title: Gene expression profiles of Chlamydophila pneumoniae during the acute and iron mediated persistent infection

status: Public on May 15 2007

city: Berlin

first: André

middle: Paul

last: Mäurer

state: Berlin

address: Charitéplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

summary:
The obligate intracellular, gram-negative bacterium, Chlamydophila pneumoniae (Cpn), has impact as an acute and chronic disease-causing pathogen. Little is known about changes in the Cpn transcriptome during its biphasic developmental cycle (the acute infection) and persistence stages that are linked to chronic diseases. To analyze Cpn CWL029 gene expression, we designed a pathogen-specific oligo microarray and optimized the extraction method for pathogen RNA. Throughout the acute infection, ratio expression profiles for each gene were generated using 48 hours post infection as a reference. Based on these profiles, significantly expressed genes were separated into 12 expression clusters using SOM clustering and manually into the ‘early’, ‘mid’, ‘late’ and ‘tardy’ cluster classes. The latter two were differentiated because the ‘tardy’ class showed steadily increasing expression at the end of the cycle. The transcriptome of the Cpn elementary body (EB) and published EB proteomics data were compared to the cluster profile of the acute infection. We found an
intriguing association between ‘late’ genes and genes coding for EB proteins, whereas ‘tardy’ genes were mainly associated with genes coding for EB mRNA. It has been published that iron depletion leads to Cpn persistence. We compared the gene expression profiles during iron depletion-mediated persistence with the expression clusters of the acute infection. This led to the finding that establishment of iron depletion-mediated persistence is more likely a mid-cycle arrest in development rather than a completely distinct gene expression pattern.
Taken together, here we describe the Cpn transcriptome during the acute infection with ‘late’ genes correlating to EB proteins and ‘tardy’ genes to EB mRNA. Expression profiles during iron mediated-persistence led us to propose the hypothesis that the transcriptomic ‘clock’ is arrested during acute mid-cycle.
Keywords: time course, iron, persistence, Chlamydia, Chlamydophila, pneumoniae, recovery, pathogen, life cycle, developmental cycle

overall_design:
A 50mer oligo array containing all open reading frames of the genome projects of CWL029 (http://www.stdgen.lanl.gov), AR39 (garnet.Berkeley.edu) and J138 (http://kantaro.grt.kyushu-u.ac.jp/J138/ident/index.html) was designed. To ensure maximum specificity, oligo sequences were compared for homology against the human genome using the BLAST algorithm. Design and spotting was done by MWG-Biotech AG (Germany). Cross-hybridization of eukaryotic RNA was confirmed to be marginal by labeling and hybridizing eukaryotic total RNA with the described procedure. Arrays were blocked prior to
hybridization by incubation for 45 min at 42°C in blocking solution (4x SSC, 0.5% SDS, 1% BSA), washed five times with H20 and dried by centrifugation (1000 rpm, RT, 2 min). Microarray experiments were done as two-color hybridizations. In order to compensate for dye-specific effects and to ensure statistically relevant data, a color swap was performed.
Reverse transcribed cDNA pools were mixed with hybridization buffer (Ambion), denatured, snap-cooled, pipetted onto the array using Lifter Slips (Erie, USA) and placed in a sealed humidified hybridization chamber (Scienion, Germany) at 42° C for 48 hours without shaking.
After hybridization the array was washed and dried according to the Ambion protocol.
Scanning of microarrays was performed with 5 μm resolution using a microarray laser scanner (Agilent). Features were extracted using the Agilent Technologies image analysis software (Version A7.5) using default settings for non-Agilent microarrays. A local background subtraction method was used and the background was adjusted globally to zero.
Dye normalization was done using the rank consistency method and applying a local weighted regression normalization (LOWESS). The ratio between both channels, the log ratio error and the p-values were calculated using default settings. Data analysis was carried
out on the Rosetta Inpharmatics platform Resolver Buildt 4.2. Transcriptome analysis was carried out with two biological replicates for 36 hpi and at least three biological replicates for all other time points. Samples were derived from independent infections, RNA preparations, labeling reactions and hybridizations. We selected genes using a 1.8-fold expression cut-off. All data of the individual sets comprising different time points were combined as Ratio Experiments using negative polarity for the color swap dye-reversal hybridizations. This was achieved by combining the Ratio Profiles, representing single hybridizations, and using an error weighted average based on p-values.

first: Andre

middle: P

last: Maeurer

first: Adrian

last: Mehlitz

first: Hans

last: Mollenkopf

first: Thomas

middle: F

last: Meyer


title: profiling of hypothalamus from mice s.c. injected with 4T-1 mammary carcinoma cells vs. PBS

status: Public on May 02 2007

city: Ciudad de Buenos Aires

first: Mariano

middle: Cesar

last: Salibe

address: Av. Patricias Argentinas 435

country: Argentina

institute: Gentron LLC

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of mammary carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the hypothalamus. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes.
Keywords: gene expression profile of the hypothalamus in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 5 samples (biological replicates) for 18 h and 4 samples for 72 h and 192 h time points.

middle: C

middle: J

last: Alvarez

first: Cintia

middle: G

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

middle: L

last: Podhajcer

first: Fernando

last: Pitossi


title: Expression profiling of T. rubrum treated with amphotericin B and ketoconazole

status: Public on May 30 2007

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

summary:
Two antifungal agents, ketoconazole (KTZ) and amphotericin B (AMB), have specific activity against dermatophytes.A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and transcriptional profiles of the responses to KTZ and AMB were determined. Some class-specific and mechanism-independent changes in gene expression were found.
Keywords: comparison of expression status

overall_design: The expression profiles of Trichophyton rubrum treated with AMB and KTZ were compared to those of Trichophyton rubrum without drug. Each treatment has three replicates.


title: Optimization and Clinical Validation of a Pathogen Detection Microarray

status: Public on May 29 2007

city: Singapore

first: Christopher

last: Wong

address: 60 Biopolis St #02-01

country: Singapore

institute: Genome Institute of Singapore

summary:
This series includes microarrays from 36 patient samples and 2 cell-culture controls, used to optimize and validate the pathogen detection microarray (Wong, et. al. 2007)
Keywords: viral pathogen detection

sample_organism: Severe acute respiratory syndrome-related coronavirus

overall_design: The microarray contains tiling probes to 35 viruses, and was used to detect the viruses present in 36 patient samples.  Viruses were reverse-transcribed and PCR-amplified using either primer A1 or AES-optimized primer A2 as described (Wong , et. al. 2007).  Those samples which were amplified using primer A2 are labelled with "A2" in the sample title.  Patient samples #122 and #412 were hybridized on multiple arrays (technical replicates).  The SARS and Dengue samples were amplified using virus-specific primers as described in Wong, et al. 2007.

middle: W

first: Charlie

last: Lee

first: Wan

middle: Y

last: Leong

first: Shirlena

last: Soh

first: Cissy

middle: B

last: Kartasasmita

first: Eric

middle: A

last: Simoes

first: Martin

last: Hibberd

first: Wing-Kin

last: Sung

first: Lance

middle: D

last: Miller


title: profiling of hypothalamus from mice s.c. injected with LL/2(LLC1) lung carcinoma cells vs. PBS

first: Mariano

last: Salibe

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold 1-5. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of lung carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the hypothalamus. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes
Keywords: gene expression profile of the hypothalamus in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 4 samples (biological replicates) for 18 h time point, 5 samples for 72 h time point, and 6 samples for 192 h time point.

last: Alvarez


title: profiling of midbrain from arthritic DBA/1 mice vs. control DBA/1 mice

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Using microarrays we studied the gene expression profile of the midbrain in DBA/1 mice strain that developed collagen induced-arthritis vs control mice.
Keywords: gene expression profile of the midbrain in response to induction of arthritis

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyze changes in gene expression profile in the midbrain of arthritic vs control mice. We performed 3 samples (biological replicates)

first: Cintia

last: Serra

last: Celi


title: 16p13 aberrations predispose to autism and MR

status: Public on May 22 2007

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

type: Genome variation profiling by genome tiling array

summary:
Autism and mental retardation (MR) are often associated, suggesting that these conditions are etiologically related.  Recently, array-based comparative genomic hybridization (array CGH) has identified submicroscopic deletions and duplications as a common cause of MR. This prompted us to search for such genomic imbalances in autism and related disorders.  Here we describe a 1.5 Mb duplication on chromosome 16p13.1, found in four autistic male patients from three families and several variably affected and unaffected relatives. A deletion of the same interval was identified in three unrelated patients with MR and other clinical abnormalities.  Duplications and deletions of this interval have not been described before, neither as copy number variants in the Database of Genomic Variants nor in >600 individuals from other cohorts examined by high resolution array CGH in our laboratory. Thus, this is the first description of a recurrent genomic imbalance predisposing to autism and/or MR.
Keywords: array CGH

overall_design: In this study, we have analysed six index patients and some of their relatives by submegabase resolution array CGH. Experiments were done without dye swap.


