title: H2O2 effect on mouse embryonic fibroblasts +/- a deletion in the helicase domain of the Werner Syndrome gene homologue

status: Public on Nov 13 2009

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary:
[original Title] Expression profiling of mouse embryonic fibroblasts with or without a deletion in the helicase domain of the Werner Syndrome gene homologue treated with hydrogen peroxide

Werner syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS is believed to be involved in different aspects of transcription, replication, and/or DNA repair. In addition to genomic instability, WS cells exhibit oxidative stress. In this report, we have examined the impact of exogenous peroxide on the expression profile of mouse embryonic fibroblasts lacking part of the helicase domain of the WRN homologue. This expression profile was compared to hydrogen peroxide treated wild type mouse embryonic fibroblasts. Interestingly, untreated mouse embryonic fibroblasts with a deletion of the helicase domain of Wrn already exhibited down regulation of several biological processes decreased by hydrogen peroxide in wild type cells.

overall_design: Microarray analyses were performed in duplicate using Agilent Whole Mouse Genome Arrays on WT mouse embryonic fibroblasts treated or not with H2O2 and mouse embryonic fibroblasts lacking part of the helicase domain of the WRN homologue treatead or not with H2O2.

first: Adam

last: Labbé

first: Ramachander

middle: V

last: Turaga

first: Chantal

last: Garand

first: Michel

last: Lebel


title: The transcriptional programme of Salmonella Typhimurium reveals a key role for tryptophan metabolism in biofilms

status: Public on Dec 14 2009

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

summary:
Background: Biofilm formation by Salmonella species enhances the capacity of these pathogenic bacteria to survive stresses that are commonly encountered within food processing and during host infection. The persistence of Salmonella within the food chain has become a major health concern, as biofilms can serve as a reservoir to contaminate food products. While the molecular mechanisms required for the survival of bacteria on surfaces are not fully understood, transcriptional studies of other bacteria have demonstrated that biofilm growth triggers the expression of specific sets of genes, compared with planktonic cells. Until now, most transcriptomic studies of Salmonella have focused on the effect of infection-relevant stressors on virulence and on comparing mutant and wild-type (WT). However little is known about the physiological responses taking place inside a Salmonella biofilm.
Results: We have determined the transcriptomic and proteomic profiles of biofilms of Salmonella enterica serovar Typhimurium. We discovered that 124 of detectable proteins were differentially expressed in the biofilm compared with planktonic cells, and that 10% (433 genes) of S. Typhimurium genes showed a biofilm-specific pattern of transcription (i.e. a 2-fold or more change in the biofilm compared with planktonic cells). The genes that were significantly up-regulated implicated specific cellular processes in biofilm development including amino acid metabolism, cell motility, global regulation and tolerance to stress. We found that the most highly down-regulated genes in the biofilm were located on Salmonella Pathogenicity Island 2 (SPI2), but that a functional SPI2 secretion system regulator (ssrA) was required for WT biofilm formation. We identified STM0341 as a gene of unknown function that was needed for WT biofilm growth. Genes involved in tryptophan (trp) biosynthesis and transport were up-regulated in the biofilm. Deletion of trpE led to a decrease in bacterial attachment and we show that this biofilm defect is restored by exogenous tryptophan or indole.
Conclusion: Biofilm growth of S. Typhimurium causes distinct changes in gene and protein expression. Our results show that aromatic amino acids make an important contribution to biofilm formation, and reveal that SPI2 genes, required for virulence in host cells, show opposing patterns of expression to biofilm-specific genes in S. Typhimurium.

overall_design: Overnight cultures of SL1344 grown in CFA broth were standardized to achieve an initial concentration of 10^6 CFU ml-1 and injected into a stirring influent flask containing 5 L of pre-warmed (25C) sterile CFA medium. The inoculated influent was then pumped through silicon tubing (5 mm internal diameter, Samco Silicon Products Ltd.) at 60 ml h-1 using a peristaltic pump (Minipulse 3, Gilson). The bacteria were allowed to flow through the closed system and either attach to a vertical piece of silicon tubing (1 meter length, 16 mm internal diameter, Samco Silicon Products Ltd.) or flow out into a waste reservoir. The tubing was positioned vertically to collect biofilm cells adherent to the tubing and minimise collecting bacteria that had simply sedimented. Possible backflow of media or bacteria into the influent from the silicon tubing was eliminated using media breaks. Samples taken to determine the pH of the medium or bacterial cell counts were removed via a media port located near the effluent and influent vessel, respectively. Planktonic cells were removed after 72 h of growth from the influent vessel to avoid any contamination with biofilm cells. The entire system was kept at a constant temperature of 25C and biofilm cells were isolated after 72 h of growth. All planktonic and biofilm samples were isolated from the same experimental system and used for both RNA and protein isolation. For this study, four biological replicates were performed at four different dates (Jun25, Jul5, Jul16, Oct11; as indicated in the sample title). For the dual-colour microarray hybridisations, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality. Individual labelled cDNA samples (RNA) were hybridised up to 4 times (technical replicates).

first: Shea

last: Hamilton

first: Roy

middle: J

last: Bongaerts

first: Francis

last: Mulholland

first: Brett

last: Cochrane

first: Jonathan

last: Porter

first: Hilary

middle: M

last: Lappin-Scott

first: Jay

middle: C

last: Hinton


title: Expression profiling of rainbow trout testicular development and spermatogenesis

status: Public on Sep 01 2009

city: Rennes

first: Florence

last: Le Gac

address: Campus de Beaulieu

department: Fish Reproduction Group

country: France

institute: Institut National de la Recherche Agronomique

summary: Trout spermatogenesis proceeds seasonally in a way that all morphological and cellular events tend to be synchronized. We thus used gonads at key stages of the male reproductive cycle together with isolated germ cell populations to study the changes in gene expression underlying testis development. Statistical analysis followed by clustering of expression profiles allowed the discrimination of sequential events of gene activation or repression during testis development and/or throughout the germline.

overall_design: 38 samples covering 6 developmental stages (as defined in Gomez et al. 1998 Biol. Reprod. 58, 483-491) and 3 isolated germ cell populations were analysed. This included: - Testes at early stages containing slowly-dividing type A spermatogonia (Stage_I, n=5) or growing numbers of actively-dividing type B spermatogonia (Stages_IIa, n= 4; Stage_IIb, n= 4) - Maturing testes containing in addition large numbers of meiotic spermatocytes (Stage_IIIb, n=3) and post-meiotic spermatids (Stage_V, n=4) - Spawning testes containing essentially mature spermatozoa (Stage_VIII, n=3) - Fractions of isolated germ cells enriched in spermatogonia (Spermatogonia, N=6), spermatocytes (Spermatocyte, N=6) and spermatids (Spermatid, N=3).

first: Antoine

middle: D

last: Rolland

first: Jean-Jacques

last: Lareyre

first: Anne-Sophie

last: Goupil

first: Jérôme

last: Montfort

first: Marie-José

last: Ricordel

first: Diane

last: Esquerré

first: Karine

last: Hugot

first: Rémi

last: Houlgatte

first: Fréderic

last: Chalmel


title: Focused DNA microarray to differentiate Clostridium botulinum type A strains

status: Public on Sep 16 2009

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

country: USA

institute: Centers for Disease Control and Prevention

summary: Strains were differentiated on the basis of hybridization to probes representing strain variable regions in C. botulinum strain ATCC 3502. Probes for selected genes (eg. toxin genes) were also featured on the microarray to allow detection of other serotypes/subtypes.

sample_organism:
Clostridium botulinum
Clostridium botulinum A str. ATCC 3502

overall_design: 27 strains were evaluated for selected gene detection and/or strain differentiation. DNA from strain ATCC 3502 was used as a control as the featured probes were based on the ATCC 3502 genome sequence.

first: Lavin

middle: A

last: Joseph

first: Loretta

last: McCroskey

first: Carolina

last: Luquez

first: Susan

middle: E

last: Maslanka


title: ML-DmBG3-c2 Replication Origins

status: Public on Jul 29 2009

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_711
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Early origins of replication were identified by treating cells with hydroxyurea (HU), a potent inhibitor of nucleotide synthesis, in the presence of the nucleotide analogue BrdU. Treatment of synchronized ML-DmBG3-c2 cells with HU stalls replication forks and activates the intra S-phase checkpoint, thereby limiting BrdU incorporation to those sequences mmediately adjacent to early activating replication origins. BrdU enriched sequences surrounding early origins of replication are then enriched by immunoprecipitation with an anti-BrdU antibody. Early origins are then detected by hybridization to Agilent genomic tiling arrays. Peaks are called using MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm)

Keywords: CHIP-chip

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Genotype: y v f mal; Sex: Unknown NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2

first: David

last: MacAlpine

first: Heather

first: Leyna

last: DeNapoli


title: ML-DmBG3-c2 Replication Timing

summary:
modENCODE_submission_670
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains.

