title: Distant cis Regulation of Myogenic Differentiation

status: Public on Feb 01 2012

city: Boston

first: Martha

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics

institute: Brigham and Women's Hospital

summary:
Identifying tissue and condition-specific gene regulatory elements and the mechanisms by which they associate with their target genes in human cells remains a significant challenge, largely due to the vast amount of non-protein-coding sequence in the human genome. Despite increasing evidence of physical interactions between distant regulatory regions and gene promoters in a variety of mammalian cell types, many searches for regulatory regions still consider only genomic regions proximal to the gene promoter. We identify a set of putative cis-regulatory modules (CRMs) of human skeletal muscle differentiation by combining new ChIP-chip data measuring the binding of myogenic TFs MyoG, MyoD, and SRF over the timecourse of differentiation with previously generated histone modification data. A substantial proportion of these putative CRMs are located distant (> 20 kb) from muscle gene promoters, and these distantly located CRMs are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding.
Examination of two distant CRMs, which were previously shown to activate transcription in differentiating muscle cells, revealed that they interact physically with their upstream or downstream gene promoters (PDLIM3 and ACTA1) specifically upon myogenic differentiation. Our results highlight the importance of considering CRMs located distant from their target genes in investigations of mammalian gene regulation and further support the hypothesis that enhancer-promoter looping contacts are a general mechanism of regulation by distant CRMs.

overall_design: ChIP-chip experiments were performed using a custom Agilent 1x244K oligonucleotide array format (AMADID # 015037) to achieve 25-bp resolution tiling of 100 kb surrounding each of 104 selected human genes as well as positive and negative control regions.  Biological and technical replicates of ChIP-chip experiments were performed using antibodies for MyoG and SRF in primary human skeletal muscle myoblasts crosslinked at 0 and 48 h relative to the removal of serum to induce differentiation.  Additional technical replicate ChIP-chip experiments were performed for MyoD at 0 and 48 hours post-differentiation and p300 at 48 h post-differentiation.  Total Input DNA for each experiment was labeled with Cy3 and used to create log-ratios with the Cy5 labeled IP data.  Negative control no antibody mock-IP ChIP experiments were performed at 0 and 48 h post-differentiation.

first: Rachel

last: McCord

first: Vicky

first: Tiffany

last: Yuh


title: NGF and proNGF activate functionally distinct mRNAs in PC12 cells: an early gene expression profiling

status: Public on Jan 09 2012

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: The biological activities of NGF and of its precursor proNGF are quite distinct, due to different receptor binding profiles, but nothing is known about how proNGF regulates gene expression. We performed experiments to address this question, by verifying whether a proNGF specific transcriptional signature, distinct from that of NGF, could be identified. To this aim, we studied gene expression regulation by proNGF and NGF in PC12 cells incubated for 1 and 4 hours with recombinant NGF and proNGF, in its wild-type or in a furin-cleavage resistant form. mRNA expression profiles were analyzed by whole genome microarrays at these early time points, in order to identify specific profiles of NGF and proNGF.

overall_design: Three-conditions experiment: PC12 cells were treated with NGF, wild type proNGF precursor (proNGF-WT), furin resistant mutated proNGF precursor (proNGF-KR) for 1 and 4 hours. Two biological replicates were performed for each condition. RNA was extracted after 1 hour and 4 hours of treatment for each treatment.

first: Mara

last: D'Onofrio

first: Francesca

last: Paoletti

first: Rossella

last: Brandi

last: Malerba

first: Luisa

last: Fasulo

first: Antonino

last: Cattaneo


title: Expression data from advanced Parkinson's disease (PD) patients leukocytes - prior to and following deep brain stimulation (DBS) treatment in on and off stimulation conditions, and matched healthy control (HC) subjects

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

summary: Sub-thalamic deep brain stimulation (DBS) reversibly modulates Parkinson’s disease (PD) motor symptoms, providing an unusual opportunity to compare leukocyte transcripts in the same subjects before and after neurosurgery and after disconnecting the stimulus (ON-and OFF-stimulus). Here, we report rapid stimulus-induced and largely reversible changes in PD leukocyte transcripts, which were larger in scope than the disease-induced changes. These transcript changes classified advanced pre- from post-surgery PD patients and discriminated patients from controls. Moreover, the extent of changes correlated with the neurological efficacy of the DBS neurosurgery, and covered both regulatory pathways and individual transcript changes, e.g. SNCA, PARK7 and the splicing factor SFRS1. Following 1 hour OFF-stimulus, these changes were largely reversed. We extracted from these differences a modified transcripts signature which discriminated controls from advanced PD patients, pre- from post-surgery and ON-from OFF-stimulus conditions. A further gene-list independent analysis detected reversed pathways. Our findings suggest future uses of this approach and the discovered molecular signature for early diagnostics of PD and for identifying novel targets for therapeutic intervention in this and other DBS-treatable neurological diseases.

overall_design: 27 Total samples were analyzed. Study design included four conditions. PD patients (n=7) leukocyte blood samples were examined at 3 time points, and healthy control subjects (n=6) were examined once each. Samples were taken 1 day prior to sub-thalamic nucleous (STN) DBS treatment, several months after STN-DBS treatment upon optimal stimulation and following one hour electrical stimulation cessation. The off stimulation caused recruitment of the disease symptoms as measured by the Unified Parkinson's Disease Rating Scale motor section (UPDRS-III). The different stages are designated: S1 (pre-treatment), S2 (post STN-DBS) and S3 (upon off stimulation). All patients were on dopamine replacement therapy (DRT) when examined pre- and post-DBS off stimulation (albeit with reduced therapy dose post-DBS). To reduce biological variability among the samples which is not related to the study, only male subjects were included in this study. Samples from six age- and gender- matched healthy control subjects served to detect disease modified transcripts and for pre- and post- treatment comparisons. The study was approved by the human review board at the Hadassah University Hospital, Ein-Kerem (no. 6-07.09.07) in accordance with the Declaration of Helsinki. All study participants signed informed consent.

first: Hagai

last: Bergman

first: Hermona

first: Zvi

last: Israel


title: High-resolution, genome-wide analysis of human metastatic neuroblastoma samples by array-Comparative Genomic Hybridization (aCGH)

status: Public on Jan 01 2012

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

institute: IRCCS Ospedale Policlinico San Martino

summary: Neuroblastoma (NB) is an aggressive tumor that affects both infants and children. The disease outcome is greatly influenced by age of patient, stage, chromosome copy number aberrations (CNAs) and gene expression abnormalities. We analyzed, by microarray technology, genome and transcriptome of 3 groups of tumors of patients with metastatic disease: G1, stage 4S and MYCN single copy; G2, stage 4 younger than 18 months of age, MYCN single copy with no disease progression and G3, stage 4, older than 19 months, with unfavorable outcome. We found an accumulation of structural copy number aberrations (CNAs) in G3 whereas G1 tumors had mostly numerical (N) CNAs and G2 showed an intermediate behavior. Pair wise comparisons demonstrated that the average of N CNAs significantly decreased from G1 to G2 to G3 (9.6 G1 < 7.2 G2 < 3.6 G3); in contrast S CNAs significantly increased in G3 (0.7 G1 < 3.7 G2 < 7.0 G3). Interestingly, we observed several intra-chromosomal rearrangements in G3 tumors on chromosomes not usually involved in NB. Excluding MYCN amplified tumors by G3 we found a high frequency of S CNAs in this group. Gene expression analysis showed a deregulation of downstream genes of Ras and Rho signaling pathway among the 3 groups. It has been also observed a progressive switch off of development and adhesion genes and a switch on of cell cycle genes from G1 to G2 to G3. Moreover, the telemorase genes were significantly expressed in G3 with respect to remaining groups. Present data show an accumulation of S CNAs from stage 4S to 4. The deregulation of genes Rho/Ras pathway may explain the increase of tumor aggressiveness from G1 to G2 to G3. The increase of cell cycle and telomerase genes expression associated with G3 would provide unlimited replicative potential for these tumors and may be responsible for accumulation of S CNAs. Finally, we can argue that accumulation of structural aberrations and gene deregulation is age-dependent and it is associated with a more aggressive tumor phenotype.

overall_design: We analyzed 133 samples of metastatic neuroblastoma from patients divided into three groups: G1 49 patients stage 4S and MYCN single copy; G2 37 patients stage 4 younger than 18 months of age at diagnosis, MYCN single copy with no disease progression; G3 47 patients stage 4 older than 19 months of age at diagnosis, with unfavorable outcome.

first: Simona

last: Coco

first: Jessica

last: Theissen

first: Paola

last: Scaruffi

first: Sara

last: Stigliani

last: Valdora


title: Gene profiles during vestibular compensation in unilateral labyrinthectomized rats

status: Public on Nov 16 2011

city: bucheon

first: moo kyun

last: park

state: Gyeonggi-do

address: jung dong 1174

department: otorhinolarynogology

country: South Korea

institute: soonchunhyang univeristy bucheon hosptial

summary:
Microarray analysis was used to examine the expression of genes upregulated or downregulated in the ipsilateral vestibular nucleus at 1 and 7 days following unilateral labyrinthectomy.
Changes in gene expression during the chronic phase of vestibular compensation following unilateral labyrinthectomy in rats

overall_design: Three conditioned experiment: nl:control with sham operation, 1day:1day after labyrninthectomy, 7day:7day after labyrinthectomy

first: Moo

middle: K

last: Park

first: Sung

middle: W

last: Chae


title: Expression data of Actinobacillus pleuropneumoniae 4074, the ΔluxS mutant and AI-2 supplemented ΔluxS mutant

status: Public on Nov 15 2011

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

summary: LuxS is an enzyme involved in the activated methyl cycle. The by-product of this cycle, autoinducer 2 (AI-2), could be an important quorum sensing signal. LuxS was conserved and regulated many behaviors in different bacteria, but in most species, whether the regulations are related to AI-2 mediated quorum sensing is still unknown. In our previous study, Actinobacillus pleuropneumoniae, the etiologic agent of porcine contagious pleuropneumonia, was found to possess the functional LuxS affecting biofilm formation and virulence. In this study, microarray was used to compare the transcriptional profiles of the A. pleuropneumoniae wildtype strain 4074, luxS mutant and its AI-2 supplemented strain in four different growth phases. The results demonstrated that both LuxS and AI-2 played important roles in metabolism of this bacterium. AI-2 did not recover the gene expression changes caused by luxS deletion but caused more extensive metabolic alterations in the luxS mutant in a concentration dependent manner. Regulations of the genes involved in iron metabolism, carbonhydrate transport and host cell adhesion were validated by real-time RT-PCR and phenotypic investigations under different conditions. The results demonstrated that sugar uptake was repressed by LuxS independent of AI-2. However, iron metabolism, an important process of infection for A. pleuropneumoniae, could be controlled by LuxS through AI-2. Adhesion to host cells was also affected by LuxS and AI-2, but exogenous AI-2 displayed more obvious effects. Our results indicated that both LuxS and AI-2 are essential in the metabolism of A. pleuropneumoniae. The function of LuxS/AI-2 displayed pleiotropic roles in different conditions. AI-2 may not serve as a quorum sensing autoinducer but a metabolite or an environmental cue to affect the metabolism and virulence traits of this important pathogen.

