title: IdentificationOf genes responsive to non-metabolised glucose analogs: approach to hexokinase-independent glucose sensing

summary:
It has been strongly argued that plant cells should have a means of sensing sugars at the cell surface, so that extracellular and intracellular sugars can be sensed separately and their metabolism coordinated (Lalonde et al., Plant Cell, 11, 707-26, 2000). There is good evidence for an intracellular hexokinase-dependent pathway of hexose sensing in plants, but very little evidence for a hexokinase-independent signalling pathway, such as that provided by SNF3 or RGT2 in yeast. Many papers on sugar sensing in plants cite work from two laboratories as evidence for hexokinase-independent hexose signalling in plants. The first is that in which cell-wall invertase and sucrose synthase genes were induced by treatment of a Chenopodium suspension culture with 30 mM 6-Deoxyglucose (6DOG) for 24 h (Roitsch et al., Plant Physiol 108, 285-294, 1995; Godt et al., J. Plant Physiol 146, 231-238, 1995). The second is that in which a patatin transgene in Arabidopsis was shown to be weakly induced by growth over several days on a mixture of 30 mM glucose plus 30 mM 3-O-methylglucose (3OMG), but strongly induced by growth on 30 mM Glc plus 90 mM 3OMG (Martin et al., Plant J, 11, 53-62, 1997). We are not aware of any examples of Arabidopsis genes which respond to 6DOG or 3OMG yet this is an area of wide significance. Identification of such a gene would help to establish if a hexokinase-independent signalling system operates in plants, and would provide a basis for establishment of a genetic screen for mutants, using the gene promoter linked to a reporter such as luciferase. The aim of this proposal is to discover any genes which are either activated or repressed by glucose AND by 3OMG and/or 6DOG, but not by mannitol (an osmotic control). The use of both 3OMG and 6DOG will help to identify non-specific effects of either. All substrates will first be analysed by HPLC to confirm that they are pure. Arabidopsis Col-0 seedlings will be grown in vitro for 7 days in the absence of sugars, then treated with 30 mM glucose or glucose analogue for 8 h (these conditions are based on concentrations and time courses of Roitsch et al.). RNA will then be isolated from multiple independent plates to minimise biological variation.

Experimenter name = Dorthe Villadsen
Experimenter phone = 0131 650 5318
Experimenter fax = 0131 650 5392
Experimenter address = Institute of Cell and Molecular Biology
Experimenter address = University of Edinburgh
Experimenter address = The King_s Buildings
Experimenter address = Mayfield Road
Experimenter address = Edinburgh
Experimenter zip/postal_code = EH9 3JH
Experimenter country = UK
Keywords: growth_condition_design

first: Dorthe

last: Villadsen

first: Steve

last: Smith


title: Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana

status: Public on Jan 08 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary:
Agrobacterium tumefaciens, a bacterial species found in temperate soils world wide, is the causative agent of crown gall disease on many plants. A. tumefaciens-induced tumours are feared in orchards and vineyards because of their pathological interference with nutrient and water supply which results in crop decline. Small wounds at the crown of the plant, usually induced by wind-bending, are potential entry sites for the bacterium. The tumorous growth is initiated by the integration and expression of the T-DNA of the bacterial Ti plasmid within the plant nuclear DNA. The T-DNA encodes enzymes catalysing the synthesis of increased concentrations of auxin and cytokinin, and of opines which stimulate cell division and enlargement. The fast growing tumours have been shown to be a strong nutrient sink on their host plants. As a matter of fact, sugar and K+ content were found to be up to 10- and 5-fold, respectively, higher in this tissue and transpiration was about 15 times increased compared to normal tissue. Whereas the morphological structure as well as some physiological and biochemical parameters of the tumour have been analysed in detail, little is known about the underlying gene expression pattern. Proliferation and growth of the tumour induced by Agrobacterium tumefaciens is obviously due to the extraordinary high concentration of phytohormons, minerals and metabolites. Their influence on regulation of gene transcription will provide information on the mechanisms underlying fast tumour growth. In a project funded by the DFG we recently started to investigate the role of solute transporter for tumour development on the model plant Arabidopsis thaliana. By comparing the expression pattern of RNA preparations from Arabidopsis tumour and non-tumour tissue, we will be able to identify genes which facilitate crown gall development. For the expression analysis with an Affymetrix full genome chip we will induce tumours at the base of an injured Arabidopsis inflorescence stalk (var. Wassilewskija, WS-2). RNA will be extraxted from tumour and injured non-tumor inflorescence stalk tissue using the RNeasy Plant Mini Kit (Qiagen), followed by a DNase treatment to eliminate DNA contamination.

This Series record represents a partial dataset. The complete dataset was submitted under GEO accession number GSE13927.

Experimenter name = Rosalia Deeken
Experimenter phone = +49 931 8886121
Experimenter fax = +49 931 8886158
Experimenter institute = Julius-von-Sachs-Institute of Biosciences Molecular Plant Physiology and Electrophysiology
Experimenter address = Julius-von-Sachs-Platz 2
Experimenter address = Wuerzburg
Experimenter zip/postal_code = D-97082
Experimenter country = Germany
Keywords: pathogenicity_design

overall_design: 4 samples were used in this experiment

first: Rosalia

last: Deeken

first: Rainer

last: Hedrich

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Functional Genomics of Ozone Stress in Arabidopsis.

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Ozone is known to induce gene expression in plants. The roles of the induced genes and the molecular basis for the induction however largely remain to be elucidated. We will expose 2 week-old Arabidopsis seedlings to 200 ppb ozone for 1 h. RNA will be extracted from control and ozone-fumigated seedlings 3 h following the end of the fumigation period. The induction of the known anti-oxidant enzyme GST will be confirmed prior to submission of the RNA samples to GARNet. Changes in gene expression will be assessed by hybridising microarrays with fluorescently labelled cDNA prepared from control and ozone-fumigated seedlings. The role of selected genes will be inferred from their sequence and further established by over expression under the control of the 35S or cell-specific promoters and by searching for mutants among single transposon or T-DNA insertion collections. Plants will be analysed on the basis of traits that are known to be affected by ozone including growth, flowering and stomatal responses. In addition, the ozone calcium signature we have reported previously (Clayton et al.1999) will be studied by crossing transgenic or mutant plants with apoaequorin or yellow cameleon 2.1-transformed plants.

