title: Global gene expression profile of small intestine from wild-type and NHE2-knockout mice.

first: Gary

last: Shull

address: 231 Albert Sabin Way ML0524

summary: The objective of this study was to identify changes in gene expression levels between wild-type and NHE2-knockout small intestine.

overall_design:
8 wild-type and 8 NHE2-knockout small intestine RNA samples were compared.  Total RNA was collected from both male and female 8-week old wild-type and NHE2-null mice on an inbred FVB\N background. All comparisons were done between wild-type and NHE2-null samples from age- and gender-matched mice.
NHE2 Small Intestine Arrays
Cy3
253 +/+  male
262 +/+  male
265 +/+  female
274 +/+  female
231 -/-  female
292 -/-   male
296 -/-   female
299 -/-   female
Cy5
247 -/-   male
263  -/-  male
264 -/-   female
275 -/-  female
229 +/+    female
290 +/+  male
295 +/+  female
302 +/+   female

middle: E

first: Emily

last: Bradford


title: Human Dox+ vs Dox-

status: Public on Dec 01 2010

city: Daejon

first: Park

last: Jinwoo

country: South Korea

institute: TOOLGEN

overall_design: This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.


title: Mouse_SAGE_P23_cerebellum

city: Columbus

first: Julie

last: Besco

state: OH

department: Pharmacology

country: USA

institute: The Ohio State University

summary: P23 C57BL6/J mouse cerebellum


title: SAGE profile of rat hippocampus mRNA from Wistar rats

city: Leiden

first: Nicole

last: Datson

department: Medical Pharmacology

country: Netherlands

institute: Leiden University


title: Association of replication restart proteins with sites of increased transcriptional activity in Bacillus subtilis

city: Nottingham

first: Panos

last: Soultanas

state: Nottinghamshire

address: University Park

department: School of Chemistry

country: United Kingdom

institute: University of Nottingham

type: Genome binding/occupancy profiling by array

summary: Antibodies against DnaD and DnaB were used to immunoprecipitate genome bound complexes of these proteins in fast growing and slow growing cells as well as in two strains with a constitutively induced Pxis promoter or repressed Pxis promoter. CHIP-chip analysis was then carried out to determine their sites of interaction in vivo. CHI-chip analysis was carried out by Oxford Gene Technology (OGT) wwho also designed and prepared the arrays.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Antibodies against DnaD and DnaB were used to immunoprecipitate genome bound complexes of these proteins in fast growing and slow growing cells, as well as in two strains with a constitutively induced Pxis promoter or repressed Pxis promoter. CHIP-chip microarray analysis was carried out by OGT who obtained the raw data. Data were visualized in CHIP Browser provided by OGT.


title: Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (wild type vs. LitR mutant)

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

summary: Bacterial small RNAs (sRNAs) are trans-encoded regulatory RNAs that typically bind mRNAs by short sequence complementarities and change the expression of the corresponding proteins. Some of the well characterized sRNAs serve critical steps in the regulation of important cellular processes, such as quorum sensing (Qrr), iron homeostasis (RyhB), oxidative stress (OxyS) and carbon metabolism (Spot42). However, many sRNAs remains to be identified, and the functional roles of sRNAs are known for only a small fraction. For example, of the hundreds of candidate sRNAs from members of the bacterial family Vibrionaceae the function is known for only nine. We have in this study significantly contributed to the discovery and verification of new sRNAs in a representative of Vibrioneceae, i.e., the A. salmonicida which causes severe disease in farmed Atlantic salmon and other fishes. A computational search for intergenic non-coding (nc) RNAs in the 4.6 Mb genome identified a total of 233 potential sRNAs and 19 other types of ncRNAs with homologs in Rfam. Depending on a set threshold value our microarray approach identified 50-80 sRNAs that are expressed under different growth conditions, twelve of which were verified by Northern blot analysis. In total our data identify nine previously unrecognized sRNAs.

overall_design: Two-condition experiment, wild type cells (control samples) vs. LitR mutants grown in LB medium (stimulated samples). Samples collected from three different optical densities (OD600nm 0.15, OD600nm 0.5 and OD600nm 0.8). Technical replicates for each sample point: 3 control, 3 stimulated, independently grown and harvested. One replicate per array.

first: Rafi

last: Ahmad

first: Geir

middle: A

last: Hansen

first: Hilde

first: May

middle: J

last: Nyrud

first: Nils-Peder

last: Willassen

first: Peik

last: Haugen


city: San Francisco

first: Lauren

middle: N

last: Booth

state: CA

address: 600 16th Street, N374

department: Micobiology and Immunology

institute: University of California, San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary:
ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1).  The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein.
For the RME1 ChIPs, the cells grown with out phosphate.  For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD.

overall_design: Epitope tagged strains were compared to untagged control strains.  Two biological replicates were preformed for the RME1 ChIP.  For the MATa1 and MATalpha2 ChIP, peaks were considered indicative of binding if both MATa1 and MATalpha2 showed enrichment above the untagged control.

first: Brian

middle: B

last: Tuch

first: Alexander

middle: D

last: Johnson


title: SAGE analysis of cardiac fibroblasts isolated from adult mouse heart

city: Dublin

first: Albert

middle: Peter

last: Smolenski

address: Belfield

department: Conway Institute

country: Ireland

institute: University College Dublin

summary:
Cardiac fibroblasts were isolated from 3-month old C57BL/6 mice.
RNA was prepared from quiescent, serum-starved cardiac fibroblasts in passage 15.
A total number of 118654 tags was sequenced. After removal of duplicate ditags and linker-derived sequences 110169 tags remained.


title: SAGE libraries from mouse

city: Baltimore

first: Kenneth

middle: R.

last: Boheler

state: MD

address: 5600 Nathan Shock Drive

department: GRC

institute: National Institute on Aging, NIH

summary: SAGE libraries from mouse


title: Molecular events of apical bud formation in white spruce

city: Edmonton

first: Chelsea

last: Ju

state: Alberta

address: CW 405, Biological Sciences Centre

department: Biological Sciences

country: Canada

institute: University of Alberta

summary: Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome-level changes that occur during bud formation of white spruce (Picea glauca [Moench] Voss.), a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day-induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod-responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for ABA, cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues.  These findings provide a temporal roadmap of bud formation in white spruce.

overall_design:
Shoot tips (terminal buds), needles, and secondary stems were collected from two-year-old white spruce plants over a 10-week time course of 0, 1, 3, 7, 14, 28, and 70 days after switching from 6 to 8 weeks of long daylight photoperiods (LD; 16 hours of light and 8 hours of dark) to short daylight photoperiods (SD; 8 hours of daylight and 16 hours of dark). Remaining plants were kept in short days for an additional 8-15 weeks, and then transferred to low temperature (LT; 2°C to 4°C) for 3 to 4 weeks with continuing SD prior to harvest. Another set of plants was grown and harvested under the same conditions as described above, but remained in LD at all times.

Four sets of dye-swap design microarray experiments were conducted. The first set of experiments (samples 1-7) studied the SD time course of buds development. Terminal buds from each time point (1d, 3d, 7d, 14d, 28d, and 70d) and LT were co-hybridized with actively growing shoot tips (0d). The same time point comparison (without LT) of shoot tips from LD-treated trees was carried out as the second set of experiments (samples 8-13). The third experiment (samples 14-20) denoted a separate LD/SD comparison at seven different time points (0d, 1d, 3d, 7d, 14d, 28d, and 70d), and the last experiment (samples 21-26) compared SD shoot tips, needles, and secondary stems with each of the other tissues at 14d and 70d. In each experiment, four biological replicates were used, with two replicates representing the dye-swaps.

first: Walid

last: El Kayal

first: Carmen

middle: C

last: Allen

first: Eri

last: Adams

first: Susanne

last: King-Jones

first: Suzanne

last: Abrams

first: Janice

last: Cooke


title: Gene Expression Arrays comparing wild-type Kluyveromyces lactis a, alpha, and a/alpha cells and a comparison between WT a cells and rme1 knock-out a cells

summary: WT and rme1 KO K. lactis cells (a, alpha, and a/alpha) were grown in YEPD, phosphate starvation and phosphate starvation with the addition of alpha pheromone. The goal was to identify cell-type regulated genes and to determine the effects of growth media on the regulation of cell-type regulated genes

overall_design: Expression was measured relative to pooled references, note that only the arrays with matched pooled references can be compared to each other


title: Chip-chip from wt and ino80 mutant cells with Htz1

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

summary:
Global regulation of H2A.Z localization by the INO80 chromatin remodeling enzyme is essential for genome integrity.
Chromatin immunoprecipitation (ChIP) of Htz1 in wild-type and ino80 mutant yeast demonstrated that Ino80 plays a role in replacing Htz1 with H2A.

overall_design:
Comparison of Htz1 localization in wt vs ino80 mutant yeast
Prior to immunoprecipitation, cells arrested with alpha-factor or nocodazole:
- The alpha-factor mating pheromone arrests yeast of the a mating type in the G1 phase of the cell cycle.
- Nocodazole disrupts the polymerization of microtubules, blocking the cells from entering mitosis and arresting them in the G2/M phase of the cell cycle.

first: Manolis

last: Papamichos-Chronakis

first: Shinya

last: Watanabe

first: Craig

last: Peterson


title: Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

institute: Toronto General Research Institute

summary:
Background: Type I interferons (IFNs) are essential to the clearance of viral diseases, in part by initiating upregulation of IFN regulated genes (IRGs).  A clear distinction between genes upregulated directly by virus and genes upregulated by secondary IFN production has not been made. Here we investigated the genes regulated by IFN-a2b compared to the genes regulated by SARS-CoV infection in ferrets.
Methods: We characterized early host immune responses in  peripheral blood and lung necropsies of ferrets injected with IFN-a2b or infected with SARS-CoV/Tor 2 strain, using microarray analysis on the Affymetrix platform.
Results: We identified a common IRG signature that was upregulated in both SARS-CoV infected ferrets as well as in ferrets injected with IFN-a2b. We also identified unique patterns of gene expression for leukocyte activation, cell adhesion and complement pathways between IFN-a2b injection and SARS-CoV infection.
Conclusions: Our results define the effects of IFN-a2b on the immune system of ferrets highlighting genes regulated by IFN during SARS-CoV infection. We have shown the similarities and differences of top funcional gene groups as well as pathways that play key roles in early immune responses in ferrets in response to IFN-a2b or SARS-CoV.
Key words: ferret, gene expression, SARS, interferon.

