title: Transcriptomic and proteomic analyses of seasonal photoperiodism in the pea aphid

status: Public on Apr 25 2009

city: Le Rheu

first: Denis

last: TAGU

department: UMR 1099 BiO3P

institute: INRA Rennes

summary: Aphid adaptation to harsh winter conditions is illustrated by an alternation of their reproductive mode. Aphids detect photoperiod shortening by sensing the length of the night and switch from viviparous parthenogenesis in spring and summer, to oviparous sexual reproduction in autumn. The photoperiodic signal is transduced from the head to the reproductive tract to change the fate of the future oocytes from mitotic diploid embryogenesis to haploid formation of gametes. Because of viviparous parthenogenesis, the whole process takes place in three consecutive generations. To understand the molecular basis of the switch in the reproductive mode, a transcriptomic approach was used to detect significantly regulated transcripts in the heads of the pea aphid Acyrthosiphon pisum. The transcriptomic profiles of the heads of the first generation were slightly affected by photoperiod shortening. This suggests that trans-generation signaling does not occur between the grand-mothers and the viviparous embryos they contain. By analogy, many of the genes regulated in the heads of the second generation are implicated in visual functions, photoreception and cuticle structure. The modification of the cuticle could decrease the storage of N-β-alanyldopamine and provoke an increase in free dopamine concentration. Based in results in Drosophila, modification of the insulin pathway could cause a decrease of juvenile hormones in short-day reared aphids.

overall_design: Biological material for microarray experiments was prepared under two dayly photoperiodic regimes both at constant temperature of 18°C: i) “Short Night” (SN) at 16h of light and ii) “Long Night” (LN) at 12h of light to induce the production of sexual morphs. To initiate the experiment, two groups of 105 L3 larvae were placed either under SN or LN condition. This corresponds to generation G0. At the middle of the photophase, 25 individual were frozen when they had reached both the L4 and the wingless adult (WA) stages, in the two photoperiod conditions. The 55 remaining WA individuals (still divided in two groups) were left on 55 plants to lay their offspring: one larva of the 1st stage (L1) was kept per WA. This larva was selected among the 20 first born larvae. This is the generation G1. At the middle of the photophase, 25 individual were frozen when they had reached both the L2 and the L4 stages, in the two photoperiodic conditions. Thus, 25 individuals from 4 different stages (L4-G0, WA-G0, L2-G1 and L4-G1) were collected in the two photoperiod conditions with 3 biological replicates, forming the 24 samples used for microarray experiments. RNAs from heads of aphids from the two photoperiodic conditions were hybridized one against the other for each stage with a dye-swap.The experimental design is thus 24 arrays which corresponds to the described samples of that series.

first: Gaël

last: LE TRIONNAIRE

first: Frédéric

last: FRANCIS

first: Stéphanie

last: JAUBERT

first: Joël

last: BONHOMME

first: Eric

last: DE PAUW

first: Jean-Pierre

last: GAUTHIER

last: HAUBRUGE

first: Fabrice

last: LEGEAI

first: Nathalie

last: PRUNIER-LETERME

first: Jean-Christophe

last: SIMON

first: Sylvie

last: TANGUY

first: Denus


status: Public on Apr 16 2009

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

country: USA

institute: Celgene Corporation

summary: Expression of known and predicted genes in tissues of Tetraodon nigroviridis (pufferfish) pooled from multiple healthy individuals.

overall_design:
Two-colour experiments with two different tissues hybridized to each array. Each tissue is arrayed in replicate with dye swaps.
Tissues: Beak, Brain, Calvaria, Connective tissue, Eye, Fin, Gallbladder, Gill, Heart, Intestine, Kidney, Liver, Ovary, Red muscle, Skin, Spleen, Stomach, Swimbladder, Testis, White muscle

first: Gerald

last: Quon

first: Gordon

last: Chua

first: Tomas

last: Babak

first: Miles

last: Trochesset

first: Ralph

middle: A

last: Zirngibl

first: Jane

last: Aubin

first: Michael

last: Ratcliffe

first: Andrew

last: Wilde

last: Brudno

first: Quaid

middle: D

last: Morris

first: Timothy

middle: R

last: Hughes


title: The time-series gene expression data in PMA stimulated THP-1

status: Public on Apr 19 2009

city: Yokohama

first: Piero

last: Carninci

department: Center for Life Science Technologies

country: Japan

institute: RIKEN

summary: (1) qPCR Gene Expression Data    The THP-1 cell line was sub-cloned and one clone (#5) was selected for its ability to differentiate relatively homogeneously in response to phorbol 12-myristate-13-acetate (PMA) (Sigma). THP-1.5 was used for all subsequent experiments. THP-1.5 cells were cultured in RPMI, 10% FBS, Penicillin/Streptomycin, 10mM HEPES, 1mM Sodium Pyruvate, 50uM 2-Mercaptoethanol. THP-1.5 were treated with 30ng/ml PMA over a time-course of 96h. Total cell lysates were harvested in TRIzol reagent at 1, 2, 4, 6, 12, 24, 48, 72, 96 hours, including an undifferentiated control. Undifferentiated cells were harvested in TRIzol reagent at the beginning of the LPS time-course. One biological replicate was prepared for each time point. Total RNA was purified from TRIzol lysates according to manufacturer’s instructions. Genespecific primer pairs were designed using Primer3 software, with an optimal primer size of 20 bases, amplification size of 140bp, and annealing temperature of 60°C. Primer sequences were designed for 2,396 candidate genes including four potential controls: GAPDH, beta actin (ACTB), beta-2-microglobulin (B2M), phosphoglycerate kinase 1 (PGK1). The RNA samples were reverse transcribed to produce cDNA and then subjected to quantitative PCR using SYBR Green (Molecular Probes) using the ABI Prism 7900HT system (Applied Biosystems, Foster City, CA, USA) with a 384-well amplification plate; genes for each sample were assayed in triplicate. Reactions were carried out in 20μL volumes in 384-well plates; each reaction contained: 0.5 U of HotStar Taq DNA polymerase (Qiagen) and the manufacturer’s 1× amplification buffer adjusted to a final concentration of 1mM MgCl2, 160μM dNTPs, 1/38000 SYBR Green I (Molecular Probes), 7% DMSO, 0.4% ROX Reference Dye (Invitrogen), 300 nM of each primer (forward and reverse), and 2μL of 40-fold diluted first-strand cDNA synthesis reaction mixture (12.5ng total RNA equivalent). Polymerase activation at 95ºC for 15 min was followed by 40 cycles of 15 s at 94ºC, 30 s at 60ºC, and 30 s at 72ºC. The dissociation curve analysis, which evaluates each PCR product to be amplified from single cDNA, was carried out in accordance with the manufacturer’s protocol. Expression levels were reported as Ct values. The large number of genes assayed and the replicates measures required that samples be distributed across multiple amplification plates, with an average of twelve plates per sample. Because it was envisioned that GAPDH would serve as a single-gene normalization control, this gene was included on each plate. All primer pairs were replicated in triplicates. Raw qPCR expression measures were quantified using Applied Biosystems SDS software and reported as Ct values. The Ct value represents the number of cycles or rounds of amplification required for the fluorescence of a gene or primer pair to surpass an arbitrary threshold. The magnitude of the Ct value is inversely proportional to the expression level so that a gene expressed at a high level will have a low Ct value and vice versa. Replicate Ct values were combined by averaging, with additional quality control constraints imposed by a standard filtering method developed by the RIKEN group for the preprocessing of their qPCR data. Briefly this method entails:   1.  Sort the triplicate Ct values in ascending order: Ct1, Ct2, Ct3. Calculate differences between consecutive Ct values: difference1 = Ct2 – Ct1 and difference2 = Ct3 – Ct2.    2.  Four regions are defined (where Region4 overrides the other regions):  Region1: difference ≦ 0.2, Region2: 0.2 < difference ≦ 1.0, Region3: 1.0 < difference, Region4: one of the Ct values in the difference calculation is 40 If difference1 and difference2 fall in the same region, then the three replicate Ct values are averaged to give a final representative measure. If difference1 and difference2 are in different regions, then the two replicate Ct values that are in the small number region are averaged instead. This particular filtering method is specific to the data set we used here and does not represent a part of the normalization procedure itself; Alternate methods of filtering can be applied if appropriate prior to normalization. Moreover while the presentation in this manuscript has used Ct values as an example, any measure of transcript abundance, including those corrected for primer efficiency can be used as input to our data-driven methods.   (2) Quantile Normalization Algorithm  Quantile normalization proceeds in two stages. First, if samples are distributed across multiple plates, normalization is applied to all of the genes assayed for each sample to remove plate-to-plate effects by enforcing the same quantile distribution on each plate. Then, an overall quantile normalization is applied between samples, assuring that each sample has the same distribution of expression values as all of the other samples to be compared. A similar approach using quantile ormalization has been previously described in the context of microarray normalization. Briefly, our method entails the following steps:      i) qPCR data from a single RNA sample are stored in a matrix M of dimension k (maximum number of genes or primer pairs on a plate) rows by p (number of plates) columns. Plates with differing numbers of genes are made equivalent by padded plates with missing values to constrain M to a rectangular structure.    ii) Each column is sorted into ascending order and stored in matrix M’. The sorted columns correspond to the quantile distribution of each plate. The missing values are placed at the end of each ordered column. All calculations in quantile normalization are performed on non-missing values.    iii) The average quantile distribution is calculated by taking the average of each row in M’. Each column in M’ is replaced by this average quantile distribution and rearranged to have the same ordering as the original row order in M. This gives the within-sample normalized data from one RNA sample.    iv) Steps analogous to 1 – 3 are repeated for each sample. Between-sample normalization is performed by storing the within-normalized data as a new matrix N of dimension k (total number of genes, in our example k = 2,396) rows by n (number of samples) columns. Steps 2 and 3 are then applied to this matrix.  (3) Rank-Invariant Set Normalization Algorithm  We describe an extension of this method for use on qPCR data with any number of experimental conditions or samples in which we identify a set of stably-expressed genes from within the measured expression data and then use these to adjust expression between samples. Briefly,    i) qPCR data from all samples are stored in matrix R of dimension g (total number of genes or primer pairs used for all plates) rows by s (total number of samples).     ii) We first select gene sets that are rank-invariant across a single sample compared to a common reference. The reference may be chosen in a variety of ways, depending on the experimental design and aims of the experiment. As described in Tseng et al., the reference may be designated as a particular sample from the experiment (e.g. time zero in a time course experiment), the average or median of all samples, or selecting the sample which is closest to the average or median of all samples. Genes are considered to be rank-invariant if they retain their ordering or rank with respect to expression across the experimental sample versus the common reference sample. We collect sets of rank-invariant genes for all of the s pairwise comparisons, relative to a common reference. We take the intersection of all s sets to obtain the final set of rank-invariant genes that is used for normalization.    iii) Let αj represent the average expression value of the rank-invariant genes in sample j. (α1, …, αs) then represents the vector of rank-invariant average expression values for all conditions 1 to s   iv) We calculate the scale f

overall_design: The THP-1 cell line was sub-cloned and one clone (#5) was selected for its ability to differentiate relatively homogeneously in response to phorbol 12-myristate-13-acetate (PMA) (Sigma). THP-1.5 was used for all subsequent experiments. THP-1.5 cells were cultured in RPMI, 10% FBS, Penicillin/Streptomycin, 10mM HEPES, 1mM Sodium Pyruvate, 50uM 2-Mercaptoethanol. THP-1.5 were treated with 30ng/ml PMA over a time-course of 96h. Total cell lysates were harvested in TRIzol reagent at 1, 2, 4, 6, 12, 24, 48, 72, 96 hours, including an undifferentiated control. Total RNA was purifed from TRIzol lysates according to manufacturer’s instructions. The RNA samples were reverse transcribed to produce cDNA and then subjected to quantitative PCR using SYBR Green (Molecular Probes) using the ABI Prism 7900HT system (Applied Biosystems, Foster City, CA,USA) with a 384-well amplification plate; genes for each sample were assayed in triplicate.

