title: Differential expression profile between MNV-1 infected and mock-infected RAW 264.7 cells.

status: Public on Apr 15 2009

city: Bethesda

first: Karin

last: Bok

state: MD

address: 50 South drive

summary: Noroviruses have been widely recognized for their importance as causative agents of non-bacterial gastroenteritis. Mouse norovirus is the only representative of the norovirus genus, family Caliciviridae, able to grow in cell culture. The aim of this study is to describe the differences in the expression profiles of MNV-1 and mock-infected macrophages (RAW 264.7 cells), in order to better understand the response of the host cell to norovirus infection.

overall_design: This study compares two type of samples (MNV-infected and mock-infected RAW cells) in biological triplicates respectively. The MNV stock used for infection was obtained in the same cell line, and purified with a sucrose cushion in order to account for expression changes caused by virus infection only.

first: Stanislav

last: Sosnovtsev

first: Kim

middle: Y

last: Green


title: Embryonic day 15 and Postnatal day 1 whole mouse brain AGTR2 knockout versus control

status: Public on Feb 28 2009

city: Greenwood

first: traci

last: pawlowski

state: SC

address: 125 Gregor Mendel Circle

department: research

country: USA

institute: Greenwood Genetic Ctr

summary:
The gene expression profiles of control vs AGTR2 knockout mouse whole brains at developmental stage E15 and postnatal day 1 were examined.

Keywords: genetic modification, brain development, AGTR2

overall_design:
Embryonic day 15: six biological control replicates and eight biological AGTR2 knockout replicates, one control and knockout replicate to an array with a dye-swap, except for 2 without a dye-swap

Postnatal day 1: four biological control replicates and four biological AGTR2 knockout replicates, one control and knockout replicate to an array with a dye-swap

first: Traci

middle: L

last: Pawlowski

first: Anand

middle: K

last: Srivastva

first: Thomas

last: Walther


title: Reliability and stability of individual differences in gene expression

city: London

first: Emma

last: Meaburn

address: PO 82, Denmark Hill

department: SGDP

country: United Kingdom

institute: Institute Of Psychiatry

summary:
Studying the causes and correlates of natural variation in gene expression in healthy populations assumes that individual differences in gene expression can be reliably and stably assessed across time. However, this is yet to be established.
We examined 4-hour test-retest reliability and 10 month test-retest stability of individual differences in gene expression in 10 12-year-old children.

overall_design: Blood was collected on four occasions: 10am and 2pm on day one and 10 months later at 10am and 2pm.  Total RNA was hybridised to Affymetrix-U133 plus 2.0 arrays.

first: Cathy

last: Fernandes

first: Leonard

last: Schalkwyk

first: Ian

middle: W

last: Craig

first: Robert

last: Plomin


title: Human endothelial gene expression under estradiol treatment

status: Public on Jun 18 2009

city: Valencia

first: Carlos

last: Hermenegildo

address: Avda. Blasco Ibanez 15

country: Spain

institute: University of Valencia

summary: DNA microarrays were used to investigate global gene expression patterns in cultured human umbilical vein endothelial cells (HUVEC) exposed to 1 nmol/L estradiol for 24 hours, compared to control cells.

overall_design: HUVEC from 9 separate cultures were exposed to control (0.1% ethanol) and 1nmol/L estradiol treatments for 24 h. Total cellular RNA was extracted. Equal amounts of RNA extracted from 3 control cells or 3 estradiol-treated cells obtained from three different cultures were pooled, achieving three biological replicates of the control and three that were treated with estradiol. Therefore, a total number of 6 microarrays were developed.

first: Agua

last: Sobrino


title: Lasp1 gene deletion: Effect on gene expression in the gastric mucosa

status: Public on Feb 13 2009

city: Augusta

first: Han

last: Zhang

state: GA

department: IMMAG

institute: Medical College of Georgia

summary:
Comparative analysis of gene expression in murine gastric fundic mucosa in wild-type and Lasp1-null littermates. The data provide a comprehensive overview of genes expressed in the mouse gastric mucosa and show that the expression of several known and unidentified genes is modified by disruption of the Lasp1 gene.

Keywords: Genotypic comparison

overall_design: Total mRNA isolated from fundic gastric mucosae of three-month old mice, C57Bl/6Ncr strain, was used for this comparison.

first: Catherine

middle: S

last: Chew

first: Xunsheng

last: Chen


title: Expression profile between internodes 1 and 9 from high and low brix plants for sucrose content

status: Public on Feb 12 2009

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

summary:
The expression profile of mature internodes (In9) and immature (In1) internodes of high brix and low brix plants was compared. Internodes were collected from plants with high brix content and from plants with low brix content from Progeny 2. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected 7 and 11 months after planting.

Keywords: Expression profiling by array

overall_design: Total RNA from internode 1 pool and total RNA from internode 9 pool from high brix plants was used for hybridization to dual channel arrays to analyze internode development in high brix plants. We also used total RNA from internode 1 pool and total RNA from internode 9 pool from low brix plants for hybridization to dual channel arrays to analyze internode development in low brix plants. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).


title: Expression profile in internodes 1, 5 and 9 from high and low brix plants for sucrose content

summary:
Summary The expression profile of internodes from high brix plant was compared to internodes from low brix plants. Mature (In9), intermediate (In5) and immature internodes (In1) were collected from two different Progenies and immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol. Progeny 1 was derived from two intra-specific polycrosses, one among Saccharum officinarum genotypes and the other combining Saccharum spontaneum genotypes. For each generation, 500 individuals were sampled for brix content and gene expression. The extreme segregants were selected for further analysis. The F3 hybrid individuals selected for molecular studies were planted in a field in single rows of 5 m using standard sugarcane cultivation practices. Brix readings and tissue samples were collected very early in the season, and in March of the following year, when plants were 10 months old. The soluble solids (brix) content of mature internodes of each sugarcane stalk was measured with a portable refractometer (N1 model, ATAGO, Japan). Individuals or pools of eight individuals had their tissues collected and RNA extracted. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected.

Keywords: Expression profiling by array

overall_design: Total RNA from internodes pool from high brix plants and low brix plants was hybridized to dual channel arrays. Internodes from the same stage of development and from the same progeny were compared. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).


title: Adipose tissue exposed to cold

status: Public on Feb 01 2009

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary:
Cold triggers VEGF dependent but hypoxia independent angiogenesis in adipose tissues and anti-VEGF agents modulate adipose metabolism

The molecular mechanisms of angiogenesis in relation to adipose tissue metabolism remain poorly understood. Here we show that exposure of mice to cold led to conversion of white adipose tissue (WAT) to brown-like adipose tissue, accompanying the switch of an active angiogenic phenotype.  Gene expression profile analysis showed VEGF was upregulated via most likely hypoxia-independent PGC-1 transcriptional activation.  Intriguingly, VEGFR2 blockage abolished the cold-induced angiogenesis, significantly impaired nonshivering thermogenesis capacity, and markedly reduced adipose metabolism.  Unexpectedly, VEGFR1 blockage resulted in opposite effects by increasing adipose vascularity and metabolism.  These findings demonstrate that VEGFR2 and VEGFR1 mediate polarized activities in modulating adipose angiogenesis and metabolism. Taken together, our findings have conceptual implications in applying angiogenesis modulators for the treatment of obesity and metabolic disorders.

Keywords: Time course

overall_design: Mice were exposed to cold and white addipose tissue was collected at different time points

first: Yiahi

last: Cao


title: Sugarcane genes associated with sucrose content relate to drought and cell wall metabolism

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

sample_organism:
Saccharum hybrid cultivar SP80-3280
Saccharum hybrid cultivar (mixed)
Saccharum hybrid cultivar SP90-1638

overall_design: Refer to individual Series


title: Identification of Common Genetic Variants that Account for Transcript Isoform Variation between Human Populations

status: Public on Mar 23 2009

city: Chicago

first: Eileen

last: Dolan

state: IL

address: 5841 S. Maryland

department: Medicine

institute: University of Chicago

summary: In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations.

overall_design: Exon level expression on 176 HapMap cell lines.

first: Wei

first: Shiwei

last: Duan

first: Wasim

last: Bleibel

first: Steven

middle: A

last: Wisel

first: Xiaolin

last: Wu

first: R

last: Huang

first: Lijun

last: He

first: Cheryl

last: Roe

first: Tyson

last: Clark

first: Tina

middle: X

first: Anthony

middle: C

last: Schweitzer

first: John

middle: E

last: Blume

first: M

first: Nancy

middle: J

last: Cox


title: Derriere targets in Xenopus posterior mesoderm

status: Public on Jan 28 2009

city: New York

first: Ali

middle: H

last: Brivanlou

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary:
Left-right axis determination is a fundamental and conserved developmental process, with consequences for human pathology. At the molecular level, this process requires at least two centers of nodal-type TGFbeta signals: the first center, containing nodal/Xn
Microarrays were used to determine differences in gene expression in posterior mesoderm of Xenopus embryos.  We compared controls and Derriere depleted embryos.

Keywords: loss of function

overall_design: Microarrays were used to determine differences in gene expression in posterior mesoderm of Xenopus embryos.  We compared controls and embryos depleted of Derriere protein using MO oligonucleotides.

first: Alin

last: Vonica

first: Alessandro

last: Rosa

first: Brigitte

last: Arduini


title: Microarray analyses of induction failure in T-ALL (COG study 9404)

status: Public on Jan 29 2009

city: Albuquerque

first: Stuart

middle: S.

last: Winter

state: NM

department: Pediatrics

institute: University of New Mexico Health Sciences Center

summary: The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure. Based on the hypothesis that microarrays might identify patients who fail therapy, we used the Affymetrix U133 Plus 2.0 chip and prediction analysis of microarrays (PAM) to profile 50 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Study 9404. We identified a 116-member genomic classifier that could accurately distinguish all 6 induction failure (IF) cases from 44 patients who achieved remission; network analyses suggest a prominent role for genes mediating cellular quiescence. Seven genes were similarly upregulated in both the genomic classifier for IF patients and T-ALL cell lines having acquired resistance to neoplastic agents, identifying potential target genes for further study in drug resistance. We tested whether our classifier could predict IF within 42 patient samples obtained from COG 8704 and, using PAM to define a smaller classifier for the U133A chip, correctly identified the single IF case and patients with persistently circulating blasts. Genetic profiling may identify T-ALL patients who are likely to fail induction and for whom alternate treatment strategies might be beneficial.

overall_design:
This was a case-controlled, retrospectively designed study. We performed expression profiles on 92 patients with T-ALL treated on Children's Oncology Group studies 8704 (42 patients) and 9404 (50 patients).
Expression profiles were obtained from patients with newly diagnosed T-ALL. NR = no response (induction failure); F= failure (relapse); C= Complete Continous Remission.
NOTE: non-sequential numbers were removed for reasons other than relapse, or poor hybridization during chip preparation.

first: Richard

last: Larson


title: Expression Profiling of HL-60 Cells Stimulated by ATRA and DMSO

status: Public on Jan 22 2009

city: Boston

first: Jessica

last: Mar

state: MA

address: 44 Binney St Smith 822

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

summary:
Stimulation of HL60 progenitor cells with either DMSO (1.25% v/v) or atRA (10E-07M) resulted in their differentiation into neutrophils within six days. Gene expression profiles across 12 600 genes were measured for the differentiation processes induced by DMSO and atRA at 0, 2, 4, 8, 12, and 18 h and daily thereafter until day 7 using oligonucleotide DNA microarrays.

