title: Transcriptome analysis of time couse of leafy spurge infection with Xam

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary: The goal of this study was to identify signaling processes associated with infection and recovery of leafy spurge inoculated with Xanthomonas axonopodis pv. manihotis (Xam).

platform_organism:
Manihot esculenta
Euphorbia esula

overall_design: Two dye-swap technical replicates for each of 3 biological replicates for each treatment were analyzed. A time course analysis of Xam infected and mock inoculated leafy spurge was performed. Time points were 1, 7 and 21 days after inoculation (or mock inoculation). Thus, 36 labeled samples were hybridized in a 2 dye rolling circle hybridization scheme to 18 arrays.

first: María

middle: A

last: Santana


title: Microarray analysis of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation: 16S rRNA

status: Public on Aug 07 2009

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

country: Canada

institute: NRC-BRI

summary: High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.

sample_organism: Bacteria Archaea

platform_organism: Bacteria Archaea

overall_design: 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years

first: Mélanie

last: Arbour

first: Roland

last: Brousseau

last: Juck

first: John

middle: R

last: Lawrence

first: Luke

last: Masson

first: Lyle

middle: G

last: Whyte

first: Charles

middle: W

last: Greer


title: Microarray analysis of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation: genomic DNA

sample_organism:
Bacteria
Escherichia coli
Archaea


title: Transcriptome patterns for Acute Cellular Rejection in Recipients with Recurrent Hepatitis C after Liver Transplantation

status: Public on Aug 05 2009

city: Suita

first: Tadafumi

last: Asaoka

address: 2-2, Yamadaoka

department: Surgery

country: Japan

institute: Osaka University

summary:
The histological evaluation of liver via biopsy remains as the standard for the diagnosis of both acute cellular rejection (ACR) and recurrent hepatitis C (RHC) after liver transplantation. Nevertheless, it is often difficult to diagnose ACR in HCV-positive recipients because of common co-existing and overlapping morphological changes with RHC. The aim of the study was to identify potential target genes for ACR in recipients with RHC. We analyzed 22 liver biopsy samples obtained from 21 HCV-positive recipients. The clinicopathological diagnoses for the biopsies were ACR-predominant with superimposed RHC in 9 samples (ACR group) and RHC with no ACR (non-ACR group) in the remaining. We compared the transcriptional alterations between the two groups with oligonucleotide microarray and selected 2206 genes which were significantly modulated in ACR. Subsequently we analyzed the regulatory networks in ACR using Ingenuity Pathway Analysis, and focused on 5 genes (IFNAR1, IL-12RB2, NFATC3, BMP2, and CASP8) from the core network as the target genes for ACR. In conclusion, our results demonstrated that novel transcriptome patterns of ACR and concurrent RHC were present and distinct from recipients with only RHC, suggesting that gene expression profiling may have a role in the diagnosis of ACR in recipients with hepatitis C.

Keywords: Gene identification in ACR with recurrent HCV infection

overall_design: Of 22 liver biopsy samples, 9 represented the clinicopathological diagnoses for ACR-predominant with superimposed RHC (ACR group) and 13 represented the clinicopathological diagnoses for RHC with no ACR (non-ACR group) .


title: Ethanol stress response in Desulfovibrio vulgaris

status: Public on Aug 08 2009

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

country: USA

institute: The University of Tennessee

summary:
Desulfovibrio vulgaris has been studied extensively for its potential in the bioremediation of heavy metals and radionuclides. Hydrocarbons and solvents, as frequent environmental co-contaminants, have been reported to inhibit microbial activities and thereby pose a limitation on bioremediation efficiency. As a part of the Genomes: GTL project to deduce the stress response pathways in metal/radionuclide reducing bacteria, we studied the responses of D. vulgaris to ethanol, which is a solvent and co-contaminant frequently encountered at contaminated DOE sites. Growth experiments in closed vessels at 37 °C indicated that D. vulgaris could maintain normal growth with 1%(v/v) ethanol. The growth rates were reduced with increasing ethanol concentrations at 2% and 5%. Growth ceased when ethanol concentration was raised to 5%(v/v). Cell lysis was apparent with decreasing optical density following 10% ethanol addition.

To assess the mechanism of ethanol inhibition, genome-wide transcriptional profiles were analyzed from D. vulgaris cultures following ethanol (5% v/v) treatment using whole-genome microarrays. The ethanol treatment altered the expression of a large number of genes in the D. vulgaris genome, of which 354 were up-regulated greater than 2 fold and 217 were down-regulated by over 2 fold. As expected, changes in the transcriptional profile were similar to those of the stress response to acetone, which is also a solvent. Transcripts highly up-regulated included genes encoding the flagella structural subunits, suggesting motility as a mechanism of solvent stress response. Another group of genes highly induced were chaperones, such as dnaJ, groES, and hsp20, indicating the importance of maintaining proper protein folding under ethanol stress. Down-regulated genes included two groups of genes, ribosomal proteins and amino acid transporters, consistent with the growth inhibition by ethanol observed in growth studies. These results were interpreted that D. vulgaris responds to elevated solvent levels by increased motility and maintenance of proper protein functions. Current work is focused on the analysis of regulatory pathways based on temporal transcriptional dynamics.
Keywords: Stress response

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Desulfovibrio vulgaris from our laboratory culture collection was cultured at 37°C in Lactate-Sulfate medium to mid-log phase. Subsequently, ethanol (5% v/v) was added into triplicate cultures. Gene expression profiles 30 and 100 minutes following ethanol exposure were compared with those of the control cultures without ethanol treatment. Total RNA was harvested from three replicate control and treated cultures at two time points following ethanol addition. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (Dye swap).

first: Jizhong

last: Zhou


title: Interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression

status: Public on Aug 14 2009

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

type: Genome binding/occupancy profiling by genome tiling array

summary:
A two-colour cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression.
We describe a fluorescent reporter system that exploits the functional genomic tools available in budding yeast to systematically assess consequences of genetic   perturbations on gene expression. We used our Reporter-Synthetic Genetic Array (R-SGA) method to screen for regulators of core histone gene expression. We discovered that the histone chaperone Rtt106 functions in a pathway with two other chaperones, Asf1 and the HIR complex, to create a repressive chromatin structure at core histone promoters. We found that activation of histone (HTA1) gene expression involves both relief of Rtt106-mediated repression by the activity of the histone acetyltransferase Rtt109 and restriction of Rtt106 to the promoter region by the bromodomain-containing protein Yta7. We propose that the maintenance of Asf1/HIR/Rtt106-mediated repressive chromatin domains is the primary mechanism of cell cycle regulation of histone promoters. Our data suggest that this pathway may represent a chromatin regulatory mechanism that is broadly used across the genome.

overall_design: The supplemental CEL files contain the raw hybridization signals from genome-wide nucleosome occupancy experiments in rtt106, hir1 and wild type strains. The .BAR files contain the normalized data for each mutant and wild-type compared to the total genomic DNA signal to identify nucleosome positions, as well as the data for each mutant normalized to the wild-type profile to visualize changes in occupancy compared to wild type conditions.

first: Jeffrey

last: Fillingham

first: Pinay

last: Kainth

first: Jean-Phillipe

last: Lambert

last: van Bakel

first: Kyle

last: Tsui

first: Lourdes

last: Pena-Castillo

first: Corey

last: Nislow

first: Daniel

last: Figeys

first: Timothy

last: Hughes

first: Jack

last: Greenblatt

first: Brenda

last: Andrews


title: Effect of High Fat Diet on gene expression of liver from obesity-prone (C57BL/6J) and obesity-resistant (A/J) mice

status: Public on Aug 09 2009

city: Lausanne

first: Carine

last: Poussin

address: Quartier UNIL-Sorge

country: Switzerland

institute: University of Lausanne

summary:
Mice were fed for 2, 10 or 30 days with a normal chow (NC) or a high fat diet (HFD). At each time point, mice were sacrificed and liver samples were collected and immediately frozen in liquid nitrogen.
Total RNA from each sample was further extracted, purified, quality-controled before and after amplification. Cy3-labeled RNA from individual liver sample was co-hybridized with a Cy5-labeled pool of RNA on the mouse 17K microarray.

Keywords: diet response, time course, mouse strains

overall_design: For a given time point, each individual RNA sample was hybridized with a pool of RNA from 6 mice

first: Diana

last: Hall

first: Bernard

last: Thorens


title: Serine hydroxamate and the transcriptome of high cell density recombinant E. coli MG1655

city: Clemson

first: Sarah

last: Harcum

state: SC

address: 105 Collings Street

department: Bioengineering

institute: Clemson University

summary:
For over 30 years, serine hydroxamate has been used to chemically stimulate a stringent response in Escherichia coli and other bacteria. These studies have elucidated numerous characteristics of the classical stringent response beyond the simple cellular response to an amino acid shortage, including phospholipid synthesis and protease up-regulation. In this study, the effects of a serine hydroxamate addition on high cell density recombinant E. coli were examined and compared to the effects of recombinant protein production to determine overlaps, as recombinant protein production stress has often been attributed to amino acid shortages.  Both the transcriptome and growth characteristics were evaluated and compared. The serine hydroxamate addition profoundly decreased the culture growth rate, whereas, recombinant protein production did not.  Conversely, the transcriptome profile of the recombinant E. coli cultures were relatively unaffected by the serine hydroxamate addition, yet recombinant protein production dramatically changed the transcriptome profile.  A subset of the classical stringent response genes were effected by the serine hydroxamate addition, whereas, recombinant protein production regulated numerous classical stringent response genes; however, not all.  The genes that were regulated by the serine hydroxamate addition include numerous fatty acid synthesis genes, in agreement with altered phospholipids synthesis reports. These results indicate that recombinant protein production and the stringent response have many overlapping responses; however, are far from identical.
It was hypothesized that recombinant protein production leads to a stringent response due to the high amino acid synthesis demands related to recombinant protein synthesis.  A comparison of the transcriptomes during recombinant protein production and a chemical imposed stringent response would assist with determining what portion of the “metabolic burden” associated with recombinant protein production is due to amino acid shortages. In this study, the transcriptome profiles of recombinant E. coli were examined and compared for the three culture conditions: 1) Normal growth, no external stress; 2) L-serine hydroxamate addition (to mediate a stringent response); and 3) IPTG-induction to produce the recombinant protein chloramphenicol acetyltransferase (CAT). The transcriptome profiles from these three conditions were analyzed using Affymetrix Anti-sense E. coli GeneChip® microarrays.

