title: Chloroplast-dependent programmed cell death is activated in Arabidopsis cell cultures after singlet oxygen production by Rose Bengal

status: Public on Mar 13 2014

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

summary: Arabidopsis thaliana cell suspension cultures (ACSC) were subjected to 30-min, mild chemical treatments with three different singlet oxygen elicitors at low-medium light conditions (150 µE m–2 s–1) with the aim of getting a better understanding of singlet oxygen-mediated defence responses in plants. The three elicitors Indigo Carmine (IC), Methylene Violet (MV) and Rose Bengal (RB) at a concentration of 0.5 µM were chosen because they exhibited different abilities to permeate the plasma membrane and to accumulate in the cell soma or organelles such as chloroplasts. In addition, ACSC were treated with 500 µM H2O2 for comparison. Confocal image analysis of Arabidopsis cells revealed that IC was not retained in cells, whereas MV and RB permeated the plasma membrane and accumulated in the chloroplast envelope and inside chloroplasts, respectively. As a consequence of their different cellular location, the physiological, transcriptional and photosynthetic responses of Arabidopsis cells to singlet oxygen production varied from each other and the activation of programmed cell death (PCD) was observed in ACSC treated with 0.5 µM RB, but not with the other elicitor nor with 500 µM H2O2. The role of chloroplasts in the activation of PCD was further investigated when this physiological response was analyzed in dark-grown cell cultures containing undifferentiated plastids. Interestingly, PCD was only activated in light-grown, but not in dark-grown, Arabidopsis cell cultures, suggesting that singlet oxygen-mediated defence responses were initiated inside chloroplasts. Genome-wide transcriptional profile analyses were performed as well and the results proved that there were only statistically significant changes in the transcript expression of light-grown ACSC treated with 0.5 µM RB and 500 µM H2O2, but not with IC nor with MV. Functional enrichment analyses revealed that GO/Biological process terms associated with defence responses were common in the treatments with 0.5 µM RB and 500 µM H2O2; however, resistance response to pathogen and PCD terms were only significantly over-represented in the RB treatment. Moreover, the analysis of the up-regulated transcripts in ACSC treated with 0.5 µM RB brought out that both specific markers for singlet oxygen from the conditional fluorescence (flu) mutant of Arabidopsis and transcripts with a key role in hormone-activated PCD (i.e. ethylene and jasmonic acid) were present, although there was no evidence for the up-regulation of EDS1 encoding the ENHANCED DISEASE SUSCEPTIBILITY PROTEIN 1. Finally, a co-regulation analysis proved that ACSC treated with 0.5 µM RB exhibited higher correlation with the flu family mutants than with other singlet oxygen producer mutants of Arabidopsis or wild-type plants of Arabidopsis subjected to high light treatments, where singlet oxygen was produced in photosystem II and an acclimatory response was activated instead of PCD.

overall_design: 18 Samples total. Six Samples are controls, 3 Samples each treated with Rose Bengal, Hydrogen Peroxide, Methyl Violet, and Indigo Carmine.

first: Jorge

last: Gutiérrez

first: Sergio

last: González-Pérez

last: García-García

first: Oscar

last: Lorenzo

first: José

middle: L

last: Revuelta

first: Paul

middle: F

last: McCabe

first: Juan

middle: B

last: Arellano


title: Transcriptomic effects of miR-30d transient over-expression in human endometrial epithelial cells.

status: Public on Feb 03 2014

city: Valencia

middle: M

last: Moreno-Moya

address: Catedrático Agustín Escardino

country: Spain

institute: FIVI

summary: microRNAs are essential regulators of gene expression. This work explores the transcriptomic effects of has-miR-30d in endometrial epithelial cells which was reported to be up-regulated during human endometrial receptivity.

overall_design: primary endometrial epithelial cells derived from four different endometrial biopsies taken on LH+0 were transiently transfected with miRNAs for 72 hours under two conditions (four scramble, four miR-30d mimic) and were evaluated for mRNA expression with Agilent’s gene expression microarray. A set of differentially expressed mRNAs were validated by qPCR.

first: Felipe

last: Vilella-Mitjana

first: Sebastián

last: Martínez

first: Antonio

last: Pellicer

first: Carlos

last: Simón


title: RNAi-mediated silencing of MLL-AF9 reveals leukemia-associated downstream targets and processes

status: Public on Feb 13 2014

city: Munich

first: Katrin

middle: K

last: Fleischmann

address: Lindwurmstrasse 2a

department: Children’s Research Center

country: Germany

institute: Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Univeristät München

summary:
The translocation t(9;11)(p22;q23) leading to the leukemogenic fusion gene MLL-AF9 is a frequent translocation in infant acute myeloid leukemia (AML). This study aimed to identify genes and molecular processes downstream of MLL-AF9 (alias MLL-MLLT3) which could assist to develop new targeted therapies for such leukemia with unfavorable prognosis.
In the AML cell line THP1 which harbors this t(9;11) translocation, endogenous MLL-AF9 was silenced via siRNA while ensuring specificity of the knockdown and its efficiency on functional protein level.
The differential gene expression profile was validated for leukemia-association by gene set enrichment analysis of published gene sets from patient studies and MLL-AF9 overexpression studies and revealed 425 differentially expressed genes. Gene ontology analysis was consistent with a more differentiated state of MLL-AF9 depleted cells, with involvement of a wide range of downstream transcriptional regulators and with defined functional processes such as ribosomal biogenesis, chaperone binding, calcium homeostasis and estrogen response.
Besides potential new therapeutic targets, the described transcription profile shaped by MLL-AF9 provides an information source into the molecular processes altered in MLL aberrant leukemia.

overall_design:
4 samples were analyzed, each corresponding to a pool of five independent replicate experiments. MLL-AF9 knockdown treatments are represented by 2 pooled samples employing two distinct siRNAs, each targeting MLL-AF9 breakpoint of THP1 cells. Control treatments are represented by 2 pooled samples employing two distinct non-targeting control siRNAs.
siRNA-3 = siRNA-A in publication
siRNA-4 = siRNA-B in publication

first: Philipp

last: Pagel

first: Irene

last: Schmid

first: Adelbert

middle: A

last: Roscher


title: Translatome of floral buds, in vivo pollinated pollen tubes, and in vitro cultured pollen grains/tubes from LAT52-HF-RPL18 Arabidopsis

status: Public on Feb 01 2014

city: Taipei

first: Shih

middle: Yun

last: Lin

state: Taiwan

address: 128 Sec. 2, Academia Rd

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: Little is known of the transcriptome of in vivo-grown pollen tubes, due to the difficulty of collection of pollen tubes elongating within the maternal gynoecium.We obtained the mRNAs undergoing translation (the translatome) of in vivo-grown pollen tubes from self-pollinated gynoecia of Arabidopsis thaliana(Col-0).

overall_design: Transgenic Arabidopsis plants (LAT52-HF-RPL18) harboring an epitope tagged ribosomal protein L18 driven by the pollen specific promoter (ProLAT52) were used for mRNA-ribosome complex isolation. After collection of polyribosomal (polysomal) complexes from self-pollinated (in vivo), unpollinated styles (buds), and in vitro-cultured pollen tubes, the actively translated mRNAs (the translatome) were purified, amplified to antisense RNA (aRNA). These aRNAs were hybridized to microarrays.Three independent biological replicates samples of aRNA from Bud, in vivo, and in vitro polysomal mRNA (translatomes) were hybridized to GeneChips to produce CEL files.

middle: Y

first: Guang-Yuh

last: Jauh

first: Piyada

last: Juntawong

first: Julia

last: Bailey-Serres


title: Effect of PCO1 overexpression [hypoxia]

status: Public on Feb 07 2014

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

country: Italy

institute: Scuola Superiore Sant'Anna

summary: The effect of the overexpression of Plant Cysteine Oxidase (PDCO1) on the transcriptome of Arabidopsis resettes was investigated with plants  subjected to a 4h hypoxia (5% O2 v/v in air). For this purpose, 4-week old rosette of wild-type and 35S:FLAG:CDO1 plants were compared. Samples were composed of pools of 5 plants.

overall_design: In total, 6 samples were analyzes, subdivided in 2 thesis with 3 replicates each. 35S:PCO1 plants (treated with hypoxia) were compared to wild-type plants (treated with hypoxia).

first: Daniël

last: Weits

first: Joost

last: van Dongen


title: Effect of PCO1 overexpression [normoxia]

summary: The effect of the overexpression of Plant Cysteine Oxidase (PCO1) on the transcriptome of Arabidopsis resettes was investigated. For this purpose, 4-week old rosette of wild-type and 35S:FLAG:CDO1 plants were compared. Samples were composed of a pool of 5 plants.

overall_design: In total, 6 samples were analyzes, subdivided in 2 thesis with 3 replicates each. 35S:PCO1 plants were compared to wild-type plants.


title: Effect of PCO1 overexpression

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

overall_design: Refer to individual Series


title: Small Cell Carcinoma of the Ovary (SCCO) vs. Normal Ovary

status: Public on Jan 17 2014

city: Dunedin

first: Heather

middle: E.

last: Cunliffe

state: Otago

address: P O Box 913

department: Department of Pathology

country: New Zealand

institute: University of Otago, Dunedin School of Medicine

summary: Transcriptional profiling of 4 SCCO tumors compared to age-matched normal ovary to investigate underlying tumor biology and potential therapeutic targets.

overall_design: RNA from 4 SCCO fresh-frozen tumors were individually hybridized to a pool of 2 commercial normal ovary RNA on Agilent 44K v2 human gene expression microarrays

middle: E

first: Megan

last: Russell

first: Pilar

last: Ramos


status: Public on Jan 16 2014

city: Xiamen

first: Shubin

last: Gao

address: Chengzhi building 110,Xiang'an South Road

department: Basic Medical Sciences

country: China

institute: Medical College,Xiamen University

summary:
Polycomb group (PcG) proteins including EZH2, SUZ12 ,BMI1,CBX8 and so on, which specifically catalyze trimethylation of histone 3 lysine 27 (H3K27me3), and methylated H3K27 can be recognized by other specific binding proteins to compress chromatin structure, leading to the transcriptional repression of the target genes. To explore a potential functional implication of PcG components in HCC, we stably transfected HepG2 cells with either vectors or constructs expressing shRNA that specifically targets EZH2, SUZ12, BMI1, or CBX8. A cDNA microarray analysis was performed on shRNA KDs of EZH2, SUZ12, BMI1, or CBX8 HepG2 cells.
To obtain a broader understanding of the molecular network of PcG in HCC, the whole genome microarray expression profiling was performed on shRNA KDs of EZH2, SUZ12, BMI1, or CBX8 HepG2 cells.