Keywords: time course, differentiation, cell fate transitions

overall_design: The experiment consists of 24 Affymetrix hgu95av2 chips. 12 chips were used for the ATRA-stimulated time course, 12 chips were used for the DMSO-stimulated time course.


title: Microarray analyses of induction failure in T-ALL

summary:
The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure. Based on the hypothesis that microarrays might identify patients who fail therapy, we used the Affymetrix U133 Plus 2.0 chip and prediction analysis of microarrays (PAM) to profile 50 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Study 9404. We identified a 116-member genomic classifier that could accurately distinguish all 6 induction failure (IF) cases from 44 patients who achieved remission; network analyses suggest a prominent role for genes mediating cellular quiescence. Seven genes were similarly upregulated in both the genomic classifier for IF patients and T-ALL cell lines having acquired resistance to neoplastic agents, identifying potential target genes for further study in drug resistance. We tested whether our classifier could predict IF within 42 patient samples obtained from COG 8704 and, using PAM to define a smaller classifier for the U133A chip, correctly identified the single IF case and patients with persistently circulating blasts. Genetic profiling may identify T-ALL patients who are likely to fail induction and for whom alternate treatment strategies might be beneficial.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series
This was a case-controlled, retrospectively designed study. We performed expression profiles on 92 patients with T-ALL treated on Children's Oncology Group studies 8704 (42 patients) and 9404 (50 patients).
Expression profiles were obtained from patients with newly diagnosed T-ALL. NR = no response (induction failure); F= failure (relapse); C= Complete Continous Remission.


title: Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes

status: Public on Jan 01 2009

city: Paris

first: Eric

last: Prina

address: 25 rue du Dr Roux

department: Parasitology and Mycology

country: France

institute: Institut Pasteur

summary: In mammals, resident dermal macrophages (MΦs) are subverted by Leishmania (L.) amazonensis amastigotes as host cells permissive for parasite multiplication. These Leishmania are living within a communal parasitophorous vacuole (PV) and are expected to trigger unique MΦ transcriptional signatures. We performed a transcription profiling of mouse MΦs harboring amastigotes to get insights into their reprogramming as host cells for parasite multiplication. BALB/c mouse bone marrow-derived MΦs were either loaded or not with four amastigotes on average. Twenty four hours later, when amastigotes multiply, total RNA from MΦ cultures was prepared, amplified and hybridized onto Affymetrix Mouse430_2 GeneChips®. The outcome recorded a total of 1,248 probe-sets showing significant differential expression. Comparable fold-change values for a handful of genes were obtained between Affymetrix technology and the more sensitive RTqPCR method. Ingenuity Pathway Analysis software® pinpointed the up-regulation of the sterol biosynthesis pathway (P-value = 1.31e-02) involving several genes (1.95 to 4.30 fold-change values), and the modulation of various genes involved in polyamine synthesis and in pro/counter-inflammatory signaling. Our findings suggest that amastigotes exploit the MΦ lipid and polyamine pathways to multiply efficiently, and induce a counter-inflammatory environment to expand their dermis niche.

overall_design:
Mice, MΦs and amastigotes:
Swiss nu/nu and BALB/c mice were used (following National Scientific Ethics Committee guidelines) for L. amazonensis (LV79 strain, MPRO/BR/1972/M1841) amastigote propagation and to prepare bone marrow-derived MΦs, respectively. Amastigotes were added at a multiplicity of 4 amastigotes per MΦ. Parasite-harboring MΦs (>98%; samples I1, I2 and I3) and parasite-free ones (samples UI1, UI2 and UI3) were cultured at 34°C (LV79 permissive temperature) for 24h.

Real-time quantitative PCR:
Total RNA from various biological samples including those used for hybridization experiments were reverse transcribed into cDNA using random hexamers (Roche Diagnostics) and Moloney Murine Leukemia Virus Reverse Transcriptase (Invitrogen Life Technologies). RTqPCR was performed using LightCycler-480 system (Roche) with primers designed with LightCycler Probe Design 1.0 software.Target genes primer sequences, amplicon melting temperatures and amplification efficiencies are available upon request. Gene expression analysis using qBase program allowed determining the normalized relative quantities between parasite-free and parasite-harboring MΦs.

first: José

last: Osorio y Fortéa

first: Emilie

last: de la Llave

first: Béatrice

last: Regnault

first: Jean-Yves

last: Coppée

first: Geneviève

last: Milon

first: Thierry

last: Lang


title: Expression data from ALL patients included in the set used to construct a classification signature (COALL cohort)

status: Public on Jan 26 2009

city: Rotterdam

first: Monique

last: Den Boer

address: POBox 2060

department: Pediatric Oncology

country: Netherlands

institute: Erasmus MC-Sophia Children's Hospital

summary:
Childhood acute lymphoblastic leukemia (ALL) comprises a large group of  genetic subtypes with a favorable prognosis characterized by a TEL-AML1-fusion, hyperdiploidy (>50 chromosomes) or E2A-PBX1 fusion and a smaller group with unfavorable outcome characterized by either a BCR-ABL-fusion, MLL-rearrangement  or T-ALL.
About 25% of precursor B-ALL are currently genetically unclassified and have an intermediate prognosis. The present study used genome-wide strategies to reveal new biological insights and advance the prognostic classification of childhood ALL.
A double-loop cross validation was used to construct a classifier based on gene expression in ALL cells from 190 newly diagnosed cases (COALL cohort, GEO GSE13425) with a prediction accuracy of 90%. T-ALL, TEL-AML1-positive, hyperdiploid and E2A-rearranged cases were identified with 100% sensitivity and ≥94% specificity.
The classifier accuracy was confirmed in an independent cohort of 107 cases (87.9%, DCOG cohort, GEO GSE13351).

Keywords: gene expression study for classification of ALL subtypes

overall_design: 190 bone marrow and peripheral blood samples were collected at diagnosis and frozen. They were later thawed and hybridized to Affymetrix U133A arrays.

last: den Boer


title: Oral dysplasias and oral squamous cell carcinoma

status: Public on Dec 31 2008

city: Vancouver

first: Ivy

last: Tsui

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

type: Genome variation profiling by genome tiling array

summary:
Analysis of DNA from 94 oral lesions by whole genome tiling-path array comparative genomic hybridization.
Keywords: array comparative genomic hybridization

overall_design: Whole genome tiling-path array CGH profiles of 94 formalin-fixed paraffin-embedded oral specimens.

middle: F

first: Lewei

last: Zhang

first: Miriam

middle: P

last: Rosin

first: Wan

last: Lam


title: Frequent PTEN genomic alterations and activated PI3K pathway in basal-like breast cancer

status: Public on Dec 03 2008

last: Dubois

address: 26 rue d'Ulm

department: Département de Transfert

institute: Institut Curie

summary:
Introduction
Basal-like (BLCs) and epidermal growth factor receptor 2 overexpressing (HER2+) carcinomas are the subgroups of breast cancers which have the more aggressive clinical behavior. In contrast to HER2+ carcinomas, no targeted therapy is currently available for the treatment of patients with BLCs. In order to discover potential therapeutic targets, we searched for deregulated signaling pathways in human BLCs.

Methods
In this study, we focused on the oncogenic phosphatidylinositol 3-kinase (PI3K) pathway in twelve BLCs, and compared it to a control series of eleven hormonal receptor negative- and grade III- matched HER2+ carcinomas. The two tumor populations were first characterized by immunohistochemistry and gene expression. The PI3K pathway was then investigated by gene copy-number analysis, gene expression profiling and at a proteomic level using reverse phase protein array technology and tissue microarray. The effects of PI3K inhibition pathway on proliferation and apoptosis was further analyzed in three human basal-like cell lines.

Results
The PI3K pathway was found to be activated in BLCs and up-regulated compared to HER2+ tumors as shown by a significantly increased activation of the downstream targets Akt and mTOR. BLCs expressed significantly lower levels of the tumor suppressor PTEN and PTEN levels correlated negatively in a significant manner with Akt activity within that population. PTEN protein expression correlated significantly with PTEN DNA copy number and more importantly, reduced PTEN DNA copy numbers were observed specifically in BLCs. Similarly to human samples, basal-like cell lines exhibited an activation of PI3K / Akt pathway and low/lack PTEN expression.  Both PI3K and mTOR inhibitors led to basal-like cell growth arrest. However, apoptosis was observed specifically after PI3K inhibition.

overall_design: The PI3K pathway was examined in 2 populations of highly proliferative, grade III, hormone receptor-negative invasive breast carcinomas. Twelve basal-like carcinomas were selected by immunohistochemistry (lack of ER, PR and HER2 staining and expression of basal cytokeratin 5/6 and/or CK14 and/or EGFR). The comparison series was composed of eleven patients with ER-/PR- and HER2+ tumors.

first: Bérengère

last: Marty

first: Virginie

last: Maire

first: Eléonore

last: Gravier

first: Guillem

last: Rigaill

first: Anne

last: Vincent-Salomon

first: Marion

last: Kappler

first: Ingrid

last: Lebigot

first: Fathia

last: Djelti

first: Audrey

last: Tourdès

first: Pierre

last: Gestraud

first: Philippe

last: Hupé

first: Emmanuel

last: Barillot

first: Francisco

last: Cruzalegui

first: Gordon

last: Tucker

first: Marc-Henri

last: Stern

first: Jean-Paul

last: Thiery

first: John

last: Hickman


title: Myd88, Trif, and Rip2-independent macrophage responses to Legionella pneumophila

status: Public on Nov 15 2008

city: New Haven

first: Sunny

last: Shin

state: CT

address: 295 Congress Ave.

department: Section of Microbial Pathogenesis

institute: Yale University School of Medicine

summary:
Microarray analysis of Myd88-/-Trif-/- and Myd88-/-Rip2-/- macrophage responses to WT or dotA mutant L. pneumophila.