overall_design: For the serine hydroxamate fermentations, cells were harvested immediately prior to the serine hydroxamate-addition (Time S0) and 1-hour post serine hydroxamate-addition (Time S1). For the IPTG-induced fermentations, cells were harvested immediately prior to the IPTG-addition (Time S0) and 1-hour post-induction (Time S1). For the uninduced (unstressed) fermentations, cells were harvested at Time S0 and Time S1, for which the timing was synchronized with the serine hydroxamate and IPTG fermentations based on OD for Time S0 and time for Time S1.  Each fermentation condition was repeated (two biological replicates). RNA from each biological replicates was purified and processed independently. Three biological replicates were obtained for the control condition (Time S0), since prior the serine hydroxamate- or IPTG- addition all fermentations were replicates.  Prior to DNA microarray hybridization, where only two biological replicates existed, one of the processed samples was divided into two technical replicates, resulting in three separate hybridized chips. All Time S1 samples contained three technical replicates from two biological duplicates, whereas the control Time S0 measurement contained three biological replicates.

first: Fu'ad

middle: T

last: Haddadin


title: Transcriptome Profiles For High-Cell-Density Recombinant and Wild-Type E. coli

summary:
The transcriptome profiles for wild-type (plasmid-free) and recombinant (plasmid-bearing) Escherichia coli during well-controlled synchronized high-cell-density fed-batch cultures were analyzed by DNA microarrays. It was observed that the growth phase significantly affected the transcriptome profiles, and the transcriptome profiles were significantly different for the recombinant and wild-type cultures. The response of the wild-type and recombinant cultures to an isopropyl-1-thio-β-D-galactopyranoside- (IPTG-) addition was examined, where IPTG induced recombinant protein production in the plasmid-bearing cultures. The IPTG-addition significantly altered the transcriptome response of the wild-type cultures entering the stationary phase. The IPTG-induced recombinant protein production resulted in a significant down-regulation of many energy synthesis genes (atp, nuo, cyo), as well as nearly all transcription- and translation-related genes (rpo, rpl, rpm, rps, rrf, rrl, rrs). Numerous phage (psp, hfl) and transposon-related genes (tra, ins) were significantly regulated in the recombinant cultures due to the IPTG-induction. These results indicate that the signaling mechanism, associated with the recombinant protein production, may induce a metabolic burden in the form of a phage defense mechanism. Taken together, these results indicated that recombinant protein production initiated a cascade of transcriptome responses that down-regulated the very genes needed to sustain productivity.
In this study, the transcriptome profiles for recombinant and wild-type E. coli cultures were compared. The recombinant and wild-type cultures were monitored during the exponential growth phase and as the cultures entered the stationary phase. Well-controlled fed-batch fermenters were used to synchronize the high-cell density cultures. E. coli MG1655 [pPROEx-CAT] and E. coli MG1655 (plasmid-free) were exposed to IPTG in the exponential phase, where chloramphenicol acetyltransferase (CAT) expression was induced in the plasmid-bearing cultures. Control cultures, not exposed to IPTG, were also examined. The gene expression profiles were determined using DNA microarrays. Recombinant protein production was shown to result in a metabolic burden due to significant down-regulation of the transcription, translation, and energy synthesis genes.  This was the first comprehensive study that has examined the transcriptome of wild-type and recombinant cultures under the same set of conditions.  This data indicated that one cannot merely extrapolate the behavior of recombinant cultures from wild-type culture data.

overall_design: All fermentations were synchronized in time to the time at which the cell density reached approximately 11.5 OD, or roughly 70% of the fermenter’s maximum cell density. IPTG (5 mM) was added when the cell density reached the targeted OD for the cultures to be induced. Cells were harvested at 0, 1, 2, 3, 4, and 5 hours relative to the synchronization time point (identified as Time S0, S1, etc). Each fermentation condition was conducted in duplicate. For the recombinant Control Time S0 sample, triplicate samples were available since prior to the IPTG-addition, all fermentations within a strain were replicates. All fermentation conditions were repeated twice (two biological replicates). RNA from each biological replicate was purified and processed independently. Three biological replicates were obtained from for the recombinant Control sample (Time S0) since the cultures prior to the IPTG-addition were replicates. Prior to hybridization, where only two biological replicates existed, one of the RNA samples was divided into two technical replicates, resulting in three separate hybridized chips. The wild-type Time S0 samples and all Time S1 and S4 samples contained data from three DNA microarrays obtained from two biological duplicates (30 DNA microarrays total).


title: Gene expression profile analysis of F2 cross between Fat and Lean chickens

status: Public on Aug 04 2009

city: Nouzilly

first: Cécile

last: Berri

address: CR INRA

department: PHASE

country: France

institute: INRA

summary: The aim of this study was to identify genes involved in the variation of the muscle glycogen content at death (estimated through the glycolytic potential, GP), a determining factor in the meat quality of chicken. The gene expression profiles of the Pectoralis major muscle were established using microarrays. We compared animals showing extreme GP values, issued from a F2 cross between Fat and Lean lines. A total of 254 genes were differentially expressed between F2 birds with low or high GP. Several of these genes were validated by qRT-PCR. For the genes with human orthologs, annotation analyses were performed and mainly revealed pathways involved in carbohydrate, fatty-acid and protein metabolism. The relationship between gene expression and meat quality has to now be validated by further e-QTL studies on the F2 population.

overall_design: 8 high GP samples compared to 8 low GP samples, 4 of these were dye-swapped.

first: Vonick

last: Sibut

first: Michel

last: Duclos

first: Christelle

last: Hennequet-Antier

first: Elisabeth

last: Lebihan-Duval


title: Design and performance of a turbot (Scophthalmus maximus) oligo-microarray based on ESTs from immune tissues

city: Lugo

first: Adrian

middle: Millan

last: Perez

state: Lugo

address: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior

department: Acuigen

country: Spain

institute: Universidad Santiago Compostela

summary: An EST database from immune tissues was used to design the first high density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60mers) were successfully designed for 2716 out of 3482 unique sequences of the database. The performance of the microarray and the sources of variation along microarray analysis were examined on spleen pools of controls and Aeromonas salmonicida challenged fish at 3 days post-infection. An asymmetric hierarchical design was employed to ascertain the noise associated with biological and technical (RNA extraction, labeling, hybridization, slide and dye bias) factors using one-colour (1C) and two-colour (2C) -labeling approaches. The high correlation coefficient between replicates at most factors tested demonstrated the high reproducibility of the signal. An analysis of random effects variance revealed that technical variation was mostly negligible and biological variation represented the main factor, even using pooled samples. One-colour approach performed at least as well as 2C. A relevant proportion of genes turn out to be differentially labelled depending on fluorophore, which alerts for the likely need of swapping replication in 2C experiments. A set of differentially expressed genes and enriched functions related to immune/defence response were detected at three days post-challenging.

overall_design: An unbalanced hierarchical design was planned to evaluate the sources of variation in microarray analysis. This design enabled us to consider most sources of noise in microarray analysis and evaluate their weight in the variability of the signal using an equilibrate number of replicates at each level and a not too large number of microarrays. According to this hierarchy, the following within slide sources of variation were assessed from top to bottom: biological (B), RNA extraction (E), labeling (L) and hybridization (H). Additionally, we studied variation between slides (S), the bias produced by labeling with different dyes (Cy3 and Cy5) and compared the performances of one-colour (1C) and two-colour (2C) -labeling approaches. A total of 24 microarrays grouped in three 8x15k slides were used for this design. One pool of five individuals was used as control and other two other pools of five individuals each (B1 and B2) were used as biological replicates. Three replicates were used for evaluating the variation associated with RNA extraction (E1, E2, E3), labeling (L1, L2, L3) and hybridization (H1, H2, H3) within slide. Some of these replicates were in turn hybridized in different slides to assess interslide variation. Three 2C hybridizations with dye swapping (6 microarrays) were performed in the same slide for comparison of 1C and 2C approaches and to analyze dye bias.   Normalization within each microarray was carried out using the loess method. Normalization using all microarray data was done by performing the Aquantile method implemented in the limma package. To estimate the variation associated with replicates at the different steps of microarray analysis or to different slides we applied the Pearson correlation coefficient using log2 absolute treatment and treatment/control ratio values. Also an ANOVA of random effects was used to split the total variance into its components.   For Dye bias evaluation and 1C vs. 2C comparisons we f estimated the proportion of common differentially expressed (DE) genes after Bonferroni correction at P <0.05 and P<0.01 at fold changes (FC) >1.5, 2 and 3. The degree of concordance between the different dyes and between 1C and 2C approaches was estimated as the proportion of common DE genes at each P and FC.

first: A

last: Millán

last: Gómez-Tato

first: C

last: Fernández

first: B

last: Pardo

first: J

last: Álvarez-Dios

first: M

last: Calaza

last: Bouza

last: Vázquez

first: S

last: Cabaleiro

first: P

last: Martínez


title: Gene expression profiling in wMelPop-infected Aedes aegypti

status: Public on Aug 03 2009

city: Oxford

first: Steven

last: Sinkins

address: South Parks Rd

department: Department of Zoology

country: United Kingdom

institute: University of Oxford

summary: Whole genome transcriptional profiling comparing  Ae. aegypti infected with Wolbachia sp. wMelPop (PGYP1) to an uninfected Ae. aegypti control line (PGYP1.tet). The objective of the experiment was to identify genes that may be involved in the life shortening phenotype associated with wMelPop infection.

overall_design: Two-colour experiment; infected vs. uninfected Ae. aegypti; 4 biological replicates; 2 dye swaps.