Experimenter name = Eleri Short
Experimenter phone = 01524 593929
Experimenter fax = 01524 843854
Experimenter department = Department of Biological Sciences
Experimenter institute = Lancaster University
Experimenter address = Department of Biological Sciences
Experimenter address = Lancaster University
Experimenter address = Lancaster
Experimenter zip/postal_code = LA1 4YQ
Experimenter country = UK
Keywords: compound_treatment_design

overall_design: 6 samples were used in this experiment

first: Eleri

last: Short

first: Alan

last: Shirras


title: AtGenExpress: Basic hormone treatment of seeds

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Basic hormone treatment of seeds
Experimenter name = Mikihiro Ogawa  , Shinjiro Yamaguchi  , Weiqiang Li  , Yuji Kamiya
Experimenter institute = AtGenExpress
Keywords: hormone treatment

overall_design: 12 samples were used in this experiment

first: Mikihiro

last: Ogawa

first: Shinjiro

last: Yamaguchi

first: Weiqiang

last: Li

first: Yuji

last: Kamiya


title: Molecular bases of zinc tolerance and accumulation by Arabidopsis halleri

summary:
This application is from a NERC-funded consortium (Mark MacNair, Nick Smirnoff, Exeter) and (Brian Ford-Lloyd, John Newbury, Birmingham). Metal tolerance is one of the classic examples of micro-evolution. Despite extensive research the physiological bases of the adaptation in plants are largely unknown. Arabidopsis halleri is a zinc tolerant, zinc accumulating species whereas Arabidopsis petraea is non-accumulating and non-tolerant.
The objective of our programme is to identify:
a) those key genes that act to determine Zn tolerance and accumulation in Arabidopsis (and which account for the difference in performance of A. halleri and A. petraea grown in the presence of elevated Zn), and
b) those _downstream_ genes that are expressed as part of the tolerance or accumulation response.
Phase 1: Total of 24 chips: Material ready by May 2003. The results will:
a) tell us how effectively material derived from other Arabidopsis species hybridises to the chips, and
b) identify genes that are differentially expressed in the two species in the presence and absence of Zn stress (thus providing initial lists of genes that may be responsible for Zn tolerance or accumulation- (but see phase 2). A. halleri exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides. A. petraea exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides.
Phase 2: Total of 48 chips: Material ready by September 2003. The results will tell us which genes, identified as having appropriate expression patterns, co-segregate with the Zn tolerance or accumulation phenotype and will provide firmer candidate genes for intensive study. Bulks will be produced from F3 progeny (from the halleri x petraea cross) following phentoypic analyses for Zn tolerance and accumulation. A bulk of F3 progeny all exhibiting high Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides. A bulk of F3 progeny all exhibiting low Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides. A bulk of F3 progeny all exhibiting high Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides. A bulk of F3 progeny all exhibiting low Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides.

Experimenter name = H. John Newbury
Experimenter phone = 0121 414 5581
Experimenter fax = 0121 414 5925
Experimenter institute = University of Birmingham
Experimenter address = School of Biosciences
Experimenter address = University of Birmingham
Experimenter address = Edgbaston
Experimenter address = Birmingham
Experimenter zip/postal_code = B15 2TT
Experimenter country = UK
Keywords: stimulus_or_stress_design;  organism_part_comparison_design; strain_or_line_design

sample_organism:
Arabidopsis lyrata subsp. petraea
Arabidopsis halleri

overall_design: 24 samples were used in this experiment

first: H

middle: J

last: Newbury


title: Dark-induced gene expression in sfr6

summary:
The sfr6 mutant was identified on the basis of its failure to cold acclimate, and exhibits a marked deficiency in cold-and osmotic stress-inducible gene expression (Knight et al., 1999). We have demonstrated that genes of this type (so-called COR genes) are misregulated if they contain the DRE (drought-responsive element, or CRT; C-repeat) cis acting element in their promoter (Boyce et al., 2003). Micro-array analysis has allowed us to identify a number of COR genes misregulated in sfr6, all of which contain the DRE element. However, these experiments have indicated that other genes, not of the COR group, are also misregulated in the mutant and these do not contain the DRE element. We chose the three non-COR genes that were most clearly down-regulated in sfr6 on our previous micro-array, and identified each as of these as dark-inducible. We now seek to address two questions: (1) Can we discover more dark-regulated genes that are down-regulated in the mutant, and thus identify a second cis-acting element with which SFR6 may be interacting? (2) Do all of the non-COR genes that are misregulated in sfr6 fall into the category of dark-inducible, or is SFR6 likely to be interacting with three or more regulons?
For this micro-array experiment, we will subject sfr6 and wild type Arabidopsis, grown in a 16/8-h light/dark cycle, to darkness for 3h or 6h at ambient growth temperature. Under these conditions we see strong up-regulation of the three genes we have identified as dark-inducible, and we see clear down-regulation of expression in sfr6.
References. Knight H, Veale E, Warren GJ, Knight MR (1999) The sfr6 mutation in Arabidopsis suppresses low-temperature induction of genes dependent on the CRT/DRE sequence motif. Plant Cell 11: 875-886. Boyce JM, Knight H, Deyholos M, Openshaw MR, Galbraith DW, Warren G, Knight MR (2003). The sfr6 mutant of Arabidopsis is defective in transcriptional activation via CBF/DREB1 and DREB2 and shows sensitivity to osmotic stress. Plant Journal 34: 395-406.

Experimenter name = Heather Knight
Experimenter phone = 01865 275023
Experimenter fax = 01865 275074
Experimenter institute = University of Oxford
Experimenter address = Department of Plant Sciences
Experimenter address = University of Oxford
Experimenter address = South Parks Road
Experimenter address = Oxford
Experimenter zip/postal_code = OX1 3RB
Experimenter country = UK
Keywords: growth_condition_design; genetic_modification_design

first: Heather

last: Knight

first: Marc


title: The effects of mutants in stress response pathways on gene expression during senescence

summary:
Many signalling pathways are involved in controlling gene expression during plant senescence. Pathways involving SA, JA and ethylene have a role in senescence but none are essential for the senescence process to occur. The aim of this experiment is to classify senescence-enhanced genes into groups depending on the signalling pathways that regulate them. This will provide useful information on the relative importance of each signalling pathway during senescence and allow us to separate potential senescence-specific genes and pathways from the stress response pathways.Mutants in genes in the ethylene pathway (ein2) and the jasmonate pathway (coi1) and the NahG transgenic plant which is defective in the salicylic acid pathway will be grown until the mid flowering stage. Fully developed green and partially senescent leaves will be harvested from the plants at this stage.  In addition, two different lines of Arabidopsis (Col5 glabrous and Col-0) will be grown as controls. Leaves will be harvested from the two control plants before flowering (green) and at mid flowering as above. The control plants will be harvested at two stages to identify the senescence- enhanced genes. The effects of each mutation on the senescence related expression of these genes will then be studied.Mutant RNAs will be isolated in duplicate. The two control accessions will act as replicates for the wild type. Two wild type accessions will be used to reduce possible differences that could be observed the mutants due to slight differences in background.