overall_design: Comparison of gene expression results from shRNA KDs of EZH2, SUZ12, BMI1 or CBX8 HepG2 cells.

first: Shu-bin

first: Bin

last: Xu


title: Identification of heat stress-targets of translational control by large scale analysis of Arabidopsis trancriptome and translatome.

status: Public on Jan 22 2014

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

type:
Expression profiling by array
Other

summary:
Heat stress is one of the most prominent and deleterious environmental threads affecting plant growth and development. Upon high temperatures, plants launch specialized gene expression programs that promote stress protection and survival. These programs involve global and specific changes at the transcriptional and translational levels. However the coordination of these processes and their specific role in the establishment of the heat stress response is not fully elucidated.
In this report, we have carried out a genome-wide analysis to simultaneously monitor the individual changes in the transcriptional and translational mRNA levels of Arabidopsis thaliana seedlings after the exposure to a heat shock stress. Our results demonstrated that, superimposed to transcription, translation exerts a wide but dual regulation of gene expression. For the majority of mRNAs, translation is severely repressed, causing a decreased of 50% of the association of the bulk of mRNAs to polysomes. However, some relevant mRNAs involved in different aspects of homeostasis maintenance follow a differential pattern of translation. Analysis of the sequence of the differentially translated mRNAs unravels that some features, like the 5´UTR G+C content and the cDNA length, may take part in the discrimination mechanisms for mRNA polysome loading.  Among the differential translated genes stand out master regulators of the stress response, highlighting the main role of translation in the early establishment of physiological response of plants to elevated temperatures.

overall_design: In total 8 ATH1 Affymetrix GeneChips were hybridized with all combinations of two factors: total mRNA/polysome-bound-RNA; 22ºC/38ºC. Two biological replicates per sample type were performed.

first: Emilio

last: Yangüez

first: Ana

last: Castro-Sanz

first: Nuria

last: Fernández-Bautista

middle: C

first: Mar

last: Castellano


title: The purine metabolite allantoin enhances abiotic stress tolerance through synergistic activation of abscisic acid metabolism

city: Higashi-Hiroshima

first: Atsushi

last: Sakamoto

address: 1-3-1 Kagamiyama

department: Graduate School of Science

country: Japan

institute: Hiroshima University

summary: Purine catabolism is regarded as a housekeeping function that remobilizes nitrogen for plant growth and development. However, emerging evidence suggests that certain purine metabolites might contribute to stress protection of plants. Here, we show that in Arabidopsis, the intermediary metabolite allantoin plays a role in abiotic stress tolerance via activation of abscisic acid (ABA) metabolism. The aln loss-of-function of ALN, encoding allantoinase, results in increased allantoin accumulation, genome-wide up-regulation of stress-related genes, and enhanced tolerance to drought-shock and osmotic stress in aln mutant seedlings. This phenotype is not caused by a general response to purine catabolism inhibition, but rather results from a specific effect of allantoin. Allantoin activates ABA production both through increased transcription of NCED3, encoding a key enzyme in ABA biosynthesis, and through post-translational activation via high-molecular-weight complex formation of BG1, a ß-glucosidase hydrolyzing glucose-conjugated ABA. Exogenous application of allantoin to wild-type plants also activates the two ABA-producing pathways that lead to ABA accumulation and stress-responsive gene expression, but this effect is abrogated in ABA-deficient and BG1-knockout mutants. We propose that purine catabolism functions not only in nitrogen metabolism, but also in stress tolerance by influencing ABA production, which is mediated by the possible regulatory action of allantoin.

overall_design: Compared analysis of the transcriptomes of 2-week-old Arabidopsis seedlings from an allantoin-accumulating mutant genotype versus wild type background Col-0 (2 independent biological replicates per genotype). The allantoin-accumulating mutant in Col-0 background was the aln-1 mutant allele in allantoinase (ALN) (abbreviated as aln).

first: Shunsuke

last: Watanabe


title: Selective mRNA sequestration by OLIGOURIDYLATE BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis

status: Public on Jan 13 2014

city: Riverside

first: Reed

middle: S

last: Sorenson

state: CA

address: 4126 Genomics Bldg

department: Botany and Plant Science

country: USA

institute: University of California, Riverside

summary: Low oxygen stress dynamically regulates the translation of cellular mRNAs as a means of energy conservation in seedlings of Arabidopsis thaliana. Most of the highly hypoxia-induced mRNAs are recruited to polysomes and actively translated, whereas other cellular mRNAs become translationally inactive and are either targeted for stabilization or degradation. Here we identify the involvement of OLIGOURIDYLATE BINDING PROTEIN 1 (UBP1), a triple RNA Recognition Motif protein, in dynamic and reversible aggregation of translationally repressed mRNAs during hypoxia. Mutation or downregulation of UBP1C interferes with seedling establishment and reduces survival of low oxygen stress. By use of messenger ribonucleoprotein immunopurification, we show that UBP1C constitutively binds a subpopulation of mRNAs characterized by U-rich 3’-untranslated regions under normoxic conditions. During hypoxia, UBP1C association with non-U-rich mRNAs is enhanced concomitant with its aggregation into microscopically visible cytoplasmic foci, referred to as UBP1 stress granules (SGs). This UBP1C-mRNA association occurs as global levels of protein synthesis decline. Upon reoxygenation, rapid UBP1 SG disaggregation coincides with the return of the stabilized mRNAs to polysomes. The mRNAs that are highly induced and translated during hypoxia largely circumvent UBP1C sequestration. Thus, UBP1 is established as a component of dynamically assembled cytoplasmic mRNPs that sequester mRNAs that are poorly translated during a transient low energy stress.

overall_design: Immunoprecipated RNA associated with Arabidopsis UBP1C (IP) was compared with total cellular RNA from light (L), mock dark (D), 2 h hypoxia, and 2 h hypoxia + 20 min reoxygenation treated samples with duplicate hybridizations to the Affymetrix ATH1 Genechip array.

first: Julia


title: Global profiling of vitamin E deficient mutant vte2 and wild type during low temperature treatment

status: Public on Jan 14 2014

city: East Lansing

first: Dean

last: DellaPenna

state: MI

address: 603 Wilson Road

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary:
Tocopherols (vitamin E) are lipid-soluble antioxidants produced by all plants and algae, and many cyanobacteria, yet their functions in these photosynthetic organisms are still not fully understood. We have previously reported that the vitamin E deficient 2 (vte2) mutant of Arabidopsis thaliana is sensitive to low temperature (LT) due to impaired transfer cell wall (TCW) development and photoassimilate export, associated with massive callose deposition in transfer cells of the phloem. To further understand the roles of tocopherols in LT induced TCW development we compared the global transcript profiles of vte2 and wild type leaves during LT treatment.
Tocopherol deficiency had no significant impact on global gene expression in permissive conditions, but significantly affected expression of 77 genes after 48 hours of LT treatment. In vte2 relative to wild type, genes associated with solute transport were repressed, while those involved in various pathogen responses and cell wall modifications, such as GLUCAN SYNTHASE LIKE genes (GSL4 and GSL11), were induced.

overall_design: The vte2 LT experiment comprised 18 chips in a factorial design. vte2 and Col plants were grown under permisive conditions for four weeks,  Three independent biological replicates were conducted for Col and vte2 at each of the three time points during LT treatment. 0h represent when they are physiologically and biochemically indistinguishable, and at two time points of LT treatment (48 h, 120 h) selected based on our previous timecourse study of the physiological and biochemical changes of vte2 and Col during LT treatment (Maeda et al., 2006). After 48 h of LT, vascular callose deposition is strongly induced and photoassimilate export capacity is significantly lower in vte2 compared to Col, though the visible whole plant phenotypes and soluble sugar accumulation between the two genotypes do not differ (Maeda et al., 2006). The 120 h LT timepoint represents a relatively late response of vte2 when soluble sugars are significantly higher and callose deposition is even more extensive and wide spread in vte2 (Maeda et al., 2006). Thus the 48 h time point should allow identification of early responses to tocopherol deficiency that are distinct from later, pleiotropic responses resulting from the strongly elevated sugar levels in vte2 after 120 h of LT. The 0 h time point represents the absence of LT treatment (see method) and serves as a critical treatment control.   7°C. Three biological replicated the 9 to 11th oldest rosetta leaves from three independent plants were harvested together into a tube filled with liquid nitrogen one hour into the light cycle after 48 and 120 hours of LT-treatment or without LT-treatment (referred to as 0 hour LT treatment).

first: Wan

last: Song

first: Hiroshi

last: Maeda


title: Identification of target genes of translation-dependent signalling in Arabidopsis

status: Public on Jan 31 2014

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary:
Changes ins organellar gene expression trigger retrograde signalling. Prolyl-tRNA synthetase (PRORS1) is located in chloroplasts and mitochondria. Thus, prors1-2 mutants are impaired in chloroplast and mitochondrial gene expression.
The effects of the prors1-2 mutation on the global transcriptome were investigated with microarray analyses.

overall_design: RNA was extracted from Col-0 (WT, 4-weeks-old) and prors1-2 (38-d-old) leaves of the same developmental stage

first: Dario

last: Leister


title: PAB/WT polysome loading and transcript levels (Arabidopsis thaliana)

status: Public on Jan 01 2014

city: Knoxville

first: Albrecht

middle: G

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

institute: The University of Tennessee

summary:
To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP.
RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels.  We used Affymetrix ATH1 microarrays.

overall_design: Each plant sample was analyzed for the mRNA abundance in total mRNA (T), polysomal mRNA (PL), and nonpolysomal mRNA (NP). Four biological replicates were collected for polysomes and three for total RNA. The pab2 pab8 double mutant was compared with wild type.

first: Byunghoon

last: Kim


title: Ovarian Cancer: 19 ovarian tumors of diverse histologic type vs. pool of all 19 tumors.

first: Heather

last: Cunliffe

summary: Transcriptional profiling of 19 ovarian tumors of 5 distinct histologic types (serous, endometrioid, clear cell, mucinous and small cell), to investigate similar and distinct biology associated with each histologic type.

overall_design: RNA from fresh-frozen ovarian tumor samples were individually hybridized to a pooled RNA from all 19 tumor cases

first: Pilar

last: Ramos

first: Megan

last: Russell


title: rpl24b/WT polysome loading and transcript levels (Arabidopsis thaliana)

summary:
To understand the contribution of the RPL24B protein, a component of the large 60S ribosomal subunit, to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and the rpl24b/stv1-1 T-DNA insertion mutant.
RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels.  We used Affymetrix ATH1 microarrays.

