title: Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

summary: Escherichia coli strain MG1655 was grown in a Zn-depleted custom-built chemostat.  Culture volume (120 ml), temperature (37 oC) and stirring speed (440 rpm) were maintained.  Steady state values for pH and OD600 were 6.9 and 0.6, respectively.  Chemostats were grown for 50 h to allow five culture volumes to pass through the vessel and allow an apparent (pseudo-)steady state to be reached.  At this point, ZnSO4.7H2O in water was added to a final concentration of 0.2 M in the chemostat.  A 10 ml sample of culture was taken using a polypropylene pipette tip immediately prior to Zn addition and 2.5, 7, 10 and 30 min after addition.  Samples were harvested into RNAprotect and total RNA was purified using Qiagen’s RNeasy Mini kit (using the supplier’s protocol) prior to use in microarray analysis.  A control experiment was also carried out in which water was added.  Biological experiments were carried out twice (i.e. control (water added) and experiment (ZnSO4 added) chemostats were grown separately twice), and a dye swap performed for each experiment, providing at least two technical repeats for each of the two biological repeats at all five time points.  Slides were analysed so that time points “with Zn” were compared to the same time point “without Zn” (e.g. 30 min after Zn was added was compared to 30 min after water being added).

overall_design:
Cells were grown in glycerol-glycerophosphate medium (GGM) lacking Zn.  Final concentrations in GGM are: MES (40.0 mM), NH4Cl (18.7 mM), KCl (13.4 mM), beta-glycerophosphate (7.64 mM), glycerol (5.00 mM), K2SO4 (4.99 mM), MgCl2 (1.00 mM), EDTA (134 microM), CaCl2.2H2O (68.0 microM), FeCl3.6H2O (18.5 microM), H3BO3 (1.62 microM), CuCl2.2H2O (587 nM), CoNO3.6H2O (344 nM), and (NH4)6Mo7O24.4H2O (80.9 nM) in MilliQ water (Millipore).  Bulk elements (MES, NH4Cl, KCl, K2SO4 and glycerol in MilliQ water at pH 7.4 (batch growth) or 7.6 (continuous culture)) were passed through a column containing Chelex-100 ion exchange resin (Bio-Rad) to remove contaminating cations.  Trace elements (with no added Zn) and a CaCl2 solution were then added to give the final concentrations shown above prior to autoclaving.  After autoclaving, MgCl2 and beta-glycerophosphate were added at the final concentrations shown above.  All chemicals were of AnalaR grade of purity or higher.  Chelex-100 was packed into a Bio-Rad Glass Econo-column (approximately 120 mm × 25 mm) that had previously been soaked in 3.5% nitric acid for 5 d.

E. coli strain MG1655 was grown a custom-built chemostat made entirely of non-metal parts.  Glass growth vessels and flow-back traps were soaked extensively (approximately two months) in 10% nitric acid before being rinsed thoroughly in MilliQ water.  Vent filters (Vent Acro 50 from VWR) were connected to the vessel using PTFE tubing.  Metal-free pipette tips were used (MAXYMum Recovery Filter Tips from Axygen).  Culture volume was maintained at 120 ml using an overflow weir in the chemostat vessel.  The dilution rate (and hence the specific growth rate) was 0.1 h-1.   The vessel was inoculated using one of the side-arms.  Flasks were placed on KMO 2 Basic IKA-Werke stirrers (arbitrary setting: 400).  Stirring speed was calibrated (440 rpm) and matched between vessels using a handheld laser tachometer (Compact Instruments Ltd).  Temperature was kept constant at 37 oC.  Twice daily, a 2-ml sample was taken and used to test the pH (which stayed constant at pH 6.9), OD600 (0.6 at steady state), glycerol limitation, and contamination on nutrient agar plates.

E. coli strain MG1655 was grown in a “Zn-free” chemostat.  Chemostats were grown for 50 h to allow five culture volumes to pass through the vessel and allow an apparent (pseudo-)steady state to be reached.   At this point, ZnSO4.7H2O in water was added to a final concentration of 0.2 M in the chemostat.  A 10 ml sample of culture was taken using a polypropylene pipette tip immediately prior to Zn addition and 2.5, 7, 10 and 30 min after addition.  Total RNA was stabilised using RNAprotect (Qiagen).  Total RNA was purified using Qiagen’s RNeasy mini kit.  A control experiment was carried out in which water was added.  Microarray slides were set up so that time points “with Zn” were compared to the same time point “without Zn” (e.g. 30 min after Zn was added was compared to 30 min after water being added).

For each time point, equal quantities of RNA obtained after addition of zinc and addition of water were labelled by using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes (Perkin Elmer).  For each microarray slide, one sample was labelled with Cy3-dCTP, while the other sample was labelled with Cy5-dCTP.  RNA (15-20 micrograms) was annealed to 9 micrograms pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC.  This was supplemented with 4 microlitres of 5× First-strand buffer (Invitrogen), 2 microlitres dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 2 microlitres 0.1 M DTT, 2 microlitres 1 mM Cy3 or Cy5 (Perkin Elmer) and 1 microlitre Superscript II reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 2 hours.  The reaction was terminated by the addition of NaOH (5 microlitres of 1M) and HCl (5 microlitres of 1M) before the addition of TE buffer (200 microlitres).  Labelled cDNA was purified using a Qiaquick PCR purification kit (Qiagen).

The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample and re-suspended in 120 microlitres salt-based hybridisation buffer (supplied with the microarray slides).  This was heated at 95 oC for 3 min then cooled on ice for 3 min.  The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated for 18 h at 42 °C.  Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 °C) SSC buffers for 5 min each at 37oC: 1× SSC/0.1 % SDS, 1× SSC, 0.2× SSC and 0.01× SSC.  Microarray slides were dried by centrifugation at 500 × g for 2 min before scanning.

Slides were scanned on an Affymetrix 428 scanner.  The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5).

Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

Biological experiments were carried out twice times, and a dye swap performed for each experiment, providing at least two technical repeats for each of the two biological repeats at all five time points.  Data from the independent experiments were combined.  Genes that were differentially expressed ≥ twofold and displayed and P value of < 0.05 (as determined by a t test) were defined as being statistically significantly differentially transcribed.

first: Alison

middle: I

last: Graham


title: Expression profiling of lung tissue from 6-, 10- and 14-week-old Fra2 transgenic male mice

status: Public on Dec 01 2011

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: The transcription factor complex AP-1 (Activator protein 1) is composed of Jun (c-Jun, JunB, JunD) and Fos proteins (c-Fos, FosB, Fra-1, Fra-2) which control a variety of stress responses, including cell proliferation, apoptosis, inflammation, wound healing, and cancer. Individual Fos proteins have been thoroughly studied in gain- and loss-of-function mouse models, which revealed important functions in bone cell proliferation and differentiation. We have recently demonstrated that loss of Fra-2 causes perinatal lethality and severe osteopenia due to several cellular defects, including a chondrocyte differentiation defect and a control of osteoclast survival and size. Moreover, we have reported a profibrogenic function of Fra-2 in transgenic mice, in which ectopic expression of Fra-2 in various organs resulted in generalized fibrosis with predominant manifestations in the lung. Fra-2 knock-out newborns have increased numbers and size of osteoclasts in vivo. The pulmonary phenotype observed in Fra-2Tg mice is characterized by vascular remodeling and obliteration of pulmonary arteries, which coincides with expression of osteopontin, an AP-1 target gene involved in vascular remodeling and fibrogenesis. These alterations are followed by inflammation; release of profibrogenic factors, such as IL-4, insulin-like growth factor 1, and CXCL5.

overall_design:
The expression profiling study was performed to analyse changes in transcript levels in lung over a period of time.
Total RNA of four mutant male animals at each time point (age: 6, 10 and 14 weeks) were hybridised versus a pool of total RNA of four wild type mice of the corresponding age. For each mutant animal, two technical chip hybridisations were performed, including a dye-swap experiment (in total, 8 hybridisation of each time point = 2 technical replicates x 4 biological replicates).

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Holger

last: Schulz

first: Alexander

last: Götz


title: Genome-wide examination of the transcriptional response to ecdysteroids 20-hydroxyecdysone and ponasterone A in Drosophila melanogaster

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

summary: The 20-hydroxyecdysone (20E) hierarchy of gene activation serves as an attractive model system for studying the mode of steroid hormone regulated gene expression and development. Primary genes are activated by the direct action of the hormone and often code for proteins with regulatory function, some of which are responsible for the perpetuation of the response through the activation of secondary genes. Here we identify 35 primary 20E-response genes that are induced by 20E in the absence of protein synthesis in the embryonic cell line Kc167, and of those with known functions, most encode proteins with catalytic activity. Comparison of the genome-wide transcriptional response to 20E and to its plant derived structural analog ponasterone A (PoA) revealed a large difference in the transcriptional targets of these molecules. Despite the structural similarity of these two compounds, many more genes related to various aspects of development appear to be significantly induced by 20E than by PoA. Furthermore, we compared the 20E response in Kc cells to that of a natural 20E target tissue where the function of 20E has been well described, the salivary glands of wandering 3rd instar larvae, and found little overlap in 20E-responsive genes. Analysis of 20E-induced transcription of EcR, a known 20E-inducible gene and regulator of early and late 20E-responsive genes, reveals differences in the fold induction of EcR isoforms EcR-RA, ER-RC, and EcR-RD/E between Kc cells and salivary glands suggesting a possible cause for the observed differences in 20E-regulated gene transcription.