Experimenter name = Vicky Buchanan-Wollaston
Experimenter phone = 01789 470382
Experimenter fax = 01789 470552
Experimenter address = Horticulture Research International
Experimenter address = Wellesbourne
Experimenter address = Warwick
Experimenter zip/postal_code = CV35 9EF
Experimenter country = UK
Keywords: genetic_modification_design; development_or_differentiation_design

overall_design: 10 samples were used in this experiment

first: Vicky

last: Buchanan-Wollaston


title: AtGenExpress: Comparison of plant hormone-related mutants

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Comparison of plant hormone related mutants
Experimenter name = Hideki Goda  , Shigeo Yoshida  , Yukihisa Shimada
Experimenter institute = AtGenExpress
Keywords: Comparison_of_plant_hormone-related_mutants

overall_design: 8 samples were used in this experiment

first: Hideki

last: Goda

first: Shigeo

last: Yoshida

first: Yukihisa

last: Shimada


title: AtGenExpress: Cytokinin treatment of seedlings

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Wild-type and ARR22 overexpressing seedlings were treated with t-zeatin for 3 hours
Experimenter name = Takatoshi Kiba  , Takeshi Mizuno
Experimenter institute = AtGenExpress
Keywords: Cytokinin treatment

first: Takatoshi

last: Kiba

first: Takeshi

last: Mizuno


title: AtGenExpress: ARR21C overexpression

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Wild-type and ARR21C overexpressing seedlings were compared.
Experimenter name = Takatoshi Kiba  , Takeshi Mizuno
Experimenter institute = AtGenExpress
Keywords: ARR21C overexpression

first: Henrik

last: Townsend

first: Zoe

last: Emmerson


title: AtGenExpress: Different temperature treatment of seeds

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Wild-type seeds were treated at 22 C and 4 C
Experimenter name = Mikihiro Ogawa  , Shinjiro Yamaguchi  , Yuji Kamiya  , Yukika Yamauchi
Experimenter institute = AtGenExpress
Keywords: temperature

first: Yukika

last: Yamauchi

first: Beatrice

last: Schildknecht


title: AtGenExpress: Pathogen Series: Response to Erysiphe orontii infection

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Responses to E. orontii infection were assayed in wild-type Col-0 plants at 6, 12, 18, 24, 48, 72, 96, and 120 hours after inoculation of adult leaves. Inoculation was done via settling tower, using 10 day old E. orontii cultures. Leaves number 7 to 10 were selected for profiling.
Experimenter name = Fred Ausubel  , Julia Dewdney
Experimenter institute = AtGenExpress
Keywords: pathogen series

overall_design: 48 samples were used in this experiment

first: Fred

last: Ausubel

first: Julia

last: Dewdney


title: AtGenExpress: Response to sulfate limitation

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
This experiment studies the effect of sulfate limitation in the roots of 10-day-old Arabidopsis seedlings from Columbia-0 ecotype
Experimenter name = Akiko Maruyama  , Hideki Takahashi
Experimenter institute = AtGenExpress
Keywords: sulfate limitation

overall_design: 22 samples were used in this experiment

first: Akiko

last: Maruyama

last: Takahashi


title: AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Responses to B. cinerea infection were assayed in wild-type Col-0 plants at 18 and 48 hours after inoculation of adult leaves. Leaves were inoculated by placing 4 5-ul drops of a 5x10e5 spore solution on each leaf. Control leaves were spotted with droplets of 24g L-1 potato dextrose broth medium.
Experimenter name = Carine Denoux  , Fred Ausubel  , Julia Dewdney  , Simone Ferrari
Experimenter institute = AtGenExpress
Keywords: pathogen series

first: Carine

last: Denoux

first: Simone

last: Ferrari


title: Seedling transcriptome affected by Norflurazon-induced photobleaching of chloroplasts

summary:
Regulation of expression of genes encoding chloroplast components is critical to the autotrophic plant and never more so than in the cotyledons of the de-etiolating seedling. Many chloroplast proteins are nuclear-encoded and a retrograde signal from the chloroplasts (the Plastid Signal) modulates nuclear transcription. However, not all chloroplast-targeted genes are subject to this control and not all plastid-dependent nuclear genes are chloroplast-targeted. We therefore aim to provide the most comprehensive screen yet of which genes are affected by plastid-signalling. To specifically knock-out positive plastid signalling in light-grown cotyledons, the herbicide Norflurazon (NF) is supplied in the growth medium, causing a carotenoid deficiency that leaves the chloroplasts vulnerable to photobleaching. This blocks the expression of a subset of nuclear genes, such as Lhcb and HEMA1.
Two pairs of RNAs will directly compare the transcription in seedlings grown under continuous white light with and without NF. A third RNA will also be compared from a mutant that shows a degree of constitutive positive plastid signalling. These two mutants act synergistically to counteract the effect of NF on nuclear transcription. The gun1,gun5 double mutant maintains a significantly higher level of Lhcb and HEMA1 expression in the presence of photobeached chloroplasts than the NF-treated wild-type. This transcriptome set will therefore complement RNA1 (wild-type+NF) and indicate which of the genes identified from the RNA1/RNA2 comparison are subject to the particular gun1/gun5 plastid signalling pathway(s).
The growth of conditions of the seedlings (namely on MS medium supplemented with 1.5% sucrose, for 3 days under continuous WL following 2 days germination in darkness) has been chosen from the results of our own recent studies using Northern blotting techniques that show these conditions to maximise the respective NF and gun mutant effects on Lhcb and HEMA1 gene expression. This experiment is part one of a two-part study to compare the transcriptional output of this NF-affected pathway with that of a newly discovered FR-mediated pathway. A subsequent array experiment will assess the nuclear response as affected by this FR/ phyA-input pathway and the two sets of array data will be compared and contrasted.
Note:
Col-0 wild-type (NASC code N1092). gun1,gun5 double mutant(obtained from Enriquez Lopez-Juez, Royal Holloway, University of London.(Mochizuki et al. 2001 PNAS 98: 2053-2058). This line cannot be donated by us as it is the IP of Joanne Chory (SALK Institute, USA). Treatment = a herbicide (Norflurazon) application which leads to chloroplast photobleaching and hence down regulation of nuclear genes dependent on plastid signalling from intact chloroplasts.

Experimenter name = Alex McCormac
Experimenter phone = 023 80594297
Experimenter fax = 023 80594319
Experimenter address = School of Biological Sciences
Experimenter address = Division of Cell Sciences
Experimenter address = University of Southampton
Experimenter address = Bassett Crescent East
Experimenter address = Southampton
Experimenter zip/postal_code = SO16 7PX
Experimenter country = UK
Keywords: genetic_modification_design

first: Alex

last: McCormac

first: Matthew

last: Terry


title: Peroxisomal mdh mutant

summary:
The aim is to study the function of peroxisomal NAD-malate dehydrogenase in fatty acid beta-oxidation, glyoxylate cycle and photorespiration. Both peroxisomal MDH genes (At2g22780 and At5g09660) have been knocked out with T-DNA insertions and a double mutant made. Double mutant seedlings are blocked in beta-oxidation - they are 2,4DB resistant and beta-oxidation genes are repressed. They carry out glyoxylate cycle as normal. Plants grow well in soil and produce seed. Microarray analysis will tell us the extent of changes in gene expression in the mutant. For microarray analysis seeds are stratified at 4 C on agar medium with 1/2 strength M&S salts and 1% sucrose for 2 days, then seedlings grown for 2 days at 20 C in the light (100 umol/m2/s). Triplicate samples will be grown for mutant and wild type (col-0) and RNA isolated from each.
Experimenter name = Itsara Pracharoenwattana
Experimenter phone = 0131 650 5316
Experimenter fax = 0131 650 5392
Experimenter department = Institute of Molecular Plant Sciences
Experimenter institute = University of Edinburgh
Experimenter address = Daniel Rutherford Building University of Edinburgh
Experimenter address = The King's Buildings
Experimenter address = Edinburgh
Experimenter zip/postal_code = EH9 3JH
Experimenter country = UK
Keywords: genetic_modification_design

first: Itsara

last: Pracharoenwattana

first: Steven

last: Smith


title: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Controls)