first: Yoshihide

last: Hayashizaki

first: Jun

last: Kawai

first: Harukazu

last: Suzuki

first: Carsten

last: Daub

first: Atsutaka

last: Kubosaki

first: Takahiro

first: Yasumasa

last: Kimura

first: Kayoko

last: Murakami

first: Fumi

last: Hori

first: David

last: Hume

first: Katharine

last: Irvine

first: Kate

last: Schroder

first: John

last: Quackenbush

first: Jess

last: Mar


first: Esther

last: Chan

summary: Expression of known and predicted genes in tissues of Gallus gallus (chicken) pooled from multiple healthy individuals.

overall_design:
Two-colour experiments with two different tissues hybridized to each array. Each tissue is arrayed in replicate with dye swaps.
Tissues: Bursa of Fabricius, Cerebellum, Cerebral cortex, Eye, Femur with bone marrow, Gallbladder, Gizzard, Heart, Intestine, Kidney, Liver, Lung, Muscle, Ovary, Oviduct, Skin, Spleen, Stomach, Testis, Thymus

first: Gerald

last: Quon

first: Gordon

last: Chua

first: Tomas

last: Babak

first: Miles

last: Trochesset

first: Ralph

last: Zirngibl

first: Jane

last: Aubin

first: Michael

last: Ratcliffe

first: Andrew

last: Wilde

last: Brudno

first: Quaid


title: Expression data from Shewanella oneidensis MR-1 wild-type, Δcrp, and ΔcyaC strains

status: Public on Apr 15 2009

city: Richland

first: Alexander

last: Beliaev

state: WA

address: 902 Battelle Blvd.

institute: Pacific Northwest National Laboratory

type: Expression profiling by genome tiling array

summary: Anaerobic respiration in the metal reducer Shewanella oneidensis MR-1, unlike other bacteria, is regulated by the cAMP receptor protein, CRP. Three putative genes, cyaA, cyaB, and cyaC, predicted to encode class I, class IV, and class III adenylate cyclases respectively, have been identified in the genome sequence of this bacterium. Functional validation through complementation of an E. coli cya mutant confirmed that these genes encode proteins with adenylate cyclase activities. Chromosomal deletion of either cyaA or cyaB did not affect anaerobic respiration with fumarate, DMSO, or Fe(III), whereas the deletion of cyaC caused deficiencies in respiration with DMSO and Fe(III), and to a lesser extent with fumarate. A phenotype similar to that of a crp mutant, which lacks the ability to grow anaerobically with DMSO, fumarate, and Fe(III), was obtained when both cyaA and cyaC were deleted. Microarray analysis of gene expression in the crp and the cyaC mutants revealed the involvement of both genes in the regulation of key respiratory pathways that include DMSO, fumarate, and Fe(III) reduction. Additionally, several genes associated with plasmid replication, flagella biosynthesis, and electron transport, were differentially expressed in the cyaC mutant, but not in the crp mutant. Our results indicated that CyaC plays a major role in regulating anaerobic respiration, and may contribute to additional signaling pathways independent of CRP.

overall_design: To  explore the roles of CyaC and CRP in the regulation of anaerobic respiration in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles of ΔcyaC and Δcrp mutants were compared to those of the wild type. Given the growth deficiencies displayed by Δcrp and ΔcyaC under anaerobic conditions, all strains were cultured in chemostats under O2 limitation. Since both Δcrp and ΔcyaC strains are not impaired in aerobic respiration, oxygen-limited conditions provided the means to maintain equal growth rates (0.06 h-1) among the mutant and wild-type strains thus eliminating the effect of growth on the overall transcriptome profiles. At the same time, while growing aerobically, the cells decreased dissolved O2 concentration in the medium below the detection threshold (DOT≤1%) allowing for the expression of anaerobic respiratory genes. The latter was confirmed by the reduction of fumarate by the wild-type culture which produced stoichiometric amounts of succinate under O2-limited conditions. The optical density (OD600) of the wild type, ΔcyaC, and Δcrp chemostat cultures used for transcriptome profiling was 0.50, 0.45 and 0.40, respectively. All the experiments were carried out in duplicate.

middle: S


title: Cell wall mediated multi-cellular development during cotton fiber elongation

city: East Lansing

first: Jeffrey

last: Landgraf

state: MI

address: 612 Wilson Rd.

department: RTSF

institute: Michigan State University

summary: Transcriptional profiling of cotton fibers during development. Time course at 6 days post anthesis (dpa), 10 dpa, 20 dpa, and 24 dpa. All referenced to 20 dpa.

overall_design: Four time points, three biological replicates with one technical replicate (dye swap) each. All referenced to 20 dpa. 18 arrays total.

first: Candace

middle: H

last: Haigler

first: Bir

last: Singh


title: Comparative analysis of gene expression profiles between four kinds of blastomere at 8-cell stage embryos.

status: Public on Apr 17 2009

city: Toba

first: Lixy

last: Yamada

state: Mie

address: 429-63 Sugashima

department: Graduate School of Science,

institute: Nagoya University

summary: The establishment of body axes and specification of early embryonic cells depend on maternally supplied transcripts and/or proteins, several of which are localized at specific regions of fertilized eggs and early embryos.  The ascidian is known to exhibit a mosaic mode of development, and this mode is largely dependent on localized maternal factors.  Using blastomere isolation, microarray and whole-mount in situ hybridization, the present study of Ciona intestinalis demonstrates that maternal transcripts of a total of 17 genes are localized at the posterior-most region of fertilized eggs and early embryos.  Ten of them are newly identified in the present study, while the remaining seven genes have already been characterized in the previous studies.  In addition, maternal transcripts of two genes, in addition to 14 genes encoded by the mitochondrial genome, showed a mitochondria-like distribution.  Despite the present comprehensive approach, we could not identify maternal transcripts that are clearly localized to the animal-pole side, the vegetal-pole side, the anterior-side or other specific regions of the early embryo.  Therefore, we concluded that the posterior-most localization and mitochondria-like distribution appear to be major specialized patterns of maternal transcripts in the early Ciona embryos.

overall_design: Four kinds of sample. Two series comparison (A4.1+a4.2+b4.2 blastomeres vs B4.1 blastomeres and Animal blastomeres vs Vegetal blastomeres) were examined including dye swap analyses.

first: Kenji

last: Kobayashi

first: Yutaka

last: Satou

first: Nori

last: Satoh


title: Transcriptomic and metabolic responses of Staphylococcus aureus exposed to supra-physiological temperatures

status: Public on Apr 22 2009

city: Geneva

first: Pierre

middle: E

last: Vaudaux

address: 24 rue Micheli-du-Crest

department: Infectious Diseases

country: Switzerland

institute: Geneva University Hospital

summary:
Previous evaluation by different molecular and physiological assays of Staphylococcus aureus (S. aureus) responses to heat shock exposure yielded a still fragmentary view of the mechanisms determining bacterial survival or death at supra-physiological temperatures. This study analyzed diverse facets of S. aureus heat-shock adjustment by recording global transcriptomic and metabolic responses of bacterial cultures shifted for 10 min from 37oC to a sub-lethal (43oC) or eventually lethal (48oC) temperature. A relevant metabolic model of the combined action of specific stress response mechanisms with more general, energy-regulating metabolic pathways in heat-shocked S. aureus was designed.
While S. aureus cultures shifted to 43oC or left at 37oC showed marginal differences in growth and survival rates, bacterial cultures exposed to 48oC showed a rapid growth arrest followed by a subsequent decline in viable counts. The most substantial heat shock-induced changes at both 43oC and 48oC occurred in transcript levels of HrcA- and CtsR-regulated genes, encoding classical chaperones DnaK and GroESL, and some Hsp100/Clp ATPases components, respectively. Other metabolic pathways up-regulated by S. aureus exposure at 48oC included genes encoding several enzymes coping with oxidative stress, and DNA damage, or/and impaired osmotic balance. Some major components of the pentose phosphate cycle and gluconeogenesis were also up-regulated, which reflected depletion of free glucose by bacterial cultures grown in Mueller-Hinton broth prior to heat shock. In contrast, most purine- and pyrimidine-synthesis pathway components and amino acyl-tRNA synthetases were down-regulated at 48oC, as well as arginine deiminase and major fermentative pathway components, such as alcohol, lactate and formate dehydrogenases. Despite the heat-induced, increased requirements for ATP-dependent macromolecular repair mechanisms combined with declining energy sources, intracellular ATP levels remained remarkably constant during heat shock.
In conclusion, the sequential loss of replication and viability at 48oC cannot be explained by significant reductions in intracellular ATP levels, but may reflect ATP rerouting for macromolecular repair mechanisms and cell survival. Our metabolic model also suggests that heat-stressed S. aureus should down-regulate the production of potential, DNA-damaging reactive oxygen species that might result from electron transport-generated ATP, involving excessive levels of free heavy metals, in particular iron.