Keywords: CHIP-chip

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: S2-DRSC Replication Origins

summary:
modENCODE_submission_710
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Early origins of replication were identified by treating cells with hydroxyurea (HU), a potent inhibitor of nucleotide synthesis, in the presence of the nucleotide analogue BrdU. Treatment of synchronized S2-DRSC cells with HU stalls replication forks and activates the intra S-phase checkpoint, thereby limiting BrdU incorporation to those sequences immediately adjacent to early activating replication origins. BrdU enriched sequences surrounding early origins of replication are then enriched by immunoprecipitation with an anti-BrdU antibody. Early origins are then detected by hybridization to Agilent genomic tiling arrays. Peaks are called using MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm)

Keywords: CHIP-chip

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Sex: Male NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC


title: Kc167 Replication Origins

summary:
modENCODE_submission_709
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Early origins of replication were identified by treating cells with hydroxyurea (HU), a potent inhibitor of nucleotide synthesis, in the presence of the nucleotide analogue BrdU. Treatment of synchronized Kc167 cells with HU stalls replication forks and activates the intra S-phase checkpoint, thereby limiting BrdU incorporation to those sequences immediately adjacent to early activating replication origins. BrdU enriched sequences surrounding early origins of replication are then enriched by immunoprecipitation with an anti-BrdU antibody. Early origins are then detected by hybridization to Agilent genomic tiling arrays. Peaks are called using MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm)

Keywords: CHIP-chip

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Genotype: se/e; Sex: Female NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line Kc167


title: S2-DSRC Replication Timing

summary:
modENCODE_submission_669
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains.

Keywords: CHIP-chip

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: Medicago truncatula germinated seedlings grown in Petri dishes for 3 days then carry out salt stress

status: Public on Nov 11 2009

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: time-course salt stress experiment of model legume Medicago truncatula roots using Affymetrix Medicago Array, aimed to dig some useful gene for improve salt resistance for legumes and other crops

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design:
4 samples of Medicago truncatula germinated seedlings
grown in Petri dishes for 3 days
180mM NaCl salt stress
material collect at 0, 6, 24, 48 hour after salt stress beginning
3 biological replicates
2 ug of total RNA was used to synthesize doublestranded cDNA


title: Transcriptome analysis of germinating maize kernels exposed to smoke-water and the active compound KAR1

status: Public on Aug 24 2009

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

summary: Smoke released from burning vegetation functions as an important environmental signal promoting the germination of many plant species following a fire . It not only promotes the germination of species from fire-prone habitats, but several species from non-fire-prone areas also respond, including some crops. Bioactivity-guided fractionation of smoke-water led to the identification of a highly active butenolide compound, 3-methyl-2H-furo[2,3-c]pyran-2-one. Several hypotheses have arisen regarding the molecular background of smoke and butenolide action. Contrary to the efforts to unravel the mode of action of smoke, the mechanism is still largely unknown. In this paper we demonstrate that although smoke-water and butenolide treatment of maize kernels results in a similar physiological response, the gene and protein expression patterns are quite different. Treatment with smoke-water enhanced the ubiquitination of proteins and activated protein-degradation-related genes. This effect was completely absent from butenolide-treated kernels, in which a specific aquaporin gene was distinctly upregulated. These findings indicate that other bioactive compounds present in smoke-water may act together, leading to accelerated protein turnover. The results highlight the importance of protein degradation and aquaporins in the seed germination process. Besides their obvious use in the sustainable agricultural practice, smoke and butenolide can be used in studies to gain further insight into the transcriptional changes during germination.

overall_design: 15 individual kernels from each of six biological replicates were chosen and equal amount of the aaRNA samples were pooled. Three technical replicates were applied at each time point for the microarray analysis. For the control versus butenolide experiment the samples were collected at 1.5, 3, 6, 9, 12 and 24 hours after treatment. For the control versus smoke experiment  the samples were collected at 1.5, 3, 6, 9, 12, 24 and 27 hours after treatment. For the delayed experiment samples were collected after 3 or 6 hours after treatment.

first: Vilmos

last: Soós


title: Kc167 Replication Timing

summary:
modENCODE_submission_668
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains.

Keywords: CHIP-chip

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Genotype: se/e; Sex: Female NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Cell Line Kc167


title: Effects of temperature on gene expression in coral larvae of Montastraea faveolata

status: Public on Aug 31 2009

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary:
Background

Coral reefs are expected to be severely impacted by rising seawater temperatures associated with climate change. This study used cDNA microarrays to investigate transcriptional effects of thermal stress in embryos of the coral Montastraea faveolata. Embryos were exposed to 27.5C, 29.0C, and 31.5C directly after fertilization. Differences in gene expression were measured after 12 and 48 hours.
Results

Analysis of differentially expressed genes indicated that increased temperatures may lead to oxidative stress, apoptosis, and a structural reconfiguration of the cytoskeletal network. Metabolic processes were downregulated, and the action of histones and zinc finger-containing proteins may have played a role in the long-term regulation upon heat stress.
Conclusions

Embryos responded differently depending on exposure time and temperature level. Embryos showed expression of stress-related genes already at a temperature of 29.0C, but seemed to be able to counteract the initial response over time. By contrast, embryos at 31.5C displayed continuous expression of stress genes. The genes that played a role in the response to elevated temperatures consisted of both highly conserved and coral-specific genes. These genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change.

overall_design: The experimental setup followed a reference design, i.e. all samples were hybridized against the same pool made up of equal amounts of RNA from all samples. We used three technical replicates for each temperature. Common reference samples were labeled with Cy3, temperature samples with Cy5. Microarrays for M. faveolata contained 1,314 coding sequences, of which 43% had functional annotations as determined by homology to known genes.

middle: R

first: Julia

last: Schnetzer

first: Leonid

last: Peshkin

first: Carly

last: Randall

first: Alina

last: Szmant

first: Monica

last: Medina


title: Identification of mRNAs enriched in G3BP immunoprecipitation

status: Public on Jul 23 2009

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu, Oko

country: Japan

institute: Kochi University Medical School

type:
Expression profiling by array
Other

summary: A phosphorylation-dependent endoribonuclease G3BP localizes in cytoplasmic stress granules (SGs). G3BP promotes SG assembly, oligomerizes, binds mRNA, and regulates levels of certain mRNAs. Transcripts bound to G3BP were identified through expression profiling of a total of 12,135 genes by immunoprecipitation (IP) with anti-G3BP or control IgG from S2-013 cells, converting the immunoprecipitated transcripts to cDNA by reverse transcription, and hybridizing these products to cDNA microarrays. Five G3BP-associated transcripts were identified.

overall_design:
In the study presented here, 1 immunoprecipitated sample with control IgG and 1 immunoprecipitated sample with anti-G3BP were used to acquire expression profiles of a total of 8,644 unique genes.

The supplementary file 'GSE17056_higher_aG3BP.txt' lists the differentially expressed genes.

middle: L

last: Kelly


title: Comprehensive Characterization of microRNAs and mRNAs in Maintenance and Differentiation of Human Embryonic Stem Cells

city: Seattle

first: Bradford

last: Stadler

state: WA

address: 815 Mercer Street; South Building, Room A581

department: Biochemistry

institute: University of Washington

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

summary: Recent advances in the study of human embryonic stem cells (hESCs) and induced-pluripotent stem cells (iPS) highlight their importance as both model systems for basic research and avenues for therapeutic applications.  To gain better insight into these cells, a clearer understanding of their molecular properties is crucial.  In this study, we analyze changes in the expression profile of microRNAs (miRNAs) and mRNAs in nine different, National Institutes of Health (NIH)-approved hESC lines.  By examining both undifferentiated hESCs and cells exposed to an undirected differentiation scheme at early stages, we found those miRNAs and mRNAs enriched in the hESC lines, and those miRNAs and mRNAs initially regulated upon commitment.  In comparing these profiles with those of an embryonal carcinoma (EC) cell line, NTera-2, we observed distinct patterns of miRNA expression in hESCs.  Furthermore, we identify several new hESC-enriched miRNAs that respond rapidly to differentiation cues, in addition to miRNAs from a large cluster of hESC-enriched miRNAs located on chromosome 19, and miRNAs from the miR-302 cluster and the miR-17~92 family of clusters. We show that key miRNAs in the chromosome 19 cluster are highly enriched in hESCs in comparison to NTera-2, and might therefore serve as future diagnostic markers for stem cell capacity.   Examination of changes in mRNA expression during early commitment further reveals that many differentiation-regulated genes are possible candidates for regulation by these hESC-enriched miRNAs.