overall_design: A. pleuropneumoniae strains were cultured in TSB medium supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v) filtered cattle serum at 37°C. For samples from the mutant supplemented with AI-2, 100μM and 25μM AI-2 precursor (DPD) were added into the medium before early exponential phase as well as one hour before late exponential phase to cover the whole growth phase respectively. The samples were collected from early, middle, late exponential phase and stationary phase respectively and the total RNA were extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions. For each time point, four biological replicates were combined into two samples. The intensities were normalized and transformed into log2 value. The values for each time point were averaged and the genes with log2 ratio >=1 or <=-1 were selected as differentially expressed genes.

first: Zhuofei

last: Xu

first: Rui

last: Zhou

first: Huanchun

last: Chen


title: Expression data of Actinobacillus pleuropneumoniae 4074 and the ΔluxS mutant of Actinobacillus pleuropneumoniae 4074

status: Public on Nov 09 2011

summary: LuxS is an enzyme involved in the activated methyl cycle and the by-product autoinducer 2 (AI-2) was a quorum sensing signal in some species. In our previous study, the functional LuxS in AI-2 production was verified in the porcine respiratory pathogen Actinobacillus pleuropneumoniae. Enhanced biofilm formation and reduced virulence were observed in the luxS mutant. To comprehensively understand the luxS function, in this study, the transcriptional profiles were compared between the A. pleuropneumoniae luxS mutant and its parental strain in four different growth phases using microarray. Many genes associated with infection were differentially expressed. The biofilm formation genes pgaABC in the luxS mutant were up-regulated in early exponential phase, while 8 genes associated with adhesion were down-regulated in late exponential phase. A group of genes involved in iron acquisition and metabolism were regulated in four growth phases. Further investigations on these virulence traits demonstrated that the luxS mutant showed enhanced biofilm formation and reduced adhesion ability and these effects were not due to lack of AI-2. But AI-2 could increase biofilm formation and adhesion of A. pleuropneumoniae independent of LuxS. Growth under iron restricted condition could be controlled by LuxS through AI-2 production. These results revealed pleiotropic roles of LuxS and AI-2 on A. pleuropneumoniae virulence traits.

overall_design: A. pleuropneumoniae strains were cultured in TSB medium supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v)filtered cattle serum at 37°C.  The samples were collected from early exponential phase, middle exponential phase, late exponential phase and stationary phase respectively and the total RNA were extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions. For each time point, four biological replicates were combined into two samples. The intensities were normalized and transformed into log2 value.The fold changes >=1.5 or <=-1.5 were selected as differentially expressed genes.


title: Verification of a custom chip which measures abundance, isoforms and alleles in Drosophila

status: Public on Sep 13 2011

city: Gainesville

first: Yajie

last: Yang

state: FL

address: 2033 Mowry Road Room 118

country: USA

institute: UF

type:
Expression profiling by array
Other

summary: Analysis of differential expression using the 3’ expression module revealed 34% probe sets showed evidence for a sex bias and alternative exon sex bias was identified for 164 genes.  Intriguingly, allelic imbalance was detected for 37% of 6,579 probe sets examined which contained heterozygous SNP loci.

overall_design: Two different isogenic strains of D. simulans, st e and C167.4 and their male and female progeny were used as the basis for the verification study. Three replicates of RNA from female and male progeny of the cross st e x C167.4 made for a total of six RNA samples. In addition, DNA was used as a control for estimating allele imbalance. Three replicates of DNA target were prepared for female st e, femaleC167.4 and the female F1 progeny of the cross st e x C167.4, for a total of 9 gDNA samples.

first: Rita

middle: M

last: Graze

first: Brandon

last: Waltz

first: Cecilia

last: Lopez

first: Henry

middle: V

last: Baker

first: Marta

middle: L

last: Wayne

first: Sergey

last: Nuzhdin

first: Lauren

last: McIntyre


title: Fibrinogen is upregulated following kidney damage and protects it against ischemia-reperfusion injury

status: Public on Oct 01 2011

first: Vishal

middle: S

last: Vaidya

department: Medicine

institute: Brigham and Women's Hospital. Harvard Medical School

summary: characterization of fibrinogen expression in the kidney, excretion in the urine following kidney damage and evaluating the therapeutic potential of fibrinogen in acute kidney injury.

overall_design: Total RNA was isolated of renal cortex and medulla from rats subjected to 20 min of bilateral ischemia followed by 6, 24 120, hr of reperfusion compared to sham  rats.

first: Aparna

last: Krishnamoorthy

first: Amrendra

last: Ajay

first: Dana

last: Hoffmann

first: Tae-Min

last: Kim

first: Victoria

last: Ramirez

first: Gabriela

last: Campanholle

first: Norma

middle: A

last: Bobadilla

first: Sushrut

last: Waikar


title: Global gene expression profiling of Plasmodium falciparum in response to the anti-malarial drug pyronaridine

status: Public on Aug 02 2011

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

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

overall_design: Refer to individual Series


title: Genome-wide gene expression profiling of fertilization competent mycelium in opposite mating types in the heterothallic fungus Podospora anserina.

status: Public on Dec 22 2011

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

country: France

institute: Institut de Génétique et Microbiologie UMR 8621

summary:
Abstract
BACKGROUND:

Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat- mating types are determined by dissimilar allelic sequences. The mat- sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation.
METHODOLOGY/PRINCIPAL FINDINGS:

The transcriptomic profiles of the mat+ and mat- strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1(-) and fpr1(-) mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat- strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species.
CONCLUSIONS/SIGNIFICANCE:

This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.

overall_design: With GPL10116 : 4 conditions each with four biological replicates :mat+, mat-, fpr1-, fmr1-; common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5

first: Jinane

last: Benkhali

first: Sandrine

last: Imbeaud

first: Robert

last: Debuchy

first: Evelyne

last: Coppin


title: Changes in gene expression in the retina of diabetic Long Evans rats after one, four, and twelve weeks of diabetes

status: Public on Oct 31 2011

city: Irvine

first: Stefanie

middle: J

last: Kirwin

state: CA

address: 18655 Teller Ave

department: Biological Sciences

institute: Allergan, Inc.

summary: Purpose. Patients with diabetic retinopathy may experience severe vision loss due to macular edema and neovascularization secondary to vascular abnormalities. However, before these abnormalities become apparent, there are functional deficits in contrast sensitivity, color perception, and dark adaptation. The goals of this study are to evaluate early changes (up to 3 months) in retinal gene expression, selected visual cycle proteins, and optokinetic tracking (OKT) in streptozotocin (STZ)-induced diabetic rats.Methods. Retinal gene expression in diabetic Long Evans rats was measured by whole genome microarray 7 days, 4 weeks, and three months after onset of hyperglycemia. Select gene and protein changes were probed by PCR and immunohistochemistry respectively, and OKT thresholds were measured using a virtual optokinetics system. Results. Microarray analysis showed that the most consistently affected molecular and cellular functions were cell-to-cell signaling and interaction, cell death, cellular growth and proliferation, molecular transport, and cellular movement. Further analysis revealed reduced expression of several genes encoding visual cycle proteins including lecithin:retinol acyltransferase (LRAT), retinal pigment epithelium (RPE)-specific protein 65kDa (RPE65) and RPE retinal G protein coupled receptor (RGR). Immunohistochemistry revealed a decrease in RPE65 in the RPE layer of diabetic rats. These molecular changes occurred simultaneously with a decrease in OKT thresholds by 4 weeks of diabetes. Conclusions. The data presented here are further evidence that inner retinal cells are affected by hyperglycemia prior to vasculopathy suggesting that glial and neuronal dysfunction may underlie some of the early visual deficits in diabetics.

overall_design: At each of the three timepoints (day 7, day 28, and day 84) one retina each from three diabetic rats were pooled for analysis on a single microarray chip. Three independent experiments were conducted for each group (n=9 animals/group). Each timepoint contained a hyperglycemic (STZ) and a control (buffer injection only) group. Additionally, on day 7 gene changes in the retina of rats which received a single injection of STZ, but did not develop hyperglycemia (STZ-non-c) were analyzed.


title: Pilot project to determine optimal bioreactor protein glycosylation conditions

status: Public on Apr 29 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
These research areas concentrate on stress induced proteases in recombinant Escherichia coli, glycosylation heterogeneity due to bioprocess conditions produced in mammalian cells, and metabolic engineering of E. coli.
The hypothesis of this project is that recombinant protein glycosylation is inefficient under normal bioreactor conditions since the additional glycosylation reactions necessary for the recombinant protein exceed the metabolic capacity of the cells. Normal bioreactor conditions have been optimized for cell growth, and sometimes for protein productivity. Only recently has it been accepted that optimal glycosylation may not occur under optimal growth or protein productivity conditions. Specific Aim: Determine the relationship between bioreactor conditions and glycosylation gene expression in NS0 cells.

