title: Identification of putative learning and memory genes in the dentate gyrus of aged rats following the Morris Water Maze

status: Public on Jul 31 2007

city: Gainesville

first: Corinna

last: Burger

state: FL

address: 1600 SW Archer Red

institute: University of Florida

summary:
The aim of this study was to investigate whether the differences in memory decline associated with aging are a result of differences in gene expression.  We first categorized age-unimpaired and age-impaired rats based on their performance in the Morris water maze, when compared to young rats. Then we isolated messenger RNA from the dentate gyrus of the hippocampus of each animal to interrogate Affymetrix RAE 230A rat genome microarrays. Supervised statistical analysis of the different groups of aged animals recognized 85 genes (p<0.005) that were significantly different in the dentate gyrus of aged rats that had learned the Morris water maze (MWM) paradigm when compared to learning impaired and a number of controls for stress, exercise and non-spatial learning.  In addition, statistical analysis of the microarray data that included young and aged rats identified 1129 genes (p<0.005) that were differentially expressed between aged and young rats independent of behavior, but due to aging alone.
Keywords: behavior comparison, age comparison

overall_design: a total of 80 samples were analyzed including aged and young rats for aged versus young comparisons. One chip was interrogated per animal.  Supervised analysis of aged rat data (aged unimpaired (HID U) versus controls : HID I, VIS, YOKE, SIT includes 39 samples (intermediate learners were not included in the analysis).  Controls include cage controls, yoke controls (no platform), visible platform controls.

first: Cecilia

last: Lopez

first: Henry

last: Baker

first: Ron

last: Mandel

first: Nicholas

last: Muzyczka


title: A transcript profile of Medicago truncatula root meristem cells

status: Public on Jul 01 2007

city: Canberra

first: Peta

last: Holmes

state: Australian Capital Territory

address: Building 46, Australian National University

department: Reseach School of Biological Sciences

country: Australia

institute: Genomic Interactions Group

summary:
The root apical meristems (RAM) is established during embryogenesis and serves as a source of stem cells for plant growth and organogenesis. Young roots have a simple structure and meristeamtic and non-meristematic cells can be differentiated based on their location.
We have used the Affymetrix Medicago Genome Array GeneChip to compare tissue from the root meristem and non-meristematic tissue to identify meristem specific candidate genes based on changes in gene expression before and after differentiation
Keywords: Cell type comparison

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Roots were sectioned separating meristematic (root-tip) and non-meristematic root tissue; total RNA was extracted and used for hybridization to Affymetrix arrays

first: Nijat

last: Imin

first: Nicolas

last: Goffard


title: Leukocytes from patients with sepsis

city: Glebe

first: Benjamin

middle: Man Piu

last: Tang

state: NSW

address: 12/29 Cook Street

department: Intensive Care Medicine

institute: Nepean Hospital

summary:
To examine whether gene-expression profiling of circulating leukocytes is different between patients with sepsis as compared to controls.  The signature genes identified will then be used to develop a prediction model to assist the diagnosis of sepsis.
Keywords: Prediction study

overall_design:
Differentially expressed genes are identified from a training set of 44 patients.  The predictive accuracy of these genes is then assessed in an independent validation set of 50 patients.

Training set: GSM134895 - GSM135279
Validation set: GSM135655 - GSM135704

middle: M

first: Anthony

middle: S

last: McLean

first: Ian

middle: W

last: Dawes

first: Stephen

middle: J

last: Huang

first: Ruby

middle: C

last: Lin


title: Structural basis for recognition of SMRT/N-CoR by the MYND domain and its contribution to AML1/ETO's activity

status: Public on Mar 21 2007

city: Hanover

first: Nancy

middle: Asmussen

last: Speck

state: NH

address: 311 Vail Bldg

department: Biochemistry

country: USA

institute: Dartmouth Medical School

summary:
To examine the effects of disrupting the AML1/ETO MYND-SMRT interaction with the W692A substitution on AML1/ETO function, the global gene expression profile of mouse bone marrow LSK cells transduced with GFP was compared to that of cells transduced with either wild-type AML1/ETO or AML1/ETO harboring the W692A substitution in the MYND domain.  Three independent biological replicates were assessed for both the control (GFP/MigR1) and AML1/ETO (intact MYND-SMRT interaction) conditions, whereas four independent biological replicates were assessed for the W692A (disrupted MYND-SMRT interaction) condition.  The three GFP replicates were used to establish a baseline signal for comparison to both the AML1/ETO and W692A samples.
Keywords: genetic modification

overall_design: Global gene expression profiles of FACS-sorted Lin-Sca1+cKit+ mouse bone marrow cells transduced with empty vector (GFP-MigR1), AML1/ETO, or AML1/ETO with the W692A substitution (W692A).

middle: A

first: Justin

last: J Gaudet

first: Yizhou

last: Liu

first: Wei

last: Chen

first: Matthew

middle: D

last: Cheney

first: Liya

last: Roudaia

first: Tomasz

last: Cierpicki

first: Rachel

last: Klet

first: Kari

last: Hartman

first: Thomas

last: Laue

first: John

middle: H

last: Bushweller


title: Pollination type recognition from a distance in the ovary is revealed by a global transcriptomic analysis.

status: Public on May 26 2010

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

summary: Sexual reproduction in flowering plants involves intimate interactions between the growing pollen tube and the female reproductive structure. These interactions start immediately after pollen landing on the stigma and continue during the pollen tube journey through the style and the ovary. Thus, well before fertilization, genes in the gynoecium are affected by the growing pollen tubes. Genes activated at a distance in the ovary before pollen tubes arrival represent one class of such genes. Using a global transcriptomic approach, expression profiles obtained from compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations revealed that these pollinations are perceived differently from a distance in the ovary. As the pollen tubes grew along the style, more and more genes became specific for each pollination type, although even early on when no difference could be observed in pollen tube growth rates, each pollination type already displayed its specific signature. Wounding experiments as well as methyl jasmonate treatment were also conducted to determine if transmitting tissue cell death caused by pollen tube growth in the style could also activate gene expression at distance in the ovary. Our data suggest that pollen tube growth in the style is at least partially perceived as a wounding aggression, and that a SI pollination is more akin to a wound response than the other pollination type tested, suggesting similarities in the signaling pathways controlling pollen recognition and stress responses. More importantly, our transcriptomic analysis reveals a highly specific recognition of various pollination types that is relayed from a distance to the ovary ahead of fertilization.

overall_design: To determine on a more global scale if interorgan communication during pollen-pistil interactions is a widespread phenomenon and does not only involve few specialized genes, we used a 7.7K cDNA microarray comprising ~6500 ovule-derived unigenes in duplicata from Solanum chacoense, a self-incompatible wild potato species (Germain et al., 2005), to conduct gene expression analyses through cDNA microarray hybridizations. Profiles obtained from compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations as well as from wounding treatments were all analyzed using the same minimal expression level critera (p < 0.05, fold change ≥± 1.5). Four independent biological replicates were produced from each time points. Ovules were collected at 6, 24 and 48 hours after each treatment and used for RNA extraction and probe preparation . compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations as well as from wounding treatments mRNA preparations were individually hybridized against unpollinated ovule mRNAs . All data was substracted from the touch control. Althought Methanol treated ovules RNA were hybridized against unpollinated ovule mRNAs from plant in closed chamber. To estimate reproducibility and to produce control data for statistical analysis, a large number of unfertilized ovules were isolated and separated between seven independent control groups. RNA from randomly selected pairs of control was hybridized on six microarrays.

first: André

last: Nantel

first: Daniel

middle: P

last: matton


title: Zymosan stimulation of MyD88-deficient bone marrow-derived macrophages

status: Public on Jan 30 2007

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

summary:
Innate immune pattern recognition receptors play critical roles in pathogen detection and initiation of antimicrobial responses. We and others have previously demonstrated the importance of the beta-glucan receptor Dectin-1 in the recognition of pathogenic fungi by macrophages and dendritic cells, and have elucidated some of the mechanisms by which Dectin-1 signals to coordinate the antifungal response. While Dectin-1 signals alone are sufficient to trigger phagocytosis and Src-Syk-mediated induction of antimicrobial reactive oxygen species, collaboration with Toll-like receptor (TLR)2 signaling enhances NF-kB activation and regulates cytokine production. In this study we demonstrate that Dectin-1 signaling can also directly modulate gene expression via activation of nuclear transcription of activated T cells (NFAT) transcription factors. Dectin-1 ligation by zymosan particles or live Candida albicans yeast triggers NFAT activation in macrophages and dendritic cells. Dectin-1-triggered NFAT activation plays a role in the induction of Egr2 and Egr3 transcription factors, and cyclooxygenase 2 (Cox-2). Furthermore, we show that NFAT activation regulates IL-2, IL-10 and IL-12 p70 production by zymosan-stimulated dendritic cells. These data establish NFAT activation in myeloid cells as a novel mechanism of regulation of the innate antimicrobial response.
Keywords: stress response

overall_design: Bone marrow-derived macrophages deficient in MyD88 were stimulated with zymosan, and total RNA was extracted 120 minutes after stimulation for comparison to macrophages grown under the same conditions, but not stimulated.

