title: Microarray analysis of V. cholerae genes differentially expressed in 12 h rabbit ileal loop fluid

summary:
Transcriptional analysis of wild-type V. cholerae isolated from the rabbit ileal loop was performed by quickly pelleting bacteria from the fluid accumulated in the ileal loops after 12 h of infection. The bacteria were then resuspended in Trizol reagent and frozen on dry ice. The wild-type bacteria from two independent experiments in two different rabbits were analyzed. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Genomic comparison of vancomycin susceptible and vancomycin intermediate Staphylococcus aureus pairs

status: Public on Nov 03 2006

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

country: Australia

institute: Austin Health

summary:
To determine if significant genomic changes are associated with the development of vancomycin intermediate Staphylococcus aureus, genomic DNA microarrays were performed to compare the initial vancomycin susceptible Staphylococcus aureus (VSSA) and a related vancomycin intermediate Staphylococcus aureus (VISA) isolate from five unique patients (five isolate pairs).
Keywords: comparative genomic hybridization

overall_design: A single 2-channel array was performed for each isolate pair using genomic DNA. Raw data was compiled using IMAGENE. Normalisation and statistical analysis was undertaken using BASE. Statistics were performed using the Wilcoxon signed ranked test.

middle: P

first: Paul

middle: D

last: Johnson

first: Peter

middle: B

last: Ward

first: Timothy

last: Stinear

first: John

middle: K

last: Davies


title: Gene expression profiling in zebrafish embryos exposed to 3,4-dichloroaniline (3,4-DCA)

status: Public on Nov 08 2006

city: Leipzig

first: Doris

last: Voelker

address: Permoser Str. 15

department: Cell Toxicology

country: Germany

institute: UFZ Centre for Environmental Research Leipzig-Halle

summary:
The zebrafish (Danio rerio) embryo toxicity test (DarT) is considered as an alternative to the acute fish toxicity test. However, DarT rarely reveals information on the mechanisms underlying a toxic effect and is relatively insensitive compared to chronic toxic effects. We hypothesized that, by using gene expression profiles as an additional endpoint, it may be possible to increase the sensitivity and predictive value of DarT. Therefore we exposed zebrafish embryos for 48 h to the reference compound 3,4-dichloroaniline and analyzed gene expression patterns with a 14 k oligonucleotide array.
Keywords: differential gene expression upon chemical exposure in zebrafish embryos

overall_design: In three independent embryo toxicity tests zebrafish embryos were either treated with the LOEC of 3,4-DCA (12.4 µM) or exposed to test medium (control samples) for 48 hours. Total RNA was extracted and reverse transcribed into aminoallyl-labeled cDNA. Samples of control and treated embryos of all three tests were labeled to Cy3 or Cy5, respectively. For every single experiment dye-swaps were performed, giving a total number of 6 hybridizations.

first: Christoph

last: Vess

first: Georg

middle: W

last: Otto

first: Robert

last: Geisler

first: Kristin

last: Schirmer

first: Stefan

last: Scholz


title: Pol II localization in yeast termination mutants

status: Public on Nov 21 2006

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

country: USA

institute: UMass Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
RNA Polymerase II was mapped over 4% of the yeast genome by ChIP, in wild-type and a handful of mutants in transcriptional termination factors.
Keywords: ChIP-chip, transcription termination

overall_design: RNA Polymerase II was mapped over 4% of the yeast genome by ChIP, in wild-type and a handful of mutants in transcriptional termination factors.  RNA polymerase was isolated by ChIP from sonicated chromatin, amplified by PCR, and labeled by Klenow labeling with direct-labeled dCTP.

first: Minkyu

last: Kim

first: Lidia

last: Vasiljeva

middle: J

first: Alexander

last: Zhelkovsky

first: Claire

last: Moore

first: Stephen

last: Buratowski


title: A high resolution map of segmental DNA copy number variation in the mouse genome

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

type: Genome variation profiling by genome tiling array

summary:
Submicroscopic (< 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals.  The biological consequences of copy number variants (CNVs) are largely undefined.  CNVs have been detected in diverse species, including mice and humans.  Published studies in mice have been limited by resolution and strain selection.  We chose to study twenty-one well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data.  We performed comparative genomic hybridization using long oligomer arrays (oligo-aCGH) to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies.  The CNVs range in size from 21-2,002 kb.  Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains.  Most of the CNVs (77.5%) contain annotated genes.  We demonstrate that this technique can identify copy number differences associated with known polymorphic traits.  The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci.  Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.
Keywords: array comparative genomic hybridization (aCGH)

overall_design: 21 strains of mouse were assayed for copy number changes.  Seven strains were assayed at least twice.  DNA was extracted from tail for all strains.  For two strains spleen DNA was also assayed on separate chips.  C57BL/6 was used as the reference sample in all experiments.

middle: A

last: Graubert

first: Deepa

last: Edwin

first: Rebecca

middle: R

last: Selzer

first: Todd

last: Richmond

first: Peggy

middle: S

last: Eis

first: William

last: Shannon

first: Xi

last: Li

first: Howard

middle: L

last: McLeod

first: James

middle: M

last: Cheverud

last: Ley


title: Gene expression alteration in human fibroblast cells after folate depletion

status: Public on Nov 02 2006

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
The molecular basis linking folate deficiency to certain health conditions and developmental defects is complex and not fully understood.  In this study, we examined the consequences of folate deficiency on global gene expression by microarray analysis and compared transcript levels in normal human fibroblast cells (GM03349) grown in folate deficient and sufficient medium.
Keywords: folate depletion, stress response, comparative genomic hybridization

overall_design: Two biological replicates are analyzed, each in quadruplicate with dye-swaps.

first: Karen

last: Katula

first: Alexandra

middle: N

last: Heinloth

first: Richard

last: Paules


title: High-throughput sequencing of small RNAs from Arabidopsis thaliana

city: Cambridge

first: Ramya

last: Rajagopalan

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research, MIT Department of Biology

type: Non-coding RNA profiling by high throughput sequencing

summary:
High-throughput sequencing of Arabidopsis thaliana endogenous small RNAs by 454 pyrosequencing.
Keywords: high-throughput sequencing

overall_design: Small RNA cDNA libraries from wildtype Arabidopsis thaliana (Columbia accession) were constructed by fractionation of total RNA using polyacrylamide gel electrophoresis, followed by adaptor ligation and reverse transcription.  Pyrosequencing from these libraries was performed.  Detailed library preparation protocol can be found in Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006) A two-hit trigger for siRNA biogensis in plants.  Cell 127:565-577.

first: David

last: Bartel


title: Gene expression profile mediated by independent E-cadherin repressors

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary:
Gene expression profiling of MDCK epithelial cells expressing different repressors (MDCK-Snail, MDCK-Slug and MDCK-E47 cells) versus control MDCK cells.
Keywords: Genetic Modification (overexpression of E-cadherin repressors)

overall_design: The Oncochip microarray platform v1.1 contains 9,726 clones corresponding to 6,386 different genes, and it includes 2,489 duplicate clones. Duplicate samples from each of the MDCK transfectants (E47, SNAIL, SLUG) were labeled with dUTP-Cy5 and hybridized against the dUTP-Cy3-labeled MDCK-CMV controls. Two additional hybridizations using reciprocal fluorochrome labeling were performed (dye-swap). Thus, a total of four hybridizations were performed for each condition.

