title: Gene expression changes in Arabidopsis thaliana treated with Myzus persicae saliva

status: Public on Nov 12 2009

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Reference: De Vos and Jander, 2009 - Plant, Cell, and Environment

Aim: Identification of genes responding to aphid saliva.

Background: During feeding on phloem sap aphids repeatedly salivate into the sieve element. It is thought that compounds in aphid saliva play a role in sustainable feeding. These compounds may include proteins and small molecules, which can function as virulence factors.

Growth conditions
Plants:  Seeds of wild-type Arabidopsis thaliana (Col-0) were obtained from the were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix with Osmocoat fertilizer. Plants were grown in Conviron growth chambers in 20- x 40-cm nursery flats at a photosynthetic photon flux density of 200 mmol m-2 s-1 and a 16-h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. Plants were grown for 3 weeks and used in experiments before flowering. Aphids:  All experiments were conducted with a tobacco-adapted red lineage of M. persicae. Aphids were raised on cabbage (Brassica oleracea) with a 16-h day (150 mmol m-2 s-1 at 24°C) and an 8-h night (19°C) at 50% relative humidity.

Experimental set-up/treatment:
Fifty aphids were allowed to feed from 50 µL artificial diet, containing sucrose and amino acids (Kim and Jander, 2007) between two layers of Parafilm. After 24 h, artificial diet from 20 aphids and control (0 aphids) diet cups was collected and infiltrated into leaves of intact Arabidopsis plants using a 1-mL syringe without the needle. Plants for control diet and aphid saliva containing diet were grown in the same pot to allow for a paired comparison. Eighteen leaves (3 leaves from 6 plants) treated with control and aphid saliva containing diet were harvested and immediately frozen in liquid nitrogen. This experiment was repeated 3 times to function as independent biological replicates.

RNA extraction + processing:
RNA was extracted using the Qiagen Plant RNeasy kit. RNA quality and quantity was assessed with an Agilent BioAnalyser 2100. Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips.

Data analysis:
Raw data from the microarrays was normalized at probe-level using gcRMA algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system. Significance of gene expression was determined using the LIMMA (Smyth, 2004) program and raw p values of multiple tests were corrected using False Discovery Rate (FDR).

overall_design: 6 samples were used in this experiment

first: Martin

last: De Vos


title: Epigenetic mutant gene expression analysis

status: Public on Nov 18 2009

city: Loughborough

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
The aim of this project is to identify endogenous targets of yet unidentified epigenetic mutants. Mutants were discovered in a forward genetic approach using T-DNA insertion mutagenesis.Pools of each 50 seedlings, grown in-vitro, will be used to examine changes in gene-expression.

Keywords: Expression profilling by array

overall_design: 9 samples were used in this experiment

first: Tuncay

last: Baubec


title: Epigenetic mutant gene expression analysis_2

status: Public on Dec 10 2009

summary: The aim of this project is to identify endogenous targets of yet unidentified epigenetic mutants. Mutants were discovered in a forward genetic approach using T-DNA insertion mutagenesis. Pools of 25 seedlings, grown in-vitro, will be used to examine changes in gene expression.

overall_design: 9 samples were used in this experiment.


title: Effect of auxin signaling on Pseudomonas syinrgae pv tomato DC3000 response

status: Public on Nov 01 2009

city: Norwich

first: Daniel

last: MacLean

address: Colney Lane

department: Bioinformatics

institute: The Sainsbury Laboratory

summary:
Expression data 24hrs after PstDC3000 inoculation in Col-0, 35S:AFB1 and 35S:miR393.
We used microarrays to investigated the effect of auxin signaling on PstDC3000 response.

Keywords: Alexandre,Robert-Seilaniantz

overall_design: Plants were syringe infiltrated with 10^6cfu/ml of PstDc3000 or water. Leaves were harvested 24hrs after inoculation

first: Dan

first: Jonathan

middle: D

last: Jones


title: Transcriptome differences between two vitamin C-deficient mutants and wild type

status: Public on Dec 05 2009

summary: The Arabidopsis mutant vtc2 is vitamin C-deficient and high light sensitive (Mueller-Moule et al., 2002. Plant Physiol 128: 970-977; Mueller-Moule et al., 2003. Plant Physiol 133: 748-760). Even though the VTC2 gene has been cloned (Jander et al., 2002. Plant Physiol 129: 440-450), its function is still unclear. The goal of this experiment is to learn more about the function of the VTC2 gene by determining differences in the transcriptomes of wild type and the vtc2-1 mutant. In order to differentiate between VTC2 gene-specific differences and vitamin C-induced differences, a second vitamin C-deficient mutant vtc1-1 (Conklin et al., 1996. PNAS 93: 9970-9974) is included in the experiment. The plants will be grown on agar plates in a growth chamber with a 16 hour light (about 40 umol photons m(-2)s(-1))/8 hour dark regime at 20C for 14 days to stage 1.04. Whole plants will be collected and total RNA will be isolated using the Qiagen Rneasy plant mini kit (Qiagen, Hilden, Germany).

first: Patricia

last: Mueller-Moule


title: Genome-wide analysis of TOC1-ox transcriptional networks

status: Public on Sep 09 2009

city: Barcelona

first: Paloma

last: Mas

address: C/ Jordi Girona 18-26

department: Genetica Molecular

country: Spain

institute: Consorcio CSIC-IRTA-UAB (CRAG)

summary: To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 overexpressor plants (TOC1-ox).

overall_design: Comparisons of WT and TOC1-ox. Three biological replicates synchronized under 12-hour light:12-hour dark (LD) cycles for 12 days. Samples were collected at Zeitgeber Time 15 (ZT15).

first: Tommaso

last: Legnaioli

first: Juan

middle: C

last: Cuevas


title: Photoperiod regulation of grape bud dormancy

status: Public on Aug 06 2009

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

summary: Bud endodormancy induction response of two genotypes (‘Seyval’ a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long (15h) and short (13h) photoperiod. Three separate replicates (5 plants/replicate) were treated to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07; V. riparia 3/26/07) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (3-25-07) they were randomized into LD or SD treatments with 25/20 + 3C D/N in climate controlled greenhouses with automated photoperiod system (VRE Greenhouse Systems). Three replications (5 vines/replication) were harvested between 5/07-6/07 and then again in 5/08-6/08 for a total of six replications. All treatments are repeated at the same time every year and harvested at the same time of day each year to minimize biological noise. At 1, 3, 7, 14, 21, 28 and 42 days of LD and SD treatment, buds were harvested from nodes 3 to 12 of each separate replicate, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein and metabolite extraction. These time points encompass early reversible phases as well as key time points during transition to irreversible endodormancy development. After photoperiod treatments and bud harvests, all pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date.  Acknowledgement:This study was funded by NSF Grant DBI0604755 and funds from the South Dakota Agriculture Experiment Station.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Anne Fennell.  The equivalent experiment is VV10 at PLEXdb.]

sample_organism:
Vitis riparia
Vitis hybrid cultivar

overall_design:
84 Samples of two genotypes compared under long and short photoperiod, 3 replicates each.
Seyval (SV, Seyve Villard 5-276) : LD, 15h : 1 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : LD, 15h : 3 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : LD, 15h : 7 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : LD, 15h : 14 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : LD, 15h : 21 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : LD, 15h : 28 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : LD, 15h : 42 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : SD, 13h : 1 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : SD, 13h : 3 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : SD, 13h : 7 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : SD, 13h : 14 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : SD, 13h : 21 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : SD, 13h : 28 days (3-replications)
Seyval (SV, Seyve Villard 5-276) : SD, 13h : 42 days (3-replications)
V. riparia (VR, PI588259) : LD, 15h : 1 days (3-replications)
V. riparia (VR, PI588259) : LD, 15h : 3 days (3-replications)
V. riparia (VR, PI588259) : LD, 15h : 7 days (3-replications)
V. riparia (VR, PI588259) : LD, 15h : 14 days (3-replications)
V. riparia (VR, PI588259) : LD, 15h : 21 days (3-replications)
V. riparia (VR, PI588259) : LD, 15h : 28 days (3-replications)
V. riparia (VR, PI588259) : LD, 15h : 42 days (3-replications)
V. riparia (VR, PI588259) : SD, 13h : 1 days (3-replications)
V. riparia (VR, PI588259) : SD, 13h : 3 days (3-replications)
V. riparia (VR, PI588259) : SD, 13h : 7 days (3-replications)
V. riparia (VR, PI588259) : SD, 13h : 14 days (3-replications)
V. riparia (VR, PI588259) : SD, 13h : 21 days (3-replications)
V. riparia (VR, PI588259) : SD, 13h : 28 days (3-replications)
V. riparia (VR, PI588259) : SD, 13h : 42 days (3-replications)

first: Anne

last: Fennell


title: Transcript profile of chitosan-treated Arabidopsis seedlings

status: Public on Oct 31 2009

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

summary:
We treated Arabidopsis seedlings with chitosan and carried out a transcript profiling analysis (GeneChip microarrays) in order to identify genes and transcription factors regulated by chitosan. The results showed that jasmonate and defense responsive genes, camalexin and lignin biosynthetic genes were among genes up-regulated by chitosan. Several transcription factors are also strongly induced by chitosan.
The results suggested that chitosan can be used as a strong elicitor of defense pathways.

overall_design:
Arabidopsis thaliana, ecotype Columbia (Col-0) seeds were sterilized for 7 min in 1.7% (v/v) bleach solution, incubated over night in 4% PPM (Plant Preservative Mixture, Plant Cell Technology, Washington DC, USA) in a full strength sterilized Murashige-Skoog (MS) salt solution with gentle shaking. Subsequently, the seeds were rinsed in abundant sterile water and transferred into 2.5 ml liquid growing media (MS half strength solution) with 0.05% PPM in 6-well plates. The plates were incubated in the dark at 4 °C for two days and finally transferred to continuous light (90µm photons/ m-2) with gentle swirling for four days in a plant growth chamber at 22 °C.
 . Treatments were performed by comparing  a control solution containing the solvent used to solubilize chitosan, and a chitosan solution concentrated 150 µg/ml.

first: Giovanni

last: Povero

first: Elena

last: Loreti


title: Comparison of gene expression regulated by WRKY6

status: Public on Dec 07 2009

city: Beijing

first: Wei-Hua

last: Wu

state: Beijing

address: No.2 Yuanmingyuan West Road

department: College of Biological Sciences

country: China

institute: China Agricultural University

summary: WRKY6-overexpressing line 35S:WRKY6-9, knockout mutant wrky6-1 and wild-type seedlings were used to analyze genes whose expression are controlled under WRKY6.

overall_design: Seven-day-old seedlings of wild-type, 35S:WRKY6-9 and wrky6-1 mutant were harvested for RNA extraction.


title: Gene expression in grapevine in response to Bois noir infection

summary:
Transcriptional changes in field-grown plants of Vitis Vinifera cultivars 'Chardonnay' and 'Incrocio Manzoni' naturally infected with  Bois Noir phytoplasma, compared to healthy samples.