first: Helen

last: Goodridge

first: Randi

last: Simmons

first: David

last: Underhill


title: Characterization of Gene Expression At the Human Maternal-Fetal Interface

status: Public on Jan 11 2007

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

summary:
Microarray analysis to globally assess gene expression at the maternal-fetal interface
Keywords: age

overall_design: 27 non-labored normal preterm and 9 non-labored normal term basal plate samples were analyzed on Affymetrix U133 chips using established protocols.   The gene expression profile of preterm was compared to term.

first: V

last: Winn

first: R

last: Haimov-Kochman

first: M

last: Gormley

first: S


title: LPS tolerance in macrophages

status: Public on Aug 10 2007

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technical University Munich

summary:
Among the multiple mechanisms that control the intensity and duration of macrophage activation, the development of a state of refractoriness to a second stimulation in cells treated with LPS has long been recognized. Release of inhibitory cytokines and alterations in intracellular signaling pathways may be involved in the development of LPS tolerance. Although a number of molecules have been implicated, a detailed picture of the molecular changes in LPS tolerance is still missing. We have used a genome-wide gene expression analysis approach to (i) define which fraction of LPS target genes are subject to tolerance induction and (ii) identify genes that are expressed at high levels in tolerant macrophages. Our data show that in LPS tolerant macrophages the vast majority of LPS-induced gene expression is abrogated. The extent of tolerance induction varies for individual genes, and a small subset appears to be excepted. Compared to other negative control mechanisms of macrophages, e.g. IL-10-induced deactivation, LPS-tolerance inhibits a much wider range of transcriptional targets. Some previously described negative regulators of TLR-signaling (e.g. IRAK-M) were confirmed as expressed at higher levels in LPS-tolerant macrophages. In addition, we discuss other potential players in LPS tolerance identified in this group of genes.
Keywords: pre and restimulation with LPS, tolerance induction

overall_design: Cells were either prestimulated (1_X) or not (0_X) for 18h with 100 ng/ml LPS. Media was exchanged and after 2h rest, cells either restimulated (X_1) or not (X_0) with again 100 ng/ml LPS. This resulted in 4 experimental conditions: 0_0, 0_1, 1_0 and 1_1. There were 3 biological replicates done, resulting in 12 arrays altogether.

first: Jörg

first: Roland

last: Lang


title: Expression data from porcelain crabs following heat stress

status: Public on Apr 16 2007

city: Tiburon

first: Jonathon

last: Stillman

address: 3152 Paradise Drive

department: Romberg Tiburon Center

institute: San Francisco State University

summary:
Porcelain crabs, Petrolisthes cinctipes, live in the marine intertidal zone and routinely experience thermal stress.  Genes involved in heat shock responses are generally upregulated following heat stress and genes involved in oxidative energy production are downregulated following heat stress
We used microarrays to detail the global programme of gene expression underlying responses to thermal stress and identified distinct classes of up-regulated and down-regulated genes during this process.
Keywords: time course

overall_design: Crabs were collected from the field and returned to the laboratory where they were given a heat stress or held under control conditions for the period of time during the heat stress.  Samples from both heat stressed and control crabs were taken after crabs were placed into a common recovery tank for periods of time ranging from 0.5 to 30h

first: Kristen

last: Teranishi


title: The Neuronal Transcriptome of Aplysia californica: A Platform for the Neurogenomics of Defined Neurons

status: Public on Jan 05 2007

city: St Augustine

first: Andrea

middle: B

last: Kohn

address: 9505 Ocean Shore Blvd

department: Whitney lab

summary:
The marine mollusc Aplysia is a well established experimental system for cellular and systems neuroscience because of the relatively simple organization of its nervous system and the presence within it of the largest nerve cells in the animal kingdom, many of which are uniquely identifiable in every member of the species. Until now, molecular analyses of Aplysia have been seriously handicapped by lack of adequate genomic information, with only 200 sequences publicly available when this project was initiated in 2003. By sequencing cDNA libraries from the central nervous system, we have identified over 175,000 ESTs (expressed sequence tags), of which 19,814 are unique neuronal gene products and 9469 has been annotated. Through comparison with the complete genomic data available for Drosophila and C. elegans, we estimate that we have sequence information for approximately 50-70% of the total transcriptome of the Aplysia nervous system. We also identified 9,223 unique gene products in a modulatory serotonergic cell and about 1,000 unique gene products from its processes. Using gene expression oligoarrays constructed using the Aplysia EST database we also have characterized the transcript profile of sensory and motor neurons. In addition to increasing the amount of publicly available gene sequences of Aplysia by two orders of magnitude, this collection of transcripts is distinctive from a comparative biology point of view. It represents the largest database available for any member of the Lophotrochozoa clade of the animal kingdom. These molecular resources should allow the detailed study of the genomics of identified cells and circuits and provide in Aplysia a much needed bridge between genes, behavior, and learning.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: High Expression Levels of Keratinocyte Antimicrobial Proteins in Psoriasis Compared with Atopic Dermatitis.

status: Public on Dec 23 2006

city: Nijmegen

first: Gys

middle: de

last: Jongh

state: Gelderland

address: Rene Descartesdreef 1

department: Dermatology

country: Netherlands

institute: Nijmegen Centre for Molecular Life Sciences

summary:
Recently, it was shown that lesional skin of atopic dermatitis patients expresses low levels of some antimicrobial peptides, compared with psoriasis patients. Here we performed microarray analysis on mRNA from purified lesional epidermal cells of patients with chronic plaque psoriasis and chronic atopic dermatitis, to investigate whether this is a general phenomenon for host defense proteins, and how specific it is for this class of molecules. We found overexpression of many antimicrobial genes in keratinocytes from psoriatic skin compared with atopic dermatitis skin. Interestingly, we observed that markers of normal differentiation and the activated/hyperproliferative epidermal phenotype were expressed at equal levels. Chronic lesions of psoriasis and atopic dermatitis patients are remarkably similar with respect to cellular proliferation. We conclude that psoriatic epidermis expresses high levels of host defense proteins compared with atopic dermatitis epidermis, and this phenomenon appears to be specific for these proteins. It remains to be investigated whether this is caused by
genetic polymorphisms in pathways leading to an epidermal antimicrobial response, or by differences in the cellular infiltrate in psoriasis compared with atopic dermatitis.

In general the microarray technique is used to probe a (very large) number of genes for say the deseased and the healthy state.Then gene ontology is used to detect the involved pathways.We did not set out to find a comprehensive list of genes involved in these skin deseases.We do suspect that the "path way" approach might be a bit anthropomorphic.Here we offered a different approach.We set out to investigate the evolutionary fitness changes from one local maximum , Psoriasis , to another , Atopie. Our hypothesis is that Psoriasis is at one extreme in the reaction of the evolution to invading micro organisms and Atopie  at an other.So the vast chemical web called human being with numorous feedback and feed forward signals would then be tilted a bit in multidimensional Gene Space and the microarray technique would show us a glimpse of the involved genes.
Keywords: Disease state analysis

overall_design: Six array’s were analysed.Each array has a sample of Psoriatic epidermis in the Cy5 channel and a sample of Atopic epidermis in the Cy3 channel.In this experiment each patient was included only once.So each array was a biological replicate and variables other than gene expression was deliberately confounded.