first: Zakaria

last: Kambris

first: Peter

last: Cook


title: Transcriptomic alterations in Trypanosoma cruzi-infected cardiac myocytes

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Trypanosoma cruzi infection is a major cause of cardiomyopathy. Gene profiling studies of hearts from infected mice have revealed prominent changes in gene expression within many functional pathways.  This variety of transcriptomic changes in infected mice raises the question of whether gene expression alterations in whole hearts are due to changes in infected cardiac myocytes or other cells or even to systemic effects of the infection on the heart. We employed microarrays to examine infected cardiac myocyte cultures 48 hr post-infection. Statistical comparison of gene expression levels of 2,258 well annotated unigenes in four independent cultures of infected and uninfected myocytes detected (p < 0.05) significant > 1.5 absolute fold changes in 221 (8.8%) of the sampled genes.  Major categories of affected genes included those involved in immune response, extracellular matrix and cell adhesion.  While changes in extracellular matrix and cell adhesion genes were anticipated, modulation of immune response genes in the infected myocytes was surprising.  These findings on infected cardiac myocytes in culture reveal that altered gene expression described in the heart in Chagas disease are the consequence of both direct infection of the myocytes and resulting from presence of other cell types in the myocardium and systemic effects of infection.

overall_design: Transcriptomic alteration in neonatal mouse cultured cardiomyocytes induced by the parasite T.cruzi were detected by profiling and compared using AECOM mouse 32k oligonucleotide arrays hybridized in the "multiple yellow" strategy described in Iacobas et al,  Biochem Biophys Res Commun. 2006 349(1):329-38.

first: Regina

middle: C

last: Goldenberg

first: Sanda

first: Leonardo

middle: L

last: Rocha

first: Fabio

middle: D

last: Fortes

first: Leandro

last: Vairo

first: Fnu

last: Nagajyothi

first: Antonio

last: Carvalho

first: Herbert

middle: B

last: Tanowitz

first: David

last: Spray


title: Acetone stress response in Desulfovibrio vulgaris

first: Qiang

last: He

summary:
Desulfovibrio vulgaris has been studied extensively for its potential in the bioremediation of heavy metals and radionuclides. Hydrocarbons and solvents, as frequent environmental co-contaminants, have been reported to inhibit microbial activities and thereby pose a limitation on bioremediation efficiency. As a part of the Genomes: GTL project to deduce the stress response pathways in metal/radionuclide reducing bacteria, we studied the responses of D. vulgaris to acetone, which is a ketone solvent frequently observed at contaminated DOE sites. Growth experiments in closed vessels at 37 °C indicated that D. vulgaris could maintain normal growth with 3%(v/v) acetone following a 1-h lag phase. When the acetone concentration was raised to 5%(v/v), we observed a 2-h lag phase followed by a growth rate which was only 15% that of normal. At an acetone concentration of 8%(v/v), no active growth was observed following 10 hours of incubation.

To assess the mechanism of acetone inhibition, genome-wide transcriptional profiles were analyzed from D. vulgaris cultures following acetone (5% v/v) treatment using whole-genome microarrays. This acetone shock altered the expression of a large number of genes in the D. vulgaris genome, of which 309 were up-regulated greater than 2 fold and 199 were down-regulated by over 2 fold. Transcripts highly up-regulated included genes encoding the flagella structural subunits, flgB (15 fold), fliE (11 fold), and flgH (10 fold). Another group of genes highly induced were chaperones, such as dnaJ (11 fold), groES (8 fold), and hsp20 (8 fold). Down-regulated genes included two groups of genes, ribosomal proteins and amino acid transporters, suggesting a state of growth arrest upon acetone addition. These results were interpreted to mean that D. vulgaris responds to elevated solvent levels by increased motility and maintenance of proper protein functions. Current work is focused on the analysis of regulatory pathways based on temporal transcriptional dynamics.
Keywords: Stress response

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Desulfovibrio vulgaris from our laboratory culture collection was cultured at 37°C in Lactate-Sulfate medium to mid-log phase. Subsequently, acetone (5% v/v) was added into triplicate cultures. Gene expression profiles 30 and 100 minutes following acetone exposure were compared with those of the control cultures without acetone treatment. Total RNA was harvested from three replicate control and treated cultures at two time points following acetone addition. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (Dye swap).

first: Zhili

first: Jizhong

last: Zhou


title: Gene expression in the liver following exposition to 1Gy ionizing radiation

city: Evry

first: Alexandre

last: Pawlik

address: 2, rue Gaston Crémieux

department: DSV/DRR

institute: CEA

summary:
Although major differences in the response of tissues were documented in the literature, the molecular mechanisms underlying tissue radiosensitivity are still fragmentary and need to be study more thoroughly. To this end, a genome wide analysis strategy was used to investigate changes in gene expression in the liver following exposition to ionizing radiation. This follows the tissue survey that was previously initiated with other organs and tends to obtain a comprehensive picture of the molecular events underlying tissue radio sensitivity.
Keywords: Ionizing radiation response

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
totalRNA sample from irradiated liver was hybridized against totalRNA sample from non-irradiated liver.
8 dye-swaps have been done.


title: Gene Expression profiling of M. bovis BCG strain under hypoxia

status: Public on Aug 06 2009

city: Lucknow

first: Ranjana

last: Srivatsava

address: Chattar Manzil Palace

country: India

institute: Central Drug Research Institute

summary:
Objective of the study is to find out the differentially regulated genes in Mycobacterium bovis BCG subjected to hypoxic condition. Gene expression profiling was carried out using Agilent microarray platform.
Keywords: Hypoxia response

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design:
Mycobacterium cells were lysed by bead beating in AL Buffer of Qiagen’s bacterial RNA kit. RNA was purified as per manufacturer’s instructions. RNA quality control was done using Agilent 2100 Bioanalyzer lab on a chip.

Total RNA (500ng) of Mycobacterium under hypoxia and log phase were labelled with Cy3 and Cy5 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol. To eliminate dye bias, technical replicates were labelled in the reverse direction i.e log phase culture with Cy5 and hypoxia with Cy3. 825ng each of labeled control cRNA was mixed with 825ng of treated labelled cRNA, mixed with appropriate amount of blocking buffer and hybridization buffer (Agilent Technologies). The hybridization mix was applied on to the backings and hybridized to custom designed 60mer M.tuberculosis H37Rv microarray using sure hyb chambers at 65degC for 17 hours. Slides were washed with gene expression wash buffer 1 and 2 (Agilent Technologies) followed by Acetonitrile and scanned at 5 micron resolution using Agilent scanner. Automated feature extraction was done using Agilent’s Feature Extraction Software. Statistical analysis of microarray data was done using GeneSpring GX and Biological analysis of the differentially regulated genes were done using Genotypics Biointerpreter -Web based tool for biological interpretation of gene list in a click of mouse.

first: Srivastav

last: BS

first: Alka

last: Saxena


title: Discovery of candidate genes and pathways in the endometrium regulating ovine blastocyst growth and conceptus elongation

status: Public on Aug 01 2009

city: College Station

first: Thomas

last: Spencer

address: 442 Kleberg Center

department: Animal Science

institute: Texas A&M University

summary: Establishment of pregnancy in ruminants requires blastocyst growth to form an elongated conceptus that produces interferon tau, the pregnancy recognition signal, and initiates implantation. Blastocyst growth and development requires secretions from the uterine endometrium. An early increase in circulating concentrations of progesterone (P4) stimulates blastocyst growth and elongation in ruminants. This study utilized sheep as a model to identify candidate genes and regulatory networks in the endometrium that govern pre-implantation blastocyst growth and development. Ewes were treated daily with either P4 or corn oil (CO) vehicle from day 1.5 after mating to either day 9 or day 12 of pregnancy when endometrium was obtained by hysterectomy.  Microarray analyses revealed many differentially expressed genes in the endometria affected by day of pregnancy and early P4 treatment.  In situ hybridization analyses revealed that many of the differentially expressed genes were expressed in a cell-specific manner within the endometrium. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to identify functional groups of genes and biological processes in the endometrium that are associated with growth and development of pre-implantation blastocysts. Notably, biological processes affected by day of pregnancy and/or early P4 treatment included lipid biosynthesis and metabolism, angiogenesis, transport, extracellular space, defense and inflammatory response, proteolysis, amino acid transport and metabolism, and hormone metabolism. This transcriptomic data provides novel insights into the biology of endometrial function and pre-implantation blastocyst growth and development in sheep.

overall_design: Ewes were mated at estrus to intact Suffolk rams and then assigned randomly to receive daily intramuscular (i.m.) injections from days 1.5 to 9 of either corn oil vehicle (CO) or 25 mg progesterone (P4) (Sigma Chemical Co., St. Louis, MO) in CO vehicle, and hysterectomized on either day 9 or day 12 of pregnancy (n=5 per day and treatment). Microarray hybridization was conducted with a bovine whole genome spotted oligonucleotide array.  This 24,000-element array was developed by the Bovine Oligo Microarray Consortium at the University of Missouri in collaboration with Texas A&M University and Iowa State University.  The array includes 16,846 probes designed from expressed sequence tags (ESTs) that were aligned to homologous vertebrate proteins and to the 6X bovine genome assembly.  The probe set was supplemented with oligos designed from 703 predicted RefSeq genes, and 5943 reproductive tissue ESTs.  A link to probe sequences and annotations is available at http://www.bovineoligo.org. The annotation included assigning a human gene symbol based on homology using BLAST.  The oligos were synthesized by Illumina and spotted onto aminosilane-coated glass slides by Dr. David Galbraith's laboratory at the University of Arizona (http://www.ag.arizona.edu/microarray/BOM.html). Hybridizations were performed with the Genisphere Array 350 kit (Genisphere Inc., Hatfield, PA) using dual channel design with dye-swapping. Preparation of cDNA was performed according to the manufacturer's instructions. Briefly, endometrial total RNA (9 µg) from each ewe (n=5 per day and treatment) was reverse-transcribed with Superscript II (Invitrogen, Carlsbad, CA) with the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labeling reagents. Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was co-hybridized with a cDNA sample from the opposite treatment for direct comparison of differences between treatments.

