title: RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Affymetrix]

status: Public on Jun 30 2016

city: Wuhan, Hubei Province

first: Zhulong

last: Chan

address: Moshan, Wuchang District

department: Wuhan Botanic Garden

institute: Chinese Academy of Sciences

summary: The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutant plants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 increased the expression of CBFs and CBF regulon genes and decreased cold-induced membrane injury. The rdm4 mutants exhibited decreased antioxidant enzyme activities and increased accumulation of reactive oxygen species. Microarray analysis indicated that a great proportion of genes affected by rdm4 overlapped with those affected by CBF2 and CBF3 in Arabidopsis. Chromatin immunoprecipitation (ChIP) results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF genes but not the promoters of up-stream regulators of CBFs. Together, these data indicate that RDM4 acts as a component of a Pol II transcription complex that regulates CBF gene expression and cold stress resistance in Arabidopsis.

overall_design: Two-week-old seedlings of rdm4 and C24 WT plant were subjected to chilling treatment for 0, 3, and 48 h treatments.Plant materials were then collected for RNA extraction.

first: Jian-Kang

last: Zhu


title: Expression data from sound vibration-treated Arabidopsis thaliana

status: Public on Jun 15 2016

city: Gyeongsan

first: Ritesh

last: Ghosh

address: 280 Daehak-Ro

department: School of Biotechnology

country: South Korea

institute: Yeungnam University

summary: Sound vibration (SV) causes various developmental and physiological changes in plants. It strongly suggests the existence of sophisticated molecular mechanisms for SV perception and signaling in plants. However, the underlying molecular mechanism of SV-mediated plant responses remains elusive. Herein, we investigated the transcript changes in Arabidopsis thaliana upon five different single frequencies of SV treatment.

overall_design: SV-treated Arabidopsis was used for RNA extraction and hybridization on Affymetrix microarrays. Arabidopsis plants (twenty-day-old) were transferred to the soundproof chamber and subjected to 5 different frequencies of SV (250, 500, 1000, 2000, and 3000 Hz) with constant amplitude (80 dB) separately for 1 h. For microarray analysis, samples were harvested right after the SV treatments of 1 h (0 h time point). Control plants were kept in a similar chamber without SV treatment.

first: Bosung

last: Choi

first: Hanhong

last: Bae


title: RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway

country: China

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

overall_design: Refer to individual Series


title: Trancriptomic analysis of PKA and PKC signalling gene cascade in cultured human ovarian granulosa cells (KGN) [PMA treatments]

status: Public on Jul 20 2016

city: Québec

first: Patricia

middle: G

last: Tremblay

state: Québec

address: 2440 Hochelaga Blvd

department: Sciences animales

country: Canada

institute: Laval University

summary: The oocyte’s capacity to complete maturation, to succeed fertilization and to reach the blastocyst stage is what defines the oocyte’s competence. The oocyte acquires this competence working closely with somatic cells of the follicle. Cumulus and granulosa cells provided support for the oocyte’s development and conversely the oocyte influence follicular cell growth and differentiation. Existing studies support the idea that follicular-stimulated hormone and luteinizing hormone play an essential role in oocyte competence acquisition through protein kinase A (PKA) and protein kinase C (PKC) signalling in granulosa cells. Therefore, human-like granulosa cells (KGN) were treated with forskolin 10 μM and phorbol 12-myristate 13-acetate 0.1 μM for 24 hours in order to process a transcriptomic analysis of differentially express genes between treatment. Over 2000 genes were founded to be differentially express at cut-off fold change of 1.5 and a p-value of 0.05. Five major upstreams, EGF, TGFB1, VEGF, FGF2 and HGF were founded to play an important role in competence acquisition thought PKA and PKC signalling. Differentially expressed targeted genes of both signalling pathways were classified in seven major ovarian functions such as PTGS2, IL8 and IL6 in inflammation, STAR, CYP11A1, CYP19A1 in steroidogenesis, VEGFC, VEGFA, CXCR4 in angiogenesis, AREG, EGFR, SPRY2 in differentiation, BAX, BCL2L12, CASP1 in apoptosis, CCND1, CCNB1, CCNB2 in division and MMP1, MMP9, TIMP1 in ovulation. Taken together, the results of this study suggest that PKA and PKC signalling potentiate their effects in some functions such as inflammation and apoptosis while some others are more specific to one or the other protein kinase like differentiation, ovulation and angiogenesis that are thought to be more PKC-dependent in human granulosa cells.

overall_design: 8 samples were analysed, 4 controls compared to 4 Phorbol 12-myristate 13-acetate treatments (total of 4 replicates).

first: Isabelle

last: Dufort

first: Marc-André

last: Sirard


title: Trancriptomic analysis of PKA and PKC signalling gene cascade in cultured human ovarian granulosa cells (KGN)


title: Trancriptomic analysis of PKA and PKC signalling gene cascade in cultured human ovarian granulosa cells (KGN) [FSK treatments]

overall_design: 8 samples were analysed, 4 controls compared to 4 Forskolin treatments (total of 4 replicates).


title: Expression profiling of Abelson interactor-1 (Abi-1) deficient hematopoietic progenitor cells.

status: Public on Jun 14 2016

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: One Hoppin street

department: Medicine/Hem-Onc

country: USA

institute: Rhode Island Hospital and Warren Alpert Medical School at Brown University

summary:
Gene expression profile of LSK-enriched population of hematopoietic progenitor cells from Abi-1 KO mice indicates activation of the NFκB pathway.
In this dataset, we include the expression data obtained from Lineage-, Sca-1+, cKit+ (LSK)-enriched population of hematopoietic progenitor cells isolated from the bone marow of Abi-1 KO and WT animals. Abi1(fl/fl);Tg (Mx1- cre(-)) or Abi1(fl/fl);Tg (Mx1-cre(+)) mice were subjected to polyinosinic:polycytidylic acid [poly(I:C)]-induced activation of the Cre recombinase under control of the Mx1 promoter to obtain animals with an  Abi1(fl/fl);Tg (Mx1-cre(-)) (Abi-1 WT) or Abi1(-/-);Tg (Mx1-cre(+)) (Abi-1 KO) genotype.

overall_design: 9 Total samples were analyzed: LSK cells from the bone marrow of 4 Abi-1 KO and 5 Abi-1 WT mice. The whole bone marrow was obtained from the individual mice by flushing cells from clavicles, scapulae, humeri, radiuses, ulnas, sternum, pelvis (iliums and ischiums), femurs, tibias, and fibulas. For LSKs sorting lineage-depleted bone marrow cells were stained with BUV395 Streptavidin, APC CD117/c-Kit (2B8), and PE.Cy7 Ly-6A/E/Sca-1 (D7) antibodies. Cells were sorted using a legacy MoFlo High Speed cell sorter equipped with four lasers (355 nm, 405 nm, 488 nm, and 633 nm).

first: Anna

last: Chorzalska

first: John

last: Morgan

first: Diana

middle: O

last: Treaba

first: Adam

middle: J

last: Olszewski

first: Nathan

last: Kingston

first: Yan

last: Cheng

first: Kara

last: Lombardo

first: Christoph

last: Schorl

first: Xiaoqing

last: Yu

first: Roberta

last: Zini

first: Annalisa

last: Pacilli

first: Alexander

last: Tepper

first: Anita

last: Hryniewicz-Jankowska

first: Ting

last: Zhao

first: Elena

last: Oancea

last: Reagan

first: Eric

last: Winer

first: Leszek

last: Kotula

first: Peter

last: Quesenberry

first: Philip

last: Gruppuso

first: Rosella

last: Manfredini

first: Alessandro

last: Vannucchi


title: Transcriptomic responses of cat2-2 and shr-6 cat2-2 to photorespiratory conditions

status: Public on Jun 10 2016

city: Helsinki

first: Cezary

last: Waszczak

address: Viikinkaari 1

department: Dept. of Biosciences

country: Finland

institute: University of Helsinki

summary: Hydrogen peroxide (H2O2) is a potent signaling molecule influencing various aspects of plant growth and development. Its limited lifetime and specific production sites in the plant cell necessitate the existence of specialized mechanisms that relay H2O2-encoded information. To discover such mechanisms, we focused on peroxisomal H2O2 production triggered by enhanced photorespiration in Arabidopsis mutants lacking catalase activity (cat2-2), and looked for second-site mutations that attenuate the negative effects (Fv'/Fm' decline and lesion formation) of H2O2 build up. A mutation residing in the GRAS family transcriptional regulator SHORT-ROOT (SHR) was found to underlie the increased performance of cat2-2 knock-outs under photorespiratory stress. In contrast to shr, introduction of the scr mutation in cat2-2 background did not improve the photorespiratory performance of plants lacking peroxisomal catalase. The absence of SHR negatively affected the activity of the photorespiratory enzymes glycolate oxidase and catalase, which was accompanied with elevated glycolate content and inability to accumulate glycine under conditions promoting photorespiration. The transcriptome signature of cat2-2 shr-6 double mutants exposed to photorespiratory stress lacked jasmonate-dependent signaling components, otherwise induced in cat2-2. The photorespiratory phenotype of cat2-2 was found to be modulated by exogenous sugars both in the presence and absence of shr. Taken together, these findings highlight a crucial role for SHR in H2O2 signal transduction and stress tolerance.

overall_design: Three-week-old cat2-2 and shr-6/cat2-2 plants were exposed to photorespiratory conditions. Rosettes were sampled in three biological replicates before (T = 0) and after 24 hours (T = 24H) of the treatment. Total RNA was extracted with Spectrum Plant Total RNA Kit (Sigma) and submitted to Arabidopsis ATH1 microarray hybridization.