Keywords: Staphylococcus aureus; heat shock; stress responses; transcriptomic profiling; physiological adjustment

overall_design: Comparative transcriptomic profiling of late log phase cultures of S. aureus ISP794, exposed to 43°C vs. 37°C, or  48°C vs. 37°C. We performed  triplicate measurements from independently grown cultures for each heat stress condition.

first: Benedicte

last: Fleury

first: William

middle: L

last: Kelley

first: Daniel

middle: P

last: Lew

first: Friedrich

last: Gotz

first: Richard

last: Proctor


title: Binding data for nine transcription factors for S. cerevisiae salt response

city: Woodbridge

first: Can

last: Bruce

state: CT

address: 5 Chestnut Lane

institute: Sciomix

type: Genome binding/occupancy profiling by genome tiling array

summary: Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets.  Recently, considerable effort has been made to analyze the binding of relevant factors to the suite of targets they regulate, thereby generating a regulatory circuit map.  However, for most studies the dynamics of binding have not been analyzed and thus the temporal order of events and mechanisms by which this occur are poorly understood.  We have globally analyzed in detail the temporal order of binding of several key factors involved in the salt response of yeast to their target genes.  Analysis of Yap4 and Sko1 binding to their target genes revealed multiple classes of binding patterns to target genes: 1) constant binding (Yap4 and Sko1 Class 1), 2) rapid induction (Yap4 and Sko1 Class 2) 3) slow induction (Yap4 Class 3) and 4) transient induction (Sko1 Class 3, Yap4 minor binding Class 4). These results demonstrate that individual transcription factors can have multiple binding patterns and help define the different types of temporal binding patterns used in eukaryotic gene regulation. To investigate these binding patterns further, we also analyzed the binding of seven other key transcription factors implicated in osmotic regulation, including Hot1, Msn1, Msn2, Msn4, Skn7 and Yap6, and found significant coassociation among the different factors at their gene targets.  Moreover, the binding of several key factors was correlated with distinct classes of Yap4 and Sko1 binding patterns and with distinct types of genes.  Correlation of each class with gene expression studies revealed association of Yap4, Sko1 and other transcription factor binding patterns with different gene expression patterns. The integration and analysis of binding and expression information reveals a complex dynamic and hierarchical circuit in which specific combinations of transcription factors target distinct sets of genes at discrete times to coordinate a rapid and important biological response.

overall_design: Yeast was grown in minimal medium to mid-log phase, then salt concentration was raised to 0.6M for various time periods before harvesting. Chromatin from a strain containing myc-labeled transcription factor and from a control strain were processed for chromatin immunoprecipitation, and hybridized to a chromosome-tiling microarray. Yap4 and Sko1 time courses data were normalized across time points using calibration curves derived from ChIP-qPCR data for various chromosomal locations. These calibration data can be obtained from http://archive.gersteinlab.org/proj/yeast_salt/. The same Web site also has the processed form of the data as it was used in the analysis reported in Ni, Bruce et al, (2009, Genes & Development).

first: Ni

last: Li

first: Christopher

last: Hart

first: Justine

last: Leigh-Bell

last: Gelperin

first: Lara

last: Umanski

first: Mark

middle: B

last: Gerstein

first: Michael

last: Snyder


title: C. elegans genomic response to Konza Prairie Soil bacterial environment

status: Public on May 02 2009

city: Manhattan

first: Joseph

last: Coolon

state: KS

address: 264 Chalmers Hall

department: Biology

institute: Kansas State University

summary: Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie.  We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure.  Here we have used transcriptional profiling to identify candidate genes involved in the interaction  of nematodes and bacteria in nature.

overall_design:
Here we have performed 36 microarrays and because channels were analyzed separately we have uploaded channels separately.  We used six biological replicates of C. elegans grown in four bacterial environments (E. coli OP50, Micrococcus luteus, Bacillus megaterium, and Pseudomonas sp.).  For each of those biological replicates we have performed three technical replicates because we made all six pair-wise comparisons amoungst the four bacterial environments.  Dye swaps were performed.

>> Biological replicates (technical replicates) <<

Micrococcus luteus 1 (GSM399039,GSM399094,GSM399119)
Micrococcus luteus 2 (GSM399426,GSM399431,GSM399459)
Micrococcus luteus 3 (GSM399467,GSM399482,GSM399486)
Micrococcus luteus 4 (GSM399489,GSM399493,GSM399500)
Micrococcus luteus 5 (GSM399514,GSM399533,GSM399534)
Micrococcus luteus 6 (GSM399539,GSM399544,GSM399547)

E. coli OP50 1 (GSM399108,GSM399118,GSM399125)
E. coli OP50 2 (GSM399427,GSM399428,GSM399465)
E. coli OP50 3 (GSM399480,GSM399485,GSM399487)
E. coli OP50 4 (GSM399490,GSM399492,GSM399495)
E. coli OP50 5 (GSM399510,GSM399513,GSM399535)
E. coli OP50 6 (GSM399541,GSM399542,GSM399546)

Bacillus megaterium 1 (GSM399089,GSM399097,GSM399123)
Bacillus megaterium 2 (GSM399429,GSM399437,GSM399458)
Bacillus megaterium 3 (GSM399468,GSM399479,GSM399484)
Bacillus megaterium 4 (GSM399496,GSM399498,GSM399505)
Bacillus megaterium 5 (GSM399512,GSM399531,GSM399536)
Bacillus megaterium 6 (GSM399538,GSM399543,GSM399549)

Pseudomonas sp. 1 (GSM399029,GSM399082,GSM399113)
Pseudomonas sp. 2 (GSM399432,GSM399457,GSM399464)
Pseudomonas sp. 3 (GSM399481,GSM399483,GSM399488)
Pseudomonas sp. 4 (GSM399491,GSM399494,GSM399509)
Pseudomonas sp. 5 (GSM399511,GSM399532,GSM399537)
Pseudomonas sp. 6 (GSM399540,GSM399545,GSM399548)

first: Bryanua

middle: C

last: Carr

first: Kenneth

last: Jones

first: Timothy

last: Todd

last: Herman


title: Phenotypic profiling of adaptation to oxidative stress

status: Public on Apr 23 2009

city: La Jolla

first: Ryan

last: Kelley

state: CA

address: 9500 Gilman Drive

department: Bioinformatics

institute: UCSD

summary: Caloric restriction extends lifespan, an effect once thought to involve attenuation of reactive oxygen species (ROS) generated by aerobic metabolism. However, recent evidence suggests that caloric restriction may in fact raise ROS levels, which in turn provides protection from acute doses of oxidant through a process called adaptation. To shed light on the molecular mechanisms of adaptation, we designed a series of genome-wide deletion fitness screens to identify genes involved in adaptation to hydrogen peroxide.

overall_design: We designed a series of yeast genome-wide phenotyping experiments using the publicly available pool of 4,831 viable single-gene deletion strains. Each strain in the pool incorporates a pair of unique oligonucleotide barcode tags, which allow the relative growth rates of all strains to be tracked in competitive growth experiments by hybridization of pooled genomic DNA to a barcode microarray. We elicited adaptation using a protocol consisting of a mild pretreatment of hydrogen peroxide (0.1 mM H2O2 for 45 min) followed by a later high dose (0.4 mM H2O2 for 1 hr). For purposes of comparison, we also conducted an acute protocol which exposed cells to the high dose only (0.4 mM H2O2 for 1 hr). In a first experiment, two identical pools of deletion mutants were treated with the adapted or acute protocol, respectively, and directly compared on a barcode array (with six biological replicates). In a second experiment, a pool subjected to the acute treatment was compared against an untreated pool (with four biological replicates).

middle: M

first: Trey

last: Ideker


title: Methylation changes occurring in early postnatal liver development

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary: Genomic DNA is isolated from C57BL6/J mice at E17.5 and postnatal d21, and we used MCAM to identify genes undergoing methylation change during late fetal to early postnatal mouse liver development.

overall_design: Two-condition experiment, P21 vs. E17.5. Biological replicates: 2 for each condition.

first: Robert

last: Waterland

first: Lanlan

last: Shen


title: Response of Lactococcus lactis to different growth rates

status: Public on Apr 28 2009

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

summary:
The development of transcriptomic tools has allowed exhaustive description of stress responses. These responses always superimpose a general response associated to growth rate decrease and a specific one corresponding to the stress. The exclusive growth rate response can be achieved through chemostat cultivation, enabling all parameters to remain constant except the growth rate.
We analysed metabolic and transcriptomic responses of Lactococcus lactis in continuous cultures at different growth rates ranging from 0.09 to 0.47 h-1. Growth rate was conditioned by isoleucine supply. Although the metabolism was constant and homolactic, a widespread transcriptomic response involving 30 % of the genome was observed. The expression of genes encoding physiological functions associated with biogenesis increased with growth rate (transcription, translation, fatty acid and phospholipids metabolism). Many phages, prophages and transposons related genes were down regulated by growth rate suggesting genome plasticity to be involved in the adaptation to slow growth. The growth rate response was compared to carbon and amino-acid starvation transcriptomic responses, revealing constant and significant involvement of growth rate regulations in these two stressful conditions (overlap 26%).
Although stringent response mechanism is considered as the one governing growth deceleration in bacteria, the rigorous comparison of the two transcriptomic responses clearly indicated the mechanisms are distinct. Moreover it was established that genes positively regulated by growth rate are preferentially located in the vicinity of replication origin while those negatively regulated are mainly encountered at the opposite. This result demonstrates the often neglected relationship between genes expression and their location on chromosome.
Keywords: growth rate impact, continuous cultures

overall_design: Continuous cultivation of Lactococcus lactis IL1403 were carried out on a chemically defined medium and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested at steady state. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 1948 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. Samples corresponding to various growth rates were analyzed simultaneously and 3 independent repetitions were performed.

first: Dressaire

last: Clémentine

first: Redon

last: Emma

first: Loubière

last: Pascal

first: Cocaign-Bousquet

last: Muriel


title: Expression data from synchronized L4 C. elegans during starvation

city: Seoul

first: Hyunsun

last: Jo

address: San 56-1, Sillim-Dong, Kwanak-Gu

country: South Korea

institute: Seoul National University

summary: The endoplasmic reticulum (ER) is an organelle associated with lipid metabolism. However, the involvement of the ER in nutritional status-dependent energy homeostasis is largely unknown. The results of this study demonstrate that IRE-1, an ER protein known to be involved in the unfolded protein response, and HSP-4, an ER chaperone, regulate expression of the novel fasting-induced lipases FIL-1 and FIL-2, which induce fat granule hydrolysis upon fasting in C. elegans. RNAi  and ectopic expression experiments demostrated that FIL-1 and FIL-2 are both necessary and sufficient for fasting-induced fat granule breakdown. Failure of ire-1 and hsp-4 mutant animals to hydrolyze fat granules during starvation impaired their motility, which was rescued by glucose supplementation of their media, implicating the importance of ire-1/hsp-4-dependent lipolysis for energy supply from stored fat during fasting. Taken together, these data suggest that the ER-resident proteins IRE-1 and HSP-4 are key nutritional sensors that modulate expression of inducible lipases to maintain whole-body energy homeostasis in C. elegans.

