title: cDNA Microarray Analysis of Soybean NILs under Fe Sufficient Hydroponic Conditions

city: Ames

first: Randy

last: Shoemaker

address: 100 Osbourne Dr. G401

department: Agronomy

institute: Iowa State University

summary:
The purpose of this experiment was to identify any genes differentially expressed between the Soybean Near Isogenic Lines iron efficient Clark and iron inefficient IsoClark under iron sufficient hydroponic conditions.  These genes would represent constituative genetic differences between the NILs.
Keywords: Near Isogenic Line Comparison of Unstressed Soybean Plants

overall_design: This experiment consists of three biological replicates each with two technical replicates (dye swaps) for a total of six hybridizations.  Arrays 195 and 196 are dye swap technical replicates of biological replicate 1, arrays 197 and 198 are dye swap technical replicates of biological replicate 2, and arrays 199 and 200 are dye swap technical replicates of biological replicate 3.

first: Jamie

last: O'Rourke

first: Dirk

last: Charlson

first: Delkin

middle: O

last: Gonzalez

first: Lila

last: Vodkin

first: Michelle

last: Graham

first: Silvia

last: Cianzio


title: Discovery of genes associated with whirling disease infection and resistance in rainbow trout using expression profiling

status: Public on Feb 20 2008

city: Davis

first: Melinda

last: Baerwald

state: CA

address: One Shields Ave

country: USA

institute: University of California, Davis

summary:
   Whirling disease, caused by the pathogen Myxobolus cerebralis, afflicts several salmonid species. Rainbow trout are particularly susceptible and suffer high mortality rates. The disease is persistent and spreading in hatcheries and natural waters of several countries, including the U.S., and the economic losses associated with whirling disease have been extremely large. In this study, gene expression profiling was conducted for resistant and susceptible rainbow trout strains following pathogen exposure with the primary objective of identifying specific genes associated with whirling disease resistance.
   Several genes were significantly up-regulated in skin following pathogen exposure for both the resistant Hofer and susceptible Trout Lodge rainbow trout strains. For both strains, response to infection appears to be associated with the interferon system. Metallothionein is differentially expressed between the resistant and susceptible strains and is a good candidate for future studies due to its diverse functional roles in inflammation and immune response.
   The present study has provided the first examination into the genetic basis underlying rainbow trout’s immune response and resistance to the whirling disease pathogen. The identified genes have allowed us to gain initial insight into the molecular mechanisms associated with a salmonid host’s immune response and resistance to whirling disease infection.
Keywords: Disease state comparison. 1st comparison: exposed vs control. 2nd comparison: resistant vs susceptible strains

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Resistant (Hofer) and susceptible (Trout Lodge) rainbow trout strains were exposed to 2,000 triactinomyxons (whirling disease pathogen) per fish. Unexposed controls for each strain were treated identically to exposed other than their lack of pathogen exposure. After twenty-four hours, caudal fin tissue was collected for RNA extraction. Amplified RNA was competitively hybridized (exposed versus control) for each strain. Four biological replicates were used for each experimental condition and a balanced block design was incorporated.

middle: R

first: Amy

middle: B

last: Welsh

first: Ronald

middle: P

last: Hedrick

first: Bernie

last: May


title: X chromosome-specific Array-CGH of XLMR patient

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

type: Genome variation profiling by genome tiling array

summary:
Mental retardation (MR) is a non-progressive cognitive impairment affecting 2 to 3% of the Western population.  So far, point mutations and subtle deletions and insertions have been shown to represent only a proportion (<40%) of genetic causes underlying X-linked mental retardation (XLMR).

We have screened a subset of 300 presumable X-linked families by X chromosome-specific array-CGH and identified 6 families with overlapping microduplications at Xp11.22 containing two candidate genes;  both of which showed overexpression in the affected individuals.  Array-CGH data revealed aberrant Cy5/Cy3 log2 ratios for different but overlapping sets of clones indicating varying sizes of these duplications in the different families.
Keywords: comparative genomic hybridization

overall_design: X chromosome-specific array-CGH performed for probands of families A, FAM3, B, MRX17, C, MRX31, and D, A057, revealing the duplications at Xp11.22. DNA from two unrelated MR patients were differentially labeled and co-hybridized onto the X-array. The patients with duplications were hybridized in Cy5 against unrelated MR patients, named Pat XY1-6, in the Cy3 channel.

first: Guy

last: Froyen

first: Paul

last: Van Hummelen


title: Expression data from Helicobacter pylori isolates infecting a gastric epithelial progenitor cell line

status: Public on Feb 22 2008

city: Saint Louis

first: Marios

last: Giannakis

state: MO

address: 4444 Forest Park Blvd.

department: Developmental Biology

institute: Washington University in Saint Louis

summary:
Helicobacter pylori clinical isolates can establish themselves in gastric epithelial stem cells and this interaction may have implications for gastric tumorigenesis. Mouse gastric epithelial progenitor cells (mGEPs) were infected for 24hrs with Helicobacter pylori clinical isolates Kx1 and Kx2. Kx1 and Kx2 were also grown in cell media in the absence of cells. Kx1 was isolated from a patient with chronic atrophic gastritis (ChAG) and Kx2 from the same patient 4 years later, when he progressed to gastric adenocarcinoma.
Keywords: RNA Expression Array

overall_design: H. pylori strains Kx1 or Kx2 that had been grown to log phase were used to infect mGEP cells.. After 24h, media and non-attached bacteria were washed off and the cells harvested by trypsinization. RNA was prepared from bacteria infecting mGEP cells or bacterial cultures of Kx1 and Kx2 grown in cell media for 24h in the absence of mGEP cells.

first: Jeffrey

middle: I

last: Gordon


title: Response of Lactococcus lactis to isoleucine starvation

status: Public on Feb 23 2008

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

summary:
For the first time in Lactococcus lactis, amino acid starvation response was characterized. The natural imposition of isoleucine starvation, by its consumption during growth, associated to transcript profiling, allowed defining exhaustively this stress stimulon. It consisted of a general induction of nitrogen metabolism (amino acid biosynthesis and transport, proteolytic system and proteases), a strong repression of genes encoding major physiological activities (translation, transcription, carbon metabolism, purine and pyrimidine biosynthesis and fatty acid metabolism) and the induction of unexpected cross responses to acid, osmotic and oxidative stresses.
Keywords: stress response, time course

overall_design: Isoleucine starvation was imposed by the consumption of this amino acid during the growth of Lactococcus lactis IL1403 on ILV0.1 medium (CDM with ten-fold reduced concentrations of isoleucine, leucine and valine) and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested in exponential phase and after 30 min, 1.7 h and 3.5 h of isoleucine starvation. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 2053 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. The 4 time-points were analyzed simultaneously and 3 independent repetitions were performed.

first: Emma

last: Redon

first: Pascal

last: Loubiere


title: Human in vivo nutrigenomic effect of olive oil

status: Public on Feb 21 2008

city: Barcelona

first: MONTSERRAT

last: FITO COLOMER

address: DR.AIGUADER 88

country: Spain

institute: IMIM

summary:
Olive oil is protective against risk factors for cardiovascular and cancer diseases. A nutrigenomic approach was performed to assess whether olive oil, the main fat of the Mediterranean diet modifies the gene expression in human peripheral blood mononuclear cells. Six healthy male volunteers ingested, at fasting state, 50 ml of olive oil, and continued with the same olive oil as a source of raw fat (25ml/day) during 3 weeks. Prior to intervention a 1-week washout period with sunflower oil as the only source of fat was followed. During the 3 days before, and on the intervention day, a very low phenolic compound diet was followed. At baseline (0h), at post ingestion (6h), and at fasting state after 3 weeks of sustained consumption of olive oil total RNA was isolated from PBMC. Gene expression was evaluated by microarray and verified by qRT-PCR.
Keywords: Olive oil, gene expression, single dose, sustained consumption

overall_design: Three pools of total RNA were prepared in triplicates (9 samples in total). Each pool refers to different time point of the study (0h-wash out, 6h postprandial and 3 weeks intervention). Pool at 0h serves as reference sample.

first: Valentini

last: Konstantinidou

first: Olha

last: Khymenets

first: Montserrat

last: Fitó

first: Rafael

last: de la Torre

first: Roger

last: Anglada

first: Pedro

last: de Alarcón

first: Ana

last: Dopazo

first: Magi

last: Farré-Albaladejo

first: Maria-Isabel

last: Covas


title: Small RNA species in the mammalian meiotic nucleus

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

summary:
MiRNAs and possibly the recently discovered piRNAs can function in reversible gene silencing.  In meiosis, transcriptional silencing of the XY bivalent and the late pairing regions of autosomes is a necessary event and defects in these processes lead to infertility.  The exact mechanisms of meiotic gene silencing are not well understood but it is thought that some RNA component might be involved at least in the XY transcriptional silencing, similar to Xist silencing of the X chromosome in females.  We wanted to investigate if small RNA species are present in the meiotic nucleus and, if so, to determine their localization pattern. We found both miRNAs and piRNAs in the nucleus of spermatogenic cells.  In Sertoli cells, miRNAs and piRNAs are localized to the fibrillogranular compartment of the nucleolus, while in meiotic cells they are found mainly in the XY-associated dense body but also are associated with chromosome cores, telomerers and the sex chromatin.  Interestingly, in MIWI null male mice, the nucleolar localization of miRNAs is decreased while the localization of piRNAs is diminished.  However, the meiotic localization of these two components is not affected.  These data suggest that small RNA species might have different roles during different stages of male gametogenesis and undergo differential regulation.  Based on the localization of miRNAs and piRNAs in the male-specific, XY-associated dense body, it is probable that at least some are involved in the silencing of the XY bivalent.  Others might be involved in translational repression of transcripts used in later stages of spermiogenesis when transcription is halted.
Keywords: total RNA direct hybridization

overall_design: Small RNAs were profiled by custom Agilent arrays with complementary probes for 257 mature mouse miRNAs.  Total RNA was directly labelled and hybridized to these arrays.  5 probes were designated for each miRNA from which a median intensity was derived and compared to 4000 intensities arising from random probe sequences.