overall_design: 2-colour microarray desgin using 18 spotted oligonucleotide microarrays printed at the Canadian Drosophila Microarray Centre. Total RNA from Kc167 cells or salivary glands from 3rd instar larvae treated with 20- hydroxyecdysone, or from Kc167 cells treated with ponasterone A, cycloheximide, or a combination of 20-hydroxyecdysone and cycloheximide were were compared to total RNA from an EtOH (the solvent for ecdysone and ponasterone A) control sample pool.

first: Sarah

last: Gonsalves


title: Transcriptional profile of Candida parapsilosis CLIB214  versus UPC2 delete, both at 1% oxygen (hypoxia)

status: Public on Nov 30 2011

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

summary: Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis UPC2 delete in hypoxia.

overall_design: RNA was isolated from CLIB214 or upc2 delete grown in YPD medium in hypoxia at 30 degree Celsius for 2 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. 2 dye swaps were perfomed so that 2 out of 4 samples isolated from CLIB214 in hypoxic culture were labeled with Cy3, and 2 were labeled with Cy5

first: Alessandro

last: Guida

first: Claudia

last: Lindstaedt

first: Chen

last: Ding


title: Transcriptional profile of Candida parapsilosis CLIB214  21% Oxygen (normoxia) versus at 1% oxygen (hypoxia).

summary: Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis in hypoxic condition.

overall_design: RNA was isolated from CLIB214 grown in YPD medium in normoxia or hypoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. Isolates from normoxic condition were labeled with Cy3 and isolates from hypoxic condition were labeled with Cy5.


title: Comparison of the global gene expression profiles between wild-type and lsg1 null strains

city: Tokyo

first: Akira

last: Yamashita

address: Hong

department: Department of Biophysics and Biochemistry

country: Japan

institute: University of Tokyo

summary: To determine the range of genes whose expression is regulated by CTDK-I under nitrogen starvation, comparison of gene expression profiles between a wild-type strain and a deletion mutant of lsg1, which encodes the gamma subunit of CTDK-I.

overall_design: Cells of the wild-type (JY450) and lsg1Δ (JT659) fission yeast strains were grown to the mid-log phase in liquid MM and shifted to nitrogen-free MM-N. The cells were harvested 2.5 h after this shift. RNA was prepared from each sample and analyzed on a DNA microarray covering 4,997 genes.

first: Yuko

last: Sukegawa

first: Masayuki

last: Yamamoto


title: Time course global expression profiles of Chlamydomonas reinhardtii during photo-biological hydrogen production

city: Bielefeld

first: Anh Vu

last: Nguyen

state: NRW

address: G2-154, CEBITEC, Universitaetsstr. 27

department: Cell and Molecular Biology

institute: Bielefeld University

summary: We used Chlamydomonas microarray v2.0 to compare the time course expression profiles of two Chlamydomonas reinhardtii strains: wild-type WT and the high hydrogen producing mutant Stm6Glc4 during sulfur starvation induced hydrogen production. Major cellular reorganizations in photosynthetic apparatus, sulfur and carbon metabolism upon H2 production were confirmed as common to both strains. More importantly, our results pointed out factors which lead to the higher hydrogen production in the mutant including higher light sensitivity and lower competitions with hydrogenase by alternative electron sinks. Under S-starvation induced H2 producing conditions the induction of LHCSR3, a chlorophyll binding protein involving in non photochemical quenching, was significantly lower in Stm6Glc4 resulting in significant higher photodamage to photosystem II. Consequently, Stm6Glc4 had a shorter aerobic phase, consumed less starch reserves, and produced H2 earlier at higher rates than WT. We also showed that the loss of mitochondrial DNA-binding protein MOC1 in both knockdown and knockout mutant resulted in higher light sensitivity and improved H2 yield. Furthermore, by comparing our data with previously published ‘omics’ data, we were able to identify genes that responded specifically to either sulfur starvation, anaerobiosis or hydrogen production as well as to provide a more complete picture of S-deprived H2 production in the green alga C. reinhardtii.

overall_design: A total of 33 microarray hydridizations were performed covering samples taken during the course of S deprivation induced H2 producction. The samples included 4 time points in the high hydrogen producing mutant Stm6Glc4 (taken at 16, 28, 52 and 76h) and 6 time points in the wildtype CC-406 (taken at 16, 28, 52, 68, 92, 116h). Samples from each time point were compared directly with the sample taken prior to S starvation from the corresponding strain. Three biological replicates were tested at each time point.

first: Anh

middle: V

first: Olaf

last: Kruse


title: Transcription landscape at the HoxD locus in developing limbs and brain

status: Public on Nov 28 2011

city: Lausanne

first: Thomas

last: Montavon

address: SV 2843, Station 19

country: Switzerland

institute: EPFL

type: Expression profiling by genome tiling array

summary:
The emergence and evolution of digits was an essential step in the success of the tetrapod lineage. Amongst the key players, Hoxd genes were functionally co-opted in the developing digital plate, where they help organize growth and patterns. To understand both the evolutionary recruitment and transcriptional regulation of this genomic locus, we analyzed its architecture and chromatin status in developing digits, combined with a deletion approach in vivo. We show that the active and inactive parts of the gene cluster adopt opposite spatial configurations, corresponding to different chromatin domains. Active genes are contacted by several regulatory islands, located within a neighboring gene desert, which contribute quantitatively or qualitatively to the global transcriptional readout. We refer to this novel type of control as a ‘regulatory archipelago’ and discuss the value of this concept to understand both the morphological flexibility of tetrapod digits and the robustness of the underlying developmental process.
Transcriptional activity at the Hoxd locus in developing limbs and brain at E12.5

overall_design: Array data were quantile normalized within cDNA/genomic DNA replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 80 bp. For each tissue, two independent RNA extractions, cDNA synthesis and array hybridizations were performed.

first: Denis

last: Duboule


title: DNA methylation data from human iPS cells, ES cells, cord blood, and keratinocytes

status: Public on Nov 29 2011

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

country: USA

institute: Johns Hopkins University School of Medicine

type: Methylation profiling by genome tiling array

summary:
Genome-wide DNA methylation was studied to determine whether iPS cells retain epigenetic memory at loci associated with its tissue of origin.
We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in human iPS cells, ES cells, and somatic cells

overall_design: We isolated genomic DNA from human stem cells  and somatic cells and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).

first: Kitai

last: Kim

first: George

middle: Q

last: Daley

first: Andrew

middle: P

last: Feinberg


title: Spatial organization of chromatin at the HoxD locus in developing limbs and brain

summary:
The emergence and evolution of digits was an essential step in the success of the tetrapod lineage. Amongst the key players, Hoxd genes were functionally co-opted in the developing digital plate, where they help organize growth and patterns. To understand both the evolutionary recruitment and transcriptional regulation of this genomic locus, we analyzed its architecture and chromatin status in developing digits, combined with a deletion approach in vivo. We show that the active and inactive parts of the gene cluster adopt opposite spatial configurations, corresponding to different chromatin domains. Active genes are contacted by several regulatory islands, located within a neighboring gene desert, which contribute quantitatively or qualitatively to the global transcriptional readout. We refer to this novel type of control as a ‘regulatory archipelago’ and discuss the value of this concept to understand both the morphological flexibility of tetrapod digits and the robustness of the underlying developmental process.
Chromosome Conformation Capture-on-chip analysis (4C) at the Hoxd locus in developing limbs and brain at E12.5

overall_design: Array data were quantile normalized within 4C/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp. At least two independant samples were analyzed for each condition.


title: Chromatin landscape at the HoxD locus in developing digits and forebrain

type: Genome binding/occupancy profiling by genome tiling array

summary:
The emergence and evolution of digits was an essential step in the success of the tetrapod lineage. Amongst the key players, Hoxd genes were functionally co-opted in the developing digital plate, where they help organize growth and patterns. To understand both the evolutionary recruitment and transcriptional regulation of this genomic locus, we analyzed its architecture and chromatin status in developing digits, combined with a deletion approach in vivo. We show that the active and inactive parts of the gene cluster adopt opposite spatial configurations, corresponding to different chromatin domains. Active genes are contacted by several regulatory islands, located within a neighboring gene desert, which contribute quantitatively or qualitatively to the global transcriptional readout. We refer to this novel type of control as a ‘regulatory archipelago’ and discuss the value of this concept to understand both the morphological flexibility of tetrapod digits and the robustness of the underlying developmental process.
Distribution of histone marks and RNA Pol2 at the Hoxd locus in developing limbs and brain at E12.5

overall_design: Array data were quantile normalized within ChIP/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp. For each tissue, two independent ChIP-chip experiments were performed with all mentionned antibodies.


title: Viral microRNA expression in two nasal NK T cell lymphoma cell lines

city: Houston

first: Paul

middle: D

last: Ling

state: Texas

address: One Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary: We have used microarray profiling to examine the expression of viral microRNAs (miRNAs) in two independently derived nasal natural killer T cell lymphoma (NKTCL) cell lines, SNK6 and SNT16.  The goal of the study was to investigate the role of the viral miRNAs in the genesis and maintenance of NKTCLs.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
Gallid alphaherpesvirus 2
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Gallid alphaherpesvirus 3
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Merkel cell polyomavirus
Macaca mulatta rhadinovirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: This experiment includes a total of 2 samples, one from SNK6 cells and the other from SNT16 cells.

first: Rajesh

last: Ramakrishnan


title: Transcriptome analysis of constitutive resistance to white pine weevil in Picea glauca-engelmannii (Interior spruce)

city: Vancouver

first: Sébastien

last: Verne

state: BC

address: 2424, Main Mall

department: Forest Sciences

institute: University of British Columbia

summary: White pine weevil is a major pest of conifers in North America, especially for Spruce trees. Constitutive defenses are important in understanding defense mechanisms because they constitute the initial barrier to attacks by weevils and other pests. Resistant and susceptible trees exhibit constitutive differences in spruce. To improve our knowledge of their genetic basis, we compared the constitutive expression levels of 17,825 genes between 20 resistant and 20 susceptible trees in interior spruce (Picea glauca).

