title: Expression data from Arabidopsis thaliana seedlings

status: Public on Dec 01 2014

city: Ciudad de Buenos Aires

first: Pablo

last: Cerdan

address: Avda Patricias Argentinas 435

country: Argentina

institute: Leloir Institute Foundation

summary:
Flowering time is a complex trait regulated by many genes that are integrated in different genetic pathways. Different genetic screenings carried out during the past decades have revealed an intrincated genetic regulatory network governing this trait. Efforts aimed at improving our understanding of how such genetic pathways respond to genetic and enviromental cues are needed.
We used microarray to identify groups of up and down-regulated genes in an early flowering mutant, suppressor of gigantea (gis5).

overall_design: gis5 and WT (Columbia, Col) 10 days-old seedlings were used for RNA extraction and hibridization on Affymetrix microarrays. Seedlings were grown on MS salts medium plates under continuos light at 23°C. We chose this particular light condition in order to avoid circadian clock effects on the global pattern of gene expression at this developmental stage.

last: Cerdán


title: Brassinosteroid-mediated gene expression changes in Arabidipsis during heat stress

status: Public on Oct 09 2014

city: Canberra

first: Uday

last: Divi

state: ACT

address: Clunies Ross St.

department: Agriculture Flagship

country: Australia

institute: The Commonwealth Scientific and Industrial Research Organisation

summary: Global analysis of brassinosteroid (BR)-mediated gene expression under abiotic stress identifies BR associated mechanisms of stress tolerance, and new stress-related genes

overall_design: We used the Arabidopsis Affymetrix ATH1 array to analyze gene expression in a synthetic BR, 24-epibrassinolide (EBR)-treated and untreated Arabidopsis seedlings before, during and after heat stress (HS) treatment. Microarray expression profiles were generated from EBR-treated (E; 1 µM EBR for 21 days) and untreated (C; 0.01% ethanol for 21 days) Arabidopsis seedlings under no-stress (0 h), HS (1 h and 3 h) at 43°C conditions. Additionally, a recovery for 6 h (6 hR) at 22°C after exposure to 3h HS at 43°C was also included

middle: K

first: Tawhidur

last: Rahman

first: Priti

last: Krishna


title: Iron-deficiency-induced changes in wild type and IRP1overexpressed transgenic Arabidopsis plants

status: Public on Oct 10 2014

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary:
a novel orphan peptide, IRON-REGULATED PROTEIN1 (IRP1) that is rapidly induced by Fe deficiency and improves growth on Fe-deplete media.
In Arabidopsis, ectopic expression of IRP1 affected the activity of several genes involved in Fe acquisition and homeostasis, causing a dramatic increase of Fe in leaves and enhanced seed Fe loading. Heterologous expression of IRP1 in tomato plants resulted in increased Fe levels in fruits. Integration of AtIRP1 into the genome of crop plants may represent a novel strategy for Fe biofortification.

overall_design: wild type Col-0 and transgenic overexpressor IRP1-OE plants were grown under normal conditions or subjected to and iron-starvation for 3 days. Roots and shoots were collected with 3 biological replicates.

first: Wenfeng

last: Li

first: Ping

last: Lan


title: Expression data for aox1a mutants, rpoTmp  mutants and aox1a:rpoTmp double mutants in Arabidopsis

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

institute: La trobe University

summary:
Common and distinct transcriptomic responses to moderate light and drought stress in the different mutants.
We used microarrays to analyse the response untreated and moderate light and drought stress in aox1a mutants, rpoTmp  mutants and aox1a:rpoTmp double mutants. This was analysed in paralell with WT (Col0) plants in order to identify the responses to stress.

overall_design: WT(Col0), aox1a mutants, rpoTmp mutants and aox1a:rpoTmp double mutants were collected under untreated conditions and after moderate light and drought stress.

first: Kristina

last: Kühn

first: Guangkun

last: Yin

first: Owen

last: Duncan

first: Simon

middle: R

last: Law

first: Szymon

last: Kubiszewski-Jakubiak

first: Parwinder

last: Kaur

first: Etienne

last: Meyer

first: Yan

last: Wang

first: Catherine

middle: C

last: des Francs Small

first: Estelle

last: Giraud

first: James

last: Whelan


title: Gene regulation by the seed maturation master regulators, LEC1, LEC2, FUS3 and ABI3 [set 2]

status: Public on Oct 01 2014

city: Nagoya

first: Tsukaho

last: Hattori

state: Aichi Prefecture

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya Universtiy

summary: During seed maturation, the embryo accumulates nutrition storage compounds such as oil and reservve proteins, and acquires dormancy and desiccation tolerance. Arabidopsis transcription factors LEC1, LEC2, FUS3 and ABI3 are known as the master regulators of seed maturation because all these events during the seed maturation are severely affected by the respective mutants. In addition, the lec1, lec2 and fus3 mutants exhibit some heterochronic characteristics, as exemplified by the development of true leaf-like cotyledons during embryogenesis. To characterize these mutants at the whole genome expression level, microarray experiments were performed.

overall_design: Developing seeds were dissected from the sliques of the abi3-6 homozygous plants or the respective wild type plants (Col-0) at 12 and 16 days after flowering. Seeds samples were obtained from triplicate batches of plants and used for RNA preparation.

first: Akiko

last: Yamamoto

first: Sachiyo

last: Tanaka

first: Tokunori

last: Hobo


title: Rootstock and soil effects on grape transcriptome

status: Public on Nov 05 2014

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

summary: Soil qualities and rootstocks are among the main factors that have been acknowledged to influence grape development as well as fruit and wine composition. Despite the role of the soil and rootstock in establishing a successful vineyard in terms of grape quality, almost no molecular evidence linking soil and rootstock properties to the gene expression have been reported. The transcriptome variation in response to different soils and rootstocks was investigated through microarray technology. The cv. Pinot Noir was grown on different soils: sand, turf and vineyard soil. The plants were grafted on the contrasting 101-14 and 1103 Paulsen rootstocks. The modulation of genes expression in response to  different soils and rootstocks was evaluated considering their potential impact on primary  (carbohydrate) and secondary (phenylpropanoid) metabolisms.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Alessio Aprile.  The equivalent experiment is VV41 at PLEXdb.]

overall_design: treatment1: Turf - treatment2: 101-14 rootstock(3-replications);  treatment1: Turf - treatment2: 1103-P rootstock(3-replications);  treatment1: Sand - treatment2: 101-14 rootstock(3-replications);  treatment1: Sand - treatment2: 1103-P rootstock(3-replications);  treatment1: Asti soil - treatment2: 101-14 rootstock(3-replications);  treatment1: Asti soil - treatment2: 1103-P rootstock(3-replications)

first: Alessio

last: Aprile

first: Luigi

last: Cattivelli


title: Gene regulation by the seed maturation master regulators, LEC1, LEC2, FUS3 and ABI3 [set 1]

overall_design: Developing seeds were dissected from the sliques of the lec1-1, lec2-1, or fus3-3 homozygous plants or the respective wild type plants (Col-0 for fus3-3, WS for lec1-1 and lec2-1) at 8 and 12 days after flowering. Seeds samples were obtained from triplicate batches of plants and used for RNA preparation.

first: Masahiro

last: Fujita

first: Nori

last: Kurata


title: Arabidopsis thaliana Col-0 leaf and root transcriptome response to Agrobacterium tumefaciens C58

status: Public on Oct 28 2014

city: London

first: Ze-Chun

last: Yuan

state: Ontario

address: 1391 Sanford Street

department: Microbiology

country: Canada

institute: Southern Crop Protection and Food Research Center, Agricultre and Agri-Foods Canada

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of grape (Vitis vinifera L.) leaves exposed to ultraviolet C radiation

status: Public on Nov 15 2014

city: Beijing

first: Huifen

last: Xi

address: Nanxincun 20, Xiangshan Southern Road

department: Institute of Botany

country: China

institute: Chinese Academy of Sciences

summary: Solar ultraviolet C（UV-C）radiation reaching the Earth’s surface is little due to the filtering effects of the stratospheric ozone layer. At present, artificial UV-C irradiation is utilized for different biological processes. Grape is a major fruit crop around the world. Research has shown that UV-C irradiation induced the biosynthesis of phenols. However, changes at the molecular level in response to UV-C and leading to these effects are poorly understood. To elucidate the effect of UV-C on expression of genes in grape and the response mechanism, transcript abundance of grape (Vitis vinifera L.) leaves was quantified using the Affymetrix Grape Genome oligonucleotide microarray (15,700 transcripts)

overall_design: Grape leaves were exposed to UV-C irradiation at 6W/m2 for 10 min. LCK-0-1, LCK-0-2 and LCK-0-3 are 0 h after the initiation of treatment and as the controls; LTR-6-1, LTR-6-2 and LTR-6-3 are for 6 h after the initiation of treatment; LTR-12-1, LTR-12-2 and LTR-12-3 are for 12 h after the initiation of treatment. Three replicates for each time point. 9 samples in all.

first: Lijun


title: HIRA regulate Arabidopsis dedifferentiation process

city: Singapore

first: Frederic

last: Berger

address: 1 research link, NUS

department: Chromatin & Reproduction

country: Singapore

institute: Temasek Lifesciences Laboratory

summary: Plant development is characterised by the capacity to reprogram differentiated cells to initiate asexual reproduction and to produce new organs such as lateral roots. To test whether HIRA could be involved in aspects of developmental reprogramming we studied the effect of HIRA during de-differentiation

overall_design: Arabidopsis root tissue was digested with enzyme to generate protoplast. This process would induce plant cell dedifferentiation. Experiments were performed in WT and hira background to understand how hira affect plant dedifferentiation process.

first: Xin

last: Nie

first: Haifeng

first: Jing

last: Li

first: Sarah

last: Holec


title: Transcriptome changes in 35S::KLU

status: Public on Sep 30 2014

city: Gent

first: Hannes

last: Claeys

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB-UGent

summary: Transcriptome changes in 35S::KLU shoots at stage 1.03 compared to wild-type (WT) Col-0 shoots

overall_design: 35S::KLU and WT seedlings were grown on 1/2 MS medium, and 5 seedlings of each were harvested at stage 1.03. Samples were obtained from three independent experiments, and both genotypes were grown on the same plate. Samples were frozen in liquid nitrogen and ground with a Retsch machine and 3-mm metal balls. RNA was extracted with TriZol (Invitrogen) and further purified with the RNeasy Mini Kit (Qiagen). DNA digestion was done on columns with RNase-free DNase I (Roche). One µg of pure RNA samples were hybridized to Affymetrix ATH1 arrays at the VIB Microarray Facility (Leuven, Belgium).

