title: Heart transplant biopsies-second test set

status: Public on Mar 15 2006

city: Bethesda

first: Natalia

last: Shulzhenko

address: 9000 Rockville Pike, Building 4, room 111

department: NIAID

summary:
MOLECULAR  PROFILING  IMPROVES DIAGNOSES  OF  REJECTION AND  INFECTION  IN  TRANSPLANTED  ORGANS.
The monitoring of transplanted hearts is currently based on histological evaluation of endomyocardial biopsies, a method that is fairly insensitive and that does not always accurately discriminate between rejection and infection in the heart.  Accurate diagnosis of rejection and infection is absolutely crucial, however, as the respective treatments are completely different.
Using microarrays we analyzed gene expression in 76 cardiac biopsies from 40 heart recipients undergoing rejection, no rejection, or T. cruzi infection.  We found a set of 98 genes whose expression patterns were typical of acute rejection, and 87 genes that discriminated between rejection and T. cruzi infection.  These sets revealed acute rejection episodes up to two weeks earlier, and trypanosome infection up to two months earlier than did histological evaluation.  When applied to raw data from other institutions, the two sets of predictive genes were also able to accurately pinpoint acute rejection of lung and kidney transplants, as well as bacterial infections in kidneys.  In addition to their usefulness as diagnostic tools, the data suggest that there are similarities in the biology of the processes involved in rejection of different grafts and also in the tissue responses to pathogens as diverse as bacteria and protozoa.
Keywords: disease state analysis

overall_design: This series includes 24 samples that were used to validate acute rejection profile descovered previously (GSE2596). This set of hybridizations was done using different from GSE2596 reference RNA (Cy5-labeled). Therefore, Cy3/Cy5 log-ratios could not be compared between these two series. There are 27 arrays in this series because 3 samples were done in duplicates that can be identified by first numbers in the title of the sample.

first: Andrey

last: Morgun

first: Ainhoa

last: Perez-Diez

first: Rosiane

last: Diniz

first: Gerdine

middle: F

last: Sanson

first: Dirceu

middle: R

last: Almeida

first: Polly

last: Matzinger

first: Maria

last: Gerbase-DeLima


title: Ad vectors in C3KO mice

status: Public on Feb 15 2006

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

country: USA

institute: Duke University

summary:
Replication-deficient adenovirus (Ad) type 5 capsids induce potent host innate immune responses.  One system pivotal in host innate immune defense is the complement system.  Intriguingly, excessive or inappropriate complement activation can result in extreme tissue damage and systemic inflammatory responses similar to those noted immediately after high dose systemic Ad vector injections.  To determine if the complement system has a significant role in intensifying Ad-associated acute toxicities, we compared complement deficient (C3-knockout (KO)) mice responses to those of wild type (WT) mice following systemic challenge with Ad vectors.  We noted not only thrombocytopenia and rapid increases in plasma IL-6, IFN-γ, TNF-α, and IL-12 levels previously reported after high dose Ad injections into WT mice, but also induction of cytokines IL-2, IL-4, IL-5 and IL-10, G-CSF and GM-CSF, and chemokines KC (CXCL1) and MIP-1.  This expanded innate response “profile” was significantly blunted in Ad injected C3-KO mice, with a near complete avoidance of thrombocytopenia.  Further validation for complement’s critical role in perturbing these innate responses against Ad were noted after comparison of gene specific RNA transcription levels in C3-KO to WT mice livers.  Finally, these disparities were not attributed to a diminished ability of the Ad vectors to transduce C3-KO mice hepatocytes.  These results suggest that Ad capsid interaction with the mammalian complement system may exacerbate the toxicity of systemic Ad injections, and thus represents a future target for manipulation in efforts to improve the efficacy and safety profile of Ad mediated gene delivery.
Keywords: adenovirus, complement system, time course, innate immune response, toxicity

overall_design: C57/Bl6 (Wild-type or C3 Knock Outs) were injected with a high dose of a 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) or mock nijected with 200ul of PBS.  Virally transduced liver cell transcriptomes were compared to mick injected mice to determine viral gene network induction or repression in vivo.

first: Anne

last: Kiang

first: Andrea

last: Amalfitano


title: Effects on gene expression of a medicinal extract from Agaricus blazei in patients with hepatitis C infection

status: Public on Feb 20 2006

city: Oslo

first: Bjorn

last: Grinde

state: Oslo

address: Geitmyrsveien 75

department: Infectious Disease Control

country: Norway

institute: Norwegian Institute of Public Health

summary:
Extracts from the mushroom Agaricus blazei Murill (AbM) are used extensively as a non-prescription remedy against cancer and infections, including hepatitis. We previously demonstrated a potent immunomodulating effect of a particular preparation on monocytes in vitro, and a protective effect on bacterial infections in mice. Here we report the effect on gene expression in peripheral blood cells from four chronic hepatitis C patients, using global (29 k) oligo-based, single channel microarrays. The viral load was slightly, but not significantly, decreased after one week of AbM treatment. The cytokine genes most strongly induced in vitro were not induced in vivo. The more notable changes in mRNA levels related to genes involved in the G-protein coupled receptor signalling pathway, in cell cycling, and in transcriptional regulation. The results suggest that the β-glucans of the extract, which presumably are responsible for cytokine induction, did not readily enter the blood, while other components, such as substances proposed to have anticancer effects, were active in the blood.
Keywords: experimental treatment, mushroom extract, hepatitis C infection

overall_design: The patients (3 males one female, 48-56 years) had chronic hepatitis C infection that did not repsond to interferon/ribavirin treatment. They were given one week treatment with Agaricus extract (Gold Label from ACE Co, Japan, 20 ml 3x daily). Blod samples were drawn before and after treatment.

first: Geir

last: Hetland

first: Egil

last: Johnson


title: Comparison of gene expression between male and female blastocysts

status: Public on Feb 03 2006

city: Bunkyo-ku

first: Shin

last: Kobayashi

state: Tokyo

address: 1-5-45 yushima

department: Medical Research Institute

country: Japan

institute: Tokyo Mdical & Dental University

summary:
Male embryos are reported to develop faster than female in the preimplantation stage.  Therefore, male and female embryos can be considered phenotypically different as early as the preimplantation stage.  Employing our sexing system of enhanced green fluorescent protein (EGFP) tagging X chromosomes, we compared the global gene expression pattern of male and female embryos at the blastocyst stage using DNA microarray.
Keywords= sex differentiation
Keywords= preimplantation embryo
Keywords= genomic imprinting
Keywords: comparative hybridization

overall_design: samples were collected from three independent preparations and the experiments were triplicated.  Scanned microarray results were processed with Feature Extraction software (ver. 7.5, Agilent). 　The hybridization experiments were duplicated in a reciprocal labeling manner to reduce dye integration bias, and total of six hybridizations were carried out for the entire analysis.　 Combining plural array results and statistical analyses were carried out by Luminator software (Rosetta).

first: Ayako

last: Isotani

first: Nathan

last: Mise

first: Yoshitaka

last: Fujihara

first: Kazuhiro

last: Kaseda

first: Tomoko

last: Nakanishi

first: Masahito

last: Ikawa

first: Kuniya

last: Abe

first: Masaru

last: Okabe


title: MCF10A_MYC_PLUS_CSN5

status: Public on Mar 01 2006

city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2142

department: Dermatology

institute: Stanford University

summary:
Gene expression signatures encompassing dozens to hundreds of genes have been associated with many important parameters of cancer, but mechanisms of their control are largely unknown. Here we present a method based on genetic linkage that can prospectively identify functional regulators driving large-scale transcriptional signatures in cancer. Using this method we show that the wound response signature, a poor-prognosis expression pattern of 512 genes in breast cancer, is induced by coordinate amplifications of MYC and CSN5 (also known as JAB1 or COPS5). This information enabled experimental recapitulation, functional assessment and mechanistic elucidation of the wound signature in breast epithelial cells.
Keywords: cell_type_comparison_design

overall_design: Computed

middle: Y

first: Adam

middle: S

last: Adler


title: Effects of inducible HIV-1 Vpr protein on cellular gene expression

status: Public on Feb 10 2006

first: Naoto

last: Yoshizuka

state: MD

institute: NCI

summary:
Three 293 cell-derivative cell line were constructed using commercially available Invitrogen Flp-In TREx 293 cells.  The cell lines express wild type HIV-1 Vpr and two mutant Vprs, F72A/R73A and R80A.  The mutant Vprs are defective in the Vpr cell cycle arrest phenotype.
The cell lines were characterized for their ability to express Vpr at the RNA and protein levels and functionally for the ability of the inducibly expressed Vprs to arrest cell cycle progression at G2/M.  To study whether certain host cell genes showed alterations in expression following induced expression of Vpr, we conducted a large scale host cell gene expression profiling study using microarray technologies. To determine whether the differential expression of certain genes was associated with Vpr-induced cell cycle arrest, we compared the gene expression pattern of wild type Vpr expressing cells with the pattern of Vpr mutant F72A/R73A- or R80A-Vpr expressing cells.  Doxycycline-induced and uninduced and Flp-In TREx 293/Vpr cells were collected 0, 1, 2, 4, 6, 8, 12, 16 and 24 hours post induction (hpi). Doxycyclineinduced and uninduced Flp-In TREx 293/Blank cells were also collected as a reference for following experiments. Total RNA was isolated using RNAeasy Midi Kit (QIAGEN), according to the manufacturer's protocol. Human long oligonucleotide microarrays were obtained from the National Cancer Institute Microarray Facility, Advanced Technology Center (Gaithersburg, MD). The microarrays (Hs Operon V2) contained 22,434 oligonucleotide (60-70 mer) spots on a glass slide. 25 µg of total RNAs isolated from doxycycline-induced Flp-In TREx 293 stably transfected blank- and FLAG tagged-Vpr cells were reverse transcribed using an oligo (dT) primer and aminoallyl-dNTP (Amersham Pharmacia). Unincorporated dNTPs were removed with QIAquick PCR purification kit (QIAGEN).
Purified cDNA was processed for coupling reaction with Cy 5 or Cy 3-ester dye, respectively.
Keywords: other

first: N


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach

status: Public on Feb 17 2006

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

summary:
Rationale: Despite the deleterious effects associated with elevated carbon dioxide (CO2), or hypercapnia, it has been hypothesized that CO2 can protect the lung from injury. However, the effects of chronic hypercapnia on the neonatal lung are unknown.
Objectives: To determine whether chronic hypercapnia alters alveolar development and to identify genes that could potentially contribute to hypercapnia-mediated lung protection.
Methods: Newborn mouse litters were exposed to 8% CO2, 12% CO2 or room air for 2 weeks. Lungs were excised and analyzed for morphometric alterations. Gene expression changes were assessed by microarray techniques and RT-PCR, and gene products by western blotting.
Results: The alveolar walls of CO2-exposed mice appeared thinner than those of controls. In addition, genes from a variety of functional categories were differentially expressed with hypercapnia, including those involved with cell growth/maintenance, signal transduction, protein metabolism, ion transport, stress response and inflammation. In particular and of major interest, gene expression was increased for surfactant proteins (SP) A and D, epithelial Na+ channel, GATA binding protein 6 and fibroblast growth factor receptor 2. In addition, SP-A and SP-D protein expression was increased with hypercapnia.
Conclusions: Our results lead us to conclude that: 1) There are potentially a number of gene families which may contribute to hypercapnia-mediated lung protection, and 2) up-regulation of SP-A and SP-D may play a role as anti-inflammatory or antioxidant agents.  Based on our genomic results, the effects of CO2 depend on the level to which the lung is exposed.
Keywords: stress response

overall_design:
Total 5 arrays including 2 dye-swaps were performed for the 8% CO2 treated animals.  Five individual animals were analyzed.
Total 4 arrays including 2 dye-swaps were performed for the 12% CO2 treated animals. Four individual animals were analyzed.

