title: Expression data of seeds imbibed at 22˚C or 4˚C for 24hr of Arabidopsis thaliana

status: Public on Jun 01 2012

city: Kaga-gun

first: Aya

last: Hatano-Iwasaki

state: Okayama

address: 7549-1 Yoshikawa, Kibichuo-cho

institute: Okayama Prefectural Technology Center for  Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences

summary: Keeping imbibed seeds at low temperatures for a certain period, so called seed vernalization (SV) treatment, promotes seed germination and subsequent flowering in various plants. Vernalization-promoting flowering requires GSH. However, the expression patterns analyzed by GeneChip arrays showed that increased GSH biosynthesis partially mimics SV treatment in Arabidopsis thaliana. SV treatment (keeping imbibed seeds at 4°C for 24 h) induced a specific pattern of gene expression and promoted subsequent flowering in wild-type plants. A similar pattern was observed at 22°C in transgenic plants (35S-GSH1 plants) overexpressing the γ-glutamylcysteine synthetase gene GSH1, coding an enzyme limiting GSH biosynthesis, under the control of the cauliflower mosaic virus 35S promoter. This pattern was strengthened at 4°C but flowering was less responsive to SV treatment. There was a difference in the transcript behaviour of the flowering repressor FLC between wild-type and 35S-GSH1 plants.  Unlike other genes responsive to SV treatment, SV-dependent decrease in FLC in wild-type plants was reversed in 35S-GSH1 plants. SV treatment increased GSSG level in wild-type seeds, whereas GSSG level was high in 35S-GSH1 plants, even at a non-vernalizing temperature.  Taking into consideration that low temperatures stimulate GSH biosynthesis and bring about oxidative stress, GSSG is considered to trigger low temperature response, but enhanced GSH synthesis was not enough for mimicking SV treatment. To complete it, it essentially required the cellular redox retransition from the oxidized to the reduced state that is observed after the seed vernalization treatment.

overall_design: Four samples (Col-0 and 35S-GSH1 seeds imbibed at 22˚C or 4˚C). Two replicates for each samples.

first: Ken'ichi

last: Ogawa


title: The AtGenExpress: hormone inhibitor or other chemical treatment of seedlings in Arabidopsis

status: Public on Jul 17 2012

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

country: Japan

institute: Yokohama City University

summary: Arabidopsis seedlings of the wild-type were treated with inhibitors.

overall_design: 60 samples were analyzed by Affymetrix GeneChip, ATH1. Sample correspondence between control (mock) and inhibitor treatment is described in brackets (F series or G series).


title: Transcript profiling of Arabidopsis msh1 mutants

status: Public on Jul 12 2012

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

country: USA

institute: University of Nebraska

summary: The Arabidopsis msh1 mutant show various growth phenotype. We use microarray analysis to characterize gene expression pattern for two of the phenotypes - variegation and stunted growth.

overall_design: Wild type and msh1 RNAi variegated and stunted tissues were collected for RNA extration and hybridization on Affymetrix.

first: Sally

middle: A

last: Mackenzie


title: Expression data from aerial parts of 14-day-old wild-type and GFP-TIE1-15 Arabidopsis seedlings

status: Public on May 27 2012

city: Beijing

first: qing

last: tao

address: 5th,Yi he yuan road, hai dian district,Beijing,China

department: Biotechnology

country: China

institute: Peking University

summary: TIE1 regulates leaf development by repressing leaf differentiation because the semi-dominant mutant tie1-D by activation tagging displays small and hyponastic leaves and the differentiation of leaf epidermal cells is delayed in the tie1-D mutant, whereas disruption of TIE1 causes epinastic leaves with early differentiated epidermal cells. We used microarrays to investigate the molecular base underpinning the phenotypes of TIE1-overexpressing plants.

overall_design: Aerial parts of 14-day-old seedlings from wild-type and GFP-TIE1-15 were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Qing

last: Tao

first: Li

middle: J

last: Qu

first: Genji

last: Qin


title: Analysis of a N-6 adenosine methylation deficient plant

status: Public on May 02 2012

city: Loughborough

first: Neil

last: Graham

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

country: United Kingdom

institute: University of Nottingham

summary: The embryo lethal adenosine methylase tDNA knockout line SALK_074069 was partially complemented with its cDNA driven by the embryo specific ABI3 promoter (A6 lines). The plants have reduced adenosine methylation and show pleiotropic phenotypes. Rosette leaves were harvested from 3 week old plants, both wild-type and mutant plants in triplicate and analysed using the Affymetrix ATH1 array.

overall_design: The 3rd to 6th rosette leaves were harvested in triplicate from 3 week old wild-type and mutant plants (A6). Total RNA was extracted and hybridised to the Affymetrix ATH1 array.

first: Z

last: Bodi

first: S

last: Zhong

last: Mehra

first: J

last: Song

first: N

last: May

first: R

last: Fray


title: The effects of infection with wild-type or mutant cucumber mosaic virus on the Arabidopsis transcriptome

status: Public on May 15 2012

first: nasc

last: nasc

address: Sutton bonington Campus

department: Plant&Crop Sciences

institute: NASC

summary: The cucumber mosaic virus (CMV) 2b counter-defense protein disrupts plant antiviral mechanisms mediated by RNA silencing and salicylic acid (SA). Using NASC ATH-1 microarrays to investigate defensive gene expression in 2b-transgenic Arabidopsis thaliana plants we found that, surprisingly, 2b inhibited expression of few SA-regulated genes and in some instances enhanced the effect of SA on certain genes. Strikingly, the 2b protein inhibited changes in the expression of 90% of genes regulated by jasmonic acid (NASCARRAYS-415: Lewsey et al. Molec. Plant-Microbe Interact. vol. 23, in press).  We will extend this work to understand the effects of the 2b protein on plant gene expression during an authentic viral infection.  By comparing the effects on the transcriptome of infection by wild-type CMV and the 2b gene deletion mutant, CMVÃ¢Ëâ 2b, we will reveal not only the influence of the 2b protein but also the effects of its interactions with other viral gene products (and the process of infection itself), on the host transcriptome.

overall_design: 9 samples were used in this experiment

first: Zhiyou

last: Du


title: Expression data in WT and erf6 mutant under high-light treatment

city: Kaifeng

first: Chun-Peng

state: Henan

address: 85 Minglun street

institute: Henan University

summary: Reactive oxygen species (ROS) have been characterized as both important signaling molecules and universal stressors that mediate many developmental and physiological responses. So far, details of the transcriptional mechanism of ROS-responsive genes are still largely unknown. In the study reported herein, we identified eight potential ROS-responsive cis-acting elements (ROSEs) from the promoters of genes upregulated by ROS. We also found that the APETALA2 (AP2/EREBP)-type transcription factor ERF6 could bind specifically to the ROSE7/GCC box. Co-expression of ERF6 enhanced luciferase activity driven by ROSE7. ERF6 interacted physically with mitogen-activated protein kinase 6 (MPK6), and also served as a substrate of MPK6. MPK6-mediated ERF6 phosphorylation at both Ser 266 and Ser 269 affected the dynamic alternation of ERF6 protein, which resulted in changes in ROS-responsive gene transcription. These data might provide new insight into the mechanisms that regulate ROS-responsive gene transcription via a complex of MPK6, ERF6, and the ROSE7/GCC box.

overall_design: To identifiy the ERF6 regualted genes under ROS and HL treatment. Three-week old Col-0 and erf6-1 mutant plants before and after exposed to 2000 umol m-2s-1 illumination for 2 h were used for RNA extracted hybridization on Affymetrix microarrays.

first: Wang

last: Pengcheng

first: Du

last: Yanyan

first: Song

last: Chun-Peng


title: Stable and inducible expression of Fbxo25  in Flp-In-293 cells: control vs. tetracycline treatment

city: Ribeirão Preto

first: Ana

middle: Carolina

last: Humanes

state: SP

address: Avenida Bandeirantes, 3900

department: Bioquímica e Imunologia

country: Brazil

institute: Universidade de São Paulo

summary: Expression profile of human Flp-In-293-WT-FBXO25 or Flp-In-293-∆F-FBXO25 cells comparing non treated cells vs. tetraciclyne treated for 24 and 48 hours. Flp-In-293-∆F-FBXO25 cells when induced express the non functional protein (without F-box domain).  The objective of the study was to identify genes up or down-regulated when Fbxo25 wild-type or Fbxo25 lacking F-box domain is superexpressed.

overall_design: Flp-In-293 WT and ∆F cells with and without tetracycline treatment.  Two timepoints, two replicates each.

first: A

middle: C


title: Hepatitis C virus-induced expression profiling of Hepatic and non-hepatic cancer cell lines [mock-treated]

status: Public on May 21 2012

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To facilitate accurate measurement of the relative expression levels in Hepatitis C virus infection, we carried out in four human cancer cell lines derived from Hepatic (Hec3B; human hepatoma and Huh7; human hepatocellular carcinoma) or nonhepatic (Hec1B; human endometrial and 293T;human embryonic kidney) cells. These experiments identified several genes , expression of which was altered in the same direction among them with real time PCR analysis.

overall_design: Hepatic (Hec3B and Huh7) or nonhepatic (Hec1B and 293T) cells were examined after HCV infection and after mock-treatment. Each cell line was run in singlet.

first: Takasuke

last: Fukuhara

first: Yoshiharu

last: Matsuura


title: Mepazine inhibitor effects DLBCL cell line HBL1

status: Public on Jul 31 2012

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

summary: The medicinal active phenothiazine mepazine acts as a small molecule inhibitor of the MALT1 protease. Mepazine selectively inhibits cleavage activity of recombinant and cellular MALT1 by a noncompetitive mechanism. MALT1 activity is required for NF-kappaB signaling and survival of aggressive lymphoma belonging to the ABC-DLBCL (activated B-cell-type of diffuse large B-cell lymphoma) entity. Gene expression profiling was carried out in the ABC-DLBCL cell line HBL1 after treatment with mepazine (20 microM) for 6, 12, and 24 hr. Mepazine inhibits anti-apoptotic NF-kB signaling and thereby survival of these cells.

overall_design: Using Agilent 2-color gene expression microarrays (GPL10332) mepazine-treated HBL1 cells were compared with DMSO in the control channels.