first: Pavel

last: Kerchev

first: Patrick

last: Willems

first: Frank

last: Van Breusegem


title: Respiratory burst oxidase homologues D and F in catalase2 deficient plants

city: Gent

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

summary: Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. Catalase deficient plants are pioneering systems which accumulate hydrogen peroxide (H2O2) from peroxisomal origin during photorespiratory challenges. Respiratory burst oxidase homologues D and F are known to participate in intracellular oxidative stress response launched in cat2 mutants (Chaouch et al., 2012). We studied the compared the transcriptional response of cat2 rbohD and cat2 rbohF double mutants versus the cat2 background to further adress their role during photorespiratory stress.

overall_design: After 3 weeks of growth, leaf tissue from the three different genotypes was harvested in triplicate.

first: Amna

last: Mhamdi

first: Graham

last: Noctor


title: Unsaturation of very-long-chain ceramides regulates hypoxia response by modulating ethylene signaling in Arabidopsis

status: Public on Jul 24 2016

city: Guangzhou

first: Lujun

last: Yu

state: Guandong

address: xingangxilu 135

institute: Sun Yat-sen University

summary: Lipid remodeling is crucial for hypoxic tolerance in animals, whilst little is known about the hypoxia-induced lipid dynamics in plant cells. Here we performed a mass spectrometry-based analysis to survey the lipid profiles of Arabidopsis rosettes under various hypoxic conditions. We observed that hypoxia caused a significant increase in total amounts of phosphatidylserine, phosphatidic acid and oxylipins, but a decrease in phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Particularly, significant gains in the polyunsaturated species of PC, PE and phosphatidylinositol, and losses in their saturated and mono-unsaturated species were evident during hypoxia. Moreover, hypoxia led to a remarkable elevation of ceramides and hydroxyceramides. Depletion of ceramide synthases LOH1, LOH2, and LOH3 enhanced plant sensitivity to dark submergence (DS), but displayed more resistance to submergence under light than wild type. Consistently, levels of unsaturated ceramide species (22:1, 24:1, and 26:1) predominantly declined in the loh1, loh2, and loh3 mutants under DS. Evidence that C24:1-ceramide interacted with recombinant CTR1 protein in vitro, enhanced ER-to-nucleus translocation of EIN2-GFP and stabilization of EIN3-GFP in vivo, suggests a role of ceramides in modulating ethylene signaling. The DS-sensitive phenotypes of loh mutants were rescued by a ctr1-1 mutation. Thus, our findings demonstrate that unsaturation of very-long-chain ceramides is a protective strategy for hypoxic tolerance in Arabidopsis.

overall_design: Arabidopsis Affymetrix GeneChip arrays were probed with RNAs isolated from leaves of untreated plants (controls) and plants upon hypoxia under light submergence for 48 h.

first: Li-Juan

last: Xie

first: Qin-Fang

last: Chen

first: Lu-Jun

first: Liang

first: Shi

last: Xiao


title: Expression profiles of OE (Overexpression of ANAC069) plants and KO (Knockout of ANAC069, SALK_095231C) plants under salt stress conditions

status: Public on Jun 07 2016

city: Harbin

first: Lin

last: He

address: 26 Hexing Road

institute: Northeast Forestry University

summary: To identify the target genes regulated by ANAC069, the expression profiles of OE (Overexpression of ANAC069) plants and KO (Knockout of ANAC069, SALK_095231C) plants under salt stress conditions were compared using Affymetrix Arabidopsis gene chips.

overall_design: Four-week-old OE (OE-3 line) and KO (KO-2 line) plants were treated with 200 mM NaCl for 3 h. Then gene expression in OE and KO plants was compared using Affymetrix Arabidopsis gene chips (ATH1 Genome Array), performed with three independent biological replicates.

first: Hongyun

last: Xu


title: Gene expressions in K67-treated or non-treated Huh1 cells

status: Public on Jun 21 2016

city: Niigata-shi

first: Tetsuya

last: Saito

state: Niigata

address: 757, Ichibancho, Asahimachidori, Chuo-ku

department: Biochemistry

country: Japan

institute: Niigata University school of medicine

summary: We have employed whole genome microarray expression profiling to identify the genes affected upon exposure of K67.

overall_design: Four independent experiments were performed using K67-treated or non-treated Huh1 cells for each experiment.

first: Yasumasa

last: Nishito

first: Masaaki

last: Komatsu


title: CTCF contributes in a critical way to spermatogenesis and male fertility

status: Public on Jun 03 2016

city: Stockholm

first: Abrahan

last: Hernández-Hernández

address: Berzeliuz väg 35

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: The CCCTC-binding factor (CTCF) is an architectural protein that governs chromatin organization and gene expression in somatic cells. Here, we show that CTCF regulates chromatin compaction necessary for packaging of the paternal genome into mature sperm. Inactivation of Ctcf in male germ cells in mice (Ctcf-cKO mice) resulted in impaired spermiogenesis and infertility. Residual spermatozoa in Ctcf-cKO mice displayed abnormal head morphology, aberrant chromatin compaction, impaired protamine 1 incorporation into chromatin and accelerated histone depletion. Thus, CTCF regulates chromatin organization during spermiogenesis, contributing to the functional organization of mature sperm.

overall_design: Tunica albuginea of wild-type and Ctcf-cKO testis was removed and seminiferous tubules were transported to the lab bench in RNA stabilization reagent RNAlater (QIAGEN). RNA was extracted and purified with the RNeasy kit (QIAGEN). Three independent wild-type and four independent Ctcf-cKO microarray analysis were performed using the GeneChip mouse transcriptome assay 1.0 (Affimetrix)

first: Ingrid

last: Lilienthal

first: Nanaho

last: Fukuda

first: Niels

last: Galjart

first: Christer

last: Höög


title: Whole transcriptome analysis of mouse brain with chronic diazepam treatment

status: Public on May 31 2016

city: Hirosaki

first: Shinya

last: Ueno

state: Aomori  Pref.

address: 5 Zaifu-cho

department: Neurophysiology

institute: Hirosaki Univ Grad Sch of Med

summary:
Global transcriptional analysis of chronic DZP administrated mouse brain using microarrays identified some up- and down- regulated genes after chronic DZP administrations.
Diazepam (DZP), a medication of the benzodiazepine family, is widely used to treat various conditions including anxiety, muscle spasms, seizures, trouble sleeping, and alcohol withdrawal syndrome. Chronic DZP treatment has significant risks such as tolerance, dependence, withdrawal effect and Alzheimer's disease. As the molecular mechanisms of these risks were complex processes, global analysis has been required.

overall_design: Control (INTRALIPID, vehicle) or DZP chronically administrated mice (n=3, respectively) were decapitated and brains were quickly removed under deep anesthesia. Total RNA were extracted from cerebral cortex, hippocampus and amygdala. The samples were named as follows: CC;control cerebral cortex, DC; DZP cerebral cortex, CH;control hippocampus, DH; DZP hippocampus, CA; control amygdala, DA; DZP amygdala. 100 ng of total RNA were subjected to GeneChip® Mouse Transcriptome Array (MTA-1_0, Affymetrix) according to manufacturer's protocol.

first: Tomonori

last: Furukawa

first: Shuji

last: Shimoyama


title: Expression data from 29-day old Arabidopsis plants

city: Bethesda

first: Laxminath

last: Tumburu

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary:
Metal oxide engineered nanoparticles, which are widely used in diverse applications, are known to impact terrestrial plants. These nanoparticles have a potential to induce changes in plant tissue transcriptomes,  and thereby the productivity. Here we looked at how the two commonly used nanoparticles, nano-titania (TiO2) and nano-ceria (CeO2) can impact the underlying mechanisms associated plant growth at genome level.
We used microarrays to detail the global programme of gene expression underlying various physiological processes associated with growth and development, and identified distinct classes of up-regulated genes during this process.

overall_design: 29  day old Arabidopsis plants were selected for RNA extraction from roots and rosette leaves, followed by hybridization on Affymetrix microarrays. Arabidopsis plants  were  exposed twice during the germination stage (Days 0 and 4), and once during the primary rosette stage (Day 17), to 500mg/L concentration of nano-titania and nano-ceria,  followed by extraction of RNA from 29-day old plant tissues (roots and rosette leaves) for Microarray analysis. 0.1mM KCl was used as control for nano-titania, whereas sterilized millipore water was used as control for nano-ceria.


title: Analysis of genes regulated by AS2 and RH10 at 22, 26°C

status: Public on May 25 2016

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

summary: AS2 encodes a protein containing AS2 domain and epigenetically regulate transcription. RH10 encodes an ortholog of human DEAD-box RNA helicase DDX47. These genes are involved in the formation of axes of leaves of Arabidopsis thaliana. To know the gene regulation in the leaf development, expression profile among wild-type, as2, rh10 and as2 rh10 double mutant plants were compared.

overall_design: Shoot apices that contain leaf primordia were selected.

first: Yoko

last: Matsumura

first: Yasunori

last: Machida


title: Tissue-based Genomics Augments Post-prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men

status: Public on May 12 2016

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

institute: GenomeDx

summary: Radical prostatectomy (RP) is a primary treatment option for men with intermediate- and high-risk prostate cancer. Although many are effectively cured with local therapy alone, these men are by definition at higher risk of adverse pathologic features. It has been shown previously that genomic data can be used to predict tumor aggressiveness. Our objective was to evaluate genomic data and it's relationship to pathological stage and grade in a cohort of men that received no treatment other than radical prostatectomy surgery.

overall_design: Retrospective case-cohort design for 260 men who underwent RP between 1992 and 2010 at intermediate or high risk and received no additional treatment until the time of metastasis. Participants met the following criteria: (1) Cancer of the Prostate Risk Assessment postsurgical (CAPRA-S) score 3; (2) pathologic Gleason score 7; and (3) post-RP prostate-speciﬁc antigen nadir <0.2 ng/ml.