first: Gema

last: Moreno-Bueno

last: Sarrió

first: Jose

last: Palacios


title: SH-SY5Y cells treated with Quercetin-3-glucoside then H2O2

status: Public on Nov 01 2006

city: Halifax

first: George

last: Robertson

state: Nova Scotia

address: 5850 College Street

department: Departments of Psychiatry and Pharmacology

country: Canada

institute: Dalhousie University

summary:
Flavonoids are polyphenolic compounds with potent anti-oxidant and free radical scavenging activities. Here, we examined the cytoprotective actions of Quercetin-3-glucoside (Q3G) against oxidative stress induced by hydrogen peroxide. Pre-treatment of the neuroblastoma cells, SH-SY5Y with Q3G for 18 h reduced cell death after a brief exposure to hydrogen peroxide. The cytoprotective effects of Q3G were associated with decreased free radical generation suggesting that this mechanism accounts for Q3G-mediated cytoprotection. To address the possibility that Q3G-mediated cytoprotection involved alterations in gene expression, cDNA microarray studies were performed. These studies identified elevated expression of 25 genes and decreased expression of 3 genes only in Q3G pre-treated cells under oxidative stress. The majority of genes up-regulated by Q3G in SH-SY5Y cells under oxidative stress encode enzymes involved in lipid biosynthesis. Quantitative Real time PCR (qRT-PCR) validated changes in gene expression that were identified by cDNA microarray analyses. The induction of multitude of genes involved in cholesterol signaling pathway by Q3G in cells under oxidative stress suggests an important role for elevated cholesterol synthesis in the cytoprotective actions of Q3G. This hypothesis was confirmed by the detection of elevated levels of cholesterol in cells pre-treated with Q3G and subjected to oxidative stress. Moreover, inhibition of cholesterol biosynthesis with mevastatin blocked the cytoprotective effects of Q3G against oxidative stress-induced cell death. Taken together, these studies suggest a novel mechanism for flavonoid-induced cytoprotection involving elevated cholesterol synthesis that may act to reduce lipid peroxidation and promote membrane repair after oxidative injury.
Keywords: cytoprotection, oxidative stress

overall_design: The SH-SY5Y cells were treated with either Q3G or vehicle (DMSO) for 6 hours, then both were subject to an H2O2 insult. The labeled cDNA derived from Q3G treated cells plus H2O2 insult represent the "Experimental sample" while the labeled cDNA from DMSO treated plus H2O2 insult samples are the "Reference sample". Two batches of cells were so treated and dye swaps were done for each, giving a total of 4 replicates.

first: Ramani

last: Soundararajan

first: Mayi

last: Arcellana-Panlilio

first: Alexander

last: Wishart

last: Rupasinghe

first: Carolanne

last: Nelson

first: Michael

last: Mayne


title: The effect of insulin, glucose and rosiglitazone on mouse 3T3-L1 mature adipocytes gene expression

city: Wageningen

first: ping

last: wang

address: bornsesteeg 45

country: Netherlands

institute: RIKILT / Maastricht University

summary:
Obesity is associated with insulin resistance and type 2 diabetes, implying a role for adipose tissue in the etiology of these disorders. We used cDNA microarrays to obtain expression profiles of adipocyte by the treatment of insulin and anti-diabetic drug rosiglitazone at both high and low glucose level. Mouse 3T3-L1 mature adipocytes were treated 2 days 1) with or without 1 µM insulin at low and high glucose level, 2) with or without 0.5 μM rosiglitazone at low and high glucose and insulin level.  1) The comparison between the insulin and non-insulin treatment at the same glucose level showed minor changes in the transcriptome. The expressions of some processing enzymes for extracellular matrix components were regulated by insulin.  2) Transcriptome data indicates that an altered energy metabolism is induced by rosiglitazone in mature adipocytes. In addition, rosiglitazone represses adipokine expression, except adiponectin and ApoE. Moreover, transcriptome changes indicate that a general repression of secreted protein encoding genes occurs.
Keywords: homone and drug response

overall_design: In the present study, large-scale gene expression analysis was performed to reveal mechanistic details of effect of insulin and rosiglitaonze. 3T3-L1 mature adipocytes were treated 1µM insulin, and/or 0.5 μM rosiglitazone. To assess the influence of glucose on the effects, high (15.75 mM) and low (4.5 mM) glucose levels as background were applied respectively.  In parallel, control cells were cultured in the same medium but without insulin or rosiglitazone. Therefore 6 conditions were used: Basal: low glucose no insulin and rosiglitazone; Glc: high glucose; Ins: high insulin; Rosi: with rosiglitazone; Ins+Glc: high glucose and high insulin, Rosi+Ins+Glc: with rosiglitazone, high insulin and high glucose. Total RNA samples (n = 5 from three independent experiments per condition) were individually hybridised to the RIKILT mouse oligo 10K DNA arrays.

first: Ping

last: Wang

first: Edwin

last: Mariman

first: Annelies

last: Bunschoten

first: Jaap

last: Keijer


title: Transcriptomes of Clostridium novyi-NT

status: Public on Nov 20 2006

first: Xin

last: Huang

address: 1650 Orleans Street, CRB I, Room 520

department: Oncology

institute: Johns Hopkins University

summary:
This study determined the patterns of gene expression of Clostridium novyi-NT in different growth phases in vitro as well as gene expression patterns from infection of tumors in vivo.
Keywords: Growth phase analysis; tumor infection

sample_organism:
Homo sapiens
Mus musculus
Clostridium novyi NT

overall_design:
For gene expression of Clostridium novyi-NT in different growth phases in vitro, we had 4 replicates for early log phase, 3 replicates for mid log phase, 4 replicates for late log phase and 5 replicates for mature spore.
For gene expression of Clostridium novyi-NT from infection of tumors in vivo, we had 5 replicates for infected CT26 tumors and 5 replicates for infected HCT116 tumors.  To control for cross hybridization with mammalian mRNAs, we also included 2 replicates for uninfected CT26 tumors and 2 replicates for uninfected HCT116 tumors for hybridization to parallel arrays.


title: Array CGH Analysis in primary gastrointestinal stromal tumors

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Gastrointestinal stromal tumors (GISTs) comprise a biologically diverse group of neoplasms with respect to activating mutations in either KIT or PDGFRA genes, histology, anatomic site of origin, and clinical aggressiveness. In this study, we applied the high resolution array-based comparative genomic hybridization (array-CGH) technology to 66 primary GISTs (40 gastric and 26 non-gastric, 48 with KIT- and 18 with PDGFRA-mutations) for identification of novel high-level alterations and for characterization of genotype-related genomic changes. All cases had genomic imbalances with the highest occurrence of chromosome 14q (73%), 1p (62%), 22q (59%), 15q (38%) and 13q (29%) losses. Our data indicate that loss of chromosome 14 and/or 22 is an early change in GIST tumorigenesis irrespective of tumor genotype. Furthermore, DNA copy number changes showed a site dependent pattern. These included lower incidence of losses at 14q (87% vs. 35%), and higher frequency of losses at 1p (45%, vs. 85%) and 15q (17% vs. 69%) in non-gastric versus gastric site (p<0.001 for all). However, in the multivariate analysis with adjustment to tumor risk stratification, only the chromosome 14q loss site-dependent pattern of distribution retained its significance. These findings suggest that loss of chromosome 14q is a relatively late genetic event in the development of non-gastric GISTs, the lack of which is most likely substituted by the accumulation of chromosomes 1p/15q and other changes. The novel minimal overlapping regions of deletion at chromosome 1p (1p36.32-1p35.2, 1p34.1, and 1p22.1-1p21.3), 13q (13q14.11-q14.2 and 13q32.3-q33.1) and 15q23 were delineated, which point to chromosomal regions that may harbor genes relevant to the development of these neoplasms.
Keywords: comparative genomic hybridization, genotype, site dependent changes

overall_design: 66 samples from GIST tumors were compared to lymphocyte samples of normal individuals. 35 samples were repeated with colour flip