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis.  The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC.
The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves.  Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways.
The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves.  We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts.  We have also demonstrated that Arabidopsis leaf development is altered by these systemmic signals and that lesions in the jasmonate and ethylene signalling pathways block these responses. Our experimental design is shown below:
We have 4 treatments and 7 timepoints. (0, 2, 4, 12, 24, 48, 96 h)
We would sample from 5 individual plants that would be pooled for each RNA preparation.
This would require 28 chips and this would include extra replication of the 0 time-point control (deemed by many as nessary).
Experimental details:
All plants were germinated for 7 days under the following conditions:
Humax multi-purpose compost, ambient carbon dioxide (370 ppm) and ambient light (250 µmol/m/s), constant temperature of 20°C and a 10 h photoperiod (8 am until 6 pm). After a week the the seedlings were potted up into 104-cell plug trays for a further 2 weeks and then potted up into 10 cm pots and the bottom part of the signalling cuvette system attached (see Lake et al., Nature 10th May 2001 Vol. 411, pp 154). Twenty four, 4 week old plants, then had the top part of the signalling system attached, trapping leaf insertions 5-13. Humidified, ambient air was passed through them at 500 mls/min via an oil-free air compressor.
The three target leaves (19-21) were then marked with non-toxic, acrylic paint. After a 24 h period (the plants were sealed into the cuvettes  from 10 am until 10am) of adjustment, the experiment was started by harvesting the target leaves from 4 plants and immediately freezing the tissue in liquid nitrogen to give the 0 h sample before RNA extraction. The remaining 20 plants were divided into 4 groups of five and given one of the following treatments:
Ambient carbon dioxide/ambient light (Control) (A)
Elevated carbon dioxide (750 ppm)/ambient light (E)
Ambient carbon dioxide/low light (50 µmol/m/s) (AS)
Elevated carbon dioxide/low light (ES)
- For the Elevated CO2, elevated CO2 was pumped in using a CT room next door set to same temperature but with a CO2 cylinder inside and the same pump as used in the ambient room to supply the elevated CO2 laden, humidified air into the signalling room using rubber tubing.
- Shade treatment consisted of neutral density filter (Cat. 210 0.6ND, Lee Filters) that had a hole cut in the middle to allow the middle developing leaves to grow through.
A timecourse of 2, 4, 12, 24, 48 and 96 h were carried out each using a batch of 24 plants. This whole process was repeated with another batch of 24 plants at the same developmental stage to give a 2, 4, 12, 24, 48 and 96 hour sample from each of the four treatments. The whole timecourse was then repeated 4 times.
For the mature leaves:
We had 8 chips left over so we devised this little experiment to assess the gene changes that were occurring in the enclosed, treated, mature leaves that were signalling the environment to the young developing leaves.

Experimenter name = Simon Coupe
Experimenter phone = 0114 222 4115
Experimenter fax = 0114 222 0002
Experimenter institute = University of Sheffield
Experimenter address = Animal and Plant Sciences
Experimenter address = University of Sheffield
Experimenter address = Western Bank
Experimenter address = Sheffield
Experimenter zip/postal_code = S10 2TN
Experimenter country = UK
Keywords: development_or_differentiation_design; growth_condition_design

first: Simon

last: Coupe

first: Paul

last: Quick


title: Growth promotion of Arabidopsis by Trichoderma hamatum

summary:
Trichoderma spp. are ubiquitous soil-borne ascomycetous fungi that have been used widely in the biological control of plant diseases. Certain strains also exhibit growth promotion of plants, but the mechanism for this phenomenon has not yet been elucidated. We have recently identified an isolate of T. hamatum that causes significant increases in the development of Arabidopsis root systems. The aim of this work is to elucidate the mechanism of root growth promotion. One approach is to analyse the transcriptome of plants grown in the presence and absence of the fungus.
Experimenter name = Christopher Thornton
Experimenter phone = 01392 264653 / 01392 264689
Experimenter department = Washington Singer Lab
Experimenter address = School of Biological and Chemical Sciences
Experimenter address = University of Exeter
Experimenter address = Perry Road, Exeter,
Experimenter zip/postal_code = EX4 4QG
Experimenter country = UK
Keywords: pathogenicity_design,  stimulus_or_stress_design

overall_design: 2 samples were used in this experiment

first: Christopher

last: Thornton

last: Townsend


title: AtGenExpress: Effect of ABA during seed imbibition

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
This experiment studies the effect of two concentrations of ABA during seed imbibition in the Col-0 ecotype.
Experimenter name = Eiji Nambara  , Kazumi Nakabayashi  , Yuji Kamiya
Experimenter institute = AtGenExpress
Keywords: Effect of ABA

first: Eiji

last: Nambara

first: Kazumi

last: Nakabayashi

first: Yuji

last: Kamiya

last: Emmerson


title: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Treatment 1: Ambient CO2 and Ambient Light)

overall_design: 26 samples were used in this experiment

first: Henrik

first: Zoe

last: Schildknecht


title: AtGenExpress: Developmental series (roots)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. The focus of this data set is on different tissues and different developmental stages in wild type Columbia (Col-0) and various mutants.
Experimenter name = Detlef Weigel  , Jan Lohmann  , Markus Schmid
Experimenter institute = AtGenExpress
Keywords: genetic_modification_design;  organism_part_comparison_design; development_or_differentiation_design

overall_design: 21 samples were used in this experiment

first: Detlef

last: Weigel

first: Jan

last: Lohmann

first: Markus

last: Schmid

first: Beatrice


title: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Treatment 2: Elevated CO2 and Ambient Light)


title: AtGenExpress: Effect of brassinosteroids in seedlings

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
det2 mutant seedlings were treated with several brassinosteroid compounds.
Experimenter name = Hideki Goda  , Yukihisa Shimada
Experimenter institute = AtGenExpress
Keywords: Effect of brassinosteroids

first: Hideki

last: Goda

first: Yukihisa

last: Shimada


title: AtGenExpress: Developmental series (leaves)

overall_design: 60 samples were used in this experiment


title: AtGenExpress: Developmental series (shoots and stems)

overall_design: 42 samples were used in this experiment


title: Cold induced changes: differences between the Arabidopsis thaliana wild type and freezing sensitive mutants.

summary:
Arabidopsis sfr mutants are deficient in cold acclimation during exposure to coolnon-freezing temperatures. Although not visibly affected by the cold they have lost the ability to survive subsequent freezing. We plan to investigate how the sfr2 and sfr6 mutants respond to low temperature on the gene expression level. Wild type plants that have undergone identical treatments in parallel are necessary controls. The cold treatment of plants in the rosette stage (soil grown in a 8/16 hours day/night cycle) will be carried out in a cooled growth chamber at 4 degrees for 24 hours (same light regimetreatment starting/ending at the 4th hour of light). The aerial parts of the treated and untreated plants will be collected and frozen immediately in liquid nitrogen for RNA extraction. Comparison of the cold response of thousands of Arabidopsis genes in the wild type to the situation in our freezing sensitive mutants will enhance our understanding of the cold response itself and illuminate the effect of the mutations on the cold acclimation process.