title: Mating response of three yeast species (S. cerevisiae, S. paradoxus and S. mikatae)

status: Public on May 20 2007

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

summary:
We examined the mating response of three yeast species, by subjecting a-type cells from each of them to alpha-factor (6uM). The expression of cells before and after (60min) addition of alpha-factor were compared using S. cerevisiae cDNA microarrays. In addition, we verified our results with a true mating experiment: the expression of a-type and alpha-type cells from S. cerevisiae were compared before and after mixing them for 90 minutes (i.e. allowing them to mate).
Keywords: yeast mating response, comparison among species

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus
Saccharomyces mikatae

overall_design: Three (or four) samples were processed in parallel for each species (biological replicates). All samples were measured by hybridization to S. cerevisiae cDNA microarray


title: Profiling miRNAs in human retinoblastoma

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

summary:
Total RNA samples from three different retinoblastoma samples were profiled for a panel of 160 human miRNAs.  Three replicates of normal retina was also included.
Keywords: disease-state analysis

overall_design: Absolute intensities were measured following hybridixzation of direct labelled total RNA from the samples listed above.

first: Jim

last: Huang

first: Timothy

middle: R

last: Hughes

last: Corson

first: Brendan

last: Frey

first: Quaid

last: Morris

first: Gordon

last: Chua

first: Benjamin

last: Blencowe


title: Interstitial del(14)(q) involving IGH: a novel recurrent aberration in B-NHL

status: Public on May 01 2007

city: Leuven

first: Helena

last: Pospisilova

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: Catholic University Leuven

summary:
Using high-resolution array comparative genomic hybridization, we mapped del(14)(q) in a series of 23 B-cell leukemia/lymphoma cases. Interestingly, 14 cases with interstitial del(14)(q) showed  involvement of IGH at 14q32.33. Whereas the proximal breakpoints of these deletions varied in 6 cases, they clustered in the 14q24.1/ZFP36L1 region in the 8 remaining cases. The latter del(14)(q24.1q32.33) covering approximately 36 Mb was further demonstrated in 12 additional patients by FISH. The majority of cases harboring this deletion were diagnosed as chronic lymphocytic leukemia (CLL) (75%), particularly atypical CLL, and were frequently associated with trisomy 12 (40%) and unmutated VH region (75%). Further analysis of the 14q32.33 breakpoints showed clustering in the constant region of IGH, proximal to the 5’ (Eµ) enhancer sequences. These findings therefore suggest that the del(14)(q24.1q32.33), and other analogous IGH-involving del(14)(q), might represent a novel aberration leading to activation of unknown oncogene(s) at 14q by its juxtaposition with regulatory elements of IGH. Extensive expression analysis via quantitative PCR and microarray profiling, however, failed to identify a gene uniformly upregulated in cases with del(14)(q24.1q32.33). Further investigations are needed to unravel the mechanism(s) and role of IGH-involving del(14)(q) in B-cell malignancies.
Keywords: comparative genomic hybridization

overall_design: 23 lymphocyte samples of B-NHL (B-cell non-Hodgkin lymhomas) were compared to lymphocyte samples of normal individuals. All experiments were carried out in sex-mismatch fashion.

first: Mathijs

last: Baens

first: Lucienne

last: Michaux

first: Michel

last: Stul

first: Paul

last: Van Hummelen

first: P

last: Van Loo

first: Joris

last: Vermeesch

first: Marie

last: Jarosova

first: Zuzana

last: Zemanova

first: Kyra

last: Michalova

first: I

last: Van den Berghe

first: HD

last: Alexander

first: Anne

last: Hagemeijer

first: Peter

last: Vanderberghe

first: Jan

last: Cools

first: Chris

last: De Wolf-Peeters

last: Marynen

first: Iwona

last: Wlodarska


title: profiling of prefrontal cortex from arthritic DBA/1 mice vs. control DBA/1 mice

first: Mariano

last: Salibe

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Using microarrays we studied the gene expression profile of the prefrontal cortex in DBA/1 mice strain that developed collagen induced-arthritis vs control mice.
Keywords: gene expression profile of the prefrontal cortex in response to induction of arthritis

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyze changes in gene expression profile in the prefrontal cortex of arthritic vs control mice. We performed 3 samples (biological replicates)

last: Alvarez

first: Cintia

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

last: Podhajcer

first: Fernando

last: Pitossi


title: HSA21 gene expression between Down Syndrome and control cell lines

city: PARIS

first: Emilie

last: Aït Yahya Graison

address: 2 place jussieu

department: UFR BIOCHIMIE

country: France

institute: UNIVERSITE PARIS 7

summary:
Background: Down syndrome is the most common genetic cause of mental retardation in humans, occurring in ~1 in 800 newborns.  It is caused by chromosome 21 trisomy.  Disruption of the phenotype is thought to be the result of gene dosage imbalance. The aim of the study was to classify chromosome 21 genes according to their level of expression in Down syndrome.
Results: Variations in chromosome 21 gene expression were analyzed in lymphoblastoid cell lines derived from 10 Down syndrome patients and 11 control individuals.  Of the 359 genes and predictions displayed on a specifically designed high content chromosome 21 oligoarray, 132 genes were expressed in lymphoblastoid cell lines.  By using a powerful statistical analysis, 58 genes were found overexpressed and 42 unchanged in cell lines from Down syndrome patients. Microarray data were validated by quantitative PCR on 10 genes.
Conclusions: The 132 chromosome 21 genes expressed by derived lymphoblastoid cell lines  were classified into four categories: Class I: 24 genes controlled by the gene dosage effect with an increase in expression in Down syndrome between 1.4 and 1.6; Class II: 14 amplified genes with expression ratio above 1.6; Class III: 32 compensated genes with expression ratio between 0.82 to 1.4 and Class IV: 30 genes with high variability between individuals.  Class I and II genes are likely to be involved in the Down syndrome phenotype, in contrast to the compensated  Class III genes; Class IV genes could account for the variable phenotypes observed in patients.
Keywords: HSA21 gene expression in Down syndrome

overall_design: We chose a design involving 40 arrays. Samples from a same patient are marked the same number of times with each fluorescent dye (Cy3 or Cy5). On each array a DS lymphoblastoid cell line and a control lymphoblastoid cell line were compared to increase the precision of the disease effect. Ten arrays compared either i) a male with DS versus a male without DS; ii) a female with DS versus a female without DS; iii) a male with DS versus a female without DS, and finally iv) a female with DS versus a male without DS.

first: Julie

last: Aubert

first: Luce

last: Dauphinot

first: Isabelle

last: Rivals

first: Marguerite

last: Prieur

first: Geoffroy

last: Golfier

first: Jean

last: Rossier

first: Léon

last: Personnaz

first: Nicole

last: Créau

first: Henri

last: Bléhaut

first: Stéphane

last: Robin

middle: M

last: Delabar

first: Marie-Claude

last: Potier


title: Transcriptional network between pCAR1 and KT2440 chromosome

city: Sendai

first: Masatoshi

last: Miyakoshi

state: Miyagi

address: Aoba-ku, Katahira, 2-1-1

department: Department of Environmental Life Sciences

country: Japan

institute: Tohoku University

summary:
The completely sequenced catabolic plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon the recipient strain Pseudomonas putida KT2440.  To study the coordinated expression of pCAR1 with its host chromosome, transcriptome of the transconjugant strain KT2440(pCAR1) was analyzed at growth with carbazole as the sole carbon source compared to succinate as an alternative carbon source.
Next, horizontal gene transfer of a plasmid potentially alters the transcriptome of its host chromosome.  Transcriptome of the transconjugant strain KT2440(pCAR1) was compared to the parental strain KT2440 at the same growth conditions.
Furthermore, pCAR1 encodes a possible global regulator designated ORF70, which belongs to the MvaT family of H-NS-like nucleoid-associated proteins in Pseudomonas.  To investigate the regulon under the control of ORF70, transcriptome of KT2440(pCAR1deltaORF70) was compared to the parental strain KT2440(pCAR1) at the same growth conditions.
Keywords: Comparative transcriptome analysis

overall_design: We conducted two independent microarray experiments (biological replicates) for each strain in exponential phase of growth. We compared three sets of strains or growth conditions; KT2440(pCAR1) at growth with carbazole vs. KT2440(pCAR1) at growth with succinate, KT2440(pCAR1) at growth with succinate vs. KT2440 at growth with succinate, and KT2440(pCAR1) at growth with succinate vs. KT2440(pCAR1deltaORF70) at growth with succinate.  We calculated the fold change as the ratio between signal averages of two controls and two treatments.

first: Masaki

last: Shintani

first: Tsuguno

last: Terabayashi

first: Hideaki

last: Nojiri


title: Sugarcane transcriptome - Response to N2-fixing endophytic bacteria association