overall_design: Each plant sample was analyzed for the mRNA abundance in total mRNA, polysomal mRNA, and nonpolysomal mRNA. Three biological replicates were collected. The rpl24b mutant was compared with wild type.


title: Expression data from Arabidopsis leaves

city: Jinan

first: Mengcheng

last: Wang

address: 27 Shandanan Road

department: School of Life Science

institute: Shandong University

summary:
Flavonols are a class of flavonoids. Unlike other classes of flavonoids, flavonols strongly accumulate in guard cells, but the role of their accumulation in guard cells is still unclear so far.The overexpression of TaFLS1, a flavonol synthase gene from wheat, improves flavonol content in guard cells of Arabidopsis, while the mutant fls1-3 of Arabidopsis AtFLS1 reduces the content. Both the increase of flavonols by TaFLS1 overexpression and the decrease in fls1-3 change stomatal apeture, showing the association between flavonols and stomatal movements.
We used microarrays to detail the global programme of gene expression underlying both the increase and decrease of flavonol content and identified possible mechanism of flavonols-mediated stomatal movement.

overall_design: Arabidipsis Col-0, TaFLS1 overexpression lines, and fls1-3 were used for analysis. Leaves of six-week old Arabidopsis seedlings grown in soils under the regime of a 16 h photoperiod at 22°C and 60% relative humidity were sampled, and RNA was extracted for microarray analysis. Each of Arabidopsis lines has three replicates.

first: Wang

last: Mengcheng

first: Li

last: Wei

first: Qian

last: Jiajia

first: Xia

last: Guangmin


title: Expression data from Arabidopsis GR-REVOLUTA and KANADI1-GR transgenic seedlings

status: Public on Dec 31 2013

city: Stanford

first: Brenda

last: Reinhart

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

summary: The REVOLUTA and KANADI1 transcription factors act in opposite directions to control polarity in Arabidopsis. By analyzing mRNA profiles following activation of REVOLUTA or KANADI1 proteins we identified genes regulated by both transcription factors, focusing on those regulated in opposite directions.

overall_design:
To coordinate transcriptional responses for microarray analysis, we constructed transgenic seedlings with the REV or KAN1 transcription factor fused to a glucocorticoid receptor (GR) domain. The GR domain tethers the transcription factor in the cytoplasm, and treatment with dexamethasone (DEX) allows movement into the nucleus. Transgenic seedlings and wild-type controls were grown simultaneously in liquid culture, treated with dexamethasone for 0min, 30min, 60min, or 120min, and total RNA was extracted and hybridized to Affymetrix arrays.
Treatment: Dexamethasone
Biological replicates

middle: J


title: Study of expression changes during RPS4-mediated resistance in Arabidopsis using a temperature-inducible system

status: Public on Dec 30 2013

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

summary:
Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The Arabidopsis Toll-related intracellular receptor RPS4 operates inside nuclei to trigger resistance to Pseudomonas bacteria expressing AvrRps4 and defence gene reprogramming through the stress response regulator, EDS1.
In this immune response, RPS4 cooperates genetically with RRS1 encoding a nuclear TIR-NB-LRR receptor with an additional C-terminal ‘WRKY’ DNA-binding domain.
Using transgenic Arabidopsis plants constitutively expressing RPS4 (35S:RPS4), an EDS1-dependent immune response can be turned on rapidly and synchronously in leaf cells after a switch from high (28°C) to moderate (19°C) temperature.
In order to determine the relative contributions of RRS1 and EDS1 to temperature-conditioned 35S:RPS4-HS transcriptional reprogramming, we performed gene expression microarray analysis of 35S:RPS4-HS, 35S:RPS4-HS rrs1-11 and 35S:RPS4-HS eds1-2 leaf mRNAs before and after temperature shift.

overall_design:
We used transgenic Arabidopsis plants over-expressing RPS4 in EDS1 WT,  eds1-2 or rrs1-11 mutant backgrounds.
35S:RPS4, 35S:RPS4 eds1-2 and 35S:RPS4 rrs1-11 plants were grown at 28°C for 3.5 weeks, and subsequently shifted to 19°C. Samples were collected before shift (0h) and 2, 8 and 24h after shift, in triplicates.

first: Katharina

last: Heidrich

first: Jane

last: Parker

first: Servane

last: Blanvillain-Baufumé

first: Bruno

last: Huettel


title: ATP effect on Arabidopsis roots

status: Public on Jan 27 2014

city: Columbia

first: Gary

last: Stacey

state: MO

address: 1201 East Rollins street C. Bond Life Sciences center R202

department: Division of Plant Sciences

institute: University of Missouri

summary: Extracellular adenosine 5’-triphosphate (ATP) is a signaling molecule. To define the global transcriptional response to ATP, we performed DNA microarray analysis using RNA derived from wild-type (Col-0) Arabidopsis and the dorn1-1 mutant, Lectin receptor kinase I.9 (At5g60300) carrying a EMS point mutation, seedlings after 100 μM ATP.

overall_design: 12 samples ( 2 genotypes, 2 treatments, 3 biological replicates)

first: Jeongmin

last: Choi

first: Kiwamu

last: Tanaka


title: Role of NPR1 in SA mediated transcription

status: Public on Dec 24 2013

city: Lucknow

first: Samir

last: Sawant

state: U.P, India

address: Rana Pratap Marg

department: Centre of Plant Molecular Biology

country: India

institute: National Botanical Research Institute

summary: Affymetrix expression analysis was used to validate the role of NPR1 in SA mediated transcription.

overall_design: The RNA of col-0 and npr1-1 mutant were isolated after 24hr water and SA treatment.The ATH1 gene chip was used for expression analysis.

first: Sumit

last: Bag

first: Mala

last: Singh

first: Archana

last: Bhardwaj


title: Genome wide identification of SHYG early target genes

status: Public on Dec 29 2013

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary: Global transcriptome patterns were performed using SHYG-IOE-5h (5h after Estradiol and Mock treatment)

overall_design: To identify genes more rapidly responding to elevated SHYG , we perfromed gene expression profiling (Affymetrix) upon 5h Est treatment of SHYG-IOE plants.

first: Mamoona

last: Rauf


title: Expression data from MTF mutant roots

status: Public on Nov 14 2013

city: West Lafayette

first: Nagesh

last: Sardesai

state: IN

address: 201 W. State St.

department: Biological Sciences

institute: Purdue University

summary:
Mutation of MTF in Arabidopsis increases Agrobacterium-mediated transformation susceptibility. Being a putative transcription factor, different genes controlling transformation may be regulated by MTF.
We used microarrays to detail the global programme of gene expression and to identify genes that play a role in transformation.

overall_design: Root samples from mutants MTF1-1 and MTF1-4, along with the wild-type, Col0, were collected after 12 days of growth in B5 liquid medium. RNA was extracted from three biological replicates, with 20 plants in each replicate, and used for hybridization to Affymetrix ATH1 microarrays.

first: Stanton

last: Gelvin


title: WWOX interacts with SMAD3 and modulates its transcriptional activity in breast cells

status: Public on Nov 28 2013

city: Smithville

first: C. Marcelo

last: Aldaz

address: POB 389

department: Molecular Carcinogenesis

institute: The University of TX M.D. Anderson Cancer Center

summary: WWOX expression is lost during tumor progression in many human malignancies including breast cancer. To understand the effects of loss of WWOX expression we analyzed the consequences of its silencing in normal human breast cells (MCF10F). WWOX silencing led to the formation of larger cell colonies, increased cell motility and decreased cell attachment.  WWOX silenced cells demonstrated deregulated expression on genes involved in cell cycle, DNA damage response and cell motility.  We detected an enrichment of targets activated by the SMAD3 transcription factor. Most notably expression of ANGPTL4, FST, PTHLH and SERPINE1 were all significantly increased upon WWOX silencing. Upregulation of these genes can be reversed by re-expressing WWOX in the previously silenced cells thus suggesting an inverse correlation between WWOX protein expression and SMAD3 transcriptional activity. Importantly, we demonstrate that WWOX physically interacts with SMAD3 protein via WW domain 1, that WWOX expression dramatically decreases SMAD3 occupancy at the ANGPTL4 and SERPINE1 promoters and significantly quenches activation of a TGFβ responsive reporter (3TP-LUX). Furthermore, WWOX expression leads to intracellular redistribution of SMAD3 protein levels redirecting protein availability from the nuclear to the cytoplasmic compartment. Interestingly, meta-analysis of gene expression breast cancer datasets indicate that WWOX and ANGPTL4 expression, encoding a secreted protein of key relevance in breast cancer lung metastatic cells, are inversely correlated and the WWOXlo/ANGPTL4hi cluster of tumors are enriched in triple-negative and basal-like sub-types.   In summary, we demonstrate that WWOX modulates SMAD3 signaling in breast cells via direct WW-domain binding and potential cytoplasmic sequestration of SMAD3 protein. Since loss of WWOX expression increases with breast cancer progression and it behaves as an inhibitor of SMAD3 transcriptional activity these observations may help explain, at least in part, the paradoxical pro-tumorigenic effects of TGFβ signaling in advanced breast cancer.

overall_design: We compared two independent shRNAs: shWWOX-A and shWWOX-B with 3 biological replicates each one, targeting different regions of the WWOX transcript as a means of ruling out any potential off-target effects.

first: Claudio


title: Microarray Analysis of myb80 versus Wild-Type Anthers

status: Public on Dec 05 2013

city: Bundoora, Melbourne

first: Song

last: Li

state: VIC

address: Kingsbury Dr

department: Botany

country: Australia

institute: La Trobe University

summary:
Arabidopsis thaliana MYB80 (formerly MYB103) is expressed in the tapetum and microspores between anther developmental  stages 6 and 10. MYB80 encodes a MYB transcription factor that is essential for tapetal and pollen development. In order to identify the genes regulated by MYB80, microarray  technology was employed to analyze the expression levels of genes  that were differentially regulated in the myb80 mutant and wild-  type anthers.
Plant Cell 23:2209–2224 (2011)

overall_design: three mutant chips vs three wild-type chips

first: Huy

last: Phan

first: Sylvana

last: Iacuone

first: Roger

middle: W

last: Parish


title: dreb1a expression data from Arabidopsis flowers under drought stress

status: Public on Nov 06 2013

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

summary: We used microarray analysis to examine transcriptomic changes upon dreb1a under drought, identifying hundreds of genes that potentially function downstream of DREB1A and mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles.