Keywords: time course

overall_design: In experiments with IFN-a2b, for peripheral blood, 15 ferrets were randomly allocated to 3 groups: Day 0, 5 ferrets (no IFN injection), day 1, 6 ferrets (injected), and day 2, 4 ferrets (injected). For lung necropsies of injected ferrets with IFN-a2b, we used 12 ferrets in 3 groups: 4 ferrets, day 0 (no IFN injection), 4 ferrets, day 1 (injected) and 4 ferrets, day 2 (injected). Experimental groups for SARS-CoV infection was as follows: For peripheral blood, 3 and 4 ferrets for day 0 (no infection) and day 2 (infection) respectively. For lung neceropsies, a total of 9 ferrets in 3 groups, each with 3 replicates for day 0 (no infection), day 1 (infection) and day 2 (infection).

first: David

last: Kelvin


title: Expression profile of contrasting maize genotypes grown in acid and control soil (leaves)

city: Campinas

first: Marcelo

last: Menossi

state: SP

address: Rua Monteiro Lobato, 255, Instituto de Biologia, Departamento de Genetica, Evolucao e Bioagentes

department: Genetica, Evolucao e Bioagentes

country: Brazil

institute: Marcelo Menossi

summary:
Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality.
We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance.

overall_design: Leaves from Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive) maize genotypes were harvested after growing on acid or control soil for 3 days. Total RNA was extracted and hybridized to Affymetrix GeneChip Maize Genome Array. Three biological replicates were used for each sample.

first: Lucia

last: Mattiello

first: Matias

last: Kirst

first: Renato

last: Jorge


title: Target of Ascl1 in CG4 cell

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: To identify the downstream targets of transcription factor Ascl1, transcriptional profiling of rat glial cell line, CG4 cell, transfected with either Ascl1 or mock control was performed.

overall_design: Comparison was performed between Ascl1 overexpressing CG4 cell and mock control transduced cell on 3D-Gene rat mRNA oligo 12k chip. Biological replication was not prepared. The results were confirmed by real time RT-PCR in several genes.

first: Toru

last: Ogata

first: Takaaki

last: Ueno


title: Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (LB medium vs. iron-limited condition)

first: Erik

last: Hjerde

overall_design: Two-condition experiment, cells grown in LB medium (control samples) vs. cells grown under iron-limited conditions (2,2`-dipyridyl) (stimulated samples). Samples collected from three different timepoints (15, 30 and 60 min). Technical replicates for each timepoint: 3 control, 3 stimulated, independently grown and harvested. One replicate per array.

first: Rafi

last: Ahmad

first: Geir

last: Hansen

first: Hilde

first: May

middle: L

last: Nyrud

first: Nils-Peder

last: Willassen

first: Peik

last: Haugen


title: MicroRNAs and Their Predicted TargetMessenger RNAs are Deregulated by Exposure to a Carcinogenic Dose of Comfrey in Rat Liver

city: Jefferson

first: Zhiguang Li

state: AR

address: HFT130, 3900 NCTR Road

department: Division of Genetic an Reproductive Toxicology

institute: National Center for Toxicological Research

summary: MicroRNAs (miRNAs) are small non-coding RNAs that function as regulators of gene expression to control cell growth and differentiation.  MiRNA levels are substantially altered in various types of tumors and have been used as biomarkers in defining malignant status.  However, studies on responses of miRNA expression to carcinogen insults in their target tissues are rare.  In this study, we analyzed miRNA expression in the livers of rats treated with carcinogenic dose of comfrey (Symphytum officinale), a rat botanical carcinogen.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Groups of 6 Big Blue Fisher 344 rats were fed a normal diet or a diet containing 8% comfrey root for 12 weeks.  The animals were sacrificed one day after the last treatment and the livers were isolated from the control and treated rats for miRNA expression analysis.  The miRNA expressions were determined using miRNA microarrays for human, mouse and rat (LC Sciences).  Data were normalized using cyclic method and statistically analyzed using Ttest.

first: Zhiguang

last: Li

first: James

last: Fuscoe

first: Tao

last: Chen


title: Smallpox vaccination with LC16m8 vaccinia virus provides a gene expression profile similar to DryVax vaccination

city: Boston

first: Judy

last: Yen

address: 620 Albany St., Rm 401H

department: NEIDL/Microbiology

institute: Boston University School of Medicine

summary: Transcriptional analysis of global gene expression changes in naïve subjects in response to smallpox vaccination with either DryVax or the replication-competent, attenuated LC16m8 vaccinia virus.

overall_design: Subjects were vaccinated with either DryVax or LC16m8 (5 from each group), and blood samples were taken at days 0, 3, 7, 10, 13, and 21 post-vaccination.  PBMCs were isolated from the samples, and were then further separated into cell subpopulations using positive selection against CD markers (CD4+, CD20+).  There are a total of 142 samples analyzed in this dataset.

middle: Y

first: Cornelia

last: Dekker

first: David

last: Relman

first: Kathleen

middle: H

last: Rubins


title: Metastatic Cascade is Reflected in the Gene Expression of Metastatic Canine Mammary Carcinomas Similar to Human Breast Cancer

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

country: Germany

institute: Charité-Universitätsmedizin Berlin

summary: Proliferation, dedifferentiation, loss of cell-cell contacts and angiogenesis are among the first steps of the metastasis cascade. The complex molecular pathways associated with these events in canine mammary tumors are mostly unknown and the value of this spontaneous canine tumor as a comparative model for human breast cancer is therefore still under debate. Messenger RNA profiles of lymph-node positive canine mammary carcinomas and normal mammary glands of the same dogs were compared by microarray analysis to elucidate molecular pathways associated with metastatic progression. Differential gene expression was analyzed by gene set enrichment and pathway analysis and compared with the gene expression data of human breast cancer. Metastatic canine carcinomas had 1,312 significantly differentially expressed genes when compared to the corresponding normal mammary gland. This expression profile included a significantly increased expression of cell division and extracellular matrix invasion genes (MMP1, MMP11, MMP13, SERPINE1, TFPI2, TIMP3). In contrast, genes associated with epithelial differentiation (EGF, EGFR, KRT17, MAP2K6, STAT5), cell adhesion (CLDN5, CLDN8, CTNNAL1, MCAM, MUC1, PECAM1) and angiogenesis (ANGPT2, ANGPTL1, ANGPTL2, ANGPTL4, FGFR1, FIGF, TIE1) were mostly down-regulated. Interestingly, tumors had a significant decrease in membrane receptors and growth factor pathway gene expression (EGFR, FGFR1, GHR, LYVE1, PDGFR, PDGFR, TGFBR, TIE1), indicating a potential independence from these proliferative stimuli. Several of the identified deregulated pathways overlap with gene expression profiles of human breast cancer. Gene expression profiling of metastatic carcinomas therefore  identified complex molecular pathways and functional gene families that are deregulated during malignant progression in the tumors. This study provides new insights into canine mammary tumor metastasis and suggests that canine mammary tumors may serve as a valuable model for the human disease.

overall_design: 13 simple mammary carcinomas with lymph node metastases at the time of tumor resection were compared with the non-neoplastic mammary gland of the same dogs. Sufficient amounts of normal mammary gland were not available for dogs no. 1 (822) and 9 (61). In addition, one normal sample without matching tumor sample was analyzed (no. 8; 2609). All patients had no radiographically detectable pulmonary metastases at the time of tumor resection. Postoperative survival was analyzed by bi-yearly telephone interviews with the owners or the attending veterinarian. Distant metastases as the cause of death were determined postoperatively by radiographic detection of metastases (nos. 1-7, 9-12) or necropsy (nos. 13 and 14). Necropsy was not authorized by the owners of dogs nos. 1-7 and 9-12. Tissue specimens of tumors and lymph node metastases were fixed in neutral-buffered 4% formalin or snap frozen in liquid nitrogen within 15 minutes after resection and stored at -80ºC until further use. Formalin-fixed tumor tissue samples were routinely embedded in paraffin and sections of 2-μm thickness were mounted on adhesive glass slides and stained with hematoxylin and eosin. Tumors and lymph nodes were evaluated histologically independently by two board-certified pathologists, following the criteria of the WHO classification of canine mammary tumors (Misdorp et al. 1999).

first: Robert

last: Klopfleisch

first: Michael

last: Hummel

first: Achim

last: Gruber


title: Pre-Collaborative Cross liver gene expression

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary:
The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics.  The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding.  Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform.  The genetic profile of these emerging lines reveals high diversity, balanced allele frequencies, and well-distributed recombination – all ideal qualities for a mapping panel.  We have mapped white spot, a discrete trait; body weight, a highly polygenic complex trait; and more than 11,000 liver gene expression traits.  These analyses provide a glimpse of the potential mapping power and resolution of the CC.
The goal of this project was to identify eQTLs for genome-wide gene expression from liver tissue in pre-CC mice.

overall_design: Gene expression profiling from liver tissue from pre-CC males. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1),  A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 4-11 generations. One animal was sampled from 157 pre-CC strain. Hybridizations were performed at the Gene Expression Core Facility at The Jackson Laboratory. Samples were divided in six batches of about 11 to 24 samples. Two batches were performed per day. Probe-level data was summarized by a custom CDF file based on Ensembl genes (NCBI 37, Ensembl 49; htttp://brainarray.mbni.med.umich.edu).  The parental strains are not part of this submission.

