title: Global Transcriptome Analysis of Tropheryma whipplei in Response to Temperature Stresses

status: Public on Dec 02 2005

city: Marseille

first: nicolas

last: crapoulet

address: 27 BD J. Moulin

country: France

institute: Unité des Rickettsies (CNRS-UMR 6020)

summary:
Microarray analysis of the global gene expression patterns of Tropheryma whipplei in response to thermal stresses showed unique transcription profiles. A few genes were regulated after 15 min exposure at 43°C, including the dnaK regulon composed of grpE, hspR, dnaK, clpB, cbpA as well as the TWT745 ORFan gene which might encode for another heat-shock protein. This operon is likely to be regulated by two HspR associated inverted repeats (HAIR motifs) found within its 5' region. Putative virulence factors like RibC and IspDF proteins were also up-regulated under such conditions. In contrast to the heat-shock response, T. whipplei transcriptome was strongly modified following cold shock at 4°C. From the 149 genes differentially transcribed, 9 regulons were evidenced, one of them being composed of 5 genes sharing similarities with ABC transporters. Up-regulation of the latter suggests an increase of nutrient uptake during cold stress. As evoked for several bacteria species, the major classes of differentially transcribed genes encode membrane proteins and enzymes involved in fatty acid biosynthesis, indicating that membrane modifications are essential. A most specific feature observed following T. whipplei in response to cold was the up-regulation of heat-shock proteins namely GroEL2 and ClpP1, as well as several genes involved in energy metabolism. All together, these data show that T. whipplei exhibits a specific adaptative response to thermic stresses which fits well to its putative environmental origin.
Keywords: thermal stresses responses

overall_design:
4 conditions of temperature
2 biological replicates per condition
1 dye-swap per condition
1 referecne sample per hybridation (37°C Day 28)
Controls inculded on microarray and added in each sample before dye-labelling
4 replicates per microarray

first: Nicolas

last: Crapoulet

first: Patricia

last: Renesto

first: Pascal

last: Barbry

first: Didier

last: Raoult


title: Gene expression responses to a Salmonella infection in the chicken intestine differ between lines.

status: Public on Dec 05 2005

city: Lelystad

first: Saskia

middle: van

last: Hemert

address: PO box 65

country: Netherlands

institute: Animal Sciences Group

summary:
Poultry products are an important source of Salmonella enterica. An effective way to reduce food poisoning due to Salmonella would be to breed chickens more resistant to Salmonella. Unfortunately resistance to Salmonella is a complex trait with many factors involved. To learn more about Salmonella resistance mechanisms in young chickens, a cDNA microarray analysis was performed to compare gene expression profiles between a Salmonella susceptible and a more resistant chicken line. Newly hatched chickens were orally infected with S. enterica serovar Enteritidis. Since the intestine is the first barrier the bacteria encountersbacteria encounter after oral inoculation, gene expression was investigated in the intestine, from day 1 until day 21 post infection. Differences in gene expression between the susceptible and resistant chicken line were found in control as well as Salmonella infected conditions. In response to the Salmonella infection, the expression of different sets of genes seemed to be affected in the jejunum of the two chicken lines. In the susceptible line this included genes that affect T-cell activation, whereas in the more resistant line, at day 1, macrophage activation seemed to be more affected. At day 7 and 9 most gene expression differences between the two chicken lines were identified under control conditions, indicating a difference in the intestinal development between the two chicken lines which might be linked to the difference in Salmonella susceptibility. The findings in this study have lead to the identification of novel genes and possible cellular pathways of the host involved in Salmonella susceptibility.
Keywords: timecourse, disease

overall_design:
8 timepoints with four groups for each timepoints. Pooled samples of 5 animals for each group. The different groups are:
slow growing control
slow growing salmonella
fast growing control
fast growing salmonella
Four comparisions for each timepoint: slow control- slow salmonella, fast control-fast salmonella, slow control-fast control, slow salmonella-fast salmonella. A dye-swap was done, so 8 slides for each timepoints, 64 arrays in total.

last: van Hemert

first: Arjan

middle: J

last: Hoekman

first: Mari

middle: A

last: Smits

first: Johanna

middle: M

last: Rebel


title: Replicative senescence in post-selection HMECs

status: Public on Dec 03 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary:
Transcriptional abundance in each of senescent populations from two post-selection HMEC lines (48R and 184) is compared with abundance in isogenic early passage proliferating cells and also with abundance in early passage quiescent cells.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Keywords: strain_or_line_design

overall_design: Computed

first: Hong

last: Zhang


title: SSH-PCR dehydrated supraoptic nucleus

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

summary:
The magnocellullar neurons (MCNs) of the supraoptic nucleus (SON) of the hypothalamus are the principle source of the neuropeptide hormone vasopressin (VP), which has a crucial role in osmoregulation. Physiological activation of the SON by dehydration results is a massive release of VP from stores in posterior pituitary axon terminals into the general circulation. By binding to V2-type receptors located in the kidney, VP decrease the amount of water lost in urine. Osmotic activation of the SON is accompanied by a dramatic morphological and functional remodelling. We have sought to understand the mechanistic basis of this plasticity in terms of the differential expression of genes. To identify such genes, we adopted a completely unbiased and global approach based on Suppressive Subtractive Hybridisation-Polymerase Chain Reaction (SSH-PCR) Using this method, we generated a library of clones putatively differentially expressed in control vs dehydrated SON. In order to rapidly screen this library, 1152 of these clones were subjected to microarray analysis, resulting in the identification of 459 differentially expressed clones, 56 of which were sequenced. Many of these clones are expressed sequences that are new to science. Four of these were shown by in situ hybridisation (ISH) to be significantly up- or down-regulated in the SON following dehydration. These genes may represent novel effectors or mediators of SON physiological remodelling.
Keywords: dehydrated, SON, clone

overall_design: 4 chips were hybridised with control SON and compared to 4 chips hybridised with dehydrated SON

first: Mohamed

last: Ghorbel

first: Greig

last: Sharman

first: Charles

middle: C

last: Hindmarch

first: Kevin

last: Becker

first: Tanya

last: Barrett


title: Replicative senescence in human fibroblasts

summary:
Transcriptional abundance in each of senescent populations from three cell lines (WS1, WI38 and BJ) is compared with abundance in isogenic early passage proliferating cells and also with abundance in early passage quiescent cells.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Keywords: strain_or_line_design


title: ILS/ISS cerebellum baseline comparison

city: Aurora

first: Erik

middle: James

last: MacLaren

state: CO

address: Mail Stop 8303, P.O. Box 6511

department: Pharmacology

institute: University of Colorado at Denver and Health Sciences Center

summary:
Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit a large difference in a number of alcohol and drug related behaviors. This study examined the expression levels of transcripts in these strains in the cerebellum, which is a major target of ethanol’s actions in the CNS, in order to find differentially expressed candidate genes for these phenotypes. Cerebellum was specifically chosen due to the fact that Purkinje cell sensitivity to ethanol in these strains is highly correlated to "sleep time", the measure of ethanol sensitivity used with these strains. Naive mice were used because differences in sensitivity are observed upon initial exposure to ethanol.
Keywords: cerebellum, naive, untreated, ethanol sensitivity

overall_design: Expression was assayed with arrays manufactured using the NIA Mouse 15K clone set. Three independant RNA pools were used for hybridization.  Each pool contained total RNA from 5 ILS and 5 ISS mice.  No individuals were used in more than one pool.

first: Beth

last: Bennett

first: Thomas

middle: E

last: Johnson

first: James

last: Sikela


title: Genomewide view of gene silencing by small interfering RNAs

status: Public on Dec 15 2005

summary:
RNA interference (RNAi) is an evolutionarily conserved mechanism in plant and animal cells that directs the degradation of messenger RNAs homologous to short double-stranded RNAs termed small interfering RNA (siRNA). The ability of siRNA to direct gene silencing in mammalian cells has raised the possibility that siRNA might be used to investigate gene function in a high throughput fashion or to modulate gene expression in human diseases. The specificity of siRNA-mediated silencing, a critical consideration in these applications, has not been addressed on a genomewide scale. Here we show that siRNA-induced gene silencing of transient or stably expressed mRNA is highly gene-specific and does not produce secondary effects detectable by genomewide expression profiling. A test for transitive RNAi, extension of the RNAi effect to sequences 5' of the target region that has been observed in Caenorhabditis elegans, was unable to detect this phenomenon in human cells.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Howard

last: Chang


title: Rat brain microvessel SAGE

city: Duluth

first: Les

last: Drewes

state: MN

address: 1035 University Drive

institute: University of Minnesota Duluth

summary:
SAGE analysis of genes expressed in rat brain microvessels.
Keywords: Novel gene identification

overall_design: Microvessels were pooled from 50 rats, a single SAGE library was constructed from the microvessel RNA

first: Bradley

last: Enerson

first: Lester

middle: R


title: Oxidative Stress 30-min interval

status: Public on Dec 01 2005

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

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

overall_design: Yeast cells in stationary-phase cultures were exposed to oxidative stress with samples harvested every 30-minutes over 8 hours.  All experimental samples are over an common reference.  There are two replicates for each time point and six replicates of T0.


title: Effects of long-term treatment with tamoxifen on endometrial gene expression in women.