overall_design: A set of 9 different NIH-approved hESC lines were treated with conditions to promote either maintenance of an undifferentiated state (mouse embryonic fibroblast- conditioned media) or undirected differentiation of the hESCs into various cell lineages (DMEM + 20% FBS). RNA was harvested from the cells and subjected to both mRNA and miRNA expression analysis on Affymetrix and Agilent microarray platforms, respectively. An embryonal carcinoma cell line, NTera-2, which shows growth characteristics similar to those of hESCs, was used an additional comparative sample. Human placental RNA samples were used as internal controls for the miRNA microarray slides (Agilent Technologies). The data were used to determine differential mRNA and miRNA expression in each specific cell line, as well as to make large-scale comparisons of the undifferentiated and differentiated hESC lines.

first: Irena

last: Ivanovska

first: Kshama

last: Mehta

first: Sunny

last: Song

first: Angelique

last: Nelson

first: Christopher

last: Darby

first: C

last: Blau

first: Carol

last: Ware

first: Garrick

last: Peters

first: Michele

last: Cleary

first: Hannele

last: Ruohola-Baker


title: Probing the endosperm gene expression landscape in Brassica napus

status: Public on May 31 2009

city: Saskatoon

first: Jitao

last: Zou

state: Saskatchewan

address: 110 Gymnasium Place

institute: Plant Biotechnology Institute, National Research Council Canada

summary:
In species with exalbuminous seeds such as crucifer oilseeds and legumes, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid endosperm, and most of the carbon resources for the ensuing stages of seed development arrive at the embryo through the endosperm. In contrast to the extensive study of species with persistent endosperm, little is known about the global gene expression pattern in the endosperm of exalbuminous seed species. We took a multiparallel approach that combines ESTs, protein profiling and microarray analyses to look into the gene expression landscape in the endosperm of the oilseed crop Brassica napus. An EST collection of over 30,000 entries allowed us to detect close to 10,000 unisequences expressed in the endosperm. A protein profile analysis of more than 800 proteins corroborated several signature pathways uncovered by abundant ESTs. Using microarray analyses, we identified genes that are differentially or highly expressed across all developmental stages. These complementary analyses provided insight on several prominent metabolic pathways in the endosperm. We also discovered that LEC1 was highly expressed in the endosperm and that the regulatory cascade downstream of LEC1 operates in the endosperm. The endosperm EST collection and the microarray dataset provide a basic genomic resource for dissecting metabolic and developmental events important for oilseed improvement. Our findings on the featured metabolic processes and the LEC1 regulatory cascade offer new angles for investigation on the integration of endosperm gene expression with embryo development and storage product deposition in seed development.

Keywords: seed development

overall_design:
We defined the developmental phase of the endosperm based on the stages of the embedded embryos. Under our growth conditions, the globular-shape embryo stage is reached approximately six days after flowering (DAF), the heart-shape embryo stage is reached after eight days, and by day 14 the seed enters the cotyledon stage.

The collected tissues allowed the construction of two cDNA libraries: one derived from endosperm of heart-shape embryo developing stage seeds and the other from endosperm of a mix of globular-shape embryo and cotyledon stage developing seeds. Heart-shaped-embryo endosperm is also ready for protein profiling analysis.

For microarray analysis, endosperms were harvested from young seeds at the globular-shape embryo, heart-shape embryo and cotyledon stages, respectively. Two biological duplicates were set up, including four technological repeats in each duplicate. A dye-swap hybridization experiment was performed for each pair of target RNA comparisons.  We performed four independent aRNA labelings for each tissue pair. For example, we used globular-shape embryo stage endosperm RNA coupled with Cy5 dye vs. heart-shape embryo stage endosperm RNA coupled with Cy3 dye, and the dye-swap experiment was with globular-shape embryo stage endosperm RNA with Cy3 dye vs. the heart-shape embryo stage endosperm RNA with Cy5 dye. Each tissue pair experiment was done with four repeats, using a total of 24 microarrays for the whole experiment.

first: Yi

last: Huang

first: Liang

last: Chen

first: Liping

last: Wang

first: Sieu

last: Phan

first: Ziying

last: Liu

first: Kannan

last: Vijayan

first: Lianglu

last: Wan

first: Andrew

last: Ross

first: Daoquan

last: Xiang

first: Raju

last: Datla

first: Youlian

last: Pan


title: Intra- and inter-individual genetic differences in gene expression (BXD Brain)

status: Public on May 19 2009

city: University of New South Wales

first: Mark

last: Cowley

state: NSW

address: School of BABS, Building D26

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Genetic variation is known to influence the amount of mRNA produced by a gene. Because molecular machines control mRNA levels of multiple genes, we expect genetic variation in components of these machines would influence multiple genes in a similar fashion. We show that this assumption is correct by using correlation of mRNA levels measured from multiple tissues in mouse strain panels to detect shared genetic influences. These correlating groups of genes (CGGs) have collective properties that on average account for 52–79% of the variability of their constituent genes and can contain genes that encode functionally related proteins. We show that the genetic influences are essentially tissue-specific and, consequently, the same genetic variations in one animal may upregulate a CGG in one tissue but downregulate the CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. Thus, this class of genetic variation can result in complex inter- and intra-individual differences. This will create substantial challenges in humans, where multiple tissues are not readily available.

overall_design: Each sample is a single hybridisation from a given BxD strain to a C57BL/6J reference sample. Two-colour glass arrays were used. No dye swaps were employed. Data from whole brain.

first: Chris

last: Cotsapas

first: Rohan

middle: B

last: Williams

first: Eva

middle: K

last: Chan

first: Jeremy

middle: N

last: Pulvers

first: Michael

middle: Y

first: Oscar

last: Luo

first: David

last: Nott

first: Peter

middle: F

last: Little


title: Gene expression in PLN vs. ILN or MLN in mice

status: Public on Apr 23 2009

city: Stanford

first: Remi

last: Creusot

state: CA

address: 269 Campus Dr, CCSR 2240

department: Medicine

institute: Stanford University

summary: Normal gene expression in pancreatic lymph nodes compared to inguinal or mesenteric lymph nodes across different strains of mice (BALB/c, FVB, NOD, NOD.B10).

overall_design: Lymph nodes were excised from 12 wk old female mice (5 mice per group), and total RNA was extracted for dual dye microarray analysis.

first: Garry

last: Fathman


title: Identification of mRNAs modulated by knockdown of CD24

first: Keisuke

last: Taniuchi

summary: We endeavored to identify factors and pathways regulated by CD24 and to obtain leads regarding the mechanism by which CD24 inhibited the invasiveness and metastasis of pancreatic cancer cells by performing cDNA microarray analysis on S2-013 CD24 RNAi clones and control clones. The group of genes showing increased expression was mainly comprised of genes for molecules with functions related to RNA metabolism, transcription factors, proteases, and molecules involved in embryonic development and cell growth. The set of genes downregulated by knockdown of CD24 included the target mRNAs of a phosphorylation-dependent endoribonuclease G3BP that interacted with CD24. The target mRNAs of G3BP were identified in GSE17056. These results suggested that CD24 inhibited the RNase activity of G3BP, and that a function of CD24 was to inhibit the degradation of specific mRNAs.

overall_design:
Transcripts upregulated or downregulated by knockdown of CD24 were identified through expression profiling of a total of 12,135 genes in S2-013 CD24 RNAi clones compared to control clones. Before labeling with Cy5 or Cy3, total RNA from two S2-013 CD24 RNAi clones were mixed and total RNA from two control clones were mixed.