first: Dirk

last: Inzé


title: Global genetic impact of surface-modified gold nanoparticles on two model human cell lines

city: Urbana

first: Elissa

middle: M

last: Grzincic

state: Illinois

address: A510 Chemical and Life Sciences Laboratory, 601 S. Goodwin Ave.

department: Chemistry

institute: University of Illinois at Urbana-Champaign

summary: Gold nanoparticles (Au NPs) are uniquely suited for various biomedical applications due to the combination of their optical properties with their easily functionalized surfaces. The Au NP surface can be tailored to improve biocompatibility while also attaching targeting ligands or drugs. However, information on how these tailored surface chemistries may affect cell gene expression is scarce. Using two model human cells line, human dermal fibroblasts and prostate cancer cells, microarray experiments measured gene expression over 27,000 human genes. Each of the cell lines was exposed to four related types of surface-modified Au NPs at two different concentrations, and the microarray data was analyzed by weighted gene correlation network analysis and gene functional annotation. Au NPs were shown to affect genes associated with a variety of cellular functions, and surface charge and chemistry were linked with the types of parthways changed and the degree of which those changes occured.

overall_design: Nanoparticle induced gene expression in PC3 and HDF cells was measured after 24 hour exposure to nanoparticles of four different surface coating types. RNA from three separate culture samples were used for each nanoparticle-cell combinations, along with three control samples not exposed to nanoparticles at all.

first: Jie

middle: A

last: Yang

first: Jenny

last: Drnevich

first: Priscila

last: Falagan-Lotsch

first: Catherine

middle: J

last: Murphy


title: Expression data from Arabidopsis thaliana WT (Ler), ebs and shl-2 mutants grown in SD conditions

status: Public on Oct 14 2014

city: Pozuelo de Alarcon

first: Alfonso

last: Mouriz-Villar

state: Madrid

address: Campus de Montegancedo

department: Biotechnology

country: Spain

institute: INIA

summary: We performed a tranascriptomic analysis of Ler, ebs and shl-2 plants in order to reveal targets whose transcription is regulated by EBS and SHL.

overall_design: The analysis was performed in WT plants (Ler), as well as mutants plants in which the expression of EBS and SHL was previously shown to be null, namely ebs and shl-2 mutant. To perform this study, plants were grown for 18 days under short days (SD) conditions (8h light, 16h darkness) in MS solid media. Three independent biological samples were hybridized separately.

first: Leticia

last: Lopez-Gonzalez

last: Mouriz

first: Jose

last: Jarillo

first: Manuel

last: Pineiro


title: TMEFF2 treated cancer cells and gastric cancer

city: Shanghai

first: jingyuan

last: fang

address: 145 Shandong Rd Middle

institute: Shanghai Institute of Digestive Disease


title: Expression data from Col-0 and sp1,spx2 under phosphate starvation stress and recovery after resupplying phosphate

city: Madrid

first: Jose M.

last: Franco-Zorrilla

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

summary: We performed a transcriptomic analysis of Pi-starvation and recovery after resupplying Pi in Arabidopsis thaliana (Columbia-0) wild type plants and double mutant spx1,spx2. Results show that SPX1 is a Pi-dependent inhibitor of the transcription factor PHR1, a central regulatory protein in the control of transcriptional responses to Pi starvation.

overall_design: The analysis was performed in wild-type and double spx1,spx2 double mutant plants grown for seven days in complete (+Pi) and Pi-lacking (-Pi) Johnson solid media. Then, plants were transferred to complete medium for 4 hours to analyze the effect of resupplying plants with Pi.

first: Maria

middle: I

last: Puga

first: Javier

last: Paz-Ares


title: Expression data from Ler and top1a-2 inflorescences

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

summary: DNA topoisomerases release supercoils in DNA introduced during replication or transcription. How DNA topoisomerases impact transcription in the context of eukaryotic chromatin is poorly understood. In this study, using a floral stem cell model in Arabidopsis, we uncovered a role of TOP1α in Polycomb Group (PcG) protein-mediated histone lysine 27 trimethylation at, and transcriptional repression of, the stem cell maintenance gene WUSCHEL (WUS). The strong genetic interactions between a top1α mutant and mutations in PcG genes and the overwhelming enrichment of PcG targets among genes affected in expression in the top1a mutant revealed a role of TOP1α in PcG-mediated regulation. Intriguingly, not only the repression of some PcG target genes but also the expression of others requires TOP1α. The mechanism that unifies the opposing effects of TOP1α on PcG target genes appears to lie in its role in decreasing nucleosome density. Genome-wide nucleosome mapping shows that TOP1α is required for the depletion of nucleosomes at regulatory regions of genes, which probably allows the binding of factors that either recruit PcG, as we show for AGAMOUS at the WUS locus, or counteract PcG-mediated regulation. This study uncovers a strong and previously unknown connection between TOP1α and PcG.

overall_design: 6 samples from wild-type and top1α-2 inflorescences, including three biological replicates per genotype.

first: Xigang

last: Liu

first: Xuemei

last: Chen


title: Transcriptome of Arabidopsis thaliana ceh1 mutant

status: Public on Sep 24 2014

city: Davis

first: Katayoon

last: Dehesh

state: CA

address: One Shilels Avenue

department: Plant Biology

institute: UNIVERSITY OF CALIFORNIA DAVIS

summary: Here we present the transcriptomic profile of mutant plants designated as ceh1 (constitutively expressing HPL).   CEH1 encodes 1-hydroxy-2-methyl-2-butenyl 4-diphosphate synthase (HDS), the enzyme controlling the bottleneck step of the biosynthesis of isopentenyl diphosphate via the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway in the plastids. Mutation of this enzyme in ceh1 mutant led to accumulation of high levels of the stress specific signaling metabolite 2c-methyl-D-erythritol 2,4-cylclodiphosphate (MEcPP), and consequently constitutive activation of a selected otherwise stress responsive genes.   This data identifies the ensemble of stress responsive genes whose expression is regulated by the MEcPP signaling cascade.

overall_design: About 20 two-week-old plants grown on 1/2 MS medium were collected to extract total RNA. Transcriptome of parent line and ceh1 mutant were compared.

first: Yanmei

last: Xiao


title: Comparison of histone deacetylase 9-1 mutant (SALK_001723) dry seed transcriptome with Col wild-type

status: Public on Sep 21 2014

city: Freiburg

first: Yong

last: Li

address: Hugstetter Str. 49

department: Institute of Genetic Epidemiology

country: Germany

institute: Medical Center - University of Freiburg

summary:
Analysis of the transcriptome of dry hda9-1 mutant seeds with those of Col wild-type seeds, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array.
The hda9-1 mutant has reduced primary seed dormancy. We used microarrays to dissect which genes are differentially expressed in the hda9-1 mutant to study the mechanisms how HDA9 affects seed dormancy and germination

overall_design: RNA was extracted from tagged dry 18-19-DAP siliques of wild-type Col and the hda9-1 mutant following an adapted protocol of the RNAqueous small scale Phenol-free total RNA isolation kit in addition with RNA isolation aid (Ambion, Austing, TX, USA), as described in Liu et al. (2011) PLoS ONE and Van Zanten et al. (2011) PNAS. Affymetrix GeneChip Arabidopsis ATH1 Genome-Micro hybridization was performed at the Max Planck Genome Centre Cologne. Three independent hybridizations of independent biological replicates, obtained from several dry siliques of at least five plants per replica, were performed.

first: Martijn

last: van Zanten

first: Christian

last: Zöll

first: Annaick

last: Carles

first: Wim

last: Soppe


title: Expression data provoked by H2O2 from plastid or peroxisomal origin

city: Düsseldorf

first: Veronica

last: Maurino

address: Universitätsstrasse 1

department: Plant Molecular Physiology and Biotechnology

institute: Heinrich-Heine-University

summary:
Reactive oxygen species (ROS) are key signalling molecules that regulate growth and development and coordinate responses to biotic and abiotic stresses. ROS homeostasis is controlled through a complex network of ROS production and scavenging enzymes. Recently, the first genes involved in ROS perception and signal transduction have been identified and, currently, we are facing the challenge to uncover the other players within the ROS regulatory gene network. The specificity of ensuing cellular responses depends on the type of ROS and their subcellular production sites. Various experimental systems, including catalase-deficient plants, in combination with genome-wide expression studies demonstrated that increased hydrogen peroxide (H2O2) levels significantly affect the transcriptome of plants and are capable of launching both defence responses and cell death events.
We used microarrays to assess differential gene expression provoked by H2O2 from plastid or peroxisomal origin, respectively.

overall_design: Columbia-0 (Col-0, wild type), catalase-deficient Salk plants  (10-15% of wild-type catalase activity; cat2-2; N576998; (Queval et  al., 2007)) and A. thaliana plants expressing glycolate oxidase in  chloroplasts (GO5 plants; (Fahnenstich et al., 2008)) were grown in  soil under a 16h light/8h dark regime at photosynthetically active  photon flux densities (PPFD) of 75 µmol quanta m-2 s-1 at 22°C  day/18°C night temperatures and a CO2 concentration of 3,000 ppm.  After three weeks of growth, plants were transferred to ambient CO2  concentration (380 ppm) and the same PPFD. Whole rosettes were  harvested at 0h and 8h after transfer. Control samples were harvested  at 8 h from plants continuously maintained in high CO2.

first: Nasser

last: Sewelam

first: Nils

last: Jaspert

first: Katrien

last: Van der Kelen

first: Jessica

last: Schmitz

first: Henning

last: Frerigmann

first: Vanesa

middle: B

last: Tognetti

first: Elia

last: Stahl

first: Jürgen

last: Zeier

first: Frank

last: Van Breusegem

middle: G


title: Transcription factor ATAF1 integrates carbon starvation responses with trehalose metabolism

status: Public on Aug 30 2014

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary: Global transcriptome patterns were obtained from ATAF1-IOE seedlings at 1 h, 2 h and 5 h after estradiol induction or mock treatment, and from mature ATAF1-IOE leaves at 5 h after estradiol induction or mock treatment.

overall_design: To identify genes rapidly responding to elevated ATAF1 expression estradiol induction experiments were performed on ATAF1-IOE seedlings after 1 h, 2 h and 5 h of ATAF1 induction. In addition, expression profiles were obtained from mature leaves after 5 h of ATAF1 induction.