overall_design: Twenty hybridizations were performed to compare untreated bark of resistant and susceptible trees.RNA isolated from each of the 20 individual untreated resistant trees was compared directly against the 20 individual untreated susceptble trees using two hybridizations with a dye flip for each tree pair.

first: Rick

last: White

first: Barry

last: Jaquish

first: Carol

last: Ritland

first: Kermit


title: multiplexage : dual-target hybridization microarray experiment-New developments towards a genetic and diagnosis use of plant mircoarrays

status: Public on Dec 08 2011

city: EVRY CEDEX

first: Elftieh

last: Samira

address: 2 rue Gaston Crémieux, CP 5708

department: Unité de Recherche en Génomique Végétale

country: France

institute: INRA

summary: gnp06-01_agriarray - multiplexage : dual-target hybridization microarray experiment - Several factors affect today a more extended use of microarrays for research and as a diagnosis tool. These factors are the experimental cost, the reproducibility of the measurements and the format of the analyses. This project aims at bringing solutions in these three domains by optimizing multiplexed analyses in order to reduce cost and enhance the number of samples treated simultaneously; by proposing new couples flurophores / slide surface in order to increase the signal precision and by developing new applications such as Comparative Genomic Hybridization (GGH) or Promoter Arrays to bring the plant microarray beyond transcriptome analyses. Altogether, these approaches will allow us to construct an optimized diagnostic tool based on 96 well microplate microarrays. This multidisciplinary project bring together biologists, chemists, physicists and mathematicians to develop innovative solutions for future application of DNA microarrays. - Dual-target hybridization microarray experiment with doble factors comparison : two mutants and its wild-types at different times. The aim of this part is to compare the classical design with the new design with a third dye.

overall_design: 47 dye-swap - genotype and ecotype comparison

first: Samira

last: Elftieh

first: Jean-Pierre

last: Renou

first: Jean-Christophe

last: Avarre

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Transcriptome of Proteus mirabilis in the murine urinary tract

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary: The enteric bacterium Proteus mirabilis is a common cause of complicated urinary tract infections. In the study, microrarrays were used to analyze P. mirabilis gene expression in vivo from experimentally infected mice.  Urine was collected at 1, 3, and 7d postinfection, and RNA was isolated from bacteria in the urine for transcriptional analysis.  Across 9 microarrays, 471 genes were upregulated and 82 were downregulated in vivo compared to in vitro broth culture.  Genes upregulated in vivo encoded MR/P fimbriae, urease, iron uptake systems, amino acid and peptide transporters, pyruvate metabolism, and portions of the TCA cycle.  Flagella were downregulated.  Ammonia assimilation gene glnA (glutamine synthetase) was repressed in vivo while gdhA (glutamate dehydrogenase) was upregulated in vivo.  Contrary to our expectations, ammonia availability due to urease activity in P. mirabilis did not drive this gene expression.  A gdhA mutant was growth-deficient in minimal medium with citrate as the sole carbon source, and loss of gdhA resulted in a significant fitness defect in the mouse model of urinary tract infection.  Unlike Escherichia coli, which represses gdhA and upregulates glnA in vivo and cannot utilize citrate, the data suggest that P. mirabilis uses glutamate dehydrogenase to monitor carbon-nitrogen balance, and this ability contributes to the pathogenic potential of P. mirabilis in the urinary tract.

overall_design: Voided urine from female CBA/J mice infected with Proteus mirabilis was collected and pooled in RNA stabilizing reagent (RNAprotect).  Urine was collected at 1, 3, and 7 d postinfection. RNA was isolated from urine and log-phase LB cultures, converted to cDNA, and labeled with CyDye. Three arrays were completed per time point (9 arrays total).  Slides were scanned with a ScanArray Express microarray scanner (Perkin Elmer) at 10 μm resolution and quantified using ScanArray Express software.   Resulting data were normalized by total intensity and median spot intensities were identified using MIDAS (v. 2.22) software.

first: Harry

middle: L

last: Mobley


title: Gene expression in helped versus helpless CD8 T cells

status: Public on Nov 26 2011

city: Amsterdam

first: Monika

last: Wolkers

address: Plesmanlaan 125

department: Research

country: Netherlands

institute: Sanquin Research

summary: CD4+ ‘helper’ T cells (TH) are pivotal for the generation and maintenance of CD8+ T cell responses. ‘Helped’ CD8+ T cells receive signals during priming that prevent the induction of the pro-apoptotic molecule TRAIL during reactivation, thereby enabling robust secondary expansion. Conversely, ‘helpless’ CD8+ T cells primed in the absence of TH induce TRAIL expression upon restimulation and undergo activation-induced cell death (AICD). We have investigated the molecular basis for the differential regulation of TRAIL in helped versus helpless CD8+ T cells by comparing their transcriptional profiles, and have identified a transcriptional corepressor, NGFI-A binding protein 2 (Nab2) that is selectively induced in helped CD8+ T cells. Enforced expression of Nab2 prevents TRAIL induction upon restimulation of primary helpless CD8+ T cells, and expression of a dominant-negative form of Nab2 in helped CD8+ T cells impairs their secondary proliferative response that is reversible by TRAIL blockade. Finally, we observe that the CD8+ T cell autocrine growth factor interleukin-2 (IL-2) coordinately increases Nab2 expression and decreases TRAIL expression. These findings identify Nab2 as a mediator of TH-dependent CD8+ T cell memory responses through regulation of TRAIL and promotion of secondary expansion, and suggest a mechanism through which this operates.

overall_design:
Helped and helpless E1B192-200-specific CD8+ T cells were generated as previously described16. Briefly, C57BL/6J mice were treated with 100 ug GK1.5 intraperitoneally (helpless) or left untreated (helped) prior to subcutaneous immunization with 1x107 irradiated (3000 rad) TAP-/-Ad5E1-MEC. 3 days post immunization, all mice were treated with 100 ug GK1.5. Spleens and draining lymph nodes were harvested 7 days post immunization, and CD8+ T cells were purified with the CD8 negative isolation kit (Miltenyi) according to the manufacturer’s protocol. Purity was 88-95%.

Microarray and data analysis
Purified CD8+ T cells from helped and helpless mice were sorted on CD44hi expression by flow cytometry. Cells were restimulated for 4h with 2ug/ml E1B192-200 peptide in the presence of 20uM qVD-OPh (R&D Systems). RNA was extracted using TriZol (Gibco BRL) according to the manufacturer's instructions. 5ug of total RNA was used to generate cDNA with RT Superscript III (Invitrogen). cDNA was indirectly labeled using Cyanine 3 and Cyanine 5 (Amersham). Labeled samples were purified and spotted in an equimolar ratio on the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) array. Images were preview scanned on an Axon 4000B and channels were balanced until an overall Cy5/Cy3 ratio of 1 was achieved before a final data scan at 5µm was performed in GenePix.  The images were manually gridded, and then saved for analysis. Data were analysed using Spotfire Decision Site.
Gene Ontology terms were downloaded from BioMart <http://www.biomart.org> version NCBI37, 09 April 2009. Genes with Biological Process term "regulation of transcription" (GO:0045449) were assumed to encode transcription factors. Of 276 probes with an absolute log2 ratio >2, 231 probes were present in BioMart; the remaining cDNA probes did not match currently known genes.

middle: C

first: Patrick

last: Fitzgerald

first: Douglas

middle: R

last: Green

first: Stephen

last: Schoenberger


title: Expression profiling of SRGs of the drought-tolerant indica rice cultivar N22 during drought stress under field conditions

status: Public on Nov 27 2011

city: Hyderabad

first: Markandeya

last: Gorantla

state: Andhra Pradesh

address: University of Hyderabad

department: Department of Plant Science

country: India

institute: university of Hyderabad

summary:
In rice, gene expression profiling under different stresses have been carried out earlier through microarrays and SAGE (Kawasaki et al., 2001; Rabbani et al., 2003,;. Yazaki et al., 2003, 2004; Walia et al., 2005; Zhou et al., 2005; Jiao et al., 2005; Zhou, 2007; Wang, et al., 2007)). The results reported so far were mostly derived from different stress treatments, array formats, species, tissue types, and time courses, which make it difficult for direct comparison among studies. Also, most of the stress experiments on expression profiles were conducted under laboratory, growth chamber or field grown plants subjected to stress in laboratory conditions, usually by inducing stress with exogenous compounds such as abscisic acid (ABA) or gibberellin (GA) genes (Yazaki et al., 2003, 2004; Rabbani et al., 2003),  salt  (Kawasaki et al., 2001; Rabbani et al., 2003; Walia et al., 2005), organ specific gene expression under high salinity (Jiao et al., 2005) and drought (Zhou et al.,  2007), comparison with different cultivars (Wang et al., 2007) and other environmental stresses such as cold and drought (Rabbani et al., 2003; Zhou et al., 2005).

However, such laboratory, growth chamber grown plants or field grown plants subjected to stress under laboratory conditions significantly differ from the field stress conditions and therefore the resultant plant response may not truly represent the actual stress conditions prevailing on field. This has been extensively reviewed by Mittler, 2006 and the need for utilizing data from multiple stress experiments for developing plants resistant to stress has been focused. The review also focuses on evaluating farmers experiences in stress management and kinds of stress that a plant is subjected prior to taking up research on stress resistances has been of significant importance. In the present study, to bridge the gap between the available data on drought stress and the gene regulation under field drought conditions has been paid attention. The outcome of this data will give new leads for breeders to design strategies to develop plants resistant to drought without much loss in yield. In the present study experiments were conducted under different field capacities using a rainout shelter to minimizing the effects of drought induction due to rains. The microarray analysis is thus expected to throw light on stress responsive gene expression in field drought conditions. Till now, to our knowledge there have been no reports on gene expression in rice under field drought conditions. Further, there is no data available on gene expression profiling during various stages of plant growth in leaf and panicle tissues under different levels of water stress. Here, we have focused on generating stress responsive gene (SRG) expression profiles in field drought conditions through the entire life cycle of rice plant.