overall_design: EXPERIMENT: Mouse NS0 myeloma cells were grown in culture, stressed with 5 mM NaCl, 10 mM proline plus 5 mM ammonia, or 5 mM ammonia, along with an unstressed control group. The growth of the cultures were followed until the late exponential phase (90 hours), at which time two 50 mLs of cells were harvested and RNA extracted. Samples were prepared in triplicate, for a total of 12 samples. The RNA was amplified and labeled by Microarray Core (E) and hybridized to the GLYCOv3 microarrays.

first: Sarah

last: Harcum

middle: R


title: A molecular and phenotypic integrative approach to identify a no effect dose level for anti-androgen induced testicular toxicity

status: Public on Mar 29 2011

city: Sophia Antipolis

first: Sophie

last: Ludwig

address: 355 Rue Dostoievski BP 153

department: Toxicology Research

institute: Bayer Cropscience

summary: With the advent of high information content technologies, especially microarrays, it is pertinent to determine the impact of molecular data on the NOAELs. Consequently, we conducted an integrative study to identify a no transcriptomic effect dose using microarray analyses coupled with qPCR and determined how this correlated with the NOAEL. We assessed the testicular effects of the antiandrogen, flutamide (FM), in a rat 28-day toxicity study using doses of 0.2-30 mg/kg/day. Concerning molecular data, we observed differential gene expression starting from 1 mg/kg/day and a deregulation of more than 1500 genes at 30 mg/kg/day. Dose-related changes were identified for the major pathways associated with the testicular lesion (eg fatty acid metabolism), that were confirmed by qPCR. These data, along with standard measurements supported the no effect dose of 0.2 mg/kg/day.

overall_design: Flutamide was administered in suspension to rats (7 weeks old at start of treatment, 10 per group) by oral gavage at a daily dose of 0 (control), 0.2, 1, 6 and 30 mg/kg body weight, for 28 consecutive days. Dose-related changes in gene expression were determined in the testes using whole genome oligonucleotide microarrays.

first: Helen

last: Tinwell


title: Comparison of developmental stage transcripts in the K1 strain

summary: To identify the developmentally regulated genes, which could confound identification of PN and CQ drug responsive genes, RNA samples from drug-free synchronized cultures from ring, trophozoite, and schizont stages were individually labelled and hybridized with a pooled sample from the three stages.  The data from this experiment were used to compare the developmental profile of the K1 strain with the data from other P. falciparum strains.

overall_design: 9 samples were obtained from three developmental stages of parasite development (3 each from ring, trophozoite and schizont synchronized parasites). Three independent cultures were obtained, synchronized on different days.

first: Kanyanan

last: Kritsiriwuthinan

first: Sastra

last: Chaotheing

first: Chayaphat

last: Wongsombat

first: Porntip

last: Chavalitshewinkoon-Petmitr

first: Sumalee

last: Kamchonwongpaisan


title: Expression profile of subcutaneous adipose samples from subjects at the time of Roux en Y gastric bypass surgery.

status: Public on Apr 01 2011

city: Seattle

first: Radu

last: Dobrin

state: WA

address: 401 Terry Ave N

institute: Merck and Co. Inc.

summary:
To map the genetics of gene expression in metabolically relevant tissues and investigate the diversity of expression SNPs (eSNPs) in multiple tissues from the same individual, we collected four tissues from approximately 1,000 patients undergoing Roux-en-y gastric bypass and clinical traits associated with their weight loss and co-morbidities. We then performed high-throughput genotyping and gene expression profiling and carried out a genome-wide association analyses for more than one hundred thousand gene expression traits representing four metabolically relevant tissues; liver, subcutaneous adipose, omental adipose and stomach. We successfully identified 24,531 eSNPs corresponding to ~10,000 distinct genes. This represents the greatest number of eSNPs identified to our knowledge by any study to date and the first study to identify eSNPs from stomach tissue.  We then demonstrate how these eSNPs provide a high quality disease map for each tissue in morbidly obese patients to not only inform genetic associations indentified in this cohort, but in previously published genome wide association studies as well.  eSNPs and gene co-expression modules identification in morbidly obese patients represent a great resource that will aid in elucidating the key networks associated with morbid obesity, response to RYGB and disease as a whole.

Keywords: Tissue profiling in a human cohort.

overall_design: Subcutaneous adipose tissue was collected from patients at the time of RYGB surgery at Massachusetts General Hospital between 2000 and 2007.  Samples were collected in RNAlater (Ambion/Applied Biosystems), stored at -80° and shipped to Rosetta Inpharmatics Gene Expression Laboratory Seattle, WA for extraction, amplification, labeling, and microarray processing.  Samples processed ranged in size from 100-200mg. Total RNA extracted from subcutaneous adipose was converted to fluorescently labeled cRNA that was hybridized to custom 44K DNA oligonucleotide microarrays manufactured by Agilent Technologies as described previously (Hughes et al. 2001; Schadt et al. 2008). Successful gene expression profiling results were collected from 701 subcutaneous adipose samples.

first: Danielle

last: Greenawalt

first: Eugene

last: Chudin

first: J

middle: I

last: Hatoum

first: Christine

last: Suver

first: John

last: Beaulaurier

first: Bin

last: Zhang

first: Victor

last: Castro

first: Jun

last: Zhu

first: Solveig

last: Sieberts

first: Susanna

last: Wang

first: Cliona

last: Molony

middle: B

last: Heymsfield

first: Daniel

last: Kemp

first: Marc

last: Reitman

first: Pek

middle: Y

last: Lum

first: Eric

middle: E

last: Schadt

first: Lee

last: Kaplan


title: Genome-wide analysis of time-dependent gene expression in MCF-10HER-2 cells treated with the HER-2-specific inhibitor CP724,714 for 45 hours

status: Public on Mar 18 2011

city: Detroit

first: Aliccia

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

summary: Results of blocking the kinase function of the activated HER-2 oncogene in MCF-10HER-2 cells by treatment with CP724,714 and measuring gene expression as a function of time provides information as to what genes are regulated by HER-2 in these breast epithelial cells that express transformed phenotypes.

overall_design: MCF-10HER-2 cells were treated with the HER-2-specific small molecule kinase inhibitor CP724,714 for 45 hours.  Total RNA was collected every 3 hours from parallel cultures throughout the 45 hour duration of treatment and genome-wide analysis of expression was performed on RNA from each time point (total 16 time points, starting at 0 hours treatment).

first: Stephen

middle: P

last: Ethier


title: Detection of duplication polymorphisms in the Drosophila simulans genome

status: Public on Sep 01 2011

city: Ithaca

first: Margarida

last: Cardoso Moreira

state: NY

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

type: Genome variation profiling by genome tiling array

summary:
In order to characterize duplication polymorphisms in Drosophila simulans, we applied comparative genome hybridization (CGH) using tiling arrays originally designed to cover the full euchromatic genome of its sister species D. melanogaster. We only used the ~900,000 probes in the tiling arrays that had a perfect and unique match to the D. simulans genome (droSim1). We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates. The probabilities of mutation were parsed to make duplication calls.
The supplementary file linked to each Sample record contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model)

overall_design: 14 lines were used in this study. Each line was represented by 3 array hybridizations, for a total of 42 hybridizations. DNA collected from 30 virgin females.

last: Cardoso-Moreira

last: Emerson

first: Manyuan

last: Long


title: Genome-wide analysis of time-dependent gene expression in MCF-10A cells treated with the HER-2-specific inhibitor CP724,714 for 45 hours

summary: Results of blocking HER-2 kinase activity in MCF-10A cells by treatment with CP724,714 and measuring gene expression as a function of time provides information as to what genes are regulated by HER-2 in these nontransformed breast epithelial cells.

overall_design: MCF-10A cells were treated with the HER-2-specific small molecule kinase inhibitor CP724,714 for 45 hours.  Total RNA was collected every 3 hours from parallel cultures throughout the 45 hour duration of treatment and genome-wide analysis of expression was performed on RNA from each time point (total 16 time points, starting at 0 hours treatment).


title: Expression profile of liver samples from subjects at the time of Roux en Y gastric bypass surgery.

first: Radu

last: Dobrin

summary:
To map the genetics of gene expression in metabolically relevant tissues and investigate the diversity of expression SNPs (eSNPs) in multiple tissues from the same individual, we collected four tissues from approximately 1,000 patients undergoing Roux-en-y gastric bypass and clinical traits associated with their weight loss and co-morbidities. We then performed high-throughput genotyping and gene expression profiling and carried out a genome-wide association analyses for more than one hundred thousand gene expression traits representing four metabolically relevant tissues; liver, omental adipose, subcutaneous adipose and stomach. We successfully identified 24,531 eSNPs corresponding to ~10,000 distinct genes. This represents the greatest number of eSNPs identified to our knowledge by any study to date and the first study to identify eSNPs from stomach tissue.  We then demonstrate how these eSNPs provide a high quality disease map for each tissue in morbidly obese patients to not only inform genetic associations indentified in this cohort, but in previously published genome wide association studies as well.  eSNPs and gene co-expression modules identification in morbidly obese patients represent a great resource that will aid in elucidating the key networks associated with morbid obesity, response to RYGB and disease as a whole.