first: Guangyu

last: Li

first: Jin

last: Xue

first: Gabriel

middle: G

last: Haddad


title: Gene expression profiling of the four human tissues by two microarray platforms and TaqMan real-time PCR

city: Foster City

first: Yulei

last: Wang

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

type:
Expression profiling by array
Expression profiling by RT-PCR

summary:
This study provides one of the largest “reference” data set of gene expression measurements using TaqMan® Gene Expression Assay based real-time PCR technology.  This data set allowed us to use an orthogonal gene expression technology to evaluate the performance of different microarray platforms.    We conclude that microarrays are indeed invaluable discovery tools with acceptable reliability for genome-wide gene expression screening, though validation of putative changes in gene expression remains advisable.   Our study also characterizes the limitations of microarrays; understanding these limitations will enable researchers to more effectively evaluate microarray results in a more cautious and appropriate manner
Keywords: cross-platform comparison of gene expression measurements

overall_design: In this study, we analyzed the gene expression profiles of three human tissues: brain, lung, liver and one universal human reference sample (UHR) using two representative commercial long-oligonucleotide microarray platforms: (1) Applied Biosystems Human Genome Survey Microarrays (based on single-color detection); (2) Agilent Whole Human Genome Oligo Microarrays (based on two-color detection).  1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan® Gene Expression Assay based real-time PCR validation.  For each platform, four technical replicates were performed on the same total RNA samples according to each manufacturer’s standard protocols.  For Agilent arrays, comparative hybridization was performed using incorporation of Cy5 for brain/lung/liver RNA and Cy3 for UHR RNA (common reference).  Using the TaqMan® Gene Expression Assay based real-time PCR data set as the reference set


title: TGFbeta Induction in Tumors

status: Public on Feb 09 2006

first: Stuart Yuspa

last: Adam Glick

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary:
TGFb1 has both tumor suppressive and pro-oncogenic functions in cancer pathogenesis but the underlying basis of this not well understood. We have developed a transgenic conditional epidermal expression model for TGFb1 in order to examine its immediate effects in benign and malignant chemically induced squamous cancers. The microarray study is an attempt to elucidate those genetic changes contributing to this behavior.
Keywords: compound treatment design

overall_design: The experiments revolve around mouse transgenics. Therefore, the hybridization design does as well. Each array represents a bigenic chemically derived tumor (exogenous TGFb expressing)versus a monogenic tumor (no exogenous TGFb expression). Tumors were separated into Papillomas ad Squamous Cell Carcinomas. In total 14 papillomas and 9 carcinomas were included. 5 reverse fluors and 5 replicates were included.


title: Response of quiescent human fibroblasts to different growth factors and serum

status: Public on Apr 12 2006

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary:
Quiescent human fibroblasts (2091 and Wi-38) were stimulated with different growth factors and serum. Cells were collected at 6 different time points followed by global transcriptional profiling.
Keywords: time course, growth factor response, cell line comparison

overall_design: RNA from cells collected from each time point were compared with universal human reference RNA on microarrays. Time points other than 0 hr were then divided by time point 0, which gives relative expression ratios for each time point to their corresponding time point zero. There are 3 biological repeats for each growth factor treatment, each cell line.

first: Jian

last: Gu

first: Vishwanath


title: Prostate cancer cell line LNCaP treated for 2, 4, 6, 8 h with the synthetic androgen R1881 (1nM)

status: Public on Apr 01 2006

city: Wageningen

first: Peter

last: Hendriksen

address: Akkermaalsbos 2

department: RIKILT

country: Netherlands

institute: Wageningen University & Research

summary:
Time series of the prostate cancer cell line LNCaP, treated for 2, 4, 6 and 8 hours with the synthetic androgen R1881. As control, the cells were cultured for 2, 4, 6 and 8 hours in the presence of the same concentration of solvent (ethanol).
With this short treatment time, we aimed to identify mainly direct targets of the androgen receptor.
LNCaP has a very low growth rate in steroid stripped medium and resumes growth on addition of androgens.
Keywords: Time course

overall_design:
The LNCaP cell line was maintained in RPMI media with 10% fetal calf serum and penicillin/streptomycin. Before R1881 treatment, cells were androgen-deprived by culture for 72 h in medium containing 10% dextran-filtered, charcoal-stripped fetal calf serum with a medium replacement after 36 h. After androgen deprivation, the medium was supplemented with R1881 to a final concentration of 1 nM. R1881 was dissolved in ethanol; the final concentration of ethanol in the media was 0.1%. In the control, ethanol was added to the same final concentration. R1881-treated and untreated cells were collected after 2, 4, 6 and 8 h.

cDNAs from R1881-treated and control cells were compared directly by hybridization to the same microarray. This was done in duplicate with reversed Cy labeling. In total, eight arrays were performed for four time points (one dye swap per time point).

first: Natasja

last: Dits

first: Jan

last: Trapman

first: Guido

last: Jenster


title: ES, EC, NS, TS, Placenta and Neural induction (N2B27) comaprison

status: Public on Jan 23 2006

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary:
Comparison among ES, EC, TS, NS, differentiated neural cells derived from NS and placenta in addition to ES-N2B27 neural induction.
Keywords: cell type comparison design,development or differentiation design,time series design

first: Kazuhiro

last: Aiba

first: Alexei

middle: A

last: Sharov

first: Mark

last: Carter

first: Chiara

last: Foroni

first: Angelo

middle: L

last: Vescovi


title: Whole genome microarray analysis of growth hormone induced genes in bone

status: Public on Feb 01 2006

city: Loma Linda

first: Hongrun

last: Yu

address: 11201 Benton Street (151)

department: Musculoskeletal Disease Center

institute: J.L. Pettis Memorial VA Medical Center

summary:
Growth hormone (GH) is important in the development and maintenance of bone; however the IGF-dependent and -independent molecular pathways involved remain to be established.  We used microarray analysis to identify genes acutely regulated by GH, in the bones of four week old GH-deficient mice at 6 or 24 hours following a single injection of GH (4 mg/kg body wt) or PBS (n = 6/group).  6,160 genes were differentially expressed at P = 0.05 and 17% of these genes were identified at both time points.  Several of the 201 genes that were up or down regulated at > 2 fold at 6 and/or 24 hours (P = 0.01) were expressed sequence tags, transcription factors, or signaling genes. In conclusion, GH caused acute changes in several novel genes, suggesting that many GH-induced signaling pathways and target genes remain to be discovered
Keywords: GH injection induced gene expression, time course

overall_design: We used 4 week old C57BL/6J-Ghrhr<lit> [GHRHR gene disruption, allele name little (lit/lit)] mice for the microarray analysis.  Twelve lit/lit mice were treated with a single injection of GH (4 mg/kg body weight), and 12 lit/lit mice were treated with PBS (controls).  At 6 hours after  injection, 6 mice each from the GH and PBS groups were euthanized by CO2 inhalation for sample preparation. RNA from two animals within each group was pooled together, generating three samples in each group.   The same procedure was applied for the remaining half of the animals at 24 hours after injection. Therefore, there were a total of six replicates in each group (3 replicates at 6 hrs and 3 at 24 hrs)

first: Kristen

middle: E

last: Govoni

first: Seong

middle: K

last: Lee

first: Robert

middle: B

last: Chadwick

first: Yuji

last: Kasukawa

first: David

middle: J

last: Baylink

first: Subburaman

last: Mohan


title: Neural induction (Embrioid bodies-Retinoic acid)

summary:
Neural induction of ES by Retinoic acid
Keywords: development or differentiation design,time series design

overall_design: Neural induction of ES by Retinoic acid


title: Single stranded DNA formation during S phase in the presence of hydroxyurea in S. cerevisiae and S. pombe

status: Public on Jan 30 2006

city: Seattle

first: Bonita

last: Brewer

state: WA

department: Genome Sciences

institute: University of Washington

summary:
We have developed a method to analyze single-stranded DNA (ssDNA) formation on a genomic scale by using microarrays.  Using this technique we have assessed the location and the amount of ssDNA in S. cerevisiae during DNA replication.  We have observed that when replication is impeded by hydroxyurea, ssDNA formation can be detected in both wild type and the checkpoint-deficient rad53 cells.  However, while wild type cells showed ssDNA formation at only a subset of origins, rad53 cells formed ssDNA at virtually all known origins.  Moreover, in rad53 cells the ssDNA regions did not expand over time, presumably due to collapsed replication forks.  We also applied this method to map origins in S. pombe, taking advantage of the conserved replication checkpoint function by Cds1, the homolog of Rad53 in S. pombe.
Keywords: ssDNA, HU, replication, time course

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design:
In order to investigate the dynamics of ssDNA formation on a genomic scale, we harvested cells at discrete times after releasing them from late G1 phase arrest with alpha factor into a synchronous S phase in the presence of 200 mM HU.  Chromosomal DNA isolated from these S phase samples and an alpha factor arrested G1 control sample were differentially labeled with Cy-conjugated deoxyribonucleotides by random priming and synthesis without denaturation of the DNA, followed by co-hybridization to a microarray.  Because the labeling was done without denaturation of the template DNA, single-stranded regions of the genome should preferentially act as templates for dye incorporation.  Comparison of experimental (S phase) and control (G1 phase) samples from the microarray hybridization revealed regions of the genome that became single-stranded in S phase.