Optimal drought simulation was achieved by conducting a drought stress experiment and validated by a series of dry runs.  The main reason for evaluating gene expression under drought in field condition is as drought itself is not limited to water stress but various other factors, such as heat, humidity, hot winds, and long day lengths effect the gene regulation.  All these are likely to trigger common pathways that are also a part of drought stress response and therefore significantly affect the expression profiles.

In the present study, field drought stress was initiated from 31 days after germination and transplantation to the field at 100%, 60%, 40% and 15% field capacities designated as A1, A2, A3, and A4. It took 7 days for the onset of the actual drought for the experimental plots to reach to their designated field capacities from 100% FC. Samples were collected from 7 days after drought stress to 33 days after drought stress to evaluate different drought stress regimes based on the developmental stages of the plant. At all the tested stress levels the data points were Hierarchically grouped and clustered sets of genes were examined and an approximate number of clusters to be formed were estimated. Finding a group of genes showing a similar pattern of gene expression by means of expression data from microarray analysis is the basis for identification of genes and pathways controlling a specific trait.  We have followed unsupervised classification and clustered the genes hierarchically after normalizing expression data to obtain a set of co-regulated genes.  Analysis of data revealed that there are at least 3 to 4 clusters which show differential regulation under each stress regime. The annotated genes falling in these clusters interestingly include a number of novel genes from N22 library along with some known candidate genes for drought tolerance which were earlier identified in our study (Markandeya et al., 2007). Expression pattern of these genes from 7 days after drought stress to 33 days after drought stress with their fold changes were evaluated in the present study. In particular, it is observed that many genes of unknown function are also co-regulated in an interesting pattern along with known genes.

overall_design:
Drought Stress Induction Under Field Conditions:
Simulation of drought under field conditions for gene expression profiling was done by constructing an experimental field plot with a rain out shelter. The experimental plots were constructed by excavation of soil up to 5 feet deep of 13 feet width and 16 feet length. A sand bed of 1 foot was laid across the length in a slanting manner such that the end of the plot has just 1 inch sand to allow drain out and prevent seepage. Eight plots (3 feet X 4 feet) were partitioned and constructed with concrete walls with water-proof agents to avoid seepage of water across plots. The inner walls were of 5 feet and the outer walls facing the exterior soil apart from the black clay soil were of 3 feet in depth. Below this, 3 feet wall, 6 inch sand was put until the base (5 feet) runs into the bottom 1 foot sand. Also, these blocks are raised enough to avoid accidental overflow from the control plots. These plots were filled to 5 feet depth with soil mixture in which the rice crop is usually cultivated with the recommended amount of farm yard manure. Rainout shelter was constructed to cover the plots during rainy days to keep the plants from rain during experiment. The drought stress induction was monitored through high-precision digital irrigation controllers (Netafim Inc, Israel). Irrigation was given taking plot A1 as 100% field capacity, which is a control plot in this experiment, and irrigation was set up in the other plots with moisture probes/timer controllers.

Rice Seedlings Growth, Transplantation and Stress Treatments Under Field Condition:
Rice seeds were surface sterilized, washed and germinated in a growth chamber. Fifteen-day-old seedlings were transplanted in the field for drought stress induction. The transplanted seedlings were grown in 100% field capacity with 2cm standing water until day 30. Field drought stress was initiated from day 31 at 100%, 60%, 40% and 15% field capacities designated as A1, A2, A3, and A4, respectively. It took 8 days for the onset of the actual drought for the experimental plots to reach to their designated field capacities from 100% FC. Samples were collected at various stages and drought stress regimes based on the developmental stages of the plant.

Phenotypic Response to Field Drought Stress:
Rice seedlings were subjected to field drought stress at various Field Capacities (FC), i.e., 60% FC (A2), 40% FC (A3) and 15% FC (A4) compared to that of the control grown at 100% FC (A1), through controlled irrigation of experimental plots. This protocol allowed us to study the response of rice plants to the desired stress levels. The field drought stress experimental set up is basically a rain out shelter with an electronically controlled irrigation system. Drought stress significantly reduced plant height, biomass and yield. Considerable variation was observed in the phenotypic response to water stress across the various stress regimes. The Relative Water Content (RWC) of the plants, measured in leaf samples periodically across the developmental stages, was in the range of 92 to 28% at various stress levels and periods.
Under mild stress (A2), plants showed, on an average, 7.5 cm (~6%) reduction in plant height by 63 DAG (Days After Germination). Similarly, there was a significant reduction (25.8%) in tiller number and about 5-fold spikelet sterility leading to a 7% yield loss, compared to that of the control. Under moderate stress conditions (A3), there was a reduction in plant height (18%), tillering (45%) and a high percentage of seed sterility (60%), leading to an yield loss of about 54%. Although milking was observed in the initial stages in all the seeds, seed setting was drastically poor, leading to a significant reduction in the yield. At about 70 DAG, the stressed seedlings started begin to lodge and eventually get desiccated by 75 DAG. Under severe stress (A4), booting was three days earlier on an average, which is a characteristic drought escaping mechanism stressing rice. Other observed drought stress responses include (a) a reduction in RWC (28%), (b) a reduction in tiller number (75.8%), and (c) stunted growth (40% reduction) compared to the control. There was complete spikelet sterility resulting in total yield loss. The plants began to lodge on 67 DAG and completely desiccated by 70 DAG.

Monitoring Expression Profiles of Stress Responsive Genes:
To monitor gene expression profiling, the target samples were prepared from field drought stressed plants under A2, A3 and A4 stresses at vegetative (DAG 45, 52), pre-anthesis (DAG 55), post-anthesis and seed setting stages (DAG 63, 67 & 71). A sampling of 5 leaves per plot were used to obtain high-quality RNA samples for labeling and hybridization for all the above targets.

Set A1 is not included in this submission.

first: V

middle: B

last: Lachagari

first: F

middle: A

last: Feltus

first: P

last: Babu

first: Andrew

middle: H

last: Paterson

first: A

last: Reddy


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus) (part 7 of 10)

status: Public on Nov 23 2011

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: Munitions constituents (MCs) including hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), 2,4,6-trinitrotoluene (TNT), and TNT derivatives are recognized to elicit aberrant neuromuscular responses in many species. The onset of seizures resulting in death was observed in the avian model Northern bobwhite after oral dosing with RDX beginning at 8 mg/kg/day in subacute (14 days) exposures, whereas affective doses of the TNT derivative, 2,6-dinitrotoluene (2,6-DNT), caused gastrointestinal impacts, lethargy, and emaciation in subacute and subchronic (60 days) exposures. To assess and contrast the potential neurotoxicogenomic effects of these MCs, a Northern bobwhite microarray was developed consisting of 4119 complementary DNA (cDNA) features enriched for differentially-expressed brain transcripts from exposures to RDX and 2,6-DNT. RDX affected hundreds of genes in brain tissue, whereas 2,6-DNT affected few (≤ 17), indicating that 2,6-DNT exposure had relatively little impact on the brain in comparison to RDX. Birds exhibiting RDX-induced seizures accumulated over 20× more RDX in brain tissues in comparison to non-seizing birds even within a common dose. In parallel, expression patterns were unrelated among seizing and non-seizing birds exposed to equivalent RDX doses. In birds experiencing seizures, genes related to neuronal electrophysiology and signal transduction were significantly affected. Comparative toxicology revealed strong similarity in acute exposure effects between RDX and the organochlorine insecticide dichlorodiphenyltrichloroethane (DDT) regarding both molecular mechanisms and putative mode of action. In a manner similar to DDT, we hypothesize that RDX elicits seizures by inhibition of neuronal cell repolarization postaction potential leading to heightened neuronal excitability and seizures facilitated by multiple molecular mechanisms.

overall_design: Northern Bobwhite 14 Day RDX High Dose Exposure, Brain Tissue Investigation (High Laser Intensity Scan): Juvenile male and female Northern bobwhite (12 weeks of age) were dosed with RDX by daily gavage (0, 20, 80, 125, or 180 mg/kg/day). Each treatment group included seven birds (at least three of each sex per treatment). All RDX doses in the 14-day high-dose experiment elicited seizures within 3 days of experiment initiation (Johnson et al., 2007). Microarray experiments were conducted using a balanced interwoven-loop design using Cyanine-3 (Cy3) and A647. This experiment investigated the 14-day RDX high-dose exposure. All RDX-dosed quail accumulated ~20 mg/kg RDX in brain tissues (Johnson et al., 2007) and exhibited seizures. Transcript expression was compared among three male and three female controls versus three male and three female RDX-seized quail incorporating two dye swaps per biological replicate totaling 24 microarrays. Hybridizations included four technical replicates and two dye swaps per biological replicate resulting in a total of 24 micorarrays assayed. To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the High Intensity Scan.

first: Mehdi

last: Pirooznia

first: Michel

middle: J

last: Quinn Jr.

first: Mark

middle: S

last: Johnson

first: Lynn

last: Escalon

first: Karl

last: Indest

first: Xin

last: Guan

first: Joan

last: Clarke

first: Youping

last: Deng

first: Ping

last: Gong

first: Edward

last: Perkins


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus) (part 4 of 10)

overall_design: Northern Bobwhite 60 Day 2,6-DNT Exposure, Brain Tissue Investigation (Low Laser Intensity Scan): Juvenile male and female Northern bobwhite (12 weeks of age) were dosed with 2,6-DNT by daily gavage (0, 5, 10, 40, or 60 mg/kg/day). Each treatment group included 12 replicates per sex. Microarray experiments were conducted in a balanced interwoven-loop design using Cyanine-3 (Cy3) and A647. This experiment investigated the 60-day 2,6-DNT exposure comparing controls and the highest affective 2,6-DNT dose (60 mg/kg/day) in males and females, with all groups including three biological replicates for a total of 24 microarrays. To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the Low Intensity Scan.


