title: Expression data from Arabidopsis wild-type, KO-nudx6, KO-nudx7, and double KO-nudx6/7 plants

status: Public on Oct 28 2015

city: Kasugai

first: Kazuya

last: Yoshimura

state: Aichi

address: 1200 Matsumoto-cho

department: Department of Food and Nutritional Science, College of Bioscience and Biotechnology,

institute: Chubu University

summary:
Arabidopsis Nudix hydrolases, AtNUDX6 and 7, exhibit pyrophosphohydrolase activities toward NADH and contribute to the modulation of various defense responses, such as the poly(ADP-ribosyl)ation (PAR) reaction and salicylic acid (SA)-induced Nonexpresser of Pathogenesis-Related genes 1 (NPR1)-dependent defense pathway, against biotic and abiotic stresses.
To identify genes (NRGs) whose expression levels positively and negatively correlated with NADH levels, a transcriptome analysis using KO-nudx6, KO-nudx7, and double KO-nudx6/7 plants, in which intracellular NADH levels increased in a step-wise manner.

overall_design: Arabidopsis wild-type, KO-nudx6, KO-nudx7, and double KO-nudx6/7 plants were grown on MS medium in a growth chamber kept at 23°C during 16 h of light (100 µmol/m2/s) and at 22°C during 8 h of darkness. Two-week-old cotyledons were collected as samples for microarray analysis.

first: Takahisa

last: Ogawa

first: Shigeru

last: Shigeoka


title: Comparison of gene expression between cna-2 phb-13 phv-11, cna-2 phb-13 phv-11 rev-6, and wild type (Col er-2) in 0.5 mm root tips of Arabidopsis.

status: Public on Dec 03 2015

city: Uppsala

first: Christina

middle: Joy

last: Müller

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary:
The class III HD-ZIP transcription factors regulate vascular patterning in Arabidopsis thaliana roots. In this expression study we compare the expression profile of the cna-2 phb-13 phv-11 and cna-2 phb-13 phv-11 rev-6 mutants to their wild type. The results are presented in PHABULOSA mediates an auxin signaling loop to regulate vascular patterning in Arabidopsis by Christina Joy Müller, Ana Elisa Valdés, Guodong Wang, Prashanth Ramachandran, Lisa Beste, Daniel Uddenberg, and  Annelie Carlsbecker, accepted for publication in Plant Physiology Nov. 2015.
Plant vascular tissues, xylem and phloem, differentiate in distinct patterns from procambial cells as an integral transport system for water, sugars and signaling molecules. Procambium formation is promoted by high auxin levels activating class III homeodomain leucine zipper (HD-ZIP III) transcription factors (TFs). In the root of Arabidopsis thaliana, HD-ZIP III TFs dose-dependently govern the patterning of the xylem axis, with higher levels promoting metaxylem cell identity in the central axis and lower levels protoxylem at its flanks. It is, however, unclear by what mechanisms the HD-ZIP III TFs control xylem axis patterning. Here we present data suggesting that an important mechanism is their ability to moderate auxin response. We found that changes in HD-ZIP III TF levels affect the expression of genes encoding core auxin response molecules. We show that one of the HD-ZIP III TFs, PHABULOSA, directly binds the promoter of both MONOPTEROS/AUXIN RESPONSE FACTOR5 (MP/ARF5), a key factor in vascular formation, and IAA20, encoding an AUX/IAA protein which is stable in the presence of auxin and able to interact with and repress MP activity. The double mutant of IAA20 and its closest homologue IAA30 forms ectopic protoxylem, while overexpression of IAA30 causes discontinuous protoxylem and occasional ectopic metaxylem, similar to a weak loss-of-function mp-mutant. Our results provide evidence that HD-ZIP III TFs directly affect auxin response and mediate a feed forward loop formed by MP and IAA20 that may focus and stabilize auxin response during vascular patterning and differentiation of xylem cell types.

overall_design: Root tips of 4 days post germination Arabidopsis thaliana cna-2 phb-13 phv-11 and cna-2 phb-13 phv-11 rev-6 mutants and Col er-2 grown vertically were manually microdissected to ca 0.5 mm. The cna-2 phb-13 phv-11 rev-6 homozygous  plants originated from a segregating cna-2 phb-13 phv-11 rev-6/+ population and were identified based on their radial cotyledon phenotype, that can be easily distinguished.  Three biological replicates were included for each genotype. RNA was prepared from the root tips and hybridized on Affymetrix ATH1 microarrays.

first: Lisa

last: Beste

first: Annelie

last: Carlsbecker


title: Bird Factors integrate positional signals to coordinate asymmetric cell division and cell fate

status: Public on Nov 02 2015

city: Durham

first: Rosangela

last: Sozzani

address: 124 Science Dr

country: USA

institute: Duke

summary: We sorted for GFP+ cells using the enhancer trap J0571 with the UAS promoter driving the expression of different BIRD genes. Different genetic backgrounds are use and listed below.

overall_design: Seedlings were grown for 5 days.  J0571 and J0571-UAS-BIRDS sorted fluorecent cells were harvested for RNA extraction.

first: Miguel

last: Moreno-Risueno

first: Philip

middle: N

last: Benfey


title: Polysome profiling in Arabidopsis thaliana over a 24-hour diurnal cycle

status: Public on Oct 15 2015

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: Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation.  We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

overall_design: 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.

first: Ben

last: Ernest

first: Anamika

last: Missra


title: Transcript levels in CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle


title: A highly conserved bacterial effector localizes to the host plasma membrane and downregulates the expression of the NDR/HIN1-like 13 (NHL13) gene requiried for antibacterial immunity in Arabidopsis

status: Public on Oct 06 2015

city: East Lansing

first: Sheng Yang

last: He

state: Michigan

address: 612 Wilson Rd, Rm106

institute: Michigan State University

summary:
Many bacterial pathogens of plants and humans cause infections by delivering effector proteins into host cells. Elucidation of how pathogen effector proteins function not only is critical for understanding bacterial pathogenesis, but also provides an important tool in discovering the functions of host genes. In this study, we characterized the Pseudomonas syringae pv. tomato DC3000 effector AvrE, the founding member of a widely distributed, yet functionally enigmatic, bacterial effector family. We show that AvrE is localized in the plasma membrane (PM) and PM-associated vesicle-like structures in the plant cell. AvrE contains two physically interacting domains, and the N terminal portion contains a plasma membrane localization signal. Genome-wide microarray analysis indicates that AvrE, as well as a functionally-redundant effector HopM1, down-regulates the expression of the NDR1/HIN1-Like 13 gene in Arabidopsis.  Mutational analysis shows that NHL13 is required for plant immunity, as the nhl13 mutant plant displayed enhanced disease susceptibility. Our results defined the site of action of one of the most important bacterial virulence proteins in plants and the anti-bacterial immunity function of the NHL13 gene.
To determine whether the type III effector AvrE’s virulence function is reflected by a possibly unique host gene expression signature, we conducted a genome-wide microarray analysis of Arabidopsis during Pst DC3000 infection. Because AvrE and another effector, HopM1, in Pst DC3000 are functionally redundant, the following bacterial strains were used to discern the shared and specific contributions of AvrE and HopM1 to host gene expression: Pst DC3000 (avrE+, hopM1+), the avrE mutant (hopM1+), the hopM1 mutant (avrE+) and the avrE hopM1 double mutant.

overall_design: Leaves of 5-week-old Arabidopsis Col-0 plants were vacuum-infiltrated with Pst DC3000, the avrE mutant, the hopM1 mutant or the avrE hopM1 double mutant at 1x108 cfu/ml. Tissue samples were collected by snap-freezing in liquid nitrogen 7 h after bacterial infiltration and RNA was extracted using RNeasy plant mini kits (Qiagen). The Gene Chip Arabidopsis ATH1 genome array (Affymetrix) was used for microarray analysis in the Research Technology Support Facility at Michigan State University.

first: Xiu-Fang

last: Xin

first: Sheng

middle: Y


title: Transcript levels in Arabidopsis thaliana over a 24-hour diurnal cycle


title: HeLa cell: DUSP2 overexpression vs. control

status: Public on Sep 30 2015

city: Tainan

first: Shaw-Jenq

last: Tsai

address: 1 , University Road

department: Department of Physiology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

summary:
The MAPK-specific phosphatase, dual-specificity phosphatase-2 (DUSP2), was negatively regulated by HIF-1a under hypoxia. To identify the downstream genes regulated by DUSP2, microarray analysis was performed.
Agilent two color microarray  was used to examine the molecular profile after DUSP2 overexpression

overall_design: Two-condition experiment, control HeLa vs. DUSP2-overexpressed-Hela cells. Biological replicates: 4 control replicates, 4 transfected replicates.

first: Shih-Chieh

last: Lin


title: Analysis of neonatal B lymphocytes

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

summary: B lymphocytes in the neonates are poorly define and some of which express the marker CD5. The experiment is based on the flow cytometry cell sorting of 2 populations of B lymphocytes defined according to their phenotype : 1/ CD5 positive sorted as CD20+CD19+CD3-CD5+CD10- ; 2/ CD5 negative B lymphocytes sorted as CD20+CD19+CD3-CD5-CD10-. Cells were isolated from fresh heparinised cord blood used within 24 hours after sample collect, without any additional treatment

overall_design: Comparison of CD5-positive and CD5-negative B lymphocytes isolated from cord blood obtained from 4 donors

first: Richard

last: Lo-Man

first: Xiaoming

last: Zhang


title: The Arabidopsis thaliana map65-3 and ugt76b1 mutant transcriptomes upon the compatible interaction with Hyaloperonospora arabidopsidis

status: Public on Sep 23 2015

city: Sophia Antipolis

first: Harald

last: Keller

address: 400 route des Chappes

department: UMR-ISA

country: France

institute: INRA

summary: We used Arabidopsis full-genome microarrays to characterize plant transcript accumulations in map65-3 and ugt76b1 mutants, 3 days after water treatment and inoculation with the biotrophic oomycete downy mildew pathogen, Hyaloperonospora arabidopsidis (Hpa)

overall_design: In two independent experiments, cotyledons from the wild-type Wassilewskija (WS) ecotype, and from the map65-3 and ugt76b1 mutants were treated with water, or inoculated with the Hpa isolate Emwa1 to establish a compatible interaction. Affymetrix ATH1 microarrays were used to profile Arabidopsis transcript accumulations at 3 days after onset of treatment. Data from the water-treated and Hpa-infected wild-type were previously deposited as GSM914964, GSM914965, GSM914966, and GSM914967. The wild-type data, and the data from the map65-3 and ugt76b1 mutant presented here were established in the same set of experiments and analyses, which also involved the previously deposited pskr1-5 mutant (GSM914968, GSM914969, GSM914970, and GSM914971).