overall_design: DREB1a mutant (CS872453) were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest. Unopened flower samples were collected from drought treated plants, at day 3, 4, 5.

last: Su

first: Hong

last: Ma


title: Gene expression data from Arabidopsis C24 wild-type and ros1-1 seedlings.

status: Public on Nov 23 2013

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

summary: We carried out a microarray experiment by using Affymetrix Arabidopsis ATH1 Genechips in order to identify genes that show reduced expression in ros1-1 plants.

overall_design: 2 samples examined: C24 wild-type and ros1-1 mutant (in C24 background).

first: Jianhua

first: Byeong-ha

last: Lee

first: Kai

last: Tang


title: Transcript profiling of Arabidopsis epiF3 plants

status: Public on Dec 01 2013

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

summary: Arabidopsis msh1 mutants display developmental reprogramming (dr) phenotypes, include reduction in growth, enhanced branching, and delayed maturation and flowering time. MSH1-epi lines were derived by crossing msh1 lines with Col-0 wild type, followed by selection for homozygous MSH1/MSH1 F2 plants and serial self-pollination. MSH1-epiF3 plants displayed phenotypic variation in plant growth, showing enhanced growth, larger rosette diameter, thicker floral stems and earlier flowering time. We carried bisulfite sequencing and uncover the methylome changes accompany the heritable MSH1-epi phenotypes that condition dramatic variation in plant growth.

overall_design: Arabidopsis Col-0 wild type and epiF3 plant tissues were collected for RNA extration and hybridization on Affymetrix.

first: Sally

last: Mackenzie


title: Transcript profiling of ERF115 transgenic Arabidopsis thaliana

status: Public on Nov 04 2013

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: This experiment was set up in order to identify the (direct) transcriptional targets of the Ethylene Response Factor 115 (ERF115) transcription factor. Because ERF115 expression occurs in quiescent center (QC) cells and strong effects on the QC cells were observed in ERF115 overexpression plants, root tips were harvested for transcript profiling in order to focus on root meristem and QC specific transcriptional targets.

overall_design: Wild-type (Col-0 ecotype), erf115 mutant (SALK_021981) and ERF115 overexpressing (p35S:ERF115 ORF) root tips (three replicates each) were harvested and subjected to transcript profiling, using the Col-0 samples as control reference.

first: Jefri

last: Heyman

first: Sandy

last: Vanderauwera

first: Lieven

last: De Veylder


title: Activation of auxin signalling counteracts photorespiratory hydrogen peroxide dependent cell death

status: Public on Nov 02 2013

city: Gent

first: Pavel

last: Kerchev

address: Technologie Park 927

department: Plant Systems Biology

summary:
The high metabolic flux through photorespiration constitutes a significant part of the carbon cycle. Although, the major enzymatic steps of the photorespiratory pathway are well characterized, little information is available on the functional significance of photorespiration beyond carbon recycling. Particularly important in this respect is the peroxisomal catalase activity which removes photorespiratory H2O2 generated during the oxidation of glycolate to glyoxylate, thus maintaining the cellular redox homeostasis governing the perception, integration and execution of stress responses. By perfroming a chemical screen, we identified 34 small molecules that alleviate the negative effects of photorespiration in Arabidopsis thaliana mutants lacking photorespiratory catalase (cat2). The chlorophyll fluorescence parameter photosystem II maximum efficiency (Fv'/Fm') was used as a high-throughput readout. The most potent chemical that could rescue the photorespiratory phenotype of cat2 is a pro-auxin that contains a synthetic auxin-like substructure belonging to the phenoxy herbicide family which can be released in planta. The naturally occurring indole-3-acetic acid (IAA) and other chemically distinct synthetic auxins also inhibited the photorespiratory-dependent cell death in cat2 mutants, implying a role for auxin signaling in stress tolerance.
We used global transcriptome profiling to characterize the effect of a novel pro-axin structure (2-(2,4-dichlorophenoxy)-N-[4-(isobutyrylamino)-3-methoxyphenyl]propanamide) on Arabidopsis Col0 seedlings

overall_design: 2-(2,4-dichlorophenoxy)-N-[4-(isobutyrylamino)-3-methoxyphenyl]propanamid (5 μM) was added to seven-day-old Arabidopsis Col0 seedlings grown in a 96-well plate setup. Control plants were treated with solvent (DMSO) only. RNA was extracted 24 h following chemical addition.

first: Frank

last: Van Breusegem


title: Expression data from Arabidopsis wild-type, sicy-192, and sicy-192 gun1-101 plants

status: Public on Sep 14 2013

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

institute: Shimane University

summary:
Plastid gene expression (PGE) acts as a signal that regulates the expression of photosynthesis-associated nuclear genes (PhANGs) via GENOMES UNCOUPLED1 (GUN1)-dependent retrograde signaling. We recently isolated Arabidopsis sugar-inducible cotyledon yellow-192 (sicy-192), a gain-of-function mutant of plastidic invertase (INV-E), and showed that following the treatment of this mutant with sucrose, the expression of PhANGs decreased while that of nitrate reductase 1 (NIA1) increased. Plastid-encoded RNA polymerase (PEP)-dependent PGE was markedly suppressed in the sicy-192 mutant by the sucrose treatment.  A double mutant of sicy-192 and gun1-101, a null mutant of GUN1, revealed that metabolic perturbation in the sucrose-treated sicy-192 mutant was, at least in part, dependent on GUN1.
To confirm whether there is a relationship between plastid sugar metabolism and nuclear gene expression, we performed a microarray analysis using Suc-treated 3 genotypes consisting of wild-type, sicy-192, and sicy-192 gun1-101 plants.

overall_design: Wild-type, sicy-192, and sicy-192 gun1-101 plants were grown on MS medium containing 100 mM sucrose in a growth chamber kept at 25°C during 16 h of light (100 µmol/m2/s) and at 22°C during 8 h of darkness for 4 days. At 4 days of age, cotyledons were collected as samples for microarray analysis.

first: Kazuya

last: Yoshimura

first: Shigeru

last: Shigeoka


title: affy_ath_2012_04-Functional characterization of JMJ24, a putative histone demethylase

status: Public on Aug 01 2013

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary: affy_ath_2012_04 - affy_ath_2012_04 - Epigenetic informations include histone post-translational modifications such as acetylation and methylation. The jumoni proteins can remove the methyl group from lysine or arginine residues of histones. The aim of this project is to compare gene expression levels between mutants of two jumonji genes and wild type at seedling stage (12 d old).-- Seeds were sterilized in bleach, washed with ethanol, dried, dispersed on Murashige and Skoog (MS) 0.5X containing 2% sucrose and kept 5 days at 4°C. - After 12 days of growth under a cool white fluorescent light (120 μmol m-2 s-1) and long day conditions (16h of light) in a growth chamber, the plants are harvested and stored at -80°C. -The RNA are extracted with the RNA Plant NucleoSpin (Machery-Nagel), quantified with Nanodrop and visualised on agarose gel. The samples are stored at -80°C.

overall_design: 8 arrays - ATH1; gene knock out

first: Stephanie

last: Huguet

first: Laure

last: Audonnet

first: Natalia

last: Silva

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: affy_ath_2012_05-Arabidopsis Ubiquitin-Like Proteases characterization

status: Public on Sep 01 2013

summary: affy_ath_2012_05 - affy_ath_2012_05 - The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.-Seeds were stratified for 3 days at 4ºC in the dark. Afterwards, seeds were surface sterilized, sown onto MS media and grown at 23ºC, with 100 µE light condition, in long days (16h L/8h D). Each MS plate was dived in four, corresponding to a genotype (Col, AB, SIZ1 or SAB), and 10 seeds were sown per genotype. After 10 days, seedlings were collected and frozen in liquid nitrogen. Each replicate was made of ~40 seedlings coming from 4 different MS plates. Frozen plant material was grounded in an eppendorf tube using a mini pestle. RNA was extracted using RNeasy Plant Mini kit (QIAGEN cat.74904), following the manufacturer instructions (QIAGEN, Hilden, Germany). The RNA samples were DNase treated (Recombinant DNase I, Takara Biotechnology, Dalian, China) and subsequently cleaned by column using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany).

overall_design:
12 arrays - ATH1; gene knock out
Col [wild type]
AB [knock out / insertional mutagen /T-Dna]
SIZ1 [knock out / insertional mutagen /T-Dna]
SAB [knock out / insertional mutagen /T-Dna]

first: Eduardo-r

last: Bejarano

first: Pedro-Humberto

last: Castro


title: Expression array from mature leaves in the genus Arabidopsis

status: Public on Sep 29 2013

city: Canberra

first: Ryo

last: Fujimoto

state: ACT

address: Cnr Clunies Ross St & Barry Dr

institute: CSIRO

summary: We compared the expression between inter-specific hybrids (A. thaliana-A. lyrata, A. thaliana-A. halleri) and mid parent values of their parental lines.

sample_organism: Arabidopsis thaliana x Arabidopsis lyrata

sample_organism: Arabidopsis thaliana x Arabidopsis halleri subsp. gemmifera

overall_design: Mature leaves in A. thaliana (Col), A. lyrata ssp. lyrata, A. halleri ssp. gemmifera and interspecific hybrid between A. thaliana and A. lyrata and between A. thaliana and A. halleri


title: Epithelial Ovarian Cancer Cells: Control vs. miR-506 Transfected

city: HOUSTON

first: wei

last: zhang

state: TX

address: 1515 Holcombe Blvd, Unit 85

department: Pathology

institute: M. D. Anderson Cancer Center

summary: Transcriptional profiling of untreated ovarian cancer cells and ovarian cancer cells miR-506 transfected with 48hours.

overall_design: Two-condition experiment, control vs. miR-506 treated cells. One replicate per array.

first: Zhang

last: Wei


title: Comparison of gene expression in Arabidopsis trichome between gtl1-1 mutant and wild type

city: Columbus

first: Kengo

last: Morohashi

state: OH

address: 1060 Carmack Rd

department: Molecular Genetics

institute: The Ohio State University

summary: Total RNA from trichomes of fifth and sixth rosette leaves of three-week-old wild-type and gtl1-1 mutants (Figure 3B) were extracted. We found a total number of 1,759 genes, corresponding to 1,694 probes on the ATH1 chip, that show differential expression of at least 1.3-fold. Out of these 1,694 genes, 47.2% are positively regulated and 52.8% are negatively regulated by GTL1.

overall_design: Compared gene expressions in fifth and sixth rosette leaves of three-week-old wild-type and gtl1-1 mutants

first: Christian

last: Breuer

first: Erich

last: Grotewold

first: Keiko

last: Sugimoto


title: HOXB7 mRNA is overexpressed in pancreatic ductal adenocarcinomas and its knockdown induces cell cycle arrest and apoptosis.