first: Prashanth

last: Garapati

first: Regina

last: Feil

first: John

middle: E

last: Lunn

first: Patrick

last: Van Dijck

first: Bernd

last: Mueller-Roeber


title: Gene regulation by the seed maturation master regulators, LEC1, LEC2, FUS3 and ABI3

first: Tsukaho

last: Hattori


title: Gene expression analysis in wild-type and OsGSTU4 overexpression line

status: Public on Aug 28 2014

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary:
Glutathione S-transferases (GSTs) are the ubiquitous enzymes, which play important role in defense against various stresses. To analyze the function of a rice GST gene, OsGSTU4, we overexpressed it into Arabidopsis constitutively. The physiological analyses revealed that overexpression of GRX gene enhanced abiotic stress tolerance in transgenic plants as compared to wild-type.
We used microarrays to study the global effect of overexpression of OsGSTU4 in Arabidopsis.

overall_design: Wild-type and transgenic Arabidopsis seedlings were grown on MS medium for 14-days in a culture room with a daily photoperiodic cycle of 16h light and 8h dark. The 500 ng of total RNA sample isolated from each tissue sample was processed for microarray analysis according to Affymetrix protocol. Two biological replicates for wild-type and GRX overexpression line were used for microarray analysis.

first: Sharma

last: Raghvendra

first: Jain

last: Mukesh


title: Expression data from Arabidopsis rosette leaves

city: San Antonio

first: Garry

last: Sunter

state: TX

address: One UTSA Circle

department: Biology

institute: The University of Texas at San Antonio

summary:
The focus of this study was to identify changes in host gene expression induced by the transcription-dependent function of the viral AC2 protein, and induced by the interaction of AC2/C2 with SnRK1.2 (AtAKIN11).
We used microarrays to identify changes in host gene expression induced by the transcription-dependent function of the geminivirus-encoded AC2 protein, and induced by the interaction of AC2 with a host serine-threonine kinase, SnRK1. Distinct classes of genes were up- and down regulated during this process. For experiment 1, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Cabbage leaf curl virus (CaLCuV) AC2 protein, a truncated version of AC2 lacking the C-terminal 29 amino acids (AC2del), or an empty vector control (530). In experiment 2, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Spinach curly top virus C2 protein, a truncated version of C2 lacking the C-terminal 29 amino acids (C2del), antisense (as) SnRK1.2 (AsAKIN11), or an empty vector control (530).

overall_design: Infused Arabidopsis rosette leaves were selected at 1, 2 or 3 days post-infusion for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of plants at each time point in order to increase the temporal resolution of expression profiles. To that end, we isolated total RNA from four individual plants, for three independent sets of plants infused with the different constructs. This resulted in three independent samples per treatment per time point.

first: Jianhua

last: Ruan


title: Transcriptome profiling of an autopolyploidy series of Arabidopsis thaliana

status: Public on Aug 01 2014

city: Galway

first: Charles

last: Spillane

state: Galway

address: University Road

department: Botany and Plant Science

country: Ireland

institute: National University of Ireland, Galway

summary: Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set

overall_design: 4 or 5 biological replicates per ploidy level, each replicate being a single two weeks old seedling

first: Antoine

last: Fort

first: Mark

last: Donoghue

first: Peter

last: McKeown

first: Marie-Luise

last: Zielinski

first: S

middle: D

last: Selcuklu

first: Ronan

last: Sulpice


title: Detection of genes acting downsteram of ectopically expressed TCP/CYC2 transcription factors in Arabidopsis thaliana

city: Osnabrueck

first: Andrea

last: Busch

address: Barbarastrasse 11

department: Botany

institute: University Osnabrueck

summary:
TCP transcription factors from the CYC2-class are involved in the development of monosymmetric flowers in all core eudicot species analysed so far. In Antirrhinum majus, the CYC2/TCP transcription factor CYCLOIDEA (CYC) is the molecular key regulator driving the development of flower monosymmetry (Luo D, Carpenter R, Vincent C, Copsey L, Coen E: Origin of floral asymmetry in Antirrhinum. Nature 1996, 383:794-799). In the Brassicaceae Iberis amara, a stronger expression of the CYC2 gene IaTCP1 in the small adaxial petals likely leads to the reduced petal size in comparison to large abaxial petals, with hardly any IaTCP1 expression. This results in the formation of the monosymmetric Iberis flower (Busch A, Zachgo S: Control of corolla monosymmetry in the Brassicaceae Iberis amara. PNAS 2007, 104:16714-16719). In contrast, the orthologous TCP/CYC2 transcription factor TCP1 from Arabidopsis thaliana, which forms equally sized and shaped petal pairs, only shows an early and transient expression in the adaxial area of floral primordia. This implies that monosymmetry in the Brassicaceae evolved through a heterochronic expression shift of the TCP/CYC2 key regulator gene IaTCP1.
Transgenic Arabidopsis plants overexpressing IaTCP1 and TCP1 develop smaller petals whereas transgenic plants overexpressing CYC from Antirrhinum majus produce larger flowers. In any case, petal size is affected. To compare the effects of the three CYC2 TCP transcription factors on downstream (regulatory) networks in Arabidopsis thaliana, a microarray analysis was conducted.

overall_design: The coding sequences of the TCP/CYC2 transcription factors IaTCP1, TCP1 and CYC were cloned into the pBAR vector (GenBank: AJ251014), resulting in the constructs #0522 (IaTCP1), #0569 (TCP1) and #0577 (CYC).  In pBAR, all genes are under the control of the CaMV35S-promoter. Arabidopsis plants were transformed (via floral dip) with respective constructs and also with the empty vector (pBar). Transgenic plants (T1) with petal size deviation from the control (plants transformed with the empty vector and wild type) were selfed and resulting T2 lines with petal size deviations from control were selected. Inflorescence buds from secondary inflorescences were harvested from transgenic T2 plants that formed smaller (#0255 or #0569) or larger (#0577) petals in the main inflorescence. Total RNA was isolated and sent to the Integrated Functional Genomics Service at the University of Münster, Germany, which carried out probe preparation, hybridization and statistical analysis of the data. Differential gene expression was always determined from a comparison of gene expression from #0522, #0569 and #0577, respectively, against the control (#pBar; inflorescence gene expression in plants transformed with an empty vector).

first: Stefanie

last: Horn

first: Sabine

last: Zachgo


title: Expression data from 35S:miR396b plants

status: Public on Jul 16 2014

city: Rosario

first: Juan

middle: Manuel

last: Debernardi

state: Santa Fe

address: Ocampo y Esmeralda

institute: IBR

summary:
Transcript profile of  apices of 20 days-old Arabidopsis plants over expressing miR396b.
We used ATH1 Affymetrics microarrays to obtain the transcription profile of plants overexpressing miR396b.

overall_design: We compared the transcriptome of 35S:miR396b plants vs wild-type plants (Col-0 accession), using ATH1 Affymetrics microarrays. For these experiments we collected vegetative apices together with the leaf primordia from plants of 20 days growth in short-day. For each genotype (Col-0, 35S:miR396b)  we collected two samples.

first: Javier

middle: F

last: Palatnik


title: Fine-tuning of the anaerobic response in plants relies on trihelix protein repression of the oxygen sensing machinery

status: Public on Jul 30 2014

city: Riverside

first: Seung Cho

last: Lee

address: 2150 Batchelor Hall

department: Botany & Plant Sciences

institute: University of California Riverside

summary: This study analyzes transcriptomic data of Arabidopsis thaliana Col-0 and overexpression lines of Hypoxia Response Attenuator (HRA1; At3g10040) with Col-0 background (OE-HRA1). Two independent transgenic lines of OE-HRA1 were considered as biological replicates (OE-HRA1#1 and OE-HRA1#2). Seven-day-old seedlings were treated either with or without hypoxia (low oxygen) stress for 2 hours. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform.

overall_design: 8 samples, 2 genotypes (Col-0 and OE-HRA1), 2 conditions (2 h non-stress and 2 h hypoxia stress), 2 independent biological replicate experiments

first: Julia

last: Bailey-Serres


title: Gene expression outcome for gastric cancer patients

first: jingyuan

last: fang

summary: The gene expression of the three cancer patients who had operation were compared with the genes of the three normal cases.

overall_design: Three gastric cancer patients were compared with the three normal persons.


title: Expression data from 12-day old Arabidopsis germinants

status: Public on Jul 29 2014

city: Bethesda

first: Laxminath

last: Tumburu

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary:
Seed germination of a terrestrial plant constitute dynamic changes in various physiological processes related to growth and development. These physiological processes can be affected by various abiotic and biotic stressors. Here we looked at how the two commonly used nanoparticles, nano-titania (TiO2) and nano-ceria (CeO2) can impact the underlying mechanisms associated with germination at genome level.
We used microarrays to detail the global programme of gene expression underlying various physiological processes associated with growth and development, and identified distinct classes of up-regulated genes during this process.

overall_design: 12 day old Arabidopsis germinants were selected for RNA extraction and hybridization on Affymetrix microarrays. Arabidopsis seeds were individually exposed to 500mg/L concentration of nano-titania and nano-ceria for 12 days, followed by extraction of RNA for Microarray analysis. 0.1mM KCl was used as control for nano-titania, whereas sterilized millipore water was used as control for nano-ceria.


title: Expression data of Arabidopsis overexpressing ERF96 gene

status: Public on Jul 31 2014

city: Taipei

first: Jeremy

last: Catinot

state: Taipei

address: n°1 sec 4 Roosevelt road

department: Institue of plant biology

institute: National Taiwan University

summary:
Arabidopsis overexpressing ERF96 are more resistant against necrotrophic pathogen such as Botrytis cinerea. ERF96 is a member of the AP2/ERF superfamily of transcription factor.
We used Microarray to determine which gene expressions are up-regulated due to an accumulation of ERF96 and to identify the putative direct target of this transcription factor.

overall_design: Microarray were performed from the RNA of a four-week old Arabidopsis overexpressing ERF96  and WT(col-0). RNA was extracted during three independant experiments

first: Laurent

last: Zimmerli


title: Expression profiling of Col-0 treated with Psm:AvrRpt2

status: Public on Jul 02 2014

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary: Identification of AvrRpt2-mediated differential gene expression in Arabidopsis

overall_design: Four-week-old leaves of Arabidopsis Col-0 plant were infiltrated with Pseudomonas syringae pv. Maculicola carring effector AvrRpt2 at OD0.01. Samples were collected at 0 or 6 hours after infiltration. Each time point contains three biological replicates.