****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Nicola Pecchioni.  The equivalent experiment is VV14 at PLEXdb.]

overall_design: genotype: Chardonnay - disease type: Bois Noir infected(3-replications);  genotype: Chardonnay - disease type: Healthy(3-replications);  genotype: Incrocio Manzoni - disease type: Bois Noir infected(2-replications);  genotype: Incrocio Manzoni - disease type: Healthy(2-replications)

first: Nicola

last: Pecchioni


title: Transcriptome of the exo70A1 mutant

summary:
We characterized two independent insertional mutants of the AtEXO70A1 gene, encoding a subunit of the exocyst complex. Homozygous mutants exhibit a suite of phenotypic defects: polar growth of root hairs and stigmatic papillae is disturbed; organs are generally smaller; plants show loss of apical dominance and an indeterminate growth where instead of floral meristems new lateral inflorescences are initiated in a reiterative manner; exo70A1 mutants have dramatically reduced fertility. These results suggest that EXO70A1 is involved in cell and organ morphogenesis.

Keywords: Expression profiling by array

overall_design: 4 samples were used in this experiment

first: Lukas

last: Synek


title: Expression analysis in HDA6 mutants

summary:
In addition to the canonical RNAi pathways that targets mRNAs in the cytoplasm, several RNA-dependent pathways operate in the nucleus to induce sequence-specific epigenetic modifications. One specialized type of RNAi-mediated pathway is RNA-directed DNA methylation (RdDM). During RdDM, nuclear DNA with sequence identity to the trigger dsRNA is de novo methylated at almost all cytosine residues, providing a mark for the formation of transcriptionally silent heterochromatin. Genetic forward screens identified the RPD3-like histone deacetylase HDA6 as the enzyme responsible for the histone deacetylation step of RdDM and suggest that HDA6 might have acquired specific functions for RNA-directed transcriptional silencing processes [Aufsatz et al., 2002a; Aufsatz et al., 2002b]. Complete loss-of-function mutants for AtHDA6 (rts1-1; RNA-mediated transcriptional gene silencing) exhibit reactivation of RdDM-silenced promoters, despite the continuous presence of the silencing-inducing RNA signal. One of the found mutant alleles, rts1-5, has an amino acid substitution located at a conserved position within the HDAC domain (Naumann et al., manuscript in preparation). This mutant is characterized by strong reactivation of an RdDM-silenced target promoter, despite maintaining wild-type levels of cytosine methylation. An evaluation of the transcription pattern among the mutants with opposite methylation phenotype and wild-type plants should show which genes are differentially regulated between the mutants in comparison to wild-type plants.

Keywords: Expression profiling by array

first: Franziska

last: Schuller


title: The transcriptional changes induced by AtLEJ1 gene expression

status: Public on Dec 20 2008

city: Seoul

first: Jung

last: Kwang Wook

address: Anam-dong 1-ga

country: South Korea

institute: Korea university

summary:
The loss-of-function mutant of AtLEJ1 had well-developed anther cells and showed an increased accumulation of JA and ET in its flower bud clusters. Conversely, overexpression of AtLEJ1 caused a delay in the development of the floral organs, arrested anther cell development and secondary cell-wall biosynthesis in the endothecium cells, and reduced JA and ET contents in the flower bud clusters, resulting in male-sterility through anther indehiscence.
We used microarrays to gain a comprehensive understanding of the transcriptional changes induced by AtLEJ1 gene expression,
Keywords: Comparison of transcripts during flower development among 35S:AtLEJ1, atlej1 and wild type.

overall_design: We performed a full genome microarray analysis (ATH1 Affymetrix chips) with the wild type, 35S:AtLEJ1/5-8 line and atlej1 mutant. Total RNAs were obtained separately from unopened flower buds at stages 1~12, when the anthers are not yet opened, and from open flowers at stages 13~14, when anthesis occurs.

first: Jeong

middle: S

last: Shin

first: Kwang

middle: W

last: Jung

first: Kyoung

last: Yoo

first: Yun

middle: Y

last: Kim

first: Mei

middle: H

last: Cui


title: Analysis of RLI on RNA stability in A. thaliana

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
A number of RNA encoding different functions have been detected in the plant vasculature. An RNase L inhibitor, similar to that present in humans have been identified in the phloem sap of cucurbits. We are interested in analyze the role of this putative inhibitor on the transcript levels that could be present in the vasculature and mainly in the phloem stream. For this purpose, we obtained an RLI T-DNA insertion mutant and generated A. thaliana overexpressing lines using the ORF of the two alleles found in the database.

Keywords: Expression profilling by array

first: Beatriz

last: Xoconostle


title: Effect of the explosive compound TNT on wild type seedlings

summary: The aim of this experiment was to identify the genes involved in the detoxification of the toxic pollutant and explosive compound 2,4,6-trinitrotolune (TNT). Fourteen-day-old, liquid culture grown, Arabidopsis seedlings, ecotype Col0 (NASC stock code N1093), were dosed with 60 uM TNT dissolved in 60 ul dimethyl formamide (DMF) solvent, or 60 ul DMF only. After six hours, RNA was extracted and used for the microarray analysis. Further details and characterisation of glucosyltransferases identified using this method are presented in citation below.

first: Elizabeth

last: Rylott


title: Treatment of Arabidopsis with low concentration of nitrate

summary:
The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 um nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism.

Keywords: Expression profilling by array

overall_design: 8 samples were used in this experiment

first: Rongchen

last: Wang


title: Transcriptome of Arabidopsis APS kinase null mutants

summary:
The aim of the experiment is to look at transcriptional changes in null mutants of APS kinase. There are four APS kinase isoforms in Arabidopsis, we are interested in the double mutant APK1/APK2, created by crossing two single salk lines. The transcriptomes of WT (Col-0) plants and the double knockout (ab) will be compared. The plants were grown under controlled environment conditions of 10h day, 14h night, 22 degrees centigrade, 60% humidity for five weeks. 10 whole rosettes were pooled for each replicate, there are three replicates for each genotype.

Keywords: Expression profilling by array

first: Sarah

last: Mugford


title: Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes

status: Public on Jun 20 2009

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
Grapevine downy mildew caused by the Oomycete Plasmopara viticola is one of the most important diseases affecting Vitis spp. However, all cultivated European grapevine varieties are susceptible to P. viticola and the resistance needs to be introduced from other Vitaceae. Segregating populations derived from Muscadinia rotundifolia, a species closely related to Vitis, lead to the identification and mapping of two resistance genes, named Rpv1 and Rpv2. The macroscopic phenotypes of the resistance mediated by the two loci are different. Rpv2 plants completely inhibit P. viticola sporulation and produce very small necrotic lesions. In contrast, Rpv1 plants allow a rather limited but visible sporulation of P. viticola. The aim of the study is to understand the gene expression changes associated with downy mildew resistance mediated by these two loci. Gene expression patterns after P. viticola inoculation or mock inoculation are compared in incompatible (resistant plants bearing Rpv1 or Rpv2 locus) and compatible (susceptible plants with no resistance loci) interactions, using the Vitis vinifera GeneChip from Affymetrix. In order to limit the effect of the genetic background, the plant material consists in three pools of genotypes called B, C and D, respectively corresponding to partially resistant plants (Rpv1+/Rpv2-), totally resistant plants (Rpv1-/Rpv2+), and susceptible plants (Rpv1-/Rpv2-) derived from a segregating population. Each pool consists in 3 different genotypes. Plant leaf discs were inoculated with P. viticola sporangium suspension (i) or mock-inoculated with water (ni) and analysed 6 hours post-inoculation. For each experimental condition, we performed two biological replicates.

Keywords: normal vs disease comparison

overall_design: 3 plant genotypes were analyzed: Rpv1+/Rpv2- (B), Rpv1-/Rpv2+ (C), and Rpv1-/Rpv2- (D). Plants were either inoculated with P. viticola (i) or mock-inoculated with water (ni). Biological replicates were performed for each experimental condition.

first: Sandrine

last: Balzergue

first: Didier

last: Merdinoglu

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Gene expression pattern similarity and differences between hair follicles and basal cell carcinomas

status: Public on Sep 02 2008

city: Vancouver

first: Kevin

last: McElwee

state: BC

department: Dermatology and Skin Science

country: Canada

institute: University of British Columbia

summary: Hair follicles (HF) and BCCs can be regarded as ordered and disordered skin appendages respectively and may utilize similar molecular mechanisms of growth. We wanted to examine the similarities and differences in gene expression patterns between BCCs and HF to define common growth mechanisms and gene expression patterns that distinguish an ordered skin appendage from a disordered skin growth. Nodular BCCs (n= 8) and non-follicular skin epithelium (n=8) were obtained. Scalp hair follicle root sheath was micro dissected from between the sebaceous gland duct and the lower one third of the HF (n=7). Microarray analysis was performed using 21K cDNA arrays and selected genes were validated using qPCR and histochemistry staining. Two differentially expressed gene sets were identified by significance analysis of microarray (SAM) in BCC and HF verses skin epithelium respectively. Based on these two lists, we conducted multiple signaling pathway analyses. The results indicated that Notch, hedgehog, and WNT signaling pathways were involved in regulating formation of both HF and BCCs. However, Notch signaling, including tumor suppressor genes Notch 1, Notch 2, Jagged ligands (JAG 1, 2), notch signaling inhibitor NUMB, Lunatic Fringe (LFNG), Deltex proteins (DTX 1, 2) which serve as important signaling components downstream of Notch, and Notch target genes HES1 ,RBPSUHL, hairless protein and HES7, all showed selective differential activation in BCCs compared to HF. The components of the notch signaling pathway may be potential new targets in the development of new therapeutic approaches to BCCs.

