title: Susceptibilities of Atlantic salmon to Piscirickettsia salmonis

status: Public on Jan 04 2013

city: Santiago de Chile

first: Calixto

last: Dominguez

state: Región Metropolitana

address: Zanartu 1482

department: Center for Bioinformatics and Genome Biology

country: Chile

institute: Fundación Ciencia y Vida

summary: The aquaculture industry has confronted severe economic losses due to infectious diseases in the last years. Piscirickettsiosis or Salmonid Rickettsial Septicaemia (SRS) is the bacterial disease caused by Piscirickettsia salmonis. This Gram-negative, non-motile, cellular pathogen has the ability to infect, survive, replicate, and propagate in salmonid monocytes/macrophages generating a systemic infection characterized by the colonization of several organs including kidney, liver, spleen, intestine, brain, ovary and gills. In this study, we attempted to determine whether global gene expression differences can be detected in different genetic groups of Atlantic salmon as a result of Piscirickettsia salmonis infection. Moreover, we sought to characterize the fish transcriptional response in order to reveal the mechanisms that might confer resistance in Atlantic salmon to an infection with Piscirickettsia salmonis. In doing so, after challenging with Piscirickettsia salmonis, we selected the families with the highest (HS) and the lowest (LS) recorded susceptibility for gene expression analysis using 32K cGRASP microarrays. Our results revealed in LS families expression changes are linked to iron depletion, as well as, low contents of iron in kidney cells and low bacterial load, indicated that the iron-withholding strategy of innate immunity is part of the mechanism of resistance against Piscirickettsia salmonis. This information contributes to elucidate the underlying mechanisms of resistance to Piscirickettsia salmonis infection in Atlantic salmon and to identify new candidate genes for selective breeding programmes.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Forty full-sibling families of Atlantic salmon (Salmo salar) were infected by intraperitoneal injection with 0.2 mL Piscirickettsia salmonis (PS889, isolated from Oncorhynchus kisutch, 1×104 PFU/mL). After forty days, the fishes were harvested and the cumulative mortality (dead fish / total fish) for each family was calculated. For the second challenge, the six families with the highest cumulative mortality levels were considered of relatively high susceptibility (HS) and the six families with the lowest cumulative mortality levels were considered of relatively low susceptibility (LS) to the infection. Five control and five infected fish from three HS and three LS families were analyzed. For each HS and LS family, pools of RNA from control and infected fish were prepared separately and were reverse transcribed. Four slides were for each used family hybridized including two dye-swaped slides. Labeled samples were hybridized on a 32K cDNA microarray, developed at the Consortium for Genomics Research on All Salmonids Project (cGRASP), GEO accession number: GPL8904.


title: Pulmonary gene expression in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles

status: Public on Apr 13 2012

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

summary: We investigated pulmonary mRNA profiles of female mice exposed to 0.018, 0.054 and 0.162 mg Printex 90 carbon black nanoparticles by single intra-tracheal instillation. We examined responses to these doses 1, 3 and 28 days after exposure, alongside respective controls. This study demonstrates widespread changes in inflammatory and acute phase response genes that persisted to 28 days at the highest exposure dose. Changes relevant to sterol and terpenoid biosynthetic pathways were also observed.

overall_design: individual total RNA (200 ng) from 6 mice per treatment group (control, 0.018mg, 0.054mg, and 0.162mg) and universal reference total RNA (Stratagene, Mississauga, ON, Canada) was used to synthesize double stranded cDNA.

first: Julie

last: Bourdon

first: Anne

last: Saber

first: Nicklas

last: Jacobsen

first: Sabina

last: Halappanavar

first: Hakan

last: Wallin

first: Carole

last: Yauk

first: Ulla

last: Vogel


title: Gene expression profiles in Sirt1/PPARalpha bigenic mice

status: Public on Dec 01 2011

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

summary: Cardiac-specific PPARalpha transgenic (Tg-PPARalpha) mice show mild cardiac hypertrophy and systolic dysfunction. The failing heart phenotypes observed in Tg-PPARalpha are exacerbated by crossing with cardiac-specific Sirt1 transgenic (Tg-Sirt1) mice, whereas Tg-Sirt1 mice themselves do not show any cardiac hypertrophy or systolic dysfunction. To investigate the mechanism leading to the failing heart phenotypes in TgPPARalpha/Tg-Sirt1 bigenic mice, microarray analyses were performed. The microarray analyses revealed that many ERR target genes were downregulated in Tg-PPARalpha and in Tg-Sirt1, and they were further downregulated in the Tg-PPARalpha/Tg-Sirt1 bigenic mice.

overall_design: Four groups of cardiac-specific transgenic mice were used for the study, i.e., control, PPARalpha, Sirt1 and PPARalpha/Sirt1. Hearts were dissected after 10-11 weeks of male FVB background transgenic mice. Total RNA was prepared from the hearts to conduct the microarray analyses.

first: O

last: Shinichi

first: J

middle: Y

first: B

last: Tian

last: Sadoshima


title: Gene-expression profiles of hepatitis C-related, early-stage liver cirrhosis

status: Public on Jan 22 2013

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

summary:
BACKGROUND & AIMS: Cirrhosis affects 1% to 2% of the world population and is the major risk factor for hepatocellular carcinoma (HCC). Hepatitis C cirrhosis-related HCC is the most rapidly increasing cause of cancer death in the United States. Noninvasive methods have been developed to identify patients with asymptomatic early-stage cirrhosis, increasing the burden of HCC surveillance, but biomarkers are needed to identify patients with cirrhosis who are most in need of surveillance. We investigated whether a liver-derived 186-gene signature previously associated with outcomes of patients with HCC is prognostic for patients with newly diagnosed cirrhosis but without HCC.
METHODS: We performed gene expression profile analysis of formalin-fixed needle biopsy specimens from the livers of 216 patients with hepatitis C-related early-stage (Child-Pugh class A) cirrhosis who were prospectively followed up for a median of 10 years at an Italian center. We evaluated whether the 186-gene signature was associated with death, progression of cirrhosis, and development of HCC.
RESULTS: Fifty-five (25%), 101 (47%), and 60 (28%) patients were classified as having poor-, intermediate-, and good-prognosis signatures, respectively. In multivariable Cox regression modeling, the poor-prognosis signature was significantly associated with death (P = .004), progression to advanced cirrhosis (P < .001), and development of HCC (P = .009). The 10-year rates of survival were 63%, 74%, and 85% and the annual incidence of HCC was 5.8%, 2.2%, and 1.5% for patients with poor-, intermediate-, and good-prognosis signatures, respectively.
CONCLUSIONS: A 186-gene signature used to predict outcomes of patients with HCC is also associated with outcomes of patients with hepatitis C-related early-stage cirrhosis. This signature might be used to identify patients with cirrhosis in most need of surveillance and strategies to prevent the development of HCC.

overall_design: 216 liver biopsy specimens

first: Augusto

last: Villanueva

first: Angelo

last: Sangiovanni

first: Manel

last: Sole

first: Joshua

last: Gould

first: Supriya

last: Gupta

first: Bradley

last: Taylor

last: Crenshaw

first: Stacey

last: Gabriel

first: Beatriz

last: Minguez

first: Massimo

last: Iavarone

first: Scott

last: Friedman

last: Colombo

first: Josep

middle: M

last: Llovet

first: Todd

middle: R

last: Golub


title: Biologic Phenotyping of the Human Small Airway Epithelial Response to Cigarette Smoking

status: Public on Oct 27 2011

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: The first changes associated with smoking are in the small airway epithelium (SAE). Given that smoking alters SAE gene expression, but only a fraction of smokers develop chronic obstructive pulmonary disease (COPD), we hypothesized that assessment of SAE genome-wide gene expression would permit biologic phenotyping of the smoking response, and that a subset of healthy smokers would have a “COPD-like” SAE transcriptome. SAE (10th-12th generation) was obtained via bronchoscopy of healthy nonsmokers, healthy smokers and COPD smokers and microarray analysis was used to identify differentially expressed genes. Individual responsiveness to smoking was quantified with an index representing the % of smoking-responsive genes abnormally expressed (ISAE), with healthy smokers grouped into “high” and “low” responders based on the proportion of smoking-responsive genes up- or down-regulated in each smoker. Smokers demonstrated significant variability in SAE transcriptome with ISAE ranging from 2.9 to 51.5%. While the SAE transcriptome of “low” responder healthy smokers differed from both  “high” responders and smokers with COPD, the transcriptome of the “high” responder healthy smokers was indistinguishable from COPD smokers. The SAE transcriptome can be used to classify clinically healthy smokers into subgroups with lesser and greater responses to cigarette smoking, even though these subgroups are indistinguishable by clinical criteria. This identifies a group of smokers with a “COPD-like” SAE transcriptome.