first: Agnieszka

last: Wozniak

first: Raf

last: Sciot

first: Louis

last: Guillou

first: Patrick

last: Pauwels

first: Bartosz

last: Wasag

first: Michel

last: Stul

first: Joris

last: Vermeesch

first: Peter

last: Vandenberghe

first: Janusz

last: Limon

first: Maria

last: Debiec-Rychter


title: Effect of day-length shortening on gene expression on pea aphid heads

status: Public on Nov 28 2006

city: Le Rheu

first: Denis

last: TAGU

department: UMR 1099 BiO3P

institute: INRA Rennes

summary:
Seasonal photoperiodism is responsable in aphid for the switch from asexual to sexual reproduction. In order to identify genes regulating the photoperiodic response, a cDNA microarray from the pea aphid was used to compare RNA populations from short- and long-day reared aphids. Analyses revealed that 64 different transcripts were significantly regulated, with a strong biological signature for cuticular proteins and proteins involved in cellular signalling or signal transduction. Quantitative PCR experiments performed on 5 transcripts confirmed microarray results. Complementary experiments eliminated moulting and circadian rhythms as putative confounding effects.
Keywords: Stress response, Environmental cue

overall_design: Two rearing conditions were compared: 16 h of light (“long-day” or LD) that maintained parthenogenesis, and 12 h of light (“short-day” or SD) that induced sexual forms after two generations. To initiate the experiment two groups of clonal third instar larvae (L3) were placed either at SD or LD photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood (wingless adults or WA) and produced offspring (G1) that were transferred onto new plants and kept under LD or SD conditions. A batch of 50 L3-G1 aphids was collected from each condition in the middle of the photophase (15:00) and immediately frozen in liquid nitrogen. Triplicates were performed. Thus, there were 6 batches of aphids: 3 reared under LD and 3 reared under SD. Heads were cut and antennae discarded. RNA was extracted from the 6 batches. Aliquot of the 3 RNA extracts form LD batches were mix to compose the REFERENCE batch. Then each RNA extract was hybridized in competition with the RNA reference: RNA from SD (replicate1) hybridized against the Reference, RNA from LD (replicate 1) hybridized against the Reference, RNA from LD, RNA from SD (replicate 2) hybridized against the Reference, RNA from LD, and so on. This is 6 arrays. A dye swap was introduced, with the Reference labelled either with Cy3 or with Cy5. The experimental design is thus 12 arrays, which corresponds to the 12 described sample of that series.

first: Gaël

last: LE TRIONNAIRE

first: Beatriz

last: SABATER-MUNOZ

first: Alessandra

last: BENEDETTO

first: Joël

last: BONHOMME

first: Stéphanie

last: JAUBERT

first: Nathalie

last: PRUNIER-LETERME

first: David

last: MARTINEZ-TORRES

first: Jean-Christophe

last: SIMON


title: H3K4me3 ChIP chips

city: Chapel Hill

first: Jason

last: Lieb

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

summary:
In yeast and other eukaryotes, the histone methyltransferase Set1 mediates methylation of lysine 4 on histone H3 (H3K4me).  This modification marks the 5' end of transcribed genes in a 5' to 3' tri- to di- to monomethyl gradient, and promotes association of chromatin remodeling enzymes that regulate transcription. In a screen to identify factors that control the distinct H3K4 methylation states, we identified Ctk1, the serine 2 C-terminal domain (CTD) kinase for RNA polymerase II (RNAP II). We found that CTK1 deletion nearly abolished H3K4 monomethylation, yet caused a significant increase in H3K4 di- and trimethylation. Both on individual genes and genome-wide, the loss of CTK1 disrupted the H3K4 methylation patterns normally observed.  H3K4me2 and H3K4me3 spread 3' into the body of genes, while H3K4 monomethylation was diminished.  These effects were dependent on the catalytic activity of Ctk1, but are independent of Set2-mediated H3K36 methylation.  Furthermore, these effects are not due to spurious transcription initiation in the body of genes, changes in RNAP II occupancy, changes in serine 5 CTD phosphorylation patterns, or to ‘transcriptional stress’. These data show that Ctk1 acts to restrict the spread of H3K4 methylation through a mechanism that is independent of a general transcription defect.  The evidence presented indicates that Ctk1 controls the maintenance of suppressive chromatin in the coding regions of genes by both promoting H3K36 methylation, which leads to histone hypoacetylation, and by preventing the 3' spread of H3K4 trimethylation, a mark associated with chromatin remodeling at the 5' end of genes.
Keywords: ChIP-chip

overall_design: Studying genome-wide distribution of H3K4me3 in ctk1del strains in Saccharomyces cerevisae

first: Bhargavi

last: Rao


title: H3K36Ac vs input ChIP chip

summary:
ChIP-chip experiments were done to analyze the global distribution of H3K36Ac in yeast
Keywords: ChIP-chip

overall_design: We analyzed 3 independent replicates

first: Rao

last: Bhargavi


title: The single ECF sigma factor of Xylella fastidiosa is involved in the heat shock response

status: Public on Nov 17 2006

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

summary:
Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an ECF sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa σE regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock identifying 23 sigmaE-dependent genes.
Keywords: stress response, heat shock, rpoE mutant strain

overall_design: Direct comparison between wild type strain J1a12 and mutant strain rpoE- at normal temperatures and at heat shock (40oC, 25min). There are at least 3 biological replicates (independent harvest) and 2 technical replicates of each array (L - left and R - right).

first: José

middle: F

last: da Silva Neto

first: Suely

last: Gomes

first: Marilis

last: Marques


title: H3K36Ac or H3K9K14 vs H3 ChIP chip

summary:
ChIP-chip experiments were done to analyze the global distribution of H3K36Ac or H3K9K14Ac in yeast compared to H3 distribution
Keywords: ChIP-chip

overall_design: We analyzed 2 independent replicates of each


title: Time course expression data of human cell lines infected with dengue virus

status: Public on Nov 16 2006

city: Singapore

first: Martin

last: Hibberd

state: Singapore

address: 60, Biopolis Street

department: Population Genetics

country: Singapore

institute: Genome Institute of Singapore

summary:
Microarray data was used to study the gene expression changes following dengue infection at various time points to identify host genes and pathways responsible for dengue virus replication
Keywords: time course

overall_design: HepG2 cell line was infected with TSV01 virus and expression profiled at 3hrs, 6hrs, 12hrs,24hrs, 48 hrs and 72hrs after infection. At each time point we profilesd the transcriptome using 3 biological repeats and each sample profiled using a technical repeat with dyes swapped

first: Subhash

last: Vasudevan

first: Ling

last: Ling

first: Joshy

last: George


title: Calcium responsiveness in Arabidopsis using calmodulin antagonists

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

summary:
The objective of this study is to identify early calcium up/down-regulated genes in response to rapid cytosolic Ca2+ transients in Arabidopsis thaliana.
Keywords: stress response

overall_design: The experimental design include 4 different experiments: 1. TFP response. 2. W7 response. 3. W7 (W7 + Ca) Vs. W7 pretreated with La3+ (W7 -Ca). 4. W7 pretreated with La3+ (W7 - Ca) Vs. DMSO pretreated with La3+ (control). For each experiment there are three independent biological repeats, including one Dye swap.

first: Boaz

last: Kaplan

first: Olga

last: Davydov

first: Heather

last: Knight

first: Marc

first: Yael

last: Galon

first: Hillel

last: Fromm


title: H3K36Ac vs H3K36me2 ChIP chip

first: Jason

last: Lieb


title: MiRNA Expression data from Tk6 cell treated with arsenic, gamma-IR, or grown under folate-deficiency

status: Public on Nov 15 2006

city: Boston

first: Carmen

last: Marsit

address: 665 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

summary:
Folate deficiency, arsenic exposure, and gamma-IR are known developmental toxicants and have carcinogenic effects.  The mechanism by which IR is known, but the effect of arsenic or folate deficiency remains unclear.  Their effect may be mediated by epigenetic alterations, leading to miRNA expression changes, and this experiment examined this hypothesis
We used microarrays to detail the miRNA expression profiles of TK6 cells treated with 2 uM sodium arsenite for 6 days, folate-deficient media for 6 days, or 2.5 Gy IR exposure either acutely at 4 hours post exposure or long-term at 6 days post exposure, as well as requiste controls, all in biological triplicate.
Keywords: exposure differences

