title: Genome-wide relationships between TAF1 and histone acetyltransferases in S. cerevisiae

status: Public on Mar 20 2006

city: University Park

first: Melissa

last: Durant

state: PA

address: 452 N Frear

institute: Penn State University

summary:
Evidence suggests that the TAF1 subunit of TFIID is a histone acetyltransferase (HAT) that is functionally redundant with the Gcn5 HAT of the SAGA and ADA complexes.  Here we test a number of predictions of this hypothesis by examining the in vivo histone acetylation targets of TAF1 and Gcn5, and re-examining the basis for the reported genome-wide functional redundancy between TAF1 and Gcn5.  Our findings do not  support a number of basic tenets of the hypothesis, thus bringing into question the physiological presence of any TAF1 HAT function in yeast.  We have also conducted genome-wide expression profiles of numerous other HATs (Elp3, Hat1, Hpa2, Sas3) in an effort identify potential functional redundancy between TAF1 and other HATs, and find none.  Further investigation of TAF1 and the Esa1 HAT re-affirm a link between histone H4 acetylation by Esa1, and TFIID binding via interactions with acetylated histone H4-binding protein Bdf1.
Keywords: genetic modification

overall_design: Experiment contains 38 total hybridizations.  Yeast cDNA dual channel (Cy3/Cy5) cohybridization.  All experiments performed in duplicate (dye swap).  Dye swap data was mode normalized using "R" software package and then corrected by B. subtilis spiking controls (added to each culture based on OD600 units).  Platform GPL1220: non-commercial nucleotide arrays. PCR amplified yeast (Saccharomyces cerevisiae) genomic DNA chip with ResGen Primer Pairs.  Amplification as described at http://cmgm.stanford.edu/pbrown/protocols/2_DNA.html.  Printed on aminosaline glass slides by the Penn State University Microarray facility


title: Salt (NaCl and KCl) Stress in Desulfovibrio vulgaris Hildenborough

status: Public on Mar 22 2006

city: Berkeley

first: Adam

middle: P.

last: Arkin

state: CA

address: 1 Cyclotron Road

department: Physical Biosciences Division

country: USA

institute: Virtual Institute for Microbial Stress and Survival

summary:
Recent interest in the ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste, has made all factors that affect its physiology of great interest. Increased salinity constitutes an important and frequent fluctuation faced by D. vulgaris in its natural habitat. Using data from microarray experiments, as well as other laboratory analyses, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. This study demonstrates that import of osmoprotectants such as glycine betaine and ectoine constitute the primary mechanism used by D. vulgaris to counter hyper-ionic stress. Several efflux systems also were highly up-regulated, as was the ATP synthesis pathway. Increase in both RNA and DNA helicases suggested that salt stress had affected the stability of nucleic acid base pairing. An immediate response to salt stress included up-regulation of chemotaxis genes though flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The extensive NaCl stress analysis was compared with microarray data from KCl stress and unlike many other bacteria, D. vulgaris responded similarly to the two stresses.
Keywords: Comparison of cells treated with either NaCl (250 mM) or KCl (250 mM) to untreated cells at times of 0, 30, 60, 120, and 240 min.

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: There are two sub series that used 250 mM NaCl as the stressor (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4504 and (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4510), and one sub series that used 250 mM KCl as the stressor (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4515).

first: Aindrila

last: Mukhopadhyay

first: Zhili

last: He

first: Terry

last: Hazen

first: Qiang

first: Katherine

last: Huang

first: Jizhong

last: Zhou

first: Jay

last: Keasling


title: Genome-wide relationships between TAF1 and histone acetyltransferases in S. cerevisiae - chIP-chip study

type: Genome binding/occupancy profiling by genome tiling array

summary:
Evidence suggests that the TAF1 subunit of TFIID is a histone acetyltransferase (HAT) that is functionally redundant with the Gcn5 HAT of the SAGA and ADA complexes.  Here we test a number of predictions of this hypothesis by examining the in vivo histone acetylation targets of TAF1 and Gcn5, and re-examining the basis for the reported genome-wide functional redundancy between TAF1 and Gcn5.  Our findings do not  support a number of basic tenets of the hypothesis, thus bringing into question the physiological presence of any TAF1 HAT function in yeast.  We have also conducted genome-wide expression profiles of numerous other HATs (Elp3, Hat1, Hpa2, Sas3) in an effort identify potential functional redundancy between TAF1 and other HATs, and find none.  Further investigation of TAF1 and the Esa1 HAT re-affirm a link between histone H4 acetylation by Esa1, and TFIID binding via interactions with acetylated histone H4-binding protein Bdf1.
Keywords: ChIP-chip, genetic modification


title: E. coli K-12 yliH and yceP biofilm expression relative to wild type

status: Public on Apr 01 2006

city: College Station

first: Thomas

middle: K.

last: Wood

state: TX

address: 220 Jack E. Brown Building

department: Artie McFerrin Department of Chemical Engineering

institute: Texas A & M University

summary:
Expression in biofilm cells of mutants yceP and  yliH relative to biofilm cells of E. coli K-12 wild type strain
Keywords: comparison of strain expression profiles

overall_design: All strain cultured in LB glu, biofilm isolated from glass wool after culturing for 24 hrs.

first: Joanna

last: Domka

first: Moshe

last: Herzberg

first: Ian

middle: K

last: Kaye

first: Jintae

last: Lee


title: NaCl Stress in Desulfovibrio vulgaris Hildenborough (Series 2)

summary:
Increased salinity constitutes an important and frequent fluctuation faced by D. vulgaris in its natural habitat. Using data from microarray experiments, we investigated the effects of excess NaCl on D. vulgaris.
Keywords: stress response, time course

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of cells treated with 250mM NaCl to untreated cells at times of 0 and 120 min.  See also Series GSE4447: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4447


title: stalk biogenesis phosphorelay

status: Public on Apr 06 2006

city: Cambridge

first: Michael

last: Laub

state: MA

address: 31 Ames St.

institute: MIT

summary:
mutants in the stalk biogenesis and sigma-54 pathways
Keywords: mutant expression patterns

overall_design: deletion mutants of each component were compared to wild type, with all strains grown to mid-log phase as mixed populations

first: Emanuele

last: Biondi


title: KCl Stress in Desulfovibrio vulgaris Hildenborough (Series 1)

summary:
Increased salinity constitutes an important and frequent fluctuation faced by D. vulgaris in its natural habitat. Using data from microarray experiments, we investigated the effects of excess KCl on D. vulgaris.
Keywords: stress response, time course

overall_design: Comparison of cells treated with 250mM KCl to untreated cells at times of 0, 30, 60, 120, and 240 min.  See also Series GSE4447: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4447


title: Effect of weeds on corn

status: Public on Mar 15 2006

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
Microarray analysis was used to identify changes in gene expression in maize leaves collected from plants at the 11-14 leaf stage that resulted from competition with velvetleaf. Genes involved in carbon and nitrogen utilization, photosynthesis, growth and development, oxidative stress, signal transduction, responses to auxin and ethylene, and zinc transport are repressed in maize growing in competition with velvetleaf. Very few genes are induced due to competition with velvetleaf, and those that are provide little indication of the physiological response of maize. No significant differences were observed in multiple genes responsive to water stress or sequestering/transporting most micronutrients indicating that these stresses are not a major component of velvetleaf competition with maize at the developmental stage tested.
Keywords: Stress response (weed competition)

overall_design: Maize plants were grown in 8 separate plots. Four of the plots were seeded with velvetleaf (1W-4W) and four were hand cultivated periodically to remove most weeds throughout the growing season (1-4). Samples of leaf material was collected from four plants in each plot and pooled. A balanced labeling comparison (R vs B) of weedy verses control was done with 10 independent hybridizations. Thus, experiment 1R4WB represents the comparison of control sample 1 labeled with Cy3 (R) to weedy sample 4 labeled with Cy5(B).

first: Sharon

last: Clay


title: Microarray Analysis of Dupuytren's Disease Tissues

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
PURPOSE: Dupuytren's disease (DD) is characterized by fibroblastic proliferation of the palmar fascia, often leading to flexion contracture in the hand. Although there is a strong genetic component the genome-wide expression of novel genes is not known. The purpose of this study was to use DNA microarray technology to identify upregulated genes in DD. METHODS: Human tissue samples were harvested from 3 patient sources: DD cord tissue (n = 20), normal-appearing adjacent control fascia (n = 15), and palmar fascia from patients having carpal tunnel release (n = 15). DNA microarray analysis was performed on amplified sample RNA. Novel genes were compared with known gene functions. A candidate gene of interest was studied further by using immunohistochemistry on DD tissue samples and controls. : Several novel genes not described previously in the study of DD were upregulated significantly, including MafB, collagen type V, alpha-2 (COL5A2), collagen type VIII, alpha-1 (COL8A1), contactin I (CNTN1), and leucine-rich repeat containing 17 (LRRC17). These upregulated genes were compared with their known gene-expression profiles in other tissues and their purported functions. MafB was found to be of particular interest because of its prominent role in tissue development and cellular differentiation. MafB immunohistochemistry showed positive staining in 50% of the DD specimens but complete absence of MafB in all control tissues (adjacent control fascia, carpal tunnel fascia). Co-localization experiments with MafB and alpha-smooth muscle actin showed staining properties in similar regions but these 2 proteins were not confined solely to the same cells. CONCLUSIONS: Microarray analysis of DD tissue has identified significant upregulated gene expression of MafB. MafB protein also is found in Dupuytren's cords but not in control fascia. Co-localization data suggest that the association of MafB with DD is not related exclusively to myofibroblast proliferation. Because of its role in fibroblastic transformation in other models MafB and its relationship to the pathogenesis of DD deserves further study.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Kenton

last: Fong


title: Genome-wide screen for salmonella genes required for long-term systemic infection of the mouse.