overall_design: Comparison of the transcriptome of small airway epithelium in healthy non-smokers, healthy smokers and smokers with COPD. One hundred and fifty-seven samples from several Series were compared.

first: Ann

middle: E

last: Tilley

first: Timothy

middle: P

last: O'Connor

first: Neil

last: Hackett

last: Strulovici Barel

first: Jacqueline

last: Salit

first: Nancy

last: Amoroso

first: Xi

middle: K

last: Zhou

first: Tina

last: Raman

first: Larsson

last: Omberg

first: Andrew

last: Clark

first: Jason

last: mezey

first: Ronald

middle: G

last: Crystal


title: Primary uveal melanoma cells, normal uveal melanocytes, neural crest stem cells, embryonic stem cells and uveal melanoma cell lines

status: Public on Feb 14 2013

city: Cleveland

first: Li

last: Zhang

state: OH

address: 9500 Euclid Ave, JJN3

department: Quantitative Health Sciences

institute: CleveLAND CLINIC LERNER COL/MED-CWRU

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

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

overall_design: Refer to individual Series


title: Gene expression in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles

status: Public on Apr 02 2012

last: Williams

overall_design: In this study, we investigate mRNA profiles in lung and liver of mice exposed to Printex 90 carbon black nanoparticles. Female mice were exposed to three doses (0.018, 0.054 and 0.162 mg printex 90) and profiles were examined 1, 3 and 28 days post-exposure. Our analyses reveal that carbon black nanoparticles cause inflammatory and acute phase responses that can trigger sterol sensitive pathways in liver.


title: Integrative Survival-Based Molecular Profiling of Human Pancreatic Cancer

status: Public on Oct 08 2011

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

type:
Expression profiling by array
Non-coding RNA profiling by array
Genome variation profiling by SNP array

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae


title: Genolyptus microarray studies of Eucalyptus grandis and Eucalyptus globulus leaf and xylem tissues

status: Public on Dec 31 2011

city: Porto Alegre

first: Giancarlo

last: Pasquali

state: RS

address: Av. Bento Gonçalves, 9500 - Pr. 43.431 - Lab. 212

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary: In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. Probes were also synthesized from ten cDNA sequences encoding known human proteins as negative controls, totaling 21,442 sequences. Leaves and xylem samples were taken from two E. grandis clonal trees, i.e., both derived from the same matrix tree and harboring the same genotype. Two additional xylem samples were collected from two other E. grandis clonal trees of a different genotype, as well as from two E. globulus clonal trees. Therefore, ten cDNA samples and ten identical chips were produced at Roche NimbleGen for the microarray assays, with a total number of 385,956 features per slide. Besides the discovery of differentially expressed genes between leaf and xylem, we wanted to test the validity of the assumed “technical” and “biological duplicates” since all trees were field-grown and four years-old in age.

sample_organism:
Eucalyptus globulus
Eucalyptus grandis

overall_design: A ten chip study using total RNA recovered from mature leaf and vascular (xylem) tissues of Eucalyptus grandis and xylem from Eucalyptus globulus trees. Two clonal trees of E. grandis (E.grandis_Clone A_Ramet 1 and E.grandis_Clone A_Ramet 2), derived from a single matrix tree and therefore genomically identical, were the source of two samples of leaf RNA and two samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Two other clonal trees of E. grandis (E.grandis_Clone B_Ramet 1 and E.grandis_Clone B_Ramet 2), derived from a different matrix tree, were the source of two additional samples of xylem RNA individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Likewise, two pairs of clonal trees of E. globulus (E.globulus_Clone A_Ramet 1 and E.globulus_Clone A_Ramet 2/ E.globulus_Clone B_Ramet 1 and E.globulus_Clone B_Ramet 2), derived from two distinct matrix trees, were the source of four additional samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Each chip measures the expression level of 21,432 genes from Eucalyptus sp. and ten human genes (negative controls) with nine 50-mer probe pairs (PM/MM) per gene in two separate blocks per chip (technical duplicate), totalizing 18 hybridization signal values per gene per chip.

first: Georgios

middle: J

last: Pappas Jr

first: Alexandre

middle: S

last: Coelho

first: Rosana

middle: V

last: Brondani

first: Sérgio

middle: H

last: Brommonschenkel

first: Júlio

middle: C

last: Cascardo

first: Gonçalo

middle: A

last: Pereira

first: Dario

last: Grattapaglia


title: Integrative Survival-Based Molecular Profiling of Human Pancreatic Cancer [SNP]

summary:
To perform an integrative profile of human pancreatic cancer (PDAC) to identify prognosis-significant genes and their related pathways.
A concordant survival-based whole genome in silico array analysis of DNA copy number, and mRNA & micro RNA (miRNA) expression in 25 early stage PDAC was performed. A novel composite score simultaneously integrated gene expression with regulatory mechanisms to identify the signature genes with the most levels of prognosis-significant evidence. The predominant signaling pathways were determined via a pathway-based approach. Independent patient cohorts (n= 150 and 42) were then used as in vitro validation of the array findings.  We find that EGFR, SRC signaling, and PI3K/AKT pathway activation are strongly linked to clinical disease progression. Furthermore, we identify two discrete subsets of pancreatic tumors characterized by either SRC or PI3K/AKT signaling that may dictate variable responses to targeted therapy.

overall_design: 42 human PDAC tumors and 7 non-malignant pancreas samples snap-frozen at the time of surgery were chosen.  Representative H&E sections of each were evaluated by a practicing gastrointestinal pathologist  to confirm diagnosis and determine relative percentage of malignant cells.  Samples with tumor cell content >30% were chosen for final multi-platform analysis (N=25).  Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 25 PDAC samples.  The HapMap270 file supplied by Affymetrix was used as the reference model for copy number inference.

first: Timothy

last: Donahue

first: Reginald

last: Hill

first: Yunfeng

last: Li

first: Anne

last: Kovochich

first: Joseph

last: Calvopina

first: Sanjeet

last: Patel

first: Nanping

last: Wu

first: Antreas

last: Hindoyan

first: James

last: Farrell

first: Xinmin

first: David

middle: W

last: Dawson

first: Hong


title: Integrative Survival-Based Molecular Profiling of Human Pancreatic Cancer [miRNA]

first: Linh

last: Tran

overall_design: 42 human PDAC tumors and 7 non-malignant pancreas samples snap-frozen at the time of surgery were chosen.  Representative H&E sections of each were evaluated by a practicing gastrointestinal pathologist  to confirm diagnosis and determine relative percentage of malignant cells.  Samples with tumor cell content >30% were chosen for final multi-platform analysis (N=25).  Genomic miRNAa of human pancreatic samples were profiled on miRCURY LNA™ microRNA Array kit v.11.0 - human, mouse & rat arrays per manufacturer's instructions.


title: Hepatic gene expression in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles

first: Andrew

last: Williams

summary: We investigated hepatic mRNA profiles of female mice exposed to 0.162 mg Printex 90 carbon black nanoparticles by single intra-tracheal instillation. We examined responses to this dose 1, 3 and 28 days after exposure, alongside respective controls. We show that genes part of the 3-hydroxy-3-methyl-glutaryl-CoA reductase pathway to be up-regulated by exposure to Printex 90.

overall_design: individual total RNA (200 ng) from 6 mice per treatment group (control and 0.162mg) and universal reference total RNA (Stratagene, Mississauga, ON, Canada) was used to synthesize double stranded cDNA.

first: Julie

last: Bourdon

last: Saber

first: Nicklas

last: Jacobsen

first: Sabina

last: Halappanavar

first: Hakan

last: Wallin

first: Carole

last: Yauk

first: Ulla

last: Vogel


title: Integrative Survival-Based Molecular Profiling of Human Pancreatic Cancer [mRNA]

overall_design: 42 human PDAC tumors and 7 non-malignant pancreas samples snap-frozen at the time of surgery were chosen.  Representative H&E sections of each were evaluated by a practicing gastrointestinal pathologist  to confirm diagnosis and determine relative percentage of malignant cells.  Samples with tumor cell content >30% were chosen for final multi-platform analysis (N=25).  Human pancreatic samples were profiled on Affymetrix HGU133 Plus 2 arrays per manufacturer's instructions.