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

summary:
Sugarcane plantlets from a variety with high inputs of N obtained from BNF (genotype SP70-1143, CTC, Brazil) free of microorganisms were obtained by sterile meristem culture and micropropagation according to the method of Hendre et al. (1983). In vitro-grown SP70-1143 rooted sugarcane plantlets were inoculated as described by James et al. (1994) with 0.1 ml of 106–107 bacterial suspension. Controls were inoculated with medium only. Endophytic diazotrophic bacteria used were Gluconacetobacter diazotrophicus (PAL5 strain) or a mixture of Herbaspirillum seropedicae (HRC54 strain) and H. rubrisubalbicans (HCC103 strain). All plants were maintained at 30°C with an irradiance of 60 µmol photons m–2 s–1 for 12 h d–1. One day after the inoculation, plant tissues were examined for bacterial colonization by the Most Probable Number (MPN) estimation, according to the methods of Reis et al. (1994) and plantlets were collected and immediately frozen in liquid nitrogen. Five plantlets were polled for each treatment. Extraction of total RNA was performed separately on each sample pool.
Keywords: comparison of associations with different endophytic bacterias

overall_design: For each endophytic bacteria association tested, RNA from experimental sample and from its respective control sample (untreated plants) was used for hybridization to dual channel arrays. Two biological replicates were used for each experimental point. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).

first: Fabiano

last: Vinagre

first: Adriana

middle: S

last: Hemerly

first: Flávia

last: Rocha

last: Papini-Terzi

last: Nishiyama-Jr

first: Ricardo

middle: Z

last: Vêncio

first: Renato

last: Vicentini

first: Gláucia

last: Souza


title: Sugarcane transcriptome - MeJa treatment

summary:
Sugarcane one-eyed seed sets (genotype SP80-3280, CTC, Brazil) were planted in 200 ml plastic cups containing a commercial planting mix (Plantmax, Eucatex) and cultivated for 20 days under greenhouse conditions. The plantlets were subsequently transferred to a growth chamber at 26°C on a 16 h/8 h light/dark cycle with a photon flux density of 70 µE.m-2.s-1 to acclimate. Plantlets were then sprayed with a 100 µmol.L-1 MeJA solution (Bedoukian Research Inc., Danbury, CT), whereas control plantlets were treated with distilled water. Leaves were collected  0, 1, 6and 12 h after exposure to MeJA and immediately frozen in liquid nitrogen. Six plantlets were used for each time point. Extraction of total RNA was performed separately on each sample pool.
Keywords: time course of hormone treatment

overall_design: RNA from experimental sample and from the control sample (0 h) was used for hybridization to dual channel arrays. Two biological replicates were used for each experimental point. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).

first: Vicente

middle: E

last: de Rosa Jr

first: Marcelo

last: Menossi

first: Eugênio

last: Ulian


title: profiling of Hypothalamus from arthritic C57Bl/6 mice s.c. vs. control C57Bl/6 mice

first: Mariano

last: Salibe

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Using microarrays we studied the gene expression profile of the hypothalamus in C57Bl/6 mice strain that developed collagen induced-arthritis vs control mice.
Keywords: gene expression profile of the hypothalamus in response to induction of arthritis.

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyze changes in gene expression profile in the hypothalamus of arthritic vs control mice. We performed 3 samples (biological replicates)

last: Alvarez

first: Cintia

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

last: Podhajcer

first: Fernando

last: Pitossi


title: D. nodosus grown in the presence/absence of ground hoof

city: Melbourne

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

summary:
This study aimed to identify genes that were differentially expressed when D. nodosus was grown on agar media supplemented with ground hoof compared to the standard agar media.
Keywords: growth response to hoof material

overall_design: Bacteria were grown on EYE agar or EYE agar with 2% ground hoof agar plates for 2 days before Trizol extraction of RNA. Four biological replicates including two dye swaps were analysed. Raw data was compiled using IMAGENE. Normalisation and statistical analysis was undertaken using BASE. Statistics were performed using the Wilcoxon signed ranked test.

first: Dane

last: Parker

first: Garry

last: Myers

first: Ruth

last: Kennan

first: Ian

middle: T

last: Paulsen


title: Soybean, resistant & susceptible response to P.sojae

city: London

first: Mark

last: Gijzen

address: 1391 Sandford St

department: Agriculture & AgriFood Canada

institute: SCPFRC London

summary:
Soybean response to P.sojae infection, Harosoy 63 (resistant cultivar) & Harosoy (susceptible cultivar) at 0,3,6,12,24,48 hours after inoculation.
Keywords: Time course

overall_design: 11 microarray slides GPL3015; 2 soybean cultivars, Harosoy63 (resistant response) and Harosoy (susceptible reponse); 2 biological reps for each infected time point with dye swap on the 2nd rep. Total RNA isolated from the etiolated hypocotyl at 0,3,6,12,24 & 48 hours after infection. Slide data was analyzed in GeneSpringGX7.3 Agilent Technologies, using background subtracted values. The ratio for resistant/susceptible was calculated from the 2 colour hybridization (same slide) and relative expression for infection development in each cultivar was calculated using all the slides as single channel data.The slide identites are biological rep1 GSM108299 toGSM108303, biological rep 2 GSM108304 to GSM108308 and water inoculated, 0 hour, GSM108309

first: Dinah

last: Qutob

first: Pat

last: Moy


title: Profiling of genes regulated by TGF-beta in immortalized skin keratinocyte cells(HaCaT).

city: Bangalore

first: Paturu

last: Kondaiah

address: C.N.R. Rao Circle

department: Molecular Reproduction, Development and Genetics

country: India

institute: Indian Institute of Science

summary:
TGF-beta is one of the key cytokines implicated in various disease processes including cancer. TGF-beta inhibits growth and promotes apoptosis in normal epithelial cells and in contrast, acts as a pro-tumour cytokine by promoting tumour angiogenesis, immune-escape and metastasis. The effect of TGF-beta on the regulation of gene expression is cell-type specific. In order to identify TGF-beta regulated genes in different cell-types, we followed the expression profiling approach.
Keywords: cell type specific response to TGF-beta

overall_design: To identify genes regulated by TGF-beta in different cell-types, we chose HaCaT cells and lung epithelial cells.  Cells were plated and propagated in designated media and TGF-beta treatments were carried out in serum free conditions at various time intervals, 1hr, 4hr and 12hr. The RNA was extracted and expression profiling was performed using microarray experiments on 19K cDNA arrays after labeling the cDNAs with Cy3 and Cy5 dyes. The image and data analysis was performed using Quantarray (P.E. Life Sciences, USA) and Avadis (Strand Life Sci. India) softwares. The results are computed as log2 transformed fold changes between treated and untreated cells.

first: Prathibha

last: Ranganathan

first: Animesh

last: Agrawal

first: Raghu

last: Bhushan

first: Ravikiran

last: Kalathur

first: Takashi

last: Takahashi


title: E. coli K-12 mutants yceP, trpE, and tnaA biofilm cell 24 hr for indole paper

city: College Station

first: Jintae

last: Lee

state: TX

department: Chemical Engineering

country: USA

institute: Texas A&M University

summary:
Gene expression of (i) K-12 yceP biofilms upon addition of 600 µM indole in LB glu medium, (ii) K-12 biofilms due to the trpE mutation in LB glu medium, and (iii) K-12 biofilms due to the tnaA mutation in LB medium.
Keywords: indole effect and cell type comparison

overall_design:
Strains:E. coli K12 BW25113 delta yceP, trpE, tnaA and wild type
Medium:LB glu or LB
Biofilm cells grown on glass wool
Harvest time:24hr

first: Thomas

middle: K

last: Wood


title: Nitrosomonas europaea cells treated with chloromethane for one hour and compared to untreated cells

status: Public on Apr 30 2007

city: Corvallis

first: barbara

last: gvakharia

state: OR

address: Cordley Hall 4097

department: Botany and Plant Pathology

institute: OSU

summary:
We analyzed the global transcriptional response of N. europaea when exposed to  chloromethane (3.2 mM for 1 h).  Chloromethane treatment led to down regulation of 175 genes and  up regulation of 67 genes. This treatment was less harmful to the cells than chloroform
Keywords: stress response, global transcription, toxin-antitoxin genes

overall_design: We selected chloromethane concentration and exposure time that caused significant changes in cell physiology but without being too severe. Our  experiments demonstrated that 3.2 mM chloromethane  caused the desired effect. Based on the physiological, proteomic and transcriptional observations, we  analyzed the whole-genome transcriptional responses of N. europaea at 1 h after the chloromethane  treatment. Cells from treated samples and untreated control samples were collected  for RNA extraction and hybridization with Affymetrix microarray GeneChip.


title: JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 genomic arrays

first: Julian

last: Rood

summary:
Comparing the genetic content of strains JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 to wild-type strain JIR3356.