Experimenter name = Irene Bramke
Experimenter phone = 01784 44 3770
Experimenter fax = 01784 43 4326
Experimenter address = Royal Holloway
Experimenter address = University of London
Experimenter address = School of Biological Sciences
Experimenter address = Bourne Building
Experimenter address = Laboratory 406
Experimenter zip/postal_code = TW20 OEX
Experimenter country = UK
Keywords: growth_condition_design; genetic_modification_design

first: Irene

last: Bramke

first: Gareth

last: Warren


title: AtGenExpress: Developmental series (flowers and pollen)

last: Nottingham Arabidopsis Stock Centre (NASC)

overall_design: 66 samples were used in this experiment


title: AtGenExpress: Stress Treatments (UV-B stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.
Experimenter name = Jakub Horak  , Klaus Harter
Experimenter institute = AtGenExpress
Keywords: growth_condition_design;  time_series_design; stimulus_or_stress_design

overall_design: 28 samples were used in this experiment

first: Jakub

last: Horak

first: Klaus

last: Harter


title: AtGenExpress: Stress Treatments (Heat stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.
Experimenter name = Lutz Nover  , Pascal von Koskull-Döring
Experimenter institute = AtGenExpress
Keywords: growth_condition_design;  time_series_design; stimulus_or_stress_design

overall_design: 32 samples were used in this experiment

first: Lutz

last: Nover

first: Pascal

last: von Koskull-Döring


title: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Treatment 3: Ambient CO2 and Low Light)

first: Simon

last: Coupe

first: Paul

last: Quick

last: Townsend


title: AtGenExpress: Stress Treatments (Wounding stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.
Experimenter name = Dierk Wanke  , Klaus Harter
Experimenter institute = AtGenExpress
Keywords: injury_design; time_series_design; stimulus_or_stress_design

first: Dierk

last: Wanke

last: Emmerson


title: AtGenExpress: Stress Treatments (Drought stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wilde Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.
Experimenter name = Cecilia D`Angelo  , Joachim Kilian  , Joerg Kudla  , Oliver Batistic  , Stefan Weinl
Experimenter institute = AtGenExpress
Keywords: growth_condition_design;  time_series_design; stimulus_or_stress_design

first: Cecilia

last: D`Angelo

first: Joachim

last: Kilian

first: Joerg

last: Kudla

first: Oliver

last: Batistic

first: Stefan

last: Weinl

first: Henrik

last: Schildknecht


title: AtGenExpress: Stress Treatments (Genotoxic stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.
Experimenter name = Holger Puchta  , I-Peng Chen
Experimenter institute = AtGenExpress
Keywords: compound_treatment_design;  time_series_design; stimulus_or_stress_design

first: Holger

last: Puchta

first: I-Peng

last: Chen

first: Zoe

first: Beatrice


title: AtGenExpress: Developmental series (siliques and seeds)

last: Nottingham Arabidopsis Stock Centre (NASC)

first: Detlef

last: Weigel

first: Jan

last: Lohmann

first: Markus

last: Schmid


title: AtGenExpress: Stress Treatments (Salt stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.
Experimenter name = Cecilia D`Angelo  , Joachim Kilian  , Joerg Kudla  , Oliver Batistic  , Stefan Weinl
Experimenter institute = AtGenExpress
Keywords: time_series_design; growth_condition_design; stimulus_or_stress_design


title: AtGenExpress: Stress Treatments (Osmotic stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 uEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.
Experimenter name = Cecilia D`Angelo  , Joachim Kilian  , Joerg Kudla  , Oliver Batistic  , Stefan Weinl
Experimenter institute = AtGenExpress
Keywords: time_series_design; growth_condition_design; stimulus_or_stress_design


title: AtGenExpress: Stress Treatments (Cold stress)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Seeds of Arabidopsis thaliana Wilde Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.

Experimenter name = Cecilia D`Angelo  , Joachim Kilian  , Joerg Kudla  , Oliver Batistic  , Stefan Weinl
Experimenter institute = AtGenExpress
Keywords: time_series_design; growth_condition_design; stimulus_or_stress_design


title: AtGenExpress: Pathogen Series: Pseudomonas half leaf injection

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Half of a Columbia plant leaf was injected with Pseudomonas syringae. The other half of the leaf was collected on a time course for analysis.
Experimenter name = Xinnian Dong
Experimenter institute = AtGenExpress
Keywords: pathogen series

first: Xinnian

last: Dong


title: AtGenExpress: Stress Treatments (Control plants)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Stress treatments
Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 uEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups.

Experimenter name = Cecilia D`Angelo, Joachim Kilian, Joerg Kudla, Oliver Batistic, Stefan Weinl
Experimenter institute = AtGenExpress
Keywords: time_series_design; growth_condition_design; stimulus_or_stress_design

overall_design: 36 samples were used in this experiment


title: Comparative transcriptome analysis of wild type and two knockout alleles of At-CAMTA

summary:
Calcium has been shown to be an important signalling molecule in the transduction of abiotic stress signals in Arabidopsis thaliana. Alteration of the calcium signature through the use of inhibitors has been shown to result in changes in the expression of certain downstream abiotic stress-induced genes. However, the communication of this signal through specific calcium-sensitive intermediate molecules has remained poorly elucidated. Various candidate molecules exist and including calcinurin, calcium-dependent protein kinases and calmodulin.
Recently, a screen of an Arabidopsis thaliana cDNA expression library with calmodulin resulted in the isolation of the protein designated calmodulin-binding transcriptional activator or AtCAMTA that may function as one of these calcium-sensitive intermediate molecules. The Arabidopsis genome contains six CAMTA genes (AtCAMTA1-6), all of which are expressed in varying tissues throughout development. AtCAMTA1 was shown to function as a transcriptional activator through the expression of a chimeric protein consisting of the bacteria LexA protein fused to various segments of AtCAMTA expressed in yeast. In order to identify putative target genes of AtCAMTA1 in Arabidopsis we plan to analyse the transcriptome of AtCAMTA1 loss-of-function mutants. The gene expression pattern of two previously characterised alleles of AtCAMTA1 will be compared to wild type.