first: Georg

last: Lenz


title: Analysis of Ripening-related Gene Expression in Papaya using an Arabidopsis-based Microarray

status: Public on May 25 2012

city: SP

first: Joao

middle: P

last: Fabi

address: Avenida Lineu Prestes, 580

department: Departamento de Alimentos e Nutrição Experimental

institute: USP

summary: Background: Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during fruit ripening and its control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana.  Results: Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes and some of them had their expression validated by qPCR. The transcription profile was then compared with that from ripening tomato and grape. Overall, the transcriptomics analysis revealed many similarities between ripening in papaya and tomato especially with respect to primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicate that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families are involved in the control of papaya ripening and reveal that cell wall-related gene expression in papaya showed similarities to the expression profiles seen in A. thaliana during hypocotyl development.  Conclusion: The cross-species array experiment was successful in identifying ripening-related genes in papaya. The data indicated common and diverse elements of transcription control between fruit bearing taxa and has also indicated a possible distinct co-evolutionary mechanism for papaya cell wall disassembling system. The present study represents new topics for future researches that would help complement the structural genomic data provided by the papaya genome, since there is no gene-chip available for this plant organism.

overall_design: Papaya ripe transcriptome was analysed using mRNA extracted from unripe and ripe fruit from 3 replicates. After microarray hybridization in ATH1-121501 chip, data were normalized against data generated by papaya DNA hybridization in another ATH1-121501 chip and analysed using perl algorithms (masks).

first: João

first: Graham

middle: B

last: Seymour

first: Neil

middle: S

last: Graham

first: John

last: Hammond

first: Martin

last: Broadley

first: Sean

middle: T

first: Franco

middle: M

last: Lajolo

first: Beatriz

middle: R

last: Cordenunsi

last: Nascimento


title: Arabidopsis thaliana wild-type and pskr1-5 transcriptome upon the compatible interaction with Hyaloperonospora arabidopsidis

status: Public on Apr 14 2012

city: Sophia Antipolis

first: Harald

last: Keller

address: 400 route des Chappes

department: UMR-ISA

country: France

institute: INRA

summary: We used Arabidopsis full-genome microarrays to characterize plant transcript accumulations in wild-type plants and pskr1-5 mutants, 3 days after water treatment and inoculation with the biotrophic oomycete downy mildew pathogen, Hyaloperonospora arabidopsidis.

overall_design: In two independent experiments, cotyledons from the wild-type Wassilewskija (WS) ecotype and from the pskr1-5 mutant were treated with water, or inoculated with the H. arabidopsidis isolate Emwa1 to establish a compatible interaction. Affymetrix ATH1 microarrays were used to profile Arabidopsis transcript accumulations at 3 days after onset of treatment.

first: N

last: Rodiuc

first: B

last: Favery

first: H


title: Expression data from 11-day-old antisense BoEMF2.1 broccoli

status: Public on Mar 31 2012

city: Taipei

first: Mao-Sen

last: Liu

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

summary:
EMF2 genes play an important function in inhibiting reproductive programs during vegetative stage of plant development. We knocked down the expression of endogenous EMF2 genes in broccoli by introduing a 35S::antisenseBoEMF2.1 contruct. The transgenic broccoli with knocking-down expression of endogenous EMF2s showed aberrant phenotypes during development.
We used microarrays to study the global programme of gene expression and to identified genes misexpressed in broccoli with knocking-down expression of endogenous EMF2 genes

overall_design: 11-day-old seedlings of broccoli harboring the empty vector pCAMBIA1380 and that harboring 35S::antisenseBoEMF2.1 (asBoEMF2.1) were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Long-Fang

middle: O

last: Chen

first: Zinmay

last: Sung


title: Expression data from 7-day-old Arabidopsis emf2 mutant, rescued emf2 mutant harboring 35S::BoEMF2.1, WT Columbia ecotype and WT harboring 35S::BoEMF2.1 named transWT

status: Public on Mar 30 2012

summary: Arabidopsis emf2 mutants bypass vegetative development and flowering upon seed germination. We introduced a broccoli BoEMF2.1 gene into emf2 mutants and obtained rescued emf2 plants that harbored 35S::BoEMF2.1. We found that BoEMF2.1 can partially rescue the phenotype of emf2 to that of WT. We used microarrays to study the global program of gene expression and to identify genes misexpressed in the Arabidopsis emf2 mutant that had been rescued by 35S::BoEMF2.1.

overall_design: 7-day-old seedlings of WT, transWT, emf2 and rescued emf2 Arabidopsis were used for RNA extraction and hybridization on Affymetrix microarrays.


title: Genome wide identification of ORE1 early target genes

status: Public on Jan 01 2013

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary: Global transcriptome patterns were performed using ORE1-IOE-2h (2h after Estradiol and Mock treatment) as well as transiently (6h) overexpressed Arabidopsis mesophyll cell protoplasts

overall_design: To identify genes more rapidly responding to elevated ORE1 expression we here repeated the previous experiment (Balazadeh et al., 2010), but shortened the EST induction time to 2 h (ORE1-IOE-2h dataset). Furthermore, to exclude potential misinterpretation due to EST treatment we also included an experiment where we transiently expressed a 35S::ORE1 construct in Arabidopsis mesophyll cell protoplasts and extracted RNA 6 h after the transfection (35S::ORE1-6h dataset);

first: Lilian

last: Matallana-Ramirez

first: Wolfgang

last: Dröge-Laser


title: Identification of Direct Targets of RPX a NAC transcription factor of Arabidopsis thaliana

city: Potsdam

first: Jos

last: Schippers

department: Plant Signaling

institute: MPIMP-golm

summary: To determine the role of RPX on cell proliferation and organ development, we performed microarray experiments in search of RPX target genes by using an estradiol-inducible RPX∆C protein.

overall_design: Estradiol-treatment allows for the nuclear translocation of the constitutively expressed chimeric transcription factor XVE and subsequent expression of RPX∆C from the LexA promoter. Stable trangenic T3 seedlings were either treated with 10 uM estradiol or ethanol (mock) for 2 hours. Three mock and three estradiol treated samples were used for RNA isolation and hybridization.

first: Hung

last: Mnguyen

first: Jozefus

middle: H

first: Bernd

last: Mueller-Roeber


title: Microarray analysis of gene expression of the Arabidopsis leaf and callus

status: Public on Apr 07 2012

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary:
Callus formation is usually a necessary step in regenerating a new plant from detached plant tissues, and the nature of the callus is similar to that of the root meristem. In this study, we intended to address the molecular basis that directs different plant tissues to form the root-meristem-like callus. We found that leaves, but not roots, of the Polycomb group (PcG) double mutant curly leaf-50 swinger-1 lost the ability to form a callus. Using ChIP-chip analysis, we identified genes that are changed markedly in the histone H3 lysine 27 trimethylation (H3K27me3) levels during callus formation from leaf explants. Among these genes, a number of leaf-regulatory genes were repressed through PcG-mediated H3K27me3. Conversely, certain auxin pathway genes and many root-regulatory genes were derepressed through H3K27 demethylation. Our data indicate that genome-wide H3K27me3 reprogramming, through the PcG-mediated H3K27me3 and the H3K27 demethylation pathways, is critical in directing cell fate transition.
This submission represents the gene expression component of the study

overall_design: Leaves from 20-day-old seedlings of wild-type Col-0 and 20-DAC calli were used for RNA preparation.

last: Xu

first: Chongsheng

last: He


title: Transcriptome profiling of LecRKVI.2 over-expressor plants.

status: Public on Mar 19 2012

city: TAIPEI

first: PRASHANT

last: SINGH

state: TAIPEI

address: Rm 1150, Life Science Building, No. 1, Sec. 4, Roosevelt Road

department: INSTITUTE OF PLANT BIOLOGY

institute: NATIONAL TAIWAN UNIVERSITY

summary:
The arabidopsis L-type lectin receptor kinase-VI.2 positively regulates bacterial PAMP-triggered immunity.
We used microarrays and performed genome-wide transcriptome analysis of LecRKVI.2 over-expressing plants and identified number of upregulated genes involved against bacterial resistance.

overall_design: Total RNA was isolated from 5-week-old Arabidopsis plants for RNA extraction and hybridisation on Affymetrix microarrays.

first: Prashant

last: Singh

first: Laurent

last: Zimmerli


title: Gene expression from cadmium treated Arabidopsis seedlings

status: Public on Feb 24 2012

city: La Jolla

first: Julian

middle: I

last: Schroeder

state: CA

address: 9500 Gilman Drive #0116

department: Biology

institute: UCSD

summary: To identify genes that are up-regulated by Cd for creation of a Cd-inducible reporter line. See PMID 22283708.

overall_design: One week old Col-0 plants were treated with/without 200uM Cd for 6 hours. Total RNA was extracted from whole seedlings and subjected to hybridization with Affymetrix ATH1 microarrays.

first: Timothy

last: Jobe


title: Genomic dna hybridizations of 10 Spring annual accessions of Arabidopsis thaliana

status: Public on Mar 12 2012

city: Austin

first: David

middle: Lee

last: Des Marais

state: TX

address: 1 University Station C0930

department: Integrative Biology

institute: The University of Texas at Austin

summary:
These data provide a basis for the detection of sequence based polymorphisms between 10 Spring annual accessions of Arabidopsis thaliana.  The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies.
Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range.  Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin.  These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.

overall_design: Each accession has 3 replicates, single channel on the ATH1 array.  Samples were processed in two balanced batches (bioprime random labeling, hybridization,scanning).  A total of 30 arrays

middle: L

last: Desmarais

first: Thomas

middle: E

last: Juenger


title: Genomic dna hybridizations of 8 winter annual accessions of Arabidopsis thaliana

overall_design: Each accession has 3 replicates, single channel on the ATH1 array.  Samples were processed in two balanced batches (bioprime random labeling, hybridization,scanning).  A total of 24 arrays


title: Identification of target genes of cancer-related microRNAs in human cancer

status: Public on Feb 09 2012

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1 Inohana,Chuo-ku

department: School of Medicine

institute: Chiba University

summary:
To identify target genes of oncogenic or tumor suppressive microRNAs in human cancer, several cell lines (bladder cancer, prostate cancer, renal cell carcinoma. lung squamous cell carcinoma and head and neck squamous cell carcinoma) were subject to Agilent whole genome microarray.
miR-183 and miR-96 function as oncogene. miR-1, miR-133a, miR-135a, miR-145 and miR-375 function as tumor suppressor

overall_design: The miRNA transfected human cancer cell lines (KK47, T24, A498, PC3, DU145, FaDu, SAS, PC10 and H157) were compared to control cell lines.


title: Synergistic Repression of Embryonic Program by SET DOMAIN GROUP 8 and EMBRYONIC FLOWER 2 in Arabidopsis Seedlings

status: Public on Dec 31 2011

city: London

first: Xurong

last: Tang

address: 1391 Sandford Street

country: Canada

institute: Agriculture and Agri-Food Canada

summary: The seed maturation program occurs only during late phase of embryo development and repression of the maturation genes is pivotal for seedling development. However, mechanisms that repress the expression of this program in vegetative tissues are not well understood. A genetic screen was performed for mutants that express maturation genes in leaves. Here, it is shown that mutations affecting SDG8 (SET DOMAIN GROUP 8), a putative histone methyltransferase, cause ectopic expression of a subset of maturation genes in leaves. Further, to investigate the relationship between SDG8 and the Polycomb Group (PcG) proteins, which are known to repress many developmentally important genes including seed maturation genes, double mutants was made and formation of somatic embryos was observed on mutant seedlings with mutations in both SDG8 and EMF2 (EMBRYONIC FLOWER 2). Interestingly, double mutant of sdg8 and mutations in VRN2 (VERNALIZATION 2), a paralog of EMF2, grow and develop normally to maturity. Analysis of histone methylation status at chromatins of a number of maturation loci revealed synergistic effect of emf2 and sdg8 on the deposition of the active histone mark, trimethylation of lysine 4 on histone 3 (H3K4me3), which is consistent with high expression of these genes (formation of somatic embryos) in emf2 sdg8 double mutants. These observations demonstrate a functional cooperative interplay between SDG8 and an EMF2-containing PcG complex in maintaining vegetative cell identity by repressing seed genes to promote seedling development. The work also indicates the functional specificities of PcG complexes in Arabidopsis.

overall_design:
Total RNA was isolated from three independent biological replicates of Wild type (ProβCG:GUS) and two independent biological replicates of sdg8-2 and essp4/sdg8-5, respectively. Four ATH1 chips were used for the two mutants and three for the wild type.