We also assessed the total percentage of ssDNA in the samples by blotting native (undenatured) genomic DNA and fully denatured genomic DNA, followed by hybridization with a genomic DNA probe.  The calculated total percentages of ssDNA in the samples were then used to normalize the raw ratio of ssDNA (S/G1) (raw data) to generate the normalized ratio of ssDNA (S/G1) (raw normalized data).  The normalized relative ratio of ssDNA was then smoothed over a 4 kb window (smoothed data) via Fourier transformation.

For origin mapping in S. pombe, we used S. pombe wild type and deltacds1 (cds1 encodes for the homolog of Rad53) cells in a comparative analysis.  DNA isolated from cells that were exposed to HU (“early S phase” sample) and cells that were starved for nitrogen source (G1 phase control sample) were differentially labeled with Cy-conjugated dUTPs without denaturation of the template DNA to enrich for labeling of ssDNA region in the genome.  These DNAs were then co-hybridized to a microarray.  The relative amount of ssDNA was quantitated as the ratio of fluorescent signal from the “early S phase” sample to that from the control sample.  The raw ratio of ssDNA (early S/G1) was then normalized by the total percentage of ssDNA in the samples similarly as for S. cerevisiae data.  The raw normalized ratio was then smoothed over a 12 kb window via Fourier transformation.

first: Wenyi

last: Feng

first: Dave

last: Collingwood

first: Mosur

last: Raghuraman


title: Gene expression profiling of a temperature-sensitive strain of Neospora caninum

city: Beltsville

middle: W

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

summary:
The gene expression profiles of a temperature-sensitive strain, ts-8, was compared agains its wild type counterpart, NC-1.
Keywords: mutant comparision, two class unpaired design

sample_organism:
Rattus norvegicus
Neospora caninum

overall_design: Eight single channel hybridization were performed (ts-8 vs NC-1), four biological replicates each.

first: Wenbin

last: Tuo


title: Cell-specific Interleukin-15 and Interleukin-15 receptor subunit expression and regulation in pneumococcal pneumonia

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary:
IL-15 has critical impact on the homeostasis and activation of NK, NKT, gdT and CD8+T cells, and contributes to antimicrobial defenses particularly at mucosal sites. The respiratory tract also comprises a large mucosal surface and harbors significant amounts of lymphocytes, but the expression pattern of IL-15 in the lung and its role in local immune responses are largely unknown. We therefore analyzed the differential expression of IL-15 and the IL-15 receptor (IL-15R) complex in the lungs of mice, and demonstrated substantial constitutive expression in bronchial and alveolar epithelial cells, alveolar macrophages, and vascular smooth muscle cells, implicating contribution to pulmonary immune cell homeostasis already under normal conditions. The induction of pneumococcal pneumonia but not the infection with Chlamydophila pneumoniae evoked a significant up-regulation of IL-15 on alveolar macrophages and bronchial epithelial cells, with the latter presenting de-novo expression of IL-15 on their basolateral surface and additional up-regulation of IL-15Ra .  Transcriptome analysis and semiquantitative PCR indicated at least partial transcriptional regulation. Finally, the increase of IL-15 was accompanied by enhanced expression of CD69, TNFa, IFNg and Bcl-2 by IL-15-dependent lymphocyte populations suggesting functional impact of IL-15 on the pulmonary immune response in pneumococcal pneumonia.
Keywords: Streptococcus pneumoniae, pneumonia, IL-15

overall_design: Microarray experiments were done as two-color hybridizations. RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies).  In order to compensate dye specific effects, and to ensure statistically relevant data, a color swap was performed.

first: Andreas

last: Hocke

first: Norbert

last: Suttorp

first: Simone

last: Rosseau


title: Gene expression profiles in resistant acute lymphoblastic leukemia

status: Public on Jan 19 2006

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Treatment resistance as indicated by the presence of high levels of minimal residual disease (MRD) after induction therapy and induction consolidation is associated with a poor prognosis in childhood acute lymphoblastic leukemia (ALL). We hypothesized that treatment resistance is an intrinsic feature of ALL cells, which is reflected in the gene expression pattern, and that resistance to chemotherapy can be predicted prior to treatment. To test these hypotheses, gene expression signatures of ALL samples with a high MRD load (MRD-HR) were compared to those of samples without measurable MRD (MRD-SR) during treatment. We identified 54 genes that clearly distinguished resistant from sensitive ALL samples. Genes low expressed in resistant samples were predominantly associated with cell cycle progression and apoptosis, suggesting that impaired cell proliferation and apoptosis are involved in treatment resistance. Prediction analysis using randomly selected samples as a training set and the remaining samples as a test set revealed an accuracy of 84%. We conclude that resistance to chemotherapy seems at least in part to be an intrinsic feature of ALL cells. As treatment response could be predicted with a high accuracy, gene expression profiling could become a clinically relevant tool for treatment stratification in the early course of childhood ALL.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

overall_design: Using regression correlation

first: Gunnar

last: Cario


title: Comparision of Total RNA from WT and RRP6delta S. cerevisiae using ORF + Intergenic Array

status: Public on Jan 15 2006

city: Santa Cruz

first: Carrie

middle: Anne

last: Davis

address: 412 Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

summary:
This data set represents the results of two reverse labeled experiments from wild-type and RRP6delta S. cerevisiae that has been hybed to arrays containing PCR products for ORFs and Intergenic Features
Keywords: genetic modification

overall_design: Dye-swap experiment from RRP6+ and RRP6delta strains (Cy3 and Cy5)

first: Manuel

last: Ares Jr


title: Human prostate cancer xenografts on intact mice or after castration.

first: Peter

last: Hendriksen

summary:
cDNA expression arrays on a panel of human prostate cancer xenografts. The xenografts can divided into three groups: 1) androgen-dependent, 2) androgen-independent with functional expression of the androgen receptor, 3) androgen-independent lacking functional expression of the androgen receptor. Four microarrays were performed per xenograft using tissue samples collected in separate experiments. Two samples were taken from intact male mice, whereas the other two samples were taken 1 to 2 weeks after castration. The panel of xenografts have been described in van Weerden and Romijn, 2000; Prostate 43:263-71.
Keywords: Different growth characteristics, androgen ablation response

sample_organism:
Homo sapiens
Mus musculus

overall_design:
A common reference is used for all hybridizations. This common reference contained two prostate cancer cell lines, Du145 and LNCaP, while the other cell lines originated from breast (MCF7 and ZR75.1), bone (MG63), colon (HT29), endothelium (Ea-hy926), ovary (A2780), skin (SK-MEL-28), B-cell leukemia (Raji), T-cell lymphoblastoma (Jurkat) and fibroblasts (N92-19N and N92-19T).
Xenograft cDNA was always labeled with Cy3; the common reference was always labeled with Cy5.

first: Natasja

last: Dits

first: Wytske

last: van Weerden

first: Jan

last: Trapman

first: Guido

last: Jenster


title: Alternative activation deprives macrophages of a coordinated defense program to Mycobacterium tuberculosis

status: Public on Jan 01 2006

summary:
A potent Th1 immune response is critical to the control of tuberculosis. The impact of an additive Th2 response on the course of disease has so far been insufficiently characterized, despite increased morbidity after coinfection with Mycobacterium tuberculosis and Th2 eliciting helminths and possible involvement of Th2 polarization in reactivation of latent tuberculosis. Here, we describe the gene expression profile of murine bone marrow derived macrophages alternatively activated by IL-4 to infection with M. tuberculosis. Comparison of transcriptional profiles of infected IL-4 and IFN-g activated macrophages revealed delayed and partially diminished responses in alternatively activated macrophages, characterized by reduced exposure to nitrosative stress and increased iron availability, respectively, to intracellular bacteria. Alternative activation of host macrophages correlated with elevated expression of the M. tuberculosis iron storage protein bfrB as well as reduced expression of the mycobactin synthesis genes mbtI and mbtJ. The extracellular matrix remodelling enzyme matrix metalloproteinase-12 (MMP-12) was induced in alternatively activated macrophages in vitro, and MMP-12 expressing macrophages were abundant at late, but not early, stages of tuberculosis in murine lungs. Our findings emphasize that alternative activation deprives macrophages of control mechanisms which limit mycobacterial growth in vivo, thus supporting intracellular persistence of M. tuberculosis.
Keywords: transcriptome, gene regulation, macrophages, IL-4, IFN-gamma, nitric oxide

overall_design: BMM were stimulated with IL-4 or IFN-gamma for validation of classical macrophage activation and compared to alternatively activated BMM infected with M. tuberculosis.

first: Antje

last: Kahnert

last: Seiler

first: Stefan

middle: H

last: Kaufmann


title: Amyotrophic lateral sclerosis: SOD1 mouse model

status: Public on Dec 31 2005

city: Göttingen

first: Bettina

last: Spielbauer

address: Humboldtallee 23

department: Neuro and Sensory Physiology

institute: University of Goettingen

summary:
Identification of familial amyotrophic lateral sclerosis (fALS) related genes.
Material from three hSOD1(G93A) transgenic mice was compared to material from three non-transgenic control mice using an alternating loop design on two-colour cDNA microarrays.
Statistical data management and analysis: postgreSQL relational database (www.postgresql.org), Perl, and R (www.r-project.org); pin-wise lowess-regression based normalisation (Yang et al., 2002 [PMID: 11842121]); mixed ANOVA-model.
Keywords = amyotrophic lateral sclerosis, ALS, SOD1 mouse model
Keywords: other

first: Jobst

last: Landgrebe

first: Bernhard

middle: U

last: Keller


title: The cellular response to 1st and 2nd generation Ad vector infection at different time points in vivo

status: Public on Dec 15 2005

first: Zachary

last: Hartman

institute: Duke University

summary:
Mice were injected intravenously with 1st generation or 2nd generation Ad vectors (each bearing a LacZ transgene) or mock infected (controls) to completely transduce the liver.  At different time points post-injection (6 hours, 3 days, and 3 weeks (21 days)), the liver was harvested and the overall transcriptome response to viral infection was assayed to measure the cellular immune response.
Keywords: Immune Response

overall_design: Roughly 3 mice per group were infected  for each vector for all three time points.  3 mice were mock injected with PBS as controls.  All samples used the same array, same dye match-ups, and same Murine Reference RNA.