first: Ashley

middle: E

last: Ross

first: Michael

middle: H

last: Johnson

first: Kasra

last: Yousefi

first: George

last: Netto

first: Luigi

last: Marchionni

first: Helen

middle: L

last: Fedor

first: Stephanie

last: Glavaris

first: Voleak

last: Choeurng

first: Christine

last: Buerki

first: Nicholas

last: Erho

first: Lucia

last: Lam

first: Elizabeth

middle: B

last: Humphreys

first: Sheila

last: Faraj

first: Stephania

last: Bezerra

first: Misop

last: Han

first: Alan

middle: W

last: Partin

first: Bruce

last: Trock

first: Edward

last: Schaeffer


title: Expression profiling of Fusarium oxysporum infected wild-type Arabidopsis and a 35S Fusarium SIX4 overexpression line.

city: Floreat

first: Louise

middle: Faye

last: Thatcher

state: WA

address: 147 Underwood Ave

department: Agriculture and Food

country: Australia

institute: CSIRO

summary:
Fungal effectors play important roles in inciting disease development on host plants. We identified an effector (Secreted in Xylem4, SIX4) in an Arabidopsis infecting isolate (Fo5176) of the root-infecting fungal pathogen Fusarium oxysporum and demonstrated this effector is required for full virulence. To  explore the role of Fo5176_SIX4 we use whole transcriptome profiling of root tissues from plants overexpressing this effector (35sSIX4) versus wild-type (Col-0) plants after F. oxysporum infection.
Published in DOI:10.1007/978-3-319-42319-7_4. Belowground Defence Strategies in Plants.

overall_design: We grew both WT and 35sSIX4 plants for four weeks in soil. After four weeks the plants were  infected with Fusarium oxyporum isolate Fo5176, trays covered with a plastic dome and incubated at 28C. There were four independent replicates of each treatment and each replicate contained root tissue from 20 plants. Each replicate (8 in total) was harvested 4 days post inoculation and the resulting RNA was used for hybridization to an Affymetrix ATH1 chip.

middle: F

first: John

last: Manners

first: Kemal

last: Kazan


title: Follicular cells in vivo and developmental competence of oocytes in human

status: Public on May 03 2016

first: Anne-Laure

last: Nivet

summary: Transcriptional profiling of in vivo follicular cells from small (S), medium sized (M) and Large (L) follicles collected individually 36hrs post hCG in superstimulated women from fertility clinic. Samples are also characterized by their respective oocyte outcome following fertilization (transferable embryo (+) or not(-))

overall_design: 3 comparisons, 3 biological replicates per comparison, one replicate per array, dye swap experiments, two colors, M- vs M+, S-vs M+, L- vs M+

first: Anne-laure

first: Marie-Claude

last: Leveillé

first: Arthur

last: Leader

first: Marc-André

last: Sirard


title: Coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/ER stress and innate immunity pathways by inducible artificial microRNA silencing of the SNF4 activator subunit of Arabidopsis SnRK1

status: Public on May 01 2016

city: Cologne

first: Csaba

last: Koncz

address: Carl-von-Linne-Weg 10

country: Germany

institute: Max-Planck Institute for Plant Breeding Research

summary:
Arabidopsis SnRK1 is structurally and functionally related to the yeast Snf1 and mammalian AMP-activated kinases, which are activated in response to carbon/glucose limitation and stress conditions causing an imbalance of energy homeostasis increasing the AMP/ATP ratio. Mutations of the SNF4 activating subunit of trimeric Arabidopsis SnRK1 complexes are not transmitted through the male meiosis. Silencing of SNF4 by a β-estradiol-inducible artificial microRNA (amiR-SNF4) constructs was used to examine how inhibition of SnRK1 affects transcriptional regulation of different cellular pathways in dark and light grown seedlings. This study shows that amiR-SNF4 silencing of SnRK1 leads to coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/endoplasmic reticulum stress and pathogen defense responses by inducing simultaneous changes in numerous other essential hormonal and metabolic pathways in Arabidopsis.
We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and β-estradiol-induced amiR-SNF4 mutant seedlings 5 days after germination in the dark or light.

overall_design:
Wild type and amiR-SNF4 mutant Arabidopsis (Col-0) seedlings were grown in either darkness or light (22°C, 400 μEinstein m−2s−1 irradiance, 8h light/16 dark) in the presence 5 µM β-estradiol on 0.5 MS medium containing 0.5% sucrose and ½ concentration of macro elements. (Koncz, C., Martini, N., Szabados, L., Hrouda, M., Bachmair, A., and Schell, J. (1994). Specialized vectors for gene tagging and expression studies. In: Plant Molecular Biology Manual, Gelvin,S., and Schilperoort, B. (eds.), Kluwer Academic Publishers, Dordrecht-Boston-London, B2, 1-22.) Seedling were collected at 4h after the start of the light period in liquid nitrogen for RNA preparation. At this stage, trypan-blue staining detected no visible signs of cell death in amiR-SNF4 seedlings.
Steady-state mRNA levels in total RNA samples of 5 days old seedlings dark and light grown were compared.

first: Marta

last: Bitrián

first: Bruno

last: Huettel


title: Human colorectal cancer cell line CRC#21: Sphere-cultured cells vs. Adherent-cultured cells

status: Public on Apr 01 2016

city: Sapporo city

first: TADASHI

last: OGAWA

state: Hokkaido

address: S-1 W-17, Chuo-ku

department: Pathology

institute: Sapporo medical University School of Medicine

summary: Transcriptional profiling of cancer stem cells (sphere-cultured cells) comparing non-cancer stem cells (adherent-cultured cells). Goal was to identity cancer stem cell-specific genes.

overall_design: Two-condition experiment, sphere-cultured cells vs. adherent-cultured cells: 1 sphere-cultured replicate and 1 adherent-culture replicate.

first: Tadashi

last: Ogawa

first: Eri

last: Saka

first: Yoshihiko

last: Hirohashi


title: Human colorectal cancer cell line CRC#21: ALDH-high cells vs. ALDH-low cells

summary: Transcriptional profiling of cancer stem cells (ALDH-high cells) comparing non-cancer stem cells (ALDH-low cells), sorted out using ALDEFLUOR assay. Goal was to identity cancer stem cell-specific genes.

overall_design: Two-condition experiment, sphere-cultured cells vs. adherent-cultured cells: 1 ALDH-high replicate and 1 ALDH-low replicate.


title: FUS3 Activates TAG Accumulation

status: Public on Apr 19 2016

city: East Lansing

last: Ohlrogge

state: MI

address: 612 Wilson Rd

department: Plant Biology

institute: Michigan State University

summary: Triacylglycerol (TAG) is the main storage lipid in plant seeds and the major form of plant oil used for food and, increasingly, for industrial and biofuel applications. Several transcription factors, including FUSCA3 (At3g26790, FUS3), are associated with regulation of embryo 3maturation and oil biosynthesis in seeds. However, the ability of FUS3 to increase TAG biosynthesis in other tissues has not been quantitatively examined. Here, we evaluated the ability of FUS3 to activate TAG accumulation in non-seed tissues. Overexpression of FUS3 driven by an estradiol-inducible promoter increased oil contents in Arabidopsis seedlings up to 6% of dry weight; more than 50 fold over controls. Eicosenoic acid, a characteristic fatty acid of Arabidopsis seed oil, accumulated to over 20% of fatty acids in cotyledons and leaves. These large increases depended on added sucrose, although without sucrose TAG increased 3-4 fold. Inducing the expression of FUS3 in tobacco BY2 cells also increased TAG accumulation, and co-expression of FUS3 and diacylglycerol acyltransferase 1 (DGAT1) further increased TAG levels to 4% of dry weight. BY2 cell growth was not altered by FUS3 expression, although Arabidopsis seedling development was impaired, consistent with the ability of FUS3 to induce embryo characteristics in non-seed tissues. Microarrays of Arabidopsis seedlings revealed that FUS3 overexpression increased expression of a higher proportion of genes involved in TAG biosynthesis than genes involved in fatty acid biosynthesis or other lipid pathways. Together these results provide additional insights into FUS3 functions in TAG metabolism and suggest complementary strategies for engineering vegetative oil accumulation.

overall_design: To  investigate gene expression patterns in vegetative tissues expressing FUS3 and the interactions between FUS3, sucrose and oil accumulation, we characterized the transcriptome of Arabidopsis seedlings that accumulated oil using Arabidopsis ATH1 microarrays. We grew ESTpro:FUS3-strong and WT plants under FUS3-inducing conditions on medium with or without sucrose, extracted total RNA from 8-day-old seedlings from triplicate biological samples, and performed transcriptome profiling using the Affymetrix GeneChip ATH1. A two-way ANOVA test was performed to evaluate differential expression across groups, and their interactions were defined based on two factors, namely, FUS3 induction and sucrose treatment.

first: Meng

last: Zhang

first: Xia

last: Cao

first: Qingli

last: Jia


title: Expression Profiling In Chromosome 1 substitution lines derived from Chinese wild mice

status: Public on May 04 2016

city: Shanghai

first: FUYI

last: XU

state: Shanghai

address: 2999 NORTH RENMING ROAD, SONGJIANG DISTRICT

department: College of Chemistry, Chemical Engineering, and Biotechnology

institute: Donghua University

summary:
Identify genes in liver tissue whose expression is under genetic and high fat diet induced regulation  in three Chromosome 1 substitution lines derived from Chinese wild mice (B6-Chr1SJ (SJ), B6-Chr1KM (KM), and B6-Chr1HZ (HZ)) and one donor strain C57B/LJ(B6)
We used microarrays to detail the global gene expression in three chromosome 1 substitution lines and one donor strain which fed with control or high fat diet.

overall_design: Male mice were first maintained on a chow diet (M01-F25, Shanghai SLAC Laboratory Animal Co., Ltd, China) for 8 weeks, then fed with 10% fat diet (D12450B, Research Diets, New Brunswick, NJ, U.S.A.) until sacrifice at 20 weeks of age.Liver tissues were collected and total RNAs were immediately extracted.RNA from two mice were pooled and assayed on one Affymetrix Mouse Transcriptome Assay 1.0 chip.