city: Leicester

first: Jerry

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

institute: University of Leicester

summary:
The aim was to examine changes in gene expression of the endometrium exposed to long-term tamoxifen treatment in comparison to age matched controls. To achieve this, endometrial tissues were obtained from women receiving tamoxifen treatment who were undergoing a hysterectomy. Using cDNA microarrays, gene expression changes in the postmenopausal endometrium of these women was compared with that in endometrium of age matched women not receiving tamoxifen.
Keywords: Gene expression changes in the postmenopausal endometrium of women following tamoxifen treatment

overall_design:
Endometrial tissue from post-menopausal women was obtained following ethical approval from the Leicester NHS Trust. None of the women had received any hormonal treatment for two months prior to the procurement of the specimens. Tissues were taken from untreated women (n=6) or those treated for 4 to 5 years with tamoxifen (20mg/day) (n=4), aged 58-82 (65 ± 9.1, mean ± SD). Total RNA was extracted. Controls were pooled.  RNA labelling, hybridisation and analysis of fluorescence was carried out as described by Turton et al (2001).  Cy3/Cy5 Dye swap labelling was carried out on samples from each patient.
Reference: Turton NJ et. al. (Oncogene (2001)  20, 1300-1306


title: NIA Neuroarray dehydration

summary:
The magnocellular neurons (MCNs) of the supraoptic nucleus (SON) and paraventricular nucleus (PVN) of the hypothalamus are the principal site of biosynthesis of prepropeptide precursor of the antidiuretic hormone vasopressin (VP). This precursor is processed during anterograde axonal transportation to terminals in the posterior pituitary gland, where biologically active VP is stored until released into the general circulation in response to physiological activation of the SON by osmotic cues. By binding to V2-type receptors located in the kidney, VP decreases the amount of water lost in urine. Osmotic activation of the SON is accompanied by a dramatic morphological and functional remodelling. We have sought to understand the mechanistic basis of this plasticity in terms of the differential expression of genes. To identify such genes, we adopted an unbiased global approach based on Suppressive Subtractive Hybridisation-Polymerase Chain Reaction (SSH-PCR) Using this method, we generated libraries of clones putatively differentially expressed in control vs dehydrated SON. In order to rapidly screen these libraries, 1152 clones were subjected to microarray analysis, resulting in the identification of 459 differentially expressed transcripts. cDNA clones corresponding 56 of these RNAs were sequenced, revealing many of them to be novel ESTs. Four transcripts were shown by in situ hybridisation (ISH) to be significantly up- or down-regulated in the SON following dehydration. These genes may represent novel effectors or mediators of SON physiological remodelling.
Keywords: dehydration, SON, NIA

overall_design: 3 chips were hybridised with control SON and compared to 3 chips hybridised with dehydrated SON


title: Effects of neonatal dosing of SERMs on CD1 mouse uterine gene expression at 3 months

summary:
Tamoxifen, a selective estrogen receptor modulator (SERM), is an effective treatment for breast cancers. In the CD-1 mouse model, neonatal oral dosing with tamoxifen leads to the development of adenomyosis.  Both 4-hydroxyestradiol and tamoxifen can form DNA-reactive metabolites and may be involved in carcinogenesis of the uterus. After comparing the uterotrophic response of several SERMs the maximal uterotrophic doses of estradiol (100mg/kg) 4-hydroxyestradiol (385mg/kg) and tamoxifen (250mg/kg) were determined. Maximal uterotrophic doses were given orally to newborn CD-1 mice on days 1 – 4 after birth and gene and pathological changes examined in the uterus at 3 months after dosing.
ERKOa knockout mice were dosed orally with tamoxifen (1mg/Kg) on days 1 – 4 after birth and uterine gene expression compared with CD-1 mice.
Keywords: Comparison of SERMs at maximal uterotrophic doses

overall_design:
Dosing groups:
Estradiol (E2): 100mg/Kg
4-hydroxyestradiol (4OHE2): 385mg/Kg
Tamoxifen : 250mg/Kg
ERKO mice dosed with tamoxifen (1mg/Kg)
4 dosed animals and 4 controls for each treatment group.  Uteri removed at 3 months after dosing and total RNA extracted. Controls were pooled.  RNA labelling, hybridisation and analysis of fluorescence was carried out as described by Turton et al (2001).  Cy3/Cy5 dye swap labelling was carried out on samples from each animal.
Reference: Turton NJ et. al. (Oncogene (2001)  20, 1300-1306


title: HapMap CEU parent custom array expression

city: Geneva

first: Emmanouil

middle: T

last: Dermitzakis

address: 1 Rue Michel-Servet

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

summary:
The exploration of quantitative variation in human populations has become one  of the major priorities for medical genetics. The successful identification of  variants that contribute to complex traits is highly dependent on reliable assays  and genetic maps. We have performed a genome-wide quantitative trait analysis  of 630 genes in 60 unrelated Utah residents with ancestry from Northern and  Western Europe (CEPH) using the publicly available phase I data of the  International HapMap project. The genes are located in regions of the human  genome with elevated functional annotation and disease interest including the  ENCODE regions spanning 1% of the genome, chromosome 21 and chromosome  20q12-13.2.  We apply three different methods of multiple test correction,  including Bonferroni, False Discovery Rate and permutations. For the 374  expressed genes, we find many regions with statistically significant association of  SNPs with expression variation in lymphoblastoid cell lines after correcting for  multiple tests.  Based on our analyses, the signal proximal (cis-) to the genes of  interest is more abundant and more stable than distal and trans across statistical  methodologies.  Our results suggest that regulatory polymorphism is widespread in the human genome and show that the 5 kb (phase I) HapMap has  sufficient density to enable linkage disequilibrium mapping in humans. Such  studies will significantly enhance our ability to annotate the non-coding part of  the genome and interpret functional variation. In addition, we demonstrate that  the HapMap cell lines themselves may serve as a useful resource for quantitative  measurements at the cellular level.
Keywords: Gene expression, Lymphoblastoid,

overall_design: Gene expression of lymphoblastoid cell lines from the 60 HapMap CEU parents was quantified with a custom Illumina bead array (see above). Two (Ambion Message Amp II) IVT reactions were performed for each cell line and each IVT was hybridised to 3 or 5 arrays, so that each sample had either 6 or 8 replicates. Arrays were run in 96-well plate format (SAM). Each array was made from a bead pool containing 1433 unique bead types (each with a unique 50mer probe). On average an array contains 30 of each bead distributed at random.

first: Barbara

last: Stranger

first: Matthew

middle: S

last: Forrest

first: Andrew

middle: G

last: Clark

first: Mark

last: Minichiello

first: Samuel

last: Deutsch

first: Robert

last: Lyle

first: Sarah

last: Kyle

first: Brenda

last: Kahl

first: Stylianos

last: Antonarakis

first: Simon

last: Tavare

first: Panagiotis

last: Deloukas


title: SAGE: unfertilized eggs

status: Public on Dec 12 2005

city: Isehara City

first: Shohei

last: Horiuchi

state: Kanagawa Pref.

address: Bohseidai

department: School of Medicine

country: Japan

institute: Tokai University

summary:
LongSAGE library was constructed by standard methods with several modifications. Additional amplification step was not performed.
Keywords: other

first: Masato

last: Ohtsuka

first: Minoru

last: Kimura


title: Ethanol-response genes and their regulation

last: Stanford Microarray Database

summary:
The nematode shows responses to acute ethanol exposure that are similar to those observed in humans, mice, and Drosophila, namely hyperactivity followed by uncoordination and sedation. We used in this report the nematode Caenorhabditis elegans as a model system to identify and characterize the genes that are affected by ethanol exposure and to link those genes functionally into an ethanol-induced gene network. By analyzing the expression profiles of all C. elegans ORFs using microarrays, we identified 230 genes affected by ethanol. While the ethanol response of some of the identified genes was significant at early time points, that of the majority was at late time points, indicating that the genes in the latter case might represent the physiological consequence of the ethanol exposure. We further characterized the early response genes that may represent those involved directly in the ethanol response. These genes included many heat shock protein genes, indicating that high concentration of ethanol acts as a strong stress to the animal. Interestingly, we identified two non-heat-shock protein genes that were specifically responsive to ethanol. glr-2 was the only glutamate receptor gene to be induced by ethanol. T28C12.4, which encodes a protein with limited homology to human neuroligin, was also specific to ethanol stress. Finally, by analyzing the promoter regions of the early response genes, we identified a regulatory element, TCTGCGTCTCT, that was necessary for the expression of subsets of ethanol response genes.
Groups of assays that are related as part of a time series.
Keywords: time_series_design


title: Lymphoblasts from healthy individuals vs. individuals with FPD-AML (familial platelet disorder - acute myeloid leukemia)

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

country: Australia

institute: The Walter and Eliza Hall Institute

summary:
RNA derived from lymphoblasts from individuals with FPD-AML is compared to that from related unaffected individuals.
Keywords: other

first: Joelle

last: Michaud

last: Escher

first: Karine

last: Buchet-Poyau

first: Wendy

middle: H

last: Raskind

first: Marshall

last: Horwitz

first: Gordon

middle: K

last: Smyth

first: Hamish

last: Scott


title: Temperature Upshift

first: Sushmita

last: Roy

summary:
Determine if cells in stationary-phase cultures respond to increased temperature.
Keywords: Time-course

overall_design: Yeast cells in stationary-phase cultures were exposed to temperature upshift (30C to 39C) with samples harvested every 30-minutes over 8 hours.  All experimental samples are over an common reference.  There are two replicates for each time point and six replicates of T0.