Comparison of JIR3356 with itself to eliminate any variation that may occur with the technique. This experiment should not produce any statistically significant expression changes.
Keywords: genomic hybridisation

overall_design: Two biological replicates were analysed per strain, which included a dye swap. Raw data was compiled using IMAGENE. Normalisation and statistical analysis was undertaken using BASE. Statistics were performed using the Wilcoxon signed ranked test.

first: J

last: Songer


title: Prediction of metastasis from low-malignant breast cancer by gene expression profiling

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

summary:
Promising results for prediction of outcome in breast cancer has been obtained by genome wide gene expression profiling. Some studies have suggested that an extensive overtreatment of breast cancer patients might be reduced by risk assessment with gene expression profiling. A patient group hardly examined in these studies is the low-risk patients who are very difficult to differentiate with currently used methods. These patients do not receive adjuvant treatment according to the guidelines of the Danish Breast Cancer Cooperative Group (DBCG). In this study a group of tumors from low-risk patients was examined with gene expression profiling. An intermediate risk group of low-malignant T2 tumors that fulfilled all other low-risk criteria than tumor size was included to increase statistical power. A 32-gene classifier, HUMAC32, was identified and it accurately predicted metastases. The classifier was also validated in an independent group of high-risk tumors resulting in comparable performance of HUMAC32 and a 70-gene classifier developed for this group. Furthermore, the 70-gene signature was tested in the present low- and intermediate-risk samples. The results indicated better performance of HUMAC32 among the low-malignant cancers compared to the 70-gene classifier. This may indicate that although the metastatic potential of a tumor is on the whole determined by the same genes in tumors with different characteristics and risk, some expression patterns have higher predictive power in the low-risk group.
Keywords: case-control design

overall_design:
In this study, a group of low-risk node-negative patients with long follow-up was studied with the aim to predict metastasis in this group by gene expression profiling using a 29K chip composed with 60-mer oligonucleotides. Thirteen patients who fulfilled the low-risk criteria, defined by DBCG, and who developed metastasis were matched with 13 patients who did not develop metastasis within 10 years (L samples). The DBCG low-risk criteria are essentially the same as the criteria defined at the eighth St. Gallen meeting in 2003: Node negative, T ≤ 20 mm, grade = 1 if ductal carcinoma NOS (not otherwise specified), receptor positive, and age ≥ 35.  In addition a group of 17 intermediate-risk tumors (Node negative, T ≤ 50 mm, grade = 1 if ductal carcinoma NOS, receptor positive, and age ≥ 35) from patients who developed metastasis and 17 matched non-metastasizing tumors was included. This group did not fulfill the DBCG low-risk criteria because the tumor size was 20-50 mm, but satisfied all other criteria (R samples)
Metastasis: A-samples
Non-metastases: B-samples

first: Qihua

last: Tan

first: Fryja

last: Eiriksdottir

first: Martin

last: Bak

first: Soeren

last: Cold

first: Torben

last: Kruse


title: regulation of Listeria monocytogenes internalin-like genes by σB and PrfA as revealed by subgenomic microarray analyses

status: Public on Apr 28 2007

city: Ithaca

first: Patrick

last: Mc Gann

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

summary:
The Listeria monocytogenes genome contains more than 20 genes that encode cell surface-associated proteins termed internalins, which are characterized by the presence of multiple leucine-rich repeats.  Subsets of internalin genes have been reported previously as transcriptionally regulated by the stress responsive sigma factor B (inlA, inlB, inlC2 and inlD) and the pleiotropic transcriptional activator PrfA (inlA, inlB, inlC).  To investigate contributions of σB and PrfA to internalin gene regulation, we designed a sub-genomic microarray containing two probes for each of the 24 internalin-like genes present in the L. monocytogenes 10403S genome.  Competitive microarray hybridization was performed on RNA extracted from (i) the 10403S parent strain and an isogenic ΔsigB strain; (ii) 10403S and an isogenic ΔprfA strain; (iii) a 10403S derivative that expresses the constitutively active PrfA* (G155S) and the ΔprfA strain; and (iv) 10403S and an isogenic ΔsigBΔprfA strain.  σB- and PrfA-dependent transcription of selected genes was further confirmed by quantitative reverse transcriptase PCR.  Statistical analyses of microarray data demonstrated that use of two probes on a microarray for a given target gene yielded more reliable transcriptional profiling information than use of a single probe.  The suitability of the PrfA* strain for examining PrfA-dependent gene expression was established quantitatively by the observation that the plcA and prfA transcript levels generated by the PrfA* strain were similar to those obtained from intracellular L. monocytogenes and significantly higher than those in a wildtype strain grown in BHI broth.  Among the 24 internalin-like genes examined, 4 and 6 were positively regulated by PrfA and σB, respectively, including inlA and inlB, which were positively regulated by both PrfA and σB.  In summary, our findings clearly establish broad roles for both PrfA and σB in regulating L. monocytogenes internalin gene expression
Keywords: Listeria monocytogenes, Internalins, sigB, PrfA, Microarrays

sample_organism:
Listeria monocytogenes
Listeria monocytogenes 10403S

overall_design: For all experiments, each strain was grown in BHI at 37oC with shaking (200 rpm) to OD600=0.4, then diluted 1:100 into fresh BHI and grown to OD600=0.4.  Cells were then exposed to conditions designed to induce PrfA or sB activity (0.2% charcoal or 0.3 M NaCl, respectively).  Specifically, to collect RNA for identification of PrfA-dependent genes, 0.2% charcoal (“BHI-charcoal”) was added to early-log phase (OD600=0.4) 10403S and DprfA cells, which were subsequently incubated with shaking for 120 min at 37°C.  To collect RNA for identification of PrfA-and sB-dependent genes, early-log phase 10403S and DprfADsigB cells were incubated with shaking for 120 min at 37°C in BHI with 0.2% charcoal.  NaCl was added (0.3 M final concentration) for the final 10 min (“BHI-charcoal+NaCl”).  To collect RNA for identification of sB-dependent genes, early-log phase 10403S and DsigB cells were incubated for 120 min in BHI with NaCl added (0.3 M final concentration) for the final 10 min (“BHI+NaCl”).  To collect RNA for identification of PrfA- dependent genes in the prfA* strain, early-log phase prfA* and DprfA cells were subsequently incubated for 120 min in BHI.  After these exposures, RNA was stabilized by the addition of two volumes of RNAprotect™ (Qiagen, CA, USA).  Bacterial cells were then harvested by centrifugation and stored at –80oC for no longer than 24 h before RNA isolation. For each growth condition described above, RNA isolations were performed on three different days to provide independent biological replicates.  Each set of RNA samples was used to perform competitive hybridization microarray experiments.

last: McGann

first: Sarita

last: Raengpradub

first: Renata

last: Ivanek

last: Wiedmann

first: Kathryn

middle: J

last: Boor


title: Methylation-silenced genes in colorectal cancer cell lines

status: Public on May 14 2007

city: Chiba

first: Satoshi

last: Fukutomi

address: 1-8-1 Inohana Chuoku

department: General Surgery

institute: Chiba University

type:
Expression profiling by array
Methylation profiling by array

summary:
Using an oligonucleotide array, we undertook a genome-wide search for genes upregulated following treatment with a demethylating agent in two CRC cell lines. Promoter methylation status was determined in 12 CRC cell lines and 11 CRC tissues. After the treatment, 350 genes were upregulated 1.5 fold or more. Six genes (PAGE-5, VCX, MAEL, GAGED2, UCHL1, and GAGE7), which contained putative 5'CpG islands in their promoter regions, were confirmed to be silenced in CRC cell lines. The median level of UCHL1 gene expression in cell lines with methylation was significantly lower than that in cell lines without methylation (P = 0.032). The level of methylation of UCHL1 was significantly higher in tumors than in corresponding normal mucosae (P = 0.005). Chemical genomic screening led to the identification of a specific promoter subject to hypermethylation in CRC. These results suggest that aberrant promoter methylation is the primary mechanism of transcriptional silencing of the UCHL1 gene and that methylation of the UCHL1 gene promoter increases during the development and progression of CRC
Keywords: Methylation Analysis

overall_design: This study explored methylation-silenced genes in colorectal cancer (CRC) cell lines. Using an oligonucleotide array, a genome-wide search for genes upregulated following treatment with a demethylating agent, 5-aza-2’-deoxycitidine, in two CRC cell lines, DLD-1 and HT-29, was performed. Promoter methylation status of candidate genes silenced and upregulated following the treatment was determined in 12 CRC cell linesby methylation-specific PCR.


title: Auratus goldfish genomics project - E2 effect on male goldfish hypothalamus

status: Public on May 10 2007

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary:
Adult male goldfish, exposed to estrogen (E2) implant, 1 day exposure

See the following for further details;
Marlatt VL, Martyniuk, CJ, Zhang, D, Xiong, H, Xia, X, Trudeau, VL, Moon, T.  Tissue-specific auto-regulation of estrogen receptor subtypes and transcript profiling of estrogen-responsive genes in the neuroendocrine brain of male goldfish (Carassius auratus) exposed to 17beta-estradiol. J. Mol. Endocrinol. (accepted).
Keywords: Estrogen effect on male goldfish hypothalamus, microarray

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design:
Slide 25 and 35 are dye swap
2-3 hypothalami per sample


title: Mesangial Cell Study

first: Maria

last: Schache

institute: St Vincents Institute

summary:
mesangical cells exposed to glycated albumin with and without aminoguanidine compared in a loop design with dye swaps and one total replication (total of 12 slides)
Keywords: loop

overall_design: loop with dye-swaps..arrayed twice

first: Schache

last: Maria


title: Ratios for G1 arrested cells (Agilent array)

status: Public on May 16 2007

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

institute: Hebrew University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states.
Keywords: Chip-chip, time course, histone turnover

overall_design: Ratios between Gal-induced H3-Flag and constitutive H3-Myc at 4 time points for G1-arrested yeast. Hybridization to 44K Agilent arrays covering the yeast genome at ~265bp-resolution.