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: TK6, were cultured in standard RPMI 1640 (Invitrogen Inc., Gaithersburg, MD) or folate-deficient RPMI 1640 (Invitrogen).  Growth media was supplemented with 10% fetal bovine serum (Invitrogen) and 1% penicillin-streptomycin; dialyzed fetal bovine serum (Invitrogen) was added to the folate-deficient medium in order to eliminate folic acid in the serum.  For controls, folate-deficiency, arsenic exposure, and 6-day ?-IR exposure groups, 106 cells were diluted into 50ml of appropriate growth media.  For the 4-hour post-?-IR exposure group, 107 cells were diluted into 50ml of growth media.   For the arsenic exposed group, sodium arsenite was added to the media to a concentration of 2 ?M.  For the ?-IR exposure groups, cells were diluted and allowed to incubate for 4 hours prior to irradiation treatment, and were exposed at a dose rate of 86.76 rad/min to a final dose of 2.5 Gy using a Philips MGC-40 X-ray source.  Following exposure, cells were returned to the incubator.  After fours hours, the short-term post-??-IR exposure group was collected for RNA isolation, as well as a mock (control) group.  All experimental and control conditions were performed in triplicate.  For all other groups, cells were cultured for 6 days, with the media changed and renewed, with the appropriate treatment, on day 3.

first: Karen

last: Eddy

first: Karl

middle: T

last: Kelsey


title: H3K36Ac in WT vs H3K36Ac in K36A ChIP chip

first: Rao

last: Bhargavi


title: Tup11-GFP ChIP-CHIP

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

summary:
We have performed a genome wide investigation for the binding locations of the transcriptional co-repressor proteins Ssn6, Tup11 and Tup12 in the fission yeast Schizosaccharomyces pombe. We have used a ChIP protocol described previously (Robyr et al, 2003) with microarrays containing ORF and IGR fragments representing the complete fission yeast genome (Wiren et al, 2005).
Keywords: ChIP-CHIP

overall_design:
Chromatin Immunoprecipitations.
Chromatin immunoprecipitations were essentially performed as described previously (Robyr et al, 2003, Wiren et al, 2005). Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking. The lysate was subjected to sonication 3x60 sec for generation of chromatin fragments with appropriate length. The lysate from the two sonications was pooled, aliquoted and subjected to immunoprecipiation with a polyclonal a-GFP antibody 1:100 (Applied Biosciences 8372-2) and protein A sepharose beads (Amersham 17-5280-01). Chromatin bound beads were washed and eluated fromm beads. DNA was purified with phenol-chloroform extraction and ethanol-sodium acetate precipitation. Precipitated chromatin and input DNA fragments from three individually separated experiments were subjected to a two step linear amplification. Round A was performed with Sequenase (USB 70775Y) and TPCRA priming. Round B was performed with Amplitaq (Roche) with TPCRB priming. Amplified material (500-1000ng) was subjected to Klenow labelling (Invitrogen 18094-011) with Cy3 and Cy5 (Amersham 53021 and 55021). Generally the input fragments was labelled with Cy3 and precipitated material was labelled with Cy5. Reportedly minimal dye swap bias has previously been observed (Robyr et al, 2003) and labelling was therefore not carried out in dye swap. Labelled fragments were hybridized to IGR+ORF microarrays from Eurogentech SA, Seraing, Belgium. Microarray signals were visualized with ScanExpress laser scanner and quantified with the TIGR spotfinder quantification software. Data was analysed and median normalized to the 50th percentile with the GeneSpring software (Silicon Genetics) to generate six data points for each binding map. Flag values were subtracted from the data set and ratios were subjected to median percentile ranking analysis described (Buck et al, 2004). Cutoff values for the generation of binding lists were set to the 85th percentile.

first: Fredrik

last: Fagerström-Billai


title: Ssn6-GFP ChIP-CHIP

overall_design: Chromatin immunoprecipitations were essentially performed as described previously (Robyr et al, 2003, Wiren et al, 2005). Cells were grown to mid log phase (107cells/ml) in rich YES media. All cells were harvested at room temperature and immediately subjected to crosslinking. The lysate was subjected to sonication 3x60 sec for generation of chromatin fragments with appropriate length. The lysate from the two sonications was pooled, aliquoted and subjected to immunoprecipiation with a polyclonal a-GFP antibody 1:100 (Applied Biosciences 8372-2) and protein A sepharose beads (Amersham 17-5280-01). Chromatin bound beads were washed and eluated fromm beads. DNA was purified with phenol-chloroform extraction and ethanol-sodium acetate precipitation. Precipitated chromatin and input DNA fragments from three individually separated experiments were subjected to a two step linear amplification. Round A was performed with Sequenase (USB 70775Y) and TPCRA priming. Round B was performed with Amplitaq (Roche) with TPCRB priming. Amplified material (500-1000ng) was subjected to Klenow labelling (Invitrogen 18094-011) with Cy3 and Cy5 (Amersham 53021 and 55021). Generally the input fragments was labelled with Cy3 and precipitated material was labelled with Cy5. Reportedly minimal dye swap bias has previously been observed (Robyr et al, 2003) and labelling was therefore not carried out in dye swap. Labelled fragments were hybridized to IGR+ORF microarrays from Eurogentech SA, Seraing, Belgium. Microarray signals were visualized with ScanExpress laser scanner and quantified with the TIGR spotfinder quantification software. Data was analysed and median normalized to the 50th percentile with the GeneSpring software (Silicon Genetics) to generate six data points for each binding map. Flag values were subtracted from the data set and ratios were subjected to median percentile ranking analysis described (Buck et al, 2004). Cutoff values for the generation of binding lists were set to the 85th percentile.


title: IL-13 and EGF receptor signaling in normal human bronchial epithelial cells

city: San Francisco

first: Agnes

last: Paquet

state: CA

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

summary:
To investigate the role of interleukin-13 (IL-13) and the epidermal growth factor (EGF) receptor pathway in controlling mucus metaplasia, normal human bronchial epithelial (NHBE) cells were cultured on air-liquid interface for 14 days and were treated with IL-13, anti-EGFR antibody or both during the final 48 h of culture.
Keywords: Stimulus response

overall_design: There were 3 independent samples for each of 3 treatment groups (IL-13 only, anti-EGFR only, IL-13 plus anti-EGFR). Each of these sample was hybridized to one of the 3 independent control samples on a separate array.

first: G

middle: H

last: Zhen

first: R

last: Barbeau

first: A

middle: C

first: D

last: Erle


title: Transcriptional response of E. coli to TPEN

first: Tara

last: Sigdel

address: 513 parnassus

department: Surgery

institute: University of California San Francisco

summary:
DNA microarrays were used to probe the transcriptional response of E. coli to N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Fifty-five transcripts were significantly up-regulated including all of the genes that are regulated by Zur and many genes regulated by Fur.  In these same TPEN-treated cells, forty-six transcripts were significantly down-regulated.
Keywords: E. coli, TPEN, zinc

overall_design: To identify genes that are differentially-expressed in response to TPEN, E. coli BL21(DE3) cells grown in minimal medium until the cultures reached mid-log phase.  TPEN was introduced and the cells were cultured for 5 hours; this time was chosen so that the results would correspond to previous transcriptional response studies with excess Zn(II). The cultures containing 5 uM TPEN were analyzed with DNA microarrays (E. coli K12 V2 array slides from MWG-BIOTECH), and the results were compared to those from E. coli cells grown in minimal medium containing no TPEN. A minimum of six slides was used for each experiment (3 slides with one combination of Cy3 and Cy5 dyes and 3 slides with swapped dyes).

