title: Expression profiles dysplastic and neoplastic rat liver lesions

status: Public on Oct 09 2010

city: Sassari

first: Rosa

middle: M.

last: Pascale

address: Via P. Manzella 4

department: Dept. of Biomedical Sciences

country: Italy

institute: University of Sassari

summary: Predisposition to hepatocarcinogenesis is under polygenic control. We analyzed gene expression patterns of dysplastic liver nodules (DN) and hepatocellular carcinoma (HCC) chemically-induced in F344 and BN rats, respectively susceptible and resistant to hepatocarcinogenesis, to evaluate effector mechanisms of predisposition genes, and commonalties between transcription signatures of rat and human liver lesions. Gene expression profiles were determined by microarray analysis and validated by quantitative RT-PCR and Western blot. Cluster analysis revealed two distinctive gene expression patterns, the first of which included normal liver of F344 and BN rats and BN rat nodules, and the second one F344 nodules and HCC of both strains. Expression of 91 and 55 genes of DN and HCC, respectively, showed significant interstrain differences. Considering genes mostly associated with cell proliferation we identified a signature predicting DN evolution to HCC. Notably, expression of oncosuppressors Csmd1, Dmbt, Dusp1, and Gnmt ,in DN, and Bhmt, Dmbt1, Dusp1, Gadd45g, Gnmt, Napsa, Pp2ca, and Ptpn13, in HCC, was higher in BN than F344 rats. Comparative genomics approach, using gene expression data from rat lesions, and human HCC with different prognosis (based on survival length), revealed expression patterns of BN and F344 lesions close to those of human HCCs with better and poorer prognosis, respectively, suggesting that similar molecular events contribute to create a phenotype prone to progression in rats and human lesions. In conclusion, we identified a molecular signature of DN prone to progress to HCC and suggest that oncosuppressor genes are determinants of the genetically transmitted resistance to hepatocarcinogenesis.

overall_design: Three-condition experiment, Normal liver vs. Dysplastic nodules and tumors. Biological replicates: 8 control replicates, 8 nodules replicates and 7 tumor replicates.


title: Transcriptome of mkk1-mkk2 mutants

status: Public on Oct 11 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: au08-02_mkk1-mkk2 - mkk1-mkk2 - Functional redundancy of the two MAPKKs MKK1 and MKK2. - mkk1 and mkk2 k.o. plants were crossed. Seedlings homozygous for mkk1 and/or mkk2, in parallel with control wild type seedlings, were grown on sterile medium. RNA was extracted from non-treated seedlings. aRNA was synthesised using the Ambion aRNA kit. Transcriptome data will be compared with those from a (already available) microarray of a mutant lacking the MAPKKkinase that is upstream of MKK1 and MKK2 (MEKK1).

overall_design: 4 dye-swap - gene knock out

first: Heribert

last: Hirt

first: Frederique

last: Bitton

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Neisseria meningitidis strain MC58 and α710 grown in RPMI and on adhesion to human epithelial cells

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

summary: Differences in the transcriptional profile of the menigococcal strains MC58 and α710 were compared upon growth in RPMI and on adhesion to FaDu cells (Human nasopharyngeal cells)

overall_design: Common reference design, MC58 and α710 grown in RPMI and adherent MC58 and α710. Aliquots from the individual samples made the common reference pool. Two replicates per array.

first: Biju

last: Joseph

first: Susanne

last: Schneiker-Bekel

first: Anja

last: Schramm-Glück

first: Jochen

last: Blom

first: Heike

last: Claus

first: Burkhard

last: Linke

first: Roland

last: Schwarz

first: Anke

last: Becker

first: Alexander

last: Goesmann

first: Matthias

last: Frosch

first: Christoph

last: Schoen


title: mRNA expression in wild type and TTHA0175-deficient Thermus thermophilus HB8 strains; rich medium with growth temperature shift from 70C to 45C

status: Public on Oct 15 2010

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

country: Japan

institute: RIKEN Harima Institute

summary: In order to find function of TTHA0175 protein, we analyzed altered expression profile of the total mRNA of TTHA0175-deficient Thermus thermophilus HB8 strain grown in a rich (TT) medium after shifted down the growth temperature from 70 oC to 45 oC, and compared to that in the cases of wild type.

overall_design: Wild-type and TTHA0175-deficient T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (0.3 ml) were inoculated into 0.15 liter of the same medium and then cultivated at 70oC. At the Abs600=0.8 (0min), cold medium was added and the temperature were shifted down to 45oC. Cells were collected at 0, 30, and 120 min after temperature shift, and then crude RNA was extracted. In order to compare mRNA expression between 45oC and 70oC both in the cases of wild-type and TTHA0175-deficient strains, the expression of each mRNA at each time point was analyzed on a GeneChip.

first: Toshiko

last: Miyazaki

first: Miwa

last: Ohmori

first: Norio

last: Nakagawa

first: Yoshihiro

last: Agari

first: Seiki

last: Kuramitsu


title: TTHB212 (anti-sigmaE)-deficient Thermus thermophilus HB8 strain: time course

summary: We observed the expression profile of the total mRNA of TTHB212-deficient of Thermus thermophilus HB8 strain grown in a rich medium at 70°C for 7 and 8 hours

overall_design: TTHB212-deficient T. thermophilus HB8 cells were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 7 or 8 h, respectively, and then, the expression of each mRNA was analyzed.

first: Keiko

last: Sakamoto


title: Discovery of biomarker genes form earthworm microarray data

status: Public on Oct 08 2010

city: Vicksburg

first: Natalie

last: Barker

state: MS

address: 3909 Halls Ferry Rd.

country: USA

institute: Engineer Research and Development Center

summary:
Motivation: Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes. Our objective was to identify biomarker genes that can separate earthworm samples into three groups: control, TNT-treated, and RDX-treated.
Results:  We developed a discriminant analysis and cluster (DAC) pipeline to analyze a 248-array dataset. First, a total of 869 significantly changed genes in response to TNT or RDX exposure were inferred by class comparison statistical algorithms. Then, nine decision tree-based algorithms were applied to generate classification rules and a set of 286 classifier genes. These classifier genes were ranked by their overall weight of significance, and were used to build support vector machines (SVMs). An SVM containing all 286 classifier genes had the highest classification accuracy (91.5%). An unsupervised clustering method was used to cluster the worm samples and results show that the use of the top 100 classifier genes can assign the largest number of worm samples into the three reference clusters obtained by using all the 14,188 filtered genes, suggesting that these top-ranked genes may be potential candidates for biomarkers. This study demonstrates that the DAC pipeline can be used to identify a small set of biomarker genes from high dimensional datasets and generate a reliable SVM classification model for multiple classes.

overall_design: Adult earthworms (E. fetida) were exposed in soil spiked with TNT (0, 6, 12, 24, 48, or 96 mg/kg) or RDX (8, 16, 32, 64, or 128 mg/kg) for 0, 4 or 14 days. The 4-day treatment was repeated with RDX concentration being 2, 4, 8, 16 or 32 mg/kg soil. Each treatment originally had 10 replicate worms with 8-10 survivors at the end of exposure. Total RNA was isolated from the surviving worms. A total of 248 worm RNA samples were hybridized to a custom-designed oligo array using Agilent’s one-color Low RNA Input Linear Amplification Kit. The array contains 15,208 non-redundant 60-mer probes, each targeting a unique E. fetida transcript (Gong et al. 2009). After hybridization and scanning, gene expression data were acquired using Agilent’s Feature Extraction Software (v.9.1.3). The 248-array dataset consists of three worm groups: 32 untreated controls, 96 TNT-treated, and 120 RDX-treated.

first: Ying

last: Li

first: Ping

last: Gong

first: Xin

last: Guan

first: Edward

last: Perkins


city: Pacific Grove

first: Brent

middle: L

last: Lockwood

state: CA

address: 120 Oceanview Blvd.

department: Biology

institute: Hopkins Marine Station of Stanford University

summary:
[original Title] Transcriptomic responses to heat-stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success.

Invasive species are increasingly prevalent in marine ecosystems worldwide. Although many studies have examined the ecological effects of invasives, little is known about physiological mechanisms that might contribute to invasive success. The mussel Mytilus galloprovincialis, a native of the Mediterranean Sea, is a successful invader on the central and southern coasts of California, where it has largely displaced the native congener, Mytilus trossulus. It has been previously shown that thermal responses of several physiological traits may underlie the capacity of M. galloprovincialis to out-compete M. trossulus in warm habitats. To elucidate possible differences in stress-induced gene expression between these congeners, we developed an oligonucleotide microarray with 8,874 probes representing 4,488 different genes that recognized mRNAs of both species. In acute heat-stress experiments, 1,531 of these genes showed temperature-dependent changes in gene expression that were highly similar in the two congeners.  In contrast, 96 genes showed species-specific responses to heat-stress, functionally characterized by their involvement in oxidative stress, proteolysis, energy metabolism, ion transport, cell signaling, and cytoskeletal reorganization. The gene that showed the biggest difference between the species was the gene for the molecular chaperone small heat shock protein 24,  which was highly induced in M. galloprovincialis and showed only a small change in M. trossulus. These different responses to acute heat-stress may help to explain—and predict—the invasive success of M. galloprovincialis in a warming world.