overall_design:
samples of human hair follicles (n=7) were collected from scalp biopsies of normal individuals undergoing cosmetic procedures while nodular BCCs (n=8) and normal skin (n=8) were obtained from patients undergoing surgical resection. Only patients that had not been treated with preoperative chemotherapy or other therapeutic approaches were selected. All samples were provided by the Department of Dermatology and Skin Science, University of British Columbia with approval from the University Clinical Research Ethics Board. Hair follicles were microdissected to remove the lower one third, including the hair bulb, leaving the root sheaths including the bulge region. Normal skin samples were microdissected to isolate skin epithelium from the dermal component. All nodular BCC samples and normal skin epithelium were taken from the facial area of donors. Collected samples were immediately stored in an RNA stabilization reagent (Qiagen Inc, Mississauga, ON). BCC morphological subtypes were described and clinically classified during surgery and clinical diagnoses were confirmed by formalin-fixed, paraffin embedded histological assessment of the tumors.
Human Operon v.2.1 (21K) glass arrays were produced (based on human 70mers from Operon Biotechnologies Inc, Huntsville, AL) by the Microarray Facility of the Prostate Centre at Vancouver General Hospital, Vancouver, Canada [17, 18]. RNAs were amplified using the SenseAmp Plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. Total RNA from test samples and universal human reference RNA (Stratagene, Cedar Creek, TX) were differentially labeled with Cy5 and Cy3 respectively, with the 3DNA array detection 350 kit (Genisphere Inc, Hatfield, PA) and cohybridized to cDNA microarrays. Following overnight hybridization and washing, arrays were imaged using a ScanArray Express scanner (PerkinElmer, Boston, MA).

last: Yu

first: David

last: Zloty

first: Robert

last: Bell

first: Bryce

last: Cowan

first: Jerry

last: Shapiro

first: Anne

last: Haegert

first: Larry

last: Warshawski

first: Nicholas

last: Carr

middle: J


title: SOL2 mutation affect gene expresstion at root apex

status: Public on Jul 31 2008

city: Bunkyo-ku

first: Kuninori

last: Iwamoto

address: Hongo 7-3-1

country: Japan

institute: University of Tokyo

summary:
Analysis of sol2 mutant. SOL2 protein is a receptor-like kinase
involved in CLE peptide signalling pathway. Results provide insignt into
the role of SOL2 in CLE signalling.
Keywords: gene expression array-based (RNA / in situ oligonucleotide)

overall_design: GeneChip analyses were performed twice for comparison of gene expression in sol2 mutant and wild type plants.

first: Hiroki

last: Miwa

first: Shigeyuki

last: Betsuyaku

first: Atsuko

last: Kinoshita

first: Hiroo

last: Fukuda

first: Shinichiro

last: Sawa


title: Expression data in individual grape berries during ripening initation

status: Public on Jul 15 2008

first: Steven

middle: T.

last: Lund

address: 241 - 2205 East Mall

department: Wine Research Centre

institute: The University of British Columbia

summary:
We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation.  By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries.
We also demonstrated that gene expression does not differ statistically significantly at a global level in berries sampled from different plants or different positions in a cluster.
Keywords: time course (berry development series)

overall_design: Individual grape berries were selected at 4 developmental stages along ripening initiation for RNA extraction and hybridization to Affymetrix Vitis Genome GeneChips. One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS). Individual berries representing each stage were collected from either the distal or the proximal position of one cluster one each of two plants used for experiments.

middle: T

first: Fred

last: Peng

first: Tarun

last: Nayar

first: Karen

middle: E

last: Reid

first: James

last: Scholesser


title: V. vinifera 'Cabernet sauvignon' and V. aestivalis 'Norton' innoculated with Erysiphe necator conidiospores

status: Public on Nov 29 2007

city: Mountain Grove

first: Wenping

last: Qiu

state: MO

address: 9740 Red Spring Road

department: Agriculture

institute: Missouri State University

summary:
we analyzed pathogen-induced changes in the transcriptome of Vitis vinifera ‘Cabernet sauvignon’ and Vitis aestivalis ‘Norton’ by conducting a large-scale study to measure transcript abundance at 0, 4, 8, 12, 24, and 48 hours post-treatment in conidiospore- and mock-inoculated leaves using Affymetrix GeneChip Vitis vinifera Genome Array
Keywords: time course

sample_organism:
Vitis aestivalis
Vitis vinifera

overall_design: sixty plants were grown in each of two identical growth chamber labeled as Inoculation and Mock-inoculation under same conditions. Pairs of vines of same size were labeled, one with an “I”, the other with a “M” prefix for “inoculated” and “mock”. The vines in each pair received the same ID number. This resulted in balanced groups for inoculated and mock-inoculated vines. “I” and “M” vines of a pair were placed in corresponding locations on the bench of the two growth chambers. The locations of the vines were determined by randomizing their ID numbers. Thus, the “I” and “M” groups were balanced according to their size and to their locations within the growth chamber.  All vines were positioned at the same height from the light source. The locations of the individual plants within the growth chamber were recorded. At a time point, 10 randomly selected pairs of plants were sampled. (For example, at 8 hours post-inoculation, vines I-3, I-17, I -23, ..etc., and vines M-3, M-17, M-23, ...etc. were sampled from the “I” and the “M” growth chambers, respectively). The 10 corresponding leaves were combined into a single sample. At the next time point, another set of randomly selected 10 pairs were sampled from among the remaining plants, and so on. This random selection was independent from the random selection implemented to determine the location of the vines in the growth chambers

first: Raymond

last: Fung

first: Martin

last: Gonzalo

first: Csaba

last: Fekete

first: Laszlo

last: Kovacs

first: Yan

last: He

first: Ellen

last: Marsh

first: Lauren

last: McIntyre

first: Daniel

last: Schachtman


title: Tween 20 inducible genes

status: Public on Nov 02 2009

city: Bochum

first: Gretel

middle: Mara

last: Hunzicker

state: NRW

address: Universitätstr. 150

department: Plant Physiology

country: Germany

institute: Ruhr-Universität

summary:
Polyethylene glycol sorbitan monoacylates (Tween) are detergents of widespread use in plant sciences. We show them, notably Tween 20, to cause a rapid and complex change in transcript abundance which bears all characteristics of a PAMP / elicitor-induced defense response, and they do so at concentrations which cause no detectable deleterious effects on plant cellular integrity. The activity does not reside in the intact Tween molecule itself, but is caused by medium-chain fatty acids, notably lauric acid (LA), which are efficiently released from the Tween-backbone by the plant. The Tween / LA-response is independent of the jasmonate signalling system. Medium-chain fatty acids are thus novel elicitors/regulators of plant pathogen defense. The results also have several practical implications: (i) The use of Tweens and, as we show, several other detergents, as solvating/wetting agents on intact plants causes profound physiological changes which may mask actual effects of test compounds; (ii) Tweens by themselves can be regarded (and probably used) as economical, non-toxic, and safe-to-apply elicitors of inducible plant immunity against pathogens.
Keywords: c: plants treated with distilled water as a control. t: plants treated with 1.6 mM f Tween 20

overall_design:
In preliminary Northern blot experiments using the Arabidopsis thaliana genes OPR1 / OPR2, strongest responses were observed between 1 h and 2.5 h after foliar treatment with 0.2 % Tween 20 solution (approx. 1.6 mM). These conditions were thus chosen for the microarray experiments. Three experiments were carried out, two 1 h after the onset of the Tween treatment (expt. IA and IB which are biological repetitions; GSM126247, GSM126248; GSM126990, GSM126991 files) and one after 2.5 h (expt. II; GSM126244, GSM126246 files, c and t respectively) to allow a distinction between fast, transient and slower, more permanent responses.
All the experiments were conducted at the same day time in the morning. For every experiment a total of three independent replicas (33 Arabidopsis thaliana Col-0 plants per experiment) were done. The plants used were 28 days old, growing under sterile conditions in 0.5 L glass jars containing MS medium. The controls were sprayed with water and the samples with 0.2 % (w/v) Tween 20 detergent. The plant material was collected in a random way from the different glass jars, the samples were dried in tissue paper, weighted (1 g) and immediately frozen in liquid nitrogen. This complete procedure took place in less than 1 min. Total RNA extraction from every individual experiment was made with TRIzol. Once the RNA quality of every independent induction experiment was satisfactory, the RNA samples were mixed.
RNA quality and quantity control, cRNA labeling, hybridizations, expression data normalization and analysis were performed in collaboration with Carsten Müssig and Thomas Altmann (Max-Planck-Institute for Molecular Plant Physiology, Golm) according to the Affymetrix manual. Clustering was performed using the Access and the MAPMAN program.

The levels of 118 transcripts were elevated (2-fold) after 1 h, i.e., in both, the IA and IB arrays, but only 12 levels were reduced (by  2-fold). In the 2.5 h array the corresponding numbers were 137 and 11. The transcript levels of 38 genes were found elevated in all three arrays. The validity of the array data was checked for 25 randomly-picked genes out of the 38 genes by RT-PCR.

middle: M

first: Elmar

last: Weiler

first: Carsten

last: Müssig


title: Expression data from xylem pole pericycle cells of Arabidopsis roots undergoing lateral root initiation

status: Public on Oct 24 2008

city: Tuebingen

first: Ive

last: De Smet

address: Auf der Morgenstelle 3

institute: University of Tübingen - Center for Plant Molecular Biology

summary:
We used microarrays to detail the global programme of gene expression during this process.
Keywords: time course

overall_design: Arabidopsis xylem pole pericycle cells were isolated at successive stages of early lateral root development for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of cells at each stage in order to increase the temporal resolution of expression profiles. To that end, we used FACS on Arabidopsis roots containing a GFP marker for the xylem pole pericycle cells at three time-points: 1) arrest of G1-to-S transition (NPA or 0h NAA), 2) auxin signaling and progression through G1-to-S (2h NAA) and 3) G2-to-M transition or asymmetric cell division (6h NAA).

first: Tom

last: Beeckman

first: Philip

middle: N

last: Benfey


title: pad4 vs. pad4 est1b

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
This experiment was designed to identify transcripts which are changed in plants deficient for evolutionary conserved EST1B gene. A mutation in est1b leads to a constitutive up-regulation of a PAD4-dependent pathogen response pathway. To eliminate secondary effects of the constitutive pathogen response in est1b mutants we will analyze transcriptoms in plants in which lack PAD4.