first: Arno

last: Pol

first: Rolph

last: Pfundt

first: Joost

last: Schalkwijk


title: Sex-biased gene expression in 18 day embryonic chicken heart, brain, and gonad

status: Public on Aug 07 2007

city: Uppsala

first: judith

last: mank

address: Norbyvägen 18D

department: evolutionary biology

country: Sweden

institute: uppsala university

summary:
The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes. In many organisms dosage compensation has thus evolved to equalize sex-linked gene expression in males and females1,2, in mammals achieved by X chromosome inactivation and in flies and worms by up- or down-regulation of X-linked expression, respectively. Another form of dosage compensation ensures that expression levels on the X chromosome and on autosomes are balanced3,4. While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW) remains an unsolved enigma5,6. Here we use a microarray approach to show that male day 18 chicken embryos generally express higher levels of Z-linked genes than female birds, both in soma and in gonads. The distribution of male-to-female fold-change values for Z chromosome genes is wide and has a mean of 1.4-1.6, which is consistent with absence of dosage compensation and sex-specific feedback regulation of gene expression at individual loci2. Intriguingly, without global dosage compensation, female chicken has significantly lower expression levels of Z-linked compared to autosomal genes, which is not the case in male birds. The pronounced sex difference in gene expression is likely to contribute to sexual dimorphism among birds, and potentially has implication to avian sex determination.
Keywords: dosage compensation, sex-biased gene expression, soma and gonad

overall_design:
Sample collection
Fertilized eggs from White Leghorn fowl were purchased from OVA Production (Morgongåva, Sweden). The eggs were incubated at 37.5C and 60% relative humidity, and were turned every 3 hours. After 18 days of incubation (ed18), the embryos were euthanized by decapitation. A piece from the apical part of the heart was collected and the left gonad and the brain were excised. The cerebellum, the optic lobes and the cerebral hemispheres were removed from the brain and, consequently, the brain sample included the intact diencephalon and remaining parts from other regions. The samples were immediately frozen in liquid nitrogen and then stored at -70 °C. The embryos were sexed by ocular inspection of the gonads and Müllerian ducts.

RNA preparation and microarray hybridization
Heart, left gonads and diencephalon from each of four male and four female embryos were homogenized by syringe and needle followed by use of the Homogenizer system (Invitrogen, Carlsbad, CA, USA). RNA was extracted from heart and brain homogenates with the PureLink Micro-to-Midi Total RNA Purification System (Invitrogen), and RNA was then DNase treated with a DNA-free kit (Ambion, Austin, TX, USA). Due to limited amounts of available tissue, gonad RNA extraction was performed with an RNeasy Micro Kit (Qiagen, Hilden, Germany) with integrated DNase treatment. RNA concentration was measured with ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA). Two micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA). Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA), the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G. In total, 24 hybridizations were made (4 individuals x 3 tissues x 2 sexes), however, three samples failed to meet Affymetrix quality control criteria and were removed from further analysis (heart and brain from one male, and gonads from one female).
Microarray data analysis. All pre-processing and statistical analysis of microarray data was performed in R version 2.4.1 using Bioconductor packages release 1.9 (ref. 29). The CEL files were processed using GCRMA30, a background adjustment method taking into account the GC content of probes when assessing non-specific binding, followed by quantile normalization and median-polish summarization of probe intensities into probe set intensities. A linear model was fitted to the log2 of the expression levels based on all probe sets and considering sex and tissue as a combined factor using the Limma package. After pre-processing and linear model fitting the probe sets were filtered on expression; an expression threshold was set on both average expression level and absent/present calls from the R implementation of the Affymetrix MAS 5.0 algorithm. Only probe sets with average expression over a defined threshold and present in more than half of the samples within at least one tissue-sex combination were considered as significantly expressed. This resulted in 15,398 probe sets for heart, 16,846 for brain and 17,438 for gonads, and these probe sets composed the reference for analysis of differently expressed genes between the sexes.

Annotation of probe sets
Annotations for the probe sets were extracted from Ensembl (www.ensembl.org) via biomRt in R. The Ensembl mapping of probe sets is based on alignments of individual probes to the chicken genome version 2.1 (WASHUC2 May 2006) and covers 21,885 of the 37,693 chicken-specific probe sets, which is close to the total number of protein-coding genes in the chicken genome identified by Ensembl. Several transcripts are represented by more than one probe set; the 21,885 probe sets with annotation corresponds to 14,414 unique transcripts. The genomic location for probe sets was taken from Ensembl.

Statistical analysis
Fold-change was calculated as the average male expression over ave
rage female expression, and a Bayesian moderated t-statistic for differential expression between males and females was then generated for each tissue. To take multiple testing into account p-values (corrected p-values) were adjusted using the Benjamini and Hochberg false discovery rate (FDR) method32. Probe sets with an absolute fold-change value larger than various threshold levels were considered sex-biased. Statistical testing of differences in levels of hybridization intensities between sex and/or chromosome categories was done by bootstrapping. The Fisher’s exact test was used to test the distribution of gene ontology terms and the distribution of sex-biased genes across chromosomes. Spearman rank correlation coefficients were calculated for the continuous fold-change values and several genomic parameters including gene density, microsatellite and CR1 retrotransposons repeat density, and GC content, all taken from Ensembl. These parameters were estimated based on averaging over a 100 kb window surrounding each gene.

first: Hans

last: Ellegren

first: Lina

last: Hultin-Rosenberg

first: Björn

last: Brunström

first: Lennart

last: Dencker

first: Kim

last: Kultima

first: Birger

last: Scholz


title: Affymetrix Research Exon Array Tissue Panel Data

status: Public on Jan 01 2007

city: Menlo Park

first: Tyson

last: Clark

address: 1380 Willow Rd.

institute: Pacific Biosciences

type: Expression profiling by genome tiling array

summary:
Manuscript Title: Discovery of tissue-specific exons using comprehensive human exon microarrays
We have designed a high-density oligonucleotide microarray with probesets for more than one million annotated and predicted exons in the human genome.  Using these arrays and a simple algorithm that normalizes exon signal to signal from the gene as a whole, we have identified tissue-specific exons from a panel of 16 different normal adult tissues.  Pair-wise comparisons between the tissues suggest that 75% of detected genes are differentially alternatively spliced.  We also demonstrate how an inclusive exon microarray can be used to discover novel alternative splicing events.  As examples, 15 new tissue-specific exons from 9 genes were validated by RT-PCR and sequencing.
Keywords: exon analysis

overall_design: 16 normal adult human tissues with 3 biological replicates each were hybridized to the Research version of the Affymetrix Human Exon Array.  We sought to identify tissue-specific exons that are included via alternative splicing.

first: Anthony

last: Schweitzer

first: Tina

middle: X

last: Chen

first: Michelle

middle: K

last: Staples

first: Gang

last: Lu

first: Hui

last: Wang

first: Alan

last: Williams

first: John

middle: E

last: Blume


title: Characterization of an Arabidopsis thaliana mutant deficient in the GAPC gene.

status: Public on Oct 31 2006

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

summary:
To investigate the role of this enzyme in different plant tissues, we characterized a mutant from Arabidopsis thaliana having an insertion at the GAPC gene locus. The homozygous mutant was determined to be null respect to GAPC, as it exhibited complete absence of both expression of GAPC mRNA and enzyme activity. Transcriptome analysis demonstrated that the insertion mutant plant shows altered expression of several enzymes involved in carbohydrate metabolism.
Keywords: 2 channel experiment in triplicate including a dye swap comparison

overall_design:
Arabidopsis oligonucleotide microarrays fabricated by the University of Arizona contain 26,000 oligonucleotides. The experimental and reference RNA samples were directly labeled with either Cy5-dUTP or Cy3-dUTP fluorescent dye (Amersham Pharmacia Biotech, Piscataway, NJ), using random hexamer primers (Invitrogen). Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen, Valencia, CA). Labeled samples were mixed and then hybridized to a microarray for 15 h at 60C. The slides were washed at room temperature in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC for 5 min each with gentle shaking. The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA). Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities. The experiments were repeated three times with samples from different experiments, as biological replicates. In dye swapping experiments, the RNA samples from different experiments were labeled reciprocally, both as a biological and technical repetition for comparing the reproducibility of the experiments.
The hybridization intensities of each microarray element were measured using ScanAlyze 4.24 (available at http://genome-www4.stanford.edu/MicroArray/SMD /restech.html). The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria: spots flagged as having false intensity caused by dust or background on the array were removed; and spots for which intensity was less than three fold above background were also eliminated. Data from multiple experiments were normalized (Bolstad et al., 2003) and signals from spots from different experiments were analyzed using Significance Analysis of Microarrays using the one class response (SAM, Tusher et al., 2001, http://www-stat.stanford.edu/~tibs/SAM/.), with a false discovery rate <10%.