status: Public on Jul 26 2013

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary: In order to determine the role of HOXB7 gene in cell lines derived from pancreatic ductal adenocarcinoma (MIA PaCa-2 e Capan-1), we performed its silencing utilizing the technique of RNA interference (RNAi). Total RNA derived from the inhibition as well as from parental cells was quantified in Bioanalyzer (Agilent,Santa Clara, CA, USA)  and  employed in the Agilent platform (4x44K). Proceeded with the guidelines of the One Color Microarray-Based Gene Expression Protocol (Agilent) and with the use of the Agilent Low Input Quick Amp Labeling Kit. HOXB7 knockdown elicited the modulation of several biological processes, especially in the MIA Paca-2 cell line, such as proteasomal ubiquitin-dependent catabolic process, synthesis of amines and cell cycle. Moreover, it showed induction of apoptosis and reduction in cell proliferation by flow cytometry and MTT assay, respectively.  In this context, HOXB7 represents another component associated with the extensive network of molecules involved in the tumorigenesis of pancreatic cancer and could be a promising target for future biologic therapies.

overall_design: The procedure was performed in duplicate for both cell lines, which were sorted into treated and untreated with RNAi.

first: Thais

last: Chile

first: Maria

middle: Z

last: Fortes

last: Correa-Giannella

first: Helena

middle: P

last: Brentani

first: Durvanei

last: Augusto

middle: D

first: Vanessa

middle: R

last: de Paula

first: Marcia

last: Kubrusly

first: Estela

last: Novak

first: Ricardo

last: Giorgi


title: Over-expression of bHLH122 in Arabidopsis

status: Public on May 07 2013

city: Haidian District,. Beijing

first: Wenxue

last: LI

state: Beijing

address: 12 Zhong-guan-cun South St.

department: Chinese Academy of Agricultural Sciences

institute: Wenxue LI

summary:
bHLH122 could be induced by salt, osmotic and drought stress except ABA, the transgentic Arabidopsis were more tolerant to abiotic stresses, such as drought and salt. What's more, in the overexpression plants, the endogenesis ABA contents were higher than WT. We found there existed an interaction between bHLH122 and CYP707A3 by virtue of EMSA and ChIP assays.
We wanted to learn more about the molecular mechanism of bHLH122 and to explore what had changed in the over-expression plant through Genechips.

overall_design: Two independent overexpression bHLH122 lines and WT Arabidopsis were chosen to  RNA extraction and hybridization on Affymetrix microarrays. The plants were sowed on MS  medium after 96 h stratification,then transferred into soil after one weeks. After 2 weeks, collected the shoot above the soil and extracted RNA, digested by DNaseⅠand hybrid on Affymetrix microarrays.

first: Wen-xue

last: Li


title: Cytosolic Fe-S cluster assembly-deficient mutant, nar1 and nbp35 mutant seedling

status: Public on May 01 2013

city: Nara

first: Miyuki

last: Nakamura

address: 8916-5 Takayama

institute: Nara Institute of Science and Technology

summary:
Expression profiling of two-weeks-old wild type, nar1-4/- and nbp35-3/-  mutant seedlings. The cytosolic Fe -S cluster assembly pathway is involved in cytosolic and nucleus Fe-S protein maturation.
The nar1 mutant was identified by the screeing for abnormal transcription feature in endosperm.We performed genome-wide transcriptional profiling of weak allele nar1-4/- using microarrays to estimate whether the  cytosolic Fe -S cluster assembly could affect on the transcriptional profile even in vegetative tissues.

overall_design: Two biological replicate were performed using two weeks seedling of wild type, nar1-4/- and nbp35-3/-. RNA was extracted using the RNeasy mini kit(QIAGEN).

first: Nakamura

last: Miyuki


title: Gene expression profiles in roots of hydroponically grown Arabidopsis treated with 0.125 mM gold

city: York

first: Elizabeth

middle: L

last: Rylott

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: University of York

summary: Gold is widely considered to be a biologically inert element; however, it can elicit a profound biological response in plants. Plants can be exposed to significant levels of this precious metal in the environment from naturally occurring sources, as the result of mining activities or more recently resulting from the escalating use of nanoparticles in industry. In this microarray study we have investigated the gene expression response of Arabidopsis thaliana (Arabidopsis) to gold. Although the uptake of metal cations by plant transporters is well characterised, little is known about the uptake of gold, which exists in soil predominantly in a zero-valent state (Au0). We used this study to monitor the expression of candidate genes involved in metal uptake and transport. These show the down-regulation of a discreet number of genes known to be involved in the transport of copper, cadmium, nickel and iron.

overall_design: The experiment comprised three replicate jars of hydropnically-grown Arabidopsis, each treated with 0.125 mM KAuCl4, and three replicate jars of hydropnically-grown Arabidopsis which were treated with water only.


title: Effects of bacterium Burkholderia phytofirmans PsJN in Arabidopsis

status: Public on May 31 2013

city: Santiago

first: Andrea

last: Vega

address: Vicuña Mackenna 4860

department: Ciencias Vegetales

country: Chile

institute: Pontificia Universidad Catolica de Chile

summary:
Plant growth promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short- term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization.
Transcriptional profiles were determined by microarray analysis (Affymetrix ATH1 Genome Array) in Arabidopsis thaliana plants inoculated with the PGPR bacterial model Burkholderia phytofirmans PsJN

overall_design: Arabidopsis seeds were sown on square Petri dishes with half strength Murashige and Skoog medium (MS) 0.8% agar, and inoculated or not (control) with strain PsJN. To assess the effect of inactivated bacteria, an inoculum was heated at 95°C for 20 min and then was used at the same dilution.Three biological replicates, consisting of ten plantlets of 13 days after sowing (DAS) each, for control and strain PsJN treatments, were used for global gene expression.

last: Poupin

first: Tania

last: Timmermann

first: Ana

last: Zuñiga

first: Bernardo

last: González


title: Three MYB Transcription Factors Control Pollen Tube Differentiation Required for Sperm Release

status: Public on Jun 18 2013

city: Providence

first: Alexander

middle: Rivinus

last: Leydon

state: RI

address: 60 Olive Street

department: MCB

institute: Brown University

summary:
Flowering plants have immotile sperm that develop within pollen and must be carried to female gametes by a pollen tube. The pollen tube engages in molecular interactions with several cell types within the pistil and these interactions are essential for successful fertilization. We identified a group of three closely related pollen tube-expressed MYB transcription factors (MYB97, MYB101, MYB120), which are required for proper interaction of the pollen tube with the female gametophyte. These transcription factors are transcriptionally induced during growth in the pistil. They regulate a transcriptional network leading to proper differentiation and maturation of the pollen tube, promoting proper pollen tube-ovule interactions resulting in sperm release and double fertilization.
We used microarrays to discover  genes regulated by the transcription factors MYB97, MYB101 and MYB120 in pollen tubes growing through the pistil at 8 hours after pollination.

overall_design: Pistils were collected from ms1 (Male Sterile 1) pistils that were unpollinated, or pollinated with either wild type (Col-0) pollen or myb triple mutant (myb97-1, myb101-4, myb120-3) pollen for 8 hours. We sought to examine transcriptional changes that were taking place in pollen tubes before they reached ovules in wild type pollen tubes, and what portion of this transcriptional regulation was due to MYB97, MYB101 and MYB120. Analysis of growth in the pistil allows discovery of transcriptional changes taking place during pollen tube growth in its native environment, as opposed to mature pollen or in vitro grown pollen, which are essentially naive conditions, as neither have interacted with the pistil environment and any signalling factors found therein.

first: Mark

middle: A

last: Johnson


title: Expression data from CD44-knockdown MDA-MB-231 human breast cancer cells.

status: Public on Apr 24 2013

city: Shiojiri

first: Toru

last: Hiraga

state: Nagano

address: 1780 Gobara-Hirooka

institute: Matsumoto Dental University

summary: CD44, an adhesion molecule that binds to extracellular matrix, primarily to hyaluronan (HA), has been implicated in cancer cell migration, invasion, and metastasis. CD44 has also recently been recognized as a marker for stem cells of several types of cancer. However, the roles of CD44 in the development of bone metastasis still remain unclear. To explore this issue, we established the MDA-MB-231 human breast cancer cells stably expressing short hairpin RNA against CD44.

overall_design: The CD44-knockdown MDA-MB-231 cells (MDA-MB-231 shCD44-2 and shCD44-3) were analyzed. As control, MDA-MB-231 cells stably expressing shRNA against firefly luciferase (shLuc) were used. Total of three samples. No replicates.


title: The rsa3-1 mutation affects global gene expression in Arabidopsis thaliana under salt stress.

status: Public on Apr 20 2013

city: College Park

first: Jianhua

last: Zhu

state: MD

address: 2102 Plant Sciences Building

department: Plant Science and Landscape Architecture

institute: University of Maryland

summary: Salt stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of salt stress RSA3 and used the Affymetrix whole-genome arrays to study the effect of rsa3-1 mutation on global gene expression under salt stress. A set of genes differentially expressed in rsa3-1 under salt stress are identified.

overall_design: Six-day-old seedlings of Arabidopsis thaliana wild type (Columbia gl1 expressing RD29A::LUC transgene) and rsa3-1 mutant seedlings subjected to salt stress at 120 mM NaCl for 24 h were used for total RNA extraction and hybridizations with Affymetrix ATH1 GeneChips. There are two biological replicates per genotype.

first: Wenbo

first: Qingmei

last: Guan

first: Zhen-Yu

last: Wang

first: Yingdian


title: Expression data from torpedo-stage embryos from different Arabidopsis accessions

status: Public on Jun 13 2013

city: Urrbrae

first: Matthew

last: Tucker

state: SA

address: Hartley Grove, Waite Campus

department: Centre of Excellence in Plant Cell Walls

institute: University of Adelaide

summary: The zll/ago10 mutant from Arabidopsis shows different expressivity of shoot stem cell defects in different Arabidopsis accessions. We used microarrays to identify changes in embryo gene expression associated with differences in zll expressivity.

overall_design: Microarrays from ZLL-dependent (Ler-1, Fe-1, Bay-0 and Nw-0) and ZLL-independent (Col-0, Van-0, Ts-1) accessions were compared (always using a minimum of 3 arrays in each group) in different combinations to identify differentially expressed genes.

first: Thomas

last: Laux


title: Expression data from Arabidopsis leavs 10 min after wounding.