Keywords: Expression profiling by microarray

overall_design: Bone marrow-derived macrophages from Myd88-/-Trif-/- and Myd88-/-Rip2-/- mice were infected with WT L. pneumophila (Lp02) or dotA mutant L. pneumophila (Lp03) for 4 hours. The RNA was extracted, processed, and hybridized onto Affymetrix 430 2.0 microarrays

first: Craig

last: Roy


title: Microarray analyses of induction failure in T-ALL (COG study 8704)

first: Stuart

last: Winter

overall_design:
The was a case-controlled, retrospectively designed study. We performed expression profiles on 92 patients with T-ALL treated on Children's Oncology Group studies 8704 (42 patients) and 9404 (50 patients).
Expression profiles were obtained from patients with newly diagnosed T-ALL. NR = no response (induction failure); F= failure (relapse); C= Complete Continous Remission.
Note: Failure (relapse) samples F8,12 and F19 were removed for reasons of failure other than relapse.

first: Richard

last: Larson


title: Gene expression profile of normal and RhoA immortal cells

status: Public on Sep 26 2008

first: Simon

last: Lin

department: Bioinformatics Core

institute: Northwestern University

summary:
Rho family small GTPases serve as molecular switches in the regulation of diverse cellular functions including actin cytoskeleton remodeling, cell migration, gene transcription, and cell proliferation.  Importantly, Rho overexpression is frequently seen in many carcinomas. However, published studies have almost invariably utilized immortal or tumorigenic cell lines to study Rho GTPase functions and there are no studies on the potential of Rho small GTPase to overcome senescence checkpoints and induce preneoplastic transformation of human mammary epithelial cells (hMECs). We found that ectopic expression of wild-type RhoA as well as a constitutively-active RhoA mutant (G14V) in  primary hMEC strains led to their immortalization and preneoplastic transformation. Significantly, RhoA-T37A mutant,  known to be incapable of interacting with many well known Rho-effectors ,was also capable of immortalizing hMECs.Our results demonstrate that RhoA can induce the preneoplastic transformation of hMECs by altering multiple pathways linked cellular transformation and breast cancer.
Through microarray analysis, we want to identify genes and pathways linked to RhoA induced hMECs immortalization.

overall_design: 4 samples,  in triplicate analyses per sample.

first: Vimla

last: Band


title: PocR regulates glycerol reduction, assembly of metabolosomes and vitamin B12 biosynthesis in Lactobacillus reuteri F275

status: Public on Oct 31 2008

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

institute: Vrije Universiteit Amsterdam

summary:
Lactobacillus reuteri has been shown to encode a vitamin B12 biosynthesis pathway that is phylogenetically related to the one present in some representatives of gamma-proteobacteria such as Salmonella and Yersinia. Here we present evidence supporting that the similarities between these otherwise unrelated organisms extend to their regulatory mechanisms.

Keywords: cell type comparison

sample_organism: Limosilactobacillus reuteri subsp. reuteri F275

overall_design: Loop design

first: F

last: Santos

first: D

first: J

last: Hugenholtz

first: B

last: Teusink


title: Small Perturbation Approach Reveals Transcriptomic Steady State

status: Public on Jan 30 2009

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

summary:
The ‘small perturbation’ approach is critical in studying the ‘steady state’ of a biological system. In our experiments, small perturbations were generated by applying a series of repeating intermittent small doses of ultraviolet radiation to a human keratinocyte cell line, HaCaT. The biological response was assessed by monitoring the gene expression profiles using a high reliability and high resolution cDNA microarray system. Following intermittent 10 J/m2 UVB small perturbations, two opposite classes of genes, down-regulated and up-regulated, exhibited an immediate response followed by relaxation between each small perturbation, but were prolonged down- or up-regulated without relaxation while larger doses (233 or 582.5 J/m2) of UVB were applied. A repeated cycle pattern of gene expression following small perturbations is an indication of the existence of steady states. This cycle pattern is suppressed when large perturbations are applied. We believe that this is a universal phenomenon. In our experiments, the functions of up-regulated genes were mainly associated with anti-proliferation, anti-mitogenesis, and apoptosis.  On the other hand, down-regulated genes were mainly related to proliferation, mitogenesis, and anti-apoptosis. In conclusion, this study experimentally proves the concept of steady state at the transcription level and demonstrates the feasibility of using small perturbation approaches for investigating steady states. This study could also set a foundation of computational systems biology, which has implicitly used the concept of steady state.
Keywords: time course

overall_design:
Three UVB exposures are indicated by UV at time points of 0, 8 and 16 hours. T1, T2, T3, T4, T5, and T6 denote the sampling time points. T1, T3 and T5 are allocated 30 minutes after the corresponding UVB irradiation. T2, T4 and T6 are allocated 8 hours after each UVB irradiation. At each sampling time point, two samples (control and UV-irradiated) are collected.

See supplementary file Loop_design.pdf for further explanation.

first: Ching-Lung

last: Huang

first: Min-Lung

last: Tsai

first: Chiu-Ting

first: Cheng-Wei

first: Hua-Kuo

first: Wen-Yi

last: Shu

first: Chi-Shiun

last: Chiang

first: Ian

last: Hsu


title: Gene expression analysis in primary human renal tumors, categorized by VHL genotype and HIF-alpha expression

status: Public on Dec 27 2008

city: Philadelphia

first: Bradley

last: Wubbenhorst

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvannia

summary:
Human renal cell carcinomas (RCC) have differential expression of HIF-1alpha and HIF-2alpha, depending on VHL genotype and other events.
Here, we have divided a series of RCC samples for HIF-alpha expression and VHL genotype, in order to define differentially expressed genes

Keywords: Patient Sample Study

overall_design: A total of 57 frozen RCC samples were stained for HIF-1alpha and HIF-2alpha, and genotyped for VHL. 5 VHL WT/HIF-negative, 8 VHL-deficient/HIF-1alpha+/HIF-2alpha+ and 8 VHL-deficient/HIF-2alpha+ tumors were selected for microarray

first: John

middle: D

last: Gordan

first: Priti

last: Lal

first: Richard

last: Letrero

first: Krishna

middle: N

last: Parekh

first: C

last: Oquendo

first: Roger

last: Greenberg

first: Keith

middle: T

last: Flaherty

first: W

last: Rathmell

first: M

last: Simon

first: Katherine

last: Nathanson


status: Public on Oct 29 2008

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary:
We identify genes presenting a specific expression profile in midgut carcinoid cells, primary carcinoids tumors and liver metastasis were gene profiled.
Gene expression profiling of classical midgut carcinoid primary tumors and liver metastasis reveal potential novel therapeutic targets and molecular signatures.
Keywords: disease state comparison

overall_design: Normal and tumoral (carcinoid) cells

first: Justyna

last: Leja

first: Ahmed

last: Essaghir

first: Kjell

last: Ö–berg

first: Thomas

last: Tötterman

first: George

last: Vasmatzis

first: Magnus

last: Essand

first: Valeria

last: Giandomenico


title: Basal and IL-4 response in DAP12 (TYROBP) KO mice

status: Public on Oct 10 2008

city: Munchen

first: Laura

last: Helming

address: Trogerstr. 30

country: Germany

institute: Institut für medizinische Mikrobiologie, Immunologie und Hygiene

summary:
DAP12 is a transmembrane protein, expressed as a disulfide-bonded homodimer and bears an immunoreceptor tyrosine-based activation motif (ITAM). DAP12 is broadly expressed in hematopoietic cells and associates with a variety of cell surface receptors in lymphoid and myeloid cells. Macrophages express several DAP12-associated receptors including triggering receptors expressed by myeloid cells (TREM)-1,2 and 3, myeloid DAP12-associating lectin (MDL)-1, CD200R like proteins CD200R3/R4 and CD300C/D/E .

Keywords: Cell type comparison

overall_design: The current experiment was designed to evaluate the effect of DAP12 knockdown on macrophage gene expression, both in basal conditions and in the response to IL-4.

first: Fernando

last: Martinez


title: Gene expression profiles of lymphatic endothelial cells after knockdown of Prox1 and/or NR2F2

status: Public on Sep 20 2008

city: Los Angeles

first: Young-Kwon

last: Hong

state: CA

address: 1450 Biggy St. NRT6501

institute: University of Southern California

summary: Gene expression profiles of primary lymphatic endothelial cells (LECs) isolated from human foreskin were analyzed after siRNA-mediated knockdown of control (firefly luciferase), Prox1, NR2F2 or Prox1/NR2F2 for 48 hours.

overall_design: Passage five human lymphatic endothelial cells (LECs) were cultured on fibronectin (10 μg/ml)-coated plates in a complete media (EBM, 20% FBS supplemented with 10 μg/ml hydrocortisone acetate, 25 ug/ml cAMP and antibiotics). LECs were harvested and electorporated with siRNA duplexes for 48 hours with siRNA duplexes against either firefly luciferase(control), Prox1, NR2F2 or Prox1/NR2F2. Total RNA was purified using Tri-reagent and was subjected to microarray analysis.

first: Sunju

last: Lee


title: PRRSV-infection of porcine alveolar macrophages

status: Public on Sep 01 2008

city: Ames

first: John

middle: D.

last: Neill

state: IA

address: 2300 Dayton Ave.

institute: National Animal Disease Center

summary:
The goal of this study was to produce a deep, global analysis of gene expression changes that occured following infection of normal porcine alveolar macrophages (PAMs) with PRRSV.  The goal was to examine the gene expression changes to help determine the mechanisms that result in reduced function and immunosuppression observed in PRRSV-infected pigs.
Keywords: time course of infection

overall_design: The PAMs were infected in culture at an MOI of 10 with PRRSV strains VR-2332 and incubated at 37C until 6, 12, 16 or 24 hours post infection.  Total cellular RNA was collected from each at the appropriate time.  SAGE libraries were prepared from each infected time point as well as from noninfected PAMs.  The SAGE libraries were sequenced to at least 95,000 tags each.