title: Modes of gene action observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents

status: Public on Dec 06 2005

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

summary:
Heterosis is the phenomenon whereby the progeny of particular inbred lines have enhanced agronomic performance relative to both parents.  Although several hypotheses have been proposed to explain this fundamental biological phenomenon, the responsible molecular mechanisms have not been determined.  The maize inbred lines B73 and Mo17 produce a heterotic F1 hybrid.  Global patterns of gene expression were compared in seedlings of these three genotypes using a microarray that contains 13,999 cDNAs.  Using an estimated 15% false discovery rate as a cut-off, 1,367 ESTs (9.8%) were identified as being significantly differentially expressed among genotypes.  All possible modes of gene action were observed, including additivity, high- and low-parent dominance, under-dominance, and over-dominance.  The largest proportion of the ESTs (78%, 1,062/1,367) exhibited expression patterns that are not statistically distinguishable from additivity.  Even so, 22% of the differentially regulated genes exhibited non-additive modes of gene expression.  Classified on the basis of significant pair-wise comparisons of genotype means, 181 of these 305 genes exhibited high-parent dominance and 23 exhibited low-parent dominance.  In addition, 44 genes exhibited under- or over-dominant gene action.  These findings are consistent with the hypothesis that multiple molecular mechanisms contribute to heterosis, including over-dominance
Keywords: Genotype Comparison

overall_design: The inbreds B73 (Schnable Lab Accession #660) and Mo17 (Schnable Lab Accession #2618) used in this study were derived by self-pollination from stocks originally obtained from Don Robertson (Iowa State University) and Mike Lee (Iowa State University), respectively.  Mo17 was crossed as a female by B73 to generate the F1.  Kernels from three different seed sources (ears) per genotype were used in the experimental design.  Prior to microarray analyses genotypes were confirmed by genotyping DNA extracted from each seed source using co-dominant IDP genetic markers that distinguish B73 from Mo17 (Fu et al., in preparation).  Ten biological replications of B73, Mo17, and their F1 (Mo17xB73) were grown under highly controlled conditions in a randomized complete block design.  For each replication, the B73, Mo17, and F1 samples were hybridized to three two-color cDNA microarrays using a loop design such that each loop included all pairwise comparisons between genotypes.  RNA pools for each genotype were alternately labeled providing dye balance within each loop.  After hybridization, one biological replicate was removed due to poor quality.  The final analysis incorporated 27 microarray slides (3 slides for each of nine high-quality biological replicates).


title: CEA_SGF:E00016#HU_response_W303a

city: Paris

first: Caroline

last: Dubacq

address: 45 rue d'Ulm

department: Biologie

institute: Ecole Normale Supérieure

summary:
Analysis of mid-term response to hydroxyurea in a yeast wild-type strain (W303a). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes were analysed compared to the same strain grown in the same medium without HU.
Keywords: repeat sample


title: Transcription factor overexpression in HeLa cell lines

summary:
Experiments measuring effects of overexpression of the transcription factors  RUNX1 and CBF-beta (in combination), and TELRUNX1 (fusion protein of TEL and RUNX1).  Overexpression is achieved via adenovirus infection of HeLa cell lines.
Keywords: other

first: Robert


title: CEA SGF:E00013#yap1 aft W303a HU response

summary:
Analysis of the response to hydroxyurea in a yeast aft1 mutant strain compared to wild-type strain (BY4741 or BY4742 backgrounds). Cells were grown in YPD rich medium containong 200 mM hydroxyurea (HU) for 2 hours.

Analysis of the response to hydroxyurea in a yeast aft1aft2 mutant strain (Y18aft2d) compared to wild-type strain (CM3260). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes due to the aft1 mutation were also analysed in absence of HU (BY4741 background).

Analysis of mid-term response to hydroxyurea in a yeast wild-type strain (W303a). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes were analysed compared to the same strain grown in the same medium without HU.
Keywords: repeat sample


title: CEA_SGF:E00015#aft_HU_response

summary:
Analysis of the response to hydroxyurea in a yeast aft1aft2 mutant strain (Y18aft2d) compared to wild-type strain (CM3260). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes due to the aft1 mutation were also analysed in absence of HU (BY4741 background).
Keywords: repeat sample


title: CEA_SGF:E00014#HU_response_long-term

summary:
Analysis of long-term response to hydroxyurea in a yeast wild-type strain (CDY59). Cells were grown in YPD rich medium containong 200 mM hydroxyurea (HU) during the indicated time (1, 2, 4 or 6 hours). Gene expression changes were analysed compared to the same strain grown in the same medium without HU.
Keywords: time-course


title: Validation of the linear amplification of single bovine embryos

status: Public on Nov 30 2005

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1392 Storrs Rd. Unit 4243

department: Center for Regenerative Biology

institute: University of Connecticut

summary:
To generate expression profiles from single embryos, a protocol for linear amplification of RNA was developed on the basis of Baugh et al. (15). Linear amplification enabled production of sufficient amounts of aRNA for the microarray experiments and has been shown to reliably amplify the initial mRNA population (15, 18-20). Approximately 5 ng of total RNA can be isolated from a blastocyst-stage embryo (21); therefore, it was necessary to carry out multiple rounds of amplification. To test the reproducibility and fidelity of the amplification procedure, a validation experiment was conducted using RNA from the kidney tissue of a newborn calf. Two replicates of the bovine kidney RNA were amplified and hybridized to the microarray. Comparisons were made between aRNA (rounds 1, 2, and 3) and unamplified RNA.
Keywords: cDNA microarray

overall_design: Hybridization of cDNA from amplified RNA/unamplified RNA to custom bovine 7,872 cDNA microarray

first: Sadie

middle: L

last: Smith

first: Robin

last: Everts

first: Fuliang

last: Du

first: Li-Ying

last: Sung

first: Sandra

last: Rodriguez-Zas

first: Byeong-Seon

last: Jeong

first: Jean-Paul

last: Renard

first: Harris

last: Lewin

first: Xiangzhong

last: Yang


title: CEA_SGF:E00013#yap1_HU_response

summary:
Analysis of the response to hydroxyurea in a yeast yap1 mutant strain compared to wild-type strain (BY4741 or BY4742 backgrounds). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours.
Keywords: repeat sample


title: Beta-naphthoflavone treated worms

status: Public on Nov 26 2005

last: Stanford Microarray Database

summary:
The soil nematode Caenorhabditis elegans is one of the simplest animals having the status of a laboratory model. Its genome contains 80 cytochrome P450 genes (CYP). In order to study CYP gene expression in C. elegans mixed stages and synchronized hermaphrodites were exposed to 18 known xenobiotic cytochrome P450 inducers. Messenger RNA expression was detected by DNA arrays and semiquantitative RT-PCR. Using subfamily-specific primers, a pooled set of exon-rich CYP fragments could be amplified. In this way it was possible to systematically check the influence of different inducers on CYP expression at the same time. The well-known CYP1A inducers beta-naphthoflavone, PCB52, and lansoprazol were the most active and in particular they strongly induced almost all CYP35 isoforms. A few number of further CYP forms were found to be inducible by other xenobiotics like phenobarbital, atrazine, and clofibrate. In addition, a transgenic C. elegans line expressing GFP under control of the CYP35A2 promoter showed a strong induction of the fusion by beta-naphthoflavone in the intestine. Copyright 2001 Academic Press.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Ralph

last: Menzel


title: Varicella-zoster virus infection of human T cells and fibroblasts in vitro and SCIDhu skin xenografts in vivo.

status: Public on Nov 24 2005

summary:
During primary infection, varicella-zoster virus (VZV) is spread via lymphocytes to skin, where it induces a rash and establishes latency in sensory ganglia. A live, attenuated varicella vaccine (vOka) was generated by using the VZV Oka strain (pOka), but the molecular basis for vOka attenuation remains unknown. Little is known concerning the effects of wild-type or attenuated VZV on cellular gene regulation in the host cells that are critical for pathogenesis. In this study, transcriptional profiles of primary human T cells and fibroblasts infected with VZV in cell culture were determined by using 40,000-spot human cDNA microarrays. Cellular gene transcription in human skin xenografts in SCID mice that were infected with VZV in vivo was also evaluated. The profiles of cellular gene transcripts that were induced or inhibited in infected human foreskin fibroblasts (HFFs), T cells, and skin in response to pOka and vOka infection were similar. However, significant alterations in cellular gene regulation were observed among the three differentiated human cell types that were examined, suggesting specific differences in the biological consequences of VZV infection related to the target cell. Changes in cellular gene transcription detected by microarray analysis were confirmed for selected genes by quantitative real-time reverse transcription-PCR analysis of VZV-infected cells. Interestingly, the transcription of caspase 8 was found to be decreased in infected T cells but not in HFFs or skin, which may signify a tissue-specific antiapoptosis mechanism. The use of microarrays to demonstrate differences in effects on host cell genes in primary, biologically relevant cell types provides background information for experiments to link these various response phenotypes with mechanisms of VZV pathogenesis that are important for the natural course of human infection.
A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
Keywords: pathogenicity_design

first: Jeremy

last: Jones


title: Pancreatic Cancer 1

summary:
This is the experiment set used for a paper written in collaboration with Hopkins. It compares genes that are differentially expressed between normal pancreas, pancreatic cell lines and pancreatic adenocarcinoma.
Pancreatic cancer is the fifth leading cause of cancer death in the United States. We used cDNA microarrays to analyze global gene expression patterns in 14 pancreatic cancer cell lines, 17 resected infiltrating pancreatic cancer tissues, and 5 samples of normal pancreas to identify genes that are differentially expressed in pancreatic cancer. We found more than 400 cDNAs corresponding to genes that were differentially expressed in the pancreatic cancer tissues and cell lines as compared to normal pancreas. These genes that tended to be expressed at higher levels in pancreatic cancers were associated with a variety of processes, including cell-cell and cell-matrix interactions, cytoskeletal remodeling, proteolytic activity, and Ca(++) homeostasis. Two prominent clusters of genes were related to the high rates of cellular proliferation in pancreatic cancer cell lines and the host desmoplastic response in the resected pancreatic cancer tissues. Of 149 genes identified as more highly expressed in the pancreatic cancers compared with normal pancreas, 103 genes have not been previously reported in association with pancreatic cancer. The expression patterns of 14 of these highly expressed genes were validated by either immunohistochemistry or reverse transcriptase-polymerase chain reaction as being expressed in pancreatic cancer. The overexpression of one gene in particular, 14-3-3 sigma, was found to be associated with aberrant hypomethylation in the majority of pancreatic cancers analyzed. The genes and expressed sequence tags presented in this study provide clues to the pathobiology of pancreatic cancer and implicate a large number of potentially new molecular markers for the detection and treatment of pancreatic cancer.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

overall_design: Using regression correlation

first: Mari

last: Olsen


title: Mouse Models for Muscular Dystrophy

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

summary:
Comparative analysis of gene expression levels from hindlimb muscle tissue from 8 week old mouse models for muscular dystrophy. We have used mouse models with dystrophin-, sarcoglycan-, sarcospan-, or dysferlin-deficiency.
Keywords = muscular dystrophy
Keywords: other

first: Ellen

last: Sterrenburg

first: Karlien

last: van der Wees

first: Emile

last: de Meijer

first: Severine

last: Groh

first: Kevin

middle: P

last: Campbell

first: Satoru

last: Noguchi

first: Gert-Jan

middle: B

last: van Ommen

first: Johan

last: den Dunnen

first: Peter

last: 't Hoen


title: Global gene expression in catfish spleen after injection of lipopolysaccharide

city: Stoneville

first: Geoffrey

middle: C.