first: Timothy

last: Donahue

first: Reginald

last: Hill

first: Yunfeng

last: Li

first: Anne


title: The DMD locus harbours multiple long non-coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms

status: Public on Jun 05 2011

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary:
The 2.2 Mb long dystrophin (DMD) gene, the largest gene in the human genome, corresponds to roughly 0.1% of the entire human DNA sequence. Mutations in this gene cause Duchenne muscular dystrophy and other milder X-linked, recessive dystrophinopathies. Using a custom-made tiling array, specifically designed for the DMD locus, we identified a variety of novel long non-coding RNAs (ncRNAs), both sense and antisense oriented, whose expression profiles mirror that of DMD gene. Importantly, these transcripts are intronic in origin and specifically localized to the nucleus and are transcribed contextually with dystrophin isoforms or primed by MyoD-induced myogenic differentiation. Furthermore, their forced ectopic expression in both human muscle and neuronal cells causes a specific and negative regulation of endogenous dystrophin full length isoforms and significantly down-regulate the activity of a luciferase reporter construct carrying the minimal promoter regions of the muscle dystrophin isoform. Consistent with this apparently repressive role, we found that, in muscle samples of DMD symptomatic female carriers, lncRNAs expression levels inversely correlate with those of muscle full length DMD isoforms.
Overall these findings unveil an unprecedented complexity of the transcriptional pattern of the DMD locus and reveal that DMD-specific lncRNAs may contribute to the orchestration and homeostasis of the muscle dystrophin expression pattern by selective targeting and down-modulation of dystrophin promoter transcriptional activity.

overall_design: We tiled the entire DMD gene, in both sense and antisense directions, using the web-based Agilent eArray database, Version 4.5 (Agilent Technologies), with 60-mer oligos every 66 bp of repeat-masked genome sequence. We defined probe sets for both orientations, encompassing the DMD exons, promoters, introns, predicted MiRNA (identified by PromiRII) and conserved non-coding sequences (CNSs) identified within dystrophin introns using the VISTA programme (http://genome.lbl.gov/vista/index.shtml). Two specific sets of probes were designed to cover, in both directions, the cDNA sequences of a group of control genes identified in the Gene Expression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/) and expressed equally in both normal and dystrophic muscles. Each probe set was opportunely distributed and replicated several times in order to obtain two 4x44k microarrays, referred to as DMD GEx Sense and DMD GEx Antisense, respectively, able to detect transcripts in the same and opposite directions as that of DMD gene transcription. Three commercial poly A+ RNAs from normal human brain, heart and skeletal muscle tissues were utilised (Ambion). Skin poly A+ RNA was isolated from total Skin RNA (Stratagene) using the Qiagen Oligotex kit. All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies), and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies).  Sample labelling and hybridisation were performed according to the protocols provided by Agilent (One-Color Microarray-Based Gene Expression Analysis version 5.0.1). The array was analysed using the Agilent scanner and Feature Extraction software (v9.1).


title: Functional genomic analysis of a nitrate reductase knockdown relative to wild-type in model-ecosystems (mesocosm)

status: Public on Jan 01 2011

city: Oak Ridge

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

summary: Current advances in genomics and computational biology have afforded novel insight as to how the phenotype is generated from the genotype – systems biology. We argue that systems biology, when viewed through an ecological lens, provides an unprecedented opportunity to understand how genes cascade through multiple levels of biological organization to alter ecosystem function. To test this approach, we established six monocultures of Arabidopsis thaliana ‘Columbia’- wild-type plants, six monocultures of a single gene variant (mutant) to the wild-type, and six mixtures with equal density plantings of each genotype in mesocosm chambers (50 x 50 x 45 cm). The mutant harbored a T-DNA insertion in the main nitrate reductase gene (nia2). This is the gateway enzyme for N metabolism, which resulted in activity levels that were 38% of the wild-type. Mesocosms were instrumented to monitor soil and air temperature, water and humidity status, and CO2 differentials. Transcript expression profiles were generated for each of the monoculture populations by collecting and processing 100 leaves per mesocosm at generation 2 and 4.

overall_design: Design:  Expression profiles were generated for each monoculture population by pooling 100 leaves per mesocosm into one sample.  This resulted in 6 biological replicates for each genotype per generation. Thus, a total of 48 samples were generated (6 wild-type + 6 nia2 mutants x 2 generations x 2 CO2 treatments) and hybridized onto microarrays. We used a direct loop design analyzing generations separately (diagrams of hybridization designs are linked as supplementary PDF files).

first: Wullschleger

middle: D

last: Stan


title: High resolution genome-wide mapping of HIF binding sites by ChIP-seq

status: Public on Apr 05 2011

city: Oxford

last: Mole

address: Roosevelt Drive

department: The Henry Wellcome Building for Molecular Physiology

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report ChIP-Seq analysis of HIF-1 alpha, HIF-2 alpha, and HIF-1 beta binding in MCF-7 breast cancer cells

overall_design: Sample analysis compared to pre-immune serum chromatin immunoprecipitation

first: Johannes

last: Schödel

first: Spyros

last: Oikonomopoulos

first: Jiannis

last: Ragousis

first: Christopher

last: Pugh

first: Peter

last: Ratcliffe


title: Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.

status: Public on Jul 31 2010

city: University of Sydney

first: Roger

last: Pamphlett

address: Blackburn Bld

country: Australia

institute: University of Sydney

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

summary: This data was divided into three experiment sets: 1. A somatic study of sporadic motor neuron disease (SMND) brain samples that were compared to the blood from the same individual, normal control brains and disease control brans (Parkinson Disease patients); 2. A twin study comparing blood and other tissue samples from twins that were discordant for MND, concordant for MND and control twins and 3. A trio study of blood samples MND patients compared to their unaffected parents.

overall_design: Study 1: 36 sporadic motor neuron disease brain (lateral frontal cortex, Brodmann area 46), 34 matched sporadic motor neuron disease blood, 26 control brain (lateral frontal cortex, Brodmann area 46), 9 Parkinson Disease brain (disease controls, lateral frontal cortex, Brodmann area 46). Study 2 and study 3: 52 twin or trio blood, 4 twin hair, 1 twin sperm. 2 replicate twin blood and 1 replicate trio blood repeated at a different time. External control blood from Coriell GM15510 and GM10851.

first: Julia

last: Morahan


title: Effect of the global regulators RpoS and cyclic-AMP/CRP on the transcriptome of Escherichia coli K12 during  carbon- and energy-limited growth

status: Public on Dec 16 2010

city: Zürich

first: Alessandro

middle: Guido

last: Franchini

address: Universitätstrasse 16

country: Switzerland

institute: Swiss Federal Institute of Technology (ETH)

summary: The faecal indicator bacterium Escherichia coli K12 was used to study the effects of the global regulators RpoS and cAMP at the transcription level using microarray technology during short-term (physiological) adaptation to slow growth under limited nutrient supply. Effects due to the absence of one global regulator were assessed by comparing the mRNA levels isolated from rpoS or cya mutants under glucose-limited continuous culture at a dilution rate of 0.3 h-1 for the rpoS mutant or 0.16 h-1 for the cya mutant with those from wt E. coli grown under the same conditions.

overall_design:
Wild-type Escherichia coli K12 MG1655 (ATCC 700926), E. coli delta-rpoS (MG1655 delta-rpoS::Tn10; Wick et al. (2002)) and AMS2 (MG1655 delta-cya-854; Schultz et al. (1988)) were grown at 37°C in mineral medium. Steady-state with respect to optical density was reached approximately 20 hours after switching on the medium feed. Samples for catabolic pathway assays and transcriptome analysis were taken 40 hours after switching to the continuous culture mode, and each experiment was done in triplicate. 800 ml of culture liquid was withdrawn from the chemostat, immediately cooled down on crushed ice and cells were collected by centrifugation at 4°C.

