cellulose synthesis by chemical inhibitors or in a mutant background leads to rapid inhibition of cell elongation. This inhibition appears to be an active process, which involves feedback signalling from the cell wall. We have isolated two loci THE1 and THE2, which are identified by mutations that partially suppress the dark-grown hypocotyl phenotype in a mutant background for cellulose synthase catalytic subunit CESA6/PROCUSTE1. THE1 encodes a receptor kinase and may play a role in this feedback signalling process. To identify genes that are regulated by THE1 and THE2, we compared the transcript profiles of 5 day-old dark-grown seedlings of the1-1/prc1-1 with prc1-1 ; the1-3/prc1-8 with prc1-8 ; prc1-8 or the1-3 with WS and the2-1/prc1-1 with prc1-1. - We have isolated two loci THE1 and THE2, which are identified by mutations that partially suppress the dark-grown hypocotyl phenotype in a mutant background for cellulose synthase catalytic subunit CESA6/PROCUSTE1. THE1 encodes a receptor kinase and may play a role in this feedback signalling process. To identify genes that are regulated by THE1 and THE2, we compared the transcript profiles of 5 day-old dark-grown seedlings of the1-1/prc1-1 with prc1-1 ; the1-3/prc1-8 with prc1-8 ; prc1-8 or the1-3 with WS and the2-1/prc1-1 with prc1-1. Keywords: gene knock out
2007-05-31 | GSE7937 | GEO