The supplementary files 'GSE17055_higher_siCD24.txt' and 'GSE17055_higher_control.txt' list the differentially expressed genes.

last: Kelly


title: Intra- and inter-individual genetic differences in gene expression (BXD Kidney)

overall_design: Common reference design where each hybridisation compares a single BxD strain to a common reference of C57BL/6J in the green channel. Two-colour, spotted glass arrays were used. No dye swaps were employed.

last: Liu


title: Gliomatosis Cerebri I

status: Public on Jun 17 2009

city: Lecce

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

country: Italy

institute: Salento University

summary: In modern clinical neuro-oncology the pathological diagnoses are very challenging creating significant clinical confusion and affecting therapeutic decisions and prognostic estimation. We investigated whether gene expression profiling, coupled with class prediction methodology, could be used to predict prognosis of gliomatosis cerebri in a more consistent manner then standard pathology. We report the results of a molecular study in  fifty-nine cases of gliomatosis cerebri, correlating these results with prognosis. TP53 and PTEN gene sequences were analyzed and microarray expression profiling were also performed. At the 24 month follow-up, 17 patients were alive, while 42 patients were died. We identified a 23 gene signature able to predict patient prognosis with microarray gene expression profiling. With the aim to produce a prognostication tool useful in clinical investigation we studied the expression of this 23 gene signature by RT-qPCR. Real time expression values relative to these 23 gene features were used to built a prediction method able to distinguish patients with good prognosis (more likely responsive to therapy) from patients with a bad prognosis (more likely irresponsive to therapy). These results demonstrated not only strong association of gene expression patterns with the survival of the patients but also a robust reproducibility of these gene expression– based predictors.

overall_design:
We have analyzed 59 gliomatosis cerebri bioptic tissue comparing them with normal brain tissue derived by non-tumor surrounding tissue or commercial brain tissue. We alternatively labeled test sample and reference with Cy3 and Cy5 so to avoid a systematic bias due to label efficiency. Since the aim of the work was to find a correlation between prognosis and expression profile we considered each sample of a one prognosis group like a replicate of that group. Median survival data allowed us to distinguish 59 gliomatosis cerebri patients in two group: bad prognosis group, counting 42 patients, with a median survival of 14.58 months and good prognosis group with a median survival of 41.20 months. Moreover TP53 and PTEN mutation analysis was performed on this patients. Kaplan-Meier survival curve with log-rank test showed like each prognosis group can be furthermore divided in 2 groups where bad prognosis group patients bringing a mutation in one of the two gene analized or both genes showed the wrong survival.
Microarray expression profile follwed by average linkage clustering analysis based on Pearson correlation coefficients was applied to all tissues on the basis of similarity in the expression pattern over all genes. As expected, it yielded two major clusters, one representing the good prognosis group and the other the bad prognosis one. Interesting these cluster are identical to cluster based on survival.

Tumour classification based upon WHO 2007.

first: Pietro

middle: I

first: Pasqualino

last: Ciappetta


title: Fibroblasts associated with tumors refractory to anti-VEGF treatment

status: Public on Jan 05 2009

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

summary:
PDGF-C mediates the angiogenic and tumorigenic properties of fibroblasts associated with tumors refractory to anti-VEGF treatment

Tumor associated fibroblasts (TAF) from different tumors exhibit distinct angiogenic and tumorigenic properties. Unlike normal skin fibroblasts (NSF) or TAF (TAF-TIB6) from TIB6 tumors that are sensitive to anti-VEGF treatment, TAF (TAF-EL4) from resistant EL4 tumors can stimulate TIB6 tumor growth even when VEGF is inhibited.  We show that platelet-derived growth factor (PDGF)-C is upregulated in TAFs from resistant tumors. PDGF-C neutralizing antibodies blocked the angiogenesis induced by such TAF in vivo and slowed the growth of EL4 and admixture (TAF-EL4 + TIB6) tumors and exhibited additive effects with anti-VEGF-A antibodies. Hence, our data reveal a novel mechanism for TAF mediated tumorigenesis and suggest that some tumors may overcome inhibition of VEGF-mediated angiogenesis through upregulation of PDGF-C

overall_design: Experiments:  two sensitive and three resistant samples.  3 replicate of each.

first: Yongping

last: Crawford

first: Ian

last: Kasman

first: Lanlan

last: Yu

first: Cuiling

last: Zhong

first: Xiumin

last: Wu

first: Zora

last: Modrusan

first: Joshua

first: Napoleone

last: Ferrara


title: Acute Dieldrin Exposure on Global Gene Transcription in Largemouth bass (Micropterus salmoides) Hypothalamus

status: Public on Sep 08 2008

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary:
Female largemouth bass were injected with 10mg/kg dieldrin and sacrificed after 7 days. Hypothalami were dissected and total RNA extracted for microarray analysis.

Exposure to dieldrin induces neurotoxic effects in the vertebrate CNS and disrupts reproductive processes in teleost fish.  Reproductive impairment observed in fish is likely the result of multiple mechanisms of action along the hypothalamic-pituitary-gonadal axis.  To better elucidate the mode of action of dieldrin in the hypothalamus, we measured neurotransmitter levels and examined the transcriptomic response of female largemouth bass (LMB) to an acute treatment of dieldrin.  Female LMB were injected with either vehicle or 10 mg/kg dieldrin and sacrificed after seven days.  The neurotransmitter γ-aminobutyric acid was significantly elevated by approximately 25-30% in the hypothalamus and cerebellum but there was no change in dopamine levels in the hypothalamus, telencephalon, or cerebellum.  We identified 270 transcripts (p<0.001) as being differentially regulated by dieldrin.  Functional enrichment analysis identified transcription, DNA repair, ubiquitin pathway, cell communication, and phosphorylation as biological processes over-represented in the microarray analysis.  Pathway analysis identified DNA damage, inflammation, regeneration, and Alzheimer’s disease as major cell processes and diseases affected by dieldrin.  Using multiple bioinformatics approaches, this study demonstrates that the teleostean hypothalamus is a target for dieldrin-induced neurotoxicity and provides mechanistic evidence that dieldrin activates similar cell pathways and biological processes that are involved in the etiology of human neurological disorders.
Key words: ubiquitin-proteasome pathway, mutagenicity, neurodegeneration, apoptosis, DNA damage

overall_design: Largemouth bass injected with single i.p. with 10 mg/kg diedrin; sacrificed 7 days later, hypothalamic tissue studied

middle: J

first: April

last: Feswick

first: Dan

last: Spade

last: Barber

first: Kevin

last: Kroll

first: Nancy

last: Denslow


title: Detecting novel genes with sparse arrays

status: Public on Aug 13 2010

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

summary:
Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions.

We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9 Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25mer microarray oligonucleotide probe was used for every 100 b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties.

overall_design: Experiment consists of three conditions relevant for study of protein secretion, growth rate D=0.03 h-1, growth rate D=0.06 h-1 and growth rate D=0.03 h-1 with high cell density. Each condition has three biological repeats thus there are nine chemostat cultivations.

first: Niina

last: Haiminen

first: Bart

last: Smith

first: Jari

last: Rautio

first: Marilyn

last: Wiebe

first: Tiina

last: Pakula

first: Deigo

last: Martinez

first: Markku

last: Saloheimo

first: Merja

last: Penttilä

first: Teemu

last: Kivioja


title: Transcriptional profiling of Ascochyta blight resistance in Lentil

status: Public on May 08 2008

city: melbourne

first: barkat

middle: murtaja

last: mustafa

state: victoria

address: Corner of Royal Parade & Tin Alley

department: School of agriculture

institute: University of melbourne

summary:
Using a cDNA microarray themed on Ascochyta-Pulse interaction resistance response was studied in two lentil varieties, specifically in response to A. lentis inoculation in a highly resistant (ILL7537) and highly susceptible (ILL6002) lentil variety. The experiments were conducted in reference design, where samples from mock-inoculated controls acted as references against post-inoculation samples and the plants were grown using a uniform and standardized experimental system that minimized environmental effects. Robust and high quality data was obtained through the use of three biological replicates (including a dye-swap), the inclusion of negative controls, and stringent selection criteria for differentially expressed genes including a fold change cutoff determined by self-self hybridizations, Students t-test and FDR (Fasle Discovary Rate) multiple testing correction (P<0.05). Microarray observations were validated by quantitative real time RT-PCR using the RNA from one of the bioassay used in the original microarray experiment. Ninety genes were differentially expressed in ILL7537 and 95 genes were differentially expressed in ILL6002. The expression profiles of the two varieties showed substantial difference in type and time of genes that were expressed in response to A. lentis. The resistant variety showed early up-regulation of PR proteins and other defence related genes. The susceptible genotype showed mainly down-regulation of defence related genes. The microarray experiment, the first in lentil, conducted with a small number of genes themed on Asochyta and Pulse interactions was able to identify different components of the defence mechanism by comparing the transcriptional profiles of the susceptible and resistant genotypes. This study will thus form the basis of future experiments to elaborate and corroborate the genomics of lentils defence to A. lentis.
Keywords: time course, disease state analysis

