Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq analysis of wild type dark grown PSB-D cell cultures

ABSTRACT: RNAseq analysis of wild type dark grown PSB-D cell cultures

PROVIDER: PRJEB10934 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1025437.fastq.gz	Fastqsanger.gz
	ERR1025438.fastq.gz	Fastqsanger.gz
	ERR1025439.fastq.gz	Fastqsanger.gz

Items per page:

1 - 3 of 3

Similar Datasets

RNAseq analysis of wild type dark grown PSB-D cell cultures

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

Identification of Peopod2 (PPD2) target genes through GSyellow-based ChIP-seq in Arabidopsis thaliana PSB-D cell cultures.

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

Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings

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

Effects of a 6h-long treatment with 90 mM sucrose to 4-d old, dark grown Arabidopsis seedlings

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

Pseudomonas sp. PsB

Project description:Pseudomonas sp. PsB Genome sequencing

| PRJNA1172183 | ENA

Light versus Dark gene expression in SAR11

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

Circadian rhythms study of the unicellular algae Ostreococcus tauri by shotgun proteomics: Dark adaptation, Global proteomics.

Project description:The overall set of experiments consist of sampling a culture of the unicellular algae Ostreococcus tauri (wild type) every 24 hours for 4 time points(ZT24, ZT48, ZT72 and ZT96). Each time point was performed with 5 replicate culture flasks, the cultures were grown under dark conditions. This proteome is associated to the transition from an 12:12 light:dark to a dark:dark regime.

2022-12-01 | PXD002909 | Pride

Transcriptome profiling of dark grown photoreceptor mutants of Arabidopsis.

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

Identification of genes involved in cell wall integrity signalling in Arabidopsis dark-grown hypocotyls

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

Transcriptome analysis of dark-grown cop1 and cop1BBX22-GFPox plants

Project description:The proper accumulation of BBX22 mediated by COP1 is crucial for plants to maintain better growth fitness when growing in the dark environment as well as responding to seasonal changes in day-length. The constitutive-photomorphogenic development of the cop1 mutant is enhanced in cop1BBX22-GFPox plants, which show a short hypocotyl, high anthocyanin accumulation and expression of light-responsive genes. Target genes responsible for the exaggerated light phenotype in cop1BBX22-GFPox plants were revealed by comparing transcriptomes among dark-grown wild-type, cop1 and cop1BBX22-GFPox plants. Expression of genes regulated by light and multiple hormones are altered in plants over-accumulating BBX22, implying a coordination role of BBX22 in light- and hormone-mediated seedling development.

2011-06-01 | GSE22983 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data