first: Sebastián

last: Rius

first: Alberto

last: Iglesias

first: Diego

middle: F

last: Gomez-Casati


title: L7 vs sensory cluster (Annotated array AAA)

first: Andrea

last: Kohn

summary:
The marine mollusc Aplysia is a well established experimental system for cellular and systems neuroscience because of the relatively simple organization of its nervous system and the presence within it of the largest nerve cells in the animal kingdom, many of which are uniquely identifiable in every member of the species. Until now, molecular analyses of Aplysia have been seriously handicapped by lack of adequate genomic information, with only 200 sequences publicly available when this project was initiated in 2003. By sequencing cDNA libraries from the central nervous system, we have identified over 175,000 ESTs (expressed sequence tags), of which 19,814 are unique neuronal gene products and 9469 has been annotated. Through comparison with the complete genomic data available for Drosophila and C. elegans, we estimate that we have sequence information for approximately 50-70% of the total transcriptome of the Aplysia nervous system. We also identified 9,223 unique gene products in a modulatory serotonergic cell and about 1,000 unique gene products from its processes. Using gene expression oligoarrays constructed using the Aplysia EST database we also have characterized the transcript profile of sensory and motor neurons. In addition to increasing the amount of publicly available gene sequences of Aplysia by two orders of magnitude, this collection of transcripts is distinctive from a comparative biology point of view. It represents the largest database available for any member of the Lophotrochozoa clade of the animal kingdom. These molecular resources should allow the detailed study of the genomics of identified cells and circuits and provide in Aplysia a much needed bridge between genes, behavior, and learning.
Keywords: Cell-type comparison

overall_design: Three biological replicates were performed on the neuron L7 verses Sensory cluster. We performed a direct comparison.

first: Thomas

last: Ha

first: Leonid

middle: L

last: Moroz


title: Sugarcane transcriptome - Drought response

status: Public on May 20 2007

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

country: Brazil

institute: Universidade de São Paulo - USP

summary:
Sugarcane one-eyed seed sets obtained from a variety sensitive to drought conditions (cv. SP90-1638, CTC, Brazil) were cultivated on moist sand for 15 days. The plants were transferred to pots containing moist sand and were irrigated with Hoagland’s solution (Hoagland and Arnon, 1950). Regular watering was maintained for 90 days and suppressed after this period for the experimental group. Leaves were collected 24 h, 72 h and 120 h after exposure to drought conditions for the control and experimental groups. Samples were collected and immediately frozen in liquid nitrogen. Leaves from six plantlets were used for each time point. Extraction of total RNA was performed separately on each sample pool.
Keywords: time course of stress response

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

first: Fabiana

last: Rodrigues

first: Sônia

middle: Z

last: di Mauro

first: Flávia

middle: R

last: Rocha

last: Papini-Terzi

middle: Y

last: Nishiyama-Jr

first: Ricardo

last: Vêncio

first: Renato

last: Vicentini

first: Gláucia

middle: M

last: Souza


title: Expression data from myogenesis

status: Public on Apr 30 2006

city: La Jolla

first: Ihsiung

middle: Brandon

last: Chen

address: 10550 N. Torrey Pines Rd.

department: Cell Biology

institute: The Scripps Research Institute

summary:
During muscle differentiation, myogenesis sepcific genes are differentially regulated, including Lamins that function at least in maintenance of nuclear architecture and regulation of gene expression.
We used microarrays to detail the global changes of gene expression in lamins and nuclear envelope assoicated proteins during myogenesis.
Keywords: comparative, myogenesis

overall_design: C2C12 were cultured either in 20% serum (undifferentiated) or in 2% horse serum (differentiated). Differentiated C2C12 cells were harvested on day 6 after induction of myogenesis in low serum. Affymetirx microarray raw data were further processed by GCRMA to globally normalized signal values and then subjected to analysis of Bayesian regularized t-test. Gene expression, that has a p-value less than 0.05 in the t-test and has more than 1.5 fold change, was considered siginificant.

first: Larry

last: Gerace


title: L7 vs sensory cluster (Discovery array DAA)

summary:
The marine mollusc Aplysia is a well established experimental system for cellular and systems neuroscience because of the relatively simple organization of its nervous system and the presence within it of the largest nerve cells in the animal kingdom, many of which are uniquely identifiable in every member of the species. Until now, molecular analyses of Aplysia have been seriously handicapped by lack of adequate genomic information, with only 200 sequences publicly available when this project was initiated in 2003. By sequencing cDNA libraries from the central nervous system, we have identified over 175,000 ESTs (expressed sequence tags), of which 19,814 are unique neuronal gene products and 9469 has been annotated. Through comparison with the complete genomic data available for Drosophila and C. elegans, we estimate that we have sequence information for approximately 50-70% of the total transcriptome of the Aplysia nervous system. We also identified 9,223 unique gene products in a modulatory serotonergic cell and about 1,000 unique gene products from its processes. Using gene expression oligoarrays constructed using the Aplysia EST database we also have characterized the transcript profile of sensory and motor neurons. In addition to increasing the amount of publicly available gene sequences of Aplysia by two orders of magnitude, this collection of transcripts is distinctive from a comparative biology point of view. It represents the largest database available for any member of the Lophotrochozoa clade of the animal kingdom. These molecular resources should allow the detailed study of the genomics of identified cells and circuits and provide in Aplysia a much needed bridge between genes, behavior, and learning.
Keywords: Cell type comparison

overall_design: Direct comparison of L7 neurons to Sensory cluster in Aplysia californica. Three biological replicated were performed

middle: b

middle: J


title: Expression profiling of bronchial epithelium

status: Public on Jul 14 2006

city: Vancouver

first: Kim

middle: Marie

last: Lonergan

state: British Columbia

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: British Columbia Cancer Research Centre

summary:
19 bronchial epithelial SAGE libraries were constructed and analyzed in this study.

Discussed in the study:

IDENTIFICATION OF NOVEL LUNG GENES IN BRONCHIAL EPITHELIUM BY SERIAL ANALYSIS OF GENE EXPRESSION Kim M. Lonergan1, Raj Chari1, Ronald J. deLeeuw1, Ashleen Shadeo1, Bryan Chi1, Ming-Sound Tsao2, Steven Jones3, Marco Marra3, Victor Ling1, Raymond Ng1,4, Calum MacAulay5, Stephen Lam5 and Wan L. Lam1
From the 1Department of Cancer Genetics & Developmental Biology,
5Department of Cancer Imaging, 3Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC, Canada, 2Ontario Cancer Institute / Princess Margaret Hospital, Toronto, ON, Canada, 4the Department of Computer Science, University of British Columbia, Vancouver, BC, Canada

A description of the transcriptome of human bronchial epithelium should provide a basis for studying lung diseases including cancer.  We demonstrate here that minute epithelial specimens obtained by bronchial brushings afford reliable profiling by serial analysis of gene expression (SAGE) leading to lung gene discovery.  We have deduced global gene expression profiles of bronchial epithelium and lung parenchyma, based upon a vast data set of nearly two million sequence tags from 21 SAGE libraries generated from individuals with a history of smoking.  Cluster and linear regression analysis demonstrate the repeatability and reproducibility of bronchial SAGE libraries, and suggest that the transcriptome of the bronchial epithelium is distinct from that of lung parenchyma and other tissue types.  This distinction is highlighted by the abundant expression of signature genes that reflect tissue-specific and region-specific functions.  Through our analysis we have identified novel bronchial-enriched genes and a novel transcript variant for surfactant, pulmonary-associated protein B in lung parenchyma.  Conspicuously, gene expression associated with ciliogenesis is evident in bronchial epithelium.  Additionally, it is noted that a large number of unmapped tags awaits further investigation.
This study represents a comprehensive delineation of the bronchial and parenchyma transcriptomes, identifying more than 20,000 known and hypothetical genes expressed in the human lung, constituting one of the largest human SAGE studies reported to date.
Keywords: bronchial epithelium

first: Raj

last: Chari

first: Ronald

last: deLeeuw

first: Ashleen

last: Shadeo

first: Bryan

last: Chi

first: Ming-Sound

last: Tsao

first: Steven

last: Jones

first: Marco

last: Marra

first: Victor

last: Ling

first: Raymond

last: Ng

first: Calum

last: MacAulay

first: Stephen

last: Lam

first: Wan


title: Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression

status: Public on Nov 21 2006

summary:
A description of the transcriptome of human bronchial epithelium should provide a basis for studying lung diseases including cancer. We demonstrate here that minute epithelial specimens obtained by bronchial brushings afford reliable profiling by serial analysis of gene expression (SAGE) leading to lung gene discovery. We have deduced global gene expression profiles of bronchial epithelium and lung parenchyma, based upon a vast data set of nearly two million sequence tags from 21 SAGE libraries generated from individuals with a history of smoking. Cluster and linear regression analysis demonstrate the repeatability and reproducibility of bronchial SAGE libraries, and suggest that the transcriptome of the bronchial epithelium is distinct from that of lung parenchyma and other tissue types. This distinction is highlighted by the abundant expression of signature genes that reflect tissue-specific and region-specific functions. Through our analysis we have identified novel bronchial-enriched genes and a novel transcript variant for surfactant, pulmonary-associated protein B in lung parenchyma. Conspicuously, gene expression associated with ciliogenesis is evident in bronchial epithelium. Additionally, it is noted that a large number of unmapped tags awaits further investigation.