Keywords: Expression profilling by array

overall_design: 6 samples were used in this experiment

first: Karel

last: Riha


title: Gene expression in roots of slim1 and the parental line grown +/-S condition

status: Public on Dec 19 2006

city: Yokohama

first: Akiko

last: Maruyama-Nakashita

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Plant Science Center

summary:
Plants utilize soil sulfate for production of sulfur-containing amino acids that serve as essential dietary sulfur sources for animals. Despite the global nutritional significance of this fundamental metabolic process in nature, transcription factors regulating the plant sulfur assimilation pathways have never been discovered. We isolated sulfur limitation1 (slim1) mutants from Arabidopsis, showing abnormally low expression of SULTR1;2 sulfate transporter, by screening responsiveness of SULTR1;2 promoter-GFP, as an indicator, to sulfur limitation.  SLIM1 encoded an EIL-family transcription factor, EIL3.
To clarify the siganificance of SLIM1 function in sulfur responsive gene expression, we analyzed the transcriptome profiles in slim1-1, slim1-2 and the parental line under +S and -S conditions.
Keywords: comparison of mutant and wild type, sulfur limitation response, nutritional stress response

overall_design: PSULTR1;2-GFP, slim1-1 and slim1-2 were vertically grown on the +S/-S (S1500/S15) agar medium. Root tissues of 10-day-old plants were used for RNA extraction and hybridization on Affymetrix microarrays. All conditions were duplicated.

first: Yumiko

last: Nakamura

first: Kazuki

last: Saito

first: Hideki

last: Takahashi


title: Heat shock response of HsfA2 knockout plants

status: Public on Nov 01 2006

city: Taipei

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

department: Agric. Biotech. Res. Center

country: Taiwan

institute: Academia Sinica

summary:
The expression of heat-shock proteins (Hsps) induced by a non-lethal heat treatment confers acquired thermotolerance (AT) to organisms against a subsequent challenge of otherwise lethal temperature. After stress signal lifted, AT gradually decayed with the decline of Hsps during recovery period. The duration of AT may be critical for sessile organisms, such as plants, to survive repeated heat stress in the environment. To identify heat-induced genes involved in duration of AT, we took a reverse-genetics approach by screening for Arabidopsis T-DNA insertion mutants that show decreased thermotolerance after a long recovery at non-stress condition following a conditioning treatment. Among the tested mutants corresponding to 47 genes, only the HsfA2 knockout mutant showed significant phenotype. The mutant plants were more sensitive to severe heat stress than the wild type after long but not short recovery following a pretreatment at 37oC, which can be complemented by introducing a wild-type copy of the gene. Quantitative hypocotyl elongation assay also revealed that AT decayed faster in the absence of HsfA2. Significant decline of the transcript levels of several highly heat-induced genes was observed in the HsfA2 knockout plants after a 4-h recovery or after 2 h of prolonged heat stress.  Immunoblot anlysis showed that Hsa32 and class I small Hsp were lower in the mutant than in the wild type after a long recovery.  Our results suggest that HsfA2 as a heat-induced transactivator sustains the post-stress expression of Hsp genes and extends the duration of AT in Arabidopsis.
Keywords: heat shock response

overall_design: Total RNA was isolated from the seedlings of 5-d old wild-type and HsfA2 knockout mutant seedlings (a pool of about 100 plants per treatment in duplicates) harvested immediately after heat shock treatment.  In this experiment, total 12 chips were used, 1 each for 2 biological replicates of the control and HS-treated samples for the wild type and mutant plants.

first: Nai-yu

last: Liu


title: Expression data from 7 day old Arabidopsis roots with 1h  Red light or dark

status: Public on Aug 15 2006

city: Gainesville

first: Melanie

last: Correll

state: FL

address: 142 Frazier Rogers Hall

department: Agricultural and Biological Engineering

institute: University of Florida

summary:
Red light can affect a variety of responses in Arabidopsis.  We characterize the early gene expression patterns of roots exposed to 1 hour of red light.  Early genes indicate elements involved in photomorphogenesis, chloroplast development, PAL pathways, root hair development are regulated by 1 hour of red light
We used microarrays to detail the gene expression underlying the effects of red light on roots.
Keywords: treatment

overall_design: 7 Day dark-grown 1 cm Arabidopsis root tips were harvested for RNA extraction and hybridization on Affymetrix microarrays. We pooled samples from several Petri plates for each experiment to obtain enough RNA for arrays.  Three experiments were performed. Treatment 1 hour of red light 630 nm (max) and dark controls

first: Maria

last: Molas

first: John

last: Kiss


title: Expression data from Arabidopsis thaliana tritrophic interaction experiment

status: Public on Nov 25 2008

city: Manchester

first: Daniel

last: Jameson

address: 3.614 Stopford Building

department: Faculty of Life Sciences

institute: University of Manchester

summary:
Multi-species interactions are a major force in the evolution and dynamics of ecosystems. These interactions may occur either when species affect each other directly or when they interact indirectly via an intermediary species. Direct interactions between species are best understood, but indirect interactions may also often be strong enough to alter the evolutionary trajectories of the target species. Little is known about the genetic basis of direct interactions within an ecosystem and even less data is available for indirect interactions. This experiment uses a simple model ecosystem to build a view at the transcriptome level of how interactions between plants (Arabidopsis) and rhizosphere bacteria (Pseudomonas) are altered by biotic stressors (insect herbivores) and abiotic stressors (UV-B).
Keywords: stress response

overall_design: Arabidopsis plants were established and then split into two cohorts at 15 days. One group were innoculated with Pseudomonas aeruginosa strain 7NR and the other not. 21 days later half of each of these groups were subjected to UV-B treatment for seven days. After this period each of the four groups of plants were further subdivided and infested with aphids, caterpillars or left alone. 24 hours after infestation the plants were harvested, individuals pooled and total RNA extracted giving 12 unique conditions. Five replicates were performed in series, yielding a total of 60 samples.

first: Rajasekaran

last: Palanisamy

first: Michael

last: Kertesz

first: Richard

middle: F

last: Preziosi


title: Overexpression of TELOMERASE ACTIVATOR 1 (TAC1)

status: Public on Sep 23 2006

city: College Station

first: Thomas

middle: D.

last: McKnight

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

summary:
The goal of this investigation was to identify putative targets of the TELOMERASE ACTIVATOR 1 transcription factor.
Keywords: Over-expression of transcription factor; mutant vs. wild type

overall_design: Total RNA was isolated from leaves of 3 week old plants.  We used three biological replicates of wild type (Columbia) and the tac1-1D activation tagged line (Ren et al., 2004. Plant Cell 16; 2910-2922).

first: Shuxin

last: Ren


title: Altered gene expression changes in Arabidopsis leaf tissues and protoplasts in response to Plum pox virus infection

status: Public on Nov 04 2008

city: London

first: Mohan

last: babu

state: Ontario

address: 1391 Sandford

department: Virology

institute: AAFC

summary:
Virus infection induces activation and suppression of global gene expression in the host. Profiling gene expression changes in the host may provide insights into the molecular mechanisms that underlie host physiological and phenotypic responses to virus infection. In this study, the Arabidopsis Affymetrix ATH1 whole genome array was used to assess global gene expression changes in Arabidopsis thaliana plants infected with Plum pox virus (PPV). To identify early genes in response to PPV infection, an Arabidopsis synchronized single-cell transformation system was developed. Arabidopsis protoplasts were transfected with a PPV infectious clone, PPV-SK68 and global gene expression changes in the transfected protoplasts were profiled.
Keywords: Time course and cell type comparison

overall_design:
For PPV infection in Arabdiopsis leaves, eight independent hybridizations were performed using total RNA isolated from three independent biological replicates of the virus-infected or mock-inoculated control samples.

For PPV infection in Arabidopsis protoplasts, 24 gene chips in total were used to hybridize with RNA isolated from protoplasts transfected with PPV infectious clone and PPV deletion mutant.

first: Aiming

last: Wang

last: Babu


title: Expression data from non-infected and Salmonella Choleraesuis infected mesenteric lymph nodes

status: Public on Sep 30 2007

first: Christopher

middle: K

last: Tuggle

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
To understand the host transcriptional response to S. enterica serovar Choleraesuis (S. Choleraesuis), the first generation Affymetrix porcine GeneChip® was used to identify differentially expressed genes in the mesenteric lymph nodes responding to infection at acute (8 hours (h), 24h, 48h post-inoculation (pi)) and chronic stages (21 days (d) pi)
The objectives of this study were to identify and examine the stereotypical gene expression response within the host mesenteric lymph nodes to S. Choleraesuis infection, and to characterize the global host responses by revealing the specific features of the host’s innate immunity.
Keywords: time course

overall_design: Fifteen piglets from Salmonella spp.-free sows were weaned at 10 days (d) of age, shipped to the National Animal Disease Center, Ames, IA and raised in isolation facilities. To confirm that all piglets were free of Salmonella spp. prior to challenge, bacteriological cultures were performed on rectal swabs twice. Seven week old pigs were randomly divided into 2 groups,  3 non-infected pigs and 12 infected pigs. Three non-infected control pigs were necropsied 3 days prior to experimental infection. On day 0, pigs in the infected groups were intranasally challenged with 1 billion CFU of Salmonella enterica serotype Choleraesuis x3246. Three infected pigs were necropsied at 8 hours post-inoculation (hpi), 24 hpi, 48 hpi and 21 day post-inoculation (dpi). Tissue samples from the mesenteric lymph nodes (MLN) were collected and immediately frozen in liquid nitrogen for RNA isolation.