Total RNA from E. coli cells was isolated (Sambrook et al., 1989). RNA in samples was quantified spectrophotometrically by measuring extinction at 260 nm, and purity (free from DNA) was checked by gel electrophoresis. Synthesis of cDNA from RNA was performed with the CyScribe First-Strand cDNA Labelling Kit (Amersham Bioscience, Little Chalfont, England). The purified cDNA was concentrated to 5 ul and was mixed with 120 ul of hybridization buffer (MWG-Biotech AG), heated to 95°C for 3 min and cooled down on ice for 3 min. The hybridization mixture was then added to the microarray slide and covered with a coverslip. The hybridization slide was incubated overnight at 42°C. After the hybridization step, the slide was washed three times, the first time for 5 min in 2x (times concentrated) SSC - 0.1 % SDS, the second time for 5 min in 1x SSC, and finally for 5 min in 0.1x SSC. SSC buffer was prepared as 20x solution containing 0.3M Na-citrate and 3M NaCl at pH 7.0. The slides were dried by centrifugation at room temperature for 2 min at 500g.

Microarray slides were scanned using the Affymetrix 428TM Array Scanner (High Wycombe, UK). Spot intensities and corresponding background signals were quantified with the Affymetrix JaguarTM software version 2.0. Further data analysis was performed with the program GeneSpring from Silicon Genetics (Redwood City, USA). Induction factors were calculated from the Cy3 and Cy5 signal intensities of the spot. Spots with signal intensity below a value of 50 were excluded from the analysis and the minimal induction factor was set to 0.01. The normalization was performed with the 50th percentile distribution of remaining spots after background correction. The mean value of the induction factors of a specific gene was calculated from three replicates. Biological experiments were carried out three times, which provided three biological repeats. Data from the independent experiment were combined, genes that were differently regulated ≥3 and ≤-3 (t-test, p ≤ 0.2) were defined as being statistically significant.

first: Julian

last: Ihssen

first: Thomas

last: Egli


title: Extremely low frequency electromagnetic fields (ELF-EMFs) effect on the genetic expression profile of a human keratinocyte line (HaCaT)

status: Public on Oct 31 2012

city: Chieti

first: Mirko

last: Pesce

address: Via Vestini

institute: University G. D'Annunzio

summary: Clinical evidence has shown that electromagnetic fields produce a benefical therapeutic result for wounds, however little is still known about their exact mechanism of action. Moreover, clinical results concerning skin tissue restoration are still debated. In the present study, we carried out gene expression profiling of a human keratinocyte line (HaCaT) submitted to 1 hour of ELF-EMF (frequency 50Hz, intensity 1 mT) in order to identify up- and downregulated genes by this stimulus, and to verify the presence of specific molecular pathways activation. Most of the genes modulated were involved in mechanisms such as protein synthesis. In particular, these genes are related to Mammalian target of Rapamycin (mTOR), which has been identified as a kinase with a pivotal role in cellular proliferation and survival in mammals.

overall_design: In this study, we analyzed the expression profiles of 3 biological replicates of HaCaT cells exposed to ELF-EMF (frequency 50Hz, intensity 1 mT) for 1 hour. All HaCaT cells exposed to ELF-EMF RNAs were hybridized against control sham-exposed HaCaT cells RNAs. Each biological sample was repeated with a technical replicate (extraction-labeling) and a dye-swap experiment.

first: Antonia

last: Patruno

first: Marcella

last: Reale

first: Paolo

last: Amerio

first: Mario

last: Felaco

first: Giovina

last: Vianale


status: Public on Aug 03 2009

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

type: Methylation profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary:
The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. In order to gain a better understanding of the epigenetic mechanisms regulating differentiation of hESCs, and produce general reference epigenome maps of the human cells, we propose to establish an Epigenome Center in San Diego. Our center will be focused on both undifferentiated hESC and four hESC-derived early embryonic cell lineages including extraembryonic endoderm, trophoblast, mesendoderm (a common precursor to mesodermal and endodermal lineages), and mesenchymal cells (a specific mesoderm derivative). We have developed and validated high throughput technologies for mapping the state of DNA methylation and chromatin modifications throughout the genome, and will use these methods to generate high-resolution maps of the reference epigenomes. Specifically, we will grow and differentiate hESCs into multiple lineages, and map DNA methylation sites using a newly developed technology that combines bisulfite conversion and whole genome shotgun sequencing. We will also determine the histone modification status in the genome by performing both ChlP-chip and ChlP-Seq analysis. We will develop advanced statistical and algorithmic solutions to facilitate high-throughput sequencing data analysis, and establish an informatics pipeline for collecting, storage, and distribution of epigenome maps. Finally, we will perform integrated data analysis to identify new epigenetic patterns in the genome that could provide insights in mechanisms of epigenetic regulation.

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

overall_design:
UCSD Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSTUDY%2FEDACC.889

first: Ryan

last: Lister

first: Mattia

last: Pelizzola

first: Robert

last: Dowen

first: R

last: Hawkins

first: Gary

last: Hon

last: Tonti-Filippini

first: Joseph

last: Nery

first: Leonard

last: Lee

first: Zhen

last: Ye

first: Que-Minh

last: Ngo

first: Lee

last: Edsall

first: Jessica

last: Antosiewicz-Bourget

first: Ron

last: Stewart

first: Victor

last: Ruotti

first: A

last: Millar

first: James

last: Thomson

first: Bing

last: Ren

last: Ecker


title: Low dose ionizing radiation treated lymphoblastoid cells

status: Public on Jul 01 2010

city: Livermore

first: Patricia

last: Wu

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

summary: Irradiated cell lines exposed to 1-10 Gy

overall_design: 2 Lymphoblastoid cell lines (GM15510 and GM15036) irradiated 1, 2.5, 5, 7.5, 10 Gy, RNA is isolated and labeled using a T7 amplification Arcturus kit for hybridization on triplicate arrays.

first: Andrew

last: Wyrobek

first: Matthew

last: Coleman


title: Microarray analysis to identify the molecular mechanisms whereby pDCs confer growth and drug resistance in MM cells

status: Public on Jul 31 2009

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: Multiple Myeloma (MM) remains incurable despite novel therapies, suggesting the need for further identification of factors mediating tumorigenesis and drug resistance. We performed microarray analysis to identify the molecular mechanisms whereby pDCs confer growth and drug resistance in MM cells.

overall_design: Comparsion of MM cells in the presence and absence of pDCs (plasmacytoid dendritic cells)

first: Dharminder

last: Chauhan

first: Ajita

last: Singh

first: Mohan

last: Brahmandam

first: Ruben

last: Carrasco

first: Madhavi

last: Bandi

first: Teru

last: Hideshima

first: Giada

last: Bianchi

first: Yu-Tzu

last: Tai

first: David

middle: L

last: Jaye

first: Shaji

last: Kumar

first: Sagar

last: Lonial

first: Paul

last: Richardson

first: Nikhil

last: Munshi

first: Kenneth

last: Anderson


title: human MRC-5 cells' gene expression difference compared with that of the adult cells including CCD-1079sk and IMR90

status: Public on Apr 01 2009

city: Shanghai

first: Jing

last: Liao

address: 320 Yue Yang Road

country: China

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

summary: human somatic cell MRC-5 had different gene expression level compared with that of the adult cells including CCD-1079sk and IMR90. This difference gave the human somatic cell MRC-5 unique characteristics which could then be compared with the human ES cells by genes comparison to show the gene expression difference between human somatic cells and human ES cells.

overall_design:
There were two replicates sample of the Human MRC-5 cells named 1, 2.
And the control cells were the mixture of CCD-1079sk and IMR90 named mix2. Human MRC-5 cells samples were labled with Cy3 and the mix2 were labled with Cy5. The data was process to show the human MRC-5 cells' gene expression difference compared with that of mix2.