first: Michael

middle: F

last: Dion

first: Minkyu

last: Kim

first: Stephen

last: Buratowski

first: Nir

last: Friedman

first: Oliver

last: Rando


title: Epigenetic natural variation in Arabidopsis thaliana

status: Public on May 09 2007

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

summary:
Ecotype-specific differences in genome methylation were assayed in Arabidopsis Col and Ler variations using genomic tiling microarrays. Comparative genome hybridization was also performed so that the contribution of ecotype-specific amplifications and deletions could be estimated and integrated into the analysis of differential DNA methylation.
Keywords: methylation analysis and comparative genome hybridization

overall_design: Methylation analysis of the two ecotypes as well as the CGH was performed in independent experiments consisting of 3 replicated dye reversal experiments each for a total of 6 measurements per probe per experiment.

middle: W

first: Milos

last: Tanurdzic

first: Zachary

last: Lippman

first: Hongmei

last: Jiang

first: Robert

last: Carasquillo

first: Pablo

last: Rabinowicz

first: Neilay

last: Dedhia

first: W

last: McCombie

first: Nicholas

last: Agier

first: Agnes

last: Bulski

first: Vincent

last: Colot

first: R

last: Doerge

last: Martienssen


title: Spermatozoal RNA Profiles (Human-6 BeadChip)

status: Public on Apr 27 2007

city: Detroit

last: Krawetz

state: MI

address: 275 East Hancock, CS Mott Center

institute: Wayne State University

summary:
Normal human spermatogenesis concludes with the formation of large numbers of  morphologically well developed spermatozoa.  While transcriptionally quiescent these cells carry  an RNA payload that reflects the final spermiogenic phase of transcription. We report here the spermatozoal  transcript profiles characteristic of normally fertile individuals and infertile males suffering from a  consistent and severe teratozoospermia in which under 4% of spermatozoa are morphologically normal.  RNA was  extracted from the purified sperm cells of ejaculate and hybridized to Illumina WG6 Microarrays.
Keywords: disease state analysis

overall_design: Spermatozoal RNAs were prepared from the semen samples of 13 individuals.  An  asymmetric dual block design was adopted with biological replicates in both blocks.  5 semen samples were  assessed from normally fertile males who had fathered at least one child.  8 semen samples were assessed from  infertile individuals with a severe and consistent heterogeneous teratozoospermia who showed no other abnormal  semen parameters.

first: Adrian

last: Platts

first: David

last: Dix

first: Hector

last: Chemes

first: Kary

last: Thompson

last: Goodrich

first: John

middle: C

last: Rockett

first: Vanesa

middle: Y

last: Rawe

first: Silvina

last: Quintana

first: Michael

middle: P

last: Diamond

first: Lillian

last: Strader


title: Comparison of gene expression in embryos in wich the nodal-related genes have been inhibited and in control embryos

status: Public on May 05 2007

city: Cambridge

first: Joana

middle: Maria

last: Ramis Morey

address: Tennis Court Road

country: United Kingdom

institute: Gurdon Institute

summary:
Embryos were injected with either water or Cerberus Short mRNA and harvested at Stage 10.5 for RNA analysis.
Keywords: Knock-down analysis

overall_design: Embryos from three different spawnings where injected at one cell stage with either water or Cerberus Short mRNA and cultured to early gastrula stage 10.5 for RNA isolation. Some embryos were cultured to further development to check their phenotypes. Each slide was hybridised with a mixture 1:1 of sample and control cDNAs, each labelled with a different dye. Hybridisations were carried out as dye-swapped technical replicates, therefore six microarray slides were hybridized

last: Ramis

first: Clara

last: Collart

first: James

last: Smith


title: Comparison of gene expression in embryos in wich Activin B has been knocked-down and in control embryos

status: Public on May 04 2007

summary:
Embryos were injected with either control or Activin antisense morpholino oligonucleotides and harvested at Stage 10.5 for RNA analysis.
Keywords: Knock-down analysis

overall_design: Embryos from three different spawnings where injected at one cell stage with either control or Activin antisense morpholino oligonucleotides and cultured to early gastrula stage 10.5 for RNA isolation. Some embryos were cultured to further development to check their phenotypes. Each slide was hybridised with a mixture 1:1 of sample and control cDNAs, each labelled with a different dye. Hybridisations were carried out as dye-swapped technical replicates, therefore six microarray slides were hybridized

middle: M


title: Ratios for unsync cells

first: Tommy

last: Kaplan

overall_design: Ratios between Gal-induced H3-Flag and constitutive H3-Myc at 8 time points for unsynchronized yeast. Hybridization to high-resolution printed arrays of ~4% of the yeast genome.

last: Dion

first: Minkyu

last: Kim

first: Stephen

last: Buratowski

first: Nir

last: Friedman

first: Oliver

last: Rando


title: Nitrosomonas europaea cells treated with chloroform for one hour and compared to untreated cells

first: barbara

last: gvakharia

summary:
We analyzed the global transcriptional response of N. europaea when exposed to  chloroform (7 µM for 1 h).  Chloroform led to down regulation of 501 genes and  up regulation of 251 genes.  These up regulated genes included genes for heat shock proteins, sigmafactors of extracytoplasmic function subfamily and newly identified genes of toxin-antitoxin loci in N. europaea. Our study showed that despite a significant decrease of transcription in response to the stress, N. europaea expresses a plethora of defense genes when exposed to chloroform.
Keywords: stress response, global transcription, toxin-antitoxin genes

overall_design: We selected chloroform concentrations and exposure times that caused significant changes in cell physiology but without them being too severe. Our  experiments demonstrated that 7 uM chloroform  caused the desired effect. Based on the physiological, proteomic and transcriptional observations, we  analyzed the whole-genome transcriptional responses of N. europaea at 1 h after the chloroform  treatment. Cells from treated samples and untreated control samples were collected  for RNA extraction and hybridization with Affymetrix microarray GeneChip.


title: SREBP1c and mock virus expression profiles in AG01518 human fibroblasts

status: Public on Apr 26 2007

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

institute: Université catholique de Louvain

summary:
Sterol-regulatory element binding proteins (SREBP) control the expression of most genes involved in fatty acid and cholesterol metabolism. In this report, using microarrays, we showed that SREBP1 also induced genes unrelated to lipid biosynthesis, such as heme oxygenase 1 (HMOX1), the phosphatidylinositol-3 kinase regulatory subunit p55-gamma, synaptic vesicle glycoprotein 2A (SV2A) and COTE1 (C1orf2). These genes were regulated by infection with adenoviruses encoding active SREBP1, sterols, statins and growth factors, as one would expect from SREBP1 target genes
Keywords: treatment comparaison

overall_design: Subconfluent AG01518 fibroblasts were infected with adenoviruses encoding SREBP1c or mock virus at 60 virus per cell for 24 h, which was shown to be optimal. Total RNA was isolated using the RNeasy kit (Qiagen) and used for microarray hybridizations as described (8). Briefly, total RNA (40 µg) from cells infected with SREBP1c or mock viruses were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/ for details and hybridization protocols). We performed three independent hybridizations, including one dye-swap control

first: Anders

last: Kallin

first: Lene

last: Johannessen

first: Patrice

last: Cani

first: Catherine

last: Marbehant

first: Ahmed

last: Essaghir

first: Pascal

last: Ferré

first: Nathalie

last: Delzenne


title: Gene expression in homozygous mbl/axin1 zebrafish

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary:
Homozygous masterblind (mbl-/-) zebrafish exhibit reduced or absent eyes and telecephalon, and the expansion of the diencephalic fates to the front of the brain. A missense mutation in the GSK3-binding domain of zebrafish axin1, a scaffolding protein in the Wnt signaling pathway, results in the mbl phenotype. In an effort to identify and study the genes affected by Wnt signaling, we used a 14,000-oligonucleotide-gene microarray to determine differentially expressed genes in mbl/axin1 (-/-) and wild type control zebrafish embryos and larvae.
Keywords: zebrafish, Danio rerio, wild-type mbl, axin1, development

overall_design: RNA was isolated from pools of approximately 50 wild-type and from approximately 50 homozygous mbl/axin1 mutant zebrafish at 24, 48, and 72 hours post-fertilization (hpf). Two separate sets of embryos or larvae were used for each time point. RNA from each replicate at each time point was separately reverse transcribed and labeled by direct incorporation with dUTP-Cy3 prior to hybridization to microarrays printed with zebrafish 50-mer oligonucleotide library (MWG) to identify genes affected in development in organisms with this mutation.