last: Waldbieser

state: MS

address: 141 Experiment Station Road

department: Agricultural Research Service

institute: U.S. Dept of Agriculture

summary:
A high-density oligonucleotide microarray for channel catfish (Ictalurus punctatus) was designed and produced with Maskless Array Synthesizer technology (MAS). The microarray contained ~379,652 24-mer oligonucleotides covering ~18,999 catfish unique sequences. The global expression profiling of the catfish spleens stimulated by lipopolysaccharide (LPS) for 2h, 4h, 8h and 24h was investigated with the microarray.  In the spleen samples, 409 genes were identified to be induced or repressed greater than 2-fold by LPS treatment.   Self-organizing maps (SOM) clustering analysis was applied to interpret gene expression patterns, and 84 of these genes were clustered into six expression patterns.  Real-time RT-PCR was used to verify the microarray results for 9 selected genes representing different expression levels. The results from real-time RT-PCR were positively correlated (R^2 = 0.87) with the results from the microarray.
Keywords: time course

overall_design: Channel catfish were injected with LPS or PBS carrier.  Fish were killed by anesthesia overdose at 2, 4, 8, or 24h post-injection and total RNA was isolated from spleen.  The experiment contained two replicate fish per time point.  Relative signal intensities for each feature were generated using the Robust Multi-Array Average algorithm and log2 transformed.  Transformed data were then processed using quantile normalization, and the average and std. error for each gene were calculated from the 10 perfectly matched oligos only.  After detransformation, the ratio (fold change) was calculated using PBS treated samples (control) as the baseline against LPS-treated samples.

first: Robert

last: Li

first: Geoff


title: PHA-4 organogenesis

summary:
The pha-4 locus encodes a forkhead box A (FoxA/HNF3) transcription factor homolog that specifies organ identity for Caenorhabditis elegans pharyngeal cells. We used microarrays to identify pharyngeal genes and analyzed those genes to determine which were direct PHA-4 targets. Our data suggest that PHA-4 directly activates most or all pharyngeal genes. Furthermore, the relative affinity of PHA-4 for different TRTTKRY (R = A/G, K = T/G, Y = T/C) elements modulates the onset of gene expression, providing a mechanism to activate pharyngeal genes at different developmental stages. We suggest that direct transcriptional regulation of entire gene networks may be a common feature of organ identity genes.
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
Keywords: genotyping_design

first: Susan

last: Mango

first: Stuart

last: Kim


title: Follicular lymphoma lymph node

status: Public on Nov 23 2005

last: Stanford Microarray Database

summary:
24 independent follicular lymphoma lymph node samples on LC microarrays was used to generate the gene lists in tables 2 and 3 of publication
patients were divided into two groups, rituximab responders (composed of  CR and PR) and non-responders (composed of NR and MR).
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Sean

last: Bohen


title: Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene.

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

summary:
Non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) is a conserved protein found in higher plants. In photosynthetic cells, the enzyme is involved in a shuttle transfer mechanism to export NADPH from the chloroplast to the cytosol. In this work, we demonstrate that GAPN gene express in leaves and roots at similar levels; showing the highest level of expression in flowers. To investigate the role of this enzyme in different plant tissues, we characterized a mutant from Arabidopsis thaliana having an insertion at the GAPN gene locus. The homozygous mutant was determined to be null respect to GAPN, as it exhibited complete absence of both expression of GAPN mRNA and enzyme activity. Transcriptome analysis demonstrated that the insertion mutant plant shows altered expression of several enzymes involved in carbohydrate metabolism. Significantly, cytosolic phosphorylating (NAD-dependent) glyceraldehyde-3-phosphate dehydrogenase mRNA levels are induced in the mutant, which correlates with an increase in enzyme activity. mRNA levels and enzymatic activity of glucose-6-phosphate dehydrogenase were also elevated, correlating with an increase in NADPH concentration. Moreover, an increased levels of oxidative stress was measured in the mutant plants. Downregulation of several glycolytic and photosynthetic genes suggests that GAPN is important for the efficiency of both metabolic processes. The results presented demonstrate that GAPN has a relevant role in plant growth and development.
Keywords: 2 color experiment in triplicate including dye-swap

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

first: Sebastián

last: Rius

first: Alberto

last: Iglesias

first: Diego

middle: F

last: Gomez-Casati


title: Genome-wide analysis of developmental and sex-regulated gene expression profiles in C. elegans

status: Public on Nov 19 2005

summary:
We have constructed DNA microarrays containing 17,871 genes, representing about 94% of the 18,967 genes currently annotated in the Caenorhabditis elegans genome. These DNA microarrays can be used as a tool to define a nearly complete molecular profile of gene expression levels associated with different developmental stages, growth conditions, or worm strains. Here, we used these full-genome DNA microarrays to show the relative levels of gene expression for nearly every gene during development, from eggs through adulthood. These expression data can help reveal when a gene may act during development. We also compared gene expression in males to that of hermaphrodites and found a total of 2,171 sex-regulated genes (P < 0.05). The sex-regulated genes provide a global view of the differences between the sexes at a molecular level and identify many genes likely to be involved in sex-specific differentiation and behavior.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Differential expression between mature zone of the olfactory organ and the dactyl of the walking legs, a taste organ

status: Public on Dec 26 2005

city: Lexington

first: Timothy

last: McClintock

state: KY

address: 800 Rose Street

department: Department of Physiology

institute: University of Kentucky

summary:
A cDNA microarray was constructed and used to assess mRNA abundance differences between two of the lobster’s major chemosensory structures, the mature zone of the olfactory organ and the dactyl of the walking legs, a taste organ.  The 115 differences detected again emphasized the abundance of neurons in the olfactory organ, especially a cluster of mRNAs encoding cytoskeletal-associated proteins and cell adhesion molecules such as 14-3-3zeta, actins, tubulins, trophonin, Fax, Yel077cp, Suppressor of profilin 2, and gelsolin.
Keywords: Differential expression

overall_design: We designed a cDNA microarray that consisted of five subarrays to cover all of the cDNA species in our library. We generated two of the sub-arrays, each with 1,152 clones spotted in duplicate, giving 2,304 spots per sub-array.  A common set of 96 clones, consisting of positive and negative control sequences, was spotted on each sub-array.  Each cloned cDNA insert was amplified by PCR and spotted on nylon membranes using an Affymetrix 417 Arrayer according to protocols supplied by Dr. Kevin Becker (Tanaka et al., 2000; Barrett et al., 2001).  Arrays were hybridized against 33P-labeled cDNA produced by oligo-dT priming of reverse transcription using the RadPrime DNA labeling kit (Invitrogen).  Hybridization was done in quadruplicate at 50˚C in 50 ml tubes in a hybridization oven as described in Barrett et al. (2001).

first: Kristen

last: Day


title: Growth phase dependent gene expression and motility_3 time courses

status: Public on Nov 22 2005

summary:
The microarrays for the three time course experiments described in the publication titled "Gene expression profiling of Helicobacter pylori reveals a growth phase dependent switch in virulence gene expression". TC1 refers to the first time course investigating gene expression changes over the time course of growth while TC2 refers to the second time course. TC Motility_broth refers to the third time course described in the manuscript used to investigate the concurrent changes in motility and the expression of the genes in the flagellar regulon. Detailed description of the growth of H. pylori for these 3 time courses can be found in the Materials and Methods section of the manuscript along with the exact filtering criteria used to download the data from these arrays. Note that in all three time courses the data for each array were transformed after download such that the abundance of each gene's transcript represented by a given spot was relative to the level of that transcript at the 6 h time point. Also duplicate spots for each ORF on the microarray were averaged for analysis after transformation.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Lucinda