summary:
This datasets includes all arrays from the first passage through 129SvJ mice (28 days) and the second independent passage (29 days).  The first passage arrays are the same as included in the experiment set "129SvJ Pass 1 28 dpi arrays" and the second passage arrays are the same as included in the experiment set "129SvJ Pass 2 28 dpi arrays".  Input arrays are also included and collectively they represent two biological replicates for negative selection at ~4 weeks post infection.
Abstract: A microarray-based negative selection screen was performed to identify Salmonella enterica serovar Typhimurium (serovar Typhimurium) genes that contribute to long-term systemic infection in 129X1/SvJ (Nramp1(r)) mice. A high-complexity transposon-mutagenized library was used to infect mice intraperitoneally, and the selective disappearance of mutants was monitored after 7, 14, 21, and 28 d postinfection. One hundred and eighteen genes were identified to contribute to serovar Typhimurium infection of the spleens of mice by 28 d postinfection. The negatively selected mutants represent many known aspects of Salmonella physiology and pathogenesis, although the majority of the identified genes are of putative or unknown function. Approximately 30% of the negatively selected genes correspond to horizontally acquired regions such as those within Salmonella pathogenicity islands (SPI 1-5), prophages (Gifsy-1 and -2 and remnant), and the pSLT virulence plasmid. In addition, mutations in genes responsible for outer membrane structure and remodeling, such as LPS- and PhoP-regulated and fimbrial genes, were also selected against. Competitive index experiments demonstrated that the secreted SPI2 effectors SseK2 and SseJ as well as the SPI4 locus are attenuated relative to wild-type bacteria during systemic infection. Interestingly, several SPI1-encoded type III secretion system effectors/translocases are required by serovar Typhimurium to establish and, unexpectedly, to persist systemically, challenging the present description of Salmonella pathogenesis. Moreover, we observed a progressive selection against serovar Typhimurium mutants based upon the duration of the infection, suggesting that different classes of genes may be required at distinct stages of infection. Overall, these data indicate that Salmonella long-term systemic infection in the mouse requires a diverse repertoire of virulence factors. This diversity of genes presumably reflects the fact that bacteria sequentially encounter a variety of host environments and that Salmonella has evolved to respond to these selective forces in a way that permits both the bacteria and the host to survive.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Kaman

last: Chan


title: Zebrafish ovarian follicle transcriptome

status: Public on Mar 17 2006

city: Talence

first: Patrick

middle: J.

last: BABIN

address: Avenue des facultés

department: UFR Biologie

country: France

institute: Université Bordeaux

summary:
SAGE analysis of fully grown ovarian follicles has been carried out to supply a resource for identification of important molecules involved in vertebrate oogenesis and in early stages of embryonic development.
Keywords: SAGE

overall_design: About 250 full-grown ovarian follicles were obtained after gentle squeezing the abdomen of five mature zebrafish females.

middle: J

last: Babin

first: Anja

last: Knoll-Gellida

first: Michele

last: Andre


title: Membrane-associated transcripts in Arabidopsis; their isolation...

city: Amsterdam

first: Mark

middle: de

last: Jong

address: Kruislaan 318

country: Netherlands

institute: University of Amsterdam

summary:
Membrane-associated, integral membrane and secreted proteins are of key importance in many cellular processes. For most of the 28 952 predicted proteins in Arabidopsis, the actual subcellular localisation has not been demonstrated experimentally. So far, their potential membrane-association has been deduced from algorithms that predict transmembrane domains and signal peptides. However, the comprehensiveness and accuracy of these algorithms is still limited. The majority of membrane-associated and secreted proteins is synthesised on membrane-bound polysomes. Therefore, the isolation and characterisation of mRNA associated with membrane-bound polysomes offers an experimental tool for the genome-wide identification of these proteins. Here we describe an efficient method to isolate mRNA from membrane-bound polysomes and report on the validation of the method to enrich for transcripts encoding membrane-associated and secreted proteins. The sensitivity and reproducibility of the isolation method was investigated by DNA microarray analysis. Pearson correlations between transcript levels obtained from three replicate isolations showed that the method is highly reproducible. A significant enrichment for mRNAs encoding proteins containing predicted transmembrane domains and signal peptides was observed in the membrane-bound polysomal fraction. In this fraction, 301 transcripts were classified by gene ontologies as ‘cellular component unknown’, and potentially encode previously unrecognised secreted or membrane-associated proteins.
Keywords: mRNA localisation, mRNA fractionation, predict protein localisation

overall_design: Membrane-bound (MBP) and free polysomes (FP) were isolated in triplicate from one batch of two weeks old aboveground parts of Arabidopsis seedlings. Each combination of isolated MBP and FP was applied to 4 microarrays, of which two were dyeswapped, giving a total of 12 arrays.

last: de Jong

first: Bas

last: van Breukelen

first: Floyd

last: Wittink

first: Frank

last: Menke

first: Peter

last: Weisbeek

first: Guido

last: Van den Ackerveken


title: Ischemic vs. nephrotoxic acute renal failure, early time points (2h and 8h)

city: Bethesda

last: Yuen

state: MD

address: 10 Center Drive, Room 3N108

department: NIDDK

institute: NIH

summary:
Acute renal failure (ARF) has high morbidity and mortality.  In animal ARF models, effective treatments must be administered before or shortly after the insult, limiting their clinical potential.  We used microarrays to identify early biomarkers that distinguish ischemic from nephrotoxic ARF, or that detect both injury types. We compared rat kidney transcriptomes 2 and 8 hours after ischemia/reperfusion and after mercuric chloride.  Quality control and statistical analyses were necessary to normalize inter-experimental groups, eliminate outliers, and exclude unaltered genes.  Principal component analysis revealed distinct ischemic and nephrotoxic trajectories, and clear array groupings. Therefore, we used supervised analysis, t-tests and fold changes, to compile gene lists for each group, exclusive or non-exclusive, alone or in combination.
Keywords: Disease classification/time course

overall_design: We used two lots of microarrays (Lot 1, n = 24, Lot 2, n = 12), for a total of 36 microarrays.  Five of them were duplicates, where two aliquots of RNA from the same rat were processed independently and hybridized to separate microarrays.  Normal rats were used in both lots (n = 3 for each lot) for normalization.

middle: S

first: Sang-Kyung

last: Jo

first: Robert

middle: A

last: Star


title: FDB1_GM-CSF_Receptor_Mutant_Factorial_Time_Course_Study

city: North Adelaide

first: Christopher

last: Wilkinson

state: South Australia

address: 72 King William Road

country: Australia

institute: Child Health Research Institute

summary:
To understand better the mechanisms controlling the balance between proliferation and self-renewal or growth suppression and differentiation during myelopoiesis we have utilized a cell line model that is responsive to myelopoietic cytokines and suited to large-scale gene-profiling. In addition to characterising differential growth or differentiation responses induced by Interleukin-3 (IL-3) and Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) respectively, we increased the power of this study by monitoring global gene expression changes in response to signalling from two activated mutant GM-CSF receptors which display differential signalling and leukaemogenic activity. A factorial time-course design generated a substantial and powerful dataset and linear modelling identified the expression changes associated with continued proliferation, differentiation or leukaemic signalling. We focussed on the changing transcription factor profile and defined a set of novel genes with potential to regulate myeloid growth and differentiation. We identified gene expression patterns associated specifically with the leukemic GM-CSF receptor mutant and have shown that these overlap with events associated with the FLT3 internal tandem duplications (ITD) frequently observed in AML. Such commonalities may be a key to leukaemic receptor signalling and could provide new targets for myeloid leukaemia therapies.
Keywords: time course, factorial design, cell line comparison, cytokine receptor, linear modelling

overall_design: Factorial design. First Factor was cell type with levels FDB1+Il-3 (Parental), FDB1+GM-CSF, FDB1 expressing V449E receptor mutant, FDB1 expressing FI-Delta receptor mutant. Second factor is time with levels 0, 6, 12, 24, 48 and 72 hours. Time course performed for FDB1+GM-CSF, V449E and FI-Delta cell lines with 0h reference. Matched time comparisons performed between V449E and FDB1+Il3 (0h only), V449E and FI-Delta, FI-Delta and FDB1+GM-CSF. Note 0hours represents time of removal of IL-3 (so that FDB1 cells in IL-3 (Parental), 0h is equilvalently FDB1+GM-CSF at 0h).

middle: R

first: Anna

middle: L

last: Brown

first: Chung

middle: H

last: Kok

first: Scott

last: Waterman

first: Diana

middle: G

last: Salerno

first: Sonya

middle: M

last: Diakiw

first: Brenton

last: Reynolds

last: Tsykin

first: Gary

middle: F

last: Glonek

first: Hamish

last: Scott

first: Gregory

last: Goodall

first: Patty

last: Solomon

first: Thomas

last: Gonda

first: Richard

last: D'Andrea


title: High-resolution gene copy number and expression profiling of human chromosome 22 in ovarian carcinomas

status: Public on Mar 08 2006

last: Stanford Microarray Database

summary:
This set contains the aCGH data for the publication. Previous low-resolution studies of chromosome 22 in ovarian carcinoma have suggested its involvement in the development of the disease. We report a high-resolution analysis of DNA copy number and gene expression of 22q in 18 ovarian carcinomas using a 22q-specific genomic microarray. We identified aberrations in 67% of the studied tumors, which displayed 3 distinct gene copy number profiles. The majority of the cases (11 of 18) demonstrated heterozygous terminal deletions of various sizes, the smallest of which was 3.5 Mb. The second profile, detected in 3 tumors, revealed the coexistence of heterozygous deletions and different patterns of low-copy-number gain that involved the proximal half of 22q. The latter finding has not been reported previously in ovarian carcinoma. One case displayed a continuous deletion encompassing the entire 22q, consistent with monosomy 22. Furthermore, we compared the results with the available data on these tumors by using cDNA microarrays to define the degree of correlation between abnormalities at the DNA level and variation in mRNA expression. By a comparison with the expression data, we were able to identify 21 deleted genes showing low mRNA levels and 12 amplified genes displaying elevated gene expression, several of which play roles in cell cycle control and the induction of apoptosis. Our results indicated significant correlation between DNA copy number aberrations and variation in mRNA expression. We also identified several regions and candidate genes on 22q that should be studied further to determine their role in the development of ovarian cancer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set, arrayCGH