first: Rajinikanth

last: Mohan

first: Xinnian

last: Dong


title: Transcriptional Profiling of Arabidopsis Root Hairs and Pollen Defines an Apical Growth Signature

status: Public on Aug 05 2014

city: Oeiras

first: Jorg

last: Becker

address: Rua da Quinta Grande No 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

summary: Despite their different origin and function, both pollen tubes and root hairs share the same sort of apical growth mechanism, i.e., the spatially focused cell expansion at the very apex. Ion fluxes, membrane trafficking, the actin cytoskeleton and their interconnection via signaling networks have been identified as fundamental processes underlying this kind of growth. Several molecules involved in apical growth have been identified, but the genetic basis is far from being fully characterized.  We have used Affymetrix Arabidopsis ATH1 GeneChips to obtain the expression profiles of isolated Arabidopsis root hairs. A comparison with the expression profile of flow-sorted pollen grains reveals an overlap in the expression of 4989 genes, which corresponds to 42% of the root hair transcriptome and 76% of the pollen transcriptome, respectively. Our comparison with transcriptional profiles of vegetative tissues by principal component analysis and hierarchical clustering shows a clear separation of these samples comprised of cell types with diffuse growth from the two cell types with apical growth. 277 genes are enriched and 49 selectively expressed, respectively, in root hairs and pollen. From this set of genes emerges an apical growth signature containing novel candidate genes for apical growth determination.

overall_design: Root hairs were isolated from Arabidopsis seedlings and total RNA was isolated for expression profiling on Affymetrix ATH1 arrays. The study was performed with biological duplicates.

first: Jörg

first: Seiji

last: Takeda

first: Filipe

last: Borges

first: Liam

last: Dolan

first: Jose

last: Feijo


title: The Arabidopsis Mediator CDK8 module genes CCT and GCT are global regulators of developmental phase transitions.

status: Public on Sep 22 2014

city: Ithaca

first: Matthew

last: Willmann

state: NY

address: B18 Weill Hall, 237 Tower Road

department: School of Integrative Plant Science

institute: Cornell University

summary:
Temporal coordination of developmental programs is necessary for normal ontogeny, but the mechanism by which this is accomplished is poorly understood.  We have previously shown that two components of the Mediator CDK8 module, CENTER CITY (CCT/MED12) and GRAND CENTRAL (GCT/MED13), are required for timing of pattern formation during embryogenesis in Arabidopsis.
Here, we performed global gene expression analyses of wild-type, cct-1, and gct-2 seedlings (above-ground portions only) to help analyze their post-embryonic phenotypes.  Our results suggest that MED12 and MED13 act as global regulators of developmental timing by fine-tuning expression of temporal regulatory genes.

overall_design: Seeds of wild-type Col-0, cct-1, and gct-2 were sown in Fafard #2 soil.  Seedlings (above-ground portions only) were harvested when the first two leaf primordia were 1 mm in length, which was at day 7 for wild-type seedlings and day 9 for the two mutants. 75-100 seedlings were used for each of three biological replicates.

first: C

middle: S

last: Gillmor

first: R

last: Poethig


title: Arabidopsis thaliana roots at 7DAG; ga1, ga1 scl3 (LOF) and ga1 SCL3 OE (GOF)

status: Public on Sep 05 2014

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

country: South Korea

institute: KonKuk University

summary: Transcriptional profiling in the root between ga1, ga1 scl3 and ga1 SCL3 OE.  We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SCL3 and gibberellin on the growth and development of the Arabidopsis root system by global transcriptome analysis and to identify new regulators in the regulatory pathway.

overall_design: Three-condition experiments, ga1, ga1 scl3 and ga1 SCL3 OE. Biological triplicates: 3 ga1-3 , 3 ga1-3 scl3 and 3 ga1-3 SCL3 OE

first: Jun

last: Lim

first: Eun

first: Jung-Ok

last: Heo

first: Kwang

last: Chang


title: Expression data from Arabidopsis seedlings heat-stressed in light environment

status: Public on Jun 19 2014

city: changsha

first: Junyi

last: Song

address: Deya Road 888

institute: National University of Defense Techonolgy

summary:
Plants transcriptome react to environment temperture changes profoundly. In Arabidopsis seedlings, genes response to temperature fluctuations to adopt the ever-changing ambient envrionment.
We used microarrays to detail the global programme of gene expression underlying heat stress response progress in Arabidopsis.

overall_design: Ten-day-old Arabidopsis seedlings were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to explore the heat stress response in transcriptome, thus we treat the plants with heat stress.  While in order to identify the interaction between light and temperature signaling pathways in plant , we treat Arabidopsis with heat stress under both light and dark conditions. To that end, our plant tissues are grouped as: HS-LIGHT, HS-DARK,CONTROL-LIGHT,CONTROL-DARK.

first: Biru

last: Hu


title: Expression data from Arabidopsis seedlings heat-stressed in light and dark environment

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

overall_design: Refer to individual Series


title: Expression data from rGRF3, 35S:GIF1 and rGRF3x35S:GIF1 plants

status: Public on Jun 17 2014

first: Juan

last: Debernardi

summary:
The Growth Regulating Factors (GRFs) are plant specific transcription factors. They form complexes with GRF Interacting Factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are regulated by microRNA miR396. A detailed analysis of GRF3 revealed that a modified transgene, insensitive to the regulation of miR396, causes a strong increase in the number of cells in leaves, while an additional increase of GIF1 expression further enhances the number of cells synergistically. Genome-wide transcript profiling revealed that simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as chromatin remodeling complexes, providing a mechanistic explanation for the additional activities of a GRF3-GIF1 complex. Interestingly, we found that the GRF system also regulates leaf longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf size and senescence can be uncoupled, demonstrating that the GRFs control different stages of leaf development. The results provide new insights into the functions of a complex regulatory network composed of microRNAs, transcription factors, and co-transcription factors.
We used microarrays to obtain the transcription profile of plants overexpressing GRF3, GIF1 or both genes toghether.

overall_design: We compared the transcriptome of 35S:GIF1, rGRF3 and rGRF3x35S:GIF1 plants vs wild-type plants (Col-0 accession), using ATH1 Affymetrics microarrays. For these experiments we collected vegetative apices together with the leaf primordia from plants of 20 days growth in short-day. For each genotype (Col-0, rGRF3, 35S:GIF1 and rGRF3x35S:GIF1)  we collected two samples.

last: Debernadi

first: Javier

last: Palatnik


title: Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

status: Public on Jun 23 2014

city: New York

first: Ying

last: Li

address: 12 Waverly Place

institute: New York University

summary:
To identify potential transient interactions between a TF and its targets, we developed an approach that can identify primary targets based either on TF-induced regulation or TF-binding, assayed in the same samples. Our studies focused on the TF bZIP1 (BASIC LEUCINE ZIPPER 1), a central integrator of cellular and metabolic signaling.
To discern the mechanisms by which bZIP1 regulates a gene netowork in response to a nitrogen (N)-signal perceived in vivo, we perturbed both bZIP1 and the N-signal that it transduces in a cell-based transient expression system called TARGET (Transient Assay Reporting Genome-wide Effects of Transcription factors).

overall_design:
To identify the genome-wide targets of bZIP1 in response to a N-signal, we transiently perturbed both the TF and the signal in the TARGET cell-based system.  Specifically, bZIP1 was transiently overexpressed in root protoplasts following transfection with a 35S::GR::bZIP1 construct containing an RFP (red fluorescent protein) selectable marker gene. bZIP1 transfected cells were sequentially treated with: i) an inorganic nitrogen signal (+/-N), ii) cycloheximide (CHX) to block the synthesis of proteins, and iii) dexamethasone (DEX) to induce nuclear import of the GR::bZIP1 protein. To identify both the TF-regulated and the TF-bound genes, transcriptome analysis of transfected cells and micro-ChIP data (using anti-GR antibodies), were carried out in parallel .

This submission represents transcriptome component of study.

first: Alessia

last: Para

first: Amy

last: Marshall-Colon

first: Kranthi

last: Varala

first: Nancy

last: Francoeur

first: Tara

last: Moran

first: Molly

last: Edwards

first: Christopher

last: Hackley

first: Bastiaan

middle: O

last: Bargmann

first: Kenneth

last: Birnbaum

first: W

last: McCombie

first: Gabriel

last: Krouk

first: Gloria

last: Coruzzi


title: Expression data from Arabidopsis seedlings heat-stressed in dark environment

first: Junyi

last: Song

summary:
Plants transcriptome react to environment temperature changes profoundly. In Arabidopsis seedlings, genes respond to temperature fluctuations to adopt the ever-changing ambient environment.
We used microarrays to detail the global programme of gene expression underlying heat stress response progress in Arabidopsis.

last: Hu


title: A genome-wide approach in Arabidopsis thaliana to assess the toxicity of cadmium sulfide quantum dots

status: Public on Jun 15 2014

city: Parma

first: Luca

last: Pagano

address: Parco Area delle Scienze 11/A

department: Chemistry Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary:
Cadmium sulfide quantum dots (CdS QDs) are widely used in novel equipment. The relevance of the research lies in the need to develop risk assessments for nanomaterials, using as basis a model plant species.
Here a screen of Arabidopsis thaliana mutant lines was performed in an attempt to identify plants tolerant to CdS QDs. Two tolerant Ds insertion mutant lines (atnp01 and atnp02) were identified. A whole-genome microarray experiment showed how genes were regulated by CdS QDs. Most of the genes involved in the response to CdS QDs were related to detoxification and general metabolism. The two mutant lines treated with CdS QDs showed different patterns of gene expression.

overall_design: The genome-wide expression profile of seedlings of the two selected resistant mutants were acquired and compared to that of wild type seedlings using the Arabidopsis ATH1 Genome Array. The wild type seedlings were exposed to either 0 mg/L, 40 mg/L (1/2 MIC) or 80 mg/L (MIC wt) CdS QDs, and each of the resistant/tolerant mutant line plants to either 0 mg/L or 80 mg/L CdS QDs for 21 days.

first: Marta

last: Marmiroli

first: Maria

middle: L

last: Savo Sardaro

first: Marco

last: Villani

first: Nelson


title: mRNA expression signatures of human glioblastoma stem cell like cells after treatment with FG-3019, irradiation and FG-3019 + irradiation

city: Heidelberg

first: Manuel

last: Roehrich

state: Baden-Württemberg

address: INF 280

department: Molecular Radiation Oncology

institute: DKFZ Heidelberg

summary: To investigate effects on mRNA expression through treatment with FG-3019, irradiation and their combination to gain mechanistic hypotheses on the effects of these treatments on glioblastoma stem cell like cells which have been observed in vitro and in vivo.