last: Aylor

first: Ralph

middle: S

last: Baric

first: Timothy

last: Bell

first: Lisa

middle: R

last: Branstetter

first: Karl

middle: W

last: Broman

first: Ryan

last: Buus

first: John

last: Calaway

first: Elissa

last: Chesler

first: Gary

last: Churchill

first: Francis

last: Collins

middle: P

last: Didion

first: Caroline

last: Durrant

first: Martin

middle: T

last: Ferris

first: Wendy

last: Foulds-Mathes

first: Jeff

last: Frelinger

first: Matt

last: Frieman

last: Gralinski

first: Mark

last: Heise

first: Kunjie

last: Hua

first: Fuad

last: Iraqi

first: Samir

last: Kelada

first: Ron

last: Korstanje

first: Yi

last: Liu

first: Leonard

last: McMillan

first: Darla

last: Miller

first: Richard

last: Mott

first: Derrick

last: Nehrenberg

first: Fernando

last: Pardo-Manuel de Villena

first: Daniel

last: Pomp

first: Christine

last: Powell

first: Abhishek

last: Sarkar

last: Schwartz

first: Jason

last: Spence

first: Jill

last: Steigerwalt

last: Threadgill


title: DEVELOPMENTAL MicroRNA EXPRESSION PROFILING OF MURINE NEURAL TUBE

city: louisville

first: Guy

last: Brock

state: KY

address: 485 E. Gray St

department: Bioinformatics and Biostatistics

institute: University of Louisville

summary:
BACKGROUND: Development of the neural tube is a highly orchestrated process relying on precise, spatio-temporal expression of numerous genes as well as hierarchies of signal transduction and gene regulatory networks. Disruption of expression of a number of genes participating in these networks is believed to underlie developmental anomalies such as neural tube defects (NTDs) resulting from anomalous neural tube morphogenesis. MicroRNAs (miRNAs), a large family of noncoding RNAs, have been shown to function as gene silencers, and thus, are key modulators of cell and tissue differentiation. To elucidate potential roles of miRNAs in murine neural tube development, miRNA gene expression profiling has been utilized in the current study, to garner novel and in-depth knowledge on the expression and regulation of genes encoding miRNAs as well as their potential target genes governing maturation of the mammalian neural tube.
METHODS: With the aim of identifying differentially expressed miRNAs during mammalian neural tube ontogenesis, miRNA expression profiles from gestation day (GD) -8.5, -9.0 and -9.5 murine neural tube tissue were compared utilizing miRXplore™ microarrays from Miltenyi Biotech GmbH. Gene expression changes observed in microarray analysis were verified by TaqManTM quantitative Real-Time PCR. clValid R package and the UPGMA (hierarchical) clustering method were utilized for cluster analysis of the microarray data. Functional associations among selected miRNAs were examined exploiting Ingenuity Pathway Analysis.
RESULTS: Expression of approximately 12% of the 609 murine miRNA genes examined was detected in murine neural tube tissues from GD -8.5, -9.0 and -9.5. Clustering analysis revealed several developmentally regulated clusters among these expressed genes. MicroRNA target analysis enabled identification of a panoply of protein-coding target genes of the differentially expressed miRNAs within such clusters. Interestingly, many of these target genes have been shown to be associated with vital cellular processes such as cell proliferation, cell adhesion, cell migration, differentiation, apoptosis and epithelial-mesenchymal transformation, all of which are essential for normal neural tube development. Utilization of Ingenuity Pathway Analysis (IPA; Ingenuity Systems) allowed identification of interactive biological networks connecting differentially expressed miRNAs and their target genes highlighting functional relationships.
CONCLUSIONS: In the present study, a unique gene expression signature of a range of miRNAs in embryonic neural tube tissue was delineated. Analysis of miRNA target genes and gene interaction pathways emphasized that expression of numerous protein-encoding genes, indispensable for normal neural tube morphogenesis, may be regulated by specific miRNAs.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Time-course experiment (Developmental Stages), ICR mice embryos on gestational days (GD) 8.5, 9.0 and 9.5.  Biological replicates: For each day of gestation, 3 independent pools of 15 to 20 staged embryos were used to procure embryonic orofacial tissues for preparation of 3 distinct pools of RNA that were independently processed and applied to individual miRXplore™ microRNA Microarray chips (Miltenyi Biotec GmbH).  Technology: 2-color spotted cDNA, Hy5 (experimental sample) vs. Hy3 (control - miRXplore Universal Reference).

first: Partha

last: Mukhopadhyay

first: Savitri

last: Appana

first: Cynthia

last: Webb

first: M

middle: M

last: Pisano

first: Robert

last: Greene


title: Stable expression of intracellular Notch suppresses v-Src-induced transformation in avian neural cells

city: orsay

first: georges

last: calothy

address: Bat.110-Centre Universitaire

country: France

institute: institut curie

summary:
We reported that stable expression of constitutively active intra cellular Notch (ICN), in quail neuroretina (QNR) cells transformed by a conditional v-Src mutant (QNR/v-src cells), resulted in the suppression of their transformed properties. Acquisition of a normal phenotype coincided with a major switch in cell identity, as these undifferentiated QNR/v-src cells acquired characteristics of glial differentiation. Similar loss of transformation and gene reprogramming can be achieved in QNR/v-src cells, stably expressing the human CBF protein, RBP-Jk, whose activity was rendered ligand independent by fusion to the VP16 transactivator. These major phenotypic changed are correlated with a dominant interference with signaling effectors, regulating cell morphology and cytoskeleton organization.
To understand the mechanisms by which Notch signaling activation suppressed v-Src induced cell transformation and induced differentiation, we compared the transcription profile of QNR cells transformed by a v-Src mutant encoding a temperature sensitive oncoprotein (QNR/v-src), with that of cells stably expressing ICN (QNR/v-src/ICN) or RBP-Jk-VP16 (QNR/v-src/RBP-Jk-VP16).

overall_design: Total RNA was extracted from QNR/v-src, QNR/v-src/ICN or QNR/v-src/RBP-Jk-VP16 cells maintained at permissive (37°C) or restrictive (41°C) temperature. cDNA from QNR/v-src cells was probed with that of QNR/v-src/ICN or QNR/v-src/RBP-Jk-VP16 at both temperature on microarrays spotted with 13,000 cDNA from chicken EST collections designed by the genomic facility of the Fred Hutchinson Cancer Research Center (Seattle). For two sets of sample, dye swap experiments were performed.

first: Samira

last: Amarir

first: Maria

last: Marx

first: Georges

last: Calothy


title: Study the epidermal regulation of mesenchymal tissue behavior using a novel rabbit animal model

city: Boulder

first: Corrie

last: Gallant-Behm

state: CO

address: 347 UCB

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado at Boulder

summary: In order to identify tissue specific differences in epithelial behavior following injury, we developed a novel animal model of epithelial-restricted injury in the New Zealand White rabbit. A grid of shallow incisional wounds, which extended through the entire epithelium but did not significantly damage the underlying connective tissue, were created on the skin and vaginal mucosa, and samples were taken at various times post-surgery for histology and molecular analysis. All wounds were completely re-epithelialized between 1 and 2 days post-surgery.

overall_design: A microarray analysis was performed on RNA extracted from the cutaneous and mucosal epithelium at 0 hour, 12 hours, 1 day, 3 days, and 5 days following injury, as well as unwounded control tissue. Multiple biological replicates (4 to 6 biological replicates) were measured at each condition. A custom Agilent 4x44K rabbit microarray was utilized.


title: Methylated DNA Immunoprecipitation (MeDIP) using a custom type 2 diabetes and related phenotypes array

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

institute: UCL Cancer Institute

type: Methylation profiling by genome tiling array

summary: Custom array designed to tile Linkage Disequilibrium Blocks of T2D GWAS SNPs, monogenic candidates for T2D and Obesity, and all plausible imprinted loci from human and mouse data.

overall_design: Case Control comparison of MeDIP for Type 2 Diabetes. MeDIP versus Input fraction.

first: Christopher

middle: G

last: Bell

middle: A


title: Metastatic Canine Mammary Carcinomas

first: Dido

last: Lenze

summary:
[original title] Metastatic Canine Mammary Carcinomas can be Identified by a Gene Expression Profile that partly Overlaps with Human Breast Cancer Profiles.

Introduction:  Similar to human breast cancer mammary tumors of the female dog are commonly associated with a fatal outcome due to the development of distant metastases. However, the molecular defects leading to metastasis are largely unknown and the value of canine mammary carcinoma as a model for human breast cancer is unclear. In this study, we analyzed the gene expression signatures associated with mammary tumor metastasis and asked for parallels with the human equivalent.
Methods:  Messenger RNA expression profiles of twenty-seven lymph node metastasis positive or negative canine mammary carcinomas were established by microarray analysis. Differentially expressed genes were functionally characterized and associated with molecular pathways. The findings were also correlated with published data on human breast cancer.
Results:  Metastatic canine mammary carcinomas had 1,011 significantly differentially expressed genes when compared to non-metastatic carcinomas. Metastatic carcinomas had a significant up-regulation of genes associated with cell cycle regulation, matrix modulation, protein folding and proteasomal degradation whereas cell differentiation genes, growth factor pathway genes and regulators of actin organization were significantly down-regulated. Interestingly, 265 of the 1,011 differentially expressed canine genes are also related to human breast cancer and, vice versa, parts of a human prognostic gene signature were identified in the expression profiles of the metastatic canine tumors.
Conclusions:  Metastatic canine mammary carcinomas can be discriminated from non-metastatic carcinomas by their gene expression profiles. More than one third of the differentially expressed genes are also described of relevance for human breast cancer. Many of the differentially expressed genes are linked to functions and pathways which appear to be relevant for the induction and maintenance of metastatic progression and may represent new therapeutic targets. Furthermore, dogs are in some aspects suitable as a translational model for human breast tumors in order to identify prognostic molecular signatures and potential therapeutic targets.

overall_design: Thirteen simple mammary carcinomas with invasive growth and lymph node metastases at the time of tumor resection and 14 simple carcinomas without lymph node metastases were included in the study. None of the patients had radiographically detectable pulmonary metastases at the time of tumor resection. Distant metastases as the cause of death were determined postoperatively by radiographic detection of metastases or necropsy. Selection criteria for carcinomas without lymph node metastases included an invasive growth, a negative lymph node status, a histological grade III and a minimal tumor diameter above the average of the lymph node positive tumors (> 2.42 cm). All animals with non-metastatic carcinomas had a survival rate of over 24 months except animal no. 22 (2627) which developed radiographic detectable lung metastases 8 months after surgery. Tumor and lymph node histologies were evaluated independently by two board-certified pathologists, following the criteria of the WHO classification of canine mammary tumors and the Nottingham grading system. All 27 tumors were simple carcinomas and characterized by an invasive, mostly solid growth pattern, marked cellular pleomorphism, anisokaryosis and 3 or more mitotic figures per high power field.