first: Han

last: Wang

first: Jason

last: Kesinger

first: Qingchun

last: Zhou

first: Gearge

last: Martin

first: Sean

last: Turner

first: Yuhong

last: Tang

first: Mark

middle: B

first: Michael

last: Centola


title: O1->O37 serogroup conversion; KanR selected

city: Stanford

first: Melanie

last: Blokesch

state: CA

address: 279 Campus Drive

department: Medical School

institute: Stanford University

summary:
These experiments were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VC73-orf6/7-Kan-A was added after 24h and the cells grown further for 24h. The VC73-orf6/7-Kan-A strain is a ATCC25873 derivative (both O37 serogroup) which harbors a Kanamycin cassette in the O37 region (as part of the operon between orf6 and orf7 w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Three clones were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone.   Comparison of A1552 versus VC73-orf6/7-Kan-A is shown as control.
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
Keywords: genotyping_design

overall_design: Computed


title: Mixed biofilm - cluster transfer O1 to O139

status: Public on Apr 25 2007

summary:
These experiments were performed to show serogroup conversion in Vibrio cholerae from O1 to O139 in a mixed communities / biofilms. For this purpose, V. cholerae O1 El Tor A1552 and VCO139-Kan strain (a MO10 derivative; O139 serogroup) were grown on crab shell fragments to induce natural competence for transformation. Transformants were selected on LB+Kan+Rif plates. O139 positive transformants have undergone a full exchange of the O1 region by the O139 region. This implies an exchange of an at least 32 kb spanning O1 genomic region by more than 42 kb of the O139 region. The transformation experiment was done at least five independent times; data from four experiments are shown; per experiment one to three clones were analysed by CGH with two experimental replicates each.
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
Keywords: all_pairs, array CGH


title: profiling of midbrain from mice s.c. injected with LL/2(LLC1) lung carcinoma cells vs. PBS

status: Public on May 02 2007

city: Ciudad de Buenos Aires

first: Mariano

middle: Cesar

last: Salibe

address: Av. Patricias Argentinas 435

institute: Gentron LLC

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold 1-5. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of lung carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the midbrain. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes.
Keywords: gene expression profile of the midbrain in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 4 samples (biological replicates) for 18 and 72 h time points, and 6 samples for 192 h time point.

last: Alvarez

first: Cintia

middle: G

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

middle: L

last: Podhajcer

first: Fernando

last: Pitossi


title: profiling of prefrontal cortex from mice s.c. injected with LL/2(LLC1) lung carcinoma cells vs. PBS

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold 1-5. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of lung carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the prefrontal cortex. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes.
Keywords: gene expression profile of the prefrontal cortex in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicate in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 5 samples (biological replicates) for 18 and 72 h time points, and 7 samples for 192 h time point.


title: Comparative genomic hybridizations of Mycobacterium avium isolates obtained from multiple host species

city: Ames

first: Mike

last: Paustian

state: IA

address: 2300 Dayton Ave

institute: National Animal Disease Center, USDA-ARS

summary:
A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species.  DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10.  ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA.  Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray.  Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates.  One of these clusters encodes glycopeptidolipid biosynthesis enzymes.  One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18.  Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements.
Keywords: Comparative genomic hybridization

overall_design: Each isolate was competitively hybridized against Map K10 with a minimum of 2 dye flip hybridizations per isolate.

first: Xiaochun

last: Zhu

first: Srinand

last: Sreevatsan

first: Suelee

last: Robbe-Austerman

first: Vivek

last: Kapur

first: John

last: Bannantine


title: O1->O139 serogroup conversion / phage selected

summary:
These experiments were performed to show a serogroup conversion of Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 El Tor (A1552) was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (4 ug each) from strain MO10, an O139 serogroup strain, was added after 24h and the cells were further grown for 24h. After detachment from the crab shell fragments, bacteria were poured into soft-agar and overlaid onto LB plates. Mukerjee's El Tor phage V (a gift of Dr. M.S. Islam) was dropped onto the surface of the bacteria containing soft-agar. The plaques formed by killing non-transformed A1552 cells possessed resistant clones which were picked and further selected for opaque morphotype and agglutination by O139-specific antiserum.
Four clones were selected from each independent experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone.
Strain Names: ApO139#2 / ApO139#4 / ApO139#6 / ApO139#8 are four clones analyzed after the first experiment; AIIpO139#3 / AIIpO139#4 / AIIpO139#5 / AIIpO139#6 are four clones analyzed after the second independent experiment. Two MA replicates for each clone were done. CGHs of A1552 versus MO10 are provided as control.
Keywords: array CGH


title: Expression of inflammatory host genes in Chlamydia trachomatis infected human monocytes

city: Hannover

first: Markus

last: Rihl

address: Carl-Neuberg-Str. 1

department: Clinical Immunology and Rheumatology

institute: Hannover Medical School (MHH)

summary:
Messenger RNA of C trachomatis infected monocytes of the three healthy donors was compared with the corresponding mock-infected samples. For mock infection, SPG buffer was used instead of the C trachomatis suspension, all other procedures were performed identically. Cells were resuspended in solution D and total RNA was extracted by application of phenol:chloroform 5:1 (pH 4.5, Ambion, Austin, TX) followed by precipitation in isopropanol at -80°C for 1 hr and incubation with RQ1 DNase (Promega, Madison, WI) at 37 °C for 1 hr. The signal intensity of the G3PDH housekeeping gene on the microarray membrane was used as indirect quality marker for the RNA utilized as only experiments were included in the analysis that revealed a G3PDH signal intensity within 1.5 times the standard deviation of all membranes evaluated in our study. The entire microarray procedure and its analysis has recently been validated and reported in detail. Total RNA of all donors was pooled and for each microarray experiment 150 µg were reverse transcribed and amplified by SMART™-PCR (BD Biosciences Clontech, Palo Alto, CA), a technology that allows reverse transcription of small amounts of total RNA and subsequent amplification of the entire cDNA. Probes were labeled with 32P and subsequently over night hybridized to a filter-based nylon membrane containing immobilized cDNA-specific sequences from a total of 1,184 genes (Human Atlas Array 1.2, BD Biosciences Clontech, Palo Alto, CA). For analysis, we focused solely on the 159 cytokines, chemokines and their receptors as given by the manufacturer. Signal intensities were retrieved by a STORM 860 scanner (Molecular Dynamics, Sunnyvale, CA) in combination with the AtlasImage 2.0 software (BD Biosciences Clontech). Data from all signal intensities were then subtracted by the local background intensity measured around each gene. The local background intensities of all individual genes were subsequently averaged, resulting in the mean background intensity of a particular membrane. Gene expression in our experiments was determined by a spot intensity of a single transcript that exceeded twice the mean background. Normalisation to background and to the G3PDH housekeeping gene was achieved by the global (sum) normalization method. Signal intensity data are given as the ratio of C trachomatis infected vs mock infected probes.
Keywords: expression analysis

overall_design: 3 control samples, 3 Chlamydia-infected samples

first: Sina

last: Schrader

first: Andreas

last: Klos

first: Simone

last: Hess

first: Henning

last: Zeidler

first: Jens

last: Kuipers


title: The intestinal adenocarcinomas of the cis-Apc/Smad4 compound mutant mice

city: Kyoto

first: Makoto

middle: Mark

last: Taketo

state: Kyoto

address: Yoshida-Konoé-cho, Sakyo

department: Pharmacology

institute: Kyoto University Graduate School of Medicine

summary:
Inactivation of TGF-beta family signaling is implicated in colorectal tumor progression. Using the cis-Apc/Smad4 mutant mice, a model of invasive colorectal cancer whose TGF-beta family signaling is blocked, we demonstrate here that a novel type of immature myeloid cells (iMCs) is recruited from the bone marrow to the tumor invasion front. These CD34+ iMCs express MMP9/2 and CC-chemokine receptor 1 (CCR1), and migrate toward its ligand CCL9. In the adenocarcinomas, expression of CCL9 is increased in the tumor epithelium. Such changes in the chemokine expression or the CD34+ iMC recruitment are not observed in the Apc (+/–) mice, a model of adenomatous polyposis. By knocking out Ccr1 gene in the cis-Apc/Smad4 mutant mice, we further demonstrate that lack of CCR1 prevents the accumulation of CD34+ iMCs at the invasion front and suppresses tumor invasion. These results indicate that loss of the TGF-beta family signaling in tumor epithelium causes accumulation of iMCs that help tumor invasion.
Keywords: disease state analysis

overall_design:
We compared the gene expression profile of the cis-Apc/Smad4 adenocarcinomas with that of the Apc (+/–) adenomas to look for chemokines that were increased in the adenocarcinomas.
To this end, we used DNA Chip Consortium Mouse Microarray v2.0 (oligonucleotide microarray) that contains 65-mer oligonuleotide probes for 21,997 mouse transcripts for three individual analyses.

first: Takanori

last: Kitamura

first: Kohei

last: Kometani

first: Hiroki

last: Hashida

first: Akihiro

last: Matsunaga

first: Hiroyuki

last: Miyoshi

first: Hisahiro

last: Hosogi

first: Masahiro

last: Aoki

first: Masanobu

last: Oshima

first: Masakazu

last: Hattori

first: Arimichi

last: Takabayashi

first: Nagahiro

last: Minato


title: profiling of midbrain from mice s.c. injected with CT-26wt colon carcinoma cells vs. PBS

first: Mariano

last: Salibe

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of colon carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the midbrain. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes.
Keywords: gene expression profile of the midbrain in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicate - extracts in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 5 samples (biological replicates) for 18 time point and 4 samples for 72 h and 192 h time points.

