title: Arabidopsis AtbHLH112 protein binds to the G-box and a novel motif GCG-box to regulate gene expression in response to abiotic stress

status: Public on Nov 14 2013

city: Harbin

first: Yujia

last: Liu

summary: Plant basic helix-loop-helix (bHLH) proteins play essential roles in physiological and developmental processes and are also involved in abiotic stresses. However, their exact roles in abiotic stress are still not fully understood, and most of them have not been functionally characterised. In the present study, we characterised the functional role of AtbHLH112 in response to abiotic stress. A WRKY gene, AtWRKY66, can regulate the expression of the AtbHLH112 via binding to W-box motifs present in its promoter. AtbHLH112 is a nuclear-localised protein, and its nuclear localisation is increased upon exposure to NaCl, mannitol and ABA. In addition to binding to the G-box motif, AtbHLH112 is found to bind to a novel motif “GGGCCGGTC” (named the GCG-box) to regulate gene expression. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with tolerance to salt and drought. AtbHLH112 can confer stress tolerance via enhanced expression of POD and SOD genes to improve ROS scavenging ability and via upregulated expression of P5CS genes and decreased expression of P5CDH and PRODH genes to improve proline levels. Our data suggested that AtbHLH112 regulates the expression of genes via binding to the G-box and the GCG-box to improve stress-related pathways, such as ROS scavenging and proline biosynthesis.

overall_design: Differentially expression genes of AtbHLH112-overexpression plants and mutant (SALK_033618C) plants of Arabidopsis thaliana were measured under salt stressed and normal condition for 3 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.

first: Yucheng

last: Wang


title: A spatiotemporal understanding of growth regulation during the salt-stress response (Agilent)

status: Public on Sep 01 2013

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

department: Plant Biology

country: USA

institute: Carnegie Institution for Science, Department of Plant Biology

summary:
A genome-scale test of dynamic gene expression changes and homeostasis in salt stress response was genereated using whole roots sample of wild type columbia. Seedlings of columbia were grown under standard conditions for 5 days, and then they were transfered to media supplemented with 140mM NaCl for a series of time: 1 hour, 3 hours, 20 hours, 2 days, 4 days and and 8 days, as well as to standard condition for the same series of time. 2 replicates for each condition was used.
Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these temporal events is controlled.  In this study we explore the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis seedling root to a rapid change in salinity.  Using live-imaging analysis, we show that growth is dynamically regulated with a period of growth quiescence followed by growth recovery and homeostasis.  Through the development and analysis of a new high-resolution spatiotemporal transcriptional map, we have identified the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action and link the activity of these pathways to the control of specific phases of growth control. Through the use of tissue-specific approaches to suppress the ABA pathway, we demonstrate that ABA signaling likely acts in select tissue layers to control spatially localized transcriptional programs and promote growth recovery.  In addition to the biological pathways directly affecting growth, we show that salt also controls many tissue-specific and time-point specific transcriptional responses that are expected to modify water transport, Casparian strip formation and protein translation.  Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment.

overall_design: To test a genome-scale dynamic changes and gene expression homeostasis of gene expression in Arabisopsis root in salt stress response, we generated this data using whole roots. Wild type plants of columbia were grown under standard conditions for 5 days, and then they were transfered to media supplemented with 140mM NaCl for a series of time: 1 hour, 3 hours, 20 hours, 2 days, 4 days and and 8 days, as well as to standard condition for the same series of time. 2 replicates for each condition was used.

first: Yu

last: Geng

first: Rui

last: Wu

first: Choon-Wei

last: Wee

first: Fei

last: Xie

first: Xueliang

last: Wei

first: Cliff

last: Tham

first: Lina

last: Duan

middle: R


title: Functional analysis of Arabidopsis MYB106 and WIN1/SHN1 transcription factors

status: Public on Sep 23 2013

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

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

overall_design: Refer to individual Series

first: Oshima

last: Yoshimi

first: Mitsuda

last: Nobutaka

first: Ohme-Takagi

last: Masaru


title: Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations

status: Public on Jan 21 2014

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

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

summary: Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary clear cell RCC tumors and 11 nontumor adjacent matched tissues were analyzed with 4k-probes microarrays. Oligoarrays with 44k-probes were used to interrogate 17 RCC samples (14 clear cell, 2 papillary, 1 chromophobe subtypes) split into four pools. Meta-analyses were performed by taking the genomic coordinates of the RCC-expressed lncRNAs, and cross-referencing them with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). An additional signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value ≤0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 25% were cis correlated (r >|0.6|) with the expression of the mRNA in the same locus across three human tissues. Gene Ontology (GO) analysis of those loci pointed to ‘regulation of biological processes’ as the main enriched category. A module map analysis of all expressed protein-coding genes in RCC that had a significant (r ≥|0.8|) trans correlation with the 20% most abundant lncRNAs identified 35 relevant (p <0.05) GO sets. In addition, we determined that 60% of these lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands and histones methylation and acetylation. Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation.

overall_design:
This SuperSeries is composed of the SubSeries listed below.
Refer to individual Series.

Data from the Fachel et al. Mol Cancer 2013 paper comes from two different microarray data sets. The ID_REF column of data table of each sample refers to the ID column of the 4K array (GPL3985) or of the 44K array (GPL4051). The gene name / gene ID are identified at the microarray platform description:
44K array: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4051 (used for expression set analysis)
4K array: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3985 (used for malignancy and survival set analysis)


title: Transcriptome analysis of Atasf1 mutants in comparison with wild type.

status: Public on Dec 31 2013

city: Shanghai

first: Yan

last: Zhu

address: 2005, Songhu Road

department: Biochemistry

country: China

institute: Fudan University, School of life sciences

summary: ASF1 is a conserved histone chaperone with affinity to histone H3-H4.  Arabidopsis thaliana genome encodes two ASF1 homologues, which play redundant roles in S-phase progression and cell proliferation in plant development. Here, in an attempt to obtain the knowledge of ASF1 role in transcriptional regulation, we perform the transcriptome analysis of each asf1 single mutant (Atasf1a and Atasf1b) as well as Atasf1ab double mutant in comparison with wild type (WT).

overall_design: 12-day-old seedlings of wild-type (WT), each single mutants and double mutant grown in normal growth condition were used for RNA extraction and microarray. Duplicate samples were analyzed.


title: S. paradoxus wt strains: glucose vs. xylulose growth

status: Public on Aug 23 2013

city: Rehovot

first: Zvi

last: Tamari

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Transcription profile of 12 wt S.paradoxus strains originating from diverse geographical origins and natural habitats. Transcription profiles in two conditioins were compared: growth on glucose and growth on the naturally rare pentose sugar xylulose.