overall_design: Synchronized L4 worms were divided into well-fed and 6 hours fasted samples for RNA extraction and hybridization on an Agilent microarray.

first: Jiwon

last: Shim

first: Junho

last: Lee

first: Jae

last: Kim


title: A C. elegans LSD1 Demethylase Contributes to Germline Immortality by Reprogramming Epigenetic Memory

city: Atlanta

first: David

middle: John

last: Katz

state: GA

address: Rollins Bldg 1510 Clifton Rd

institute: Emory University

summary: Microarray-based expression profiling of mixed stage populations taken from generation 1,13 and 26 spr-5 mutant animals as well as wild-type animals reveals a large class of spermatogenesis-expressed genes whose expression coordinately increased from generations 1 to 13 and then decreased from generations 13 to 26 in spr-5(by101) mutants. These results suggest that a failure to reset spermatogenesis acquired H3K4me2 may result in the progressive sterility that is observed in spr-5 mutants.

overall_design: 8ug of total RNA was hybridized pair-wise, along with a dye flip, from N2 (wild-type) f1 and spr-5(by101) mutant f1, f13 and f26, for a total of 12 arrays. RNA was labelled with the Genisphere Array350 system.

middle: J

first: Thomas

last: Edwards

first: Valerie

last: Reinke

first: William

middle: G

last: Kelly


title: Phenotype and expression profile of S. erythraea rifampicin-resistant (rif) mutants affected in erythromycin production

status: Public on Apr 12 2009

city: Segrate - Milan

first: Giorgio

last: Corti

address: via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

summary:
In this study we have used the rifampicin selection as a tool to genetically improve the erythromycin producer Saccharopolyspora erythraea. Two rifampicin-resistant (rif) mutants, rif1 and rif6, have been characterized in more detail. With respect to the parental strain NRRL2338, rif1 (harboring the missense S444F) exhibited higher respiratory performance and final erythromycin yields; in contrast, rif6 (harboring the missense Q426R) was slow-growing, developmental-defective and severely impaired in erythromycin production. The results of genome-wide analysis of expression profiles using DNA micro-arrays demonstrated that these mutations deeply changed the transcriptional profile of S. erythraea with marked regional distribution.

Keywords: mutants versus wild type comparison in a time course experiment

overall_design: Total of 12 Samples

first: P

last: Alifano

first: C

last: Peano

first: G

first: S

last: Bicciato

last: De Bellis


title: Multisampled Lethal Metastatic Prostate Cancer Copy Number Analysis

city: Baltimore

first: George

middle: S.

last: Bova

state: MD

address: 600 N. Wolfe St

department: Pathology

institute: Johns Hopkins University

summary: Many studies have shown that primary prostate cancers are multifocal1-3, and are composed of multiple genetically distinct cancer cell clones4-6. Whether or not multiclonal primary prostate cancers typically give rise to multiclonal or monoclonal prostate cancer metastases is largely unknown, although studies at single chromosomal loci are consistent with the latter. Here we show through a high-resolution genome-wide SNP and copy number survey that most if not all metastatic prostate cancers have monoclonal origins and maintain a unique signature copy number pattern of the parent cancer cell while also accumulating a variable number of separate subclonally sustained changes. We find no relationship between anatomic site of metastasis and genomic copy number change pattern.  Taken together with past animal and cytogenetic studies of metastasis7, and recent single-locus genetic data in prostate and other metastatic cancers8-10, it appears that despite common genomic heterogeneity in primary cancers, most metastatic cancers arise from a single precursor cancer cell.  Methodologically, this study establishes that genomic archeology of multiple anatomically separate metastatic cancers in individuals can be used to define the salient genomic features of a parent cancer clone of proven lethal metastatic phenotype.

overall_design: Purified cancer DNA from frozen metastatic cancer tissue obtained at autopsy studied by Affymetrix Genome-Wide Human SNP (single nucleotide polymorphism) Array 6.0 analysis (Affy6).


title: miRNA expression profiling of stage specific monocyte derived dendritic cell differentiation

city: Los Angeles

first: Sara

middle: Tajyar

last: Hashimi

address: 657 Charles E Young Dr. East

department: MIMG

institute: UCLA

summary: MicroRNAs (miRNAs, miRs) modulate a multitude of cellular events.  Here, we identify functional miRNA-protein networks that regulate human monocyte-derived dendritic cell (MDDC) differentiation. MiRNA profiling revealed stage-specific differential expression of 20 miRNAs during days 1, 3 and 5 of MDDC differentiation. To identify and prioritize miRNA-protein networks for functional validation, we developed a target ranking algorithm that incorporates many features of miRNA regulatory networks.  This system prioritized miR-21, miR-34a, and their cognate targets WNT1 and JAG1 for functional validation. Inhibition of both miR-21 and miR-34a stalled MDDC differentiation, as quantified by DC-SIGN/CD14 expression ratios, showing cooperative involvement of these miRNAs in MDDC differentiation.  We confirmed that the 3’ UTRs of WNT1 and JAG1 were functional targets of these miRNAs and provide evidence that these targets were translationally suppressed.  Significantly, exogenously added Wnt-1 and Jagged-1 also stalled MDDC differentiation, suggesting that miRNA mediated inhibition of endogenous WNT1 and JAG1 expression was important for proper MDDC differentiation. Finally, inhibition of miR-21 and miR-34a, or addition of Wnt-1 and Jagged-1 led to a decrease in endocytic capacity, a key function of immature DCs.  Thus, our novel approach identified and validated some miRNA-protein networks involved in phenotypic and functional MDDC differentiation.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: monocytes were cultured with GM-CSF and IL-4 for the indicated days (0,1, 3, and 5). Each timepoint was repeated in 3 independent donors (donor 1 , 2, and 3).

first: Jennifer

last: Fulcher

first: Margaret

last: Chang

first: Lanny

last: Gov

first: Shuo

last: Wang

first: Benhur


title: Gene expression in cell cycle of Cyanidioschyzon merolae_1

status: Public on May 08 2009

city: Toshima-ku

first: Takayuki

last: Fujiwara

department: Life Science

institute: Rikkyo University

summary:
To analyze mitotic cycle and organelle proliferation cycle, we investigated C.merolae cells across two cell cycles synchronized by light and dark cycles. C.merolae has one nucleus, mitochondria and chloroplast (Kuroiwa et al,1993. Protoplasma). Their division are strictly regulated by cell cycle and can be synchronized by light/dark cycle (Misumi et al,2005. Plant Physiol). These characteristics enable microarray system to analyze the proliferation cycle of not only the nucleus but also organelle.
Keywords: Time course in cell cycle

overall_design: Analysis of C.merolae cells across two cell cycles, a length of 50 hours after onset of synchronizied culture by light/dark cycles. Gene expression examined at 2-hours intervals.

first: Misumi

last: Osami

first: Kousuke

last: Tashiro

first: Keiji

last: Nishida

first: Fumi

last: Yagisawa

first: Yamato

last: Yoshida

first: Toshiyuki

last: Mori

first: Masaki

last: Sakajiri

last: Hashimoto

first: Haruko

last: Kuroiwa

first: Tsuneyoshi


title: Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas

city: Cambridge

first: David

middle: T W

last: Jones

address: Box 231, Level 3 Lab Block, Addenbrooke's Hospital

country: United Kingdom

institute: University of Cambridge

type: Genome variation profiling by genome tiling array

summary:
Pilocytic astrocytomas (PAs), WHO Grade I, are one of the most frequently occurring childhood brain tumors. We have used microarray comparative genomic hybridization (aCGH) to study copy number changes on chromosome 7 in a series of PAs (n=44).
Keywords: Comparative Genomic Hybridization

overall_design: Single hybridization per case. 44 pilocytic astrocytomas WHO grade I were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

first: Sylvia

last: Kocialkowski

first: Lu

last: Liu

first: Danita

last: Pearson

first: Magnus

last: Backlund

first: Koichi

last: Ichimura

first: V

last: Collins


title: Gene expression profiling in equine polysaccharide storage myopathy

status: Public on Apr 08 2009

city: EVRY

first: ERIC

last: BARREY

address: 3bis Christophe Colomb

institute: INSERM-INRA

summary:
Standardized muscular biopsies of the dorsal compartment of the gluteus medius muscle were performed in 7 horses suffering from equine polysaccharide storage myopathy (PSSM) and 6 sound Norman Cob horses .
Gene expression analysis was performed using an equine oligonucleotide microarray which included 384 equine gene probes of the nuclear genome and all the mitochondrial genes.

overall_design: All the samples of PSSM muscles were hybridized against the reference control muscles. This reference was made by pooling together all the mRNA extracted after in vitro transcription from the 6 control muscles of the sound horses. Briefly, the hybridization protocol was adapted from Le Brigand et al. (2006). An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res. 2006 Jul 19;34(12).

first: E

last: Barrey

last: Mucher

first: N

last: Jeansoule

first: O

last: Alibert

first: G

last: Maltere

first: X

last: Gidrol


title: Genetic control of human brain transcript expression in Alzheimer’s disease.

status: Public on Apr 10 2009

city: Miami

first: Amanda

last: Myers

state: FL

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

institute: Miller School of Medicine, University of Miami

summary: We recently surveyed the relationship between the human brain transcriptome and genome in a series of neuropathologically normal postmortem samples. We now have analyzed additional samples with a confirmed pathologic diagnosis of late onset Alzheimer's disease (LOAD, final n=187 controls, 176 cases). Nine percent of the cortical transcripts we analyzed had expression profiles correlated with their genotypes in the combined cohort and approximately 5% of transcripts had SNP-transcript relationships that could distinguish LOAD samples. Two of these transcripts have been previously implicated in LOAD candidate gene SNP-expression screens. This study shows how the relationship between common inherited genetic variants and brain transcript expression can be used in the study of human brain disorders. We suggest that studying the transcriptome as a quantitative endo-phenotype has greater power to find risk SNPs influencing expression than the use of discrete diagnostic categories such as presence or absence of disease. see DOI:10.1016/j.ajhg.2009.03.011 for further details and complete author list.

overall_design: Expression quantitative trait loci study using human brain from 363 cortical samples. Affymetrix 500K chip for genotyping, Illumina ref-seq 8 chip for expression. Genotyping data will be available at dbGAP.

first: Jennifer

last: Webster

first: Raphael

last: Gibbs


title: Arabidopsis transcriptome microarray from virus infected roots. Functional Genomic study in virus-infected plants.

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary:
au07-02_trv - arabidopsis transcriptome microarray from virus infected roots. - mRNA expression profile in virus-infected Arabidopsis. - Arabidopsis miRNA/transcriptome microarray from virus infected roots of plants.