first: Edyta

last: Marcon

first: Gordon

last: Chua

first: Tim

last: Hughes

first: Peter

last: Moens


title: Gene expression variation among eight maize inbreds - 70mer oligo array

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary:
Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation.  This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10237).
Keywords: Genotype comparison series

overall_design: Expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for eight different inbred lines; B37, B73, B84, Mo17, Oh43, B14a, Wf9 and W22.

first: Jack

last: Gardiner

first: Vicki

middle: L

last: Chandler

first: Nathan

last: Springer


title: Dynamics of Ecoli Aerobic to Anaerobic Switch Response

status: Public on Feb 19 2008

city: Los Angeles

first: Jason

last: Ernst

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary:
The experiment is a time course for the aerobic to anaerobic switch response in E. coli.  The data was used to validate the utility of a set of predicted transcription factor gene interactions for modeling the dynamic regulatory response networks of this response.  The transcription factor gene interaction predictions were generated by a semi-supervised classification method that takes advantage of a separate compendium of gene expression and a data set of curated interactions.
Keywords: time course, environment change response

overall_design: In total there are 11 samples measuring the gene expression response at the different time points from the change from aerobic to anaerobic conditions.  The control sample was based on completely aerobic conditions before shutting off oxygen. The test samples correspond to 0min, 2min, 5min, 15min, 25min, 35min, 45min, and 55min after shutting off Oxygen.  Technical replicates were taken for the 5min, 25min, and 55min time points.  Two channel microarray labeling was used with Cy5 and Cy3 labels. The standard aerobic was labeled with Cy5 in the 0min, 2min, 5min replicate 1, and both 25min replicates.  In all other experiments the standard was labeled with Cy3.

first: Qasim

middle: K

last: Beg

first: Krin

middle: A

last: Kay

first: Gabor

last: Balazsi

first: Zoltan

middle: N

last: Oltvai

first: Ziv

last: Bar-Joseph


title: Comprehensive Serial Analysis of Gene Expression of the Cervical Epithelium Transcriptome

city: Vancouver

first: Ashleen

last: Shadeo

address: 675 West 10th Ave

institute: BCCRC

summary:
In this study, we sequenced 691,390 SAGE tags from four libraries.  Cervical L-SAGE libraries N1, N2, C1, and C2 were sequenced to 165,624, 181,224, 173,534, and 171,008 tags, respectively.  Duplicate ditags were eliminated from analysis resulting in 136,276, 139,656, 154,828 and 136,386 useful tags respectively and a total of 24 058 unique tags. 15,438 of the unique tags mapped to annotated UniGene identifiers.  We characterized the transcriptome of normal cervical tissue and evaluated the highly expressed genes in terms of tissue specificity, conserved expression among the normal libraries and their altered expression in CIN III lesions.
Keywords: Cervical Epithelium, Long SAGE

overall_design: Four Long SAGE libraries were created from cervical epithelium biopsies. Two were CIN III and two were normal cervical tissue.

first: Raj

first: Greg

last: Vatcher

first: Jennifer

last: Campbell

first: Kim

last: Lonergan

first: Jasinka

last: Matisic

first: Dirk

last: Van NieKirk

first: Thomas

last: Ehlen

first: Dianne

last: Miller

first: Michele

last: Follen

first: Wan

last: Lam

first: Calum

last: MacAulay


title: MTG16, a target of the t(16;21), regulates hematopoietic stem cell mobilization and progenitor cell proliferation.

city: Nashville

first: Isabel

last: Moreno-Miralles

state: TN

address: 512 PRB 23rd and Pierce Ave

department: Biochemistry

institute: Vanderbilt University School of Medicine

summary:
A single normal hematopoietic stem cell (HSC) is sufficient to regenerate the entire blood system after bone marrow transplantation. This process requires not only rapid mobilization of the stem cell into the cell cycle, but also the proliferation of committed progenitor cells to provide functional mature cells until HSC progeny have accumulated to sufficient numbers1. Gene disruption strategies have dissected the regulatory pathways and identified critical factors that mediate the decision of a stem cell to self-renew and quiesce or to enter the rapidly expanding progenitor cell pool to populate the various hematopoietic cell lineages.  However, only a very limited number of the transcriptional regulators and chromatin remodeling factors that are recruited by DNA binding factors have been pinpointed as contributors to stem cell functions. Here, we show that the transcriptional co-repressor Myeloid Translocation Gene on chromosome 16 (Mtg16), which is targeted by the t(16;21) in acute myeloid leukemia, is required for long-term hematopoietic stem cell functions and suppression of stem cell mobilization.  Although there are no dramatic defects in the allocation of cells to any of the major hematopoietic cell lineages, inactivation of Mtg16 impairs the rapid expansion of stem/progenitor cells, which is required after bone marrow transplantation.  This impairment appears to be a failure to proliferate rather than an induction of cell death, as expression of c-Myc complements the Mtg16-/- defect.
Keywords: Knock-out analysis, genetic modification

overall_design:
The lineage negative fraction of bone marrow from 4 age and sex match wild type (WT_BM) or Mtg16-null (NULL_BM) mice was pooled for total RNA extraction.
The samples were analyzed in two different microarray lots (rep1 and rep2).

first: Brenda

middle: J

last: Chyla

first: Melissa

last: Steapleton

first: MaryAnn

last: Thompson

first: Srividya

last: Bhaskara

first: Michael

last: Engel

first: Scott

middle: W

last: Hiebert


title: Stable nucleosome positions in HOX clusters; human K562 and HeLa cells

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes where nucleosome positions have not been examined beyond isolated loci and promoter regions. Towards this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of inter-nucleosome distances, specific loci contain regular nucleosomal arrays with 195bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3’ ends of genes. Through comparison of different cell lines, we find that increased gene expression correlates with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes.
Keywords: human chromatin nucleosome positions, nucleosomes, ChIP-chip

overall_design: Samples include mononucleosome samples resulting from MNase digestion in two cell lines, pan-H3 and rabbit IgG ChIP-chip validation, MNase sequence bias on bare genomic DNA.

middle: V

first: Caroline

last: Woo

middle: Y

last: Tolstorukov

first: Robert

middle: E

last: Kingston

last: Park


title: Acid-Shifted Time Course of Gene Expression Profiles of Aerobically Grown Escherichia coli K-12

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

summary:
The effect of an extracellular acid shift on gene expression profiles of Escherichia coli K-12 W3110 was observed using Affymetrix E. coli arrays. In order to maximize aeration and maintain logarithmic growth, the overnight culture (LBK broth medium) was diluted 500-fold into a 250-ml baffled flask containing 55 ml of 20mM HOMOPIPES buffered medium (pH 7.6). Cultures were grown to OD600=0.2. A shift to acid external pH was conducted by rapid addition of 840 µl 1M HCl, which lowered the pH of the medium to pH 5.5. For each of five biological replicates, 10-ml samples were taken at times 0, 1, 5, and 10 min post addition of HCl. Each sample was added to 1 ml 10% phenol-ethanol stop solution in <5 sec. For each sample, cDNA synthesized from total RNA was hybridized onto Affymetrix E. coli arrays. Model-based gene expression intensities were determined using GCOS software. Gene-by-gene temporal differential expression was analyzed as a mixed-effects model using polynomial time functions as fixed effects and flask variation as a random effect.
Keywords: Time Course

overall_design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of time versus change in external pH. Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 20 mM HOMOPIPES at 7.6. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 225 rpm, incubated at 37°C to an optical density at 600 nm of 0.2. External pH was lowered to pH 5.5 by adding 840 µl of 1M HCl to 40 mls of culture within 5 seconds. Four samples were taken from each of  five replicate cultures, corresponding to time 0 (before HCl addition),1, 5, and 10 min post HCl addition.

first: Geetha

last: Kannan

first: Jessica

middle: C

last: Wilks

first: Sandra

middle: S

last: BonDurant

first: Brian

middle: D

last: Jones


title: Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis - 70mer

last: Stupar

summary:
Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236).
Keywords: Genotype comparison series

overall_design: Expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for nine different genotypes; B37, B73, B84, Mo17, Oh43, B37xB73, B84xB73, Oh43xB73 and Oh43xMo17.