Experimenter name = Sarah Scrase-Field
Experimenter phone = 01865 275062
Experimenter fax = 01865 275074
Experimenter department = University of Oxford
Experimenter address = Department of Plants Sciences
Experimenter address = University of Oxford
Experimenter address = South Parks Road
Experimenter address = Oxford
Experimenter zip/postal_code = OX1 3RB
Experimenter country = UK
Keywords: genetic_modification_design

overall_design: 4 samples were used in this experiment

first: Sarah

last: Scrase-Field

first: Marc

last: Knight


title: Newbury: Molecular bases of zinc tolerance and accumulation by Arabidopsis halleri

summary:
This application is from a NERC-funded consortium (Mark MacNair, Nick Smirnoff, Exeter) and (Brian Ford-Lloyd, John Newbury, Birmingham).
Metal tolerance is one of the classic examples of micro-evolution. Despite extensive research the physiological bases of the adaptation in plants are largely unknown. Arabidopsis halleri is a zinc tolerant, zinc accumulating species whereas Arabidopsis petraea is non-accumulating and non-tolerant. The objective of our programme is to identify
a) those key genes that act to determine Zn tolerance and accumulation in Arabidopsis (and which account for the difference in performance of A. halleri and A. petraea grown in the presence of elevated Zn) and
b) those _downstream_ genes that are expressed as part of the tolerance or accumulation response.
Phase 1: Total of 24 chips: Material ready by May 2003 The results will a) tell us how effectively material derived from other Arabidopsis species hybridises to the chips, and b) identify genes that are differentially expressed in the two species in the presence and absence of Zn stress (thus providing initial lists of genes that may be responsible for Zn tolerance or accumulation- but see phase 2)· A. halleri exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides· A. petraea exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides
Phase 2: Total of 48 chips: Material ready by September 2003
The results will tell us which genes, identified as having appropriate expression patterns, co-segregate with the Zn tolerance or accumulation phenotype and will provide firmer candidate genes for intensive study. Bulks will be produced from F3 progeny (from the halleri x petraea cross) following phentoypic analyses for Zn tolerance and accumulation.· A bulk of F3 progeny all exhibiting high Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting low Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting high Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting low Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides

Experimenter name = H. John Newbury
Experimenter phone = 0121 414 5581
Experimenter fax = 0121 414 5925
Experimenter department = Newbury lab
Experimenter institute = University of Birmingham
Experimenter address = School of Biosciences
Experimenter address = University of Birmingham
Experimenter address = Edgbaston
Experimenter address = Birmingham
Experimenter zip/postal_code = B15 2TT
Experimenter country = UK
Keywords: stimulus_or_stress_design;  organism_part_comparison_design;  strain_or_line_design

first: H

last: Newbury

last: Townsend


title: AtGenExpress: Response to Phytophthora infestans

summary:
AtGenExpress:  A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC)
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate.
Series 2: Base line experiment for pathogen infection. Growth and infection conditions: Seeds will be stratified for 3 days at 4°C and sown on soil. Plants are grown at 22°C under a 8/16 hour light/dark regime in Percival growth chambers. All pathogen treatments will be performed on leaves of 5-weeks old plants. Bacterial infiltrations will be performed with 10-8 cfu/ml in 10 mM MgCl2. 5x105 spores of Phytophthora infestans in water will be applied to leaf surfaces. LPS (100 µg/ml), HrpZ (1 µM), NPP1 (2 µM) or flagellin (1 µM flg22) will be applied in water. Experiments should be performed in triplicate at the time points indicated below.
Experimenter name = Dierk Scheel  , Frederic Brunner  , Lore Westphal
Experimenter institute = AtGenExpress
Keywords: genetic_modification_design;  organism_part_comparison_design; development_or_differentiation_design

overall_design: 18 samples were used in this experiment

first: Dierk

last: Scheel

first: Frederic

last: Brunner

first: Lore

last: Westphal

last: Emmerson


title: Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)

summary:
The aim of this study is to study gene expression in Brassica oleracea in shoot tissues of plants grown under contrasting P supplies (see Hammond JP et al., 2003, Plant Physiology, 132, 578-596 for background). Seeds of B. oleracea (var. alboglabra, A12dH) were first washed in 70% (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50% (v/v) domestic bleach/water. Seeds were rinsed and imbibed for 3 to 5 days in sterile distilled water at 4°C to break dormancy. Following imbibition, B. oleracea seeds were sown in un-vented, polycarbonate culture boxes (Sigma-Aldrich Company Ltd., Dorset UK). Seedlings were grown for 21 days on perforated polycarbonate discs (diameter 91 mm by 5 mm) placed on 75 ml of 0.8% (w/v) agar containing 1% (w/v) sucrose and a basal salt mix. Roots grew into the agar, but shoots remained on the opposite side of the disc. After 21 days, seedlings were transferred, still on polycarbonate discs, to a hydroponics system situated in a Saxcil growth cabinet (16 h daylength, set to 22°C and 80% humidity). Each polycarbonate disc was placed on a light-proof 500 ml beaker over 450 ml of nutrient solution. After 7 days, half the plants were transferred to nutrient solution containing no phosphate and the other half remained on full nutrient solution (control plants). Shoots were harvested 100 h after the withdrawal of P. !Samples were snap frozen in liquid nitrogen. RNA was extracted using the TRIzol extraction method and cleaned through a Qiagen RNeasy column.

Experimenter name = Martin Broadley
Experimenter phone = 0115 951 6382
Experimenter fax = 0115 951 6334
Experimenter institute = University of Nottingham
Experimenter address = Plant Sciences Division
Experimenter address = School of Biosciences
Experimenter address = University of Nottingham
Experimenter address = Sutton Bonington
Experimenter address = Loughborough
Experimenter zip/postal_code = LE12 5RD
Experimenter country = UK
Keywords: growth_condition_design

overall_design: 6 samples were used in this experiment

first: Martin

last: Broadley


title: Circadian expression of genes: modelling the Arabidopsis circadian clock

summary:
Our aim is to study the circadian expression of genes to aid in our attempt of modelling the Arabidopsis circadian clock. Circadian microarray data have previously been published for plants after white light (WL)-dark cycles, using the 8k chip (Harmer et al. 2000). We intend to repeat this experiment using the 26k chips and are coordinating with Dr. Harmer, who is pursuing complementary experiments in UC Davis. Plants will be transferred to continuous WL after entrainment to 12h:12h light dark cycles. RNAs will be harvested every 4 hours over two days, with the same accession and sampling intervals used previously by Harmer et al. The two days of sampling provide internal replication. Our experience shows that this is the most economical design: it is easier to identify rhythms over a two-day timecourse than in two replicates of a single day. Hence: 13 RNA samples on 13 chips in total.
METHOD: Seed was sown on MS agar plates with 3% sucrose, imbibed at 4 C for 96 hours.  Seed was then entrained for 7 days at 22C, in cycles of 12 hours white light, 12 hours darkness. After 7 days they were transferred to constant white light at 22 C: this is time 0h. Tissue harvested at the time points shown after time 0.