Keywords: Tissue profiling in a human cohort.

overall_design: Liver tissue was collected from patients at the time of RYGB surgery at Massachusetts General Hospital between 2000 and 2007.  Samples were collected in RNAlater (Ambion/Applied Biosystems), stored at -80° and shipped to Rosetta Inpharmatics Gene Expression Laboratory Seattle, WA for extraction, amplification, labeling, and microarray processing.  Samples processed ranged in size from 100-200mg. Total RNA extracted from liver was converted to fluorescently labeled cRNA that was hybridized to custom 44K DNA oligonucleotide microarrays manufactured by Agilent Technologies as described previously (Hughes et al. 2001; Schadt et al. 2008). Successful gene expression profiling results were collected from 651 liver samples.

first: Danielle

last: Greenawalt

first: Eugene

last: Chudin

first: J

last: Hatoum

first: Christine

last: Suver

last: Beaulaurier

last: Zhang

last: Castro

first: Steven


title: Differential gene profile of resorbed embryos following paternal tamoxifen treatment

status: Public on Feb 07 2011

city: Mumbai

first: Nafisa

middle: H

last: Balasinor

state: Maharashtra

address: J.M.Street, Parel

country: India

institute: National Institute for Research in Reproductive Health

summary: Studies from our laboratory have demonstrated that treatment of adult male rats with tamoxifen, a selective estrogen receptor modulator, at a dose of 0.4 mg/kg/day for 60 days resulted in an increase in post-implantation loss at around mid gestation. The present study was done to assess global gene expression profile using Agilent Rat Whole Genome Microarray slides. Differential gene expression profile of resorbed to normal embryos at embryonic day (E) 11 and 13 was studied to identify the causes of resorption. Gene Ontology classification based on biological function revealed significant down regulation of genes associated with development, differentiation, metabolism, transcription, chromatin binding and cell cycle in the resorbed embryos from both the groups at E13. Genes associated with immune response, inflammatory response and angiogenesis were found to be up regulated in the resorbed embryos. Temporal analysis at E11 in the treated resorbed embryos revealed no increase in immune response and inflammation associated genes as seen on E13, indicative of this being a secondary effect. Down regulation of genes associated with development, differentiation, metabolism, transcription, chromatin binding, cell cycle was also evident on E11 in the resorbed embryos. Differential gene expression profile also revealed stochastic expression of imprinted genes, known to modulate embryo-placental growth namely Dlk1, p57, Mash2, Peg3, Lot1 etc. in the resorbed embryos as compared to the normal ones.

overall_design:
Organism used: Rat, Holtzman
Slides: Agilent Rat Whole Genome Microarray Slides (4x44K)
Starting material: Whole Embryo Lysate in TRIzol
RNA Samples used:
CN-E13-1, CR-E13-1, CN-E13-2, CR-E13-2,
TN-E13-1, TR-E13-1, TN-E13-2, TR-E13-2,
TN-E11-1, TR-E11-1, TN-E11-2, TR-E11-2,
Labeling kit: Agilents Low input RNA linear amplification Kit Cat # 5184-3523
Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA
Total RNA and cRNA Purification Kit: Qiagen’s RNeasy minikit Cat#74104
Hybridization Kit: Agilent’s In situ Hybridzation kit 5184-3568
RNA quality was checked using Bioanalyzer.

first: NeelamKedia

last: Mokashi

first: Raja

middle: C

last: Mugasimangalam

first: Aiyaz

last: Mohamed

first: Shrabani

last: Mukherji


title: Importance of genetic background for risk of relapse shown in altered prefrontal cortex gene expression during abstinence following chronic alcohol intoxication.

status: Public on Jan 05 2011

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

summary: Alcoholism is a relapsing disorder associated with excessive consumption after periods of abstinence. Neuroadaptations in brain structure, plasticity and gene expression occur with chronic intoxication but are poorly characterized. Here we report identification of pathways altered during abstinence in prefrontal cortex, a brain region associated with cognitive dysfunction and damage in alcoholics. To determine the influence of genetic differences, an animal model was employed with widely divergent responses to alcohol withdrawal, the Withdrawal Seizure-Resistant (WSR) and Withdrawal Seizure-Prone (WSP) lines. Mice were chronically exposed to highly intoxicating concentrations of ethanol and withdrawn, then left abstinent for 21 days. Transcriptional profiling by microarray analyses identified a total of 562 genes as significantly altered during abstinence. Hierarchical cluster analysis revealed that the transcriptional response correlated with genotype/withdrawal phenotype rather than sex. Gene Ontology category overrepresentation analysis identified thyroid hormone metabolism, glutathione metabolism, axon guidance and DNA damage response as targeted classes of genes in low response WSR mice, with acetylation and histone deacetylase complex as highly dimorphic between WSR and WSP mice. Confirmation studies in WSR mice revealed both increased neurotoxicity by histopathologic examination and elevated triidothyronine (T3) levels. Most importantly, relapse drinking was reduced by inhibition of thyroid hormone synthesis in dependent WSR mice compared to controls. These findings provide in vivo physiological and behavioral validation of the pathways identified. Combined, these results indicate a fundamentally distinct neuroadaptive response during abstinence in mice genetically selected for divergent withdrawal severity. Identification of pathways altered in abstinence may aid development of novel therapeutics for targeted treatment of relapse in abstinent alcoholics.

overall_design: A total of 32 microarrays were run with 4 biological replicates per treatment, line, and sex.  Selection replicates (i.e. WSP-1 and WSP-2) for each treatment, line, and sex were collapsed to improve statistical power (n=4) and to facilitate in the identification of phenotype related effects and exclude selection artifacts.  For comparisons, EtOH regulation was determined by comparing 4 arrays from (for example) Male WSR EtOH treated versus 4 arrays from Male WSR Air treated arrays.

first: Kristine

last: Wiren

first: Joel

middle: G

last: Hashimoto


title: The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc, and its association with wing shape in Drosophila melanogaster

status: Public on Jan 19 2011

city: East Lansing

first: Ian

last: Dworkin

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

institute: Michigan State University

summary:
An analysis of the transcriptional profiles of weak genetic perturbations generated via P-elements measured as heterozygotes in wing imaginal discs of Drosophila melanogaster.

Abstract:
A major objective of genomics is to elucidate the mapping between genotypic and phenotypic space as a step toward understanding how small changes in gene function can lead to elaborate phenotypic changes. One approach that has been utilized is to examine overall patterns of co-variation between phenotypic variables of interest, such as morphology, physiology and behavior, and underlying aspects of gene activity, in particular transcript abundance on a genome wide scale. Numerous studies have demonstrated that such patterns of co-variation occur, although these are often between samples with large numbers of unknown genetic differences (different strains, or even species) or perturbations of large effect (sexual dimorphism, or strong loss of function mutations), that may represent physiological changes outside of the normal experiences of the organism. We used weak mutational perturbations in genes affecting wing development in Drosophila melanogaster, that influence wing shape relative to a co-isogenic wild-type. We profiled transcription of 1150 genes expressed during wing development in 27 heterozygous mutants, as well as their co-isogenic wild type and one additional wild-type strain.
Despite finding clear evidence of expression differences between mutants and wild-type, transcriptional profiles did not co-vary strongly with shape, suggesting that information from transcriptional profiling may not generally be predictive of final phenotype. We discuss these results in the light of possible attractor states of gene expression, and how this would affect interpretation of co-variation between transcriptional profiles and other phenotypes.

overall_design: Total RNA was extracted from pools of wing imaginal discs for each mutant strain as well as for their co-isogenic wild-type, and one additional wild-type strain. RNA was extracted using a modified protocol using the Qiagen RNAeasy kit.


title: Pyronaridine and chloroquine responses in the K1 strain

first: Philip

last: Shaw

summary:
Pyronaridine (PN) and chloroquine (CQ) are structurally related anti-malarial drugs with primarily the same mode of action. However, PN is effective against several multidrug-resistant lines of Plasmodium falciparum, including CQ-resistant lines, suggestive of important operational differences between the two drugs.

Synchronized trophozoite-stage cultures of P. falciparum strain K1 (CQ resistant) were exposed to 50% inhibitory concentrations (IC50) of PN and CQ, and parasites were harvested from culture after 4 and 24 hours exposure. Global transcriptional changes effected by drug treatment were investigated using DNA microarrays.

overall_design: Plasmodium falciparum in vitro cultures were synchronized to trophozoite stage (22-24h post infection) and exposed to either CQ or PN at IC50 concentrations. 18 sample pairs (drug treated/untreated) were analyzed; 9 for CQ and 9 for PN. All drug-treated samples were labelled with Cy5 and untreated controls were labelled with Cy3.

first: Kanyanan

last: Kritsiriwuthinan

first: Sastra

last: Chaotheing

first: Chayaphat

last: Wongsombat

first: Porntip

last: Chavalitshewinkoon-Petmitr

first: Sumalee

last: Kamchonwongpaisan


title: Elucidation of cell type specific Ecdysone Receptor Binding

status: Public on Apr 30 2011

city: Athens

first: Melissa

last: Davis

state: GA

address: 500 DW Brooks Dr S 270C

department: Genetics  and MCG/UGA Medical Partnership

institute: University of Georgia

type: Genome binding/occupancy profiling by genome tiling array

summary: Cell lines from two tissue types (embryonic and imaginal discs) were utilzed in a DAM-ID  study in order to identify tissue specific receptor binding sites. We have found novel binding sites, unique to each cell type, with about 20% overall overlap and about 50% overlap between cells from common tissues.

overall_design: 46 arrays were utilized. For each cell type, three replicates each of hormone treated and untreated cells, with an EcR-DAM fusion construct as well as a DAM-only construct (hormone treatment and no treatment)

first: Kevin

last: White


title: Plasmodium falciparum CNV-SNP chip optimization

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

institute: University of Notre Dame

summary: Optimize SNP genotyping probes and demonstrate a new P. falciparum microarray platform that includes CGH and resequencing probes on the same chip

overall_design: 3D7 common reference; lab samples: HB3, Dd2, SC05, 7C126; field patient samples: M1176, M1069, M1094, M1321, M1064, M1111

middle: T


title: Thrombopoietin (TPO) protects against heart damage induced by doxorubicin and infarction in rat models

status: Public on Dec 29 2010

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: In order to examine the mechanism of TPO on cardiac protection against DOX damage, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to delineate the TPO cardioprotective mechanism against DOX-induced cardiomyopathy

overall_design: Dox and TPO induced gene expressions in rat heart were measured at day 6. Two biological replicates were performed for each treatment group.