status: Public on Jul 11 2013

city: Rehovot

first: Robert

last: Fluhr

address: Hertzel st. 234

department: Plant science

country: Israel

institute: Weizmann institute of science

summary:
Rapid responses to biotic and abiotic insults are crucial for plant survival. We examined the very early (10 min) wound transcriptome in order to increase our understanding regarding this critical intial phase of the plant response to stress. Our analysis revealed a rapid induction of stress-related transcripts that was distinct from the long term events which are dominated by jasmonic pathway responses.
The transcriptome showed high correlation between the early wound response and other early but not late responses to innate immune interactions and other abiotic stresses. In addition those early responses were correlated with transcriptomes of response to singlet oxygen as displayed in the flu mutant. Singlet oxygen appears to be a signaling intermediate in the plant response to multiple stresses.

overall_design: 6 samples were analysed in total with 2 replicates from each type of treatment; control (unwounded plants), local (woundedd plants) and systemic (unwounded leaves from wounded plants).

first: Hadas

last: Sibony-Benyamini

first: Avishai

last: Mor


title: Positive and Negative Spatial Gradients of High Wall Shear Stress Have Different Effects on Endothelial Gene Expression

city: Buffalo

first: Jennifer

last: Dolan

state: NY

address: 3435 Main Street

department: Neuroscience

institute: University at Buffalo

summary: Intracranial aneurysms tend to form at bifurcation apices, where flow impingement causes high frictional force (or wall shear stress, WSS) and flow acceleration and deceleration that create positive and negative streamwise gradients in WSS (WSSG), respectively. In vivo, intracranial aneurysms initiate under high WSS and positive WSSG. Little is known about the responses of endothelial cells (ECs) to either positive or negative WSSG under high WSS conditions. We used cDNA microarrays to profile EC gene expression exposed to positive WSSG vs. negative WSSG for 24 hours in a flow chamber with converging and diverging channels, respectively.  WSS varied between 3.5 and 28.4 Pa in each gradient channel. GO and biological pathway analysis indicated that positive WSSG favored proliferation, apoptosis, and extracellular matrix processing while decreasing expression of pro-inflammatory genes. A subset of characteristic genes was validated using qPCR: Genes for ADAMTS1, CKAP2 and NCEH1 had higher expression under positive WSSG compared to negative WSSG while TAGLN, THBS1, VCAM1, CCL2, and CSF2 had lower expression. To determine if these patterns of expression are also exhibited in vivo, we tested whether the extracellular matrix related protein ADAMTS1 and proliferation were modulated by positive WSSG during intracranial aneurysm initiation. An aneurysm was induced at the basiliar terminus in rabbits by bilateral carotid ligation. WSSG at the bifurcation was determined by computational fluid dynamic simulations from 3D angiography and mapped on immunofluorescence staining for ADAMTS1 and the proliferation marker, Ki-67. Endothelial ADAMTS1 protein and Ki-67 were significantly higher in regions with positive WSSG compared to adjacent sites where WSSG was negative. Our results indicate that WSSG can elicit distinct gene expression profiles in ECs.  Increased matrix processing and high levels of proliferation under positive WSSG could contribute to intracranial aneurysm initiation by causing transient gaps in the endothelium or disrupting EC signals to smooth muscle cells.

overall_design: Time-matched bovine aortic endothelial cells were exposed to positive wall shear stress gradient, negative wall shear stress gradient, and two no gradient samples: uniform WSS of 3.5 Pa and high WSS of 28.4 Pa for 24 hrs in an in vitro flow loop system. RNA was extracted and hybridized on Affymetrix microarrays. There were 12 samples in total, four flow conditions with three replicates each.

middle: M

first: Hui

last: Meng

first: Fraser

last: Sim

first: John

last: Kolega


title: Influence of ATL-type Helios overexpression or WT-Helios/Ikaros knockdown on gene expression profile in Jurkat cells

status: Public on Mar 31 2013

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: It has been known that aberrant isoforms of Ikaros family ptoteins are expressed in malignant cells. We identified that PBMC of ATL (acute T-cell leukemia) patients expresses different patterns of Helios isoforms compared with normal PBMC. In order to investigate the biological impact of ATL-type Helios isoform, we conducted complehensive gene expression analyses in Jurkat cells overexpressing ATL-type Helios. Also, we investigated the influence of WT-Helios or WT-Ikaros knockdown on the gene expression profile and compared with that of the cells with ATL-type Helios overexpression.

overall_design: Total RNA samples from Jurkat cells were subjected to Cy-3 labeling followed by human whole genome gene expression microarray analyses.

first: Nakano

last: Kazumi

first: Satomi

last: Asanuma

first: Toshiki

last: Watanabe


title: Effect of GSH on the gene expression profile of Arabidopsis thaliana

status: Public on Apr 02 2013

city: Kolkata

first: Sharmila

last: Chattopadhyay

state: West Bengal

address: 4, Raja S.C. Mullick Road,

institute: CSIR-Indian Institute of Chemical Biology, Kolkata

summary: GSH, being a versatile molecule, is actively involved in various bilogical processe of plant system. Our previous studies identifies an active role of GSH in plant defense signaling network. Here, we used microarray under GSH treated condition to obtain a global expression profiling under this altered GSH conditions.

overall_design:
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
A.thaliana, much accalimed model system of plant biology and being fully sequenced, we used this system to explore the specific relation of GSH with metabolic processes, phisiological conditions, etc.

first: Ragini

last: Sinha

first: Riddhi

last: Dutta

first: Deepak

last: Kumar


title: Expression data from arabidopsis wild type (Col-0) and JAV1 RNAi plant

city: Beijing

first: Daoxin

last: Xie

address: tsinghua univercity

institute: tsinghua univercity

summary:
JAV1 functions as a negative regulator to control plant defense. Defense-related genes were highly induced in JAV1 RNAi plants compared to wild-type plants in response to wounding or jasmonate treatments.
We used microarrays to detail the global programme of gene expression underlying JAV1 effects on expression of genes involving in defense response, lipid metabolism and regulating transcription.

overall_design: For the Affymetrix microarray assay with 100 uM MeJA treatment, 21-day-old seedlings grown in MS medium were treated with 100 μM MeJA for various time periods (0, 1, and 4 hours). For the Affymetrix microarray assay with wounding treatment, JAV1 RNAi line Ri17 versus wild-type was utilized after mechanical wounding for various time periods. Four rosette leaves from 21-day-old plants were crushed across the midrib with a forceps. About 30% of each leaf was damaged. Wounded leaves were harvested at various time periods (0, 0.5, and 1 hour) for RNA extraction. Control plants were untreated and leaves were harvested for RNA extraction.

first: Po

last: Hu

first: Wu

last: Zhou


title: WT and dTLec1-1 plants systemic wounding

first: Robert

last: Fluhr

department: Plant Sciences

institute: Weizmann Institute of Science

summary: Innate immune responses in animals and plants involve receptors that recognize microbe-associated molecules. In animals, activation of the Toll-NFkappaB pathway involves the recruitment of a series of TIR-domain containing adaptors that activate NFkappaB transcription factors. Plants contain many TIR modules as part of a large multi-gene TIR-NBS-LRR R-gene innate immune defense system as well as TIR-motif containing genes that lack LRR and whose functions are unknown. Molecular interactions for any TIR module signaling pathway has yet to be shown. Here we investigated the functional role of a TIR module linked to a lectin-containing motif, TIR-Lec1 (TLec1). We show that TLec1 acts as a positive modulator of the systemic JA-dependent wound response. TLec1 transcripts are rapidly induced in a JA-independent pathway and insertional mutants that TLec1 transcripts fail to show the full systemic wound response

overall_design: 2 replicates. 2 genotypes (wt and dTLec), 2 treatments (control and systemic wounding)

first: Yehudit

last: Zohar

first: Alex

last: Keshet

first: Dina

last: Volodarsky

first: Otto

last: Miersch

first: Claus

last: Wasternack

first: Olga

last: Davydov


title: Genome wide expression analysis of EST-induced EBE-XVE  using Affymetrix ATH1 array

status: Public on Mar 30 2013

city: Potsdam

first: Mohammad

last: Mehrnia

state: Brandenburg

address: Am Muhlenberg 1

department: Stitt

institute: Max-Planck-Institut für Molekulare Pflanzenphysiologie

summary:
Global transcriptome patterns were determined in XVE-14 and wild-type seedlings induced for 45 min b-estradiol in order to identify the genes early regulated by EBE transcription factor.
We used microarrays to identify genes differentially expressed in EST-inducible EBE over-expression line #14 compared to wild-type plants, 45 min after 2µM EST induction. Three independent biological replications were performed.

overall_design: In order to identify potential direct/early target genes of EBE transcription factor, estradiol inducible overexpression system was used. Three week old Arabidopsis EBE-XVE (line 14) and WT seedlings were treated with ß-estradiol (2µM) for 45 min. RNA was isolated from shoot and subjected to hybridization on Affymetrix microarrays. Experiment was performed in 3 biological replications and genes differentially expressed between estradiol treated EBE-XVE and WT plants were identified as potential early targets of EBE.


title: A key role for a glutathione transferase in multiple herbicide resistance in grass weeds

status: Public on Mar 13 2013

first: David

last: Wortley

state: North Yorkshire

summary:
The gene encoding a protein (AmGSTF1) associated with multiple herbicide resistance (MHR) in black-grass was transgenically expressed in Arabidopsis thaliana.The goal of this study was to determine if AmGSTF1 could elicit an MHR phenotype in the transgenic host.
Affymetix microarrays were used to detect changes in transcriptional regulation between amgstf1-expressors and wild-type Arabidopsis plants (ecotype Col0).

overall_design: Total RNA was isolated from amgstf1-expressors and wild-type Arabidopsis plants (ecotype Col0) respectively, grown under identical growth room conditions. Performed in biological triplicate.

first: Ian

last: Cummins

first: Federico

last: Sabbadin

first: Zhesi

last: He

first: Christopher

last: Coxon

first: Hannah

last: Straker

first: Jonathan

last: Sellars

first: Kathryn

last: Knight

first: Lesley

last: Edwards

last: Hughes

first: Shiv

last: Kaundun

first: Sarah-Jane

last: Hutchings

first: Patrick

last: Steel


title: Expression data for plant compensatory responses

status: Public on Mar 02 2013

city: Utbana

first: Madhura

middle: H

last: Siddappaji

state: IL

address: 515 Morrill Hall

institute: UIUC

summary:
Plant compensatory responses depends on transcriptional reprogramming. We used microarray analysis to understand the differential gene expression pattern between clipped (herbivore browsed)
and unclipped plant.