This study represents a comprehensive delineation of the bronchial and parenchyma transcriptomes, identifying more than 20,000 known and hypothetical genes expressed in the human lung, constituting one of the largest human SAGE studies reported to date.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
This reference Series links data in the following related Series:

GSE3707 Expression profiling of bronchial epithelium
GSE3708 Expression profiling of normal lung parenchyma


title: Sample Matching by Inferred Agonal Stress in Gene Expression Analyses of the Brain

city: Ann Arbor

first: Fan

last: Meng

state: MI

address: 205 Zina Pitcher Place

department: Psychiatry

institute: U of Michigan

summary:
Gene expression patterns in the brain are strongly influenced by the severity of physiological stress at death.  This agonal effect, if not well controlled, can lead to spurious findings in case-control comparisons.  While many recent studies match samples by tissue pH and clinically recorded agonal conditions, we found that these commonly used indicators were sometimes at odds with observed stress-related patterns of gene expression, and that matching by these criteria still sometimes results in identifying differences between cases and controls that are primarily driven by residual agonal effects.  This problem is analogous to the one in genetic studies, where race and ethnicity are often imprecise proxies for complex environmental and genetic factors.
We developed an Agonal Stress Rating (ASR) system that evaluates each sample’s degree of stress based on gene expression data, and used ASRs in post hoc sample matching or covariate analysis.  While we found that gene expression patterns are generally correlated across different regions of the same brain, we also found strong region-region differences in empirical ASRs in many subjects that are likely due to inter-individual variabilities in local structure or function, resulting in region-specific vulnerability to agonal stress.
Variation of agonal stress from one region of the brain to another differs between individuals, revealing a new level of complexity for gene expression studies of brain tissues.  The Agonal Stress Ratings provide a direct assessment of the regulatory responses to agonal stress in individual samples, and allow a strong control of this important confounder.  Our strategy is analogous to sample matching by inferred ancestral proportions in genetic association studies to control subtle confounding by ancestry.
Keywords: Agonal Stress Rating comparison

overall_design: We examined the relationship between the Agonal Stress Ratings (ASRs) and conventional pre hoc indicators such as pH and clinically derived Agonal Factor Scores (AFS), compared the stress ratings across six brain regions in up t0 126 samples, and assessed the performance of different sample matching strategies.

first: Jun

last: Li

first: Larisa

last: Tsavaler

first: Simon

last: Evans

first: Prabhakara

middle: V

last: Choudary

first: Hiroaki

last: Tomita

first: Marquis

middle: P

last: Vawter

first: David

last: Walsh

first: Vida

last: Shokoohi

first: Tisha

last: Chung

first: William

last: Bunney

first: Edward

middle: G

first: Huda

last: Akil

first: Stanley

last: Watson

first: Richard

last: Myers


title: Expression data from B. melitensis infected mouse macrophages

status: Public on Jun 30 2006

first: Yongqun

last: He

address: 018 ARF, 1150 W. Medical Center Dr.

institute: University of Michigan

summary:
Facultative intracellular Brucella infect and survive inside macrophages, and the outcome of macrophage-Brucella interaction is a basis for establishment of a chronic Brucella infection. The majority of Brucella are killed at the early infection stage. A subpopulation of virulent Brucella strains is instead trafficked to an intracellular replicative phagosome, and are resistant to further attack and begin to multiply dramatically. Virulent Brucella also inhibit macrophage apoptosis that in turn favors pathogen survival and replication.
We used the Affymetrix mouse GeneChip 430 2.0 array to analyze mouse macrophage gene expression profiles during the time course of virulent B. melitensis strain 16M infection.
Keywords: time course

overall_design: Murine J774.A1 macrophage cells were infected with B. melitensis strain 16M at a MOI of 200:1. Brucella cultures derived from different Brucella colonies were used to infect different groups of macrophage cells to reflect independent infections. Following 4 h incubation, the cells were washed with PBS and treated with 50 ug/ml gentamicin to kill extracellular Brucella. At 0 h (no Brucella infection), 4 h, 24 h, and 48 h post-infection, cells were individually collected, and total RNA was isolated. The Affymetrix mouse GeneChip 430 2.0 array was used for microarray hybridization. Microarray intensity data were obtained by using Affymetrix GCOS software and further analyzed by GeneSpring and other software programs.

first: Sherry

last: Reichow

first: Sheela

last: Ramamoorthy

first: Xicheng

last: Ding

first: Nammalwar

last: Sriranganathan

first: Stephen

last: Boyle


title: Gene Expression in Naive and Tolerant Macrophages stimulated with LPS

status: Public on Apr 22 2007

city: New Haven

first: Simmie

last: Foster

state: CT

address: 300 Cedar St

department: Immunobiology

institute: Yale University School of Medicine

summary:
The inflammatory response initiated by microbial products signaling through Toll-like receptors (TLRs) of the innate immune system is essential for host defense against infection. Because inflammation can be harmful to host tissues, the innate response is highly regulated.  Negative regulation of TLR4, the receptor for bacterial lipopolysaccharide (LPS), results in LPS tolerance, defined as hyporesponsiveness to repeated stimulation with LPS.  LPS tolerance is thought to protect the host from excessive inflammation by turning off TLR4 signal, which then shuts down TLR-induced genes. However, TLR signaling induces hundreds of genes with very different functions.  We reasoned that genes with different functions should have different requirements for regulation. Specifically, genes encoding proinflammatory mediators should be transiently inactivated to limit tissue damage, while genes encoding antimicrobial effectors, which directly target pathogens, should remain inducible in tolerant cells to protect the host from infection. Using an in vitro system of LPS tolerance in macrophages, here we show that TLR-induced genes may indeed be divided into two distinct categories based on their functions and regulatory requirements.  Further, we show these distinct groups are regulated by gene-specific, and not signal-specific mechanisms.
Keywords: Treatment Comparison

overall_design: We examined gene expression using affymetrix genechips in 3 groups of murine bone-marrow derived macrophages: Naive (untreated), Naive stimulated with LPS, and Tolerant stimulated with LPS.  Two biological replicates were performed for each group.

first: Diana

middle: C

last: Hargreaves

first: Ruslan

last: Medzhitov


title: Expression data from mouse bone marrow macrophages from a strain intercross

status: Public on Jul 19 2007

city: Cleveland

first: Jonathan

middle: David

last: Smith

state: OH

address: 9500 Euclid Avenue

institute: Cleveland Clinic

summary:
Bone marrow macrophages were cultured from 16 week old apoE-deficient F2 mice from an AKRxDBA/2 intercross
Gene expression profiling was performed using Affy 430v2 arrays, and 1967 informative SNP markers were genotyped for each mouse

Supplementary file of SNP data attached below from ParAllele 5K mouse linkage panel

Keywords: Genetic-genomic

overall_design: Expression QTLs and sex effects on gene expression and eQTLs were determined

middle: D

first: Jeffrey

last: Bhasin


title: Sugarcane transcriptome - ABA treatment

first: Milton

last: Nishiyama Jr

summary:
Plants (genotype SP80-3280, CTC, Brazil) cultivated in axenic cultures were transferred to a growth chamber at 26°C on a 16 h/8 h light/dark cycle with a photon flux density of 70 µE.m-2.s-1 and cultivated for 4 weeks. After this period, the phytohormone ABA (Sigma Chem. Co) was added to the culture medium to a final concentration of a 100 µmol.L-1. Control plants were treated with distilled water. Leaves were collected 0 h, 30 min, 1 h, 6 h and 12 h after exposure to ABA and immediately frozen in liquid nitrogen. Six plantlets were used for each time point. Extraction of total RNA was performed separately on each sample pool.
Keywords: time course of hormone treatment