first: Jack

last: Gardiner

first: Vicki

last: Chandler

first: Nathan

last: Springer


title: Genome-wide analysis for rice small RNAs by MPSS

status: Public on Feb 15 2008

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a novel class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. We provide evidence that the miRNAs function by inducing mRNA cleavage in the middle of their complementary site. Their production requires DCL1 activity, which is essential for canonical miRNA biogenesis. All of the nat-miRNAs identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and for the formation of functional miRNA loci. These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes
Keywords: small RNA sequencing by MPSS

overall_design: Six rice samples are included in this study. They are 1) immature panicles, 2) germinating seedlings (control for Magnaporthe treatment), 3) germinating seedlings infected with Magnaporthe grisea,4)stems, 5) three-week-old seedlings (control for ABA treatment), 6) three-week-old seedlings treated with ABA.


title: A tri-species Aspergillus array (oryzae arrays)

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

summary:
The full genome sequencing of the ﬁlamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Aﬀymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identiﬁed to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics.
Keywords: Physiological response

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Two conditions (glucose and xylose) and three biological replicates

first: Wanwipa

last: Wongsangnak

first: Gianni

last: Panagiotou

first: Margarita

middle: P

last: Salazar

first: Linda

last: Lehmann

first: Jens

last: Nielsen


title: Expression of Mouse and Human Sense-Antisense Transcript

city: Tsuruoka City

first: Yuki

last: Okada

address: Nipponkoku 403-1, Daihouji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

summary:
Increasing numbers of sense–antisense transcripts (SATs), which are transcribed from the same chromosomal location but in opposite directions, have been identified in various eukaryotic species, but the biological meanings of most SATs remain unclear. To improve understanding of natural sense–antisense transcription, we performed comparative expression profiling of SATs conserved among humans and mice. Using custom oligo-arrays loaded with probes that represented SATs with both protein-coding and non-protein–coding transcripts, we showed that 33% of the 291 conserved SATs displayed identical expression patterns in the two species. Among these SATs, expressional balance inversion of sense–antisense genes was mostly observed in testis at a tissue-specific manner. Northern analyses of the individual conserved SAT loci revealed that: (1) a smeary hybridization pattern was present in mice, but not in humans, and (2) small RNAs (about 60 to 80 nt) were detected from the exon-overlapping regions of SAT loci. In addition, further analyses showed marked alteration of sense–antisense expression balance throughout spermatogenesis in testis. These results suggest that conserved SAT loci are rich in potential regulatory roles that will help us understand this new class of transcripts underlying the mammalian genome.
Keywords: Expression profile of mouse and human sense-antisense transcript

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The RNA samples used for the mouse oligo-array experiments came from the brain, NIH3T3 cells (fibroblast cell line), liver, heart, and testis. RNA from mouse tissue (C57BL/6J, 8 to 10 weeks, male and female mixed) and mouse fibroblast line NIH3T3 was isolated by using Trizol reagent (Invitrogen). The mouse custom oligo DNA microarray chip (microarray format: 11K) contained 3896 probes that represented genes in 1948 exon-overlapping SAT (sense-antisense transcript) pairs.The same total RNA samples were reciprocally labeled with Cy3 or Cy5, hybridized to the oligo DNA on the chip, and dye-normalized. The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. The total mean signal on the mouse chip in each hybridization experiment was adjusted with to a value of 4872.3. The RNA samples used for human microarray experiments came from brain, HF19 cells (fibroblast cell line), heart, liver and testis. The total brain, heart, and testis RNA used in the array experiments was purchased from Ambion. Total RNA was isolated from the fibroblast cells by using Trizol reagent (Invitrogen). The same total RNA samples were labeled with single color Cy3, hybridized to the oligo DNA on the chip, and dye-normalized; the processed signals were obtained by using Feature Extraction software (Agilent Technologies). The custom oligo DNA microarray chip (microarray format: 11K) contained 2793 probes for 1486 pairs of exon-overlapping SATs. The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. For further analysis, the Cy3-labeled processed signal was used as the processed signal from the expression of a particular gene. The total mean signal on the human chip in each hybridization experiment was adjusted to 1491.6, so that the relative differences in gene expression could be compared among cell lines and tissues.

first: Chiaki

last: Tashiro

first: Koji

last: Numata

first: Kazufumi

last: Watanabe

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Kazue

last: Okubo

first: Rieko

last: Ikeda

first: Rintaro

last: Saito

first: Akio

last: Kanai

first: Kuniya

last: Abe

first: Masaru

last: Tomita

first: Hidenori

last: Kiyosawa


title: cDNA Microarray Analysis of NILs under Fe Deficient Hydroponic Conditions

first: Randy

last: Shoemaker

state: IA

summary:
This experiment was designed to identify candidate genes related to iron deficiency chlorosis in soybeans that are differentially expressed between near isogenic lines developed for their differential tolerance to low iron conditons.
Keywords: Stress Response Analysis

overall_design: This experiment was a linear dye swapped experiment consisting of 3 biological replicates each wtih two technical replicates for a total of six hybridizations.

first: Jamie

last: O'Rourke

first: Dirk

last: Charlson

first: Delkin

middle: O

last: Gonzalez

first: Lila

last: Vodkin

first: Michelle

last: Graham

first: Silvia

last: Cianzio


title: Effect of amphotericin B on Aspergillus fumigatus

status: Public on Feb 14 2008

city: San Jose

first: Jata

last: Shankar

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

summary:
Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections including invasive aspergillosis. We aimed  to understand molecular targets of AMB in Aspergillus fumigatus (Afu) by genomic approaches.
Keywords: Aspergillus fumigatus treated with amphotericin B for 24 hours

overall_design: Experiment was performed in dye swap manner from two different biological replicates

first: Poonam

last: Gautam

first: Seemi

middle: F

last: Basir

first: Puranam

middle: U

last: Sarma

first: Taruna

last: Madan


title: A tri-species Aspergillus array (niger arrays)

first: Mikael

last: Andersen

first: Wanwipa

last: Wongsangnak

first: Gianni

last: Panagiotou

first: Margarita

last: Salazar

first: Linda

last: Lehmann

first: Jens

last: Nielsen


title: Distinctive microRNA profiles relating to patient survival in esophageal squamous cell carcinoma

status: Public on Feb 18 2008

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

summary:
We have investigated expressed microRNA in cryo-preserved esophageal cancer tissues using advanced microRNA microarray techniques.  Our microarray analyses reveal a unique microRNA expression signature composed of 40 genes which can distinguish normal from malignant esophageal tissue.  Some microRNAs could be correlated with the different clinico-pathological classifications.  For example, high hsa-miR-103, -107, -23b expression correlated with poor overall disease-free survival of esophageal cancer patients.  These results indicate that microRNA expression profiles are important diagnostic and prognostic markers of esophageal cancer, which might be analyzed simply using economical approaches such as RT-PCR.
Keywords: microRNA, esophageal squamous cell carcinoma

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: cancer vs adjacent normal tissues

first: Yong

last: Guo


title: Cervical Tissue Long SAGE

first: Ashleen

last: Shadeo

summary:
16 Long SAGE libraries
Keywords: Various degrees of cervical dysplasia

overall_design:
Normal Cervical Tissue (N1, N2, N3, N4)
CIN III, severe dysplasia cervical tissue (C1, C2, C3, C4, C5, C6)
CIN I, mild dysplasia, cervical tissue (M1, M2, M3)
CIN II, moderate dysplasia, cervical tissue (M4, M5, M6)

first: Wan

middle: L

last: Lam


title: A tri-species Aspergillus array (nidulans arrays)

overall_design: Two conditions (glucose and xylose) and three biological replicates of each.


title: Global transcriptome analysis of Lactobacillus reuteri in sourdough fermentation.

status: Public on Feb 13 2008

city: Stuttgart

first: Eric

last: Huefner

address: Garbenstrasse 28

department: Food Microbiology

country: Germany

institute: University of Hohenheim

summary:
In this study, we investigated the transcriptional response of the human isolate L. reuteri ATCC 55730 during sourdough fermentation by using whole-genome microarrays. Significant changes of mRNA levels were found for 101 genes involved in diverse cellular processes, e.g., carbohydrate and energy metabolism, cell envelope biosynthesis, exopolysaccharide production, stress responses, signal transduction and cobalamin biosynthesis. Our results evidence extensive changes of the organism’s gene expression to the growth in sourdough as compared to the growth in chemically defined medium, and thus allowed us to uncover pathways involved in the adaptation of L. reuteri to the ecological niche of sourdough. An impact of several genes of L. reuteri for effective growth in sourdough was shown by implementation of mutant strains in sourdough fermentation. This study contributes to the understanding of the molecular fundamentals of L. reuteri’s ecological competitiveness, and provides a basis for further exploration of genetic traits involved in adaptation to the food and/or intestinal environment.
Keywords: environment-specific gene expression, sourdough fermentation, chemically defined medium, dye swap

overall_design: RNA of exponetially growing cells grown in chemically defined medium CDML and sourdough was isolated three times (biological replicates). cDNA was synthesized from RNA of each biological replicate, and labeled with both Cy3 and Cy5 separately. cDNA of CDML and sourdough cultures were hybridized in a dye-swap duplicate for each biological replicate, resulting in 6 hybridizations. The duplicate genome per slide results in 12 replicate hybridizations per spot/gene.