first: Carey

last: Satterfield

first: Gwonhwa

last: Song

first: Kelli

middle: J

last: Kochan

first: Penny

middle: K

last: Riggs

first: Rebecca

middle: M

last: Simmons

first: Christine

last: Elsik

last: Adelson

first: Fuller

last: Bazer

first: Huaijun

middle: E


title: Genomic Response of Escherichia coli during coexpression of a bacteriocin release protein

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

country: Germany

institute: Universität Hannover

summary:
Secretion of recombinant proteins to the culture medium after transport to the periplasm of gram-negative bacteria often facilitates downstream-processing. It could lead to more biological active and correct folded proteins and low contamination with host proteins, thereby reducing the costs of the production process. However, Escherichia coli K12 secrets only little amount and few substrates naturally. This is one of the major drawbacks for the applicability of this strain in the biotechnology industry, when large amounts of biological active proteins are desirable.
Therefore, different attempts were made to enhance the level of secreted proteins. Coexpression of bacteriocin release proteins makes the outer membrane permeable for proteins. A detailed insight into the complex underlying regulatory mechanism and metabolic changes when such release proteins are expressed could be very useful for successful optimisation strategies. The identification of potential optimisation targets can be achieved by DNA-microarray-technology, as proven in many cases before. In this work DNA-microarrays were used for the identification of differentially expressed genes of an inducible E.coli secretion strain expressing reporter proteins bacterial alkaline phosphatase, PhoA and beta-lactamase, Bla and their release to the culture medium by coexpression of the BRP of CloDF13. Based on the data of whole genome experiments and on the different databases genes which are regulated after induction of BRP expression are identified and discussed. BRP activity was found to cause a substantial cellular response and considerable changes in global gene expression. Additionally, performed cluster-analysis using k-means algorithm identified clusters containing promising candidates for new optimisation strategies aiming for an enhanced protein secretion.

overall_design: time series of BRP Induction, every sample was labeled with Cy3 and Cy5 (Dye Swap) to compensate dye-specific effects.

first: Michael

last: Reck

first: Karl

last: Friehs

last: Scheper

first: Cornelia

last: Repenning

first: Benjamin

last: Sommer


title: Response of Blastocladiella emersonii to hypoxia, iron deprivation and geldanamycin treatment followed by hypoxia.

city: São Paulo

first: Cesar

middle: Moises

last: Camilo

state: SP

address: Av. Prof. Lineu Prestes

department: Departamanto de Bioquímica

country: Brazil

institute: Instituto de Química - USP

summary: Due to its aquatic saprophytic lifestyle, the fungus Blastocladiella emersonii seems to be adapted to low aerated environments and thus can be an interesting model of study of the hypoxic stress response. Iron deprivation, a hypoxia-mimicking stimulus due to HIF-1 stabilization, and geldanamycin, that causes HIF-1 depletion by HSP90 inhibition, are helpful parameters to find an evidence of an oxygen-dependent regulatory mechanism in B. emersonii similar to the metazoan HIF-1 pathway.

overall_design: Direct transcript comparison between cells grown under normoxic conditions (70%sat. O2 in air) and cells submitted to oxygen deprivation (direct and gradual) and iron (II) deprivation. It was also compared transcripts of cells submitted to direct 1-hour hypoxia (1%sat. O2) with cells treated with geldanamycin for 1 hour, followed to 1-hour hypoxia (1%sat. O2). There are at least 3 biological replicates (independent harvest) and 2 technical replicates of each array (L - left and R - right).

first: Suely

last: Gomes


title: A putative network of actin-associated cytoskeletal proteins in glomerular podocytes defined by co-purified mRNAs

city: Philadelphia

first: Russ

middle: P

last: Carstens

state: PA

address: 411 Hill Pavilion, 380 S. University Ave.

department: Medicine

institute: University Of Pennsylvania School of Medicine

summary:
Identification of a putative network of actin-associated cytoskeletal proteins in glomerular podocytes defined by co-purified mRNAs.
An experimental purification in which a presumed RNA binding protein was used for an RNA immunoprecipitation and microarray analysis (RIP-CHIP).  Total cell extracts were harvested from the conditionally immortalized mouse MPC-5 podocyte cell line 14 days after transfer from 33 to 37 degrees Celsius.  The MPC-5 cell lines were stably expressing the Wilm's Tumor protein (+KTS) isoform carrying a modified TAP tag.  A fraction of each extract (Input samples) was saved and the remaining extract was applied to a sepharose IgG column, washed, and eluates were harvested after addition of TEV protease and elution in microbiospin columns.  Four input and four eluate samples were then used to harvest RNA using Trizol.

overall_design:
Total RNA was harvested from 4 input samples and 4 eluate samples.  RNAs that were enriched in the eluate samples relative to input samples were further investigated and characterized.  These RNAs were shown to be enriched in the eluates independent of the TAP-tagged protein.

Complete data matrices reporting all 46,657 unique probe IDs (i.e., including the 14 control IDs not reported in the Sample data tables) are linked below as supplementary files.

first: Behnam

last: Nabet

first: Arthur

last: Tsai

first: John

last: Tobias


title: Trout_Muscle_diet&selection

city: saint-pée sur nivelle

first: catherine

last: kolditz

address: quartier Ibarron

summary: Comparative transcriptomic analysis: dietary treatment, genetic selection, and muscle fat content

overall_design: We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al., Am J Physiol Regul Integr Comp Physiol 294: R1154–R1164, 2008.  There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual muscle of these fish. For each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array. The study consisted of 19 samples total.

first: C

last: Kolditz

first: E

last: Plagnes-Juan

last: Quillet

first: Florence

last: Lefèvre

first: Françoise

last: Médale


title: Transcriptome Analysis of North Atlantic Right Whale Kidney Fibroblast Cell line exposed to cadmium

city: Charleston

first: Marine

last: Genomics

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

summary: An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes and used to measure the transcriptome level effects of right whale kidney fibroblast cells exposed to cadmium. Cells were exposed to three concentrations of cadmium chloride (CdCl2) for three exposure times. Cells exposed to 10-6M CdCl2 for 4 hours and 24 hours showed upregulated genes involved in protection from metal toxicity, oxidative stress, protein renaturation, apoptosis inhibition, and several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as mitochondrial membrane potential collapse, reactive oxygen species (ROS) influx, and cell cycle arrest. The results confirm the right whale microarray as a reproducible tool in measuring differentiated gene expression and should be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols.

platform_organism:
Tursiops truncatus
Eubalaena glacialis

overall_design: 35 Samples were analyzed representing 3 biological replicates for each treatment and corresponding controls except treatment 4hour_0.01uMCdCl2 had only two biological replicates due to spot intensity values. There are 3 spot replicates/probe on the array, along with Agilent control grid specific for 8X15K arrays, and 4 Karenia brevis sequences used as a negative control (K.brevis.chlorophyllA/Bbindingprotein, K.brevis.flavodoxin,K.brevis.photolyase,K.brevis.photosystemcoreprotein).

first: Jessalyn

last: Ierardi

first: Gregory

last: Warr


title: Transcript Profiling of Different CNS Regions in Response to Experimental Restraint Stress on Rats

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

country: China

institute: Shanghai Biochip Co., Ltd.

summary:
It generally believes that moderate stress could have protective and adaptive effects, but less is known about the moderate or experimental stress on CNS in stimulated animals. This study aims to investigate the potential gene expression in nociception-related central regions induced by moderate experimental stress in rats. Rats were given moderate restrain for 50 min and using cDNA microarrays to compare different gene expression in central regions. Transcriptome profiling analysis showed that stress-related genes at acute stage were up-regulated in Arc; rhythmic process-related genes were up-regulated in PAG, while glutamine metabolism-, arginine metabolis-related genes were up-regulated in DH. At late stage, immune related genes were broadly up-regulated in the CNS regions. These results suggest that specific GO categories? genes could be regulated in the specific CNS regions correlated with relative function in response to external stimuli at the beginning period. It also suggest that moderate stress could enhance neuroendocrine and immune function in broad CNS regions at late stage, and experimental stress should be careful considered, especially in neuroendocrine and immune studies. Furthermore, Sgk1 was verified by qRT-PCR and western blot. The significant up regulation implied Sgk1 in the CNS may play an important role in the response to stress.

Keywords: Transcriptome analysis

overall_design: Rats were exposed to moderate restrain for 50 min and nociceptive testing and returned to home cages for 1 hours or 24 hours before sacrificed, termed as restrain_nociceptive_test_group 1 (RT1) and restrain_nociceptive_test_group 24 (RT24) respectively. Subsequently analyzed their nociception-related central regions transcript profile using cDNA microarrays, the rats were without receiving restraint stress and nociceptive testing as control. The tissue of arcuate nucleus (Arc), periaqueductal gray (PAG) and dorsal horn (DH) of the fifth and sixth lumbar (L5 and L6) of five rats were selected for transcript analysis in each group. The five control rats were mixed and labeled with cy5 according to different CNS regions, each RT1 or RT24 rats were labeled with cy3.

first: Ke

first: Fei

last: he

first: Libo

last: Lin

first: Qinghua

last: Zhang


title: Gene expression profile analysis of Fat and Lean chickens

first: Cécile

last: Berri

summary: The aim of this study was to identify genes involved in the variation of the muscle glycogen content at death (estimated through the glycolytic potential, GP), a determining factor of meat quality in chicken. Gene expression profiles of Pectoralis major muscle were established using microarrays. We compared Fat and Lean chickens issued from two lines divergently selected for abdominal fatness and also differed for muscle GP. A total of 197 genes were differentially expressed between Fat and Lean pure chickens. Several of these genes were validated by qRT-PCR. For the genes with human orthologs, annotation analyses were performed and mainly revealed pathways involved carbohydrate, fatty-acid, and protein metabolism. The relationship between gene expression and meat quality has to now be validated by further e-QTL studies on the F2 population.

overall_design: 8 samples from Fat chickens were compared to 8 samples from Lean chickens, 4 of these were dye-swapped.