first: Yun

last: Wang


title: Rice Seedling Stress treatment

city: Tsukuba

first: Shoshi

last: Kikuchi

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

country: Japan

institute: National Institute of Agrobiological Sciences

summary:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours (stress treated sample). Seedlings were exposed to one of the following for 24 h: cold stress, incubation at 10 °C; salt stress by adding 150 mM sodium chloride to the planter box; osmotic stress by adding 260 mM mannitol to the planter box; and drought stress by adding 25% polyethylene glycol 6000 to the planter box. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer.
Keywords = Rice
Keywords = Seedling
Keywords = stress treatment
Keywords = flood
Keywords: other

first: Hitomi

last: Yamada-Akiyama

first: Jung-Sook

last: Lee


title: NaCl Stress in Desulfovibrio vulgaris Hildenborough (Series 1)

first: Adam

last: Arkin

overall_design: Comparison of cells treated with 250mM NaCl to untreated cells at times of 0, 30, 60, 120, and 240 min.  See also Series GSE4447: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4447


title: Ecoli DH5alpha, pUC overexpression in LB + Amp vs no pUC

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary:
Responses of Escherichia coli DH5alpha as they overexpress pUC at different ODs in LB + Amp
Keywords: time course

overall_design: Escherichia coli DH5alpha expressing pUC sampled at different ODs (0.2, 0.5, 0.9) in LB + Amp vs cells not producing pUC

first: Friedrich

last: Srienc

first: Arkady

last: Khodursky


title: Transcriptional consequences of DNA gyrase inhibition

status: Public on Mar 10 2006

city: Saint Paul

first: Kyeong Soo

last: Jeong

state: MN

institute: University of Minnesota

summary:
DNA gyrase is an essential enzyme whose activity is required for DNA replication and chromosome maintenance. Inhibition of gyrase results in multiple physiological effects including changes in DNA superhelicity, replication arrest and DNA damage. Using genetic, genomic, statistical and biochemical techniques, we have untangled the contribution of individual effects, assessed their relative significance and concluded that: i) DNA replication is required for the formation of spatial transcriptional domains; ii) transcriptional response to gyrase inhibition is coordinated between at least two modules involved in DNA maintenance, relaxation and damage response; iii) genes whose transcriptional response to gyrase inhibition does not depend on the activity of topoisomerase I can be classified on the basis of the GC excess in their upstream and coding sequences into, respectively, activated and repressed by gyrase inhibition; iv) relaxation by topoisomerase I dominates the transcriptional response upon gyrase inhibition, followed by the effects of replication and RecA.
Keywords: time course

overall_design: Isogenic mutants (recA-, topA- and dnaC(Ts)) are deficient in one of cellular processes upon gyrase inhibition: DNA repair, DNA relaxation and DNA replication. With time course (0, 5, 10, 15 and 20 min) treatment of gyrase inhibitor, transcriptional responses are dissected in terms of three celluar processes. Reference samples are collected from non-treated cells at 0 min.


title: The gene expression profile of PDGF-treated neural stem cells corresponds to partially differentiated neurons and glia

status: Public on Mar 12 2006

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary:
Understanding and controlling stem cell differentiation in vitro is critical for the development of stem cell-based therapies. We have previously shown that platelet-derived growth factor AA (PDGF-AA) stimulates the expansion of neuronal progenitors from neural stem cells, but is unable to replace fibroblast-growth factor 2 (FGF-2) as a stem cell mitogen. In the present study, we compared gene expression in neural stem cells that were grown in the presence of FGF-2 to that of cells cultured with PDGF-AA or in the absence of growth factor, which induces differentiation. Most of the transcripts enriched in FGF-2-treated cells were connected to cell division (70%) and showed limited overlap with previously described stem cell transcriptional signatures. PDGF-AA significantly regulated 156 genes, 146 of which were also modified by differentiation in the absence of growth factor. The latter condition affected the expression of 153 additional genes which were regulated less than two fold by PDGF-AA. Among the genes induced by differentiation was the PDGF-A gene itself, suggesting that in the absence of exogenously added growth factors, cells make their own PDGF-AA in an autocrine manner. In addition, we identified several poorly characterized transcripts that were highly regulated and may play a role in stem cell differentiation. Our results suggest that the genetic program elicited by PDGF-AA is not unique, but an intermediate between the ones of FGF-2-cultured stem cells and differentiated cells. These observations are compatible with the hypothesis that PDGF-AA induces a partial differentiation of neural stem cells, which retain the ability to proliferate.
Keywords: treatment comparison

overall_design: Neural stem cells were grown in the presence of FGF2 (reference), in the absence of growth factor, which induces differentiation, or in the presence of PDGF for 12 hours or 6 days. Hybridizations were carried out in quadrulicates from at least two independent RNA preparations. Cy3 and cy5 dyes were swapped in two out of four replicates.

first: Mia

last: Enarsson

first: Ahmed

last: Essaghir

first: Karin

last: Forsberg-Nilsson

first: Carl-Henrik

last: Heldin


title: Genetic regulators of large-scale transcriptional signatures in cancer

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.
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
Keywords: cell_type_comparison_design

first: Howard

last: Chang


title: Gamma treatment in Davis, timecourse

summary:
Responses of Escherichia coli as they are treated to Gamma radiation in Davis medium
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (5, 10, 20, 40, 60 min) after Gamma treatment in Davis vs 0 min untreated


title: Normal placenta

status: Public on Mar 09 2006

first: Ruchira

last: Sood

address: 3373 Hillview avenue Room 220

department: Pathology

institute: Stanford University

summary:
Total RNA was isolated from all the placental tissues using Trizol, and mRNA was isolated using FastTrack Kit. We used a placenta reference as a standard for all these array hybridizations. The placenta reference is a mixture of placenta mRNA with CRG.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Novobiocin treatment in LB

summary:
Responses of Escherichia coli at 5 mins as they are treated to different concentrations of Novobiocin in LB
Keywords: dosage course

overall_design: Escherichia coli LE234 acrD- treated with 5, 20, 50, 200 ug/ml Novobiocin in LB and response at 5 mins compared with 0 min untreated


title: Genome-wide mapping of DNA re-replication in S. cerevisiae

city: San Francisco

first: Joachim

last: Li

address: 600 16th Street S376

department: Microbiology and Immunology

institute: University of California, San Francisco

type: Genome variation profiling by genome tiling array

summary:
To maintain genomic stability, re-initiation of eukaryotic DNA replication within a single cell cycle is blocked by multiple mechanisms that inactivate or remove replication proteins after G1 phase.  Consistent with the prevailing notion that these mechanisms are redundant, we previously showed that simultaneous deregulation of three replication proteins, ORC, Cdc6 and Mcm2-7, was necessary to cause detectable bulk re-replication in G2/M phase in Saccharomyces cerevisiae.  In this study, we used microarray comparative genomic hybridization (CGH) to provide a more comprehensive and detailed analysis of re-replication.  This genome-wide analysis suggests that re-initiation in G2/M phase primarily occurs at a subset of both active and latent origins, but is independent of chromosomal determinants that specify the use and timing of these origins in S phase.  We demonstrate that re-replication can be induced within S phase, but differs in amount and location fr  om re-replication in G2/M phase, illustrating the dynamic nature of DNA replication controls.  Finally, we show that very limited re-replication can be detected by microarray CGH when only two replication proteins are deregulated, suggesting that the mechanisms blocking re-replication are not redundant.  Therefore we propose that eukaryotic re-replication at levels below current detection limits may be more prevalent and a greater source of genomic instability than previously appreciated.
Keywords: comparative genomic hybridization (CGH), DNA replication, re-replication

overall_design: Genomic DNA was purified from non-replicating and (re-)replicating cells, differentially labeled with Cy3 and Cy5, and competitively hybridized to a spotted microarray containing ORF and intergenic PCR products.  Cy5/Cy3 ratios are normalized so that the average ratio of all elements equals the DNA content of the cells (as determined by flow cytometry).  For most experiments, two hybridizations were performed from each of two independent genomic DNA preparations.  (In some cases, two hybridizations were performed from a single genomic DNA preparation.)  Experiments differ in the cell cycle position, whether re-replication was induced and combination of mutations in ORC, MCM and CDC6.  Series contains a total of 50 hybridizations.

first: Brian

last: Green

first: Richard

last: Morreale

first: Bilge

last: Ozaydin

first: Joseph

last: DeRisi


title: Anaerobic growth in M9 + glucose + fumarate

summary:
Responses of Escherichia coli MG1655 as they grow anaerobically in M9 + glucose + fumarate (as electron acceptor) vs Aerobic growth OD 0.4
Keywords: time course

overall_design: Escherichia coli cells sampled at several points (OD 0.15, 0.30, 0.63, 0.85, 1.07, 1.29) in anaerobic growth in M9 + glucose vs Aerobic growth OD 0.4


title: Anaerobic growth in M9 + glucose + fumarate,genomic DNA reference

summary:
Responses of Escherichia coli MG1655 as they grow anaerobically in M9 + glucose + fumarate
Keywords: time course

overall_design: Escherichia coli cells sampled at several points (OD 0.05, 0.21, 0.43, 0.7, 1.2, stationary) in anaerobic growth in M9 + glucose + fumarate,, vs genomic DNA reference


title: Anaerobic growth in M9 + glucose, genomic DNA reference

summary:
Responses of Escherichia coli MG1655 as they grow anaerobically in M9 + glucose
Keywords: time course

overall_design: Escherichia coli cells sampled at several points (OD 0.03, 0.2, 0.35, 0.6, 0.9, stationary) in anaerobic growth in M9 + glucose, vs genomic DNA reference


title: Ecoli W3110_0.01 M sodium azide treatment vs untreated, timecourse

summary:
Responses of Escherichia coli W3110 after treatment with 0.01 M Sodium Azide in Bonner-Vogel medium + 50 ug/ml Tryptophan
Keywords: time course

overall_design: Escherichia coli W3110 cells sampled at several time points (5, 15, 30, 60 min) after addition of 0.01 M sodium azide in Bonner-Vogel + 50 ug/ml Tryptophan, vs untreated