platform_organism:
Cicer arietinum
Lathyrus sativus
Lens culinaris

overall_design: Total RNA was extracted from pooled stem and leaf samples for each genotype at each time-point (including control samples) using the RNeasy® Plant Mini Kit (Qiagen, Valencia, CA). The quantity, quality and integrity of the total RNA samples were assessed by OD260/OD280 ratios and by gel electrophoresis. Fifty  μg of total RNA from each sample was reverse transcribed using Superscript II (Invitrogen) with incorporation of amino-allyl dUTP (Sigma) into the cDNA for post labeling  with Cy3- or Cy5-NHS esters (Amersham). For each time point after inoculation, hybridisations were performed with six technical replicates (corresponding to the six complete grids on each microarray slide) and three biological replicates and included a dye-swapping (i.e. reciprocal labeling of Cy3 and Cy5) to eliminate any dye bias. In total 180 images were analysed from 30 slides, resulting in 18 data points for each time-point of each genotype. An Affymetrix® 428™ array scanner (Santa Clara, CA) was used to scan hybridized microarray slides at 660 nm for Cy5 (red laser) and 532 nm for Cy3 (green laser) at 10 µm resolution and the image was captured with Affymetrix® Jaguar™ software (v. 2.0, Santa Clara, CA). Scanned image was analysed and quantified using Imagene™ 5 (BioDiscovery, Marina Del Rey, CA) software. Transformation of quantified spot data with GeneSight™ 3 (BioDiscovery, Marina Del Rey, CA) consisted of a local background correction (subtracting mean background intensity from mean signal intensity for each spot), omitting flagged spots (i.e. empty spots, negative spots (signal mean<background mean), poor spots and spots with mean signal intensity less than two times the local background), LOWESS normalisation of the entire population, creating a test/reference mean signal ratio, taking a shifted log (base 2), and combination of duplicated spot data. For identifying differentially expressed (DE) genes, expression ratios were filtered to eliminate genes whose  mean fold change (FC) was less than 1.83-fold up or down at 95% confidence interval followed by Students t test and  False Discovery Rate (FDR) multiple testing correction to retain only genes in which expression ratio changes were significant at P < 0.05. Datasets for ILL7537 and ILL6002  was built from mean expression ratios of a non-redundant list of genes differentially expressed at any time-point for any  genotype at This dataset was then used to perform Figure of Merit (FOM) and k-means clustering using euclidean distance metrics with the MeV software.

first: Barkat

middle: M

last: Mustafa

first: Tristan

last: Coram

first: Eddie

last: Pang

first: Paul

last: Taylor

first: Rebecca

last: Ford


title: Murine spleen B cells miR181b vs control (G4122A)

status: Public on Aug 20 2008

city: Madrid

first: Almudena

middle: R.

last: Ramiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary:
Transcriptional profile of mouse primary spleen B cells overexpresing miR181b-GFP vectors compared to B cells overexpressing control-GFP vectors

Keywords: Genetic modification

overall_design: Two-condition experiment: B-miR181b vs. B-control. Biological replicates: 1 control, 1 miR181b.

first: A

first: V

middle: G

last: de Yebenes


title: Microarray analysis of phosphate regulation in Synechococcus sp. WH8102

status: Public on Jun 15 2009

city: Sydney

first: Ian

last: Paulsen

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

institute: Macquarie University

summary: Primary productivity of open ocean environments, such as those inhabited by marine picocyanobacteria Synechococcus sp.WH8102, are often limited by low inorganic phosphate (P). To observe how this organism copes with P starvation, we constructed a full genome microarray and examined differences in gene expression under P-limited and P-replete growth conditions. To determine the temporal nature of the responses, comparisons were made for cells newly entered into P-stress (at a time point corresponding to the induction of extracellular alkaline phosphatase activity) and a later time point (late log phase). In almost all instances the P starvation response was transitory, with 36 genes showing significant upregulation (>log2 fold) while 23 genes were highly downregulated at the early time point; however, these changes in expression were maintained for only five of the upregulated genes. Knockout mutants were constructed for genes SYNW0947 or SYNW0948, comprising a two component regulator hypothesized to play a key role in regulating the response to P-limitation. A high degree of overlap in the sets of genes affected by P-limited conditions and in the knockout mutants supports this hypothesis; however there is some indication that other regulators may play a role in this response in Synechococcus sp. WH8102. Consistent with what has been observed in many other cyanobacteria, the Pho regulon of this strain is comprised largely of genes for alkaline phosphatases, P transport or P metabolism. Interestingly, however, the exact composition and arrangement of the Pho regulon appears highly variable in marine cyanobacteria.

overall_design: In this series four conditions have been analyzed.  These are low phosphate stress during early log phase, low phosphate stress during late log phase, SYNW0947 mutation, and SYNW0948 mutation.  There are six slides per condition, each with two biological replicates.  There are three technical replicates for each biological replicate including one flip-dye comparison.  The exception is the low phosphate stress during late log phase experiment which has a total of five slides, two biological replicates with three and two technical replicates, respectively, and one flip-dye comparison for each biological replicate.  Each slide contains six replicate spots per gene.

first: Brian

last: Palenik

first: Sasha

last: Tetu

first: Katherine

last: Phillippy

first: Bianca

last: Brahamsha

first: Daniel

middle: A

last: Johnson

first: Vera

last: Tai

first: Lori

last: Crumblis

first: Rob

last: Herman

first: Chris

last: Dupont


title: Liver Cyprinus carpio PFOS experiment

status: Public on Aug 15 2008

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary:
Perfluorooctane sulfonate (PFOS) has been manufactured for over 50 years in increasing quantities and has been used for several industrial and commercial aims. Due to the persistence and the bioaccumulation of this pollutant, it can be found worldwide in wildlife and humans. Biochemical effects of PFOS exposure are mainly studied in mammalian model species and information about effects on fish species remain largely scarce. This lack of toxicity data points out that there is an urgent need for the mechanistic molecular understanding of the mode of action of this pollutant. In the present study, common carp (Cyprinus carpio) was exposed through water for 14 days at concentrations of 0.1; 0.5 and 1 mg/l PFOS. Liver was selected as target tissue. Custom microarrays were constructed from cDNA libraries obtained with Suppression Subtractive Hybridization-Polymerase chain reaction (SSH-PCR) experiments. Microarray data revealed that the expression of several genes in the liver was influenced by PFOS exposure and real-time PCR was used to confirm these gene expression changes. The affected genes were mainly involved in energy metabolism, reproduction and stress response. Furthermore, the relative condition factor and the hepatosomatic index of the exposed fish were significantly lower after 14 days of exposure as well as the available glycogen reserves. At all levels of biological organization, indications of a trade-off between the metabolic cost of toxicant exposure on one hand and processes vital to the survival of the organism on the other hand were seen. Our results support the prediction that increases in energy expenditure negatively affects processes vital to the survival of an organism, such as growth.
Keywords: PFOS, common carp, microarray, condition factor, energy reserves, metabolic cost

overall_design: There were 3 biological replicates for each exposure concentration. For each biological replicate control versus exposed hybridizations were carried out. The mean of the biological replicates was calculated for the differentially expressed genes.

first: Dries

last: Knapen

first: Izak

last: Meyer

first: Wim

last: De Coen


title: 'Bois noir' phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine

status: Public on Mar 21 2008

city: Ljubljana

first: Kristina

last: Gruden

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary:
Transcriptional profiling of Vitis vinifera cv. Chardonnay healthy vs. Phytoplasma-infected plants (Bois noir phytoplasma). Study was conducted on grapevine plants grown in the same vineyard (leaf midribs were sampled).
Keywords: disease state analysis

overall_design: Two-condition experiment: healthy vs. infected plants/shoots. Biological replicates: 4 healthy, 4 infected. No replicates. Each sample was prepared as a pool of several samples (each sample was collected from a different shoots/plants) of the same disease status. Each sample was co-hybridized to a common reference cRNA (pool of all samples).

first: Matjaz

last: Hren

first: Ana

last: Rotter

first: Marina

last: Dermastia

first: Petra

last: Nikolič

first: Tomaž

last: Curk

first: Maja

last: Ravnikar

first: Paolo

last: Ermacora

first: Ruggero

last: Osler

first: Piero

last: Bianco

first: Luigi

last: Carraro

first: Nancy

last: Terrier

first: Serge

last: Delrot


title: Gene expression response to copper toxicity between coastal and open ocean strains of marine Synechococcus

status: Public on Jul 01 2009

first: Ian

last: Paulsen

summary: Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock.  Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays.  Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability.  This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus.  The two strains additionally showed a reduction in photosynthetic gene transcripts.  Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response.  In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer.  Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner.