first: Valérie

last: Allasia

first: Michael

last: Quentin

first: Isabelle

last: Baurés

first: Bruno

last: Favery


title: Polysome profiling in CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle


title: Analysis of gene expression changes in KPT-185-treated HMLE cells transduced to stably overexpress SNAI1

status: Public on Aug 31 2015

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary:
HMLE-SNAIL cell cultures were  treated with KPT-185 drug (KPT, 150 nanomolar) or vehicle (DMSO) for 24 hours, in parallel quadruplicates. KPT-185 is an Exportin 1 (XPO1) inhibitor with possible pluripotent or unexpected effects on cell signaling.
Total RNA was isolated and analyzed in an Agilent two-color experiment, where four biological replicates of each condition were directly compared, expression ratios are KPT-treated condition relative to control (DMSO vehicle-treated).

overall_design: The experiment object was to identify genes that displayed significantly altered expression in response to KPT treatment inorder to confirm on-target drug impact and elucidate other potential effects in this cell line model.

first: Asfar

last: Azmi


title: Expression of Vitis amurensis NAC26 in Arabidopsis enhances drought tolerance by modulating jasmonic acid synthesis

status: Public on Aug 14 2015

city: Wuhan

first: Lingye

last: Su

address: Lumo Road, Moshan

country: China

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

summary: The growth and fruit quality of grapevine are widely affected by abnormal climatic conditions such as water deficit. But how grapevine responds to drought stress is still largely unknown. Here we found that VaNAC26, a member of NAC transcription factor family, was up-regulated dramatically during cold, drought and salinity treatments in Vitis amurensis, a cold and drought-hardiness wild Vitis species. Ectopic overexpression of VaNAC26 enhanced the drought and salt tolerances in transgenic Arabidopsis. Higher activities of antioxidant enzymes and the lower concentration of H2O2 and O2- were found in VaNAC26-OE lines than in wild type plants under drought stress. These results indicate that the reactive oxygen species (ROS) scavenging was enhanced by VaNAC26 in transgenic lines. Microarray based transcriptome analysis reveals that genes related to jasmonic acid (JA) synthesis and signaling were up-regulated in VaNAC26-OE lines under both normal and drought conditions. VaNAC26 showed a specific binding ability on NACRS motif, which was broadly existent in the promoter regions of up-regulated genes in transgenic lines. Endogenous JA content was found increased obviously in VaNAC26-OE-2/3 lines. Our data suggests that VaNAC26 responds to abiotic stresses and may enhance the drought tolerance by transcriptional regulation of JA synthesis in Arabidopsis.

overall_design: Leaves from wild-type and three transgenic lines were collected before and after 5 d of drought stress. An equal amount of leaves from three independent transgenic lines that were harvested in same day was pooled as OE lines for RNA isolation. Four samples were collected, which including WT 0d, OE 0d, WT 5d and OE 5d and each sample were represented by two replicates.

first: Linchuan

last: Fang

last: Sun

first: Xinbo

last: Li

first: Mengxiang

first: Shaohua

first: Haiping


title: Transcriptomic profiling of Arabidopsis exposed to E-2-hexenal

status: Public on Sep 08 2015

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

country: Netherlands

institute: University of Amsterdam

summary:
Plants are known to be responsive to volatiles, but knowledge about the molecular players involved in transducing their perception remain scarce.
Here the response of Arabidopsis thaliana to E-2-hexenal, one of the green leaf volatiles that are produced upon wounding, herbivory or infection with pathogens is studied. We have taken a transcriptomics approach to identify genes that are induced by E-2-hexenal but not by defense hormones.

overall_design: In three independent biological experiments, Arabidopsis plants, ecotype Columbia (Col-0), were exposed either to 3 µM aerial E-2-hexenal or to the carrier MeOH for the mock treatment and rosette leaves were harvested after 1h, 3h and 24h.

first: Rossana

last: Mirabella

first: Alessandra

last: Scala

first: Timo

middle: M

last: Breit

first: Michel

middle: A

last: Haring

first: Robert

middle: C

last: Schuurink


title: The tinkerbell (tink) mutation identifies the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a novel regulator of organ size in Arabidopsis.

status: Public on Jul 30 2015

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants.  In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway.  Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development.  We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.

overall_design: 6 samples, three mutant replicates, three wild type replicates.

first: Kim

middle: L

last: Johnson

first: Sascha

last: Ramm

first: Christian

last: Kappel

first: Sally

last: Ward

first: Ottoline

last: Leyser

first: Tomoaki

last: Sakamoto

first: Tetsuya

last: Kurata

middle: W

last: Bevan


title: Polysome profiling in wild type and CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle

first: Albrecht

last: von Arnim

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

overall_design: Refer to individual Series


title: Comparison of low water potential (drought) regulated gene expression in wild type (Col-0) and egr1-1egr2-1 (At3g05640/At5g27930) mutant.

status: Public on Oct 08 2015

city: Taipei

first: Bhaskara

last: Goivnal Badiger

address: 128 Sec. 2, Academia Rd, Nankang, Taipei 11529 Taiwan, R.O.C.

department: Institue of Plant and Microbial Biology

institute: Academia Sinica

type:
Expression profiling by array
Third-party reanalysis

summary:
Two Clade E Growth Regulating PP2Cs EGR1 and EGR2 (EGR1, At3g05640; EGR2, At5g27930) are strongly up regulated by low water but much less affected by ABA.  EGR mutants maintained higher seedling root elongation and dry weight at low water potential and higher levels of stress protective metabolite proline.

Phosphoproteomics of egr1egr2 double mutant showed an increased phosphopeptide abundance of several cytoskeleton and plasma membrane-associated proteins, and consistent to this, egr mutants had more extensive microtubules recovery during low water potential acclimation.

Microarray experiments were used to identify genes differentially expressed in egr1-1egr1-2 (SALK_011589/salk_048861) versus wild type under both unstress control conditions and after low water potential (ie: drought, water deficit).  A relatively long term (96 h) low water potential treatment was used as phenotypes of egr1-1egr2-1 were most apparent after this longer term low water potential treatment.

overall_design:
Seven-day-old seedlings of wild type (Col-0) or egr1-1egr1-2 were transferred from agar plates of control media to low water potential stress (PEG-infused agar plates at -1.2 MPa) or to fresh control media (-0.25 Mpa).  Samples (whole seedlings) were collected 96 h after transfer.  Three independent experiments were conducted with one sample of each treatment (wild type stress and control, egr1-1egr2-1 stress and control) collected from each experiment.
Gene expression data of Col-0 samples were the same set of samples which were previously (GSE35258) compared with the gene expression of Clade A PP2C, Highly ABA Induced 1 (HAI1).
Microarray experiments of Col-0, hai1-2 and egr1-1egr2-1 were performed at the same time.
Here, we are using same set of Col-0 expression profile to compare with the expression profile of egr1egr2.

last: Govinal Badiger

first: Thao

middle: T

last: Nguyen

first: Paul

middle: E

last: Verslues


title: Expression data from WT Col-0 and the pdx1.3 ko mutant of Arabidopsis

status: Public on Jul 25 2015

city: Geneva

first: Teresa

last: Fitzpatrick

address: 30 Quai E. Ansermet

department: Botany and Plant Biology

country: Switzerland

institute: University of Geneva

summary:
We performed a microarray experiment to assess the global changes in transcription occurring in leaves and roots of the vitamin B6 deficient pdx1.3 knockout mutant in comparison to WT. Vitamin B6 (pyridoxal 5′-phosphate) is an essential cofactor of many metabolic enzymes. Plants biosynthesize the vitamin de novo employing two enzymes, pyridoxine synthase1 (PDX1) and PDX2. In Arabidopsis (Arabidopsis thaliana), there are two catalytically active paralogs of PDX1 (PDX1.1 and PDX1.3) producing the vitamin at comparable rates. Since single mutants are viable but the pdx1.1 pdx1.3 double mutant is lethal, the corresponding enzymes seem redundant.
However, the single mutants exhibit substantial phenotypic differences, particularly at the level of root development, with pdx1.3 being more impaired than pdx1.1. Here, we investigate the impact of possible global changes in gene expression in the pdx1.3 mutant compared to WT on the phenotype.

overall_design: Four different types of samples (conditions) were analyzed, namely pdx1.3 leaves, pdx1.3 roots, WT leaves and WT roots with three biological replicates per condition (12 samples altogether). WT samples served as reference (control) for the respective pdx1.3 samples.

first: Svetlana

last: Boycheva

middle: B


title: Genome-wide Immune Modulation of TLR3-mediated Inflammation in Intestinal Epithelial Cells Differ between Single versus Multi-Strain Probiotic Combination

status: Public on Aug 25 2015

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

country: Canada

institute: Lallemand Health Solutions Inc.