overall_design: Two condition experiment, growth on glucose and on xylulose, 12 wt S.paradoxus strains


title: JA-INDUCIBLE MYC2-LIKE1 acts as a repressor and negatively regulates jasmonate signaling in Arabidopsis

status: Public on Jul 03 2013

summary: Jasmonate (JA) is a plant hormone that controls trade-offs between plant growth and responses to biotic and abiotic stresses. Although recent studies uncover core mechanism for JA-induced responses in Arabidopsis thaliana, it remains elusive how plants attenuate those responses. We report here that a basic-helix-loop-helix type transcription factor named JA-INDUCIBLE MYC2-LIKE1 (JAM1) acts as a transcriptional repressor and negatively regulates JA signaling. Arabidopsis plants expressing the chimeric repressor for JAM1 exhibited a substantial reduction of JA responses, including JA-induced inhibition of root growth, accumulation of anthocyanin, and male fertility. These plants were also compromised in resistance to attack by Spodoptera exigua. Conversely, jam1-4 loss-of-function mutants showed enhanced JA responsiveness, including increased resistance to the insect attack. Competitive binding of JAM1 and MYC2 to the target sequence of MYC2 suggested negative regulation of JA signaling by JAM1 and suppression of MYC2 function. These results indicate that JAM1 plays a pivotal role in fine-tuning of JA-mediated stress responses and plant growth by negatively regulating JA signaling.

overall_design: Transcriptomes of ProJAM1:JAM1-SRDX, ProMYC2:MYC2-SRDX and wild-type Arabidopsis seedlings with or without jasmonic acid were compared.

first: Nakata

first: Moreno

middle: E

last: Javier

first: Herde

last: Marco

first: Koo

middle: J

last: Abraham

first: Howe

middle: A

last: Gregg

first: Suzuki

last: Kaoru

first: Ohme

middle: T


title: S. cerevisiae wt strains: glucose vs. xylulose growth

summary: Transcription profile of 12 wt S.cerevisiae strains originating from diverse geographical origins and natural habitats. Transcription profiles in two conditioins were compared: growth on glucose and growth on the naturally rare pentose sugar xylulose.

overall_design: Two condition experiment, growth on glucose and on xylulose, 12 wt S. cerevisiae strains, two biological replicates


summary: Antirrhinum R2R3 MYB transcription factor MIXTA is known to regulate epidermal cell outgrowth in petal. Arabidopsis has three MIXTA-like proteins NOECK(NOK)/MYB106, MYB16 and MYB17 and nok mutant exhibits over-branched trichomes in rosette leaves. On the other hand, Arabidopsis AP2/ERF transcription factor WAX INDUCER1/SHINE1 is well known to induce cuticle development. Here, we report the transcriptional cascade of MYBs-WIN/SHNs coordinately regulates the epidermal cuticle development.  The constitutive expression of MYB106 chimeric repressor, in which strong repression domain was fused with MYB106 (35S:MYB106SRDX), induced cuticle deficiency characterized by organ adhesion, reduction of epicuticular wax crystals and staining by toluidine blue in broad region of aerial parts in addition to the over-branched trichomes. Most these phenotypes were partially reproduced in T-DNA knockout plants and also similarly induced by the chimeric repressors of WIN1/SHINE1(SHN1), SHN2 and SHN3, which are AP2/ERF transcription factors previously shown as positive regulators of cutin. Microarray experiments revealed that MYB106SRDX and WIN1SRDX plants have similar transcriptomes, in which the expression of wax and cutin biosynthetic genes was suppressed. Conversely, VP16-fused MYB106 which has high activation ability induced ectopic production of cutin nanoridges in the transgenic plants and enhanced the reporter driven by promoters of WIN1 and wax-related genes in transient expression assay. These results suggest that  MIXTA-like proteins regulate cutin biosynthesis partially via WIN1 and directly regulate wax accumulation as well as their known roles in epidermal cell differentiation.

overall_design: Transcriptomes of 35S:MYB106VP16 and wild-type Arabidopsis seedling were compared.


title: Identification of WRKY22 targets under submergence in Arabidopsis

city: Taipei

first: Fu-Chiun

last: Hsu

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

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

type: Genome binding/occupancy profiling by genome tiling array


title: Microarray analysis of elp2 and wild type (Col-0) infected with the necrotrophic fungal pathogen Botrytis cinerea

status: Public on Jul 01 2013

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

summary: The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutant elp2 and wild type in response to infection of the necrotrophic fungal pathogen Botrytis cinerea. Results indicated that, compared with the wild type, the WRKY33/OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59 (ORA59)/ETHYLENE RESPONSE FACTOR1 transcriptional cascades are down-regulated, whereas the MYC2 transcriptional cascade is up-regulated in the elp2 mutant.

overall_design: Three biological replicates with leaves from 8-12 plants per sample were collected at 0, 3, 6, 12, 24, and 48 hours after inoculation with the necrotrophic fungal pathogen Botrytis cinerea. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Equal amount of RNA from the 3 biological replicates were used for microarray analysis. The channels of the dual-channel arrays were analyzed independently.

first: Chenggang

last: Wang

first: Yezhang

last: Ding

first: Jin

last: Yao

first: Yanping

last: Zhang

first: Yijun

last: Sun


title: Virulence effects and signaling partners modulated by Brucella melitensis light-sensing histidine kinase

status: Public on Jun 15 2013

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Drive

department: PBS

institute: UW-Madison

summary: A whole genome expression comparision between wild type B. melitensis 16M and ΔBM-LOV-HK (ΔBMEII0679) B. melitensis strains grown in broth culture to determine genes directly and indirectly regulated by BM-LOV-HK.

overall_design: 6 samples, 3 wild type B. melitensis 16M replicates, 3 ΔBM-LOV-HK B. melitensis replicates

first: Christopher

last: Gourley

first: Erik

middle: M

last: Petersen

first: Jerome

middle: H

last: Harms

middle: L


title: longitudinal expression profiling in whole blood of multiple sclerosis patients and controls [IFN_discovery dataset]

status: Public on Jun 17 2013

city: San Francisco

first: Sergio

last: Baranzini

state: CA

address: 675 Nelson Rising Lane, Room S-215

department: Neurology

institute: University of California San Francisco

summary:
Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis.
Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the discovery data set (n=318) when we compared gene expression in untreated MS patients (n=62) to IFN treated patients (n=58).

overall_design: The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.