last: Thompson


title: A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP

status: Public on Nov 21 2005

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

institute: University of Birmingham

summary:
The fumarate and nitrate reductase regulator protein, FNR, is a global transcription factor that regulates major biochemical changes as Escherichia coli adapts from aerobic to anaerobic growth.  The ability of an fnr mutant to grow anaerobically in the presence of trimethylamine-N-oxide (TMAO) as the terminal electron acceptor was exploited in microarray experiments designed to determine a minimum number of Escherichia coli K-12 MG1655 operons that are regulated directly by FNR.  In an anaerobic glycerol-TMAO-fumarate medium, the fnr mutant grew as well as the parental strain, enabling us to reveal the response of the E. coli transcriptome to oxygen, nitrate and nitrite in the absence of glucose repression or artefacts due to variations in growth rate.  Many of the discrepancies between previous microarray studies of the E. coli FNR regulon were resolved in this study.  First data for 43 previously characterised FNR-dependent operons were analysed.  The current microarray data confirmed 32 of these 43 assignments, but alone did not confirm FNR-activation of 5 operons (adhE, glpTQ, cydDC, hlyE and arcA), or FNR repression of 6 operons (hemA, narXL, tpx, yeiL, norVW or ubiCA).  Thirty-six operons not previously known to be included in the FNR regulon were activated by FNR and a further 26 operons appeared to be repressed.  For each of these operons, an excellent match to the consensus FNR-binding site sequence was identified.  The FNR regulon therefore minimally includes at least 94, and possibly as many as 105, operons.
	Many FNR-activated promoters are also regulated by one or both of two nitrate- and nitrite-responsive two-component regulatory systems, NarX-NarL and NarQ-NarP.  Comparison of transcripts in the parental strain and a narXL deletion mutant revealed that transcription of 51 operons is activated, directly or indirectly, by NarL in response to nitrate, and a further 41 are repressed.  As phosphorylated NarL can bind to the NarP DNA target sequence, the narP gene was also deleted from the narXL mutant to reveal the extent of regulation by phosphorylated NarP.  Fourteen promoters were more active in the narP+ strain than in the mutant, and a further 37 were strongly repressed.  This is the first report that NarP might function as a global repressor as well as a transcription activator.  The data also revealed possible new biochemical defence mechanisms against reactive nitrogen species.
Keywords: genetic modification, growth conditions

overall_design:
An fnr mutant is either unable to grow anaerobically in the presence of most terminal electron acceptors and a non-fermentable carbon source such as glycerol or lactate, or grows far more slowly than the parental strain.  Under such conditions, any differences in the transcriptomes of an fnr mutant and its parental strain would be due to both direct effects of FNR, and to differences in growth rate.  As glucose represses expression from some FNR-activated promoters replacement of glucose by a less repressing fermentable carbohydrate would decrease effects due to glucose repression, but to an unknown extent.  We therefore exploited the fact that fnr mutants can be grown anaerobically in the presence of the non-fermentable and non-repressing carbon source, glycerol, in the presence of trimethylamine-N-oxide (TMAO) in addition to fumarate as the terminal electron acceptor.  Furthermore, the presence of TMAO has a minimal effect on NarX-NarL or NarQ-NarP-dependent induction or repression.  Under these conditions, the fnr mutant grows as well as the parental strain and the use of the glycerol-TMAO-fumarate medium enables us to reveal the response of the E. coli transcriptome to nitrate, nitrite and the two-component regulator system, NarX-NarL.
In each large set of experiments a common pool of reference RNA isolated from bacteria that had been grown anaerobically, and in which FNR-activated genes were expressed at a significant level.  A potential disadvantage of this approach was the risk that some promoters repressed by FNR would be expressed at such a low level that the microarray signals would be too low to yield reliable data.  To check for this artefact, further experiments were completed in which the reference RNA was a pool of samples isolated from bacteria in the early exponential phase of aerobic growth.
“Reference” RNA was isolated from at least four independent cultures grown to OD 0.5 to 0.6. “Test” RNA was isolated from three independent cultures grown to OD 0.5 to 0.6.

last: Overton

first: Jon

last: Hobman

first: Lesley

last: Griffiths

first: Mala

middle: D

last: Patel

first: Charles

middle: w

last: Penn

first: Jeff

middle: A

last: Cole


title: Differential gene expression of Vicia species using a soybean cDNA microarray

city: Fort Collins

first: Kathleen

last: Yeater

address: 2150 Centre Avenue

institute: USDA-ARS

summary:
Hairy vetch (Vicia villosa Roth) is recognized as a beneficial winter cover crop in the Midwestern U.S.  DNA microarrays are used for assessing gene expression significance.  The objective of the study was to identify a set of genes expressed in hairy vetch, that could be further analyzed for their potential in improving the crop.  The RNA of four targets (soybean (Glycine max), hairy vetch, Vicia pannonica PI 170008, and Vicia pannonica PI 515988) were purified, labeled, and hybridized to 142 cDNA clones of biotic stress genes and gene sequences of soybean that were robotically spotted onto aminosilicated slides with duplicate spots and three arrays per slide.  The microarray experiments were completed in a reference design experiment incorporating a two-dye system.  The data were analyzed using the individual fluorescence intensities to fit two statistical models in a mixed model analysis of variance.  In this analysis, systematic error effects were observed to account for 24% of the total variation.  The use of a Bonferroni adjusted significance threshold allowed for adequate control over the number of falsely identified significant genes showing expression in the different target comparisons.  We observed that 64 of the 142 gene sequences (45%) were differentially expressed in at least one of the target comparisons.  Two of these expressed genes in hairy vetch encoded for a cold tolerance indicator, proline, and two other gene sequences encode for stress tolerance indicators, myo-inositol and calmodulin.  A soybean cDNA microarray was used effectively to differentiate gene expression in hairy vetch.
Keywords: comparative genomic hybridization (cross-species)

sample_organism:
Glycine max
Vicia villosa
Vicia pannonica

overall_design: In this study, the targets consist of the 4 sources of RNA, Soybean cultivar Burlison (Glycine max), Common Hairy Vetch (Vicia villosa),  Vicia pannonica PI 170008, and Vicia pannonica PI 515988.  The four targets were hybridized in a reference design with dye-label swap, where the common hairy vetch target served as the reference sample.  There were three independent replications.

middle: M

first: A

last: Rayburn

first: M

middle: J

last: Iqbal

first: Donald

last: Bullock

first: Sandra

last: Rodriguez-Zas

first: German

last: Bollero


title: Barley1 salinity stress study

status: Public on Nov 18 2005

city: Riverside

first: HARKAMAL

last: WALIA

address: Department of Botany & Plant Sciecnes

institute: University of California

summary:
Shoot tissue from 17 day old barley plants was used for expression analysis.  Targets from three biological replicates of each were generated and the expression profiles were determined using Affymetrix Barley1 Genechip arrays.  Comparisons between the control and stressed samples at three time points (3, 8 and 27 h) allow the identification of salt stress responsive genes.
Keywords: repeat

overall_design: 3 control and 3 salt stressed biological replicates were analyzed at 3, 8 and 27 h.

first: Harkamal

last: Walia

last: Close


title: Molecular classification of failing hearts from coronary and myopathic patients

city: Trondheim

first: Vidar

last: Beisvag

address: Olav Kyrres gt 3

country: Norway

institute: Deparment of Circulation and Imaging, Norwegian University of Science and Technology

summary:
RNA form the heart a goupe of 9 patients with end stage cardiomyopathy (CAD) and 11 patiensts with coronary artery disease (CAD) was hybridized against pooled RNA form 4 normal nonfailing hearts.
Keywords: repeat sample

first: Per

last: Lehre

first: Herman

last: Midelfart

first: Halfdan

last: Aass

first: Odd

last: Geiran

first: Astrid

last: Lægreid

first: Jan

last: Komorowski

first: Øyvind

last: Ellingsen


city: Mountain View

first: Mark

last: Fielden

address: 325 East Middlefield Road

institute: Iconix Biosciences

summary:
A Gene Expression Signature that Predicts the Future Onset of Drug-Induced Renal Tubular Toxicity
These data support the publication titled "A Gene Expression Signature that Predicts the Future Onset of Drug-Induced Renal Tubular Toxicity"
Copyright (c) 2005 by Iconix Pharmaceuticals, Inc.

Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf
Keywords: time course

overall_design: replicated drug treatments with controls

middle: R

first: Barrett

last: Eynon

first: Georges

last: Natsoulis

first: Kurt

last: Jarnagin

first: Deborah

last: Banas

first: Kyle

last: Kolaja


title: Carbon starvation and pectin utilization in Aspergillus nidulans

status: Public on Jan 01 2006

city: Stillwater

first: Patricia

last: Ayoubi

state: OK

address: 246 Noble Research Center

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

summary:
We have a cDNA microarray to investigate changes in gene expression following transfer of fungal cultures from growth on glucose to growth on pectin or no carbon source.  Our goal was to asses the roles of release from carbon catabolite repression and specific induction on proteins needed for metabolism (or utilization) of a single class of complex polysaccharide.
Keywords = Aspergillus
Keywords = Pectin
Keywords = central metabolism
Keywords = pectin
Keywords = carbon catabolite repression
Keywords = polysaccharide
Keywords = exopolygalacturonase
Keywords: time-course

first: Anamika

last: Ray

first: Hua

last: Weng

first: Sunita

last: Macwana

first: Rolf

last: Prade

first: Andrew

last: Mort


title: T-cell co-stimulation

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 agonists elicited a multifaceted temporally choreographed gene expression program. The principal effect of simultaneous engagement of CD28 was to increase the amplitude of the CD3 transcriptional response. The induced genes whose expression was most enhanced by costimulation were significantly enriched for known targets of nuclear factor of activated T cells (NFAT) transcription factors. This enhancement was nearly abolished by blocking the nuclear translocation of NFATc by using the calcineurin inhibitor FK506. CD28 signaling promoted phosphorylation, and thus inactivation, of the NFAT nuclear export kinase glycogen synthase kinase-3 (GSK3), coincident with enhanced dephosphorylation of NFATc proteins. These results provide a detailed picture of the transcriptional program of T cell activation and suggest that enhancement of transcriptional activation by NFAT, through inhibition of its nuclear export, plays a key role in mediating the CD28 costimulatory signal.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Max

last: Diehn


title: human medulloblastoma

city: Heidelberg

first: Frank

last: Mendrzyk

country: Germany

institute: German Cancer Research Center (DKFZ)

type: Genome variation profiling by genome tiling array

summary:
Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH). Tumor DNA was hybridized against a single standard reference DNA-pool of the opposite sex than the patient. Every experiment was performed as dye-swap.
Keywords: repeat sample


title: Insights into Dahl salt-sensitive hypertension revealed

status: Public on Nov 17 2005

city: Milwaukee

first: Mingyu

last: Liang

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

summary:
The results of this study identified a number of pathways potentially important for the amelioration of hypertension and renal injury in SS-13BN/Mcw rats, and these results generated a series of testable hypotheses related to the role of the renal medulla in the complex mechanism of salt-sensitive hypertension.
Keywords: time course, microarray; 11ß-hydroxysteroid dehydrogenase; glucagon receptor; extracellular matrix; apoptosis

overall_design: Rats were paired for microarray hybridization, and the results were analyzed. Each of the four between-group comparisons comprised three pairs of rats examined by six microarrays with dye switching for each pair. Dye switching was not necessary for within-group comparisons, because the two rats of each pair were equivalent in terms of their treatment status. The expression data from the present study were combined with those from 24 microarrays hybridized in our previous study and used to identify genes exhibiting the most distinct temporal patterns of expression between SS and SS-13BN/Mcw over the time course studied.