Matrices comprising the signal intensity value of each gene per replicate hybridization and the averaged data of each gene generated from three replicate hybridizations of the wild type and two replicate hybridizations of mutant samples, respectively, are linked below as supplementary files.

first: Julie

last: Pelletier

first: Mingjuan

first: Vi

last: Nguyen

first: Wilfred

last: Keller

first: Aiming

last: Wang

first: Steven

last: Rothstein

first: John

last: Harada

first: Yuhai

last: Cui


title: Expression data from Arabidopsis and Maize leaves

status: Public on Dec 23 2011

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

institute: John Innes Centre

summary: Many animal and plant species exhibit increased growth rates, reach larger sizes and, in the cases of crops and farm animals, produce higher yields when bred as hybrids between genetically differing strains, a phenomenon known as hybrid vigour or heterosis.  Despite the importance of heterosis, and its extensive genetic analysis, there has been little understanding of its molecular basis.  We aimed to determine whether characteristics of the leaf transcriptome, as an indicator of the innate functional genetic architecture of a plant line, could be used as markers to predict heterosis and the performance of hybrids, a methodology we term Association Transcriptomics. Relationships between transcript abundance of specific genes and the values of heterosis and heterosis-dependent traits were identified and mathematical models were constructed that relate gene expression characteristics in inbred lines of Arabidopsis thaliana and maize with vegetative biomass and for grain yield, respectively, in corresponding hybrids.

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays

overall_design:
Plants used for transcriptome analysis were grown from seeds for 2 weeks.  Aerial parts above the coleoptiles were excised, weighed and frozen in liquid nitrogen.  All plants were harvested as close as practicable to the middle of the photoperiod.
Plants used for transcriptome analysis were grown from seeds for 2 weeks. Maize seeds were first imbibed in distilled water for 2 days in glasshouse conditions to break dormancy, before transfer to peat and sand P7 pots. They were grown in long day glass house conditions (16 hours photoperiod) at 22 degrees Celsius.  Aerial parts above the coleoptiles were excised, weighed and frozen in liquid nitrogen.  All plants were harvested as close as practicable to the middle of the photoperiod.  Plants for yield trials were grown in the field at Clayton, NC, U.S.A. in 2005.  Forty plants of each hybrid were grown in duplicate 0.0007 hectare plots.


title: Identify differentially expressed genes in 14-day-old pkl seedlings

status: Public on Jan 01 2012

first: Heng

last: Zhang

state: Shanghai

address: 300 Fenglin Rd, Room 705

institute: Shanghai Center for Plant Stress Biology

summary:
CHD3 proteins are ATP-dependent chromatin remodeling factors that are components of diverse multisubunit complexes that can either repress or activate gene expression. In plants, the CHD3 protein PICKLE (PKL) is necessary for repression of seed-specific genes during germination and promotes deposition of the repressive epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3). It is unknown, however, if PKL acts directly at H3K27me3-enriched loci.  We undertook a microarray analysis of 14-day-old plants and found that PKL continues to play an important role in expression of H3K27me3-enriched genes and in specification of developmental identity after germination.
We used microarray to identify genes that are differentialy expressed in 14-day-old pkl seedlings and used chormatin immunoprecipitation to identify genes that are the direct targets of PKL.

overall_design: Wild-type (Col-0) and pkl-1 seedlings were grown on 1/2 MS plates with constant light and harvsted after 14-day growth. Three biological replicates.

first: Joe

last: Ogas

first: Ann

last: Feil


title: Physiological genomics of response to soil drying in diverse Arabidopsis accessions

status: Public on Mar 09 2012

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Effect of biotin deficiency on gene expression in Aravbidopsis leaves

status: Public on Dec 22 2011

city: Seibersdorf

first: Günter

last: Brader

address: AIT

department: Health & Environment Department

country: Austria

institute: Austrian Institute of Technology

summary:
In addition to its essential metabolic functions biotin is suggested a critical role in regulating gene expression. The first committed enzyme in biotin biosynthesis in Arabidopsis, 7-keto-8-aminopelargonic acid synthase is encoded by At5g04620 (BIO4). We isolated a novel T-DNA insertion mutant of BIO4 (bio4-1) showing a spontaneous cell death phenotype that could be rescued both by exogenous biotin and genetic complementation. The bio4-1 plants exhibited massive accumulation of hydrogen peroxide.
The T-DNA insertion in the bio4-1 mutant contains a Methionine Sulfoxide Reductase B9 (AT4G21850) under a constitutive 35S CaMV promoter. To dissect the specific effects of biotin defiency on gene expression on a genome wide scale, we compared expression of wt Col-0 leaves with bio4-1 mutants and bio4-1 mutants complemented with D-biotin.

overall_design: Expression in leaves of Col-0 wt, bio4-1 mutants with a T-DNA insertion in the 5`-UTR of BIO4, and bio4-1 mutants complemented with watering with 200µM D-biotin.

first: Jing

last: Li

first: Elina

last: Helenius

first: Tarja

last: Kariola

first: E-Tapio

last: Palva


title: Gene regulation by phosphomimetic Myc (MycD), cytosine arabinoside (AraC) and retinoic acid (RA)

status: Public on Jan 05 2012

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

summary: We aimed to investigate whether the previously observed synergistic effects of AraC and RA in stimulating leukemia differentiation could be at least partially dependent on Pak2-mediated phosphorylation of Myc. Genome-wide analysis of NB4 cells treated with RA, AraC with RA, or MycD with RA revealed a significant 60% overlap between RA-target genes superactivated by AraC with RA, or MycD with RA, with respect to RA alone.

overall_design: NB4 cells infected with ER-tagged inducible empty vector (CTL), MycD or MycA were treated with 4-OHT (200 nM, 16 h) to induce MycD-ER and MycA-ER expression. CTL cells were either vehicle or AraC (25 μM) treated for 16 h. Short treatment of RA (10 nM, 4 h) was performed in CTL, AraC and MycD-expressing cells. Four biologically independent experiments were performed at each time.

first: Iris

last: Uribesalgo

first: Guglielmo

last: Roma


title: Expression analysis of developmental stages of Arabidopsis roots exposed to sulfur deficient media

status: Public on Nov 23 2011

city: Durham

first: Anjali

last: Iyer-Pascuzzi

state: NC

institute: Duke University

summary:
To understand the effect of sulfur deficiency on developmental stages in the root, we dissected the root into four developmental zones after exposure to sulfur deficiency and expression profiled each zone.
Stress responses in plants are tightly coordinated with developmental processes, but the interaction between these pathways is poorly understood. Here we use genome-wide assays at high spatial and temporal resolution to understand the processes that lnk development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. Common stress responses appear to exists and, analagous to animal systems, many of them show cell-type specificity, suggesting a convergent evolutionary theme in multicellular organisms. Common stress responses may be mediated by cell identity regulators, as mutations in these genes resulted in altered responses to stress. Our results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide datasets to elucidate biological processes.

overall_design: 2 replicates each of 4 developmental stages exposed to sulfur deficient media

first: Terry

last: Jackson

first: Philip

middle: N

last: Benfey


title: An O-acetylserine(thiol)lyase homolog regulates cysteine homeostasis in Arabidopsis thaliana

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

summary: Cysteine occupies a central position in plant metabolism due to its biochemical functions. Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Because they are localized in the cytosol, plastids and mitochondria, this results in multiple subcellular cysteine pools. Much progress has been made on the most abundant OASTL enzymes; however, information on the less abundant OASTL-like proteins has been scarce. To unequivocally establish the enzymatic reaction catalyzed by the minor cytosolic OASTL isoform CS-LIKE (AT5G28030), we expressed this enzyme in bacteria and characterized the purified recombinant protein. Our results demonstrate that CS-LIKE catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate. Thus, CS-LIKE is a novel L-cysteine desulfhydrase (EC 4.4.1.1), and we propose to designate it DES1. The impact and functionality of DES1 in cysteine metabolism was revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. Mutation of the DES1 gene leads to premature leaf senescence, as demonstrated by the increased expression of senescence-associated genes and transcription factors. Also, the absence of DES1 significantly reduces the total cysteine desulfuration activity in leaves, and there is a concomitant increase in the total cysteine content. As a consequence, the expression levels of sulfur-responsive genes are de-regulated, and the mutant plants show enhanced antioxidant defenses and tolerance to conditions that promote oxidative stress. Our results suggest that DES1 from Arabidopsis is an L-cysteine desulfhydrase involved in maintaining cysteine homeostasis, mainly at late developmental stages or under environmental perturbations.

overall_design: Using the Affymetrix ATH1 GeneChips, we performed a comparative transcriptomic analysis on leaves of the des1-1 and wild type plants grown on soil for three weeks. Three biological replicates were performed for each sample and hybridized to the chips. We made the comparison of des1-1 leaves versus wild-type leaves to classify the differently expressed genes in the mutant plant.

first: Consolación

last: Álvarez

first: Irene

last: García

first: Luis

last: Romero


title: Expression data from dark-grown AtGATA2 (At2g45050) overexpression transgenic line, homozygous bri1-116 and Col-0 wild type

status: Public on Nov 09 2011

city: Beijing

first: wenhui

last: lin

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, CAS

summary:
Molecular genetic analyses support important roles for the AtGATA2 gene in brassinolide (BR) and light regulation of plant development. The overexpression line 6-9 of AtGATA2 suppresses the etiolated phenotype of Col-0 grown in the dark.
Using microarray analysis, we identified genes differentially expressed in the AtGATA2ox transgenic line 6-9 compared to wild type, and genes differentially expressed in the AtGATA2ox transgenic line 6-9 compared to the bri1-116 single mutant.  Consistent with the phenotypic similarity of bri1-116 and AtGATA2, overall about 93% of the co-regulated genes were affected in the same way by GATA2-ox and bri1-116.