overall_design: Arabidopsis ecotypes Columbia and Landsberg erecta were chosen due to their differential compensatory response. The plants were grown in greenhouse. At bolting stage the plants were clipped to imitate herbivore damage. Following day the samples were collected from clipped and unclipped plants.

first: Ken

last: Paige

first: Daniel

last: Scholes

first: Martin

last: Bohn


title: Transcriptome in Col, C24, and their F1 at 10 DAS

status: Public on Feb 19 2013

city: Canberra

first: Ryo

last: Fujimoto

address: Cnr Clunies Ross St & Barry Dr

institute: CSIRO

summary: We compared the expression among three lines, Col, C24, and their hybrids at 10 days after sowing (DAS).

overall_design: Whole plants without root in Col, C24, and their F1 hybrids with three replications.


title: Expression analysis of Arabidopsis ein2 and bak1 mutants treated with the elicitors elf18 and Pep2.

status: Public on Mar 05 2013

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

summary: Recognition of microbial patterns and host derived damage signals by host pattern recognition receptors is a key step in immune activation in multicellular eukaryotes. Here we show how mutations in ethylene signaling and the coreceptor bak1 affect host immune responses triggered by elicitors.

overall_design: A 51 DNA microarray study using total RNA from Arabidopsis mutants (ein2-1, bak1-3, efr-1 and pepr1-1 pepr2-3) as well as wild type treated with elf18 or Pep2 with three biological replicates.

first: Nico

last: Tintor

first: Yusuke

last: Saijo


title: Analysis of genes regulated by AS1 and AS2

status: Public on Mar 01 2013

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

summary: AS1 and AS2 encode MYB related protein and AS2-domain containing protein, respectively and may regulate transcription. These genes are involved in the determination of axes of leaves of Arabidopsis thaliana. To know the gene regulation in the leaf development, expression profile among wild-type, as1 and as2 mutants and AS2 overexpression plants were compaired.

overall_design: shoot apices from as1-1, as2-1, AS2 overexpressing, and wild type embryos

first: Hidekazu

last: Iwakawa

first: Chiyoko

last: Machida


title: Light- and Phytochrome-Dependent Regulation of Hypocotyl Elongation in Arabidopsis thaliana

city: East Lansing

first: Sookyung

last: Oh

state: MI

address: 612 Wilson Road, Rm. 322

department: Plant Research Laboratories

institute: Michigan State Univ.

summary: To identify and characterize genes required for tissue-specific phytochrome responses during hypocotyl development in far-red-light grown bvr lines, we performed gene transcriptional profiling using bvr lines with mesophyll-specific phytochrome inactivation (cab3: :pBVR2). We identified several candidate genes whose expression is significantly altered in lines with mesophyll tissue-specific BVR expression (Cab3::pBVR2), compared to constitutive phytochrome inactivation lines, i.e. 35S-driven BVR lines (35S::pBVR3). No-0 is used as wild-type (WT)

overall_design: Seeds of No-0 WT, 35S::pBVR3 and CAB3::pBVR2 on MS plates were exposed to Red (R) light of 75 µmol m-2 s-1 for 5 min and imbibing seeds were cold-stratified at 4 °C in darkness for 3 d. Seedlings were grown under continuous far-red illumination for 7 d. Seven-day-old vegetative whole seedlings (300 – 500 mg) were quickly (<1 min) harvested and immediately frozen in liquid nitrogen inside the FR chamber. Seedlings were grown under continuous far-red illumination for 7 d.

first: Sankalpi

last: Warnasooriya

first: Beronda

last: Montgomery


title: Expression data in whole Arabidopsis seedlings after treatment with Rhizoctonia solani AG8 and AG2-1

status: Public on Feb 01 2013

city: Floreat

first: Rhonda

last: Foley

address: Underwood Ave

department: Plant Industry

summary: Rhizoctonia solani is an economically important soil-borne necrotrophic fungal pathogen, with a broad host range and for which little effective resistance exists in crop plants.  Arabidopsis is resistant to the R. solani AG8 isolate but susceptible to R. solani AG2-1.  Affymetrix microarray analysis was performed to determine genes that are affected in common and specifically by AG8 and AG2-1.

overall_design: 3 biological samples were taken from 3 treatments: non-infected control, R. solani AG8 infection and R. solani AG2-1 infection.

first: Cynthia

last: Gleason

first: Jonathan

last: Anderson

first: Thorsten

last: Hamann

first: Karam

last: Singh


title: Transcriptional responses to water deficit and Xylella fastidiosa (Pierce's disease) in Vitis vinifera

status: Public on Feb 12 2013

city: Davis

first: Douglas

last: Cook

state: California

address: One Shields Aave

institute: University of California-Davis

summary: Pierce’s disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grapes. To test the long-standing hypothesis that Pierce’s disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a massive redirection of gene transcription involving 822 genes with a minimum 2-fold change (p<0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis related (PR) proteins, absisic acid (ABA)/jasmonic acid (JA)-responsive transcripts, and down-regulation of transcripts related to photosynthesis, growth and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis, and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlation of the classical concept of the disease triangle where environment impacts disease severity.

overall_design: Mature leaves were sampled from 2-year old V. vinifera cv. Cabernet sauvignon clone 8 vines 4 and 8 weeks post-mock or inoculation with Xylella fastidiosa (Pierce's disease). Vines were grown in growth chambers under non-water limiting and water limiting condtions (moderate and severe water stress)

first: Hong-Kyu

last: Choi

first: Alberto

last: Landolino

first: Francisco

last: Goes da Silva


title: Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB

status: Public on Jan 29 2013

city: Frederick

first: Xiaolin

last: Wu

address: 8560 Progress Drive, C3001

department: Cancer Research Technology Program

institute: Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc

summary:
Transcriptome analysis of control and MALAT1 lncRNA-depleted RNA samples from human diploid lung fibroblasts [WI38]
The long noncoding MALAT1 RNA is upregulated in cancer tissues and its elevated expression is associated with hyper-proliferation, but the underlying mechanism is poorly understood.  We demonstrate that MALAT1 levels are regulated during normal cell cycle progression. Genome-wide transcriptome analyses in normal human diploid fibroblasts reveal that MALAT1 modulates the expression of cell cycle genes, and is required for G1/S and mitotic progression. Depletion of MALAT1 leads to activation of p53 and its target genes. The cell cycle defects observed in MALAT1-depleted cells are sensitive to p53 levels, indicating that p53 is a major downstream mediator of MALAT1 activity. Furthermore, MALAT1-depleted cells display reduced expression of B-MYB (Mybl2), an oncogenic transcription factor involved in G2/M progression, due to altered binding of splicing factors on B-MYB pre-mRNA and aberrant alternative splicing. In human cells, MALAT1 promotes cellular proliferation by modulating the expression and/or pre-mRNA processing of cell cycle-regulated transcription factors. These findings provide mechanistic insights on the role of MALAT1 in regulating cellular proliferation.

overall_design: We analyzed RNA from control and MALAT1 depleted WI38 cells using the Affymetrix Human Exon 1.0 ST platform. Array data was analyzed by Partek Genomic Suite software.

first: Ashish

last: Lal

first: Vidisha

last: Tripathi

first: Prasanth

middle: V

last: Kannanganattu


title: Comparative transcriptome analysis of responses of Arabidopsis ecotypes to cold stress

status: Public on Dec 01 2012

first: Zhulong

last: Chan

state: Hubei

address: Wuchang District, Moshan

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

summary: Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects.  In these studies we sought to examine differential gene expression in response to cold for two widely used Arabidopsis thaliana ecotypes, C24 and Columbia (Col).

overall_design: Two Arabidopsis genotypes were grown in 1/2 MS plate. Forteen-day-old seedlings were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and cold treatment combination.


title: Transcriptional regulation of Sox17 in HUVEC

status: Public on Dec 17 2012

city: Daejeon

first: Hanseul

last: Yang

address: Korea Advanced Institute of Science and Technology

country: South Korea

summary: We identified Sox17 as a novel angiogenic transcription factor in the context of tumor. Our data revealed that Sox17 promotes tumor angiogenesis and tumor vessel abnormality. We found that Sox17 is specifically expressed in tumor endothelial cells within tumors. Our study elucidates a novel transcriptional regulation for tumor angiogenesis

overall_design: Control HUVECs vs. Sox17 knockdown HUVECs. Biological replicates: 3 control replicates, 3 transfected replicates.

first: Injune

last: Kim


title: Expression data from Arabidopsis grown in perlite and compost

status: Public on Nov 09 2012

city: Barcelona

first: guillem

last: segarra

address: Diagonal 643

department: Plant Biology

country: Spain

institute: Universitat de Barcelona

summary:
Composts are the products obtained after the aerobic degradation of different types of organic matter wastes and can be used as substrates or substrate/soil amendments. There are a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost as growing medium compared to standard substrates. The purpose of this study was to unravel the gene expression alteration produced by the compost to gain knowledge about the mechanisms involved in the compost-induced systemic resistance.
A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis compared to the standard substrate perlite. Microarray analyses revealed that 178 genes were differently expressed with a fold change cut off of 1 from which 155 were upregulated and 23 were down regulated in compost-grown compared to perlite-grown plants. Functional enrichment study of up regulated genes revealed that 38 Gene Ontology terms were significantly enriched.  Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched terms as well as immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants.  Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA dependent/independent abiotic stress responses.

overall_design: Global gene expression of plants grown in compost (3 biological replicates) versus plants grown in perlite (2 biological replicates) was studied.

first: Guillem

last: Segarra

first: Gabriel

last: Santpere

first: Georgina

last: Elena

first: Isabel

last: Trillas


title: Actin Cytoskeleton Integrates Auxin and Brassinosteroid Signaling in Plants.

status: Public on Nov 21 2012

city: Campus de Cantoblanco

first: Antonio

last: Leyva

state: Madrid

address: Darwin 3

department: Plant Molecular Genetics

institute: CNB-CSIC

summary: We describe a new mutant allele of the ACTIN2 gene with enhanced actin dynamics, displaying a broad array of twisting and bending phenotypes that resemble BR-treated plants. Moreover, auxin transcriptional regulation is enhanced on the mutant background, supporting the idea that shaping actin filaments is sufficient to modulate BR-mediated auxin responsiveness. The actin cytoskeleton thus functions as a scaffold for integration of auxin and BR signaling pathways.

overall_design: Three biological replicates were performed for each sample (wild-type and actin2-5) and hybridized to the the Affymetrix ATH1 GeneChips.