sample_organism:
Mytilus trossulus
Mytilus galloprovincialis

platform_organism:
Mytilus californianus
Mytilus galloprovincialis

overall_design:
Two species (Mytilus galloprovincialis, Mytilus trossulus), heat ramp with three treatment groups (24, 28, 32 degrees-C), three control groups sampled at the same time as treatment groups (13 degrees-C), one control group sampled at the beginning (13 degrees-C).  Biological replicates: 6 in each treatment group, 6 in each control group. Heterologous and homologous hybridization to microarray constructed from Mytilus californianus and Mytilus galloprovincialis sequences.
To accurately compare the transcriptomes of Mytilus galloprovincialis and M. trossulus, we chose to develop a common microarray format that could be used for both species. This microarray design consisted of probe sequences generated from the out-group species, M. californianus. M. trossulus and M. galloprovincialis are approximately 7.6 million years diverged from M. californianus, yet only 3.5 million years divergent from each other (Seed, 1992). Therefore, heterologous hybridization to the microarray allowed us to compare transcriptional responses of M. galloprovincialis and M. trossulus without the inherent sequence biases that would result from a microarray that was designed from sequences of either M. galloprovincialis or M. trossulus. A limited number of sequences (556) from ESTs from M. galloprovincialis that matched M. californianus ESTs were included on the microarray to test for the effects of sequence mismatches. To further control for sequence biases only probes that performed well for both M. galloprovincialis and M. trossulus were used in our analyses. In order to determine significant changes in expression, we conducted a two-way ANOVA, in which temperature and species were modeled as fixed effects, and focused on genes that were significant for the temperature effect or the species x temperature interaction. We ignored the species term from the ANOVA as this effect could have highlighted genes that differentially bound to probes on the microarray due to differences in sequence homology, thus not reflecting true differences in gene expression. In accordance with statistical convention, all genes with a significant species x temperature interaction were deemed not to have significant temperature effects, even if the temperature term from the ANOVA had a low P-value. All genes with FDR-corrected (Benjamini and Hochberg, 1995) P-values less than 0.01 were considered significant. Analyses were conducted in the R statistical programming environment (R Development Core Team, 2009).

first: Jon

middle: G

last: Sanders

first: George

middle: N

last: Somero


title: Comparison of two clones of Myzus Persicae (Sulzer) (Hemiptera: Aphididae)

status: Public on Oct 07 2010

city: Harpenden

first: Chris

last: Bass

state: Hertfordshire

address: West Common

department: Biological Chemistry

country: United Kingdom

institute: Rothamsted Research

summary: The aim of this experiment was to compare the transciptome of the peach-potato aphid (Myzus persicae) clone 4106a (a laboratory insecticide-susceptible standard collected from potato in Scotland in 2000) with clone 5191A (an insecticide resistant aphid clone collected from tobacco in Greece in 2007) to identify which genes are over or underexpressed in the resistant phenotype.

overall_design: Two-condition experiment, 4106a vs. 5191a Myzus persicae clones. Biological replicates: 4 pools of RNA extracted from ten 15 day old aphids of each clone. Technical Replicates: Two technical reps incorporating a dye swap. Total replication: eight replicates for each clone.


title: Apoptosis gene signature of Survivin and its splice variant expression in breast carcinoma

status: Public on Oct 06 2010

city: Brussels

first: Olivier

last: Feron

address: 53 Avenue E. Mounier, bte B1.53.09

department: Pole of Pharmacology and Therapeutics (FATH)  Institute of Experimental and Clinical Research (IREC)

country: Belgium

institute: Université catholique de Louvain

summary: Background: Survivin was described as strongly expressed in human cancer. To date, little is known about the association between Survivin splice variants and the other apoptosis-related genes. In this study, we analyzed the apoptosis gene signature of Survivin and its variant expression in breast cancer. Methods: Expression of the 5 transcripts was measured by RT-PCR in 135 breast carcinomas. Human Apoptosis Gene Arrays were used to screen the genes that could be associated with Survivin variants. Cox survival analysis was analyzed according to the breast cancer patient outcome. Results: Significant associations between Survivin transcript and the apoptotic gene array were found. Interestingly, Survivin-3B variant showed major inverse correlations with the pro-apoptotic gene array. Overexpression of Survivin-3B strongly inhibits 5-fluorouracil/epirubicin/Cyclophosphamide induced-apoptosis in breast tumor cell lines. In breast carcinomas, uni- and multivariate analysis showed patients with high level of survivin-3B expression had a shorter overall (p=0.030 and p=0.042, respectively) and disease-free (p=0.024 and p=0.009) survival. Conclusion: Our data indicate Survivin-3B could have an anti-apoptotic activity and its expression level might be used as a prognostic marker in breast carcinoma.

overall_design: The expression of 96 apoptosis genes and  was analyzed in 41 breast carcinomas and 1 pool of normal mammary tissues. In parallel, every survivin isoform expression was quantified by real-time quantitative PCR. Data obtained with the macro-array were correlated with survivin isoform levels detected by RT-PCR.

first: Frédérique

last: Végran

first: Romain

last: Boidot

first: Franck

last: Bonnetain

first: Muriel

last: Cadouot

first: Sandy

last: Chevrier

first: Sarab

last: Lizard


title: Neuroinflammation in Advanced Canine Glaucoma

city: Iowa City

first: Markus

middle: H

last: Kuehn

state: IA

address: 375 Newton Road

department: Ophthalmology and Visual Sciences

institute: University of Iowa

summary: Dogs frequently develop glaucoma, a disease that leads to vision loss due to loss of retinal ganglion cells and degeneration of axons within the optic nerve.  We used Affymetrix Gene chips to characterize transcriptional changes between healthy and glaucomatous retinas.

overall_design: These data describe gene expression changes in the canine retina with glaucoma. RNA was isolated from the retinas of 5 dogs with advanced glaucoma and from 5 normal individuals.

first: S

last: Grozdanic

first: M

first: R

last: Kardon

middle: M

last: Harper

first: Grazyna

last: Adamus

first: Bing

last: Jiang

first: Helga

last: Kecova


title: Transcriptionnal analysis of a Photorhabdus luminescens TT01 variant, named VAR*, which is a colonial and phenotypic variant displaying delayed pathogenicity in the insect, Spodoptera littoralis.

status: Public on Oct 13 2010

city: Montpellier

first: Sophie

last: Gaudriault

address: case courrier 54, Place Eugène Bataillon

institute: Université Montpellier 2 - Institut National de la Recherche Agronomique

summary:
Photorhabdus luminescens lives in a mutualistic association with entomopathogenic nematodes and is pathogenic for insects. Variants of Photorhabdus frequently arise. VAR* is a colonial and phenotypic variant displaying delayed pathogenicity in the insect, Spodoptera littoralis. In this study, we evaluated the role of transcriptomic modulation in determining the phenotypic variation and delayed pathogenicity of VAR* with respect to the corresponding wild-type form, TT01alpha.
A P. luminescens microarray was used to determine changes in transcript profiles in the exponential and stationary phase growth phase  of VAR* and TT01alpha grown in LB broth.

sample_organism: Photorhabdus laumondii subsp. laumondii TTO1

overall_design: Direct transcriptomic comparisons were carried out between VAR* and TT01alpha grown in LB broth. RNA were extracted from bacterial cells in the exponential growth phase (6-hour-old culture, 5 x 107 cfu/ml) and stationary phase (45-hour-old culture, 5 x 108 cfu/ml). Each microarray comparison (TT01alpha versus VAR* growth in exponential growth or stationary phase) included six slides, with three dye-swapping replicates. Each microarray comparison is done twice with two independant biological extractions (repbiol1 or 2).

first: Anne

last: Lanois

first: Stéphane

last: Bourot

first: Anne-Sophie

last: Canoy


title: Widespread over-expression of the X chromosome in sterile F1 hybrid mice

status: Public on Oct 05 2010

city: Leipzig

first: Thomas

last: Giger

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max-Planck-Institute of Evolutionary Anthropology

summary: We used a reciprocal cross of Mus musculus and M. domesticus in which F1 males are sterile in one direction and fertile in the other direction, in order to associate expression differences with sterility.

sample_organism: Mus musculus musculus x M. m. domesticus

overall_design: Four different crosses were performed. A cross between two strains within each mouse species (M. musculus, PWK/PhJ and CZECHII/EiJ; M. domesticus, LEWES/EiJ and WSB/EiJ). And two reciprocal crosses between a domesticus (LEWES/EiJ) and a musculus (PWK/PhJ) strain. The cross between a musculus female and a domesticus male produces sterile male offspring - whereas all other crosses produced fertile male offspring. Testis tissue from three male mice (60 days old) from all four crosses were analysed on the Affymetrix MG 430.2. Array.

first: Jeffrey

last: Good

first: Matthew

middle: D

last: Dean

first: Michael

middle: W

last: Nachman


title: Microarray analysis of Gene expression in limb muscles of three mouse models of Kennedy disease/SBMA

status: Public on Oct 12 2010

city: Mississauga

first: Ashley

last: Monks

state: Ontario

address: 3359 Mississauga Road

department: Dept. of Psychology

country: Canada

institute: University of Toronto

summary:
Emerging evidence implicates transcriptional dyseregulation within skeletal muscle in the pathogenesis of Kennedy disease/spinal bulbar muscular atrophy (KD/SBMA). We therefore broadly characterized gene expression in skeletal muscle of three independently generated mouse models of this disorder. The mouse models included a polyglutamine expanded (polyQ) AR knock-in model (AR113Q KI), a polyQ AR transgenic model (AR97Q Tg), and a transgenic mouse which overexpresses wild type AR solely in muscle (HSA-AR Tg). We performed microarray analysis of lower hindlimb muscles taken from these three models using high density oligonucleotide arrays. Changes in gene expression relative to wild type controls were evaluated separately in each strain. We validated our results using quantitative RT-PCR. Patterns of gene expression that are common to all lines and unique to each are described.  When considered globally, the degree of overlap between the three models is approximately equivalent, and several patterns of gene expression relevant to the disease process were observed. Notably, patterns of gene expression typical of loss of AR function were observed in all three models, as were alterations in genes involved in cell adhesion, energy balance, Huntington’s disease, muscle atrophy and myogenesis. By comparing patterns of gene expression in three independent models of KD/SBMA, we have been able to identify candidate genes that might mediate the core myogenic features of KD/SBMA.
Keywords: Gene expression in transgenic mice and disease state analysis

overall_design: We used microarray (38.5K oligo mouse array, which contain 35,302 of 70mer oligonucleotide probes largely derived from constitutively expressed exons and 3,482 of controls) to analyze gene expression in limb muscles of transgenic mice. Three mouse models of KD/SBMA were used: HSA-AR, AR113Q knock-in and AR97Q. HSA-AR transgenic male mice (n=5) and their WT brothers (n=8, all mice were 110-130 days of age) were used in this experiment. ARQ113-Knock In males (n=3, 3-4 months of age), and transgenic AR97Q males and WT brothers (n= 6 of each) were used in this study. For both HSA-AR and AR113Q samples, the log2 ratio of experimental samples (Cy5) and reference RNA(Cy3) was obtained, and log2 ratios from mutant samples were then subtracted from log2 ratios from WT controls. AR97Q males (Cy5) were simply compared with their WT brothers (Cy3) using a log2 ratio, rather than being first compared with reference RNA.

