Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of Arabidopsis thaliana stems to investigate the transcriptome of myb103 mutants to better understand the mechanism underlying MYB103 action

ABSTRACT: Two null mutants of MYB103 were found to have decreased expression of FERULATE-5-HYDROXYLASE and reduced syringyl lignin in the basal inflorescence stem. The aim with this microarray experiment was to investigate the transcriptome of these myb103 mutants to better understand the mechanism underlying MYB103 action.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: David Ohman

PROVIDER: E-MEXP-3680 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

MYB103 is required for FERULATE-5-HYDROXYLASE expression and syringyl lignin biosynthesis in Arabidopsis stems.

Öhman David D Demedts Brecht B Kumar Manoj M Gerber Lorenz L Gorzsás András A Goeminne Geert G Hedenström Mattias M Ellis Brian B Boerjan Wout W Sundberg Björn B

The Plant journal : for cell and molecular biology 20121019 1

The transcription factor MYB103 was previously identified as a member of the transcriptional network regulating secondary wall biosynthesis in xylem tissues of Arabidopsis, and was proposed to act on cellulose biosynthesis. It is a direct transcriptional target of the transcription factor SECONDARY WALL ASSOCIATED NAC DOMAIN PROTEIN 1 (SND1), and 35S-driven dominant repression or over-expression of MYB103 modifies secondary wall thickness. We identified two myb103 T-DNA insertion mutants and che ...[more]

PMID: 22967312

Similar Datasets

Gene expression over the course of xylem tracheary element formation in cell suspension cultures of Arabidopsis thaliana

Project description:Transcriptomic analysis of gene expression during the differentiation of cell suspension cultures into tracheary elements using the biological system published by Pesquet et al., Current Biology (2010): tracheary element differentiation was triggered by externally supplying hormone-free habituated cell suspension cultures of Arabidopsis thaliana Col-0 with auxin, cytokinin and epibrassinolides; RNA samples extracted from 3 independent time-courses every 12h from 0h to 4 days were analyzed using ATH1 Arabidopsis Affymetrix micro-array Time-course design during tracheary element differentiation (3 independepent time-course were harvested from initiation 0h to 4 days every 12h) - total of 27 samples corresponding to the 3 replicates of 9 time point time-courses - gene expression was monitored along the time-course compared to 0h

2015-09-18 | E-GEOD-73146 | biostudies-arrayexpress

Temporal dependency of the transcriptional response to carbohydrate depletion contrasts with conservation of the rapid response to sucrose readdition

Project description:To investigate whether the transcriptional response to carbon (C) depletion and sucrose re-addition depend on the duration of C-depletion, Arabidopsis thaliana seedlings growing in liquid culture in weak continuous light were harvested 3, 6, 12, 24, 48 and 72 h after removing sucrose from the medium, and 30 min after resupplying sucrose at each of these times. After removing sucrose, soluble sugars fell strongly within 3 h, and starch was gradually depleted over 24 h, and hexose phosphates and ATP declined gradually over 72 h. Expression profiling using ATH arrays pointed to Overall the transcriptional response pointed to early transcriptional remodelling of metabolism to conserve C, followed by induction of photosynthesis and pathways that recycle C, and repression of growth-related processes. The time-dependent transcriptional response to C-depletion differed from that during a light/dark cycle and an extended night. Re-supplying sucrose for 30 min led to near-complete recovery of seedling sucrose levels, partial recovery of reducing sugars and phosphorylated intermediates, but no immediate change of starch or ATP. The rapid transcriptional response to sucrose readdition was conserved across the entire C-depletion time course, became larger with time. , and was highly enriched for regulatory genes. Whilst there was a rapid decrease of many C-depletion-induced transcripts, fewer transcripts increased. The majority of the transcripts that responded rapidly after resupplying sucrose also decreased after treating C-depleted seedlings with the transcriptional inhibitor cordycepin A, pointing to an important role for transcript turnover in the rapid response to sucrose.

2015-10-12 | E-MTAB-3143 | biostudies-arrayexpress

Sumoylation at Chromatin Governs Coordinated Repression of a Transcriptionnal Program Essential for Cell Growth and Proliferation 3

Project description:mRNA profiling of WI38 expressing shCt or shUbc9 4 days post-infection. The goals of this study is to analyse transcriptionnal changes in cells were sumoylation pathway is inactivated and to compare them with ChIPseq data for several histones marks and proteins of the SUMO machinery.

2013-11-25 | E-MEXP-3778 | biostudies-arrayexpress

Gene expression profiling of Fibroblasts of Sanfilippo syndrome type B patient

Project description:Gene expression profiling of human fibroblasts from patients with Sanfilippo syndrome type B (MPSIIIB) before and after correction of the Alpha N-acetylglucosaminidase (NAGLU) enzyme defect.

2011-03-15 | E-MEXP-3033 | biostudies-arrayexpress

Regulation of endometrial bleeding by uNK cells

Project description:Uterine NK cells (uNK) play a role in the regulation of placentation but their functions in non-pregnant endometrium are not understood. We have previously reported suppression of endometrial bleeding and alteration of spiral artery morphology in women exposed to asoprisnil, a progesterone receptor modulator (PRM). We now compare global endometrial gene expression in asoprisnil-treated versus control women and demonstrate a statistically significant reduction of genes in the IL-15 pathway, known to play a key role in uNK development and function. Suppression of IL-15 by asoprisnil was also observed at mRNA level (p<0.05), and immunostaining for NK cell marker CD56 revealed a striking reduction of uNK in asoprisnil-treated endometrium (p<0.001). IL-15 levels in normal endometrium are progesterone-responsive. Progesterone receptor (PR) positive stromal cells transcribe both IL-15 and IL-15RA. Thus, the response of stromal cells to progesterone will be to increase IL-15 trans-presentation to uNK, supporting their expansion and differentiation. In asoprisnil-treated endometrium, there is a marked down-regulation of stromal PR expression and virtual absence of uNK. These novel findings indicate that the IL-15 pathway provides a missing link in the complex interplay between endometrial stromal cells, uNK and spiral arteries affecting physiological and pathological endometrial bleeding. 39 Samples