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus) (part 5 of 10)

overall_design: Male Northern Bobwhite 14 Day 2,6-DNT Exposure, Brain Tissue Investigation (High Laser Intensity Scan): Juvenile male and female Northern bobwhite (12 weeks of age) were dosed with 2,6-DNT by daily gavage (0, 50, 100, 190, or 350 mg/kg/day). Each treatment group included seven birds (at least three of each sex per treatment). This microarray data set represents investigation of the male birds. Microarray experiments were conducted using an interwoven-loop design using Cyanine-3 (Cy3) and A647. This experiment investigated the effects of the 14-day 2,6-DNT exposure in males including controls and 60 mg/kg/day treatments, each including 3 biological replicates. To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the High Intensity Scan.


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus) (part 3 of 10)

overall_design: Northern Bobwhite 60 Day 2,6-DNT Exposure, Brain Tissue Investigation (High Laser Intensity Scan): Juvenile male and female Northern bobwhite (12 weeks of age) were dosed with 2,6-DNT by daily gavage (0, 5, 10, 40, or 60 mg/kg/day). Each treatment group included 12 replicates per sex. Microarray experiments were conducted in a balanced interwoven-loop design using Cyanine-3 (Cy3) and A647. This experiment investigated the 60-day 2,6-DNT exposure comparing controls and the highest affective 2,6-DNT dose (60 mg/kg/day) in males and females, with all groups including three biological replicates for a total of 24 microarrays. To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the High Intensity Scan.


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus) (part 6 of 10)

overall_design: Male Northern Bobwhite 14 Day 2,6-DNT Exposure, Brain Tissue Investigation (Low Laser Intensity Scan): Juvenile male and female Northern bobwhite (12 weeks of age) were dosed with 2,6-DNT by daily gavage (0, 50, 100, 190, or 350 mg/kg/day). Each treatment group included seven birds (at least three of each sex per treatment). This microarray data set represents investigation of the male birds.  Microarray experiments were conducted using an interwoven-loop design using Cyanine-3 (Cy3) and A647. This experiment investigated the effects of the 14-day 2,6-DNT exposure in males including controls and 60 mg/kg/day treatments, each including 3 biological replicates. To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the Low Intensity Scan.


title: The unfolded protein response supports cellular robustness as a broad-spectrum compensatory pathway.

city: Singapore

first: Guillaume

last: Thibault

address: 1 Research Link, National University of Singapore

department: Cell Stress and Homeostasis

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: Stress pathways monitor intracellular systems and deploy a range of regulatory mechanisms in response to stress. One of the best-characterized pathways, the unfolded protein response (UPR), is responsible for maintaining endoplasmic reticulum (ER) homeostasis. The highly conserved Ire1 branch regulates hundreds of gene targets by activating a UPR specific transcription factor. To understand how the UPR manages ER stress, a novel genetic approach was applied to reveal how the system corrects disequilibria. The data show that UPR can address a wide range of dysfunctions that is otherwise lethal if not for its intervention. Transcriptional profiling of stress alleviated cells shows that the program can be modulated, not just in signal amplitude, but also through differential target gene expression depending on the stress. The breadth of the functions mitigated by the UPR further supports its role as a major mechanism maintaining systems robustness.

overall_design: Genes expression from early log phase of ALG5, LHS1, and SCJ1 knockout cell and untreated and DTT-treated WT cells. RNA was prepared from independent triplicate samples.

first: Davis

middle: T

last: Ng


title: The role of transcription factor Gata4

city: Bethesda

first: Natalia

last: Shulzhenko

address: 9000 Rockville Pike

department: Laboratory of Cellular and Molecular Immunology

institute: NIAID, USA

summary:
Using a systems biology approach, we discovered and dissected a three-way interaction between the immune system, the intestinal epithelium, and the microbiota. We found that mice lacking B lymphocytes, or lacking IgA, have low intestinal expression of lipid metabolism genes regulated by the transcription factor GATA4, and a consequent decrease in fat absorption in the intestine.  The defect disappeared in germ free mice, suggesting that it is dependent on the microbiota; and sequencing analysis of the bacteria showed subtle differences between normal and B-cell deficient mice. Analysis of gene expression of gut biopsies from patients with common variable immunodeficiency and intestinal dysfunction revealed a high similarity to mouse B-cell knockout profiles. These data provide an explanation for a longstanding enigmatic association between immunodeficiency and defective lipid absorption in humans.
This series represents the subsection of the study where we address the role of transcription factor Gata4. The data are from conditional KO (Gata4KOvil) and  corresponding control mice.

overall_design: Intensity of each channel was extracted from two-color arrays.  We used direct dye swap design and performed paired analysis between small intestine of KO and control mice. Corresponding paires of KO and control were hybridized on the same array, except pair X

first: Andrey

last: Morgun


title: The role of immunoglobulin A

summary:
Using a systems biology approach, we discovered and dissected a three-way interaction between the immune system, the intestinal epithelium, and the microbiota. We found that mice lacking B lymphocytes, or lacking IgA, have low intestinal expression of lipid metabolism genes regulated by the transcription factor GATA4, and a consequent decrease in fat absorption in the intestine.  The defect disappeared in germ free mice, suggesting that it is dependent on the microbiota; and sequencing analysis of the bacteria showed subtle differences between normal and B-cell deficient mice. Analysis of gene expression of gut biopsies from patients with common variable immunodeficiency and intestinal dysfunction revealed a high similarity to mouse B-cell knockout profiles. These data provide an explanation for a longstanding enigmatic association between immunodeficiency and defective lipid absorption in humans.
This series represents the subsection of the study where we adress the role of immunoglobulin A. The data is from IgA KO and  corresponding control mice.

overall_design: Intensity of each channel was extracted from two-color arrays.  We used direct dye swap design and performed paired analysis between small intestine of KO and control mice. Corresponding paires of KO and control were hybridized on the same array and can be matched by the array name.


title: Gene expression profiling in caprine milk somatic and white blood cells upon intramammary challenge with Staphylococcus aureus

city: Lodi

first: Marcello

last: Del Corvo

address: via Einstein - Loc. Cascina Codazza

department: Bioinformatics

country: Italy

institute: CNR-Ibba

summary: In dairy ruminants transcriptome profiling has enabled the identification of genes, pathways and regulatory networks activated in mammary tissues during experimental infection by various pathogens, including E. coli, S. aureus and S. uberis. Information in goats are still low and many host-pathogen interaction mechanisms have to be explained. The objectives of the present study were (1) to identify the network of genes that becomes activated in caprine blood and milk somatic cells in early response towards a S. aureus challenge in order to better understand the local and sistemic response and (2) to search any difference in this immune response by using two animal groups belonging to a caprine reference family established based on founders with adverse SCC breeding values.

overall_design: Udders from ten healthy French Alpine goats  were infected with S. aureus and samples of blood and milk cells were collected at 0, 24 and 30 hours after infection. Alterations in the transcriptome profile were investigated using a custom bovine DNA microarray containing 43.822 unique gene probes.


title: Identification of potential biomarkers for patients with neurodegenerative parkinsonian syndromes using serum cytokine microarray analysis; series 8

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

summary: Background: Microarray technology may offer a new opportunity to gain insight into disease-specific global protein expression profiles. The present study was performed to apply a serum cytokine-array to screen for potential molecular biomarkers for Parkinson's disease (PD), multiple system atrophy (MSA), progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS). Methodology/Principal Findings: Serum samples were obtained from patients with clinical diagnoses of PD (n=117), MSA (n=31) and PSP/CBS (n=38) and 99 controls. Cytokine profiles of sera of patients and controls were analyzed with a semiquantitative human cytokine antibody array. In a next step, significantly altered cytokines were individually validated by immunoassays. The cytokine array revealed a significantly altered expression of 12 cytokines. Immunoassay validation confirmed a significant increase of PDGF-BB in PSP/CBS, MSA and PD and a decrease of Prolactin in PD (Kruskal-Wallis p<0.05). A multivariate analysis taking into account diagnoses anti-Parkinsonian treatment, sex and age revealed that PDGF-BB levels were influenced only by the diagnoses (p<0.001), whereas Prolactin levels were influenced only by anti-Parkinsonian treatment (p<0.001). These findings could be corroborated by a subgroup analysis in untreated patients. Conclusions/Significance: In our unbiased cytokine array screening approach we found PDGF-BB to be elevated in PSP/CBS, MSA and PD. Increased PDGF-BB levels might be of relevance in a model of molecular biomarkers for Parkinsonian syndromes.

overall_design: Screen serum samples from patients with Parkinson's disease, progressive supranuclear palsy, corticobasal syndrome, multisystem atrophy and controls for deregulation of serum proteins using a cytokine-array detecting 174 secreted signaling proteins.

first: Phillip

last: Mahlknecht

first: Sylvia

last: Stemberger

first: Fabienne

last: Sprenger

first: Eva

last: Hametner

first: Rudolf

last: Kirchmair

first: Christoph

last: Grabmer

last: Scherfler

first: Gregor

middle: K

last: Wenning

first: Klaus

last: Seppi

first: Werner

last: Poewe

first: Markus

last: Reindl


title: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) [miRNA]

city: Pittsburgh

first: Pruthvi S. R.