Experimenter name = Kieron Edwards
Experimenter phone = 024 7652 8374
Experimenter fax = 024 7652 3701
Experimenter department = Department of Biological Sciences
Experimenter institute = University of Warwick
Experimenter address = Department of Biological Sciences
Experimenter address = University of Warwick
Experimenter address = Gibbet Hill Road
Experimenter address = Coventry
Experimenter zip/postal_code = CV4 7AL
Experimenter country = UK
Keywords: time_series_design, growth_condition_design

overall_design: 13 samples were used in this experiment

first: Kieron

last: Edwards

first: Andrew

last: Millar

last: Schildknecht


title: Gene expression profile of nickel-stimulated HUVEC

status: Public on Dec 31 2006

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

country: Germany

institute: Hannover Medical School

summary:
Nickel compounds, important carcinogens and prime inducers of contact allergy in humans, are potent activators of endothelial cells (ECs). To elucidate the signaling pathways mediating the cellular responses to nickel we performed Affymetrix gene profiling of human primary ECs.
Keywords: stress response

overall_design: HUVEC cultured under standard conditions were treated for 5h with 1.5 mM NiCl2 or left untreated before total RNA isolation and processing for microarray hybridization. Four independent experiments were performed, i.e. 8 samples (Control and experiment) were analyzed.

last: Schmidt

first: Klaus

last: Tenbrock

first: Sybille

first: Verena

last: Müller

first: Kerstin

last: Klimmek

first: Stephan

last: Ludwig

first: Johannes

last: Roth

first: Matthias

last: Goebeler


title: House keeping gene analysis - carcinoids and normal mucosa

city: New Haven

first: Mark

last: Kidd

state: CT

address: 333 Cedar Street

department: Surgery

country: USA

institute: Yale University School of Medicine

summary:
Accurate and reproducible quantitation of target genes depends on correct normalization. Historically, genes with variable tissue transcription e.g. GAPDH, have been used as normalization factors which is problematic, particularly in clinical samples which often are derived from different tissue sources. Using a large-scale gene database (GeneChip (Affymetrix U133A) dataset of 36 gastrointestinal tumors and normal tissues), we identified 8 candidate reference genes that were highly expressed with low variability and established expression levels by real-time RT-PCR in an independent set of GI tissue samples (n=42).
Keywords: house-keeping, intestine, carcinoid

overall_design: (GeneChip (Affymetrix U133A) dataset of 36 gastrointestinal tumors and Affymetrix protocol: http://keck.med.yale.edu/affymetrix/analysis.htm

middle: S

first: Irvin

middle: M

last: Modlin

first: Shrikant

last: Mane

first: Boaz

last: Nadler


title: Expression data from quadriceps muscle of young DMD patients and age matched controls

status: Public on Dec 25 2006

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

summary:
Albeit increased serum CK level and abnormal muscle histology are always present, boys with DMD are phenotipically indistinguishable from the normal ones at birth and, in their first years of life, acquire early motor milestones at normal times. A clear defect in muscle function becomes generally apparent by the end of the second year. As the disease is typically diagnosed between the ages of 3 and 7, the first two years are often considered and referred to as clinically presymptomatic.
As a defined gene expression signature was shown to characterize these symptomatic patients we sought to investigate whether and to which extent alterations may be also present in muscle from presymptomatic DMD infants. To this aim, we used the Affymetrix technology to compare the individual expression profiles of 19 DMD patients with age at biopsy scattered along the first two years of the disease with those of 14 age matched controls. This approach allowed us to describe with high resolution the altered transcriptional state that characterizes this early, presymptomatic phase of the disease and highlight some molecular pathways as potential critical targets in the pathophysiology of the disease.
Keywords: two populations study

overall_design:
-Subjects
Relevant data about the participants are posted under supplementary material (Table ST1). All DMD patients (n=22) had diagnosis of Duchenne Muscular Dystrophy based on the absence of dystrophin immunoreactivity on quadriceps muscle sections. None of the participants at the time of biopsy was or had been under corticosteroid treatment. Control biopsies (n=14) were selected from diagnostic specimens which were not given a diagnosis of neuromuscular disease nor showed any non-specific myopathic signs. A MIAME compliant description of this study is posted under supplementary Material (MIAME compliance).
-RNA extraction.
Total RNA was extracted from frozen quadriceps muscle biopsies by TriZol. (TriZol reagent, Invitrogen). RNA was further purified using the RNAeasy mini kit following the RNA cleanup protocol as indicated by the manufacturer (QIAGEN). RNA purity and integrity was assessed by spectophotometric analysis and agarose gel electrophoresis.
-Affymetrix Genechips.
In this work we made use of one chip type: the affymetrix HG-U133A genechipCRNA synthesis was performed using 5ug of total RNA as template, as described in the Affymetrix Gene Expression Manual. Genechips were washed and stained in an Affymetrix fluidic station 430. To avoid overcorrelation, samples were processed 8 at the time and arranged to have both DMD and control samples in each experimental session.

first: Enzo

last: Ricci

first: Camilla

last: Bernardini

first: Pietro

middle: A

last: Tonali


title: AtGenExpress: Developmental series (seedlings and whole plants)

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana.
The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. The focus of this data set is on different tissues and different developmental stages in wild type Columbia (Col-0) and various mutants.
Experimenter name = Detlef Weigel  , Jan Lohmann  , Markus Schmid
Experimenter institute = AtGenExpress
Keywords: genetic_modification_design;  organism_part_comparison_design; development_or_differentiation_design

overall_design: 24 samples were used in this experiment

first: Detlef

last: Weigel

first: Jan

last: Lohmann

first: Markus

last: Schmid

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Expression data from tocopherol deficient seedlings of Arabidopsis

status: Public on Dec 29 2006

city: East Lansing

first: Scott

middle: E.

last: Sattler

state: MI

address: room 201 Biochem Bldg

department: Biochemistry and Molecular Boliogy

institute: Michigan State University

summary:
Tocopherols (Vitamin E) are lipophilic antioxidants that are synthesized by all plants and are particularly abundant in seeds.  Two tocopherol deficient mutant loci were used to examine how tocopherol deficiency impacts global gene expression during the critical peroid of germination and early seedling development when tocopherols are essential.  vte1 lacks all tocopherols, but accumulates the tocopherol pathway intermediate DMPBQ,.  vte2 which lacks all tocopherols and pathway intermediates.
We used microarrays to examine the global gene expression in early seedlings and identify distinct classes of genes whose expression is affected by tocopherol deficient mutants vte1 and vte2.
Keywords: genetic modification

overall_design: Arabidopsis seedlings were grown on media containing MS salts at 22C and RNA was extracted from 1 (1D)and 3 (3D)day old seedlings following cold treatment to break dormancy and synchronize germination (5 days at 6C) .   We sought to compare the two tocopherol deficient mutants vte1 (VTE1) and vte2 (VTE2) with each other and the corresponding wild-type background Columbia-0 (COL).