first: Yanfang

first: Long

last: Qu

first: Jolita

last: Uthe

first: Shawn

last: Bearson

last: Kuhar

first: Joan

last: Lunney

first: Oliver

middle: P

last: Couture

first: Dan

last: Nettleton

first: Jack

last: Dekkers


title: Expression data from Arabidopsis 14-day-old  seedlings

status: Public on May 03 2006

city: Columbia

first: Gary

last: Stacey

address: 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri-Columbia

summary:
Chitin, a polymer of N-acetyl-glucosamne, is a component of the cell walls of many plant fungal pathogens. During the infection process, the released chitin fragments (such as chitooctaose) from fungal cell walls by plant enzymes can trigger plant defense response and gene activation. The current work studies the regulation of Arabidopsis genes by the purified chitin fragment chitooctaose.
We used the Affymetric Arabidopsis whole gene arrays to study the gene expression caused by chitin (chitooctaose).
Keywords: chitooctaose vs water treatments, with 3 biological replicates

overall_design: Arabidopsis seedlings grown hydroponically for 14 days were treated with the purified chitin fragment chitooctaose at a final concentration of 1 um for 3 minutes. The controls were similarli treated with an equivalent amount of ddH2O. Three biological replicates were obtained.

first: Jinrong

last: Wan


title: Difference in expression between SA- and mock-treated leaves 2 hours after application

status: Public on Mar 30 2006

city: Rockville

first: Francoise

last: Thibaud-Nissen

state: MD

address: 9712 Medical Center Dr

institute: The Institute for Genomic Research

summary:
Arabidopsis plants, ecotype Columbia, were sprayed with surfactant alone (0.01% Silwet) or surfactant and 1mM salicylic acid until all leaves were wet, 3 to 4 weeks after germination (before flowering). Leaves were harvested and frozen in liquid nitrogen. Three biological replicates were obtained over a period of 6 months. For each replicate, RNA was extracted using standard phenol/chloroform protocol and biotin-labeled cRNA was synthesized. cRNA was hybridized to 6 ATH1 GeneChip arrays. Cel files produced by the Affymetrix software were imported into R. Background subtraction, normalization and probe summaries were performed with the rma, quantile.normalization and median polish options of the rma function. Comparison of the SA- versus mock-treated tissue provides insight on the genes involved in systemic acquired resistance in Arabidopsis.
Keywords: salicylic acid, Arabidopsis, stress response, defense,

overall_design: 3 mock-treated and 3 SA-treated biological replicates were analyzed (one array each)

first: Julia

middle: C

last: Redman

last: Johnson

first: Jonathan

last: Arias

first: Chris

middle: D

last: Town


title: Analysis of Arabidopsis thaliana gene expression in response to the bacterial pathogen Pseudomonas syringae ES4326

status: Public on Mar 09 2007

city: Saint Paul

first: Raka

middle: Mustaphi

last: Mitra

state: MN

address: 1500 Gortner Avenue

department: Plant Biology

institute: University of Minnesota

summary:
In order to protect themselves from pathogens, plants activate a battery of defense pathways, many of which involve changes in gene expression.  We are interested in identifying plant genes that are differentially expressed in response to pathogen exposure, with the ultimate goal of studying the roles of these genes in plant defense.
Keywords: disease response

overall_design: Whole plants are grown in soil, and individual leaves from 3-4 week old plants are injected with a bacterial suspension, or a mock (5mM MgSO4) control. Approximately five leaves are harvested 24 hours after inoculation and used for RNA preparation, labeling and Affymetrix hybridization.

first: Jane

last: Glazebrook


title: Gain-of-function mutants of SOC1 vs soc1-2

status: Public on Jan 01 2006

first: Horim

last: Lee

address: San56-1, Seoul National University, Shillim-dong, Kwanak-gu

department: Biological Sciences

institute: Seoul National University

summary:
To find downstream target of SOC1, we attemted global expression profiles in gain-of-function mutants of SOC1

To find downstream target of SOC1, we attemted global expression profiles in soc1-101D:
Expt. 1 GSM73643, GSM73646
Expt. 2 GSM73647, GSM73648
Expt. 3 GSM73649, GSM73650

To find downstream target of SOC1, we attemted global expression profiles in soc1-2: GSM73649, GSM73651

To find downstream target of SOC1, we attemted global expression profiles in gain-of-function mutants of SOC1:
GSM73643, GSM73646, GSM73647, GSM73648, GSM73649, GSM73650
Keywords: genetic modification

overall_design: To more completely identify the downstream targets of SOC1, we attemted to compare the expression profiles of g-o-f mutant of SOC1 with the results of soc1-2 mutant

first: Ilha


title: effect of sucrose feeding to detached leaves

status: Public on Jan 05 2008

city: Potsdam

first: Joost

last: van Dongen

address: Am Muehlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

summary:
The effect of sucrose feeding on gene expression in Arabidopsis thaliana leaves was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis.
Keywords: sucrose feeding

overall_design: The effect of sucrose feeding on gene expression was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis.

first: Anna

last: Kolbe

first: Alisdair

middle: R

last: Fernie

first: Peter

last: Geigenberger


title: effect of redox on gene expression

status: Public on Apr 10 2006

summary:
In this study, we used GC-MS analysis in combination with flux analysis and the Affymetrix ATH1 GeneChip to survey the metabolome and transcriptome of Arabidopsis leaves in response to manipulation of the thiol-disulfide status. Feeding low concentrations of the sulfhydryl reagent dithiothreitol (DTT) for one hour at the end of the dark period led to post-translational redox-activation of ADP-glucose pyrophosphorylase and major alterations in leaf carbon partitioning, including an increased flux into major respiratory pathways, starch- cell-wall-, and amino-acid synthesis and a reduced flux to sucrose. This was accompanied by a decrease in the levels of hexose-phosphates, while metabolites in the second half of the TCA cycle and various amino acids increased, indicating a stimulation of anaplerotic fluxes reliant on α-ketoglutarate. There was also an increase in shikimate as a precursor of secondary plant products and marked changes in the levels of the minor sugars involved in ascorbate synthesis and cell wall metabolism. Transcript profiling revealed a relatively small number of changes in the levels of transcripts coding for components of redox-regulation, transport processes and cell wall, protein and amino acid metabolism, while there were no major alterations in transcript levels coding for enzymes involved in central metabolic pathways. These results provide a global picture of the effect of redox and reveal the utility of transcript and metabolite profiling as systemic strategies to uncover the occurrence of redox-modulation in vivo.
Keywords: redox regulation

overall_design: Leaf discs were incubated with or without 5mM DTT for one hour to affect the redox status of the cells. The effect of this treatment on global gene expression was analysed using affymetrix ATH1 microarrays. The experiments contains one control (-DTT) and one treatment (+DTT) and is performed with 2 biological replicas.

first: Sandra

last: Oliver

first: Mark

last: Stitt


title: The molecular basis of plant insect interactions.

status: Public on Jan 22 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary:
The aim of this study is to identify Arabidopsis genes whose expression is altered by aphid feeding. An understanding of the plant aphid interaction at the level of the plant transcriptome will 1) consolidate current areas of investigation focused on the phloem composition (the aphid diet), 2) open up areas of plant aphid interactions for ourselves and other workers, 3) Contribute to understanding the use of new molecular technologies in an environmental context and  4) contribute to existing and development of novel control strategies.Our Arabidopsis/Myzus persicae system provides a valuable model for the study because of: a) the advantages of using Arabidopsis, b) The ability to use clonal insects, c) phloem feeding aphids facilitate focus on a specific cell type, d) aphid stylectomy allows collection of pure phloem sap to monitor ‘phloem phenotype’ of the plant and the insect diet, e) we have techniques to monitor the reproductive performance and feeding behaviour aphids.Our strategy has been to test the function of selected genes, particularly those regulating phloem composition (the feeding site of the aphid) based on current phloem models of phloem function. Gene choice is limited the simplicity of current models of phloem aphid interaction.We propose a simple two treatment (aphid infested vs control plants) experiment that will identify novel target genes for future analysis. Arabidopsis plants (variety Columbia) will be grown in 16/8 light/dark in temperature controlled growth rooms. At growth stage 3.90, when rosette growth is complete, 10 clonal adult Myzus persicae will be caged in clip cages on the two largest leaves on each plant. Control plants will be treated identically except that the cages will be empty. Leaves will be harvested 8 h after infestation. This time point is selected as we know that 90% of aphids are plugged into the sieve element within 2h and that a 6h lag phase has period has previously been used when examining gene expression affected by wounding. In subsequent experiments we will examine time courses of expression of relevant genes using other approaches. Pooling two leaves from each of ten plants will generate the RNA sample, ensuring that expression signals are representative of the population of plants.
Keywords: pathogenicity_design

overall_design: Number of plants pooled:10

first: Jeremy

last: Pritchard


title: AtFBP7 mutant analysis

status: Public on Dec 31 2005

city: Freising

first: Claus

last: Schwechheimer

address: Emil-Ramann-Str. 4

department: Plant Systems Biology

institute: TUM

summary:
Transcript profiling analysis of AtFBP7 mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array.
Keywords: 5 day old light grown seedlings, wild type and mutant

overall_design: Three replicate samples were harvested and prepared from 5 day-old light grown wild type and fbp7-3 mutant seedlings. RNA for microarray analysis was extracted using the RNeasyTM kit (Quiagen, Hilden, Germany). Complementary RNA was prepared from 6 µg of total RNA as described in Affimetrix _Expression Analysis Technical Manual using the One-Cycle Target Labeling and Control Reagents (Affimetrix, Santa Clara, CA). In brief, double-stranded cDNA was synthesized. Biotin-labeled target cRNA was prepared by cDNA in vitro transcription in the presence of biotinylated UTP and CTP. After purification, cRNA was fragmented and used to hybridize to the Arabidopsis ATH1 GeneChip array (Affimetrix, Santa Clara, CA). Hybridization, washing, staining, scanning and data collection were performed in an Affymetrix GeneChip® Fluidics Station 450 and GeneArray® Scanner. The microoarray computaional analysis was performed on *.CEL and *.CHP data files.