first: Vonick

last: Sibut

first: Michel

last: Duclos

first: Christelle

last: Hennequet-Antier

first: Elisabeth

last: Lebihan-Duval


title: Genome-wide analysis of murine cardiomyocytes at different developmental stages

city: Lund

first: Stefan

last: Jovinge

address: Klinikgatan 26

country: Sweden

institute: Lund Strategic Center for Stem Cell Biology and Cell Therapy

summary: Cardiomyocytes exhibit differential growth patterns throughout development. In fetal life the increase in cardiac mass is associated with hyperplastic growth and cardiomyocyte proliferation. The majority of fetal cardiomyocytes are also mononucleated. During the early neonatal period in mice there is a switch from hyperplastic to hypertrophic growth of cardiomyocytes. This period is characterized by bi-nucleation and polyploidization of cardiomyocyte nuclei and a decreased capacity for cardiomyocytes to proliferate and complete cytokinesis. Increases in myocardial mass occur predominantly via hypertrophic growth. Adult mammalian cardiomyocytes are generally accepted to have little or no proliferative capacity and to be terminally withdrawn from the cell cycle. The vast majority of adult murine cardiomyocytes are bi-nucleated. The present study sought to accurately establish the growth pattern of cardiomyocytes throughout development in mice and identify genes associated with the switch from hyperplastic to hypertrophic growth. These cell cycle associated genes are crucial to the understanding of the mechanisms of bi-nucleation, polyploidization and hypertrophy in the neonatal period. Cardiomyocytes were FACS sorted from the hearts of ED11-12 embryos, neonatal day 3-4 and adult (10 week) eGFP ?-MHC mice whereby GFP expression is driven constitutively by the ?-MHC promoter. Gene analyses identified  genes whose expression was predicted to be particular to day 3 -4 neonatal cardiomyocytes, compared to embryonic or adult cells. Cell cycle associated genes are crucial to the understanding of the mechanisms of bi-nucleation and hypertrophy in the neonatal period, and offer attractive candidates for manipulation.

overall_design: Total RNA obtained from isolated cardiomyocytes from ED11-12; Neonatal day 3-4 and adult timepoints compared with each other. Several hearts per sample, RNA was pooled within samples. FACS samples were prepared in the following manner: embryonic, neonatal and adult hearts were dissected and dissociated to single cell solution with Liberase Blendzyme 3 (0.1 mg/ml) (Roche Diagnostics), washed and spun down and resuspended in cardiomyocyte isolation buffer (130 mM NaCl;  5 mM KCl; 1.2 mM KH2PO4; 6 mM HEPES; 5 mM NaHCO3; 1 mM MgCl2; 5 mM Glucose).

first: Stuart

last: Walsh

first: Annica

last: Pontén


title: Deletion of Clr3 restores expression of a subset of genes in gcn5- mutant cells

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

institute: Karolinska Institute

summary:
Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation.
The related data for this are GSE13790 and GSE5227

overall_design: Data showed expression pattern of gcn5- vs gcn5-clr3-   and clr3- vs wild type under KCl stress in S. pombe. Two biological replicates  are used  with dye-swap labeling.

first: Anna

last: Johnsson

first: Mickael

last: Durand-Dubief

first: Yongtao

last: Xue-Franzén

first: Karl

last: Ekwall

first: Michelle

last: Rönnerblad


title: Gene expression-based comparison of PQQ and known transcriptional regulators

city: Davis

first: eskouhie

middle: Hagop

last: Tchaparian

state: CA

address: UC Davis, One Shields Ave

department: Nutrition

institute: University of Ca, Davis

summary: Pyrroloquinoline quinone (PQQ) is a naturally occurring compound and known to improve growth and reproductive performance when added to diets of PQQ-deprived rodents. To understand its mechanism action, changes in hepatic gene expression were measured in rats fed diets with or without added PQQ.  Gene expression changes for PQQ supplemented (EC50 ~ 3 nmol PQQ/Kg diet) or deficient rats were assayed by expression microarray analysis and compared to those for known transcriptional regulators (epicatechin; Epi; dexamethasone, Dex; clofibrate, Clo; phenobarbital, Pb).  Two principal expression clusters were observed; one for Dex and another for Pb, Epi, Clo, and PQQ.  Within the latter, a PQQ subcluster  containing a unique group of genes for cell signaling and transport functions.  Next, short and long term PQQ depletion and repletion protocols (48 or 36 h, respectively) were performed, leading to changes in hepatic gene expression for both time periods.  Of the ~10,000 genes and ESTs analyzed, 4.7% of the transcripts were sensitive to changes in PQQ dietary status.  PQQ deprivation generally caused down regulation of genes associated with mitochondriogenesis, cell differentiation, and immune function.  These gene expression changes provide the basis for most of the previously published functional observations associated with PQQ deficiency and PQQ administered in pharmacological amounts. To assess PQQ’s potential functions, we used gene expression profiling through microarray technology as part of a comprehensive approach to identify potential pathways and mechanisms.  Given that the systemic effects of PQQ deprivation are influenced at levels of dietary intake in the micromolar range, highly purified diets were used to reduce expression from other bioactive factors and xenobiotics, such as those found in typical rodent chow diets.  To establish if the changes in gene expression in response to PQQ exposure will follow a similar pattern as other xenobiotics, the responses to PQQ exposure were contrasted with those from exposure to epicatechin (Epi), dexamethasone (Dex), clofibrate (Clo), or phenobarbital (Pb).  Dietary conditions were also chosen to clarify the response to short- and longer-term PQQ deprivation.  A goal was to determine if specific changes in dietary protocol or patterns could be used to identify genes important to the function of PQQ.  Because it has been observed that mitochondrial-related functions are influenced by PQQ, we hypothesized that changes in genes important to fatty acid and amino acid metabolism and mitochondrial function would be likewise affected by dietary levels of PQQ. The overall study was carried out using two experiments. In this specific experiment, the gene expression profiles of Sprague Dawley (SD) rats treated with different xenobiotics were compared to the gene expression profile of PQQ treated SD rats.

overall_design: In this experiment, a Codelink® ADME Rat Bioarray was used, which is specifically designed for analysis of genes involved in absorption, distribution, metabolism, and toxicology.  Labeled liver RNA from 6 rats was pooled and hybridized in duplicate for the ADME arrays.

first: Eskouhie

first: Lisa

last: Marshall

first: Gene

last: Cutler

first: Kathryn

last: Bauerly

first: Winyoo

last: Chowanadisai

first: Calliandra

last: Harris

first: Robert

last: Rucker


title: Expression profiling of Ovine Herpesvirus 2-infected lymph nodes from Bos taurus

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

type: Expression profiling by genome tiling array

summary:
We hypothesized that the gene expression pattern of OvHV-2 may be important to understand the pathogenesis of malignant catarrhal fever (MCF). Therefore, RNA was extracted from lymph nodes of animals with MCF and healthy controls to be analyzed by a custom-made microarray. Two regions on the viral genome were transcriptionally active, one encoding a homologue to the latency-associated nuclear antigen (ORF73) of other gamma herpesviruses, the other with no predicted open reading frame.

Keywords: Disease state analysis

platform_organism:
Bos taurus
Ovine gammaherpesvirus 2

overall_design: Two biological replicates with two technical replicates each, with one of the technical replicates being a dye-swap.

first: Claudia

middle: S

last: Meier-Trummer

first: Andrea

last: Patrignani

first: Ulrich

last: Wagner

first: Mathias

last: Ackermann


title: Engineered ECMs modulate the expression profile of bone marrow-derived human MSC: implications for HSC self-renewal

city: Dresden

first: Philipp

middle: Friedrich

last: Seib

address: Hohe Strasse 6

department: Max Bergmann Centre for Biomaterials Dresden

institute: Leibniz Institute for Polymer Research

summary:
The bone marrow harbours multipotent mesenchymal stromal cells (MSCs) that nurture haematopoietic stem cells (HSCs). The extracellular matrix (ECM) is an integral part of the bone marrow, and the aim of this study was therefore to (a) examine the effect of engineered ECM substrates on MSC gene expression over time, and (b) to determine the functional ability of ECM-cultured MSCs to support HSCs. ECMs were surface immobilised using films of maleic anhydride to covalently immobilise tropocollagen or fibrillar collagen type I to the substrate. Where indicated, collagen type 1 fibrils were supplemented with heparin or hyaluronic acid. All surfaces maintained MSC viability, though cell expansion was ECM dependent. Microarray analysis indicated that both time in culture and culture substrate were important factors regulating gene expression. Surprisingly, a number of MSC genes critical for the support of HSC self-renewal were down regulated during the study period. The functional effects of the different substrates were quantitatively assessed by determining cobblestone area-forming cell frequencies and colony-forming units (CFUs). Progenitor frequencies were similar for all substrates during the first 3 weeks in culture, but thereafter the reference material, plasma-treated polystyrene (PTP), outperformed ECM-based culture substrates, as predicted from expression studies. Likewise, PTP was able to maintain CFUs for extended periods, whereas HSCs rapidly exhausted themselves when cultured on any of the ECM substrates tested. The ability to regulate the expression of stromal factors using reconstituted ECM is exciting and warrants further studies to identify the ECM components/combinations that maximise the expansion of clonogenic HSCs.
Keywords: time course, human MSC, extracellular matrix

overall_design:
15 hybridizations on PIQOR Human Stem Cell Microarray chips.
Exact details can be found in the publication accompanying this study.

first: Friedrich

first: Katrin

last: Müller

first: Martina

last: Franke

first: Milauscha

last: Grimmer

first: Martin

last: Bornhäuser

first: Carsten

last: Werner


title: Gene expression profiling in sinonasal adenocarcinoma.

status: Public on Jul 31 2009

city: Brest

first: Sylvia

last: Quéméner

address: 49 rue Felix le Dantec

summary:
Transcriptional profiling of ethmoïd tumors samples comparing normal samples from the controlateral sinus. RNA were extracted from biopsies.
Sinonasal adenocarcinomas are uncommon tumors developping in ethmoid sinus after wood dust exposure. Although the etiology of these tumors is well defined very little is known regarding the molecular basis of these tumors. In an attempt to identify genes involved in this disease we proceed to a gene expression profiling using cancer-dedicated microarrays, on matched samples of nine sinonasal adenocarcinomas and non-tumoral sinusal tissue. Among the genes with significant differential expression we selected: LGALS4, ACS5, CLU, BAX, PDGFRa, SRI and CCT5 for further exploration by quantitative real-time reverse-transcription-PCR on a larger set of tumors and confirmed the microarray data. Protein expression alterations were shown for LGALS4, ACS5, and CLU by immunohistochemistry. Our results suggest that two genes might be involved in the pathogenesis of these tumors: LGALS4 highly up-regulated, particularly in the most differentiated tumors, and CLU, whose expression was lost. After further evaluation these genes could be used as markers for a better characterization of these tumors and will potentially help to an earlier detection of cancer in woodworkers, who have high risk of developing sinonasal adenocarcinomas.