summary: Genome-wide transcriptional analysis in intestinal epithelial cells (IEC) can aid in elucidating the impact of single versus multi-stain probiotic combinations on immunological and cellular mechanism of action. In this study we used an in vitro intestinal epithelial cell model to investigate the impact of three probiotic bacteria individually or in combination and a surface-layer protein (SLP) partially purified from one of the bacteria on HT-29 cells’ response to a known pro-inflammatory stimulus, polyinosinic:polycytidylic, poly(I:C). Human expression microarray chips were used to evaluate the effect of Lactobacillus helveticus R0052, Bifidobacterium longum subsp. infantis R0033 and Bifidobacterium bifidum R0071 individually, in combination and of a surface-layer protein (SLP) partially purified from R0052 on HT-29 cells’ transcriptional profile to poly(I:C)-induced inflammation. Hierarchical heat map clustering, Set Distiller and String analyses revealed that the effects of R0052 and R0071 diverged from that of R0033 and R0052-SLP. It was evident from the global analyses with respect to the immune, cellular and homeostasis related pathways that the co-challenge with probiotic combination (PC) vastly differed in its effect from the single strains and R0052-SLP treatments. The multi-strain PC resulted in a greater reduction of modulated genes, found through functional connections between immune and cellular pathways. Cytokine and chemokine analyses based on specific outcomes from the TNF-α and NF-κB signaling pathways revealed single, multi-strain and R0052-SLP specific attenuation of the majority of proteins measured (TNF-α, IL-8, CXCL1, CXCL2 and CXCL10), indicating potentially different mechanisms. These findings indicate a synergistic effect of the bacterial combinations relative to the single strain and R0052-SLP treatments in resolving toll-like receptor 3 (TLR3)-induced inflammation in IEC and maintaining cellular homeostasis, reinforcing the rationale for using multi-strain formulations as a probiotic.

overall_design: The overall study design consisted of 8 different treatments/challenges of HT-29. Briefly, HT-29 cells were co-challenge for 3 h with either the single strains (R0033, R0052 or R0071) or probiotic combination (PC) alone or in combination with poly (I:C) at 10 µg/mL. Also, a specific surface layer protein purified from R0052 (R0052-SLP) was also co-challenged with poly (I:C) in HT-29 cells. Treatment/challenges of poly (I:C)-only, surface layer protein-only (R0052-SLP-only) and probiotic combination-only or PC-only were also evaluated. All challenges and co-challenges were compared to unchallenged control HT-29 cells. 4 biological reps were performed for each of the 8 samples/treatments.

first: Chad

last: MacPherson

first: Padmaja

last: Shastri

first: Olivier

last: Mathieu

first: Pierre

last: Burguière


title: Crosstalk between two bZIP signaling pathways orchestrates salt-induced metabolic reprogramming in Arabidopsis roots

status: Public on Sep 02 2015

city: Umea

first: Johannes

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

institute: Umeå Plant Science Centre

summary: Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.

overall_design: RNA from roots from Control and salt treated hydroponically grown seedligs were extracted and subjected to microarray analysis

first: Wolfgang

last: Dröge-Laser


title: Comparative analysis of transcriptional profiles of adult Schistosoma japonicum from different laboratory animals and the natural host, water buffalo

status: Public on Jul 19 2015

city: Beijing

first: Shuai

last: Liu

address: Dong Dan San Tiao 9, Beijing, China

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Although numerous researches on schistosomiasis japonica have been performed using laboratory animal models, the comparison of gene expression profiles of S. japonicum from the different laboratory animals and natural hosts is still a gap. We systematically compared the gene expression profiles of schistosomes from different laboratory animals and water buffaloes. The findings of this study provide the basis for schistosomiasis research in different mammalian hosts at transcriptional level and valuable resource for the screening of anti-schistosomal intervention targets.

overall_design: Three biological replicates of  adult male and female worms from BALB/c mice, C57BL/6 mice, New Zealand white rabbits and water buffaloes were analyzed.

first: Xianyu

last: Piao

first: Xiaosu

last: Zhou

last: Hou

first: Qijun

last: Chen


title: Gene expression changes in venous segments of overflowing arteriovenous fistulae

status: Public on Jul 17 2015

city: Hirosaki

first: Yasuhiro

last: Hashimoto

state: Aomori

address: 90 Yamazaki Kozawa

department: Urology

country: Japan

institute: Oyokyo Kidney Research Institute Hirosaki Hospital

summary: This study characterized the coordinated molecular changes evoked in the structure and composition of the wall of a venous segment exposed to high fistula flow.

overall_design: Venous tissues were obtained from the venous segments of overflowing arteriovenous (AV) fistulae present in 6 hemodialysis patients and from normal cephalic veins of 4 hemodialysis patients. Total RNA was extracted from these samples, and gene expression was compared between groups using a Whole Human Genome DNA microarray 44K kit.

first: Chikara

last: Ohyama


title: Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana [expression]

status: Public on Jul 22 2015

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary: Histone phosphorylation plays key roles in stress-induced transcriptional reprogramming in metazoans but its function(s) in land plants has remained relatively unexplored. Here we report that an Arabidopsis mutant defective in At3g03940 and At5g18190, encoding closely related Ser/Thr protein kinases, shows pleiotropic phenotypes including dwarfism and hypersensitivity to osmotic/salt stress. The double mutant has reduced global levels of phosphorylated histone H3 threonine 3 (H3T3ph), which are not enhanced, unlike the response in the wild type, by drought-like treatments. Genome-wide analyses revealed increased H3T3ph, slight enhancement in trimethylated histone H3 lysine 4 (H3K4me3), and a modest decrease in histone H3 occupancy in pericentromeric/knob regions of wild type plants under osmotic stress. However, despite these changes in heterochromatin, transposons and repeats remained largely transcriptionally repressed. In contrast, this reorganization of heterochromatin was mostly absent in the double mutant, which even under normal conditions exhibited lower H3T3ph levels in pericentromeric regions, and a few transposons and repeat sequences showed modest transcriptional activation. Interestingly, within actively transcribed protein-coding genes, H3T3ph density was minimal in 5’ genic regions, coincidental with a peak of H3K4me3 accumulation. This pattern was not affected in the double mutant, implying the existence of additional H3T3 protein kinases in Arabidopsis. Our results suggest that At3g03940 and At5g18190 are involved in the phosphorylation of H3T3 in pericentromeric/knob regions and that this repressive epigenetic mark may be important for maintaining proper heterochromatic organization and, possibly, chromosome function(s).

overall_design: Columbia-0 and double mutant at3g03940/at518190 knockdown plants were grown in 12 hr light for 3 weeks in pots in well-watered state. RNA was isolated from rosettes in triplicate for analysis on microarray.

first: Zhen

last: Wang

first: Armando

last: Mollano

first: Jianping

last: Xu

first: Chi

last: Zhang

first: Heriberto

last: Cerutti


title: Genome-wide expression analysis of bri1-5 and its suppressors brs1-1D, bak1-1D, bri1-1D

status: Public on Jul 14 2015

city: Lanzhou

first: Tao

last: Shi

state: Gansu

address: 222 South Tianshui Road

department: School of Life Sciences

institute: Lanzhou University

summary: bri1-5 is a weak mutant of Brassinosteroid Insensitive 1 (BRI1). Suppressors by activation tagging bri1-1D, brs1-1D and bak1-1D can recover bri1-5 phenotype. We use microarray to investigate which pathways or functional categories have been transcriptionally regulated by bri1-1D, brs1-1D and bak1-1D.

overall_design: Whole seedlings from wild-type (WS2), bri1-5, bri1-5/brs1-1D, bri1-5/bak1-1D, bri1-5/bri1-1D. Three biological replicates for each genotype.

first: Dongzhi

first: Xiaoping

last: Gou

first: Jia

last: Li


title: Gene expression profiling in synovial fluid derived stem cells (SFSCs)

status: Public on Jul 01 2015

city: Incheon

first: Eui-jin

last: Lee

address: 665-8 Bupyong 6 Dong, Bupyong-Gu

department: Institute of Catholic Integrative Medicine

country: South Korea

institute: Incheon St. Mary's hospital

summary: To explore mRNA expression profiling in synovial fluid derived stem cells (SFSCs), gene expression analysis was performed on 3 SFSCs and 1 BMMSC.

overall_design: 3 synovial fluid derived stem cells and 1 bone marrow mesenchymal stem cells

first: Euj-Jin

first: Yun-Jung

last: Yang

first: Yeon-Pyo

last: Hong

first: Sung

middle: S

last: Choi

first: Sun-Uk

last: Kim

first: Moon-Seo

last: Park

first: Hong

middle: J


title: Remodeling of major genomic fabrics and their interplay in metastatic clear cell renal carcinoma

status: Public on Aug 24 2015

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Clear cell renal carcinoma (CCRC) accounts for >80% of all kidney cancers but what triggers the tumorigenesis in the kidney and metastases in the bones are still under debate. Our hypothesis is that remodeling of the genomic fabrics of certain functional pathways and their interplay beyond critical limits are key causes of CCRC. We profiled the transcriptomes of metastatic chest wall and of two primary cancerous sites of the renal medulla and compared them with that of non-cancerous kidney resection margins. Samples were collected from a 74 years old male with metastatic carcinoma, consistent with renal cell carcinoma, clear cell type, Fuhrman grade 3, who undergone total right kidney nephrectomy and resection of a chest wall mass. Transcriptomic analysis pointed the tumor region in the right kidney that led to the chest wall metastases. The tumor proved heterogeneous not only in the expression level but also in the expression control, coordination and interplay of pathways responsible for cellular processes and genetic and environmental information processing. The differently regulated pathways in the two sides of the tumor: CCRC, and HIF-1, Vegfa and mTor signaling indicate activation of distinct mechanisms.

overall_design: Four-conditions (CTR = control - non-cancerous kidney resection margins, PTA = primary tumor side  A, PTB = primary tumor side B, MET = chest wall metastasis. Four biological replicates of each condition.

first: Sanda


title: Expression data of Arabidopsis seedlings in response to ARR1 or cytokinins, in the presence and absence of DELLA proteins

status: Public on Jun 13 2015

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

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

summary:
DELLA proteins interact with ARR1 and modulate its activity.
We have investigated the effect of DELLA proteins on transcriptional regulation by ARR1

overall_design: A dominant hyperactive allele of ARR1 was induced with dexamethasone in seedlings preincubated with paclobutrazol (allowing DELLA acummulation) or paclobutrazol+GA3 (promoting DELLA degradation)

first: Nora

last: Marin-de la Rosa

first: Jan

last: Lohmann

last: Alabadí

first: Miguel

last: Blázquez


title: Gated SA effect on transcriptome

status: Public on Jun 22 2015

city: Ames

first: Wei

last: Wang

state: IA

address: 415 Bessey Hall

department: Department of Plant Pathology and Microbiology

institute: Iowa State University

summary: We used microarrays to identify genes that respond to SA differently during the subjective morning and subjective night.