first: Luz-Irina

last: Calderon-Villalobos


title: VFB mutant analysis

summary:
Transcript profiling analysis of vfb (Vier F-Box) mutant  seedlings compared to wild type using Arabidopsis ATH1 GeneChip array.
Keywords: 10 day old light grown seedlings, wild type and mutant

overall_design: Three replicate samples were harvested and prepared from 10 day-old light grown wild type and vfb mutant seedlings. RNA for micro array analysis was extracted using the RNeasyTM kit (Quiagen, Hilden, Germany). Complementary RNA was prepared from 6 µg of total RNA as described in Affimetrix _Expression Analysis Technical Manual using the One-Cycle Target Labeling and Control Reagents (Affimetrix, Santa Clara, CA). In brief, double-stranded cDNA was synthesized. Biotin-labeled target cRNA was prepared by cDNA in vitro transcription in the presence of biotinylated UTP and CTP. After purification, cRNA was fragmented and used to hybridize to the Arabidopsis ATH1 GeneChip array (Affimetrix, Santa Clara, CA). Hybridization, washing, staining, scanning and data collection were performed in an Affymetrix GeneChip® Fluidics Station 450 and GeneArray® Scanner. The microarray computaional analysis was performed on *.CEL and *.CHP data files


title: DCL4 Functional Analysis

status: Public on Sep 30 2005

city: Corvallis

first: Edwards

last: Allen

state: OR

address: 3021 Ag Life Sciences Building

department: Botany and Plant Pathology

institute: Oregon State University

summary:
Rosette leaves (5-8) and inflorescence stages (1-12) from dcl1-7, rdr6-15, and dcl4-2 mutants, involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays.  Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and trans-acting siRNAs).
Keywords: other

first: Zhixin

last: Xie

first: April

last: Wilken

first: James

last: Carrington


title: Tropic-stimulus induced changes in gene expression

status: Public on Jan 09 2006

first: Emmanuel

last: Liscum

address: Rollin Rd

institute: University of Missouri

summary:
Plants, although sessile, can reorient growth axes in response to changing environmental conditions.  Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively.  The nearly 80-year-old Cholodny-Went theory Went, F.W. & Thimann, K.V. Phytohormones (1937) (Macmillan, New York) predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature.  Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient.  Yet, the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive.  Here we report the discovery of a suite of tropic stimulus-induced (TSI) genes in Brassica oleracea that are responsive to an auxin gradient, and exhibit morphologically graded expression concomitant with, or before, observable curvature responses.  These results provide compelling molecular support for the Cholodny-Went theory, and suggest that morphologically-graded transcription represents an important mechanism for interpreting tropically-stimulated gradients of auxin.  Intriguingly, two of the TSI genes, EXPA1 and EXPA8, encode enzymes involved in cell wall extension, a response prerequisite for differential growth leading to curvatures, and are upregulated prior to curvature in the flank that will elongate.  This observation suggests that morphologically-graded transcription likely leads to the graded expression of proteins whose activities can directly regulate the establishment and modulation of tropic curvatures.
Keywords: tropic response, repeat

overall_design: A 15° ophthalmic scalpel (Feather, Osaka, Japan) was used to isolate tissue flanks (~1 cm in length, see Fig. 1A) from etiolated B. oleracea seedlings that had received one of three treatments: 1) a mock stimulation; 2) a 2 h phototropic stimulation; or 3) a 2 h gravitropic stimulation.  Only the outer third of the hypocotyl was collected for each flank section, and opposing flanks were collected into separate pools.  Hence there were five distinct tissue samples (two flanks for each of two tropic stimulations plus one set of control flanks) with each sample being generated and collected in triplicate for a total of fifteen biological samples.  Tissue flanks were immediately quick frozen in liquid N2 and stored at –80°C until RNAs were isolated.  Total RNA was extracted from frozen tissue using the RNeasy kit (Qiagen, Valencia, CA), followed by cRNA synthesis (ENZO Diagnostics, Farmingdale, NY).  cRNA probe generation, as well as microarray hybridization, washing and scanning were performed as described by manufacturer protocols (Affymetrix, Santa Clara, CA).

first: Cairn

middle: A

last: Esmon

first: Amanda

middle: G

last: Tinsley

first: Karin

last: Ljung

first: Goran

last: Sandberg

first: Loenard

middle: B

last: Hearne


title: Transcriptome profiling of dark grown photoreceptor mutants seedlings of Arabidopsis  ATH1

status: Public on Sep 04 2005

city: Capital Federal

first: Maria

middle: Agustina

last: Mazzella

state: Buenos AIres

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI

summary:
Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment.
Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses

overall_design: We analysed the transcriptome profile in dark grown seedlings of the WT, and phyA phyB photoreceptor mutants. All seedlings have the same treatment (3d grown in complete darkness). We have two samples for each genotype that represent two replicates in each case.

middle: V

last: Arana

first: Roberto

last: Staneloni

first: Susana

last: Perelman

first: MAria

middle: J

last: Rodriguez Batiller

first: Jorge

last: Muschietti

first: Pablo

last: Cerdan

first: Kenhua

last: Chen

first: Rodolfo

last: Sanchez

first: Tong

last: Zhu

first: Joanne

last: Chory

last: Casal


title: ATH1 Transcriptome profiling of dark grown photoreceptor mutants seedlings of Arabidopsis

summary:
Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment.

Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses

overall_design: We analysed the transcriptome profile in dark grown seedlings of the WT, phyA and phyB photoreceptor single mutans and the phyAphyB double mutant. All seedlings have the same treatment (3d grown in complete darkness). We have two samples for each genotype that represent two replicates in each case.

last: Muschhietti

first: Kenua


status: Public on Apr 03 2005

city: Berlin

first: Wolfram

last: Brenner

address: Albrecht-Thaer-Weg 6

department: Applied Genetics

institute: Institute of Biology

summary:
Time course of Arabidopsis seedlings treated with 6-Benzyl adenine dissolved in diluted KOH for 15 min or 2 hours
Keywords: other

first: W

first: Lukas

last: Bürkle

first: Georgy

last: Romanov

first: Thomas

last: Schmülling


title: Expression profiling of A.thaliana with the posttranscriptionally silenced Myosin XI-K

status: Public on Aug 04 2006

first: Valera

last: Peremyslov

address: 2082 Cordley Hall

summary:
This study was aimed to determine roles of individual myosins in organelle trafficking in plant cell.  Expression of Myosin XI-K was suppressed in transgenic A.thaliana by using RNAi approach. To ensure that the RNAi-induced gene silencing was specific and did not affect expression of other myosins, a microarray analysis was performed.
Keywords: RNAi-mediated posttranscriptional gene silencing, Myosin expression levels

overall_design: Total RNA was purified from A.thaliana plants transformed with an inverted repeat construct harbouring a sequence derived from Myosin XI-K ORF. 3 independent groups of plants were used for comparison of the expression profiles of 17 myosin RNAs to a control group comprised of plants constitutively expressing GUS ORF as a transgene.


title: Overexpression of miR164b and 172a (vegetative apex)

status: Public on Feb 01 2005

first: Javier

middle: Fernando

last: Palatnik

address: 37-39 Spemannstrasse

department: Molecular Biology

institute: Max Planck Institute

summary:
RNA was isolated from vegetative apices of 7d-old short-day grown plants. Overexpression of miR164b and miR172a versus control.
Keywords: parallel sample

first: Rebecca

last: Schwab

first: Carla

last: Schommer

first: Detlef

last: Weigel


title: Expression during deetioaltion under Rc in wt and phy mutant seedlings

status: Public on May 15 2006

city: Albany

first: james

middle: m

last: tepperman

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

summary: Etiolated seedling response to one hour of continuous red light. Four-day-old dark-grown wild-type RLD and phyA101, phyB1  and phyAphyB  mutant seedlings were transferred to Rc (680 nm, 8  mol m-2 s-1) for 1 h or retained in darkness as controls. Three different biological replicates of each treatment were grown separately and extracted, processed, and analyzed independently.RNA was extracted and subjected to expression analysis by using the Affymetrix ATH1 microarray containing approximately 22,000 Arabidopsis genes .

overall_design: 3 dark and 3 1hr Rc samples ( biological replicates) were analyzed for each genotype

first: James

middle: M

last: Tepperman


title: Overexpression of miR319a (SD Leaves)

city: Tuebingen

summary:
jaw-D plants grown in SD compared to columbia wt.
Keywords: parallel sample

middle: F


title: Heat shock response in Arabidopsis Hsa32 knockout mutant

status: Public on Mar 20 2006

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

institute: Academia Sinica

summary:
Plants and animals share similar mechanisms in the heat-shock (HS) response, such as synthesis of the conserved HS proteins (Hsps). However, because plants are confined to a growing environment, in general they require unique features to cope with heat stress. We have analyzed the function of a novel Hsp, heat-stress-associated 32-kD protein (Hsa32), which is highly conserved in land plants but absent in most other organisms. The gene responds to HS at the transcriptional level in moss, Arabidopsis, and rice. Like other Hsps, Hsa32 protein accumulates greatly in Arabidopsis seedlings after HS treatment. Disruption of Hsa32 by T-DNA insertion does not affect growth and development under normal conditions. However, the acquired thermotolerance in the knockout line was compromised following a long recovery period (> 24 h) after an acclimation HS treatment, when a severe HS challenge killed the mutant but not the wild-type plants, but no significant difference was observed if they were challenged within a short recovery period. Microarray analysis of the knockout mutant indicates that only the expression of Hsa32 was significantly altered in HS response. Taken together, our results suggest that Hsa32 is not required for the induction but maintenance of acquired thermotolerance.  This report provides direct evidence that a plant-specific Hsp plays an important role in thermotolerance.
Keywords: heat shock response

overall_design: Total RNA was isolated from the shoots of 15-d old wild-type and Hsa32 knockout mutant seedlings (a pool of about 100 plants per treatment in duplicates) harvested immediately after treatment at 37C (HS) or 22C (control) for 2 h.  In this experiment, total eight chips were used, 1 each for 2 biological replicates of the control and HS-treated samples for the wild type and mutant plants.

first: Nai-yu

last: Liu


title: flk_vs_wt

status: Public on Sep 01 2004

city: La Jolla

first: Todd

middle: C.

last: Mockler

department: Plant Biology Laboratory

institute: The Salk Institute for Biological Studies

summary:
Examination of Columbia-O wildtype and flk mutant tissues under the following conditions:

7 day-old long-day grown, collected 1hr after dawn (exp3: GSM26236-GSM26241);

16 day-old continuous-light-grown (exp2: GSM26230-GSM26235);

16 day-old long-day grown,  collected at 16hrs after dawn (exp1: GSM26224-GSM26229).