first: Karen

last: Li

first: Rita

last: Sung


title: Sheep longissimus dorsi (LD) muscle from 40 individual progeny belonging to six Poll Dorset industry sires

status: Public on Nov 30 2010

city: Brisbane

first: Ross

last: Tellam

state: QLD

address: 306 Carmody Road St.Lucia

department: Level 6 Queensland Biosciences Precinct

country: Australia

institute: CSIRO Animal, Food and Health Sciences

summary:
Expression profiling of sheep born to Australian industry sires with high and low genetic merit (Estimated Breeding Values or EBVs) for eye muscle depth (EMD). Progeny (40) from six Poll Dorset sires representing well defined extremes of EBVs for Eye Muscle Depth (low EBV EMD and high EBV EMD) were selected for analysis. The six sires were Australian industry sires with three sires representative of low EBV EMD and three representing high EBV EMD.
Microarrays were used for transcription profiling of skeletal muscle samples taken from 40 individual progeny belonging to six Poll Dorset industry sires, with 3 sires extreme for high and 3 sires extreme for low muscling (based on EBV for EMD).

overall_design: Sheep longissimus dorsi (LD) skeletal muscle samples were collected from 40 individual progeny belonging to six Poll Dorset industry sires, with 3 sires extreme for high and 3 sires extreme for low muscling (based on EBV for EMD).

first: Tony

last: Vuocolo

first: Keren

last: Byrne


title: Expression profile of liver, omental adipose, and subcutaneous adipose samples from subjects at the time of Roux en Y gastric bypass surgery.

first: Radu

last: Dobrin

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

overall_design: Refer to individual Series

first: Danielle

middle: M

last: Greenawalt

first: Eugene

last: Chudin

first: J

last: Hatoum

first: Christine

last: Suver

first: John

last: Beaulaurier

first: Bin

last: Zhang

first: Victor

last: Castro

first: Jun

last: Zhu

first: Solveig

middle: K

last: Sieberts

first: Susanna

last: Wang

first: Cliona

last: Molony

first: Steven

last: Heymsfield

first: Daniel

last: Kemp

first: Marc

last: Reitman

first: Pek

last: Lum

first: Eric

last: Schadt

first: Lee

last: Kaplan


title: Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes (Illumina expression data)

status: Public on Jan 01 2011

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

summary: Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Using a combination of genome-wide and gene-specific approaches, we provide evidence that rather than representing off/on transitions, Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early (I/E) and late response genes results from a sequential process in which signal-independent factors, exemplified by Gabpa, initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. Promoters of I/E genes are distinguished from those of late genes by the use of distinct sets of signal-dependent transcription factors, preferential binding of TBP and basal enrichment for RNA Pol II immediately downstream of transcriptional start sites. Global nuclear run-on (GRO) sequencing and total RNA sequencing further indicates that TLR4 signaling markedly increases efficiency of transcriptional elongation of nearly all I/E genes, while RNA splicing is largely unaffected. NCoR/SMRT co-repressor complexes are unexpectedly found to be associated with H3K4me3-positive promoters of TLR4-responsive genes that exhibit a broad range of basal expression levels, implying a dynamic, rather than static role in regulation of gene expression. Collectively, these findings reveal mechanisms underlying temporally distinct patterns of TLR4-dependent gene activation required for homeostasis and effective immune responses.

overall_design: ChIP-Seq, Total RNA-Seq, Gro-Seq, and gene expression profiling was performed in macrophages treated with Kdo2 Lipid A. Control samples for H3K4me3 and Input in Macrophages and B cells, in addition to control microarray data are included in GEO accession# GSE21512

first: Laure

last: Escoubet-Lozach

first: Minna

middle: U

last: Kaikkonen

first: Jean

last: Lozach

first: Sven

last: Heinz

first: Nathanael

last: Spann

first: Andrea

last: Crotti

first: Josh

last: Stender

first: Serena

last: Ghisletti

last: Glass


title: Expression profile of omental adipose samples from subjects at the time of Roux en Y gastric bypass surgery.

first: Radu

last: Dobrin

overall_design: Omental adipose tissue was collected from patients at the time of RYGB surgery at Massachusetts General Hospital between 2000 and 2007.  Samples were collected in RNAlater (Ambion/Applied Biosystems), stored at -80° and shipped to Rosetta Inpharmatics Gene Expression Laboratory Seattle, WA for extraction, amplification, labeling, and microarray processing.  Samples processed ranged in size from 100-200mg. Total RNA extracted from omental adipose was converted to fluorescently labeled cRNA that was hybridized to custom 44K DNA oligonucleotide microarrays manufactured by Agilent Technologies as described previously (Hughes et al. 2001; Schadt et al. 2008). Successful gene expression profiling results were collected from 848 omental adipose samples.

first: Danielle

last: Greenawalt

first: Eugene

last: Chudin

first: J

last: Hatoum

first: Christine

last: Suver

first: John

last: Beaulaurier

first: Bin

last: Zhang

first: Victor

last: Castro

first: Jun

last: Zhu

first: Solveig

last: Sieberts

first: Susanna

last: Wang

last: Molony

middle: L


title: Borna disease virus phosphoprotein expression affects glial functions in the C6 glioma cells

status: Public on Feb 17 2011

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Borna disease virus (BDV) is a highly neurotropic negative-strand RNA virus that belongs to the Mononegavirales. Many reports demonstrated that natural infection of BDV occurs worldwide in a variety of vertebrate species, suggesting that host range of this virus includes all warm-blooded animals. BDV persistently infects the central nervous system (CNS) of many animal species and causes neurobehavioral disorders resembling autism, such as anxiety, aggression, hyperactivity, abnormal play behavior, and cognitive deficits. We previously reported the generation of transgenic mice expressing BDV phosphoprotein (P) selectively in astrocytes. This transgenic mouse, P-Tg, showed striking neurobehavioral abnormalities resembling those in BDV-infected animals, such as enhanced intermale aggressiveness, hyperactivity and spatial reference memory deficit. To reveal the molecular mechanisms how glial cells induce these abnormalities, we performed microarray analysis using C6 rat glioma cells expressing either GFP (C6-GFP) or BDV P (C6-P). Sixty-eight genes are significantly affected in C6-P cells.  The genes, whose products are localized at the extracellular region, were enriched in the differentially expressed genes in C6-P cells. Furthermore, gene ontology analysis revealed an emphasis on genes involved in morphogenesis. It is highly likely that the secretion of astrocyte factors may be widely dysregulated in the P-Tg, leading to the astrocyte hypofunction in the brain.

overall_design: The labeled cRNAs were hybridized on 4X44K Agilent Whole Rat Genome dual colour Microarrays (G4130F) in two dye swap experiments, resulting in four individual microarrays.

first: Tomoyuki

last: Honda

first: Keizo

last: Tomonaga


title: Human postmortem hippocampus: Major depressive disorder  (MDD) vs. Control

status: Public on Oct 17 2010

city: New Haven

first: Vanja

last: Duric

state: CT

address: 34 Park Street

institute: Yale University

summary: We examined the genetic profile of postmortem brain (hippocampal) samples; 15 brains from patients diagnosed with MDD were matched to brains from healthy subjects based on gender, race and age.  Gene expression profiles in the dentate gyrus and CA1 subregions of the hippocampus were assessed by cDNA hybridization to 48K human HEEBO whole genome microarrays (Microarray, Inc).

overall_design:
Two-group comparison: MDD (13 male, 8 female) vs. Control (11 male, 7 female).  Dentate Gyrus (DG): 15 pairs of samples (1 array per pair); CA1: 15 pairs of samples (1 array per pair).  Biological replicates.
We can not provide a list of normalized values for each individual hybridization (per chip), but rather have a list of average expression values for all hybridizations used in the experiment (n=15).  See supplementary files below.

CODES:
AAm, African American; C, Caucasian; CO, carbon monoxide; CVD, cardiovascular disease; ETOH, ethanol; F, female; Hx, history of alcohol abuse but not currently active; M, male; MDD, Major Depressive disorder, ND, no psychotropic medication detected; NOS, not otherwise specified, OD, drug overdose; PE, prior episode of major depression with psychotic features; PMI, postmortem interval (hours); SIGSW, self-inflicted gunshot wound; [1], Psychotrophic prescriptions within last month; [2], MDD in remission;  [3], prescriptions for six days prior to death; *, samples present only in array sets for the dentate gyrus; **, samples present only  in array sets for CA1.

first: Mounira

last: Banasr

first: Pawel

last: Licznerski

first: Heath

middle: D

last: Schmidt

first: Craig

middle: A

last: Stockmeier

first: Arthur

last: Simen

first: Samuel

middle: S

last: Newton

first: Ronald

last: Duman


title: Sexual Dimorphic Regulation of Liver Gene Expression by Glucocorticoids

status: Public on Oct 02 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Males and females exhibit differences in the incidence of many major diseases including auto-immune diseases, hepatocellular carcinoma, diabetes, and osteoporosis, which all have important inflammatory components in their etiology. Glucocorticoids are the primary physiological anti-inflammatory hormone in all mammals and synthetic derivatives of these hormones are widely prescribed as anti-inflammatory agents irrespective of gender. Surprisingly we report a marked sexually dimorphic regulation of gene expression by glucocorticoids in the rat liver. Eight distinct patterns of glucocorticoid regulated genes were identified and two revealed genes that respond to glucocorticoid treatment in both sexes in opposite directions (anti-correlated genes. We also identified gender-specific groups of genes regulated by glucocorticoids. Pathways analysis identified sex-specific glucocorticoid regulated gene expression in several canonical pathways that have been implicated in human disease in which disease susceptibility is sex-biased. For example, comparison of number of genes involved in inflammatory disorders between sexes, revealed 84 additional glucocorticoid responsive genes in the male rat. Our data suggests that glucocorticoids thorough sexually-dimorphic regulation of gene expression modulate gender specific homeostatic functions in male and female liver.