first: Pablo

last: Catarecha

first: Mónica

last: Lanza

first: Yolanda

last: Leo


title: Partial deficiency of isoleucine impairs alters transcript levels of the genes involved in branched-chain amino acid and glucosinolate metabolism in Arabidopsis

status: Public on Nov 07 2012

first: Dong

last: Liu

address: School of Life Sciences

institute: Tsinghua University

summary: Isoleucine (Ile) is one of the branched-chain amino acids (BCAAs) that are essential substrates for protein synthesis in all organisms. In this study, we characterized an Arabidopsis mutant, lib (low isoleucine biosynthesis), that has defects in both cell proliferation and cell expansion processes during root development. This mutant carries a mutation in OMR1 gene that encodes a threonine deaminase/dehydratase (TD) which results in a defect in isoleucine production. Microarray analysis indicated that the partial deficiency of Ile in the lib mutant triggers a decrease in transcript levels of the genes encoding the major enzymes involved in the BCAA degradation pathway; the analysis also indicated that many genes involved in the biosynthesis of methionine-derived glucosinolates are up-regulated.

overall_design: Total RNAs were isolated from three replicate samples of the root tissues of 8-day-old wild type (w) and lib mutant (m)seedlings grown on 1/2 MS medium and hybridized on Affymetrix ATH1 microarrays. The changes of gene expression in the lib mutant (m) was compared with the wild type (w). The corrected P value of <0.05 was used to select the genes for comparison, and only those genes whose expression was two-fold higher or lower in lib than in the WT were used for analysis.

first: Hailan

last: Yu


title: Arabidopsis thaliana roots at 7DAG; Col-0, scl3 (LOF) and SCL3 OE (GOF)

status: Public on Oct 13 2012

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

institute: KonKuk University

summary: Transcriptional profiling of root part comparing wild type with scl3 mutant and SCL3 OE.  We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SCL3 on growth and development of Arabidopsis root system by global transcriptome analysis and to identify new regulators in the regulatory pathway.

overall_design: Three-condition experiments, Col-0, scl3 and SCL3 OE. Biological triplicates: 3 WT, 3 scl3 and 3 SCL3 OE

first: Kwang

last: Chang

first: Jun

last: Lim

first: Jung-Ok

last: Heo


title: Gene alteration in A549 cells by disinfectant PHMG

status: Public on Sep 27 2012

city: Cheonan

first: Yong-Sik

address: Soonchunhyang-2gil 8

department: Microbiology

institute: College of Medicine, Soonchunhyang University

summary: Polyhexamethyl guanidine is widely used as a disinfectant in various places such as hospitals and restaurants. In order to examine of PHMG cytotoxicity in lung adenocarcinoma A549 cells we treated 5 ug/ml PHMG for 24 h.

overall_design: To investigate cytotoxicity of commonly used bactericidal reagent PHMG, A549 cells were treated 5 ug/ml PHMG for 24 h. After then purified the total RNA from treated and untreated cells using the Rneasy mini kit (Qiagen). The concentration and purity of the total RNA was measured and performed gene array.

first: Hana

last: Jung

first: Ho-Yeon

last: Song


title: Transcriptomic analysis during heat stress and after the following recovery in grapevine (Vitis vinifera L.) leaves

status: Public on Oct 10 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: To elucidate the effect of heat stress and the following recovery on grapevines and identify some regulated genes representing the classical heat stress response and thermotolerance mechanisms, transcript abundance of grapevine (Vitis vinifera L.) were quantified using the Affymetrix Grape Genome oligonucleotide microarray (15,700 transcripts), followed by quantitive Real-Time PCR validation for some transcript profiles. The treatment: heat stress(5h) and the following recovery (18.5h), sampling were conducted at two time respectively.  ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Lijun Wang. The equivalent experiment is VV40 at PLEXdb.]

overall_design: temperature: 45 C(3-replications); temperature: 25 C(3-replications); temperature: 45-25 C(3-replications); temperature: 25-25 C(3-replications)

first: Lijun

last: Wang

first: Shaohua

last: Li


title: Carbon-Deprivation-Driven Transcriptome Reprogramming in Detached Developmentally-Arresting Arabidopsis Inflorescences

status: Public on Sep 25 2012

city: Pisa

first: Alice

last: Trivellini

address: Viale delle Piagge

institute: University of Pisa

summary: Senescence is genetically-controlled and activated in mature tissues during ageing. However, immature plant tissues also display senescence-like symptoms when continuously exposed to adverse energy-depleting conditions. We used detached dark-held immature inflorescences of Arabidopsis thaliana to understand the metabolic reprogramming occurring in immature tissues transitioning from rapid growth to precocious senescence. Macroscopic growth of the detached inflorescences rapidly ceased upon placement in water in the dark at 21°C. Inflorescences were completely de-greened by 120 h of dark incubation and by 24 h had already lost 24% of their chlorophyll and 34% of their protein content. Comparative transcriptome profiling at 24 h revealed that inflorescences response at 24 h had a large carbon-deprivation component. Genes that positively regulate developmental senescence (ANAC092) and shade avoidance syndrome (PIF4 and PIF5) were up-regulated within 24 h. Mutations in these genes delayed de-greening of the inflorescences. Their up-regulation was suppressed in dark-held inflorescences by glucose treatment, which promoted macroscopic growth and development and inhibited de-greening of the inflorescences. Detached inflorescences held in the dark for 4 days were still able to re-initiat development to produce siliques upon being brought out to light indicating the transcriptional reprogramming at 24 h was adaptive and reversible. Our results suggest that the response of detached immature tissues to dark storage involves interactions between carbohydrate status sensing and light deprivation signaling and that the dark adaptive response of the tissues appears to utilize some of the same key regulators as developmental senescence.

overall_design: Detached arabidopsis inflorescences were harvested and either immediately snap-frozen in liquid nitrogen and stored at -80°C, or placed at 21°C on blotting paper moistened with water inside a 2-L black plastic container for RNA extraction and hybridization on Affymetrix microarrays. Ten inflorescences from 10 independent plants were pooled for each time point (0 h or 24 h).

first: Rubina

last: Jibran

first: Lyn

last: Watson

first: Erin

last: O’Donoghue

last: Ferrante

first: Kerry

last: Sullivan

first: Paul

last: Dijkwel

first: Donald

last: Hunter


title: Expression data of Arabidopsis pollen tube of an AGP6 AGP11 double null mutant

status: Public on Oct 31 2012

city: Porto

first: Sílvia

last: Coimbra

address: Rua do Campo Alegre

department: Biology

country: Portugal

institute: University of Porto

summary:
Arabinogalactan proteins are proteoglycans known to have important roles during cell growth and development, namelly during pollen tube growth.
A microarray experiment was performed on agp6 agp11 pollen tubes to search for genetic interactions in the context of pollen tube growth.

overall_design: RNA from wt and mutant pollen tubes was extracted after 8h of in vitro germination and hybridized on Affimetrix microarrays.

first: Mário

last: Costa

first: Margarida

last: Nobre

first: Jörg

last: Becker

first: Simona

last: Masiero

first: Maria

middle: I

last: Amorim

first: Luís

last: Pereira


title: Expression data from Arabidopsis under hydrogen peroxide and light treatment

status: Public on Sep 05 2012

city: Hong Kong

first: Han

last: Cheng

address: Shatin

department: School of Life Science

institute: The Chinese University of Hong Kong

summary:
Green plants are more robust to hydrogen peroxide (H2O2) stress and contain high endogeneous H2O2 levels which is generated during photorespiration and photosynthesis. Therefore, exgeneous H2O2 application mostly impose oxidative stress. To reduce endogenous H2O2 background, we adopted a strategy which is to grow Arabidopsis seedlings in the dark to eliminate light-induced H2O2 production, thus to reduce the endogenous H2O2 level. Exogenous H2O2 was then applied to induce transcriptome changes.
Global gene expression is studied and compared between samples collected under 7d dark, 7d H2O2 treatment under dark and 7d light conditions.

overall_design: We cultured seedlings in the dark to reduce endogenous H2O2. Three conditions were used for transcriptome profiling: dark grown (dark); dark grown with exogenous H2O2 treatment (H2O2); and light grown (light). Three types of conditions were used for Arabidopsis seedling culture: dark, dark with 5 mM H2O2 treatment and light. Each condition was performed with two biological replicates. The seedlings were harvested at 7 days old.

first: Dianjing

last: Guo


title: Expression profiling of Arabidopsis wild type Col-0 and pmr5 mutant

status: Public on Sep 01 2012

city: San Francisco

first: Bradley

middle: Robert

last: Dotson

state: CA

address: 55 Boardman Place Apt C

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary: The rosettes from genotype Col-0 and pmr5 mutant were collected for RNA expression profiling when the plants were 3 weeks old.

overall_design: The rosettes were collected when the plants were 3 weeks old for RNA extraction and hybridization on Affymetrix microarrays.

first: Shauna

last: Somerville


title: Expression data from Arabidopsis petioles in early stage dense canopy

status: Public on Sep 04 2012

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

summary:
Growth in dense stands induces shade avoidance responses. Early responses to neighbors seem to be assoctaed with touch, not light signalling.
We studied gene expression in petioles during early canopy development when leaf hyponasty was visible but altered phytochrome signalling was not yet detectable.

overall_design: Plants were grown in small pots that were either kept single, or put in a high density of 2066 plants/m2. Gene expression measured in petioles when canopies had reached a leaf area index of 0.9.

first: Mieke

last: de Wit


title: Expression data from 10-days old dark grown Arabidopsis seedlings of wild type (Col-0), sps1 line and L17 line.

status: Public on Jul 01 2012

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Applied Science

institute: University of Arkansas at Little Rock

summary: In the present work, experiments were carried out to understand the molecular mechanism underlying phyA’ silencing.The EMS-mutagenesis of phyA’ line, L17, generated suppressor mutations that activate phyA’ locus. Detailed study of one suppressor line, sps1, indicated that methylation of specific CG site within the phyA coding region is critical for maintaining phyA’ silencing. In order to study the possible genomic targets of the putative SPS1 factor, microarray analysis using ATH1 genome array chip was done on sps1, L17 and Col-0.

overall_design: 9 samples in total were analyzed. Each line (WT, sps1, L17) were analyzed in triplicate.

first: Vibha

last: Srivastava


title: The AtGenExpress: Basic hormone treatment of seedlings in Arabidopsis

status: Public on Jul 17 2012

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

institute: Yokohama City University

summary: Arabidopsis seedlings of the wild-type or hormone mutants were treated with plant hormones.

overall_design: 72 samples were analyzed by Affymetrix GeneChip, ATH1