Keywords = Arabidopsis
Keywords = flowering
Keywords = flk
Keywords: other


title: Nep1 Treatment

status: Public on Apr 11 2006

city: Beltsville

first: Hanhong

last: Bae

address: 10300 Baltimore Ave

institute: USDA-ARS-PSI

summary:
In order to study the Nep1 responsive genes in Arabidopsis, experiments were performed with the Affymetrix GeneChip Arabidopsis ATH1 Genome Array (Santa Clara, CA; Cat # 900385).
Keywords: Arabidopsis, Nep1, Affymetrix GenChip

overall_design: Seven-day old Arabidopsis seedlings were exposed to Nep1 (10 ug/mL) treatment or using sterilized, deionized H2O as a control for 30 min.  Two independent biological replications were conducted using two independent samples and two microarrays.

first: Moon

middle: S

last: Kim

first: Richard

last: Sicher

first: Hyeun

first: Bryan

last: Bailey


title: Histone acetylation during seed germination

status: Public on Dec 10 2005

city: Fredericton

first: Helen

middle: H

last: Tai

email: htai@nrcan.gc.ca, taihelen@yahoo.com

state: New Brunswick

address: 1350 Regent St.

department: Natural Resources Canada

institute: Canadian Forest Service

summary:
Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes.  Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression.  To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds.  GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination.   Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA).  A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate.  In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated.  Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Arabidopsis WT and vip mutants (vip5 and vip6)

city: East Lansing

first: Sookyung

last: Oh

state: MI

department: Horticulture

institute: Michigan State University

summary:
Comparison of gene expression profiles of wild-type, vip5 mutant, and vip6 mutant  Arabidopsis.
Keywords = VIP
Keywords: repeat sample

first: Hua

last: Zhang

first: Philip

last: Ludwig

first: Steve

last: van Nocker


title: ETHYLENE-INSENSITIVE5 encodes a 5' to 3' exoribonuclease required for posttranscriptional regulation

status: Public on Aug 08 2006

first: Joseph

middle: R.

last: Ecker

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

summary:
Ethylene is a gaseous plant growth regulator that controls a multitude of developmental and stress responses. Recently, the levels of Arabidopsis EIN3 protein, a key transcription factor mediating ethylene-regulated gene expression, have been demonstrated to increase in response to the presence of ethylene gas. Furthermore, in the absence ethylene, EIN3 is quickly degraded through a ubiquitin/proteasome pathway mediated by two F box proteins, EBF1 and EBF2 (1-3). Here, we report the identification of ETHYLENE INSENSITIVE5 as the 5’?3’ exoribonuclease XRN4. Specifically, we demonstrate that EIN5 is a component of the ethylene signal transduction cascade acting downstream of CTR1 that is required for ethylene-mediated gene expression changes. Furthermore, we find that the ethylene insensitivity of ein5 mutant plants is a consequence of the over-accumulation of EBF1 and EBF2 mRNAs resulting in the under-accumulation of EIN3 even in the presence of ethylene gas. Together, our results suggest that the role of EIN5 in ethylene perception is to antagonize the negative feedback regulation on EIN3 by promoting EBF1 and EBF2 mRNA decay, which consequently allows the accumulation of EIN3 protein to trigger the ethylene response.
Keywords: total RNA profiling, proteolysis, plant hormoine, ethylene

overall_design: Cold-treated seeds in MS plates were placed in chambers at 24oC in the dark with hydrocarbon-free airflow for three days, after which some of the chambers were connected to ethylene gas at 10 ppm while the others remained on air treatment. Four hours later the seedlings of each plate were quickly collected and frozen in liquid nitrogen.  Total RNA was prepared from both air-treated and ethylene-treated etiolated seedlings of Arabidopsis Col-0, ein2-5 and ein5-1 using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Biotinylated target RNA was prepared from 16 ?g of total RNA using the procedure described by the manufacturer (Affymetrix, Santa Clara, CA). Briefly, a primer encoding a T7 RNA polymerase promoter fused to (dT)24 (Genset Oligos, La Jolla, CA) was used to prime double-stranded cDNA synthesis using the SuperScript Choice System (Life Technologies). The resulting cDNA was transcribed in vitro using the BioArray High-Yield RNA Tran-script Labeling Kit (Enzo Biochem, New York, NY) in the presence of biotinylated UTP and CTP to produce biotinylated target complementary RNA (cRNA). The labeled target cRNA was purified, fragmented, and hybridized to Arabidopsis microoarrays (Affymetrix whole genome tiling, and ATH1 gene expression arrays) according to protocols provided by the manufacturer in a hybridization oven model 640 (Affymetrix, Santa Clara, CA). The arrays were washed and stained with streptavidin-phycoerythrin using a GeneChip Fluidics Station model 400 and then scanned with a Gene Array Scanner (Hewlett-Packard, Palo Alto, CA). Scanned images were processed and quantified using GeneChip Suite 3.2. Genespring software (Silicon Genetics, Redwood City, CA) was used to manage and filter the array data. Each measurement was divided by the 50.0th percentile of all measurements in that sample.  The percentile was calculated with all normalized measurements above 10.  For samples where the bottom tenth percentile was less than the negative of the 50.0th percentile, it was used as a background, and subtracted from all the other genes first. Experiments were carried out in duplicate and hybridized to two sets of expression chips.  Expression values were analyzed using GeneSpring™ software version 4.2 (Silicon  Genetics, Redwood, California).

first: Gabriela

last: Olmedo

first: Hongwei

last: Guo

first: Brian

last: Gregory

first: Saied

last: Nourizadeh

first: Laura

last: Aguilar-Henonin

first: Hongjiang

last: Li

first: Fengying

last: An

first: Plinio

last: Guzman

first: Junshi

last: Yazaki


title: Overexpression of miR159a

first: Javier

last: Palatnik

summary:
Flowers stage 15: Comparison of miR159a overexpressers to empty-vector control.
Keywords: parallel sample

first: Rebecca

last: Schwab

first: Carla

last: Schommer

first: Detlef

last: Weigel


title: Cell culture treatment study

status: Public on Dec 01 2005

city: Crawley

first: Rachel

last: Clifton

state: Western Australia

address: 4th Floor CMS Building M310, University of Western Australia

department: Biochemistry, UWA

country: Australia

institute: Plant Energy Biology, ARC Centre of Excellence

summary:
Profiling the transcriptome of Arabidopsis suspension cells in response to a range of abiotic treatments.
Keywords: treatment response

overall_design:
variable_1 = 3 h
variable_2 = 12 h
variable_3 = untreated, control
variable_4 = hydrogen peroxide
variable_5 = N2 air replacement
variable_6 = chitin
variable_7 = cold
variable_8 = cysteine
variable_9 = flagellen
variable_10 = mannitol
variable_11 = norflurazon
variable_12 = oligomycin 0.125 uM
variable_13 = oligomycin 1.25 uM
variable_14 = roteonone
variable_15 = salicylic acid 10 uM
variable_16 = salicylic acid 100 uM
variable_17 = chloramphenicol

first: Ryan

last: Lister

first: Pia

last: Sappl

first: Karen

last: Parker

first: James

last: Whelan

first: A

last: Millar

first: Karem

last: Singh


title: BR effects on WT and yucca seedlings

status: Public on Aug 31 2004

first: Jennifer

last: Nemhauser

department: PBIO

institute: Salk Institute

summary:
Ten-day old light-grown Arabidopsis seedlings were immersed in 1 µM brassinolide in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA) or media alone for 2.5 hours
Keywords: repeat sample

middle: L

first: Todd

middle: C

last: Mockler

first: Joanne

last: Chory


title: Auxin effects on seedlings

status: Public on Jul 31 2004

summary:
Five-day old light-grown Arabidopsis seedlings were immersed 10 µM indole-3-acetic acid (auxin) or water
Keywords: repeat sample

first: Yunde

last: Zhao

first: Xinhua

last: Dai

first: Helen

middle: E

last: Blackwell

first: Stuart

last: Schreiber


title: Arabidopsis thaliana gene expression in response to IAA challange

status: Public on Mar 09 2004

first: Julia

last: Redman

address: 9712 Medical Center Dr

department: Plant Genomics

institute: The Institute for Genomic Research

summary:
Arabidopsis seedlings (Col-0) were grown in suspension in half-strength MS medium with agitation at ~100 rpm at ~22 C under ~50 microeinsteins m-2s-1 cool white fluorescent continuous illumination as described by (Xiao et al., Plant Physiol. 2002 Dec;130(4):2118-28). Seedlings were treated at 10-12 days by addition of freshly made IAA (0.1 or 1.0uM) to each flask, and harvested after a 1 or 3 hour incubation.  Controls were not treated and harvested at 0hr.  All tissue harvested.  Total RNA was extracted using TRIzol (Invitrogen) as described by the manufacturer and then filtered using QIAGEN RNeasy columns.  cDNA was synthesized from total RNA using a Superscript double-stranded cDNA synthesis kit (Invitrogen) and a T7-dT24 primer. cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling kit (Affymetrix p/n 900182) and fragmented by Mg2+ hydrolysis.  15ug per ATH1 array was hybridized overnight at 45 C. Arrays were then washed and scanned using the GeneChip FS400 fluidics station and Agilent GeneArray scanner.  Images were analyzed using Affymetrix Microarray Suite 5.0, scaling to a target average intensity of 500.  Spiking controls were added to the total RNA before cDNA synthesis and additional spiking samples were added to the resulting cDNA prior to cRNA synthesis.