overall_design: Two-condition experiment tumor samples from frozen section vs normal samples. There were two arrays by sample when it was possible.

first: Dominique

last: Tripodi

first: Karine

last: Renaudin

first: Christophe

last: Ferron

first: Olivier

last: Malard

first: Isabelle

last: Guisle

first: Véronique

last: Sébille

first: Christian

last: Verger

last: Géraut

first: Catherine

last: Gratas


title: E. coli imp fabI(G93V) Mutant Cells: Control (E. coli imp fabI(G93V) ) vs. NTG-treated E. coli imp fabI(G93V)

city: Daejeon

first: BJ

last: Yu

address: 52 Eoeun-dong Yuseong-gu

department: Systems Microbiology Research Center

country: South Korea

institute: KRIBB

summary: Transcriptional profiling of NTG-treated E. coli imp fabI(G93V) cells compared to control cells (E. coli imp fabI(G93V) ) in the absence or presence of sub-lethal concentration of triclosan.

overall_design: Two-condition experiments with NTG-treated E. coli imp fabI(G93V) vs. control E. coli imp fabI(G93V). Biological replicates: 1 control (E. coli imp fabI(G93V) cell), 1 sample (NTG-treated E. coli imp fabI(G93V) cell), independently grown and harvested. Two replicate per array.

first: Jae

middle: G

last: Pan

first: Byung


title: Transcriptome analysis of the Trypanosoma cruzi life-cycle

city: Athens

first: Todd

middle: A

last: Minning

state: GA

address: Rm 310 Coverdell

department: CTEGD

institute: University of Georgia

summary:
To generate a high quality, annotated gene expression database of T. cruzi trypomastigotes(TRP), amastigotes (AMA), epimastigotes (EPI), and metacyclic trypomastigotes (MET). The global assessment of transcript abundances in each life-cycle stage of T. cruzi will identify stage-regulated genes and provide an essential element of an integrated database of T. cruzi genomic, proteomic, and transcriptomic data. RNAs from 3 biological replicates from a single time point in each stage will be subjected to DNA microarrays containing probes for the complete, annotated T. cruzi genome, as it is currently known. The arrays for this project will be provided by the Pathogen Functional Genomics Resource Center (PFGRC) at The Institute for Genomic Research (TIGR) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID), and will contain long oligonucleotides complementary to every annotated gene in the newly sequenced T. cruzi genome. The resulting data and analysis results will be deposited in TcruziDB (http://TcruziDB.org).

Keywords: Gene expression comparisons between the four life-cycle stages of T. cruzi

overall_design: Six hybridizations were performed for each life-cycle stage.  The hybridizations consisted of three dye-swap experiments from three independent samples (biological replicates).  In each case, the experimental sample was from a single life-cycle stage and the control sample was an equal mixture of all four life-cycle stages. A total of 24 hybridizations were preformed.

first: D

last: Weatherly

first: Rick

last: Tarleton


title: Down-regulation of MYC and TP63 in human keratinocytes

status: Public on Jul 30 2009

city: Grenoble

first: Ning

last: WU

address: 17 rue des Martyrs

summary: This transcriptome study is intended to discover the effects of MYC and TP63 on human keratinocytes differentiation at the genome level.

overall_design: Human keratinocyte cell line, HaCaT cells were transfected by siRNAs with the help of transfection reagent, INTERFERin. 48 hours post-transfection, total RNA was extracted from cells. We used a non-targeting siRNA as a negative control. siRNA targeting MYC or TP63 was obtained from QIAGEN, and RNAs from wild type HaCaT cells were used as reference samples. We did 3 biological replicates and 2 'dye swap' for each sample. Totally we got 12 samples, with 2 dye-swap for each sample, and 48 arrays used for all hybridization.

first: Jérôme

last: ROLLIN


title: Detection of Cancer with Serum miRNAs on an Oligonucleotide Microarray

city: Mukilteo

first: Michael

middle: Joseph

last: Lodes

state: WA

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

institute: CombiMatrix Corp

summary: Micro RNAs (miRNAs) are a class of small, non-coding RNA species that play critical roles throughout cellular development and regulation. miRNA expression patterns taken from various tissue types often point to the cellular lineage of an individual tissue

overall_design: Arrays for serum miRNA analysis were constructed with 547 human miRNA sequences obtained from the Sanger Database version 10.0 which appeared on 8/2/07. Because of limited space on the array, the probe list was modified to exclude a few newer miRNAs that had recently been added. The array includes miRNA probes for all studies referenced by this paper. Three probes were written for each miRNA: an anti-sensed wild-type version, a double-mutant control probe, and a sense control version.  Antisense controls were not included if the corresponding antisense miRNA existed in the databases. The double mutant control mutations were screened in order to maintain the same notional melting temperature (Tm) as the wild-type Tm. They were also designed to avoid perturbing or creating any secondary structure that might appear in the wild-type probe. In addition to the 547 human miRNAs, we also included as controls, four sheep, three C. elegans, and two human sequences.

first: Marcelo

last: Caraballo

first: Dominic

last: Suciu

first: Sandra

last: Munro

first: Amit

last: Kumar

first: Brooke

last: Anderson


title: mRNA expression in ttcsp1 deletion mutant and wild type Thermus thermophilus HB8 strains grown on a rich medium

city: Toyonaka

first: Miyazaki

last: Toshiko

state: Osaka

address: 1-1 Machikaneyama

department: science

institute: Osaka univ.

summary:
We observed the expression profile of the total mRNA of ttcsp1 deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TR) medium at 45oC compared with that of 70oC.

Keywords: temperature comparison

overall_design: Wild-type and ttcsp1 mutant T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (0.3 ml) were inoculated into 0.15 liter of the same medium and then cultivated at 70oC. At the Abs600=0.8 (0min), cold medium was added and the temperature were shifted down to 45oC. Cells were collected at 0min and 30min after temperature shift, and then crude RNA was extracted. In order to compare mRNA expression in the ttcsp1 mutant between 45oC and 70oC, the expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

first: Noriko

last: Nakagawa

first: Seiki

last: Kuramitsu

first: Akeo

last: Shinkai


title: Evaluation of a New High-Dimensional miRNA Profiling Platform

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: We evaluated a new miRNA profiling platform that utilizes Illumina’s existing robust DASL chemistry as the basis for the assay.  Using total RNA from five colon cancer patients and four cell lines, we evaluated the reproducibility of miRNA expression levels across replicates and with varying amounts of input RNA.  The beta test version was comprised of 735 miRNA targets of Illumina’s miRNA profiling application.

overall_design: The study used four SAMs to assess variability due to separate total RNA extractions, technical replicates of each extraction and varying total RNA input.  Total RNA extracted from five patient samples (IDs 45, 165, 565, 919, 133) and RNA from four cell lines (HeLa, PC3, 293 and MCF-7) supplied by Illumina, was evaluated on each of 4 SAMs.  SAM 1 was hybridized in week one, SAMs 2 and 3 were hybridized in week two and SAM 4 (with cell line RNA only) was hybridized in week three of the study. Sample allocation on SAM 1 was designed to assess reproducibility between two separate total RNA extractions, between duplicate samples (technical replicates) and between two input RNA amounts.  Sample allocation on SAM 2 was designed to assess technical reproducibility and the effect of six input levels of total RNA.  Sample allocation on SAM 3 was designed to assess technical replication.  The four cell lines, but none of the 5 patient RNA, were run on a fourth SAM .  Reproducibility across all four SAMs was also assessed.

first: Julie

last: Cunningham

first: Ann

last: Oberg

first: Pedro

last: Borralho

first: Betsy

middle: T

last: Kren

first: Amy

last: French

first: Liang

last: Wang

first: Brian

last: Bot

first: Bruce

middle: W

last: Morlan

first: Kevin

last: Silverstein

first: Rod

last: Staggs

last: Zeng

first: Anne-Francoise

last: Lamblin

first: Christopher

last: Hilker

first: Jian-Bing

last: Fan

first: Clifford

last: Steer

first: Stephen

middle: N

last: Thibodeau


title: Expression analysis of the Theileria parva subtelomere-encoded variable secreted protein gene family

city: New York

first: Simon

last: Kang'a

state: NY

address: 341 East 25th Street

department: Medical Parasitology

institute: New York University School of Medicine

summary:
The protozoan parasite Theileria parva infects and transforms bovine lymphocytes inducing uncontrolled proliferation.  The transforming schizont resides free in the host cell cytoplasm and it is assumed that proteins released from the parasite contribute to host cell transformation and parasite persistence.  The identification and characterisation of parasite genes encoding candidate secreted proteins constitutes a first step towards elucidating this complex process.   In earlier work, it was shown that the genes encoding subtelomere-encoded variable secreted proteins (SVSPs) are located at the subtelomeres of all four T. parva chromosomes and, with 85 members, form the largest Theileria gene family.  The majority of predicted proteins contain signal peptides, suggesting secretion into the host cell cytoplasm. We analysed SVSP expression in T. parva-transformed cell lines established in vitro by infection of T or B lymphocytes with cloned T. parva parasites.  Preliminary microarray followed by quantitative real-time PCR analysis revealed mRNA expression for a wide range of SVSP genes.  The pattern of mRNA expression was neither influenced by the cell type transformed by T. parva, nor by the animal background.  Instead, the pattern of SVSP mRNA expression was largely defined by the parasite genotype and found to be relatively stable when monitored in vitro over a period of two months.  Experiments using antibodies raised against the SVSP TP03_0882 provided first evidence for protein expression.  Interestingly, results indicate that SVSP expression in cell lines established from a cloned parasite is limited to only a small percentage of parasites, suggesting SVSP expression by individual parasites is restricted.  Expression of epitope-tagged TP03_0882 in mammalian cells revealed nuclear translocation and localisation to different nuclear compartments, including nucleoli, nucleoplasm and other nuclear bodies.  Nuclear translocation to the mammalian cell nucleus was shown to involve two different types of nuclear localisation signals present in the conserved C-terminal region of TP03_0882.  This first characterisation, opens up possibilities for future studies on the regulation of gene expression and the biological role of these enigmatic proteins.
Expression patterns of SVSP genes in different T. parva-infected cloned cell lines