last: Alvarez

first: Cintia

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

last: Podhajcer

first: Fernando

last: Pitossi


title: profiling of hypothalamus from mice s.c. injected with CT-26wt colon carcinoma cells vs. PBS

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of colon carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the hypothalamus. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes.
Keywords: gene expression profile of the hypothalamus in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 5 samples (biological replicates) for 18 h and 4 samples for 72 h and 192 h time points.


title: profiling of prefrontal cortex from mice s.c. injected with 4T-1 mammary carcinoma cells vs. PBS

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of mammary carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the prefrontal cortex. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes.
Keywords: gene expression profile of the prefrontal cortex in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 5 samples (biological replicates) for 18 h and 3 samples for 72 h and 192 h time points.


title: profiling of prefrontal cortex from mice s.c. injected with CT-26wt colon carcinoma cells vs. PBS

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in a model of colon carcinoma, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the prefrontal cortex. These changes occur as early as 18 h after tumour cell injection and involve specific signalling pathways. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes.
Keywords: gene expression profile of the prefrontal cortex in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 3 samples (biological replicates) for 18 time point, 4 samples for 72 h time point, and 4 samples for 192 h time point.


title: profiling of prefrontal cortex from arthritic C57Bl/6 mice s.c. vs. control C57Bl/6 mice

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Using microarrays we studied the gene expression profile of the prefrontal cortex in C57BL/6 mice strain that developed collagen induced-arthritis vs control mice.
Keywords: gene expression profile of the prefrontal cortex in response to induction of arthritis.

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyze changes in gene expression profile in the prefrontal cortex of arthritic vs control mice. We performed 3 samples (biological replicates)


title: profiling of liver from mice s.c. injected with LL/2(LLC1) lung carcinoma cells vs. PBS

summary:
The main function of the nervous system is to maintain homeostasis by sensing and reacting to signals that reach a certain threshold. For example, the brain can sense immune peripheral events through soluble compounds or the vagus nerve and can react through activation of the hypothalamus-pituitary-adrenal axis, resulting in the modulation of an ongoing immune response. Cancer progression is characterized by high mutation rates, with each mutation potentially promoting alarm signals during the 10 to 15 years of cancer development before clinical detection. It is not known, however, whether the brain can recognize the presence of a peripheral tumour, and if this recognition can be molecularly assessed. Using genome-wide expression analysis in three mouse tumour models, we show that a tumor growing at the periphery can indeed promote changes in the expression levels of defined sets of genes in the brain, but not in the liver. These changes are cancer type - and brain region-specific, occur as early as 18 h after tumour cell injection, involve specific signalling pathways and differ from changes in gene expression induced during arthritis. The brain and specially the hypothalamus can discriminate among different cancer types and between cancer and arthritis by expressing specific sets of genes, highlighting the role of specific brain regions as early sensors of signals emanating from chronic peripheral diseases. These findings prove that cancer-derived signals are effective in eliciting specific changes in gene expression in discrete brain regions and open a question regarding the potential role of brain genes in cancer outcomes
Keywords: gene expression profile of the liver in response to peripheral tumor cells

overall_design: We used two-color oligonucleotides in-house printed microarrays in a case-control direct design with two technical replicates in a dye swap design. We analyzed 3 different time points: 18, 72 and 192 h after tumor cells or PBS injection. We performed 4 samples (biological replicates) for the three time points.


title: Genome-wide association analysis in diverse inbred mice: power and population structure

status: Public on Apr 18 2007

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
The discovery of quantitative trait loci (QTL) in model organisms has relied heavily on the ability to perform controlled breeding to generate genotypic and phenotypic diversity.  Recently, we and others have demonstrated the use of a set of diverse inbred mice as a QTL mapping population.  The use of this population has many advantages, including increased phenotypic diversity, a higher recombination frequency and the ability to collect genotype data in community databases.  However, these methods are complicated by inherent population structure and the inability to accurately assess statistical power.  To address these issues, we measured gene expression levels in hypothalamus across the diverse inbred mapping population.  We then mapped these phenotypes as quantitative traits with our association algorithm, resulting in a large set of expression QTLs.  We utilized these eQTLs (and specifically the cis-eQTLs) to devise a relative measure of statistical power which does not rely on parametrically simulated data.  Finally, we utilized this approach to develop and optimize a novel method of accounting for population structure in the Mouse Diversity Panel.
Keywords: strain and gender

overall_design: samples were taken from naïve mice of different strains and both genders

first: Phillip

last: McClurg

first: Jeff

last: Janes

first: Chunlei

last: Wu

first: David

last: Delano

first: Joseph

middle: S

last: Takahashi

first: Kazu

last: Shimomura

first: Akira

last: Kohsaka

last: Bass

first: Tim

last: Wiltshire

first: Andrew

middle: I

last: Su


title: Natural variation in gene expression between normal human individuals studies using Hu2304 cDNA arrays

city: Delhi

first: Anu

last: Sharma

email: anukaush@gmail.com, ramuigib@gmail.com

state: Delhi

address: Mall Road, Near Jubilee Hall

department: Functional Genomics Unit,

institute: Institute of Genomics and Integrative Biology

summary:
Hu2304 arrays have been printed on aminosilane glass slides using 50% DMSO as the spotting solution (Quackenbush protocol; chapter 4). It has 2304 gene probes (including positive and negative controls) printed in duplicates. The probes for this array were primarily selected from the 384 well plates that contained maximum representation of genes expressed in blood (based on EST information).
Keywords: Studying natural variation

overall_design: Eleven normal human individuals with a wider age group of 10-58 years were recruited . These eleven individuals comprised of four male individuals (M9, M22, M182, M185), three female individuals (F15, F183, F184) and a dizygotic female twin pair (F18, F19). Eight pair wise comparisons (somewhat randomly without loop strategy due to sample limitations) were carried out between these ten individuals using Hu2304 arrays including seven pair wise comparisons between unrelated individuals (M9:M182, F15:F183, F15:F184, F15:M185, F18:M22, F18:M23 and F19:F24) and one pair wise comparison between dizygotic female twin pair (F18:F19).

first: Samir

middle: K

last: Brahmachari

first: Srinivasan

last: Ramachandran


title: Transcriptional analysis of select CfMNPV genes and some antisense transcripts by an oligonucleotide microarray

city: Guelph

first: Dan-Hui

last: Yang

state: Ontario

address: 488 Gordon Street

department: Dept. of Molecular and Cellular Biology

institute: University of Guelph

summary:
The temporal expression of the 23 CfMNPV genes representing all four temporal classes including its 7 unique genes were determined by a modified oligonucleotide-based two-channel DNA microarray. Transcription of the non-coding (antisense) strands of some of the CfMNPV select genes including the polyhedrin gene was also detected by the array analysis. The expression of four host genes varied several fold throughout virus infection. The microarray chip contained oligonucleotide probes for 23 CfMNPV ORFs and their complements. We first developed a novel normalization protocol using Cy5-labeled CfMNPV viral genomic DNA (vgDNA) as equimolar reference standards for each probe in order to overcome the inherent variability problem of the traditional microarray normalization procedures including use of internal standards. Cy3-labeled cDNA was from total RNA isolated at different times post infection of Cf203 insect cells infected with CfMNPV. Host genes were unsuitable for normalization between microarrays. The DNA microarray results were selectively validated by quantitative RT-PCR (qRT-PCR). The nature of the polyhedrin antisense transcription was further investigated using long range RT-PCR analysis.
Keywords: Time course, detection of antisense transcripts, viral genomic DNA normalization

sample_organism: Choristoneura fumiferana multiple nucleopolyhedrovirus

overall_design: Total RNA was isolated from Cf203 cells at 0, 3, 6, 12, 24 and 48 h post infection, as well as from mock-infected Cf203 cells. The Cy3-labeled cDNA derived from 20 μg total RNA was co-hybridized with 10 ng/μl vgDNA to each array at 42ºC. Seven hybridizations in each experiment, two independent hybridization experiments were performed, and therefore 14 samples were analyzed and included in the sample submission including the mock-infected sample.

first: Peter

middle: J

last: Krell

first: Mehrnoosh

last: Barari

first: Basil

last: Arif

last: Leishman

first: Qili

last: Feng

first: Margaret

last: Howes

first: Melanie

last: Arbour


title: Developmentally regulated piRNA clusters implicate MILI in transposon control

status: Public on Apr 20 2007

city: Cold spring Harbor

first: ravi

last: Sachidanandam

address: 1 bungtown road

institute: Cold Spring Harbor Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary:
Nearly half of the mammalian genome is composed of repeated sequences. In Drosophila, PIWI proteins exert control over transposons. However, mammalian PIWI proteins, Miwi and Mili, partner with piRNAs that are depleted of repeat sequences, raising questions about a role for mammalian PIWIs in transposon control. A search for murine small RNAs that might program PIWI proteins for transposon suppression revealed developmentally regulated piRNA loci, some of which resemble transposon master control loci of Drosophila. We also find evidence of an adaptive amplification loop in which PIWI catalyzes formation of piRNA 5’ ends. Mili mutants de-repress L1 and IAP and lose DNA methylation of L1 elements, demonstrating an evolutionarily conserved role for PIWI proteins in transposon suppression.
Keywords: small RNA profile, piRNA

overall_design: Mili RNP complexes were immunoprecipitated from testes extract of 10 day old CD-1 mice using polyclonal antibodies against two MILI peptides (MILI-N, amino acids 2-18 and MILI-N2, amino acids 107-122).   Immunoprecipitation of MILI RNP complexes and RNA isolation was performed as described in A. Aravin et al., Nature 442, 203 (2006). Two cDNA libraries were created and sequenced separately.  After preliminary analysis, sequences were pooled. Small RNA cloning and 454 sequencing of small cDNA libraries were performed as described in J. Brennecke et al., Cell 128, 1089 (2007).