first: Kaiguo

last: Mo

first: John

middle: T

last: Westwood

first: Douglas

middle: A


title: Dissecting the transcriptional response to DNA damage in Helicobacter pylori.

status: Public on Oct 04 2010

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: We have completed transcriptional profiles of H. pylori cells undergoing DNA damage, caused by either failure to repair endogenous damage (addA- cells) or exposure to ciprofloxacin, which binds DNA gyrase, thus inducing double strand breaks.  The goals of this study were to elucidate factors required to sustain the transcription response to DNA damage.

overall_design: All mutants are complete deletions of the coding sequence.  The recA and comB10 genes are disrupted with the chloramphenical acetyl transferase (CAT) gene, encoding chloramphenicol resistance.  The addA gene is disrupted with the aph3 gene, which encodes resistence to kanamycin.  All mutant phenotypes can be complemented by expression of the gene at a heterologous locus.

first: Marion

last: Dorer


title: A developmental atlas of transcription in the sea hare Aplysia californica

city: Guelph

first: Andreas

last: Heyland

state: ON

address: 50 Stone Rd East

department: Integrative Biology

institute: University of Guelph

summary: The monitoring of global transcription patterns during development is a useful first step to understand mechanisms underlying growth, differentiation and patterning in a given species. However such large scale developmental studies are so far only available from a few selected model organisms such as mouse, Drosophila and the nematode C. elegans. Genomic scale information from the lophotrochozoa is now emerging. The recently characterized neuronal transcriptome of the sea hare Aplysia californica (~200’000 ESTs and ~40,000 unique non-redundant sequences representing about 55-70% of all neuronal transcripts including splice forms and non-coding RNAs) provides new insights and opportunities into problems of molluscan development and specifically neurogenesis. Regulatory genes used in development are recruited for the functions of adult nervous systems such as synaptogenesis, specific wiring in networks and structural changes underlying synaptic plasticity. While this similarity reflects a basic concept in biology, namely the recruitment of the same genes for different functions, it has never been tested on a large scale genomic level. We used representative oligo-arrays constructed from transcripts obtained from the Aplysia nervous system to explore the following two questions: 1) What neuronal genes are differentially expressed during embryonic development of the sea hare Aplysia. 2) What gene expression changes can be observed in correlation with gastrulation, metamorphosis, and larval neurogenesis. For this purpose we hybridized RNA from 3 embryonic (64 cells, gastrula, trochophore) and 4 larval stages (pre-hatching, post-hatching, pre-metamorphosis, postmetamorphosis) against a reference sample consisting of equal contributions from all stages. Our analysis revealed that all embryonic and larval stages can be distinguished based on their transcription profiles. A comparison of the Aplysia atlas with similar studies in Drosophila and mouse reveals interesting differences. We identified several new transcription factors which are differentially expressed during early embryonic development. Various other transcripts involved in metabolism and differentiation were characterized. These genes can be candidate targets for understanding neuronal growth, synaptogenesis and memory mechanisms.  We conclude that the microarray technology provides us with a powerful tool for efficient survey and functional annotation of the neuronal transcriptome in Aplysia.

overall_design: We used a reference design for this study  where we hybridized each of the 8 developmental stages of Aplysia (cleavage, gastrula, trochophore, first veliger, hatching veliger, pre-metamorphosis (stage 6), post-metamorphosis (stage 7), post-metamorphosis 60 hours (pm60)

first: Monica

last: Medina

first: Chris

last: Voolstra

first: Zer

last: Vue

first: Leonid

last: Moroz


title: Chip-chip from HCT116 cells with YBX1

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

type: Genome binding/occupancy profiling by genome tiling array

summary:
YBX1 is a multifunctional protein involved in the control of transcription and translation. We identified YBX1 as an target of MEK/ERK signaling in colorectal cancer cell lines.
We performed a ChIP-chip analysis of HCT116 cells to identify new potential target genes of YBX1.

overall_design: Comparison of input DNA fragments with fragments coprecipitated with YBX1 in HCT116 cells.

first: Reinhold

last: Schäfer


title: Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes

status: Public on Oct 02 2010

city: La Jolla

first: Neekesh

middle: V

last: Dharia

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

type: Genome variation profiling by genome tiling array

summary: Plasmodium vivax causes 25-40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the P. vivax reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole genome sequencing (30X coverage). This analysis revealed over 18,261 single nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Sal1 strain obtained in 1970. This full-genome sequence of a P. vivax isolate, the second overall and first of an uncultured patient isolate, shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous to synonymous SNPs encode two AP2 transcription factors and the P. vivax multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in P. falciparum. This analysis provides a new data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies.

overall_design: Genome DNA from Peruvian P. vivax Isolate IQ07 vs. Reference Sal1

first: N

first: E

last: Winzeler


title: Mutant K-ras promotes carcinogen-induced murine colorectal tumourigenesis, but does not alter tumour chromosome stability

city: Cambridge

first: Mark

middle: J

last: Arends

address: Hills Road

department: Pathology

institute: University of Cambridge

summary:
K-ras mutations are observed in around 40% human colorectal adenomas and carcinomas and contribute to the pathogenesis of human and rodent colorectal tumour formation. Previously, we developed and characterised a strain of transgenic mice with inducible intestinal epithelial expression of K-rasVal12 via a Cre/LoxP system. To evaluate the influence of mutant K-ras on carcinogen-induced colorectal tumourigenesis, we induced neoplastic alterations in the large intestines of wild-type and K-rasVal12 mice using the colon-selective carcinogen 1, 2-dimethylhydrazine (DMH), which has been widely used to study chemically induced colorectal tumours that are histopathologically similar to those observed in humans. K-rasVal12 expression significantly promoted DMH-induced colorectal tumourigenesis: the average life span of the mice decreased from 38.52±1.97 weeks for 40 wild-type mice to 32.42±2.17 weeks for 26 K-rasVal12 mice (mean+SEM, P<0.05) and the large intestinal tumours increased from 2.27±0.15 per wild-type mouse to 3.85±0.20  in K-rasVal12 mice (mean+SEM, P<0.01). Adenomas from DMH-treated K-rasVal12 mice showed significantly higher levels (10.9±1.69%) of Ki-67-positive proliferating cells compared with those from DMH-treated wild-type mice (7.77±1.15%) (mean+SD, P<0.01) and a mild increase in apoptotic nuclei staining for cleaved caspase-3 (1.94+0.51% compared with 1.15±0.34%, mean+SD, P<0.01).
In the adenomas from DMH-treated K-rasVal12 mice, K-rasVal12 transgene recombination and expression were confirmed and shown to promote strong Erk and mild Akt activation compared with adenomas from DMH-treated wild-type mice. Microarray hybridization and cluster analysis demonstrated different expression profiles in adenomas from DMH-treated wild-type and DMH-treated K-rasVal12 mice, indicating involvement of different molecular mechanisms, but array-comparative genomic hybridisation analysis showed chromosome stability in both, with very few chromosome alterations observed in adenomas from either of the two groups. Taken together, these data show that mutant K-ras promotes DMH-induced colorectal tumourigenesis, conferring a proliferative effect, but does not alter chromosome stability in the tumours.

overall_design: This study has 7 samples analysed, 4 Kras mutants and 3 controls, on the Illumina Mouse-6 Beadchip array.

first: Feijun

last: Luo

first: George

last: Poulogiannis

first: Hongtao

last: Ye

first: Rifat

last: Hamoudi

first: Wenyan

last: Zhang

first: Gehong

last: Dong


title: Transcriptome analysis of a breeding program pedigree

city: Ames

first: PLEXdb Curator

middle: Sudhansu

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: Transcriptome comparison of 15 lines representing the University of Minnesota six-rowed malting breeding program  at two time points of the malting process: 'out of steep' and '3 days of germination'. Three replicates of each genotype and time point were accomplished.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Maria Muñoz-Amatriain.  The equivalent experiment is BB91 at PLEXdb.]

overall_design: genotype: Bonanza - time: 0 days(3-replications);  genotype: Bonanza - time: 3 days(3-replications);  genotype: Cree - time: 0 days(3-replications);  genotype: Cree - time: 3 days(3-replications);  genotype: Dickson - time: 0 days(3-replications);  genotype: Dickson - time: 3 days(3-replications);  genotype: Excel - time: 0 days(3-replications);  genotype: Excel - time: 3 days(3-replications);  genotype: Lacey - time: 0 days(3-replications);  genotype: Lacey - time: 3 days(3-replications);  genotype: M1 - time: 0 days(3-replications);  genotype: M1 - time: 3 days(3-replications);  genotype: M44 - time: 0 days(3-replications);  genotype: M44 - time: 3 days(3-replications);  genotype: M46 - time: 0 days(3-replications);  genotype: M46 - time: 3 days(3-replications);  genotype: M55 - time: 0 days(3-replications);  genotype: M55 - time: 3 days(3-replications);  genotype: M66 - time: 0 days(3-replications);  genotype: M66 - time: 3 days(3-replications);  genotype: M78 - time: 0 days(3-replications);  genotype: M78 - time: 3 days(3-replications);  genotype: Manker - time: 0 days(3-replications);  genotype: Manker - time: 3 days(3-replications);  genotype: Morex - time: 0 days(3-replications);  genotype: Morex - time: 3 days(3-replications);  genotype: Robust - time: 0 days(3-replications);  genotype: Robust - time: 3 days(3-replications);  genotype: Stander - time: 0 days(3-replications);  genotype: Stander - time: 3 days(3-replications)

first: Maria

last: Muñoz-Amatriain


title: Gene expression changes in response to drought stress in Arabidopsis reveal early responses leading to acclimation in plant growth

status: Public on Oct 01 2010

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

summary: Plant drought stress response and resistance are complex biological processes that merit systems-level analyses to dissect drought stress encountered by crops in the field. We have used gene expression profiling of Arabidopsis plants subjected to a controlled, sublethal, moderate drought (mDr) treatment to characterize early and late response to drought. We have also compared these profiles to those from plants treated with soil water deficit (progressive) drought (pDr) to reveal acclimation responses in plants.