last: Miller

first: Gregory

last: Harhay


title: Genome-Wide Microarray Analysis Reveals Massive Changes in Gene Expression During Conjugation in Tetrahymena thermophila

status: Public on Oct 01 2008

city: Rochester

first: Martin

last: Gorovsky

address: Hutchison Hall 432

department: Department of Biology

institute: University of Rochester

summary:
A genome wide microarray platform containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila is described, validated and used to study gene expression in growing, starved and conjugating cells. Of the ~27,400 predicted open reading frames in Tetrahymena, transcripts homologous to 5876 are not detectable in one or more of these life cycle stages, indicating that this organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels 5X background and 95 genes are expressed at 250X background in all stages. Transcripts homologous to 94 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, and 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1073 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the previously described developmental stages of meiosis, nuclear differentiation and DNA elimination. Genes encoding proteins known to be complexed show similar expression patterns, indicating that co-ordinate expression with putative genes of known function should identify new genes with related functions.
Keywords: growth (three cell densities); Starvation (seven time points); Conjugation (ten time points)

overall_design:
For growth, CU428 cells at low, medium and high cell densities (~100Kcells/ml, ~350Kcells/ml and ~1000Kcells/ml; referred to as L-l, L-m and L-h) were collected.
For starvation, CU428 cells were starved at 2x105 cells/ml in 10 mM Tris (pH 7.5) for 3, 6, 9, 12, 15 and 24 hours （referred to as S-0, S-3, S-6, S-9, S-12, S-15 and S-24.
For conjugation, B2086 and CU428 cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 2x105 cells/ml, mixed, and samples were collected at 2, 4, 6, 8, 10, 12, 14, 16, 18 hours after the mixture （referred to as C-0, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16 and C-18).
For each growing and starved Tetrahymena sample, hybridizations were performed on three independent microarrays (e.g. L1, L2 and L3; S1, S2 and S3). For analysis of conjugation, hybridizations were performed on two independent microarrays (e.g. C1 and C2).
Each individual microarray represents a separate experiment; total RNA was isolated from independent cell cultures then independently labeled and hybridized.

first: Wei

last: Miao

first: Jie

last: Xiong

first: Josephine

last: Bowen


title: Wnt and FGF signals interact to coordinate growth with cell fate specification during limb development

status: Public on Aug 15 2008

first: Derk

last: ten Berge

address: Wytemaweg 80

department: Cell Biology

institute: ErasmusMC

summary:
A fundamental question in biology is how an undifferentiated field of cells acquires spatial pattern and undergoes coordinated differentiation. The development of the vertebrate limb is an important paradigm for understanding these processes. The skeletal and connective tissues of the developing limb all derive from a population of multipotent progenitor cells located in its distal tip. During limb outgrowth, these progenitors segregate into a chondrogenic lineage, located in the center of the limb bud, and soft connective tissue lineages located in its periphery. We report that the interplay of two families of signaling proteins, fibroblast growth factors (FGFs) and Wnts, coordinate the growth of the multipotent progenitor cells with their simultaneous segregation into these lineages. FGF and Wnt signals act together to synergistically promote proliferation while maintaining the cells in an undifferentiated, multipotent state, but act separately to determine cell lineage specification. Withdrawal of both signals results in cell cycle withdrawal and chondrogenic differentiation. Continued exposure to Wnt however, maintains proliferation and re-specifies the cells towards the soft connective tissue lineages. We have identified target genes that are synergistically regulated by Wnts and Fgfs, and show how these factors actively suppress differentiation and promote growth. Finally, we show how the spatial restriction of Wnt and FGF signals to the limb ectoderm and to a specialized region of it, the apical ectodermal ridge, controls the distribution of cell behaviors within the growing limb, and guides the proper spatial organization of the differentiating tissues.

Keywords: transcriptional response to growth factor treatment

overall_design: Cells derived from mouse embryonic stage 11.5 limb buds were cultured and treated with purified Wnt3a protein or vehicle controls. The transcriptional response was detected using spotted cDNA microarrays after 2 hrs or 4 hrs of treatment. 4 biological replicates were used per condition.

first: Roel

last: Nusse


title: Expression data of LPS-stimulated macrophages from wild-type and Zc3h12a-/- mice.

status: Public on Feb 19 2009

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

country: Japan

institute: Kyoto University

summary:
Lipopolysaccharide (LPS), a Toll-like receptor (TLR) 4 ligand, induces the expression of various genes including proinflammatory cytokines, and the expression is modified by the presence of Zc3h12a.
We used microarrays to examine influence of Zc3h12a deficiency in LPS-inducible gene expression.

Keywords: Time course after LPS (100 ng/ml) stimulation

overall_design: Peritoneal macrophages from wild-type and Zc3h12a-/- mice were stimulated with LPS for 0, 1, 2 and 4 hours, followed by RNA extraction. Then hybridization on affymetrix microarrays was performed.

first: Kazufumi

last: Matsushita


title: Identification of genomic regions regulated by the Xrn1 and Upf1 proteins

status: Public on Aug 21 2008

first: Guillaume

middle: Francois

last: Chanfreau

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

type: Expression profiling by genome tiling array

summary:
Comparison of WT, xrn1 delta and upf1 delta strains were used in a tiling array to yield genomic regions regulated by these proteins
The supplementary CHP files record either the signal in log2 space or the p-values in linear space, per TAS output.  The CHP files are further divided between UPF1 delta vs. WT and XRN1 delta vs. WT.

overall_design: Four biological replicates of WT, upf1 delta, and xrn1 delta from the BY4741 background were grown independently and analyzied by Affymetrix yeast tiling microarray analysis.

first: Shakir

last: Sayani

first: Michael

last: Janis

first: Chrissie

first: Isabelle

last: Toesca


title: Expression Data from Sod2-/- and Sod2+/+ Mouse Erythroblasts.

status: Public on Aug 06 2008

city: La Jolla

first: Florent

middle: M.

last: MARTIN

address: 10550 North Torrey Pines Road, MEM-151

department: Department of Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
The mitochondrial superoxide dismutase (SOD2) is a major antioxidant protein which detoxifies superoxide anion radicals generated by mitochondrial respiration (Weisiger and Fridovich, J. Biol. Chem. 1973).  We designed a model of oxidative stress-induced anemia caused by SOD2-deficiency (Friedman et al. J. Exp. Med. 2001).  Our previous work showed that mice reconstituted with SOD2-deficient hematopoietic stem cells develop an anemia with striking similarity to human sideroblastic anemia (SA) (Friedman et al. Blood 2004; Martin et al. Exp Hematol 2005).  Our overall goal was to define early events in the pathogenesis of SOD2-deficiency SA and, in particular, to identify genes involved in the response of erythroid progenitors to oxidative stress.  We compared gene expression of sorted TER-119+ CD71+ erythroblasts from SOD2-/- ('KO') versus Sod2+/+ ('WT') hematopoietic stem cell recipients using cDNA microarrays.
Samples used in this study were re-hybridized with GLYCOv2 oligonucleotide arrays.  GLYCOv2 oligonucleotide arrays are custom Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA) designed for the Functional Glycomics Gateway, collaboration between the Consortium for Functional Glycomics (CFG, http://www.functionalglycomics.org/) and Nature Publishing Group.  A complete description of the array can be found at http://www.functionalglycomics.org/static/consortium/resources/resourcecoree.shtml .  Hybridization results and quality control details can be found at https://www.functionalglycomics.org/glycomics/publicdata/microarray.jsp , by clicking on the ‘Raw Data’ icon link for microarray experiment ‘Jeff Friedman 1: Sod2 KO anemic mice’. Briefly but importantly, one Sod2-/- sample, which was prepared separately, and whose GAPDH 3'/5' ratio was off range, was legitimately removed from the analysis of the GLYCOv2 and 430 2.0 arrays.
Keywords: Genotype comparison, genetic modification

overall_design: We sorted Sod2-/- and Sod2+/+ size-matched mouse erythroblasts based on the expression of two developmental surface markers, CD71 and TER-119.  Total RNA from 4 biological replicates per genotype were extracted and hybridized on 8 Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA).  After quality controls (see scan protocol), analysis was performed with GeneSifter (VizX Labs, Seattle, WA) using 4 Sod2+/+ (control samples, WT) and 3 Sod2-/- (KO) replicates.

middle: M

last: Martin

first: Timothy

last: Gilmartin

first: Jeffrey

last: Friedman


title: Rat right heart pulmonary embolism microarray

status: Public on Jul 01 2008

city: Charlotte

first: Nina

last: Sanapareddy

state: NC

address: 1542 Garden Terrace

institute: Carolinas Healthcare system

summary:
Time and dose related expression profiles of rat right heart tissue in microsphere bead model for Pulmonary embolism
Keywords: Time course and dose response in experimental PE

overall_design: Rat right tissues of the Vehicle(no beads- control), low dose and high dose from rat bead model for Pulmonary Embolism were collected after 2, 6 and 18 hour time points. The extracted RNA was hybridized to Affymetrix Rat 230-2.0 microarrays to look for the dose and/or time related transcriptional changes associated with experimental Pulmonary Embolism.

first: John

last: Watts

last: Gellar

last: Kline

last: Zagorski


title: Gene expression changes with inducible expression of activated ras and ras effector domain mutants

status: Public on Aug 01 2008

city: Bethesda

first: Kathleen

last: Kelly

address: 37 Convent Drive

department: Cancer and Cell Biology Branch

institute: National Institutes of Health

summary:
The goals of this study were to identify gene transcription changes in cells expressing activated H-RasV12 or activated versions of the ras effector domain mutants RasV12G37, RasV12S35, and RasV12C40 for the purpose of identifying common or unique transcription alterations in cells transformed by different ras signal transduction pathways.
Keywords: genetic modification design

overall_design: HME16C mammary epithelial cells infected with pLRT control vector, or H-RasV12-, V12G37-, V12S35-, or V12C40-expressing vectors were each treated with 250ng/mL doxycycline and total RNA prepared at two separate times to give two biological replicates. Then dye swap experiments were performed with each biological replicate.