overall_design: mRNA expression was measured 6 h after treatment with FG-3019, irradiation and their combination. 3 biological replicates were analyzed for each treatment condition (control, FG-3019, irratiation and FG-3019+irradiation)

first: Mengxian

last: Zhang

first: Peter

last: Huber


title: Expression data from 10-day old Arabidopsis seedlings treated with protease IV from Pseudomonas aeruginosa PA14

city: Boston

first: Zhenyu

last: Cheng

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary:
Immune responses in plants are triggered in part by conserved microbe-associated molecular pattern (MAMP) molecules such as bacterial flagellin. Upon MAMP perception, plants rapidly turn on the induction of numerous defense-related genes. We have identified a novel type of plant innate immunity elicitor, protease IV from Pseudomonas aeruginosa. Genome-wide transcriptomic profiles obtained with Affymetrix Arabidopsis ATH1 GeneChips® of 10-day old Arabidopsis seedlings treated with 20 nM purified protease IV for 1 hour were compared to published bacterial flagellin- and oligogalacturonide-triggered responses.
We used microarrays to characterize the global transcriptomic changes in Arabidopsis seedlings upon protease IV treatment.

overall_design: Ten-day old Arabidopsis seedlings were treated with mock control or 20 nM purified protease IV from Pseudomonas aeruginosa for 1 hour for RNA extraction and hybridization on Affymetrix microarrays.

first: Frederick

last: Ausubel


title: Targets of ALTERED PHLOEM DEVELOPMENT (APL)

status: Public on Aug 25 2014

city: Helsinki

first: Ykä

last: Helariutta

address: Viikinkaari 1

department: University of Helsinki

country: Finland

institute: Institute of Biotechnology

summary:
We profiled transcripts from sorted phloem cells of wild-type and apl mutants to identify the genes regulated by APL in phloem.
We profiled transcripts from sorted phloem cells of wild-type and apl mutants to identify the genes regulated by APL in phloem.

overall_design: Three biological replicates for control WT and apl mutants were used in thes study. Root tissue was protoplasted and sorted using fluorescence-activated cell sorting (FACS). Total RNA was extracted from GFP+ protoplasts.

first: L

last: Satu

first: O

last: Lindgren

first: B

last: De Rybel

first: T

last: Beeckman

first: Helariutta

last: Ykä


title: Impact of monomeric and oligomeric flavanols (MOF) consumption on the gene expression profile of leukocytes (human)

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

country: France

institute: INRA

summary: Background: In a recent intervention study, the daily supplementation with 200mg monomeric and oligomeric flavanols (MOF) from grape seeds for 8 weeks revealed a vascular health benefit in male smokers. The objective of the present study was to determine the impact of MOF consumption on the gene expression profile of leukocytes and to assess changes in DNA methylation. Methodology/Principal Findings: Gene expression profiles were determined using whole genome microarrays (Agilent) and DNA methylation was assessed using HumanMethylation450 BeadChips (Illumina). MOF significantly modulated the expression of 869 genes. The majority of the affected genes are involved in chemotaxis, cell adhesion, cell infiltration or cytoskeleton organisation, suggesting lower immune cell adhesion to endothelial cells. This was corroborated by in vitro experiments showing that MOF exposure of monocytes attenuates their adhesion to TNFα-stimulated endothelial cells. Nuclear factor-kappa B reporter gene assays confirmed that MOF decrease the activity of NF-κB. Strong inter-individual variability in the leukocytes DNA methylation was observed. As a consequence, on group level, changes due to MOF supplementation could not be found. However, in individuals, significant changes in DNA methylation of genes involved in leukocyte rolling, adhesion and cytoskeleton remodelling were seen. At the group level, the variation in DNA methylation related to life style and clinical parameters appeared to overrule the magnitude of effects of supplementation with MOF. Conclusion: Our study revealed that regular consumption of MOF modulates the expression of genes in immune cells which, however, cannot be correlated to alterations in the DNA methylome. Remarkably, at the individual level, genes related to leukocyte adhesion pathways present complex variation in DNA methylation. As such, the individual transcriptional and epigenetic modulation of genes involved in early manifestation of cardiovascular diseases constitutes important subcellular mechanisms by which MOF promote vascular health in humans.

overall_design: Two-colors experiment, 7 volunteers : blood samples of 7 men, before and after an intervention of 8 weeks with daily intake of MOF (14 samples).

first: Dragan

last: Milenkovic

first: Wim

last: Vanden Berghe

first: Céline

last: Boby

first: Christine

last: Leroux

first: Aalt

last: Bast

first: Antje

last: Weseler


title: Analysis of gene expression controlled by light and brassinosteroids

status: Public on Jul 01 2014

first: Sunghwa

last: Choe

address: Gwanak-Gu Shillim-Dong

department: Biological sciences

institute: Seoul National University

summary: Plant photomorphogenesis and skotomorphogenesis depend on interplay of various plant hormones. Brassinosteroids (BRs) play crucial roles during hypocotyl establishment both in the light and darkness. Arabidopsis brassinosteroid insensitive1 (bri1-5) is a partial loss-of-function mutant, and the short-hypocotyl phenotype of bri1-5 is greatly suppressed by a long-hypocotyl mutant phytochrome B (pbyB-77) at the double mutant for the two in the light conditions to display additive phenotypes of both. To identify the genes responsible for this genetic interaction, we employed microarray analysis with the RNAs prepared from wild type, bri1-5, phyB-77, and bri1-5 phyB-77 double mutant. Microarray analysis supported the notion that PHYB acts upstream of BRs.

overall_design: Total RNAs were isolated from four different genotypes: wild type, bri1-5, gul2-1/phyB-77, bri1-5 gul2-1 double mutant, and the RNAs were subjected to microarray analysis using Affymetrix GenChip arrays. Three biological replicates for each genotype resulted in 12 experiments.

first: Bokyung

last: Kim

first: Seoae

last: Cho

first: Taesung

last: Park


title: Dissecting physiological and transcriptional responses of nitric oxide to drought stress by increasing in vivo nitric oxide content in Arabidopsis

status: Public on Jun 03 2014

city: Wuhan, Hubei Province

first: Zhulong

last: Chan

address: Moshan, Wuchang District

department: Wuhan Botanic Garden

institute: Chinese Academy of Sciences

summary: Nitric oxide (NO) is involved in all major environmental stresses. However, most of these understandings were mainly based on pharmacological study using NO modulator compounds. Recently, our studies together with others provided a new class of plant experimental system with specific in vivo NO release through constitutively overexpressing rat neuronal NO synthase (nNOS) in plants. In this study, we found that the nNOS transgenic Arabidopsis plants displayed lower level of H2O2 content, but higher levels of antioxidant enzyme activities and osmolytes under drought stress conditions. Transcriptomic analysis identified 490 and 20 genes that were differentially expressed in wild type (WT) and nNOS transgenic plants under control and drought stress conditions, respectively. Pathway analysis revealed that many genes involved in photosynthesis, cell, misc, co-factor and vitamin metabolism, major CHO metabolism, OPP and secondary metabolism were largely changed in nNOS vs. WT under control or drought stress conditions. Interestingly, CBF1/2 and 13 zinc finger family proteins, known as important family of transcription regulators in modulating several stress-responsive genes, were differentially expressed by nNOS transgenic effect. Additionally, some genes were commonly regulated by nNOS transgenic and abscisic acid (ABA) effects, indicating new insights to cross-talk between ABA and NO. Taken together, in vivo NO modulated antioxidant enzyme activities, osmolyte level, and the expression of genes involved in several pathways, thereby resulting in enhanced stress tolerance in nNOS transgenic plants. These observations might provide some insights to understand the physiological and molecular mechanisms of NO in response to drought stress in Arabidopsis.

overall_design: Two transgenic Arabidopsis lines (nNOS-2 and nNOS-25) with the nNOS gene under the control of the cauliflower mosaic virus (CaMV) 35S promoter, as well as Col-0 (WT), were used in this research. RNA samples from two nNOS transgenic lines were pooled for cRNA labelling and chip hybridization.

first: Haitao

last: Shi


title: MiRNome and transcriptome aided pathway analysis in human regulatory T cells

status: Public on May 23 2014

city: München

first: Thomas

last: Magg

address: Lindwurmstr. 2a

institute: Dr. von Haunersches Kinderspital der LMU München

summary: Owing to their manifold immune regulatory functions, regulatory T cells (Treg) have received tremendous interests as targets for therapeutic intervention of diverse immunological pathologies or cancer. Directed manipulation of Treg will only be achievable with extensive knowledge about the intrinsic programs that define their regulatory function. We simultaneously analyzed miR and mRNA transcript levels in resting and activated human Treg cells in comparison to non-regulatory conventional T cells (Tcon). Based on experimentally validated miR-target information, both transcript levels were integrated into a comprehensive pathway analysis. This strategy revealed characteristic signal transduction pathways involved in Treg biology such as TCR-, TLR-, TGF-, JAK/STAT- and mTOR signaling and allowed for the prediction of specific pathway activities on the basis of miR and mRNA transcript levels in a probabilistic manner. These data encourage new concepts for targeted control of Treg cell effector function.

overall_design: Differential gene expression was measured in highly pure, FACS-sorted, resting regulatory T cells and conventional T cells and stimulated  regulatory T cells and conventional T cells. Two independent experiments using pooled samples from 5 different donors were performed for each cell type and activation condition.

first: Michael

middle: H

last: Albert

first: Joachim

last: Mannert

first: Katrin

middle: K

last: Fleischmann

first: Matthias

last: Schiemann

first: Philipp

last: Pagel

first: Irene

last: Schmid


title: Whole genome gene expression profiling in CD4+ T-cells, FACS-sorted based on CADM1/CD7 expression levels, in Adult T-cell Leukemia-lymphoma (ATL) patients, HTLV-1 carriers, and in healthy volunteers.

status: Public on Jun 02 2014

city: Tokyo

first: Kazumi

last: Nakano

address: 4-6-1, Sirokanedai, Minatoku

department: Department of Medical Genome Sciences, Graduate School of Frontier Sciences

institute: The University of Tokyo

summary: CADM1 overexpresion and stepwise downregulation of CD7 in CD4+T-cells from ATL patients and HTLV-1 carriers accurately reflect the process of disease, i.e., oligoclonally and clonally exanding cells are accumulated in D (CADM1posCD7dim) and N (CADM1posCD7neg) populations, respectively. Moreover, gene expression profiling of each subpopulation supported that notion.

overall_design: PBMCs of asymptomatic carriers (ACs) and ATLs were subgrouped based on CADM1 and CD7 expression levels by multicolor flow cytometry. FACS-sorted subpopulations were then subjected to extraction of total RNA, followed by Cy-3 labeling and human whole genome gene expression microarray analyses.