2013-08-23 | E-GEOD-47577 | biostudies-arrayexpress

Sumoylation at Chromatin Governs Coordinated Repression of a Transcriptionnal Program Essential for Cell Growth and Proliferation

Project description:mRNA profiling of WI38 wild-type or overexpressiong the SUMO E3 ligase PIASy in human primary fibroblasts 24h post-infection. The goal of this study is to analyse transcriptional changes in cells over-expressing the SUMO E3 ligase PIASy and to compare them with ChIPseq data for several histones marks and proteins of the SUMO machinery including PIASy

2013-11-25 | E-MEXP-3776 | biostudies-arrayexpress

Gene expression profiling of parkinsonian substantia nigra

Project description:Affymetrix HG-Focus array was used to determine a global gene expression profile of clinically and neuropathologically confirmed cases of sporadic Parkinson's disease compared to controls. Major alterations were detected in signal transduction, protein degradation, dopaminergic transmission/metabolism, energy pathways/glycolysis, cell adhesion/cytoskeleton, extracellular matrix components and cell cycle functional classes. Post-mortem human brains were obtained from moderately to severe parkinsonism individuals based on the Hoehn & Yahr criteria. All the subjects were negative for AD pathology according to Braak & Braak. The average age for PD and control is 76.6 and 77.8 years, respectively. The average postmortem delay for PD and control is 26.2 and 19.8 hours, respectively.

2010-03-23 | E-GEOD-20333 | biostudies-arrayexpress

ADAR1 regulates the resistance of melanoma cells to T cells via miR-222 and ICAM1

Project description:The blossom of immunotherapy in melanoma highlights the need to delineate mechanisms of immune resistance. Recently, we have demonstrated that the RNA editing protein, adenosine deaminase acting on RNA-1 (ADAR1) is down-regulated during metastatic transition of melanoma, which enhances melanoma cell proliferation and tumorigenicity. Here we investigate the role of ADAR1 in melanoma immune resistance. Importantly, knockdown of ADAR1 in human melanoma cells induces resistance to tumor infiltrating lymphocytes in a cell contact-dependent mechanism. We show that ADAR1, in an editing-independent manner, regulates the biogenesis of miR-222 at the transcription level and thereby Intercellular Adhesion Molecule 1 (ICAM1) expression, which consequently affects melanoma immune resistance. ADAR1 thus has a novel, pivotal, role in cancer immune resistance. Corroborating with these results, the expression of miR-222 in melanoma tissue specimens was significantly higher in patients who had no clinical benefit from treatment with ipilimumab as compared to patients that responded clinically, suggesting that miR-222 could function as a biomarker for the prediction of response to ipilimumab. These results provide not only novel insights on melanoma immune resistance, but also pave the way to the development of innovative personalized tools to enable optimal drug selection and treatment. 13 formalin fixed paraffin embedded (FFPE) melanoma tissues were stained with hematoxilin and eosin for examination by an expert pathologist. Non-tumor tissue was removed. Total RNA was isolated using miRNeasy FFPE kit (Qiagen) according to the manufacture guidelines.

2015-12-31 | E-GEOD-67496 | biostudies-arrayexpress

Alexandraki-S.cerevisiae-WT SC BCS BPS

Project description:Reference experiment of wild type Saccharomyces cerevisiae cells of the BJ5457 background. Cells were grown in synthetic complete medium (SC) with the addition of the necessary aminoacids and factors (leucine, uracil, histidine, tryptophane) and harvested in exponential phase (OD=0.7-1). Cells were grown in the presence of BCS and BPS chelators. <br>

2014-11-01 | E-MEXP-3838 | biostudies-arrayexpress

Gene expression profiling of Fast vs. Slow Chinese Hamster Ovary cell lines using Wye3aHamster array

Project description:A 3rd generation Wye3aHamster microarray chip was used to carry out a differential expression microarray study of a panel of 30 slow- and fast-growing production cell lines, identifying a priority list of 240 transcripts (110 Up; 130 Down) that passed a statisical filter (ANOVA p-value <0.05, 1.3 fold-change) when the samples were grouped into fast versus slow and pairwise compared and a minimum Pearson Correlation Coefficent (PCC) of >0.7 when growth rate was used as a continuous variable (i.e. included genes have to satisfy BOTH criteria, not just one). This yielded a list of 240 genes. The 240-member genelist yielded 223 Annotated IDs, 203 of which are Unique and all of which are associated with contributing to a high rate of growth in production CHO cell lines. Prospective samples were isolated from 2 distinct groups of clones (slow growers and fast growers), all chosen from the same project (transfection of product transgene into parent line) generated at Pfizer Inc., Bioprocess R&D, Andover, MA, USA. Each group comprised 5 distinct clones, all of which had comparable Qp characteristics. The clones were passaged for 3 or 4 passages over 3-4 days to stabilise the phenotype and freeze stocks. Samples for array hybridization were generated in batch shake flask culture (60ml working volume) with AS1 medium and without feeds or temperature shift. Samples were collected at a single time point (72hrs - mid/late log) and each clone was grown in triplicate flasks, yielding a total of 30 samples for collection and processing. Two bioprocess-relevant variables, viable cell density (VCD) and viability were measured. From the VCD, the growth rate (h-1) was calculated.

2013-01-01 | E-GEOD-37251 | biostudies-arrayexpress

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