overall_design: Controlled moderate drought (mDr) was maintained by giving Arabidopsis (Columbia) plants water to keep the soil moisture level at 30% of field capacity, which is 200% or 2 g H2O g-1 dry soil. Water was withheld at 30 days after sowing (DAS). For progressive drought (pDr) treatment, plants were grown in a growth room as described above, water was withheld at 35 DAS, and were allowed to dry until the required pDr level was reached. For RNA isolation, two biological replicate samples of 5 pooled plants were collected at early (day1) and late stage (day10) for mDr, and first day of wilting for pDr, along with controls for mDr and pDr. Samples were hybridized to the Affymetrix (ATH1 25K) GeneChip.

first: Amal

last: Harb

first: Arjun

last: Krishnan

first: Madan

last: Ambavaram


title: Expression analysis of 6 serotypes of Actinobacillus pleuropneumonia during iron deprivation

city: Copenhagen

first: Kirstine

last: Klitgaard

address: Bulowsvej 27

country: Denmark

institute: National Veterinary Institute, Technical University of Denmark

summary: Investigation of whole genome changes in six serotypes of Actinobacillus pleuropneumoniae in control cultures compared to bacteria grown in media containg the iron chelator 2,2'-dipyridyl.

sample_organism: Actinobacillus pleuropneumoniae serovar 5

sample_organism: Actinobacillus pleuropneumoniae serovar 7

sample_organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

sample_organism: Actinobacillus pleuropneumoniae serovar 3

sample_organism: Actinobacillus pleuropneumoniae serovar 2 str. 4226

sample_organism: Actinobacillus pleuropneumoniae serovar 6

overall_design: A 48 chip study using total RNA recovered from four different control cultures and four different iron depleted cultures of Actinobacillus pleuropneumoniea serotype 1 (4074), serotype 2 (4226), serotype 3 (1421), serotype 5b(L209, serotype 6 (7712640) and serotype 7 (WF87).

first: Carsten

last: Friis

first: Mette

last: Boye

first: Oystein

last: Angen


title: Expression analysis of a respiration-deficient mutant of Zymomonas mobilis

city: Beppu

first: Takeshi

last: Hayashi

address: Kitaishigaki 82

department: Faculty of Food and Nutrition

institute: Beppu university

summary:
Investigation of whole-genome gene expression level changes in RDM-4 strain of Zymomonas mobilis respiration-deficient mutant compared to the wild-type strain. The mutant strains were isolated from the antibiotics-resistant mutants of Z. mobilis ZM6.
The RDM strains exhibited much higher ethanol fermentation abilities than the wild-type strain under aerobic conditions. The strains also gained thermotolerance and exhibited higher ethanol productivities at high temperature (39 ºC) under both non-aerobic and aerobic conditions compared with the wild-type strain. To evaluate the mechanisms of aerobic fermentation and thermotolerance of the RDM strain, we performed the microarray experiments.

sample_organism: Zymomonas mobilis subsp. mobilis ATCC 29191

platform_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: A four-chip study using total RNA recovered from the shaking cultures of wt and RDM-4 strains grown at 30ºC, a non-aerobic culture of wt strain grown at 30ºC, and a non-aerobic culture of RDM-4 strain grown at 38ºC. Each chip measures the expression level of 1,998 genes from Z. mobilis.


title: Transcriptional profiling of the yeast forkhead transcription factor Hcm1

city: Lleida

first: Cabiscol

last: Elisa

address: Montserrat Roig, 2

department: Ciencies mediques Basiques

country: Spain

institute: Universitat de Lleida

summary: In S. cerevisiae, the forkhead transcription factor Hcm1 has been involved in chromosome segregation, spindle pole dynamics and budding. We found that, in response to oxidative stress stimuli, Hcm1 shifts from cytoplasm to the nucleus, interacting with the histone deacetylase Sir2, which regulates Hcm1 localization. Hcm1-overexpressing cells showed increased resistance to oxidative stress which can be attributed to increased catalase and Sod2 activities. Microarray analysis revealed that genes corresponding to mitochondrial function and transition from exponential to stationary phase are clearly induced in these cells which consistently showed higher rates of oxygen consumption due to an increase in mitochondria – possibly triggered by higher amounts of Abf2, a protein involved in mitochondrial biogenesis. In wild-type cells, when glucose levels decreased by 50%, we observed Hcm1 translocation to the nucleus and increased Hcm1 levels. We conclude that Hcm1 may act as an early regulator to respond to nutrient limitation, increasing stress resistance and mitochondrial function and thereby allowing the cells to adapt to nutrient limitations by shifting from fermentative to respiratory metabolism.

overall_design: Four strains were used: WT (strain CML128), Δhcm1 (a deleted strain derived from CML128), HCM1HA (an HA tagged strain derived from CML128), and tetHCM1HA (an overexpressor of Hcm1 with a tet promoter regulatable with doxycycline derived from HCM1HA. Addition of doxy repressed Hcm1 expression). We compared the expression profile of Δhcm1 vs WT; tetHCM1HA vs HCM1HA, tetHCM1HA vs tetHCM1HA + 10h doxycycline. As controls we also compared HCM1HA vs WT; HCM1HA + 4h doxycycline vs HCM1; HCM1HA + 10h doxycycline vs HCM1. A Dye-swap was carried out for each RNA sample.   Total number of chips analyzed: 12

first: M

last: Rodriguez-Colman

first: Gemma

last: Reverter-Branchat

last: Sorolla

first: Jordi

last: Tamarit

first: Joaquim

last: Ros

first: Elisa

last: Cabiscol


title: Human peripheral blood cells: systemic lupus erythematosus vs healthy individual.

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

institute: Wakayama Medical University

summary: Gene expression profiling of peripheral blood cells from patients with  systemic lupus erythematosus (SLE)  vs healthy individual (HI).

overall_design: Peripheral blood was obtained from patients with SLE (n=21) and HI (n=45). Blood samples from 45 HI are used as control.

first: Hidehiko

last: Sugino

first: Chieko

last: Aoki

first: Satoru

last: Ishikawa

first: Hooi-Ming

last: Lee

first: Yasuo

last: Adachi

first: Kenichi

last: Matsubara


title: Next-generation sequencing identifies the natural killer cell microRNA transcriptome

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

summary:
Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation.  Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g. granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate the translation of their mRNA targets, and are therefore candidates mediating this control process.  While the expression and importance of miRNAs in T and B lymphocytes has been established, little is known about miRNAs in NK cells.  Here, we utilized two next-generation sequencing (NGS) platforms to define the miRNA transcriptomes of resting and cytokine-activated primary murine NK cells, with confirmation by RT-qPCR and microarrays.  We delineate a bioinformatics analysis pipeline that identified 302 known and 28 novel mature miRNAs from sequences obtained from NK cell small RNA libraries.  These miRNAs are expressed over a broad range, exhibit isomiR complexity, and a subset is differentially expressed following cytokine-activation.  Using this miRNA NGS data, miR-223 was identified as a mature miRNA present in resting NK cells with decreased expression following cytokine-activation.  Further, we demonstrate that miR-223 specifically targets the 3’UTR of murine GzmB in vitro, indicating that this miRNA may contribute to control of GzmB translation in resting NK cells.  Thus, the sequenced NK cell miRNA transcriptome provides a valuable framework for further elucidation of miRNA expression and function in NK cell biology.
Illumina GA (SRR036363, SRR036364) and SOLiD (SRR036206, SRR036210) sequencing data have been submitted to the NCBI Sequence Read Archive (SRA).

overall_design: The study uses a custome made array to characterize miRNA of activated and resting murine splenic natural killer cells

first: Todd

last: Fehniger


city: Bloomington

first: Krystyna

last: Kazmierczak

state: IN

address: 1001 E. Third St.

institute: Indiana University

summary: Streptococcus pneumoniae D39 AdcR (adhesion competence repressor) is the first metal-sensing member of the MarR (multiple antibiotic resistance repressor) family to be characterized.  Expression profiling of a ∆adcR strain grown in liquid culture under microaerobic conditions revealed that transcript amounts for 13 genes were up-regulated relative to the wild-type strain, among them adcR, adcCBA, encoding a high affinity ABC uptake system for zinc, and genes encoding cell-surface zinc-binding pneumococcal histidine triad (pht) and adcII (lmb, laminin binding) proteins. Down-regulated transcripts included those encoding two putative zinc-containing alcohol dehydrogenases.

overall_design:
Bacterial strains were grown exponentially in rich (BHI) media at 37C and an atmosphere of 5% CO2 to OD620~0.2, and were processed as described in the related Sample records.  Samples were collected from three independent biological replicates and included one dye swap.
Data were normalized using the Lowess (block) method without background subtraction.
Changes in relative transcript amounts of positive or negative 2-fold with Bayesian P value of <0.001 were considered significant, and were included as supplementary material for the accompanying manuscript (The metalloregulatory site in Streptococcus pneumoniae AdcR, a zinc-activated MarR-family repressor; Reyes-Caballero, H. et al, manuscript in preparation).

first: Hermes

last: Reyes-Caballero

first: Alfredo

last: Guerra

first: Faith

middle: E

last: Jacobsen

first: Darin

last: Cowart

first: Uma

last: Mahendra Kumar Koppolu

first: Robert

last: Scott

first: Malcolm

last: Winkler

first: David

middle: P

last: Giedroc


title: C. perfringens 13 strain vs 13∆cpe1786 erm strain

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Transcriptional profiling of C. perfringens 13 strain compared with strain 13∆cpe1786 erm after growth in minimal medium with 0.5 mM cystine.