first: Fuyi

last: Xu


title: A jumonji protein with E3 ligase and histone binding activities regulates transposon silencing in Arabidopsis

status: Public on Mar 18 2016

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: Transposable elements (TEs) make up a large proportion of eukaryotic genomes. As their mobilization creates genetic variation that threatens genome integrity, TEs are epigenetically silenced through several pathways and this may spread to neighboring sequences. JUMONJI (JMJ) proteins can function as anti-silencing factors and prevent silencing of genes next to TEs. Whether TE silencing is counterbalanced by the activity of anti-silencing factors is still unclear. Here, we characterize JMJ24 as a regulator of TE silencing. We show that loss of JMJ24 results in increased silencing of the DNA transposon AtMu1c, while overexpression of JMJ24 reduces silencing. JMJ24 has a JumonjiC (JmjC) domain and two RING domains. JMJ24 auto-ubiquitinates in vitro, demonstrating E3 ligase activity of the RING domain(s). JMJ24-JmjC binds the N-terminal tail of histone H3 and full-length JMJ24 binds histone H3 in vivo. JMJ24 activity is anti-correlated with histone H3 lysine 9 dimethylation (H3K9me2) levels at AtMu1c. Double mutant analyses with epigenetic silencing mutants suggest that JMJ24 antagonizes histone H3K9me2, and requires H3K9 methyltransferases for its activity on AtMu1c. Genome-wide transcriptome analysis indicates that JMJ24 affects silencing at additional TEs. Our results suggest that the JmjC domain of JMJ24 has lost demethylase activity but has been retained as a binding domain for histone H3. This is in line with phylogenetic analyses indicating that JMJ24 [with the mutated JmjC domain] is widely conserved in angiosperms. Taken together, this study assigns a role in TE silencing to a conserved JmjC-domain protein with E3 ligase activity, but no demethylase activity.

overall_design: 9 samples, three mutant replicates, three overexpresser replicates, three wild type replicates.

first: Tina

last: Kabelitz

first: Krzysztof

last: Brzezinka

first: Thomas

last: Friedrich

first: Christian

last: Kappel


title: Analysis of Pichia pastoris cultivated in chemostat and retentostat culture

status: Public on May 10 2016

city: Wien

first: Alexandra

middle: Bettina

last: Graf

address: Muthgasse 18

department: Applied Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna

summary: Transcriptional profiling of Pichia pastoris cultivated at different specific growth rates in carbon and energy-limited aerobic chemostats and retentostats

overall_design: Reference design, samples R1-3, R6, R8, C01, C0025, C0050, C0075 hybridized against a pool sample [mixed pool of Pichia pastoris cells sampled from various conditions including cells grown on glycerine, glucose and methanol, on full andminimal medium, in stationary and exponential growth phase, and in different stress states].

first: Corinna

last: Rebnegger

first: Tim

last: Vos

first: Minoska

last: Valli

first: Jack

middle: T

last: Pronk

first: Pascale

last: Daran-Lapujade

first: Diethard

last: Mattanovich


title: IL-17A plays a central role in the expression of psoriasis signature genes through induction of IkappaB-zeta in keratinocytes

status: Public on Mar 08 2016

city: Sapporo

first: Ryuta

last: Muromoto

address: Kita 12 Nishi 6, Kita-ku

department: Faculty of Pharmaceutical Sciences

institute: Hokkaido University

summary: In psoriasis lesions, a diverse mixture of cytokines is upregulated which influence each other generating a complex inflammatory situation. Although this is the case, the inhibition of Interleukin-17A (IL-17A) alone showed unprecedented clinical results in patients, indicating that IL-17A is a critical inducer of psoriasis pathogenesis. To elucidate IL-17A-driven keratinocyte-intrinsic signaling pathways, we treated monolayers of normal human epidermal keratinocytes in vitro with a mixture of 6 cytokines (IL-17A, TNF-a, IL-17C, IL-22, IL-36g and IFN-g) involved in psoriasis, to mimic the inflammatory milieu in psoriasis lesions. Microarray and gene set enrichment analysis revealed that this cytokine mixture induced similar gene expression changes with the previous transcriptome studies using psoriasis lesions. Importantly, we identified a set of IL-17A-regulated genes in keratinocytes, which recapitulate typical psoriasis genes exemplified by DEFB4A, S100A7, IL19 and CSF3, based on differences in the expression profiles of cells stimulated with 6 cytokines versus cells stimulated with only 5 cytokines lacking IL-17A. Furthermore a specific IL-17A-induced gene, NFKBIZ, which encodes IkappaB-zeta, a transcriptional regulator for NF-kappaB, was demonstrated to have a significant role for IL-17A-induced gene expression. Thus, we present novel in vitro data from normal human keratinocytes that would help elucidating the IL-17A-driven keratinocyte activation in psoriasis.

overall_design: Cytokine mixture-induced gene expression in primary normal human epidermal keratinocytes (NHEKs) was measured at 24 hours after exposure.  NHEKs were exposed to the combination of selected six cytokines (IL-17A: 100 ng/ml, TNF-a: 10 ng/ml, IFN-g: 10 ng/ml, IL-17C: 100 ng/ml, IL-22: 100 ng/ml, IL-36g: 500 ng/ml) , or to the different combinations of five of the six cytokines (in total, 7 different treatments and one untreated control). No replicate experiments were conducted.

first: Toru

last: Hirao


title: Expression data from Arabidopsis thaliana seedlings under shade avoidance condition at two different temperatures

status: Public on Mar 07 2016

city: Albany

first: ByungHoon

middle: Brian

last: Kim

state: GA

address: 504 College Dr.

institute: Albany State University

summary: We carried out microarray analysis to investigate the global gene expression pattern in response to supplemental far-red light under different temperature contexts.

overall_design: Three biological replicates of four different conditions were used, in which two different signals (light quality and temperature), were indipendently varied.


title: Role of GEMC1 controls the MCC transcriptional program

status: Public on Apr 05 2016

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary:
The generation of multiciliated cells requires a highly regulated but poorly understood transcriptional program. The deletion of GEMC1 in mice leads to the loss of multiciliated cells in the brain, respiratory system and oviduct indicating that it plays a key role in this process.
We used microarrays to examine the influence of GEMC1 on transcription in tissues with high numbers of multiciliated cells (trachea and oviduct).

overall_design:
The trachea and oviduct were isolated from  wild type and GEMC1 null mice of 39 (trachea, males) or 65 (oviduct, females) days of age. mRNA was extracted for array analysis.
IFOM-Cogentech (contributor)

last: Stephan-Otto Attolini

first: Travis

last: Stracker


title: Expression data from gbf1, gbf1 hy5, and gbf1 hyh mutants

city: New Delhi

first: Sudip

last: Chattopadhyay

state: Delhi

address: Aruna Asaf Ali Marg, JNU Campus

department: Development Biology

country: India

institute: National Institute of Plant Genome Research

summary: Three bZIP transcription factors (TFs), namely GBF1, HY5, and HYH, form heterodimers with each other and regulate photomorphogenesis in an interdependent manner. GBF1 acts as both a positive and negative regulator of photomorphogenesis, whereas HY5 and HYH mainly act as positive regulators of photomorphogenesis. To study the effect of HY5 and HYH on GBF1-mediated genome-wide expression, transcript profiling was performed in the gbf1 single mutant and gbf1hy5 and gbf1hyh double mutants. Our study revealed that GBF1 mainly acts antagonistic to HY5 and HYH for genome-wide expression.

overall_design: Four-day-old constant white-light grown Arabidipsis seedlings of wild-type (Col-0), gbf1 mutant, gbf1 hy5 double mutant and gbf1 hyh double mutant were harvested for total RNA extraction and Affymetrix microarray hybridisation. Two biological replicates of each sample were used for hybridisation and data analysis. Data were analysed using GeneSpring software by utilising the RMA algorithm. To draw the conclusions from this study, probe level intensity of gbf1, gbf1 hy5, and gbf1 hyh was normalised against the probe level intensity of wild-type, and also the probe level intensity of gbf1 hy5 and gbf1 hyh double mutants was normalised against the probe level intensity of the gbf1 single mutant.

first: Hathi

last: Ram

first: Mukesh

last: Jain


title: Gene expression analysis between CD20- CD138- and CD20+ CD138+ subpopulations using sorted MWCL-1

status: Public on Feb 17 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: For the complete cure of tumors, it is essential to eliminate cancer-initiating cells (CICs). Immunohistochemically, most tumor cells were CD20 and/or CD138 positive in clinical samples of lymphoplasmacytic lymphoma (LPL), and CD20- CD138- cells were hardly detected. Therefore, useful positive markers expressing in a candidate of CICs of LPL are necessary. First, we performed gene expression microarray analysis between CD20- CD138- and CD20+ CD138+ subpopulations using sorted Waldenstrom macroglobulinemia cell line (MWCL-1).

overall_design: Two dye-swap experiment was performed onto Human GE 4×44K V2 arrays (G4845A; Agilent Technologies).