first: Lei

last: Xiao

first: Chun

last: Cui

first: Huasheng

first: Xiaokun

last: Teng

first: Yi

last: Zhang


title: Gene Expression in Blood in Scizophrenia and Bipolar Disorder

status: Public on Oct 02 2009

first: Ming

last: Tsuang

address: 9500 Gilman Drive

institute: UCSD

summary:
Schizophrenia (SCZ) and bipolar disorder (BPD) are polygenic disorders with many genes contributing to their etiologies. The aim of this investigation was to search for dysregulated molecular and cellular pathways for these disorders as well as psychosis. We conducted a blood-based microarray investigation in two independent samples with SCZ and BPD from San Diego (SCZ=13, BPD=9, control=8) and Taiwan [data not included](SCZ=11, BPD=14, control=16). Diagnostic groups were compared to controls, and subjects with a history of psychosis [PSYCH(+): San Diego (n=6), Taiwan (n=14)] were compared to subjects without such history [PSYCH(-): San Diego (n=11), Taiwan (n=14)]. Analyses of covariance comparing mean expression levels on a gene-by-gene basis were conducted to generate the top 100 significantly dysregulated gene lists for both samples by each diagnostic group. Gene lists were imported into Ingenuity Pathway Analysis (IPA) software. Results showed the ubiquitin proteasome pathway (UPS) was listed in the top ten canonical pathways for BPD and psychosis diagnostic groups across both samples with a considerably low likelihood of a chance occurrence (p = .001). No overlap in dysregulated genes populating these pathways was observed between the two independent samples. Findings provide preliminary evidence of UPS dysregulation in BPD and psychosis as well as support further investigation of the UPS and other molecular and cellular pathways for potential biomarkers for SCZ, BPD, and/or psychosis.
The aim of this investigation was to search for dysregulated molecular and cellular pathways for these disorders as well as psychosis.

overall_design: Blood-based microarray investigation in two independent samples with SCZ and BPD from San Diego (SCZ=13, BPD=9, control=8).

first: Chad

last: Bousman

first: Gursharan

last: Chana

first: Stephen

last: Glatt

first: Sharon

last: Chandler

first: Ginger

last: Lucero

first: Erick

last: Tatro

first: James

last: Lohr

first: William

last: Kremen

first: Ian

last: Everall

middle: T


title: Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Training Set, HCC)

status: Public on Oct 15 2008

first: Yujin

last: Hoshida

summary:
Background: It is a challenge to identify those patients who, after undergoing potentially curative treatments for hepatocellular carcinoma, are at greatest risk of recurrence. Such high-risk patients could receive novel interventional measures. An obstacle to the development of genome-based predictors of outcome in patients with hepatocellular carcinoma has been the lack of a means to carry out genomewide expression profiling of fixed, as opposed to frozen, tissues.
Methods: We aimed to demonstrate the feasibility of gene-expression profiling of more than 6000 human genes in formalin-fixed paraffin-embedded tissues. We applied the method to tissues from 307 patients with hepatocellular carcinoma, from four series of patients, to discover and validate a gene-expression signature associated with survival.
Results: The expression-profiling method for formalin-fixed, paraffin-embedded tissue was highly effective: samples from 90% of the patients yielded data of high quality, including samples that had been archived for more than 24 years. Gene-expression profiles of tumor tissue failed to yield a significant association with survival. In contrast, profiles of the surrounding nontumoral liver tissue were highly correlated with survival in a training set of 82 Japanese patients, and the signature was validated in tissues from an independent group of 225 patients from the United States and Europe (p = 0.04).
Conclusions: We have demonstrated the feasibility of genomewide expression profiling of formalin-fixed, paraffin-embedded tissues and have shown that a reproducible gene-expression signature correlating with survival is present in liver tissue adjacent to the tumor in patients with hepatocellular carcinoma.
Keywords: Hepatocellular carcinoma, Expression array, Illumina, Signatures, Outcome prediction

overall_design: Training cohort: 80 tumor and 82 non-tumor liver tissues surgically resected from patients with hepatocellular carcinoma (HCC); Validation cohort: 225 non-tumor liver tissues surgically resected from patients with HCC.

first: Augusto

last: Villanueva

first: Masahiro

last: Kobayashi

first: Judit

last: Peix

first: Derek

last: Chiang

first: Amy

last: Camargo

first: Supriya

last: Gupta

first: Jamie

last: Moore

first: Matthew

last: Wrobel

first: Jim

last: Lerner

first: Michael

last: Reich

first: Jennifer

last: Chan

first: Kenji

last: Ikeda

first: Masashi

last: Hashimoto

first: Goro

last: Watanabe

first: Sasan

last: Roayaie

first: Myron

last: Schwartz

first: Swan

last: Thung

first: Stacey

last: Gabriel

first: Vincenzo

last: Mazzaferro

first: Jordi

last: Bruix

first: Scott

last: Friedman

first: Hiromitsu

last: Kumada

first: Josep

middle: M

last: Llovet

first: Todd

middle: R

last: Golub


title: Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma

first: Yujin

last: Hoshida

summary:
Background: It is a challenge to identify those patients who, after undergoing potentially curative treatments for hepatocellular carcinoma, are at greatest risk of recurrence. Such high-risk patients could receive novel interventional measures. An obstacle to the development of genome-based predictors of outcome in patients with hepatocellular carcinoma has been the lack of a means to carry out genomewide expression profiling of fixed, as opposed to frozen, tissues.
Methods: We aimed to demonstrate the feasibility of gene-expression profiling of more than 6000 human genes in formalin-fixed paraffin-embedded tissues. We applied the method to tissues from 307 patients with hepatocellular carcinoma, from four series of patients, to discover and validate a gene-expression signature associated with survival.
Results: The expression-profiling method for formalin-fixed, paraffin-embedded tissue was highly effective: samples from 90% of the patients yielded data of high quality, including samples that had been archived for more than 24 years. Gene-expression profiles of tumor tissue failed to yield a significant association with survival. In contrast, profiles of the surrounding nontumoral liver tissue were highly correlated with survival in a training set of 82 Japanese patients, and the signature was validated in tissues from an independent group of 225 patients from the United States and Europe (p = 0.04).
Conclusions: We have demonstrated the feasibility of genomewide expression profiling of formalin-fixed, paraffin-embedded tissues and have shown that a reproducible gene-expression signature correlating with survival is present in liver tissue adjacent to the tumor in patients with hepatocellular carcinoma.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Training cohort: 80 tumor and 82 non-tumor liver tissues surgically resected from patients with hepatocellular carcinoma (HCC); Validation cohort: 225 non-tumor liver tissues surgically resected from patients with HCC.

Clinical data has been withheld from GEO due to privacy concerns.

first: Augusto

last: Villanueva

first: Masahiro

last: Kobayashi

first: Judit

last: Peix

first: Derek

last: Chiang

first: Amy

last: Camargo

first: Supriya

last: Gupta

first: Jamie

last: Moore

first: Matthew

last: Wrobel


title: Expression data from MCF-7aro aromatase inhibitor-resistant, tamoxifen-resistant and LTEDaro lines.

status: Public on Mar 22 2008

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
MCF-7aro cells were used to generate a cell culture model system that is resistant to 3 aromatase inhibitors (AIs), letrozole, anastrozole and exemestane.  For comparison, the MCF-7aro cells were also used to generate the tamoxifen-resistant cells as well as long-term estrogen deprived, LTEDaro.
Affymetrix microarray analysis was performed to determine changes in gene expression that are unique to AI-resistance.
Keywords: cell lines, aromatase inhibitor resistance, tamoxifen resistance

overall_design: For control purposes, MCF-7aro cells were cultured without any hormone or inhibitor as well as a hormone-only control (T-only).  Resistant cells were grown in the presence of testosterone, T+LET R (letrozole), T+ANA R (anastrozole), T+EXE R (exemestane), T+TAM R (Tamoxifen).  In addition, testosterone-free resistant lines were generated, LTEDaro, ANA R and EXE R.  6 replicates were generated for the hormone-containing resistant lines and 3 replicates for the hormone-free resistant lines.

first: Shiuan

last: Chen

first: Selma

last: Masri


title: Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Validation Set)

institute: University of Texas Southwestern Medical Center

first: Jim

last: Lerner

first: Michael

last: Reich

first: Jennifer

last: Chan

first: Kenji

last: Ikeda

first: Masashi

last: Hashimoto

first: Goro

last: Watanabe

first: Sasan

last: Roayaie

first: Myron

last: Schwartz

first: Swan

last: Thung

first: Stacey

last: Gabriel

first: Vincenzo

last: Mazzaferro

first: Jordi

last: Bruix


title: Gene expression changes in mouse aorta during activation of or interference with PPAR gamma signaling.