overall_design: two-condition experiment, 13 vs 13∆cpe1786 erm, 4 biological replicates for each condition

first: Gaëlle

last: André

first: Marc

last: Monot


title: Gene expression profiles in ruminal tissue from cows fed high or low concentrate diets

city: Tsukuba

first: Masaaki

last: Taniguchi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

summary: Cattle are often fed high concentrate diets to increase energy intake and improve overall animal performance.  Such diets also cause changes in fermentation patterns and epithelial function.  However, the molecular mechanisms involved in regulating epithelial function for cattle fed high concentrate diets have not been elucidated.  In this study, we aimed to gain a broad overview of the involved molecular mechanisms by detecting differentially expressed genes (DEG) in rumen tissue from dairy cows fed a low concentrate (LC; 8%) compared to a high concentrate (HC; 64%) diet using a bovine-specific microarray platform containing 16,846 unique gene loci and 5,943 ESTs from the bovine genome.  Feeding the HC diet increased the total volatile fatty acid concentration and markedly reduced ruminal pH, suggesting that the dietary treatments used did induce changes in ruminal fermentation.  In response to changes in the ruminal environment, a total of 5,200 elements were detected as DEG in ruminal tissue with >1.5-fold expression change (P < 0.05) for cows fed HC relative to LC.  Of the 5,200 DEG, 2,233 and 2,967 were up- and down-regulated, respectively. The GENECODIS analysis elucidated that relationships among the DEG represented 19 annotations characterized with GO molecular function and KEGG pathways with 26 DEG identified in multiple annotations such as calcium signaling and gap junction pathways. Among those DEG that were identified numerous times, catalytic subunit of cAMP-dependent protein kinase (PRKACB) was down-regulated in ruminal tissue from cows fed HC, suggesting that this gene may have important roles including regulation of cell proliferation and differentiation, and intracellular pH regulation.

overall_design: Two-condition experiment, High concentrate vs. Low concentrate diets. Biological replicates: 5 high concentrate fed, 5 low concentrate, independently grown and harvested. Two replicates per array.

first: Le

last: Guan

first: Urmila

last: Basu


title: Testicular gene expression profiles in infertile patients with AZFc deletions of the Y chromosome

city: Chieti

first: Florina

last: Raicu

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

institute: G. d’Annunzio University Foundation Chieti

summary: In the present study we carried out testicular gene expression profiling of patients with AZFc microdeletion, idiopathic infertility and normal spermatogenesis, in order to identify up- and downregulated genes in the different conditions, and to verify the presence of specific  molecular pathways leading to the spermatogenic damage in patients with AZFc deletions. All samples of patients with AZFc deletion clustered together, showing downregulation of several genes related to spermatogenesis.

overall_design: In this study, we analyzed testis expression profiles of 16 patients with different phenotypes, including men with AZFc deletions and men with idiopathic infertility. All pathological human testis RNAs were hybridized against normal testis reference RNA samples (obstructive azoospermia), while  the three samples with normal spermatogenesis were hybridized against  a control represented by an home-made RNA universal reference consisting of a commercial human purified tissue RNA pool (brain, liver, muscle and lung) (Clontech, Terra Bella, CA, USA) . These latter hybridizations were carried out in order to generate  a profile of genes specifically expressed in normal testis.

first: Liborio

last: Stuppia

first: Valentina

last: Gatta

first: Carlo

last: Foresta

first: Alberto

last: Ferlin


title: Transcriptional profiles uncover Aspergillus flavus induced resistance in mature maize kernels

city: New Orleans

first: Meng

last: Luo

state: LA

address: 1100 Robert E Lee Blvd

department: FFS

institute: SRRC, USDA-ARS

summary: Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and during storage. Previous studies indicate that both constitutive and induced resistance are involved in maize kernel defense against A. flavus infection, little is known about molecular mechanisms of mature kernels in response to fungal infection. The purpose of this study is to determine gene expression differences in maize kernels between resistant and susceptible lines in response to A. flavus challenge. To avoid the environmental effects in the field inoculation, a laboratory based inoculation technique Kernel Screening Assay (KSA) was used to challenge kernels with A. flavus. After 72 hours incubation of inoculated and noninculated mature kernels, gene expression profiles of two Near Isogenic Lines (NIL) of Eyl25 (A. flavus resistant) and Eyl31 (A. flavus susceptible) were compared using oligonucleotide array.

overall_design: Direct comparisons were designed. The comparisons of NIL Eyl25 and Eyl31 include: Treated/Control, Control/Control and Treated/Treated. After 72 hours incubation under KSA conditions, forty seeds used in each A. flavus inoculated and noninculated group were bulked to extract total RNA. Four technical replications were performed in each comparison including two dye-swaps, total 16 hybridization reactions.

last: Brown

first: Zhiyuan

last: Chen

first: Abebe

last: Menkir

first: Jiujiang

last: Yu

first: Deepak

last: Bhatnagar


title: Expression data from maize endosperm

city: Taian

first: xiang

last: li

address: No. 61 Daizong street

department: College of life science

country: China

institute: Shandong Agricultural University

summary:
Despite much knowledge is well-known on the transcriptional and enzymological regulation of  many genes in starch synthesis, including SBEⅡb, Waxy, and SUS-SH1 genes, less information is available on their expression profiles as a consequence of their dysfunction. Hence, transcriptional adjustments in response to mutations were required for a better understanding of starch biosynthesis pathway, others metabolism and cell response.
We used microarrays to detail the transcriptional adjustments in the endosperms of ae wx and sh1 at 15 days after pollination (DAP) compared to B73.

overall_design: Maize endosperms at 15 DAP were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain  homologic endosperms of middle ears in order to increase the temporal resolution of expression profiles.

first: Xiang

last: Li

first: Xian

middle: S

last: Zhang


city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

summary:
Analysis of the effect of G-alpha or GPCR mutation on the Arabidopsis Transcriptome
Keywords: Comparitive Genome Hybridization

overall_design: The transcriptomes of wild type and mutants (G-alpha and GPCR) were compared in the current study. The study was carried out on four whole genome oligo arrays. The G-alpha mutant and its corresponding wild type variety were compared on a single array by means of a dual channel experiment (Cy3 and Cy5 labeling). The experiment was repeated on a different array as a flip-dye replicate and the data from both the sets analyzed further.

first: Priyanka

last: Sharma

first: Ravi

middle: R

last: Pathak

first: Beena

last: Pillai


title: Microarray analysis of S. pyogenes Type M1-CdhA55(-) mutant

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

institute: Ohio State University

summary: A total of 192 genes were found to be differentially expressed; 38 genes of them were up regulated and 154 genes were down regulated. Most notably the functional categories that were affected include carbohydrate metabolism  and cell envelop realted genes ( 56, 29.1% of the total),Virulence genes (12 genes  6.25% of the total significantly differentiated genes),  and aminoacid transport genes (7 genes, 3.6 %).  Among the virulence-related genes, the most notable ones were those belong to the production of capsule, the M protein, exotoxin, NAD glycohydrolase and Streptolysin S.  Some of the capsule related genes were down regulated by more than 64 fold. Additionally 11 differentially expressed lipid metabolism related genes  and four aminoacid transport and metabolism-related genes were upregulated. These results indicate that the C-terminal CHAP domain of CdhA (group A Streptococcal Cell division controlling and Chain-forming cell wall hydrolase) plays an important role in the regulation of virulence. Since these mutant lack cell wall hydrolase activity but are not defective in cell division or growth, we believe that CdhA isa multifunctional protein with N-terminal region controlling cell division and c-terminal region responsible for regulating bacterial virulence.

overall_design:
S. pyogenes strain SF370 (wild-type) was procured from ATCC (ATCC 700294). M1-CdhA55(-) mutant strain was obtained using pFW5 vector containing spectinomycin resistance marker (aad9). The mutant expressing truncated CdhA that lack C-terminal 55 residues constituting catalytic site of the CHAP domain is  not defective in cell division and growth,  but lacks antiphagocytic property and attenuated for virulence.
Both strains  (M1-Wild-type and M1-CdhA55(-) were grown in Todd-Hewitt broth to their late log phase. Bacteria  were harvested by centrifugation and washed twice with sterile PBS. Total RNA was isolated from  these washed streptococci using Qiagen RNeasy Mini kit.

For synthesis and labeling of cDNA, 20 ug of total RNA, 1.5 ug of random hexamer, 0.5mM dNTPs (except that 0.2mM of dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) were used in each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen).

Purified cDNA preparations from the wild-type and  M1-CdhA55(-) mutant strains were labeled with either Alexafluor-555 or Alexafluor-647 depending on the experimental design ( i.e. dye swap experiment). Differentially labeled probes were then combined and purified.  Using three independently isolated RNA preparations (biological replicates), a total of 7 experiments (incorporating  dye swaps) were performed. Accordingly 7 hybridization measurements for this mutant were performed. Thus
Exp-1 and  2 (GSM389993, GSM389994) are the technical replicates of the biological sample-1, Exp-3 and 4 (GSM389995, GSM390054) are technical replicates of biological sample-2 and Exp-5,-6, and -7 (GSM390055,GSM390056, and GSM390057) are technical replicates of the biological sample-3.

Signals of the bound reagents on the microarray spots in terms of relative fluorescence values were measured and quantified by a laser scanner (GenePix 4100 ) at 10um/pixel resolution. The resulting images were processed using Gene Pix Pro  software (version 4.0, Axon instruments). The raw data were obtained in the form of GenPix  *.gpr output files.