overall_design: 23-day-old wild type Arabidopsis seedlings. 24 samples total. Three biological replicates were used

first: Mian

last: Zhou

first: Xinnian

last: Dong


title: Root transcriptome of ninja-1

status: Public on May 28 2015

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

institute: UNIL

summary:
A major role of NINJA is to repress root jasmonate signalling and allow normal cell elongation.
To further characterize the transcriptional changes occurring in the root in the absence of a NINJA-dependent repression mechanism, we conducted a microarray analysis of ninja-1 versus WT roots.

overall_design: Root transcriptome of Col-0 (WT) versus ninja-1, both carrying the JAZ10pro-GUSPlus (JGP) reporter, grown in basal aseptic conditions. Biological replicates: 3 for the WT control and 3 for the ninja-1 mutant.

first: Debora

last: Gasperini

first: Aurore

last: Chételat

first: Ivan

middle: F

last: Acosta

first: Jonas

last: Goossens

first: Laurens

last: Pauwels

first: Alain

first: René

first: Esteban

last: Alfonso

first: Edward

last: Farmer


title: Transcriptomic signatures in whole blood of patients who suffer a Chronic Inflammatory Response Syndrome (CIRS) as a result of exposure to the marine toxin ciguatoxin

status: Public on Jun 01 2015

city: Vero Beach

first: James

last: Ryan

state: FL

institute: ProteoGenomics, LLC

summary: This study compares the transcriptional profiles of 11 patients with ciguatera induced Chronic Inflammatory Response Syndrome to 11 normal controls using whole blood perserved in PAXgene blood collection tubes and Agilent whole genome microarrays. In our analysis, we found nearly 200 genes significantly, differentially expressed in patients compared to controls.

overall_design: Gene expression of normal controls was compared to ciguatera fish poisoning patients using whole genome microarrays with technical replicates for each sample.

first: Ritchie

last: Shoemaker


title: Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma

status: Public on Jun 03 2015

city: shanghai

first: Mingjie

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

summary: Natural killer/T-cell lymphoma (NKTCL) is a malignant proliferation of CD56+/cytoCD3+ lymphocytes and constitutes a heterogeneous group of aggressive lymphomas prevalent in Asian and South American populations. Molecular pathogenesis of NKTCL remains largely elusive. Here we identified somatic mutations in RNA helicase gene DDX3X. Gene expression profiling revealed an association of DDX3X mutations with activation of NF-kB and MAPK pathways. Together, our work suggests the heterogeneity of gene mutational spectrum in NKTCL.

overall_design: We identified somatic mutations in RNA helicase gene DDX3X. To determine whether these mutations have influence on gene expresson, whole genome expression microarray was employed on 5 Natural killer/T-cell lymphoma patients with mutations in DDX3X and 5 patients without these mutations. The expression profile of NK cell line KAI3 was also detected on 2 samples with different mutations (E348K andA404P) and 1 wildtype sample.

first: Zhu

last: Chen

first: Sai-Juan


title: MYC-ER and MYC-ER V394D induced gene expression changes in MCF10A cells

status: Public on Jul 10 2015

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: Oncogenic levels of Myc expression sensitize cells to multiple apoptotic stimuli and this protects long-lived organisms from cancer development. How cells discriminate physiological from supra-physiological levels of Myc is largely unknown. Here we show that induction of apoptosis by Myc in breast epithelial cells requires association of Myc with Miz1. Gene expression and ChIP-sequencing experiments show that oncogenic levels of Myc, but not of MycV394D, a point mutant that does not bind Miz1, recruit Miz1 to core promoters and enable binding of Myc/Miz1 complexes to low-affinity target sites, correlating with repression of a specific set of target genes. Repressed genes encode proteins involved in cell adhesion, migration and wound healing; their promoters are enriched for binding sites of the serum response (SRF) factor. Restoring SRF activity attenuates Myc-induced apoptosis in response to glutamine starvation, exposure to Trail and to DNA damage. We propose that supra-physiological levels of Myc engage Miz1 in repressive DNA binding complexes and suppress transcriptional progr

overall_design: 4 different experimental conditions were analyzed: MYC-ER 4-OHT treated versus MYC-ER ctr-treated (EtOH), MYC-ER V394D 4-OHT treated versus MYC-ER V394D ctr-treated; 3 biological replicates for every condition.

first: Katrin

last: Wiese

first: Lukas

last: Rycak

first: Michael

last: Krause


title: Gene expression of Arabidopsis leaves under heat stress and during recovery

status: Public on May 27 2015

city: Yokohama

first: Yasuhiro

last: Higashi

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

institute: RIKEN

summary: To understand plant adaptation to heat stress, gene expression profiles of Arabidopsis leaves under heat stress, during recovery and control condition were obtained using microarray. Microarray data listed responsible candidate genes for glycerolipid metabolism.

overall_design: Arabidopsis thaliana ecotype Columbia (Col-0) seeds were surface-sterilised and sown on an agar-solidified Murashige and Skoog medium. Plants were grown at 22ºC under a 16-h-light/8-h-dark cycle. Vegetative plants were subjected to high temperature for a day, then continued to be grown under normal condition for a day.

first: Yozo

last: Okazaki

first: Fumiyoshi

last: Myouga

first: Kazuo

last: Shinozaki

first: Kazuki

last: Saito


title: Expression data from wildtype and spy-3 roots

status: Public on May 16 2015

city: Tallahassee

first: Hongchang

last: Cui

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

summary:
SPY is an O-linked N-acetylglucosamine transferase involved in many signaling and developmental processes in Arabidopsis. SPY also has a role in root development. In the spy mutant, a middle cortex is produced prematurely.
To understand how SPY regulates root cortex proliferation, we sought to identify the genes affected by the spy mutation in the root.

overall_design: The transciptomes from the root of one-week-old seedlings, Col or spy-3 mutant, were compared. The seedlings were grown on a nylon membrane placed on 1X MS agar medium and the plates are positionally vertically in a Pecival growth chamber with 16 hr light and 8 hr dark. Three biological replicates were performed.


title: Expression data from Arabidopsis wild type and ibr1 ibr3 ibr10 triple mutant seedlings root tip segments treated with indole-3-butyric acid (IBA)

status: Public on May 12 2015

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The root cap-specific conversion of the auxin precursor indole-3-butyric acid (IBA) into the main auxin indole-3-acetic acid (IAA) generates a local auxin source which subsequently modulates both the periodicity and intensity of auxin response oscillations in the root tip of Arabidopsis, and consequently fine-tunes the spatiotemporal patterning of lateral roots. To explore downstream components of this signaling process, we investigated the early transcriptional regulations happening in the root tip during IBA-to-IAA conversion in Col-0 and ibr1 ibr3 ibr10 triple mutant after 6 hours of IBA treatment.

overall_design: Arabidopsis thaliana (L). Heynh., Col-0 and ibr1ibr3ibr10 seeds were germinated vertically on solid medium derived from standard Murashige and Skoog (MS) medium. Three days after germination, Col-0 and ibr1ibr3ibr10 seedlings were transferred to a fresh MS medium supplemented with or without 10 μM indole-3-buytric acid (IBA) for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction. For each treatment, at least 120 individual Col-0 or ibr1ibr3ibr10 mutant root tip segments were sampled and three independent biological replicates were performed. Hormone and DMSO solution were filer-sterilized before being added to the medium.

first: Wei

last: Xuan

first: Dominique

last: Audenaert

first: Boris

last: Parizot

first: Tom

last: Beeckman


title: Gene expression profile after Spring Viraemia Carpae Virus (SVCV) infection in zebrafish mutants rag1 -/- versus wt

status: Public on May 10 2015

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

summary:
Immune responses in higher vertebrates are classically separated into innate and adaptive (or specific) immunity. However, important gaps of knowledge about how adaptive responses are generated in lower vertebrates still remain unsolved.
In order to explore the relative importance of adaptive and innate immune responses, we have studied zebrafish  transcriptional responses to an infection with the Spring Viraemia of Carp virus  (SVCV) in rag1-/- zebrafish mutants compared to wild type zebrafish by using both genome wide and immunological-targeted gene expression microarrays.

overall_design: Both wild type (wt) and mutant (rag1) zebrafish were divided in two groups  with 3 individuals per group. First group was infected with 10^5 pfu per ml of SVCV, second group was mock-infected. Two days after challenge zebrafish were sampled, head kidney and spleen of each fish were extracted and pooled between each group. The experiment was repeated once to obtain two biological replicates.


title: Genetic analyses of interactions between ABA and GA in the control of leaf development in Arabidopsis thaliana

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

institute: Academia Sinica, Taiwan

summary:
Although abscisic acid (ABA) and gibberellins (GAs) play pivotal roles in many physiological processes in plants, their interaction in the control of leaf growth remains elusive. In this study, genetic analyses of ABA and GA interplay in leaf growth were performed in Arabidopsis thaliana. The results indicate that for ABA and GA interaction, leaf growth of both the aba2/ga20ox1 and aba2/GA20OX1-OE plants exhibits partially additive effects but is similar to the aba2 mutant. Consistent with this result, transcriptome analysis suggests that a substantial proportion (45-65%) of the gene expression profile of aba2/ga20ox1 and aba2/GA20OX1-OE plants overlaps and shares a similar pattern to the aba2 mutant. Thus, these data support that ABA deficiency dominates leaf growth regardless of GA levels. Moreover, gene ontology (GO) analysis indicates gene enrichment in the categories of hormone response, developmental and metabolic processes, and cell wall organization in these three genotypes. Leaf developmental genes are also involved in ABA-GA interaction. Collectively, these data support that the genetic relationship of ABA and GA interaction involves multiple coordinated pathways rather than a simple linear pathway in the regulation of leaf growth.
To better understand the molecular basis of ABA and GA interaction, transcriptome analysis was performed among the genotypes used in this study.

overall_design: Plants were grown in soil for 21 days, and the aerial parts were used for microarray analysis. Genotypes included aba2, ABA2-OE, ga20ox1, GA20OX1-OE, aba2/ga20ox1 and aba2/GA20OX1-OE. The mutants and transgenic lines all had a background of Col-0 ecotypes of Arabidopsis thaliana.