Keywords: normal vs disease comparison

overall_design: 3 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Agnes

last: Yu

first: Cesar

last: Llave

first: Marie-Laure

last: Martin-Magniette


title: An Rtt109-independent role for Vps75 in transcription-associated nucleosome dynamics

status: Public on Apr 11 2009

city: South Mimms

first: Luke

last: Selth

state: Herts.

address: Blanch Lane

institute: Cancer Research UK

summary:
This is the microarray data accompanying the aforementioned manuscript.  Summary: The histone chaperone Vps75 forms a complex with, and stimulates the activity of, the histone acetyltransferase Rtt109. However, Vps75 can also be isolated on its own and might therefore play a role in histone-related cellular processes independently of Rtt109. Using the E-MAP approach, we compared the genetic interaction profiles for VPS75 and RTT109 and found that, whereas deletion of RTT109 behaved like DNA replication/repair mutants, vps75Δ genetically interacted with genes linked to transcriptional regulation.  Further genetic and biochemical experiments indicated an intimate relationship with RNA polymerase II, and chromatin immunoprecipitation showed that Vps75 is recruited to activated genes in an Rtt109-independent manner. Expression microarray analysis identified a limited number of genes whose normal expression depends on VPS75. Interestingly, histone H2B dynamics at some of these genes were consistent with a role for Vps75 as a histone H2A/H2B eviction factor during transcription-associated nucleosome disassembly. Indeed, reconstitution of nucleosome disassembly using the ATP-dependent chromatin remodeler Rsc and Vps75 showed that these proteins can cooperate to remove H2A/H2B dimers from nucleosomes. Together, these results indicate a role for Vps75 in nucleosome dynamics during active transcription, and that this function is likely to be independent of the histone acetyltransferase Rtt109.

Keywords: Array-based; Chip-chip

overall_design: ChIP-chip analysis of the distribution of Vps75 on budding yeast chromosomes. Experiment type: ChIP-chip = Chromatin immunoprecipitation (ChIP) followed by hybridization to a high-density oligonucleotide microarray (chip).    Number of hybridizations performed: 2 ChIP-chip samples and 2 SUPernatant samples for each type of tiling array (whole genome and chromosome VI). Analysis: ChIP samples were normalized against SUPernatant fractions. Quality control: Confirmation of results by duplication of experiments and by hybridization to two different types of Saccharomyces cerevisiae tiling arrays (whole genome and chromosome VI). Also, whole cell extract, SUPernatant, and ChIP fractions were checked by Western blotting.

middle: A

first: Yahli

last: Lorch

first: Maria

middle: T

last: Ocampo-Hafalla

first: Richard

last: Mitter

first: Michael

last: Shales

first: Nevan

last: Krogan

first: Roger

last: Kornberg

first: Jesper

middle: Q

last: Svejstrup


title: Arabidopsis transcriptome microarray from virus infected plants. Functional Genomic study in virus-infected plants.

summary:
au07-02_trv - arabidopsis transcriptome microarray from virus infected plants. - mRNA expression profile in virus-infected Arabidopsis. - Arabidopsis transcriptome microarray from virus infected plants.

Keywords: normal vs disease comparison


title: Gene expressional change along crypt-villus in rats jejunum

status: Public on Apr 05 2009

city: Shizuoka

first: Toshinao

last: Goda

address: 52-1 Yada, suruga-ku

department: Department of Nutrition

institute: University of Shizuoka

summary: Transcriptional profiling of jejunal gene expression during the differentiation from crypt to villus cells in rats, using cryostat sections of the villus-crypt columns.

overall_design: Total RNA were extracted from each samples (Crypt part, Middle of villus part and Top of villus part), which were separated along the crypt-villus columns of rats jejunum by cryostat technique. In this study, we compared with the gene expression in different part of rats jejunum along the crypt-villus columns. Crypt vs. Middle of villus vs. Top of villus.

first: Takuji

last: Suzuki

first: Kazuki

last: Mochizuki


title: Mutational analysis of progesterone receptor delineates different sets of regulated genes

status: Public on Apr 27 2009

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

summary: Steroid hormone receptors act directly in the nucleus over the chromatin organization and transcriptional activity of several cellular promoters. On the other hand, they have an indirect effect on cytoplasmic signal transduction pathways, including MAPK, impacting ultimately on gene expression. We are interested on distinguishing between direct effects of progesterone receptor (PR) and those mediated by signal transduction pathways on transcription of hormone-responsive genes and cell proliferation. For this, we have stably expressed in a PR-negative breast cancer cell line, tagged forms of the PR isoform B mutated at regions involved either in DNA binding (DBD), or in its ability to interact with estrogen receptor and activate the c-Src/MAPK/Erk/Msk cascade (ERID). Both mutants impair PR-mediated activation of a well-understood model promoter in response to progestin, as well as hormone-induced cell proliferation. Additional mutants affecting transactivation activity of PR (AF2) or a Zn-finger implicated in dimerization (D-box) have also been tested. Microarrays and gene expression experiments in these cell lines define the subsets of hormone-responsive genes regulated by the different modes of action of PRB, as well as genes where the nuclear and nongenomic pathways of PRB cooperate. Correlation between CCND1 expression in the different PR mutants expressing cell lines and their ability to support hormone-induced cell proliferation, confirms CCND1 as a key controller gene.

overall_design: A customized human cDNA microarray containing 826 genes of interest in breast cancer or steroid hormone regulation was used to identify subsets of genes that retain response to progestin in cells expressing defective PRB variants. Previous kinetic experiments performed with T47D cells on this array platform have shown that at 6 h of R5020 treatment, an extensive number of genes change its expression, being a compromise between rapid and long-term effects of this hormone on gene expression (unpublished results). TYML cells containing the empty vector, WT PRB, AF2, DBD and ERID, and T47D parental cells were serum-starved for 24 h and hormone (10 nM R5020) or vehicle-treated for 6 h. Cells were collected and RNA was extracted for microarray hybridization.

first: Ignacio

last: Quiles

first: Albert

last: Jordan

first: Belen

last: Minana

first: Cecilia

last: Ballare

first: Miguel

last: Beato

first: Lluis

last: Millan-Ariño

first: Alicia

last: Subtil


title: Human Cell Toxicogenomic Analysis of Bromoacetic Acid: A Regulated Drinking Water Disinfection By-product

city: Urbana

last: Plewa

state: IL

address: 1101 W Peabody Dr

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

summary: In this study we linked the biological end point of genomic DNA damage from our quantitative, comparative disinfection by-product (DBP) database, with toxicogenomic analysis using a Super Array RT2 Profiler™ PCR Array containing primers for 84 genes related to human DNA damage and repair and  84 genes whose expression level is indicative of stress and toxicity.

overall_design: We used a non-transformed, normal, fetal human small intestinal epithelial cell line (FHs 74 Int), along with PCR arrays, to measure the modulation of gene expression after exposure to the regulated DBP bromoacetic acid (BAA). Human cells were exposed to 60 µM BAA for either 30 min or 4 h to measure early and late gene responses using the Superarray DNA damage signaling APHS-029B and the Human Stress & Toxicity PathwayFinder PCR Array PAHS-003A.

first: Mark

last: Muellner

first: Matthew

last: Hudson

first: Matias

middle: S

last: Attene-Ramos

first: Elizabeth

middle: D

last: Wagner


title: DNA methylation status of CpG islands in normal and atherosclerotic human arteries

status: Public on Apr 04 2009

city: COPENHAGEN

first: Silvio

last: Zaina

address: Blegdamsvej 9

department: Clinical Biochemistry

country: Denmark

institute: Rigshospitalet

type: Methylation profiling by genome tiling array

summary: Abnormal epigenetic gene regulation may play a pivotal role in atherogenesis. In particular, global DNA hypomethylation potentially leading to proatherogenic gene expression, occurs in atherosclerotic lesions in humans and animal models. In order to identify genomic sequences targeted for DNA hypomethylation in atherosclerosis, we analysed the methylation status of CpG islands (CGIs) in 45 human arteries with advanced atherosclerotic lesions and 16 normal counterparts by a microarray approach. Methylation data for 10,367 CGIs revealed that a subset (1.5%) of such sequences was hypermethylated in normal arteries, in accordance with data previously obtained in peripheral blood cells. Ninety-four per cent of this CGI subset was demethylated in atherosclerotic tissue, while only 17 of normally hypomethylated CGIs was hypermethylated in diseased tissue. A functional classification of genes physically associated with differentially methylated CGIs revealed a bias towards transcription factors (42%). The latter include HOX members, NOTCH1 and FOXP1, which are known to regulate angiogenesis, dedifferentiation, cell migration and macrophage function. The methylation status of selected CGIs was validated in further 10 subjects for either group. Expression patterns of these factors were compatible with the observed differential methylation. Our data suggest that one of the molecular changes associated with aberrant DNA methylation in advanced atherosclerosis is the regulation of critical transcription factor genes for the induction of a proatherogenic cellular phenotype.

overall_design: Two-condition experiment, i.e. normal vs. atherosclerotic arteries. 16 and 45 normal and atherosclerotic samples, respectively, were pooled and used to interrogate CpG island arrays in triplicate, for a total of six arrays. Each array was co-hybridized with untreated DNA (reference) and hypermethylated DNA obtained by biochemical filtration.

first: Silvia

last: Castillo-Díaz

first: María

middle: E

last: Garay-Sevilla

first: Martha

last: Hernández-González


title: Differential gene expression in Ki-RAS and Ha-RAS cell lines.

status: Public on Apr 07 2009

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary:
Comparison of gene expression in Ha-RAS  transformed cells versus untransformed Caco-2.
Comparison of gene expression in Ki-RAS  transformed cells versus untransformed Caco-2.

overall_design:
2 x biological replicates of each RAS isoform vs 2 x control replicates.