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

first: Vicente

middle: E

last: de Rosa Jr

first: Marcelo

last: Menossi

first: Flávia

last: Rocha

middle: S

last: Papini-Terzi

last: Nishiyama-Jr

first: Ricardo

last: Vêncio

first: Renato

last: Vicentini

first: Eugênio

last: Ulian

first: Gláucia

last: Souza


title: Gene Expression profiling of pterygium

status: Public on Mar 03 2006

city: Singapore

first: Yong Wee

last: Wong

state: Singapore

address: 11, Third Hospital ave

department: SERI Lab

country: Singapore

institute: Singapore Eye Research Institute

summary:
Gene Expression profiling of pterygium. Analysis of conjunctiva and pterygium samples.
Keywords = pterygium
Keywords: repeat sample

first: Jaime

last: Chew

first: Henry

last: Yang

first: Doan

last: Nguyen

first: Leonard

last: Ang

first: Donald

last: Tan

first: Roger

last: Beuerman


title: Trichophyton rubrum germination study

status: Public on Mar 27 2007

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

summary:
Conidia are considered to be the primary cause of skin and nail infections by Trichophyton rubrum. A cDNA microarray containing 10112 ESTs was developed and used to estimate the relative gene expression levels and changes of gene expression during conidial germination in time-course experiments.
Keywords: time course

overall_design:
In order to monitor the expression profings of germination, T. rubrum conidia were induced into Sabouraud liquid medium. Sample were collected  in 1 hr intervals throughout the 15 hr conidial germination. We established two parallel experiments in the whole process and in every parallel experiments, two duplicates were settled. So, including the 0 hr, 64 samples were collected from 16 time points during germination.
Sample mRNA was extracted and reverse transcribed into cDNA and labeled with a fluorescent dye (Cy3 or Cy5). Also, the reference genome DNA isolated in the hyphal stage was labeled. Test samples and reference samples were dye-swapped to avoid variation arising from the dyes.


title: Female BALB/c Mouse Testosterone-Treated Submandibular/Lacrimal/Meibomian Glands

status: Public on Jan 10 2006

city: Boston

first: Nathaniel

last: Treister

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
Our objective was to determine the nature and extent of androgen regulation of gene expression in the female lacrimal, meibomian,and submandibular glands, and to explore the degree to which this control is the same as in male glands.
Keywords: Hormone treatment

overall_design: Series includes pooled (n = 5-6 mice per biological replicate) samples from lacrimal, meibomian, and submandibular glands of male palcebo- and testosterone-treated BALB/c mice. All experiments were run in triplicate (pooled biological replicates) on CodeLink Mouse Uniset I Microarrays

first: David

last: Sullivan

first: Stephen

last: Richards

first: Tomo

last: Suzuki


title: Human cerebellum, frontal cortex [BA4, BA9] and caudate nucleus HD tissue experiment

status: Public on Feb 08 2006

city: Cardiff

first: Lesley

last: Jones

address: Heath Park

department: Psychological Medicine

country: United Kingdom

institute: Cardiff University School of Medicine

summary:
Post mortem human brain tissue comparison between HD patients and controls from 3 brain regions - cerebellum, frontal cortex [BA4, BA9] and caudate nucleus.  Gene expression analysed using linear models from LIMMA package in Bioconductor suite.
Keywords: disease state analysis

overall_design: Large sample sizes were used to examine brain tissue gene expression at various stages of HD pathology.  Three brain regions were profiled, compared and analysed for differential gene expression.  The broad aim was to capture early stage gene expression changes in HD brains.

first: Angela

last: Hodges

first: Andrew

last: Strand

first: Aaron

middle: K

last: Aragaki

first: Alexander

last: Kuhn

first: Thierry

last: Sengstag

first: Gareth

last: Hughes

first: Lyn

middle: A

last: Elliston

first: Cathy

last: Hartog

first: Darlene

last: Goldstein

first: Doris

last: Thu

first: Zane

last: Hollingsworth

first: Francois

last: Collin

first: Beth

last: Synek

first: Peter

last: Holmans

first: Anne

middle: B

last: Young

first: Nancy

last: Wexler

first: Mauro

last: Delorenzi

first: Charles

last: Kooperberg

first: Sarah

last: Augood

first: Richard

middle: L

last: Faull

first: James

last: Olson

first: Ruth

last: Luthi-Carter


title: Gefitinib sensitivity in NSCLC cell lines

status: Public on Aug 31 2006

city: Aurora

first: Christopher

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

summary:
Eleven NSCLC cell lines with widely divergent gefitinib sensitivities were compared using gene expression.  Genes associated with gefitinib response were used to classify additional NSCLC lines with unknown gefitnib sensitivity.
A subset of the test set data was tested for gefitinib sensitivity, and results correlated strongly with the gene expression-based predictions

All eleven training set lines, and seven test set lines had both HGU133A and B chips done, while other test set lines had only HGU133As.
Keywords: cell response comparison

overall_design: Baseline (unstimulated) gene expression was measured in a large panel of NSCLC cell lines

first: Barbara

last: Helfrich

first: Samir

last: Witta

first: Michio

last: Sugita

first: Razvan

last: Lapadat

first: Chan

last: Zeng

first: Anna

last: Barón

first: Wilbur

last: Franklin

first: Fred

middle: R

last: Hirsch

first: John

last: Minna

first: Mark

middle: W

last: Geraci

first: Paul

last: Bunn Jr


title: Expression profiling in adipocytes of obese humans

status: Public on Jan 01 2006

city: Phoenix

first: Yong-Ho

last: Lee

state: AZ

department: Phoenix Epidemiology and Clinical Research Branch

institute: NIDDK, NIH

summary:
Microarray analysis comparing gene expression profiles of adipocytes from non-diabetic lean vs non-diabetic obese Pima Indian subjects to identify differentially expressed adipocyte genes with obesity. RNA samples of isolated abdominal subcutaneous adipocytes from 20 lean (10 Males / 10 Females, aged 31±6 year, Body Mass Index 25±3 kg/m2 ) and 19 obese (9M/10F, 29±5y, 55±8 kg/m2 ) subjects were hybridized individually to Affymetrix  oligonucleotide arrays HG-U95A, B, C, D, and E.
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression
Keywords: other

first: Saraswathy

last: Nair

first: Emma

last: Rousseau

first: David

last: Allison

first: Grier

last: Page

first: P-Antonio

last: Tataranni

first: Clifton

last: Bogardus

first: Paska

last: Permana


title: Molecular subclasses of high-grade glioma: prognosis, disease progression, and neurogenesis

status: Public on Mar 15 2006

city: South San Francisco

first: Thomas

middle: D.

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

summary:
Novel prognostic subclasses of high-grade astrocytoma are identified and discovered to resemble stages in neurogenesis.  One tumor class displaying neuronal lineage markers shows longer survival, while two tumor classes enriched for neural stem cell markers display equally short survival.  Poor prognosis subclasses exhibit either markers of proliferation or of angiogenesis and mesenchyme.  Analysis of gene expression data is described in Phillips et al., Cancer Cell, 2006.
Keywords: Disease state comparison

overall_design: 77 primary high-grade astrocytomas and 23 matched recurrences were profiled to identify changes in gene expression that relate to both survival and disease progression.  Samples include WHO grade III and IV astrocytomas with a wide range of survival times.