first: Seiichiro

last: Kobayashi

first: Toshiki

last: Watanabe

first: Kaoru

last: Uchimaru


title: Whole genome transcript profiling upon 4 days of salt treatment

status: Public on Jun 01 2014

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

institute: MPIMP

summary:
Our study identified long term salt stress treatment to induce symptoms similar to developmental senescence. In order to identify possible crosstalk components shared between developmental and salt-triggered senescence.
We first obtained the expression profile of Arabidopsis leaves under the condition of salt-induced senescence (4 days) and then compared it with the transcriptome of developmental leaf senescence.

overall_design: Wild type Arabidopsis Col-0 plants were grown hydroponically and treated with or without 150mM NaCl and harvested after 4 days of treatment.

first: Annapurna

last: Allu

first: Bernd

last: Mueller-Roeber


title: Expression data from Arabidopsis flowers under moderate drought stress

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

institute: The Penn State University

summary: We also used microarray analysis to examine transcriptomic changes under moderate drought, identifying thousends of genes that potentially mediate moderate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles.

overall_design: Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when moderate drought treatment was started by withholding water (defined as day 0 for moderate drought treatment). The relative soil moisture content decreased rapidly and, after about 48 hours the relative soil moisture content was near 50% of the soil water-holding capacity (first moderate drough treated sample M3 were collected at day 3 (72 h after withholding water)). The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened floral bud samples were collected at day 0, 3, 4, 5, 10.

first: Xuan

last: Ma

last: Su

first: Hong


title: The Enzyme-Like Domain of Arabidopsis Nuclear Beta-Amylases is Critical During DNA Sequence Recognition and Transcriptional Activation

status: Public on Jun 10 2014

city: Tuebingen

first: Dierk

last: Wanke

address: Auf der Morgenstelle 32

department: Plant Physiology

institute: University of Tuebingen

summary:
Plant BZR1-BAM transcription factors contain a β-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be non-catalytic, but determine the function of the Arabidopsis thaliana BZR1-BAMs (BAM7 and BAM8) during transcriptional initiation. Microarray experiments with plants overexpressing different mutant versions of the proteins show that only functional BZR1-BAM variants deregulate gene expression and cause leaf developmental abnormalities. Transcriptional changes caused by overexpression of the BZR1 domain alone indicate that the BAM domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element).
In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes.

overall_design: Arabidopsis thaliana (accession Columbia) were grown in a nutrient-rich, medium-grade, peat-based compost in Percival AR95 growth chambers (CLF Plant Climatics) at a constant temperature of 20°C, 70% humidity and a 12-h light period with constant, uniform light intensity of 150 μmol•m-2•s-1. Three-week-old plants were harvested 4 h after onset of the light period and immediately frozen in liquid nitrogen. Fourteen individual plants were pooled per replicate.

first: Sebastian

last: Soyk

first: Klára

last: Šimková

first: Luise

last: Brand

first: Samuel

middle: C

last: Zeeman


title: Expression data from leafminer-damaged Arabidopsis thaliana

status: Public on May 26 2014

city: Beijing

first: Sufang

last: Zhang

address: No.2 Dong Xiao Fu, Wan Shou Shan, Haidian District

institute: Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry

summary: Plants have developed a complicated resistance system, and they exhibit various defense patterns in response to different attackers. However, the determine factors of plant defense patterns are still not clear. Here, we hypothesized that damage patterns of plant attackers play an important role in determining the plant defense patterns. To test this hypothesis, we selected leafminer, which has a special feeding pattern more similar to pathogen damage than chewing insects, as our model insect, and Arabidopsis thaliana as the response plants. The local and systemic responses of Arabidopsis thaliana to leafminer feeding were investigated using the Affymetrix ATH1 genome array.

overall_design: Damaged leaves of Arabidopsis thaliana for local damage analysis and the intact leaves on the same plant for systemic damage analysis were separately frozen by liquid nitrogen. Then, we used an Affymetrix ATH1 Arabidopsis microarray to study the expression changes pattern of Arabidopsis thaliana to pea leafminers damage, both locally (LI) and systemically (SI). We downloaded data from the web database and used hierarchical clustering to explore the relationships of Arabidopsis thaliana expression pattern to different kinds of attackers.

first: Le

last: Kang


title: Sugar-dependent gene expression in xylose grown A. thaliana cell suspension culture

status: Public on May 16 2014

city: UMEÅ

first: Leszek

last: Kleczkowski

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

summary: Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars.  This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source.  The functional genomics approach was used to identify sugar responsive genes, which rapidly (within 1 h) respond specifically to low concentration (1 mM) of glucose, fructose and/or sucrose.

overall_design: A habituated A. thaliana cell culture grown in a hormone free full strength MS media in the dark was adapted to growth on xylose as the only carbon source in the media.The cells were subjected to a 1 hour treatment with 1 mM of either Fru, Glc, Suc or Xyl (control). The experiments were carried out in 3 biological repeats per treatment. Whole genome expression analysis was conducted by hybridization of the extracted RNA to the Affymetrix Arabidopsis ATH1 Genome Array.

first: Sabine

last: Kunz

first: Edouard

last: Pesquet


city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

summary:
Mitochondrial stress stimuli such as AA caused a transient suppression of auxin signaling and conversely, auxin treatment represses a part of the response to AA treatment.
Expression data of Col:LUC Arabidopsis treated with antimycin A (AA) in the presence or absence of a synthetic auxin analogue

overall_design: Total RNA extraction was carried out on 80 mg of  Col:LUC Arabidopsis seedlings grown on B5 media for 10 days and transferred to fresh plates, containing either B5 media or B5 media supplemented with 4.5 µM NAA for an additional 3 days. Seedlings were treated with 50 µM AA for 3 hours.

first: Aneta

last: Ivanova

middle: R

first: Reena

last: Narsai

first: Owen

last: Duncan

first: Jae-Lee

last: Hoon

first: Botao

first: Olivier

last: Van Aken

first: Jordan

last: Radomiljac

first: Margaretha

last: van der Merwe

first: KeKe

last: Yi

first: James

last: Whelan


title: Micro-array analysis of WT and AtISWI in callus formation

status: Public on May 15 2014

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: Plant regeneration could be achieved via formation of a pluripotent cell mass termed callus, nature of which is a group of fast-dividing root primordium cells. However, mechanisms that strictly control the stem cell fate transition in regeneration of callus remain elusive. Here we show that the Arabidopsis ISWI type chromatin remodelers specifically promote the second-step cell fate transition from root founder cells to root primordium cells in the leaf-to-callus transition.

overall_design: Leaf explants cultured in CIM from Col-0 or chr11-1 chr17-1 at time 0 and 8 days after culture (8 DAC) were used for RNA preparation. Microarray was performed using the AffymetrixGeneChip system. Three independent experiments were performed.

last: Xu

first: Shujing

last: Liu


title: Cell type specific gene expression map of Arabidopsis thaliana SAM.

city: SAS Nagar

first: Ram

middle: Kishor

last: Yadav

state: Punjab

address: Sector 81

institute: Indian Institute of Science Education and Research Mohali

summary:
Shoot apical meristem (SAM) of higher plant composed of a few distinct cell types.  All the cells in a mature plant’s SAM derived from 30~35 stem cells reservoir which are located at the tip of the apex.  Plants ability to give rise diverse cell types from a pool of pluripotent stem cells requires orchestrated gene network that controls the cell fate commitment during the meristem development.  To understand, how gene regulatory networks control cell identities switches during cell differentiation requires resolution in recording their gene expression pattern at single cell resolution. An earlier expression map involving three-cell population of stem cell niche revealed complex expression pattern among the cell types1.  We developed this approach further and report here a gene expression map using cell-sorting methods for fluorescent protein marked cells in Arabidopsis shoot. The map covered 10 cell populations.
This gene expression map represents data from 10 different cell types from Arabidopsis SAM. It will be first step in defining the function of many unknown genes in model plant Arabidopsis.

overall_design: Based on the in situ hybridization we identified 7 new cell types specific gene expression patterns. The promoters of these genes were used to generate fluorescent reporters. After treating the SAM with protoplasting cocktail, we sorted the fluorescent protein tagged cells using fluorescent activated cell sorter (FACS).  The purified cell population was used to isolate RNA. Two round of RNA amplification was performed before microarray hybridization.

first: R

first: G

middle: V

last: Reddy


title: Expression profiling of uninfected and Golovinomyces orontii infected Arabidopsis thaliana wild type Col-0 and del1-1 mutant

status: Public on Apr 30 2014

city: Berkeley

first: Mary

last: Wildermuth

address: 221 Koshland Hall MC3102

institute: University of California Berkeley

summary: In plants, the activation of immunity is often inversely correlated with growth. Mechanisms that plant growth in the context of pathogen challenge and immunity are unclear. Investigating Arabidopsis infection with the powdery mildew fungus, we find that the Arabidopsis atypical E2F DEL1, a transcriptional repressor known to promote cell proliferation, represses accumulation of the hormone salicylic acid (SA), an established regulator of plant immunity. DEL1 deficient plants are more resistant to pathogens and slightly smaller than wild type. The resistance and size phenotypes of DEL1 deficient plants are due to the induction of SA and activation of immunity in the absence of pathogen challenge. Moreover, Enhanced Disease Susceptibility 5 (EDS5), a SA transporter required for elevated SA and immunity, is a direct repressed target of DEL1. Together, these findings indicate that DEL1 control of SA levels contributes to regulating the balance between growth and immunity in developing leaves.

overall_design: Mature, fully expanded leaves of 41/2-week-old Col-0 and del1-1 plants were harvested at 5 days after G. orontii infection and from uninfected control plants for RNA extraction and hybridization on Affymetrix microarrays.

first: Divya

last: Chandran


title: CSB3 transcriptome analysis (Arabidopsis thaliana)

status: Public on Apr 25 2014

city: Valencia

first: Pablo

last: Vera

email: vera@ibmcp.upv.es, oliveros@cnb.csic.es

state: Valencia

address: Camino de Vera s/n

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP) UPV-CSIC

summary: In this study we show the comparative transcriptome of constitutive subtilisin3 (csb3) plants, an Arabidopsis mutant showing strikingly enhanced resistance to biotrophic pathogens. CSB3 encodes a 1-hydroxy-2-methyl-2-butenyl 4-diphosphate synthase, the enzyme controlling the penultimate step of the biosynthesis of isopentenyl diphosphate via the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway in the chloroplast. It has been proposed that CSB3 represents a point of metabolic convergence modulating the magnitude of SA-mediated disease resistance to biotrophic pathogens. We show that csb3 have increased expression  of a set of genes encoding defense-related proteins and enzymes,  which includes two subtilisins. In essence our results substantiates an important role of these two subtilases in the activation of defense-related signaling pathways against biotrophic pathogens.