sample_organism:
Synechococcus sp. CC9311
Parasynechococcus marenigrum WH 8102

overall_design: In this series four conditions have been analyzed. These are moderate copper shock for Synechococcus sp. WH8102 and CC9311 (pCu 11.1 and pCu 10.1, respectively), and high copper shock for WH8102 and CC9311 (pCu 10.1 and pCu 9.1, respectively). For each slide, an experimental RNA sample was labeled with Cy3 or Cy5 and was hybridized with a reference RNA from a non-copper-shocked sample labeled with the other Cy dye. There are six or eight slides per condition, each with two biological replicates. There are three or four technical replicates for each biological replicate including at least one flip-dye comparison. Each slide contains six replicate spots per gene.

first: Rhona

last: Stuart

first: Chris

last: Dupont

first: Daniel

last: Johnson

middle: T

first: Brian

last: Palenik

first: Katherine

middle: H

last: Phillippy


title: Transcriptional profiling of Candida albicans wild-type CAI-4 strans treated by Hst5

status: Public on Jul 18 2007

city: Buffalo

first: Wansheng

last: Li

state: NY

address: 3435 main st.

department: Oral Biology

institute: University at Buffalo

summary:
The experiment was designed to study the transcriptional profiling of Candida albicans wild-type CAI-4 strains and corresponding Histatin 5 treated strains. Since Histatin 5 will kill Candida albicans, the focus will be on how many and which genes are significantly affected with the treatment of Histatin 5. Currently, we only conducted the microarray experiments at one concentration of Histatin 5 and one time point of treatment.
Keywords: cell type comparison

overall_design:
Direct balanced design (without reference sample)
Four samples/arrays were used  in the experiment, which includes 2 dye swap replicates and 2 duplicate experiments. The details are
CAI-4-Cy5 <-> Hst5_CAI-4-Cy3
CAI-4-Cy5 <-> Hst5_CAI-4-Cy3
CAI-4-Cy3 <-> Hst5_CAI-4-Cy5
CAI-4-Cy3 <-> Hst5_CAI-4-Cy5

CAI-4 is wild-type strain
Hst5_CAI-4 is CAI-4 treated with Histatin 5 for 1hr. under specific conditions.

first: Slavena

last: Vylkova


title: Diet and phenobarbital affect cholesterol homeostasis and drug metabolism

status: Public on Nov 27 2007

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

institute: Faculty of Medicine, University of Ljubljana

summary:
High cholesterol diet and xenobiotic treatment induce changes in cholesterol homeostasis and drug metabolism. Mice were either 7 days on high cholesterol diet or were treated with phenobarbital. Liver samples were analyzed using Sterolgene v0 cDNA microarrays. Sterolgene microarray is a tool designed to enable focused studies of cholesterol homeostasis and drug metabolism. We show that one week of cholesterol diet down-regulates cholesterol biosynthesis and up-regulates xenobiotic metabolism (Cyp3 family). Phenobarbital treatment also up-regulates xenobiotic metabolism (Cyp2b and Cyp3a families). We can conclude that the Sterolgene series of cDNA microarrays represent novel original tool, enabling focused and cost-wise studies of cholesterol homeostasis and drug metabolism.
Keywords: Treatment and diet effects

overall_design: One group of mice was treated i.p. with 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). Untreated group was injected vehicle. Third group was 7 days on 1 % (w/w) cholesterol diet prior vehicle treatment. After 10 h animals were sacrificed and livers were stored. Pools of total RNA from two animals were mixed. Three pools of untreated and phenobarbital treated groups, and two pools of cholesterol diet group were co-hybridized with liver reference on Sterolgene v0 cDNA microarray. No dye-swaps were performed.

first: Tadeja

last: Režen

first: Adrian

last: Roth

first: Klementina

last: Fon Tacer

first: Urs

last: Meyer

first: Damjana

last: Rozman


title: Interdependence between DNA methylation and transcription

status: Public on Nov 26 2006

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

summary:
Cytosine methylation, a common form of DNA modification that antagonizes transcriptional initiation, is found at transposons and repeats in vertebrates, plants, and fungi.  Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution.  DNA methylation covers transposons and is present within about 20% of Arabidopsis genes.  Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit.  Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, while genes at either extreme are least likely.  Small RNAs are enriched at methylated genes, which suggests that aberrant transcription triggers genic methylation.  Transcription is in turn influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription.  Our results indicate that genic transcription and DNA methylation are closely interwoven processes.
Keywords: whole genome profiling, DNA methylation, met1-6 expression

overall_design: All experiments were done using two channels per chip.  Two microarray experiments compared immunoprecipitated, methylated DNA to control genomic DNA.  A third microarray experiment used a methylation sensitive restriction enzyme (HpyCH4 IV) to determine regions of differential DNA methylation in met1-6 mutant plants.  Two microarray experiments for expression analysis of met1-6 mutants were done using biological replicates.  Oligo (dT) primed cDNA from mutant plants was compared to oligo (dT) primed cDNA from wild type plants.

last: Zilberman

first: Mary

last: Gehring

first: Robert

last: Tran

first: Tracy

last: Ballinger

first: Steven


title: Expression Profiling of Circulating Red Blood Cells and Non Red Blood Cells in the Chicken Embryo (E4 and E6)

status: Public on Dec 17 2007

city: Kobe

first: Brendan

last: McIntyre

state: Hyogo

address: 2-2-3 /minatojima-minamimachi

institute: Kobe RIKEN Center for Developmental Biology

summary:
Blood was extracted from embryonic hearts at E4 and E6 and non-red blood was separated by density gradient centrifugation
Keywords: Cell type comparison

overall_design: There are a total of 9 samples which have one biological replicate each, except negative control E6 embryonic heart (used to screen heart contamination in our blood samples - which were drawn from the heart) which has only one sample.

first: Guojun

last: Sheng


title: TNFalpha interferes with adaptation to starvation and activates pro-atherogenic processes

summary:
Pathenogenesis of atherosclerosis results from the interactions between disrupted lipid homeostasis and immune response, but the molecular bridges between the major players are still a matter of controversy. We performed a systemic study of the imflammatory cytokine tumor necrosis factor alpha (TNF alpha), a well established anorexia agent, in the livers of the mice exposed to 20h-cytokine/starvation. We show that treatment with TNF-alpha reverses adaptations to fasting. Moreover, it up-regulates cholesterol biosynthesis and down-regulates bile acids synthesis, which leads to disrupted cholesterol homeostasis and pro-atherogenic changes. Interestingly, we found that TNF alpha also interferes with gene regulation of the xenobiotic metabolism.
Keywords: treatment and diet effects

overall_design: Mice have been either saline treated (nontreated group), saline treated and fasted for 20h (fasted group), and TNF-alpha treated (30 mikrograms per animal) and fasted for 20h (TNF-alpha group). 3 biological replicas from fasted and TNF-alpha groups were co-hybridized with pool of nontreated group. No dye-swaps were performed.


title: FolR1 gene ablation-induced changes in gene expression in mouse conotrucus tissue and developing heart

status: Public on Feb 20 2006

city: Houston

first: Huiping

last: Zhu

state: TX

address: 2121 W. Holcombe Blvd

department: Center for Environmental and Genetic Medicine

institute: Institute of Biosciences and Technology, TAMUSHSC

summary:
Defective function of FolR1 in mice results in inadequate transport, accumulation, or metabolism of folate during cardiovascular morphogenesis. We have observed cardiovascular abnormalities including outflow track defects and aortic arch artery defects in these genetically compromised mice. In order to investigate the mechanisms underlying the failure to complete cardiac development in the transgenic mouse model, we studied gene expression difference between FolR1 knockout embryos and normal embryos during outflow track septation (GD11:12,
GSM78976 ... GSM78987), and
studied gene expression difference between FolR1 knockout embryos and normal embryos during embryonic heart development(GD9:00 and GD10:00, GSM79024 ... GSM79035).
Keywords: gene ablation response

overall_design:
Pregnant FolR1 heterozygotic dams were supplemented with s-folinic acid 6.25mg/kg/day p.o. At GD11:12, 3 control embryos and 3 null embryos were harvested from 6 different dams. From these embryos, the conotruncus tissue of developing heart was dissected and RNA extracted. These RNA samples were used for hybridization on commercially available CodeLink UniSet 10K Bioarray.