Raw non-normalized data analyzed in BeadStudio:
Normalization method = None
Analysis Type = Differential Expression
Error Model = Illumina Custom

first: Tobias

last: Joyce

first: Daniela

last: Cantarella

first: Claudio

last: Isella

first: Alexander

last: Pintzas


title: Mycobacterium tuberculosis clinical isolates in China: extensively drug-resistant tuberculosis vs drug sensitive one

city: Beijing

first: Zhaogang

last: Sun

state: Beijing

address: No. 97, Machang Road, Tongzhou District

department: Microbiology and Immunology

country: China

institute: Beijing Tuberculosis & Thotacic Tumor research Institute

summary: Transcriptional profiling of mycobacterium tuberculosis clinical isolates in China comparing extensively drug-resistant tuberculosis with drug sensitive one.

overall_design: The same condition experiment. The samples were from the different drug-resistant strains. Only one replicate.

first: Xuxia

last: Zhang


title: human primary monocytes: Control vs. oxLDL(oxidized low density lipoprotein)-stimulated 6h vs oxLDL-stimulated 12h

status: Public on Apr 03 2009

city: shanghai

first: ting

last: chen

address: kongjiang road 1665

institute: shanghaixinhua hospital

summary: total RNA profiling of human primary monocytes comparing control untreated oxLDL cells with oxLDL cells for different time (6h and 12h),  The latter makes monocytes to macrophage and foam cells.

overall_design: Three-condition experiment, human primary monocytes control vs oxLDL stimulated 6h  vs oxLDL stimulated 12h . Biological replicates: 3 control, 3 oxLDL stimulated 6h, 3 oxLDL stimulated 12h, independently grown and harvested. seven replicate per array.

first: Changqian

last: Wang

first: Ting

last: Chen


first: Soubigou-Taconnat

last: Ludivine

summary:
au06-03_tsn_fj - tsn_fj - Root transcriptome of the tsn1 tsn2 double mutant - Comparison of a tsn1 tsn2 double mutant line (A10.9.3- or A13.3.11-) and an isogenic line complemented by TSN2 (A10.9.5) or TSN1 (A13.3.2)

Keywords: gene knock in (transgenic),gene knock out

overall_design: 6 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Fabien

last: Jammes

first: Michele

last: Bianchi

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Ftz and Eve ChIP data

status: Public on Apr 02 2009

city: Chicago

first: Kevin

last: White

address: 400 CLSC

institute: University of Chicago

summary: Genome wide mapping of Ftz and Eve transcription factor binding sites in early Drosophila embryos

overall_design:
Ftz has one replicate and dyes swapping
Eve has two replicates with one dye swap
Mock IPs were used as controls
Slides were hybridized with two color samples, but individual channels were uploaded seperately to GEO

first: Murad

last: Ghanim

first: Sujun

last: Hua

first: Christopher

last: Brown


title: The genomic analysis of erythrocyte microRNA expression in sickle cell diseases

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary:
Background
Since mature erythrocytes are terminally differentiated cells without nuclei and organelles, it is commonly thought that they do not contain nucleic acids. In this study, we have re-examined this issue by analyzing the transcriptome of a purified population of human mature erythrocytes from individuals with normal hemoglobin (HbAA) and homozygous sickle cell disease (HbSS).

Methods and Findings
Using a combination of microarray analysis, real-time RT-PCR and Northern blots, we found that mature erythrocytes, while lacking ribosomal and large-sized RNAs, contain abundant and diverse microRNAs.  MicroRNA expression of erythrocytes was different from that of reticulocytes and leukocytes, and contributed the majority of the microRNA expression in whole blood. When we used microRNA microarrays to analyze erythrocytes from HbAA and HbSS individuals, we noted a dramatic difference in their microRNA expression pattern. We found that miR-320 played an important role for the down-regulation of its target gene, CD71 during reticulocyte terminal differentiation. Further investigation revealed that poor expression of miR-320 in HbSS cells was associated with their defective downregulation CD71 during terminal differentiation.

Conclusions
In summary, we have discovered significant microRNA expression in human mature erythrocytes, which is dramatically altered in HbSS erythrocytes and their defect in terminal differentiation.  Thus, the global analysis of microRNA expression in circulating erythrocytes can provide mechanistic insights into the disease phenotypes of erythrocyte diseases.
Keywords: Sickle cell disease RBC profiling

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The microRNA of purified erythrocytes from 7 normal and 12 HbSS individuals

first: Shao-Yin

first: Yulie

first: Marilyn

last: Telen


title: Differential expression of certain genes during somatic embryogenesis in leaf explants of Cichorium intybus

status: Public on Apr 06 2009

city: Villeneuve d'Ascq

first: Anca

last: Lucau

address: Cité Scientifique

department: Biology

institute: University Lille 1

summary: In Cichorium intybus, macroscopic and histological modifications were identified during in vitro cell reactivation and morphogenesis events. The relationships between these modifications and transcript profiles of genes were investigated. Two chicory genotypes derived from the Hungarian landrace Koospol, were tested: K59 is a responsive genotype (embryogenic), as it undergoes cell de- and re-differentiation that leads to somatic embryogenesis (SE). C15 is an unresponsive genotype (nonembryogenic), unable to express this morphogenetic pattern. Previously studies showed that addition of beta-D-glucosyl Yariv reagent (BGlcY), a synthetic phenyl-glycoside that specifically binds arabinogalactan-proteins (AGPs), to the culture medium blocked somatic embryogenesis in chicory root explants in a concentration-dependent manner with complete inhibition of induction occurring at 250 µM of BGlcY (Chapmann et al. 2000a). A putative AGP (DT212818) encoding gene was previously found significantly over-expressed in the K59 as compared to the C15 and was suggested to be involved in chicory re-differentiation. To better understand the cell reactivation events, a treatment with BGlcY was applied in order to precipitate AGPs in muro and to block the in vitro cell re-differentiation processes. The two different genotypes together with BGlcY represented an original tool to discriminate cell reactivation events from cell fate determination. Microscopy, biochemical and transcriptome analyses showed that in vitro SE in chicory was blocked during BGlcY-treatment but cell reactivation still occurred. Consequently, AGP (DT212818) seems to be only important in cell fate determination leading to SE commitment. Gene expression profiles showed in addition to the AGP, other proteins could play a role in SE determination: 26S proteasome AAA ATPase subunit 6 (RPT6), remorin (REM), metallothionein 1 (MT1), 3-hydroxy-3-methylglutaryl-CoA reductase (HMG-CoA reductase). Cell wall events during BGlcY-treatment were observed and discussed.

overall_design: Gene expression of K59 explants induced (d4) was compared with gene expression of K59 explants without induction (d0). Gene expression of K59 explants induced in the presence of BGlcY (Y+; d4) was next compared with gene expression of K59 explants induced in the absence of BGlcY (Y-; d4). Similar comparisons were made for C15 leaf explants. To link up both genotypes, direct comparison was done between gene expression of K59 explants without induction (d0) and C15 explants without induction (d0). Three biological replicates were used for each analysed condition. Dye labelling for each paired sample was reversed in two subsequent individual hybridizations giving rise to a total of six hybridizations per condition except for the K59_D0_vs_C15_D0 condition.

first: Laurent

last: Laborde

first: Sylvain

last: Legrand

first: Ludovic

last: Huot

first: David

last: Hot

first: Yves

last: Lemoine

first: Simon

last: Hawkins

first: Jean-Louis

last: Hilbert

first: Marie-Christine

last: Quillet

first: Theo

last: Hendriks

first: Anne-Sophie

last: Blervacq


title: miRNA profiling of human adipose stem cells

city: Seoul

first: Kyo Won

last: Lee

address: 108 Pyung-Dong, Jongro-Gu

department: Obsterics & Gynecology

institute: Adult Stem Cell Research Institute

summary: miRNA profiling of undifferentiated and neuro-differentiated adipose-derived stem cells.

overall_design: Adipose-derived stem cells obtained from 4 different donors were divided into 2 groups, undifferentiated "control" group and neurally-differentiated "neuro" group. miRNA of each cells were analyzed using Agilent miRNA microarray.

first: KyoWon

first: SuMan


title: A transcriptomic analysis of super-hybrid rice LYP9 and its parental lines

first: lihuang

last: Zhu

address: Datun Road, Chaoyang District,100101 Beijing China

department: Plant Gene Research Center

institute: The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS)

summary: Using a whole-genome oligonucleotide microarray designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of super hybrid rice LYP9 and its parental cultivar 93-11 and PA64s. We detected 22,266 expressed genes out of 36,926 total gene set collectively from seven tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicle at filling stage. Clustering result showed that expression profiles between F1 and its parental lines were always more similar than that between the two parental lines. Out of the total gene set, 7,078 were shared by all sampled tissues and 3,926 (10.6%) were differentially-expressed genes (DG). As we divided DG into those between the parents (DGPP) and between the hybrid and its parents (DGHP), the comparative results showed that genes in the two categories, Energy metabolism and transport, were enriched in DGHP rather than in DGPP. The majority of genes were identified as additive expression, and non-additive expression only took a minority (0.53%-1.35%) of the total genes. In addition, we correlated the concurrence of DG and yield-related QTL, providing a potential group of genes as heterosis-related.

overall_design: We investigated transcriptome profiles in developing leaves and panicles of super hybrid rice LYP9 and its parental cultivar 93-11 and PA64s for seven tissues, and there are at least three independent replicates for each sample pair.

first: Wei

last: Gang

first: Tao

last: Yong

first: Liu

last: Guozhen

first: Chen

last: Chen

first: Luo

last: Renyuan

first: Xia

last: Hongai

first: Gan

last: Qiang

first: Zeng

last: Haipan

first: Lu

last: Zhike

first: Han

last: Yuning

first: Li

last: Xiaobing

first: Song

last: Guisheng

first: Zhai

last: Hongli

first: Peng

last: Yonggang

last: Dayong

first: Xu

last: Honglin

last: Xiaoli

first: Cao

last: Mengliang

first: Deng

last: Huafeng

first: Yuan

last: Longping

first: Yu

last: Jun

first: Zhu

last: Zhen

last: Lihuang


title: Gene expression of E. coli MG1655 at attachment, colony formation and maturation during biofilm formation

status: Public on Apr 01 2009

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

institute: Hokkaido University

summary:
Gene expression changes during biofilm formation processes were investigated. The gene expression was compared at attachment, colony formation and maturation during biofilm formation. At the same time, the gene expressions were also compared with exponential phase and stationary phase in planktonic cells. The gene expression pattern at attachment and colony formation processes showed similar pattern with those in planktonic exponential phase, and the gene expression pattern at maturation process showed similar pattern with those in planktonic stationary phase. During the maturation process, metabolic activities of the cells in the biofilms decreased, and the genes involved in the anaerobic respiration and efflux pumps were induced. The analysis revealed that gene expression pattern was changed and the physiological states were changed dramatically during maturation process in the biofilms.