title: response to LPS of WT and IRAK4 kinase dead mouse bone marrow macrophages

status: Public on Jun 25 2008

city: Basel

first: Anton

last: Glück

country: Switzerland

institute: Novartis Institutes for BioMedical Research

summary:
IRAK-4 is an essential component of the signal transduction complex downstream of the IL-1- and Toll-like receptors. Though regarded as the first kinase in the signaling cascade, the role of IRAK-4 kinase activity versus its scaffold function is still controversial. In order to investigate the role of IRAK-4 kinase function in vivo, ‘knock-in’ mice were generated by replacing the wild type IRAK-4 gene with a mutant gene encoding kinase deficient IRAK-4 protein (IRAK-4 KD). Analysis of bone marrow macrophages obtained from WT and IRAK-4 KD mice with a number of experimental techniques demonstrated that the IRAK-4 KD cells greatly lack responsiveness to stimulation with the Toll-like receptor 4 (TLR4) agonist LPS. One of the techniques used, microarray analysis, identified IRAK-4 kinase-dependent LPS response genes and revealed that the induction of LPS-responsive mRNAs was largely ablated in IRAK-4 KD cells. In summary, our results suggest that IRAK-4 kinase activity plays a critical role in TLR4-mediated induction of inflammatory responses.
Keywords: genetic modification, strain comparison, cell stimulation, time course, anti-bacterial response, innate immune response, inflammatory response

overall_design: The response of mouse bone marrow macrophages from WT and IRAK4 kinase dead animals to stimulation with LPS at two time points was determined. There were 12 samples in total, 6 from WT and 6 from IRAK4 kinase dead cells; for each strain there were 3 conditions: growth for 4 hours without stimulation (the strain-specific control), growth for 1 hour with stimulation, and growth for 4 hours with stimulation; for each condition there were two biological replicates.

first: Magdalena

last: Koziczak-Holbro

first: Hermann

last: Gram

first: Bernd

last: Kinzel

last: Glueck

first: Nicole

last: Hartmann

first: Martin

last: Letzkus


title: Expression data from human mesenchymal stem cells (six batches)

status: Public on Jun 06 2008

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

institute: National Institute of Health Sciences

summary:
Human mesenchymal stem cells (hMSCs), which are multipotent cells to differentiate into several cell types, are expected to be a useful tool for cellular therapy. In some clinical settings, hMSCs have immuno-suppressive effects for GVHD (Graft-versus-host disease) and are expanded in vitro before application. To find biomarkers that indicate the culture stage of hMSCs, we performed microarray analysis for hMSCs derived from bone marrow, using Affymetrix GeneChip Human Genome U133 Plus 2.0 (54,613 probe sets).
Keywords: mesenchymal stem cells, culture stage

overall_design: We profiled the gene expression in 6 different batches of hMSCs. The cells were cultured and subjected to total RNA extraction. We performed microarray analysis using 6 batches provided by 6 different individuals in early stage (passage #4 or 5), middle stage (#7 or 9) or senescing stage (#22, 24, or 28).

first: Yoji

last: Sato

first: Takayoshi

last: Suzuki

first: Kazuhiro

first: Taku

last: Nagao

first: Teruhide

last: Yamaguchi


title: Rice Gene Network Inferred from Expression Profiling of Plants Overexpressing OsWRKY13

status: Public on Jul 02 2008

city: Wuhan

first: Deyun

last: Qiu

state: Hubei

address: Luoshi Road

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

summary:
Accumulating information indicates that plant disease resistance signaling pathway frequently interact with other pathways regulating developmental processes or abiotic stress responses. However, the molecular mechanisms of these types of crosstalk remain poorly understood in most cases. Here we report that OsWRKY13, an activator of rice resistance to both bacterial and fungal pathogens, functions as a convergent point of the crosstalk between pathogen-induced salicylate-dependent defense pathway and at least five other physiological pathways. Genome-wide analysis of the expression profiling of OsWRKY13-overexpressing lines showed that OsWRKY13 directly or indirectly regulates the expression of more than 500 genes, which are potentially involved in different physiological processes according to the classification of Gene Ontology database. Comparing the expression patterns of genes functioning in known pathways or cellular processes upon pathogen infection and the phenotypes between OsWRKY13-overexpressing and susceptible wild-type plants, we find that OsWRKY13 is also regulator of other physiological processes during pathogen infection. OsWRKY13-involved disease resistance pathway synergistically interacts with glutathione/glutaredoxin system and flavonoid biosynthesis pathway via OsWRKY13 to monitor redox homeostasis and may enhance the biosynthesis of antimicrobial flavonoid phytoalexins. Meanwhile, OsWRKY13-invloved disease resistance pathway antagonistically interacts with SNAC1-mediated abiotic-stress defense pathway, JA signaling pathway, and terpenoid metabolism pathway via OsWRKY13 to suppress salt and cold defense responses as well as may retard rice growth and development.
Keywords: abiotic stress, bacterial blight, microarray, Oryza sativa, signal transduction, WRKY transcription factor

overall_design: To determine the genes directly or indirectly regulated by OsWRKY13 genome-widely, we performed the microarray analysis using the Affymetrix Genechip Rice Genome Array containing total 57381 probe sets. Two independent OsWRKY13-overexpressing rice lines, D11UM 1-1 and D11UM 7-2 (Qiu et al., 2007), and wild-type Mudanjiang 8, which was susceptible to Xoo and M. grisea, were used for the analyses.The experiment was repeated three times.

first: Jun

last: Xiao

first: Weibo

last: Xie

first: Hongbo

last: Liu

first: Xianghua

last: Li

first: Lizhong

last: Xiong

first: Shiping

last: Wang


title: Identification of mesendoderm precursor- and neurectoderm precursor-enriched genes in Zebrafish embryos

status: Public on Jun 17 2008

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

summary:
We have developed a method for rapidly identifying early, regionally-expressed molecules: FACS-Assisted Microdissection of Photolabeled cells (FAM-P). For our first FAM-P project, we injected embryos with purified Kaede protein, a stony coral protein that fluoresces at 514 nm (green) prior to- and 582 nm (red) after photoconversion at 405 nm.  We used the scanning laser of a confocal microscope to photolabel late blastula-stage embryos along 4-6 tiers of marginal cells, comprising the mesoderm and endoderm germ layer precursors.  This procedure left the neurectoderm precursor cells marked by green fluorescence and the mesendoderm precursor cells marked by red fluorescence.  Embryonic cells were dissociated and subjected to FACS, separating red mesendoderm precursors from green neurectoderm precursors.  RNA was extracted and linearly amplified once, then dye-labeled and co-hybridized to a microarray with over 30,000 oligos representing more than 20,000 unique zebrafish genes.  In validation of our strategy, many genes known to have elevated expression in the late blastula margin (e.g., squint, fgf8, lim1 and gata5) and several genes known to be specific to the early neurectoderm (e.g., sox31 and otx2) were independently identified by this approach.  In addition to known genes, our method has identified dozens of previously uncharacterized genes that are enriched in the pre-mesendoderm or pre-neurectoderm.
Keywords: 40% epiboly-stage embryos, injected with purified Kaede protein, differentially photolabeled, disaggregated and FACS sorted

overall_design: 34k expression arrays were generated by printing Oligo nucleotides from three different sets (MWG, Compugen and Operon) onto epoxy slides. Total RNA from Kaede protein-injected and FAM-P treated zebrafish embryos was amplified using an Ambion kit (Cat#1753), labeled with Cy dyes and hybridized overnight to the oligo chip in a MAUI chamber.  The experiment comparing mesendoderm was performed four times (twice with WIK/AB hybrid strain embryos, once with EK strain embryos and once with AB strain embryos) each time including a dye swap, for a total of eight (four forward and four dye-swap) hybridizations.  Three control cRNA probes were also generated from AB-strain embryos, namely: (1) whole 40% epiboly stage embryos, (2) FACS-sorted green cells from dissociated 40% epiboly embryos that were Kaede-injected but NOT photolabeled and (3) FACS-sorted red cells from dissociated 40% epiboly embryos that were Kaede-injected AND photolabeled.  These probes were each generated three times, each time including a dye swap and co-hybridized as follows: (1) whole embryo cRNA vs green cell cRNA (three forward and three dye-swap hybridiizations) and (2) green cell cRNA vs. red cell cRNA (three forward and three dye-swap hybridizations).

first: Jamie

last: Boorech

first: Houtan

last: Noushmehr

first: Martha

last: Kirby

first: Abdel.

middle: G

last: Elkahloun

first: Benjamin

last: Feldman


title: Mapping the Genetic Architecture of Gene Expression in Human Liver

status: Public on May 08 2008

city: Seattle

first: eric

middle: e

last: schadt

state: WA

address: 401 Terry Ave N

department: Genetics

institute: Merck

summary:
To uncover the genetic determinants affecting expression in a metabolically active tissue relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting greater than 40,000 transcripts and genotyped DNA from each of these samples at greater than 1,000,000 SNPs.  The relatively large sample size  of this study and the large number of SNPs genotyped provided the means to assess the relationship between genetic variants and gene expression and it provided this look for the first time in a non-blood derived, metabolically active tissue.  A comprehensive analysis of the liver gene expression traits revealed that thousands of these traits are under the control of well defined genetic loci, with many of the genes having already been implicated in a number of human diseases.

Clincal data was requested, but not provided by submitter.
Keywords: eQTL

overall_design: Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.

first: Eric

last: Schadt

first: Cliona

last: Molony

first: Eugene

last: Chudin

first: Ke

last: Hao

first: Xia

last: Yang

first: Pek

last: Lum

first: Andrew

last: Kasarskis

first: Bin

last: Zhang

first: Susanna

first: Christine

last: Suver

last: Zhu

first: Joshua

last: Millstein

first: Solveig

last: Sieberts

first: John

last: Lamb

first: Debraj

last: Guhathakurta

first: Johnathan

last: Derry

last: Storey

first: Margarete

last: Mehrabian

first: Thomas

middle: A

last: Drake

first: Aldons

last: Lusis

first: Ryan

last: Smith

first: Peter

last: Guengerich

first: Stephen

last: Strom

first: Erin

last: Schuetz

last: Rushmore

first: Roger

last: Ulrich


title: Mapping of transcription factor binding sites in mouse embryonic stem cells

status: Public on Jun 12 2008

city: Singapore

first: Chia-Lin

last: Wei

address: 60 Biopolis Street #02-01

department: Genome Technology & Biology

country: Singapore

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Transcription factors and their specific interactions with targets are crucial in specifying gene expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem cells, we use chromatin immunoprecipitation coupled to ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of thirteen sequence specific transcription factors (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1 and CTCF) and two transcription regulators (p300 and Suz12). These factors are known to play different roles in ES cell biology as components of the LIF and BMP signaling pathways, self-renewal regulators and key reprogramming factors. Our study provides insights into the integration of the signaling pathways to the ES cell-specific transcription circuitries. Intriguingly, we find specific genomic regions extensively targeted by different transcription factors. Collectively, the comprehensive mapping of transcription factor binding sites identifies important features of the transcriptional regulatory networks that define ES cell identity.
Keywords: Transcription factor binding sites in undifferentiated mouse embryonic stem cells

overall_design: ChIP-enriched DNA from pooled ChIP samples were analyzed by Solexa sequencing.