Pregnant FolR1 heterozygotic dams were supplemented with s-folinic acid 6.25mg/kg/day p.o. At GD9:00 and GD10:00, 3 control embryos and 3 null embryos were harvested from 6 different dams for each timepoint. From these embryos, the heart tissue of developing heart was dissected and RNA extracted. These RNA samples were used for hybridization on commercially available CodeLink UniSet 20K Bioarray.

last: Cabrera

first: Daniel

last: Bozinov

first: Bogdan

last: Wlodarczyk

first: Richard

last: Finnell

first: Deli

last: Wang


title: Transcriptional profiling of bovine endometrial tissue at day 17 of the reproductive cycle

status: Public on Dec 01 2009

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

summary: Over the past three decades, there has been a significant decline in dairy cattle fertility.  A large proportion of pregnancy losses are believed to occur during the pre-implantation period, when the developing embryo is elongating rapidly and signaling its presence to the maternal system. The molecular mechanisms that prevent progression of the estrous cycle and allow the allogenic embryo to survive within the maternal environment are not well understood. To gain a more complete picture of these molecular events, global transcriptional profiling was performed using endometrial tissues from reproductive day 17 pregnant and non-pregnant (cycling) Holstein-Friesian dairy cattle.

overall_design: 22 animals were enrolled in this study, 2 samples from each animal were used for microarray analysis consisting of caruncular and intercaruncular endometrium. A reference design was used for hybridisation, whereby each of the 44 samples were hybridised to individual microarrays along with a pooled reference sample. The reference sample was generated by taking equal concentrations of each of the experimental samples.

first: Mathew

middle: D

last: Littlejohn

first: Susanne

last: Meier

first: John

middle: R

last: Roche

first: Murray

last: Mitchell


title: Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise

status: Public on Mar 31 2007

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

summary:
Salt Stress response of salt-tolerant genotype Golden Promise compared to Maythorpe
Barley1 GeneChip was used to find differential expression between two barley genotypes under control and salt stress conditions at vegetative stage of growth
Keywords: genotype and treatment comparison

overall_design: Roots (tips) and shoot (crown and growing point) tissue was used for hybridization to GeneChips

first: Timothy

last: Close


title: Environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

status: Public on Oct 15 2007

city: Brisbane

first: Karin

middle: Sonja

last: Kassahn

state: QLD

address: Queensland Bioscience Precinct

department: Institute for Molecular Bioscience

institute: University of Queensland

summary:
Transcriptional profiling of gene responses in liver in the coral reef fish Pomacentrus moluccensis in response to different types of environmental stress: cold, heat, hypoxic and hyposmotic shock. Goal was to determine the common effects of different types of environmental stress on gene expression as well as responses unique to different stressors.

Abstract from Kassahn et al. BMC Genomics (2007) 8:358
Background
While our understanding of the importance of transcriptional regulation for biological function is continuously growing, we still know comparatively little about how environmentally-induced stress affects gene expression in vertebrates and how consistent transcriptional stress responses are across different types of environmental stress.
Results
In this study, we looked for a genetic measure of environmental stress and used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. We identified a series of gene functions that were consistently involved in all stress responses examined here, suggesting common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes and the responses of individual genes varied greatly across different stress types. However, we were able to identify groups of co-regulated genes, the genes within which shared similar functions. Given current estimates of climatic change, we were particularly interested in the response to prolonged heat exposure.  In total, 324 gene loci were differentially expressed following exposure to heat over five days. The functions of these heat-responsive genes suggest that prolonged heat stress leads to oxidative stress and protein damage, challenge of the immune system, and a re-allocation of energy sources.
Conclusion
This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. This study offers insight into the effects of environmental stress on biological function and sheds light on the expected sensitivity of coral reef fishes to elevated temperatures in the future.
Keywords: Stress response

overall_design: Balanced design with dye-swaps and biological replicates representing comparisons of environmentally-stressed fish compared against fish kept at ambient conditions and comparisons involving fish exposed to different types of environmental stress. No technical replicates were employed. In total 59 dual channel microarray hybridisations were performed using 118 different individuals. Thus, each microarray hybridisation employed two individual fish (no sample pooling).

middle: S

first: Ross

last: Crozier

first: Alister

middle: C

last: Ward

first: Glenn

last: Stone

first: M

last: Caley


title: Microarray analysis of the effect of Cipro on wt and lexA mutant S. aureus cells

status: Public on Nov 30 2006

city: San Diego

first: Marcus

last: Jones

address: 4120 Torrey Pines Road

institute: JCVI

summary:
Staphylococcus aureus is a leading cause of human disease and can be difficult to treat due to both multi-drug resistance and the organism’s remarkable ability to persist in the host, which is thought to result from several complex regulatory networks that modify transcription in response to environmental stress. In this study, we characterize the global transcriptional response of S. aureus strain 8325 to the antibiotic ciprofloxacin. We find that ciprofloxacin induces prophage mobilization and also significant alterations in metabolism, most notably an upregulation of the tricarboxylic acid cycle. In addition, ciprofloxacin induces the SOS response, which based on a comparison of the wild-type and lexA mutant strains, we show includes the de-repression of sixteen genes. In addition to RecA, LexA, and the hypothetical proteins encoded by SACOL0436, SACOL1375, SACOL1986 and SACOL1999, the S. aureus SOS genes encode proteins involved in DNA metabolism and induced mutation. Finally, we show that rendering LexA uncleavable significantly sensitizes the pathogen to ciprofloxacin therapy in vivo. These observations suggest that the SOS response may play a critical role in the pathogenicity of S. aureus.
Keywords: time course

overall_design:
Sample preparation for transcriptional analysis. For each strain, 3 clones were inoculated in TSB and incubated for 18 hours. Cultures were diluted 1:100 and incubated until they reached early log phase (OD600 ~0.5-0.6) at which point ciprofloxacin was added to a final concentration of 0.8 •g/ml. Immediately prior to ciprofloxacin addition, and again 30 and 120 minutes following addition, appropriate volumes from each of the 3 cultures per strain were pooled and added to 2 volumes of RNAprotect reagent (Qiagen). Cultures were centrifuged and cell pellets were stored at 4 ºC until RNA extraction. During the experiment, OD600 and viable cfu per ml were monitored for each of the cultures (Figure 2A and 2B). Total RNA was extracted using the RNeasy Mini kit (Qiagen) at the end of the sample collection period. This procedure was repeated 3 independent times to generate 3 samples at each time point for each strain.

Generation of probes for microarray experiments. cDNA probes for microarray experiments were generated as follows. Briefly, 2 μg of total RNA in a mixture containing 6 μg of random hexamers (Invitrogen); 0.01 M dithiothreitol; an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma); reaction buffer (Clontech); and 400 units of Powerscript reverse transcriptase (Clontech) were incubated at 42 °C overnight. The resulting RNA template was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 65 °C for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The cDNA probes were eluted with phosphate buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature and incubated for 2 h. Uncoupled label was removed using a Minelute column (Qiagen).

Microarray hybridization, scanning, image analysis, normalization, and
analysis. Epoxy-coated slides were prehybridized in 5´ SSC (1´ SSC, 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 °C for 60 min. The slides were then washed at room temperature with distilled water, dipped in isopropanol, and spun dry. Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5´ SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were denatured by heating to 95ºC prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 °C. Hybridized slides were washed sequentially in solutions of 1´ SSC-0.2% SDS, 0.1´ SSC-0.2% SDS, and 0.1´ SSC at room temperature, dried, and then scanned with an Axon GenePix 4000 scanner. Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at http://www.tigr.org/software/tm4). Microarray data were normalized by LocFit (LOWESS) Normalization in block mode using TIGR MIDAS software (available at http://www.tigr.org/software/tm4). Median spot intensity values were used to calculate the log2 ratio and fold change. Oligos with intensities less than 10,000 units were subtracted from the analysis to rule out background. All hybridizations were performed with a minimum of 1 flip dye experiment. Each hyb has 3 inslide replicates per oligo to rule out bias data.


title: Transcriptome changes in Emericella nidulans due to oxidative stress - normalized experimental data

status: Public on Jan 05 2006

city: Debrecen

first: Istvan

last: Pocsi

address: Egyetem tér 1.

department: Dept.of Microbiology and Biotechnology

institute: University of Debrecen

summary:
Late exponential growth phase (18 h) Emericella nidulans mycelia were transferred to minimal media also supplemented with 1.8 mM diamide, 75 mM H2O2 or 0.8 mM menadione (sodium bisulfite addition compound) and transcriptome profiles were recorded at 0.25, 0.5, 1, 3, 6 and 9 h incubation times. Double printed EST-based (3533 unique sequences) DNA chips were used to monitor changes in cDNA populations prepared from mRNA pools isolated from oxidative stress exposed and untreated control cultures. Gene expression ratios were estimated with Genisphere (Hatfield, PA, USA) 3DNA Submicro EX Expression Array Detection Kit. Expression data were read with a GenePix 4000B microarray scanner (Axon Instruments). Intensity ratios were calculated with GenePix Pro 3.0 software. Gene expression ratios were subjected to LOESS-type block-by-block normalization using SAS for Windows, version 8. (SAS Institute Inc., Cary, NC, USA.) software. Global gene expression profiles were correlated to physiological changes quantified by intracellular reactive oxygen species levels and redox balances.