last: Hüfner

first: Robert

middle: A

last: Britton

first: Stefan

last: Roos

first: Hans

last: Jonsson

first: Christian

last: Hertel


title: Blue light inhibition of tuberization

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

summary:
A tuberization inhibitor has long been postulated, but not yet found. We found that blue light inhibits tuberization in Norland, a day-neutral variety of Solanum tuberosum L. Tissue-cultured plants formed tubers within 8 weeks under continuous darkness, and white, red, or far-red light. Preliminary experiments indicated that a one- or two-day exposure to blue light after 3-4 weeks of dark treatment will inhibit tuber formation in ‘Norland’ plants. Using this system and expression profiling, we may be able to identify candidate tuberization inhibitors. 'Norland' plants (subcultured from existing cultures and grown for two weeks under continuous 100 umol/m2-s white fluorescent light) were placed in tuber-inducing media containing 6% sucrose, vitamins, MS salts, and kinetin (2.5 mg/L). Tubes containing plants were wrapped in two layers of aluminum foil. After 3 weeks and 2 days, half of the tubes were exposed to 6-7 umol/m2-s blue light. The other half of the tubes were left in darkness (controls). After 2 days, all plants were harvested and frozen in liquid nitrogen. Plants exposed to blue light were harvested under blue light. Control plants were harvested under < 2 umol/m2-s light conditions. All plant transfers were done at 1700 (5 PM) to avoid possible complications due to circadian effects. Experiments were performed four times, from subculture to harvest. RNA was extracted from stem and leaf tissue of plants using the Qiagen RNeasy Plant Mini kit. Extracted RNA was then converted to dsDNA using the Invitrogen protocol and reagents for double stranded cDNA synthesis. The resulting dsDNA was in vitro transcribed into amplified RNA using the Ambion procedure and reagents for in vitro transcription. cDNA was purified using Qiagen MinElute columns and protocol. Amplified RNA was purified using Ambion columns or Qiagen RNeasy columns and the Ambion protocol, and quantified using RiboGreen dye fluorometry.
Keywords: Direct comparison

overall_design: 6 hybs total

first: Cindy

last: Tong


title: Local and systemic gene expression in potato infected with PVY

summary:
The goal of these studies is analysis of gene expression profiles in potato plants infected with potato virus Y (necrotic strain - PVYN). A prototypic plant pathogen interaction system used to study disease resistance is tobacco (Nicotiana tabacum) and tobacco mosaic virus (TMV). In tobacco, the resistance response comprises two phenomena, known as the hypersensitive response (HR) and systemic acquired resistance (SAR). HR is typically characterized by a local necrosis surrounding the site of viral entry leading to restriction of pathogen replication and spread. SAR is the enhanced ability of the plant to resist a secondary challenge by the same or a different pathogen inoculated elsewhere on the plant. The identity of the signal(s) that induces HR and SAR is still poorly understood. Plants of S. tuberosum cv. Rywal, resistant to all known (N, 0, NTN) PVY strains, were grown in growth chambers using 16 h period of light (22°C) and 8 h of darkness (18°C). For all experiments, 6-week-old plants were used. For inoculation with PVY, carborundum-dusted leaves were rubbed with water (mock control) or PVYN solution (1 µg ml-1). Two to four leaves were inoculated on each plant and harvested together at 1, 3, and 6 days post inoculation (dpi). Separately, noninoculated leaves were harvested at the same time points (upper leaves). The first time point (1 dpi) has been chosen to study the early stage of plant response before necrotic lesion formation. At 3 dpi necrotic lesions start to appear, and at 6 dpi necroses are fully developed which correlates with the maximum of salicylic acid increase in virus inoculated leaves.
Keywords: Direct comparison

overall_design: 26 hybs total

first: Kamil

last: Witek


title: Integrating whole transcriptome assays on a lab-on-a-chip for single cell gene profiling

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

institute: INSERM U1127-CNRS UMR7225-UPMC

summary:
To correlate gene expression profiles to fundamental biological processes such as cell growth, differentiation and migration, it is essential to work at the single cell level. Gene expression analysis always starts with the relatively low efficient reverse transcription (RT) of RNA into complementary DNA (cDNA), an essential step as unprocessed RNAs will not be analyzed further. In this paper, we present a novel method for RT that uses microfluidics to manipulate nanoliter volumes. We compare our method to conventional protocols performed in microliter volumes. More specifically, reverse transcription was performed either in a poly-dimethylsiloxane (PDMS) rotary mixer or in a tube, using single cell amount of mouse brain RNA (10 pg), and was followed by a template-switching PCR (TS-PCR) amplification step. We demonstrate that, using the microfluidic protocol, 74% of the genes expressed in mouse brain were detected, while only 4% were found with the conventional approach. We next profiled single neuronal progenitors. Using our microfluidic approach, i.e. performing cell capture, lysis and reverse transcription on-chip followed by TS-PCR amplification in tube, a mean of 5000 genes were detected in each neuron, which corresponds to the expected number of genes expressed in a single cell. This demonstrates the outstanding sensitivity of the microfluidic method.
Keywords: Single cell, transcriptome, PDMS, microfluidic, reverse-transcription (RT), template-switching, lab-on-a-chip

overall_design:
To validate our approach, we first reverse-transcribed 10pg of mouse forebrain RNA, which corresponds to the RNA content of a single cell, either in a microcentrifuge tube, in 10 µL, or in a 7 nL rotary mixer. Then, the cDNAs were all amplified in tubes by template-switching PCR (TS-PCR, 40 cycles). We also performed control experiments using 15µg of RNA without amplification. The gene expression profiles were  compared using pangenomic microarrays.
Single embryonic neuronal cells were dissociated from CGE explants and trapped into the microfluidic device. Cell lysis and reverse-transcription reactions were performed in the rotary mixer. cDNAs were then amplified by TS-PCR in tubes. In parallel, 5µg of RNA from the explant were reverse-transcribed without amplification. Gene expression profiles were next examined using pangenomic microarrays.

first: Nathalie

last: Bontoux

first: Tania

last: Vitalis

first: Vincent

last: Studer

last: Chen

first: Jean

last: Rossier

first: Marie-Claude

last: Potier


title: The birth and death of microRNA genes in Drosophila

city: Chicago

first: Chung-I

last: Wu

state: IL

address: 1101 57th East

department: Ecology and Evoluation

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary:
MicroRNAs (miRNAs) are small, endogenously expressed RNAs
that regulate mRNAs post-transcriptionally. The class of miRNA
genes, like other gene classes, should experience birth, death
and persistence of its members. We carried out deep
sequencing of miRNAs from three species of Drosophila, and
obtained 107,000 sequences that map to no fewer than 300
loci that were not previously known. We observe a large class
of miRNA genes that are evolutionarily young, with a rate of
birth of 12 new genes per million years (Myr). Most of these
new miRNAs originated from non-miRNA sequences. Among
the new genes, we estimate that 96% disappeared quickly in
the course of evolution; only 4% of new miRNA genes were
retained by natural selection. Furthermore, only 60% of these
retained genes became integrated into the transcriptome in the
long run (60 Myr). This small fraction (2.5%) of surviving
miRNAs may later on become moderately or highly expressed.
Our results suggest that there is a high birth rate of new
miRNA genes, accompanied by a comparably high death rate.
The estimated net gain of long-lived miRNA genes, which
is not strongly affected by either the depth or the breadth
(number of tissues) of sequencing, is 0.3 genes per Myr
in Drosophila
Keywords: 454 microRNA deep sequencing

sample_organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans

overall_design: Three small RNA samples from male heads of D. melanogaster, D. simulans and D. pseudoobscura were analyzed. The small RNAs were sequenced by 454 technology. After removing the flank adaptor sequences, the inserted sequences greater than 18nt were extracted.

first: Jian

last: Lu

first: Yang

last: Shen

first: Qingfa

first: Supriya

last: Kumar

first: Bin

last: He

first: Suhua

last: Shi

first: Richard

last: Carthew

first: SanMing

last: Wang


title: Recurrent 15q13 microdeletions

status: Public on Feb 17 2008

city: Seattle

first: Heather

last: Mefford

state: WA

address: 1705 NE Pacific St

department: Genome Sciences

institute: University of Washington

summary:
We report a recurrent microdeletion syndrome causing mental retardation, epilepsy and variable facial and digital dysmorphisms. We describe nine patients, including six probands; two with de novo deletions, two who inherited the deletion from an affected parent, and two with unknown inheritance. The proximal breakpoint of the largest deletion is contiguous with breakpoint 3 (BP3) of the Prader-Willi/Angelman region extending 3.95 Mb distally to BP5. A smaller 1.5 Mb deletion has proximal breakpoint within the larger deletion (BP4) and shares the same distal BP5. This recurrent 1.5 Mb deletion contains six genes, including a candidate gene for epilepsy (CHRNA7) that is likely responsible for the observed seizure phenotype. The BP4-BP5 region undergoes frequent inversion, suggesting a possible link between this inversion polymorphism and recurrent deletion. The frequency of these microdeletions in mental retardation cases is ~0.3% (6/2082 tested), a prevalence comparable to that of the Williams, Angelman, and Prader-Willi syndromes.
Keywords: microdeletion, genomic disorder, mental retardation, epilepsy

overall_design: Patients were intially screened by BAC array CGH (n=290) or qPCR (n=1040). Patients with potential 15q13 deletions were then analyzed on a custom oligonucleotide array targeted to the 15q13 region, results of which are shown here.