first: Alexei

middle: A

last: Aravin

first: Ravi

first: Angelique

last: Girard

first: Katalin

last: Fejes-Toth

first: Gregory

last: Hannon


title: SpxB regulates O-acetylation dependent resistance of Lactococcus lactis peptidoglycan to hydrolysis

status: Public on Apr 17 2007

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary:
Endogenous peptidoglycan (PG) hydrolysing enzymes, the autolysins, are needed to relax the rigid PG sacculus to allow bacterial cell growth and separation. PG of pathogens and commensal bacteria may also be degraded by hydrolases of animal origin (lysozymes), which act as antimicrobials. The genetic mechanisms regulating PG resistance to hydrolytic degradation was dissected in the Gram-positive bacterium Lactococcus lactis. We found that the ability of L. lactis to counteract PG hydrolysis depends on the degree of acetylation. Overexpression of PG O-acetylase, encoded by oatA, led to bacterial growth arrest, indicating potential lethality of oatA and a need for its tight regulation. A novel regulatory factor SpxB (previously denoted as YneH), exerts a positive effect on oatA expression. Our results indicate that SpxB binding to RNA polymerase constitutes a previously missing link in the multi-step response to cell envelope stress, provoked by PG hydrolysis with lysozyme. We suggest that the two component system CesSR responds to this stress by inducing SpxB, thus favoring its interactions with RNA polymerase. Induction of PG O-acetylation by this cascade renders it resistant to hydrolysis.
Keywords: mutant, lysozym

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: RNA was isolated from 3 independent cultures of L. lactis MG1363/pVE3916 (VES4075) and L. lactis MG1363/pspxB+ (VES3910). Slide data were processed and normalized using MicroPrep software as described in this article. Expression of a gene was considered to be significantly altered when the Cyber T baysian P-value 0.001.

first: Patrick

last: Veiga

first: Carmen

last: Bulbarela-Sampieri

first: Sylviane

last: Furlan

first: Aurélie

last: Maisons

first: Marie-Pierre

last: Chapot-Chartier

first: Michael

last: Erkelenz

first: Peggy

last: Mervelet

first: Philippe

last: Noirot

first: Dorte

last: Frees

first: Oscar

last: Kuipers

first: Jan

last: Kok

first: Alexandra

last: Gruss

first: Girbe

last: Buist

first: Saulius

last: Kulakauskas


title: Expression array data for oleate-specific transcriptional regulatory network analysis

status: Public on Apr 19 2007

city: Seattle

first: Jennifer

middle: Joy

last: Smith

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

summary:
The goal of the study was to determine the expression profiles of transcription factor deletion strains in the presence of oleate.
The data were used for a larger study described below:
A novel network topology-based clustering approach was used to characterize a dynamic transcriptional regulatory network responsive to the fatty acid oleate.  Condition-specific large-scale chromatin localization data were generated for four fatty-acid related regulators, and used to construct physical interaction networks.  Data integration and simple statistical analysis of dynamic network architecture led to the identification of a regulatory role for a previously uncharacterized protein, and unique mechanism for coordination and regulation of multiple biological responses through the formation of related parallel combinatorial control motifs.  Temporal coordination and specificity are achieved through the ability of a regulator (Oaf1p) to have multiple context-specific activities under the same condition.  The analysis suggests that active paths for a transcriptional response can be highly interconnected in parallel and involve multiple functions for individual regulators through combinatorial control.
Keywords: expression analysis of gene deletion strains

overall_design:
Experiments 1-4:
mRNA levels in each of four deletion strains (delta_OAF1, delta_PIP2, delta_ADR1 or delta_OAF3) were compared to those in wild type cells by microarray analysis.  All strains were induced for 5h in the fatty acid oleate.
Experiment 5:
mRNA levels in wild-type cells grown in the presence of 0.1% glucose were compared to those in wild-type cells grown in oleate for 5h by microarray analysis.
Control Experiment 6:  mRNA levels in wild-type cells were compared to mRNA levels in wild-type cells by microarray analysis.  All strains were induced for 5h in the fatty acid oleate.
For all 6 experiments, cells were harvested, and poly A+ RNA was extracted and labeled with Cy3 and Cy5 fluorescent dyes, and equimolar amounts of each label were mixed and hybridized to yeast ORF oligonucleotide microarrays as previously described (Smith et al., 2002).  There were two biological replicates for each experiment, and for each replicate both label orientations were analyzed on arrays containing 4 replicate spots of each gene, resulting in a total of 16 replicate spots per gene.

first: Stephen

last: Ramsey

first: Marcello

last: Marelli

first: Bruz

last: Marzolf

first: Daehee

last: Hwang

first: Ramsey

last: Saleem

first: Richard

last: Rachubinski

first: John

middle: D

last: Aitchison


title: M1 serotype (strain SF370): pharyngeal cell adherence vs. association

city: New York

first: Patricia

middle: A.

last: Ryan

address: 1230 York Ave

department: Bacterial Pathogenesis and Immunology

institute: Rockefeller University

summary:
We developed spotted oligonucleotide arrays of the S. pyogenes SF370 (an M1 serotype) genome and compared the transcriptomes of streptococci that adhere to Detroit 562 human pharyngeal cells to non-adherent (“associated”) streptococci within the same experiment.  We replicated experiments independently and used dye-swaps to incorporate biological and technical variation, biological replicate experiments. Following filtering and normalization, we analyzed data from four biological replicates with robust summary statistics, Bayesian statistics and permutation algorithms to identify genes differentially expressed with significance during pharyngeal cell adherence. This analysis identified 79 genes (4% of the genome) exhibiting statistically significant fold changes in expression (PF value < 0.05) during adherence from 1769 open reading frames represented on the array. The genes encoding several known virulence factors (e.g. cysteine protease SpeB and streptolysin O) were differentially expressed with significance; however, many were either never before associated with adherence (e.g. phage-encoded genes including speH), or of undefined function.  Genes demonstrating up-regulation (n= 45) and down-regulation (n= 34) included virulence factors, prophage-encoded transcripts, metabolic genes and transcriptional regulators (Table 2). Undefined or hypothetical genes comprised 27% of differentially expressed genes (n= 21; 11 chromosomally-encoded, 10 phage-encoded). We conducted TaqMan (qRT-PCR) analysis of 11 differentially expressed genes to validate selected microarray hybridization results. We further analyzed the data with neighbor clustering, using a set of novel computational algorithms (termed “GenomeCrawler”) for evaluating bacterial microarray data, which couples the expression profiles of genes with their physical location on the chromosome. When applied to the microarray data from this study, neighbor clustering identified a greater number of differentially expressed genes, which facilitated the reconstruction of known multimeric proteins, complete metabolic pathways and intact virulence loci that would not have been possible without its application. These data sets and algorithms are freely available for download at www.rockefeller.edu/vaf.
Keywords: Pharyngeal cell adherent vs. associated

overall_design: Series contains 4 biological replicates including dye-swap experiments

first: P

first: V

last: Fischetti


title: Spermatozoal RNA Profiles (HumanRef-8 BeadChip)

last: Krawetz

summary:
Normal human spermatogenesis concludes with the formation of large numbers of  morphologically well developed spermatozoa.  While transcriptionally quiescent these cells carry  an RNA payload that reflects the final spermiogenic phase of transcription. We report here the spermatozoal  transcript profiles characteristic of normally fertile individuals and infertile males suffering from a  consistent and severe teratozoospermia in which under 4% of spermatozoa are morphologically normal.  RNA was  extracted from the purified sperm cells of ejaculate and hybridized to Illumina WG ref8 Microarrays.
Keywords: disease state analysis

overall_design: Spermatozoal RNAs were prepared from the semen samples of 10 individuals.  An  asymmetric dual block design was adopted with biological replicates in both blocks.  4 semen samples were  assessed from normally fertile males.  6 semen samples were assessed from  infertile individuals with a severe and consistent teratozoospermia (predominantly DFS).

first: Adrian

middle: E

last: Platts

first: David

last: Dix

first: Hector

last: Chemes

first: Kary

last: Thompson

first: Robert

last: Goodrich

middle: C

last: Rockett

first: Vanesa

middle: Y

last: Rawe

first: Silvina

last: Quintana

first: Michael

middle: P

last: Diamond

first: Lillian

middle: F

last: Strader