first: Dorothee

last: Nickles

first: Jorge

last: Oksenberg


title: bHLH transcription factors facilitating K+ uptake during stomatal opening are repressed by abscisic acid through phosphorylation

city: Fukuoka

first: Yohei

last: Takahashi

address: 6-10-1, Hakozaki

institute: Kyushu university

summary: Stomata open in response to light and close following exposure to abscisic acid (ABA). They regulate gas exchange between plants and atmosphere, allowing plants to adapt to changing environmental conditions. ABA binding to receptors initiates a signaling cascade that involves protein phosphorylation. Here we show that ABA induced phosphorylation of three basic helix-loop-helix (bHLH) transcription factors, called AKSs (ABA-RESPONSIVE KINASE SUBSTRATES; AKS1, AKS2, AKS3), in Arabidopsis guard cells, and that they facilitated stomatal opening through the transcription of genes encoding inwardly-rectifying K+ channels. aks1aks2-1 double mutant plants showed decreases in light-induced stomatal opening, K+ accumulation in response to light, activity of inwardly-rectifying K+ channels, and transcription of genes encoding major inwardly-rectifying K+ channels. Overexpression of POTASSIUM CHANNEL IN ARABIDOPSIS THALIANA 1 (KAT1), which encodes a major inwardly-rectifying K+ channel in guard cells, rescued the phenotype of aks1aks2-1 plants. AKS1 bound directly to the promoter of KAT1, an interaction that was attenuated after ABA-induced phosphorylation. The ABA agonist pyrabactin induced phosphorylation of AKSs. Our results demonstrate that the AKS family of bHLH transcription factors facilitates stomatal opening through transcription of genes encoding inwardly-rectifying K+ channels, and that ABA suppresses the activity of inwardly-rectifying K+ channel activity by triggering the phosphorylation of these transcription factors.

overall_design: To find the affect of AKS1 and AKS2 transcription factors on gene expression, Arabidopsis guard cell protoplasts from wild type and aks1aks2-1 mutant  were compared. Three independent experiments were performed.

first: Ken-ichiro

last: Shimazaki


title: Simultaneous application of heat, drought and virus to Arabidopsis thaliana plants reveals significant shifts in signaling networks [triple_stress]

status: Public on Jun 10 2013

city: Erlangen

first: Christian

last: Prasch

address: Staudtstrasse 5

department: Biochemistry division

country: Germany

institute: FAU Universität Erlangen-Nürnberg

summary: Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment.

overall_design: Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. Four biological replicates have been hybridized for each treatment.

first: Prasch

last: Christian

first: Sonnewald

last: Uwe


title: Simultaneous application of heat, drought and virus to Arabidopsis thaliana plants reveals significant shifts in signaling networks [triple_wdh]

overall_design: Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. In parallel, a homozougus T-DNA insertion line SALK_021115C  (N672283), located in the Arabidopsis gene  At5g45000 has been exposed to the same stress conditions. Four biological replicates have been hybridized for each treatment.


title: Simultaneous application of heat, drought and virus to Arabidopsis thaliana plants reveals significant shifts in signaling networks [severe_triple]

overall_design: Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. Four biological replicates have been hybridized for each treatment. Furthermore, Arabidopsis plants were exposed to a single severe heat stress (37°C day/33°C night) to mimic the severity of the triple stress experiment.


title: Simultaneous application of heat, drought and virus to Arabidopsis thaliana plants reveals significant shifts in signaling networks


title: Microarray analysis of  scap1 mutant and wild type in Arabidopsis thaliana guard cell protoplast

status: Public on Feb 28 2013

first: Juntaro

last: Negi

address: 6-10-1 Hakozaki, Higashi-ku

department: Biology

institute: Kyushu University

summary: Stomata are highly specialized organs which consist of pairs of guard cells and regulate gas and water vapor exchange in plants. While early stages of guard cell differentiation have been described and were interpreted in analogy to processes of cell type differentiation in animals, the downstream development of functional stomatal guard cells remains poorly understood. We have isolated an Arabidopsis mutant, scap1 (stomatal carpenter 1), that develops irregularly shaped guard cells and lacks the ability to control stomatal aperture, including CO2-induced stomatal closing and light-induced stomatal opening. SCAP1 was identified as a plant-specific Dof-type transcription factor expressed in maturing guard cells but not in guard mother cells. SCAP1 regulates the expression of genes encoding key elements of stomatal functioning and morphogenesis, such as a K+ channel protein, MYB60 transcription factor, and pectin methyl esterase. Consequently, ion homeostasis was disturbed in scap1 guard cells, and esterification of extracellular pectins was impaired so that the cell walls lining the pores did not mature normally. We conclude that SCAP1 regulates essential processes of stomatal guard cell maturation and functions as a key transcription factor regulating the final stages of guard cell differentiation.

overall_design: We isolated guard cell protoplasts from 4-week-old WT(Col-0) and scap1 mutant plants and extracted RNA independently. Four biological replicates were performed for each experiment.

first: Koh

last: Iba


title: Plant growth in Arabidopsis is assisted by whole soil microbial communities

status: Public on Mar 09 2013

city: Saint Lucia

first: Lilia

last: Costa Carvalhais

state: QLD

address: The University of Queensland John Hines Blg 5th floor room 517A

country: Australia

institute: The University of Queensland

summary: Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments.

overall_design: Four samples were analysed in total. One corresponded to a pooled sample of RNA extracted from root tissues of 60 plants. The other three were biological replicates from shoot tissues, each of which contained 20 plants. Controls were used as reference and corresponded to tissues of plants grown in sterile conditions.

middle: C

last: Carvalhais

first: Peer

last: Schenk

first: Frederico

last: Muzzi

first: Chin

last: Hong-Tan

first: Jin

last: Hsien-Choo


title: Microarray analysis of med14 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

status: Public on May 18 2013

first: Zhonglin

last: Mou

summary: The goal of the microarray experiment was to determine the induction kinetics of transcriptome changes and to identify differentially expressed genes in the Arabidopsis mutant med14 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2.  Results indicated that med14 exhibited slower kinetcis of transcriptional changes than the wild type after Pst DC3000/avrRpt2 infection, and the induction of a large group of defense genes was suppressed in the med14 mutant.

overall_design: Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 12 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Each replicate was used as one sample for microarray analysis.

first: Xudong

last: Zhang

last: Yao

first: Yanping

first: Yijun

last: Sun


title: Arabidopsis ult1-3 mutant restored LFYasEMF1's phenotype

status: Public on Mar 01 2013

first: Mao-Sen

last: Liu

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

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

summary: Arabidopsis ult1-3 mutant was shown to rescue the phenotype of LFYasEMF1 to that of WT. We performed microarray analysis of 7-d-old and 15-d-old seedlings of WT, LFYasEMF1, ult1-3 and LFYasEMF1/ult1-3 grown under short day to study the underlie mechanism of this phenotypic rescuing.

overall_design: Gene expression of 7 and 15 day old WT, LFYasEMF1, ult1-3 and LFYasEMF1/ult1-3 seedlings grown under short day condition were performed and compared.

first: Zinmay

last: Sung

first: Long-Fang

middle: O

last: Chen


title: Microarray analyses of pathogen-induced transcriptome changes in the Arabidopsis mutant med14

overall_design: Refer to individual Series


title: Expression data of WT (NCED3pro:LUC transgenic plants, gl1 Columbia background) and ced2 under osmotic stress

status: Public on Feb 21 2013

city: Thuwal

first: zhenyu

last: wang

address: PSGC

country: Saudi Arabia

institute: KAUST

summary: ced2 mutant has reduced expression of NCED3 in response to osmotic stress (PEG, polyethylene glycol) treatments compared to the wild type. Other ABA biosynthesis genes are also greatly reduced in ced2 under osmotic stress. We used microarrays to detail the global programme of gene expression under osmotic stress treatment and identified distinct classes of up/down-regulated genes in the stress pathway.