first: Chia-lin


title: p53 independent TAF6delta target genes.

status: Public on Jun 26 2008

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

summary:
To elucidate the impact of TAF6d on cell death and gene expression, here we have employed modified antisense oligonucleotides to enforce expression of endogenous TAF6d. The induction of endogenous TAF6d triggered apoptosis in tumor cell lines, including cells devoid of p53. Microarray experiments revealed that TAF6d activates gene expression independently of cellular p53 status. Our data define TAF6d as a pivotal node in a signaling pathway that acts immediately downstream of p53 to control gene expression programmes and apoptosis.
Keywords: Treatment with splice site switching antisense oligonucleotides, induction of apoptosis

overall_design: Biological triplicates, 4 conditions: isogenic p53+/+ and -/- cells; control oligonucleotide,  TAF6 AS2 oligonucleotide

first: Emmanuelle

last: Wilhelm

first: François-Xavier

last: Pellay

first: Brendan

last: Bell


title: Spatial and Temporal Analysis of Gene Expression During Growth and Fusion of the Mouse Facial Prominences

status: Public on Aug 30 2008

city: Aurora

first: Trevor

last: Williams

state: CO

department: Craniofacial Biology

institute: UCHSC at Fitzsimons

summary:
Growth and patterning of the face relies on several small buds of tissue, the facial prominences, which surround the primitive mouth. Beginning around E10 of mouse development the prominences undergo rapid growth and morphogenesis. By E11.5 the medial nasal prominences are in close apposition in the midline, as are the maxillary and medial nasal prominences on either side of the developing face. Subsequently, by E12.5 the nasal and maxillary prominences fuse to form a continuous shelf at the front of the face - the primary palate. Individual prominences are associated with specific developmental processes, and this is reflected by patterns of differential gene expression that give the prominences their unique identities. Thus, only the mandibular and maxillary prominences give rise to dentition while the frontonasal prominence has a unique role in olfaction, and the mandibular prominence in taste. We used microarrays to detail the differential gene expression program in each of the mandibular, maxillary, and frontonasal prominences during the key developmental timepoints of E10.0 through E12.5.
Keywords: time course

overall_design: Analysis of gene expression during growth and fusion of the facial prominences in the C57BL/6J mouse strain between embryonic (E) day 10.0 and 12.5. At the earliest timepoint, E10, only the mandibular prominence is a distinct entity that can be readily identified and dissected. The frontonasal prominence and the maxillary prominence are very small and not discrete from other components of the head such as the forebrain until E10.5. Analysis of these tissues at earlier timepoints would require laser capture and preamplification steps - techniques that were not used for the later timepoints. Thus samples were isolated from the mandibular prominence at E10.0 and from the mandibular, maxillary and frontonasal prominences of mouse embryos from E10.5 to E12.5, at 0.5 day intervals. In order to obtain sufficient sample for hybridization, each sample represents a pool of between 3 and 48 embryos depending on the timepoint. Specifically, the number of embryos were 40-48 for E10.0 (mandibular prominence only), 24-8 for E10.5, 8-9 for E11.0 and E11.5 and 3-4 for E12.0 and E12.5. Seven replicate samples were taken for each of the later five timepoints in each of the three prominences, with an additional seven samples for the mandibular E10.0 timepoint, for a total of 112 samples.

first: Weiguo

last: Feng

first: Sonia

last: Leach

first: Tzulip

last: Phang

first: Hannah

last: Tipney

first: Larry

last: Hunter

first: Mark

last: Geraci

first: Richard

last: Spritz


title: Molecular profiling of LGL leukemia reveals role of sphingolipid signaling of cytotoxic lymphocytes

status: Public on May 01 2008

city: Washington, DC

first: Norman

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

summary:
We used microarrays to expression profile peripheral blood mononuclear cells (PBMCs) from LGL leukemia patients and control subjects to identify survival pathways that render leukemic LGL resistant to activation induced cell death.
Keywords: granular lymphocyte leukemia, PBMC

overall_design: Leukemic PBMC RNA from 30 patients was extracted for target preparation and hybridization onto Affymetrix microarrays. We also isolated PBMCs and PBMCs subjected to enrichment for CD8+ cells from control patients.  RNA from these cells (naïve or activated with phytohemagglutinin) was extracted for target preparation and hybridization onto Affymetrix microarrays.

first: Thomas

last: Loughran Jr


title: Expression data from MALP-2-stimulated macrophages from wild-type, IRAK-2-/- and IRAK-1-/IRAK-2-/- mice

status: Public on Mar 08 2008

first: Osamu

last: Takeuchi

summary:
IL-1R-associated kinases (IRAKs) participate in Toll-like receptor (TLR) signal transduction. MALP-2 is a TLR2 ligand, and stimulation of macrophages with MALP-2 activates expression of various genes including proinflammatory cytokines.
We used microarrays to examine influence of IRAK-2 or IRAK-1/IRAK-2 deficiency in MALP-2-inducible gene expression.
Keywords: Time course after MALP-2 stimulation

overall_design: Peritoneal macrophages from wild-type, IRAK-2-/- and IRAK-1/IRAK-2 mice were stimulated with MALP-2 for 0, 2, 4, and 8 hours, followed by RNA extraction. Then hybridization on affymetrix microarrays was performed.

first: Tatsukata

last: Kawagoe


title: Array-based comparative genomic hybridisation analysis at 1Mb resolution of 44 pilocytic astrocytomas

status: Public on Apr 28 2008

city: Cambridge

first: David

middle: T W

last: Jones

address: Box 231, Level 3 Lab Block, Addenbrooke's Hospital

department: Pathology

institute: University of Cambridge

summary:
Pilocytic astrocytomas (PAs), WHO Grade I, are one of the most frequently occurring childhood brain tumors. We have used microarray comparative genomic hybridization (aCGH) at 1Mb resolution to study copy number changes in a series of PAs (n=44).
Keywords: Comparative Genomic Hybridization, aCGH

overall_design: Single hybridization per case. 44 pilocytic astrocytomas WHO grade I were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

first: Lu

last: Liu

first: Danita

last: Pearson

first: Karen

last: Plant

first: Koichi

last: Ichimura

first: V

last: Collins


title: Gene expression data throughout the normal lifespan of rhesus macaque corpora lutea during natural menstrual cycles.

status: Public on Feb 08 2008

city: Beaverton

first: Randy

middle: Lloyd

last: Bogan

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: Oregon National Primate Research Center

summary:
The molecular and cellular processes required for development, function, and regression of the primate corpus luteum (CL) are poorly defined. We hypothesized that there are dynamic changes in gene expression occurring during the CL lifespan, which represent proteins and pathways critical to its regulation. Therefore, a genomic approach was utilized to systematically identify differentially expressed genes in the rhesus macaque CL during the luteal phase of natural menstrual cycles. CL were collected between days 3-5 (early stage), 7-8 (mid), 10-12 (mid-late), 14-16 (late), or 18-19 (very-late) after the midcycle LH surge. From the early through very-late stages, 3234 transcripts were differentially expressed, with 879 occurring from the early through late stages that encompass the processes of luteinization, maintenance, and functional regression. To characterize gene changes most relevant to these processes, ontology analysis was performed using the list of 879 differentially expressed transcripts. Four main groups of related genes were identified with relevance to luteal physiology including: 1) immune function; 2) hormone and growth factor signaling; 3) steroidogenesis; and 4) prostaglandin biosynthesis, metabolism, and signaling. A subset of genes representing each of the four major categories was selected for validation of microarray results by quantitative real-time PCR. Results in mRNA levels were similar between the two methodologies for 17 of 18 genes. Additionally, protein levels for 3 genes were determined by Western blot analysis to parallel mRNA levels. This database will facilitate the identification of many novel or previously underappreciated pathways that regulate the structure and function of the primate CL.
Keywords: time course

overall_design: The sole experimental factor is the stage of the luteal phase when the CL was collected. There were five stages: 1) between days 3-5 post LH-surge (early stage), 2) 7-8 (mid stage), 3) 10-12 (mid-late stage), 4) 14-16 (late stage), and 5) 18-19 (very-late stage). The early CL are undergoing luteinization, the mid are fully functional CL that are at their peak progesterone producing capacity, the mid-late stage is a transitionary period where CL are still producing significant quantities of progesterone but are nearing the time when luteolysis initiates in non-conception cycles, the late stage corresponds to CL undergoing functional regression (cessation of progesterone secretion), and the very-late stage (menses) is when the structural remodeling and apoptosis associated with luteolysis is occurring. Measuring mRNA levels in CL collected during these periods provides a comprehensive analysis of the primate transcriptome throughout CL lifespan. There were 20 biological replicates: n = 4 per stage, 5 stages in total. The early CL were used as the baseline reference for gene expression.

middle: L

first: Melinda

last: Murphy

last: Stouffer

first: Jon

last: Hennebold


title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

status: Public on Mar 01 2008

city: Birmingham

first: Grier

last: Page

state: AL

institute: University of Alabama at Birmingham

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

summary:
three replicates of HT29 cells per conditionwere grown under normoxic and hypoxic conditions. RNA and miRNA was extracted from each replicate and run on the GPL570 and GPL5106 arrays respectively.
Low levels of oxygen in tissues, seen in situations such as chronic lung disease, necrotic tumors, and high altitude exposures, initiate a signaling pathway that results in active transcription of genes possessing a hypoxia response element (HRE).  To identify changes induced by hypoxia and determine whether miRNA may have effects on gene expression, we conducted mRNA- and miRNA-array-based analysis on HT29 cells, and developed methods for the comparative analysis of these data sets.  To date, no studies have examined the effects of an environmental perturbation on miRNA levels and their relationship to gene expression.  Comparison of miRNAs with the expression of their predicted targets indicated a lower level of concordance than expected.  We did, however, find preliminary evidence of combinatorial regulation of mRNA expression by miRNA.  The methods described here for comparative analysis of miRNA and mRNA profiling will be useful for better understanding genome wide regulatory responsiveness, and to refine miRNA predictive algorithms under development for that purpose.
Keywords: miRNA, hypoxia, HT29, cystic fibrosis