last: Klopfleisch

first: Michael

last: Hummel

first: Achim

last: Gruber


city: Nanjing

first: miao

last: weiguo

address: Weigang

country: China

institute: Nanjing Agricultural Uiversity

summary:
Hpa1Xoo-Mediated Transcriptome in Transgenic Cotton Reveals the Constitutively Expressed Diverse Defense genes in Multiple Signaling Pathways Associated with Hypersensitive Cell Death

Like other harpins, harpinXoo enables plants to acquire multiple resistance to pathogen and insect attack. However, the molecular model is not fully understood, especially in transgenic plant harpinXoo for genome-wide constitutive expression. Here, we showed that 530 cDNAs differentially expressed in transgenic hpa1Xoo-harboring cotton (T-34) compared to its receiptor (Z35), through analyzing the transcriptome profile in a customized cotton 12k cDNA microarray, which was enriched in 34 pathways. Among them, 123 genes were identified from T-34 as hypersensitive reaction-mediated defense genes, involved in reactive oxygen species-, salicylic acid-, jasmonates-, ethylene-, auxin-, abscisic acid-, and Ca2+-mediated signaling pathways, and we uncovered various components of defense responses associated with recognition of the pathogen-derived elicitor. Apart from elevated genes for basic defense, harpinXoo activated leucine-rich-repeat plant receptor kinases and mitogen-activated protein kinase cascade to strengthen downstream defense responses, including production of antimicrobial compounds in T-34. Defense genes from T-34 were expressed at a much higher level in response to pathogen infection compared with Z35. Simultaneous up- and down-regulation in differentially-expressed genes, and increased expression of genes encoding energy producing and consuming pathways, suggested that energy balance was maintained in the genetically modified cotton without biotic stress. High-energy demand only occurred following pathogen infection.

overall_design: Using kanamycin-resistance tests, positive plants were successfully screened from transgenic cotton T-34 T6 progenies; all the receiptor Z35 plants gave negative results. We randomly selected three positive plants for polymerase chain reaction (PCR) analysis; the different positive bands (420, 310 and 180 bp) were confirmed as harpinXoo, the 35s promoter, and the NOS terminator, respectively, by sequencing and BLAST searches (www.ncbi.nlm.nih.gov.). For further analysis, the positive results were confirmed by Southern and western blots. Three positive bands were obtained in each T-34 sample located at about 4, 6 and 10 kb in the Southern blot. This pattern suggests that T-34 incorporated the harpinXoo transgene at multiple chromosomal locations. Western blot analysis showed that the harpinXoo protein was constitutively expressed in T-34 transgenic lines, whereas it was barely detectable in Z35 (data not shown).   The transgenic plants contained a selectable ‘marker’ gene, neomycin phosphotransferase II (nptII). Previous research showed that expression of marker genes (e.g. nptII, uidA, hph and uidA-gfp) did not contribute to visible phenotypes in transgenic plants. The non-targeted transgenic and non-transgenic plants were equivalent in their global patterns of transcription (El Ouakfaoui and Miki, 2005). Thus, the present study examined the many differences between T-34 and its receiptor Z35 in regard to the whole genome expression of G. hirsutum using microarrays to monitor changes in individual gene expression level effected by harpinXoo. All experiments were conducted using the 12k cotton cDNA microarray, and cotton true leaves and roots at the 4–5-true-leaf-stage. The use of this microarray enabled a quantitative approach to examine changes in transcript level for all genes within the G. hirsutum genome; as a result, inferences can be drawn regarding the molecular effects of transgenic cotton expressing harpinXoo. There were three biological replicates in the experiment for each organ.

first: Weiguo

last: Miao

first: Jinsheng

last: Wang


title: BES performance of S. oneidensis pure- and co-culture

city: Ithaca

first: Miriam

last: Rosenbaum

state: NY

address: 325 Riley-Robb Hall

department: Biological and Environmental Engineering

institute: Cornell University

summary: Bioelectrochemical systems employing mixed microbial communities as biocatalysts are gaining importance as potential renewable energy, bioremediation, or biosensing devices. While we are beginning to understand how individual microorganism species interact with an electrode as electron donor, not much is known about the interactions between different microbial species in a community. Here, we compare the bioelectrochemical performance of Shewanella oneidensis in a pure-culture and in a co-culture with the homolactic acid fermenter Lactococcus lactis. While S. oneidensis alone can only use lactate as electron donor for current production, the co-culture is able to convert glucose into current with a similar coulombic efficiency of approximately 17%, respectively. With (electro)-chemical analysis and transcription profiling, we found that the BES performance and S. oneidensis physiology were not significantly different whether grown as a pure- or co-culture. These co-culture experiments represent a first step in understanding microbial interactions in BES communities with the goal to design complex microbial communities, which specifically convert target substrates into electricity. Further, for the first time, we elucidated S. oneidensis gene expression with an electrode as the only electron acceptor. The expression pattern confirms many previous studies regarding the enzymatic requirements for electrode respiration, and it generates new hypotheses on the functions of proteins, which are so far not known to be involved in electrode respiration.

overall_design: The BES was either operated with S. oneidensis alone, fed with lactate, or it was operated with S. oneidensis and L. lactis with glucose as primary substrate. The basic medium was a modified M4 medium containing 0.5 g/L yeast extract, 0.5 g/L trypton and 5 g/L glycerol phosphate, besides the commen M4 incredients. S. oneidensis oxidizes lactate to acetate and electrons in a BES - the latter generate a current at a graphite anode. The anode biofilm was harvested after about 4 weeks of continuous BES operation and subjected to total RNA extraction.

first: Haim

last: Bar

first: Qasim

last: Beg

first: Largus

last: Angenent


title: Transcriptome analysis of Escherichia coli O157:H7 EDL933 inside Acanthamoeba using microarrays

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

summary: The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of intracellular life within a ruminant and environmental protozoan on E. coli O157:H7, global transcript levels of strain EDL933 cells inside Acanthamoeba were compared to cell grown in the protozoan media (ATCC PYG712) by microarray.

overall_design: Nine independent RNA samples from cell from within Acanthamoeba were paired with seven independent RNA samples from control cultures for hybridization to nine two-color microarrays. For four arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other five arrays to overcome dye bias.

last: Carruthers


title: Transcriptome analysis of Escherichia coli O157:H7 EDL933 during rumen fluid exposure using microarrays

summary: The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of rumen fluid on E. coli O157:H7, global transcript levels of strain EDL933 cells resuspended in heat clarified rumen fluid for 15 min were compared to cells resuspended in fresh LB using microarrays.

overall_design: Seven independent RNA samples from rumen fluid treated cultures were paired with seven independent RNA samples from control cultures for hybridization to seven two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other four arrays to overcome dye bias.

first: Nancy

last: Cornick


title: Transcriptome analysis of Escherichia coli O157:H7 EDL933 during anaerobic growth using microarrays

summary: The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of an anaerobic environment on E. coli O157:H7, global transcript levels of strain EDL933 cells grown aerobically were compared to cells grown anaerobically using microarrays.

overall_design: Eight independent RNA samples from aerobic cultures were paired with eight independent RNA samples from anaerobic cultures for hybridization to eight two-color microarrays. For four arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.

first: F.


title: Human lung tissue

status: Public on Nov 30 2010

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
Dr. Clausen's laboratory is interested in the structure, biosynthesis and genetic regulation of glycoconjugates, with a major focus on mucins. This laboratory is studying the glycosylation and secretion process of mucins and biological functions involving mucins. This lab is also interested in receptor modulation mediated by glycosylation or through glycosphingolipids.
We have a particular interest in understanding how mucin type O-glycosylation is regulated. Mucin type O-glycosylation is controlled by the ppGalNAc-transferase multigene family. An estimated 23 iso-forms belong to this family, so the specific involvement of each individual iso-form in any given organ seems complex to understand. An initial attempt to comprehend how this multigene family regulates mucin type O-glycosylation, is to get insight into which iso-forms are expressed in different organs and cell types. For this reason we have generated monoclonal antibodies towards 7 iso-forms, and the list of ppGalNAc-T iso-form specific monoclonals is currently growing. We have done some immuno histochemistry on lung using the available monoclonals, but are keen on assessing the number of ppGalNAc-T's expressed in lung as determined this Glyco-array. We have focused on lung because a number of ppGalNAc-T acceptor polypeptides, belonging to the mucin gene family, are expressed in this organ.

platform_organism:
Homo sapiens
Mus musculus

overall_design: An RNA sample pooled from two independent adult human healthy lung tissue samples was analyzed

first: Hentik

last: Clausen


title: microRNA profiling of mesenchymal stem cells from adipose tissue of differentially aged mice

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

country: Italy

institute: University of Verona

summary: The data presented here is part of a study aimed to investigate whether the gene expression profile of Polycomb, Trithorax and interacting molecules might be related to different states of differentiative potential.

overall_design: microRNA profiling (Exiqon miRCURY LNA array Version 9.2) has been performed on mesenchymal stem cells isolated from the inguinal fat pad of mice of 1 (n=2), 3(n=2), 6(n=2), 12(n=2) and 24(n=1) months of age.

first: Daniele

last: Peroni

first: Ilaria

last: Scambi


title: Gene expression analysis at the intersection of ploidy and hybridity in maize.

city: St. Louis

first: Nicole

middle: Christina

last: Riddle

state: MO

address: 1 Brookings Dr.; CB1137

department: Biology

institute: Washington University

summary: Heterosis and polyploidy are two important aspects of plant evolution. To examine these issues, we conducted a global gene expression study of a maize ploidy series as well as a set of tetraploid inbred and hybrid lines. This gene expression analysis complements an earlier phenotypic study of these same materials. We find that ploidy change affects a large fraction of the genome, albeit at low levels; gene expression changes rarely exceed 2-fold and are typically not statistically significant. The most common gene expression profile we detected is greater than linear increase from monoploid to diploid, and reductions from diploid to triploid and from triploid to tetraploid, a trend that mirrors plant stature. When examining heterosis in tetraploid maize lines, we found a large fraction of the genome impacted but the majority of changes were not statistically significant at 2-fold or less. Non-additive expression was common in the hybrids, and the extent of non-additivity increased both in number and magnitude from duplex to quadruplex hybrids. Overall, we find that gene expression trends mirror observations from the phenotypic studies; however, obvious mechanistic connections remain unknown.