overall_design: Arabidopsis seedlings were selected at 14 days with 6hr PEG treatment for RNA extraction andhybridization to the Arabidopsis ATH1 Gene expression arrays (Agilent Technologies). From Northern data we have known some of well-known stress responsive gene were significantly changed. We sought to obtain whole gene expression to analysis which genes were affected in the osmotic stress pathway.

first: Zhenyu

last: Wang

first: Liming

last: Xiong


title: The expression profiles of WT and sgs1△ after tangeretin treatment

status: Public on Jan 29 2013

first: SHIN YEN

last: CHONG

address: No. 1, Sec. 4, Roosevelt Road,

department: Institute of Food Science and Technology

institute: National Taiwan University

summary: Tangeretin is a member of the polymethoxyflavones in citrus peel, which have been of interest due to their anti-atherogenic, anti-inflammatory, and anti-carcinogenic properties. However, their detailed target pathways have not been fully discovered. We applied the notion of chemical-genetic and genetic interactions in budding yeast, screening the putative targeting pathways of tangeretin, and we found that sgs1△ yeast was sensitive to tangeretin treatment. Therefore, we applied this microarray test to investigate the potential pathways influenced by tangeretin in sgs1. The gene expression profiles of WT and sgs1△ mutated yeast under tangeretin treatment were compared.

overall_design: The gene expression profiles of S. cerevisiae WT and sgs1△ strains under 30 μM tangeretin treatment for 4 hours were compared. Triplicated tests were made for each sample (tangeretin-treated WT, control-treated WT, tangeretin-treated sgs1△, control-treated sgs1△).

first: Shin

middle: Y

last: Chong

first: Yi

last: Lo


title: Microarray analysis of med14, med16, npr1, and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

summary: The goal of the microarray experiment was to identify genes that are differentially expressed among the Arabidopsis mutant med14, med16, npr1, and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2.  Results indicated that the induction of a large group of defense genes was suppressed in the med14 mutant compared with both med16 and the wild type.

overall_design: Three biological replicates with leaves from 8 plants per sample were collected at 0 and 4 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Each replicate was used as one sample for microarray analysis.


title: Evolutionary principles of modular gene regulation in Yeasts

status: Public on Jun 20 2013

city: Cambridge

first: Dawn

last: Thompson

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts

sample_organism:
Schizosaccharomyces pombe
Schizosaccharomyces japonicus
Lachancea waltii
Saccharomyces bayanus
Saccharomyces cerevisiae
Lachancea kluyveri
Yarrowia lipolytica
Debaryomyces hansenii
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Saccharomyces paradoxus
Kluyveromyces lactis
Vanderwaltozyma polyspora
Saccharomyces mikatae

platform_organism:
Schizosaccharomyces pombe
Schizosaccharomyces japonicus
Lachancea waltii
Saccharomyces bayanus
Saccharomyces cerevisiae
Yarrowia lipolytica
Debaryomyces hansenii
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Saccharomyces paradoxus
Kluyveromyces lactis
Vanderwaltozyma polyspora
Saccharomyces mikatae
Lachancea kluyveri NRRL Y-12651

overall_design: Each of the following species-specific, growth curve derived samples competitively hybed to their own mid-log samples: lag phase, late log, diauxic shift, post-shift, plateau

first: Sushmita

last: Roy


title: Expression data in an Arabidopsis cytokinin (CK)-signaling mutant, ahp2,3,5 and its wild type plant (Col-0) under drought and well-water (control) conditions.

status: Public on Feb 15 2013

city: Yokohama

first: Rie

last: Nishiyama

state: Kanagawa

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

department: Plant Science Center

institute: RIKEN

summary: To understand the role of CK-signaling components, AHPs (His-containing phosphotransfer proteins) in drought stress response, we have employed transcriptional profiling of ahp2,3,5 and it's wild type plant, Col-0 under drought and well-water (control) conditions. Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and ahp2,3,5 mutant plants were transferred from GM plates to soil and grown for an additional week. Three week-old plants were exposed to drought stress for 10 days or grown under well-watered condition in parallel. All rosette leaves of independent 31d-old plants were corrected. Total RNA was prepared and used for the microarray hybridization. Three replicative hybridization experiments were carried out for each independent biological sample.

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Lam

middle: S

last: Tran


title: Trichoderma-plant root colonization: escaping early plant defense responses and activation of the antioxidant machinery

status: Public on Nov 09 2012

city: Potsdam

first: Yariv

last: Brotman

address: Am Mühlenberg 1

institute: Max-Planck-Institute of Molecular Plant Physiology

summary: Trichoderma spp. are versatile opportunistic plant symbionts which can colonize the apoplast of plant roots. Microarrays analysis of Arabidopsis thaliana roots inoculated with Trichoderma asperelloides T203, coupled with qPCR analysis of 137 stress-responsive genes and transcription factors, revealed wide gene transcript reprogramming, preceded by a transient repression of the plant immune responses supposedly to allow root colonization. Enhancement in the expression of WRKY18 and 40, which stimulate JA-signaling via suppression of JAZ repressors and negative-regulate the expression of the defense genes FMO1, PAD3 and CYP71A13, was detected in Arabidopsis roots upon Trichoderma colonization. Reduced root colonization was observed in the wrky18/wrky40 double mutant line, while partial phenotypic complementation was achieved by over-expressing WRKY40 in the wrky18 wrky40 background. On the other hand, an increased colonization rate was found in roots of the FMO1 knockout mutant.

overall_design: Two-condition experiment: Roots treated with Trichoderma vs. Control untreated roots. Biological replicates: 2 control replicates, 2 treated replicates. 1 dye-swap.

first: Alvaro

last: Cuadros-Inostroza

first: Ada

last: Viterbo


title: Transcriptional Analysis of lsm1a lsm1b Arabidopsis mutant.

status: Public on Jan 16 2013

city: Madrid

first: Carlos

last: Perea-Resa

address: Ramiro de Maeztu,9

country: Spain

institute: CIB-CSIC

summary: Characterization of the lsm1a lsm1b transcriptional profile. LSM1 protein is involved in RNA decay through decapping facilitation. The performed array help us to understand the transcription level alterations produced by the absence of LSM1.

overall_design: One-condition experiment, Col-0 vs. lsm1a lsm1b plants. Biological replicates: 3 control replicates.