first: Naoki

last: Wada

first: Eiichi

last: Morii


title: The purine metabolite allantoin can activate the jasmonate signaling pathway in a MYC2-regulated and ABA-dependent manner

status: Public on Mar 01 2016

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

summary:
Allantoin is a metabolic intermediate of purine catabolism that often accumulates in stressed plants. Recently, using Arabidopsis knockout mutants (aln) of ALLANTOINASE, we showed that this purine metabolite activates ABA production, thereby stimulating stress-related gene expression and enhancing seedling tolerance to abiotic stress. A detailed re-examination of the microarray data of an aln mutant (aln-1) not only confirmed increased expression of ABA-inducible genes, but also revealed altered expression of genes involved in jasmonic acid (JA) responses, likely under the control of MYC2, a master switch in the JA signaling pathway. Consistent with the transcriptome profiles, the aln-1 mutant displayed increased JA levels and enhanced responses to mechanical wounding and exogenous JA. Moreover, aln mutants demonstrated modestly increased susceptibility to hemibiotrophic and necrotrophic pathogens, probably reflecting the antagonistic action of MYC2 on the defense against these bacteria. Exogenously administered allantoin elicited the expression of JA-responsive genes including MYC2 in wild-type plants, supporting that allantoin might be responsible for the observed JA-related aln phenotypes. However, the effect of exogenous allantoin was suppressed by mutations deficient in bioactive JA (jar1-1), insensitive to JA (myc2-3) and deficient in ABA (aba2-1 and bglu18). The suppressive effect of jar1-1 and bglu18 mutations was further confirmed in the aln-1 background (jar1-1/aln-1 and bglu18/aln-1). These results indicate that allantoin can activate the MYC2-regulated JA signaling pathway through ABA production. Overall, this study provides evidence for the possible connection of purine catabolism with stress hormone homeostasis and signaling, and highlights the importance of allantoin in these interactions.
Evidence has been presented only recently for the involvement of purine catabolism in stress protection of plants and the mechanism behind this remains obscure. Here we show that in Arabidopsis, the intermediary metabolite allantoin can activate the MYC2-regulated jasmonate signaling pathway via the mechanism involving ABA, providing the link between the metabolism and two interactive signaling pathways of stress hormones that play critical roles in plant adaptation to environmental adversity.

overall_design: Two replicates of the mutant were compared with controls. This series is a re-analysis of GSE44922.

first: Hiroshi

last: Takagi

first: Yasuhiro

last: Ishiga

first: Mayumi

last: Egusa

first: Shunsuke

last: Watanabe

first: Nobuhiro

last: Akiyoshi

first: Takakazu

last: Matsuura

first: Izumi

middle: C

last: Mori

first: Takashi

last: Hirayama

first: Hironori

last: Kaminaka

last: Shimada

first: Atsushi

last: Sakamoto


title: Somatic mutation spectrum in monoclonal gammopathy of undetermined significance indicates a simpler genomic landscape compared to multiple myeloma

status: Public on Feb 18 2016

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

type: Genome variation profiling by genome tiling array

summary: Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma (MM) with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about the molecular mechanism of malignant transformation. We have performed whole-exome sequencing together with CGH+SNP array analysis in 33 flow-cytometry separated abnormal plasma cell samples from MGUS patients to describe somatic gene mutations and chromosome changes at the genome-wide level. Non-synonymous mutations and copy-number alterations were present in 97.0% and in 60.6% of cases, respectively. Importantly, the number of somatic mutations was significantly lower in MGUS compared to MM (p<10-4) and we have identified six genes that are significantly mutated in MM (KRAS, NRAS, DIS3, HIST1H1E, EGR1 and LTB) in the MGUS dataset. We also found a positive correlation with increasing chromosome changes and somatic mutations. IGH translocations were present in 27.3% of cases comprising t(4;14), t(11;14), t(14;16) or t(14;20) and were in a similar frequency to MM, which corresponded with the primary lesion hypothesis. Data from this study showed MGUS is a genetically comprehensive disease, however, overall genetic instability is significantly lower compared to MM.

overall_design: Overall, 33 MGUS patients were included in this study. Genomic DNA was isolated from flow-cytometry separated abnormal plasma cells and analysed by CGH+SNP arrays to describe somatic gene mutations and chromosome changes at genome-wide level. Agilent Human Reference DNA was used as reference DNA.

first: Christopher

middle: P

last: Wardell

first: Alexander

last: Murison

first: Eileen

last: Boyle

first: Zuzana

last: Kufova

first: Ludek

last: Pour

first: Viera

last: Sandecka

first: Martina

last: Almasi

first: Evzen

last: Gregora

first: Petr

last: Kuglik

first: Roman

last: Hajek

first: Gareth

last: Morgan

first: Brian

middle: A

last: Walker


title: Expression data from VND7 induction line

status: Public on Feb 22 2016

city: Melbourne

first: Zheng

last: Li

address: Grattan Street,  Parkville, Victoria

institute: The University of Melbourne

summary:
Plants typically contain two different types of cell walls: a primary wall that is being deposited around all growing cells, and a secondary wall that is produced in cells with specialized functions once they have ceased to grow. In Arabidopsis, VND7 is a transcription factor that is sufficient to activate secondary cell wall synthesis. To artificially turn on the secondary cell wall synthesis, VND7 was fused to the activation domain of the herpes virus VP16 protein and the glucocorticoid receptor (GR) domain. Thus, the transgenic plants harbouring the constructs can then be treated with dexamethasone (DEX), a glucocorticoid derivative, to induce the secondary cell wall formation.
We used microarrays to investigate the global program of gene expression during the secondary cell wall development and identified up- and down-regulated genes associated with this process.

overall_design: Cultures were harvested at indicated time points after induction (1, 3, 6, 9, 12, 24, 30, 48 h) and at time point zero (0). Uninduced cultures (DMSO instead of DEX) served as controls for each time point, and thus, 48 microarray analyses for 8 time points (3 biological reps) for +/- induced VND7-VP16-GR cultures, and 3 arrays for time 0h. To ensure that the DEX did not influence the measurements, an empty vector construct (EV), i.e., without the VND7 gene, VP16-GR, was used at three time points, i.e., VP16-GR +/- DEX at 9h, 12h, and 24h after DEX induction.

first: Nooshin

last: Omranian

first: Lutz

last: Neumetzler

first: Staffan

last: Persson


title: Expression changes in lymphoid cells on excision of Runx1

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube Estate

institute: The University of Glasgow

summary: The Runx genes function as dominant oncogenes that collaborate potently with Myc or loss of p53 to induce lymphoma when over-expressed. Here we examined the gene changes in an Eµ-Myc model of Burkitt’s lymphoma on deletion of Runx1, and found a gene signature that was associated with lymphoid proliferation, survival and differentiation.

overall_design: We treated triplicate Mx1Cre+/EµMyc+/p53+/- lymphoma lines (3s) containing floxed endogenous Runx1 with or without IFNβ in order to excise Runx1, before extracting RNA and performing microarray analysis. To account for IFNβ responses, parallel experiments with phenotypically similar control cells with wild type Runx1 that cannot be excised (30s) were performed.

first: Gillian

last: Borland

first: Anna

last: Kilbey

first: James

last: Neil


title: The Adaptive Immune System Restrains Alzheimer’s Disease (AD) Pathogenesis by Modulating Microglial Function

status: Public on Mar 03 2016

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 3014 Gross Hall

department: Department of Neurobiology & Behavior

institute: University of California, Irvine

summary:
Neuroinflammation and activation of innate immunity are pathological hallmarks of Alzheimer’s disease (AD).  In contrast, very few studies have examined the impact of the adaptive immune system in AD pathogenesis. In this study, we find that genetic deletion of peripheral immune populations significantly accelerates amyloid pathogenesis, worsens neuroinflammation, and alters microglial activation state.
We used microarray analysis to profile gene expression underlying genotype related changes at the cellular level in the context of AD .

overall_design: To examine the impact of the adaptive immune system on AD pathogenesis, we backcrossed a well-established AD transgenic line, 5xfAD mice [Oakley et al., 2006], on to a Rag2-/-/Il2rγ-/- double knockout background, creating mice that lacked T-cells, B-cells, and NK-cells.  In the process of generating these immune-deficient “Rag-5xfAD” and “Rag-WT” littermates, we also produced strain-matched equivalent immune-competent AD transgenic and wild-type mice termed “WT-5xfAD” and “WT-WT” respectively.

first: Anita

last: Lakatos

first: Sam

last: Marsh


title: Expression profiling of wild-type Arabidopsis and an activation-tagged jaz7-1D line.

status: Public on Feb 08 2016

city: Floreat

first: Louise

last: Thatcher

address: 147 Underwood Ave

institute: CSIRO

summary: Jasmonate (JA) signaling plays a key role in mediating both resistance and susceptibility to the root-infecting fungal pathogen Fusarium oxysporum. Within this system, the roles of the JA-signaling repressor gene family of JASMONATE ZIM-domain (JAZ) genes had not been investigated. By screening JAZ T DNA insertion lines for altered resistance or susceptibility to F. oxysporum, we identified a JAZ7 mutant (jaz7-1D) highly susceptible to F. oxysporum infection. Further analyses revealed jaz7-1D exhibits constitutively active JAZ7 expression, enhanced expression of JA-defense marker genes, and increased sensitivity to JA-inhibition of root elongation. To further explore altered JA-signaling and JA-responses in this mutant, we use whole transcriptome profiling of jaz7-1D versus wild-type (Col-0) plants after mock/control and JA treatment.

overall_design: We grew both WT and jaz7-1D plants for four weeks in soil. After four weeks the plants were treated with 1 mL of 5% MeJA (dissolved in 100% ethanol) or 1 mL of Mock solution (100% ethanol) by applying the solutions to a cotton ball attached to a tray cover which was then used to enclose individual trays. Each tray and cover was then sealed by two layers of opaque plastic bags and secured with masking tape. There were four independent replicates of each treatment and each replicate contained leaf tissue from 20 plants. Each replicate (16 in total) was harvested after 6 hours and the resulting RNA was used for hybridization to an Affymetrix ATH1 chip.