title: Recovery from stationary phase in 10 mM Na-P (pH 7.5) + 0.2 % glucose

summary:
Responses of Escherichia coli as they recover from one stationary phase in 10 mM Na-P + 0.2 % glucose at OD 0.4
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (0, 15, 30, 45, 60, 75, 90 min) as they recover from stationary phase in 10 mM Na-P (pH 7.5) + 0.2 % glucose at OD 0.4vs Bonner-Vogel medium OD 0.5


title: Recovery from stationary phase in 10 mM Na-P (pH 7.5)

summary:
Responses of Escherichia coli as they recover from one stationary phase in 10 mM Na-P
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (0, 15, 30, 45, 60, 75, 90 min) as they recover from stationary phase in 10 mM Na-P (pH 7.5) vs Bonner-Vogel medium OD 0.5


title: Ecoli C600  Norfloxacin treatment (50 ug/ml) in LB, timecourse

summary:
Responses of Ecoli  as they are treated to 50 ug/ml Norfloxacin in LB
Keywords: time course

overall_design: Escherichia coli   cells sampled at several time points (2, 5, 10, 20, 30 min) after addition of 50 ug/ml Norfloxacin in LB vs 0 min untreated


title: Ecoli C600 (gyrArparCr) Norfloxacin treatment (50 ug/ml) in LB, timecourse

summary:
Responses of Ecoli (gyrArparCr) as they are treated to 50 ug/ml Norfloxacin in LB
Keywords: time course

overall_design: Escherichia coli (gyrArparCr)  cells sampled at several time points (2, 5, 10, 20, 30 min) after addition of 50 ug/ml Norfloxacin in LB vs 0 min untreated


title: Balanced growth of Ecoli MG1655/pTrc99a(NOX+) at different growth rates

summary:
Responses of Escherichia coli MG1655/pTrc99a(NOX+) grown at different growth rates in chemostat in M9 + salts
NOX: NADH oxygenase converts NADH to NAD. Cells with NOX are able to recycle the excess NADH generated during rapid growth, leading to lesser accumulation of acetate
Keywords: different growth rates in parallel

overall_design: Escherichia coli MG1655/pTrc99a(NOX+) cells sampled at different growth rates ( 0.13,0.21,0.28,0.34,0.4 1/hr) vs balanced growth at 0.06 1/hr


status: Public on Mar 11 2006

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 3333 Burnet Ave

department: Develpomental Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved.  Here we used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation.  We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators as well as over a hundred uncharacterized genes.  Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodals, Mixer and Sox17 have both shared and distinct sets of downstream targets and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, Sox17 and Bix1, 2, 4 and between Sox17 and Xnr4. We find that Mixer does not function primarily via Sox17 as previously proposed. This data provides a new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network.
Keywords: Embryonic, Development. Endoderm, Xenopus, nodal, Sox17, Mixer, microarray, gene regulatory network

overall_design: Define a set of transcripts with enriched expression in the gastrula endoderm of the Xenopus laevis embryo and determine how these are regulated by nodal signaling, Mixer and Sox17 using loss-of-function experiments. For more specific details see Sinner et al., (2006) Global analysis of the transcriptional network controlling Xenopus endoderm formation.

first: Debora

last: Sinner

first: Pavel

last: Kirilenko

first: Scott

last: Rankin

first: Eric

last: Wei

first: Laura

last: Howard

first: Mathew

last: Kofron

first: Janet

last: Heasman

first: Hugh

last: Woodland


title: Balanced growth of Ecoli MG1655/pTrc99a(NOX-) at different growth rates

first: Dipen

last: Sangurdekar

summary:
Responses of Escherichia coli MG1655/pTrc99a(NOX-) grown at different growth rates in chemostat in M9 + salts
Keywords: different growth rates in parallel

overall_design: Escherichia coli MG1655/pTrc99a(NOX-) cells sampled at different growth rates (growth rate 0.19,0.3,0.41,0.49,0.6 1/hr) vs balanced growth at 0.1 1/hr

first: Friedrich

last: Srienc

first: Arkady

last: Khodursky


title: Ecoli C600 (gyrArparCr) Norfloxacin treatment (15 ug/ml) in LB, timecourse

summary:
Responses of Ecoli (gyrArparCr) as they are treated to 15 ug/ml Norfloxacin in LB
Keywords: time course

overall_design: Escherichia coli (gyrArparCr)  cells sampled at several time points (2, 5, 10, 20, 30 min) after addition of 15 ug/ml Norfloxacin in LB vs 0 min untreated


title: Recovery from stationary phase in LB + glucose at OD 0.4

summary:
Responses of Escherichia coli as they recover from one stationary phase in rich media at OD 0.4
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (0, 15, 30, 45, 60, 75, 90 min) as they recover from stationary phase in LB at OD 0.4 vs Bonner-Vogel medium OD 0.5


title: Recovery from stationary phase in LB + glucose at OD 1.0

summary:
Responses of Escherichia coli as they recover from one stationary phase in rich media at OD 1.0
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (0, 15, 30, 45, 60, 75, 90 min) as they recover from stationary phase in LB at OD 1.0 vs Bonner-Vogel medium OD 0.5


title: Indol-acrylate (10 ug/ml) treatment  in Bonner-Vogel, timecourse

summary:
Responses of Escherichia coli as they are treated to 10 ug/ml Indol-acrylate in Bonner-Vogel
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (5, 15, 30, 60 min) after addition of Indol-acrylate (10 ug/ml) in Bonner-Vogel vs 0 min untreated


title: Recovery from stationary phase in LB + 0.2 % glucose

summary:
Responses of Escherichia coli as they recover from one stationary phase in rich media
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (0, 78, 105, 133, 163, 191, 218, 261, 313, 446, 1440 min) as they recover from stationary phase vs Bonner-Vogel medium OD 0.5


title: Kanamycin treatment (100 ug/ml) in M9 + glucose, timecourse

summary:
Responses of Escherichia coli as they are treated to 100 ug/ml Kanamycin in M9 + glucose
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (5, 10, 20, 30, 40, 50 min) after addition of 100 ug/ml Kanamycin in M9 + glucose vs 0 min untreated


title: Ecoli_CaCl2 wash vs before wash, timecourse

summary:
Responses of Escherichia coli as they are washed with 0.1 M CaCl2 + 15 % glycerol and kept on ice vs unwashed
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (2, 5, 10, 20, 40, 60 min) after washing with 0.1 M CaCl2 + 15 % glycerol and kept on ice vs unwashed at OD 0.43


title: Stationary phase in LB, genomic DNA reference

summary:
Responses of Escherichia coli MG1655 in stationary phase in LB
Keywords: time course

overall_design: Escherichia coli cells sampled at several points (OD 2.4, 2.8 and 3.1 (at 0, 20, 40 and 60 min)) in LB, vs genomic DNA reference


title: Normoxia versus hypoxia exposure

city: Bern

first: Christoph

last: Däpp

department: Functional Anatomy

country: Switzerland

institute: University of Bern

summary:
Exposure to 20.9% or 10.5% O2 for 24 hours of wildtype control mice, mice reloaded after hindlimb suspension and control HIF-1 alpha heterozygote mice, respectively.
Keywords: ordered

first: Max

last: Gassmann

first: Hans

last: Hoppeler

first: Martin

last: Flück

first: Silvia

last: Schmutz


title: Breast tumors

status: Public on Mar 07 2006

last: Stanford Microarray Database

summary:
Additional experiments used for intrinsic gene selection. Sorlie et al. Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74.
This Series accompanies Series GSE4335.
Experiments that were used to make the "intrinsic" gene list from.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Therese

last: Sorlie

first: Charles

last: Perou


title: Norway/Stanford Breast Tumors

summary:
Characterization of patterns of gene expression measured by cDNA microarrays to subclassify tumors  into clinically relevant subgroups. In this study, we have refined the previously defined subtypes  of breast tumors that could be distinguished by their distinct patterns of gene expression.  A total of 115 malignant breast tumors and 7 benign tissues were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into a basal epithelial-like, an ERBB2-overexpressing, two luminal epithelial-like and a normal breast tissue-like subgroup. The genes used for classification were selected based on their similar expression levels between pairs of consecutive samples taken from the same tumor separated by 15 weeks of neoadjuvant treatment.
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: Computed


status: Public on Mar 06 2006

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary:
Genome wide patterns of histone modifications in fission yeast
Keywords: High resolution maps of nucleosome modifications

overall_design: We have used oligonucleotide tiling arrays to construct genome-wide high-resolution histone acetylation maps for fission yeast. The maps are corrected for nucleosome density and reveal surprisingly uniform patterns of modifications for five different histone acetylation sites. We found that histone acetylation and methylation patterns are generally polar, i.e. they change as a function of distance from the ATG codon. A typical fission yeast gene shows a distinct peak of histone acetylation around the ATG and gradually decreased acetylation levels in the coding region. The patterns are independent of gene length but dependent on the gene expression levels. H3K9Ac shows a stronger peak near the ATG and is more reduced in the coding regions of genes with high expression compared with genes with low expression levels. H4K16Ac is strongly reduced in coding regions of highly expressed genes. A second microarray platform was used to confirm the 5’ to 3’ polarity effects observed with tiling microarrays. By comparing coding region histone acetylation data in HDAC mutants and wild type, we found that hos2 affects primarily the 5’ regions, sir2 and clr6 affect middle regions, and clr6 affects 3’ regions. Thus, mechanisms involving different HDACs modulate histone acetylation levels to maintain a 5’ to 3’ polarity within the coding regions.