first: Tamara

last: Hernández-Verdeja

first: Julio

last: Salinas


title: Transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis

status: Public on Oct 19 2012

city: beijing

first: Jinsong

last: Zhang

address: No.1 West Beichen Road,Chaoyang District

institute: IGDB

summary: Plant-specific DOF-type transcription factors regulate various biological processes. Here, we characterized a silique-abundant gene AtDOF4.2 for its functions in Arabidopsis. AtDOF4.2 is localized in the nuclear region and has transcriptional activation activity in both yeast and plant protoplast assays. The Thr-Met-Asp motif in AtDOF4.2 is essential for its activation. AtDOF4.2-overexpressing plants exhibit an increased branching phenotype, and the mutation of Thr-Met-Asp motif in AtDOF4.2 significantly reduces the branching in transgenic plants. AtDOF4.2 may achieve this function through the upregulation of three branching-related genes, AtSTM, AtTFL1 and AtCYP83B1. The seeds of an AtDOF4.2-overexpressing plant show collapse-like morphology in epidermal cells of the seed coat. Mucilage contents and the concentration and composition of mucilage monosaccharides are significantly changed in the seed coat of transgenic plants. AtDOF4.2 may exert its effects on the seed epidermis through the direct binding and activation of the cell wall loosening-related gene AtEXPA9. The dof4.2 mutant did not exhibit changes in branching or its seed coat; however, the silique length and seed yield were increased. AtDOF4.4, which is a close homolog of AtDOF4.2, also promotes shoot branching and affects silique size and seed yield. Manipulation of these genes should have a practical use in the improvement of agronomic traits in important crops.

overall_design: Two-week-old seedlings (aerial part) of Col-0 and AtDOF4.4-overexpressing transgenic lines 4.4-1 and 4.4-5, grown on MS, were used for extraction of total RNA and subjected to chip analysis using Agilent Arabidopsis Oligo Microarray (4X44K) in SHANGHAIBIO CORPORATION (www.ebioservice.com; Shanghai, China).

first: Hong-Feng

last: Zou

first: Jin-Song


title: Identification of target genes of the DELLA protein RGL2 during the repression of seed germination

status: Public on Aug 31 2012

city: Singapore

first: Petra

last: Stamm

address: Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National Univerisity of Singapore

summary: To shed light on the genetic events downstream of DELLA proteins, we have employed a microarray expression profiling of Arabidopsis thaliana seeds to identify target genes of the DELLA protein RGL2. Seeds of the germinating ga1-3 rga-t2 rgl2-1 and the non-germinating ga1-3 rga-t2 mutant were stratified, and RNA was extracted after five days. Transcript profiles of the non-germinating seeds closely resemble profiles of dormant seeds, and several transcription factors involved in light- and phytohormone-regulated signalling pathways appear to be up-regulated, suggesting that RGL2 controls various physiological aspects to inhibit seed germination.

overall_design: Gene expression  five days after stratification was measured in ga1-3 rga-t2 seeds, using seeds of the ga1-3 rga-t2 rgl2-1 mutant as reference. Two biological replicates were performed for each sample.

first: Pratibha

last: Ravindran

first: Bijayalaxmi

last: Mohanty

first: E

last: Tan

first: Hao

last: Yu

first: Prakash

middle: P

last: Kumar


title: Arabidopsis thaliana vegetative part: Col-0 vs. shr scl23 scr triple mutant

status: Public on Oct 11 2012

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

country: South Korea

institute: KonKuk University

summary: Transcriptional profiling of the vegetative part of Arabidopsis comparing wild type with the shr scl23 scr triple mutant. The latter is produced by crossing the strong null alleles of shr (shr-2), scl23 (scl23-1) and scr (scr-5). The goal was to determine the effects of the GRAS transcription factors SHR, SCL23 and SCR on growth and development of the Arabidopsis shoot system by global transcriptome analysis.

overall_design: Two-condition experiment: Col-0 vs. shr scl23 scr triple mutant. Biological replicates: 2 WT vs. triple mutant replicates, 2 WT vs. triple mutant replicates dye-swap replicates.

first: Mi

last: Lee

first: Eun

middle: K

first: Jun

last: Lim


title: Global transcriptome analysis of tarani (tni)

status: Public on Sep 01 2012

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To gain insight molecular function of tarani with respect to cell division.

overall_design: Agilent one-color experiment. Organism: Arabidopsis thaliana, Agilent-021169 Gene Expression Arabidopsis 4x44k, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: K

last: Premananda

first: Challa

last: Krishna Reddy

first: Nath

last: Utpal


title: Transcript expression data from  Populus euphratica leaves subjected to drought

status: Public on Jul 01 2012

city: Haidian

first: Dong-hui

last: YAN

state: Beijing

address: 1#, Dong Xiao Fu

institute: Chinese Academy of Forestry

summary:
Populus euphratica is a natural population grown in semirid areas. The molecular response of the poplar to drought maintain to be elucided, especially at global genome level.
We used Affymetrix poplar genome genechip microarrays to analyze the full transcript expression underlying different drought intensities and identified significantly differently expressed genes during this process.

overall_design: Uniformly developed seedlings of P. euphratica grown in gradually long-term drought throught water-withholding treatment. Affymetrix poplar genechip was hired to investigate the full transcripts changed of the poplar response to different drought intensity levels.

last: Yan

first: Weilun

last: Yin


title: Transcriptional analysis for cell-cell communication during graft union development in Arabidopsis

status: Public on May 03 2012

city: Lanzhou

address: Tianshuinanlu 222

department: Life Science School

institute: Lanzhou university

summary: Grafting is an ancient cloning method that has been used widely for thousands of years in agricultural practices. However, the molecular mechanisms for graft union development are still largely unknown. The developmental stage of graft union was characterized based on micrografting method. Microarray data revealed a signal exchange process between cells of scion and stock at 1dag, which reestablished the communication network in graft union. This process was concomitant with the cleaning of cell debris, and both of the processes were initiated by a wound-induced program. The results demonstrate the feasibility and potential power of investigating various plant developmental processes by this method and represent a primary and significant step in interpretation of the molecular mechanisms underlying graft union development.

overall_design: WT/WT seedling grafts of 22-26 hours after grafting were collected for microarray, intact WT seedlings and ungrafted scions and stocks were as control. All three types of sample, grafts (marked as A: whole graft), ungrafted scions and stocks (marked as B: mixture of ungrafted scions and stocks) and intact seedlings (marked as C: whole seedling), were collected at the same time of 22-26 hours after grafting. For sample B, scions and stocks were cut at the same time during grafting. For sample C, intact seedlings were also reserved during grafting. Data were firstly compared between sample A and C, differential expressed probe sets were than tested based on A and B to obtain graft-specific probes.

first: Guochang

last: Zheng

first: Heng

last: Liu


title: dehydration response: dcp5-1 and WT

status: Public on Apr 06 2012

city: New York

last: Xu

address: 1230 york avenue

institute: Rockefeller University

summary: Transcriptional profiling of Arabidopsis dcp5-1 comparing control WT with 30min dehydration treatment. Goal was to determine the effects of DCP5 on global transcript abundance during dehydration response.

overall_design: Two-condition experiment, time0 and 30min dehydration. Biological replicates: 4 WT replicates, 4 dcp5-1 replicates.