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two group experiment (noroxia and hypoxia) three replicates per condition


title: MDP- and Pam3CSK4-induced genes in naïve and tolerant macrophages

status: Public on Mar 15 2008

city: Ann Arbor

first: Yun-Gi

last: Kim

state: MI

address: 1500 E. Medical Center Dr. 4111 CCGC

institute: University of Michigan

summary:
Most of the genes were self-tolerized by Pam3CSK4 and MDP but there was no or minimal cross-tolerization.
The transcriptome induced via Nod2 stimulation is greatly expanded in TLR2-tolerant macrophages.
Keywords: self and cross tolerance by MDP or Pam3CSK4

overall_design: Genes induced by Pam3CSK4 or MDP were selected based on a three-fold increase over expression levels in unstimulated  macrophages.  Tolerized genes are defined as genes downregulated more than 2-fold in tolerant macrophages stimulated with  Pam3CSK4 or MDP.

first: Jong-Hwan

last: Park

first: Michael

middle: H

last: Shaw

first: Luigi

last: Franchi

first: Naohiro

last: Inohara

first: Gabriel

last: Núñez


title: The expression patterns of 17b-estradiol responsive genes in wt MCF7, OHT resistant MCF7 and ICI resistant MCF7

status: Public on Sep 14 2007

city: Bloomington

first: Henry

last: Paik

state: IN

department: Medical Sciences

institute: Indiana University

summary:
Compare the expression pattern of 17b-estradiol responsive genes in parent, OHT-resistant and ICI-resistant breast cancer cells.
Keywords: 17b-estradiol responsive genes, OHT resistance, Fulvestrand resistance

overall_design:
Data for 4 replicate experiments performed with biologically independent samples.

KN01M001v0   DMSO (control)   wt MCF7 -> GSM136152
KN01H002v0   DMSO (control)   wt MCF7 -> GSM136148
KN01H003v0   DMSO (control)   wt MCF7 -> GSM136150
KN01H004v0   DMSO (control)   wt MCF7 -> GSM136152

KN01M005v0   17b-estradiol (10nM 4h)   wt MCF7 -> GSM136153
KN01H006v0   17b-estradiol (10nM 4h)   wt MCF7 -> GSM136154
KN01H007v0   17b-estradiol (10nM 4h)   wt MCF7 -> GSM136155
KN01H008v0   17b-estradiol (10nM 4h)   wt MCF7 -> GSM136156

first: Meiyun

last: Fan


title: Evaluation of Genetic Variation Contributing to Differences in Gene Expression between Populations

city: Chicago

first: Eileen

last: Dolan

state: IL

address: 5841 S. Maryland

department: Medicine

institute: University of Chicago

summary:
Gene expression is a complex quantitative trait partially regulated by genetic variation in DNA sequence. Population differences in gene expression could contribute to some of the observed differences in susceptibility to common diseases and responses to drug treatments. We characterize gene expression in the full set of HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry for 9,156 transcript clusters (gene-level) evaluated using the Affymetrix GeneChip® Human Exon 1.0 ST Array. Gene expression was found to differ significantly between these samples for 383 transcript clusters. Biological processes including ribosome biogenesis and antimicrobial humoral response were found to be enriched in these differential genes, suggesting their possible roles in contributing to the population differences at a higher level than mRNA expression and the population differences in response to environmental information. Genome-wide association studies for local or distant genetic variants that correlate with the differentially expressed genes enabled identification of significant associations with one or more single nucleotide polymorphisms (SNPs), consistent with the hypothesis that genetic factors and not simply population identity or other characteristics (age of cell lines, length of culture etc.) contribute to differences in gene expression in these samples. Our results provided a comprehensive view of the genes differentially expressed between populations and the enriched biological processes involved in these genes. We also provided an evaluation of the contribution of genetic variation and non-genetic factors to the population differences in gene expression.
Keywords: exon array

overall_design: Gene expression on 176 HapMap cell lines.

first: Wei

last: Zhang

first: Shiwei

last: Duan

first: Emily

middle: O

last: Kistner

first: Wasim

middle: K

last: Bleibel

first: R

middle: S

last: Huang

first: Tyson

last: Clark

first: Tina

middle: X

last: Chen

first: Anthony

middle: C

last: Schweitzer

first: John

middle: E

last: Blume

first: Nancy

middle: J

last: Cox

first: M


title: Critically ill patients with either gram-positive sepsis or gram-negative sepsis

status: Public on Dec 01 2007

city: Glebe

first: Benjamin

middle: Man Piu

last: Tang

state: NSW

address: 12/29 Cook Street

department: Intensive Care Medicine

country: Australia

institute: Nepean Hospital

summary:
Objective:  It is unclear whether the host response of gram-positive sepsis differs from gram-negative sepsis at a transcriptome level.  Using microarray technology, we compared the gene-expression profiles of gram-positive sepsis and gram-negative sepsis in critically ill patients.

Design:  A prospective cross-sectional study.

Setting:  A 20-bed general intensive care unit of a tertiary referral hospital.

Patients:  Seventy-two patients admitted to the intensive care unit.

Interventions:  Intravenous blood was collected for leukocyte separation and RNA extraction.  Microarray experiements were then performed examing the expression level of 19,232 genes in each sample.

Measurements and Main Results:  There was no difference in the expression profile between gram-positive and gram-negative sepsis.  The finding remained unchanged even when genes with lower expression level were included or after statistical stringency was lowered.  There were, however, ninety-four genes differentially expressed between sepsis and control patients.  These genes included those involved in immune regulation, inflammation and mitochondrial function.  Hierarchical cluster analysis confirmed that the difference in gene expression profile existed between sepsis and control patients, but not between gram-positive and gram-negative patients.

Conclusion:   Gram-positive and gram-negative sepsis share a common host response at a transcriptome level.   These findings support the hypothesis that the septic response is non-specific and is designed to provide a more general response that can be elicited by a wide range of different micro-organisms.
Keywords: disease state analysis, gram-positive sepsis, gram-negative sepsis

overall_design:
The study included seventy-two critically ill patients admitted to the intensive care unit (ICU) of Nepean Hospital, Sydney, Australia.  Of these, fifty-five patients were diagnosed to have sepsis, as confirmed by microbiological culture.  The remaining seventeen patients did not have sepsis and were therefore used as controls.  The study was approved by the hospital ethics committee and informed consent was obtained from all patients or their relatives.

Patient Samples. Whole blood was taken from each patient on admission to ICU.  Neutrophils were separated from whole blood using density-gradient separation with Ficoll-PaqueP P(Amersham).  Subsequent neutrophil RNA extraction was performed using guanidinium thiocyanate (Ambion).

Microarray Experiment. The neutrophil RNA was converted to cDNA, fluorescently labeled and hybridized to its complimentary sequences on the microarray (Invitrogen).   The fluorescent signals on each micrroarray were captured using the GenePix 4000B laser scanner (Axon Instruments).  Expression level of each gene was represented by the intensity of its fluorescent signal.

Data Extraction. All signal intensity values were processed using background-subtraction method.  Prior to analysis, all values were log-transformed and normalized by fitting a print-tip group Lowess curve.   Normalization minimizes bias due to dye chemistry, signal intensity or location of a gene on the array.  It ensures the detection of genes that are truly differentially expressed, instead of those caused by experimental artifacts or variation in the hybridization process.  After normalization, genes that had more than 50% of data missing were removed.   We then selected genes that had at least 80% of the data showing two-fold changes from the gene’s median values.  After filtering, 1617 genes were available for further analysis.


status: Public on Sep 29 2007

city: Taipei

first: Ming-Ta

last: Hsu

address: 155, Li-Nong St., Sec.2, Peitou, Taipei, Taiwan, R.O.C.

institute: National Yang-Ming University

summary:
We have developed a method for mapping unmethylated sites in human genome based on the resistant of TspR1 digested ends to exoIII nuclease degradation.  Digestion with TspR1 and methylation-sensitive restriction endonuclease, HpaII, followed by exoIII and single strand DNA nuclease allows the removal of DNA fragments containing unmethylated HpaII sites.  We then use array CGH to map the sequences depleted by this procedures in human genomes derived from five human tissues, a primary breast tumor and two breast tumor cell lines.  Analysis of methylation patterns of the normal tissue genomes indicates that the hypomethylated sites are enriched in the 5’ end of widely expressed genes including promoter, first exon and first intron.  In contrast, genomes of the MCF-7 and MDA-MB-231 cell lines show extensive hypomethylation in the intragenic and intergenic regions whereas primary tumor exhibits intermediate pattern between normal tissue and cell lines.  A striking characteristic of tumor genomes is the presence of megabase-sized hypomethylated zones.  These hypomethylated zones are associated with large genes, fragile sites, evolutionary breakpoints, chromosomal rearrangement breakpoints, tumor supperessor genes, and with regions containing tissue-specific gene clusters or with gene poor region containing novel tissue-specific genes.  Bisulfite sequencing analysis shows a novel mosaic methylation pattern with alternative methylated and unmethylated zones was found in human histone gene clusters in chromosome 6.  Correlation with microarray analysis show that genes with hypomethylated sequence 2kb up- or down-stream of transcription start site are highly expressed whereas genes with extensive intragenic and 3’ UTR hypomethylation are silenced. The method described herein can be used for large scale screening of changes in methylation pattern in the genome of interest.
Keywords: Genome-Wide Mapping of Hypomethylated Sites in Human Genomes

overall_design:
Protected from Exonuclease III digestion by TspR1 ends.
1~2μg DNA was digested with methylation sensitive restriction enzyme in 10μl of total volume for 2hrs, 1μl(10units) TspR1 was then added and reacted at 65℃ for two hours using hot top PCR machine. 10unit of Exonuclease III enzyme was then added and total volume was brought to 20μl by addition of water and 10X buffer. Reaction was carried out at 30℃ for 1hr. Exonuclease III was heat inactive by 70℃ for 20min. 30units RecJf was added to remove single-strand DNA and the enzyme was inactivated by heating at 65℃ for 20min. DNA was then phenol/chloroform extracted and ethanol precipitate.

Array-CGH protocols.
7 µg of the undigested and digested DNA were labeled with Cy3 or Cy5 respectively according to the manual of Agilent Oligo Microarray Kit. The log2 ratio (log2 Cy3/Cy5) were calculated and compared.