first: Zachry

middle: C

first: Anne

last: Kiang

first: Ruth

last: Everett

first: Andrea

last: Amalfitano


title: Defining a developmental path to neural fate by global expression profiling of mouse ESCs and adult NS cells

first: Minoru

last: Ko

summary:
Defining a developmental path to neural fate by global expression profiling of mouse embryonic stem cells and adult neural stem/progenitor cells.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Kazuhiro

last: Aiba

first: Alexei

last: Sharov

first: Mark

last: Carter

first: Chiara

last: Foroni

first: Angelo

last: Vescovi


title: Global analysis of X chromosome dosage compensation

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary:
We have conducted a global analysis of somatic dosage compensation and also asked if germ cell dosage compensate by microarray analysis of gene expression in wild-type tissues. To obviate the confounding effects of scatter and especially the skewed genomic distributions of genes with sex-biased expression in both the soma and germline [there are fewer X chromosome genes with male-biased expression], we used mutations that transform sexual identity.  In the soma we used gain-of-function transformer to turn X;AA flies into somatic females with tumorous germlines.  The gonadectomized somas of these X;AA female flies were compared to similarly prepared XX;AA females.  The X;AA ovarian tumors, which are possibly the result of germline sex transformations,  were compared to the similar XX;AA ovarian tumors generated with loss-of-function alleles of ovarian tumor and Sex-lethal. We used alleles of transformer-2 and doublesex to transform XX;AA flies into somatic males with atrophic germlines.
Keywords: other

first: Vaijayanti

last: Gupta

first: Michael

last: Parisi

first: David

last: Sturgill

first: Rachel

last: Nuttall

last: Doctolero

first: James

middle: D

last: Malley

first: Olga

last: Dudko

first: Scott

last: Eastman


title: Sugar turns benefit of cholesterol into immune evasion in Helicobacter pylori infected C57BL/6 mice

status: Public on Dec 22 2005

first: Hans-Joachim

last: Mollenkopf

summary:
Following the initial demonstration of Helicobacter pylori’s pathogenic potential, evidence has been accumulated that H. pylori is the leading cause of gastric ulcers, carcinoma and lymphoma3. Cholesterol is a physiological constituent of membranes critical for their biophysical properties, but is stigmatised as mediating detrimental effects in obesity and cardiovascular disease. Since H. pylori is auxotrophic for cholesterol, we explored the assimilation of cholesterol by H. pylori upon infection. Here we show that H. pylori follows a cholesterol gradient and extracts the lipid from plasma membranes of epithelial cells for subsequent glycosylation. Cholesterol promotes phagocytosis of H. pylori by antigen-presenting cells such as macrophages and dendritic cells and enhances antigen-specific T cell responses. Consistently, cholesterol-rich diet during bacterial challenge leads to a reduction of the H. pylori burden in the stomach. Intrinsic a-glycosylation of cholesterol abrogates phagocytosis of H. pylori and subsequent T cell activation. Hence, we propose a novel mechanism regulating host-pathogen interaction which describes glycosylation of a lipid tipping the scales towards immune evasion or response.
Keywords: disease state analysis

overall_design: color-swap dye-reversal hybridizations

first: Christian

last: Wunder

first: Thomas

middle: F

last: Meyer

first: Florian

last: Winau


title: Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

status: Public on Dec 20 2005

city: St Lucia

first: Darrin

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

summary:
Expression profiling of multiple mouse tissues against 57931 RIKEN cDNAs
Keywords: dual color nucleotide, tissue comparison

overall_design: Comparison of of whole mouse tissues/organs against a common reference.

first: Hidemasa

last: Bono

first: Ken

last: Yagi

first: Takeya

last: Kasukawa

first: Itoshi

first: Naoko

last: Tominaga

first: Rika

last: Miki

first: Yosuke

last: Mizuno

first: Yasuhiro

last: Tomaru

first: Hitoshi

last: Goto

first: Hiroyuki

last: Nitanda

first: Daisuke

last: Shimizu

first: Hirochika

last: Makino

first: Tomoyuki

last: Morita

first: Junshin

last: Fujiyama

first: Takehito

last: Sakai

first: Takashi

last: Shimoji

first: DavidA

last: Hume

first: Yoshihide

last: Hayashizaki

first: Yasushi

last: Okazaki

first: S

middle: M

last: Grimmond


title: Gene expression profiling in colonic adenoma and carcinoma in situ

city: Seoul

first: Inchul

last: Lee

address: 388-1 Poongnap-Dong, Songpa-Gu

department: Pathology

country: South Korea

institute: University of Ulsan College of Medicine

summary:
The majority of colon carcinomas are known to develop in tubular adenomas through multi-stage carcinogenesis.  Recently, we have reported a simple and reproducible method for the expression profiling using microdissected cells from formalin-fixed tissue samples (Lee et al, World J Gastroenterol, 11:1937-1945, 2005).  Using the method, we analyzed the expression profiling in colon tubular adenoma/carcinoma sequence.  Epithelial cells of carcinoma, tubular adenoma, and normal colon mucosa were microdissected from colon tubular adenomas containing focal adenocarcinomas.
Keywords: disease (colon cancer) state analysis

overall_design:
Microarray (GenePlorer TwinChip Human-8K)  hybridizations were duplicated for adenomas, and carcinoma.

normal  vs adenoma :4 array  repeated
normal vs carcinoma : 4 array  repeated

first: Seunghyun

last: Bang


title: RNA polymerase II

status: Public on Dec 01 2005

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

summary:
Determine if increase in transcript abundance was the result of de novo transcription
Keywords: Time-course

overall_design: Three strains, RNA polymerase II mutant, Partental, and Wild type S288c yeast cells in stationary-phase cultures were exposed to oxidative stress with samples harvested at 2 and 30 minutes.  All experimental samples are over an common reference.  There are two replicates of T0 for each strain.


title: Oxidative Stress 1-min interval

summary:
Determine if yeast cells in stationary-phase cultures respond to oxidative stress
Keywords: Time-course

overall_design: Yeast cells in stationary-phase cultures were exposed to oxidative stress with samples harvested every 1-minute over 35 minutes, with a final time point at 60 minutes.  All experimental samples are over an common reference.  There are two replicates for each time point and six replicates of T0.


title: Protease Treatment

summary:
Determine if transcripts are released by protease treatment
Keywords: Comparison of protease treatments

overall_design: During total RNA isolation cell free lysates from stationary-phase cultures or exponential cultures were treated with one of three proteases or buffer alone.  All experimental samples are over a common reference.  There are two replicates for each sample.


title: Neural induction (N2B27 monolayer cluture)

first: Minoru

last: Ko

summary:
Neural induction of ES by N2B27 monolayer culture
Keywords: development or differentiation design,time series design

first: Kazuhiro

last: Aiba

first: Alexei

last: Sharov

first: Mark

last: Carter

first: Chiara

last: Foroni

first: Angelo

last: Vescovi


title: Parallel Hybridizations of six organs

status: Public on Dec 02 2005

city: Stillwater

first: Zhongming

last: Chen

state: OK

address: 264 McElroy Hall

department: Deptment of Physiological Sciences

institute: Oklahoma State University

summary:
Labeled organ cDNA samples from six organs were hybridized on one glass slide with identical conditions. The hybridizations were repeated for 19 times with 4 biological replications each with 5 technical replications.
Keywords: repeat sample


title: Transcriptomes of Alveolar epithelial cells

status: Public on Jan 14 2006

summary:
Freshly isolated type I and type II alveolar epithelial cells were investigated for transcriptomes with dual-color DNA microarray using 3DNA 50 kit.
Keywords: parallel sample

first: Jiwang

first: Nili

last: Jin

first: Telugu

last: Narasaraju

first: Narendranath

last: Chinagari

first: Lin

last: Liu


title: A Distinctive Alveolar Macrophage Activation State Induced by Cigarette Smoking

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

summary:
This series represents alveolar macrophages from a mouse model of emphysema, deletion of the integrin beta6
Keywords: parallel sample

first: Laura

last: Koth

first: Prescott

last: Woodruff

first: Jean-Yee-Hwa

last: Yang

first: Madeleine

last: Rodriguez

first: Silvio

last: Favoretto

first: Gregory

last: Dolganov

first: Agnes

last: Paquet

first: David

last: Erle


title: Oxidative stress in stationary-phase cultures

status: Public on Dec 03 2005

first: Sushmita

last: Roy

summary:
Background: As carbon sources are exhausted, Saccharomyces cerevisiae cells exhibit reduced metabolic activity and cultures enter stationary phase.  We asked whether cells in stationary-phase cultures respond to additional stress at the level of transcript abundance.
Results:  Microarrays were used to quantify changes in transcript abundance in cells from stationary-phase cultures.  In response to oxidative stress, more than 800 mRNAs increased within 1 minute.  A significant number of these mRNAs encode proteins involved in stress responses.  We tested whether mRNA increases were due to new transcription, rapid poly-adenylation of message (which would not be detected by microarrays), or potential release of mature mRNA sequestered in the cell but insoluble during RNA isolation.  Examination of the response to oxidative stress in an RNA polymerase II mutant, rpb1-1 suggested new transcription was not required.  Quantitative RT-PCR analysis of a subset of these transcripts further suggested that essentially all isolated transcripts were polyadenylated.  In contrast, over 1000 transcripts increased after protease treatment of cell-free lysates from stationary-phase but not exponentially growing cultures.  We also determined that oxidative stress and temperature upshift led to the release of different transcripts, suggesting that mRNA release is stress specific.
Conclusions:   A large number of mRNAs are sequestered in a protease-labile, rapidly releasable form in cells in stationary-phase cultures but not exponentially growing cultures.  The differences between mRNAs released by protease treatment and those observed with oxidative stress and temperature upshift, suggest different stresses cause the release of different transcripts.  We hypothesize that P-bodies are involved in this sequestration.
Keywords: stress response

overall_design:
This reference Series links data in the following related Series:
GSE2263        10s oxidative stress
GSE3683        Oxidative Stress 30-min interval
GSE3684        Hot phenol
GSE3685        RNA polymerase II
GSE3686        Protease Treatment
GSE3687        Temperature Upshift
GSE3688        Oxidative Stress 1-min interval


title: Thermoprotection in the Drosophila hsf4 mutant

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

country: Canada

institute: University of Toronto

summary:
In Drosophila larvae, acquired synaptic thermotolerance following heat shock has previously been shown to correlate with the induction of heat shock proteins (Hsps) including HSP70. We tested the hypothesis that synaptic thermotolerance would be significantly diminished in a temperature-sensitive strain (hsf4) which has been reported not to be able to produce inducible Hsps in response to heat shock.  Contrary to our hypothesis, considerable thermoprotection was still observed at hsf4 larval synapses following heat shock. To investigate the cause of this thermoprotection, we conducted DNA microarray experiments to identify heat-induced transcript changes in these organisms. Transcripts of the hsp83, dnaJ-1(hsp40) and gstE1 genes were significantly up-regulated in hsf4 larvae after heat shock.  In addition, increases in the levels of Hsp83 and DnaJ-1 proteins but not in the inducible form of Hsp70 were detected by Western blotting.   The mode of heat shock administration differentially affected the relative transcript and translational changes for these chaperones.  These results indicate that the compensatory up-regulation of constitutively expressed Hsps, in the absence of the synthesis of inducible Hsps including HSP70, could still provide substantial thermoprotection to both synapses and the whole organism.
Keywords: heat shock response

overall_design: Two strains were used in this study; the mutant cn bw hsf4 strain, and the dp cn bw cl control strain from which the mutant was derived.  For each strain, co-reared larvae were separated into a control group and a treatment group at random.  RNA from the heat-shocked larvae and from the respective controls were directly compared on cDNA microarrays (GPL311).  Two independent biological samples from each genotype were collected.  In addition, an inter-strain comparison was made using the RNA from the untreated controls from each genotype.  This was also performed in duplicate.