last: Nagilla

state: PA

address: 416 Parran Hall, 130 DeSoto Street

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh

summary: Host cells respond to exogenous infectious agents such as viruses, including HIV-1. Studies have evaluated the changes associated with virus infection at the transcriptional and translational levels of the cellular genes involved in specific pathways. While this approach is useful, in our view it provides only a partial view of genome-wide changes. Recently, technological advances in the expression profiling at the microRNA (miRNA) and mRNA levels have made it possible to evaluate the changes in the components of multiple pathways. To understand the role of miRNA and its interplay with host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative global miRNA and mRNA microarray using human PBMCs infected with HIV-1. The PBMCs were derived from multiple donors and were infected with virus generated from the molecular clone pNL4-3. The results showed that HIV-1 infection led to altered regulation of 21 miRNAs and 444 mRNA more than 2-fold, with a statistical significance of p<0.05. Furthermore, the differentially regulated miRNA and mRNA were shown to be associated with host cellular pathways involved in cell cycle/proliferation, apoptosis, T-cell signaling, and immune activation. We also observed a number of inverse correlations of miRNA and mRNA expression in infected PBMCs, further confirming the interrelationship between miRNA and mRNA regulation during HIV-1 infection. These results for the first time provide evidence that the miRNA profile could be an early indicator of host cellular dysfunction induced by HIV-1.

overall_design: Total RNA isolated from PBMC subjected to 7 days of HIV-1 infection compared to uninfected control PBMC

first: Pruthvi

first: Velpandi

last: Ayyavoo


title: Identification of potential biomarkers for patients with neurodegenerative parkinsonian syndromes using serum cytokine microarray analysis; series 7


title: Identification of potential biomarkers for patients with neurodegenerative parkinsonian syndromes using serum cytokine microarray analysis; series 6


title: σB-dependent yabJ-spoVG operon involved in regulation of extracellular nuclease, lipase and protease expression in Staphylococcus aureus

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: The alternative sigma factor σB of Staphylococcus aureus is involved in the coordination of the general stress response, expression of virulence determinants and modulation of antibiotic resistance levels. It controls a large regulon, either directly by recognizing conserved σB promoter sequences, or indirectly via σB-dependent elements. The σB-controlled yabJ-spoVG operon encodes two such putative downstream elements. We report here transcriptome analysis in S. aureus Newman showing that inactivation of the yabJ-spoVG operon had primarily a repressing effect on a small subregulon comprising mainly virulence factors, including a nuclease (nuc), a protease (splE) and a lipase (lip).. As a consequence extracellular nuclease, protease and lipase activities were reduced in a yabJspoVG mutant. Trans-complementation by SpoVG was sufficient to restore their reduced phenotypic expression and lowered transcription due to yabJ-spoVG deletion. It did not restore, however, the changes triggered by σB inactivation, indicating that both regulons do only partially overlap, despite the σB dependency of the yabJ-spoVG expression. Thus, σB is likely to control additional, SpoVG-independent factors affecting the expression of numerous hydrolytic enzymes. SpoVG, on the other hand, seems to fine-tune the σB-dependent regulation of a subset of virulence factors by antagonizing the σB effect.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

platform_organism: Staphylococcus aureus subsp. aureus Mu50

platform_organism: Staphylococcus aureus subsp. aureus N315

platform_organism: Staphylococcus aureus subsp. aureus MRSA252

platform_organism: Staphylococcus aureus subsp. aureus MSSA476

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Newman wild type strain compared to double mutant spoVG and yabJ or to sigB truncated mutant

first: Bettina

last: Schulthess

first: Dominik

last: Bloes

first: Patrice

last: François

first: Myriam

last: Girard

first: Jacques

last: Schrenzel

last: Bischoff

first: Brigitte

last: Berger-Bächi


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus) (part 1 of 10)

status: Public on Nov 22 2011

first: Kurt

last: Gust

overall_design: Female Northern Bobwhite 14 Day 2,6-DNT Exposure, Brain Tissue Investigation (Low Laser Intensity Scan):  Juvenile female Northern bobwhite (12 weeks of age) were dosed with 2,6-DNT by daily gavage (0, 50, 100, 190, or 350 mg/kg/day). Each treatment group included seven birds (at least three of each sex per treatment). Microarray experiments were conducted using an interwoven-loop design using Cyanine-3 (Cy3) and A647. This experiment investigated the effects of the 14-day 2,6-DNT exposure in females including controls, 60, and 100 mg/kg/day treatments, each including 3 biological replicates. To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the Low Intensity Scan.

first: Mehdi

last: Pirooznia

first: Michel

last: Quinn Jr.

first: Mark

last: Johnson

first: Lynn

last: Escalon

first: Karl

last: Indest

first: Xin

last: Guan

first: Joan

last: Clarke

first: Youping

last: Deng

first: Ping

last: Gong

first: Edward

last: Perkins


title: Structural and functional characterization of a winter malting barley

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: Transcriptome comparison of the winter malting barley '88Ab536' with the spring malting variety 'Morex' at two time points of the malting process: 'out of steeping' and '3 days of germination'. Three replicates of each genotype and time point were accomplished.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Maria Munoz-Amatriain.  The equivalent experiment is BB76 at PLEXdb.]

overall_design: genotype: 88Ab536 - time: 0 days(3-replications);  genotype: 88Ab536 - time: 3 days(3-replications);  genotype: Morex - time: 0 days(3-replications);  genotype: Morex - time: 3 days(3-replications)

first: Maria

last: Munoz-Amatriain

first: Gary

last: Muehlbauer


title: Neurotoxicogenomic investigations to assess mechanisms of action of the munitions constituents RDX and 2,6-DNT in Northern bobwhite (Colinus virginianus) (part 2 of 10)

overall_design: Female Northern Bobwhite 14 Day 2,6-DNT Exposure, Brain Tissue Investigation (High Laser Intensity Scan): Juvenile female Northern bobwhite (12 weeks of age) were dosed with 2,6-DNT by daily gavage (0, 50, 100, 190, or 350 mg/kg/day). Each treatment group included seven birds (at least three of each sex per treatment). Microarray experiments were conducted using an interwoven-loop design using Cyanine-3 (Cy3) and A647. This experiment investigated the effects of the 14-day 2,6-DNT exposure in females including controls, 60, and 100 mg/kg/day treatments, each including 3 biological replicates. To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the High Intensity Scan.


title: Expression and functional validation of new p38α transcriptional targets in tumorigenesis

city: Barcelona

first: Angel

last: Nebreda

state: Barcelona

address: C/ Baldiri Reixac 10

country: Spain

institute: Institute for Research in Biomedicine (IRB Barcelona)

summary: p38α MAP kinase plays an important tumor suppressor role, which is mediated by both its negative effect on cell proliferation and its pro-apoptotic activity. Surprisingly, most tumor suppressor mechanisms coordinated by p38α have been reported to occur at the post- translational level. This contrasts with the important role of p38α in the regulation of transcription and the profound changes in gene expression that normally occur during tumorigenesis. We have analyzed whole genome expression profiles of Ras-transformed wild- type and p38α-deficient cells and have identified 202 genes that are potentially regulated by p38α in transformed cells. Expression analysis has confirmed the regulation of these genes by p38α in tumors, and functional validation has identified several of them as likely mediators of the tumor suppressor effect of p38α on Ras-induced transformation. Interestingly, about 10% of the genes that are negatively regulated by p38α in transformed cells contribute to EGF receptor signalling. Our results suggest that inhibition of EGF receptor signalling by transcriptional targets of p38α is an important function of this signalling pathway in the context of tumor suppression.

overall_design: We have investigated how transcriptional regulation contributes to the tumor suppressor effect of p38α, by comparing whole-genome expression profiles of wild-type (WT) and p38α- deficient (p38α-/-) mouse embryo fibroblasts (MEFs) expressing oncogenic H-RasG12V

first: Aneta

last: Swat

first: Ignacio

last: Dolado

first: Ana

last: Igea

first: Gonzalo

last: Gomez-Lopez

first: David

middle: G

last: Pisano

last: Cuadrado


title: Microarray of barley genes in wheat-barley chromosome addition lines

summary: Transcript levels of barley genes were examined in the wheat-barley chromosome addition lines having one of six barley chromomes, 2H, 3H, 4H, 5H, 6H and 7H.    ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Seungho Cho.  The equivalent experiment is BB8 at PLEXdb.]

sample_organism:
Hordeum vulgare
Triticum aestivum

overall_design: genotype: chr2H(3-replications);  genotype: chr2HL(3-replications);  genotype: chr3H(3-replications);  genotype: chr4H(3-replications);  genotype: chr5H(3-replications);  genotype: chr6H(3-replications);  genotype: chr6HL(3-replications);  genotype: chr6HS(3-replications);  genotype: chr7H(3-replications);  genotype: Betzes(3-replications);  genotype: Chinese Spring(3-replications)

first: Seungho

last: Cho


title: Characterization of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumors

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

type: Genome variation profiling by genome tiling array

summary: Amplification of chromosomal region 11q13, containing the cell cycle regulatory gene CCND1, is frequently found in breast cancer and other malignancies. It is associated with the favourable oestrogen receptor (ER) positive breast tumour phenotype, but also with poor prognosis and treatment failure. 11q13 spans almost 14 Mb and contains more than 200 genes and is affected by various patterns of copy number gains, suggesting complex mechanisms and selective pressure during tumour progression. In the present study we used 32k tiling BAC array CGH to analyse 94 CCND1-amplified breast tumours from sporadic, hereditary and familial breast cancers to fine map chromosome 11q13. A set containing 281 CCND1-non-amplified breast tumours was used for comparisons. We used gene expression data to further validate the functional effect of gene amplification. We identified six core regions covering 11q13.1-q14.1 that were amplified in different combinations. The major core contained CCND1, whereas two cores were found proximal of CCND1 and three distal. The majority of the CCND1-amplified tumours were ER-positive and classified as luminal B. Furthermore, we found that CCND1 amplification is associated with a more aggressive phenotype within histological grade 2 tumours and luminal A subtype tumours. Amplification was equally prevalent in familial and sporadic tumours, but strikingly rare in BRCA1- and BRCA2- mutated tumours. We conclude that 11q13 includes many potential target genes in addition to CCND1.