first: Nam-Hai

last: Chua


title: Identification of target genes of ABI3 [Agilent 44k]

status: Public on Jun 01 2012

city: Gatersleben

first: Gudrun

last: Moenke

address: Corrensstr. 3

institute: IPK

summary:
ABI3 is a key regulator of seed development in Arabidopsis and other plants.To identify genes regulated by ABI3 we performed array based transcriptome analysis of Dexamethasone inducible ABI3 transgenic seedlings.
ABI3 mostly in concert with abscisic acid (ABA) was found to activate genes specifically expressed during the maturation phase of seed development.

overall_design: Two weeks old wildtype and 35S::ABI3::GR seedlings were treated with ABA, Dexamethasone (DEX) and ABA plus Dexamethasone for 4 h. Two biological independent experiments were performed. Wildtype was induced to control for DEX-induction of genes.

first: Astrid

last: Junker

first: Michael

last: Seifert

first: Lothar

last: Altschmied


title: Comparison of normalized signal intensities of various miRNAs in the exsosomes isolated by Exoquick or ultracentrifugation

status: Public on Jan 26 2012

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary:
MicroRNAs (miRNAs), small (18–22 nucleotides) non-coding RNAs, suppress the translation of target mRNAs by binding to their 3′ untranslated region. Evidence suggests that miRNAs are key regulators of several cellular processes, including angiogenesis. Recent findings indicate that Secreted miRNAs enclosed in exosomes also play an important role in cell–cell communication.
To elucidate whether miRNAs secreted from neoplastic cells transfer into endothelial cells and are functionally active in the recipient cells, we investigated the interaction of a leukemia cell line and human umbilical vein endothelial cells (HUVECs).

overall_design: The culture medium was collected and centrifuged at 3000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration. Exosome pellets were resuspended with 500 µl of the serum-free AIM V medium (Invitrogen).   K562 cells or K562/Cy3-miR-92a cells (K562 cells transfected with Cy3-labeled pre-miR-92a) were pre-cultured in serum-free AIM V medium (Invitrogen). The cells were cultured in 200 ml of AIM V medium (twenty 100 mm culture dishes). For exosome preparation, the culture media were collected and centrifuged at 2,000 × g for 10 min at room temperature, and the supernatant was centrifuged again at 12,000 × g for 30 min at room temperature, then the supernatant was ultracentrifuged at 110,000 × g for 70 min at 4 ºC. The pellets were washed with PBS, after ultracentrifugation, they were used for Microarray analysis.


title: Expression data in an Arabidopsis cytokinin-deficient mutant, ipt1,3,5,7 and its wild type plant (Col-0) under high salinity and control conditions.

status: Public on Jan 23 2012

first: Rie

last: Nishiyama

summary: To understand the role of cytokinins (CKs) in salt stress response, we have employed transcriptional profiling of the CK-deficient mutant, ipt1,3,5,7 and wild type plant, Col-0 under high salinity and control conditions to identify genes differentially expressed in ipt1,3,5,7 under salt stress and control conditions. Agilent's Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K) was used.

overall_design: 10-d-old plants grown on GM medium (22ºC, 16-h-light/8-h-dark) were transfered onto 1/2 MS agar plates without sucrose containing either 0 or 200 mM NaCl. Independent biological samples, 10 plants/each biological replicate, were collected after 24 hours. Total RNA was prepared and used for the microarray hybridization. Three replicative hybridization experiments were carried out for each independent biological sample.

first: Dung

last: Le

first: Yasuko

last: Watanabe

first: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Motoaki

last: Seki

first: Kazuko

last: Yamaguchi-Shinozaki

first: Kazuo

last: Shinozaki

first: Lam

last: Tran


title: Identification of target genes of ABI3

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Expression analysis of RCc3:OsNAC5 and GOS2:OsNAC5 transgenic rice plants

status: Public on Mar 01 2012

city: Yongin

first: Jin

middle: Seo

last: Jeong

state: Gyeonggido

address: San 38-2 Namdong, Cheoin-gu

institute: Myongji University

type: Expression profiling by genome tiling array

summary: For identification of genes up-regulated in RCc3:OsNAC5, GOS2:OsNAC5 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions.

overall_design: Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC5, GOS2:OsNAC5 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.

first: Youn

last: Kim

first: Harin

last: Jung

first: Mark

last: Redillas

first: Yang

middle: D

last: Choi

first: Christophe

last: Reuzeau

first: Ju-Kon


title: Nimblegen 385K array CGH on NCI-60 cancer cell lines

status: Public on Oct 24 2011

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

type: Genome variation profiling by genome tiling array

summary: The NCI-60 cancer cell lines have been used for studying cancer pathogenesis and for drug discovery. This dataset adds to the growing number of datasets on various genomic platforms that have been made public on Cellminer (http://discover.nci.nih.gov/cellminer/)

overall_design: 61 cell lines (including PR:DU145 and its drug resistant derivative PR:RC01) were arrayed. Of these, 56 were done one time, four cell lines were done with either two or three replicates, and one cell line (LC:A549) was done with three replicates and two dye flips. Two color arrays were used, with Cy3 mostly used for sample and Cy5 for the reference pool of 6 normal male samples.

first: William

last: Reinhold

first: Rebecca

middle: R

last: Selzer

first: John

middle: N

last: Weinstein

first: Peggy

last: Eis


title: Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat

status: Public on Dec 02 2011

city: Nashville

last: Tansey

address: 425 @1st Avenue South

institute: Vanderbilt University

type: Expression profiling by high throughput sequencing

summary: In Saccharomyces cerevisiae, ubiquitylation of histone H2B signals methylation of histone H3 at lysine residues 4 (K4) and 79. These modifications occur at active genes but are believed to stabilize silent chromatin by limiting movement of silencing proteins away from heterochromatin domains. In the course of studying atypical phenotypes associated with loss of H2B ubiquitylation/H3K4 methylation, we discovered that these modifications are also required for cell wall integrity at high temperatures. We identified the silencing protein Sir4 as a dosage-suppressor of loss of H2B ubiquitylation, and showed that elevated Sir4 expression suppresses cell wall integrity defects by inhibiting the function of the Sir silencing complex. Using comparative transcriptome analysis, we identified a set of euchromatic genes - enriched in those required for cellular response to heat - whose expression is attenuated by loss of H2B ubiquitylation, but restored by disruption of Sir protein function. Finally, using DNA adenine methyltransferase identification, we found that Sir3 and Sir4 associate with genes that are silenced in the absence of H3K4 methylation. Our data reveal that H2B ubiquitylation/H3K4 methylation play an important role in limiting ectopic association of silencing proteins with euchromatic genes important for cell wall integrity and the response to heat.