overall_design: We examined gene expression in a ploidy series (1n to 4n) of the maize line B73 and in a variety of hybrid tetraploid lines using a complex loop design.  Pooled RNA samples from 10 plants were used (2 independent RNA isolations/sample), and all comparisons were made using replicate dye swaps (16 slide sets/comparison).  For the ploidy analysis, all expression changes were computed relative to the diploid as well as between 2n + 3n and 3n + 4n.  For the expression analysis of hybrids, hybrid expression levels were compared to the parental expression levels as well as to mid-parent levels.

first: Hongmei

last: Jiang

first: Lingling

last: An

first: Rebecca

last: Doerge

first: James

last: Birchler


title: PcG/TrxG profiling of differentially aged adipose-derived mesenchymal stem cells

summary: The microarray reported here is part of a study aimed to investigate whether the gene expression profile of Polycomb, Trithorax and interacting molecules (collectively referred to PcG/TrxG genes) might be related to different states of differentiative potential. In particular , this microarray profiles the expression of PcG/TrxG genes in adipose-derived mesenchymal stem cells isolated from the inguinal fat depot of mice of different age.

overall_design: MSC have been isolated from the inguinal fat pad of FVB mice aged 1, 3, 6, 12 or 24 months.


title: Biological cost of rifampicin resistance in Helicobacter pylori

city: Moscow

first: Kuvat

last: Momynaliev

address: Malaya Pirogovskaya 1A

country: Russia

institute: Research Institute for Phys-Chim Medicine

summary: The present study was aimed at analyzing (i) the biological cost of RNA polymerase (rpoB) mutations conferring rifampin resistance on H.pylori,  (ii) the relationship between the cost of rpoB mutations and the chromosomal mutaion, (iii) the relationship between the cost of rpoB mutations and the transcription profile of sensitive and resistantrif strains of H.pylori  (iv) and rpoB mutations in view of the possible fitness burden associated with resistance to another antibiotics.

overall_design: H.pylori reference strain 26695 was routinely maintained on Columbia agar plates  and H. pylori-selective antibiotic mix Dent. Liquid culture was grown in BHI broth. Both plates and broth cultures were incubated at 37C under atmosphere enriched with 5% CO2  for 2-3 days . Mutant strains were selected by culturing  H. pylori 26695 on selective plates containing rifampicin. In 5 days resistant colonies were picked up and passed under rifampicin pressure. RNA isolated was reverse transcribed and used to probe H. pylori home-made arrays

first: K

first: A

last: Klubin


title: Consequences of an in utero TCDD exposure on the male reproductive function in 5 postnatal days rat

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary:
Our project focuses on the effects of an in utero TCDD exposure on the male reproductive function.

Keywords: transcriptionnal analysis

overall_design: Pregnant rats were given either one oral dose of 2,3-7,8 TCDD (200 ng/kg) or equal volume of vehicule (sesame oil). Male rats were sacrified 5 postnatal days and testes were harvested. RNA were extracted with Rneasy mini kit. A pool of RNA from vehicule group was used as the reference group. Each rat submitted to TCDD was compared to reference group. Four biological replicates were processed in a dye swap experimental plan.

first: Diane

last: Rebourcet

first: Emmanuelle

last: Meugnier

first: Sandra

last: Pesenti

first: Hubert

last: Vidal

first: Brigitte

last: Le Magueresse-Battistoni


title: miRNA profiling by Agilent mouse miRNA microarray

city: Shanghai

first: Wenchao

last: Hu

address: 320 Yueyang Road

department: Functional Genomics Group

institute: CAS-MPG Partner Institute for Computational Biology

summary: miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. Mammalian hibernation is a physiological process involving dramatic metabolic suppression and cellular reorganization, during which miRNAs may play an important role. We systematically analyzed the miRNAs in the liver of an extreme hibernating species, arctic ground squirrels (Spermophilus parryii), during two stages of hibernation compared to non-hibernating animals by massively parallel Illumina sequencing technology. We identified more than 200 ground squirrel miRNAs including novel miRNAs specific to ground squirrel and a fast-evolving miRNA cluster that also showed significant differential expression during hibernation. Integrating with Agilent miRNA microarray and Real-time PCR results, we identified that mir-211, mir-378, mir-184, mir-200a, and mir-320 were significantly under-expressed during hibernation, whereas mir-144, mir-486, mir-451, mir-142-5p, and mir-1 were over-expressed. Analyses of the their target genes suggested that these miRNAs could play an important role to suppress tumor progression and cell growth during hibernation.

overall_design: Three total RNA pools from arctic ground squirrel livers in Early Arousal(EA), Late Topor(LT), and Post-Reproduction(PR) stages were hybridized to three Agilent mouse miRNA microarrays.

first: Yuting

last: Liu

first: Haifang

last: Wang

first: Chunxuan

last: Shao

first: Zheng

last: Yan

first: Sen

last: Zhao

first: Jun


title: Vastus lateralis muscle biopsy: post-expedition vs. pre-expedition

status: Public on Nov 27 2010

city: Chieti

first: Rosa

last: Mancinelli

state: Chieti

address: via Dei Vestini 29

department: Dept. Basic and Applied Medical Sciences

institute: University "G. d'Annunzio" Chieti-Pescara, Chieti

summary: To define the skeletal muscle adaptations induced by exercise performed at high altitude hypoxia, we investigated if the gene expression profile of Vastus lateralis muscle was affected by 5000 m-above-sl-expedition.

overall_design: Two-condition experiment, Vastus lateralis muscle biopsy post-expedition vs Vastus lateralis muscle biopsy pre-expedition. Five volunteers/climbers. Biological replicates: 1 pre-expedition sample, 1 post-expedition sample.


title: Phylogenetic, microbiological and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor

status: Public on Nov 29 2010

city: Raleigh

first: Robert

last: Kelly

state: MI

address: Campus Box 7905

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Phylogenetic, microbiological and comparative genomic analysis was used to examine the diversity among members of the genus Caldicellulosiruptor with an eye towards the capacity of these extremely thermophilic bacteria for degrading the complex carbohydrate content of plant biomass. Seven species from this genus (C. saccharolyticus, C. bescii (formerly Anaerocellum thermophilum), C. hydrothermalis, C. owensensis, C. kronotskyensis, C. lactoaceticus, and C. kristjanssonii) were compared on the basis of 16S rRNA phylogeny and cross-species DNA-DNA hybridization to a whole genome C. saccharolyticus oligonucleotide microarray. Growth physiology of the seven Caldicellulosiruptor species on a range of carbohydrates showed that, while all could be cultivated on acid pre-treated switchgrass, only C. saccharolyticus, C. besci, C. kronotskyensis, and C. lactoaceticus were capable of hydrolyzing Whatman No. 1 filter paper. Two-dimensional gel electrophoresis of the secretomes from cells grown on microcrystalline cellulose revealed that species capable of crystalline cellulose hydrolysis also had diverse secretome fingerprints.  The two-dimensional secretome of C. saccharolyticus revealed a prominent S-layer protein that appears to be also indicative of highly cellulolytic Caldicellulosiruptor species, suggesting a possible role in cell-substrate interaction.  These growth physiology results were also linked to glycoside hydrolase and carbohydrate-binding module inventories for the seven bacteria, deduced from draft genome sequence information.  These preliminary inventories indicated that the absence of a single glycoside hydrolase family and carbohydrate binding motif family appear to be responsible for some Caldicellulosiruptor species’ diminished cellulolytic capabilities. Overall, the genus Caldicellulosiruptor appears to contain more genomic and physiological diversity than previously reported, and is well suited for biomass deconstruction applications.

sample_organism:
Caldicellulosiruptor bescii
Caldicellulosiruptor saccharolyticus
Caldicellulosiruptor owensensis
Caldicellulosiruptor acetigenus
Caldicellulosiruptor hydrothermalis
Caldicellulosiruptor kronotskyensis

overall_design: Six dye-flip experiments were conducted using C. saccharolyticus genomic DNA as the reference in each dye-flip, and one of six different Caldicellulosiruptor spp. as a tester in each dye-flip

first: Sara

middle: E

last: Blumer-Schuette

first: Derrick

last: Lewis


title: Genome-wide copy number variation in human metastatic melanoma cell lines

status: Public on Nov 26 2010

city: Los Angeles

first: Mikyung

last: Lee

address: UCLA Med-Derm BOX 951781, 13-942 Factor, 13-952 Factor Los Angeles, CA 90095-1781

institute: UCLA

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Illumina HumanExon510S-DUO bead arrays (Illumina Inc) were performed according to the manufacturer's protocol.

overall_design: Genome-wide copy number variation analysis was performed on the genomic DNA of two pairs of cell lines comprising of parental melanoma cell lines and corresponding resistant sub-lines.

first: Roger

last: Lo

first: Ramin

last: Nazarian

first: Qi


title: Gene expression studies in apparently normal, paired normal and malignant gastric tissues

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

summary:
Gene expression profiling of apparently normal gastric tissue (obtained from patients undergoing gastric surgery for Non-gastric cancers), paired normals (obtained from the same stomach as the gastric cancer but confirmed by frozen section not to harbour any tumour cells) and gastric cancer, with an intent to identify genes involved in the malignant transformation of normal gastric mucosa and to identify genes which can be used as biomarkers for early diagnosis and potential targets for treatment
Identification of novel prognostic markers using microarray gene expression studies.