first: Heidi

last: Phillips

first: Samir

last: Kharbanda

first: Ruihuan

last: Chen

first: William

last: Forrest

first: Robert

last: Soriano

first: Anjan

last: Misra

first: Janice

last: Nigro

first: Howard

last: Colman

first: Liliana

last: Soroceanu

first: P

middle: M

last: Williams

first: Zora

last: Modrusan

first: Burt

last: Feuerstein

first: Ken

last: Aldape


title: Expression profiling in preadipocytes in obese Pima Indians/humans

status: Public on Jul 28 2005

first: Saraswathy

last: Nair

address: 4212 N. 16th Street

summary:
Microarray analysis comparing gene expression profiles of primary cultured preadipocytes from non-diabetic lean vs non-diabetic obese Pima Indian subjects (a subset of the subjects from the adipocyte genechip project, GSE2508). Primary cultured  abdominal subcutaneous preadipocytes from 14 lean (7 Males / 7 Females) and 14 obese (7M/7F) subjects were hybridized individually to Affymetrix  oligonucleotide arrays HG-U133A and B.
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue
Keywords: other

first: Yong-Ho

last: Lee

first: Emma

last: Rousseau

first: Margaret

last: Cam

first: P. Antonio

last: Tataranni

first: Leslie

middle: J

last: Baier


title: Differential susceptibility to Candida albicans in mice

status: Public on Nov 01 2005

city: Montreal

first: Gundula

last: Min-Oo

state: Quebec

institute: McGill University

summary:
C5-deficiency in the A/J and recombinant congenic strain, BcA17, is linked to a dysregulated inflammatory response to Candida albicans infection and high morbidity compared to C5-sufficient C57Bl/6J (B6) mice. The recombinant congenic BcA70 strain thus provides an ideal model to study the effect of C5-deficiency on a B6 genetic background. We have used the A/J and BcA70 strains to carry out a detailed analysis of the pathophysiological effects of the uncontrolled inflammatory activity as a result of Candida infection.  We present several lines of evidence to indicate that the heart of C5-deficient mice is severely affected by infection, although the kidney is the site of highest fungal replication. Histological sections of Candida-infected cardiac and kidney tissues from A/J mice reveal cellular infiltration in the vicinity of hyphal foci in the heart, leaving more dense fungal colonies in the kidney unaffected. As well as high-level inflammatory activity in the infected heart tissue, gene expression profiles revealed a striking lack of cardio-protective stress response linked to C5-deficiency.  An inability of the A/J and BcA17 hearts to make the appropriate adaptive changes resulted in lower levels of both fatty acid and glucose metabolism, leading to cardiac failure.
Keywords: differential response to infection; genetic variation

overall_design: 4 biological replicates were used for each strain for both uninfected and infected samples and BcA70 was hybridized against control C57Bl/6 on chip. Dye swaps were included and normalization was performed using dye swap correction and intensity dependent normalization on GeneSpring.

first: Alaka

last: Mullick

first: Zully

last: Leon

first: Joanne

last: Berghout

first: Rita

last: Lo

first: Eugene

last: Daniels

first: Philippe

last: Gros


title: The in vivo cellular response to adenovirus and its regulation through MyD88

status: Public on Apr 04 2006

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

summary:
While recent studies of immunity have uncovered many aspects of the innate immune system, there has been precious little investigation of the cellular response to viruses in vivo.  To this end, we exploited high titer adenoviral (Ad) vectors to investigate the cellular response to non-enveloped viral infection in vivo.  Our results indicate a potent cellular transcriptome response early after infection, with global assessments revealing significant dysregulation in ~15% of measured transcripts derived from Ad infected tissue.  Transcriptome analysis revealed a complex interplay between the innate and adaptive responses, with suppression of metabolism and mitochondrial genes akin to those observed when mice are challenged with LPS.  But despite this common response profile, there were many unique aspects of the Ad dependent trancriptome response, including upregulation of several RNA regulatory mechanisms and apoptosis-related pathways, accompanied by suppression of lysosome, endocytic, Wnt, and Calcium signaling pathways.  Investigations into the TLR pathway using MyD88KO mice revealed that Ad induction of the TLR, MAPK, and cytokine receptor genes are significantly dependent on MyD88, as well as five other functional gene modules (mitochondrial, RNA regulation, cell cycle and growth, extracellular, and immune response genes).  Absence of MyD88 also resulted in a greatly diminished Th1 response and acute phase response at later time points, confirming the important role MyD88 plays as an anti-adenoviral immunity amplifier and regulator in vivo.   However, continued activation of immune response genes in Ad infected MyD88KO mice indicates that MyD88 is not the only component of the Ad ‘sensing mechanism’ in vivo.
Keywords: Infectious response, pathogen response

overall_design: Mice were either mock infected with PBS or Ad infected with 1.5x10E11 particles of a 1st generation LacZ Adenoviral vector.  At 6 hours post-infection, mice were sacrificed and liver transcriptomes (whole livers) were evealuated (complete transduction).

first: Anne

last: Kiang

first: Ruth

last: Everett

first: Andrea

last: Amalfitano


title: Normal and glaucomatous astrocytes

status: Public on Mar 09 2005

city: Chicago

first: M Rosario

last: Hernandez

state: IL

address: 330 Chicago Avenue

department: Ophthalmology

institute: Northwestern University

summary:
Astrocytes from optic nerve head from donors with and without glaucoma
Keywords: parallel sample

first: M

last: Hernandes

first: Olga

last: Agapova

first: Ping

last: Yang


title: Malignant pleural mesothelioma

status: Public on Jun 01 2005

first: Gavin

last: Gordon

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

summary:
Malignant pleural mesothelioma (MPM) is a highly lethal, poorly understood neoplasm that is typically associated with asbestos exposure. We performed transcriptional profiling using high-density oligonucleotide microarrays containing approximately 22,000 genes to elucidate potential molecular and pathobiological pathways in MPM using discarded human MPM tumor specimens (n=40), normal lung specimens (n=4), normal pleura specimens (n=5), and MPM and SV40-immortalized mesothelial cell lines (n=5). In global expression analysis using unsupervised clustering techniques, we found two potential subclasses of mesothelioma which correlate loosely with tumor histology. We also identified sets of genes with expression levels that distinguish between multiple tumor subclasses, normal and tumor tissues, and tumors with different morphologies. Microarray gene expression data were confirmed using quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and protein analysis for three novel candidate oncogenes (NME2, CRI1, and PDGFC) and one candidate tumor suppressor (GSN). Finally, we used bioinformatics tools (i.e. software) to create and explore complex physiological pathways that may be relevant in mesothelioma tumorigenesis, pathobiology, or both.

Tissues and cell lines profiled using microarrays. Discarded MPM surgical specimens (n=40), normal pleura specimens (n=5), and normal lung specimens (n=4) were freshly collected (and snap frozen) from patients who underwent surgery at Boston's Brigham and Women's Hospital (BWH) between October 1998 and August 2000. All of these patients underwent extrapleural pneumonectomy with heated intra-pleural cisplatin chemotherapy delivered after the specimens were removed. All normal specimens were obtained from patients who were never diagnosed with MPM. Two human MPM cell lines (MS589 and MS428) were kindly provided by Jonathan A. Fletcher, M.D., Department of Pathology, BWH. The JMN1B MPM cell line19,20 has been described previously. The SV40-immortalized, non-tumorigenic mesothelial cell line (Met-5A)21 and the MPM cell line MSTO-211H22 were purchased from the American Type Culture Collection. Normal tissues were obtained from additional consented patients undergoing treatment for diseases other than MPM. All MPM samples used in these studies contained relatively pure tumor (greater than 50% tumor cells per high power field examined in a section adjacent to the tissue used). The microscopic slides from the patients' resection specimens were reviewed by one of the authors (J.G.), and the diagnosis and histologic subclassification of MPM confirmed in all cases. Linked clinical and pathological data were obtained for all patients who contributed tumor specimens. Specimens and data were rendered anonymous to protect patient confidentiality. Studies utilizing human tissues were approved by and conducted in accordance with the policies of the Institutional Review Board at BWH.


title: Burn20

status: Public on May 07 2004

first: Muralikrishna

last: Vemula

department: Center for Engineering in Medicine/Department of Surgery

institute: Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children

summary:
Type of experiment: Comparison of liver samples between sham (control) and 20% TBSA (total burn surface area) burn rats collected at 1h, 4h, 8h, and 24h.

Experimental factors:  Burn injury and time

Experiment design: All experimental liver samples collected after 1h, 4h, 8h, and 24h after burn injury were compared to a common reference (sham control treated as 0h time point)

Bio source: Sprague-Drawley male rats weighing 150-200 g supplied through Charles river laboratories, MA (www.criver.com)

Bio material manipulations: Rats (n=3 for each scald-burn and sham-burn time point) were individually housed in a temperature-controlled (25oC) and light-controlled room (12h light-dark cycle) and allowed to adjust to their new surroundings for at least 5 days prior to the experiment.  Water and rat chow were provided ad libitum to the animals.  On the day of the treatment, the animals were randomly divided into two groups, burned and sham-burned.  The burn injury consisted of a full-skin-thickness scald burn of the dorsum, calculated to be ~ 20% of the rat’s total body surface area (TBSA), induced by immersing the designated area in boiling water for 10 s [Yamaguchi, 1997 #416].  Rats were resuscitated with an intra-peritoneal injection of sterile saline solution (1.5 mL/Kg body weight/% TBSA) immediately after burn.  At each time point, three animals belonging to each group was sacrificed, the serum collected, and stored at –80oC.