overall_design: The transcriptome of four strains, wildtype, htbK123R, sir4delta,and htbK123R sir4delta, were sequenced using Illumina sequencing technology

first: Amy

last: Leung

first: Ivelisse

last: Cajigas

first: Peilin

last: Jia

first: Elena

last: Ezhkova

first: Jason

last: Brickner

first: Zhongming

last: Zhao

first: Fuqiang

last: Geng


title: Arabidopsis thaliana ecotype Columbia [Col-0]: incubated with E. coli vs. Control

status: Public on Dec 01 2010

city: Brisbane

first: chanyarat

last: Paungfoo-Lonhienne

address: The University of Queensland

department: Science

institute: The University of Queensland

summary: To explore mechanisms involved in the plant-microbe interactions, we proceeded with genome-wide transcriptome analysis of Arabidopsis roots incubated with E. coli Bl21 for 24 hours. Control plants did not receive E. coli.

overall_design: Two-condition experiment, E. coli vs. Control. Biological replicates: 3 E. coli replicates, 3 control replicates

first: Chanyarat


title: Global Analysis of the Expression of Salmonella RyhB regulon

status: Public on Jan 08 2010

city: Fayetteville

first: Jeong Nam

last: Kim

state: AR

address: 1260 W Maple St. POSC L-115

department: Cell and Molecular Biology

institute: University of Arkansas

summary: Analysis of the Expression Change of RyhB Regulon in RyhB-deleted Mutant Strains.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Wild-type Salmonella 14028 vs. three mutant strains (∆ryhB1, ∆ryhB2, and ∆ryhB1&∆ryhB2); One condition experiment, Iron-depleted condition by adding 200 µM of 2,2’-dipyridyl (dip).

first: Jeong

first: Young

last: Kwon


title: RgfC/A regulated genes in Streptococcus agalactiae strain A909

status: Public on Apr 29 2010

city: Seattle

first: Lakshmi

last: Rajagopal

state: WA

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

summary:
Genes that showed altered expression between wild type A909 and isogenic rgfC/A mutant were identified. A strain with a deletion in RgfC/A (SAK_1917/SAK_1918) was derived and microarray analysis was performed to identify genes regulated by the RgfC/A two component system.
strain comparison, global regulation, two component system

overall_design: Deletion mutant was compared to the wild type strain A909 for changes in gene expression

first: Melissa

last: delosReyes


title: The Arabidopsis Aminopeptidase LAP2 Regulates Plant Growth, Leaf Longivity and Stress Response

status: Public on Jun 02 2010

city: Tsukuba

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: Peptidases are known to play key roles in multiple biological processes in all living organisms.  In a model plant Arabidopsis, the vast majority of many putative aminopeptidases remain uncharacterized.  We therefore aim to explore physiological function of uncharacterized aminopeptidase in higher plants using Arabidopsis as a model to study.We performed functional and expression analyses of the Arabidopsis LAP2 through cDNA cloning, isolation of T-DNA insertional mutants, characterization of the enzymatic activity, characterization of gene expression, and transcriptomic and metabolomic analyses of the mutants.  We found that LAP2, one of the 28 aminopeptidases in Arabidopsis, regulates plant growth, leaf longevity and stress response by controlling intracellular protein turnover.  Loss-of-function alleles of LAP2 reduced in vegetative growth, accelerated leaf senescence and rendered plants more sensitive to various stresses.  LAP2 is highly expressed in the quiescent center cells in the root meristem, cotyledons and leaf veins.  Integration of global gene expression and metabolite analyses suggest that LAP2 controlled intracellular protein turnover.  The mutant maintained free leucine by up-regulating key genes for leucine biosynthesis, however, this influenced the flux of glutamate strikingly.  As a result, gamma-aminobutyric acid, a metabolite which is derived from glutamate, was diminished in the mutant.  Decrements in these nitrogen-rich compounds are associated with morphological alterations and stress sensitivity of the mutant.Our results provide molecular and biochemical evidence that LAP2 is indeed an enzymatically active aminopeptidase. LAP2 plays key roles in senescence, stress response and protein turnover.  Regulated proteolysis is an important mechanism in all stages of the plant life cycle.  The present study would contribute to further understanding of the aminopeptidases which have several implications in higher plants.

overall_design: Comparison between wild-type and mutant (LAP2-1) plants was performed. Two biological replicates (20 pooled plants in each replicate) were used, and each replicate was dye-swaped.

first: Rungaroon

last: Waditee-Sirisattha

first: Junko

last: Shibato

first: Randeep

last: Rakwal

first: Sophon

last: Sirisattha

first: Akira

last: Hattori

first: Takeshi

last: Nakano

first: Teruhiro

last: Takabe

first: Masafumi

last: Tsujimoto


title: Expression profiling defines a recurrence signature in lung adenocarcinoma

status: Public on May 01 2007

first: Jill

middle: Everland

last: Larsen

state: Queensland

address: Rode Road, Chermside

department: Thoracic Medicine

institute: The Prince Charles Hospital

summary:
Lung cancer remains the leading cause of cancer death worldwide. Overall 5-year survival is about 10-15% and despite curative intent surgery, treatment failure is primarily due to recurrent disease. Conventional prognostic markers are unable to determine which patients with completely resected disease within each stage group are likely to relapse. To identify a gene signature associated with recurrent adenocarcinoma (AC) of lung, we analyzed primary tumour gene expression for a total of 48 stage I ACs on 22,323 element microarrays, comparing expression profiles for individuals who remained disease-free for a minimum of 36 months with those from individuals whose disease recurred within 18 months of complete resection. Genome-wide profiling has revealed a distinct gene expression profile for recurrent lung AC which may be clinically useful as a prognostic tool.
Keywords: non-small cell lung carcinoma, squamous cell, tumor recurrence, expression profiling

overall_design: Expression profiling using 22K element microarrays of 48  adenocarcinomas.

middle: E

first: Sandra

last: Pavey

first: Belinda

last: Clarke

first: Rayleen

middle: V

last: Bowman

first: Nicholas

last: Hayward

first: Kwun

last: Fong


title: Global expression profiles in one hour biopsy of human kidney transplantation from donors after cardiac death

status: Public on Feb 08 2008

city: Toyoake

first: Mamoru

last: Kusaka

state: Aichi

address: 1-98 Kutsukake

department: Department of Urology

institute: Fujita-Health University

summary:
Because of world-wide shortage of renal grafts, kidney transplantation (KTx) from donors after cardiac death (DCD) is an alternative way to KTx from brain-dead donors. Although the prognosis of DCD KTx is gradually improving, the graft often undergoes delayed graft function (DGF) rendering the control of DGF essential for post-KTx patient care. To know the etiology of the DGF, we performed genome-wide gene expression profiling using renal biopsy samples performed at 1 hour after KTx from DCD and compared the data with those of KTx from living donors (LD). A total of 526 genes were differentially expressed between them. Genes involved in acute inflammation were activated, while metabolic pathways were consistently down-regulated in DCD. All of these findings imply inferior performance of the DCD grafts relative to LD grafts. We identified several genes of which expression levels were correlated well with parameters indicating short- and long-term prognosis of the DCD patients. In addition, we identified several genes encoding secretory proteins that might reflect the performance of the graft and be potent non-invasive biomarkers. Our data provide good source for candidates of biomarker that are potentially useful for control of DGF.
Keywords: disease state analysis