Keywords: Patient tissue samples

overall_design: Two-dye experiments using Universal control RNA (Stratagene) and RNA from tissues. Biological replicates: Apparently Normal = 5; Paired Normal = 20; Gastric cancers = 24. One replicate per array.

first: T

last: Rajkumar


title: Expression analysis of GFP+ and GFP- populations of B.subtilis strain DS901

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

institute: TNO

summary: Investigation of whole genome gene expression level changes in GFP+ and GFP- populations of B.subtilis strain DS901

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: An 8 chip study using total RNA recovered from B.subtilis strain DS901 (Phag-gfp). With a Cytopeia Influx cell sorter, cells were sorted in GFP+ and GFP- populations. Each B. subtilis subsp. subtilis strain 168 NC_000964 chip measures the expression level of 4,104 genes in two-fold from with eight 60-mer probe pairs (PM/MM) per gene.


title: Consequences of an in utero TCDD exposure on the male reproductive function in 28 postnatal days rat

first: emmanuelle

last: meugnier

overall_design: Pregnant rats were given either one oral dose of 2,3-7,8 TCDD (200 ng/kg) or equal volume of vehicule (sesame oil). Male rats were sacrified 28 postnatal days and testes were harvested. RNA were extracted with Rneasy mini kit. A pool of RNA from vehicule group was used as the reference group. Each rat submitted to TCDD was compared to reference group. Four biological replicates were processed in a dye swap experimental plan.

first: Diane

last: Rebourcet

first: Emmanuelle

last: Meugnier

first: Sandra

last: Pesenti

first: Hubert

last: Vidal

first: Brigitte

last: Le Magueresse-Battistoni


title: ArrayCGH of Trichoderma reesei strains QM9123, QM9414, NG14 and RutC-30

city: VTT, Espoo

first: Marika

last: Vitikainen

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre

type: Genome variation profiling by genome tiling array

summary:
Trichoderma reesei is the main industrial producer of cellulases and hemicellulases used to depolymerize biomass in many biotechnical applications. Many production strains in use have been generated by classical mutagenesis. In this study we characterized genomic alterations in hyperproducing mutants of T. reesei by high-resolution comparative genomic hybridisation tiling array.
We carried out aCGH analysis of four hyperproducing strains (QM9123, QM9414, NG14 and RutC-30) using QM6a genome as a reference. ArrayCGH analysis identified dozens of mutations in each strain analyzed.

overall_design: 2.1 million oligonucleotide probe custom aCGH (HD2 format, RocheNimblegen) was designed according to T. reesei strain QM6a genome v2.0 (http://genome.jgi-psf.org/Trire2/Trire2.home.html). 14 samples are included in this set; 3 replicates of each strain (except two replicates of QM9123) were analyzed (four mutant strains and QM6a control strain for self-hybridization)

first: Mikko

last: Arvas

first: Markku

last: Saloheimo


title: PI3K/mTOR specific phospho-antibody microarray to study the effect of rapamycin to the innate immune respsonse

status: Public on Nov 25 2010

city: louisville

first: huizhi

last: wang

state: kY

address: 501 S.Preston St. Room 211B

department: PEDH

institute: University of Louisville

summary: To comprehensively analyze the effects of mTORC1 inhibition on GSK3, we employed the use of a PI3K/mTOR-specific phospho-antibody microarray that analyzed the site-specific phosphorylation of over 130 kinases within the PI3K/mTOR pathway.  The phosphorylation levels of different kinases in monocytes were measured when stimulated with LPS in the presence or absence of a kind of mTORC1 inhibitor, rapamycin

overall_design: More than 130 highly specific and characterized phospho-antibodies for the human mTOR signaling pathway were immobilized and replicated six times on glass slides. The same non-phosphorylated target antibodies were included to allow the determination of the relative level of phosphorylatioin

first: Michael

last: Martin

first: Ruqiang

last: Liang

first: Huizhi


title: Induction of virulence genes in Listeria monocytogenes serotype 4b upon exposure to concentrations of biocides

type: Expression profiling by genome tiling array

summary: Study on genome-wide expression in L.monocytogenes str4b F2365 exposed to five different biocides at three different concentrations

sample_organism: Listeria monocytogenes serotype 4b str. F2365

overall_design: The study was carried out with a total of 34 microarrays using total RNA recovered from L.monocytogenes str4b F2365, which has been exposed for 1 hour (t =1) to five different biocides at three different concentrations (sub-inhibitory as well as inhibitory) in two-fold (30 exps). As reference samples, RNA of untreated cells were used in two-fold directly after pre-culturing (t=0) and after one hour of preculturing (t=1 hour; 4 exps). Each microarray read out includes expression levels of 2,821 genes from L.monocytogenes str4b F2365in two-fold, with a total of twelve 60-mer probe pairs (PM/MM) per gene.

first: Alie

middle: K

last: Angelino


title: Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer

city: Melbourne

first: Holger

last: Schlueter

state: Victoria

address: Locked Bag 1

country: Australia

institute: Peter Mac Callum cancer Centre

summary: Study aims: to identify critical genes involved in non-small cell lung cancer (NSCLC) pathogenesis that may lead to a more complete understanding of this disease and identify novel molecular targets for use in the development of more effective therapies. Methods: Both transcriptional and genomic profiling were performed on 69 resected NSCLC specimens and results correlated with mutational analyses and clinical data to identify genetic alterations associated with groups of interest.   Results: Combined analyses identified specific patterns of genetic alteration associated with adenocarcinoma vs. squamous differentiation; KRAS mutation; TP53 mutation, metastatic potential and disease recurrence and survival. Amplification of 3q was associated with mutations in TP53 in adenocarcinoma. A prognostic signature for disease recurrence, reflecting KRAS pathway activation, was validated in an independent test set.   Conclusions: These results may provide the first steps in identifying new predictive biomarkers and targets for novel therapies, thus improving outcomes for patients with this deadly disease.

overall_design: Transcriptional profiling of 82 samples of NSCLC using Peter MacCallum in-house 10,500 element cDNA microarray. RNA from 11 pooled cell lines used as reference for each sample. Replicate of 6 samples included.

first: Genni

last: Newnham

first: Matthew

last: Conron

first: SueAnne

last: McLachlan

first: Alexander

last: Dobrovic

first: Hongdo

last: Do

first: Jason

last: Li

first: Kenneth

last: Opeskin

first: Natalie

last: Thompson

first: Gavin

last: Wright

first: David

last: Thomas


title: Rat & M. fortis - lung and liver

first: Weibin

last: Jiang

address: 518,Ziyue ARd

institute: Shanghai Institute of Veterinary Research, Chinese Academy of Agricultural Sciences

summary: More than 40 kinds of mammals in China are known to be naturally infected with Schistosoma japonicum (S. japonicum); Microtus fortis (M. fortis), a species of vole, is the only mammal in which the schistosomes cannot mature or cause significant pathogenic changes. In the current study, we compared the differences in pathology by Hematoxylin-eosin staining and in changes in the T cell subsets with flow cytometry as well as gene expression using genome oligonucleotide microarrays in the lung and liver, before challenge and 10 days post-infection with schistosomes in a S. japonicum-susceptible mouse model of infection, a non-susceptible rat model and the non-permissive host, M. fortis. The results demonstrated that S. japonicum promoted a more intensive immune response and more pathological lesions in M. fortis and rats than in mice. Hematoxylin-eosin staining revealed that the immune effector cells involved were mainly eosinophilic granulocytes supplemented with heterophilic granulocytes and macrophages. The analysis of splenic T cell subsets showed that CD4+ T cell subsets and the CD4+/CD8+ ratio were increased while the CD8+ T cell subsets decreased remarkably in rats; whereas the CD8+ T cell subsets were increased but the CD4+/CD8+ ratio was decreased significantly in mice. The analysis of the pattern of gene expression suggested that some immune-associated genes and apoptosis-inducing genes upregulated while some development-associated genes were downregulated in the infected M. fortis compared to the uninfected controls; the three different hosts have different response mechanisms to schistosome infection. The results of this study will be helpful for identifying the key molecules in the immune response to S. japonicum in M. fortis and for understanding more about the underlying mechanism of the response, as well as for elucidating the interaction between S. japonicum and its hosts.

sample_organism:
Rattus norvegicus
Alexandromys fortis

overall_design:
Genes Differentially Expressed in lung and liver （rat and microtus fortis）before challenge and 10 days post-infection with Schistosoma japonicum.
Total RNA from the control tissue and infected tissue were used to generate target cDNA, and then hybridized to 27k Rat Genome Array Genechips, representing about 22000 characterized rat genes.

first: Jiaojiao

last: Lin


title: BA-Sulfate vs Sulfate starvation

city: Thiverval-Grignon

first: Marie-Pierre

last: FORQUIN

address: Aveniue de la Bretigniere

department: MICA

institute: INRA

summary: Study of sulfur metabolism in BA

overall_design: 3 biologic replicates

last: Forquin

first: Caroline

last: Proux


title: Instability of Acetate Kinase Mutants and Their Effects on Acetyl Phosphate and ATP Amounts in Streptococcus pneumoniae

city: Bloomington

first: Krystyna

last: Kazmierczak

state: IN

address: 1001 E. Third St.

institute: Indiana University

summary: Acetyl phosphate (AcP) is a small-molecule metabolite that can act as a phosphoryl group donor for response regulators of two-component regulatory systems (TCSs). Streptococcus pneumoniae (pneumococcus) synthesizes AcP by the conventional pathway involving the phosphotransacetylase and acetate kinase enzymes encoded by the pta and ackA genes, respectively. In addition, pneumococcus synthesizes copious amounts of AcP and hydrogen peroxide (H2O2) by the pyruvate oxidase enzyme encoded by spxB. To access possible roles of AcP in pneumococcal TCS regulation and metabolism, we constructed combinations of spxB, pta, and ackA mutants and determined their ATP, AcP, and H2O2 production. Epistasis and microarray experiments were consistent with a role for the AcP biosynthetic pathway in basal-level phosphorylation of WalRSpn and possibly other response regulators involved in sensing cell wall status. However, this basal phosphorylation likely does not play an active physiological role in sensing in S. pneumoniae.

overall_design:
Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.1 and were processed as described in the related Sample records. Strain IU1781 (D39 rpsL1) served as the reference for all strain comparisons. Samples were collected from the indicated number of independent biological replicates:
1) WalK-Janus_vsWT (Winkler strain IU1885 versus IU1781), 2 replicates including one dye swap
2) DeltaSpxB_vsWT (Winkler strain IU2173 versus IU1781), 2 replicates including one dye swap
3) DeltaPta_vsWT (Winkler strain IU2687 versus IU1781), 3 replicates including one dye swap
4) DeltaSpxBPta_vsWT (Winkler strain IU2689 versus IU1781), 2 replicates including one dye swap
5) DeltaSpxBPtaAckA_vsWT (Winkler strain IU2837 versus IU1781), 4 replicates including two dye swaps
6) DeltaSpxBPtaAckAWalK_vsWT (Winkler strain IU3107 versus IU1781), 2 replicates including one dye swap
7) DeltaSpxBAckA_vsWT (Winkler strain IU3590 versus IU1781), 2 replicates including one dye swap
8) DeltaSpxBAckAWalK_vsWT (Winkler strain IU4319 versus IU1781), 1 replicate.