Keywords: time course

overall_design: Affymetrix E. coli antisense genome array was used to compare the gene expression among biofilm formation processes (attachment, colony formation and maturation) and planktonic cells (exponential phase and stationary phase). All samples were grown in MOPS minimal media with 0.2% glucose at 37ºC. Biofilms were grown on glass surface in flow cells (1 x 4 x 40 mm), and samples were taken at 2 h, 24 h and 72 h. Planktonic cell were grown for 6 h (exponential phase) and 24 h (stationary phase). Experiments were repeated 3 times, which resulted in 3 replicates of 5 different samples.

first: Asami

last: Taniuchi

first: Thithiwat

last: May

first: Koji

last: Kawata

first: Satoshi

last: Okabe


title: Adaptive differences in gene expression associated with stress tolerance in the soil arthropod Orchesella cincta

city: Amsterdam

first: Dick

last: Roelofs

state: Noord-Holland

address: De Boelelaan 1085

department: Animal Ecology

country: Netherlands

institute: VU University

summary: Field-selected tolerance to heavy metals has been reported for Orchesella cincta (Arthropoda: Collembola) populations occurring at metal-contaminated mining sites. This tolerance is correlated with heritable increase of metal excretion efficiency; less pronounce cadmium induced growth reduction and, over-expression of the metallothionein gene. We applied transcriptomics to determine differential gene expression caused by this abiotic stress in reference and cadmium tolerant populations. Many cDNAs responded to cadmium exposure in a reference population. Significantly fewer clones were cadmium responsive in tolerant animals. Analysis of variance revealed transcripts that interact between cadmium exposure and population. Hierarchical clustering of these clones revealed two major groups. The first one contained cDNAs that were up regulated by cadmium in the reference culture, but non-responsive or down regulated in tolerant animals. This cluster was also characterized by elevated constitutive expression in the tolerant population. Gene ontology analysis revealed that these cDNAs were involved in structural integrity of the cuticle, anti-microbial defense, calcium-channel blocking, neurotransmitter transport, chromatin remodeling and, endoplasmatic vesicle activity. The second group consisted of cDNAs down regulated in reference animals but not responding or slightly up regulated in tolerant animals. Their functions involved carbohydrate metabolic processes, Ca2+ dependent stress signaling, proteolysis and digestion. The reference population showed a strong signature of stress-induced genome-wide perturbation of gene expression, whereas the tolerant animals maintained normal gene expression upon cadmium exposure. We confirmed the micro-evolutionary processes occurring in soil arthropod populations and suggest a major contribution of gene regulation to the evolution of a stress-adapted phenotype.

overall_design:
Orchesella cincta (Collembola) from the laboratory population (LC) at the department of Animal Ecology, Vrije Universiteit Amsterdam were taken as the reference group. This population originated from a pine forest from the reference area (Roggebotzand, the Netherlands, latitude N = 52 º 34’17’’, longitude E = 5 º 47’56’’) that contains on average < 0.5 μg cadmium per gram litter and humus. Tolerant animals were collected from randomly selected litter samples at two areas of the abandoned, but still heavily polluted lead/zinc mining site of Plombières (Belgium, latitude N = 50˚44’03’’, longitude E = 5˚58’02’’): the locations contain an average cadmium concentration between 10 and 52 μg.g-1 soil (Lock et al. 2003; Sterenborg 2003; Van Straalen et al. 1987). To diminish putative environmental effects from the field the animals were reared in a climate room (20°C, 75% humidity, LD 12 h:12 h) in PVC jars on a moist plaster of Paris layer feeding on algae present on twigs for at least three generations before experimental treatment.
Animals were exposed to cadmium (nominal concentration of 112,4 μg cadmium.g-1 dry algae) for 3 days, directly after molting, via algal food. Control groups received the same treatment except that water was spiked into the algal food instead of cadmium solution. The cadmium exposure concentration is two times the no observed effect concentration (NOEC) for reproduction in chronically exposed animals. Total RNA was extracted from times 12 pooled animals per treatment using SV Total RNA Isolation system (Promega) and quantified on a Nanodrop ND-1000 Spectrophotometer (Nanodrop Technologies). Total RNA was visualized on a 1.5% agarose gel to verify its integrity. Each experimental group (pool of 12 animals) was replicated 8 times. Dyes were swapped between biological replicates: 4 Cy-3 labeled replicates and 4 Cy-5 lebeled replicates per experimental group
Microarray experiment was designed in a closed loop Lab culture clean vs Cd, Lab culture Cd vs Tolerant culture Cd, Tolerant culture Cd vs Tolerant culture clean, Tolerant culture clean vs lab culture clean

first: Thierry

last: Janssens

first: Martijn

last: Timmermans

first: Ben

last: Nota

first: Janine

last: Marien

first: Zoltan

last: Bochdanovits

first: Bauke

last: Ylstra

first: Nico

last: van Straalen


title: Evidence for Antisense Transcription Associated with microRNAs in Arabidopsis

city: Los Altos

first: Manoj

last: Samanta

address: 2240 Homestead Court #309

institute: Systemix Institute

type: Non-coding RNA profiling by genome tiling array

summary: Exploring miRNA-related antisense transcription in Arabidopsis through RNA transcript profiling of smRNA pathway-defective mutants on a custom high-resolution oligonucleotide array.

overall_design: Two custom arrays were designed with 15,000 oligonucleotide (25-mer and 36-mer) probes in each array. The probes were selected tiling 200 base upstream and downstream (3 n.t. resolution) of miRNA target sites in Arabidopsis thaliana. The arrays were fabricated by Agilent Technologies, Santa Clara, CA.  The 22 target genes on the arrays were chosen based on the  abundance of associated smRNAs that mapped to the loci, the amplitude of the antisense  transcription signals in published whole genome tiling microarray experiments and a  representative cross section of miRNA families.  For 15k arrays  with 24 selected miRNA targets, a dye swap loop experiment design was utilized with 12  blocks for 7 genotypes on two chip arrays. The details of the experimental design are in  Supplemental Table V of the manuscript. For the hen1-1 versus Ler-0 experiment, a dye swap with two versus  three biological replicates and four array blocks was performed.

first: Qing-Jun

last: Luo

middle: P

first: Fatih

last: Köksa

first: Jaroslav

last: Janda

first: David

middle: W

last: Galbraith

first: Casey

middle: R

last: Richardson

first: Fangqian

last: Ou-Yang

first: Christopher

last: Rock


title: Angiogenesis study of Gd@C82(OH)22 nanoparticle

first: Huan

last: Meng

address: Mailbox 918, Yuquan Road 19

institute: Lab of Bioeffects of Nanosized Materials, Institute of High Energy Physics

summary:
we report a novel nanomedicine (Gd@C82(OH)22 ) effectively inhibit  human breast tumor growth by antiangiogenesis in vivo. To further identify which angiogenic factor(s) were affected on mRNA level, the "RT² Profiler™ PCR Array Mouse Angiogenesis (APMM-024, SuperArray Bioscience Corporation)" was used.
Keywords: nanomedicine, Gd@C82(OH)22, angiogenesis, MCF-7, breast cancer

sample_organism:
Homo sapiens
Mus musculus

overall_design: In the experimental group, the tumor bearing mice were administered intraperitoneally (i.p.) [Gd@C82(OH)22]n saline solution once a day at the dose of 2.5mM/kg, after the tumor tissue implantation into the animal for 7 days, continuing until the mice were sacrificed. The 0.9% saline soultion was used as control. At the end of the experiment, parts of the tumor tissue was collected, and further be analyzed by PCR-array.

first: Gengmei

last: Xing

first: Yuliang

last: Zhao

first: Chengcheng

last: Zhang

first: Zhen

last: Chen

first: Ning

first: Hui

last: Yuan

first: Feng

first: Chunying

first: Hao

last: Lei

first: Xuxia

last: Wang

first: Xingjie

last: Liang


title: Influence of Fatty Acid Diets on Gene Expression in Rat Mammary Epithelial Cells

city: RTP

first: Johannes

middle: M

last: Freudenberg

address: 111 TW Alexander Dr

department: Biostatistics Branch

institute: NIEHS

summary:
Background: This study examines the impact of dietary fatty acids on regulation of gene expression in the mammary epithelial cells before and during puberty.
Methods: The diets primarily consisted of n-9 monounsaturated fatty acids (olive oil), n-6 polyunsaturated fatty acids (safflower), saturated acids (butter), and the reference AIN-93G diet (soy oil).  The dietary regimen mimics the repetitive nature of fatty acid exposure in Western diets. Dietary-induced changes in gene expression were examined in the LCM (Laser Capture Microdissected) captured mammary ductal epithelial cells at day of weaning (21 days) and at the end of puberty (50 days after birth). PCNA immunohistochemistry analysis was used to compare proliferation rates between diets.
Results: Genes differentially expressed between each of the test diets and the reference diet in both age groups were significantly enriched by cell cycle genes.  Some of these genes were involved in the activation of the cell cycle pathway or the G2/M check point pathway. Although there were some differences in the level of differential expression, all diets showed qualitatively same pattern of differential expression compared to the reference diet. Cluster analysis identified an expanded set of cell cycle as well as immunity and sterol metabolism related clusters of differentially expressed genes.
Conclusion: Fatty acid-enriched diets significantly up-regulated proliferation above the normal physiological level at day 50.  The higher cellular proliferation during puberty caused by enriched fatty acid diets pose a potential increase risk of mammary cancer in later life.  The human homologs of 27 of 62 cell cycle cluster of rat genes are included in a human breast cancer cluster of 45 cell cycle related genes further emphasizing the importance of our findings in the rat model.

overall_design: Female, virgin Spraque-Dawley rats were obtained from Taconic Farms (Germantown, NY) at approximately 7 weeks of age and placed on one of 9 pelleted purified diets for one month. After one month of diet exposure, female rats were bred with male Sprague-Dawley rats of approximately 3 months of age. Litters were weighed and monitored throughout gestational period. Pups had access to dam’s milk as well as tap water and food throughout gestation. Pups were weaned at DOL 21 and individually housed with tap water and diets ad libitum. Rats were killed by CO2 asphyxiation and decapitated at the following two ages, DOW (DOL21) and DOL 50 with no other treatments.

first: Mario

last: Medvedovic

first: Robin

last: Gear

first: Robert

last: Bornschein

first: Meenakshi

last: Mistry

first: Holly

last: Hendrix

first: Saikumar

last: Karyala

first: Sue

last: Heffelfinger

first: Deborah

last: Clegg

first: Marshall

last: Anderson


title: Microarray Analysis of Toxicogenomic Effects of peracetic acid on Mycobacterium bovis BCG

status: Public on Mar 31 2009

city: Fort Meade

first: Chantal

middle: Wheko

last: Nde

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

summary:
In the present study, we employed Affymetrix Mycobacterium bovis BCG GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Mycobacterium bovis BCG to Peracetic acid, which involved initial growth inhibition and metabolism.