first: Baozhi

last: Yuan

first: Elizabeth

last: Rute

last: Greene

first: Michael

last: Olivier

first: Allen

middle: W

last: Cowley Jr.


title: Genotyping Tool for Studying Epidemiologically Related Isolates

status: Public on Nov 16 2005

summary:
Replicates of strains used in comparison of microarray to RAPD analysis for the publication. Findings from use of an open-reading frame-specific Campylobacter jejuni DNA microarray to investigate genetic diversity among clinical isolates associated with 5 independent clusters of infection were compared with data from random amplified polymeric DNA (RAPD) and Penner serotyping analyses. The DNA microarray provides a highly specific epidemiological typing tool for analysis of C. jejuni isolates and reveals both divergent and highly conserved gene classes among isolates
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed

first: Nina

last: Salama

first: Edward

last: Leonard


title: Stereotyped and specific gene expression programs in human innate immune responses to bacteria.

summary:
The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene expression program in human peripheral blood mononuclear cells responding to bacteria and bacterial products. We found a remarkably stereotyped program of gene expression induced by bacterial lipopolysaccharide and diverse killed bacteria. An intricately choreographed expression program devoted to communication between cells was a prominent feature of the response. Other features suggested a molecular program for commitment of antigen-presenting cells to antigens captured in the context of bacterial infection. Despite the striking similarities, there were qualitative and quantitative differences in the responses to different bacteria. Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Jennifer

last: Boldrick


title: Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis

city: Newcastle upon Tyne

first: Nicholas

last: Allenby

state: Tyne and Wear

address: Leech Building, Medical School

department: Institute for Cell and Molecular Biosciences

institute: The University of Newcastle upon Tyne

summary:
Bacillus subtilis responds to phosphate starvation stress by inducing the PhoP and SigB regulons. While the PhoP regulon provides a specific response to phosphate starvation stress, maximizing the acquisition of phosphate (Pi) from the environment and reducing the cellular requirement for this essential nutrient, the SigB regulon provide non-specific resistance to stress by protecting essential cellular components such as DNA and membranes.  We have characterized the phosphate starvation stress response of B. subtilis at a genome-wide level using DNA macroarrays. A combination of outlier and cluster analyses identified putatively new members of the PhoP regulon, namely yfkN (2',3'-cyclic-nucleotide 2'-phosphodiesterase), yurI (ribonuclease), yjdB (unknown) and vpr (extracellular serine protease). YurI is thought to be responsible for the non-specific degradation of RNA, whilst the activity of YfkN on various nucleotide phosphates suggests that it could act on substrates liberated by YurI which produces 3` or 5` phosphoribonucleotides.
The putative new PhoP regulon members are either known or predicted to be secreted and are likely to be important for the recovery of inorganic phosphate from a variety of organic sources of phosphate in the environment.
Keywords: other

first: Nicholas E.

middle: E

first: Nicola

last: O’Connor

first: Zoltán

last: Prágai

first: Alan

middle: C

last: Ward

first: Anil

last: Wipat

first: Colin

last: Harwood


title: Primary pneumonic vs cultured Y. pestis

status: Public on Nov 10 2005

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

summary:
Although pneumonic plague is the deadliest manifestation of disease caused by the bacterium Yersinia pestis, there is surprisingly little information on the cellular and molecular mechanisms responsible for Y. pestis-triggered pathology in the lung. Therefore, to understand the progression of this unique disease, we developed an intranasal mouse model of primary pneumonic plague. Mice succumbed to a purulent multifocal severe exudative bronchopneumonia that closely resembles the disease observed in humans. In order to assess the adaptation of Y. pestis to a mammalian environment, we employed DNA microarray technology to analyze the transcriptional responses of the bacteria during interaction with the mouse lung as compared to bacteria cultured in vitro.
Keywords: Infectious expression analysis

overall_design: A Y. pestis genespecific microarray, consisting of 70-mer oligonucleotides representing 100% of the ORFs of strain CO92, was constructed. Two groups of 10 mice each were independently infected with Y. pestis strain CO92 as described above. After 48 hours, mice were sacrificed and RNA derived from infecting bacteria was extracted, amplified, and hybridized to the arrays. Each experiment consisted of a pair-wise competitive hybridization of amplified RNA (aRNA) samples from mouse and culture derived RNA and a reciprocal dye-flip replicate. Since 4 biological duplicates were tested, a total of eight DNA microarrays were used for comparison for each set of RNA amplifications.  The scanner photomultiplier tube (PMT)values were set for optimal intensity with minimal background. An additional scan was done for each slide (low PMT) with the PMT such that <1% of the elements are saturated in order to characterize spots which were saturated at the higher PMT setting.

first: Wyndham

last: Lathem

first: Virginia

last: Miller

first: William

last: Goldman


title: Expression profiling of responsiveness to infliximab in rheumatoid arthritis patients

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

institute: Faculty of Medicine and Pharmacy

summary:
Identifying gene expression profiles as predictors of a good vs poor response to a combined infliximab/methotrexate treatment in rheumatoid arthritis patients.
Keywords: drug response

overall_design: The PBMCs were isolated from venous blood by Ficoll-Hypaque and total RNAs were extracted, measured at 260 nm and frozen at -80°C until further used. An internal, arbitrary standard was made of a mixture of total RNAs from PBMCs taken from 3 healthy donors. The oligodT-primed poly(A) mRNAs were labelled with [α33P]dCTP as previously described [Coulouarn et al 2004], and the resulting, labelled cDNAs were immediately used for hybridization. Our array covering 12,000 cDNA probes for 10,000 non-redundant genes and various negative controls as well as nylon arraying of PCR-amplified probes and hybridization of [α33P]dCTP-labelled mRNAs have all been extensively described in a previous report [Coulouarn et al 2004]. All arrays were made from a single batch of cDNA probes. Every RNA sample was hybridized at least twice on separate arrays. Image analysis with the XDotsReader software, version 1.8 (COSE, Le Bourget, France), substractions of noise and spot background, and image normalization with the median value of all signals per image were done as in [Coulouarn et al 2004]. A transcript was considered to be expressed if at least two hybridizations provided a positive signal. The resulting, normalized values were used for a selection of significantly regulated mRNAs, i.e. those with an abundance that differed in two or more comparisons between two samples, using a funnel-shaped confidence interval (p<0.05) calculated from every mRNA detected per hybridization [Coulouarn et al 2004]. This results in a false discovery rate (FDR) that is below 10% of the total number of regulated mRNAs [Coulouarn et al 2005]. Statistical analyses were done with the R software [Ihaka and Gentleman 1996]. The TIGR Multiexperiment viewer (Tmev version 2.2, http://www.tm4.org) was used for i) unsupervised hierarchical clustering (HC) using the average dot product and complete linkage options, ii) the supervised statistical tool Significance Analysis of Microarrays (SAM) [Tusher et al 2001] for identification of discriminant transcripts. Gene profiling in PBMCs of responders and non-responders (total, 13 patients) were compared.

first: Thierry

last: Lequerré

first: Anne-Christine

last: Jauneau

first: Maryvonne

last: Daveau

first: Xavier

last: Le Loêt

first: Jean-Philippe

last: Salier


title: Post-hepatitis C and post-alcoholism hepatocellular carcinomas: series 3

summary:
The aim of this study is to compare post-Hepatitis C (HCV) and post-Alcoholism (ALC) Hepatocellular Carcinoma gene expression profiling. Owing to transcriptome analysis with a cDNA array virtually covering every transcript in liver, we compared tumors vs paired cirrhosis or tumors vs controls as a function of etiology, i.e. alcoholism (ALC) vs hepatitis C virus (HCV). The so-called Significance Analysis of Microarray was used to identify those genes with the most informative changes in transcript levels. Comparisons of tumor/cirrhosis ratios or tumor/controls ratios between 12 alcoholic vs 10 HCV patients identified a total of 31 transcripts whose altered ratios appropriately clustered the patients according to etiology.
Keywords: etiology analysis

overall_design: The tumoral (TU) part and paired-cirrhosis (CIR) taken away from tumor were analyzed for 22 patients with hepatocellular carcinoma (Pat1-22). Five controls (Control1-5) have been included. All data in the current study were obtained from 3 separate hybridizations per RNA sample (except for Control4-5 : 2 replicates).

first: Céline

last: Derambure

first: Cédric

last: Coulouarn

first: Frédérique

last: Caillot

first: Grégory

last: Lefebvre

first: Martine

last: Hiron

first: Michel

last: Scotte

first: Arnaud

last: François

first: Odile

last: Goria

first: Catherine

last: Cavard

first: Benoît

last: terris


title: primary stem development

city: Vancouver

first: Carl

last: Douglas

state: BC

department: Department of Botany

country: Canada

institute: University of British Columbia

summary:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Four replicate arrays (double dye-flip) were hybridized for each comparison.
Keywords = fiber
Keywords = lignin
Keywords = stem developmet
Keywords: time-course

first: Juergen

last: Ehlting

first: Joerg

last: Bohlmann

first: Brian

last: Ellis


title: Histopathological stages of disease in Helicobacter-induced mucosa-associated lymphoid tissue lymphoma.