first: Andrew

middle: J

last: Sharp

first: Evan

last: Eichler


title: Physiological and Transcriptional Responses of Nitrosomonas europaea to Toluene and Benzene Inhibition

city: Corvallis

first: Tyler

middle: Steven

last: Radniecki

state: OR

address: 101 Gleeson Hall

department: CBEE

institute: Oregon State University

summary:
The effects of the aromatic hydrocarbons benzene and toluene on Nitrosomonas europaea, a nitrifying bacterium that plays an important role in the removal of nitrogen from wastewater treatment plants, were studied in batch reactors.  Exposure to 20  M toluene and 40  M benzene resulted in a 50% reduction in nitrifying activity after 1 h.   However, Affymetrix microarray experiments detected no significant changes in gene expression in toluene exposed cells.  Cells exposed to benzene were found to up-regulate a gene cluster (NE 1545 - NE 1551).  This gene cluster appears to be involved with fatty-acid metabolism, lipid and membrane protein biosynthesis.  TEM experiments reveal that cells exposed to benzene decrease the thickness of their membrane and the membrane becomes more structured.
Keywords: stress response, benzene, toluene

overall_design:
40 uM benzene caused 50 % inhibition in physiological response following 1 hour incubation. Transcriptional levels of the cells inhibited by benzene were compared with the cells under control conditions (ie, no benzene).
20 uM toluene also caused 50 % inhibition in physiological response following 1 hour incubation. Transcriptional levels of the cells inhibited by toluene were compared with the cells under control conditions (ie, no toluene).

first: Lew

last: Semprini


title: Gene expression during innate immunity in tobacco triggered by bacteria.

first: Jia

last: Liu

summary:
To study basal resistance we inoculated tobacco plants with Pseudomonas syringae pv. syringae 61 hrcC mutants (gift of A. Collmer). To compare the expression profiles of basal resistance to hypersensitive response, we used P. syringae pv. syringae 61. Gene activation triggered by the live compatible pathogen P. syringae pv. tabaci was compared to kanamycine-inactivated P. tabaci (10 min in 100 ug/ml KM, then washed 2x in H2O). Water-infiltrated control leaves were used. The aim of another set of experiments was to investigate the influence of various signal transduction pathways on basal resistance. Control plants were infiltrated with P. syringae pv syringae hrcC mutant bacteria. These were compared to treatments, in which the bacterial suspensions were supplemented with inhibitors that can block a specific type of signal transduction pathway. The inhibitors represented Ca2+ signaling, lipid derived signals generated by phospholipase C and A, protein phosphorilation (kinases) and protein degradation (degradation of transcription repressors or activators). The used inhibitors were LaCl3, neomycin, aristolochic acid, K252a and MG115 respectively. 2-2.5 months old tobacco plants (Nicotiana tabacum cv. Samsun nn) were grown in a greenhouse in soil with cca. 16/8 hr light/dark period at 20°C, then in a growth chamber 2 days before and during experiments, under identical conditions. A syringe was used for the injection of bacteria or chemical solutions into the tobacco leaves. At 6 or 48 hours post inoculation, leaf samples were taken, and frozen in liquid nitrogen.  Every experiment was carried out in 3 independent replicates. Total RNA was extracted using the Quiagen RNeasy Plant Mini kit and the Quiagen Rnase-free Dnase Set, then re-purified and concentrated on Microcon-30 (Millipore) columns. The concentration and quality of isolated RNA was estimated by measuring its absorbency at 260 and 280 nm and running on 1% agarose gel.
Keywords: Direct comparison

sample_organism: Nicotiana langsdorffii x Nicotiana sanderae

overall_design: 30 hybs total

first: Agnes

last: Szatmari


title: Comparative Solanum wild species transcription profiles under controlled water stress conditions

summary:
The aim of the present work is to apply microarrays to identify candidate genes associated with the strategies adopted by different Solanum wild species to maintain their metabolism and limit the harm under water stress conditions. Wild genotypes are a rich source of novel genes for introduction into cultivated species to enhance stress tolerance. The mechanisms in which genes act can involve different pathways inside the cell, resulting in the expression of stress responsive genes. We will identify genes whose expression change in the leaves of potato plants subjected to drought stress. We will analyze different Solanum genotypes in six moments of water stress (0,1,3,5,7 & 10 days after initiation of stress). We will selected 4 time-points (days 0,5,7 & 10) and 2 genotypes (with divergence behavior) for microarrays analysis. The candidate genes obtained with this approach will be validated by semi-quantitative northern blot analysis (Typhoon scanner) and/or RT-PCR in each time-point of treatment and with all wild genotypes in study. This will help us to get a better understanding respect the dynamics of expression of a great number of genes in response to stress, as well as to establish functional relations between the involved genes. Research Plan: 5-weeks-old Solanum wild species plants were randomly sorted in 2 groups (25 plants per group). One group was submitted to non-irrigated conditions, withholding water and the other was normally watered. For microarray analysis, leaflets tissue from 4 plants per group of 4 time-points (days 0,5,7, & 10) were pooled, frozen in liquid nitrogen and stored at –80°C.RNA of the pool was extracted following TRIZOL method (Invitrogen). RNA integrity was verified on agarose gel. Hybridizations were performed with n genotypes,t time-points and r repeats. The hybridizations proposed in this experiment to enhance statistical robustness of data will be: 32 slides = n*t*r ; (2 genotypes; 4 time-points; 4 repeats (dye-swap).
Keywords: Direct comparison

overall_design: 32 hybs total

first: María-Florencia

last: Lucca


title: Signalling events triggered in response to gibberellins during potato tuber sprouting

summary:
The aim of this study is to analize the genes that are up or down-regulated in response to sprouting promoting effectors such as GAs and light, in order to elucidate the signalling cascades triggered during this process. Half sections of certified pathogen tested Spunta tubers were put into sterile MS-agar (0.7%) containing flasks at 16„aC and subjected to different treatments:  Dark controls: Tuber sections were incubated for 10 or 35 days in complete darkness. Light control: Tuber sections were incubated  for 10 days under continuous light conditions.   Treatments performed in complete darkness during 35 days: a) GA treatment: 5 uM gibberellic acid (C19H22O6) = GA3 (Sigma) b) Sucrose treatment: 1% sucrose  c) GA & sucrose treatment: 5 uM GA3 (Sigma) + 1% sucrose  Treatments performed in light (10 days)d) GA treatment  : 5 uM GA3 (Sigma).   Three independent biological replicates of each condition (3 controls and 4 treatments) wereperformed. At the moment of harvest (10 or 35 days) sprout length was measured and photographs of the different samples were taken. Sprouts were excised and frozen in liquid Nitrogen. Total RNA was obtained using the Trizol reagent (Invitrogen) according to the manufacturer¡¦s instructions. RNAs were quantified by OD: 260/280 and checked in agarose gels.
Keywords: Loop design

overall_design: 25 hybs total

first: Rita-María

last: Ulloa


title: Maize primary roots: inbred lines vs. hybrids

status: Public on Feb 16 2008

city: Bonn

first: Frank

last: Hochholdinger

state: BW

address: Katzenburgweg 1a

department: INRES - Crop Functional Genomics

institute: University of Bonn

summary:
The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. To achieve this goal a two step strategy was selected. First, a microarray preselection of non-additively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high throughput qRT-PCR experiments. Initial microarray experiments identified 1941 non-redundant genes which displayed non-additive gene expression in at least one of the twelve analyzed hybrids compared to the midparent value of their parental inbred lines. Comparison of these 1941 genes with non-additively expressed genes identified in maize shoot apical meristems via the same experimental procedure in the same genotypes revealed significantly less overlap than expected by pure chance supporting. This supports the notion of organ specific patterns of non-additively expressed genes.  qRT-PCR analyses of 64 of the 1941 non-additively expressed genes in four different hybrids revealed that the majority of non-additively expressed genes were expressed between the high and low parent expression values and only a small fraction of genes was expressed below low or above high parent levels. Subsequently, 22 of the 64 genes that displayed non-additive expression in all four hybrids were analyzed in twelve hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all twelve hybrids and might thus play a protective role in antioxidative defense in the primary root of maize hybrids. These findings are consistent with the hypothesis that global expression trends but also the consistent differential expression of key genes might be relevant during the organ-specific manifestation of heterosis.
Keywords: Comparative genomic hybridization

overall_design: Comparison of four inbred lines and the resulting twelve reciprocal hybrids. Samples from all 16 genotypes were paired on 85 arrays following a hybridization scheme including a dye-swap according to Keller et al. (2005). A tailor-made design was developed for this purpose using simulated annealing that was optimized for estimating non-additive effects while at the same time allowing estimation of additive effects with comparable precision. Optimizing precision for estimation of non-additivity required the design to be unbalanced with respect to the number of genotype pairings and the number of replications per genotype. Hence, two RNA samples were hybridized to each of the 85 microarray chips. Each RNA sample represented an independent biological replicate