first: Indranil

last: Sinha

first: Marianna

last: Wiren


title: Indol-acrylate (15 ug/ml) treatment  in Bonner-Vogel, timecourse

summary:
Responses of Escherichia coli as they are treated to 15 ug/ml Indol-acrylate in Bonner-Vogel
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (5, 15, 30, 60 min) after addition of Indol-acrylate (15 ug/ml) in Bonner-Vogel vs 0 min untreated


title: Anaerobic growth in M9 + glucose

summary:
Responses of Escherichia coli MG1655 as they grow anaerobically in M9 + glucose vs Aerobic growth OD 0.4
Keywords: time course

overall_design: Escherichia coli cells sampled at several points (OD 0.08, 0.15, 0.34, 0.73, 1.02, 1,27) in anaerobic growth in M9 + glucose vs Aerobic growth on M9 + glucose,OD 0.4


title: Ampicillin treatment (100 ug/ml) in M9 + glucose, timecourse

summary:
Responses of Escherichia coli as they are treated to 100 ug/ml Ampicillin in M9 + glucose
Keywords: time course

overall_design: Escherichia coli cells sampled at several time points (5, 10, 20, 30, 40, 50 min) after addition of 100 ug/ml Ampicillin in M9 + glucose vs 0 min untreated


title: Gene expression in lung fibroblasts of patients with emphysema

status: Public on Mar 02 2006

city: Grosshansdorf

first: Olaf

last: Holz

address: Woehrendamm 80

country: Germany

institute: KH Grosshansdorf

summary:
Exploratory design using pooled samples of 3 patients with emphysema and 3 patients without COPD
Aim: 1.Search for expressed genes to select for a custom designed array (200 genes, n=50). 2. Find highly differentially expressed genes as targets for qPCR
3. Search for regulated senescent associated genes
Keywords: disease comparison

overall_design: Three cultures of lung fibroblast from patients with emphysema with a very low proliferation rate in culture were selected and compared with 3 patients without COPD an normal proliferation rate in culture.

first: Rudolf

last: Jorres

first: Lutz

last: Welker

first: Dieter

last: Branscheid

first: Kai-Christian

last: Mueller

first: Helgo

last: Magnussen


title: Comparative study of gene expression in human colorectal cancer tissues and normal mucosa

status: Public on Mar 01 2006

city: Buenos Aires

first: Michele

last: Bianchini

address: Cramer 1180

department: Centro de Investigaciones Oncologicas

country: Argentina

institute: Instituto Alexander Fleming

summary:
The purpose of our study was to better understand the genetic mechanism of oncogenesis for human colorectal cancer and to identify potential new tumour markers of use in clinical practice.
Results: Comparing cancerous tissues with normal colonic mucosa we identified 584 known genes (3%) differentially expressed to a significant degree (p<0.001). Many of the transcripts that were more abundant in tumours than in non-neoplastic tissues appear to reflect important events for colon carcinogenesis. For example, a significant number of these genes serve as apoptotic inhibitors (e.g. BFAR, BIRC1, BIRC6). Furthermore, we observed the simultaneous upregulation of HLA-E and the downregulation of b2-microglobulin; these genes strongly support a potential tumour escape strategy from immune surveillance in colon cancer tissues.
Conclusions: Our study provides new gene candidates in the pathogenesis of human CRC disease. From our results we hypothesise that CRC cells escape immune surveillance through a specific gene expression alteration; moreover, overexpression of several survival genes seems to confer a more anti-apoptotic phenotype. These genes are involved in pathways not previously implicated in CRC pathogenesis and they may provide new targets for therapy.
Keywords: disease state analysis

overall_design: We used cDNA microarrays to compare gene expression profiles of colorectal biopsies from 25 CRC patients and 13 normal mucosa from adjacent noncancerous tissues. Normal samples were pooled in equimolar amounts to generate a single standard reference RNA employed as a control in each microarray hybridisation. For half of microarray hybridisations, total RNA isolated from each tumour sample were retrotranscribed and labelled with Cy5-dCTP and cDNA obtained from the standard reference RNA was labelled with Cy3-dCTP; the fluorochromes were inverted in the second half of microarrays with the purpose of reducing dye bias. Findings were validated by real time PCR; in addition, western blotting and immunochemistry analysis were carried out as further confirmation of differential expression at a protein level.


title: Time course analysis of genes regulated by E. coli sigma 32 (rpoH) after overexpression

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

institute: UCSF

summary:
DNA microarray analysis of genes regulated by the alternative sigma factor, sigma 32 (rpoH). Sigma 32-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma 32, with a strain over-expressing sigma 32 (following induction of rpoH from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses. Because sigma 32 is negatively regulated, its activity decreases 10 min after overexpression. Consequently, to identify genes regulated by sigma 32 we analyzed the expression data for 10 min after overexpression using SAM (Statistical Analysis of Microarrays). We identified 105 genes organized in 66 separate transcription units. This study is detailed in Nonaka et al 2006 (submitted).
Keywords: time course

overall_design: This series consists of 4 replicated time courses from separate biological samples. Each time course consists of a comparison between wild type E.coli MG1655 that has a low level of sigma 32, and an over-expressing sigma 32 strain following induction of rpoH from an inducible promoter by IPTG. Both strains were grown to mid log and then induced with IPTG and incubation resumed. Samples were removed for comparative microarray analysis immediately prior to induction, and at 2.5, 5, 10, and 20 min after induction. To correct for changes in growth state, control and over-expressed samples were always compared from the same time point. Note time course 4 only contains the 10 min samples.

first: Gen

last: Nonaka

first: Matthew

last: Blankschien

first: Christophe

last: Herman

first: Carol

last: Gross


title: Adult fly versus embryo (0-16h)

status: Public on Feb 28 2006

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

institute: Swiss Federal Institute of Technology

summary:
Total RNA was isolated from wild-type adult flies (yellow white) and from embryos (cs, 0-16h) with TRIZOL reagent.  12 microgram of each total RNA were labeled with fluorescent dyes, following cDNA synthesis with amino-allyl dUTP in addition to the four natural dNTPs using a 1:1 mixture of oligo(dT) and random nonamer primers.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs


title: Acute Lymphedema

status: Public on Mar 04 2006

first: Roger

last: Wagner

department: Falk Cardiovascular Research Center

institute: Stanford University School of Medicine

summary:
Mouse surgical model of acute lymphedema induction. We performed three sets of microarrays with three replicates each for a total of 9 arrays.  Each array was run using pooled RNA from three animals.  The three conditions were Normal tail skin (no intervention), Lymphedema tail skin(due to surgical lymphatic vessel blockage), and Surgical Sham control tail skin(surgical incision with no lymphatic vessel blockage).  15ug of test and reference (e17.5 mouse whole embryo) RNA was used for labeling.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Stanley

last: Rockson

first: Lauren

last: Cheung


title: Form deprivation modulates retinal neurogenesis in primate experimental myopia

status: Public on Feb 27 2006

city: Boston

first: Andrei

middle: V

last: Tkatchenko

address: 220 Longwood Avenue, B2-201

department: Neurobiology

institute: Harvard Medical School

summary:
Juvenile primates develop myopia when their visual experience is degraded by lid fusion. In response to the abnormal visual input, retinal neural networks cause an excessive growth of the postequatorial segment of the eye, but the mechanism underlying this axial elongation is unknown. By combining analysis of gene expression, injection of the thymidine analog 5-bromo-2'-deoxyuridine and immunocytochemistry, we show that the retinal periphery in both juvenile rhesus macaques and green monkeys harbors a population of mitotically active neuroprogenitor cells that proliferate when the visual experience is altered by lid fusion. Furthermore, the number of dividing cells is highly correlated with the axial elongation of the eye and the resulting myopic refractive error. Thus, the retina undergoes active growth during the postnatal development of the primate eye. This growth is modulated by the visual input and accelerates considerably when the eye develops axial myopia.
Keywords: disease state analysis

overall_design: cDNA subtractions, construction of cDNA libraries and differential screening were performed as previously described (Tkatchenko et al, 2000). Two subtractions were carried out resulting in two cDNA libraries. One library was enriched in clones potentially up-regulated in the retina of the closed eye and the other was enriched in cDNAs potentially down-regulated. One thousand clones from each library were analyzed, and 535 differentially-expressed cDNAs were amplified by PCR and spotted onto glass slides coated with poly-L-lysine (five duplicates for each cDNA). The slides were then processed, hybridized with Cy3- and Cy5-labeled complex cDNA probes and washed in 0.2xSSC as described at http://cmgm.stanford.edu/pbrown/protocols/. Two hybridizations with color swap were carried for each monkey. After hybridization, slides were scanned using a GenePix 4000B microarray scanner (Axon Instruments, Union City, CA). The images were acquired and processed using the GenePix Pro 5.1 software package (Axon Instruments). The data obtained were normalized against GAPDH expression level and mean values (the reported values) and P-values (probability associated with a Student's t-test) were calculated for duplicate experiments (n = 10) with color swap using Microsoft Excel. Genes were defined as differentially regulated if P< 0.05. Cluster analysis was performed using the Genesis software package (provided by Alexander Sturn, Graz University of Technology, Austria).

first: Pamela

last: Walsh

first: Tatiana

first: Stefano

last: Gustincich

first: Elio

last: Raviola


title: Ovarian cancers

status: Public on Feb 25 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
Schaner M., et al.; Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 1
Unsupervised hierarchical clustering of ovarian cell lines and ovarian cancers. Cell lines were not co-clustered with the tumor specimens, because these cell lines have a very prominent proliferation cluster (Perou et al., 1999; Ross et al., 2000) that significantly influences the clustering of the tumor samples if the two sample sets are not analyzed separately.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Marci

last: Schaner

first: Douglas

last: Ross


title: Hypoxic changes in gene expression: effect of vhl and p53 genotype

first: Nicholas

last: Denko

address: Rm 1245 269 campus dr

department: Radiation Oncology

summary:
Microarrray experiments were performed in order to identify genes whose expression is altered under hypoxic conditions and to determine whether these changes are dependant on the p53 and HIF tanscription factors. In order to determine HIF dependance, isogenic RCC4 cell lines were used that were either wildtype of null for vhl, the gene responsible for degrading HIF under normoxic conditions. In order to determine p53 dependance, isogenic HCT116 and H1299 cell lines that were wildtype or null for p53 were used. Gene expression was measured after exposure of cells in monolayer culture to hypoxia (<0.01% O2) for various times.
Keywords: hypoxia, time course, genetic modification, cell line comparison

overall_design: Affymetrix genechips were used to measure expression in cells exposed to hypoxia in monolayer culture for different times. One replicate was analysed at each time point, except for the control (0 hr) and 18 hr time points in the RCC4 cells, where two independant replicates were performed.