first: Ming-Hau

last: Chiang

first: Hwei-Ling

last: Shen


title: Expression data from MCF-7 breast cancer cells treated with Plumbagin (PL) and its derivative Acetyl Plumbagin (AP)

status: Public on Apr 28 2015

city: Thuwal

first: Mandeep

last: Kaur

address: Building 2, Level 4

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: The study aimed at finding the molecular mechanism of action of PL and AP in breast cancer cells. The dataset shows the comparison of gene expression in Plumbagin/Acetyl Plymbagin treated MCF-7 cells when compared with untreated samples.

overall_design: 11 samples were analyzed. MCF-7 cells treated with 10 uM PL or AP for 6 hours. Please note that three samples were done in triplicates and one sample MCF-7 treated with 10uM PL was done in duplicates as one of the replicate RNA didn't show up a good RIN number, SAMPLE1 &2 are replicates, SAMPLE 3,4 &5 are triplicates, SAMPLE 6,7 & 8 are triplicates and SAMPLE 9,10 & 11 are triplicates (SAMPLE numbers are indicated in the description field).

first: Luke

last: Esau

first: Sunil

last: Sagar

first: Dhinoth

middle: K

last: Bangarusaamy


title: High REDOX RESONSIVE TRANSCRIPTION FACTOR1 levels result in accumulation of reactive oxygen species in Arabidopsis thaliana shoots and roots [mature leaves]

status: Public on Apr 23 2015

city: Kyoto

first: Mitsuhiro

last: Matsuo

address: 1-5 Hangi-cho, Shimogamo, Sakyoku

department: Graduate School of Life and Environmental Sciences

institute: Kyoto Prefectural University

summary: Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H202, as well as biotic and abiotic induced redox signals. Inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Overexpressor (oe) lines are impaired in root and shoot development, light sensitive and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors which scavenge ROS. More than 850 stress-, redox-, ROS regulated-, ROS scavenging-, defense-, cell death- and senescence-related genes are regulated by RRTF1, ~ 30% of them have ROS related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box and GCC-box like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli as well as H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains GCC-box like sequene in its promoter, but RAP2.6 oe lines do not accumulate higher ROS levels. RRTF1 stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the highly conserved RRTF1 rapidly, transiently and systemically induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals. Necrotrophs stimulate RRTF1 expression, while symbiotic interactions of Arabidopsis with (hemi)-biotrophs and P. indica do not affect or repress RRTF1 expression.

overall_design: Mature leaves of 5 weeks-old Col-0 wild type and RRTF1-overexpressor Arabidopsis (called oe18), which were grown on soil under short-day condition at 20˚C, were subjected to RNA extraction and Affymetrix microarray analysis. Three biological independent experiments for both Col-0 and oe18 were performed.

first: Joy

last: Johnson

first: Ayaka

last: Hieno

first: Mutsutomo

last: Tokizawa

first: Mika

last: Nomoto

first: Yasuomi

last: Tada

first: Rinesh

last: Godfrey

first: Junichi

last: Obokata

first: Irena

last: Sherameti

first: Yoshiharu

last: Yamamoto

first: Frank

middle: D

last: Böhmer

first: Ralf

last: Oelmüller


title: Transcript profiling of Arabidopsis plasma membrane proton pump mutants

status: Public on Apr 01 2015

city: Madison

first: Miyoshi

last: Haruta

state: WI

address: 425 Henry Mall

department: Biotechnology Center

institute: University of Wisconsin Madison

summary: Plasma membrane proton pump maintains proton electrochemical gradient and provides energy to secondary transporters. Arabidopsis mutant plants with reduced proton pump activity grow normal under ideal growth conditions; however their growth are reduced compared with wildtype plants when placed under the conditions that stress on protonmotive force (high external pH or high external potassium).

overall_design: Seedlings of wildtype, aha1, and aha2 mutant plants were grown under ideal growth condition. Total RNA from those seedlings were subjected to transcriptome analyses using Affymetrix Gene Chip.

first: Michael

middle: R

last: Sussman


title: Expression data from Arabidopsis C3H14/15 overexpressors, c3h14c3h15 double mutant vs wild type

status: Public on Apr 07 2015

city: Qingdao

first: Chai

last: Guohua

state: Shandong

address: No.189 Songling Road, Laoshan District

department: Qingdao Institute of BioEnergy and Bioprocess Technology

institute: Chinese Academy of Sciences

summary:
In plants, CCCH zinc finger proteins involved in secondary wall formation and anther development are poorly understood. We have functionally identified two homologous genes C3H14 and C3H15 and found that the two genes differentially regulate secondary wall formation and anther development. C3H14 contributes more to secondary wall thickening, whereas, C3H15 is more important for anther development.
We performed microarray analyses on C3H14/15 overexpressors and c3h14c3h15 double mutant to to ientify differentially-expressed genes involved in the two developmental processes.

overall_design: Our microarray data show that C3H14 and C3H15 regulate the expression of a number of genes involved in various biological activities, particularly those associated with secondary wall metabolism and pollen formation.

first: Guohua

last: Chai

first: Gongke

last: Zhou


title: Comparative transcriptional profiling between the organs of the scion and rootstock of a homograft (Arabidopsis thaliana)

status: Public on Apr 14 2015

city: Mohali

first: Sudhir

middle: P

last: Singh

state: Punjab

address: NABI, C127, Indus Area, Phase8

country: India

institute: National Agri-Food Biotechnology Institu

summary: Analyses of expression differences in flower bud and leaf of scion and rootstock, in homografts of Arabidopsis

overall_design: Gene expression data of unopened developing flower buds and leaves, newly emerged after homografting, from the scion and the rootstock

first: Anita

last: Kumari

first: Jitendra

last: Kumar


title: Genetic Suppression of Plant Development and Chloroplast Biogenesis by SCO3 and PhyB Pathways

status: Public on Mar 24 2015

city: Philadelphia

first: Diep

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary:
In this study we used genetic approaches and transcriptome profiling to unravel the complex interaction of different developmental pathways required for chloroplast development in plants. The recently described snowy cotyledon 3 (sco3) mutant as well as the Phytochrome B (phyb) mutant revealed, in the double mutant, a complex suppressive or additive genetically linked regulation of chloroplast development, flowering time and transcription regulation.
Transcriptional profilling of mutants with aberrant chloroplast development: sco3, phyb and the double mutant sco3phyb.

overall_design: Analysis of differences in gene expression profiles between Col-0 (reference line), sco3, phyb and sco3phyb was performed using Affymetrix Gene Chip Arabidopsis ATH1 genome arrays in biological triplicate. Total mRNA was collected from 4 day old seedlings, grown on sterile Murashige Skoog media with 0.8% Agar under long day conditions  (16hr light/8h dark, 21°C), was isolated and DNAse treated using the Spectrum Total RNA Kit (Sigma, USA). These were sent for sample quality control, labelling, hybridization and scanning at the Ramaciotti Centre (Sydney). Results were received as raw CEL files, which were subsequently analyzed.

first: Peter

last: Crisp

first: Klaus

last: Harter

first: Barry

last: Pogson

first: Verónica

last: Albrecht-Borth


title: A transcriptional map following the developmental trajectory of the Arabidopsis stomatal lineage

status: Public on Apr 06 2015

city: Stanford

first: Dominique

last: Bergmann

state: CA

address: 371 Serra Mall

department: Biology Department

institute: Stanford University

summary: Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression.

overall_design: To obtain pure cell populations corresponding to different stomatal lineage cell types we used Fluorescent Activated Cell Sorting (FACS) in combination with markers of early (SPCHp::SPCH-YFP, SSY), middle (MUTEp::nucGFP, MG), and late (FAMAp::GFP-FAMA, FGF) precursor stages, as well of mature stomata (enhancer trap E1728::GFP, E1728G) and a marker of the entire epidermis (ML1p::YFP-RCI2A, ML1Y). To minimize transcriptional differences due to age, all cell types were sorted from 14-day old aerial rosettes, and the specificity of expression pattern at this common time point confirmed via confocal microscopy. Total RNA was extracted from purified protoplasts (2,000 to 20,000 cells/replicate; 3 replicates/marker line) and transcript abundance measured using ATH1-121501 microarrays.

first: Jessika

last: Adrian

first: Jessica

last: Chang

first: Bastiaan

middle: O

last: Bargmann


title: Transcriptomic response of the Arabidopsis provascular tissue to Brassinosteroids

status: Public on Mar 22 2015

city: Bellaterra

first: Ana

last: Cano-Delgado

state: Barcelona

address: Edificio CRAG- Bellaterra (Cerdanyola del Vallés)

institute: CRAG

summary: These data represents a microgenomic approach to dissect the response of the plant steroid hormone, brassinosteroid, in the provascular tissue of the arabidopsis thaliana primary roots. We used two different provascular markers, wooden leg (WOL) and corona (ATHB15) to profile the provascular response to BRs. We used a timecourse analysis with 4 different timepoint; 0.5, 1, 2 and 4 hours treated with BRs in the WOL domain. Additional trasncriptomic responses of the ATHB15 domain were analyzed after 2 hours BRs treatment.

overall_design: We perform timecourse profiling of pWOL (labeling stele cells) at 0.5, 1, 2, 4 hours after 10 nM BL treatment. Additionally we profile Athb15 (labeling provascular cells) at 2 hours after BL treatment. Note that for athb15 we did 3 replicates of the controls conditions.