first: Nadine

last: Hoecker

first: Barbara

last: Keller

first: Nils

last: Nuthreich

first: Didier

last: Chollet

first: Patrick

last: Descombes

first: Hans-Peter

last: Piepho


title: Transcriptional profiling of NF-kB's Rel and RelA proteins

city: Piscataway

first: Celine

last: Gelinas

state: NJ

address: 679 Hoes Lane

department: UMDNJ-Robert Wood Medical School

institute: Center for Advanced Biotechnology and Medicine

summary:
Rel and RelA proteins were stably expressed in the chicken DT40 pre-B cell line and analyzed by transcription profiling to identify  transformation-impacting genes regulated by NF-kB’s oncogenic v-Rel and c-Rel proteins. This analysis uncovered both common and differential  gene expression profiles in cells expressing Rel vs. RelA proteins, and revealed that Rel protein expression can lead to gene-specific  transcriptional repression, as seen for key B-cell receptor (BCR) components and signaling molecules like B-cell linker (BLNK), the B-cell  adaptor for PI3K (BCAP) and Igλ. These were also downregulated in cells expressing a transformation-competent chimeric RelA/v-Rel protein,  suggesting a correlation with the capacity of Rel proteins to transform lymphocytes. DNA binding, ChIP and transformation assays indicate  that downregulation of BLNK and BCAP is an important contributing factor to the malignant transformation of lymphocytes by Rel and suggest that gene repression may be as important as transcriptional activation for the transforming activity of Rel proteins.
Keywords: Comparative transcriptional profiling

overall_design:
v-Rel, c-Rel (chicken, mouse, human), RelA (mouse, human) or a human RelA/v-Rel chimera were stably expressed at equivalent levels in the  chicken pre-B-cell line DT40. Three independent cell clones were analyzed for each protein, using dye-swap experiments. Their gene expression profiles were compared to that of parental DT40 cells by cDNA microarray. Triplicate data sets were averaged to identify changes in gene expression in response to expression of each of these proteins.

Differential expression analysis was performed using CyberT (Baldi and Long, Bioinformatics, 2001), a Bayesian t-statistic methodology that is designed for microarray analyses in studies with low replicate numbers. For our CyberT analysis, we employed the default parameters. Differential gene expression was identified by ranking each gene's corresponding Bayesian p-values and applying a false discovery rate correction of 5% (Benjamini and Hochberg, J R Statistical Soc Ser B - Methodological, 1995). In addition, we applied a fold-change threshold of ± 1.5 as an additional criterion. Accordingly, relative expression levels for a given gene with a p-value that satisfies the FDR condition and fold-change criteria were identified as differentially expressed.  Note: relative expression levels were transformed to natural log  (ln) for CyberT analysis and the results are reported in those units.

Results of differential expression analysis are reported in the supplementary table "Differentially-expressed genes for each condition" where 1=TRUE, 0=FALSE.

first: Nupur

last: Gupta

first: Jeffrey

last: Delrow

first: Amar

last: Drawid

first: Anirvan

last: Sengupta

first: Gaofeng

last: Fan

first: Céline

last: Gélinas


title: Heat-stress of maturing microspores derived from wild type and starch-less mutant plants of Nicotiana sylvestris

first: Jia

last: Liu

summary:
Pollen development is one of the most heat-sensitive developmental stages in a wide range of crops. Our longer-term goal is to understand the mechanism how starch metabolism in maturing pollen grains of the Solanaceae family contributes to maintaining higher pollen quality under heat-stress conditions. The specific aim of the suggested proposal is to characterize N. sylvestris WT and mutant (starch-deficient) transcriptomes during microgametogenesis under ambient and heat-stress conditions. Expression profiles of maturing microspores derived from flower buds at developmental stage of 4 to 2 days before flower opening will be obtained. Pollen was derived from WT and mutant plants exposed to either ambient or heat-stress conditions (exposing the plants to 45oC for 2.5 hours).
Keywords: Loop design

overall_design: 12 hybs total

first: Nurit

last: Furon


title: Potato Encyclopedia

summary:
The purpose of this study is to survey gene expression of potato (solanum tuberosum gilroy) in a variety of tissues and life cycle timepoints.  Potato plants were grown from true seeds, planted in either soil or MS media, and grown in growth chambers.  Four biological replicates each of twenty different tissue samples were collected at the appropriate timepoints.  The samples were immediately frozen at -80.  The tissues were then ground into a powder in liquid nitrogen, and RNA was extracted using Qiagen's QiaShredder columns and Qiagen's Rneasy MinElute Kit.  The RNA was amplified using Arcturus' RiboAmp RNA Amplification Kit.  1ug of amplified RNA was used in TIGR's indirect labelleling procedure.  All hybridaztions were applied to TIGR's 10kV4 potato array.
Keywords: Loop design

overall_design: 36 hybs total

first: Robin

last: Buell


title: Escherichia coli treated with 13 antibiotics, 3 synergistic combinations, and IPTG

status: Public on Feb 12 2008

city: La Jolla

first: Michael

last: Sykes

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
Microarrays allow us to monitor the change in transcription of every gene in the genome in response to a change in cellular state.  We use cDNA microarrays to measure the response of E. coli to 13 different antibiotics and 3 synergistic combinations.  Hierarchichal clustering reveals 4 distinct classes of antibiotics distinguished by their modes of action, and allows us to predict the mechanism for promethazine, a drug whose mode of action has not previously been established.
The expression profiles of the synergistic combinations exhibit a complex relationship between the two component antibiotics, with similarity to one of the two drugs, as well as a surprising number of new gene responses exhibited by E. coli in response to neither drug alone.  The subset of drugs which act in synergy with each other suggests that only very specific combination of mechanisms give rise to synergistic behavior.
Keywords: stress response, antibiotic response, synergy

overall_design:
Each array has two spots to monitor the response of E coli to one of the treatments, and two control spots (ie no treatment).  These are background corrected, normalized for total intensity, and then the average volume difference is calculated.  Each treatment has two replicates, and the result is average across these two replicates.  Our final processed data is a relative volume difference, in which the aforementioned volume difference is divided by an estimate of the error in the data.  This relative volume difference gives us greater confidence that the changes we see are real.  Any relative volume difference >= 2 or <= -2 (ie where the absolute volume difference is twice as much as the estimated error or more) is considered to be significant.
Total of 68 hybridizations: 17 samples X 2 replicates for each sample X (1 sample + 1 control for each replicate)

first: Plachikkat

last: Radha

middle: T

first: James

last: Williamson


title: Transcriptional profiling of two stress responses in potato

summary:
Potato (cv. King Edward and Bintje) tubers were obtained from local suppliers, and synchronized by storage in darkness for 3 weeks at +4 C followed by +20 C for two days. Tubers were then stressed in a time-course experiment either by exposure to white light (0 to 96h) or wounded by sectioning into 5mm pieces (0 to 48h).
Keywords: Reference design

first: Sitbon

last: Folke


title: Transcriptional rearrangements in tomato in response to herbivory and signals of competition

summary:
In plants, an increase in resource allocation to growth (primary metabolism) associated with the presence of neighbors is likely to reduce defense-related production (secondary metabolism), making plants more vulnerable to herbivory. Even though there is increasing evidence supporting this “trade-off hypothesis”, the underlying mechanisms are still unclear. Far red (FR) radiation reflected from plant tissues serves as an early warning signal of future competition, triggering a suite of plastic morphological adjustments that improve plant’s ability to compete for light in crowded populations. Recent evidence from our lab showed that, when competition signals are present, plant defenses are severely reduced. Besides direct effects of herbivory and competition signals on target plants, second order effects occurs on neighboring plants through plant volatiles (PVs) communication. PVs play a key role in plant-plant and plant-insect interactions, changing its content and composition in response to environmental conditions. To increase our understanding of the molecular mechanisms underlying those interacting signaling webs, we performed a field study with tomato plants (cv Moneymaker), in which plants of EMITTER plots (six plants plot-1) were subjected to herbivory (nine larvae of Spodoptera eridania plant-1) and competition signals (increased FR radiation) in a factorial design. Light treatment started 28 days after sowing (DAS), and herbivory treatment and volatiles conduction started 34 DAS. Volatiles were conducted from EMITTER to RECEIVER plots (five plants plot-1) using a 5 inch, 1.4 m long tube fitted with a computer-type fan. 40 and 45 DAS, larval performance was measured on EMITTER plots as well as naturally-occurring insect colonization on RECEIVER plots. Finally (46 DAS), samples for bulk phenolic content were taken on every plot, and plant material from 4th and 5th leaves was collected for microarray analysis. There were three real biological replicates.
Keywords: Reference design

overall_design: 18 hybs total

first: Mazza

last: Carlos


title: Analysis of Potato Smooth Skin Mutant Susceptible to Powdery Scab Disease

summary:
Russet Nugget and the corresponding smooth skin mutant tubers harvested from disease and healthy filed plots. Tubers were washed with 10% Clorox and dried before harvesting tissue. Cortex and peel tissue was collected from healthy and infected regions of the mutant. Healthy peel and cortex tissue was collected from Russet Nugget (wild-type) potato tuber and snap-frozen in liquid nitrogen and stored at -80 °C. RNA was extracted from frozen tissues using a hot phenol method in triplicate from the different sets of tuber tissue. Extracted RNA was purified by Qiagen kits after treatment with DNAse. In all of these experiments RNA from Russet Nugget peel and cortex tissue will be used as reference samples where as mutant tissue will be used as query samples.
Keywords: Direct comparison

overall_design: 15 hybs total

first: Sastry

last: Jayanty


title: Gene expression of D. vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

institute: University of Calgary

summary:
The gene expression profile of wild-type Desulfovibrio vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells over-expressed two hydrogenases, the hyn1 genes for [NiFe] hydrogenase-1, and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high molecular weight cytochrome (Hmc) complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also over-expressed. In contrast, cells grown on gaseous hydrogen over-expressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also over-expressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn1-, hyd-, and hmc-mutant biofilms, as compared to wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion.
Keywords: Growth on Iron Electrode and Biofilm formation