Keywords: Gene expression

overall_design: We performed a three-condition experiment comparing SVSP gene transcription in three T. parva infected cell lines: (1) 211T-A3 (consisting of CD4+ T cells), (2) 211B-A3 (consisting of B cells), and 951T-F44 (consisting of CD4+ T cells). We used direct two-color experiment design, comparing each cell line with the other, i.e. (1) 211T-A3 vs 211B-A3,  (2) 211T-A3 vs 951T-F44 and (3) 211B-A3 vs 951T-F44. There were two biological replicates for each hybridization and dye-flips for each hybridization pair. Microarray consisted of four in-slide replicates peer gene as well as no-DNA spots as negative controls.

first: Jacqueline

last: Schmuckli-Maurer

first: Carlo

last: Casanova

first: Stéfanie

last: Schmied

first: Sarah

last: Affentranger

last: Kang’a

first: Vishvanath

last: Nene

first: Frank

last: Katzer

first: Declan

last: McKeever

first: Joachim

last: Müller

first: Richard

last: Bishop

first: Dirk

last: Dobbelaere


title: Human nasopharyngeal carcinoma

city: Miaoli County

first: Shu-Chen

last: Liu

address: 35 Keyan Road,Zhunan

country: Taiwan

institute: National Health Research Institutes

summary:
To uncover the oncogenic pathways of nasopharyngeal carcinoma, gene expression profiles of  primary NPC cell strains and NPC-derived cell lines were conducted and analyzed in depth.

Keywords: Oncogenesis

overall_design: Gene expression profiles of 9 primary NPC cell strains and 5 NPC-derived cell lines were analyzed. Forty μg total RNA from one NPC sample was needed for a dye-swap experiment. Total RNA from 32 normal nasopharyngeal epithelial cell strains was pooled to serve as a universal reference.

first: Shih-Sheng

last: Jiang

first: Chao

last: Hsiung

first: Jyh-Lyh

last: Juang


title: A binary redox control mode in gene expression and metabolism of plants

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

summary:
To analyze the impact of photosynthetic redox signals, light sources with spectral qualities that preferentially excite either Photosystem I (PSI light) or Photosystem II (PSII light) were used. The light sources have been described in (Fey et al., 2005). Strong reduction and oxidation signals were induced by light shifts from PSI to PSII light (PSI-II) and the reverse light shift (PSII-I), respectivly. The acclimation responses were monitored at 0.5, 2, 8, and 48h after a light shift. Samples taken prior to changing the light quality (0h) served as control.
Keywords: photosynthesis, redox regulation, light acclimation, retrograde signalling, long term response

overall_design:
Experiments were performed with plant material corresponding to pools of at least 250-500 individuals of Arabidopsis thaliana (Col-0). To abtain healthy and unstressed plants, seedlings were initially grown for 21 days under white light (short day periods, 8-h light/16-h dark) on soil. Plants were then pre-acclimated to PSI-light for 3 days and reference samples were taken. Plants were then shifted to PSII light and tissue was harvested at the described time points. Similarly, samples were harvested before and after the reverse light shift. As additional control, plants acclimated to white light were also analyzed.
RNA isolation: Leaf material was harvested and frozen in liquid N2 under the respective light source. Isolation of total RNA was performed as adapted from (Westhoff et al., 1991). Array analyses using the 3292-GST nylon array were performed as described earlier (Richly et al., 2003; Fey et al., 2005). Three independent experiments with different filters and independent cDNA probes were performed (for each timepoint).

last: noutsos

first: Dario

last: Leister

first: Alexander

last: Biel

first: Katharina

last: Bräutigam

first: Thomas

last: Pfannschmidt


title: MicroRNAome of highly metastatic and non-metastatic human breast cell lines

status: Public on Jul 28 2009

city: New Orleans

first: Suresh

last: Alahari

state: LA

address: 1901 Perdido Street

department: Biochemistry

institute: LSU School of Medicine

summary: MicroRNAs are noncoding, endogenous small RNAs that regulate target genes by cleavage of the targeted mRNA or translational repression. We investigated the microRNAome using 2-color microarrays in a highly invasive human breast cancer cell line, MDA-MB-231 (sub line 4175) and a non-invasive breast epithelial cell line, MCF10A. We found 13 miRNAs that were up-regulated and 9 were down-regulated significantly in 4175 cells (p <0.05, fold change >2) compared with MCF10A cells.

overall_design: We compared the highly metastatic human breast cell lines MDA-MB-231 (4175 subline)  with non-metastatic MCF10A cell lines. Two 4175 sublines and two MCF10A cell lines, independently grown and harvested. Dye swap was performed.

first: Yanfang

last: Wang


title: Estimation of miRNAs

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

summary:
Our analyses of microRNA expression profiles involve the hybridization of fluorescently labeled miRNA samples to custom made, DNA microarrays based on the GAPSII coated slides.  We hybridized different amounts of microRNAs from the mirVana miRNA Reference Panel v9.1 to microarrays.
Keywords: Expression

overall_design: Three different concentrations of miRNAs from the commercial standrads were labelled and hybridized to three microarrays.

first: Yan

last: Zeng


city: Musashimiurayama-shi

first: Hideki

last: Hasegawa

state: Tokyo

address: Gakuen 4-7-1

department: Influenza Virus Research Center

institute: National Institute of Infectious Diseases

summary:
Transcriptional profiling of cytokines and its receptors in primary murine lymphoblastoid cells (pML cells), which are lymphomatous cells from HTLV-1 TAX transgenic mice.
ATL is a T-cell malignancy caused by HTLV-I, and presents as an aggressive leukemia with characteristic widespread leukemic cell infiltration into visceral organs and skin. The molecular mechanisms associated with leukemic cell infiltration are poorly understood. We have employed mouse models of ATL to investigate the role of chemokines in this process. Transfer of splenic lymphomatous cells from transgenic to SCID mice rapidly reproduces a leukemia and lymphoma which is histologically identical to human disease. It could be shown that lymphomatous cells exhibit specific chemotactic activity in response to SDF-1α. Lymphomatous cells exhibited surface expression of CXCR4, the specific receptor of SDF-1α and chemotaxis was associated with down regulation of CXCR4 expression and phosphorylation of intracellular ERK1/2. AMD3100, a CXCR4 antagonist, was found to inhibit both SDF-1α - induced migration and phosphorylation of ERK1/2. Investigation of cultured cells from human ATL patients revealed identical findings. Employing the SCID mouse model it could be demonstrated that AMD3100 inhibited infiltration of lymphomatous cells into liver and lung tissues in vivo. These results demonstrate the involvement of the SDF-1α /CXCR4 interaction as one mechanism of leukemic cell migration and this may provide a novel target as part of combination therapy for ATL.

overall_design: pML cells vs. pan T cells from C57BL6 mice.

first: A

last: Kawaguchi

first: Y

last: Orba

first: T

last: Kimura

first: H

last: Iha

first: M

last: Ogata

last: Tsuji

last: Sata

first: W

last: Hall

last: Sawa


title: MicroRNA expression profiling in human tumor cell lines treated with interferon-alpha-2a

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

institute: University Hospital Bern

summary: MicroRNAs are positive and negative regulators of eukaryotic gene expression that modulate transcript abundance by specific binding to sequence motifs located prevalently in the 3’ untranslated regions (3’-UTR) of target messenger RNAs (mRNA). Interferon-alpha-2a (IFNα) induces a large set of protein-coding genes mediating anti-proliferative and antiviral responses. Here we use a global microarray-based microRNA detection platform to identify genes that are induced by IFNα in hepatoma- or melanoma-derived human tumor cell lines. Despite the enormous differences in expression levels between these models, we were able to identify microRNAs that are upregulated by IFNα in both lines, suggesting the possibility that interferon-regulated microRNAs (IRmiRs) are involved in the transcriptional repression of mRNA relevant to cytokine responses.

overall_design: Total RNA obtained from a melanoma cell line and a hepatoma cell line grown in triplicates treated with 1000 U / mL interferon alpha2a for 4 or 24 hours compared to mock-treated cell cultures.

first: Ulrich

last: Certa


title: Illumina HapMap YRI (Human660W-Quad_v1)

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

summary: HapMap samples

overall_design: 90 samples from Human660W-Quad_v1_90YRI_FinalReport.txt


title: Illumina HapMap CEU (HumanCNV100Wv1.0)

summary: HapMap samples

overall_design: 89 samples from HumanCNV100W_89CEU_Final_Report.txt


title: Illumina HapMap CHB and JPT (HumanCNV100Wv1.0)

summary: HapMap samples

overall_design: 90 samples from HumanCNV100W_90CHB-JPT_Final_Report.txt


title: DNA methylation of promoters plus CpG islands in mouse embryos at early neurulation

city: Indianapolis

first: GUOHUA

last: WANG

state: IN

address: 410 West 10th Street, Suite 5000

institute: Indiana University Center for Computational Biology and Bioinformatics

type: Methylation profiling by genome tiling array

summary:
To gain insights into the function of DNA methylation and its impact on gene expression, we measured methylation in 19,530 mouse promoters and CpG islands.
Keywords: DNA methylation, MeDIP

overall_design: The chosen array from NIMBLEGEN (2007-02-27_MM8_ CpG island _ promoter array) represents putative mouse promoters plus CpG islands, each covered by oligonucleotide probes spanning 1.3 kb upstream and 0.5 kb downstream of the transcription start site.

first: Yunlong

last: Liu

first: Yokesh

last: Balaraman

first: Guohua

first: Lijun

last: Ni

first: Kenneth

last: Nephew

first: Feng

last: Zhou


title: Expression profiling identifies genes involved in neoplastic transformation of serous ovarian cancer