overall_design: Genomic profiling of 94 CCND1-amplified breast tumors using tiling BAC aCGH. A number of cases were hybridized as replicates or replicate as dye-swaps.

first: Karolina

last: Holm

first: Göran

last: Jönsson

last: Vallon-Christersson

first: Haukur

last: Gunnarsson

first: Adalgeir

last: Arason

first: Linda

last: Magnusson

first: Rosa

last: Barkardottir

first: Cecilia

last: Hegardt

first: Markus

last: Ringnér

first: Åke

last: Borg


title: Functional Genomic Analysis Of Barley(Hordeum vulgare L.) Grain Protein Accumulation

first: PLEXdb Curator

summary: Effect of high grain protein locus on barley grain protein accumulation. Gene expression levels were analysed in Karl, a low grain protein variety with its near-isogenic line 10_11(has high grain protein locus, chromosome 6)using Barley1 22k affymetrix chip.    ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Aravind Jukanti.  The equivalent experiment is BB53 at PLEXdb.]

overall_design: developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications);  developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications);  developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications);  developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications);  developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications);  developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications);  developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications);  developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications)

first: Aravind

last: Jukanti


title: Barley cv Morex inoculated with Fusarium graminearum and water as mock control

summary: Barley cv. Morex inoculated with Fusarium graminearum (isolate Butte 86) or water (mock). Sampled at 24, 48, 72, 96 and 144 hours after treatment.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Jayanand Boddu.  The equivalent experiment is BB9 at PLEXdb.]

overall_design: time: 24 - Treated or untreated: WATER(5-replications);  time: 24 - Treated or untreated: Fusarium(5-replications);  time: 48 - Treated or untreated: WATER(4-replications);  time: 48 - Treated or untreated: Fusarium(4-replications);  time: 72 - Treated or untreated: WATER(5-replications);  time: 72 - Treated or untreated: Fusarium(5-replications);  time: 96 - Treated or untreated: WATER(4-replications);  time: 96 - Treated or untreated: Fusarium(4-replications);  time: 144 - Treated or untreated: WATER(4-replications);  time: 144 - Treated or untreated: Fusarium(4-replications)

first: Jayanand

last: Boddu

first: Gary

last: Muehlbauer


title: SRE1 Regulates Iron-Dependent Gene Expression in the Fungal Pathogen Histoplasma capsulatum

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

institute: University of California

summary: Regulation of iron acquisition genes is critical for microbial survival under both iron-limiting conditions (to acquire essential iron) and iron-replete conditions (to limit iron toxicity). In fungi, iron acquisition genes are repressed under iron-replete conditions by a conserved GATA transcriptional regulator. Here we investigate the role of this transcription factor, Sre1, in the cellular responses of the fungal pathogen Histoplasma capsulatum to iron. We showed that cells in which SRE1 levels were diminished by RNA interference were unable to repress siderophore biosynthesis and utilization genes in the presence of abundant iron, and thus produced siderophores even under iron-replete conditions. Mutation of a GATA-containing consensus site found in the promoters of these genes also resulted in inappropriate gene expression under iron-replete conditions. Microarray analysis comparing control and SRE1-depleted strains under conditions of iron limitation or abundance revealed both iron-responsive genes and Sre1-dependent genes, which comprised distinct but overlapping sets. Iron-responsive genes included putative oxidoreductases, metabolic and mitochondrial enzymes, superoxide dismutase, and nitrosative-stress response genes; Sre1-dependent genes were of diverse function. Genes regulated by iron levels and Sre1 included all of the siderophore biosynthetic genes, a gene involved in reductive iron acquisition, an iron-responsive transcription factor, and two catalases. Based on transcriptional profiling and phenotypic analyses, we conclude that Sre1 plays a critical role in the regulation of both traditional iron-responsive genes and iron-independent pathways such as regulation of cell morphology. These data highlight the evolving realization that the effect of Sre1 orthologs on fungal biology extends beyond the iron regulon.

overall_design: For microarray studies, initial cultures of HcLH120 (Control RNAi-1) or 123 (SRE1 RNAi-2) yeast cells were grown in 5 mL HMM, and then passaged 1:25 into 100 mL HMM. After 2 days of growth, the cultures were pelleted, washed in 100 mL of PBS, resuspended in 100 mL of mRPMI pH 6.5 and diluted to an OD600~2 in 1 L of mRPMI. After 24 hours of growth, 200 mL of culture was harvested for each of the three zero time points. Then the cultures were split into 2 X 400 mL, and 10 uM FeSO4 (final concentration) was added to one set of cultures. At each time point (.5, 1, 4, or 8 hours), 100 mL of culture was harvested for RNA extraction.

first: Lena

last: Hwang

first: Erica

last: Seth

first: Anita

last: Sil


title: Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines

summary: We utilized the Barley1 Affymetrix GeneChip for comparative transcript analysis of Betzes barley, Chinese Spring wheat, and Chinese Spring–Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations.  We mapped barley genes to chromosome arms (1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL) based on their transcript levels in the ditelosomic addition lines.     ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Hatice Bilgic.  The equivalent experiment is BB55 at PLEXdb.]

overall_design: genotype: CS (Chinese Spring)(3-replications);  genotype: Betzes(3-replications);  genotype: 1HS(3-replications);  genotype: 2HS(3-replications);  genotype: 3HS(3-replications);  genotype: 3HL(3-replications);  genotype: 4HS(3-replications);  genotype: 4HL(3-replications);  genotype: 5HS(3-replications);  genotype: 5HL(3-replications);  genotype: 7HS(3-replications);  genotype: 7HL(3-replications)

first: Hatice

last: Bilgic


title: Transcriptome analysis of wild barley (H. vulgare ssp spontaneum) after pathogen inoculation

summary: Hordeum vulgare ssp. spontaneum, accession Shechem 12-32, was    submitted to 4 experimental treatments (C. sativus (spot blotch), P.    hordei (leaf rust), and water and oil controls) to examine gene    transcription differences triggered by biotrophic and hemi-biotrophic    pathogens.  Inoculated plants were arranged in a split plot design.     Samples were collected at 12, 24, 36, & 48 hours after inoculation. A    total of 48 samples (4 treatments x 4 time points x 3 replicates) were    subjected to GeneChip analysis.    Made public: 2009-12-02   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Ben Millett.  The equivalent experiment is BB61 at PLEXdb.]

overall_design: treated or untreated: C. sativus (spot blotch) - time: 12 hrs(3-replications);  treated or untreated: C. sativus (spot blotch) - time: 24 hrs(3-replications);  treated or untreated: C. sativus (spot blotch) - time: 36 hrs(3-replications);  treated or untreated: C. sativus (spot blotch) - time: 48 hrs(3-replications);  treated or untreated: water control - time: 12 hrs(3-replications);  treated or untreated: water control - time: 24 hrs(3-replications);  treated or untreated: water control - time: 36 hrs(3-replications);  treated or untreated: water control - time: 48 hrs(3-replications);  treated or untreated: P. hordei (leaf rust) - time: 12 hrs(3-replications);  treated or untreated: P. hordei (leaf rust) - time: 24 hrs(3-replications);  treated or untreated: P. hordei (leaf rust) - time: 36 hrs(3-replications);  treated or untreated: P. hordei (leaf rust) - time: 48 hrs(3-replications);  treated or untreated: oil control - time: 12 hrs(3-replications);  treated or untreated: oil control - time: 24 hrs(3-replications);  treated or untreated: oil control - time: 36 hrs(3-replications);  treated or untreated: oil control - time: 48 hrs(3-replications)

first: Ben

last: Millett


title: Barley host response to the direct application of the trichothecene mycotoxin deoxynivalenol

summary: Barley florets (cv. Morex) were treated with 2.0 microgram deoxynivalenol per floret via a 10 microliter solution or mock inoculated with water. Samples were collected at 1, 12, 24, and 48 hours after inoculation.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Stephanie A. Gardiner.  The equivalent experiment is BB62 at PLEXdb.]

overall_design: time: 1 hai - treated or untreated: Deoxynivalenol(3-replications);  time: 1 hai - treated or untreated: Water(3-replications);  time: 12 hai - treated or untreated: Deoxynivalenol(3-replications);  time: 12 hai - treated or untreated: Water(3-replications);  time: 24 hai - treated or untreated: Deoxynivalenol(3-replications);  time: 24 hai - treated or untreated: Water(3-replications);  time: 48 hai - treated or untreated: Deoxynivalenol(3-replications);  time: 48 hai - treated or untreated: Water(3-replications)

first: Stephanie

last: Gardiner


title: Transcriptome analysis of trichothecene-induced gene expression in barley

summary: Fusarium Head Blight susceptible barley variety, Morex, was infected with deoxynivalenol production deficient mutant strain (GZT40) and wild type stains (Z3639) of Fusarium graminearum. The RNA was sampled at 48 and 96 hours after inoculation. and was used hybridize to Barley_1 GeneChip.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Jayanand Boddu.  The equivalent experiment is BB52 at PLEXdb.]