first: Scott

last: Neal

first: Shanker

last: Karunanithi

first: Adrienne

last: Best

first: Anthony

last: So

first: Robert

last: Tanguay

first: Harold

last: Atwood

first: J

middle: T

last: Westwood


title: Global gene expression profiles of NT, AI and IVF bovine blastocysts, examination of nuclear reprogramming

status: Public on Nov 30 2005

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1392 Storrs Rd. Unit 4243

department: Center for Regenerative Biology

institute: University of Connecticut

summary:
Nuclear transfer (NT) has potential applications in agriculture and biomedicine, but the technology is hindered by low efficiency. Global gene expression analysis of clones is important for the comprehensive study of nuclear reprogramming. Here, we compared global gene expression profiles of individual bovine NT blastocysts with their somatic donor cells and fertilized control embryos utilizing cDNA microarray technology. The NT embryos’ gene expression profiles were drastically different from those of their donor cells and closely resembled those of the naturally fertilized embryos. Our findings demonstrate that the NT embryos have undergone significant nuclear reprogramming by the blastocyst stage; however, problems may occur during re-differentiation for tissue- and organogenesis, and small reprogramming errors may be magnified downstream in development.
Keywords: cDNA microarray

overall_design: expression profiling of single bovine blastocysts using custon 7,872 cDNA microarray

first: Sadie

last: Smith

first: Robin

last: Everts

first: Fuliang

last: Du

first: Li-Ying

last: Sung

first: Sandra

last: Rodriguez-Zas

first: Byeong-Soen

last: Jeong

first: Jean-Paul

last: Renard

first: Harris

last: Lewin

first: Xiangzhong


title: Cold hardening gene expression

first: Zak

last: Razak

summary:
Cold hardening treatment, a brief exposure to low temperatures (e.g. 0°C for 2 h), can protect certain insects against subsequent exposure to temperatures sufficiently low to cause damage or lethality. Microarray analysis to examine the changes in transcript abundance associated with cold hardening has been undertaken in Drosophila melanogaster in order to gain insight into this phenomenon. Transcripts associated with 36 genes were identified, a subset of which appeared to be also differentially expressed after heat shock treatment. Quantitative RT-PCR was used to independently determine transcript abundance of a subset of these sequences. Taken together, these assays suggest that stress proteins, including Hsp23, Hsp26, Hsp83 and Frost as well as membrane-associated proteins may contribute to the cold hardening response.
Keywords: cold stress response

overall_design: Co-reared flies were separated into a control group and a treatment group at random.  RNA was isolated from the cold-shocked flies and the respective controls and was used for direct comparisons on cDNA microarrays.  Treatments were not varied as they had been optimized in previous studies.  A pilot experiment was performed using the Drosophila 7k2 array (GPL311) and subsequently three pairs of independent biological samples were evaluated with the Drosophila 12k1 array (GPL1467).

first: Wensheng

last: Qin

first: Scott

first: R

last: Robertson

first: Virginia

last: Walker


title: Sox4 null mice e12.5 pancreas

first: Michael

middle: Scott

last: German

address: 513 Parnassus, HSW 1090

department: Diabetes Center

institute: University of California San Francisco

summary:
The purpose of this experiment was to assess global changes in gene expression pattern in the pancreas from Sox4-/- embryos vs. pancreas from Sox4 wild-type embryos at embryonic day 12.5. [Sox4 gene knock-out (Schilham, M. W. et al. (1996) Defects in cardiac outflow tract formation and pro-B-lymphocyte expansion in mice lacking Sox-4. Nature 380, 711-4.)]
Embryonic pancreases from homozygous mutants and their wild-type littermates were harvested. Total RNA was isolated amplified using a linear amplification kit and used to prepare the hybridization samples through indirect labeling.
Keywords = Pancreas Sox4 null e12.5
Keywords: parallel sample

first: Anna

last: Kalousova

first: Caroline

last: Mrejen

middle: S


title: HapMap Yoruban individuals vs CEPH reference

status: Public on Nov 17 2005

city: Hinxton

first: Dan

last: Andrews

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Sanger Institute

type: Genome variation profiling by genome tiling array

summary:
It is becoming clear that copy number polymorphism in the human genome is a significant form of genetic variation. We have developed a new method that uses SNP genotype data from parent-offspring trios and applied it to HapMap to conduct high-resolution detection of deletion polymorphism. Of the delections uncovered, approximately 100 have been experimentally validated using comparative genome hybridization on these tiling-resolution oligonucleotide microarrays. We identified a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the parent-offspring trios.  This new method will permit future identification of deletion polymorphisms from high density SNP data derived from parent-offspring trios or other family relationships.
Keywords: comparative genomic hybridisation

overall_design: Eight array CGH assays/hybridisations of 131 suspected genomic regions with copy number polymorphisms.

first: Donald

last: Conrad

first: Nigel

middle: P

last: Carter

first: Matthew

last: Hurles

first: Johnathon

last: Pritchard


title: Expression analyses to identify genes involved in testis-specific vascular development

status: Public on Nov 24 2005

city: Durham

first: Douglas

last: Coveney

address: Research Drive

department: Cell Biology

institute: Duke University Medical Center

summary:
One of the earliest morphological changes during testicular differentiation is the establishment of an XY specific vasculature. The testis vascular system is derived from mesonephric endothelial cells that migrate into the gonad. In the XX gonad, mesonephric cell migration and testis vascular development is inhibited by WNT4 signaling. In Wnt4
mutant XX gonads, endothelial cells migrate from the mesonephros and form a male-like coelomic vessel. Consequently, the XX Wnt4 mutant mice presented an opportunity to focus a
gene expression screen on the processes of mesonephric cell migration and testicular vascular development. We compared differences in gene expression between XY Wnt4+/+ and XX Wnt4+/+ gonads and between XX Wnt4-/- and XX Wnt4+/+ gonads to identify genes similarly upregulated in wildtype XY gonads and XX mutant gonads that might play important roles in testis-specific vascular development.
Keywords: genetic sex and phenotypic comparisons

overall_design: Expression profiling was performed on gonads collected from XY Wnt4+/+, XX Wnt4+/+ and Wnt4-/- embryos at 12.0 days post coitum, using arrays spotted with the Operon Mouse Genome Oligo Set, version 2.0. Competitive dual-color hybridizations with dye-swap controls were performed in duplicate for each of two comparisons: XY Wnt4+/+, versus XX Wnt4+/+, and XX Wnt4-/- versus XX Wnt4+/+. For both comparisons, the wild-type XX sample is used as the reference.

first: Andrea

last: Ross

first: Blanche

last: Capel


title: Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives

status: Public on Jan 02 2006

city: Ann Arbor

last: Tomlins

state: MI

address: 1400 E. Medical Center Dr., 5410 CCGC

institute: University of Michigan

summary:
Type of experiment:  This study used microarray experiments to evaluate the reproducibility and fidelity of Whole Transcriptome Amplification (WTA).
Experimental factors:  This study contains multiple categories of microarray experiments.  Self-self hybridizations from WTA amplified total RNA were performed to evaluate the reproducibility of WTA.  To evaluate the fidelity of WTA, the same total RNA, isolated from tissue samples or cell lines, was either directly used for microarray analysis or subjected to WTA amplification before hybridization.  The amount of input total RNA for WTA amplification was varied for different hybridizations.  To demonstrate the usefulness of WTA, benign epithelia, cancerous epithelia and stroma isolated by laser capture microdissection from frozen prostate tissue specimens were subjected to WTA and hybridized.  To demonstrate the fidelity of WTA with degraded samples, total RNA from cell lines was artificially degraded before WTA and hybridization.  Total RNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues containing benign and cancerous prostate tissue were also subjected to WTA and hybridized.
Keywords: other

middle: A

first: Rohit

last: Mehra

first: Daniel

middle: R

last: Rhodes

first: Rajal

last: Shah

first: Mark

last: Rubin

first: Eric

last: Bruening

first: Vladimir

last: Makarov

first: Arul

last: Chinnaiyan


title: Time course Healthy DMD myogenesis

status: Public on Nov 15 2005

city: Leiden

first: Ellen

last: Sterrenburg

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

summary:
Primairy human myoblast cell cultures
Healthy
DMD
Keywords: time-course


title: Hot phenol

first: Sushmita

last: Roy

summary:
Determine differences between RNA isolation methods.
Keywords: Comparison of RNA isolation techniques

overall_design: Total RNA was isolated from yeast cells in stationary-phase cultures using three different isolation methods.  All experimental samples are over an common reference.  There are two replicates for each sample.