middle: I

last: Caño Delgado


title: Identification of hsa-miR-135a target genes in the prostate cancer cell line LNCaP

status: Public on Mar 18 2015

city: Lyon Cedex 07

first: Nathalie

last: ALLIOLI

address: 46 Allée d'Italie

department: Institut de Génomique Fonctionnelle de Lyon (IGFL)

institute: Ecole Normale Supérieure de Lyon (ENS)

summary: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs. They act as negative regulators of protein-coding gene expression at the post-transcriptional level via sequence-specific interaction with the 3' UTR of targeted mRNAs. A miR-135a dysregulation has been observed in various cancers, where a dual role of oncomiR or of tumor suppressor has been reported for the cancers profiled to date; however, knowledge is limited to explain these contentious data. In the present study, we investigate the regulation and mechanism of action of miR-135a, including identification of functionally targets that contributes to its actions, in prostate cancer progression. We demonstrate that the expression of miR-135a is regulated by androgens, in a time- and dose-dependent manner and identify miR-135a as a direct target gene of the androgen receptor AR. A functional androgen response element (ARE) is identified in the promoter region of the miR-135a gene and ChIP assay reveal AR protein binding to. Anti-androgen treatment and AR-targeted siRNA knockdown strategy suggest a novel function for miR-135a in AR signaling. In silico prediction, transcriptomic and proteomic combined analyses lead to identify ROCK-1/-2 as two miR-135a-targeted genes. Luciferase reporter assays indicate that these two proteins are miR-135a's direct targets. We finally demonstrate that miR-135a acts through ROCK-1/-2 pathways to affect migration and invasion cellular processes. MiR-135a expression level was lower in surgical cancerous samples compared to paired adjacent non-tumoral tissues and was gradually diminished consistent with cancer progression, suggesting the significance of miR-135a-mediated prostate cancer transformation. Our findings define miR-135a as a candidate tumor suppressor and potential prognostic marker in human prostate cancer.

overall_design:
Transcriptional profiling of the LNCaP cell line that over-expressed hsa-miR-135a.
LNCaP cells were transfected with the hsa-miR-135a mimic (Ambion) and compared to control cells transfected with the negative control.

last: Allioli

first: Auriane

last: Kroiss

first: Séverine

last: Vincent

first: Jacques

last: Samarut


title: Expression data from Col, brm-1, clf-29 and brm-1 clf-29 14-d-old seedlings

status: Public on Mar 09 2015

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

summary: To understand how actions of the chromatin-remodeler BRAHMA (BRM) and Polycomb Group (PcG) proteins are coordinated during plant development, we performed a genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed upon removal of the CURLING LEAF (CLF) H3K27me3 methyltransferase. ChIP experiments demonstrated that BRM directly binds to a subset of genes and prevents the inappropriate association of PcG proteins at some of the loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG protein complexes during plant development.

overall_design: 12 samples from wild-type, brm-1, clf-29 and brm-1 clf-29 14-d-old seedlings with three biological replicates

first: Chenlong

last: Li

first: Yuhai

last: Cui


title: The Arabidopsis GAGA-binding factor BPC6 recruits PRC1 component LHP1 to GAGA DNA-motifs

status: Public on Apr 30 2015

city: Tuebingen

first: Dierk

last: Wanke

address: Auf der Morgenstelle 32

department: Plant Physiology

institute: University of Tuebingen

summary:
Plant BBR/BPC transcription factors contain the conserved Basic-Pentacystein (BPC) DNA-binding domain. Arabidopsis group II BBR/BPC proteins interact with PRC1 component LHP1 in vivo. Microarray experiments with Arabidopsis bpc4 bpc6, lhp1-4 and lhp1-4 bpc4 bpc6 suggest an importance of this interaction in the concerted repression of homeotic genes.
In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes.

overall_design: Arabidopsis thaliana (accession Columbia) were grown in the greenhouse under constant temperature of 20°C, 35% humidity and a 18-h light period. 18 days old plants were harvested and immediately frozen in liquid nitrogen. Six individual plants were pooled per replicate.

first: Andreas

last: Hecker

first: Luise

middle: H

last: Brand

first: Sébastien

last: Peter

last: Simoncello

first: Joachim

last: Kilian

last: Harter

first: Valérie

last: Gaudin


title: CaSki cells: adherent cultured cell vs. sphere cells

status: Public on Mar 04 2015

city: Sapporo

first: Takuya

last: Asano

address: South 1 West 16, Chuo-ku

department: Pathology

institute: Sapporo Medical University School of Medicine

summary: Transcriptional profiling of human cervical squamous cell carcinoma cell line CaSki comparing adherent cultured cells with spheres cultured in serum free culture medium.  Goal was to identify candidate antigens for immunotherapy targeting cancer stem cells.

overall_design: Two-condition experiment, CaSki vs. CaSki-sphere cells.


title: Transcription factor WRKY46 regulates osmotic stress responses and stomatal movement tissue specifically and independently in Arabidopsis

status: Public on Feb 01 2015

city: Hangzhou

first: Shao Jian

last: Zheng

address: Yuhangtang Rd 866#

department: College Life Sciences

institute: Zhejiang University

summary:
Drought and salt stress severely inhibit plant growth and development. However, the regulatory mechanisms of plants in response to these stresses are not fully understood. Here we find that the expression of a WRKY transcription factor WRKY46 is rapidly induced by drought, salt and oxidative stresses. Mutations of WRKY46 by T-DNA insertion lead to more sensitive to drought and salt stress, whereas, overexpression of WRKY46 exhibits hypersensitive in soil culture with higher water loss rate, but increased tolerance on the agar plates. ABA induced stomatal closing is impaired in the WRKY46 overexpressing line (OV46), which is potentially due to the lower ROS accumulation in the guard cells. Real-time qPCR and GUS activity assay further demonstrate that WRKY46 is expressed in guard cells, but its expression is not affected by dehydration treatment, suggesting different regulatory mechanisms for WRKY46 between guard cells and other WRKY46 expressed tissues. The stomatal movement and conductance assay indicate that WRKY46 is involved in light-dependent stomatal opening. Further microarray analysis reveals that WRKY46 regulates a set of genes involved in cellular osmoprotection and redox homeostasis under dehydration stress. Determinations of ROS and MDA content confirm its role in oxidative detoxification under stress. Furthermore, we find that WRKY46 modulates light-dependent starch metabolism in guard cells via regulating QQS gene expression. Taken together, we demonstrate that WRKY46 plays a role in modulating cellular osmoprotection and redox homeostasis under drought and salt stress, and functions independently in stomatal movement via regulating light-dependent starch metabolism and ROS levels in guard cells.
We used microarrays to identify the certain downstream genes regulated by WRKY46 under normal and dehydration conditions.

overall_design: One-week-old Arabidopsis seedlings of wild-type Col-0 (WT) and WRKY46 overexpressing line (46T) with or without dehydration treatment for 1 h were harvested and used for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays. The experiment includes 3 biological replicates.

first: Z

last: Ding

first: S


title: Global Functional Targets of the Histone Methyltransferase SDG8 Uncover a Role for Histone Modification in Energy Metabolism

status: Public on Mar 01 2015

city: New York

first: Ying

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

summary: Histone methylation modulates gene expression in response to external and internal cues. We uncovered a non-redundant role for the Arabidopsis histone methyltransferase, SDG8, which provides a unique opportunity to study the global function of a specific histone methyltransferase within in a multicellular organism. We previously used a promoter responsive to light and carbon in a positive genetic screen to identify an Arabidopsis carbon and light insensitive mutant cli186.  In this study, we characterize the mutant cli186  as a complete deletion of a histone methyltransferase gene SDG8 (now renamed sdg8-5). To assess the global role of SDG8, we compared the global histone methylation patterns and the transcriptome of sdg8-5 to wild type (WT) in the context of a transient carbon and light treatment. We showed that the complete deletion of SDG8 in sdg8-5 is associated with a dramatic reduction of H3K36me3 towards the 3’ of the gene body, which correlates with significant reduction in gene expression.  We uncovered 1,084 “high confidence” functional targets of SDG8 – affected in both H3K36me3 marks and gene expression – that are associated with specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 71% of these functional targets are responsive to carbon and/or light. Our model suggests that SDG8 functions to mark specific sets of genes with H3K36me3 in the gene body for active transcription, to tune genes involved in primary metabolism that are responsive to the energy level in the environment.

overall_design: Wild type Arabidopisis and sdg8-5 plants were grown in hydroponics system for three weeks, then starved for carbonhydrate and light for 24 h. They were then treated with  carbon and/or light or remained untreated as controls.Three biological replicates were collected, resulting in 24 samples (2 genotypes X 2 carbonhydrate treatmens X 2 light treatments X3 biological replicates).

last: LI

first: Indrani

last: Mukherjee

first: Karen

last: Thum

first: Milos

last: Tanurdzic

first: Manpreet

last: Katari

first: Mariana

last: Obertello

first: W

last: McCombie

first: Robert

middle: A

last: Martienssen

first: Gloria

middle: M

last: Coruzzi


title: Impact of NRT1.1 point mutants on gene expression under high NH4NO3 supply

status: Public on Jan 15 2015

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

institute: CNRS

summary: NRT1.1 is a nitrate transceptor involved in many nitrate responses including the regulation of gene expression through (i) the Primary Nitrate Response (PNR) and (ii) the regulation the NRT2.1 gene under continuous high NH4NO3 conditions. Phosphorylation of NRT1.1’s T101 residue is involved in the modulation of the PNR whereas nitrate transport by NRT1.1 is not. Here we used various NRT1.1 point mutants to study the impact of NRT1.1 on the whole transcriptome under high NH4NO3 supply. Col is the WT control, chl1-5 and chl1-12 are KO mutants, chl1-9 is defective in nitrate transport but not in PNR induction, T101D and T101A mimick the phosphorylated and not phosphorylated forms of NRT1.1 respectively.

overall_design: This work studies the impact of various NRT1.1 mutations on the transcriptome under 10mM NH4N03 supply.

first: Eléonore

last: Bouguyon

first: Amy

last: Marshall-Colon

first: Alain

last: Gojon

first: Philippe

last: Nacry


title: Auxin Induced Endodermal to QC Transdifferentiation Time Series and Downsteam of JKD Analysis

first: Kenneth

middle: David

last: Birnbaum

summary:
First series collects endodermal cells using the SCR::GFP promoter after treatment with auxin
Second series includes comparative samples of jkd vs. wild type plants for specific tissues; QC and meristem

overall_design: In first series, plants are grown under normal conditions, then transferred to auxin analog 2,4-D and endodermis is collected at time points 0hrs, 24hrs, 48hrs, 72hrs, 96 hrs.

first: Ken

first: Shuai

last: Yuan


title: Ovarian cancer cell line RMG1: ALDEFLUOR positive vs. negative

first: Tasuku

last: Mariya

state: Hokkaido

institute: Sapporo Medical University

summary: Transcriptional profiling of ALDH1 high cancer stem like cells of ovarian cancer cell line, sorted out using ALDEFLUOR assay.