Hybridization extract: Total RNA was isolated from approximately 50 mg of pooled liver tissue using the Nucleospin II RNA isolation kit from Clontech (Palo Alto, CA), as per the manufacturer’s instructions.

Labeling protocol: Labeling was performed as instructed by Affymetrix, Inc (www.affymetrix.com). In brief, 10 μg of total RNA was used for the double-stranded cDNA synthesis using the T7-oligo (dT) promoter primer kit (Affymetrix Inc.) and superscript RT II enzyme (Invitrogen). 1 μg of cDNA was labeled through invitro transcription reaction using T7 DNA polymerase in the presence of biotin labeled ribonucleotides. The cRNA was cleaned up using the Qiagen RNeasy columns following manufactures instructions. The cRNA (20 μg) was fragmented using the fragmentation buffer supplied as part of the Gene Chip Sample Cleanup Module (Affymetrix).

Image analysis and raw data description: The images were analyzed using MAS V.0 software provided by Affymetrix, Inc. The raw data output consists of several metrices: Signal, Detection, Detection p-value, Stat pairs, Stat pairs used. Signal is a measure of the abundance of the transcript. Detection is call that indicates whether the transcript is detected (P, present), undetected (A, absent), or at the limit of detection (M, marginal). Detection p-value is a measure of the significance of the detection call. Stat pairs, is the number of probe pairs for a particular probe set on an array. Stat pairs used, is the number of probe pairs per probe set used in the analysis.

Normalized and summarized data: All chips were scaled to a target intensity of 500 to account for differences between the replicate chips and their hybridization efficiencies using Affymetrix GENECHIP MAS V.0 software.  The entire dataset is available at gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE802. Three filters were serially used to obtain the list of annotated genes that demonstrated differential expression in intensity between sham and burn injured animals.  In the first filter, only genes that were flagged as ‘present’ by the MAS V.0 analysis software in at least one of the time points in all replicate chips were considered for further analysis.  This step eliminated all genes for which the expression data was not reproducible between the replicate chips.  The genes that passed this criterion were subjected to a second filter where ANOVA was performed to test each gene independently for a statistical difference in expression between groups (0, 1, 4, 8 and 24 h). The output of the analysis is the probability (p value) that a difference in expression can be observed by chance i.e., probability of getting a false positive.  While the occurrence of false positives can be controlled by choosing a higher significance level (0.01 or 0.001) it also concomitantly increases the false negatives.  Therefore, in this study we have chosen to work with ANOVA p-value cut-off 0.05.  To reduce the occurrence of the false positives, we have used the false discovery rate (FDR) method (33) which adjusts the ANOVA p-value (cut-off 0.05) while taking the dependencies between the genes into consideration.  The 695 genes that demonstrated a significant ANOVA p-value were then selected and their expression values averaged.  The third filter selected 339 genes that were either up-regulated or down-regulated by at least 2-fold between any one time point (1, 4, 8 or 24h) and the 0h time point (Sham control).  To determine the temporal profiles in the data, gene expression values were hierarchically clustered using the dChip software (www.dChip.org). The expression values for a gene across all samples were standardized by setting the mean to 0 and standard deviation to 1.  The software then builds a hierarchical cluster tree based on centroid-linkage method using Pearson correlation coefficient as the distance metric.  A set of genes were assigned to cluster groups empirically based on visual inspection of their temporal expression patterns.
Keywords = Rat
Keywords = burn
Keywords = microarrays
Keywords = fatty acids
Keywords = cholesterol
Keywords = inflammation
Keywords: time-course

first: Francois

last: Berthiaume

first: Arul

last: Jayaraman

first: Martin

last: Yarmush


title: CD3+ T cells derived from bone marrow or peripheral blood of aplastic anemia patients

status: Public on Dec 26 2005

city: Braunschweig

first: Susanne

last: Pfoertner

address: Mascheroder Weg 1

institute: German Research Centre for Biotechnology (GBF)

summary:
CD3+ T cells derived from bone marrow aspirates and peripheral blood samples of newly diagnosed AA patients and healthy volunteers were  analysed using Affymetrix HG_U133A GeneChips. Additionally, two patients were studied after achieving a partial remission (post-Therapy).
Keywords: disease vs health vs response to therapy

overall_design: Altogether, we analysed 8 different samples. Pool I contained three female and one male patients, 19 to 70 years old, suffering from (severe) aplastic anemia. From these four donors, samples derived from bone marrow aspirates and from peripheral blood, were pooled on total-RNA basis. Pool II consisted of additional two patients, one male (64 years old) and one female (70 years old). From both donors, total-RNA was extracted and pooled from CD3+ T cells derived either from bone marrow or peripheral blood, each prior and post therapy. Healthy control pools included three donors for the peripheral blood sample and two donors for bone marrow derived T cells.


title: Allergy response

status: Public on Nov 13 2004

city: Nashville

first: Zheng

last: Liu

state: TN

institute: Vanderbilt University

summary:
Background  Atopic diseases, resulting from hypersensitivity to a wide variety of allergens, affect 10-20% of the population. Immunotherapy is an effective treatment for atopic diseases, but its mechanisms are not fully understood.
Objective  We studied gene expression profiles in the peripheral blood mononuclear cells and examined whether the individuals with allergic rhinitis have a unique gene expression profile and how the immunotherapy affect the gene expression profiles.
Method  We used cDNA microarray and “Expression Analysis Systemic Explorer” to examine the gene expression profiles in the peripheral blood mononuclear cells of atopic subjects and other groups.
Results  We identified a highly conserved gene expression profile in atopic subjects that permitted their accurate segregation from control or autoimmune subjects.  A major feature of this profile was the under-expression of a variety of genes that encode proteins required for apoptosis and over-expression of genes that encode proteins critical for stress responses and signal transduction.  We also identified 563 genes that can segregate individuals with allergic rhinitis based upon receipt of immunotherapy.
Conclusion  There is a highly conserved gene expression profile in the peripheral blood mononuclear cells of individuals with allergic rhinitis. This profile can be used to identify individuals with allergic rhinitis and to evaluate responses to immunotherapy.  Quantitative endpoints, such as gene expression, may assist clinicians faced with clinical decisions in the diagnosis of patients and the evaluation of response to therapy.  The knowledge of the possible genetic basis for immunotherapy efficacy may also lead to novel therapeutic approaches for atopic diseases.
Keywords: other

first: Thomas

last: Aune


title: Genomic copy number alterations as predictive markers of neoadjuvant chemotherapy response in breast cancer

status: Public on Jan 17 2008

city: Seoul

first: Wonshik

last: Han

address: 28 Yongon-dong, Chongno-gu

department: Dept. of Surgery

country: South Korea

institute: Seoul National University College of Medicine

type: Genome variation profiling by genome tiling array

summary:
Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess different copy number changes between chemotherapy responsive and non-resposive breast cancer tissues.
Keywords: Array CGH

first: Jihyoung

last: Cho

first: Eun-Mi

last: Jeong

first: Song-Ju

first: Dong-Young

last: Noh


title: An expression signature for p53 in breast cancer predicts mutation status, transcriptional effects, and patient survival

status: Public on Oct 21 2005

first: Lance

last: Miller

address: 60 Bioplois Street, #02-01 Genome

department: Microarray and Expression Genomics

institute: Genome Institute of Singapore

summary:
The biological tumor samples (ie, breast tumor specimens) consisted of freshly frozen breast tumors from a population-based cohort of 315 women representing 65% of all breast cancers resected in Uppsala County, Sweden, from January 1, 1987 to December 31, 1989.  Estrogen receptor status was determined by biochemical assay as part of the routine clinical procedure. An experienced pathologist determined the Elston-Ellis grades of the tumors, classifying the tumors into low, medium and high-grade tumors.  The clinico-pathological characteristics accompanying each tumor include p53 status, ER status, tumor grade, lymph node status and patient age.
Keywords: Tumor sample comparisons

overall_design: All tumor specimens were assessed on U133 A and B arrays.

first: L

first: J

last: Smeds

last: George

first: V

last: Vega

last: Vergara

first: A

last: Ploner

first: Y

last: Pawitan

first: P

last: Hall

first: S

last: Klaar

first: E

middle: T

last: Bergh