overall_design: AtGATA2-regulated genes have been identified by comparing genes differentially expressed by the Col control and bri1-116, which could find the crosslink between light and BR regulations of plant development.

first: Zhiyong

last: Wang


title: Chemokine expressions in breast cancer patients

status: Public on Nov 05 2011

city: Timisoara

first: Diana

last: Narita

address: 2 Eftimie Murgu

department: Biochemistry

country: Romania

institute: University of Medicine and Pharmacy Victor Babes Timisoara

summary:
Our aim was to evaluate the expression of chemokines in breast cancers before treatment to identify a molecular signature that could distinguish between women with or without cancer. We identified a panel of chemokines clearly deregulated in breast cancer that could be further investigated for prospective novel markers or therapeutically approaches.
Samples for gene expression were obtained during surgical resection and after macroscopic pathological assessment. Laser-capture microdissection was used to select and procure only the desired cell types (malignant groups of cells or normal mammary acini), under direct microscopic visualization

overall_design: Chemokine expression profiles using cDNA microarray was evaluated on homogenous, laser-capture microdissected breast cancer specimens before treatment.


title: Gene expression changes in response to the overexpression of the Arabidopsis RKD4 gene

status: Public on Sep 22 2011

city: Ikoma

first: Keiji

last: Nakajima

state: Nara

address: 8916-5 Takayama

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

summary: The Arabidopsis RWP-RK protein RKD4 is expressed specifically in early embryogenesis and triggers embryonic cell division sequences. We used Affymetrix ATH1 microarrays to analyze the pattern of gene expression changes in response to induced ectopic expression of RKD4 in post-embryonic organs.

overall_design: Plants of a dexamethasone (DEX)-inducible overexpression line and a control line were grown under normal conditions for 2 days and then treated with DEX for 1 day. RNA was extracted from two independent pools for each genotype.


title: Exogenous slaicylic acid (SA) treatment of Arabidopsis thaliana Col-0

status: Public on Nov 03 2011

city: Berkeley

first: Mary

last: Wildermuth

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

summary: 0.5 mM SA plus 0.02% Silwet or 0.02% Silwet (control) was sprayed on leaves of 3.5 week old Arabidopsis plants.  Samples were harvested at 0 (prior to treatment) , 3, 6, 12, and 24 hours post treatment.  A subset of these samples were processed.

overall_design: Arabidopsis plants grown in parallel under standardized conditions were treated with SA + Silwet or Silwet alone (control).  Only mature leaves of the same developmental age were harvested using leaves from 2-4 plants, totalling ~0.2 grams per sample.  Plants were not resampled.  In our hands, experimental replicates are highly reproducible.  This was an exploratory experiment to look for candidate genes impacted by exogenous SA treatment.  We were only able to process a subset of samples and chose to process key time points, sacrificing replicates at each time point.

first: Jennifer

last: Harrower


title: Expression data from arabidopsis root in response to boron toxicity

status: Public on Nov 01 2011

city: Santiago

first: Andrea

last: Vega

address: Vicuña Mackenna 4860

department: Ciencias Vegetales

country: Chile

institute: Pontificia Universidad Catolica de Chile

summary: Boron is an essential micronutrient for plants and is taken up in the form of boric acid (BA). Despite this, a high BA concentration is toxic for the plants, inhibiting root growth and is thus a significant problem in semi-arid areas in the world. In this work, we report the molecular basis for the inhibition of root growth caused by boron. We used microarrays to detail the global gene expression underlying boron toxicity in roots.

overall_design: 5-day-old arabidopsis plants were transferred to medium with high boron concentration (½ MS medium supplemented with 5mM BA) and control conditions (½ MS medium). We determined that 5 mM BA is the minimum concentration that produces the maximum effect, stunting root growth by ~50% after 5 days as compared with control conditions. We analyzed the transcript profiles in roots by microarray analysis (Affymetrix ATH1 Genome Array). We compared the transcripts obtained at 12 hrs of BA treatment.

first: Felipe

last: Aquea

first: Fernan

last: Federici

first: Cristian

last: Moscoso

first: Pastor

last: Jullian

first: Jim

last: Haseloff

first: Patricio

last: Arce-Johnson


title: Identification of target genes of the NMD factor SMG7b

status: Public on Oct 07 2011

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary: Nonsense-mediated mRNA decay (NMD) is a conserved mRNA quality control mechanism that identifies and destroys aberrant mRNAs that contain premature termination codons (PTCs). The NMD core comprises seven proteins, from SMG1 to SMG7. Arabidopsis has orthologues of most of these proteins. Studies on yeast, Drosophila, Humans and Arabidopsis reveal that NMD not only functions to target PTC-containing mRNAs but also acts as a global regulator of gene expression. It has also been reported that the NMD pathway branches with some target genes being dependent on specific NMD factors. In order to determine the extent to which different NMD factors co-regulate or independently regulate Arabidopsis genes, transcriptome analysis of smg7b-1 mutants will be carried out and added to existent data of upf1, upf3 and smg5 NMD mutants for comparison. RNA will be extracted from 17 day-old mutant and wild type seedlings grown at 22-24 C under constant light.

overall_design: 4 samples were used in this experiment

last: Arciga-Reyes


title: Genes co-regulated by the NMD factors UPF2 and SMG5

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary: Eukaryotic cells have evolved a mechanism called nonsense mediated mRNA decay (NMD) that detects and degrades aberrant mRNAs that contain premature termination codons (PTCs).  NMD has recently acquired broader importance as it has been found to regulate not only aberrant mRNAs but also a great diversity of transcripts, including wild type genes in mammals, Drosophila and yeast.  Seven proteins are the core of the NMD complex: SMG1, SMG2 (UPF1), SMG3 (UPF2), SMG4 (UPF3), SMG5, SMG6 and SMG7. Plants have orthologues of most of these proteins. We have identified and characterized a number of alleles of UPF1, UPF3 and SMG5 and made 35S:UPF2 RNAi (upf2i) transgenic plants, all of which share some phenotypic characteristics. Transcriptome analysis of upf1 and upf3 mutants has identified a subset of genes coregulated by UPF1 and UPF3 and, therefore, by NMD (unpublished data). By doing further transcriptome analysis on smg5 mutants and upf2i plants we aim to build a more robust subset of NMD targets in Arabidopsis.  RNA will be extracted from 17 day-old mutant, transgenic and wild type seedlings grown at 22-24 C under constant light.

overall_design: 6 samples were used in this experiment


title: Transcriptomic analysis of the myb3r1 myb3r4 double mutant in Arabidopsis thaliana

status: Public on Sep 07 2011

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: R1R2R3-Myb proteins represent an evolutionarily conserved class of Myb family proteins important for cell cycle regulation and differentiation in eukaryotic cells. In plants, this class of Myb proteins are believed to play important roles in cell cycle regulation through transcriptional regulation of G2/M phase-specific genes by binding to common cis-elements, called MSA elements. In Arabidopsis thaliana, MYB3R1 and MYB3R4 act as transcriptional activators and positively regulate cytokinesis by activating transcription of KNOLLE, which encodes a cytokinesis-specific syntaxin. Here, we show that the double mutation myb3r1 myb3r4 causes pleiotropic developmental defects, some of which are due to deficiency of KNOLLE whereas other are not, suggesting multiple target genes are involved. Consistently, microarray analysis of the double mutant revealed altered expression of many genes, among which G2/M-specific genes showed significant overrepresentation of the MSA motif and a strong tendency to be down-regulated by the double mutation. Our results demonstrate, on a genome-wide level, the importance of the MYB3R-MSA pathway for regulating G2/M-specific transcription. In addition, MYB3R1 and MYB3R4 may have diverse roles during plant development by regulating G2/M-specific genes with various functions, as well as genes possibly unrelated to the cell cycle.

overall_design: Comparison between the myb3r1 myb3r4 double mutant and wild type in three paired replicates.

first: Nozomi

last: Haga

first: Kosuke

last: Kobayashi

first: Takamasa

last: Suzuki

first: Kenichiro

last: Maeo

first: Minoru

last: Kubo

first: Misato

last: Ohtani

first: Taku

last: Demura

first: Kenzo

last: Nakamura

first: Gerd

last: Jürgens

first: Masaki

last: Ito


title: Grape skin transcriptome in the berries cultured in vitro treated with exogenous abscisic acid

status: Public on Aug 26 2011

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary:
The softened green berries of Cabernet Sauvignon were cultured in a Petri dish. 0.3M sucrose solution with (±)-abscisic acid (ABA) and without (±)-ABA (control) were applied to the Petri dishes. The berry skins were sampled at 3 and 10 days after the application.
PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Kazuya Koyama.  The equivalent experiment is VV17 at PLEXdb.

overall_design:
ABA treated - time: 3 days(2-replications);
ABA treated - time: 10 days(2-replications);
Non-treated (control) - time: 3 days(2-replications);
Non-treated (control) - time: 10 days(2-replications)

first: Kazuya

last: Koyama


title: High temperature effect on Cabernet Sauvignon berries

summary:
The experiment was conducted using four 11-year-old potted  grapevines of V. vinifera L. cv. Cabernet Sauvignon grafted on  SO4 (Selection Oppenheim No. 4) grown in a phytotron. Vines  were trained on a Guyot trellising system and each vine carried  4-10 clusters of grapes. The experiment started approximately  1 week before veraison, when berry softening started, and continued  to fruit maturity. The two temperature regimes consisted of a high  day (06.00–20.00 h) temperature (max.35C) and a control (max.  25C). Under both conditions, the night-time (20.00–06.00 h)  temperature was 20C.
PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Kentaro Mori.  The equivalent experiment is VV9 at PLEXdb

overall_design:
developmental stage: 2 weeks - temperature: High (2-replications);
developmental stage: 2 weeks - temperature: Control(2-replications);
developmental stage: 4 weeks - temperature: High (2-replications);
developmental stage: 4 weeks - temperature: Control(2-replications);
developmental stage: 6 weeks - temperature: High (2-replications);
developmental stage: 6 weeks - temperature: Control(2-replications)

first: Kentaro

last: Mori


title: Expression data from NPA treated stems of Arabidopsis thaliana.

status: Public on Sep 01 2011

city: Wien

first: Javier

last: Agusti

address: Dr. Bohr-Gasse 3

institute: Gregor Mendel Institute

summary:
In-vivo induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under NPA treatments.
We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium.

overall_design: 3 mm stem pieces were collected after being in treated with NPA for a week in order to stop the polar auxin transport and induce secondary growth. Collected samples were used for RNA extraction and hybridization on Affymetrix microarrays. We aimed to obtain genes responsible for auxin-indueced cambium establishment and activity.

first: Thomas

last: Greb


title: Gene expression associated with compatible viral diseases in berry

summary:
To understand the fruit changes and mechanisms involved in the compatible grapevine-virus interaction, we analyzed the berry transcriptome in two stages of development (veraison and ripening) in the red wine cultivar Cabernet Sauvignon infected with Grapevine leaf-roll-associated virus-3 (GLRaV-3). Analysis of global gene expression patterns indicate incomplete berry maturation in infected berries as compared to uninfected fruit suggesting viral infection interrupts the normal berry maturation process.

PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Andrea Vega.  The equivalent experiment is VV28 at PLEXdb.

overall_design:
GLRaV-3 virus-infected, developmental stage: Veraison(3-replications);
GLRaV-3 virus-infected, developmental stage: Ripening(3-replications);
Virus-free, developmental stage: Veraison(4-replications);
Virus-free, developmental stage: Ripening(4-replications)

first: Andrea

last: Vega

first: Patricio

last: Arce-Johnson


title: Long-term Salt & Water Stress in Grapes

summary:
Potted Cabernet Sauvignon vines in the greenhouse were exposed to irrigated controls, non-irrigated water-deficits, and saline treatments for 16 days. Plant shoot tips were harvested every 4 days (0,4,8,12, and 16 days) to measure the progression of changes of global gene expression due to the stress.
PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Grant Cramer.  The equivalent experiment is VV2 at PLEXdb.

overall_design:
time: Day 0 - stress: Control(3-replications);
time: Day 4 - stress: Control(3-replications);
time: Day 4 - stress: Water-Deficit(3-replications);
time: Day 4 - stress: Salinity(3-replications);
time: Day 8 - stress: Control(3-replications);
time: Day 8 - stress: Water-Deficit(3-replications);
time: Day 8 - stress: Salinity(3-replications);
time: Day 12 - stress: Control(3-replications);
time: Day 12 - stress: Water-Deficit(3-replications);
time: Day 12 - stress: Salinity(3-replications);
time: Day 16 - stress: Control(3-replications);
time: Day 16 - stress: Water-Deficit(3-replications);
time: Day 16 - stress: Salinity(3-replications)

first: Grant

last: Cramer


title: Pinot Noir berry transcriptome during ripening.

status: Public on Aug 27 2011

summary:
Global gene expression analysis of grapevine cv. Pinot Noir berries during development and ripening. Time-course comparison of samples collected at three developmental stages (stages 33, 34 and 36 according to the modified E-L system, ref: Coombe BG, Aust J Grape Wine Res 1995, 1: 104-110) during three seasons (2003, 2005 and 2006).    Data for each of the three seasons were normalized independently within each season, using gcRMA.
PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Stefania Pilati.  The equivalent experiment is VV11 at PLEXdb.

overall_design:
year: 2003 - developmental stage: UD:0000034 33E-L (3-replications);
year: 2003 - developmental stage: UD:0000035 34E-L (3-replications);
year: 2003 - developmental stage: UD:0000037 36E-L (3-replications);
year: 2005 - developmental stage: UD:0000034 33E-L (3-replications);
year: 2005 - developmental stage: UD:0000035 34E-L (3-replications);
year: 2005 - developmental stage: UD:0000037 36E-L (3-replications);
year: 2006 - developmental stage: UD:0000034 33E-L (3-replications);
year: 2006 - developmental stage: UD:0000035 34E-L (3-replications);
year: 2006 - developmental stage: UD:0000037 36E-L (3-replications)

first: Stefania

last: Pilati

first: Claudio

last: Moser


title: Grape skin transcriptome in the berries grown on the vine treated with exogenous abscisic acid

summary:
The experiment was conducted using grapevines of Cabernet Sauvignon grown in a field. At veraison, the clusters in the vines were sprayed with a 400 mgl-1(+)-abscisic acid (ABA) solution. The ABA treated berries and non-treated berries (control) were harvested at 14 and 28 days after veraison and peeled.
PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Kazuya Koyama.  The equivalent experiment is VV16 at PLEXdb.

overall_design:
ABA treated - developmental stage name: 14 days after veraison(3-replications);
ABA treated - developmental stage name: 28 days after veraison(3-replications);
untreated (control) - developmental stage name: 14 days after veraison(3-replications);
untreated (control) - developmental stage name: 28 days after veraison(3-replications)


title: short term abiotic stress Cabernet Sauvignon

status: Public on Aug 23 2011

summary: Cabernet Sauvignon plants grown in a hydroponic drip system were treat with 120 mM salt  (10:1 NaCl:CaCl), Polyethylene Glycol, cold  (5 C) or unstressed. Shoots with leaves were collected at 0, 1, 4, and 8 hours for all treatments, and at 24 hours for all except cold.  ****[PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Elizabeth Tattersall. The equivalent experiment is VV1 at PLEXdb.]

overall_design: time: 0 h - treatment: unstressed (3-replications); time: 1 h - treatment: unstressed (3-replications); time: 1 h - treatment: salt (3-replications); time: 1 h - treatment: PEG (3-replications); time: 1 h - treatment: cold  (5 C) (3-replications); time: 4 h - treatment: unstressed (3-replications); time: 4 h - treatment: salt (3-replications); time: 4 h - treatment: PEG (3-replications); time: 4 h - treatment: cold  (5 C) (3-replications); time: 8 h - treatment: unstressed (3-replications); time: 8 h - treatment: salt (3-replications); time: 8 h - treatment: PEG (3-replications); time: 8 h - treatment: cold  (5 C) (3-replications); time: 24 h - treatment: unstressed (3-replications); time: 24 h - treatment: salt (3-replications); time: 24 h - treatment: PEG (3-replications)

first: Elizabeth

last: Tattersall


title: Effect of gibberellins on metabolism during rosette growth in Arabidopsis

status: Public on Jun 03 2011

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

institute: MPIMP-golm

summary: To understand the effect of high and low GA levels on plant metabolism and development in Arabidopsis we made use of the GA biosynthesis inhibitor paclobutrazol (PBZ) and  exogenously applied GA. The whole genome response at the translation level was assessed by immunopurification of polysomes from PBZ- and GA treated plants expressing FLAG-tagged ribosomal protein L18 (RPL18B). Polysomal associated RNA was isolated and subjected to affymterix ATH1 CHIP analysis. A total of 140 genes were statistically determined to be differentially translated after GA treatment whereas 89 genes where affected PBZ treatment. Our analysis revealed that GA and PBZ have opposing effects on the expression of cell wall and wax layer biosynthesis related genes. In addition, many genes involved in secondary metabolism are upregulated upon PBZ treatment. A set of SAUR-like genes important for mediating auxin responses are downregulated by PBZ, which is of interest to coordinatian of GA levels with growth and development. Interestingly, GA treatment induces the upregulation of  transcription factors related to plant defense and senescence, which is in agreement with the early flowering upon GA treatment. Our study provides a first picture of the response of Arabidopsis to altered GA levels at the translation level, and thus will be valuable for understanding gene regulation at the polysome level.

overall_design: Two replicates for each treatment including GA, PBZ and control samples.

first: Dimas

last: Ribeiro

first: Jozefus

first: Bernd

last: Mueller-Roeber


title: affy_l2bctv_ath-Expression viral protein L2 BCTV in Arabidopsis thaliana

status: Public on Aug 30 2011

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary:
affy_l2bctv_ath - affy_l2bctv_ath - Geminivirus diseases are among the most important economic impact on crops, including beans, cassava, cotton, cucurbits, corn, peppers and tomatoes. Geminiviruses have a genome composed of one or two molecules of single-stranded DNA, depending on mono or bipartite. The BCTV genome consists of a single strand of DNA that contains six reading frames for proteins CP, V2, Rep, C2, Ren, and C4. To determine the mechanism by which C2 of BCTV induce genes, we performed transgenic Arabidopsis expressing BCTV C2. We are interesting to study the difference between the wild type and two mutants. -10 days old plants were grown in MS at 24 degrees in long day. We used the different lines: wt, L2.4 mutants and L2.5 mutants. We performed three repetitions each.

Keywords: gene knock in (transgenic)

overall_design: 9 arrays - ATH1

first: Stephanie

last: Huguet

first: Eduardo

last: Rodriguez Bejarano

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Expression data from 35S::VvCBF4-overexpressing grapevines

status: Public on Jul 09 2011

city: Reno

first: Richard

middle: Leonard

last: Tillett

state: NV

address: University of Nevada Reno Mailstop 330

department: Department of Biochemistry & Molecular Biology

institute: University of Nevada Reno

summary:
Overexpression of a grapevine C-repeat binding factor (CBF) gene, VvCBF4 in cv. “Freedom” was found to improve freezing survival in non-cold-acclimated vines.
To understand the mechanistic basis of VvCBF4 transgene action, a transgenic line (‘9-12’) was genotyped using microarray-based mRNA expression profiling.

overall_design: Young grapevines (cv. 'Freedom') were grown in soil for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare vines transformed with the VvCBF4 transcription factor, expressed under the 35S CaMV promoter (line '9-12') vs. an empty vector transformant (line '8-6'). We harvested the whole aerial tissues of four biological replicates, each.

first: Karen

middle: A

last: Schlauch

first: John

last: Cushman


title: TEAD4 regulated genes in differentiated C2C12 myoblasts

status: Public on Aug 22 2011

city: Illkirch

first: Celine

last: Keime

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

type: Expression profiling by high throughput sequencing

summary: The TEAD (1-4) transcription factors comprise the conserved TEA/ATTS DNA binding domain recognising the MCAT element in the promoters of muscle-specific genes. Despite extensive genetic analysis, the function of TEAD factors in muscle differentiation has proved elusive due to redundancy amongst the family members. Expression of the TEA/ATTS DNA binding domain that acts a dominant negative repressor of TEAD factors in C2C12 myoblasts inhibits their differentiation, while selective shRNA knockdown of TEAD4 results in abnormal differentiation characterised by the formation of shortened myotubes. RNA-seq identifies a novel set of TEAD4 target genes encoding muscle structural and regulatory proteins and those required for the unfolded protein response. In contrast, TEAD4 represses expression of the growth factor CTGF and Cyclin D1 to promote differentiation. Together these results show that TEAD factor activity is essential for normal C2C12 cell differentiation and define a novel and non-redundant role for TEAD4 in regulating expression of the unfolded protein response genes.

overall_design: C2C12 cells were infected with lentiviral vectors expressing either a control shRNA or two independent shRNAs directed against TEAD4. The cell populations were selected with puromycin and then differentiated for 7 days to form myotubes.