status: Public on Dec 12 2007

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

summary:
Ligand-mediated activation of the nuclear hormone receptor PPAR gamma lowers blood pressure and improves glucose tolerance in humans.  Two naturally occurring mutations (P467L, V290M) in the ligand binding domain of PPAR gamma have been described in humans that lead to severe insulin resistance and hypertension.  Experimental evidence suggests that these mutant versions of PPAR gamma act in a dominant negative fashion.  To better understand the molecular mechanisms underlying PPAR gamma action in the vasculature, we determined the gene expression patterns in mouse aorta in response to activation or interference with the PPAR gamma signaling pathway.
Keywords: time course, dose response

overall_design: To assess the response to PPAR gamma interference, we used adult mice containing a dominant negative form of PPAR gamma. These mice have a targeted P465L mutation, which is equivalent to the P467L mutant, described in human patients. Wild-type littermates were used as the genetic control. The PPAR gamma signaling pathway was activated by administration of rosiglitazone for either 2 or 14 days to adult mice (C57BL/6J strain) at a dose of 3 or 10 mg/kg/day via the food. Control mice were fed standard mouse chow. For the microarray hybridizations, 2-3 biological replicates from each experimental group were used.  Biological replicates were RNA pooled from 8 different mouse aortas. All the microarray procedures were conducted at the University of Iowa DNA Core facility using standard Affymetrix protocols.  In brief, approximately 3 ug of total RNA was used as input to a one-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array.

first: Curt

last: Sigmund

first: Andreas

last: Beyer

first: Carmen

last: Halabi

first: Willem

last: de Lange

first: Frank

last: Faraci


title: Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Training Set, Liver)

city: Dallas

first: Yujin

last: Hoshida

first: Augusto

last: Villanueva

first: Masahiro

last: Kobayashi

first: Judit

last: Peix

first: Derek

last: Chiang

first: Amy

last: Camargo

first: Supriya

last: Gupta

first: Jamie

last: Moore

first: Matthew

last: Wrobel

first: Jim

last: Lerner

first: Michael

last: Reich

first: Scott

last: Friedman

first: Hiromitsu

last: Kumada

first: Josep

last: Llovet

first: Todd

last: Golub


title: Human metapneumovirus strain associated with critical respiratory illness in an elderly male with leukemia Stanford HMPV

status: Public on Mar 01 2008

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
This series includes 1 microarray used to detect a human metapneumovirus strain associated with critical respiratory illness in an elderly male with leukemia (Chiu, et al 2006)
Keywords: viral detection

overall_design: The series includes 1 bronchoalveolar lavage sample.

first: Chiu

middle: Y

last: Charles

first: Ash

last: Alizadeh

first: Silvi

last: Rouskin

first: Jason

last: Merker

first: Bruce

last: Patterson

first: Don

last: Ganem

first: Joseph


title: Expression data for stress treatment in rice seedlings

status: Public on May 17 2007

city: New Delhi

first: Akhilesh

middle: K.

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary:
Drought, salinity and sub-optimal temperatures are stresses that cause adverse effects on the growth of plants and the productivity of crops. In this study, we have analyzed the expression profiles of rice genes under control and abiotic stress conditions using microarray technology to identify the genes differentially expressed during various abiotic stresses.
Keywords: Stress treatment

overall_design: Seven-day-old light-grown rice seedlings grown under controlled conditions and those subjected to various abiotic stress conditions were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. For salt treatment (SS), the rice seedlings were transferred to a beaker containing 200 mM NaCl solution for 3 h. For desiccation (DS), rice seedlings were dried for 3 h between folds of tissue paper at 28±1 degree C, in a culture room. For cold treatment (CS), the seedlings were kept at 4±1 degree C for 3 h. The seedlings kept in water for 3 h, at 28±1 degree C, served as control (Seedling).

middle: K

first: Sanjay

last: Kapoor

first: Jitendra

middle: P

last: Khurana

first: Swatismita

last: Ray


title: Expression data from yeast with modulated expression of base excision repair players

status: Public on Nov 30 2007

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
We are investigating the transcriptional response of yeast to modulation of the expression of base excision repair players, these generate different dna lesions of abasic sites of strand breaks
We used microarrays to detail the global programme of gene expression underlying the DNA damage response in yeast
Keywords: dose

overall_design: Yeaststrains with different expression levels of players in base excision repair (in biological triplicate)  were grown to mid log phase. The expression responses were compared to each other and we have deciphered a gene expression profile that is specific for DNA damage in yeast.

first: Ivan

last: Rusyn

first: Thomas

middle: J

last: Begley

first: Joanna

last: Klapacz

first: Peter

last: Svensson

first: Mark

last: Ambrose

first: Leona

last: Samson


title: Expression profiling of human adult postmortem brain tissue from Down syndrome and healthy control subjects

status: Public on Jul 27 2007

city: Cambridge

first: Sabine

last: Bahn

address: Tennis Court Road

institute: University of Cambridge

summary:
Down syndrome (DS) is the result of trisomy chromosome 21 but the mechanisms by which the genotype leads to the characteristic disease phenotype are unclear. We performed a microarray study using human adult brain tissue (dorsolateral prefrontal cortex) from DS subjects and healthy controls to characterise for the first time the human adult Down syndrome brain
Keywords: disease state analysis

overall_design: RNA extracted from human postmortem brain tissue from adult subjects with Down syndrome and healthy controls was hybridised to Affymetrix HG-U133A GeneChips to identify differentially expressed genes in the disease state.

first: Helen

middle: E

last: Lockstone

first: Laura

last: Wiseman Harris

first: Jane

last: Swatton

first: Matthew

last: Wayland

first: Edmund

middle: S

last: Jackson


title: Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary:
Chromosomal instability (CIN) is the hallmark of colorectal adenoma to carcinoma progression in 85% of cases, with 20q gain as the most prominent aberration. Yet, the oncogenes at this chromosomal gain are still largely unknown. Here, we aimed to identify oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of  20q gain on gene expression in this amplicon. Segmentation of DNA copy number changes on 20q was performed by array CGH in 67 colorectal adenomas and carcinomas. Additionally, robust analysis of mRNA expression in these segments was performed in 68 adenomas and carcinomas. This approach revealed seven genes to be important in CIN related adenoma to carcinoma progression. These genes may both serve as highly specific biomarkers for presence of high-risk precursor lesions as well as potential targets for pharmaceutical intervention.
Keywords: Integration of array CGH and expression microarrays in colorectal cancer progression

overall_design:
We performed array CGH on a panel of 41 progressed adenomas, from which the adenoma and carcinoma components were separately analysed (total, 82 samples). The DNA obtained from these samples was extracted from formalin-fixed, paraffin-embedded material. Additionally we analysed a series of independent frozen adenomas and carcinomas by array CGH (34 adenomas and 33 carcinomas) and expression microarrays (37 adenomas and 31 carcinomas).
For array-CGH we used as reference DNA for all samples, a pool of 10 normal individuals. For expression microarrays we used as reference a commercial available RNA (pool of different cancer cell lines), from Strategene. No replicates nor dye swaps were done.

first: Beatriz

last: Carvalho

first: Cindy

last: Postma

first: Sandra

last: Mongera

first: Erik

last: Hopmans

first: Sharon

last: Diskin

last: van de Wiel

first: Wim

last: van Criekinge

first: Olivier

last: Thas

first: Anja

last: Matthäi

first: Miguel

last: Cuesta

first: Jochim

last: Terhaar

first: Mike

last: Craanen

first: Evelin

last: Schröck

first: Bauke

last: Ylstra

first: Gerrit

last: Meijer


title: NATURI V1 Nasal Lavage - Viro3

status: Public on Nov 07 2007

first: Amy

last: Kistler

institute: UCSF

summary:
BACKGROUND:  50% to 80% of asthma exacerbations are precipitated by viral upper respiratory tract infections (RTI), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood due to the limited scope and throughput of conventional viral detection methods.  METHODS: We investigated the capability of the Virochip, a DNA microarray-based viral detection platform, to characterize the viral diversity in RTIs in asthmatic and non-asthmatic adults.  RESULTS:  The Virochip detected viruses in a higher proportion of samples (65%) than culture isolation (17%), while exhibiting high concordance (98%), sensitivity (97%) and specificity (98%) with pathogen-specific PCR.  A similar spectrum of viruses was identified in the RTIs from each patient subgroup; however, unexpected diversity among the coronaviruses (HCoVs) and HRVs was revealed.  All but one of the HCoVs corresponded to the newly-recognized HCoV-NL63 and HCoV-HKU1 viruses, and over 20 different serotypes of HRVs were detected, including a set of 5 divergent isolates that form a distinct genetic subgroup.  CONCLUSIONS:  The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger scale studies will be necessary to determine if particular substrains of viruses confer an elevated risk of asthma exacerbation
Keywords: Virus detection

overall_design: We analyzed a series of 82 microarrays on which were hybed  RNA randomly amplified from nasal lavage of outpatient cold specimens.