first: Ioanna

last: Papandreou

first: Rob

last: Cairns

first: Lucrezia

last: Fontana

first: Ai

last: Lim

middle: C


title: Breast and ovarian carcinoma

summary:
Schaner, M., et al.;  Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 4
Clustering of breast and ovarian carcinoma cases. 68 breast and 57 ovarian cases were co-clustered to discern both similarities and disparities between the two sample sets. An ovarianspecific set of highly expressed transcripts was identified in comparison to breast across the 3363 transcripts.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Charles

last: Perou


city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary:
Gene expression measured at maximal Salmonella growth rate in different media
Keywords: other

first: Gyejung

last: Yun

first: Steffen

last: Porwollik

first: Pui

last: Cheng

first: Carlos

last: Santiviago


title: cDNA microarray analysis of human skeletal muscle after endurance exercise

status: Public on Feb 17 2006

city: Ottawa

middle: Joseph

last: Mahoney

state: ON

address: 401 Smyth Rd

department: Apoptosis Research Center

country: Canada

institute: CHEO Research Institute

summary:
We examined global mRNA expression using cDNA microarrays in skeletal muscle of humans before, and 3h and 48h after a single bout of exhaustive endurance exercise (cycling).
Keywords: Time course

overall_design: Healthy, non-trained university-aged subjects performed a single bout of exhaustive cycling.  Skeletal muscle biopsies were taken from the vastus lateralis before, 3h and 48h after the exercise bout.  Total RNA was extracted, amplified, reverse transcribed, and cDNA was analyzed on a custom made cDNA microarray.  Four subjects were analyzed, and samples were not pooled between subjects (i.e. individual microarrays were used for baseline vs. 3H and baseline vs. 48h for EACH subject; repeated measures design).

first: Gianni

last: Parise

first: Simon

last: Melov

first: Adeel

last: Safdar

first: Mark

last: Tarnopolsky


title: Expression Changes Relevant for Apoptosis in K562 Cells Co-Treated with Amifostine and Imatinib

first: Michele

last: Bianchini

summary:
We had previously demonstrated an increased proapoptotic effect of Imatinib (STI571) in combination with Amifostine (AMI) in K562 cell line. In this study we used genomic scale gene expression profiling to monitor changes at transcriptional level in K562 cells during the treatment with AMI+STI571. We identified a transcriptional repressor of survival genes, known as BTF, which triggers a pro-apoptotic signal, potentially helpful to overcome the resistance to STI571. This finding could be particularly useful to design novel therapeutic strategies for leukaemia patients.
Keywords: Pharmacogenomic

overall_design:
cRNA from Control and Treated K562 cells were mixed in equal amounts and incubated with a microarray slide for hybridisation. RNA from six independent paired experiments was subjected to transcriptional profiling.
To identify a list of genes that best distinguishes the joint effect of the two drugs from what might be predicted on the basis of their effects alone, we decided to apply a class of experimental design named multifactorial design, as described by Y.H. Yang and T. Speed (15). If we let C denote mRNA that is derived from the untreated cells (Control), and A and S denote mRNA that is derived from the cells that were treated by AMI and STI571 separately, we can then use AS to denote cells that were treated with both drugs simultaneously. Since our main interest was to identify gene variations due to the drug interaction (named “AS effect”), experimental design that offers the best precision, is a balance of direct and indirect comparison.


title: Global Identification of Noncoding RNAs in S. cerevisiae

city: Moffett Field

first: Waraporn

last: Tongprasit

institute: NASA Ames Research Center

type: Expression profiling by genome tiling array

summary:
Genome-wide detection of novel non-coding RNAs in S. cerevisiae by
modulating an RNase P pathway through the depletion of a component RPP1.
Keywords: time course

overall_design:
Nearly 400,000 36-mer oligonucleotide probes, tiling the entire yeast
genome including the mitochondrial chromosome with an average gap of 10
bases between two consecutive probes, were synthesized on glass slides
using a mask-less array synthesizer. RNA samples for hybridizing to the
arrays were extracted from a conditional lethal allele of S. cerevisiae
created by placing the RPP1 gene under control of GAL10 promoter. It
allowed the expression of RPP1 in galactose-containing culture medium but
suppressed its expression in glucose-containing medium. A wild-type
isogenic strain was used as a control. Both strains were initially grown
in galactose-containing medium and subsequently transferred and
resuspended into glucose-containing medium. Eight arrays were hybridized
with RNA extracted from the Rpp1-depleted cells at 0, 4, 7, 12, 16, 21,
30h, and the control cell at 30h, after initial transfer to
glucose-containing medium.

first: Manoj

middle: P

last: Samanta

first: Himanshu

last: Sethi

first: Chen-shan

last: Chin

first: Viktor

last: Stolc


title: Breast Cancer Cell Lines

status: Public on Feb 16 2006

city: Vancouver

first: Ashleen

last: Shadeo

state: BC

address: 675 west 10th Ave

institute: British Columbia Cancer Research Center

summary:
7 breast cancer cell lines were differentially labeled and each competitively hybridized against female genomic DNA using the 32K SMRT Array
Keywords: None

first: Wan

last: Lam


title: Expression Profile of Signal Transduction Components in a Sugarcane Population Segregated for Sugar Content

status: Public on Feb 14 2006

city: Campinas

first: Renato

last: Vicentini

state: SP

address: Cidade Universitaria "Zeferino Vaz"

department: Centro de Biologia Molecular e Engenharia Genetica - CBMEG

country: Brazil

institute: Universidade Estadual de Campinas - UNICAMP

summary:
Sucrose is the major product of photosynthesis in many higher plants. It is transported from the source tissue through the phloem to various sink tissues to support plant growth, development and reproduction. Knowledge of the signal transduction pathways involved in carbohydrate metabolism is limited. Genes involved in the regulation of sucrose synthesis and accumulation could be used as tools in the development of genetically manipulated plants with higher sucrose content or aid in breeding programs as molecular markers. Using the SUCEST (Sugarcane EST) database information and a microarray approach, the expression profiles of 1920 sugarcane (Saccharum spp.) genes encoding signal transduction elements, transcription factors and stress-related proteins were analyzed. In order to assess their involvement in sucrose metabolism, the expression profiles of individuals from a sugarcane population segregated for sugar content were compared. From a population of 500 F1 individuals, the seven with the highest and the seven with the lowest sugar contents were selected, pooled and profiled using cDNA microarrays. Twenty-four genes were identified as differentially expressed. Five of them were more expressed in the plants with the highest sugar contents and 19 in the plants with the lowest sugar contents. RNA-blot hybridization was used to validate the expression profiles obtained for individuals in each group. These genes were shown to have differential expression throughout the growing season and in the different tissues. Our data supports the view that sugar levels modulate a complex signal transduction network that seems to involve responses related to stress.
Keywords: Segregated population

overall_design: Our experiment consisted in two microarrays hybridizations comparing two pooled samples, high and low sugar content sugarcane leaves. The replication of this experiment was only technical replication and we did also a dye-swap.


title: Wild-type versus Pumilio mutant flies

first: Andre

last: Gerber

summary:
Total RNA was isolated with TRIZOL reagent from wild-type flies (yellow white, yw) and Pumilio mutant flies (pum13; Barker DD. et al. (1992) Genes Dev 6, 2312-26). 12 microgram of total RNA was used for cDNA synthesis using a 1:1 mixture of oligo(dT) and random nonamer primers and in the presence of amino-allyl dUTP.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed


title: GLA and profiling of proteasome, Spt23 and Mga2

first: Pamela

last: Silver

address: 200 Longwood Ave

department: Systems Biology

type: Genome binding/occupancy profiling by array

summary:
The proteasome can regulate transcription through proteolytic processing of transcription factors and via gene locus binding, but few targets of proteasomal regulation have been identified.  Using genome-wide location analysis and transcriptional profiling in Saccharomyces cerevisiae, we have established which genes are bound and regulated by the proteasome, and by Spt23 and Mga2, transcription factors activated by the proteasome.   We observed proteasome association with gene sets that are highly transcribed, controlled by the mating-type loci, and involved in lipid metabolism.  At ribosomal protein genes, proteasome and RNA polymerase II binding was enriched in a proteasome mutant, indicating a role for the proteasome in dissociating elongation complexes.  The genomic occupancies of Spt23 and Mga2 overlapped significantly with the genes bound by the proteasome.  Finally, the proteasome acts in two distinct ways, one dependent and one independent of Spt23/Mga2 cleavage, providing evidence for cooperative gene regulation by the proteasome and its substrates.
Keywords: ChIP-chip; genetic modification transcriptional profiling

overall_design: Six genomic localization analysis (GLA, ChIP2) experiments are represented by 18 samples. Six transcriptional profiling experiments (prof) are also represented. Experiments were generally done in triplicate, with fluors swapped on the third replicate.

first: Kathryn

last: Auld

first: Christopher

last: Brown

first: Jason

last: Casolari

first: Suzanne

last: Komili


title: High Resolution Mapping of DNA Copy Alterations in Human Chromosome 22 Using High Density Tiling Oligonucleotide Arrays

city: New Haven

first: Jan

middle: Oliver

last: Korbel

state: CT

address: 266 Whitney Avenue

institute: Yale University

summary:
Deletions and amplifications of the human genomic sequence (Copy Number Polymorphisms, or 'CNPs') are the cause for numerous diseases and a potential cause of phenotypic variation in the normal population. Comparative Genomic Hybridization (CGH) has been developed as a useful tool for detecting alterations in DNA copy number that involve blocks of DNA several kilobases or greater in size. We have developed High-Resolution CGH (HR-CGH) to detect accurately and with relatively little bias the presence and extent of chromosomal aberrations in human DNA. Maskless array synthesis was used to construct arrays containing 393,000 oligonucleotides with
isothermal probes of 45-85 bp in length; arrays tiling the β-globin locus and chromosome 22q were prepared. Arrays with 9 bp tiling path were used to map a 622 bp heterozygous deletion in the β-globin locus. Arrays with an 85 bp tiling path were used to analyze DNA from patients with copy number changes in the pericentromeric region of chromosome 22. Heterozygous deletions and duplications as well as partial triploidies and partial tetraploidies of portions of chromosome 22q were mapped with high resolution in each patient, and the precise breakpoint of two deletions was confirmed by DNA sequencing. Additional peaks potentially corresponding to
known and novel additional CNPs were also observed. Our results demonstrate that HR-CGH allows the detection of copy-number changes in any given region of the human genome comprehensively and at an unprecedented level of resolution.
Keywords: high resolution comparative genome hybridization (HR-CGH)

overall_design: The overall goal of the study was the detection of the precise boundaries of chromosomal aberrations involved in disease. Maskless array synthesis was used to construct custom isothermal arrays containing up to 385,000 oligonucleotides, either tiling the non-repetitive regions of chromosome 22, or focussing on the beta-globin locus on chromosome 11. Genomic DNA isolated from patients (Cy3) was co-hybridized with a reference DNA pool (Promega; Cy5).