first: Ataailah

last: Benhaddou

first: Tao

last: Ye

first: Aurore

last: Morlon

first: Isabelle

last: Michel

first: Bernard

last: Jost

first: Gabrielle

last: Mengus

first: Irwin

last: Davidson


title: Identification of Direct Targets of SND1 and VND7

status: Public on Aug 01 2011

city: Athens

first: Zheng-Hua

state: GA

address: 2502 Miller Plant Sciences

department: Plant Biology

institute: University of Georgia

summary: This study was to find genes directly regulated by SND1 and VND7.

overall_design: SND1XVE- or VND7XVE-expressing cells were treated with cycloheximide alone (control) or with cycloheximide plus estradiol (experimental) to identify genes directly activated by SND1 or VND7.


title: Differential expression between frb1 mutant Arabidopsis and wild-type

status: Public on Jul 30 2011

city: Oshawa

first: Dario

last: Bonetta

state: ON

address: 2000 Simcoe St N

department: Science

institute: Ontario Institute of Technology

summary:
Cell adhesion in plants is mediated predominantly by pectins, a group of complex cell wall associated polysaccharides. An Arabidopsis mutant, friable1 (frb1), was identified through a screen of T-DNA insertion lines that exhibited defective cell adhesion. Interestingly, the frb1 plants displayed both cell and organ dissociations and also ectopic organ fusions. The FRB1 gene encodes a Golgi-localized, plant specific protein with only weak sequence similarities to known proteins (DUF246). Unlike other cell adhesion deficient mutants, frb1 mutants do not have reduced levels of adhesion related cell wall polymers, such as pectins. Instead, FRB1 affects the abundance of galactose- and arabinose-containing oligosaccharides in the Golgi. Furthermore, frb1 mutants displayed alteration in pectin methylesterification, cell wall associated extensins and xyloglucan microstructure. We propose that abnormal FRB1 action has pleiotropic consequences on wall architecture, affecting both the extensin and pectin matrices, with consequent changes to the biomechanical properties of the wall and middle lamella, thereby influencing cell-cell adhesion.
Microarrays were used to determine the differences in global expression of friable1 mutant plants, which have cell adhesion defects, and compared these to wild-type plants.

overall_design: RNA was extracted from seedlings grown on 0.5X MS for 10 days under constant illumination.

first: Shelley

last: Lumba


title: Overexpression of Cbx4 wild type and of a Cbx4 sumoylation mutant in human epidermal stem cells

status: Public on Aug 02 2011

city: Barcelona

first: Salvador

middle: Aznar

last: Benitah

address: Baldiri Reixac 10

department: Oncology

institute: Institute for Research in Biomedicine (IRB, Barcelona)

summary: Human epidermal stem cells transit from a slow cycling to an actively proliferating state to contribute to homeostasis. Both stem cell states differ in their cell cycle profiles but must remain guarded from differentiation and senescence. Here we show that Cbx4, a Polycomb Repressive Complex-1 (PRC1)-associated protein, maintains human epidermal stem cells slow-cycling and undifferentiated, while protecting them from senescence. Interestingly, abrogating the polycomb activity of Cbx4 impairs its anti-senescent function without affecting stem cell differentiation, indicating that differentiation and senescence are independent processes in human epidermis. Conversely, Cbx4 inhibits stem cell activation and differentiation through its SUMO ligase activity. Global transcriptome and chromatin occupancy analyses indicate that Cbx4 regulates modulators of epidermal homeostasis and represses factors, such as Ezh2, Dnmt1, and Bmi1, to prevent the activate stem cell state. Our results suggest that distinct Polycomb complexes balance epidermal stem cell dormancy and activation, while continually preventing senescence and differentiation.

overall_design: Primary human keratinocytes were infected with control vector pBABE, Cbx4 wildtype and a Sumoylation mutant version of Cbx4 (the two Sumo Interaction Motifs were deleted), both fused to a Estrogen Receptor to render their activaty inducible by addition of 4OHT to the media. Cells were cultured for 5 days (after infection and selection) under 4OHT treatment, after which total RNA was collected.

first: Nuno

last: Luis


title: Analysis of gene expression in the nectarless mutant cwinv4-1

city: minneapolis

first: wayne

last: xu

state: MN

address: 117 Pleasant ST

department: supercomputing Institute

institute: university of minnesota

summary: Many flowering plants attract pollinators by offering a reward of floral nectar. Remarkably, the molecular events involved in the development of nectaries, the organs that produce nectar, as well as the synthesis and secretion of nectar itself, are poorly understood. We previously identified a mutant, cwinv4-1, for the gene CELL WALL INVERTASE 4 that failed to produde nectar. This study was undertaken to understand transcriptional changes that occur in cwinv4-1 mature lateral nectaries.

overall_design: RNA was isolated from Stage 14-15 lateral nectaries (secretory stage) of wild-type and cwinv4-1 (mutant) Arabidopsis thaliana ecotype Columbia flowers. Two biological replicates were performed for cwinv4-1 and a single biological replicate was performed for wild-type. Normalization was also performed with other pre-existing wild-type lateral nectary array data.

first: Brian

middle: W

last: Kram

first: Wayne

last: Xu

first: Clay

middle: J

last: Carter


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

status: Public on Jun 01 2011

city: Taipei

first: Chiung-Swey

middle: Joanne

last: Chang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

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

overall_design: Three biological replicates for 4-day-old etiolated seedlings of wild type (Col-0) and two mutants (cop1-4 and cop1-4BBX22-GFPox).

first: Shu-Hsing

last: Wu


title: LEAFY target genes reveal a link between flower development and biotic stimulus response (III)

status: Public on May 11 2011

city: Philadelphia

first: Cara

middle: Michele

last: Winter

address: 421 Curie Blvd.

institute: University of Pennsylvania

summary:
The transition from vegetative growth to flower formation is critical for the survival of flowering plants. The plant-specific transcription factor LEAFY (LFY) has central, evolutionarily conserved roles in this process, both in the formation of the first flower and later in floral patterning. We performed genome-wide binding and expression studies to elucidate the molecular mechanisms by which LFY executes these roles. Our study reveals that LFY directs an intricate regulatory network in control of floral homeotic gene expression and, unexpectedly, controls the expression of genes regulating the response to external stimuli in Arabidopsis. We further show that LFY dampens responses to a bacterial MAMP (microbe-associated molecular pattern) and to pathogen challenge. Our findings suggest a molecular mechanism for the coordination of reproductive stage development and disease response programs in plants. Regulation of these distinct survival programs by a single transcription factor may ensure optimal allocation of plant resources for reproductive fitness.
Expression array analysis used to identify genes differentially expressed upon LFY induction in 9-day-old shoot apices.

overall_design: Expression array analysis of 9-day-old 35S::LFY-GR dexamethasone-treated seedlings compared to 9-day-old WT dexamethasone-treated seedlings. Four biological replicate samples.

first: Doris

last: Wagner


title: Gene expression from Arabidopsis  under high light conditions

status: Public on May 05 2011

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

summary:
We have investigated the genomic response of Arabidopsis cell suspension culture under high light. Our main goal has been twofold: first, to establish whether chloroplasts in Arabidopsis cell suspension culture are functional and, as such, can act as sensors of adverse external stimuli leading to the activation of genomic defence responses in a manner similar to that described in whole plants exposed to a wide range of environmental stresses and; second, to distinguish which of the ROS that would be probably generated in the chloroplasts is predominant.
Our functional genomic analysis has led us to conclude that singlet oxygen is the major ROS in Arabidopsis cell suspension culture under high light stress and that singlet oxygen production is responsible for a genomic activation associated with the biosynthesis and signalling pathway of several phytohormones that ultimately triggers accelerated cell death.

overall_design: After the ninth day of growth, a volume of 200 mL of Arabidopsis cell suspension culture with a cell density of approximately 150-200 mg/mL was placed in a glass vessel surrounded by a water bath to maintain constant temperature during the light treatment. Nine microarray experiments were designed and classified as follows: control 1–3 (50 microE/m2/s), 1-h dark 1–3 and high light 1–3 (1800 microE/m2/s); where 1–3 stands for the number of biological replicates. After each treatment, sample RNA was extracted and its quality evaluated. The transcriptomic analysis was performed using Affymetrix GeneChip Arabidopsis genome ATH1 arrays.

first: Juan

middle: B

last: Arellano

first: Joaquín

last: Dopazo

last: García-García

first: Sergio

last: González-Pérez

first: Oscar

last: Lorenzo

first: Daniel

last: Osuna

first: José

last: Revuelta


title: Expression data from Arabidopsis Col-0 expressing FLAG-SUB1A or FLAG-SUB1C rice ERFs

status: Public on May 02 2011

city: Tuxtepec, OAX

first: Julian

middle: M

last: Pena-Castro

state: South America

address: Circuito Central 200

department: Biotechnology

country: Mexico

institute: Universidad del Papaloapan

summary: In rice (Oryza sativa L.), the haplotype at the multigenic SUBMERGENCE 1 (SUB1) locus determines survival of prolonged submergence. SUB1 encodes two or three group VII Ethylene Response Factor (ERF) family transcription factors, SUB1A, SUB1B and SUB1C. A highly submergence-inducible SUB1A allele is present in lines that are submergence tolerant. This gene is the determinant of submergence tolerance. Here, the heterologous ectopic expression of rice SUB1A and SUB1C in Arabidopsis thaliana was employed to assess the transcriptional network mobilized by ectopic expression of SUB1A and SUB1C.

overall_design: Arabidopsis thaliana Col-0 plants were stably transformed with constructs allowing the expression of 35S:FLAG-SUB1A and 35S:FLAG-SUB1C. Affymetrix ATH1 arrays were hybridized with RNA isolated from 7-day-old whole seedlings at midday (growth chamber, 0.5X MS-agar plates, 1 %(w/v) sucrose, 23 ºC, 16 h light/ 8 h dark, 125 uE m-2 s-1). Two biological replicates each.

first: J

last: Bailey-Serres

last: Peña-Castro


title: Rice A20/AN1 zinc-finger containing stress-associated proteins (SAP1/11) and a receptor-like cytoplasmic kinase (OsRLCK253) interact via A20 zinc-finger and confer abiotic stress tolerance in transgenic Arabidopsis plants

status: Public on May 01 2011

city: New Delhi

first: Akhilesh

middle: Kumar

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus,  Benito Juarez Road  India

summary: The inbuilt mechanisms of plant survival have been exploited for improving tolerance to abiotic stresses. We have investigated the subcellular interactions of rice stress-associated proteins (SAPs) using yeast two-hybrid and FRET approaches and found that A20 domain mediates the interaction of OsSAP1 with self, its close homolog OsSAP11, and a rice receptor-like cytoplasmic kinase, OsRLCK253. Such interactions between OsSAP1/11 and with OsRLCK253 occur at nuclear membrane, plasma membrane and in nucleus. Functionally, both OsSAP11 and OsRLCK253 could improve the water-deficit and salt stress tolerance in transgenic Arabidopsis plants via a signaling pathway affecting the expression of several common endogenous genes. The yield in transgenic plants is also protected indicating the agronomic relevance of OsSAP11 and OsRLCK253 in conferring abiotic stress tolerance.