overall_design: This investigation was approved by the Institutional Review Boards of our centers. Written informed consent was obtained from each patient or legal guardian before enrollment. Consecutive patients undergoing either a living (n =15) or DCD KTx (n = 14) at this center were prospectively enrolled. The immunosuppressive regimen was similar in all patients, consisting of basiliximab, tacrolimus or cyclosporine with prednisone and mycophenolate mofetil. All kidney grafts were procured at this canter using in situ regional cooling technique from DCD. All donors after cardiac death from this hospital were classified as type IV in this study. The cause of donor death was cerebrovascular disease in all cases. Although most of those cases required HD (0-22 days) after KTx because of DGF, the function of all of transplanted kidneys eventually recovered. All kidney grafts from LD were procured by open nephrectomy in this study. All graft biopsies were performed one hour after reperfusion during kidney transplant operation using biopsy needles. All biopsy samples were stored immediately in RNA later (Applied Biosytems). Total cellular RNA was extracted from frozen samples using RNeasy (Qiagen, Valencia, CA, USA). For DNA microarray experiments, 200 ng aliquots of total RNA were labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, CA) according to the manufacturer'€™s instructions. RNA purified from each kidney graft was used for microarray analysis (Cy5-labeled), with pooled RNA derived from normal kidneys (Homan Kidney Total RNA #636529 BD, Franklin Lakes, NJ, USA) as a template control (Cy3-labeled). After checking the labeling efficiency, 1 ug aliquots of Cy3-labeled normal control RNA and Cy5-labeled RNA from individual grafts were mixed, and then hybridized to Agilent Human 1A (Ver. 2) Microarrays (Product No.G4110B) according to the manufacturerâ€™s hybridization protocol. After washing, the microarray slides were analyzed with an Agilent Microarray scanner and software (scanner model G2565BA). Data analysis was performed using Agilent Feature Extraction software (Ver. A.7.1.1), and Excel 2007 (Microsoft).


title: Efficient Yeast ChIP-Seq using Multiplex Short-Read DNA Sequencing

status: Public on Oct 24 2008

city: Palo Alto

first: Ghia

last: Euskirchen

address: 1501 S. California Ave.

department: Genetics

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Short-read DNA sequencing technologies provide new tools to answer biological questions.  However, high cost and low throughput limit their widespread use, particularly in organisms with smaller genomes such as S. cerevisiae.  Although ChIP-Seq in mammalian cell lines is replacing array-based ChIP-chip as the standard for transcription factor binding studies, ChIP-Seq in yeast is still underutilized compared to ChIP-chip.  We developed a multiplex barcoding system that allows simultaneous sequencing and analysis of multiple samples using Illumina’s platform.  We applied this method to analyze the chromosomal distributions of three yeast DNA binding proteins (Ste12, Cse4 and RNA PolII) and a reference sample (input DNA) in a single experiment and demonstrate its utility for rapid and accurate results at reduced costs.  We developed a barcoding ChIP-Seq method for the concurrent analysis of transcription factor binding sites for yeast. Our multiplex strategy generated high quality data that was indistinguishable from data obtained with non-barcoded libraries.  None of the barcoded adapters induced differences relative to a non-barcoded adapter when applied to the same DNA sample. We used this method to map the binding sites for Cse4, Ste12 and Pol II throughout the yeast genome and we found 148 binding targets for Cse4, 823 targets for Ste12 and 2508 targets for PolII.  Cse4 was strongly bound to all yeast centromeres as expected and the remaining non-centromeric targets correspond to highly expressed genes in rich media, the latter constituting a novel finding.  We designed a multiplex short-read DNA sequencing method to perform efficient ChIP-Seq in yeast and other small genome model organisms.  This method produces accurate results with higher throughput and reduced cost.  Given constant improvements in high-throughput sequencing technologies, increasing multiplexing will be possible to further decrease costs per sample and to accelerate the completion of large consortium projects such as modENCODE.

overall_design: Examination of the distribution of PolII (4 biological replicates), Cse4 (3 biological replicates) and Ste12 (3 biological replicates) using barcoded adapters and non-barcoded genomic DNA Illumina adapters. Input DNA was used as a reference sample and for scoring as well.

first: Philippe

last: Lefrançois

first: Raymond

last: Auerbach

first: Joel

last: Rozowsky

first: Theodore

last: Gibson

first: Christopher

last: Yellman

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: Copper(II) Sulfate treatment with 10 mM for 2 h

status: Public on Nov 01 2007

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

summary:
The effect of the heavy metal copper on the expression of a wide spectrum of genes was analyzed by using a DNA microarray.  Gene expression profile of baker’s yeast Saccharomyces cerevisiae grown in a media containing sub-lethal concentration of cupric sulfate was compared with those of yeast grown in a normal media.  Among about 6200 ORFs of yeast, 143 ORFs were induced more than two-fold to resist against copper toxicity after exposure to copper.  As was expected, FRE1, FRE7, and CTR1, genes controlled by Mac1p, were strongly down-regulated.  Copper metallothionein CUP1-1 and CUP1-2 were induced more than 20-fold.  Some genes related to sulfur metabolism and oxidative stress response were also up-regulated.  This DNA microarray technology indicated that plasma membrane, cell wall, protein, and DNA, were molecular targets of copper toxicity.
Keywords: stress response

overall_design: Series containes 3 hybridization results from independent biological samples, and each experiment have high and low power scanned data respectively. However, the low data from array-1 and array-3 was eliminated because of the data quality (the data from array-1 with low power scanning was not submitted in this series, whereas that from array-3 was submitted).

first: Daisuke

last: Yasokawa

first: Hitoshi

last: Iwahashi


title: Mammary gene expression profile of goats receiving high or low forage diets supplemented or not with lipids

status: Public on Nov 29 2009

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

country: France

institute: INRA

summary: Animal nutrition considerably affects milk composition that influences its nutritional quality. Milk component synthesis and secretion by the mammary gland involve the expression of a large number of genes whose nutritional regulation remains poorly defined. In this study, 16 lactating goats received 4 experimental diets differing in either forage to concentrate ratio (high forage, HF, or low forage, LF) supplemented, or not, with lipids (whole rapeseeds, RS, or sunflower oil, SO) in a 4 x 4 Latin Square design. To investigate the pathways regulated by nutrition, we examined the effect of these diets on the expression of approximately 8400 genes in caprine mammary gland using a bovine oligonucleotide microarray.

overall_design: Due to the limited quantity of mammary RNA available, equal amounts of total RNA sample from mammary gland of each goat belonging to the same Latin Square group were mixed together before labeling. Each mammary pooled sample (4 by dietary treatment) was then co-hybridized with a standard reference corresponding to a mixture of purified total RNA from several caprine tissues. Each hybridization was repeated in a dye-swap manner for a total of 32 slides (8 slides and 4 independent comparisons by dietary treatment).

first: Séverine

last: Ollier

first: Anne

last: De La Foye

first: Yves

last: Chilliard