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

middle: M

first: Hung-So

last: Park

first: Jenny

last: Been

first: Paul

last: Gordon

first: Christoph

middle: W

last: Sensen

first: Gerrit

last: Voordouw


title: Non-cancerous liver infiltrating lymphocytes of hepatitis C and tumor-infiltrating lymphocytes

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

institute: Kanazawa University

summary:
Study goal is to disclose features of gene expressio profile of non-cancerous liver-infiltrating lymphocytes of type C hepatitis patients with hepatocellular carcinomas and  tumor-infiltrating lymphocytes of type C hepatitis patients with hepatocellular carcinomas.
Keywords: gene expression profile, non-cancerous liver-infiltrating lymphocytes, tumor-infiltrating lymphocytes, type C hepatitis, hepatocellular carcinoma

overall_design:
Non-cancerous liver-infiltrating lymphocytes were obtained by laser capture microdissection from surgically resected liver tissues of 12 type C hepatitis patients with hepatocellular carcinoma. The mRNA was amplified and expression profile was comprehensively analyzed with reference RNA using oligo-DNA chip.
Tumor-infiltrating lymphocytes were obtained by laser capture microdissection from surgically resected cancer tissues of 12 type C hepatitis patients with hepatocellular carcinoma. The mRNA was amplified and expression profile was comprehensively analyzed with reference RNA using oligo-DNA chip.

first: Masao

last: Honda

first: Isamu

last: Tatsumi

first: Haruo

last: Fujinaga

first: Shuichi

last: Kaneko


title: Electric current induced genes in Escherichia coli

city: Knoxville

middle: Thomas

last: Fleming

address: 676 Dabney Hall

department: Center for Environmental Biotechnology

institute: University of Tennessee

summary:
The control of cellular processes by direct electronic interface will facilitate the development of biosensors, synthetic biology, and nanobiotechnology by providing the means to pass information from synthetic to living elements of hybrid systems.  To investigate the potential of manipulating cellular gene expression by means of electric current, Escherichia coli cultures were screened for electric current inducible genes using global gene expression profiling.  Cells in stationary phase were subjected to a DC current density of 2.5 mA/cm2 for 2 min after which the cells were lysed and the total RNA extracted.   Of the 4290 expressed genes in E. coli , 432 genes were found to be significantly differentially expressed at an effective alpha value of 5.8 X 10-6.    Of these, 333 genes were induced and 99 repressed.  Several genes were verified as differentially expressed by quantitative real-time RT-PCR. The set of differentially expressed genes were examined for the presence of regulatory factors, subsidiary regulon genes, and biological function, particularly redox functions.  Transcripts for the regulatory proteins fnr, sspB, soxS, oxyR,  creB and yeiL were found to be up-regulated, and crp was down regulated.  While soxS and oxyR were up-regulated, the downstream genes controlled by these regulatory proteins were not differentially expressed, suggesting that the oxidative stress level of low-current electric exposure is small.  Genes controlled by FNR and CRP, many of which have redox function, were found to be differentially expressed suggesting modulation by direct reduction that can only be partially explained as a  response to the reducing environment created by the electrolytic generation of H2 at the cathode. Genes associated with phosphate metabolism and membrane proteins were also differentially expressed.
Keywords: electric current induced gene expression

overall_design: Three biological replicates were exposed to electric current along with three biological replicate controls.

first: Donald

last: Fox

first: Michael

last: Simpson

first: Gary

last: Sayler


title: Identifying Compartment-specific Alloimmune Targets After Renal Transplantation by integrated genomics

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

summary:
Microarray technology has evolved as a powerful tool over the last decade, to identify biomarkers and study the mechanisms of diseases. We propose a novel application of integrated genomics by combining transcriptional levels with serological antibody profiling after kidney transplantation, with the aim of uncovering the relative immunogenicity of seven different renal compartments after allo-transplantation. Thirty-six paired pre- and post-transplant serum samples were examined from eighteen transplant recipients, across 5,056 protein targets on the ProtoArray V3.0 platform. Normal renal compartment-specific gene expression data from a cDNA platform were re-analyzed and both the cDNA and the ProtoArray platforms were re-annotated to most up-to-date NCBI gene identifiers; 3,835 genes/proteins are measured on both platforms. Antibody levels were ranked for individual patients and the hypergeometric enrichment statistic was applied on mapped compartment-specific expression data. We discovered that after transplantation, in addition to HLA and MICA responses, temporal alloimmune responses are seen against non-HLA antigens specific to different compartments of the kidney, with highest level responses noted against renal pelvis and cortex specific antigens. The renal medulla is of low immunogenicity as none of the outer or inner medulla specific targets generated significant post-transplant antibody responses. Immunohistochemistry confirmed pelvis and cortex specific localizations of selected targeted antigens, supporting the robust nature of this discovery. This study provides a road map of renal compartment-specific non-HLA antigenic targets responsible for generating alloimmune responses, opening the door for clinical correlations with post-transplant dysfunctional states to be determined.
Keywords: alloimmune response after kidney transplantation

overall_design:
Plasma profiling using Protein Microarray: Serum antibodies were profiled using Invitrogen ProtoArray® Human Protein Microarray v3.0 technology (Invitrogen, Carlsbad, CA). This platform contains 5,056 non-redundant human proteins expressed in a baculovirus system, purified from insect cells and printed in duplicate onto a nitrocellulose-coated glass slide. Five mL serum diluted in PBST buffer at 1:150 was applied for 90 minutes onto the Protoarray, after blocking with blocking buffer for 1 hour. The slides were then washed with 5ml fresh PBST buffer, 4 times for 10 minutes each, and probed with secondary antibody (goat anti-human Alexa 647, Molecular Probes, Eugene, OR) for 90 minutes. Finally, after a second washing with PBST buffer, the slides were dried and scanned using a fluorescent microarray scanner (GSI Luminoics Perkin-Elmer scanner). All steps were carried out on a rotating platform at 4 ºC.
ProtoArray data acquisition and measurement:
The slides were scanned at a PMT gain of 60% with a laser power of 90% and a focus point of 0 μm. Fluorescence intensity data were acquired using GenePix Pro 6.0 software (Molecular devices, Sunnyvale, CA) with the appropriate “.gal” file downloaded from the ProtoArray central portal on the Invitrogen website (http://www.invitrogen.com/protoarray) by submitting the barcode of each ProtoArray slide.

first: Persis

last: Wadia

first: Rong

last: Chen

first: Neeraja

last: Kambham

first: Maarten

last: Naesens

first: Tara

last: Sigdel

first: David

last: Miklos

first: Minnie

last: Sarwal

first: Atul

last: Butte


title: Architecture of thermal adaptation in Exiguobacterium sibiricum strain 255-15: A genome and transcriptome approach

status: Public on Feb 11 2008

city: East Lansing

first: Debora

middle: Frigi

last: Rodrigues

state: MI

address: 540 Plant and Soil Science Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary:
Several microorganisms have wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments. To better understand thermal adaptation of psychrotrophs, Exiguobacterium sibiricum strain 255-15 was used, a psychrotrophic bacterium that grows from -5°C to 39°C. Its genome is approximately 3 Mb in size, has a GC content of 47.7% and includes 2,978 putative protein-encoding genes (CDS). The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of about 27%, 3.2% and 5.2% of E. sibiricum strain 255-15 CDS spotted on the DNA microarray yielded differentially expressed genes in cells grown at -2.5°C, 10°C and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89% and 2.3% of the CDS differentially expressed when grown at -2.5°C, 10°C and 39°C versus 28°C. The transcriptome analyses showed that E. sibiricum is constitutively adapted to cold temperatures since little differential gene expression was observed at growth temperatures of 10°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, much more differential gene expression occurred. The genes that responded were more typically associated with stress response.
Keywords: stress response to cold and hot temperatures

overall_design: Six-condition experiment: -2.5°C vs10°C, -2.5°C vs 28°C, -2.5°C vs 39°C, 28°C vs10°C, 28°C vs 39°C, 10°C vs 39°C. Biological replicates: 6 replicates grown and harvested independently for each different temperature (-2.5°C, 10°C, 28°C and 39°C). One replicate per array.