overall_design: Arabidopsis transgenic plants expressing rice genes OsSAP11 and OsRLCK253  were compared with untransformed plants at seedling level

first: Jitender

last: Giri

middle: K


title: Expression data from Arabidopsis thaliana seedlings with reduced synthesis of 5-aminolevulinic acid

status: Public on Apr 01 2011

city: Berlin

first: Bernhard

last: Grimm

state: Berlin

address: Philippstr. 13, building 12

department: Institute of Biology

institute: Humboldt University Berlin

summary:
5-aminolevulinic acid (ALA) is the common precursor of all biological synthezised tetrapyrroles. Inhibition of ALA synthesis results in decreased amounts of chlorophylls, heme, siroheme and phytochrome. It was previously shown that 4 out of 5 Arabidopsis mutants uncoupling nuclear gene expression from the physiological state of the chloroplast are affected in plant tetrapyrrole biosynthesis. It is common to all four mutants to show a reduced ALA formation.
We investigate the impact of reduced plastidic ALA synthesis on nuclear gene expression by inhibition of ALA formation using gabaculin and compare these effects with  the gun4-1 mutant.

overall_design: Formation of 5-aminolevulinic acid was inhibited in Arabidopsis thaliana Col-0 seedlings by application of 10 µM gabaculin. Additionally the Arabidopsis gun4-1 mutant was investigated. Seedlings were etiolated for 3 days on MS medium in absence or presence of gabaculin and subsequently deetiolated for 6 hours. Total RNA was extracted and used for microarray hybridisation.

first: Olaf

last: Czarnecki


title: Differential gene expression in ref6-1

status: Public on May 25 2011

city: Boston

first: Falong

last: Lu

state: Massachusetts

address: 200 Longwood Ave, WAB 159

department: Program of Cellular and Molecular Medicine

institute: Boston Children's Hospital / HHMI

summary: We demonstrate that REF6/JMJ12 (RELATIVE OF EARLY FLOWERING 6/Jumonji domain-containing protein 12) is an H3K27me3 and H3K27me2 demethylase. Plants overexpressing REF6/JMJ12 resemble mutants defective in H3K27me3-mediated gene silencing. Genetic interaction tests indicate that REF6/JMJ12 acts downstream of H3K27me3 methyltransferases. Moreover, loss of REF6/JMJ12 leads to ectopic and increased H3K27me3 and decreased mRNA expression of a large spectrum of genes involved in development and hormone responses to stimuli.

overall_design:
Expression array to identify differentially expressed genes in ref6-1.

For genome-wide expression analysis of ref6/jmj12, two replicates of Col and ref6/jmj12 samples (RNA from 10-day-old whole seedlings on MS plates in long day conditions at 23 degrees) were analyzed on an Affymetrix ATH1 chip by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer's protocols. Genes showing a 20.6-fold change with a q-value < 0.05 were considered as differentially expressed.

first: Xia

last: Cui

first: Xiaofeng

last: Cao


title: apum23_col3

status: Public on Mar 01 2011

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary:
Gene expression analyses of three-week old soil grown wild-type (Col-3) and apum23-1 mutant.
Expression profiling was conducted as an attempt to identify the genes differentially regulated in apum23-1 mutant This study was under taken to characterize a member of pumilio family, APUM23 in Arabidopsis. Pumilio, an RNA-binding protein (RBP) containing tandem repeat PUF domains, has been known to repress translational activity in early embryogenesis and polarized cells of non-plant species. Although Pumilio proteins have been characterized in many eukaryotes, their roles in plants are unknown. We detail the characterization of an Arabidopsis Pumilio gene, APUM23. APUM23 is constitutively expressed with higher level in metabolically active tissues, and upregulated in the presence of either glucose or sucrose. The T-DNA insertion mutants apum23-1 and apum23-2 showed slow growth with serrated and scrunched leaves, abnormal venation pattern, and distorted organization of the palisade parenchyma cells, a phenotype reminiscent of nucleolin and ribosomal protein gene mutants. Intracellular localization studies indicate that APUM23 predominantly localizes to the nucleolus. Based on the localization, rRNA processing was examined in apum23 mutant. In apum23, 35S pre-rRNA and unprocessed 18S and 5.8S poly(A) rRNAs were accumulated without affecting steady-state levels of mature rRNAs, indicating that APUM23 participates in the degradation of rRNA by-products. The apum23 mutant showed increased levels of 18S rRNA biogenesis-related U3 and U14 snoRNAs, and accumulated RNAs within nucleolus. Our results suggest that APUM23 plays an important role in plant development via rRNA processing and ribosome biogenesis.

overall_design: To identify the genes affected in apum23-1 as compared to wild-type (Col-3) under normal growth conditions using Arabidopsis ATH1 Genome arrays (Affymetrix). RNA samples from these plants were used to generate biotin labelled (cDNA) probes, which were then hybridized to the microarray. For data set generation, three independent samples were used, three from Col-3 and three from apum23-1 plants grown on soil for 21 days.

first: Sang-Bong

last: Choi

first: Nazia

last: Abbasi


title: Analysis of the Aloe vera transcriptome using the Affymetrix ATH1 GenChip

status: Public on Mar 27 2011

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

summary: The Aloe vera transcriptome was analysed by hybridising triplicate samples of root and leaf tissue to the Affymetrix Arabidopsis ATH1 array.

overall_design: In total, 7 samples were hybridised to the array. Samples consisted of 1 genomic DNA, and triplicate samples of leaf and root RNA.

first: Zoe

middle: F

last: Emmerson

first: Neil

middle: S

last: Graham

first: Sean

middle: T

last: May


title: Expression data in double knockout of HsfA1d and HsfA1e Arabidopsis mutants (KO-HsfA1d/A1e) at 30 min under high-light stress

status: Public on Mar 26 2011

city: Tottori

first: Yukinori

last: Yabuta

address: 4-101 Koyama-Minami

institute: Tottori University

summary: The transcript levels of 560 genes were decreased (less than two-fold), while those of 312 genes were increased (more than two-fold) in the KO-HsfA1d/A1e plants compared with the wild-type plants.  The transcript levels of  HsfA2, HsfA7a, HsfA7b, HsfB1, and HsfB2a were down-regulated in the KO-HsfA1d/A1e

overall_design: Arabidopsis thaliana ecotype Columbia plants were grown (16 h light, 25°C/8 h dark, 22°C) on MS medium under a light intensity of 100 µE m-2 sec-1.  Two-week-old seedlings were subjected to high-light stress (400 µE m-2 sec-1, 25°C).

first: Ayako

last: Nishizawa-Yokoi

first: Ryota

last: Nosaka


title: Expression data of wild-type and dcl1-15 torpedo-staged embryos

status: Public on Feb 17 2011

city: Ithaca

first: Matthew

middle: R

last: Willmann

state: NY

address: B18 Weill Hall, 237 Tower Road

department: School of Integrative Plant Science

institute: Cornell University

summary:
Severe loss-of-function alleles of DCL1 are embryonic lethal.  Defects in cell division were seen as early as the globular stage in the strong loss-of-function allele dcl1-15.  Phenotypic work with dcl1-15 and the null allele dcl1-5 suggested that, in addition to the severe patterning defects, the mutants were maturing earlier than wild-type embryos.
We performed global gene expression analysis of dcl1-15 and wild-type torpedo staged embryos to examine this maturation phenotype further.  The results suggested that DCL1 is a heterochronic gene.  Comparisons to a time series of embryo development (http://www.seedgenenetwork.net/arabidopsis) showed that the genes differentially expressed in dcl1-15 embryos behaved more like green-cotyledon stage embryos than torpedo embryos.

overall_design: Seeds of a DCL1/dcl1-15 plant were sown.  For each wild-type sample, 300 torpedo stage embryos were selected from wild-type siblings.  For each mutant replicate, 300 dcl1-15/dcl1-15 embryos were selected from the siliques of DCL1/dcl1-15 where the wild-type embryos were at the torpedo stage.

first: Pablo

middle: D

last: Jenik


title: G3P triggered changes in systemic transcriptome

status: Public on Mar 15 2011

city: LEXINGTON

first: Mihir

last: Mandal

state: KENTUCKY

address: 201 F Plant science Building

department: Plant Pathology

institute: University of Kentucky

summary:
Goal of this study was to determine changes in transcription profile in mock versus G3P treated plants. Arabidopsis (Col-0 ecotype) plants were infiltrated with petiole exudate, with or without G3P, and distal leaves were sampled 24 h post treatments.

Keywords: Glycerol-3-Phosphate, Exudate, Salicylic acid, Arabidopsis, Systemic Acquired Resistance, Defense

overall_design:
3 mock-treated and 3 G3P-treated biological replicates were analyzed (one array each)
Total RNA was isolated from four-week-old plants using TRIZOL method.  The experiment was carried out in triplicate and a separate group of plants was used for each set. RNA was processed and hybridized to the Affymetric Arabidopsis ATH1 genome array GeneChip following the manufacturers instructions (http://www.affymetrix.com/Auth/  support/downloads/manuals/expression_analysis_technical_manual.pdf <http://www.affymetrix.com/Auth/%20support/downloads/manuals/expression_analysis_technical_manual.pdf> ). All probe sets on the Genechips were assigned hybridization signal above background using Affymetrix Expression Console Software v1.0 (http://www.affymetrix.com/Auth/support/downloads/manuals  /expression_console_userguide.pdf <http://www.affymetrix.com/Auth/support/downloads/manuals%20/expression_console_userguide.pdf> ). Data was analyzed using the nonparametric Wilcoxen Rank Sum test. Fold changes are reported as ratios of medians. The P values were calculated individually for each probe set.

first: Pradeep

last: Kachroo


title: Whole genome analysis of pollen-pistil interactions in Arabidopsis thaliana: time course

status: Public on Feb 14 2011

city: Oeiras

first: Filipe

last: Borges

state: Lisbon

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

summary:
Plant reproduction depends on the concerted activation of many genes to assure the correct communication between pollen and pistil. Here we queried the whole transcriptome of Arabidopsis thaliana in order to identify genes with specific reproductive functions.
We used the ATH1 whole genome array to profile wild-type unpollinated pistils and unfertilized ovules in comparison with the expression profile of pistils 0.5, 3.5 and 8.0 hours after pollination

KEYWORDS: time course

overall_design: Flowers at the developmental stage 12c were emasculated 24 hours before pollination. Pistils were collected at 0, 0.5, 3.5 and 8 Hours After Pollination (HAP) and immediately frozen in liquid nitrogen. Unfertilized ovules were collected by the funiculus from dissected UP and immediately frozen in liquid nitrogen. To minimize biological variation 20 pistils were collected from a minimum of 10 plants and for ovule isolation 50 pistils were used from about 30 plants to isolate approximately 1500 ovules for each replicate experiment.

first: Leonor

middle: C

last: Boavida

first: Jörg

last: Becker

first: José

last: Feijó


title: Auxin stimulates brassinosteroid biosynthesis in Arabidopsis roots

status: Public on Feb 15 2011

city: Seoul

first: Sunghwa

last: Choe

address: Gwanak-Gu Shillim-Dong

department: Biological sciences

institute: Seoul National University

summary:
We found that auxin stimulates gene expression of DWF4, which encodes a rate-dertermining step in brassinosteroid biosynthesis pathways. This increased gene expressioin subsequently led to elevation of the biosynthetic flux in Arabidopsis roots.
To determine the list of genes that are regulated by auxin-synthesizing brassinosteroids, we challenged Arabidopsis seedlings with either auxin only or auxin plus brassinosteroid biosynthetic inhibitor brassinazole.