overall_design:
Adult males and females adrenalectomized Sprague-Dawley rats (8-10 weeks of age) (females Distrous 1) were treated with vehicle (Phosphate Buffered Saline – 400 µl) or Dexamethasone (1mg/Kg i.p.) purchased from Steraloids (Newport, RI). Liver was harvested 6 hours after treatment and kept in RNA later solution at 4oC over night. Samples were frozen and stored at -80oC.
Three replicate microarrays were completed for each group (male vehicle, male dexamethasone, female vehicle and female dexamethasone) for a total of 12 microarrays. Each microarray was hybridized using a pooled RNA sample, and each pool was created from equal amounts of total RNA from three independent RNA samples, representing individual animals (n=9 animals per group). This approach provides appropriate biological replication within the constraints of a limiting number of microarrays (C. Kendziorski, R. A. Irizarry, K. S. Chen, J. D. Haag, M. N. Gould, Proc Natl Acad Sci U S A 102, 4252 Mar 22, 2005).

first: Danielle

last: Duma

first: Jennifer

last: Collins

first: Jeff

middle: W

last: Chou

first: John

last: Cidlowski


title: Neonatal Hydrocephalus: Saline Control vs. Kaolin-Induced

status: Public on Jul 01 2010

city: Salt Lake City

first: Kelley

last: Deren

state: UT

address: 175 N Medical Drive East CNC 3305

department: Neurosurgery

institute: University of Utah

summary: Transcriptional profiling of the parietal cortex was performed in postnatal day 22 rats with obstructive hydrocephalus.  An intracisternal injection of kaolin was done on postnatal day one, and severe hydrocephalus developed over 3 weeks.  Hydrocephalic animals were compared to age-matched saline controls.  The goal was to determine the effects of kaolin-induced neonatal hydrocephalus on gene expression.

overall_design: Two-condition experiment: kaolin-induced vs. saline-injected controls. Replicates: 5 treatment samples and 5 saline controls.

last: Forsyth

first: Brett

last: Milash

first: James

last: McAllister


status: Public on Jun 01 2010

first: Ross

last: Tellam

summary:
Expression data from Sheep longissimus dorsi (LD) muscle during development;  fetal lambs (80, 100, 120 days gestation), new born lambs at birth (150 d) and lambs at 12 weeks (230 d)

The fetal to neonatal developmental transition corresponds with profound changes in skeletal muscle function as it adapts to the new physiological demands of locomotion and postural support against gravity. The mechanisms underpinning this adaption process are unclear but are likely to be initiated by changes in hormone levels occurring during the major developmental transition. We tested the hypothesis that this period is associated with changes in the transcription of skeletal muscle genes, particularly genes involved in oxidative metabolism.  Using an ovine model, transcriptional profiling was performed on longissimus dorsi skeletal muscle taken at three fetal developmental time points (80, 100 and 120 d of fetal development) as well as two postnatal time points, one within 3 days after birth and a second at 12 weeks of age. The developmental time course was dominated by large changes in the expression of 2471 genes during the period from late fetal development (120 d fetal development) to birth (within 1-3 days of birth). Analysis of the functions of the genes that were uniquely up-regulated in this period showed strong enrichment for oxidative metabolism and the TCA cycle indicating enhanced mitochondrial activity. Indeed, histological examination of tissues from these developmental time points directly demonstrated a marked increase in mitochondrial activity between the late fetal and early post-natal samples. The genes that were down-regulated in this period suggested de-emphasis of an array of biological functions including Wnt signaling, cell adhesion and differentiation. There were also changes in the expression of genes prior to this late fetal – postnatal transition and between the two postnatal time points that involved a variety of biological functions. It is concluded that there is substantial and coordinated changes in the transcription of a large number of genes in skeletal muscle which underpin the adaption of muscle to the new physiological demands in the postnatal environment.
Microarrays were used for transcription profiling of skeletal muscle samples taken from fetal lambs (80, 100, 120 days gestation), new born lambs at birth (150 d) and lambs at 12 weeks (230 d)

overall_design: Sheep used in this experiment were bred from a research flock of Dorset/Suffolk/Rambouillet cross-bred sheep raised at Utah State University and cared for and euthanased for sample collection in accordance with the animal ethics guidelines of Utah State University (Utah, USA).  Longissimus dorsi (LD) skeletal muscle samples were taken from fetal lambs at 80, 100 and 120 days of gestation, new born lambs within 1 to 3 days of birth (i.e. 150 days of development) and young lambs at 12 weeks of age (230 days of development). Three individuals were sampled at each developmental time

first: Tony

last: Vuocolo

first: Keren

last: Byrne

first: Cedric

last: Gondro

first: Jason

last: White

first: Noelle

last: Cockett

first: Tracey

last: Hadfield

first: Christopher

last: Bidwell

first: Jolena

middle: N

last: Flemming-Waddell


title: Expression data from unactivated vs. activated PBMCs (ion array)

status: Public on Jun 17 2010

city: Hamburg

first: Christoph

last: Ogrodowczyk

address: Falkenried 94

department: Institute for Neural Signal Transduction

country: Germany

institute: ZMNH

summary: Long-lasting activation of T cells requires up-regulation of many genes, for example of transcription factors, cytoskeletal proteins and cell surface proteins encluding ion channels.  An increase of ion channel density at the cell surface reflects the needs to manage increased  Ca2+ influx into the activated T cell. Using oligonucleotide-based arrays we have surveyed  changes in ion channel mRNA expression that occur upon T cell activation.

overall_design: We isolated PBMCs from blood of healthy donors and divided those into two parts. One was activated for 72 hr by adding PHA-L whereas the other part was incubated in the same way but not stimulated.

first: C

first: O

last: Pongs


title: Human and Mouse Cells Time of Replication (ToR)

status: Public on May 25 2010

city: Jerusalem

first: Itamar

last: Simon

address: Ein Karem Campus

department: Molecular Biology

country: Israel

institute: The Hebrew university

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: MicroRNA Profiling in Ischemia-Reperfusion Injury of the Gracilis Muscle in Rats

status: Public on Apr 22 2010

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

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


title: Potential Target Genes of MicroRNA-21 In Ischemia-Reperfusion Injury Of The Gracilis Muscle In Rats

summary:
Transcriptional profiling of rat gracilis muscle after ischemia 4h and reperfusion for 1d, 3d, 7d and 14d v.s. sham control, and correlate the downregulated transcripts to the computational predicted gene targets of ron-miR-21
Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, three miRNAs (miR-21, miR-200c, and miR-205) of 350 tested rat miRNAs were found to have an increased expression in the miRNA array.The expression of the mRNA in the muscle specimens after 4 h of ischemia and reperfusion for 1, 3, 7, and 14 d were detected with the Agilent Whole Rat Genome 4 × 44 k oligo microarray. A combined approach using a computational prediction algorithm that included miRanda, PicTar, TargetScanS, MirTarget2, RNAhybrid, and the whole genome microarray experiment was performed by monitoring the mRNA:miRNA association to identify potential target genes.

overall_design: Four-condition experiment, Gracilis muscle after ischemia-reperfusion injury for 1d, 3d, 7d and 14d v.s.Gracilis muscle (sham control), Biological replicates: 1 control replicate, 1 experiement replicate (each condition).


title: Network analysis of differentially expressed genes in a rat model of neonatal HI encephalopathy +/- antioxidant

status: Public on Mar 05 2010

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary: Neonatal hypoxic-ischemic (HI) encephalopathy can lead to severe brain damage, and  is a common cause of neurological handicaps in adulthood. The modified Levine method (Rice model) has been widely used as an animal model of this condition, which can be rescued by the administration of an antioxidant such as 3-methyl-1-phenyl-2-pyrazolin-5-one (MCI-186). In the present study, by using the Rice model, we performed comprehensive gene expression and gene network analyses of neonatal HI brain insult with and without MCI-186 administration via a DNA microarray to help elucidate the molecular events responsible for the selective vulnerability of neurons to an HI insult and the underlying mechanisms of the effect of MCI-186 on the pathophysiological events. A large difference in gene expression was observed between the Rice model and the control. By performing a clustering analysis of the gene expression pattern after the HI brain insult, we found the following 3 clusters: (i) a cluster of strongly upregulated genes mainly consisting of genes related to immune responses; (ii) a cluster of mildly upregulated genes mainly consisting of genes related to cellular movement, growth and proliferation, and cell death; and (iii) a cluster of downregulated genes mainly consisting of genes related to neuronal activity. The effect of MCI-186 administration on gene expression was much less than and contrary to that of the HI brain insult. The genes upregulated and downregulated on MCI-186 administration were closely related to neuronal activity and immune responses, respectively, thereby reflecting the protective effect of MCI-186 on an HI brain insult.

overall_design: Seven-day-old Wistar rats were assigned to two groups: control group and Rice group. The Rice group rats were subjected to a modified Levine’s procedure to produce the HI brain injury. Each rat was anesthetized with ether, and the left carotid artery was sectioned between double ligatures with 4-0 surgical silk. The rats were allowed to recover for 1–2 h and then exposed to 1 h of hypoxia in a plastic chamber, which was perfused with a mixture of humidified 8% oxygen balanced with nitrogen. The temperature inside the chamber was maintained at 33 °C, the usual temperature while huddling with the mother. Immediately after removal from the hypoxia chamber, the pups were intraperitoneally injected with 100 ul normal saline or 9 mg/kg MCI-186 dissolved in normal saline. The injection was repeated after 30 min. The control group rats were not exposed to HI brain insult but received an intraperitoneal injection of 100 ul saline or 9 mg/kg MCI-186 dissolved in normal saline. There were three pups per condition in both the groups. The cerebral cortexes ipsilateral to the HI brain insult and those of the same side of the control animals were used for the experiment.