Affymetrix analysis.
Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to the manual of Affymetrix Microarray Kit.


title: A transcriptional repressor and co-repressor induced by the STAT3-regulated anti-inflammatory signaling pathway.

city: Memphis

first: Peter

last: Murray

state: TN

address: 332 Nth Lauderdale

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

summary:
IL-10 regulates anti-inflammatory signaling via the activation of STAT3, which in turn controls the induction of a gene expression program whose products execute inhibitory effects on pro-inflammatory mediator production. Here we show that IL-10 induces the expression of an ETS family transcriptional repressor, ETV3 and a helicase family co-repressor, SBNO2 (Strawberry notch homolog 2) in mouse and human macrophages. IL-10-mediated induction of ETV3 and SBNO2 expression was dependent upon both STAT3, and co-stimulus through the TLR pathway. We also observed that ETV3 expression was strongly induced by the STAT3 pathway induced by IL-10 but not STAT3 signaling activated by IL-6, which cannot activate the anti-inflammatory signaling pathway. ETV3 and SBNO2 specifically repressed NF-kB-mediated transcription and can physically interact. Collectively our data suggest that ETV3 and SBNO2 are components of the pathways that contribute to the downstream anti-inflammatory effects of IL-10.
We compared expression profiles of macrophages isolated from IL-10 -/- mice. Macrophages were treated with either LPS or LPS plus IL-10. Treatment times were 10, 20 and 30 minutes.
Keywords: time-course, treatment response, gene expression analysis

overall_design: Mouse IL-10 -/- macrophages were isolated and purified and set up in culture medium containing LPS or LPS plus IL-10. A total of 18 samples were analyzed. This set contains three replicates of each treatment condition where treatment (LPS versus LPS plus IL-10) and time (10min, 20min and 30min) were varied.


title: Genomic copy number alterations as predictive markers 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

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

overall_design: Refer to individual Series


title: High gene expression of inflammatory markers and IL-17A in Atlantic salmon vaccinated with oil-adjuvanted vaccines

status: Public on Aug 21 2007

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

summary:
	Two decades after the introduction of oil-based vaccines in the control of bacterial and viral diseases in farmed salmonids, the mechanisms of induced side effects manifested as intra-abdominal granulomas remain unresolved. Side effects have been associated with generation of auto-antibodies and autoimmunity but underlying profile of the inflammatory and immune response has not been characterized. This study was undertaken with the aim to elucidate the inflammatory and immune mechanisms of granuloma formation at gene expression level associated with high and low side effect (granuloma) indices.
	Groups of Atlantic salmon parr were injected intraperitoneally with oil-adjuvanted vaccines containing either high or low concentrations of Aeromonas salmonicida or Moritella viscose antigens in order to induce polarized (severe and mild) granulomatous reactions. The established granulomatous reactions were confirmed by gross and histological methods at 3 months post vaccination when responses were known to have matured. The corresponding gene expression patterns in the head kidneys were profiled using salmonid cDNA microarrays followed by validation by real-time quantitative PCR (qPCR). qPCR was also used to examine the expression of additional genes known to be important in the adaptive immune response. Granulomatous lesions were observed in all vaccinated fish. Presence of severe granulomas were associated with a profile of up-regulation of innate immunity-related genes such as complement factors C1q and C6, mannose binding protein, lysozyme C,
C-type lectin receptor, CD209, Cathepsin D, CD63, LECT-2, CC chemokine and metallothionein. In addition, IL-17A (Th17) was significantly up-regulated (p=0.009) in the group with severe granulomas as were arginase and IgM. None of the genes directly reflective of Th1 T cell lineage (IFN-γ, CD4) or Th2 (GATA-3) differentiation were differentially expressed.
	Granulomatous reactions following vaccination with oil-based vaccines in Atlantic salmon has the profile of strong expression of genes related to innate immune responses. The expression of IL-17A suggests an involvement of Th17 T cell lineage and is in conformity with strong infiltration of neutrophils and macrophages into inflamed areas. Arginase upregulation shows that macrophages in these reactions are alternatively activated, indicating a Th2-bias. To what extent the IL-17A profile reflects an autoimmune vaccine-based reaction remains elusive but would be in conformity with previous observations of autoimmune reactions in salmon vaccinated with oil-based vaccines.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: RNA from 12 head kidney samples (12 fish) per group were pooled into groups of 4. The RNA was amplified prior to hybridization to arrays. Three biological and 2 technical replicates (dye-swapped) were utilized in different combinations to hybridize to 18 arrays using RNA from fish with the least injection-site inflammatory reactions (FO-1) as the reference group. The assignment of microarrays to treatment groups for hybridization was randomised by using a random number generator. To minimize technical variability, target synthesis was done in batches of 6 where all treatment groups were equally represented.

first: Stephen

last: Mutoloki

first: Glenn

last: Cooper

first: Inderjit

last: Marjara

first: O

last: Evensen


title: Comparison of gene expression pattern between Wild-type and Trib1-deficient mice (Gene chip data for JEM 20070183)

status: Public on Aug 17 2007

city: Suita

first: Masahiro

last: Yamamoto

state: Osaka

address: 2-2, Yamada-oka

institute: Osaka University

summary:
The purpose of this experiment was to compare the gene expression pattern between wild-type and Trib1-deficient macrophages in response to LPS.
Keywords: Comparison of gene expression pattern between Wild-type and Trib1-deficient mice

overall_design: Two samples to define "LPS-inducible gene" and 4 samples (2 for wild-type and the rests for Trib1-deficient mice) for comparison.

first: Shizuo

last: Akira


title: Comparison of splenic and small intestine lamina propria macrophages

status: Public on Aug 24 2007

city: La Jolla

first: Tim

last: Denning

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Allergy and Immunology

summary:
The intestinal immune system must elicit robust immunity against harmful pathogens but restrain immune responses directed against commensal microbes and dietary antigens. The mechanisms that maintain this dichotomy are poorly understood.  Here we describe a population of CD11b+F4/80+CD11c– macrophages in the lamina propria (LP) that express several anti-inflammatory molecules including interleukin 10 (IL-10), but little or no pro-inflammatory cytokines, even upon stimulation with Toll-like receptor (TLR) ligands. These macrophages induced, in a manner dependent on IL-10, retinoic acid and exogenous transforming growth factor-β, differentiation of FoxP3+ regulatory T cells. In contrast, LP CD11b+ dendritic cells elicited IL-17 production. This IL-17 production was suppressed by LP macrophages, indicating that a dynamic interplay between these subsets may influence the balance between immune activation and tolerance.
Splenic or small intestine lamina propria CD11b+11c- cells were isolated for RNA extraction and hybridization on Affymetrix microarrays. We sought to determine the unique genetic profile of small intestine lamina propria CD11b+11c- cells.
Keywords: cell type comparison

overall_design: 4 samples analyzed, 2 spleen and 2 intestine

first: Bali

last: Pulendran


title: Micrometastasis primary tumors

status: Public on Aug 13 2007

city: Oslo

first: Therese

last: Sorlie

address: Montebello

country: Norway

institute: The Norwegian Radium Hospital

summary:
Primary tumors from a series of breast cancer patients evaluated for the presence of tumor cells in bone marrow. Samples were taken at primary surgery, RNA isolated from fresh frozen tumors, amplified and hybridized to 42k cDNA arrays.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

overall_design: Computed


title: Hypertensive Study

city: Phildelphia

first: Rishi

last: Khan

state: PA

address: 1020 Locust Street Room 381

institute: Thomas Jefferson University

summary:
Animals. Male Sprague–Dawley rats (Charles River Laboratories, Wilmington, MA) weighing about 250g were used. The study was approved by the Thomas Jefferson University Institutional Animal Care and Use Committee and was conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The animals were housed in Thomas Jefferson University's animal care facilities. Animals were anesthetized with isoflurane dissolved in O2 (5% induction; 1% maintenance) and one femoral artery and vein were cannulated (PE-50 tubing) via a small medial incision for measurement of arterial pressure and infusion of drugs, respectively. The cannulae were run subcutaneously to an exit incision between the scapulae. The leg wound was sutured and topical anesthetic (lidocaine) was applied to both skin incisions. Following surgery, after one hour of stable and normal resting blood pressure and heart rate, intravenous infusion was initiated of approximately 1 mL saline, as a control, or phenylephrine (200 µg/mL; 1 mL/hr), to induce hypertension. We followed standard methods in the use of phenylephrine (PE) to elevate blood pressure. PE does not cross the blood brain barrier and the elevated blood pressure it produces has been shown to cause molecular effects in the NTS principally via increased baroreceptor afferent drive by both pharmacological and sinoaortic denervation studies. We titered the PE dose to maintain intermediate levels of elevated blood pressure 25 mmHg above resting blood pressure.
Keywords: Hypertension, time series

sample_organism:
Rattus norvegicus
unidentified

overall_design: In keeping with practice of previous studies we induced a defined period of hypertension and then measured effects on the NTS at time points following that standard period of blood pressure disturbance. The previous studies show that blood pressure elevations of 25-30mmHg above baseline induce c-fos expression in the NTS after 30-40 minutes. Based on this result, we estimated that transcriptional regulation in the NTS might be observed after 60 minutes. For this reason we used a standard 60 minute acute hypertension experimental treatment. We took the first samples immediately after the 60 minutes of PE or saline infusion at 15 minute intervals. Our experimental design is for time series data at 60, 75, 90, 105 and 120 minutes (see Figure 1). Gas anaesthesia has previously been reported to induce p-ERK1/2 phosphorylation in some central autonomic structures so the present study reports only differential data that compares to controls that experience the same surgery and fluid (saline) infusion. In order to maximize the statistical power of the experimental design  and capture biological variability we did not pool mRNA across animals, but used one array per animal. Four control and four treated animals were taken for each time point and condition for a total of 40 animals. In our previous studies, we found that four replicates in each condition were necessary to accurately and reproducibly measure small, physiologically relevant fold changes as low as 1.2-fold.

first: Rajanikanth

last: Vadigepalli

first: Mary

last: McDonald

first: Robert

last: Rogers

first: Guang

middle: R

last: Gao

first: James

last: Schwaber


title: Effect of active smoking on bronchial epithelial transcriptome (24 SAGE libraries)

status: Public on Aug 08 2007

city: Vancouver

first: Raj

last: Chari

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

summary:
24 SAGE libraries comprising of 8 current smokers, 12 former smokers and 4 never smokers.
Keywords: SAGE, gene expression, current, former, never, smokers

overall_design: Raw tag counts for each tag in each library are provided