first: James

last: Easton

first: Michael

last: Crowder


title: Erythroid progenitors stimulated with EPO

status: Public on Nov 10 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
CD34+ progenitors were isolated from the bone marrow of three healthy volunteers. CD34+CD71+CD45RA- were FACS sorted to enrich for erythroid progenitors. The cells were cultured for four hours with or without EPO in combination with LY294002, and harvested for RNA extraction, amplification and expression analysis.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Compound Based Treatment: EPO
Keywords: compound_treatment_design

overall_design: Computed

first: Einar

last: Sivertsen


title: Ultra high resolution array painting

city: Hinxton

first: Nigel

middle: Paul

last: Carter

state: Cambirdge

address: Wellcome Trust Genome Campus

department: Molecular Cytogenetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

summary:
Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting
Keywords: Breakpoint mapping

overall_design: The two derivative chromosomes from 4 patients with balanced translocations were flow sorted, differentially labelled and hybridised to custom oligonucleotide arrays designed to cover the potential breakpoint region at high resolution.  Single hybridisations with no replicates.


title: Evidence that Loading of Cohesin Onto Chromosomes Involves Opening of Its SMC Hinge

status: Public on Nov 05 2006

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

summary:
	Cohesin is a multisubunit complex that mediates sister-chromatid cohesion. Its Smc1 and Smc3 subunits possess ABC-like ATPases at one end of 50 nm long coiled coils. At the other ends are pseudosymmetrical hinge domains that interact to create V-shaped Smc1/Smc3 heterodimers. N- and C-terminal domains within cohesin's kleisin subunit Scc1 bind to Smc3 and Smc1 ATPase heads respectively, thereby creating a huge tripartite ring. It has been suggested that cohesin associates with chromosomes by trapping DNA within its ring. Opening of the ring due to cleavage of Scc1 by separase destroys sister-chromatid cohesion and triggers anaphase. We show that cohesin's hinges are not merely dimerization domains. They are essential for cohesin's association with chromosomes, which is blocked by artificially holding hinge domains together but not by preventing Scc1's dissociation from SMC ATPase heads. Our results suggest that entry of DNA into cohesin's ring requires transient dissociation of Smc1 and Smc3 hinge domains.
Keywords: Cohesin loading, Scc1, Smc1, Smc3, Hinge opening, ChIP-chip

overall_design:
•	Experimental factors
	Distribution of the mutant and wild type form of cohesin in mitotic G2 phase.
•	Experimental design
	ChIP analysis: In all cases, hybridization data for ChIP fraction was compared with SUP (supernatant) fraction. SUP fraction is equal to WCE (Whole Cell Extract) fraction. Essentially WCE or SUP fraction of any cell cycle phase can be used for normalization, and there was no effect on protein binding profiles. Cerevisiae chromosome VI array was used.

•	Quality control steps taken
	Confirmation using different tags. Confirmation by q-PCR. Checking of the ChIP fraction by Western blotting. Mock hybridisation of samples immuno-precipitated from cells containing no tag recognized by antibody used.
Samples used, extract preparation and labelling:
•	The origin of each biological sample
	Saccharomyces cerevisiae (W303).
•	Manipulation of biological samples and protocols used
	Chromatin immunoprecipitation (ChIP) and hybridization to Affimetrix high-density oligonucleotide arrays of S. cerevisiae chromosome VIwere performed essentially as previously described (Katou et al., 2003, nature) (Lengronne et al., 2004, nature).
•	Technical protocols for preparing the hybridization extract
	The chromatin-immunprecipates were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp. After Dnase I inactivation at 95ºC. DNA fragments were end-labeled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) for 1 hour at 37ºC as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.
•	Hybridization procedures and parameters:
	Hybridization, blocking and washing were carried out as previously described (Lengronne et al. Nature 2004). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3’biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100ºC for 10 minutes, and then put on ice before being hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).
•	Measurement data and specifications:

	Arrays were scanned using the Genechip Scanner3000 7G following the library array description. All the cel files data and processed data files can be downloaded from GEO database. The primary analysis of tiling chip data was performed following exactly the statistical algorithm used for Affymetrix GeneChip Operating Software (GCOS). The detailed information for the algorithm used can be downloaded from the Affymetrix web site. The analysis is available on request. For the ChrVI array, one unit for analysis (locus) was set to 300bp. Fold change value, change p-value, and detection p-value for each locus were obtained by primary analysis. For the discrimination of positive and negative signals for the binding, we used three criteria as follows. First, the reliability of the signal strength was judged by detection p-value of each locus (p-value≤0.025). Secondly, reliability of binding ratio was judged by change p-value (p-value≤0.025). Thirdly, clusters consisting of at least 900bp contiguous loci that satisfied the above two criteria were selected, because it is known that a single site of protein-DNA interaction resulted in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors.

•	Array Design:

		General array design: in situ synthesized arrays by Affymetrix
		Availability of arrays: commercially available from Affymetrix
		Location and ID of each spot on arrays: available from Affymetrix on 			request
		Probe type: oligonucleotide
		The arrays used in this study can be purchased from Affymetrix:
			Chromosome VI S.cerevisiae: rikDACFC6, P/N# 510636

first: Stephan

last: Gruber

first: Prakash

last: Arumugam

first: Yuki

last: Katou

first: Daria

last: Kuglitsch

first: Wolfgang

last: Helmhart

first: Kim

last: Nasmyth


title: Distinctive gene expression of prostatic stromal cells cultured from diseased versus normal tissues

summary:
To obtain a comprehensive view of the transcriptional programs in prostatic stromal cells of different histological/pathological origin, we profiled 18 adult human stromal cell cultures from normal transition zone (TZ), normal peripheral zone (PZ), benign prostatic hyperplasia (BPH), and prostate cancer (CA) using cDNA microarrays.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Hongjuan

last: Zhao


title: Genomic profiling of aged rat skeletal muscle

city: Stockholm

first: Mikael

last: Altun

address: Retzius väg 8

department: Neuroscience

institute: Karolinska Institutet

summary:
a genomic profile of aged rat sceletal muscle with diffrent degrees of sensorimotor disturbances.
Keywords: age skeletal muscle sensorimotor disturbances

overall_design:
Experimental animals
Male Sprauge-Dawley rats (strain Bkl; Harlan Sprauge-Dawley, Houston, TX), including a total of five adults (4 months old) and seven aged rats (30 months) were used. The animals were delivered by a local breeder (B and K, Stockholm, Sweden) at 2 months of age and were kept thereafter under standardized barrier-breeding conditions at our department (12-hour light/12-hour dark cycle) with free access to water and food (R70 with reduced protein content: Lactamin, Vadstena, Sweden). All experiments were approved by the Local Ethical Committee (Stockholm’s Norra Djurförsöksetiska Nämnd; project no. N54/00).

Stage ranking of animal
Under these conditions the median survival time is 30 months (plus/minus 2 months across cohorts), and based on this the 30-month-old rats are defined as aged. All aged rats used in this study showed signs of behavioral sensorimotor disturbances, defined by using two parameters as a guide to select a stage, namely: (a) is a limb weight bearing? (b) does a limb show a complete gait cycle coordinated with the other limb(s)? The animals were ranked in stage 0-III: Stage 0 animals show no signs of insufficiency concerning these two variables; Stage I animals show some signs, including a lowering of the trunk towards the supportive surface and minor signs of gait cycle aberrations; Stage II animals show clear gait cycle aberrations, often involving a poorer coordination between limbs. Body weight bearing is often clearly incapacitated in at least one limb; Stage III animals show severe gait cycle aberrations, often involving a poorer coordination between limbs. Only minor efforts to initiate a gait cycle may.