title: Gene expression profiling of the 20 human early breast carcinomas by three miaroarray platforms

city: Foster City

first: Yulei

last: Wang

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

summary:
In this study, we profiled gene expressions on 20 biopsy tissues of early stage breast carcinoma using Applied Biosystem’s Human Genome Survey Microarrays. Two main previously defined clinically relevant subtypes of breast tumors, Luminal A (longest survival time) and Basal (shortest survival time) were identified. Statistical analysis identified 1210 genes as signature genes characterizing the two subtypes of breast cancer. PantherTM functional classification and biological pathway analysis on these signature genes depicts a more detailed molecular portrait of these expression-based subtypes: Genes over expressed in Luminal A subtype were over-represented by biological function/processes such as cell structure and amino acid metabolism, while genes over expressed in the Basal subtype are over-represented by kinases, oncogenesis, cell cycle regulatory genes and TGF-beta signaling pathways. Our results provided further evidence that these breast tumor subtypes represent biologically distinct disease entities. In an attempt to identify the best set of genes as potential biomarkers for sub-classifying breast cancer, parallel data were generated on the same 20 patients samples using Stanford 42K cDNA Arrays and Agilent Human Whole Genome Arrays. Same subtypes of breast cancer were identified and the results from the three microarray platforms were found to be highly correlated. Using PAM (Prediction Analysis of Microarray) analysis, a minimal numbers of genes were selected to best characterize and distinguish the Luminal A and Basal subtypes of tumors. These classifier genes were further verified by TaqMan assays. Validated by multiple gene expression platforms, the classifier genes identified in this study defined potential prognostic molecular markers for breast cancers.
Keywords: sub-classification and characterization of early breast carcinomas

overall_design: We analyzed 20 early breast carcinomas on Applied Biosystem Human Whole Genome Survey Arrays ( 40 arrays, with 2 replicates per sample), on Stanford 42k cDNA microarrays (20 arrays, no replicate), and Agilent Whole Human Genome Oligo Microarrays (20 arrays, no replicate)

first: Therese

last: Sorlie


title: In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part 3

status: Public on Oct 28 2005

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

institute: NIH

summary:
E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples at various input levels. A "full-scale" reference was prepared using the standard input level of 6.0 ug total RNA, and one round of amplification was performed with 250 ng and 50 ng total RNA inputs.  For 10 ng and 2 ng inputs, two rounds of amplification were used.  Targets were compared on a microarray platform designed for this test using a "dye-swapped" experimental design, and sets of significantly differential genes were compared to the full scale reference's list to determine specificity and sensitivity in terms of detection of significant expression differences.
Keywords: dye swap design,quality control testing design

middle: G

last: Carter

first: Toshio

last: Hamatani

first: Alexei

last: Sharov

first: Condie

middle: E

last: Carmack

first: Yong

last: Qian

first: Kazuhiro

last: Aiba

first: Naomi

first: Dawood

middle: B

last: Dudekula

first: Pius

last: Brzoska

first: Stuart

last: Hwang


title: Haa1 regulated transcription

status: Public on Oct 25 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
The Saccharomyces cerevisiae genome contains a predicted gene, YPR008w, homologous to the gene encoding the copper-activated transcription factor Ace1. The product of the YPR008w gene, designated Haa1, regulates the transcription of a set of yeast genes, many of which encode membrane proteins. Two main target genes of Haa1 are the multidrug resistance gene YGR138c and the YRO2 homolog to the plasma membrane Hsp30. Haa1 is localized to the nucleus. Haa1-induced expression of YGR138c and YRO2 appears to be direct. Induction of HAA1 using a GAL1/HAA1 fusion gene resulted in rapid galactose-induced expression of both HAA1 and target genes. Although Haa1 has a sequence very similar to the Cu-activated DNA binding domain of Ace1, expression of Haa1 target genes was found to be independent of the copper status of cells. Haa1 does not exhibit metalloregulation in cells incubated with a range of transition metal salts. Haa1 does not exhibit any cross-talk with Ace1. Overexpression of Haa1 does not compensate for cells lacking a functional Ace1. The lack of metalloregulation of Haa1 despite the strong sequence similarity to the copper regulatory domain of Ace1 is discussed.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Esha

last: Ray


title: CEA_SGF:E00020#Dose_Effect_Blood

status: Public on Oct 26 2005

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

country: France

institute: Institut de Radioprotection et de Surete Nucleaire

summary:
In this study, we asked whether expression profiling could generate a “signature” of a dose of exposure to a toxic in general and to gamma rays in particular. To characterize genes that could potentially “sign” an exposure to irradiation and could allow the estimation of the received dose, we have performed DNA microarray experiments. Responses to gamma rays were analysed by genome-wide expression profiling at different doses in blood leucocytes of c57bl/6 mice. Twenty four mice were divided into five groups and exposed to 0.02Gy, 0.2Gy, 0.5Gy, 2Gy and 5Gy, five mice by dose except for 5Gy where we used only four mice.
Keywords: dose response


title: In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part1

department: National Institute on Aging

summary:
E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.
Keywords: dye swap design,quality control testing design

first: Mark


title: In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part2

summary:
E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples and compared on a novel microarray design to validate the system. A "self-versus-self" experimental design was used to assess the false-positive rates in the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.
Keywords: self vs self design


title: Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (WGA 2.1 Spike Test)

summary:
E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells were compared on a novel microarray design to validate the system.  The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 44,000 DNA features, and was designed to detect transcripts from all known genes, as well as about 5,000 potential genes, as identified by the NIA Mouse Gene Index 2.0. Seven external RNA controls were derived from intronic and intergenic yeast genome sequences, and 60-mer probes were spotted 10 time each on the slides. These spike-in RNA controls were diluted to cover 7 orders of magnitude in initial concentration, and used to define a function relating signal intensity to transcript abundance.
Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design

first: Vincent

last: VanBuren

first: Charlie

last: Nelson


title: Murine ES Cells: Control vs. Triple-Fusion Transfected

status: Public on Oct 12 2005

first: Joshua

middle: M.

last: Spin

institute: Stanford University

summary:
Transcriptional profiling of mouse embryonic stem cells comparing control untreated ES cells with ES cells transfected with a pUb-fluc-mrfp-ttk triple fusion reporter gene. The latter makes ES visualization possible by FACS and single cell microscopy, high throughput bioluminescence imaging, and PET. Goal was to determine the effects of triple-fusion (TF) gene transfection on global ES gene expression.
Keywords: Genetic modification

overall_design: Two-condition experiment, ES vs. TF-ES cells. Biological replicates: 4 control, 3 transfected, independently grown and harvested. One replicate per array.

first: Joseph

last: Wu

first: Feng

last: Cao

first: Shaun

last: Lin

first: Olivier

last: Gheysens

first: Ian

middle: Y

last: Chen

first: Anya

last: Tsalenko

first: Sanjiv

last: Ghambhir

first: Thomas

last: Quertermous


title: Iron uptake in yeast

status: Public on Oct 22 2005

summary:
Analysis of iron-regulated gene expression in Saccharomyces cerevisiae using cDNA microarrays has identified three putative cell wall proteins that are directly regulated by Aft1p, the major iron-dependent transcription factor in yeast. FIT1, FIT2, and FIT3 (for facilitator of iron transport) were more highly expressed in strains grown in low concentrations of iron and in strains in which AFT1-1(up), a constitutively active allele of AFT1, was expressed. Northern blot analysis confirmed that FIT1, FIT2, and FIT3 mRNA transcript levels were increased 60-230-fold in response to iron deprivation in an Aft1p-dependent manner. Fit1p was localized exclusively to the cell wall by indirect immunofluorescence. Deletion of the FIT genes, individually or in combination, resulted in diminished uptake of iron bound to the siderophores ferrioxamine B and ferrichrome, without diminishing the uptake of ferric iron salts, or the siderophores triacetylfusarinine C and enterobactin. FIT-deletion strains exhibited increased expression of Aft1p target genes as measured by a FET3-lacZ reporter gene or by Arn1p Western blotting, indicating that cells respond to the absence of FIT genes by up-regulating systems of iron uptake. Aft1p activation in FIT-deleted strains occurred when either ferrichrome or ferric salts were used as sources of iron during growth, suggesting that the FIT genes enhance uptake of iron from both sources. Enzymatic digestion of the cell wall resulted in the release of significant amounts of iron from cells, and the relative quantity of iron released was reduced in FIT-deletion strains. Fit1p, Fit2p, and Fit3p may function by increasing the amount of iron associated with the cell wall and periplasmic space.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Tracy

last: Ferea


title: Novel Roles of Osteopontin and CXC Chemokine Ligand 7 in the Defense against Mycobacterial Infection

status: Public on Oct 05 2005

city: Fukuoka

first: Vahid

last: Khajoee

state: Fukuoka

address: 3-1-1 Maidashi, higashi-ku

department: Pediatrics

institute: Kyuhsu University

summary:
Granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced human monocyte-derived macrophage (GM-Mphage) or macrophage CSF (M-CSF)-induced human monocyte-derived Mphage (M-Mphage) are distinct in terms of the resistance to Mycobacterium tuberculosis (M. tuberculosis). To elucidate the role of molecules involved in the functional differences between these Mphages, we investigated the gene expression profiles using microarray.
After culture of CD14+ monocytes with CSFs, Mphages were cultured with or without BCG (GM-Mf-BCG and M-Mf-BCG). The gene expression profiles from these cells were compared. Chemokines highly expressed in M-Mphages were selected and evaluated for antimycobacterial activity and superoxide production.
FN1 and FCGR2B were the most up-regulated genes in GM-Mphage and M-Mphage, respectively. After the stimulation with BCG, 3 chemokine genes (Osteopontin (SPP1), CXC chemokine ligand 7 (CXCL7), and CC chemokine ligand 11 (CCL11)) were highly expressed in M-Mphage-BCG when compared to those in GM-Mf-BCG. A significantly increased resistance to M. tuberculosis H37Ra was observed after the stimulation of GM-Mphage with SPP1 or CXCL7. Superoxide production levels of SPP1- or CXCL7-stimulated GM-Mphages were higher than those of GM-Mphages without stimulation.
These results indicate that both SPP1 and CXCL7 might have a role in the resistance against mycobacteria, at least in part, through augmenting reactive oxygen intermediates production in Mphages.

overall_design: Fluorescence signals for approximately 30,000 spots in slides were detected by fluorescent image analyzer FLA-8000 (Fuji film, Tokyo, Japan) for Cy3 and Cy5, separately. Hybridization intensities were processed using Arrayvision software ver. 6.0 (Imaging Research, Ontario, Canada). Signal and background intensities were determined by the median pixel values. Local background values were determined as the average of four background spots around each gene spot. All spots in the image (for both Cy3 and Cy5 signals) were evaluated for a possibility of dusts, to lower the probability of false data in all experiments. GeneSpring ver. 6.2. (Silicon genetics, Redwood city, CA) was used for data analysis. According to the GeneSpring instruction, normalization of the data was done using "Lowess method" [20]. Spots with dust, or with signal value of which the Cy5 or Cy3 channels were less than three times of background, were excluded.

first: Hidetoshi

last: Takada

first: Toshiro

last: Hara


title: Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (22k Linearity)

first: Minoru

last: Ko

summary:
E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation.  These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene).  Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta.
Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design

last: Carter

first: Alexei

last: Sharov

first: Dawood

last: Dudekula

first: Condie

last: Carmack


title: Transcriptional programs activated by exposure of human prostate cancer cells to androgen.