middle: E

first: Dean

last: DellaPenna


title: Human myeloma cell lines gene expression profiling

status: Public on Dec 28 2006

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
In order to investigate the patterns of genetic lesions in a panel of 23 Human Multiple Myeloma Cell Lines (HMCLs), we made a genomic integrative analysis involving FISH and both gene expression and genome-wide profiling approaches. The expression profiles of the genes targeted by the main IGH translocations showed that the WHSC1/MMSET gene involved in t(4;14)(p16;q32) was expressed at different levels in all of the HMCLs, and that the expression of the MAF gene was not restricted to the HMCLs carrying t(14;16)(q32;q23). Supervised analyses identified a limited number of genes specifically associated with t(4;14) and involved in different biological processes. The signature related to MAF/MAFB expression included the known MAF target genes CCND2 and ITGB7, as well as genes controlling cell shape and cell adhesion. Genome–wide DNA profiling allowed the identification of a gain on chromosome arm 1q in 88% of the analyzed cell lines, together with recurrent gains on 8q, 18q, 7q and 20q; the most frequent deletions affected 1p, 13q, 17p and 14q; and almost all of the cell lines presented LOH on chromosome 13. Two hundred and twenty-two genes were found to be simultaneously overexpressed and amplified in our panel, including the BCL2 locus at 18q21.33. Our data further support the evidence of the genomic complexity of multiple myeloma and reinforce the role of an integrated genomic approach in improving our understanding of the molecular pathogenesis of the disease.
Keywords: cell line comparison

first: Luigia

last: Lombardi

first: Giulia

last: Poretti

first: Michela

last: Mattioli

first: Sonia

last: Fabris

first: Silvio

last: Bicciato

first: Ivo

last: Kwee

first: Andrea

last: Rinaldi

first: Domenica

last: Ronchetti

first: Donata

last: Verdelli

first: Giorgio

last: Lambertenghi-Deliliers

first: Francesco

last: Bertoni

first: Antonino

last: Neri


title: Distinct transcriptional and genetic features associated with chromosome 13 deletion in multiple myeloma

status: Public on Jan 01 2007

summary:
Background and objective: The chromosome 13 deletion (del(13)) represents one of the most frequent chromosomal alterations in multiple myeloma (MM). del(13) is associated with an unfavorable prognosis, although there is an increasing agreement that its prognostic relevance has to be related to the ploidy status and the presence of different chromosomal translocations. This study is aimed at providing a comprehensive analysis of the transcriptional features of del(13) in MM. Design and methods: Highly purified plasma cells from 80 newly diagnosed MM patients were characterized by means of FISH and high-density oligonucleotide microarray for gene expression profiling and chromosomal alterations. Results: We identified 67 differentially expressed genes in the del(13)+ and del(13)- groups, all of which downregulated in the del(13)+ cases: 44 mapped along the whole chromosome 13, seven on chromosome 11 and three on chromosome 19. Functional analyses of the selected genes indicated their involvement in protein biosynthesis, ubiquitination and transcriptional regulation. An integrative genomic approach based on regional analyses of the gene expression data identified distinct chromosomal regions whose global expression modulation could differentiate del(13)+, in particular the upregulation of 1q21-1q42 and the downregulation of 19p and almost the entire chromosome 11. FISH analyses confirmed the close relationship between del(13)+ and the presence of extracopies of 1q21-1q42 (P=6x10-4) or the absence of chromosome 11 and 19 trisomy (P=5x10-4). Interpretation and conclusions: Our results indicate that distinct types of chromosomal aberrations are closely related to the transcriptional profiles of del(13)+, suggesting that the contribution of del(13) on the malignancy should be considered together with associated abnormalities.
Keywords: disease state analysis

overall_design: This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 90 newly diagnosed multiple myeloma (MM). PCs were purified from bone marrow specimens, after red blood cell lysis with 0.86% ammonium chloride, using CD138 immunomagnetic microbeads. The purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases. 5 micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the Agilent GeneChip Scanner G2500A. The images were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted and quantile-quantile normalised.

last: Baldini

first: Fortunato

last: Morabito

last: Callegaro


title: Expression profiling of A. thaliana wild type Columbia-0 and mutant gh3.5-1D in response to pathogen Pst DC3000(avrRpt2)

status: Public on Dec 18 2006

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of plant physiology & ecology, SIBS, CAS

summary:
To reveal the underlying molecular mechanism of GH3.5 action in modulating the SA and auxin pathways, we performed transcriptional profiling of gh3.5-1D plants after infection with or without Pst DC3000(avrRpt2) on a global scale using the Affymetrix Arabidopsis ATH1 GeneChip
Keywords: Pathogen-response

overall_design: Each 3 leaves of plants of 5-week-old wild type Columbia-0 and mutant gh3.5-1D (heterozygous) were inoculated with Pst DC3000(avrRpt2)at 105 cfu mL-1. Leaves were harvested at 0 h (uninoculated) and 48 hours after inoculation. Three biological repeats were performed on Columbia-0 (wild-type, Col-0) and gh3.5-1D (mutant) after infection with or without Pst DC3000(avrRpt2), respectively.

first: Zhongqin

last: Zhang

first: Qun

last: Li

first: Zhimiao

first: Paul

last: Staswick

first: Muyang

last: Wang

first: Ying

last: Zhu

first: Zuhua

last: He


title: Role of coactivator SRC-1/NcoA-1 for IL-6 target gene induction in HepG2 cells

city: Leipzig

first: Friedemann

last: Horn

address: Johannisalle 30

department: Institute of Clinical Immunology and Transfusion Medicine

institute: University of Leipzig

summary:
This experiment series addresses the role of coactivator SRC-1/NcoA-1 for the induction of interleukin-6 (IL-6) target genes in HepG2 cells. For that purpose, HepG2 human hepatocellular carcinoma cells were manipulated to stably express an shRNA that knocks down SRC-1 expression yielding the HepG2-∆Src1 cells. Either unmanipulated HepG2 or HepG2-∆Src1 cells were then treated for various periods with IL-6.
Keywords: time course, genetic modification

overall_design: HepG2 or HepG2-∆Src1 (with silenced SRC-1/NcoA-1 expression) cells were either left untreated or treated with 10 ng/ml IL-6 for 1 or 4 hours. Every experiment was carried out in replicate.

first: Helena

last: Cvijic


title: IMR-90 cells: Tissue Culture Polystyrene or Collagen Mesh Time Course

status: Public on Dec 03 2006

city: Boston

first: Catherine

last: Klapperich

state: MA

address: 44 Cummington St. 7th Floor

department: Biomedical and Manufacturing Engineering

institute: Boston University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series