overall_design: time: 48 hai. - Treated or untreated: WATER(3-replications);  time: 48 hai. - Treated or untreated: MUTANT(3-replications);  time: 48 hai. - Treated or untreated: WILD TYPE(3-replications);  time: 96 hai. - Treated or untreated: WATER(3-replications);  time: 96 hai. - Treated or untreated: MUTANT(3-replications);  time: 96 hai. - Treated or untreated: WILD TYPE(3-replications)


title: Necrotic mutants in barley cv. Steptoe

summary: FN044, FN211, FN242 and FN303 are the fast neutron generated mutants in cv. Steptoe background. These 4 mutants have lesion mimic phenotype and increase disease resistance to stem rust.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  ling zhang.  The equivalent experiment is BB54 at PLEXdb.]

overall_design: line: nad1-1(3-replications);  line: nad1-2(3-replications);  line: nad1-3(3-replications);  line: nad1-4 (FN242)(3-replications);  line: Steptoe(3-replications)

first: ling

last: zhang


title: mlo5-mediated resistance responses in barley

summary: Gene expression of a near-isogenic pair of barley lines differing in absence or presence of the mlo5 resistance gene in response to attack by barley powdery mildew (Bgh).   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Achim Fischer.  The equivalent experiment is BB7 at PLEXdb.]

overall_design: disease type: Control - genotype: Mlo(1-replications);  disease type: Control - genotype: mlo5(1-replications);  disease type: Treated (Pathogen Infection) - genotype: Mlo(1-replications);  disease type: Treated (Pathogen Infection) - genotype: mlo5(1-replications)

first: Achim

last: Fischer


title: Mla-specified Transcriptional Responses in Barley-Powdery Mildew Interactions

summary: A large-scale parallel expression analysis was conducted to elucidate Mla-specified responses to powdery mildew infection using 22K Barley1 GeneChip probe arrays. Our goal was to identify genes  differentially expressed in incompatible (resistant) vs. compatible (susceptible) and Mla-specified Rar1-dependent vs. -independent interactions. A split-split-plot design with 108 experimental units (3 replications x 2 isolates x 3 genotypes x 6 time points) was used to profile near-isogenic lines containing the Mla1, Mla6, and Mla13 resistance specificities in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6) and K1 (AvrMla1, AvrMla13).    ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Rico Caldo.  The equivalent experiment is BB4 at PLEXdb.]

overall_design: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 0 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 8 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 16 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 20 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 24 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 32 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 0 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 8 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 16 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 20 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 24 hai(3-replications);  genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 32 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 0 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 8 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 16 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 20 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 24 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 32 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 0 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 8 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 16 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 20 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 24 hai(3-replications);  genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 32 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 0 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 8 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 16 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 20 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 24 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 32 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 0 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 8 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 16 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 20 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 24 hai(3-replications);  genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 32 hai(3-replications)

first: Rico

last: Caldo

first: Roger

last: Wise


title: Genetics of gene expression in barley

summary: Comparison of mRNA accumulation in segregating doubled haploid barley lines   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  .  The equivalent experiment is BB21 at PLEXdb.]

overall_design: genetic line: SM004(3-replications);  genetic line: SM007(3-replications);  genetic line: SM012(3-replications);  genetic line: SM013(3-replications);  genetic line: SM022(3-replications);  genetic line: SM024(3-replications);  genetic line: SM027(3-replications);  genetic line: SM041(3-replications);  genetic line: SM043(3-replications);  genetic line: SM044(3-replications);  genetic line: SM046(3-replications);  genetic line: SM061(3-replications);  genetic line: SM063(3-replications);  genetic line: SM073(3-replications);  genetic line: SM074(3-replications);  genetic line: SM079(3-replications);  genetic line: SM085(3-replications);  genetic line: SM088(3-replications);  genetic line: SM089(3-replications);  genetic line: SM116(3-replications);  genetic line: SM130(3-replications);  genetic line: SM135(3-replications);  genetic line: SM136(3-replications);  genetic line: SM140(3-replications);  genetic line: SM141(3-replications);  genetic line: SM146(3-replications);  genetic line: SM152(3-replications);  genetic line: SM155(3-replications);  genetic line: SM160(3-replications);  genetic line: SM167(3-replications);  genetic line: SM169(3-replications);  genetic line: SM173(3-replications);  genetic line: SM177(3-replications);  genetic line: SM184(3-replications);  genetic line: SM200(3-replications);  genetic line: Steptoe(3-replications);  genetic line: Morex(3-replications)


title: A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning

summary: Trancript Based Cloning (TBC) uses standard Gene Expression techniques to quickly isolate genes of interest and begin to determine their function. Using a particular mutant phenotype, identified during a programme of mutagenesis and screning, and a wild-type control we can quickly determine a list of genes that is likely to contain the gene responsible for the phenotype.  TBC is a general method for identifying and cloning important plant genes that is fast and may be applicable to almost any plant species  Transcript abundance assays on the barley rar1-2 mutant and Sultan5 wild type were performed by using standard methods for the Affymetrix barley genome array (Affymetrix). For each genotype, two independent biological replicates were analyzed and pooled for analysis.  Data were analyzed with DCHIP VERSION 1.3 (www.dchip.org),using data from only perfect-match oligonucleotides. Model-based analysis was performed by using perfect match-only analysis, compiling data from two biological replicates for each condition. Pairwise comparisons were analyzed for each condition, and a lower 90% confidence bound (LCB) and fold change were determined for each comparison. Gene expression changes were considered significant if the LCB was 1.4-fold or higher and if the intensities between the two conditions differed by >100.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  james hadfield.  The equivalent experiment is BB5 at PLEXdb.]

overall_design: genotype: rar1-2 (mutant)(2-replications);  genotype: Sultan 5 (wild type)(2-replications)

first: james

last: hadfield


title: Transcription profiling of barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes

summary: A split-split-plot design with 144 experimental units (3 replications x 4 genotypes x 6 time points x 2 treatment types) was used to profile barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6).  Barley leaves were harvested from inoculated and non-inoculated plants at 6 time points (0,8,16,20,24 and 32 hrs) after Bgh inoculation.    ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Rico Caldo.  The equivalent experiment is BB10 at PLEXdb.]

overall_design: genotype: Mla1 - time: 0 - Treated or untreated: Inoculated (3-replications);  genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla1 - time: 8 - Treated or untreated: Inoculated (3-replications);  genotype: Mla1 - time: 8 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla1 - time: 16 - Treated or untreated: Inoculated (3-replications);  genotype: Mla1 - time: 16 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla1 - time: 20 - Treated or untreated: Inoculated (3-replications);  genotype: Mla1 - time: 20 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla1 - time: 24 - Treated or untreated: Inoculated (3-replications);  genotype: Mla1 - time: 24 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla1 - time: 32 - Treated or untreated: Inoculated (3-replications);  genotype: Mla1 - time: 32 - Treated or untreated: Non-inoculated(3-replications);  genotype: m508  - time: 0 - Treated or untreated: Inoculated (3-replications);  genotype: m508  - time: 0 - Treated or untreated: Non-inoculated(3-replications);  genotype: m508  - time: 8 - Treated or untreated: Inoculated (3-replications);  genotype: m508  - time: 8 - Treated or untreated: Non-inoculated(3-replications);  genotype: m508  - time: 16 - Treated or untreated: Inoculated (3-replications);  genotype: m508  - time: 16 - Treated or untreated: Non-inoculated(3-replications);  genotype: m508  - time: 20 - Treated or untreated: Inoculated (3-replications);  genotype: m508  - time: 20 - Treated or untreated: Non-inoculated(3-replications);  genotype: m508  - time: 24 - Treated or untreated: Inoculated (3-replications);  genotype: m508  - time: 24 - Treated or untreated: Non-inoculated(3-replications);  genotype: m508  - time: 32 - Treated or untreated: Inoculated (3-replications);  genotype: m508  - time: 32 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla6 - time: 0 - Treated or untreated: Inoculated (3-replications);  genotype: Mla6 - time: 0 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla6 - time: 8 - Treated or untreated: Inoculated (3-replications);  genotype: Mla6 - time: 8 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla6 - time: 16 - Treated or untreated: Inoculated (3-replications);  genotype: Mla6 - time: 16 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla6 - time: 20 - Treated or untreated: Inoculated (3-replications);  genotype: Mla6 - time: 20 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla6 - time: 24 - Treated or untreated: Inoculated (3-replications);  genotype: Mla6 - time: 24 - Treated or untreated: Non-inoculated(3-replications);  genotype: Mla6 - time: 32 - Treated or untreated: Inoculated (3-replications);  genotype: Mla6 - time: 32 - Treated or untreated: Non-inoculated(3-replications);  genotype: 9472  - time: 0 - Treated or untreated: Inoculated (3-replications);  genotype: 9472  - time: 0 - Treated or untreated: Non-inoculated(3-replications);  genotype: 9472  - time: 8 - Treated or untreated: Inoculated (3-replications);  genotype: 9472  - time: 8 - Treated or untreated: Non-inoculated(3-replications);  genotype: 9472  - time: 16 - Treated or untreated: Inoculated (3-replications);  genotype: 9472  - time: 16 - Treated or untreated: Non-inoculated(3-replications);  genotype: 9472  - time: 20 - Treated or untreated: Inoculated (3-replications);  genotype: 9472  - time: 20 - Treated or untreated: Non-inoculated(3-replications);  genotype: 9472  - time: 24 - Treated or untreated: Inoculated (3-replications);  genotype: 9472  - time: 24 - Treated or untreated: Non-inoculated(3-replications);  genotype: 9472  - time: 32 - Treated or untreated: Inoculated (3-replications);  genotype: 9472  - time: 32 - Treated or untreated: Non-inoculated(3-replications)