overall_design: 5 five-week-old plants were collected, frozen in liquid nitrogen and stored at -80ºC. Samples from Col-0 and csb3 were compared.

first: Vicente

last: Ramírez

first: María

middle: J

last: Gil

first: Ana

last: López


title: The Arabidopsis spaceflight transcriptome: a comparison of whole plants to discrete root, hypocotyl and shoot responses to the orbital environment

status: Public on Apr 10 2014

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary:
transcriptome response of Arabidopsis cultivar Columbia and WS whole plants and plant tissue roots, hypocotyls and shoots to the spaceflight environment
Arabidopsis thaliana was evaluated for its response to the spaceflight environment in three replicated experiments on the International Space Station. Two approaches were used; GFP reporter genes were used to collect gene expression data in real time within unique GFP imaging hardware, and plants were harvested on orbit to RNAlater for subsequent analyses of gene expression with using Affymetrix and SAGE transcriptome analyses. Three tissue types were examined (leaves, hypocotyls and roots) and compared to analyses conducted with whole plants.  Transcriptome analyses with whole plants suggested that the spaceflight environment had little impact on the transcriptome of arabidopsis, however, closer examination of selected tissues revealed that there are a number of tissue-specific responses that arabidopsis employs to respond to this novel environment.

This experiment was launched on STS-131 in 2010 and was supported by NASA grant NNX07AH27G - Transgenic Plant Biomonitors of Space Flight Exposure to R.J. Ferl and A-L. Paul.

overall_design: whole plants total samples 6: spaceflight 3 samples vs unit gravity ground control' 3 samples; plant tissue total samples 30: shoots: spaceflight 5 samples vs unit gravity ground control' 5 samples; hypocotyls: spaceflight 5 samples vs unit gravity ground control' 5 samples; roots: spaceflight 5 samples vs unit gravity ground control' 5 samples;

first: Anna-Lisa

last: Paul

first: Agata

last: Zupanska

first: Yanping

last: Zhang

first: Yijun

last: Sun


title: A New Mediator of Singlet Oxygen Responses in Chlamydomonas and Arabidopsis

status: Public on Apr 21 2014

city: Potsdam

first: Ning

last: Shao

address: Wissenschaftpark Golm

institute: Max-Planck Institute for Molecular Plant Physiology

summary: We identified a small zinc finger protein, MBS, as a new mediator of singlet oxygen responses in Chlamydomonas and Arabidopsis.  MBS is required for induction of singlet oxygen-dependent gene expression and, upon oxidative stress, accumulates in distinct granules in the cytosol of Arabidopsis cells. First, we recorded changes in light stress-regulated gene expression profiles after genetically perturbing MBS function by isolating mutants for the two MBS genes (MBS1 and MBS2) and by overexpression of MBS1 in Arabidopsis thaliana. Then, these light stress-related gene expression profiles were analyzed with respect to genes specifically responding to singlet oxygen and hydrogen peroxide/superoxide.  The results indicated that MBS inactivation leads to an impaired response to singlet oxygen signaling under light stress.

overall_design: Knock-out or knock-down of the MBS1 and MBS2 genes and overexpression of MBS1 in Arabidopsis thaliana were compared with the wild type and the flu mutant as controls under light stress. Arabidopsis seedlings of mbs1-1, RNAi-MBS2/mbs1-1, 35S:MBS1, the wild type and the flu mutant were harvested at 0 h and 3 h of light stress (HL, 1000 µE m−2 s−1). Total RNA was extracted and cDNA was hybridized to Affymetrix ATH1 microarrays in three biological replicates.

first: N

last: Duan

last: Bock


title: Transcription profiling by array of the response of Arabidopsis cultivar Columbia etiolated seedlings and undifferentiated tissue culture cells to the spaceflight environment

summary:
transcriptome response of Arabidopsis cultivar Columbia etiolated seedlings and undifferentiated tissue culture cells to the spaceflight environment
We address a key baseline question of whether gene expression changes are induced by the orbital environment, and then we ask whether undifferentiated cells, cells presumably lacking the typical gravity response mechanisms, perceive spaceflight. Arabidopsis seedlings and undifferentiated cultured Arabidopsis cells were launched in April, 2010, as part of the BRIC-16 flight experiment on STS-131. Biologically replicated DNA microarray and averaged RNA digital transcript profiling revealed several hundred genes in seedlings and cell cultures that were significantly affected by launch and spaceflight. The response was moderate in seedlings; only a few genes were induced by more than 7-fold, and the overall intrinsic expression level for most differentially expressed genes was low. In contrast, cell cultures displayed a more dramatic response, with dozens of genes showing this level of differential expression, a list comprised primarily of heat shock-related and stress-related genes. This baseline transcriptome profiling of seedlings and cultured cells confirms the fundamental hypothesis that survival of the spaceflight environment requires adaptive changes that are both governed and displayed by alterations in gene expression. The comparison of intact plants with cultures of undifferentiated cells confirms a second hypothesis: undifferentiated cells can detect spaceflight in the absence of specialized tissue or organized developmental structures known to detect gravity.

This experiment was launched on STS-131 in 2010 and was supported by NASA grant NNX10AF45G - The Impact of Spaceflight on Arabidopsis: Deep Sequencing and DNA Arrays as Collaborative Readouts of the Transcriptome of Arabidopsis Seedlings and Undifferentiated Cells in Space to A-L. Paul and R.J. Ferl.

overall_design: undifferentiated cultured cells total samples 12: spaceflight 6 samples vs unit gravity ground control' 6 samples; etiolated seedlings total samples 12: spaceflight 6 samples vs unit gravity ground control' 6 samples

first: Dejerianne

middle: T

last: Ostrow

first: Jian-Liang

last: Li


title: WRKY6 Transcription Factor Restricts Arsenate Uptake and Transposon Activation in Arabidopsis

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Stress constantly challenges plant adaptation to the environment.  Of all stress types, arsenic was a major threat during the early evolution of plants.  The most prevalent chemical form of arsenic is arsenate, whose similarity to phosphate renders it easily incorporated into cells via the phosphate transporters.  Here we found that arsenate stress provokes a notable transposon burst in plants, in coordination with arsenate/phosphate transporter repression, which immediately restricts arsenate uptake.  This repression was accompanied by delocalization of the phosphate transporter from the plasma membrane.  When arsenate was removed, the system rapidly restored transcriptional expression and membrane localization of the transporter.  We identify WRKY6 as an arsenate-responsive transcription factor that mediates arsenate/phosphate transporter gene expression and restricts arsenate-induced transposon activation.  Plants therefore have a dual WRKY-dependent signaling mechanism that modulates arsenate uptake and transposon expression, providing a coordinated strategy for arsenate tolerance and transposon gene silencing.

overall_design: Three biological replicates were performed for each sample type. Single channel hybridizations were carried-out using either Affymetrix ATH1 platform or Nimblegen Gene Expression 12x135K platform (Arabidopsis thaliana).

first: Gabriel

last: Castrillo

first: Eduardo

last: Sánchez-Bermejo

first: Laura

last: de Lorenzo

first: Pedro

last: Crevillen

last: Fraile-Escanciano

first: Mohan

last: TC

first: Alfonso

last: Mouriz

last: Catarecha

last: Sobrino-Plata

first: Sanna

last: Olsson

first: Yolanda

last: Leo del Puerto

first: Isabel

last: Mateos

first: Enrique

last: Rojo

first: Luis

middle: E

last: Hernández

first: Jose

middle: A

last: Jarillo

first: Manuel

last: Piñeiro

first: Javier

last: Paz-Ares

first: Antonio

last: Leyva


title: Identification of ZIC2 target genes in human pancreatic cancer cell lines PANC-1 and KP-4

status: Public on Apr 14 2014

city: Nagakute

first: Shingo

last: Inaguma

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Pathology

institute: Aichi Medical University School of Medicine

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
PANC-1Tet/ZIC2 and PANC-1Tet/empty were established from human pancreatic cancer cell line PANC-1. PANC-1Tet/ZIC2 cells express FLAG-tagged human ZIC2 on the withdrawal of DOX. On the other hand, PANC-1Tet/empty was transfected an empty vector for the control experiment. To identify ZIC2 target genes, total RNAs were purified from the cells before and 48 hours after the DOX withdrawal. Gene expression profiles were analyzed by AGILENT human 4x44k cDNA microarray.
As well as ZIC2-inducible system, we performed ZIC2-knockdown experiments in PANC-1 human pancreatic cancer cells. After 96 hours transfection of siRNAs for ZIC2 and its control, total RNAs were purified and gene expression profiles were analyzed by AGILENT human 4x44k cDNA microarray.

overall_design:
ZIC2 target genes were identified in PANC-1 cells. Gene expression profiles of PANC-1Tet/ZIC2 and PANC-1Tet/empty cells were analyzed by AGILENT human 4x44k cDNA microarray before and 48 hours after the DOX withdrawal.
As well as ZIC2-inducible system, gene expression profiles of control- and ZIC2-knocdown PANC-1 cells were also analyzed by AGILENT human 4x44k cDNA microarray.

first: Kenji

last: Kasai

first: Hiroshi

last: Ikeda


title: A comparison of gene expression between human dermal fibroblasts and neurons infected by varicella zoster virus

status: Public on Apr 22 2014

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

summary: The cellular transcriptomes of VZV-infected fibroblasts and T-lymphocytes have been reported, but not that of human neurons. In order to determine the transcriptional response of human neurons to VZV infection, we generated 95%-pure populations of neurons from hESC, infected them with recombinant GFP-expressing cell-free VZV, and compared their transcriptome to that of human foreskin fibroblasts infected in parallel, using Agilent microarrays.  Applying a twofold-change as the cutoff (p-value<0.05), we observed that transcription of 1654 fibroblast and 340 neuronal genes were upregulated, and 955 fibroblast and 38 neuronal genes were downregulated by VZV infection. 223 of these infection-regulated genes were unique to neurons. Gene ontology enrichment analysis revealed several clusters of genes regulated by VZV in neurons and fibroblasts differed. For example, neurons did not show upregulation of innate immune responses, NF-kappaB, response to stress and DNA repair clusters, in contrast to fibroblasts that upregulated these groups. This is the first study of the response of genetically normal human neurons to viral infection.