first: Volkan

last: Cevik

first: Murray

last: Grant

first: Bing

last: Zhai

first: Jonathan

middle: D

last: Jones

first: John

last: Manners

first: Kemal

last: Kazan


title: Role of root-specific transcription factor MYB72 in regulation of Pseudomonas fluorescens WCS417-mediated changes in gene expression in roots of Arabidopsis thaliana

status: Public on Feb 11 2016

city: Utrecht

first: Corné

last: Pieterse

address: Padualaan 8

department: Biology

country: Netherlands

institute: Utrecht University

summary: • Selected soil-borne rhizobacteria can trigger an induced systemic resistance (ISR) that is effective against a broad spectrum of pathogens. In Arabidopsis thaliana, the root-specific transcription factor MYB72 is required for the onset of ISR, but is also associated with plant survival under conditions of iron deficiency. Here we investigated the role of MYB72 in both processes.  • To identify MYB72 target genes, we analyzed the root transcriptomes of wild-type Col-0, mutant myb72, and complemented 35S:FLAG-MYB72/myb72 plants in response to ISR-inducing Pseudomonas fluorescens WCS417.  • Five WCS417-inducible genes were misregulated in myb72 and complemented in 35S:FLAG-MYB72/myb72. Amongst these, we uncovered β-glucosidase BGLU42 as a novel component of the ISR signaling pathway. Overexpression of BGLU42 resulted in constitutive disease resistance, whereas bglu42 was defective in ISR. Furthermore, we found 195 genes to be constitutively upregulated in MYB72-overexpressing roots in the absence of WCS417. Many of these encode enzymes involved in the production of iron-mobilizing phenolic metabolites under conditions of iron deficiency. We provide evidence that BGLU42 is required for their release into the rhizosphere.   • Together, this work highlights a thus far unidentified link between the ability of beneficial rhizobacteria to stimulate systemic immunity and mechanisms induced by iron deficiency in host plants.

overall_design: Total 18 samples of RNA extracted from Arabidopsis roots: Three genotypes: 1) Wild-type Arabidopsis thaliana accession Col-0, 2) mutant myb72-2 (Col-0 background), 3) Transgenic 35S:FLAG-MYB72 (oxMYB72) in the myb72-2 background; Two treatments: 1) non-treated control, 2) Roots colonized by beneficial Pseudomonas fluorescens WCS417 rhizobacteria; Replicates: three biological replicates per genotype/treatment combination

middle: M

first: Christos

last: Zamioudis


title: Expression data from Arabidopsis thaliana root protoplast

city: New York

first: joan

last: doidy

state: NY

address: 12 Waverly place

institute: NYU

summary:
BACKGROUND:Dynamic transcriptional regulation is critical for an organism's response to environmental signals and yet remains elusive to capture. Such transcriptional regulation is mediated by master transcription factors (TF) that control large gene regulatory networks. Recently, we described a dynamic mode of TF regulation named "hit-and-run". This model proposes that master TF can interact transiently with a set of targets, but the transcription of these transient targets continues after the TF dissociation from the target promoter. However, experimental evidence validating active transcription of the transient TF-targets is still lacking.

RESULTS:Here, we show that active transcription continues after transient TF-target interactions by tracking de novo synthesis of RNAs made in response to TF nuclear import. To do this, we introduced an affinity-labeled 4-thiouracil (4tU) nucleobase to specifically isolate newly synthesized transcripts following conditional TF nuclear import. Thus, we extended the TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) to include 4tU-labeling and named this new technology TARGET-tU. Our proof-of-principle example is the master TF Basic Leucine Zipper 1 (bZIP1), a central integrator of metabolic signaling in plants. Using TARGET-tU, we captured newly synthesized mRNAs made in response to bZIP1 nuclear import at a time when bZIP1 is no longer detectably bound to its target. Thus, the analysis of de novo transcripomics demonstrates that bZIP1 may act as a catalyst TF to initiate a transcriptional complex ("hit"), after which active transcription by RNA polymerase continues without the TF being bound to the gene promoter ("run").

CONCLUSION:Our findings provide experimental proof for active transcription of transient TF-targets supporting a "hit-and-run" mode of action. This dynamic regulatory model allows a master TF to catalytically propagate rapid and broad transcriptional responses to changes in environment. Thus, the functional read-out of de novo transcripts produced by transient TF-target interactions allowed us to capture new models for genome-wide transcriptional control.

overall_design: Root protoplasts were transfected with 35S::GR::bZIP1 or Empty vector (EV=pJD385_35S::GR) constructs and cells were sequentially treated with: i) the nitrogen signal (N), ii) cycloheximide (CHX), iii) dexamethasone (DEX; for review see Bargmann et. al 2013). Cells were exposed to 4tU to affinity-label newly synthesized transcripts prior RNA extraction followed by specific pull down of 4tu-fractions and hybridization on Arabidopsis ATH1 microarray chips.

first: Joan

last: Doidy

first: Ying

last: Li

first: Benjamin

last: Neymotin

first: Molly

last: Edwards

first: Kranthi

last: Varala

first: David

last: Gresham

first: Gloria

last: Coruzzi


title: Expression data from Arabidopsis plants under varying zinc supply.

status: Public on Jan 28 2016

city: Vairao

first: Antonio

last: Muñoz

state: Porto

address: Rua Padre Armando Quintas, 7 (Campus Agrario)

country: Portugal

institute: CIBIO-InBIO (University of Porto)

summary:
Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, generating a negative impact on crop quality and yield. Nevertheless, there is insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition.
Hydroponically-grown Arabidopsis thaliana plants (WT Col-0 and the T-DNA insertion double mutant bzip19 bzip23)  were subjected to zinc deficiency, sufficiency and excess. The particular role of the bZIP19 and bZIP23 transcription factors was investigated via the bzip19 bzip23 double mutant.

overall_design: Fourty two Affymetrix ATH1 microarray hybridizations were carried out, to resolve the transcriptome under three variables: genotype (WT vs. Mutant), tissue (Shoot vs. Root) and zinc supply (Defficiency vs. Sufficiency vs. Excess).

first: Herlânder

last: Azevedo

first: Sarah

middle: G

last: Azinheiro

last: Muñoz-Mérida

first: Pedro

last: Castro

first: Bruno

last: Huettel

first: Mark

last: Aarts

first: Ana

last: Assunção


title: Characterization of LncRNA BC012900 among long non-coding RNAs differentially expressed in ulcerative colitis

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: In this report, we provide a comprehensive assessment of the expression of  ~17000 lncRNAs on 60 colonic samplesin colon tissues from patients with IBD, irritable bowel syndrome, infectious colitis and healthy controls. We also explored the possibility of using cRNAs as biomarkers distinguish active UC from normal.  To investigate the mechanism offunctional role these IBD-associated lncRNAs in the development of IBD, we  then focused on a ncRNA highlyexpressed in the UC-associated lncRNAactive UC, BC012900.  We , to characterized its cellular localization, expression regulation and biological function. We . We found that BC012900 and its adjacent gene, dual specificity phosphatase 4 (DUSP4) are functionally distinct, with BC012900 modulating. Overexpression of BC012900 resulted in usceptibility  to apoptosis. Our study provides the first evidence that lncRNAs may play potential roles in development and persistence of active UC.

overall_design: LncRNAs microarray and quantitative RT-PCR were performed on 60 sigmoid biopsies from patients with active ulcerative colitis (UC) and relevant controls.

first: Feng

last: Wu

first: Fengshi

last: Dong

first: John

last: Kwon


title: Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations (part 4)

status: Public on Feb 01 2016

city: Chapel HIll

first: Ryan

last: Miller

state: North Carolina

institute: University of North Carolina

summary: We used genetically-engineered mice (GEM) to target constitutive RTK effector pathway (KrasG12D and/or Pten deletion) mutations in G1/S checkpoint-defective adult mouse astrocytes.  Genetic lineage tracing showed that these mutations potentiated tumor initiation in cortical, diencephalic, brainstem, and olfactory bulb astrocytes, producing low-grade astrocytomas (LGA).  LGA lacked copy number abnormalities (CNA), but showed oncogenic driver- and astrocyte location-specific transcriptome profiles, suggesting that both driver mutations and cellular origin contribute to LGA genomic heterogeneity.  Progression to high-grade astrocytomas (HGA) occurred stochastically, in part through location-specific acquisition of CNA.  HGA transcriptomes were heterogeneous and consisted of three subtypes that were also evident in GEM HGA with different oncogenic drivers and cellular origins.  HGA subtypes expressing immune/invasion, proliferation, and neuronal genes mimicked human mesenchymal, proneural, and neural GBM, respectively.  HGA subtypes also expressed distinct neural lineage signatures and were correlated with astrocyte location, but not oncogenic driver mutations.  These results suggest that oncogenic drivers influence LGA subtype and that regional astrocyte identity and progression-acquired CNA contribute strongly to HGA transcriptomal heterogeneity.  Defining tumor-initiating and progression-acquired mutations and the cells in which they occur would facilitate molecular classification and development of molecularly targeted strategies to manage GBM.

overall_design: CGH microarray analysis was completed for 41 high-grade astrocytoma (HGA) dissected from neurollogically symptomatic mice.  Frequency of genomic mutations varied by genotype and brain region, and 93% of HGA had genomic gains and losses, in contrast to neurologically asymptomatic mice with low-grade astrocytoma (LGA).  These results suggest that most HGA acquire CNA during progression from LGA

last: Vitucci

first: Christopher

middle: R


title: Genes regulated by 4D09 effector from cyst nematode Heterodera schachtii and its host target (14-3-3Ɛ) in Arabidopsis roots

status: Public on Jan 21 2016

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the transgenic plants overexpressing 4D09 effector gene from the cyst nematode Heterodera schachtii and the wild-type (C24). Also, Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the transgenic plants overexpressing 14-3-3Ɛ gene from Arabidopsis and the wild-type (Col-0).     Wild-type (Arabidopsis thaliana, ecotypes C24 and Col-0 ), and  the transgenic plants overexpressing 4D09 effector gene or overexpressing 14-3-3Ɛ gene from Arabidopsis   were grown in vertical culture dishes on modified Knop’s medium for 2 weeks and then root tissues were collected for RNA extraction.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Tarek Hewezi.  The equivalent experiment is AT144 at PLEXdb.]