first: Yuto

last: Ueda

first: Naoki

last: Adati

first: Aya

last: Kitamoto

first: Akira

last: Sato

first: Ming-Chih

last: Huang

first: Jesmine

last: Noor

first: Hiroshi

last: Sameshima

first: Tsuyomu

last: Ikenoue


title: Cotranscriptional exon skipping in the genotoxic stress response

status: Public on May 20 2010

city: ORSAY

first: Martin

last: Dutertre

address: Rue Henri Becquerel

institute: INSERM

summary: Pre-mRNA splicing is functionally coupled to transcription, and genotoxic stresses can enhance alternative exon inclusion by affecting elongating RNA polymerase II. We report here that various genotoxic stress inducers, including camptothecin, inhibit the interaction between EWS, an RNA polymerase II-associated factor, and YB-1, a spliceosome-associated factor. This results in the cotranscriptional skipping of several exons of the MDM2 gene encoding the main p53 ubiquitin-ligase. This reversible exon skipping participates in the timely regulation of MDM2 expression, and may contribute to the accumulation of p53 during stress exposure and its rapid shut off when stress is removed. Finally, a splicing-sensitive microarray identified numerous exons that are skipped in response to camptothecin and EWS/YB-1 depletion. These data demonstrate genotoxic stress-induced alteration of the communication between the transcriptional and splicing machineries, resulting in widespread exon skipping and playing a central role in the genotoxic stress response.

overall_design: 6 samples of MCF7 cells exposed to different treatments were analyzed: 3 x control_6 hours; 3 x camptothecin_6 hours.

first: Gabriel

last: Sanchez

first: Marie-Cécile

last: de Cian

first: Jérôme

last: Barbier

first: Etienne

last: Dardenne

first: Lise

last: Gratadou

first: Gwendal

last: Dujardin

first: Catherine

last: Le Jossic-Corcos

first: Laurent

last: Corcos

first: Didier

last: Auboeuf


title: Cold-induced silencing mediated by long antisense FLC transcripts

status: Public on Dec 31 2009

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary: Hight throughput techniques have revealed huge complexity in antisense RNAs in many organisms. We have explored the complexity of this class of transcripts and functional links to Polycomb silencing thought analysis of non-coding RNAs of Arabidopsis FLC. FLC is repressed and epigenetically silenced by prolonged cold, enabling plants to undergo the floral transition. Single nucleotide resolution tiling array revealed long non-coding transcripts covering the entire FLC locus. The most abundant of these are capped and polyadenylated, initiate over a 100 nucleotide window just downstream of the sense polyA site, are differentially spliced and terminate either within the sense gene or its promoter. Their levels correlate with FLC sense transcripts in all mutants and conditions tested except cold treatment. The antisense transcripts were strongly but transiently cold-induced, much earlier than other vernalization markers, and this coincided with reduction in sense FLC transcription but not sense FLC mRNA levels. Addition of the FLC antisense 5'/sense 3' region to a GFP transgene was sufficient to confer cold-induced silencing of thet fusion; however this silencing was not epigenetically manteined. These processes were all independent of the function of the Polycomb proteins required for maintenance of FLC silencing. Our data suggest that FLC antisense transcripts induce transient FLC transcriptional silencing, possibly through promoter interference, with the epigenetic silencing requiring subsequent recruitment of Polycomb machinery.

overall_design: Total seedling RNA from different genotypes and different conditions: WT, FRIGIDA, 35s::FCA (giving overexpression of FCA), FRIGIDA + 2 weeks cold, FRIGIDA + 2 weeks cold + 7 days warm.

first: Szymon

last: Swiezewski

first: Fuquan

last: Liu

first: Andreas

last: Magusin

first: Caroline

last: Dean


title: Temporal Gene Expression Profiling of Bone Repair in a Rat Calvarial Defect

status: Public on Mar 25 2010

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

summary: Microarray analysis of gene expression was performed in the healing and non-healing calvarial defects of 12-week old male rats during various stages of bone repair: 1, 3, 5, 7, 10, 14, and 21 days post surgery.

overall_design: Eight (CSD) or four (non-CSD) mm circular defects were created in the calvaria. The disc was removed, leaving the underlying dura mater intact. At the respective time post-injury, the region of regeneration was harvested, and RNA isolated using Tri Reagent. Next, labeling and hybridization to Agilent rat whole genome microarrays was performed.

first: Arlene

last: Siller-Jackson


title: High weight differences between donor and recipient affect early kidney graft function -a role for IL-6 signaling

status: Public on Jul 22 2009

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: The frequency of delayed function of kidney transplants varies greatly and is associated with the quality of graft, donor age, and the duration of cold ischemia time. Body weight differences between donor and recipient can affect primary graft function. The underlying mechanism is poorly understood. Here, we have transplanted kidney grafts from commensurate body weight (L-WD) or reduced body weight (H-WD) donor rats into syngeneic or allogeneic recipients. 24 hours post-transplantation, serum creatinine level in H-WD recipients was significantly higher compared to that of L-WD recipients indicating impaired primary graft function. We detected a 10 fold higher transcription of IL-6 and dramatically increased tubular destruction in grafts from H-WD recipients. This was accompanied by decreased expression of genes associated with kidney function and an up-regulation of other genes such as cytochrome P450 isoforms, FosL and Trib3 as revealed by DNA microarray analysis. A single application of IL-6 into L-WD recipients is sufficient to impair primary graft function and to cause tubular damage. Whereas, immediate neutralization of IL-6 receptor signaling rescued primary graft function resulting in low serum creatinine levels, well-preserved kidney graft architecture and a normalized gene expression profile. These findings have strong clinical implication as anti-IL6R treatment of patients receiving grafts from lower-weight donors could be used to improve primary graft function.

overall_design: The dataset comprises eight samples divided into four sample groups. Each group represents rat kidneys collected after allogeneic transplantation under a certain condition and includes two biological replicates. The first group is characterized by a high body weight difference between donor and recipient, rats in the second group exhibit a low weight difference. Group three and four are similar to group one, but underwent an additional treatment with anti-IL6R mAb or prednisolone immediately after transplantation.

first: Weihua

last: Gong

first: Maren

last: Klöpfel

first: Anja

last: Reutzel-Selke

first: Anke

last: Jurisch

first: Katrin

last: Vogt

first: Stefanie

last: Haase

first: Conny

last: Höflich

first: Dietrich

last: Polenz

first: Bernhard

last: Gerstmayer

first: Hans-Dieter

last: Volk

last: Pascher

first: Birgit

last: Sawitzki


title: Analysis of ETS gene expression patterns uncovers novel ETS mediated gene silencing pathways in prostate cancers

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary:
Deregulated expression of ETS transcription factors with oncogenic and tumor suppressor function occurs frequently in prostate cancer leading to profound alterations of the cancer transcriptome.  By integrating genomic and functional studies we identified key targets of the aberrantly expressed ETS factors, ERG and ESE3. Altered expression of ETS factors led to the induction of the polycomb group protein EZH2 and silencing of the tumor suppressor Nkx3.1.  Nkx3.1 was controlled by ERG and ESE3 both directly via binding to ETS binding sites in the gene promoter and indirectly via EZH2-induced histone H3K27 methylation.  This may represent a general mechanism linking aberrantly expressed ETS with deregulation of epigenetic pathways and global reprogramming of the prostate epithelial cell transcriptome in prostate tumorigenesis.

Keywords: prostate cancer, gene expression profiling, ETS genes

overall_design: In this study we show that deregulated expression of ETS factors with opposite functions is highly frequent in prostate cancer.  Our study uncovers a previously unrecognized link between aberrant expression of ETS factors, deregulation of epigenetic pathways and silencing of tumor suppressor genes in prostate cancer and shows that partially distinct transcriptional programs are associated with different ETS gene expression patterns. The presence of distinct prostate cancer subgroups with different biological features may have important clinical implications and suggests that assessment of ETS expression levels might be useful to distinguish tumors with different clinical outcome.

first: Paolo

last: Kunderfranco

first: Maurizia

last: Mello-Grand

first: Romina

last: Cangemi

first: Stefania

last: Pellini

first: Afua

last: Mensah

first: Veronica

last: Albertini

first: Anastasia

last: Malek

first: Giovanna

last: Chiorino

first: Carlo

middle: V

last: Catapano

first: Giuseppina

last: Carbone


title: No-match ORESTES explored as tumor markers

status: Public on Apr 13 2009

city: Sao Paulo

first: Barbara

middle: Pereira

last: Mello

state: SP

address: R. Prof. Antonio Prudente, 211

department: Centro de Pesquisa

country: Brazil

institute: Hospital A. C. Camargo

summary: Sequencing technologies together with new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this major objective by generating data from about 1.2 million expressed sequence tags (ESTs). Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3,421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences, with fold differences between tumor and normal samples of at least two, in one or more different tissues, was 1,007. Also, about 28% of analyzed sequences could represent non-coding RNAs (ncRNAs). Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of 3 out of 8 potentially tumor markers in prostate tissues. A list of 1,007 differentially expressed sequences, as well as the 291 potentially non-coding molecular markers for different tumors was provided.

overall_design: Experiments were performed in duplicate, using dye-swap method. We used linearly amplified RNA samples (T7-based protocol), derived from 56 normal or tumor tissues from 12 distincts body localization, and a pool of RNAs obtained from 15 distinct human cell lines as reference. cDNA was synthesized in the presence of aminoallyl-dUTP (Sigma-Aldrich) and labeled using Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen).

first: Eduardo

middle: F

last: Abrantes

first: César

last: Torres

first: Rogério

last: Fonseca

first: Ariane

last: Machado-Lima

first: Dirce

last: Carraro

first: Ricardo

middle: R

last: Brentani

first: Luiz

last: Lima Reis

first: Helena


title: Rat heart cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

status: Public on Apr 01 2009

city: Shanghai

first: Jing

last: Liao

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology  Shanghai Institutes for Biological Sciences  Chinese Academy of Science

summary: Rat somatic heart cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic heart cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic heart cells and rat iPS cells.

overall_design: There were two replicates sample of the rat somatic heart cell  named 1, 2.And the control cells were the mixture of rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF) named mix1. Rat somatic heart cells samples were labled with Cy3 and the mix1 were labled with Cy5. The data was process to show the rat somatic heart cells' gene expression difference compared with that of mix1.