Analysis of chips
GenePix Pro software (Axon Instruments, CA) was used for the analysis of the image. The signal of each spot was calculated as the average intensity of the spot minus the background. Spots with intensity that were at least 1.6 times above the background were included in the study. Dye swaps were used in one of the chips in each group of runs. Normalization between the two fluorescent images was performed, as described previously [Ross DT et al., 2000], by applying a scaling factor to all intensities measured for the Cy5 channel so that the mean log (Cy5/Cy3) for the subset of spots that were not flagged was 0. Expression ratios calculated as Cy5/Cy3 signals was normalized using the “LOWESS” method in the SMA (Statistical Analysis of Macroarrays) package [Dudoit S et al., 2002]; [Yang YH et al., 2002] SMA is an add-on library written in the public domain statistical language R [Ihaka R et al., 1996]. The LOWESS (locally Weighted Scatter Plot Smoother) algorithm performs a local fit to the data in an intensity-dependent manner. The intensity value for each spot is normalized based on data distribution in the immediate neighborhood of the spot’s intensity. Genes with missing data in more than one of the three triplicates of the studied cases were excluded. The significance of the expression ratios of the aged animals in the different stage groups was estimated using the SAM software [Tusher VG et al., 2001]. SAM is a statistical technique for finding significantly regulated genes in a set of microarray experiments. For each gene, i, in the array SAM compute the T-statistics di, a score derived from changes of gene expression in relation to the standard deviation of repeated measurements for that gene. A threshold can be set based on di to identify potentially significant changes in gene expression. The threshold can be adjusted based on an associated false discovery rate (FDR) value: the percentage of genes expected to be false identified as differentially expressed when certain threshold (d value) is set. To each of the genes in the array a q-value was assigned. This value is similar to the commonly used p-value and measures the lowest FDR at which the gene is called significant. In this study, initially genes with a q-value of more than 5% in either if the stage groups in the same gene were excluded for further analysis.

first: Erik

last: Edström

first: Eric

last: Spooner

first: Amilcar

last: Flores-Moralez

first: Esbjörn

last: Bergman

first: Petra

last: Tollet-Egnell

first: Gunnar

last: Norstedt

first: Benedikt

last: Kessler

first: Brun

last: Ulfhake


title: Gene Transcription Profiles during Development of Mucosal Immunity

city: Brookings

first: Xiuqing

last: Wang

state: SD

address: NPB 252, SDSU

department: Department of Biology and Microbiology

institute: South Dakota State University

summary:
Avian infectious bronchitis virus (IBV) infection is a major chicken viral respiratory disease that causes significant economic losses to the poultry industry worldwide. The local mucosal immune response plays a vital role against the infection of this respiratory virus. Previous studies have indicated that a variety of innate immunity and a Th1 based adaptive immunity are activated in the host’s early defense (3 days post inoculation, dpi) against IBV invasion and they are responsible for the rapid clearance of virus from the local infection. In the present study, we propose to use IBV as a model system to uncover the molecular mechanism of mucosal immunity development by characterizing the kinetics of the local gene transcription profiles in trachea tissues after administration with an attenuated IBV strain (IBV-Mass). More specifically, immune-related gene transcription profiles in trachea at 1, 3, 5, 8, 12 and 21 days after the primary immunization and at 1 and 2 days after a second immunization were monitored using chicken 13K cDNA Microarray.
Keywords: time course, cDNA 13k chicken array from FHCRC, IBV-chicken model

overall_design: The goal of the study was to uncover the molecular mechanism of mucosal immunity development using avian infectious bronchitis virus (IBV) as a model system. To achieve this goal, we monitored the kinetics of local gene transcription profiles in trachea tissues after administration of animals with an attenuated IBV strain (IBV-Mass) using chicken 13K cDNA Microarray. More specifically, immune-related gene transcription profiles in trachea at 1, 3, 5, 8, 12 and 21 days after the primary immunization and at 1 and 2 days after a second immunization were characterized.  There are total 9 groups including 8 time points for vaccinated groups and 1 pooled age-matched control group. RNAs from each group were used to compare with RNAs from other four groups as determined by the loop-design. Four different RNA samples at each time point were used for hybridization with the respective four other groups.  The use of loop-design allows the direct comparisons between the 9 groups, which would enhance the statistical power and lower the variation. This design is preferred over other methods when the goal of the study is to uncover the kinetics of gene transcription profiles.

first: Xueshui

last: Guo

first: Din

last: Chen

first: Artur

last: Rosa


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris

first: Yasuhiro

last: Oda

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

summary:
We used transcriptome analysis to identify genes that were differentially expressed between wild-type (CGA010) and hupV mutant cells (CGA009) grown photoheterotrophically with malate under nitrogen-fixing conditions. We also compared the transcriptome of a hupS mutant with that of the wild type.
Keywords: Genetic modification

overall_design: RNA was isolated from various Rhodopseudomonas palustris strains that were grown to the mid-logarithmic phase of growth. Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction. The hybridization mixtures containing the two labeled cDNA samples to be compared were applied to microarray slides that had been covered with Lifterslips (Erie Scientific Company, Portsmouth, NH). The slides were assembled with hybridization chambers (Corning, Corning, NY) and submerged in a 65ºC water bath. After 14-16 h of hybridization, the slides were washed and scanned with a ScanArray 4000XL scanner (PerkinElmer, Boston, MA). Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA). The software package lcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Duplicate calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides for each (10 slides in total) were used to generate each data set.

first: Federico

middle: E

last: Rey

first: Caroline

last: Harwood


title: Microarray identification of PCa markers highlights HOXB13

status: Public on Oct 28 2006

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

summary:
In a strategy aimed at identifying novel markers of human prostate cancer, we performed expression analysis using microarrays of clones randomly selected from a cDNA library prepared from the LNCaP prostate cancer cell line. Comparisons of expression profiles in primary human prostate cancer, adjacent normal prostate tissue, and a selection of other (nonprostate) normal human tissues, led to the identification of a set of clones that were judged as the best candidate markers of normal and/or malignant prostate tissue. DNA sequencing of the selected clones revealed that they included 10 genes that had previously been established as prostate markers: NKX3.1, KLK2, KLK3 (PSA), FOLH1 (PSMA), STEAP2, PSGR, PRAC, RDH11, Prostein and FASN. Following analysis of the expression patterns of all selected and sequenced genes through interrogation of SAGE databases, a further three genes from our clone set, HOXB13, SPON2 and NCAM2, emerged as additional candidate markers of human prostate cancer. Quantitative RT-PCR demonstrated the specificity of expression of HOXB13 in prostate tissue and revealed its ubiquitous expression in a series of 37 primary prostate cancers and 20 normal prostates. These results demonstrate the utility of this expression-microarray approach in hunting for new markers of individual human cancer types.
Keywords: Tumour vs normal comparison

overall_design: 23 samples  - Expression microarray of 11 Primary Prostate Tumours and 12 Normal Tissues versus PNT2