first: Pedro

middle: C

last: Avila

first: Silvi

last: Rouskin

first: David

last: Wang

first: Theresa

last: Ward

first: Shigeo

last: Yagi

last: Schnurr

first: Joseph

last: DeRisi

first: Homer

last: Boushey


title: CGH analysis between Xcc strains and transcriptome analysis of Xcc 8004 grown in NYG and XVM2

status: Public on Jan 01 2007

city: Beijing

first: Liang

last: Zhang

address: 18 Life Science Parkway,Changping District

institute: CapitalBio Corporation

type:
Expression profiling by array
Genome variation profiling by array

summary:
Xanthomonas campestris pathovar campestris (Xcc), the causal agent of black rot disease of cruciferous plants worldwide, is composed of phenotypically heterogeneous groups of strains. The knowledge about the genome diversity and phylogenetic relationships between Xcc strains with different origins are of great interest as they provide insight into the mechanisms of pathogenicity, host preferences and evolution of this pathogen. In our present work, eighteen Xcc strains collected from different geographical area of China mainland were investigated concerning of the genome composition by comparative genomic hybridization (CGH) using   microarray slides spotted with PCR-based intragenic DNA fragments of 4273 open reading frames (ORFs) representing the non-redundant genome content of Xcc strain 8004. The common genome backbone of Chinese strains was estimated to contain about 3404 ORFs, which was considered to maintain the basic characteristics of Xcc, i.e. the yellow mucoid colony on nutrient solid medium as well as the pathogenicity to induce black rot disease on host plants. A flexible gene pool of 729 ORFs in Xcc was characterized, of which 402 ORFs were clustered in twenty-seven highly variable genomic regions in Xcc 8004. Of these highly variable genomic regions, five are absolutely absent from Chinese strains, which constitutes the main genomic differences between the Xcc 8004 and Chinese strains. Transcriptome analysis of Xcc 8004 grown in the rich medium NYG and the defined medium XVM2 indicated that the expression of some certain genes in highly variable genomic regions are significantly activated in XVM2, which included the predicted pathogencity and avirulence genes. Candidate genes for cultivar-specificity of Xcc were identified in the variable genomic regions: the avrXccC and avrXccE1 were demonstrated to confer the avirulence on the host plants Mustard cultivar (cv.) Guangtou and Chinese cabbage cv. Zhongbai 83, respectively; and the avrBs1 showed to correlate with the hypersensitive reaction (HR) on the non-host plant pepper ECW10R. This study revealed the common genome backbone of Xcc maintained the basic function in essential metabolisms and basic pathogencity, and the variable genomic determinants contributed to the cultivar-specificity of the pathogen, suggesting that the Xcc genome, with a compact function core carrying essential genes for survival, reproduction, and invasion, is constantly diversifying by acquiring and losing DNA segments, or by DNA degeneration, to improve the genetic novelty for the adaptation during the evolution.
Keywords: CGH analysis and transcriptome analysis

overall_design: We analyzed 26 arrays for aCGH and 2 arrays for expression profilings.

first: Yong

middle: Q

last: He


title: NATURI V1 Nasal Lavage - MegaViro

middle: A


title: Pan-viral screening of respiratory tract infections in asthmatic and non-asthmatic adults

summary:
BACKGROUND: 50% to 80% of asthma exacerbations are precipitated by viral upper respiratory tract infections (RTI), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood due to the limited scope and throughput of conventional viral detection methods. METHODS: We investigated the capability of the Virochip, a DNA microarray-based viral detection platform, to characterize the viral diversity in RTIs in asthmatic and non-asthmatic adults. RESULTS: The Virochip detected viruses in a higher proportion of samples (65%) than culture isolation (17%), while exhibiting high concordance (98%), sensitivity (97%) and specificity (98%) with pathogen-specific PCR. A similar spectrum of viruses was identified in the RTIs from each patient subgroup; however, unexpected diversity among the coronaviruses (HCoVs) and HRVs was revealed. All but one of the HCoVs corresponded to the newly-recognized HCoV-NL63 and HCoV-HKU1 viruses, and over 20 different serotypes of HRVs were detected, including a set of 5 divergent isolates that form a distinct genetic subgroup. CONCLUSIONS: The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger scale studies will be necessary to determine if particular substrains of viruses confer an elevated risk of asthma exacerbation

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series.
We analyzed a series of 82 microarrays on which were hybed RNA randomly amplified from nasal lavage of outpatient cold specimens.


title: Bovine skeletal muscle gene network

status: Public on Aug 30 2006

city: St Lucia

first: Yonghong

state: Queensland

address: 306 Carmody Road

department: Livestock Industries

institute: CSIRO

summary:
We present the application of large-scale multivariate mixed-model equations to the joint analysis of nine gene expression experiments in beef cattle muscle and fat tissues with a total of 147 hybridizations, and exploring 47 experimental conditions or treatments. Using a correlation-based method, we constructed a gene network for 822 genes. Modules of muscle structural proteins and enzymes, extracellular matrix, fat metabolism and protein synthesis were clearly evident. Detailed analysis of the network identified groupings of proteins on the basis of physical association. For example, expression of three components of the z-disk, MYOZ1, TCAP and PDLIM3, was significantly correlated. In contrast, expression of these z-disk proteins was not highly correlated with the expression of a cluster of thick (myosins) and thin (actin and tropomyosins) filament proteins, or titin, the third major filament system. However, expression of titin was itself not significantly correlated with the cluster of thick and thin filament proteins and enzymes. Correlation in expression of many fast twitch muscle structural proteins and enzymes was observed, but slow twitch specific proteins were not correlated with the fast twitch proteins or with each other. In addition, a number of significant associations between genes and transcription factors were also identified. Our results not only recapitulate the known biology of muscle, but have also started to reveal some of the underlying associations between and within the structural components of skeletal muscle.
Keywords: gene network

overall_design: Analysis of nine gene expression experiments in beef cattle muscle and fat tissues with a total of 147 hybridizations, and exploring 47 experimental conditions or treatments.


title: Genome-wide expression and location analyses of the Candida albicans Tac1p regulon

status: Public on Mar 15 2008

city: Memphis

first: Katherine

last: Barker

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary:
A major mechanism of azole resistance in Candida albicans is the over-expression of the genes encoding the ABC transporters Cdr1p and Cdr2p.  Constitutive over-expression of these efflux pumps is due to mutations in the gene encoding Tac1p, resulting in hyperactivity of this zinc cluster transcription factor.  In order to identify the transcriptional targets of Tac1p, we examined four matched sets of clinical isolates representing the development of CDR1- and CDR2-mediated azole resistance, using gene expression profiling analysis.  We identified 31 genes that were consistently up-regulated with CDR1 and CDR2, including TAC1 itself, as well as 12 consistently down-regulated genes.  When a resistant strain deleted for TAC1 was similarly examined, the expression of almost all of these genes was returned to levels similar to those in the matched azole-susceptible isolate.
Keywords: gene expression profiling

overall_design: Four clinical match isolates (azole susceptible and resistant) were grown as three independent replicates for each set to mid-log phase.  A TAC1 knockout derived from resistant isolate 5674 was also grown as three independent replicates.  Each resistant isolate was compared to its susceptible parent, and the TAC1 knockout was compared to the susceptible parent (5457) of the resistant isolate, 5674.

first: Teresa

last: Liu

first: Sadri

last: Znaidi

first: Lijing

last: Xu

first: Ramin

last: Homayouni

first: Saloua

last: Saidane

first: Joachim

last: Morschhauser

first: Andre

last: Nantel

first: Martine

last: Raymond

last: Rogers


title: Comparative transcript profiling of interaction events in Pinus sylvestris root tissues following challenge (15dpi).