The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data.  All raw data (in the form of  *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signal was applied and within microarray normalization was achieved using the Lowess method.  Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were given a weight of zero. The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. CARMAweb allows to set Log2 cut-off values for both the M (regulation) and the A (average expression) values. Differentially expressed genes (Log2 values of Mutant647-red vs. wild-type555-green or Log2 values Mutant-555(green) vs Wild-type 647-red) were defined based on cut-off value >1 Log2< i.e. all genes that show a two or more-fold up- or down-regulation.  BioConductors Multtest package provided suitable method to adjust P values according to multiple hypothesis testing problems.

first: Hong

last: Jin


title: OsMYB4-Regulated Transcriptional Network of Rice

status: Public on Sep 30 2010

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

institute: University of Maine

summary: The OsMyb4 transcription factor of rice represents a more recent example of a regulatory gene used in various attempts to develop stress-tolerant crops by regulon engineering. Although OsMyb4 confers tolerance to low temperature and drought by affecting the biosynthesis of compatible osmolytes and the phenylpropanoid metabolic process, the exact composition and scope of the OsMyb4 network has not been established from the previous analysis of heterologous overexpression in Arabidopsis. Further characterization of the OsMyb4 regulon at the global scale will facilitate understanding of the intricate underpinnings of a pathway independent of the DREB/CBF network. To dissect the OsMyb4 network of rice in relation to chilling stress response mechanisms, we conducted a gene expression profiling using transgenic rice overexpressing the OsMyb4 cDNA.

overall_design: This experiment describes the analysis of the gene expression changes as a result of supra-optimal expression of transcription factor (OsMYB4) overexpressed as transgenic in the cv. Nipponbare. Control (WT) and transgenic (OsMYB4-OX) samples were labeled with Cy3 and Cy5, respectively. No dye-swap replicates was performed in this experiment. The microarray platform used in this study was the 45k oligonucleotide microarray (www.ricearray.org), which comes in pairs of slides A and B (each containing about 50% of the total number of features). The data described in this series includes all hybridizations with slide A and with slide B. Experiments were performed with two independent biological replicates (R1 and R2) for each transgenic line.

first: Myoung-Ryoul

last: Park

first: Kil-Young

last: Yun

first: Venura

last: Herath

first: Song-Joong

last: De Los Reyes


title: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (mm8 tiling array)

city: Los Angeles

first: Yi

last: Sun

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

type: Methylation profiling by genome tiling array

summary: MicroRNAs (miRNAs) are a class of small non-coding RNAs that function as post-transcriptional regulators of gene expression. Many miRNAs are expressed in the developing brain and regulate multiple aspects of neural development including neurogenesis, dendritogenesis and synapse formation. Rett syndrome (RTT) is a progressive neurodevelopmental disorder caused by mutations in the gene encoding Methyl-CpG binding protein 2 (MECP2). While Mecp2 is known to act as a global transcriptional regulator, miRNAs that are directly regulated by Mecp2 in the brain are not known.  Using massively parallel sequencing methods, we have identified miRNAs whose expression is altered in cerebella of Mecp2-null mice before and after the onset of severe neurological symptoms.  In vivo genome-wide analyses indicate that promoter regions of a significant fraction of dys-regulated miRNA transcripts, including a large polycistronic cluster of brain-specific miRNAs, are DNA methylated and directly bound by Mecp2. Functional analysis demonstrates that the 3’ untranslated region (UTR) of messenger RNA encoding Brain-derived neurotrophic factor (Bdnf) can be targeted by multiple miRNAs aberrantly up-regulated in absence of Mecp2.  Taken together, these results suggest that dys-regulation of miRNAs may contribute to RTT pathoetiology, and also provide a valuable resource to further investigate the role of miRNAs in RTT.

overall_design: Chromatin extracted from postnatal 6-8 week old cerebellar (CB) tissues of wild-type (WT) or Mecp2-null (KO) male mice was immunoprecipitated with indicated antibodies and analyzed by a NimbleGen mouse 385K genomic tiling microarray (the array set26 of a 37-array set, which covers the mouse chromosome 12 that includes the entire Dlk1-Gtl2 imprinting domain).  Whole cell extract (WCE) was used as input controls for ChIP or MeDIP/WCE experiments. For ChIP/ChIP experiments, immunoprecipitated DNA from WT and KO CB was directly compared on the same microarrays.  DNA methylation profiles in WT CB were also analyzed by methylated DNA immunoprecipitation (MeDIP) followed by hybridization to the same genomic tiling microarrays (MeDIP-chip).

first: Hao

last: Wu


title: Expression analysis of Sphingomonas paucimobilis sp. EPA505 during biodegradation kinetics of various PAHs and detection of gene in a contaminated soil S3

city: AUBIERE

first: TERRAT

last: Sebastien

address: 24, avenue des Landais, Campus des Cézeaux

department: Génomique Intégrée des Interactions Microbiennes

institute: UMR CNRS 6023

summary:
Studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. During the biodegradation kinetics with phenanthrene, fluoranthene or a mix of both pollutants, we identified the targeted set of genes induced by these pollutants, compared to basal expression detected with glucose.
Hybridizing total DNA extracted from S3, we show the efficiency of our probe design to study a complex environment. Despite the relative small size of our probes (23-mers), their sensitivity is reliable as we can detect the presence of genes in this complex mixture.
Obtained results are further described in Sébastien Terrat, Eric Peyretaillade, Olivier Gonçalves, Eric Dugat-Bony, Fabrice Gravelat, and Pierre Peyret. 2010 - Studying the ‘Unkown’ with Metabolic Design, a new probe design software for explorative functional microarrays development. Nucleic Acids Research (submited).

sample_organism:
Sphingomonas paucimobilis
uncultured organism

overall_design: A 17 chip study was realized using total RNA recovered from separate cultures of Sphingomonas paucimobilis sp. EPA505 with phenanthrene, fluoranthene or a mix of these both pollutants as sole carbon and energy source. A negative kinetic expermient was realized with glucose as sole carbon and energy source. Each chip measures the expression level of 8 genes from Sphingomonas paucimobilis sp. EPA505 with 23-mer probes (a total of 8,048 probes) using a new design approach. We also assess metabolic capacities of microbial communities in an aromatic hydrocarbons contaminated soil named S3. Each probe was spotted in triplicate, and a total of 8,863 random probes was used to determine the background noise.

first: Sébastien

last: TERRAT

first: Eric

last: PEYRETAILLADE

first: Olivier

last: GONCALVES

last: DUGAT-BONY

first: Fabrice

last: GRAVELAT

first: Pierre

last: PEYRET


title: Microarray analysis for Streptococcus pyogenes M1-CdhA (-) mutant

summary: A total of 163 genes were found to be differentially expressed; 38 genes of them were up regulated and 125 genes were down regulated. Most notably the functional categories that were affected include Virulence genes (18 genes  11% of the total significantly differentiated genes), carbohydrate metabolism  and cell envelop realted genes ( 31, 19.1% of the total),  and aminoacid transport genes (21genes, 12.9%).  Among the virulence-related genes, the most notable one were those belong to the production of capsule, the M protein, exotoxin, NAD glycohydrolase and Streptolysin S. Some of the capsule related genes were down regulated by more than 64 fold. These results indicate that CdhA (group A Streptococcal Cell division controlling and Chain-forming cell wall hydrolase) plays an important role in the regulation of virulence.

overall_design:
S.pyogenes strain SF370 (wild-type) was procured from ATCC (ATCC 700294). M1-CdhA(-) mutant strain was obtained using pFW5 vector containing spectinomycin resistance marker (aad9). The mutant lacking CdhA is highly defective in cell division and growth,  lacks antiphagocytic property and attenuated for virulence.
Both strains  (M1-Wild-type and M1-CdhA(-) were grown in Todd-Hewitt broth to their late log phase. Bacteria  were harvested by centrifugation and washed twice with sterile PBS. Total RNA was isolated from  these washed streptococci using Qiagen RNeasy Mini kit.

For synthesis and labeling of cDNA, 20 ug of total RNA, 1.5 ug of random hexamer, 0.5mM dNTPs (except that 0.2mM of dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) were used in each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen).

Purified cDNA preparations from the wild-type and  M1CdhA(-) mutant strains were labeled with either Alexafluor-555 or Alexafluor-647 depending on the experimental design ( i.e. dye swap experiment). Differentially labeled probes were then combined and purified.  Using three independently isolated RNA preparations (biological replicates), a total of 11 experiments (incorporating  dye swaps) were performed. Accordingly eleven hybridization measurements for this mutant were performed. Thus
Exp-1 to -4 (GSM388703, GSM388717, GSM388718 and GSM388719) are the technical replicates of the biological sample-1, Exp-5 to 8(GSM388732, GSM388733, GSM388734, and GSM388735) are technical replicates of biological sample-2 and Exp-9,-10, and -11 (GSM388736,GSM388737, and GSM388738) are technical replicates of the biological sample-3.

Signals of the bound reagents on the microarray spots in terms of relative fluorescence values were measured and quantified by a laser scanner (GenePix 4100 ) at 10um/pixel resolution. The resulting images were processed using Gene Pix Pro  software (version 4.0, Axon instruments). The raw data were obtained in the form of GenPix  *.gpr output files.

The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data.  All raw data (in the form of  *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signal was applied and within microarray normalization was achieved using the Lowess method.  Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were given a weight of zero. The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. CARMAweb allows to set Log2 cut-off values for both the M (regulation) and the A (average expression) values. Differentially expressed genes (Log2 values of Mutant647-red vs. wild-type555-green or Log2 values Mutant-555(green) vs Wild-type 647-red) were defined based on cut-off value >1 Log2< i.e. all genes that show a two or more-fold up- or down-regulation.  Bioconductors Multtest package provided suitable method to adjust P values according to multiple hypothesis testing problems.


title: Number of vertebrae is fine-tuned by Notch signaling via control of period of the somite segmentation clock.

city: Ikoma

first: Woong

last: Kim

state: Nara

department: Biosciences

institute: NAIST

summary: The number of vertebrae is strictly defined for any given species1, and depends on the number of somites, which are periodically formed as perfectly matched cell masses during mid-embryogenesis, where the somite segmentation clock prescribes the timing2. The tempo of the clock is affected by surrounding condition, despite which the same number of somites is formed3, suggesting that the clock may be tunable to adapt to the environmental condition. Here, we demonstrate a tunability of the segmentation clock in the period depending on the level of Notch signaling that senses the surrounding information to adjust the number of somites and vertebrae precisely, in which we propose a mechanism of the clock with a feedback loop of Notch signaling by Notch-regulated ankyrin repeat protein (Nrarp). Disruption of Nrarp in mouse resulted in the loss of two vertebrae, due to 4-min extension of the period of the clock elicited by the up-regulation of Notch activity, whereas pharmacological diminishment of Notch activity shortens it by a few min. The Notch inhibitor rescues the phenotype of Nrarp knockout mice in the period. These results are comprehended by mathematical analyses, in which the period of the clock is fine-tuned by Notch activity that Nrarp adjusts. Overall, our results are the first to provide molecular evidence of fine-tuning of the segmentation clock that preserves the number of somites and vertebrae.

overall_design: Nrarp mutant mouse which have LacZ gene instead of Nrarp coding region was generated by homologous recombinant. Fragnant female heterozygous mutant mice, mated with heterozygous mutant male, were dissected at embryonic day 10.5 (E10.5). 12 PSMs were collected in each genotype to extract total RNA.