Data were analyzed using software from the TM4 Microarray Software Suite (www.tm4.org). GenePix results files (.gpr) were converted to TIGR MultiExperiment Viewer file format (.mev) using ExpressConverter 2.1 software and median spot intensities. Lowess (block) normalization was performed on non-background subtracted data using TIGR MIDAS 2.21 software. For strain comparisons replicated at least three times, the cut-off for statistical significance of differential expression was set at Bayesian P =0.001 and an average up or down fold change of at least 1.8 fold. For strain comparisons replicated two times, the cut-off for statistical significance of differential expression was set at an average up or down fold change of at least 1.8 fold. In addition, we required that the value obtained upon addition or subtraction of the standard error of the mean (SEM) from the average fold change was -1.7 or smaller (for negative fold changes) or 1.7 or greater (for positive fold changes).

first: Smirla

last: Ramos-Montañez

first: Kristy

last: Hentchel

first: Malcolm

last: Winkler


title: differential gene expression dynamics of Pseudomonas putida KT2440 under matric stress

status: Public on Nov 24 2010

city: Kgs Lyngby

first: Gamze

last: Gulez

address: Miljoevej 113

department: Environmental Engineering

country: Denmark

institute: Technical University of Denmark

summary: Our first aim was understand whole genome expression dynamics of Pseudomonas putida KT2440 surface colonies under water stress. Therefore, we wanted to identify significantly differentially expressed genes of at -0.4 MPa matric potential relative to the -0.5 kPa (near saturation condition) at different stress durations. Aliquots of overnight grown P. putida KT2440 cells were inoculated (approx. 100 µl and 1x107 cells) on the surface of ceramic plates. Prior to matric stress, the cells were incubated for 120, 116, 96, and 48 hr at-0.5 kPa to allow formation of a mature cell loan. -0.4 MPa matric potential was applied for the last 0 (control), 4, 24, and 72 hr of incubation periods, respectively, so that the total incubation time (at (-0.5 kPa) and (-0.4 MPa)) was kept constant as 5 days. Our second aim was to find out how the gene expression profile would change when we use PEG-8000 to simulate matric stress. To that effect, similar incubations were performed where the direct matric potential was -0.5 kPa, but supplemented with PEG-8000 to set a matric potential equivalent of -0.5 or -1.0 MPa. Incubations were again 5 days. In addition, we tested the effect of gas pressure on gene expression profile of cells in liquid medium.  20 ml of overnight grown KT2440 cells were exposed to 0.4 MPa (gauge) and 0.1 MPa (atmospheric) pressures.

overall_design: Matric Stress Experiments: we had 3 to 4 replicates for each time point and controls (-0.5 kPa). These were kept under -0.4 MPa stress at 4 hr  (P4), 24 hr (P24), 72 hr (P72), and controls kept at -0.5 kPa (C).

first: Arnaud

last: Dechesne

first: Chris

last: Workman

first: Barth

middle: F

last: Smets


title: BA-Sulfate vs Cystine

summary: Study of sulfur metabolism in BA

overall_design: 2 biologic replicates


title: BA-Methionine plus Cystine vs Sulfate

summary: Study of sulfur metabolism in BA


title: Spore formation of Lentinula edodes (LongSAGE)

city: Shatin

first: Hoi Shan

last: Kwan

state: Hong Kong SAR

institute: The Chinese University of Hong Kong

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

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

To facilitate comparison of LongSAGE and SAGE data in GEO, LongSAGE tags (15bp) were trimmed to become 10bp and uploaded in previous submission (GSM87320, GSM87321). The current submission are actual LongSAGE experimental data without any extrapolation from SAGE data.

first: HS

first: WWY

last: Chum


title: Time course study of confinement stress in HR and LR trout lines

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

institute: NUI Galway

summary: Farmed fish are unavoidably exposed to husbandry-related stressors which can result in outbreaks of disease, reduced reproductive success and poor growth. Biomarkers are needed for the establishment of selective breeding approaches for the production of stress resistant fish. In this context, microarray analysis has been carried out on liver tissues of two genetic lines of rainbow trout, high responders (HR) and low responders (LR), after confinement for various time periods. Microarray hybridisations provided gene expression profiles for pools of fish (stress: n=5; control: n=3) after 6h, 24h and 168h of confinement stress. Keywords : stress response, pools, time course, comparison of two lines.

overall_design: Samples were hybridised directly to each other in a parallel loop design. Each treatment (LC, LS, HC, HS) was hybidised in a loop of all 3 time points and each treatment loop was interconnected by hybridisations at a specific time. The publication will have this figure.

first: Thomas

last: Pottinger

first: Kalyani

last: Pemmasani


title: BA-Methionine plus Cystine vs Cystine

summary: Study of sulfur metabolism in BA


title: Lactobacillus johnsonii NCC comparative genomics with L. iatae

city: Lausanne 26

first: Bernard

last: Berger

address: Vers-Chez-Les-Blanc

department: Nutrition & Health

country: Switzerland

institute: Nestlé Research Center

summary: Whole genome DNA microarray designed for the probiotic L. johnsonii strain NCC533 was used for comparative genomic hybridization (CGH) of L. johnsonii ATCC 33200T, L. johnsonii BL261, L. gasseri ATCC 33323T and L. iatae BL263 (CECT 7394T). In these experiments, the fluorescence ratio distributions obtained with L. iatae and L. gasseri showed characteristic inter-species profiles. The percentage of conserved L. johnsonii NCC533 genes was about 83% in the L. johnsonii strains comparisons and decreased to 51% and 47% for L. iatae and L. gasseri, respectively. These results confirmed the separate status of L. iatae from L. johnsonii at the level of species, and also that it is closer to L. johnsonii than L. gasseri.

sample_organism:
Lactobacillus gasseri
Lactobacillus johnsonii
Lactobacillus iatae

overall_design: L. johnsonii, L. gasseri, and L. iatae strains were hybridized versus L. johnsonii NCC533, some with replicates

first: Deborah

last: Moine


title: Transcriptional Responses of Karenia brevis to Acute Stresses

city: Charleston

first: Frances

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

country: USA

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

summary: Dinoflagellates have evolved a nuclear organization unlike that of any other eukaryotic group.  Recent studies find a predominance of post-transcriptional control of dinoflagellate gene expression.  This study investigated regulation of the environmental stress response in the red tide dinoflagellate, Karenia brevis using an Agilent custom oligonucleotide microarray.  K. brevis cultures were exposed to 5°C or 10°C heat shock, or three different sources of oxidative stress: 60 µM H2O2, 10 mM NaNO2, or 12 µM PbCl2 over acute time courses. Ribosomal genes, genes involved in RNA processing, translation, and chaperones were among the classes of genes consistently downregulated across treatments, although within these functional classes the same genes did not always respond to different stressors.  Genes involved in the photosystem and mitochondrial and chloroplast ATP generation dominated the down-regulated genes. Heat shock and oxidative stress response genes were not induced under any treatment, even under conditions that resulted in decreased viability.  We subsequently identified the presence of a trans-spliced leader sequence on many stress response gene transcripts, which suggests that they may be transcribed constitutively and their expression regulated at the level of translation.

overall_design: Cultures of were grown to mid-log phase.  For each treatment, five replicate untreated control cultures and five replicate treated cultures were harvested at several time points following treatment.  The following time courses were used:  5°C heat shock - 5, 15, 30, 60, and 240 min;  10°C heat shock - 60 min;  60 µM H2O2 - 5, 15, 30, 60, and 240 min; 10 mM NaNO2 -1, 4, and 7 hours; 12 µM PbCl2 -1, 4, and 7 hours.  For each treatment, RNA was pooled from the controls and treated cultures at each timepoint. Two color arrays were then run comparing each the transcriptome at timepoint with the pooled control for that treatment.  A technical dye swap array was run at each timepoint.

middle: B

last: Lidie

first: Jeanine

last: Morey


title: Individual variation in confinement response at 168h

summary: Farmed fish are unavoidably exposed to husbandry-related stressors which can result in outbreaks of disease, reduced reproductive success and poor growth. Biomarkers are needed for the establishment of selective breeding approaches for the production of stress resistant fish. In this context, microarray analysis has been carried out on liver tissues of two genetic lines of rainbow trout, high responders (HR) and low responders (LR), after confinement for various time periods. Microarray hybridisations provided gene expression profiles for 10 individual fish (5 of the HR line and 5 of the LR line) after 168h of confinment stress. Keywords : stress response, individual variation, fixed time point, comparison of two lines

overall_design: All 10 samples were hybridised against a common reference source that contained equal amounts of all 10 samples. Each sample was hybridised twice against this reference using a dye-swap setup.


title: Arabidopsis Col-5 challenged with Ralstonia solanacearum BCCF401

status: Public on Nov 22 2010

city: Pretoria

first: Dave

state: Gauteng

address: Room 6-26, Agricultural Sciences Building, University of Pretoria, Lunnon Rd

department: Plant Science, Forestry & Agricultural Biotech. Instit. (FABI)

country: South Africa

institute: University of Pretoria

summary:
Arabidopsis plants were challenged with Ralstonia solanacearum isolate BCCF401 and expression profiles investigated during early and late wilt symptom development.