status: Public on Jul 31 2006

city: Raleigh

first: Chris

last: Smith

state: NC

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU

summary:
The response mechanisms, recognition and specificity of conifer trees during interaction with pathogenic, saprotrophic or symbiotic ectomycorrhizal fungus were investigated. The roots of Pinus sylvestris were challenged for fifteen days with either Heterobasidion annosum (a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees); Laccaria bicolor (an obligate ectomycorrhizal symbiont); or Trichoderma aureoviride (an obligate saprotroph). The gene expression data from cDNA micro-arrays consisting of 2176 Pinus taeda genes were analysed using 2-interconnected mixed linear model statistical approach. The result of the pairwise comparisons of the different treatments against un-inoculated control led to identification of genes specifically differentially expressed in the pathogenic, saprotrophic and symbiotic interactions. The results were compared with similar data obtained for two other interaction stages: 1 and 5 days post inoculation. The result of this comprehensive expression profiling will hopefully shed more light on the mechanistic basis for recognition and response of conifer trees to pathogenic and non-pathogenic fungi.
Keywords: stress response

overall_design: Three replicates (A,B, and C) of 12 arrays each. In each replicate each of the 4 samples is paired with each of the other 3 samples in both dye assignment possibilities (i.e. a dye-swap is performed).

first: Gregory

last: Heller

first: Aleksandra

last: Adomas

first: Guosheng

last: Li

first: Ake

last: Olson

first: Jason

last: Osborne

first: Debbie

last: Craig

first: Len

last: van Zyl

first: Ron

last: Sederoff

first: Ralph

last: Dean

first: Jan

last: Stenlid

first: Roger

last: Finlay

first: Frederick

middle: O

last: Asiegbu


title: Comparative transcript profiling of interaction events in Pinus sylvestris root tissues following challenge (5dpi).

summary:
The response mechanisms, recognition and specificity of conifer trees during interaction with pathogenic, saprotrophic  or symbiotic ectomycorrhizal fungus were investigated. The roots of Pinus sylvestris were challenged for five days with either Heterobasidion annosum (a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees); Laccaria bicolor (an obligate ectomycorrhizal symbiont); or Trichoderma aureoviride (an obligate saprotroph). The gene expression data from cDNA micro-arrays consisting of 2176 Pinus taeda genes were analysed using 2-interconnected mixed linear model statistical approach. The result of the pairwise comparisons of the different treatments against un-inoculated control led to identification of genes specifically differentially expressed in the pathogenic, saprotrophic and symbiotic interactions. The results were compared with similar data obtained for two other interaction stages: 1 and 15 days post inoculation. The result of this comprehensive expression profiling will hopefully shed more light on the mechanistic basis for recognition and response of conifer trees to pathogenic and non-pathogenic fungi.
Keywords: stress response

first: Åke

first: Tzu-Ming

last: Chu

first: Russ

last: Wolfinger


title: SAGE profiles from cultured keratinocytes and human epidermis

status: Public on Feb 22 2002

city: Nijmegen

first: Bastiaan

last: Jansen

address: PO Box 9101

department: Tumor Immunology

institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen

summary:
SAGE libraries from cultured, differentiated keratinocytes and human epidermis, both normal and affected by actinic keratosis
Keywords = Keratinocyte, Epidermis, Homo sapiens, Actinic Keratosis, TNF alpha

first: Fred

last: Van Ruissen

first: Gys

last: De Jongh

first: Ivonne

last: Van Vlijmen-Willems

first: Joost

last: Schalkwijk

first: Patrick

last: Zeeuwen


title: Gene expression profiling in human glial brain tumors

status: Public on Jan 27 2006

city: Stanford

first: Markus

last: Bredel

institute: Stanford University School of Medicine

summary:
Gene expression profiling in 50 glial brain tumors and 4 normal brains using 42,000-feature cDNA microarrays (from total RNA). Tumors: 50 fresh-frozen glioma specimens subjected to standard WHO classification. Specimens included astrocytic [2 juvenile pilocytic astrocytomas, 1 low-grade astrocytic glioma, 1 anaplastic astrocytomas, 31 glioblastomas (of these 2 secondary glioblastomas and 2 gliosarcomas)], oligodendroglial [5 oligodendrogliomas, 3 anaplastic oligodendrogliomas], and 6 anaplastic oligoastrocytomas tumors. One tumor had been classified as glioneuronal neoplasm. Normal brain was purchased from Stratagene. Stratagene Universal Common Reference was used as reference RNA. The results provide insights into molecular mechanisms and pathways associated with gliomagenesis.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
type: Logical Set
Keywords: other


title: Array-CGH in human glial brain tumors

status: Public on May 27 2005

summary:
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Characterization of DNA copy number changes in 54 glial brain tumors using a cDNA microarray-based comparative genomic hybridization method. Tumors: 54 fresh-frozen glioma specimens subjected to standard WHO classification. Specimens included astrocytic [3 juvenile pilocytic astrocytomas, 1 low-grade astrocytic glioma, 3 anaplastic astrocytomas, 31 glioblastomas (of these 3 secondary glioblastomas and 2 gliosarcomas)], oligodendroglial [5 oligodendrogliomas, 3 anaplastic oligodendrogliomas], and 7 anaplastic oligoastrocytomas tumors. One tumor had been classified as glioneuronal neoplasm. Human male and female genomic reference DNA was purchased from Promega (Promega, Madison, WI). The results provide insights into molecular genetic changes associated with gliomagenesis.
Keywords: other


title: Expression data for reproductive development in rice

first: Sanjay

last: Kapoor

summary:
Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development.
Keywords: Development time course

overall_design: Various rice tissues/organs (seedling root, mature leaf and Y leaf) and stages of reproductive (panicle and seed) development were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. We sought to obtain developmental and temporal gene expression profiles at each stage to identify the differentially expressed genes. Different stages of panicle and seed development have been categorized according to panicle length and days after pollination, respectively, based on landmark developmental events as follows: up to 0.5 mm, shoot apical meristem and rachis meristem (SAM); 0-3 cm, floral transition and floral organ development (P1); 3-10 cm, meiotic stage (P2 and P3); 10-15 cm, young microspore stage (P4); 15-22 cm, vacuolated pollen stage (P5); 22-30 cm, mature pollen stage (P6); 0-2 dap, early globular embryo (S1); 3-4 dap, middle and late globular embryo (S2); 5-10 dap, embryo morphogenesis (S3); 11-20 dap, embryo maturation (S4); 21-29, dormancy and desiccation tolerance (S5). These stage specifications are approximations based on information from Itoh et al., 2005, Plant Cell Physiol, 46, 23-47.

first: Akhilesh

last: Tyagi

first: Jitendra

last: Khurana

first: Rita

last: Arora

first: Pinky

last: Agarwal

first: Aashima

last: Nijhawan

first: Pooja

last: Sharma

first: Mukesh

last: Jain


title: S. coelicolor M145 Time-course Study in R5- medium (Culture# 3)

status: Public on Jun 19 2007

city: Minneapolis

first: Salim

last: Charaniya

state: MN

address: 421 Washington Ave SE., 151 Amundson Hall

department: Chemical Engineering and Materials Science

institute: University of Minnesota

summary:
Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators.  Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined.  In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M145 wild type and disruption mutants of regulatory genes (afsS and absA1) known to affect antibiotic biosynthesis.
Keywords: Time course

overall_design: The time-course study involved analysis of 13 samples (10h, 13h, 14h, 16h, 18h, 20h, 22h, 24h, 27h, 29h, 32h, 34h, 37h). Of these, 13h, 14h, 16h, 18h, 20h, 22h, 24h, 32h, and 37h sample were analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.

first: Wei

last: Lian

first: Karthik

last: Jayapal

first: Wei-Shou

last: Hu


title: Intra-MZ pair discordance and longitudinal variation of whole-genome scale DNA methylation in adults

status: Public on Oct 30 2013

last: Zhang

address: 1347 West Guangfu Rd.

institute: Institute of Forensic Science, Ministry of Justice

type: Methylation profiling by genome tiling array

summary: In this study, we used Illumina Infinium HumanMethylation450 Beadchips to compare DNA methylation profiles in blood from 10 pairs of MZ twins and 8 individuals recruited at 0, 3, 6, and 9 months.

overall_design: MZ Group (Group A) contained 10 pairs of MZ twins ranging from 23 to 74 years old, including 8 female and 12 male subjects.Longitudinal study group (Group B) included a pair of MZ (male) twins and 6 unrelated individuals (3 male, 3 female), aged from 24 to 39. Except subject H, all participants in Longitudinal study group (Group B) were recalled every 3 months for 9 months (0, 3, 6, and 9 m). Subject H was studied only at 0, 6, and 9 months. Bisulphite converted DNA from the 60 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Shumin

last: Zhao

first: Su-Hua

first: Jingzhong

last: Chen

first: Daru

last: Lu

first: Min

last: Shen

first: Chengtao

last: Li