overall_design: genotype: Arabidopsis thaliana ecotypes C24(3-replications);  genotype: Arabidopsis thaliana ecotypes Col-0(3-replications);  genotype: P35S:4D09 overexpression(3-replications);  genotype: P35S:14-3-3Ɛ overexpression(3-replications)

first: Tarek

last: Hewezi

first: Thomas

last: Baum


title: Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations (part 1)

overall_design: 78 olfactory bulb and forebrain samples of various genotypes showed oncogenic driver- and astrocyte location-specific transcriptome profiles


title: MiR-511 dependently expressed genes in monoblastic cell line THP1

status: Public on Jan 16 2016

city: Munich

first: Katrin

middle: K

last: Fleischmann

address: Lindwurmstrasse 2a

department: Children’s Research Center

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

summary: To experimentally investigate the function of hsa-miR-511-5p in AML monoblasts, we employed miRNA mimic mediated up-regulation of miR-511 in THP1 cells and subsequently analyzed a comprehensive gene expression profile.

overall_design: 4 samples of two independent miRNA mimic experiments were analyzed. THP1 monoblasts were transfected with 30 nM of Ambion Pre-miR miRNA Precursors (hsa-miR-511-5p AM10237 or negative Control #1 AM17110, Life Technologies).

first: Philipp

last: Pagel

first: Julia

last: von Frowein

last: Magg

first: Adelbert

last: Roscher

first: Irene

last: Schmid


title: Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations (part 3)

overall_design: CGH microarray analysis was completed for 10 low-grade astrocytoma (LGA) dissected from neurollogically asymptomatic mice at least a year after induction.  LGA showed few and infrequent CNA.


title: Expression profling of Arabidopsis  sto2 mutant

status: Public on Jan 01 2016

first: Staffan

last: Persson

address: Parkville, 3010,

department: School of Biosciences

institute: University of Melbourne

summary:
STO2 is a novel MYB like protein which belongs to one of the most important transcription factors in planta.
Microarray analysis of sto2 null mutant compared to Columbia with three-week-old soil-grown plants revealed that STO2 function in ABA and salt stress response.

overall_design: To find the potantial downstream target of STO2 protein, microarray was performed and samples from expanding rosette leaves (from 3th to 6th leaves) of three-week-old soil-grown sto2 mutant plants with those of wild-type were collected. Both Wild-type (Col-0) and sto2 null mutant have three biological replicates, respectively.

first: Ting

last: Wang


title: A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly

status: Public on Jan 08 2016

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

summary: Gene expression microarray was designed, based on two recently published versions of the N. benthamiana transcriptome (v.3 and v.5). Based on homology searches and hybridization tests we identified the sense strand in 106,684 transcriptome contigs and used this information to design a Nb-105k microarray on Agilent eArray platform. By the hybridization of N. benthamiana roots vs leaves RNA samples we showed high specificity and sensitivity of the new microarray in detection of differentially expressed transcripts.

overall_design: Agilent microarrays in 2x105k format (two microarrays per slide) were used  for hybridization of labeled RNA from leaves vs roots of N. benthamiana plants. Four biological replicates were used for two-color design in a dye-swap manner.

first: Michal

last: Goralski

first: Paula

last: Sobieszczanska

first: Aleksandra

last: Obrepalska-Steplowska

last: Swiercz

first: Marek

last: Figlerowicz


title: Central Role of Th2 and Tc2 Lymphocytes in Multiple Sclerosis Pattern II Demyelinating Lesions

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system with marked heterogeneity in several aspects including pathological processes. Four histopathological patterns of MS have been described. Pattern II is characterized by antibody and complement deposition. MS is considered a prototypic T cell-mediated disease, but until now the study of pathogenic T cells has encountered major challenges, most importantly the limited access of brain-infiltrating T cells. Here, we used next generation sequencing to identify clonally expanded T cells in demyelinating pattern II brain autopsy lesions and subsequently isolated these as T cell clones from autologous cerebrospinal fluid. The functional characterization shows that T cells releasing Th2 cytokines and able to provide B cell help dominate the T cell infiltrate in pattern II brain lesions. Our data provide the first functional evidence for a role of Th2/Tc2 cells in pattern II MS.

overall_design: Two stimulated CD4+ Th2 brain infiltrating T cell clones compared with stimulated circulaiting memory CD4+ T cells and two stimulated CD8+ T cell clones (one Tc1 and one Tc2) compared with each other.

first: Roland

last: Martin

first: Mireia

last: Sospedra

first: Raquel

last: Planas


title: Expression of lncRNAs in mouse heart 4 weeks after myocardial infarction

status: Public on Dec 30 2015

city: Harbin

first: Xuefeng

last: Qu

state: Heilongjiang

address: 157 Baojian Road

department: Department of Pharmacology

institute: Harbin Medical University

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

summary: The expression signature of lncRNAs and mRNAs was analyzed in fibrotic tissue from peri-infarct region of mouse heart. We fund that fifty seven differentially expressed lncRNAs and 20 differentially expressed mRNAs are associated with 8 signaling pathways which are involved in the development of cardiac fibrosis, indicating a potential role of lncRNAs in cardiac fibrosis.

overall_design: Male C57BL/6 mice was used to establish a myocardial infartion model by ligating the left anterior descending coronary artery.  After 4 weeks, we collected the peri-infarct tissues from MI mice and corresponding region from sham-operated group for RNA extraction and hybridization on Affymetrix microarrays.

first: Xiaotong

last: Song

first: wei

last: Yuan

first: You

last: Shu

first: Lihua

last: Sun

first: Yanjie

last: Lu


title: Grape_Bud_Dormancy

status: Public on Jan 13 2016

first: PLEXdb Curator

summary: Bud endodormancy induction response of two genotypes (‘Seyval’ a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long and short photoperiod. Three separate replicates (5 plants/replicate) were treated in each of 2 separate years (2007 and 2008) to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07, 3/18/08; V. riparia 3/26/07, 3/24/08) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes they were randomized into groups for differential photoperiod treatments.  On 4/30/07 and 4/28/08 LD and SD (13 h) treatments were imposed with automated photoperiod system (VRE Greenhouse Systems).  Temperatures were maintained at 25/20 + 3C D/N.  Three replications (5 vines/replication) were harvested between 5/07-6/07 and then again in 5/08-6/08.  At 1, 3, 7, 14, 21, 28 and 42 days of differential photoperiod treatment, buds were harvested from nodes 3 to 12 (from the base of the shoot) of each separate replicate, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein and metabolite extraction. These time points encompass early reversible phases as well as key time points during transition to irreversible endodormancy development. After photoperiod treatments and bud harvests, all pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date.  Acknowledgement:This study was funded by NSF Grant DBI0604755 and funds from the South Dakota Agriculture Experiment Station.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Anne Fennell.  The equivalent experiment is VV18 at PLEXdb.]

sample_organism:
Vitis riparia
Vitis hybrid cultivar

overall_design: genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 1 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 3 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 7 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 14 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 21 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 28 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 15 h - time: 42 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 1 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 3 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 7 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 14 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 21 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 28 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 1 - photoperiod: 13 h - time: 42 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 1 days(2-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 3 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 7 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 14 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 21 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 28 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 15 h - time: 42 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 1 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 3 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 7 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 14 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 21 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 28 days(3-replications);  genotype: Seyval (SV, Seyve Villard 5-276) - year: 2 - photoperiod: 13 h - time: 42 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 1 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 3 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 7 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 14 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 21 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 28 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 15 h - time: 42 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 1 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 3 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 7 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 14 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 21 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 28 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 1 - photoperiod: 13 h - time: 42 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 1 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 3 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 7 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 14 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 21 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 28 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 15 h - time: 42 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 1 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 3 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 7 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 14 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 21 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 28 days(3-replications);  genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 42 days(3-replications)

first: Anne

last: Fennell


title: DELAY OF GERMINATION 1 plays a role in Arabidopsis seed maturation

status: Public on Jan 14 2016

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

institute: Wageningen University

summary:
We analysed the transcriptome of dry seeds (the end product of seed maturation) of three genotypes with different DOG1 expression levels. These included the WT Ler (low DOG1 expression), the near isogenic line NILDOG1-Cvi (strong DOG1 expression) and the non-dormant dog1-1 mutant (absence of DOG1 expression). NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006). The dog1-1 mutant is in the NILDOG1-Cvi genetic background.
The aim was to obtain a global overview of the effect of different levels of DOG1 expression during seed maturation on the dry seed transcriptome.

overall_design: Gene expression in dry seeds of three genotypes was compared: Ler, NILDOG1 and the dog1-1 mutant. For each genotype, three replicates were used.

first: Bas

middle: J

last: Dekkers

first: Hanzi

last: He

first: Johannes

last: Hanson

first: Leo

last: Willems

first: Gwendal

last: Cueff

first: Loïc

last: Rajjou

first: Henk

last: Hilhorst


title: Analysis of the effect of auxin biosynthesis inhibitor L-AOPP on the gene expression profile (shoot apical meristem)

status: Public on Dec 31 2015

city: Hayama

first: Eriko

last: Sasaki

state: Kanagawa

institute: Graduate University for Advanced Studies

summary: Recently, 2-aminoxy-3-phenylpropionic acid (L-AOPP) had been demonstrated to possess an inhibitory activity against IAA biosynthesis but the molecular basis of the action was unclear. To investigate the function of L-AOPP, we conducted microarray analysis using the shoot apical meristem (SAM) part of A. thaliana in addition to whole plants after the treatment of L-AOPP.

overall_design: We performed microarray analysis using the shoot apical meristem (SAM) part of A. thaliana (Columbia-0) to investigate function of 2-aminoxy-3-phenylpropionic acid (L-AOPP) in relation to inhibition of auxin biosynthesis. Total RNA was extracted from SAM part of 7-day-old seedlings grown on 1/2 MS medium containing L-AOPP (50 µM),L-AOPP (50 µM) + Indole-3-acetic acid (IAA 10 nM) or Dimethyl sulfoxide (DMSO 0.1%).

first: Takehiko

last: Ogura

first: Yukihisa

last: Shimada


title: Analysis of the effect of auxin biosynthesis inhibitor L-AOPP on the gene expression profile (whole plant)

summary: Recently, 2-aminoxy-3-phenylpropionic acid (L-AOPP) had been demonstrated to possess an inhibitory activity against IAA biosynthesis but the molecular basis of the action was unclear. To investigate the function of L-AOPP in relation to Auxin biosynthesis, we conducted microarray analysis.