first: S

last: Edwards

first: C

last: Campbell

first: P

last: Flohr

first: J

last: Shipley

first: I

first: R

last: te-Poele

first: A

last: Dodson

last: Foster

last: Clark

last: Jhavar

first: G

last: Kovacs

last: Cooper


title: Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain Dependent

city: Glasgow

first: Tim

last: Mitchell

address: 120 University Place

department: IBLS

institute: University of Glasgow

summary:
Recent murine studies have demonstrated that the role of response regulator 09 (RR09) of S. pneumoniae in virulence varies between strains. In the present study, we used a murine pneumonia model of infection to assess the virulence of a TIGR4 rr09-mutant, and found that TIGR4Δrr09 was attenuated after intranasal infection. Further, we investigated the in vitro transcriptional changes in pneumococcal rr09 mutants of two strains, D39 and TIGR4, by microarray analysis. The transcriptional profiles of the rr09 mutants in both strains displayed clear differences compared to their parental wild-type. In D39Δrr09 but not TIGR4Δrr09, genes involved in competence (e.g. comAB) were upregulated. In TIGR4, genes located on the rlrA pathogenicity islet, absent in the D39 genome, appeared to be regulated by RR09. Furthermore, several phosphotransferase systems (PTSs), believed to be involved in sugar uptake (e.g., sp0060-sp0066), were strongly downregulated in D39Δrr09, while not regulated by RR09 in TIGR4. To address the role of one of these PTS in virulence, D39Δsp0063 was constructed and tested in a murine infection model. No difference in virulence compared to the wild-type was found, indicating that downregulation of this gene alone is not the cause of the avirulent phenotype of D39Δrr09. Finally, expression of rr09 and three of our identified RR09 targets were assessed during infection in mice. This in vivo experiment confirmed differences in expression between TIGR4 wild-type and rr09-mutant, as well as between wild-type D39 and TIGR4. In conclusion, our results indicate strain specific regulation of pneumococcal gene expression by RR09.
Keywords: Genetic modification

overall_design: The full genome array of S. pneumoniae microarray v.2 consists of amplicons representing segments of 2,131 open reading frames from S. pneumoniae reference strain TIGR4 (Tettelin et al., 2001) spotted in quadruplicate on glass slides. Also, the array contains an additional 118 open reading frames from strains R6 (164) (Hoskins et al., 2001) and G54 (399). The RNA for wild-type and rr09 strains was isolated in 2 independent biological replicates which were hybridised (dye-swap) into 4 slides for D39 and 2 slides for TIGR4.

first: Nuno

last: Silva

first: Gavin

last: Paterson


title: Comparison of miRNA profile of Foxp3-transduced activated T cells with control vector-transduced activated T cells

status: Public on Oct 26 2006

city: Cambridge

first: James

last: Smith

address: Tennis Court Road

department: Gurdon Institute

institute: Cambridge University

summary:
Activated T cells were transduced with either Foxp3-IRES-GFP or IRES-GFP control vector. Low molecular weight RNA from cells was extracted 72h or 96h later and hybridised to microarrays containing oligonucleotide probes corresponding to known miRNA sequences.
Keywords: cell type comparison

platform_organism:
Homo sapiens
Mus musculus

overall_design: Four arrays representing two timepoints dyeswaps of each.

first: Bradley

last: Cobb

first: Arnulf

last: Hertweck

first: Frederick

last: Livesey

first: Matthias

last: Merkenschlager


title: Comparison of miRNA profile of activated T cells to naive T cells

summary:
T cells were activated for 1, 3 or 10 days using plate-bound anti-TCR and anti-CD28. Low molecular weight RNA from conventional T cells and activated T cells was hybridised to microarrays containing oligonucleotide probes corresponding to known miRNA sequences.
Keywords: cell state analysis

overall_design: Five arrays, with T cells having been activated for varying lengths of time, including dye swaps.


title: CpG-mediated changes in gene expression

status: Public on Oct 30 2006

city: Frederick

first: Dennis

last: Klinman

department: CIP

institute: NCI Frederick

summary:
The current study was designed to identify reproducible changes in gene activation over time induced by CpG DNA stimulation. Towards that end, the expression of 11,300 genes was examined at 2, 4 and 8 h after murine spleen cells were treated with CpG ODN. Results provide insight into the nature, breadth and magnitude of the response elicited by CpG DNA, and identify genes that play a central role in the up- and down-regulation of CpG mediated cellular activation.
Keywords: time series design

overall_design: BALB/c spleen cells were cultured with 1 uM of CpG ODN for 2, 4 or 8 h. mRNA was isolated from these cells, and converted into Cy5-labeled cDNA. All samples were hybridized to a murine microarray in the presence of the same Cy3-labeled murine cDNA reference standard. Two control groups were included in all experiments. The first group consisted of spleen cells incubated in medium alone, compensating for any effect of cell manipulation or in vitro culture on gene expression. The second group consisted of spleen cells incubated with 1 uM of non-CpG ODN, controlling for any sequence-independent ODN activity. Reproducible changes in gene expression were identified by combining results generated from 3-4 independent experiments.


title: A role for Dicer in immune regulation

summary:
A study of the miRNA profile CD4 T cells compared to T reg cells; of activated and naive T cells; and the miRNA profile conferred by enforced expression of Foxp3.
Keywords: cell type comparison

overall_design: Fifteen arrays broken down into three broader experiments as referenced by series GSE6003 - a comparison of miRNA profile of natural T reg cells with conventional CD4+CD25- T cells; GSE6006 - a comparison of miRNA profile of activated T cells to naive T cells; and GSE6007 - comparison of miRNA profile of Foxp3-transduced activated T cells with control vector-transduced activated T cells.


title: Gene profiling of cells expressing different FGF-2 forms

last: Stanford Microarray Database

summary:
Fibroblast Growth Factor-2 (FGF-2) induces cell proliferation, cell migration, embryonic development, cell differentiation, angiogenesis and malignant transformation. The four forms of FGF-2 (Low Molecular Weight) and (High Molecular Weights) are alternative translation products, and have a different subcellular localization: the high molecular weight (HMWFGF-2) forms are nuclear while the low molecular weight form, (LMWFGF-2) is mainly cytoplasmic. Our previous work demonstrated NIH 3T3 cells expressing different FGF-2 forms, displayed a different phenotype, suggesting that nuclear and cytoplasmic forms of FGF-2 may have different functions. Here we report a cDNA microarray-based study in NIH 3T3 fibroblasts expressing different FGF-2 forms. Several candidate genes that affect cell-cycle, tumor suppression, adhesion and transcription were identified as possible mediators of the HMWFGF-2 phenotype and signaling pattern. These results demonstrated that HMWFGF-2 and LMWFGF-2 target the expression of different genes. Particularly, our data suggest that HMWFGF-2 forms may function as inducers of growth inhibition and tumor suppression activities.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Kenton

last: Fong


title: SH-SY5Y cells treated with Quercetin-3-glucoside (10 uM) for 6 hr

city: Halifax

first: George

last: Robertson

address: 5850 College Street

department: Departments of Psychiatry and Pharmacology

institute: Dalhousie University

summary:
Flavonoids are polyphenolic compounds with potent anti-oxidant and free radical scavenging activities. Here, we examined the cytoprotective actions of Quercetin-3-glucoside (Q3G) against oxidative stress induced by hydrogen peroxide. Pre-treatment of the neuroblastoma cells, SH-SY5Y with Q3G for 18 h reduced cell death after a brief exposure to hydrogen peroxide. The cytoprotective effects of Q3G were associated with decreased free radical generation suggesting that this mechanism accounts for Q3G-mediated cytoprotection. To address the possibility that Q3G-mediated cytoprotection involved alterations in gene expression, cDNA microarray studies were performed. These studies identified elevated expression of 25 genes and decreased expression of 3 genes only in Q3G pre-treated cells under oxidative stress. The majority of genes up-regulated by Q3G in SH-SY5Y cells under oxidative stress encode enzymes involved in lipid biosynthesis. Quantitative Real time PCR (qRT-PCR) validated changes in gene expression that were identified by cDNA microarray analyses. The induction of multitude of genes involved in cholesterol signaling pathway by Q3G in cells under oxidative stress suggests an important role for elevated cholesterol synthesis in the cytoprotective actions of Q3G. This hypothesis was confirmed by the detection of elevated levels of cholesterol in cells pre-treated with Q3G and subjected to oxidative stress. Moreover, inhibition of cholesterol biosynthesis with mevastatin blocked the cytoprotective effects of Q3G against oxidative stress-induced cell death.  Taken together, these studies suggest a novel mechanism for flavonoid-induced cytoprotection involving elevated cholesterol synthesis that may act to reduce lipid peroxidation and promote membrane repair after oxidative injury.
Keywords: cytoprotection

overall_design: The SH-SY5Y cells were treated with either Q3G or vehicle (DMSO) for 6 hours and total RNA was extracted. The labeled cDNA derived from Q3G treated cells represent the "Experimental sample" while the labeled cDNA from DMSO treated samples are the "Reference sample".  Two batches of cells were so treated and dye swaps were done for each, giving a total of 4 replicates.