title: MicroRNA expression profiling of 3T3-L1 adipogenesis

city: Cambridge

first: Tarjei

last: Mikkelsen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: 3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogeneic media.

overall_design: One sample from each of four time points relative to induction of adipogenesis (day 0)

first: Zhao

last: Xu

first: Jeffery

last: Gimble

last: Lander

first: Evan

last: Rosen


title: Microarray analysis of V. cholerae genes differentially expressed in 8 h rabbit ileal loop mucus

status: Public on Sep 29 2010

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary: The mucus and cell-associated bacteria were isolated as a single fraction from ileal loops eight hours post inoculation by scraping the epithelial surface of the intestine with a disposable plastic cell scraper after the loops had been cut open and gently rinsed in PBS buffer to wash away remaining luminal fluid. The mucus gel/cell associated fraction was suspended in Trizol and frozen on dry ice. Total RNA, which includes RNA from the infecting bacteria and from the host (see below), was isolated from the thawed Trizol suspension, treated with DNaseI (Applied Biosystems, Austin, TX) and cleaned by using the RNeasy kit (Qiagen, Valencia, CA).

overall_design: Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

first: Nadia

last: Dolganov


title: Comparison of copy number variations between wildtype and BCL6 knockout BCR-ABL1-driven acute lymphoblastic leukemia

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: This comparative genomic hybridization (CGH) study investigated the effect of BCL6 on clonal evolution in BCR-ABL1-driven acute lymphoblastic leukemia (ALL). The frequencies of copy number alterations in BCR-ABL1-transformed BCL6+/+ and BCL6-/- leukemias were determined.

overall_design: Three BCR-ABL1-transformed BCL6+/+ and BCL6-/- ALL samples derived from mice were maintained for 4 month in cell culture and were subjected to CGH analysis. As control samples, normal untransformed splenoytes were used.

first: Cihangir

last: Duy

first: Christian

last: Hurtz

first: Leandro

last: Cerchietti

first: Lars

last: Klemm

first: Srividya

last: Swaminathan

first: Seyedmehdi

last: Shojaee

first: Weimin

last: Ci

first: Huimin

last: Geng

first: Melanie

last: Braig

first: Wolf-Karsten

last: Hofmann

first: H

last: Koeffler

first: J

last: Yu

first: Rahul

last: Nahar

first: Soo-mi

last: Kweon

first: Lothar

last: Hennighausen

first: Sebastian

last: Herzog

first: Hassan

last: Jumaa

first: John

last: Groffen

first: Nora

last: Heisterkamp

first: B

last: Ye

first: Ari

last: Melnick


title: Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop mucus

last: Stanford Microarray Database

summary: The mucus and cell-associated bacteria were isolated as a single fraction from ileal loops twelve hours post inoculation by scraping the epithelial surface of the intestine with a disposable plastic cell scraper after the loops had been cut open and gently rinsed in PBS buffer to wash away remaining luminal fluid. The mucus gel/cell associated fraction was suspended in Trizol and frozen on dry ice. Total RNA, which includes RNA from the infecting bacteria and from the host (see below), was isolated from the thawed Trizol suspension, treated with DNaseI (Applied Biosystems, Austin, TX) and cleaned by using the RNeasy kit (Qiagen, Valencia, CA).

first: Nadia

last: Dolganov


title: microRNA profiles of schwannomas

city: Charlestown

first: Okay

last: Saydam

address: Building 149, 13th st. 6th Floor, Room:6101

department: Neurology

institute: MGH

summary: MicroRNAs (miRNAs) negatively regulate protein-coding genes at the post-transcriptional level and are critical in tumorigenesis. Schwannomas develop from proliferation of dedifferentiated Schwann cells, which normally wrap around nerve fibers to help support and insulate nerves. In this study, we carried out high-throughput miRNA expression profiling of human vestibular schwannomas using an array representing 407 known miRNAs in order to explore the role of miRNAs in tumor growth. Twelve miRNAs were found to be significantly deregulated in tumor samples as compared with control nerve tissue, defining a schwannoma-typical signature. Among these miRNAs, we focused on miR-7 which was one of the most downregulated in these tumors and has several known oncogene targets, including mRNAs for epidermal growth factor receptor (EGFR) and p21-activated kinase 1 (Pak1). We found that overexpression of miR-7 inhibited schwannoma cell growth both in culture and in a xenograft tumor model in vivo, which correlated with downregulation of these signaling pathways. Furthermore, we identified a novel direct target of miR-7, the mRNA for associated cdc42 kinase 1 (Ack1), with the expression levels of miR-7 and Ack1 being inversely correlated in human schwannoma samples. These findings are the first analyzing miRNA profiles of schwannomas and support a “tumor suppressor” function for miR-7 in these tumors by targeting proteins in three major oncogenic pathways, EGFR, Pak1, and Ack1. Moreover, our result also suggest that miR-7 may serve as a potential therapeutic molecule for schwannomas and that drugs which inhibit these signaling pathways could suppress growth of these benign tumors.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Schwannoma tumor samples are compared to nerve controls


title: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (mm8 promoter arrays)

first: Yi

last: Sun

type: Non-coding RNA profiling by genome tiling array

overall_design: Chromatin extracted from postnatal 6-8 week old cerebellar (CB) tissues of wild-type (WT) or Mecp2-null (KO) male mice was immunoprecipitated with indicated antibodies and analyzed by NimbleGen custom mouse 385K promoter tiling microarrays (a 2-array set covering the promoter regions of all Refseq protein-coding genes and miRNA transcripts with predicted transcription start sites).  Whole cell extract (WCE) was used as input controls in all experiments.  DNA methylation profiles in WT CB were also analyzed by methylated DNA immunoprecipitation (MeDIP) followed by hybridization to the same promoter tiling microarrays (MeDIP-chip).

first: Hao

last: Wu


title: Effect of enzyme IIANtr on gene expression in Escherichia coli

status: Public on Sep 28 2010

city: Seoul

first: Yeong-Jae

last: Seok

address: San 56-1, Shillim-dong, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: Enzyme IIANtr (encoded by ptsN gene) is a component of the nitrogen phosphotransferase system (PTS). It has previously been shown that the dephosphorylated form of EIIANtr is required for the derepression of ilvBN encoding acetohydroxy acid synthase I (AHAS I) catalyzing the first step common to biosynthesis of branched-chain amino acids. Here we examine the effect of deletion of ptsN gene on global gene expression by microarray analysis. Most of the genes down-regulated in a ptsN mutant are controlled by sigma 70, while all the up-regulated genes are controlled by sigma S. As intracellular levels of sigma factors in the ptsN mutant were similar to those of the wild-type strain, this implied that the balance of sigma activities is modified by ptsN deletion.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: The E. coli K12 strain MG1655 and its isogenic ptsN mutant were used in all experiments. Overnight bacterial cultures were incubated in M9 minimal medium containing 0.5% glucose as carbon source. Cells from duplicate experiments were harvested in exponential growth phase when cultures reached an A600 of 0.4. RNA was extracted from each sample using a QIAGEN RNA extraction kit according to the manufacturer's instruction.

first: Chang-Ro

last: Lee

first: Seung-Hyon

last: Cho

first: Hyun-Jin

last: Kim

first: Miri

first: Alan

last: Peterkofsky


title: Transcript Profiling of Elf5+/- Mammary Glands During Pregnancy Identifies Novel Targets of Elf5

status: Public on Sep 27 2010

city: Darlinghurst

first: Renee

last: Rogers

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: Elf5, an epithelial-specific Ets transcription factor, plays a crucial role in the pregnancy-associated development of the mammary gland.  However, the molecular mechanisms employed by Elf5 to exert its effects on the mammary gland are largely unknown. Transcript profiling was used to investigate the transcriptional changes that occur as a result of Elf5 haploinsufficiency.  We show that the development of the Elf5+/- gland is delayed at a transcriptional and morphological level, due to the delayed increase in Elf5 protein in these glands. We also identify a number of potential Elf5 target genes, including Mucin 4, whose expression, is directly regulated by the binding of Elf5 to an Ets-binding site within its promoter. We identify novel transcriptional targets of Elf5 and show that Muc4 is a direct target of Elf5, further elucidating the mechanisms through which Elf5 regulates proliferation and differentiation in the mammary gland.

overall_design: We used Compugen 22,000 oligo arrays from the Adelaide Microarray Centre to determine the transcriptional effects of the loss of one Elf5 allele on mammary gland development. We examined Elf5+/+ and Elf5+/- mammary glands over 5 timepoints of mammary gland development in three experiments.  Each experiment used the pooled RNA of 2  mice, resulting in a total of 6 individual mice at each timepoint per genotype.  Replica 1 of each condition was labelled with the one fluorophore, and replicas 2 and 3 with the other fluorophore.  A common reference design was used for this experiment.  RNA extracted from eight pooled 17.5dpc C57BL/6 mouse embryos was used as the reference sample. In total, we performed 30 micraoarray hybridisations, examining 5 timepoints of mammary gland development in 2 genotypes (Elf5+/+ and Elf5+/-).  This experiment was repeated with a total of three biological replicates.

middle: L

first: Isabelle

last: Van Seuningen

first: Jodee

last: Gould

first: Paul

last: Hertzog

first: Matthew

last: Naylor

first: Melanie

last: Pritchard


title: MicroRNA expression profiling of human adipose stromal cell (hASC) adipogenesis

first: Tarjei

last: Mikkelsen

summary: Human abdominal adipose tissue was obtained with informed consent from a 33-year old Caucasian female (BMI = 32.96 Kg/m2) undergoing lipoaspiration. Adipose stromal cells (hASCs) were isolated and differentiated into adipocytes in vitro.

overall_design: Two technical replicates from 9 time points relative to induction of adipogenesis (day 0). Also, one sample from pre-adipocytes (day -2) grown without FGF.

first: Zhao

last: Xu

first: Jeffery

last: Gimble

first: Eric

last: Lander

first: Evan

last: Rosen


title: Expression profile of TTHA0995-deficient Thermus thermophilus HB8 strain

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

summary: In order to find function of TTHA0995 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0995-deficient strain grown in a rich medium at 70°C for 680 min.

overall_design: Three TTHA0995-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 680 min, and then, the expression of each mRNA was analyzed.

first: Yoshihiro

last: Agari

first: Miwa

last: Ohmori

first: Seiki

last: Kuramitsu


title: Gene Expression Profiling of Malignant Peritoneal Mesothelioma Patient Tumor Samples

city: Baltimore

first: Sheelu

last: Varghese

state: MD

address: 655 W Baltimore Street

department: surgery

institute: University of Maryland, Baltimore

summary: Gene expression profiles were generated from 41 consecutive surgically resected fresh frozen malignant peritoneal mesothelioma patient tumor samples to identify molecular prognostic factors.

overall_design: Patient tumor samples hybridized against the common reference (complementary DNA generated from human universal RNA), 41 tumor samples.

first: H

last: Alexander


title: Diversity of Human Copy Number Variation and Multicopy Genes

status: Public on Sep 24 2010

first: Peter

last: Sudmant

address: 77 Massachusetts Ave

institute: MIT

summary: Copy number variants (CNVs) affect both disease and normal phenotypic variation but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrate accurate estimation of absolute copy number for duplications as small as 1.9 kbp, ranging from 0-48 copies. We identified 4.1 million ‘singly unique nucleotide’ (SUN) positions informative in distinguishing specific copies, and use them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000  genes accessible to genetic studies of disease association.

overall_design:
This dataset complements the results from short read sequencing by performing validation on five individuals.