overall_design: Two-condition experiment, ALDEFLUOR positive vs. negative cells. Biological replicates: 1 ALDEFLUOR positive replicate, 1 negative replicate.

first: Akari

last: Takaya

first: Yoshihiko

last: Hirohashi


title: Intersystem photosynthetic redox signal in retrograde chloroplast-to-nucleus communication

status: Public on Mar 23 2015

city: Grenoble

first: Thomas

last: Pfannschmidt

address: 17 rue des Martyrs

department: Institut de Recherches en Technologies et Sciences pour le Vivant

institute: CNRS/UJF/INRA/CEA Grenoble

summary:
To analyze the impact of photosynthetic redox signals, light sources with spectral qualities that preferentially excite either Photosystem I (PSI light) or Photosystem II (PSII light) were used. The light sources have been described in (Wagner et al, Planta 2008). Strong reduction signals were induced by light shifts from PSI to PSII light (PSI-II). In order to find primary regulated genes the acclimation responses were monitored at 30 min and 60 min after a light shift. The control was continuous Psi light at the same time. We used stn7 (a thylakoid redox regulated kinase) to specifically block transduction of photosynthetic redox signal in order to compare “real” redox regulated with that of other light acclimation pathways.
Keywords: photosynthesis, redox regulation, light acclimation, retrograde signalling, long term response

overall_design: Experiments were performed with plant material corresponding to pools of at least 250 individuals of Arabidopsis thaliana (Col-0 and stn7; SALK_073254 in Col-0 background). To abtain healthy and unstressed plants, seedlings were initially grown for 20 days under continuous white light on soil. Plants were then pre-acclimated to PSI-light for 3 days. Plants were then shifted to PSII light and tissue was harvested at the described time points. As control we utilized the stn7 knockout mutant which does not perceive PQ- related photosynthetic redox signals. RNA isolation: Leaf material was harvested and frozen in liquid N2 under the respective light source. Isolation of total RNA was performed as adapted from Logemann et al Analytical Biochemistry, 1987.

first: Lars

last: Dietzel


title: High REDOX RESONSIVE TRANSCRIPTION FACTOR1 levels result in accumulation of reactive oxygen species in Arabidopsis thaliana shoots and roots

city: Jena

first: khabat

last: vahabi

state: Deutschland

address: Dornburger Straße 159

department: plant physiology

institute: Friedrich-Schiller-Universität

summary: Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H202, as well as biotic and abiotic induced redox signals. Inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Overexpressor (oe) lines are impaired in root and shoot development, light sensitive and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors which scavenge ROS. More than 850 stress-, redox-, ROS regulated-, ROS scavenging-, defense-, cell death- and senescence-related genes are regulated by RRTF1, ~ 30% of them have ROS related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box and GCC-box like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli as well as H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains GCC-box like sequene in its promoter, but RAP2.6 oe lines do not accumulate higher ROS levels. RRTF1 stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the highly conserved RRTF1 rapidly, transiently and systemically induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals. Necrotrophs stimulate RRTF1 expression, while symbiotic interactions of Arabidopsis with (hemi)-biotrophs and P. indica do not affect or repress RRTF1 expression.

overall_design: The seedlings were grown on MS medium with 1.37% sucrose under short day conditions and low light intensity (30 µmol m-2s-1) at 20˚C for 14 days. Transcriptome analysis was performed for the rrtf1 knock-out line and a RRTF1-overlexpressor line (called oe18) in comparison to wild-type seedlings.

first: Mitsuhiro

last: Matsuo

first: Joy

last: Johnson

first: Ayaka

last: Hieno

first: Mutsutomo

last: Tokizawa

first: Mika

last: Nomoto

first: Yasuomi

last: Tada

first: Rinesh

last: Godfrey

first: Junichi

last: Obokata

first: Irena

last: Sherameti

first: Yoshiharu

last: Yamamoto

first: Frank-D

last: Böhmer

first: Ralf

last: Oelmüller


title: Expression data from Arabidopsis wild-type (Col-0) and KO-nudx19  plants, which lacks nudix hydrolase 19, a NADPH hydrolase

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

institute: Shimane University

summary:
The NADPH status, which is regulated by AtNUDX19, a NADPH pyrophosphohydrolase, is involved in the regulation of stress and hormonal responses.
To clarify how the status is involved in the regulation, we performed a microarray analysis using 3-week-old wild-type and KO-nudx19 leaves grown under normal light conditions.

overall_design: Wild-type and KO-nudx19 plants were grown on MS medium containing 3% 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 1 week, and then transferred to and further grown on soil for 2 weeks in the same chamber. At 3 weeks, leaves were collected as samples for microarray analysis.

first: Kazuya

last: Yoshimura

first: Shigeru

last: Shigeoka


title: Expression data from Arabidopsis myb3r mutants

status: Public on Mar 31 2015

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: NAIST

summary: Temporal and spatial regulation of cell division is central for generating multicellular organs with predictable sizes and shapes. However, it remains largely unclear how genes with mitotic functions are transcriptionally regulated during organogenesis in plants. Here, we showed that a group of R1R2R3-Myb transcription factors are responsible for developmentally controlled downregulation of variety of mitotic genes in Arabidopsis. Loss of their functions resulted in elevated expression of mitotic genes in quiescent cells including those underwent terminal differentiation. Concomitantly, their mutations enhanced cell division activities in various aspects of plant development, generating organs with increased sizes and irregular architectures. In addition, we showed that this type of R1R2R3-Myb proteins are required for oscillated expression of G2/M-specfiic genes, most likely by inhibiting transcription outside of G2/M in the cell cycle. Our finding uncovered a novel plant-specific mechanism in which scheduled expression of G2/M-specific genes may require their global repression both in the cell cycle and during development.

overall_design: Seedlings (9d-old) or leaves (5d or 15d-old) of the wild type or myb3r mutants were sampled for RNA extraction and hybridization on Affymetrix microarrays.

first: Taku

last: Demura

first: Kosuke

last: Kobayashi

first: Masaki

last: Ito


title: Human HL-60 Cells: all-trans retinoic acid (ATRA) vs. ATRA plus arsenic trioxide (ATO)

city: Tokushima

first: Daigo

last: Sumi

institute: Tokushima Bunri University

summary: Transcriptional profiling of human leukemia　HL-60  cells comparing ATRA treated HL-60 cells with ATRA plus ATO. Goal was to determine the effects of ATO on ATRA induced differentiation of HL-60 cells.

overall_design: Two-condition experiment, ATRA vs. ATRA plus ATO treated HL-60 cells.

first: Kazumi

last: Suzukawa

first: Seiichiro

last: Himeo


title: Identification of hsa-miR-135a target genes in LNCaP and HeLa cell lines

first: Nathalie

last: ALLIOLI

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

overall_design: Refer to individual Series


title: Transcriptome analysis of plant sulphate starvation and resupply

city: Potsdam-Golm

first: Rainer

last: Hoefgen

address: Am Mühlenberg 1

institute: Max-Planck Institute for Molecular Plant Physiology

summary: Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using ‘omics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

overall_design: Arabidopsis seedlings were grown in 30 mL of sterile liquid full nutrition (FN) medium (3 mM sulphate) or 150 μM sulphate medium. Transferring pre-grown 7-days old seedlings to a sulphate depleted medium (0 μM sulphate) assured immediate and continued sulphate starvation during the next two days of plant cultivation. On day 9 subsets of the sulphate depleted cultures were supplied with sulphate (500 μM) and samples taken 30 min and 3 hours after re-supply. Four time points (full nutrition (FN), plants starved for 48 h (-S), plants re-supplied with sulphate for 30 minutes (30’ S) and plants re-supplied with sulphate for 3 hours (3 h S)) were subjected to the microarray analysis. Two biological repetitions of each sample were analyzed.


title: The G1 arrest and maintenance mechanism between the long-term G1-arrested and the G1-arrested cells.

status: Public on Jan 27 2015

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary:
Non mitotic tumor cells are resistant to conventional chemotherapeutic drugs. However, the mechanisms underlying this phenomenon remain unclear. Here, we found a population that is viable but remains in the G1 phase for an extended period of time (up to 48 h) by Long-term time-lapse observations in Fucci-HCT116 cells and then we conducted DNA microarray-based comparative analyses between the RR (the long-term G1-arrested cells) and R (the G1-arrested cells) fractions, to determine the molecular basis of the G1 arrest/maintenance mechanism.
This study is related to GSE34940.

overall_design: The labeled cRNAs were hybridized on 4X44K v2 Agilent Whole Human Genome dual color Microarrays (G4845A) in two dye swap experiments, resulting in four individual microarrays.

first: Atsushi

last: Naito

first: Yoshinori

last: Kagawa


title: Arabidopsis thaliana shoots at 10 DAG; pSHR:SHR-GR in shr-2

status: Public on Nov 12 2014

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

institute: KonKuk University

summary: Transcriptional profiling in the shoot after SHR induction by DEX.  We used Affymetrix ATH1 microarrays to identify new target genes of SHR and the effect of SHR on growth and development of the Arabidopsis shoot system by global transcriptome analysis.

overall_design: Five-condition experiments: Control, DEX3hr, DEX6hr, DEX12hr and DEX24hr  Biological replicates: 2 Control, 2 DEX3hr, 2 DEX6hr, 2 DEX12hr and 2 DEX24hr

first: Jun

last: Lim

first: Eun


title: AtNIGT1/HRS1 TARGET approach

status: Public on Jan 05 2015

first: Gabriel

last: Krouk

summary: This work studies the impact of AtNIGT1/HRS1-GR entrance in the nucleus upon DEX treatment in protoplasts.

overall_design: AtNIGT1/HRS1 TARGET. The whole procedure has been performed as previously described in Bargmann et al Mol Plant 2013. In brief, the protoplasts were transfected with the plasmid pBeaconRFP_GR-HRS1 that trigger the expression of HRS1 protein fused with the glucocorticoid receptor under control of CaMV35S promoter. Protoplasts were treated with 35µM cycloheximide (CHX) to inhibit translation and to select only direct target genes and 10µM dexamethasone (DEX) to induce HRS1-GR entry in the nucleus. Nitrate is maintained during the whole TARGET procedure. The Red Fluorescent Protein was used as marker selection for fluorescent-activated cell sorting (FACS) of successfully transformed protoplasts. RNA were extracted and amplified in order to be tested with ATH1 Affymetrix™ chips.