first: Natalia

last: Ivannova

first: Jizhong

last: Zhou

first: Zhili

last: He

first: Marianne

last: Huebner

first: James

last: Tiedje


title: Low temperature sweetening of potato tubers

first: Jia

last: Liu

summary:
This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers.
Keywords: Reference design

first: Paul

last: Bethke


title: Expression profile of peripheral blood mononuclear cells obtained from type C cirrhotic patients

first: Yoshio

last: Sakai

summary:
Study goal is to disclose features of gene expression profile of peripheral blood mononuclear cells obtained from type C cirrhotic patients with or without hepatocellular carcinomas.
Keywords: gene expression profile, peripheral blood mononuclear cells, type C liver cirrhosis

overall_design: Peripheral blood mononuclear cells were obtained from 32 type C cirrhotic patients without hepatocellular carcinoma (LC) or from 30 type C cirrhotic patients with hepatocellular carcinoma (HCC). The mRNA was amplified and expression profile was comprehensively analyzed with reference RNA using oligo-DNA chip.

first: Masao

last: Honda

first: Isamu

last: Tatsumi

first: Haruo

last: Fujinaga

first: Shuichi

last: Kaneko


title: Gene expression profiling of caffeic acid phenethyl ester-treated human umbilical vein endothelial cells-1

city: San Antonio

first: Xinyu

last: Wang

state: TX

address: 3400 Rawley E. Chambers Ave., Bldg. 3611

institute: US Army Institute of Surgical Research

summary:
Caffeic acid phenethyl ester (CAPE), derived from various plant sources, has been shown to ameliorate ischemia/reperfusion (I/R) injury in vivo, and this has been attributed to its ability to reduce the oxidative stress. Here we investigated the cytoprotection of CAPE against menadione (MD)-induced oxidative stress in human umbilical vein endothelial cells (HUVEC) to evaluate potential gene expression involvement. CAPE exhibited dose-dependent cytoprotection of HUVEC that required preincubation. A gene screen with microarrays was performed to identify the potential cytoprotective gene(s) induced by CAPE. Heme oxygenase-1 (HO-1) was highly upregulated by CAPE and this was confirmed with reverse transcriptase polymerase chain reaction (RT-PCR) and western blotting.
Keywords: Gene expression in HUVEC, CAPE cytoprotective dose response

overall_design: Confluent HUVEC were incubated with cytoprotective dose of CAPE at 5 µg/ml or 0.1% DMSO as vehicle control for 6 hrs. Both treatments were done in triplicates. Total RNA was isolated at the end of the treatment and applied to microarray experiments in order to identify transcriptional response of HUVEC to CAPE. Microarray experiments were based on a two-color reference design using human universal reference RNA to compare results bwtween CAPE treatment and vehicle control groups.

first: Phillip

last: Bowman


title: PARP-1 and H1 custom ChIP-chip

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary:
PARP-1 and H1 ChIP-chips were performed to compare the genomic binding patterns of these chromatin binding factors
Keywords: ChIP-chip

overall_design: Two PARP-1 and two H1 ChIP-chip biological replicates are included. An H3 ChIP-chip sample is included as a control

first: William

first: Raga

last: Krishnakumar

first: Matthew

last: Gamble


title: Genetic variation in Glp1r expression influences the rate of gastric emptying

city: Baton Rouge

first: Brenda

last: Richards

state: LA

address: 6400 Perkins Rd.

department: Basic Science

institute: Pennington Biomedical Research Center

summary:
A C57BL6/J (B6) x CAST/Ei (CAST) strain intercross has revealed a new quantitative trait locus (QTL) on Chromosome (Chr) 17 controlling total food volume (Tfv1; LOD=7.6).  Compared with B6, the CAST mice consume 39% more food volume per body weight in a macronutrient diet selection paradigm.  Linkage analyses of total food volume revealed the presence of suggestive QTL on Chrs 2, 6, and 15 and a significant locus on Chr 17.  An interval-specific congenic strain, B6.CAST-17, was then developed which verified the QTL.  Microarray analysis of stomach in congenic and wildtype B6 mice revealed Glp1r as an expression candidate with physiological relevance to food intake. Further functional analysis of this gene revealed this gene as potential candidate for total food volume trait in mice
Keywords: Comparative gene expression analysis

overall_design: RNA obtained from six male B6.CAST-17 homozygous congenic mice and six male wild type B6 mice. Each strain was represented by two pools, each containing equal amounts of RNA from three animals, for a total of four samples.  Thus, two biological replicates were analyzed for each strain.

first: Karunakaran

middle: G

last: Kumar

middle: K

last: Smith-Richards


title: MicroRNA profiles of 84 colon adenocarcinomas and paired nontumorous

city: Bethesda

first: Curtis

middle: C

last: Harris

address: Building 37, Room 3068A

department: Center for Cancer Research

institute: National Cancer Institute

summary:
The goal of this study was to identify microRNAs that were differentially expressed in colon tumors and determine if microRNA expression profiles could predict poor cancer survival.
Keywords: disease state design

overall_design: For these experiments, we used RNA extracted from pairs of colon adenocarcinoma tissue and adjacent nontumorous tissue. RNA from pairs of tissues were hybridized on the same day with up to 12 pairs of tissues being hybridized on a given day. To identify differentially expressed microRNAs, paired class comparison in BRB array tools was used.  Samples were paired in the individual from where the tissues originated. Therefore, every tumor tissue has it's own nontumorous reference for comparison.


title: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae knockout mutants at different hybridization conditions and PMTs

status: Public on Feb 08 2008

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

summary:
Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are important bacterial pathogens of the worldwide staple and grass model, rice. Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice throughout the world. Xoc colonizes the parenchyma tissue to cause bacterial leaf steak, a disease of emerging importance. We have designed oligonucleotide probes (50-70-mers) represented 2,858 Xoo genes and 1,816 Xoc genes annotated by The Institute for Genomic Research (TIGR). To validate the Xo arrays, self-hybridization samples and tests of the non-specific hybridization using randomly spotted oligonucleotides corresponding to the hygromycin phosphotransferase gene (hph), and blank spot and of the correlation coefficient between biological replicates as well as between duplicate spots revealed that the data generated from our oligo array were highly reliable and consistent.
To optimize the suitable protocol for hybridizing sample onto XOarray slides, we performed hybridization with 4 temperature levels (42 0C, 44 0C, 48 0C, and 52 0C) and 5 numbers of template amounts (10 pMol, 20 pMol, 30 pMol, 40 pMol, and 50 pMol) for hybridization process. Two level of PMT (Power of the scanner photomultiplicator) exposed to hybridized glass slides. Total samples is 36 slides (4 temperatures x 2 technical replicates x 2 PMT level = 16 slides and 5 numbers of template amount x 2 technical replicates x 2 PMT level = 20 slides).
Keywords: Condition Optimization

sample_organism: Xanthomonas oryzae pv. oryzae KACC 10331

overall_design: Two different Xanthomonas oryzae pv. oryzae knockout mutant strains, phoP and rpfC, were cultured ion PSB media. 2 technical replicates.  4 sets for hybridization temperature optimization. 5 sets for template amount optimization. Every experimental set slides were scanned with two different PMT level, highPMT and lowPMT.

first: Young-Su

last: Seo

first: Li

first: Jirapa

last: Phetsom

first: Ki-Hong

last: Jung

first: Michael

last: Shultz

first: H

middle: H

last: Chou

first: Adam

last: Bogdanove

first: Pamela

last: Ronald


title: IAH Salmonella infected chicken caecal contents

city: Roslin

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

country: United Kingdom

institute: The Roslin Institute

summary:
RNA from in vitro grown Salmonella typhimurium is compared with RNA extracted from Salmonella typhimurium from infected chick caecums using a common DNA reference.
Keywords: Disease state analysis, infected versus uninfected, common reference

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
Five replicates from infected chick caecal contents compared to a common reference.

Three replicates from in vitro grown Salmonella compared to a common reference.

The common reference was genomic DNA and always occupies the Cy3 channel (channel 2).

first: Paul

last: Barrow

first: Philippa

last: Adam


title: Gene expression profiling of caffeic acid phenethyl ester-treated human umbilical vein endothelial cells-2

first: Xinyu

last: Wang

summary:
Caffeic acid phenethyl ester (CAPE), derived from various plant sources, has been shown to ameliorate ischemia/reperfusion (I/R) injury in vivo, and this has been attributed to its ability to reduce the oxidative stress. Here we investigated the cytoprotection of CAPE against menadione (MD)-induced oxidative stress in human umbilical vein endothelial cells (HUVEC) to evaluate potential gene expression involvement. CAPE exhibited dose-dependent cytoprotection of HUVEC that required preincubation. A gene screen with microarrays was performed to identify the potential cytoprotective gene(s) induced by CAPE. Heme oxygenase-1 (HO-1) was highly upregulated by CAPE and this was confirmed with reverse transcriptase polymerase chain reaction (RT-PCR) and western blotting.
Keywords: gene expression in HUVEC, CAPE cytoprotective dose response

first: Phillip

middle: D

last: Bowman