last: Stanford Microarray Database

state: CA

department: Stanford University, School of Medicine

summary:
Long-term colonization of humans with Helicobacter pylori can cause the development of gastric B cell mucosa-associated lymphoid tissue lymphoma, yet little is known about the sequence of molecular steps that accompany disease progression. We used microarray analysis and laser microdissection to identify gene expression profiles characteristic and predictive of the various histopathological stages in a mouse model of the disease. The initial step in lymphoma development is marked by infiltration of reactive lymphocytes into the stomach and the launching of a mucosal immune response. Our analysis uncovered molecular markers of both of these processes, including genes coding for the immunoglobulins and the small proline-rich protein Sprr 2A. The subsequent step is characterized histologically by the antigen-driven proliferation and aggregation of B cells and the gradual appearance of lymphoepithelial lesions. In tissues of this stage, we observed increased expression of genes previously associated with malignancy, including the laminin receptor-1 and the multidrug-resistance channel MDR-1. Finally, we found that the transition to destructive lymphoepithelial lesions and malignant lymphoma is marked by an increase in transcription of a single gene encoding calgranulin A/Mrp-8.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Anne

last: Mueller


title: Follicular lymphoma and normal lymphoid tissue comparisons

summary:
20 FL lymph node samples from 16 patients and four normal lymphoid tissues (two tonsil and two spleen) from four different patient.  Data can be viewed on the supplemental website at http://genome-www.stanford.edu/rituximab/.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Sean

last: Bohen


title: MI: 1 and 7 days post-op

city: Oslo

first: Kristin

last: Andersson

address: Ullevål University Hospital

institute: Institute for Experimental Medical Research

summary:
1-day and 7-day sham and MI hearts
Keywords = Heart
Keywords = Mycardial infarction
Keywords = 1 day post-MI
Keywords = 7 day post-MI
Keywords: parallel sample

first: Geir

last: Florholmen

first: Lisbeth

last: Winer

first: Theis

last: Tonnessen

last: Christensen


title: cDNA array of the new human breast cancer cell line EM-G3 derived from breast cancer progenitor cells

status: Public on Nov 08 2005

city: Prague 2

first: Zdenek

last: Kleibl

address: U nemocnice 5

department: Dept. of Biochemistry and Experimental Oncology

country: Czech Republic

institute: First Faculty of Medicine, Charles University in Prague

summary:
Analysis of gene expression with cDNA array showed high expression levels of apoptosis activator Apaf1, membrane proteins CD44 and TGFR1β, integrin family members α2, α3, α6, αV and β1, p53 regulator MDM2, p21Ras GTP-ase activating molecule RasA1, and extracellular matrix-associated protein thrombospondin I. Expression of EGFR confirmed the immunocytochemical results, and expression of integrin α6 and CD44 support basal epithelial character of the EM-G3 cells.
Keywords: cDNA array, breast cancer cell line

overall_design: GEArray Q series Human Cancer PathwayFinder array kit was obtained from SuperArray Inc (see www.superarray.com for details). RNA (3 μg) from EM-G3 cells was used as a template to generate 32P-dCTP (Amersham Biosciences) labeled cDNA probes, according to the manufacturer's instructions. The cDNA probes were denatured and hybridized overnight at 60°C with the SuperArray membrane. The membrane was washed, and analyzed by scanning the Kodak BioMax X-Omat X-ray film (Amersham Biosciences).

first: Marketa

last: Brozova

first: Eva

last: Matouskova

first: Jan

last: Sevcik


title: Listeria infection of Caco-2 cells

status: Public on Nov 05 2005

summary:
This experiment set contains all of the arrays described in Baldwin et al., Genome Biology, 2002.  All experiments are time courses, with the exception of multiple measurements for the zero time point in the parallel time course for the purpose of zero transformation.  The parallel four hour time course was performed on a single day and three independent measurements were taken prior to infection.  The eight hour time courses were each performed on different days, with single time zero measurements.  Each array represents a measurement of human mRNA from cultured intestinal epithelial cells (red channel), relative to the control reference pool of mRNA (green channel), at different time points during the course of an infection by Listeria monocytogenes, or the mutants actA (defective in actin-based motility) and prfA (defective in virulence factor gene expression).
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: David

last: Baldwin


title: Microbial diversity of an uncontaminated and a 2,4,6-TNT contaminated soil sample with CodeLink microarrays

city: Louvain-la-Neuve

first: Laurent

last: Eyers

address: Place Croix du Sud 2/19

department: Unit of bioengineering

country: Belgium

institute: Catholic University of Louvain

summary:
Comparison of probe-target dissociations of probe Eub338 and Gam42a with native RNA of P. putida, in vitro transcribed 16s rRNA of P. putida, in vitro transcribed 16S rRNA of a 2,4,6-trinitrotoluene contaminated soil and an uncontaminated soil sample. Functional ANOVA revealed no significant differences in the dissociation curves of probe Eub338 when hybridised to the different samples. On the opposite, the dissociation curve of probe Gam42a with native RNA of P. putida was significantly different than the dissociation curves obtained with in vitro transcribed 16S rRNA samples.
Keywords: Microbial diversity, thermal dissociation analysis, CodeLink microarray

sample_organism:
Pseudomonas putida
unidentified

overall_design: Four samples: 1) native RNA of P. putida, 2) in vitro transcribed 16S rRNA of P. putida, 3) in vitro transcribed 16S rRNA of an unconontaminated soil sample, 4) in vitro transcribed 16S rRNA of a 2,4,6-trinitrotoluene contaminated soil sample. Each hybridisation experiment was done in triplicate.

first: James

last: Smoot

first: Laura

first: Céline

last: Bugli

first: Hidetoshi

last: Urakawa

first: Zack

last: McMurry

first: Slil

last: Siripong

first: Said

last: El Fantroussi

first: Philippe

last: Lambert

first: Spyros

middle: N

last: Agathos

last: Stahl


title: Genomic comparison of Salmonella enterica serovars and Salmonella bongori

status: Public on Nov 04 2005

last: Stanford Microarray Database

summary:
This experiment set includes 64 arrays representing 26 serovars and strains of Salmonella spp. including many representatives of subspecies I, Arizona from subsp. IIIa, and S. bongori from subsp. V.  The genomic DNA from all strains were labeled with Cy5 and hybridized against an equal amount (1.5 ug) of S. typhimurium SL1344 reference genomic DNA that was labeled with Cy3, all on an S. typhimurium SL1344 spotted DNA microarray.  Most of the arrays are present in triplicate to account for variability in probe generation, hybridization, and slide quality.  Several are represented in duplicate, and a few without any replicates.
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: Distinct Sets of Genetic Alterations in Melanoma

city: San Francisco

first: Boris

last: Bastian

department: Laboratory Medicine

institute: UCSF Cancer Center

summary:
We compared genome-wide DNA copy number alterations and mutational status in BRAF and RAS genes of 126 primary melanomas arising in four groups in which UV exposure differ: skin with (n=30), and without chronic sun damage (n=40); palms, soles and subungual (acral) sites (n=36) (which have very little sun exposure); and mucosa (n=20) (no sun exposure).
Keywords: other

first: J

last: Curtin

last: Fridlyand

first: T

last: Kageshita

first: H

last: Patel

first: K

last: Busam

last: Kutzner

middle: H

last: Cho

first: S

last: Aiba

first: E

last: Bröcker

first: P

last: LeBoit

first: D

last: Pinkel

first: B


title: Correlation between expression levels of different tumors measured by poly(A)+RNA and aRNA

summary:
Zhao et al. Amplification Table 7
This experiment was designed to determine the correlation between expression levels of defferent tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor. Total RNA was amplified using the Jeffrey lab protocol with G50 cleanup.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Hongjuan

last: Zhao


title: Effect of column cleanup on T7 based RNA linear amplification

summary:
Zhao et al. Amplification Table 4
This experiment was designed to evaluate the effect of column cleanup on the fidelity and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with or without G50 cleanup.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Effect of ligase on T7 based RNA linear amplification

summary:
Zhao et al. Amplification Table 3
This experiment was designed to evaluate the effect of ligase used in the second strand cDNA synthesis on the fidelity of T7 based RNA linear amplification. BC2 total RNA was amplified with or without ligase using Affymetrix protocol.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Renal medullary genes in salt-sensitive hypertension

first: Mingyu

last: Liang

summary:
Substitution of chromosome 13 from Brown Norway BN/SsNHsd/Mcw (BN/Mcw) rats into the Dahl salt-sensitive SS/JrHsd/Mcw (SS/Mcw) rats resulted in substantial reduction of blood pressure salt sensitivity in this consomic rat strain designated SSBN13. In the present study, we attempted to identify genes associated with salt-sensitive hypertension by utilizing a custom, known-gene cDNA microarray to compare the mRNA expression profiles in the renal medulla (a tissue playing a pivotal role in long-term blood pressure regulation) of SS/Mcw and SSBN13 rats on either low-salt (0.4% NaCl) or high-salt (4% NaCl, 2 wk) diets.
Keywords: Dahl S rat; blood pressure; kidney; consomic rats

overall_design: To increase the reliability of microarray data, we designed a four-way comparison experiment incorporating several levels of replication and developed a conservative yet robust data analysis method. Using this approach, from the 1,751 genes examined (representing more than 80% of all currently known rat genes), we identified 80 as being differentially expressed in at least 1 of the 4 comparisons.