overall_design: Two-condition experiment, VZV-GFP23- fibroblast cells vs. fibroblast cells, and VZV-GFP23- neuron cells vs. neuron cells. Data from two biological replicates and two technical replicates were used for each condition.

first: Amos

last: Markus

first: Paul

last: Kinchington

first: Ronald

last: Goldstein


title: Gene expression in Arabidopsis ddm1 mutants with high levels of Transposable Element activity

status: Public on Apr 07 2014

city: Columbus

first: Richard

middle: Keith

last: Slotkin

state: OH

address: 318 West 12th Ave.

department: Molecular Genetics

institute: The Ohio State University

summary:
Background: Transposable elements are known to influence the regulation of some genes. We aimed to determine which genes show altered gene expression when transposable elements are epigenetically activated.
Results: We find over 2000 genes with altered steady-state expression levels in ddm1 mutants. Some of these genes are influenced by neighboring transposable element fragments, while other genes are targeted by transposable element derived 21 nucleotide siRNAs.
Conclusion: The regulation of the genic portion of the Arabidopsis genome is heavily influenced by the epigenetic regulation of transposable elements. The regulation of genes by transposable elements can occur through multiple mechanisms.

overall_design: Three biological replicates for two genotypes

first: R

first: Kaushik

last: Panda


title: Cell type-specific transcriptional responses of Arabidopsis to salinity

city: Adelaide

first: aurelie

last: evrard

address: Hartley Grove, Urrbrae

country: Australia

institute: ACPFG

summary:
Microarray data were generated to investigate the changes in gene expression for two cell types of the root: pericycle and cortical cells in response to salt treatment. The transcription profile of both cell types were also generated.
Cell-types of interest expressing specifically Green Fluorescent Protein (GFP) were isolated from the rest of the root using fluorescence-activated cell sorting (FACS).

overall_design: 11 arrays were generated from plants grown in control and salt conditions. All seedlings grew in one tank were collected and correspond to one biological sample. Two control biological replicates were used for pericycle and 3 for cortical cells. By comparison from control microarray, 6 others arrays from salt treated plant (3 for each cell types) were used to identified salt responsive genes. The salt treatment was done on day 6 and 7 with increment of 25mM every 24h.

first: Aurelie

last: Evrard

first: Alex

last: Johnson

first: Ute

last: Baumann

first: Mark

last: Tester

first: Baastian

last: Bargmann

first: Kenneth

last: Birnbaum


title: Heterodimerization of GBF1 with HY5 and HYH is crucial for its genome wide binding and target gene regulation

status: Public on Mar 24 2014

city: New Delhi

first: Sudip

last: Chattopadhyay

state: Delhi

address: Aruna Asaf Ali Marg, JNU Campus

department: Development Biology

institute: National Institute of Plant Genome Research

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: Developmental stage specificity of transcriptional, biochemical and CO2 efflux responses of leaf dark respiration to growth of Arabidopsis thaliana at elevated [CO2]

status: Public on Apr 04 2014

city: Urbana

first: Robert

middle: John Cody

last: Markelz

state: IL

address: 1206 W Gregory Dr

department: Plant Biology

country: USA

institute: University of Illinois

summary: Plant respiration responses to elevated growth [CO2] are key uncertainties in predicting future crop and ecosystem function. In particular, the effects of elevated growth [CO2] on respiration over leaf development are poorly understood. This study tested the prediction that, due to greater whole-plant photoassimilate availability and growth, elevated [CO2] induces transcriptional reprogramming and a stimulation of nighttime respiration in leaf primordia, expanding leaves, and mature leaves of Arabidopsis thaliana. In primordia, elevated [CO2] altered transcript abundance, but not for genes encoding respiratory proteins. In expanding leaves, elevated [CO2] induced greater glucose content and transcript abundance for some respiratory genes, but did not alter respiratory CO2 efflux. In mature leaves, elevated [CO2] led to greater glucose, sucrose and starch content, plus greater transcript abundance for many components of the respiratory pathway, and greater respiratory CO2 efflux. Therefore, growth at elevated [CO2] stimulated dark respiration only after leaves transitioned from carbon sinks into carbon sources. This coincided with greater photoassimilate production by mature leaves under elevated [CO2] and peak respiratory transcriptional responses. It remains to be determined if biochemical and transcriptional responses to elevated [CO2] in primordial and expanding leaves are essential prerequisites for subsequent alterations of respiratory metabolism in mature leaves.

overall_design: Arabidopsis plants were grown in either ambient (370 ppm) or elevated (750 ppm) CO2. Leaf number 10 was harvested when it was a primordia, expanding, or mature in each of the CO2 treatments.

first: Andrew

middle: D

last: Leakey


title: Argentinean high altitude adaptation

status: Public on Feb 20 2014

city: Cambridge

first: Christina

last: Eichstaedt

address: Fitzwilliam Street

department: Biological Anthropology

institute: University of Cambridge

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: This study evaluates genetic and phenotypic variation in the high altitude Colla population living in the Argentinean Andes above 3500 m. They were compared to the Wichí population living in the nearby lowlands of the Gran Chaco region. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to hypobaric hypoxia. We have genotyped 25 individuals from both populations for 730,525 SNPs.

overall_design: DNA from 25 saliva samples from Collas living >3500 m and 25 saliva samples from Wichí living <500 m from the Province of Salta in Argentina was genotyped

first: Maru

last: Mormina

first: Toomas

last: Kivisild

first: Tiago

last: Antão

first: Luca

last: Pagani

first: Alexia

last: Cardona


title: Expression data from 10 day old Arabidopsis thaliana seedlings

status: Public on Mar 07 2014

city: Regensburg

first: Klaus

last: Grasser

address: Universtitätsstr. 51

institute: University of Regensburg

summary: Microarrays were used to detail the global programme of gene expression comparing wild-type and RNAi knock-down plants of SPT4-1 and SPT4-2

overall_design: Arabidosis seeds were stratified for 2 days and grown for 10 days on solid (0.8% Agar) MS in an plant incubator in a 16 hours day, 8 hours night rythm.  Only the aerial part was harvested 2h after turning on the light.

first: J

last: Dürr

first: C

last: Möhle


title: Expression data from  Arabidopsis wild type and cdm1 young floral buds

status: Public on Mar 11 2014

first: Pingli

last: Lu

address: 220 Handan Road

department: School of Life Sciences

institute: Fudan University

summary: We used microarray analysis to examine transcriptomic changes in cdm1 mutant, identifying genes potentially regulated by CDM1 by comparing gene expression between cdm1 and wild type young floral buds. Among 375 genes that showed differential expression (P-value <0.05) with >1.5-fold changes between wild type and cdm1, 185 genes were down-regulated by 1.5 to 7.10-folds, whereas 190 genes were up-regulated by 1.5 to 5.82-folds.

overall_design: Wild type and cdm1 young floral buds were used to isolate total RNA, with two biological replicates for each. Microarray analysis was performed using 500ng of total RNA per sample as described in the Genechip Expression Analysis Technical Manual.

first: Hong

last: Ma


title: Transcription profiling by array of wild type and arr1,10,12 mutant Arabidopsis seedlings treated with the cytokinin benzyladenine

status: Public on Feb 12 2014

city: Hanover

first: George

last: Schaller

state: NE

address: 339 Life Sciences Center, HB 6044

department: Biological Sciences

institute: Dartmouth College

summary:
Effect of the cytokinin BA on wt and arr1,10,12 mutant seedlings
The type B Arabidopsis Response Regulators (ARRs) of Arabidopsis thaliana are transcription factors that act as positive regulators in the two-component cytokinin signaling pathway. We employed a mutant-based approach to perform a detailed characterization of the roles of ARR1, ARR10, and ARR12 in plant growth and development. The most pronounced phenotype was found in the arr1-3 arr10-5 arr12-1 triple loss-of-function mutant, which showed almost complete insensitivity to high levels of exogenously applied cytokinins. The triple mutant exhibited reduced stature due to decreased cell division in the shoot, enhanced seed size, increased sensitivity to light, altered chlorophyll and anthocyanin concentrations, and an aborted primary root with protoxylem but no metaxylem. Microarray analysis revealed that expression of the majority of cytokinin-regulated genes requires the function of ARR1, ARR10, and ARR12. Characterization of double mutants revealed differing contributions of the type B ARRs to mutant phenotypes. Our results support a model in which cytokinin regulates a wide array of downstream responses through the action of a multistep phosphorelay that culminates in transcriptional regulation by ARR1, ARR10, and ARR12.  This data was originally made available through ArrayExpress under the accession number E-MEXP-1573.

overall_design: A benzyladenine treatment of 10 uM or a control treatment with equal DMSO was applied to A thaliana seedlings which were either knock outs for ARR1,10,12 or wild type.

first: Rebecca

last: Argyros

first: Dennis

last: Mathews

first: Chiang

last: Yi-Hsuan

first: Christine

middle: M

last: Palmer

first: Derek

last: Thibault

first: Naomi

last: Etheridge

first: D

first: Michael

middle: G

last: Mason

first: Joseph

last: Kieber


title: miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis [Affymetrix]

status: Public on Mar 18 2014

city: Cold Spring Harbor

first: Kate

last: Creasey

address: 1 Bungtown Road

department: Plant Sciences

institute: Cold Spring Harbor Laboratory

summary: Utilizing Affymetrix ATH1 microarrays to analyze transposon expression in DNA methylation mutants, and RNAi mutants, compared to wildtype.

overall_design: Total RNA extracted from plant inflorescence tissue.

first: K

first: R

last: Martienssen


title: Pre-mRNA splicing factor atsf1-2 mutant seedlings

status: Public on Mar 31 2014

city: Seoul

first: Jeong-Kook

last: Kim

address: 5-1, Anam-Dong, Seongbuk-Gu

department: Life Sciences

institute: Korea University

summary:
Analysis of atsf1-2 mutant seedlings for pre-mRNA splicing defect.  The atsf1-2 mutant is a homozygous T-DNA insertion line isolated from a SALK line, SALK_062177.  Results identify transcripts with altered alternative splicing pattern in the atsf1-2 mutant.
We used microarrays to examine the transcriptome profile in the atsf1-2 mutant and identified genes of  which transcript levels were changed significantly.

overall_design: Arabidopsis seedlings were grown for 9 days under long day condition.  They were then used for RNA extraction and hybridization on Affymetrix ATH1 Genome Array.  Three replicates for Col-0 (control) and atsf1-2 (mutant) were compared respectively.

first: Yun-Hee

last: Jang