Keywords: Hormone treatment

overall_design: Arabidopsis seedlings (Columbia ecotype) were grown for 10 d on 1× MS agar-solidified media under long-day conditions (16:8, white light and dark cycle). The seedlings were then transferred to 2 different liquid media containing either 10–7 M 2,4-D or 10–7 M 2,4-D plus 10–6 M brassinazole. After 8 h of treatment, the seedlings were blotted with paper towels to remove excess media and subject to total RNA isolation. Total RNAs isolated from each batch were prepared from 3 replicate seedlings using an RNeasy plant mini kit (Qiagen, Germany).


title: Microarray hybridization data from the root tips of 5-day-old Arabidopsis thaliana seedlings grown on tilted, hard agar surfaces

status: Public on Mar 31 2011

city: Madison

first: Laura

last: Vaughn

state: WI

address: 425-G Henry Mall

department: Genetics

institute: University of Wisconsin

summary:
The growth behavior of plant roots on tilted, hard agar surfaces is determined by many basic cellular processes, including microtubule dynamics and cell wall expansion.  Among Arabidopsis thaliana accessions there is natural variation for these behaviors, including one known as skewing or slanting.  The root skewing pattern on hard, tilted agar surfaces may be a clue to adaptations of an accession to its environment.
Here, we compare expression profiles of two accessions with diverse skewing behavior grown on the wave assay, which consists of seedlings growing two days vertically and 3 days tilted on hard agar plates.  Cvi has a strong skew on tilted, hard agar sufaces, and Ler-2 has a weaker one.  We also include a near isogenic line, 170G-55-16 a.k.a HGI2.1, that is mostly Ler-2 in background but has a segment of Cvi introgressed into chromosome 2.  This line has an intermediate skew between its two parents.

overall_design: 3 biological replicates of each of 3 genotypes (Cvi, Ler-2, and 170G-55-16/HGI2.1) were subjected to the wave assay.  After the assay, approximately 600 root tips from each biological replicate were pooled for RNA extraction and hybridization on the Affymetrix ATH1 microarray.

first: Patrick

middle: H

last: Masson


title: Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories.

status: Public on Jan 14 2011

city: Newark

first: Linda

last: Rymarquis

state: DE

address: 15 Innovation way rm 241

institute: University of Delaware

summary: One of the major players controlling RNA decay is the cytoplasmic 5'-to-3' exoribonuclease, which is conserved among eukaryotic organisms. In Arabidopsis, the 5'-to-3' exoribonuclease XRN4 is involved in disease resistance, the response to ethylene, RNAi, and miRNA-mediated RNA decay. Curiously, XRN4 appears to display selectivity among its substrates because certain 3' cleavage products formed by miRNA-mediated decay, such as from ARF10 mRNA, accumulate in the xrn4 mutant, whereas others, such as from AGO1, do not. To examine the nature of this selectivity, transcripts that differentially accumulate in xrn4 were identified by combining PARE and Affymetrix arrays. Certain functional categories, such as stamen-associated proteins and hydrolases, were over-represented among transcripts decreased in xrn4, whereas transcripts encoding nuclear-encoded chloroplast-targeted proteins and nucleic acid-binding proteins were over-represented in transcripts increased in xrn4. To ascertain if RNA sequence influences the apparent XRN4 selectivity, a series of chimeric constructs was generated in which the miRNA-complementary sites and different portions of the surrounding sequences from AGO1 and ARF10 were interchanged. Analysis of the resulting transgenic plants revealed that the presence of a 150 nucleotide sequence downstream from the ARF10 miRNA-complementary site conferred strong accumulation of the 3' cleavage products in xrn4. In addition, sequence analysis of differentially accumulating transcripts led to the identification of 27 hexamer motifs that were over-represented in transcripts or miRNA-cleavage products accumulating in xrn4. Taken together, the data indicate that specific mRNA sequences, like those in ARF10, and mRNAs from select functional categories are attractive targets for XRN4-mediated decay.

overall_design: Mixed-stage inflorescences from Col-0 and xrn4-5 plants were harvested.  Total RNA was extracted and hybridized to the ATH1 array to determine genes differentially expressed in xrn4-5 compared to Col-0. 2 replicates each.

middle: A

first: Frederic

last: Souret

first: Pamela

last: Green


title: Expression data from micropropagated Vitis vinifera when transferred to ex vitro conditions

status: Public on Feb 10 2011

city: Lisboa

first: Luisa

last: Carvalho

address: Tapada da Ajuda

department: DRAT-CBAA

institute: Instituto Superior de Agronomia, Univarsidade Técnica de Lisboa

summary:
Oxidative stress can arise when in vitro propagated plants developed under low light conditions are exposed to high light during transfer to ex vitro conditions. In such a situation, among the many potential stresses to which the transferred plant can be exposed, oxidative stress is commonly experienced, most likely brought about by absorption of light energy in excess of that required for very low levels of photosynthetic metabolism. In vitro propagated grapevine when transferred to ex vitro conditions with a 4 fold increase in PPFD shows an initial inhibition of PET accompanied by an accumulation of H2O2, suggesting a signal for the upregulation in gene expression and antioxidant enzyme activity, which peaked at 48h after transfer of in vitro grapevine to ex vitro growing conditions.
When in vitro propagated plants are exposed to high light upon transfer to ex vitro oxidative stress symptoms occur. To determine whether the underlying pathways activated at the transfer of in vitro grapevine to ex vitro conditions reflect the processes occurring upon light stress we used microarrays.

overall_design: Leaves were harvested from in vitro grown plants immediately prior to transfer to ex vitro condition and 48h after transfer to compare gene expression before and after exposure of these plants to the high light conditions typical of ex vitro growth.

first: Luísa

first: Belmiro

last: Vilela

first: Jorg

first: Sara

last: Amâncio


status: Public on Mar 08 2012

city: Bochum

first: Stephan

last: Hahn

address: Universitaetsstrasse 150

department: MGO

institute: Ruhr-University Bochum

summary: Global mRNA expression profiling of HCT116 cells overexpressing miR30a-5p were collected using Agilent human whole genome array (G4845A AMADID  026652, cRNA 4x44k V2) . Two different sources of RNA were analyzed: 1.) HCT116 colon cancer cells overexpressing human mir-30a-5p together with a sponge vector expressing binding sites for the antisense sequence of sh30a-5p vector construct to compete out possible miRNAs derived from the anti-guide strand of this vector. 2.) HCT116 colon cancer cells expressing control vector (pLKO.1-LV) and the sponge vector described above.

overall_design: Two conditions (sponge-LV vs sponge-sh30a-5p), each condition is represented by 3 biological replicates


title: Expression data from dark-grown BR double mutant bzr1-1D;bri1-116, single mutant bri1-116, and wildtype

status: Public on Dec 31 2010

city: Stanford

first: Yu

last: Sun

state: CA

address: 260 panama street

department: plant biology

institute: Carnegie Institution of Washington

summary:
Molecular genetic analyses support a central role of BZR1 in Brassinosteroid (BR) regulation of plant development. The dominant bzr1-1D mutation, which stabilizes the BZR1 protein, completely suppresses the de-etiolated phenotype of the null bri1-116 mutant grown in the dark.
Using microarray analysis, we identified genes differentially expressed in bri1-116 compared to wild type and genes differentially expressed in the bzr1-1D;bri1-116 double mutant compared to the bri1-116 single mutant.  Consistent with the phenotypic suppression of bri1-116 by bzr1-1D, about 80% of the genes affected in bri1-116 were affected oppositely  by bzr1-1D

overall_design:
BZR1 regulated genes were generated from comparing genes differentially expressed by bzr1-1D;bri1-116 and bri1-116.  Genes affected by BRI1 were generated from comparing differentially expressed genes of bri1-116 and Col control.
ANOVA was used to find genes whose expression was different between bzr1-1D;bri1-116 and bri1-116 or between bri1-116 and Col samples [see Supplementary file below].

first: Zhiyong

last: Wang


title: Brassinosteroid (BR) plant hormone signaling

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: H. arabidopsidis EMWA1 infection, time course experiment

city: Durham

first: Jinyoung

middle: Yang

last: Barnaby

state: NC

address: 4204 FFSC Bldg (Box 90338)

department: Biology

institute: Duke Univeristy

summary: We used microarrays to identify differentially expressed genes. We focused on those genes that were dramatically induced (>2-fold) in WT but not in the rpp4 mutant at 2 dpi when WT and rpp4 first showed distinct phenotypes

overall_design: 2-week old Col wild-type plants and rpp4 mutants were infected with spores from 10-day old H. arabidopsidis EMWA1. Leaves were harvested at 0, 0.5, 2, 4, 6 days post-inoculation. Replicates are derived from two independent biological experiments, with no overlap in growing periods.

middle: Y


title: Expression data in whole Arabidopsis seedlings after treatment with the herbicide dicamba

status: Public on Dec 10 2010

city: Wembley

first: Cynthia

last: Gleason

state: WA

address: Private Bag #5

department: Plant Industry

country: Australia

institute: CSIRO

summary:
Dicamba is an auxin-like herbicide that can stimulate the production of ethylene and ABA biosynthesis.  The subsequent stomatal closure and build-up of reactive oxygen species is hypothesized to contribute to plant death.
In order to further understand the herbicide dicamba's mode of action at the molecular level, we used microarrays to dissect global gene expression in Arabidopsis seedlings 10 hrs after dicamba treatment.

overall_design: 4 day old Arabidopsis seedlings (a Columbia line containing a -800GSTF8::LUC reporter) were flooded with water or 7mM dicamba  for 40 minutes before the treatment was poured off.  Ten hours after the start of the treatment, whole seedlings were collected

first: Karam

last: Singh