title: Variation in cDNA microarray analysis of gene expression using unamplified poly(A)+ RNA

summary:
Zhao et al. Amplification BC2 uM
This experiment was designed to assess the reproducibility of microarray hybridization using poly(A)+RNA. BC2 total RNA was isolated from which poly(A)+RNA was subsequently isolated. Three arrays were hybridized on the same day using arrays from the same batch. Two were done three months later using poly(A)+RNA freshly isolated from the same total RNA.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Keywords: replicate_design


title: Effect of the amount of input total RNA on T7 amplification

summary:
Zhao et al. Amplification Table 9
This experiment was designed to evaluate the effect of the amount of input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol. Different amounts of T7 primer were used according to the quantity of input total RNA. Multiple amplifications were done for each quantity of input total RNA to minimize experimental variations.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Effects of template switching (TS) primer and cDNA cleanup columns on T7 based RNA linear amplification

summary:
Zhao et al. Amplification Table 1
This experiment was designed to determine the effects of template switching (TS) primer and the type of columns used in ds cDNA cleanup on the fidelity of the T7 based RNA linear amplification. BC91 total RNA was amplified with or without TS primer and with two different ds cDNA cleanup protocols.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection.

summary:
TC1: gastric epithelial (AGS) cells infected with wild type H. pylori (G27) and isogenic mutants in cagA and vacA for 0, 0.5, 3, 6, and 12 hours.  Total RNA was used to make single stranded Cy5 labelled probe and compared to Cy3 labelled probe from uninfected AGS cells. Hybridizations of G27 (trial 4) and cagA- (trial 3) timecourses were done in parallel.  A technical replicate of the G27 time course (trial 5) and hybridization of vacA- (trial 3) time course were done in parallel.  The cagA 6 and 12 hour time points were technically replicated (trial 4) (the cagA 6 hour sample of trial 3 was lost). TC2: Biological replication and expansion of TC1, using more isogenic mutants and timepoints.  AGS cells were mock infected, infected with G27, and isogenic mutants in cagN, cagA, cagE, and a deletion of the cag PAI for 0. 1, 3, 6, 12, and 24 hours.  Probe synthesis and hybridization was done as in TC1. Note: there may have been a sample mix-up with PAI 12, swapping it with G27 or cagN 12.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Karen

last: Guillemin


title: BMP4 initiates human ES cell differentiation

last: Stanford Microarray Database

summary:
The excitement and controversy surrounding the potential role of human embryonic stem (ES) cells in transplantation therapy have often overshadowed their potentially more important use as a basic research tool for understanding the development and function of human tissues. Human ES cells can proliferate without a known limit and can form advanced derivatives of all three embryonic germ layers. What is less widely appreciated is that human ES cells can also form the extra-embryonic tissues that differentiate from the embryo before gastrulation. The use of human ES cells to derive early human trophoblast is particularly valuable, because it is difficult to obtain from other sources and is significantly different from mouse trophoblast. Here we show that bone morphogenetic protein 4 (BMP4), a member of the transforming growth factor-beta (TGF-beta) superfamily, induces the differentiation of human ES cells to trophoblast. DNA microarray, RT-PCR, and immunoassay analyses demonstrate that the differentiated cells express a range of trophoblast markers and secrete placental hormones. When plated at low density, the BMP4-treated cells form syncytia that express chorionic gonadotrophin (CG). These results underscore fundamental differences between human and mouse ES cells, which differentiate poorly, if at all, to trophoblast. Human ES cells thus provide a tool for studying the differentiation and function of early human trophoblast and could provide a new understanding of some of the earliest differentiation events of human postimplantation development.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

overall_design: Using regression correlation

first: Xin

last: Chen


title: Conventional renal cell carcinomas

status: Public on Nov 01 2005

department: Urology, Edwards Building R116

institute: Stanford University

summary:
Our goal was to identify gene expression features, using comprehensive gene expression profiling, that correlate with survival in conventional renal cell carcinomas (cRCCs). We profiled 177 cRCCs using high-density cDNA microarrays. Unsupervised hierarchical clustering analysis segregated cRCC into five gene expression subgroups. Expression subgroup was correlated with survival in long-term follow-up and was independent of grade, stage, and performance status. The tumors were then divided evenly into training and test sets that were balanced for grade, stage, performance status, and length of follow-up. A semisupervised  learning algorithm (supervised principal components analysis) was applied to identify transcripts whose expression was associated with survival in the training set, and the performance of this gene expression-based survival predictor was assessed using the test set. With  this method, we identified 259 genes that accurately predicted disease-specific survival among patients in the independent validation group (p < 0.001 ). In multivariate analysis, the gene expression predictor was a strong predictor of survival independent of tumor stage, grade, and performance status (p < 0.001).
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Comprehensive analysis of the gene expression profiles in human gastric cancer cell lines

status: Public on Nov 03 2005

summary:
Gastric adenocarcinoma is one of the major malignancies worldwide. Gastric cell lines have been widely used as the model to study the genetics, pharmacology and biochemistry of gastric cancers. Here we describe a comprehensive survey of the gene expression profiles of 12 gastric carcinoma cell lines, using cDNA microarray with 43 000 clones. For comparison, we also explored the gene expression patterns of 15 cell lines derived from lymphoid, endothelial, stromal and other epithelial cancers. Expression levels of specific genes were validated through comparison to protein expression by immunohistochemistry using cell block arrays. We found sets of genes whose expression corresponds to the molecular signature of each cell type. In the gastric cancer cell lines, apart from genes that are highly expressed corresponding to their common epithelial origin from the gastrointestinal tract, we found marked heterogeneity among the gene expression patterns of these cell lines. Some of the heterogeneity may reflect their underlying molecular characteristics or specific differentiation program. Two putative gastric carcinoma cell lines were found to be B-cell lymphoma, and another one had no epithelial specific gene expression and hence was of doubtful epithelial origin. These cell lines should no longer be used in gastric carcinoma research. In conclusion, our gene expression database can serve as a powerful resource for the study of gastric cancer using these cell lines
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

last: Chi


title: Gene expression of gastric mucosa during therapeutic acid inhibition

first: Kristin

last: Nørsett

department: Dept of Cancer Research and Molecular Medicine

institute: Norwegian University of Science and Technology

summary:
The effect on mucosal gene expression of potent acid inhibition with proton pump inhibitors (PPI’s) given to humans in ordinary, therapeutic doses is virtually unknown. Eight patients suffering from gastro-oesophageal reflux disease were included in this study. Endoscopic biopsies were taken from the corpus mucosa before and towards the end of a three-month treatment with the PPI esomeprazole 40 mg daily. Total RNA was extracted and samples (2 microgram total RNA) were labeled for microarray analysis. For each patient, RNA from both time points were labeled and hybridized to a single array. The gene expression patterns for 7700 genes were analyzed and differentially expressed genes were identified using one-sample Student t test. The aim of this study was, by use of cDNA microarray, to get an overview of the gene expression pattern in gastric corpus mucosa in patients after three months’ treatment with the proton pump inhibitor esomeprazole. Further characterization of the functional roles of genes whose expression is modulated by potent acid inhibition may give new insight into the molecular responses to this therapeutic intervention, including the mucosal response to the moderately increased gastrin levels encountered in clinical practice.
Keywords: Repeat sample group, treatment analysis

overall_design: The series is composed of 8 hybridizations for analysis of differentially expressed genes in the gastric mucosa of patients treated with 40 mg omeprazole (Losec, Astra AB, Gothenburg, Sweden) once daily for 90 days. Biopsy speciments were taken form the oxyntic mucosa before treatment and during the last week of treatment. Total RNA from patients before treatment (2 microgram each) and patients after treatment (2 microgram each) were reverse transcribed and labeled with Cy3- and Cy5-attached dendrimer, respectively, mixed and hybridized using 3DNA Array Detection Submicro kit as described in the manufacturer's protocols (Genisphere, Montvale, NJ). The labeling reactions were also spiked with exogenous control RNAs (Stratagene). No technical replicates or dye-swabs were included.

middle: G

first: Astrid

last: Lægreid

first: Waclaw

last: Kusnierczyk

first: Mette

last: Langaas

first: Helge

middle: L

last: Waldum

first: Arne

middle: K

last: Sandvik


title: Mutational state FLT3-ITD and GATA2 overexpression could define a subgroup of AML-M1 patients with normal karyotype

status: Public on Oct 27 2005

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

summary:
More than 40% of patients with AML have a normal karyotype and are included in the intermediate prognostic group, in which risk classification is currently poor defined and more molecular markers are needed to achieve treatment stratification. EVI1 overexpression (OE) has been reported to discriminate in this group those with a worse prognosis. The EVI1 mice homolog has a role in the HSC proliferation through Gata2 expression, therefore, GATA2, a transcription factor with a relevant role in hematopoiesis, could be a candidate gene in the leukemogenic transformation in AML in patients with normal karyotype, and in other subgroups. GATA2 OE was detected in 46% of cases with normal karyotype, and was more frequent among samples with FLT3-ITD (p=0.0021), especially among the AML-M1 cases. We found a mutational pattern FLT3-ITD/GATA2-OE/WT1-OE that could define a subgroup of patients with normal karyotype and AML-M1, with a different gene expression array pattern and a poor prognosis. Our results show that GATA2 OE is a common event in AML cases with normal karyotype (46%). The deregulation of the expression of the GATA2 transcription factor would lead to a hematopoietic differentiation impairs, focusing GATA2 as a candidate gene that fits in the cooperating model for the multistep pathogenesis that causes AML transformation.
Keywords: Disease state analysis

overall_design: Nine slides were hybridized, one for each patient, being three patients per group. Each patient sample is labeled with cy5 and the reference sample, the same for all slides, is a pool of nine bone marrows from healthy patients, labeled with cy3.

first: Idoya

last: Lahortiga

first: Eva

last: Bandrés

first: María

last: Odero