status: Public on Oct 15 2005

last: Stanford Microarray Database

summary:
Androgens are required for both normal prostate development and prostate carcinogenesis.  We used DNA microarrays, representing approximately 18,000 genes, to examine the temporal program of gene expression following treatment of the human prostate cancer cell line LNCaP with a synthetic androgen.  We observed statistically significant changes in levels of transcripts of more than 500 genes.  Many of these genes were previously reported androgen targets, but most were not previously known to be regulated by androgens.  The androgen-induced expression programs in 3 additional androgen-responsive human prostate cancer cell lines, and in 4 androgen-independent subclones derived from LNCaP, shared many features with those observed in LNCaP, but some differences were observed.  A remarkable fraction of the genes induced by androgen appeared to be related to production of seminal fluid and these genes included many that play roles in protein folding, trafficking, and secretion.  Prostate cancer cell lines retain features of androgen responsiveness that reflect normal prostatic physiology. These results provide a broad view of the effect of androgen signaling on the transcriptional program in these cancer cells, and a foundation for further studies of androgen action
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Samuel

last: DePrimo


title: Heat-shock (Temp43, 30min, 60 min)

status: Public on Sep 21 2005

city: Tsukuba

first: Rena

last: Matsumoto

state: Ibaraki

address: 1-1-1 Higashi

institute: National Institute of Advanced Industrial Science and Technology

summary:
JN54 (wild-type) cells were incubated in YPD medium at 30 degrees C to a logarithmic phase (OD660=1), followed by treatment with mild heat-shock at 43 degrees C for 30 min in pre-warmed (43 degrees C) 100ml of YPD medium using 500 ml Erlenmeyer flask.

JN54 (wild-type) cells were incubated in YPD medium at 30 degrees C to a logarithmic phase (OD660=1), followed by treatment with mild heat-shock at 43 degrees C for 60 min in pre-warmed (43 degrees C) 100ml of YPD medium using 500 ml Erlenmeyer flask.
Keywords: Stress response

overall_design: Series containes 3 independent experiment and high and low power scanns for each independent experiment

first: Kuniko

last: Akama

first: Randeep

last: Rakwal

first: Hitoshi

last: Iwahashi


title: DNA damage responses and Mec1p

status: Public on Sep 24 2005

summary:
Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. The human ATR kinase and its homolog in yeast, MEC1, play central roles in transducing the damage signal. To characterize the role of the Mec1 pathway in modulating the cellular response to DNA damage, we used DNA microarrays to observe genomic expression in Saccharomyces cerevisiae responding to two different DNA-damaging agents. We compared the genome-wide expression patterns of wild-type cells and mutants defective in Mec1 signaling, including mec1, dun1, and crt1 mutants, under normal growth conditions and in response to the methylating-agent methylmethane sulfonate (MMS) and ionizing radiation. Here, we present a comparative analysis of wild-type and mutant cells responding to these DNA-damaging agents, and identify specific features of the gene expression responses that are dependent on the Mec1 pathway.  Among the hundreds of genes whose expression was affected by Mec1p, one set of genes appears to represent an MEC1-dependent expression signature of DNA damage. Other aspects of the genomic responses were independent of Mec1p, and likely independent of DNA damage, suggesting the pleiotropic effects of MMS and ionizing radiation. The complete data set as well as supplemental materials is available at http://www-genome.stanford.edu/mec1
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Audrey

last: Gasch


title: Chronic hypoxia alters the level, maturation and control of gene expression in mouse kidney

status: Public on Sep 13 2005

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary:
Transcriptomic studies were undertaken to investigate the effect of hypoxia on kidney in early life to elucidate the genomic basis of renal injury and adaptation when oxygen is deprived.
Fluorescently labeled, reverse-transcribed kidney RNA from 18 male and 18 female P2 mice, subjected for one, two or four weeks to normal atmospheric conditions (NAC) or to chronic constant (CCH) or intermittent (CIH) hypoxia were hybridized with 18 cDNA microarrays ("multiple yellow strategy", MYS). Expression level, stability, coordination and maturation of 1775 distinct genes were studied in each treatment-duration condition. Results: Both CIH and CCH change the expression level, stability and coordination of numerous genes that are involved in most major functional pathways. The fold change was significantly higher in female mice after one week of hypoxia and significantly higher in males after two and four weeks of hypoxia. Most solute carrier genes, including NHE1, are up-regulated and few down-regulated. There are genes coordinately expressed but others are much less so, with a remarkable overlap between the genes that are coexpressed in NAC and coregulated in CCH and CIH.
Conclusion. Hypoxia is a major stress that alters the profile, stability and coordination of the kidney transcriptome in early life and slows down its maturation.
Keywords: stress response

overall_design: Several litters of CD1 mice at P2 were split in nine groups and subjected for 1, 2 and 4 weeks to NAC (N), hypoxia in which [O2] was kept constant at 11% (CCH or C) and hypoxia in which [O2] was switched between 21% and 11% every four minutes (CIH or I). We have used the "multiple yellow strategy" (MYS) in which each slide was hybridized with Cy5-cDNA from the kidneys of one male mouse and Cy3-cDNA from the kidneys of one female mouse, both animals subjected to the same condition as described in Physiol Genomics. 22: 292-307. Data were processed as described in Physiol Genomics 20: 211-223, 2005.

first: Chenhao

last: Fan

first: Sanda

first: Gabriel

last: Haddad


title: Thyroid hormone induced changes in Xenopus laevis tadpole brain

status: Public on Oct 04 2005

summary:
Premetamorphic Xenopus laevis tadpoles brain ventricle cells respond to thyroid hormone by proliferation and subsequent differentiation. The goal of this experiment is to identify the genes involved in the TH-induced proliferation pathway in tadpole brain and compare it to TH-induced proliferation and differentiation program in tadpole limb. Xenopus tadpoles (NF54) were treated with 1 mM methimazole in 0.1 X MMR solution for 1 week to block the endogenous TH production and reduce the TH present in the system of the tadpole. They were then treated with 100 nM T3 in 1 mM methimazole and 0.1 x MMR for another 24h and 48h or without T3 for 48h (control group). Brains from the tadpoles were dissected at the end of the experiment.
Keywords: development or differentiation design,organism part comparison design,reference design,replicate design,time series design

sample_organism:
Xenopus laevis
unidentified

first: Biswajit

last: Das

first: Liquan

last: Cai

first: Mark

first: Yu-Lan

last: Piao

first: Donald

last: Brown


title: How different diets alter skeletal muscle in pig

status: Public on Aug 31 2005

city: Trieste

first: Alberto

last: Pallavicini

address: 9 Piazzale Valmaura

department: Biology

country: Italy

institute: University of Trieste

summary:
we want to test how different diets (high energy diet HED and low energy diet LED) alter muscle methabolism in pigs.
we perform different array experiments using an human platform (GPL2011) and RNA extracted from pig skelethal muscle.
thank's this we also test cross-species hybridisation.
Keywords: comparative genomic hybridisation

overall_design:
extraction of RNA from pig skeletal muscle by a modification of Chomczynski protocol.

cDNA was purified and labelled with Cy3 and Cy5 fluorochromes using the cDNA labeling purification module kit (Invitrogen). The HED samples were analysed in comparison to LED samples, used as reference. The labelled cDNA were appropriately coupled and used for competitive hybridisation on the same microarray at 42°C for 16h. The relative intensity of labelled cDNA in HED and LED was acquired with ScanArray LITE scanner (PerkinElmer Life Sciences, Inc).

platform used for our experiments is GPL2011.


title: Comparison of monocytes from G-CSF mobilized and normal peripheral blood

city: Seattle

first: Lynn

last: Graf

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary:
A prospective randomized trial has shown that there is a survival advantage for allogeneic transplant patients receiving Granulocyte Colony Stimulating Factor (G-CSF) stimulated peripheral blood mononuclear cells (GPBMC) versus bone marrow (BM) as a source of stem cells. The biological basis for this advantage is not clear, and may be attributable to qualitative as well as quantitative differences in the CD34 cells, T-cells and/or the monocytes transplanted. To begin to address this issue, gene expression patterns in monocytes isolated from G-CSF mobilized peripheral blood were compared those from normal, non-mobilized peripheral blood to identify functional pathways that may distinguish these two populations.
Keywords: Cell type comparison

overall_design: Six samples were analyzed, 3 from normal peripheral blood donors and 3 from normal donors who had been treated with G-CSF by a protocol designed to mobilize bone marrow stem cells into the peripheral blood.

first: Beverly

last: Torok-Storb

first: Shelly

last: Heimfeld

first: Mineo

last: Iwata

first: Christoph

last: Kahl


title: Heart transplant biopsies

status: Public on Oct 24 2005

city: Bethesda

first: Natalia

last: Shulzhenko

address: 9000 Rockville Pike, Building 4, room 111

department: NIAID

summary:
MOLECULAR PROFILING IMPROVES DIAGNOSES OF REJECTION AND INFECTION IN TRANSPLANTED ORGANS.
The monitoring of transplanted hearts is currently based on histological evaluation of endomyocardial biopsies, a method that is fairly insensitive and that does not always accurately discriminate between rejection and infection in the heart.  Accurate diagnosis of rejection and infection is absolutely crucial, however, as the respective treatments are completely different.
Using microarrays we analyzed gene expression in 76 cardiac biopsies from 40 heart recipients undergoing rejection, no rejection, or T. cruzi infection.  We found a set of 98 genes whose expression patterns were typical of acute rejection, and 87 genes that discriminated between rejection and T. cruzi infection.  These sets revealed acute rejection episodes up to two weeks earlier, and trypanosome infection up to two months earlier than did histological evaluation.  When applied to raw data from other institutions, the two sets of predictive genes were also able to accurately pinpoint acute rejection of lung and kidney transplants, as well as bacterial infections in kidneys.  In addition to their usefulness as diagnostic tools, the data suggest that there are similarities in the biology of the processes involved in rejection of different grafts and also in the tissue responses to pathogens as diverse as bacteria and protozoa.