Keywords: Transcriptome study

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Peracetic acid. We calculated fold change as the ratio between the signal averages of three untreated (control) and three Peracetic acid-treated (experimental) cultures for 0, 10 and 20 min exposures.

first: Freshteh

last: Toghrol

first: William

last: Bentley


title: Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock using microarrays

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

summary:
The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of heat shock on E. coli O157:H7, global transcript levels of strain EDL933 cells shifted from 37°C to 50°C for 15 min were compared to cells left at 37°C using microarrays.
Keywords: Stress Response

overall_design: Twelve independent RNA samples from heat shocked cultures were paired with twelve independent RNA samples from control cultures for hybridization to twelve two-color microarrays. For six arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.

first: Michael

last: Carruthers


title: MicroRNA expression in the newborn mouse cochlea and vestibule

city: Tel Aviv

first: Karen

middle: B

last: Avraham

address: Levanon St.

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: MicroRNAs (miRNAs) inhibit the translation of target mRNAs and affect, directly or indirectly, the expression of a large portion of the protein-coding genes. This study focuses on miRNAs that are expressed in the mouse cochlea and vestibule, the two inner ear compartments. To identify miRNAs that are expressed in the vertebrate developing inner ear, we used miRNA microarrays. Similar miRNA profiles were found in newborn (P0) mouse whole cochleae and vestibules. 105 miRNAs were found to be expressed in the whole P0 cochlea and 114 miRNAs expressed in the whole P0 vestibule with average intensities higher than twice the global background, out of 206 included in the arrays. Only 24 miRNAs were found to have different levels of expression in these whole organs, and these differences were mild (15-40%). The microarray results were intersected with two bioinformatic complementary approaches in order to choose candidate miRNAs that are predicted to be expressed specifically in the inner ear sensory epithelia (see the paper).

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Six small (<40 nt) RNA samples were hybridized with 4 microarrays (to save costs, some of the microarrays were hybridized with two different samples, labeled with different CyDyes – Cy3 and Cy5). Each RNA sample contains small RNAs (<40 nt) pooled from at least 20 newborn cochleae or vestibules, and there are 3 different samples for each organ. However, one of the samples (WT_P0_whole_Cochlea_3_V4) was hybridized with a different array than the other samples (printed from the same probes, but at a different date), and therefore excluded from the analysis described in the paper.

Each microarray contains at least 4 identical spots per each probe that may be considered as technical replicates.
Four of the samples were hybridized in parallel at the same day to two microarrays, and the dyes were swaped:
First microarray: WT_P0_whole_Cochlea_1 (Cy3) [GSM388075] and WT_P0_whole_Vestibule_2 (Cy5) [GSM388635]; second microarray: WT_P0_whole_Cochlea_2 (Cy5) [GSM388633] and WT_P0_whole_Vestibule_1 (Cy3) [GSM388634].
The other 2 samples: WT_P0_whole_Vestibule_3 (Cy3) [GSM388637] and WT_P0_whole_Cochlea_3_V4 (Cy3) [GSM388660] were hybridized to two individual microarrays, at different dates.

The miRNA profile in the cochlear and vestibular samples were compared: the vestibular samples are considered as the “experiment” samples, and the cochlear samples – as “reference”.

Positive control probes (labeled as “control 1” in raw data) were added to RNA samples before labeling. The average of empty and buffer spots was used to calculate the global background of each array, and only miRNAs with an average expression higher than twice the fold of the array global background at least in one of the tissues were considered as expressed.

first: Lilach

last: Friedman

first: Noam

last: Shomron

first: Eran

last: Hornstein


title: Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (Illumina)

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

summary:
Gene expression profiling of 17 fresh frozen chondrosarcoma biopsies using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA). DNA copy number analyses was also performed in these tumors.

Keywords: chondrosarcoma, gene expression profiling, Illumina

overall_design: Samples displaying a tumor content of >70%, as determined from haematoxylin and eosin-stained frozen sections, were analyzed using the Homo sapiens-6 v2 Expression BeadChips (Illumina Inc., San Diego, CA, USA), containing more than 48,000 transcript probes. In samples demonstrating a lower amount of tumor versus normal tissue, macrodissection of tumor material was performed. For each hybridization, 200 ng of total RNA were processed according to the Illumina® TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX, USA), to produce double-stranded cDNA and subsequently to generate biotin-labelled cRNA. Following the manufacturer’s specifications (Illumina), 1.5 µg of the biotin labeled cRNA were hybridized onto the Homo sapiens-6 v2 Expression BeadChips overnight, and subsequently detected with streptavidin-Cy3 using an Illumina® BeadArray Reader. Image analysis was performed using the Illumina® BeadStudio Application Software.

first: KH

last: Hallor

first: J

last: Staaf

first: JVMG

last: Bovée

first: PCW

last: Hogendoorn

first: AM

last: Cleton-Jansen

first: S

last: Knuutila

last: Savola

first: O

last: Brosjö

first: HCF

last: Bauer

first: F

last: VultvonSteyern

first: K

last: Jonsson

first: M

last: Skorpil

first: N

last: Mandahl

last: Mertens


title: Differential gene expression of hair and wool sheep infected with Haemonchus contortus

city: College Station

first: Kathryn

last: MacKinnon

address: 2881 F&B Road

institute: USDA-ARS-SPARC

summary: Our objective was to investigate differences in gene expression between 24 parasite-resistant hair and 24 susceptible wool lambs to determine genetic mechanisms involved in resistance to H. contortus.  Half of the animals of each breed were infected and sacrificed at 3 or 27 days post-infection; the remaining animals were uninfected controls.  Breed differences in abomasum and abomasal lymph node tissue gene expression were assessed using bovine cDNA microarrays.   Over 60 transcripts differed between breeds for each tissue and infection status.  Genes differentially expressed between hair and wool sheep 3 days PI were assessed for gene function and mechanisms for greater immune cell infiltration, abomasal tissue repair, Th17 response, and anticoagulation were present in parasite-resistant hair sheep.  By 27 days PI, hair sheep had greater expression of genes involved in gut motility, inflammatory cytokines, and cell proliferation and differentiation compared to wool sheep.  Changes in these processes indicate Caribbean hair sheep have a stronger inflammatory response when infected with H. contortus which may facilitate the increased parasite resistance observed in these sheep.

overall_design:
This experiment utilized 24 hair and 24 wool lambs.  Wool lambs were from a composite line of 50% Dorset, 25% Rambouillet, and 25% Finnsheep breeding established in 1983.  Hair lambs were derived from St. Croix and Barbados Blackbelly ancestors and were at least 87.5% St. Croix.  Lambs were born in January, raised under field conditions with no effort to prevent parasite infection, and were 4 to 5 months of age at the start of the study.  Equal numbers of female and castrated male lambs were represented, and body weights ranged from 14 to 35 kg.  Levels of parasitemia were not quantified before the start of the study, but signs of clinical haemonchosis had not been observed for any of the experimental animals.  However, to further standardize prior exposure levels, all lambs were drenched weekly with 3,000 infective third-stage larvae (L3) of H. contortus for 4 consecutive weeks before initiation of the study.  The experiment was thus designed to compare breed differences in acquired immunity. Six infected animals of each breed were sacrificed at both 3 and 27 days after infection.  These days were selected to represent the response to larvae (day 3) and adult worms (day 27).  Control animals were sacrificed at day 17, 27, and 38, relative to day 0 of infected animals.
The cDNA from one wool and one hair lamb were hybridized on each slide.  Pairings were made randomly within the same infection status and collection day, resulting in 24 microarrays per tissue.  Direct comparisons were thus made on each array for hair versus wool sheep within each infection status group and day of sampling, and the experimental unit for the study was a hair and wool lamb pair with the same infection status and day of sacrifice.   To minimize effects of dye bias, an equal number of hair and wool sheep samples were labeled with Cy3 and Cy5 dye.  Thus for each collection time, breed, and infection status, random assignment of Cy3-dye labeling for hair lambs and Cy5-dye labeling for wool lambs was made for one half of the samples. The remaining hair sheep samples were labeled with Cy5 dye and remaining wool sheep samples were labeled with Cy3 dye.

first: David

last: Notter

first: Jeanne

last: Burton

first: Anne

last: Zajac


title: THP-1 cells infected with the clinical isolates of extensively drug-resistant and drug sensitive tuberculosis

first: Zhaogang

last: Sun

address: No. 97, Machang Road, Tongzhou District

institute: Beijing Tuberculosis & Thotacic Tumor research Institute

summary: Extensively drug resistant tuberculosis (XDR-TB) showed many different characteristics including the extreme drug resistance versus the drug sensitive clinical isolates (DS-TB), to know better about the reasons we used the tuberculosis host cells named as THP-1  (one kind of the macrophage cells) to be infected by the XDR-TB and DS-TB.DS strain A36 and the XDR strain B42 and was typical and selected by our lab. Then the total RNA of infected or uninfected THP-1 cells was extract and purified for the analysis by the chip (22K Human Genome chip representing the 21522 ORF of human with the oligonucleotide probe of 70 mer from CapitalBio Corp., Beijing, China). The results reflected the different expressed genes involved in apoptosis, secreted cytokines and signal pathway and so on. Those results might indicate the how the XDR-TB cause the pathogenesis.

overall_design: In this study, the well grown THP-1 cells were separated and cultured in three ampoules. Cells in one ampoules were infected with XDR-TB strain of B42. Cells in another ampoules were infected with DS-TB strain of A36, with the cells in the third one were not infected and just treated with PBS as the control. Then the dual channel method was used for detecting the hybridization of B42 vs the control or A36 vs control. This work was repeated for three times.

first: Yi

last: Liu


title: Gene expression signature of cerebellum hypoplasia in a mouse model of Down syndrome (Part I).

city: Paris

first: Julien

last: Laffaire

address: 10 rue Vauquelin

institute: ESPCI - CNRS UMR 7637

summary:
We designed a large scale gene expression study in Ts1Cje mice between P0 and P10 in order to measure the effects of trisomy 21 on a large number of samples (56 in total) in a tissue that is affected in Down syndrome (the cerebellum) and to quantify the defect during development in order to correlate gene expression changes to the phenotype observed.
Keywords: Down syndrome, Ts1Cje, cerebellum, development, hypoplasia

overall_design: We analyzed gene expression in the cerebellum of Ts1Cje and euploid mice at P0, P3, P7 and P10 using pangenomic two colors microarrays containing 25 344 probes representing approximately 15 574 mouse genes. 56 samples from individual cerebellum were hybridized on 28 microarrays. On each microarray we hybridized a Ts1Cje sample versus an euploid sample and always a male versus a female. In addition on the same microarray we always compared samples from mice of the same age or with a maximum difference of 4 days (P0 versus P3, P3 versus P7 or P7 versus P10).

first: Isabelle

last: Rivals

first: Luce

last: Dauphinot

first: Tania

last: Vitalis

first: Jean

last: Rossier

first: Yann

last: Herault

first: Marie-Claude

last: Potier