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

summary:
Background - The malignant potential of serous ovarian tumors, the most common ovarian tumor subtype, varies from benign to low malignant potential (LMP) tumors to frankly invasive cancers. Given the uncertainty about the relationship between these different forms, we compared their patterns of gene expression. Methods - Expression profiling was carried out on samples of 7 benign, 7 LMP and 28 invasive (moderate and poorly differentiated) serous tumors and surface epithelium of four normal whole ovaries using oligonucleotide microarrays representing over 21,000 genes.
Results - We identified 311 transcripts that distinguished invasive from benign tumors, and 20 transcripts that were significantly differentially expressed between invasive and LMP tumors at p < 0.01 (with multiple testing correction). Five genes that were differentially expressed between invasive and either benign or normal tissues were validated by real time PCR in an independent panel of 46 serous tumors (4 benign, 7 LMP, 35 invasive). Overexpression of SLPI and WNT7A and down-regulation of C6orf31, PDGFRA and GLTSCR2 were measured in invasive and LMP compared with benign and normal tissues. Over-expression of WNT7A in an ovarian cancer cell line led to increased migration and invasive capacity. Conclusions - These results highlight several genes that may play an important role across the spectrum of serous ovarian tumorigenesis.

overall_design: Common reference design.

first: Melissa

last: Merritt

first: Peter

last: Parsons

first: Tanya

middle: R

last: Newton

first: Adam

middle: C

last: Martyn

first: Penelope

last: Webb

first: Adele

last: Green

first: David

last: Papadimos


title: Illumina HapMap YRI (HumanCNV100Wv1.0)

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

summary: HapMap samples

overall_design: 90 samples from HumanCNV100W_90YRI_Final_Report.txt


title: Illumina HapMap CHB and JPT (Human660W-Quad_v1)

summary: HapMap samples

overall_design: 89 samples from Human660W-Quad_v1_89CHB-JPT_FinalReport.txt


title: MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer from never-smokers

status: Public on Jul 29 2009

first: Tetsuya

last: Okano

address: 37 Convent Drive, Bldg 37

department: NCI

institute: NIH

summary: Approximately 15% of lung cancer cases are not associated with smoking and show molecular and clinical characteristics distinct from those in smokers.  Epidermal growth factor receptor (EGFR) gene mutations, which are correlated with sensitivity to EGFR-tyrosine kinase inhibitors (EGFR-TKIs), are more frequent in never-smoker lung cancers.  In this study, microRNA (miRNA) expression profiling of 28 never-smoker lung cancer cases identified aberrantly expressed miRNAs, which were much fewer than in lung cancers of smokers and included miRNAs previously identified (e.g., upregulated miR-21) and unidentified (e.g., downregulated miR-138) in those smoker cases.  The changes in expression of some of these miRNAs were more remarkable in cases with EGFR mutations than in those without: the most upregulated miRNA, miR-21, was more abundant in cancers with EGFR mutation.  A significant correlation between phosphorylated-EGFR (p-EGFR) and miR-21 levels in lung carcinoma cell lines and the suppression of miR-21 by an EGFR-TKI, AG1478, suggested that the EGFR signaling pathway positively regulated miR-21 expression.  In a never-smoker-derived lung adenocarcinoma cell line H3255 with mutant EGFR and high levels of p-EGFR and miR-21, antisense inhibition of miR-21 enhanced AG1478-induced apoptosis.  In a never-smoker-derived adenocarcinoma cell line H441 with wild-type EGFR, the antisense miR-21 not only showed the additive effect with AG1478 but also induced apoptosis by itself.  These results suggest that aberrantly increased expression of miR-21, which is further enhanced by the activated EGFR signaling pathway, plays a critical role in lung carcinogenesis in never-smokers and is a potential therapeutic target in both EGFR mutant and wild-type cases.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Twenty-eight pairs of lung cancer tissues and corresponding noncancerous lung tissues were obtained from never-smokers who had undergone surgical resection from 2000 to 2004 at the University of Maryland Medical Center (n=15), Mayo Clinic (n=7) in United States and Hamamatsu University School of Medicine (n=6) in Japan.

first: Masahiro

last: Seike

first: Akiteru

last: Goto

first: Elise

middle: D

last: Bowman

first: Aaron

middle: J

last: Schetter

first: Izumi

last: Horikawa

first: Ewy

last: Mathe

first: Jin

last: Jen

first: Ping

last: Yang

first: Haruhiko

last: Sugimura

first: Akihiko

last: Gemma

first: Shoji

last: Kudoh

first: Carlo

last: Croce

first: Curtis

last: Harris


title: Illumina HapMap CHB and JPT (HumanCytoSNP-12v2)

last: Illumina Inc.

summary: HapMap samples

overall_design: 89 samples from Human_CytoSNP-12v2_89CHB-JPT_FinalReport.csv


title: Illumina HapMap YRI (HumanCytoSNP-12v2)

summary: HapMap samples

overall_design: 90 samples from Human_CytoSNP-12v2_90YOR_FinalReport.csv


title: Illumina HapMap (Human-1)

summary: HapMap samples

overall_design: 118 samples from Human1_Final_BSGT_118dna_FinalReport.txt


title: Regulation of Vertebrate Nervous System-Specific Alternative Splicing and Development by an SR-Related Protein

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

summary: Alternative splicing is a key process underlying the evolution of increased proteomic and functional complexity and is especially prevalent in the mammalian nervous system. However, the factors and mechanisms governing nervous system-specific alternative splicing are not well understood. Through a genome-wide computational and expression profiling strategy, we have identified a tissue- and vertebrate-restricted Ser/Arg (SR)-repeat splicing factor, the neural-specific SR-related protein of 100 kDa (nSR100). We show that nSR100 regulates an extensive network of brain-specific alternative exons enriched in genes that function in neural cell differentiation. nSR100 acts by increasing the levels of the neural/brain-enriched polypyrimidine tract binding protein and by interacting with its target transcripts. Disruption of nSR100 prevents neural cell differentiation in cell culture and in the developing zebrafish. Our results thus reveal a critical neural-specific alternative splicing regulator, the evolution of which has contributed to increased complexity in the vertebrate nervous system.

overall_design: A microarray platform to profile alternative splicing levels for 8714 cassette-type alternative exons across a diverse spectrum of mouse tissues.

first: John

last: Calarco

first: Simone

last: Superina

first: Dave

last: O’Hanlon

first: Ursula

last: Skalska

first: Mathieu

last: Gabut

first: Bushra

last: Raj

first: Laura

last: Clarke

first: Danielle

last: Gelinas

first: Derek

last: van der Kooy

first: Mei

last: Zhen

first: Brian

last: Ciruna

first: Benjamin

last: Blencowe


title: Lung adenocarcinoma and mesothelioma DNA methylation

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

summary: Pathologic differentiation of tissue of origin in tumors found in the lung can be challenging, with differentiation of mesothelioma and lung adenocarcinoma emblematic of this problem. Indeed, proper classification is essential for determination of treatment regimen for these diseases, making accurate and early diagnosis critical. Here we investigate the potential of epigenetic profiles of lung adenocarcinoma, mesothelioma, and non-malignant pulmonary tissues (n=285) as differentiation markers in an analysis of DNA methylation at 1413 autosomal CpG loci associated with 773 cancer-related genes. Using an unsupervised recursively-partitioned mixture modeling technique for all samples, the derived methylation profile classes were significantly associated with sample type (P < 0.0001). In a similar analysis restricted to tumors, methylation profile classes significantly predicted tumor type (P < 0.0001). Random forests classification of CpG methylation of tumors - which splits the data into training and test sets - accurately differentiated MPM from lung adenocarcinoma over 99% of the time (P < 0.0001). In a locus-by-locus comparison of CpG methylation between tumor types, 1266 CpG loci had significantly different methylation between tumors following correction for multiple comparisons (Q < 0.05); 61% had higher methylation in adenocarcinoma. Using the CpG loci with significant differential methylation in a pathways analysis revealed significant enrichment of methylated gene-loci in Cell Cycle Regulation, DNA Damage Response, PTEN Signaling, and Apoptosis Signaling pathways in lung adenocarcinoma when compared to mesothelioma. Methylation-profile-based differentiation of lung adenocarcinoma and mesothelioma is highly accurate, informs on the distinct etiologies of these diseases, and holds promise for clinical application.

overall_design: Mesotheliomas (n=158) and grossly non-tumorigenic parietal pleura (n=18) were obtained following surgical resection at Brigham and Women’s Hospital through the International Mesothelioma Program  from a pilot study conducted in 2002 (n=70) and an incident case series beginning in 2005 (n=88) with a participation rate of 85%.  We used biopsy specimens from patients treated for NSCLC at the Massachusetts General Hospital from 1992 – 1996 (18) including lung adenocarcinomas (n=57) and non-malignant pulmonary tissues (n=48) (of which 22 (39%) were taken from the adenocarcinoma patients) (18). Additional normal lung tissues were obtained from the National Disease Research Interchange from donors free of lung malignancy (n=4).

first: Karl

last: Kelsey


title: Illumina HapMap YRI (HumanCytoSNP-12v1)

summary: HapMap samples

overall_design: 90 samples from HumanCytoSNP-12_90YOR_FinalReport.txt


title: Illumina HapMap CEU (HumanCytoSNP-12v2)

summary: HapMap samples

overall_design: 88 samples from Human_CytoSNP-12v2_88CEU_FinalReport.csv


title: Illumina HapMap CHB and JPT (HumanCytoSNP-12v1)

summary: HapMap samples

overall_design: 89 samples from HumanCytoSNP-12_89CHB-JPT_FinalReport.txt


title: Illumina HapMap CEU (Human660W-Quad_v1)

summary: HapMap samples

overall_design: 89 samples from Human660W-Quad_v1_89CEU_FinalReport.txt


title: Illumina HapMap (HumanHap300-Duov2)

summary: HapMap samples

overall_design: 120 samples from Hap300v2_318237_SNPs_120_Final_Samples_OfficialManifest_FinalReport.txt