first: Alexander

middle: E

last: Urban

middle: O

first: Rebecca

last: Selzer

first: Todd

last: Richmond

first: Joseph

last: Cubells

first: George

last: Popescu

first: April

last: Hacker

first: Roland

last: Green

first: Beverly

last: Emanuel

middle: B

last: Gerstein

first: Sherman

last: Weissman

first: Michael

last: Snyder


title: Resveratrol-Induced Gene Expression Profiles in Human Prostate Cancer Cells

last: Stanford Microarray Database

department: Stanford University, School of Medicine

summary:
Cell Culture and Treatments The LNCaP cell line was obtained from American Type Culture Collection (Manassas, VA) and maintained in RPMI medium with 10% fetal bovine serum (CDT; Hyclone Laboratories, Logan, UT) and penicillin/streptomycin (Mediatech, Herndon, VA) in an environment of 95% air and 5% CO2 at 370C. Upon reaching 75% confluence, cells were treated with either DMSO control or purified resveratrol at several concentrations (LKT Laboratories, St. Paul, MN), dissolved in DMSO, and incubated for varying lengths of time. Final concentration of DMSO in media was 0.01%. Total RNA was prepared from cells using TRIzol (Invitrogen Life Technologies, Carlsbad, CA).
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

overall_design: Computed

first: Sunita

last: Jones

first: Samuel

last: DePrimo


title: Deciphering cellular states of innate tumor drug responses

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

summary:
Clinical drug resistance is one major concern in the treatment of human cancers, most of them being found resistant to therapy at the time of drug presentation. Deciphering the molecular mechanisms that contribute to such innate drug resistance should improve both the prediction of treatment failure and the development of new strategies to overcome resistance. Our study reports for the first time a systems approach toward understanding the in vivo cellular states of clinical samples collected from colorectal cancer (CRC) patients prior to their exposure to combined chemotherapy of folinic acid (FA), 5-fluorouracil (5-FU) and irinotecan (CPT-11).
Vigilant experimental design, power simulations and robust statistics were used to restrain the rates of false negative and false positive hybridizations, allowing successful discrimination between drug resistance and sensitivity states with restricted sampling. A list of 679 genes was established which intrinsically differentiate, for the first time prior to drug exposure, subsequently diagnosed chemo-sensitive and resistant patients. Independent biological validation performed through quantitative-PCR confirmed the expression pattern on two additional patients. Careful annotation of interconnected functional networks provided a unique representation of the cellular states underlying drug responses.
Molecular interaction networks were described that provide a solid foundation on which to anchor working hypotheses about mechanisms underlying in vivo innate tumor drug responses. These broad-spectrum cellular signatures represent a starting point from which by-pass chemotherapy schemes, targeting simultaneously several of the molecular mechanisms involved, may be developed for critical therapeutic intervention in CRC patients. The demonstrated power of this research strategy makes it generally applicable to other physiological and pathological situations.
Keywords: Drug response

overall_design:
Microarray analyses were applied to tumor biopsies (including 9 tumor colons, 13 liver metastases, 6 adjacent non tumoral colons) from 13 individuals following a randomized and blinded unbalanced design. RNA labelling, hybridization and analysis of fluorescence was carried out, considering that uneven numbers of samples were randomly allocated to each of the engineers who were not aware of sample phenotypes. To assess data reproducibility and minimize dye bias effects, each of the samples was measured four times, twice with Cy3 and twice with Cy5. To ensure robustness and flexibility in data analysis, a reference design was used with a universal reference sample (Stratagene, USA) serving as a baseline for the comparisons of tumor samples.
Hybridizations were performed onto an 11K human array (GPL3282), which provides a genome-wide coverage of functional pathways. Raw data were obtained using the ArrayVision™ 7.0 software (Imaging Research Inc., USA); the resulting 3.2x106 hybridization data points collected from 70 arrays were stored in a database and pre-processed for normalization and filtering.
Statistical comparison was done considering that biopsies collected prior to drug exposure may be subsequently categorized in two groups of chemo-sensitive or resistant samples in view of the initial response rates of individual patients to combined chemotherapy. The initial response rate to combined chemotherapy (complete or partial regression, stabilization or progression of disease) was evaluated after two treatment cycles as described in [Ychou, et al. (2004) J of Clinical Oncology. 22 (Supp 14S):3601, Douillard, et al. (2000) Lancet. 355:1041-7], according to the complete guideline to evaluate the response to treatment described in [Therasse, et al. (2000) J Natl Cancer Inst. 92:205-16].

first: Esther

last: Graudens

first: Virginie

last: Boulanger

first: Cindy

last: Mollard

first: Régine

last: Mariage-Samson

first: Xavier

last: Barlet

first: Guilaine

last: Grémy

first: Christine

last: Couillault

first: Malika

last: Lajémi

first: Dominique

last: Piatier-Tonneau

first: Patrick

last: Zaborski

first: Eric

last: Eveno

first: Charles

last: Auffray


title: Ovarian cell lines

summary:
Schaner, M., et al.  Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 1
Ovarian Cell Lines
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Marci

last: Schaner


title: Taxane-selected ovarian cancer cell lines

last: Stanford Microarray Database

type:
Expression profiling by array
Genome variation profiling by array

summary:
Each of the six ovarian carcinoma cell lines was exposed to docetaxel or paclitaxel at IC50 levels (the concentration required to kill 50% of the population). After several passages at this initial concentration of taxanes, drug concentrations were escalated, and this process was repeated until variants displayed at least a 10-fold resistance to the selecting agents. mRNA and genomic DNA were isolated from the parental and resistant variants, and hybridized onto Stanford human cDNA microarrays containing about 42000 elements. We analyzed the gene expression profiles and copy number alterations, and identified a cluster of genes co-activated with MDR1 on chromosome arm 7q21. In six of these variants, regional activation was driven by gene copy number alterations, with low-level gains or high-level amplifications spanning the involved region. However, three variants displayed a regional increases in gene expression even without concomitant gene copy number changes. These results suggest that regional gene activation may be a fundamental mechanism for acquired drug resistance, with or without changes in gene dosage. In addition to numerical and structural chromosomal changes driven by genome instability in cancer cells, other mechanisms might be involved in MDR1 regional activation, such as chromatin remodeling and DNA or histone modifications of the 7q21 region.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Keywords: compound treatment design, arrayCGH, expression profiles

first: Yan

last: Wang


title: Transcriptome analysis of a cnidarian – dinoflagellate mutualism reveals complex modulation of host gene expression

status: Public on Feb 21 2006

city: Corvallis

first: Mauricio

last: Rodriguez-Lanetty

state: OR

address: 3029 Cordley Hall

department: Zoology

institute: Oregon State University

summary:
Background: Cnidarian – dinoflagellate intracellular symbioses are one of the most important mutualisms in the marine environment.  They form the trophic and structural foundation of coral reef ecosystems, and have played a key role in the evolutionary radiation and biodiversity of cnidarian species.  Despite the prevalence of these symbioses, we still know very little about the molecular modulators that initiate, regulate, and maintain the interaction between these two different biological entities. In this study, we conducted a comparative host anemone transcriptome analysis using a cDNA microarray platform to identify genes involved in cnidarian – algal symbiosis.

Results: We detected statistically significant differences in host gene expression profiles between sea anemones (Anthopleura elegantissima) in a symbiotic and non-symbiotic state.  The group of genes, whose expression is altered, is diverse, suggesting that the molecular regulation of the symbiosis is governed by changes in multiple cellular processes.  In the context of cnidarian – dinoflagellate symbioses, we discuss pivotal host gene expression changes involved in lipid metabolism, cell adhesion, cell proliferation, apoptosis, and oxidative stress.