first: Lei

last: Xiao

first: Chun

last: Cui

first: Huasheng

first: Xiaokun

last: Teng

first: Yi

last: Zhang


title: Differential expression of whole transcriptome in Synechocystis sp. PCC 6803

status: Public on May 20 2009

city: Freiburg

first: Bjoern

last: Voss

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg

summary:
The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey of differential expression with a focus on antisense (as)RNAs and non-coding (nc)RNAs. A microarray was constucted with on average 5 probes for each transcript known thus far, including ncRNAs and asRNAs. The resulting 20,431 individual probes are duplicated on the array (Agilent 4x44k custom array) representing a technical replicate.
Hybridization of this array with total RNA isolated from cultures raised under different growth conditions identified transcripts from intergenic spacers and in antisense orientation to known genes (natural cis-asRNAs) with differential expression compared to control hybridizations. This shows the involvement of such transcripts in the regulation of adaptation to various stresses.

overall_design: 12 RNA hybridizations (1 control & 3 stress conditions, 3 times each)

first: Jens

last: Georg

first: Björn

first: Ingeborg

last: Scholz

first: Jan

last: Mitschke

first: Annegret

last: Wilde

first: Wolfgang

last: Hess


title: Transcriptome/Expression analysis in Mycoplasma pneumoniae

status: Public on Dec 11 2009

city: Barcelona

first: Marc

last: Güell

address: C/ Dr.Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

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

overall_design: Refer to individual Series


title: Subtypes of familial breast tumors revealed by expression and copy number profiling

status: Public on Dec 16 2009

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

institute: Queensland Centre for Medical Genomics

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: We analysed a cohort of 75 BRCA1, BRCA2 and non-BRCA1/2 breast tumors by gene expression profiling and found that 74% BRCA1 tumors were basal-like, 73% of BRCA2 tumors were luminal A or B, and 52% non-BRCA1/2 tumors were luminal A. Thirty-four tumors were also analysed by single nucleotide polymorphism-comparative genomic hybridization (SNP-CGH) arrays. Copy number data could predict whether a tumor was basal-like or luminal with high accuracy, but could not predict its mutation class. Basal-like BRCA1 and basal-like non-BRCA1 tumors were very similar, and contained the highest number of chromosome aberrations. We identified regions of frequent gain containing potential driver genes in the basal (8q and 12p) and luminal A tumors (1q and 17q). Regions of homozygous loss associated with decreased expression of potential tumor suppressor genes were also detected, including in basal tumors (5q and 9p), and basal and luminal tumors (10q). This study highlights the heterogeneity of familial tumors and the clinical consequences for treatment and prognosis.

overall_design: RNA was extracted from 75 Familial breast tumours, which were more than 50% tumour cells, comprising BRCA1 (19), BRCA2 (30), non-BRCA1/2 (25) and one familial tumour of unknown mutation status. DNA was also extracted from 34 of these samples which were more than 75% tumour.


title: Rat medial prefrontal cortex gene expression following heroin self-administration, abstinence, and extinction

status: Public on Jan 30 2009

city: Hershey

first: Kent

middle: E.

last: Vrana

state: PA

address: 500 University Drive

department: Pharmacology

institute: Penn State College of Medicine

summary:
Several studies have investigated changes induced by drug exposure, but few reports have described changes that persist following relapse.  In the present study, genome-wide analysis of gene expression was conducted in rats that expressed behavioral incubation of heroin-seeking and goal-directed behavior.  The medial prefrontal cortex (mPFC) is important in mediating goal-directed behavior and also was the target of this analysis.  Rats were trained to self-administer heroin (0.06 mg/0.2 ml infusion) during 3 hour daily sessions for 14 days.  Following the self-administration period, rats were reintroduced to the self-administration chambers for a 90-minute extinction session.  The extinction session occurred either 1 day or 14 days following the final self-administration session.  Behavioral data demonstrated incubation (increased expression) of heroin-seeking and goal-directed behavior after the 14 day abstinent period.  Whole genome analysis was performed and selected results were confirmed by quantitative real-time PCR (RT-qPCR).  Microarrays identified 66 genes whose expression was identified as changed by at least 1.4 fold (p<0.02) following 14 days of abstinence and the 90-minute extinction session, and seven of the genes on which RT-qPCR was performed were confirmed (BDNF, Calb1, Dusp5, Dusp6, EGR1, NPY, RGS2).  Ontological analysis indicates that several of the genes with changed expression in this study are important for behavior and learning.  The importance of drug-seeking behavior and memory of previous sessions of drug-taking suggest that such genes may be important for relapse.  The global gene expression analysis adds to the knowledge of heroin-induced changes and further highlights similarities between heroin and other drugs of abuse.

Keywords: heroin self-administration

overall_design: cRNA from 6 rats that self-administered heroin was compared to cRNA from 5 rats that received yoked infusions of saline.

middle: E

first: Kara

last: Kuntz-Melcavage


title: Gene expression profiling of distinct serotypes of Actinobacillus pleuropneumoniae

status: Public on Mar 31 2010

city: Wuhan

first: Lu

last: Li

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

summary:
To further confirm the genetic diversity and virulence evolution of A. pleuropneumoniae
To determine the gene sets with different expression levels (high, normal and low, respectively)

Keywords: serotype comparison

overall_design: A. pleuropneumoniae strains were grown in TSB medium supplemented with 10 μg/ml nicotinamide adenine dinucleotide and 10% (v/v) filtered cattle serum at 37°C. The intensities were normalized and transformed into log2 value. The values for each time point were averaged and the genes with log2 ratio >=1 or <=-1 were selected as differentially expressed genes.

first: Zhuofei

last: Xu

first: Rui

last: Zhou

first: Huanchun

last: Chen


title: Rat iPS M13 cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

first: Jing

last: Liao

department: Institute of Biochemistry and Cell Biology

summary: Rat iPS M13 cells had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave rat iPS M13 cells unique characteristics which could then be compared with other species' ES cells or iPS cells like human ES cells and mouse ES cells by the homologue genes comparison to show which species' ES cells or iPS cells were more competitive with the other.

overall_design: There were three replicates sample of the Rat iPS M13 cells named 1, 2, 3. And the adult cells were the mixture of rat bone marrow cells and rat primary ear fibroblasts named mix1. Rat iPS M13 cells samples were labled with Cy3 and the mix1 were labled with Cy5. The data was process to show the Rat iPS M13 cells' gene expression difference compared with that of mix1.

first: Lei

last: Xiao

first: Chun

last: Cui

first: Huasheng

first: Xiaokun


title: Rat lung cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

summary: Rat somatic lung cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic lung cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic lung cells and rat iPS cells.

overall_design: There were two replicates sample of the rat somatic lung cell  named 1, 2.And the control cells were the mixture of rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF) named mix1. Rat somatic lung cells samples were labled with Cy3 and the mix1 were labled with Cy5. The data was process to show the rat somatic lung cells' gene expression difference compared with that of mix1.

last: Teng

first: Yi

last: Zhang


title: Identification of brain transcriptional variability reproduced in peripheral blood: an approach for mapping brain eQTLs

status: Public on Aug 21 2009

city: Pittsburgh

first: Anna

middle: J

last: Jasinska

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

summary: Genome-wide gene expression studies may provide a comprehensive insight in gene activities and biological pathways differing between individuals and tissues (even closely related tissues building complex organs such as the brain). Our research addressed both kinds of gene expression variation – between brain regions and between individuals – by expression profiling in brain tissues derived from eight brain regions and blood from 12 vervet monkeys (Chlorocebus aethiops sabaeus). We employed the non-human primate model to assure tissue quality and to enhance the probability of precise dissection of the brain tissues, which is difficult to realize in human subjects. We characterized brain regional differences in gene expression levels which may relate to specific functions of brain tissues including disease symptoms affecting specific brain regions. We focused on inter-individual variability of brain transcript levels in different regions that correlates well between blood and brain tissues and therefore could be further reliably studied in easily accessible blood samples. Applying very stringent transcript selection criteria including 1). considerable similarities between brain and blood tissues, 2). consistent repeat measurements in blood, 3). higher inter-individual than intra-individual variability and 4). detection in all tissue samples, allowed us to identify transcripts in which inter-individual variation in brain expression profiles indicates possible genetic factors regulating gene transcript levels. High heritabilities of these transcript levels indicated that our approach focusing on transcripts showing higher inter-individual variability than intra-individual variability identifies transcripts with a strong genetic component.

overall_design: Total RNA was isolated from 8 brain regions (cerebellar vermis, pulvinar, head of caudate, hippocampus, frontal pole, dorsolateral prefrontal cortex (DLPFC), orbital frontal cortex and occipital pole) and peripheral blood from vervet monkey (Chlorocebus aethiops sabaeus), according to standard protocols. Tissue specimens were collected from vervet monkeys that were related members of the Vervet Research Colony (VRC) pedigree. We created three tissue sets. Set one (AGMBB) consists of brain and blood samples collected from 12 monkeys and allows comparison of gene expression between brain and peripheral blood. Set two (AGMBR) consists of replicate blood samples collected from 18 monkeys (the average kinship coefficient among these is 0.026) and enables gene expression analysis of biological replicate samples. Set three (AGMPED) consists of blood samples collected from vervets in the entire pedigree N=347 and enables estimation of heritability of gene expression data. RNA expression profiles were determined using an Illumina HumanRef-8 v2 Expression BeadChip system. A transcript was called detectable by BeadStudio (Illumina) when the detection p-value was <0.01. Background correction was performed in Bead Studio. Signal intensities were VST transformed (variance-stabilizing transformation) and RSN normalized (robust spline normalization) using the Lumi package.

first: Oi-wa

last: Choi

first: Joseph

last: Deyoung

first: Olivera

last: Grujic

first: Matthew

last: Jorgensen

first: Lynn

last: Fairbanks

first: Roger

last: Woods

first: J

last: Jentsch

first: Nelson

middle: B

last: Freimer