overall_design: We performed microarray analysis to investigate function of 2-aminoxy-3-phenylpropionic acid (L-AOPP) in relation to inhibition of auxin biosynthesis.  Then L-AOPP (final concentration is 50 μM) was added to tubes and seedlings were incubated for additional 3 hours. To investigate effects on L-AOPP treatment, IAA (1 μM) or IPyA (100 μM) were added to the medium 1 hour after L-AOPP was added.


title: Analysis of the effect of auxin biosynthesis inhibitor L-AOPP on the gene expression profile

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

overall_design: Refer to individual Series


title: Expression data from pam48 (mterf6-1) mutants

status: Public on Dec 10 2015

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary:
Of the members of mitochondrial transcription termination factors (mTERFs) found in metazoans and plants known to regulate organellar gene expression at various levels, plant mTERF6 promotes maturation of a tRNA
We used microarrays to analyze whole-genome transcriptome changes in pam48 (mterf6-1) mutants compared to wild type.

overall_design: Arabidopsis thaliana Col-0 and pam48 (mterf6-1) leaves were harvested at the 8-leaf stage for RNA extraction and hybridization on Affymetrix microarrays.

first: Dario

last: Leister


title: Expression data from wild and ind-6 mutant Arabidopsis silique  during three development stages of  fruit dehiscence

status: Public on Dec 28 2015

city: Guangzhou

first: JIANG

middle: Xin

last: Shan

state: Guangdong

address: Zhongshan Road No. 55, Tianhe District

department: school of life sciences

institute: South China Normal University

summary:
Fruit dehiscence is an essential developmental process of some economic crops that impacts dramatically on crop yields and involves altered regulation of thousands of genes, ind-6 gene is a transcription factor play important role during fruit dehiscence. Gene expression were examined in wild-type and ind-6 mutants at three development stages of fruit dehiscence to explore the molecular mechanism of ind-6 in fruit dehiscence.
We used microarrays to examine changes in gene expression during fruit dehiscence  and identified distinct classes of up- and down-regulated genes in wild-type and ind-6 mutant genotypes.

overall_design: Two Arabidopsis genotypes (wild-type and ind-6 mutant) were grown in a growth room with a 16-h-light/8-h-dark cycle at 22°C. Silique for stage 11(dehiscence zone did not start differentiate), stage 15 (fruit dehiscence zone started asymmetric cell division), stage 17( dehiscence zone just completed the differentiation)  were used for microarray experiments. Three biological replicates for Arabidopsis silique in each stage and genotypes were prepared. Total RNA was isolated by RNAiso for Polysaccharide-rich Plant Tissue (TAKARA) and purified using a QiagenRNeasy Micro kit (Qiagen, Venlo, Netherlands), then hybridization on Affymetrix microarrays

first: Xinshan

last: Jiang

first: Hong

last: Wu

first: Xiaojing

last: Wang


title: Expression data from Arabidopsis thaliana treated with NO donor SNP, compared to NO depletion by cPTIO

status: Public on Dec 21 2015

city: Madrid

first: Maria

last: FernandezMarcos

state: Madrid

address: Darwin 3

department: Genomic

institute: CNB-CSIC

summary: Nitric oxide (NO) is considered a key regulator of plant developmental processes and defense. Characterization of root-related phenotypes and the involvement of NO in the regulation of primary root growth.

overall_design: Three-experimental condition, SDW, SNP and cPTIO. Biological replicates: 3 control replicates (SDW) , 3  replicates treated with sodium nitroprusside (SNP), 3 replicates treated with 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO)

first: María

last: Fernández-Marcos

first: Luis

last: Sanz

first: Daniel

last: Osuna

first: Irene

last: López-Vidriero

first: Roberto

last: Solano

first: Montserrat

last: Dueñas

first: Celestino

last: Santos-Buelga

first: Dolores

last: Rodríguez

first: Oscar

last: Lorenzo


title: The Arabidopsis DRYK, AtYAK1 regulates the development of the male gametophyte

city: Taipei

first: Shu-Hsing

address: 128, Sec 2, Academia Road

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica

summary: Pollen is the male gametophyte of land plants. Proper development and maturation of pollen is necessary for the successful reproduction of seed plants. This process involves sophisticated coordination between sporophytic and gametophytic tissues in anthers. To advance the mechanistic studies of anther development, additional players need to be discovered for a comprehensive understanding of the underlying regulatory network. Here we show that the Arabidopsis dual specificity tyrosine phophorylated and regulated kinase (DRYK), AtYAK1, is essential for development of rosette leaves and the male but not female gametophyte in Arabidopsis. Arabidopsis mutant plants carrying a mutation in AtYAK1 produce developmentally stalled microspores, likely because of the defects in the two consecutive mitosis steps in the post-meiotic maturation process of pollen. The mutation of AtYAK1 has a significant effect on gene expression programs in developing pollen. Transcritpome analysis of atyak1 revealed downstream genes in families of protein kinases, transporters and transcription factors, which potentially contribute to pollen development. This study represents the first molecular characterization of DYRK in the plant kingdom. Our results also imply that the regulation of cytokinesis by DYRKs is evolutionally conserved in fungus, fruit fly, animals and plants.

overall_design: 2 biological replicates were performed for wt and 2 different alleles of ayak1 mutants (atyak1-1 and atyak1-2)

first: Yi-Chen


title: Comparison of gene expression between athb8-11 cna-2 phb-13 phv-6 (bvca) 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

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 athb8 cna phb phv quadruple mutant to its 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 athb8-11 cna-2 phb-13 phv-6 and Col er-2 grown vertically were manually microdissected to ca 0.5 mm. 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: Human glioma cells: chronophin (CIN/PDXP) knockdown vs. control or rescue

status: Public on Nov 25 2015

city: Regensburg

first: Markus

last: Schulze

address: Franz-Josef-Strauss Allee 11

department: Neuropathology

institute: University Hospital Regensburg

summary: Transcriptional profiling of human glioma cells to elucidate the role of chronophin (CIN/PDXP) for glioma pathogenesis

overall_design: three-condition experiment: control cells vs. knockdown and knockdown vs. rescue

first: Antje

last: Gohla


title: gcn2/WT polysome loading and transcript level in Arabidopsis thaliana

status: Public on Dec 01 2015

city: Knoxville

first: Albrecht

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

institute: The University of Tennessee

summary:
To understand the role of GCN2 in regulating translation, we compared the polysome loading state and overall transcript level between Arabidopsis thaliana wild type (ecotype Landsberg erecta)  and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory)  seedlings with or without herbicide chlorosufuron treatment
RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels.  We used Affymetrix ATH1 microarrays.

overall_design: wild type and gcn2 mutant were compared in their total transcript and translation state. RNA was fractionated using sucrose gradients into nonpolysomal and polysomal RNAs.   The sucrose gradient fractions and the total RNA were analyzed using Affymetrix ATH1 microarrays (platform  GPL198).

first: Byung-Hoon

last: Kim


title: Gene expression in 0.5 mm root tips of Arabidopsis


title: miR396 overexpression in Arabidopsis thaliana roots

status: Public on Nov 18 2015

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

summary: Analysis of gene expression in the meristematic zone of Arabidopsis roots overexpressing miR396

overall_design: Meristems of wt and 35S:miR396 were microdissected and subjected to microarray analysis

middle: E

first: Javier

last: Palatnik


title: Genome wide expression analysis of EST-induced MYB112 (MYB112-IOE) using Affymetrix ATH1 array

status: Public on Nov 03 2015

city: Potsdam-Golm

first: Magda

middle: Ewa

last: Lotkowska

address: Karl-Liebknecht-Str.24-25, Haus 20

institute: Potsdam University

summary:
Global transcriptome patterns were determined in MYB112-IOE seedlings induced for 3 h and 5 h with b-estradiol in order to identify the genes early regulated by MYB112 transcription factor.
We used microarrays to identify genes differentially expressed in EST-inducible MYB112 over-expression line #1, 3 h and 5 h after 10µM EST induction, compared to mock treated plants. Two independent biological replications were performed for 5 h timepoint and one replicate for 3 h timepoint.

overall_design: In order to identify potential direct/early target genes of MYB112 transcription factor, estradiol inducible overexpression system was used. Two week old Arabidopsis MYB112-IOE (line 1) were treated with ß-estradiol (10µM) for 3 h and 5 h. Control plants were treated with DMSO. RNA was isolated from shoot and subjected to hybridization on Affymetrix microarrays. Experiment was performed in two biological replications for the 5 h timepoint and one biological replicate for the 3 h timepoint. Genes differentially expressed between estradiol treated MYB112-IOE and DMSO treated MYB112-IOE were identified as potential early targets of MYB112.


title: Gene expression in 0.5 mm root tips of Arabidopsis upon induction of pCRE1>>MIR165A

summary:
The class III HD-ZIPtranscription factors regulate vascular patterning in Arabidopsis thaliana roots. In this expression study we compare the expression profile in root tips upon miR165 induction, after 6h, 10h and 24h. 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: Seedlings harbouring pCRE1_XVE::MIR165A, that allows ß-estradiol induction of miR165 from the stele specific CRE1 promoter, were grown vertically and transferred to mock plates (plate containing no estradiol; called 0h) or plates containing 5µM ß-estradiol for 6 hours on ß-estradiol (6h), 10 hours on ß-estradiol (10h) and 24 hours on ß-estradiol (24h). Inductions and collections were staggered such that seedlings were the same age (+/- 4.5h) when collected. The age of the plants were 4 days post germination. Material from three biological replicates were collected.  Root tips (0.5 mm) of 200 seedlings per replicate were dissected after the specified time, and the RNA was extracted and subsequently hybridized to Affymetrix ATH1 microarrays.