Conclusion: Our data do not support the existence of symbiosis-specific genes involved in controlling and regulating the symbiosis.  Instead, it appears that the symbiosis is maintained by altering expression of existing genes involved in vital cellular processes.  Specifically, the finding of key genes involved in cell cycle progression and apoptosis have led us to hypothesize that a suppression of apoptosis, together with a deregulation of the host cell cycle, create a platform that might be necessary for symbiont and/or symbiont-containing host cell survival. This first comprehensive molecular examination of the cnidarian – dinoflagellate associations provides critical insight into the maintenance and regulation of the symbiosis.
Keywords: comparative genomic hybridization

overall_design: We applied a multiple dye-swap experimental design for the two conditions, aposymbiotic and symbiotic anemone groups, compared in our experiment. For this experiment, there were no reference samples. Six biological replicates per condition were used as recommended for this type of two-comparison experimental design.  There were not technical replicates on the array.

first: Wendy

middle: S

last: Phillips

first: Virginia

last: Weis


title: Fur mutant analysis

status: Public on Feb 03 2006

summary:
Wildtype G27 and it's Fur mutant derivative were exposed to pH 5.0 for the indicated length of time.  Bacterial cells in the exponential phase of growth (denoted log) and stationary phase of growth were used.  fur1 denotes a single fur mutant while fur2 denotes an additional fur mutant.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Douglas

last: Merrell


title: Mesothelioma differential expression

city: Nancy

first: Bertrand

last: Rihn

address: 5 rue A Lebrun

department: Faculté de Pharmacie

institute: Université de Lorraine

summary:
To investigate the molecular events controlling malignant transformation of human pleural cells, we compared constitutive gene expression of mesothelioma cells to that of pleural cells. Using cDNA microarray and high-density filter array, we assessed expression levels of > 6500 genes. Most of the highly expressed transcripts were common to both cell lines and included genes associated with stress response and DNA repair, outcomes consistent with the radio- and chemo-resistance of mesothelioma. Interestingly, of the fewer than 300 genes that differed between cell lines, most functioned in (i) macromolecule stability, (ii) cell adhesion and recognition, (iii) cell migration (invasiveness), and (iv) extended cell division
Keywords: c-DNA array from Incyte Pharmaceuticals™, cell line comparison

overall_design: Target cDNA was generated from 1 μg polyadenylated mRNA that was reverse transcribed to produce cDNA and labeled either with Cy3 (MSTO-211H) or Cy5 (Met-5A) dUTP. The average intensity of the Cy3 fluorescence divided by the average intensity of the Cy5 fluorescence equaled 0.97 (balance coefficient), indicating similar labeling efficiency for each set of target cDNAs. Target cDNA was hybridized on Incyte Pharmaceuticals™ arrays containing 6356 probes with sequences complementary to 4311 human genes and 2045 human expressed sequence tags (ESTs) (Unigem V™, Genome Systems Inc., St Louis, MO, USA). Dye-swaps were performed. More than 600 probes were internal and external controls. Inclusion criteria were derived from an image recognition algorithm for each cDNA in the analysis and included a fluorescent signal from the cDNA exceeding a signal to background ratio of 2.5 and the cDNA covering its grid location on the microarray for >40%. In this study, genes were considered differentially expressed (DE) if the change was >2.0-fold. The cDNAs corresponding to genes of known function were sorted by enzyme, function or pathway cluster analysis using a Gemtools software (v2.4.2, Incyte Pharmaceuticals, Freemont, CA, USA).

first: Steve

last: Mohr


title: Virulent and nonvirulent Entamoeba species comparison

status: Public on Feb 02 2006

summary:
Entamoeba histolytica is a protozoan parasite that causes colitis and liver abscesses. Several Entamoeba species and strains with differing levels of virulence have been identified. E. histolytica HM-1:IMSS is a virulent strain, E. histolytica Rahman is a nonvirulent strain, and Entamoeba dispar is a nonvirulent species. We used an E. histolytica DNA microarray consisting of 2,110 genes to assess the transcriptional differences between these species/strains with the goal of identifying genes whose expression correlated with a virulence phenotype. We found 415 genes expressed at lower levels in E. dispar and 32 genes with lower expression in E. histolytica Rahman than in E. histolytica HM-1:IMSS. Overall, 29 genes had decreased expression in both the nonvirulent species/strains than the virulent E. histolytica HM-1:IMSS. Interestingly, a number of genes with potential roles in stress response and virulence had decreased expression in either one or both nonvirulent Entamoeba species/strains. These included genes encoding Fe hydrogenase (9.m00419), peroxiredoxin (176.m00112), type A flavoprotein (6.m00467), lysozyme (6.m00454), sphingomyelinase C (29.m00231), and a hypothetical protein with homology to both a Plasmodium sporozoite threonine-asparagine-rich protein (STARP) and a streptococcal hemagglutinin (238.m00054). The function of these genes in Entamoeba and their specific roles in parasite virulence need to be determined. We also found that a number of the non-long-terminal-repeat retrotransposons (EhLINEs and EhSINEs), which have been shown to modulate gene expression and genomic evolution, had lower expression in the nonvirulent species/strains than in E. histolytica HM-1:IMSS. Our results, identifying expression profiles and patterns indicative of a virulence phenotype, may be useful in characterizing the transcriptional framework of virulence.
A species experiment design type assays differences between distinct species.
Keywords: species_design

overall_design: User Defined

first: Ryan

last: Macfarlane

first: Michael

last: Howitt


title: Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor

summary:
A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Jane

last: Huang


title: A DNA integrity network in the yeast Saccharomyces cerevisiae

city: Baltimore

first: Daniel

last: Yuan

address: 733 N. Broadway, Suite 351

department: Molecular Biology and Genetics

institute: Johns Hopkins Univ School of Medicine

summary:
A network governing DNA integrity was identified in yeast by a global genetic analysis of synthetic fitness or lethality defect (SFL) interactions. Within this network, multiple functional modules or mini-pathways were defined according to their common patterns of global SFL interactions and available protein-protein interaction information. Modules or genes involved in DNA replication, DNA replication checkpoint signaling, and oxidative stress response were identified as the major guardians against lethal spontaneous DNA damage, efficient repair of which requires the functions of the DNA damage checkpoint signaling and multiple DNA repair pathways. This genome-wide genetic interaction network also revealed potential roles of a number of genes and modules in mitotic DNA replication and maintenance of genomic stability. These include DIA2, NPT1, HST3, HST4, and the CSM1/LRS4 module (CSM1m). Likewise, the CTF18 module (CTF18m), previously implicated in sister chromatid cohesion, was found to participate in the DNA replication checkpoint.
Keywords: dose response

overall_design: This study surveyed the effects of second-site ("query") null mutations, or exposure to genotoxic agents, on the viability of strains already carrying a null mutation in another gene. Of the 119 datasets, 72 datasets were for different query genes, while 25 other datasets were added for 21 of the query genes to confirm and extend the analysis. The remaining 22 datasets were dose-response studies involving a total of four genotoxic agents.

first: Xuewen

last: Pan

first: Ping

last: Ye

first: Xiaoling

first: Joel

last: Bader

first: Jef

middle: D

last: Boeke


title: Spore formation of Lentinula edodes

status: Public on Feb 09 2006

city: Shatin

first: Hoi Shan

last: Kwan

state: Hong Kong SAR

department: Biology

country: China

institute: The Chinese University of Hong Kong

summary:
Gene expression profiles before and after spore formation of Lentinula edodes (L54)grown at sawdust.
Keywords: time-course

overall_design:
SAGE were used to generate tags from RNA of fruit bodies of L. edodes. RNA were extracted from the fruit bodies before and after spore observed.
Gene expression profiles of both stages were compared to screen out genes may relate to spore formation.

first: Hoi-Shan

first: Wing-Yan

middle: W

last: Chum


title: Response to antimycin A in wild type Arabidopsis and in alternative oxidase overexpresser

city: East Lansing

first: Jianping

last: Yu

state: MI

address: Michigan State University

department: Plant Research Laboratory

institute: Michigan State University

summary:
In higher plants, various developmental and environmental conditions enhance expression of the mitochondrial alternative oxidase (AOX). In this work transgenic Arabidopsis thaliana plants were generated that either overexpress AOX or inhibit its synthesis. Gene expression following antimycin A treatment, which inhibits the cytochrome pathway in mitochondria, was studied in an AOX overexpressor line. An accumulation of AOX protein blocked normal responses of a number of genes, including some AOX genes. This result indicates that AOX can generate feedback to inhibit induction of its own synthesis.
Keywords: stress response

overall_design:
Two wild type replicates: Poly-A RNA from two batches of plants were labeled with dye-swaps then hybridized to custom-designed arrays containing two sets of spotted DNA elements.
Two S5 replicates: Poly-A RNA from two batches of plants were labeled with dye-swaps then hybridized to custom-designed arrays containing three sets of spotted DNA elements.

first: Lee

last: McIntosh

first: Roxy

last: Nickels

first: Per

last: Gardestrom


title: The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans

status: Public on Feb 01 2006

last: Stanford Microarray Database

state: CA

summary:
This set of arrays contains all microarray experiments done involving comparisons among C. elegans natural isolates and mutation-accumulation lines.
Abstract: The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection, whereas others claim that most between-species regulatory changes are neutral or nearly neutral. We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Dee

last: Denver


title: Hyperplastic gastric tumor of K19-C2mE transgenic mouse

city: Sakyo-ku, Kyoto-shi

first: Akihiro

last: Matsunaga

state: Kyoto

address: Yoshida-konoe-cho

department: Medicine

institute: Kyoto University

summary:
Cyclooxygenase-2 (COX-2), the rate-limiting enzyme for prostanoid biosynthesis, plays a key role in gastrointestinal carcinogenesis. Among various prostanoids, prostaglandin E2 (PGE2) appears to be most responsible for cancer development. To investigate the role of PGE2 in gastric tumorigenesis, we constructed transgenic mice simultaneously expressing COX-2 and microsomal prostaglandin E synthase (mPGES)-1 in the gastric epithelial cells. The transgenic mice developed metaplasia, hyperplasia and tumorous growths in the glandular stomach with heavy macrophage infiltrations. Although gastric bacterial counts in the transgenic mice were within the normal range, treatment with antibiotics significantly suppressed activation of the macrophages and tumorous hyperplasia. Importantly, the antibiotics treatment did not affect the macrophage accumulation. Notably, treatment of the transgenic mice with lipopolysaccharides induced proinflammatory cytokines through Toll-like receptor 4
in the gastric epithelial cells. These results indicate that an increased level of PGE2 enhances macrophage infiltration, and that they are activated through epithelial cells by the gastric flora, resulting in gastric metaplasia and tumorous growth. Furthermore, Helicobacter infection upregulated epithelial PGE2 production, suggesting that the COX-2/mPGES-1 pathway contributes to the Helicobacter associated gastric tumorigenesis.
Keywords: disease state analysis

overall_design: We used DNA Chip Consortium Mouse Microarray v2.0 (oligonucleotide microarray) to examine the gene expression profile in the hyperplastic gastric tumors of K19-C2mE transgenic mice. Each DNA chip contains 65-mer oligonuleotide probes for 21,997 mouse transcripts. We examined expression profile in the hyperplastic gastric tumors of the K19-C2mE transgenic mice compared with normal glandular stomach of the littermate wild-type mice by analyses of three individual arrays from both groups.

first: Hiroko

last: Oshima

first: Makoto

last: Taketo

first: Masanobu