pre-rejection:
GSM47949, GSM48048, GSM49625

non-rejection:
GSM47957, GSM48045, GSM48049, GSM48057, GSM48072, GSM48089, GSM48092, GSM49624, GSM49654, GSM49656, GSM49657, GSM49658, GSM49661, GSM49666, GSM49748, GSM49750, GSM49751, GSM49752, GSM49754, GSM49756, GSM49757, GSM49758, GSM49762, GSM49765, GSM49766, GSM49767, GSM49769, GSM49771, GSM49773, GSM49774, GSM49781, GSM49782, GSM49783, GSM49784

acute rejection:
GSM48040, GSM48043, GSM48046, GSM48047, GSM48050, GSM48053, GSM48056, GSM49655, GSM49747, GSM49749, GSM49755, GSM49759, GSM49761, GSM49763, GSM49764, GSM49780

pre-Chagas disease reactivation:
GSM48089, GSM49756, GSM49757, GSM49758, GSM49767, GSM49769, GSM49771

Chagas disease reactivation:
GSM49753, GSM49760, GSM49768, GSM49772, GSM49775, GSM49776, GSM49777, GSM49778

Toxoplasma myocarditis:
GSM48058

first subset ("summer"):
GSM47949, GSM47957, GSM48040, GSM48043, GSM48045, GSM48046, GSM48047, GSM48048, GSM48049, GSM48050, GSM48053, GSM48056, GSM48057, GSM48058, GSM48072, GSM48089, GSM48092, GSM49624, GSM49625, GSM49654, GSM49655, GSM49656, GSM49657, GSM49658, GSM49661, GSM49666, GSM49747, GSM49748, GSM49749, GSM49750, GSM49751, GSM49752

second subset ("winter"):
GSM49753, GSM49754, GSM49755, GSM49756, GSM49757, GSM49758, GSM49759, GSM49760, GSM49761, GSM49762, GSM49763, GSM49764, GSM49765, GSM49766, GSM49767, GSM49768, GSM49769, GSM49770, GSM49771, GSM49772, GSM49773, GSM49774, GSM49775, GSM49776, GSM49777, GSM49778, GSM49780, GSM49781, GSM49782, GSM49783, GSM49784
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Keywords: repeat sample

overall_design:
This is a series that includes training and first test set of samples. Number of biological samples: 52. Eleven samples were done in replicates as identified below.
RNA was isolated from endomyocardial biopsies, amplified and labeled with Cy3. Reference RNA was labeled with Cy5.

first: Andrey

last: Morgun

first: Ainhoa

last: Perez-Diez

first: Rosiane

middle: V

last: Diniz

first: Gerdine

last: Sanson

first: Dirceu

last: Almeida

first: Polly

last: Matzinger

first: Maria

last: Gerbase-DeLima


title: High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridiz

status: Public on Aug 30 2005

first: Minoru

last: Ko

summary:
We attempted to identify candidate genes that are expressed more highly in the ICM than in TE cells. Mouse ES cells are cultured from the ICM, whereas mouse TS cells are cultured from the TE. Although these cells have been cultured in vitro, they represent the in vitro equivalents of the ICM and TE. Therefore, genes which are expressed more highly in ES than TS in microarray studies were good candidates for genes predominantly expressed in the ICM in blastocysts.
Keywords: strain or line design

first: Toshiyuki

last: Yoshikawa

first: Yulan

first: Jinhui

last: Zhong

first: Ryo

last: Matoba

first: Mark

last: Carter

first: Yuxia

last: Wang

first: Ilya

last: Goldberg


title: Bone marrow microenvironment: interaction of monocytes and stromal cells

first: Lynn

last: Graf

summary:
Two human stromal cell lines, HS-5 and HS-27a, represent functionally distinct components of the bone marrow microenvironment.  A third influential component of the microenvironment is resident monocytes and macrophages. The baseline expression profile of normal peripheral blood monocytes was determined and their effect on the gene expression of the stromal cells was investigated in a co-culture sytem. Control RNA for all samples was Stratagene Universal human reference RNA.
Keywords: Cell Line Comparison and Culture Comparison

overall_design: We analyzed 5 arrays for the HS-5 cell line, 5 arrays for the HS-27a cell line and 3 arrays for normal peripheral blood monocytes. Four arrays for HS-5 were biological replicates with cells cultured alone; one is from HS-5 cultured in the presence of monocytes. Four arrays for HS-27a were biological replicates with cells cultured alone; one is from HS-27a cultured in the presence of monocytes. Peripheral blood monocytes were biological replicates from multiple normal donors.

first: L

first: M

last: Iwata

first: N

last: Awaya

first: B

last: Torok-Storb

last: Pillai

first: C


title: Partially degraded RNA from bladder washing is a suitable sample for studying gene expression profiles of bladder cancer

status: Public on Aug 25 2005

city: Barcelona

first: Moises

middle: Burset

last: Albareda

state: Barcelona

address: Cartagena, 340-350

department: Molecular biology

country: Spain

institute: Fundacio Puigvert

summary:
The aims of this study were to determine the impact of different levels of RNA degradation as well as to ascertain if the gene expression profiles obtained from bladder washing correlates to that obtained from the related bladder tumor.
Keywords: RNA degradation, bladder washing, bladder tumor, bladder cancer

overall_design: We obtained tissue tumor and bladder washing tumor samples from the same individual. We degraded each intact RNA to 3 different degradation states with dye swap (2x4x2 arrays). All tumor RNAs were compared against a pool of 4 healthy control samples with intact RNA (named as C0).


title: Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

status: Public on Aug 24 2005

last: Stanford Microarray Database

department: Stanford University, School of Medicine

summary:
There are about 800 genes in Saccharomyces cerevisiae whose transcription is cell-cycle regulated. Some of these form clusters of co-regulated genes. The 'CLB2' cluster contains 33 genes whose transcription peaks early in mitosis, including CLB1, CLB2, SWI5, ACE2, CDC5, CDC20 and other genes important for mitosis. Here we find that the genes in this cluster lose their cell cycle regulation in a mutant that lacks two forkhead transcription factors, Fkh1 and Fkh2. Fkh2 protein is associated with the promoters of CLB2, SWI5 and other genes of the cluster. These results indicate that Fkh proteins are transcription factors for the CLB2 cluster. The fkh1 fkh2 mutant also displays aberrant regulation of the 'SIC1' cluster, whose member genes are expressed in the M-G1 interval and are involved in mitotic exit. This aberrant regulation may be due to aberrant expression of the transcription factors Swi5 and Ace2, which are members of the CLB2 cluster and controllers of the SIC1 cluster. Thus, a cascade of transcription factors operates late in the cell cycle. Finally, the fkh1 fkh2 mutant displays a constitutive pseudohyphal morphology, indicating that Fkh1 and Fkh2 may help control the switch to this mode of growth.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Paul

last: Spellman


title: Thyroid hormone induced resorption of tail in  Xenopus laevis tadpole

summary:
Premetamorphic Xenopus laevis tadpole tail respond to thyroid hormone by resorption. The goal of this experiment is to identify the genes involved in the TH-induced resorption tadpole tail and compare it to TH-induced proliferation and differentiation program in tadpole limb and brain. Xenopus tadpoles (NF54) were treated with 100 nM T3 in 0.1 x MMR for another 24h and 48h or without T3 for 48h (control group). NF 61 tadpoles were in 0.1 X MMR till they reached NF stage 62. The tails were dissected after the experiment.
Keywords: development or differentiation design,organism part comparison design,reference design,replicate design,time series design

first: Biswajit

last: Das

first: Liquan

last: Cai

first: Yu-Lan

last: Piao

first: Alexei

last: Sharov

first: Donald

middle: D

last: Brown


title: Rap1, Sir2, Sir3, Sir4 immunoprecipitations

summary:
All Rap1, Sir2, Sir3, Sir4, and mock immunoprecipitation experiments associated with Lieb et al. Nature Genetics, August 2001, Volume 28, Issue 4
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Jason

last: Lieb


title: Thyroid hormone induced changes in Xenopus laevis tadpole limb bud

first: Minoru

last: Ko

summary:
Premetamorphic Xenopus laevis tadpoles limb bud cells respond to thyroid hormone by proliferation and subsequent differentiation. The goal of this experiment is to identify the genes involved in the TH-induced proliferation pathway in developing tadpole limb bud and compare it to TH-induced proliferation and differentiation program in tadpole brain. Xenopus tadpoles (NF54) were treated with 1 mM methimazole in 0.1 X MMR solution for 1 week to block the endogenous TH production and reduce the TH present in the system of the tadpole. They were then treated with 100 nM T3 in 1 mM methimazole and 0.1 x MMR for another 24h and 48h or without T3 for 48h (control group). Limb buds were dissected at the end of the experiment.
Keywords: development or differentiation design,organism part comparison design,reference design,replicate design,time series design

first: Mark

last: Carter


title: Immediate/Early Response to Trypanosoma cruzi Infection Involves Minimal Modulation of Host Cell Transcription

status: Public on Oct 20 2005

summary:
Host cell infection by the intracellular pathogen, Trypanosoma cruzi, involves activation of signaling pathways, cytoskeletal reorganization, and targeted recruitment of host cell lysosomes. To determine the consequences of T. cruzi invasion on host cell gene expression, high density microarrays consisting of approximately 27,000 human cDNAs were hybridized with fluorescent probes generated from T. cruzi-infected human fibroblasts (HFF) at early time points following infection (2-24 h). Surprisingly, no genes were induced > or =2-fold in HFF between 2 and 6 h post-infection (hpi) in repeated experiments while immediate repression of six host cell transcripts was observed. A significant increase in transcript abundance for 106 host cell genes was observed at 24 hpi. Among the most highly induced is a set of interferon-stimulated genes, indicative of a type I interferon (IFN) response to T. cruzi. In support of this, T. cruzi-infected fibroblasts begin to secrete IFNbeta at 18 hpi following the induction of IFNbeta transcripts. As compared with global transcriptional responses evoked by other intracellular pathogens, T. cruzi is a stealth parasite that elicits few changes in host cell transcription during the initiation of infection.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Barbara

last: Burleigh


title: ssa1/2 deletion mutant

first: Rena

last: Matsumoto

summary:
Yeast strain lacking the two genes SSA1 and SSA2, which encode cytosolic chaperones, acquires thermotolerance as well as the mild heat-shocked wild-type yeast strain.
Keywords: Stress response

overall_design: Series containes 3 independent experiments.

first: Kuniko

last: Akama

first: Randeep

last: Rakwal

first: Hitoshi

last: Iwahashi


title: CEA_SGF:E00001#SPvsMP

status: Public on Oct 01 2005

city: EVRY

first: Michèle

last: Martin

address: 2, rue Gaston Crémieux

department: DSV/DRR

institute: CEA

summary:
Characterization of the transcriptional profile of SP human keratinocytes from primary cultures.
Keywords: repeat sample