Keywords: Disease state analysis

overall_design: A direct comparison was performed. Two replicate biological experiments were performed and two technical replicates with dye swap were included in each biological replicate.

first: Sanushka

last: Naidoo

first: Katherine

middle: J

last: Denby


title: Heat stress expression data from developing barley caryopses

city: Tuebingen

first: Joachim

last: Kilian

address: Auf der Morgenstelle 1

department: ZMBP Plant Physiology

institute: University of Tuebingen

summary:
High temperature stress, like any abiotic stress, impairs the physiology and development of plants, including the stages of seed setting and ripening.
In this study we used the 22K Barley1 GeneChip microarray to investigate the response of developing barley (Hordeum vulgare) caryopses at 12 days post anthesis to 0.5h, 3h and 6h of heat stress exposure.

overall_design: Developing barley caryopses were harvested at different time-points of a day during heat stress (42°C) (2:00 PM, 5:00 PM and 8:00 PM). Heat stress started at 1:30PM. Pooled caryopses (form 3 plants) from the respective time points were used for RNA extraction and hybridization on Affymetrix microarrays (Barley1 GeneChip; GEO accsession GPL1340). Biological replicates were performed.

first: Elke

last: Mangelsen

first: Dierk

last: Wanke

first: Klaus

last: Harter

first: Christer

last: Jansson

first: Eva

last: Sundberg


title: Transcriptional Characteristics of Xa21-mediated Defense Responses in Rice

status: Public on Nov 21 2010

city: Beijing

first: Guozhen

last: Liu

address: Beijing Airport Industrial Zone B-6

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

summary: Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice.  The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races.  To identify other genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 hours post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively.  A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated Differentially expressed Genes), were identified.  Based on their functional annotations, the XDGs were assigned to 14 categories some of which encode resistance/defense related proteins and signaling regulators.  Interestingly, most signaling-related genes were down-regulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response.  Moreover, a number of pathogenesis-related genes were induced at 72 and 120 hpi.  Comparison of expression profiles mediated by other resistance genes revealed an interesting common responses in the plant immune system.  Comparison analyses also suggest possible overlaps with hormone signaling pathways and with defense systems including basal defense and hypersensitive responses.

overall_design: We investigated the transcriptional characteristics of Xa21-mediated defense responses in rice using whole-genome oligonucleotide microarray, by comparing the expression profiles between incompatible interactions and mock treatments at five time-points and between incompatible and compatible interactions at 4 hours post inoculation. Microarray hybridization at each time point was carried out in three replications including two biological replications and one technological replication. To detect the genes that are significantly regulated and to eliminate those that have inconsistent expression data among replicated experiments, a cutoff of 1.5 fold change and 1.96 for intensity-dependent Z-scores were required in at least two experimental samples.

first: Qiang

last: Gan

first: Hui

last: Bai

first: Xianfeng

last: Zhao

first: Yong

last: Tao

first: Haipan

last: Zeng

first: Yuning

last: Han

first: Lihuang

last: Zhu

first: Wenyuan

last: Song


title: Silencing factors induce the elimination of nucleosome-free regions in S. pombe heterochromatin

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
Abstract: In the yeast S. pombe, multiple chromatin-modifying enzymes are required for heterochromatin formation, yet how their actions alter chromatin structure to block access to DNAby the transcriptional machinery is unknown. We constructed high-resolution nucleosome occupancy maps of heterochromatic regions in wild-type strains and in mutants lacking the H3K9 methyltransferase Clr4 or one of the two activities of the silencing effector complex SHREC.  Fourier analysis reveals that these enzymes do not increase the regularity of nucleosome spacing.  Rather, their principal effect was to induce the elimination of nucleosome-free regions (NFRs).  Both NFRs associated with transcription initiation sites as well as those not associated with promoters are affected. As in S. cerevisiae, repressed genes in euchromatin retain their NFRs.  Thus, NFR elimination cannot be explained as a secondary consequence of repression. The maps also show that TFIIIC boundary elements have NFRs resistant to silencing, suggesting a potential
role in preventing lateral spread of heterochromatin. NFR elimination offers a mechanism by which heterochromatin restricts access of the transcriptional machinery to DNA.

overall_design:
Nucleosome positions in either heterochromatin or euchromatin were mapped in various mutants to determine whether chromatin structure is altered upon heterochromatic silencing. Eight strains were assayed for nucleosome positioning in heterochromatin while two strains were assayed for nucleosome positioning in euchromatin.  Two biological replicates were assayed for each strain.  No dye swaps were done.

RNA transcripts were also mapped using the heterochromatin tiling arrays to determine where RNA transcripts accumulate in heterochromatin.  Three strains were assayed for transcripts in heterochromatin by hybridizing cy5-labeled cDNA created from total RNA against cy3-labeled cDNA created from RNA synthesized from sonicated genomic DNA.  Two biological replicates were assayed for each strain.

first: Jennifer

last: Garcia

first: Phillip

last: Dumesic

first: Paul

middle: D

last: Hartley

first: Hana


title: Expression Analysis of Geobacter sulfurreducens Current-Consuming Biofilm versus Current-Producing Biofilm

status: Public on Nov 23 2010

city: Washington

first: Sarah

last: Strycharz

state: DC

address: 4555 Overlook Ave.

department: CBMSE

institute: Naval Research Laboratory

summary: There is a wide diversity of potential applications for direct electron transfer from electrodes to microorganisms, which might be better optimized if the mechanisms for this novel electrode-biofilm interaction were better understood.  Geobacter sulfurreducens is one of the few microorganisms available in pure culture that is known to be capable of directly accepting electrons from a negatively poised electrode. A microarray comparison of cells accepting electrons from the electrode versus cells donating electrons to the electrode reveals that the genes previously observed to be upregulated in current-producing biofilms are not highly expressed in current-consuming biofilms.

overall_design: Current-consuming biofilms were grown under anoxic conditions in freshwater medium in a potentiostat-poised (-500 mV vs. Ag/AgCl), dual-chambered electrode system where the electrode served as the electron donor and fumarate as the electron acceptor. Current-producing biofilms were grown under identical condition, except the electrode served as the electron acceptor (+300 mV vs. Ag/AgCl) and acetate as the electron donor. Triplicate electrode systems of either current-consuming biofilms or current-producing biofilms were harvested for total RNA.

first: Kelly

last: Nevin

first: Lorrie

last: Perpetua

first: Anna

first: Derek

last: Lovley


title: Expression Analysis of Geobacter sulfurreducens Current-Consuming Biofilm versus No-Current Biofilm

summary: There is a wide diversity of potential applications for direct electron transfer from electrodes to microorganisms, which might be better optimized if the mechanisms for this novel electrode-biofilm interaction were further understood.  Geobacter sulfurreducens is one of the few microorganisms available in pure culture that is known to be capable of directly accepting electrons from a negatively poised electrode. Gene transcript abundance in cells of G. sulfurreducens using electrons delivered from a graphite electrode as the sole electron donor for fumarate reduction was compared with transcript abundance in cells growing on the same graphite material, but without an electrical connection and acetate as the electron donor.

overall_design: Wild type G. sulfurreducens was inoculated into a anaerobic, dual-chambered electrode system with the working electrode poised using a potentiostat at -500 mV (vs. Ag/AgCl) in order to serve as the electron donor and fumarate (40 mM) provided as the electron acceptor. An identical system in which the working electrode was left disconnected (no-current biofilm), with acetate provided as the electron donor and fumarate as the electron acceptor, served as the control. Both the experimental and control biofilms were harvested for RNA extraction once fully grown.

last: Liu


title: Role of microRNA-214-targeting PTEN in advanced glycation end product-induced apoptosis delay of monocytes

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: We studied genome-wide miRNA expression in THP-1 cells treated with/without AGEs. Significant upregulation of miR-214 was observed in THP-1 cells treated with/without AGEs.

overall_design: Two samples, one treated with AGE-BSA and one without AGEs.

first: Dong-Xia

last: Hou

first: Li-Min

last: Li


title: Candida Iron deprived Cells: Control vs. BPS treated

status: Public on Nov 17 2010

city: New Delhi

first: Rajendra

last: Prasad

state: Delhi

address: New Mehrauli Road

department: School of Life Sciences

institute: Jawaharlal Nehru University

summary: Transcriptional profiling of iron deprived Candida cells comparing the WT vs BPS (Iron deprived) cells

overall_design: One-condition experiment, WT vs. BPS treated cells. Biological replicates: 3 control, 3 treated, independently grown and harvested.

first: Saif

last: Hameed


title: Gene Expression Patterns of Dengue Virus-Infected Children from Nicaragua Reveal a Distinct Signature of Increased Metabolism

status: Public on Nov 20 2010

first: Sajeev

last: Batra

institute: UCSF

summary: Infection with dengue viruses (DENVs) leads to a spectrum of disease outcomes. The pathophysiology of severe versus non-severe manifestations of DENV infection may be driven by host responses, which could be reflected in the transcriptional profiles of peripheral blood immune cells. We conducted genome-wide microarray analysis of whole blood RNA from 34 DENV-infected children in Nicaragua collected on days 3–6 of illness, with different disease manifestations. Gene expression analysis identified genes that are differentially regulated between clinical subgroups. The most striking transcriptional differences were observed between dengue patients with and without shock, especially in the expression of mitochondrial ribosomal proteins associated with protein biosynthesis. In the dengue hemorrhagic fever patients, one subset of differentially expressed genes encode neutrophil-derived anti-microbial peptides associated with innate immunity.

overall_design: We analyzed 44 HEEBO arrays on which were hybridized RNA amplified from whole blood collected into PAXgene tubes. 34 samples were collected from DENV-infected patients who presented between days 3-6 of illness. Six convalescent samples collected 14-19 days after onset of symptoms were from two dengue fever patients, one dengue hemorrhagic fever patient and three dengue shock syndrome patients. Additionally, samples from four normal healthy individuals were also analyzed.

first: P’ng

last: Loke

first: Samantha

middle: N

last: Hammond

first: Jacqueline

last: Leung

first: Charles

middle: C

last: Kim

first: Crisanta

last: Rocha

first: Angel

last: Balmaseda

first: Eva

last: Harris


title: Gene expression patterns of biopsies from a colonoscopy taken in 2008 of an ulcerative colitis patient infected with Trichuris trichiura

summary: Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the second (out of three) series of arrays from this patient from a colonoscopy in 2008 when the patient was suffering from severe colitis but still had worms in the ascending colon.

overall_design: We analyzed 12 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 4 samples were from the ascending colon, which was colonized by worms at the time. 4 samples were from the transverse colon, which was no longer colonized by worms at the time. 4 samples were from the recto-sigmoid colon, which was suffering from severe colitis at the time.

first: Mara

last: Broadhurst

first: Vikram

last: Kashyap

first: Joseph

last: McCune

first: Uma

last: Mahadevan

first: James

middle: H

last: McKerrow

first: P'ng