Primary unprocessed experimental data are summarized Series GSE2100.
Keywords: time-course

first: Marton

last: Miskei

first: Zsolt

last: Karanyi

first: Tamas

last: Emri

first: Patricia

last: Ayoubi

first: Tunde

last: Pusztahelyi

first: Gyorgy

last: Balla

first: Rolf

last: Prade


title: Trichostatin A (TSA) inhibition of histone deacetylase in Arabiodopsis thaliana

status: Public on Dec 10 2005

city: Fredericton

first: Helen

last: Tai

email: htai@nrcan.gc.ca, taihelen@yahoo.com

state: New Brunswick

address: 1350 Regent St.

department: Natural Resources Canada

institute: Canadian Forest Service

summary:
     Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes.  Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression.  To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds.  GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination.   Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA).  A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate.  In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated.  Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes.
Keywords: histone deacetylase inhibitor, developmental effects

overall_design: Two samples  (TSA-treated v.s. untreated).  Two replicates for each sample.

first: George

first: Tannis

last: Beardmore


title: Intra- and inter-individual genetic differences in gene expression (C57BL/6J vs DBA/2J)

status: Public on May 18 2005

first: Peter

last: Little

institute: School of Biotechnology and Biomolecular Sciences, The University of New South Wales

summary: Genetic variation is known to influence the amount of mRNA produced by a gene, but the effects in different tissues is unclear. We studied gene expression levels in whole brain, kidney or liver, comparing 8 week old, male C57BL/6J to DBA/2J mice. Genes differentially expressed due to genetic background in one tissue were not differentially expressed in other tissues, suggesting that genetic variation of gene expression is tissue specific in inbred mice. Data used in a comparison to the BXD panel of mice in GSE8355, GSE8356, GSE6621 and to SJL/J in GSE8358.

overall_design: Each sample is a single hybridisation from a common pool of C57BL/6J or DBA/2J. Two-colour glass arrays were used. No dye swaps were employed. Data from whole brain, kidney or liver.

first: Chris

last: Cotsapas

first: Jeremy

middle: N

last: Pulvers

first: Rohan

middle: B

last: Williams

first: David

last: Nott

first: Eva

last: Chan

first: Mark

last: Cowley

middle: F


title: Transcriptome changes in Emericella nidulans due to oxidative stress - primary experimental data

first: Istvan

last: Pocsi

summary:
Late exponential growth phase (18 h) Emericella nidulans mycelia were transferred to minimal media also supplemented with 1.8 mM diamide, 75 mM H2O2 or 0.8 mM menadione (sodium bisulfite addition compound) and transcriptome profiles were recorded at 0.25, 0.5, 1, 3, 6 and 9 h incubation times. Double printed EST-based (2x4352 spots) DNA chips were used to monitor changes in cDNA populations prepared from mRNA pools isolated from oxidative stress exposed and untreated control cultures. Gene expression ratios were estimated with Genisphere (Hatfield, PA, USA) 3DNA Submicro EX Expression Array Detection Kit. Expression data were read with a GenePix 4000B microarray scanner (Axon Instruments). Intensity ratios were calculated with GenePix Pro 3.0 software. Note, processed data after LOESS-type normalization are presented on Series GSE2085 and all the signs were also reversed during data processing to reach proper log2(treated/control) channel intensity ratios.
Keywords: time-course

first: Marton


title: Prostaglandin J2 alters gene expression patterns and 26S proteasome assembly in human neuroblastoma cells

status: Public on Jun 01 2006

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

summary:
Many neurodegenerative disorders are characterized by two pathological hallmarks: progressive loss of neurons and occurrence of inclusion bodies containing ubiquitinated proteins. The mechanisms responsible for these pathological features remain elusive. Inflammation may be critical to neurodegeneration associated with ubiquitin-protein aggregates. We previously showed that prostaglandin J2 (PGJ2), one of the endogenous products of inflammation, induces neuronal death and accumulation of ubiquitinated proteins into distinct aggregates. We now report that temporal microarray analysis of human neuroblastoma SK-N-SH cells treated with PGJ2 revealed changes relevant to neurodegeneration. PGJ2 triggered a “repair” response including increased expression of heat shock, protein folding, stress and cellular defense genes. PGJ2 also decreased expression of DNA repair genes and increased expression of apoptotic genes. Overtime pro-death responses prevailed over pro-survival responses, leading to cellular demise. Furthermore, PGJ2 increased the expression of proteasome and other ubiquitin-proteasome pathway genes. This increase failed to overcome PGJ2-inhibition of 26S proteasome activity. Ubiquitinated proteins are degraded by the 26S proteasome, shown here to be the most active proteasomal form in SK-N-SH cells. We demonstrate that PGJ2 impairs 26S proteasome assembly, which is an ATP-dependent process. Interestingly, PGJ2 is known to perturb mitochondrial function, which could be critical to the observed 26S proteasome disassembly and suggest a crosstalk between mitochondrial and proteasomal impairment. In conclusion neurotoxic products of inflammation, such as PGJ2, may play a role in neurodegenerative disorders associated with the aggregation of ubiquitinated proteins by impairing 26S proteasome activity and inducing a chain of events that culminates in neuronal cell death.
Keywords: Drug response time course

overall_design: SK-N-SH cells were treated with 20uM PGJ2 for 4, 8, 16 and 24h. Each time point was repeated two times. For each time point, total RNA from untreated control and PGJ2-treated cells was isolated, labeled and co-hybridized onto Human 19K oligonucleotide arrays.

first: Zhiyou

last: Wang

first: Kenyon

last: Ogburn

last: Soteropoulos

first: Maria

middle: E

last: Figueiredo-Pereira


title: Sex-specific gene expression in the mouse heart

status: Public on Jul 09 2006

city: Berlin

first: Joerg

last: Isensee

address: Hessische Str. 3-4

department: Center for Cardiovascular Research

country: Germany

institute: Charite Berlin

summary:
In this study cDNA microarrays were used to identify genes with sex-biased expression in mouse whole hearts of two age classes (2 months and 8 months of age).
Keywords: cDNA microarray hybridization, sex-specific expression

overall_design: A total of 24 male and female C57BL/6 mice were sacrificed at two and eight months of age, respectively (n=6 per group). Isolated total RNAs were pooled according to sex and age and hybridized on Agilent cDNA microarrays (age-matched, male vs. female or vice versa). Four technical replicates were carried out with exchanged dye-labelled RNA probes (dye-swap) on two of them.

middle: J

first: Henning

last: Witt

first: Patricia

middle: P

last: Ruiz


title: Aromatics Degradation in Geobacter metallireducens

status: Public on Jul 03 2007

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

summary:
Geobacter metallireducens serves as the model for Geobacter species that anaerobically oxidize aromatic contaminants with the reduction of Fe(III) oxides in contaminated sediments.  Analysis of the complete G. metallireducens genome sequence revealed a 307 kb region, designated the aromatics island, not found in closely related species that do not degrade aromatics.  This region encoded enzymes for the degradation of benzoate and other aromatic compounds with the exception of the genes for the conversion of toluene to benzyol-CoA which were in a different region of the genome.  Predicted aromatic degradation pathways were similar to those described in more well-studied organisms except that no genes encoding a benzoyl-CoA reductase were present. A genome-wide comparison of gene transcript levels during growth on benzoate versus growth on acetate demonstrated that the majority of the most significant increases in transcript levels were among genes within the aromatics island. Of particular interest were highly expressed genes that encode redox proteins of unknown function, one of which had a homolog outside the aromatics island that was also highly expressed. There was also an apparent shift in the acetyl-CoA oxidation pathway to the use of a putative ATP-yielding succinyl-CoA synthase during growth on benzoate.  These results provide new insights into the pathways for the degradation of aromatic compounds in G. metallireducens, indicate genes whose role in benzoate metabolism need to be evaluated further, and suggest target genes whose expression may be monitored in order to better assess the degradation of aromatic compounds in contaminated environments.
Keywords: Metabolism

overall_design: G. metallireducens GS-15 from our laboratory culture collection was cultured at 30°C in electron donor limited chemostats.  The dilution rate was 0.05 h-1 with acetate (5 mM) or benzoate (1.25 mM) provided as the electron donor and ferric citrate (55mM) as the electron acceptor. Cells were harvested from three replicate chemostats for each of the electron donors. 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) The dye swap hybridization was repeated for all samples, yielding 12 hybridizations in total.

first: Jessica

last: Butler

first: Zhili

first: Jizhong

last: Zhou

first: Kelly

last: Nevin

first: Derek

last: Lovley