first: Anna

last: Medici

first: Amy

last: Marshall-Colon

first: Sandrine

last: Ruffel

first: Gloria

last: Coruzzi


title: Gene is expression in 2 mutant alleles of the freezing-sensitive mutant sfr6 subjected to cold.

status: Public on Dec 22 2014

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: The sfr6-1 mutant of Arabidopsis has been shown to be defective in freezing tolerance and fails to express a number of cold-regulated genes to normal wild type levels. The aim of this experiment was to test whether two other mutant alleles, sfr6-2 and sfr6-3 showed similar defects in cold-inducible gene expression.

overall_design: Two experiments were performed. In each, one sfr6 mutant was cold-treated alongside its corresponding wild type.

first: Heather

last: Knight

first: Marc


title: Dose dependent toxicological response of lung cells exposed to silica nanoparticles

city: Bagnols sur Cèze

first: Odette

last: Prat

address: Site de Marcoule

department: Life Science

institute: CEA

summary: We have employed whole genome microarray expression to distinguish the effect of Fumed Silica Nanoparticles on human alveolar epithelial A549 lung cells. Cells were exposed in vitro, and datasets of differentially expressed genes were identified for NPs versus control samples.

overall_design: NPs induced gene expression in A549 cells was measured at 24 hours and 72 hours after exposure. Minimum three independent experiments were performed for each experiment.

first: Cedric

last: Pisani


title: Genome-wide gene expression analysis of MNT-1 cell under hyperosmotic condition

status: Public on Dec 31 2014

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: In order to investigate the effect of hyperosmotic stress on melanoma cell line, we performed a gene expression microarray analysis from RNAs isolated from MNT-1 cells treated by sucrose or not

overall_design: Duplicate experiments were performed on MNT-1 cells before and after sucrose treatments for 7 days. In each experiment, the total RNA was isolated from the MNT-1 cells that had been independently cultured using trizole (Invitrogen). The total RNA was reverse-transcribed, amplified, and hybridized onto an Agilent Human GE 4x44K V2 chip according to the manufacturer’s protocol.

first: Tae

last: Lee

first: Eun-Gyung

last: Cho

first: Daehee

last: Hwang

first: Bum-Ho

last: Bin

first: Jinhyuk

last: Bhin


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

status: Public on Oct 28 2014

city: London

first: Ze-Chun

last: Yuan

state: Ontario

address: 1391 Sanford Street

department: Microbiology

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

summary:
As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency.
Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes.

overall_design: 3-week-old A.thaliana Col-0 seedlings were selected for growth in hydroponic systems. A. tumefaciens C58 was inoculated into the hydroponic system and co-cultivation persisted for 8 hours. Root tissue was seperated for RNA extraction and hybridization to the ATH1 Affymetrix microarray.

first: Naeem

last: Nathoo


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

summary:
As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency.
Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes.

overall_design: 3-week-old A.thaliana Col-0 seedlings were selected for growth in hydroponic systems. A. tumefaciens C58 was inoculated into the hydroponic system and co-cultivation persisted for 8 hours. Leaf tissue was seperated for RNA extraction and hybridization to the ATH1 Affymetrix microarray.


title: Effect of NJ15 on gene expression profiles in Arabidopsis thaliana seedlings

status: Public on Nov 03 2014

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Brassinosteroid (BR) and auxin co-regulate plant growth in a process termed cross-talking. Based on the assumption that their signal transductions are partially shared, inhibitory chemicals for both signal transductions were screened from a commercially-available library. A chemical designated as NJ15 (ethyl 2-[5-(3,5-dichlorophenyl)-1,2,3,4-tetrazole-2-yl]acetate) diminished the growth promotion of both adzuki bean epicotyls and Arabidopsis seedlings, by either the application of BR or auxin. To understand its target site(s), bioassays with a high dependence on either the signal transduction of BR (BR-signaling) or of auxin (AX-signaling), were performed. NJ15 inhibited photomorphogenesis of Arabidopsis seedlings grown in the dark, which mainly depends on BR-signaling, while NJ15 also inhibited their gravitropic responses mainly depending on AX-signaling. On the study for the structure-activity relationships of NJ15 analogues, they showed strong correlations on the inhibitory profiles between BR- and AX-signalings. These correlations imply that NJ15 targets the downstream pathway after the integration of BR- and AX-signals.

overall_design: Arabidopsis thaliana ecotype Col-0 was used as the wild type (WT) in this study. The Col-0 plants, grown vertically as a gravitropic response assay for 4 days on MS plates, were sprayed with mock or with 10 µM NJ15 (ethyl 2-[5-(3,5-dichlorophenyl)-1,2,3,4-tetrazole-2-yl]acetate) and were gravistimulated by turning then 90° relative to the first direction. After 8 h, plants were harvested and total RNA was extracted with a Total RNA Extraction Kit Mini for plant (RBC Bioscience), then total RNA was subjected to microarray analysis.

first: Naiyanate

last: Jaroensanti

first: Jung-Min

last: Yoon

first: Ikuya

last: Shirai

first: Masato

last: Otani

first: Seung-Hyun

last: Park

first: Ken-ichiro

last: Hayashi

first: Masatoshi

last: Nakajima

first: Tadao

last: Asami


title: Expression data from early Arabidopsis thaliana embryo

status: Public on Oct 23 2014

city: Tübingen

first: Daniel

last: Slane

state: Baden-Württemberg

address: Spemannstrasse 35

department: Cell Biology

institute: Max Planck Institute for Developmental Biology

summary: After zygote division, the resulting daughter cells progressively give rise to two very different tissue types. With the use of microarrays, global nuclear expression profiles were generated.

overall_design: Tissue-specific marker lines were used to isolate nuclei from early Arabidopsis embryos by flow cytometry. Additionally, cellular RNA from intact whole embryos was extracted. Subsequently, extracted RNA was biotinylated and  hybridized to Affymetrix ATH1 chips.

first: Jixiang

last: Kong

first: Kenneth

middle: W

last: Berendzen

first: Joachim

last: Kilian

first: Agnes

last: Henschen

first: Martina

last: Kolb

first: Markus

last: Schmid

first: Klaus

last: Harter

first: Ulrike

last: Mayer

first: Ive

last: De Smet

first: Martin

last: Bayer

first: Gerd

last: Jürgens


title: Time course microarray analysis during xylem cell differentiation in leaf-disk culture system

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

summary:
We established a novel in vitro culture system, in which vascular development can be induced in Arabidopsis thaliana leaf-disks using the specific GSK3s inhibitor.
To elucidate gene expression profiles during vascular development, we performed GeneChip analysis using our newly established culture system.

overall_design: Arabidopsis leaf disks cultured with the induction medium were sampled at every 12 hours from 0 to 48 hours.

first: Sayaka

last: Isu

first: Yukiko

last: Sugisawa


title: Transcriptional profiling of the Arabidopsis root quiescent center

status: Public on Dec 17 2014

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

summary:
The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the WOX5 marker.
To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5.

overall_design: Three replicates of FACS-sorted GFP-positive cells from WOX5:GFP roots.

first: Shuai

last: Yuan

last: Birnbaum


title: Expression data from RECA1-overexpressing plants

status: Public on Oct 15 2014

first: Hyesung

last: Jeon

address: Shillim-Dong

department: Agricutural Biotechnology

institute: Seoul National University

summary:
Arabidopsis nuclear RecA homologue RA51D were reported to be involved in plant defense responses. Plant organelles such as mitochondria and chloroplast also have their own RecA homologues. We focused on chloroplast RecA homologue RECA1 because it has been well known that the precursors of phytohormones and secondary metabolites related to plant defense responses are synthesized in chloroplast and recent studies have identified several chloroplastic proteins invoved with plant defense responses.
We used microarrays to investigate the global gene expression changes by RECA1.

overall_design: 2-week-old Col-0 and RECA1(at1g79050)-overexpressing plants without any treatments were used for RNA extraction and hybridization on Affymetrix microarrays. Col-0 plants were used as control and T3 RECA1-overexpressing transgenic plants were used in this study.

first: Minkyun

last: Kim


title: AtC3H14, a direct target of MYB46, suppress cell elongation and involved in the secondary wall formation.

status: Public on Dec 05 2014

city: Yongin

first: Jae-Heung

last: Ko

state: Gyeonggi

address: 1 Seocheon-dong, Giheung-gu

department: Plant & Environmental Resources

institute: Kyung Hee University

summary: Recently, AtC3H14, a CCCH-type zinc finger protein, was identified as one of the direct targets of MYB46, which is known as a master regulator of secondary wall biosynthesis. AtC3H14 and their homologs (i.e., AtC3H15 and PtrC3H14-1 from Arabidopsis and poplar, respectively) are predominantly expressed in the secondary wall forming tissues. Transgenic Arabidopsis plants overexpressing AtC3H14 (i.e., 35S::AtC3H14 plants) produced dwarfing phenotypes. 35S::AtC3H14 plants developed phloem fibers earlier than wild-type and this phenotype was more pronounced in the roots. Interestingly, ectopic secondary wall thickenings were found in both stems and roots. These phenotypic consequences are successively reproduced from the 35S::AtC3H15 and 35S::PtrC3H14-1 plants. Whole transcriptome GeneChip analysis identified that the ‘cell wall’ and ‘extracellular’-related genes are extremely over-represented in the stem tissues of 35S::AtC3H14 plants. These results suggest that AtC3H14 may act as a negative regulator of cell elongation with modification of cell wall reassembly and be involved in the secondary wall formation in Arabidopsis.

overall_design: To gain insights into the AtC3H14-mediated transcriptional regulation, we used ATH1 GeneChip microarray to obtain transcriptome profiles of Arabidopsis stem overexpressing AtC3H14 compared to that of wild type plant.

first: Kyung-Hwan

last: Han