We analyzed the 17q21.1 locus in 5 HapMap individuals by array CGH on a custom Agilent 4-plex 310k array performing 1 experiment for each sample.  This array was targeted at high density (1 probe/105bp) to 7 genomic loci, including 17q21.  The reference individual used was NA19240.

middle: H

first: Jacob

middle: O

last: Kitzman

first: Francesca

last: Antonacci

last: Eichler


title: Effects of Bifidobacterium bifidum PRL2010 on gene expression in intestinal epithelial cells

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

institute: University of Aberdeen

summary:
Analysis of gene expression in Caco-2 intestinal epithelial cells stimulated with Bifidobacterium bifidum PRL2010.
We used microarrays to investigate gene expression in intestinal epithelial cells in response to Bifidobacterium bifidum PRL2010, in particular genes involved in mucin pathways.

overall_design: Caco-2 cells were grown in transwell plates to 4 days post-confluence. Cells were then incubated for 2h and 4h with Bifidobacterium bifidum PRL2010. The experiment was performed in duplicate. Caco-2 RNA was extracted and hybridized to Affymetrix NuGO_Hs1a52018 arrays.

first: Imke

last: Mulder


title: Differential expression analysis of T. thermophilus HB8 wild-type strain in response to iron

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0 and 30 min after the addition of FeSO4.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 4 mL of synthetic medium. The cells (2 mL) were inoculated into 200 mL of the same medium and then cultivated at 70°C for 9 hours (A600 value being ~0.31). Then the 1.0 mM of FeSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of iron ion, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.


title: Dynamic, mating-induced gene expression changes in female head and brain tissues of Drosophila melanogaster

first: Justin

last: Dalton

address: 1050 Child's Way, RRI

summary: Temporal gene expression changes in head tissues from mated females was determined at four time points post-mating, from 0-2 hours out to 72 hours. Each time point assayed post-mating showed a unique post-mating gene expression response, with 48 hours post-mating having the largest number of genes with expression changes.  At most time points, a marked change in expression of genes expressed in the head fat body and encode products that function in metabolism was observed. Additionally, gene expression was analyzed at 24 hours post-mating in brain tissues, identifying the repressed expression of several genes encoding ion channels.

overall_design: All microarrays were dual channel with direct comparisons of mated females versus virgin females. For each experiment, four independent biological samples were analyzed using a dye-swap design. Samples consisted of adult heads or dissected CNS collected either at 0-2, 24, 48, or 72 hours post-mating.

first: Tanvi

last: Kacheria

first: Simon

last: Knott

first: Matthew

last: Lebo

first: Allison

middle: M

last: Nishitani

first: Laura

last: Sanders

first: Emma

last: Stirling

first: Ari

last: Winbush

first: Michelle

middle: N

last: Arbeitman


title: Microarray analysis of V. cholerae genes differentially expressed in 8h rabbit ileal loop fluid.

last: Stanford Microarray Database

summary: Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 8 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from three independent experiments in three different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States).

first: Nadia

last: Dolganov


title: Expression profiling in grapevine berry during development and withering processes

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

summary: Grapevine is a commercially important fruit crop that provides berries for direct consumption, juice pressing, drying (raisins), and fermentation to produce wine. The economic value of the crop has encouraged many researchers to study the physiological and molecular basis of berry development, particularly processes that affect wine quality. Post-harvest withering of grapevine berries is used in the production of dessert and fortified wines to alter must quality characteristics and to increase the concentration of simple sugars.

overall_design: Vitis vinifera cv Corvina berries were sampled during the 2006 growing season at four developmental time points and three additional time points during the 91-day post-harvest withering process. The four developmental time points were 59, 71, 98 and 112 days after fruit set, corresponding to pre-veraison, veraison, early ripening and late ripening, and the three withering time points (WI, WII and WIII) were 35, 56 and 91 days after harvest. Three biological replicates were taken at each time point resulting in a total of 21 samples.

first: Mariasole

last: Di Carli

first: Flavia

last: Guzzo

first: Matteo

last: Stocchero

first: Sara

last: Zenoni

first: Alberto

last: Ferrarini

first: Ketti

last: Toffali

first: Angiola

last: Desiderio

first: Kathryn

last: Lilley

first: Enrico

last: Pè

first: Eugenio

last: Benvenuto

first: Massimo

last: Delledonne

first: Mario

last: Pezzotti


title: Transcriptome changes in splicing inhibited cells

city: Toyama

first: Daisuke

last: Kaida

state: Toyama

address: 2630 Sugitani

department: Frontier Research Core for Life Sciences

institute: University of Toyama

type: Expression profiling by genome tiling array

summary: In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. This did not occur when splicing was inhibited with U2 snRNA antisense morpholino oligonucleotide or the U2-snRNP-inactivating drug spliceostatin A unless U1 antisense morpholino oligonucleotide was also included. We further show that U1 snRNA–pre-mRNA base pairing was required to suppress premature cleavage and polyadenylation from nearby cryptic polyadenylation signals located in introns. These findings reveal a critical splicing-independent function for U1 snRNP in protecting the transcriptome, which we propose explains its overabundance.

overall_design: Treated HeLa cells with antisense oligos for U1 snRNP or U2 snRNP or control oligo, or methanol or spliceosotain A for 8 hours followed by analysis of total RNA on human tiling 2.0R E array. Three biological replicates were used for each treatment.

first: Gideon

last: Dreyfuss


title: LNCaP Atlas: Gene expression associated with in vivo progression to castration-recurrent prostate cancer

city: Vancouver

first: Marianne

middle: D.

last: Sadar

state: British Columbia

address: 675 W. 10th Ave

department: Genome Sciences Centre

institute: British Columbia Cancer Agency

summary: Background: There is no cure for castration-recurrent prostate cancer (CRPC) and the mechanisms underlying this stage of the disease are unknown. Methods: We analyzed the transcriptome of human LNCaP prostate cancer cells as they progress to CRPC in vivo using replicate LongSAGE libraries. We refer to these libraries as the LNCaP atlas and compared these gene expression profiles with current suggested models of CRPC. Results: Three million tags were sequenced using in vivo samples at various stages of hormonal progression to reveal 96 novel genes differentially expressed in CRPC. Thirty-one genes encode proteins that are either secreted or are located at the plasma membrane, 21 genes changed levels of expression in response to androgen, and 8 genes have enriched expression in the prostate. Expression of 26, 6, 12, and 15 genes have previously been linked to prostate cancer, Gleason grade, progression, and metastasis, respectively. Expression profiles of genes in CRPC support a role for the transcriptional activity of the androgen receptor (CCNH, CUEDC2, FLNA, PSMA7), steroid synthesis and metabolism (DHCR24, DHRS7, ELOVL5, HSD17B4, OPRK1), neuroendocrine (ENO2, MAOA, OPRK1, S100A10, TRPM8), and proliferation (GAS5, GNB2L1, MT-ND3, NKX3-1, PCGEM1, PTGFR, STEAP1, TMEM30A), but neither supported nor discounted a role for cell survival genes. Conclusions: The in vivo gene expression atlas for LNCaP was sequenced and support a role for the androgen receptor in CRPC. BMC Medical Genomics 2010, 3:43

overall_design: RNA from the hollow fibres of three mice (biological replicates) representing different stages of prostate cancer progression (AS, RAD, and CR) were used to make a total of nine LongSAGE libraries.

first: Tammy

last: Romanuik

first: Gang

last: Wang

first: Olena

last: Morozova

first: Allen

last: Delaney

first: Marco

last: Marra

middle: D


title: miRNA profiling in adult rat cardiomyocytes and myocyte-derived progenitor cells

status: Public on Sep 22 2010

city: Honolulu

first: Yiqiang

last: Zhang

state: HI

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

summary: TLDA miRNA profiling on purified rat cardiomyocytes (Myo) (Ctl) and myocyte-derived progenitor cells (MDCs) demonstrated significant dedifferentiation of myocytes and identity of stemness, cell cycle progression and proliferation in MDCs after continuous culture in mitogen-rich medium for about 2 weeks.

overall_design: Total RNA was extracted from 3 batches of myocytes or MDCs; 100ug each was subjected to TLDA microRNA profiling after preamplification using ABI's kit. Cardiomyocyte (Myo, Ctl) was used as calibrator sample.

last: ZHANG


title: A novel copper-responsive regulon in Mycobacterium tuberculosis

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

summary: In this study, we report the identification and characterization of several regulators in Mycobacterium tuberculosis.

overall_design: WT and mutant Mtb cells were grown in 7H9 minimal media to early stationary phase (OD580 = 2 and 4)

first: Richard

middle: A

last: Festa

first: Macus

last: Jones

first: Susan

last: Bulter-Wu

first: Daniel

last: Sinsimer

first: Russell

last: Gerads

first: Willianm

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