In comparison table below:
SIGNAL_LOG_RATIO = Mean of log to base two of the experimental divided by control signal ratios across all probe pairs in a set.
CHANGE = Qualitative measurement indicating whether the probe set signal is increased (I), marginally increased (MI), not changed (NC), marginally decreased (MD), or decreased (D) as compared to a control hybridization across all probe pairs, based on a p-value calculation.
change_p-value = Measures the probability that all probe pairs in the set indicate a change, with 0 indicating strong likelyhood for increase, 0.5 indicating little probability for difference, and 1 indicating strong probability for decrease.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Keywords = Arabidopsis
Keywords: dose response

first: Brian

last: Haas

first: Gene

last: Tanimoto

first: Christopher

middle: D

last: Town


title: Comparison of AG and ATH1 using IAA

summary:
Arabidopsis seedlings (Col-0) were grown in suspension in half-strength MS medium with agitation at ~100 rpm at ~22 C under ~50 microeinsteins m-2s-1 cool white fluorescent continuous illumination as described by (Xiao et al., Plant Physiol. 2002 Dec;130(4):2118-28). Seedlings were treated at 10-12 days by addition of freshly made IAA
(0.1 or 1.0uM) to each flask, and harvested after a 1 or 3 hour incubation.  Controls were not treated and harvested at 0hr.  All tissue harvested.  Total RNA was extracted using TRIzol (Invitrogen) as described by the manufacturer and then filtered using QIAGEN RNeasy columns.  cDNA was synthesized from total RNA using a Superscript double-stranded cDNA
synthesis kit (Invitrogen) and a T7-dT24 primer. cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling kit (Affymetrix p/n 900182) and fragmented by Mg2+ hydrolysis.  15ug per array was hybridized overnight at 45 C. Arrays were then
washed and scanned using the GeneChip FS400 fluidics station and Agilent GeneArray scanner.
Images were analyzed using Affymetrix Microarray Suite 5.0, scaling to a target average
intensity of 500.  Spiking controls were added to the total RNA before cDNA synthesis and additional spiking samples were added to the resulting cDNA prior to cRNA synthesis.

Probe samples were recovered for use in replicate hybridizations, 2 per array for a total of 4 hybridizations.  The purpose of this was the statistical comparison of the two different versions of Affymetrix Arabidopsis probe arrays, AG and ATH1, as part of the process of characterization of the newer array, ATH1.

A complete dose response assay using ATH1 and the data represented below may be found in series file GSE1110.

In comparison table below:
SIGNAL_LOG_RATIO = Mean of log to base two of the experimental divided by control signal ratios across all probe pairs in a set.
CHANGE = Qualitative measurement indicating whether the probe set signal is increased (I), marginally increased (MI), not changed (NC), marginally decreased (MD), or decreased (D) as compared to a control hybridization across all probe pairs, based on a p-value calculation.
change_p-value = Measures the probability that all probe pairs in the set indicate a change, with 0 indicating strong likelyhood for increase, 0.5 indicating little probability for difference, and 1 indicating strong probability for decrease.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Keywords = Arabidopsis
Keywords: parallel sample


title: Arabidopsis pen3 mutant and wild type Col-O comparison under host inoculation, nonhost inoculation and no inoculation.

city: Stanford

first: Shauna

last: Somerville

address: 260 Panama Street

institute: Carnegie Institution of Washington

summary:
Arabidopsis is a host to the fungal powdery mildew pathogen, Erysiphe cichoracearum, and a nonhost to Blumeria graminis f.sp. hordei, the powdery mildew pathogenic on barley. A screen for mutants that allowed increased entry by this inappropriate or nonhost pathogen on Arabidopsis led to the identification of PEN3. While pen3 mutants permitted both increased penetration and increased hyphal growth by B. g. hordei, they were unexpectedly resistant to E. cichoracearum. This resistance was correlated with the appearance of chlorotic patches and was salicylic acid-dependent. Consistent with this observation, microarray analysis revealed that the salicylic acid defense pathway was hyper-induced in pen3 relative to wild type following inoculation with either E. cichoracearum or B. g. hordei. The pen3 phenotypes result from a loss of function of AtPDR8, a ubiquitously and highly expressed ATP binding cassette transporter. PEN3 protein tagged with green fluorescent protein localized to the plasma membrane in uninfected cells. In infected leaves, the protein concentrated to high levels at infection sites and surrounded fungal penetration pegs. We hypothesize that PEN3 may be involved in exporting toxic substrates to sites of infection and that accumulation of these substrates intracellularly in the pen3 mutant may secondarily activate the salicylic acid pathway.
Keywords: disease state comparison

overall_design: Three week-old wild-type Col and mutant pen3 Arabidopsis thaliana plants were inoculated with Erysiphe cichoracearum, Blumeria graminis hordei, or not inoculated.  1 day post inoculation 16 rosettes were harvested per replicate. 4 replicates were perfomerd per treatment.

first: Monica

last: Stein

first: Bi-Huei

last: Hou


title: A genome-wide housekeeping role for TFIID and a highly stress-related role for SAGA in Saccharomyces cerevisiae

status: Public on Mar 01 2004

city: University Park

first: Frank

last: Pugh

state: PA

address: 452 North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

summary:
TFIID and SAGA are the only two known yeast complexes that modify chromatin and deliver TBP to promoters.  Previous genome wide expression studies indicated that TFIID and SAGA positively regulate most but not all yeast genes.  Using a relatively low noise microarray approach, we have re-examined the genome-wide dependence on TFIID and SAGA.  We find that TFIID and SAGA contribute to the expression of virtually the entire genome, with TFIID being preferred at ~90% of the genes, and SAGA being preferred at ~10%.  SAGA-dominated genes were found to overlap substantially with a previously described set of highly active genes that are attenuated in part by the TBP regulator NC2, and an auto-inhibitory function of TFIID.  These SAGA-dominated genes also encompass most of the previously reported “TAF-independent” genes.  These results build upon and refine the generally held view that activators recruit either TFIID or SAGA to promoters which then bind and acetylate nucleosomes locally, thereby enhancing TBP delivery to the TATA box.  Promoter-specific differences in the ability to alleviate auto-inhibitory activities associated with TFIID and SAGA might contribute to the preferential use one complex versus the other.
Keywords = Chromatin Immunoprecipitation
Keywords = genome-wide binding
Keywords: other

first: Kathryn

last: Huisinga

first: B Franklin

first: Sara

last: Zanton


title: Transcriptome analysis of ROP10 GTPase-mediated abscisic acid (ABA) signaling in Arabidopsis

status: Public on Nov 14 2005

city: Bronx

first: Zhi-Liang

last: Zheng

state: NY

address: 250 Bedford Park Blvd W

institute: Lehman College of City University of New York

summary:
In this study, we have identified genes that are respectively activated and repressed by the low concentration of ABA and show that ROP10 gates a specific subset of genes that are responsive only to a low ABA concentration.
Keywords: Whole seedlings of wild-type (Ws) and the mutant (rop10-1) treated with or without ABA

overall_design: 12 Arabidopsis ATH1 chips were purchased from Affymetrix. Total RNA was extracted and purified from 1µM ABA-treated or non-treated Ws and rop10-1. Each genotype/treatment has three biological replicates. Probe labeling, array hybridization and scanning were done by the University of California-Irvine DNA Microarray Facility.

first: Zeyu

last: Xin

first: Yihong


title: Brassinosteroid mutant (bzr1-1D and det2) analysis

status: Public on May 24 2005

first: Joshua

middle: Martin

last: Gendron

address: 260 Panama Rd.

institute: Carnegie Institution of Washington/Stanford University

summary:
Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth
and development of plants. BR signaling through cell-surface receptor
kinases and intracellular components leads to dephosphorylation and
accumulation of the nuclear protein BZR1. How BR signaling regulates gene
expression, however, remains unknown. Here we show that BZR1 is a
transcriptional repressor that has a previously unknown DNA binding domain
and binds directly to the promoters of feedback-regulated BR biosynthetic
genes. To identify additional BZR1-regulated genes and to understand the
BR-regulated transcriptional pathways, we examined the effects of bzr1-1D
and det2 mutations on the expression of BR-regulated genes by using the
Arabidopsis full-genome oligo microarray (Affymetrix). Microarray analyses
identified additional potential targets of BZR1 and illustrated, together
with physiological studies, that BZR1 coordinates BR homeostasis and
signaling by playing dual roles in regulating BR biosynthesis and downstream
growth responses.
Keywords: other

first: Zhi-yong

last: Wang


title: YODA lof and gof seedlings

status: Public on Feb 22 2004

first: Dominique

last: Bergmann

address: 260 Panama St

institute: Carnegie Institution

summary:
comparison of 7dpg seedlings of wildtype yda(C24) and N-term deletion of YDA (Ler) for stomatal development comparisons
Keywords: repeat sample

first: Chris


title: Control vs. 35S:AtRALF1-1

status: Public on Feb 06 2004

city: Pullman

first: Daniel

middle: Scherer de

last: Moura

state: WA

institute: Institute of Biological Chemistry

summary:
This series (two repeats) compares the transcriptional changes caused by the overexpression of the AtRALF1-1 cDNA.  AtRALF1-1 is one of the nine Arabidopsis isoforms of the polypeptide hormone RALF (PNAS 98, 12843).
Keywords: other

first: Gregory

last: Pearce

first: Clarence

middle: A

last: Ryan


title: Seed germination in presence and absence of histone deaceatylase inhibitor, Trichostain A (TSA).

first: Helen

last: Tai

summary:
   Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes.  Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression.  To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds.  GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination.   Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA).  A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate.  In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated.  Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes.
Keywords: histone deacetylase inbibition, developmental effects

overall_design: Three samples:  Unimbibed seeds, untreated imbibed seeds, TSA-treated imbibed seeds.

first: George

first: Tannis

last: Beardmore