first: Ramani

last: Soundararajan

first: Mayi

last: Arcellana-Panlilio

first: Alexander

middle: D

last: Wishart

last: Rupasinghe

first: Carolanne

last: Nelson

first: Michael

last: Mayne


title: SAGE libraries derived from Bombyx ovaries

city: Tokyo

first: shunsuke

last: funaguma

address: Yayoi 1-1-1, Bunkyo-ku

summary:
These two 3' Long SAGE libraries were constructed from stage 1-3 or stage 2-3 Bombyx egg chambers.
Keywords: 3' Long SAGE libraries

overall_design: These libraries were constructed as described in Saha et al, 2002.

first: Shunsuke

last: Funaguma

first: Shin-ichi

last: Hashimoto

first: Yutaka

last: Suzuki

first: Naoko

last: Omuro

first: Sumio

last: Sugano

first: Kazuei

last: Mita

first: Susumu

last: Katsuma

first: Toru

last: Shimada


title: Acute and Chronic Environmental Tobacco Smoke Condensate Exposure to Primary Human Bronchial Epithelial Cells

status: Public on Dec 25 2006

city: Albquerque

first: Susan

middle: Esther

last: Boggs

state: NM

address: 2425 Ridgecrest Dr SE

institute: Lovelace Respiratory Research Institute

summary:
The goal was to assess global gene expression changes in primary human bronchial epithelial cells exposed to environmental tobacco smoke (ETS) condensate.  ETS-C was standardized by HPLC analysis and two timepoints of exposure in two different donor bronchial epithelial cell populations were assessed.  These findings demonstrate that even short exposure (4.5 h) to ETS is sufficient to induce a stress response, as reflected by decreased antioxidant levels, induced HSP family members, and modulation of the family of glutathione metabolism enzymes in primary human lung cells.  Upon longer exposures (48 h) with ETS-condensate, bronchial epithelial cells arrest at the G2/M phase of the cell cycle.  Taken together, these data support a stress-induced state in primary human bronchial epithelial cells that culminates in cell cycle arrest.
Keywords: time course, comparative, stress response

overall_design: Two donors and two time points of exposure were assessed by hybridizing to filter arrays.  Each biological sample was exposed and hybridized in triplicate to the same filter array.  A total of four filter arrays were used.  Filter arrays were stripped per manufacturer's recommendations.

first: Chris

last: Beenhouwer

first: Brandy

last: Crowder

first: James

last: Aden

first: Cindy

last: Knall


title: H3K4me3  vs input DNA ChIP chip in WT

city: Chapel Hill

first: Jason

last: Lieb

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

summary:
ChIP-chip experiments were done to analyze the global distribution of H3K4me3 in WT
Keywords: ChIP-chip

overall_design: We analyzed 3 independent replicates.

first: Rao

last: Bhargavi


title: Survival Prediction of HNSCC using FFPE samples

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

summary:
Recently it was shown that gene expression signatures generated from DNA microarray analyses have promise as biomarkers of clinical outcome and that the molecular characteristics of tumors could be elucidated. Through this study, we have determined a high-risk signature for recurrence as a prognostic biomarker using formalin-fixed HNSCC tumors and tested the results to an independent data set obtained from fresh frozen tumors as a comparison. Also, we have shown the genes that are involved in epithelial to mesenchymal transition and nuclear factor-ĸB signaling deregulation are the most prominent molecular characteristics of the high-risk tumors. Forty samples including 34 formalin-fixed tissues and 6 matched frozen tissues from 29 HNSCC patients were analyzed for gene expression. The formalin-fixed tumors were classified based on their gene expression by intrinsic analysis and the intrinsic gene list was tested on the classification of previously published 60 frozen HNSCC tumors which highly correlated. Based on the molecular classification, a 75-gene list that is predictive of high-risk for recurrence was determined by training on the formalin-fixed tumor set and tested on the independent frozen tumor set. The difference in recurrence-free survival (RFS) between the high-risk vs. low-risk groups in the training and test sets were statistically significant (Log-rank test, p=0.002 and p=0.03, respectively). Also, the gene expression data was interrogated using Gene Set Enrichment Analysis to determine functional significance. The most significant sets of genes that are enriched in the high-risk tumors were genes involving epithelial to mesenchymal transition (EMT), NF-ĸB activation and cell adhesion. In conclusion, global gene expression analysis is feasible using formalin-fixed tissue, and the data from different sample preparations and array platforms can be reliably combined for analyses. The 75-gene list can be utilized as a prognostic biomarker of recurrence and the molecular characteristics of EMT and NF-ĸB activation can be targeted as the novel therapy in the identified high-risk patients.
Keywords: FFPE, survival analysis

overall_design: 34 HNSCC samples from FFPE tissue and 6 HNSCC samples from fresh frozen tissue.  Each independtly hybridized using Affymetrix X3P chips.

first: Joel

last: Parker

first: Kim

last: Ely

first: Jesse

last: Carter

first: Barbara

last: Murphy

first: Yajun

last: Yi

first: Adam

first: Kian

middle: K

last: Ang

first: Adel

last: El-Naggar

first: Anthony

last: Cmelak

first: Robert

last: Slebos

first: Shawn

last: Levy

first: Wendell

middle: G

last: Yarbrough


title: A high-resolution transcriptome map of the sea urchin embryo

status: Public on Oct 23 2006

city: Los Altos

first: Manoj

last: Samanta

address: 2240 Homestead Court #309

institute: Systemix Institute

type: Expression profiling by genome tiling array

summary:
The sea urchin S. purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low leveles in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.

Keywords: high-resolution tiling array, sea urchin, embryo
Keywords: other

overall_design: Poly-A RNA from egg, early blastula (15hr.), early gastrula (30hr.) and late gastrula stage (45hr.) embryos of sea urchin were mixed in equal quantities. The RNA sample was converted to cDNA and fluorescently labeled. Single hybridization experiment was performed.

middle: P

first: W

last: Tongprasit

first: S

last: Istrail

first: R

middle: A

last: Cameron

first: Q

last: Tu

first: E

last: Davidson

first: V

last: Stolc


title: Time-course studies of three cell wall interfering drugs on gene expression in yeast

status: Public on Nov 03 2006

city: Toulouse

first: Serguei

last: Sokol

address: 135 av de Rangueil

department: Lab. Biotech. and Bioprocess

institute: INSA

summary:
Caffeine is a natural purine analog that elicits pleiotropic effects, which ultimately lead to cell death by a mechanism that is still largely uncharacterized. This drug can activate the PKC1-MAPK cell integrity pathway, as shown by phosphorylation of Mpk1 kinase. However, and contrary to expectation, the caffeine-induced hyperphosphorylation of Mpk1 was accompanied by a negligible activation of its downstream targets Rlm1 and SBF transcription factors, which suggested that the fortification of the cell wall induced by caffeine was independent on the MAP kinase activation. This result was consistent with the finding that the loss of RLM1 had no consequence on the increased resistance of caffeine-treated cells to zymolyase, and was further consolidated by a genome-wide microarray analysis showing that, contrary to the cell wall drugs Congo Red and Calcofluor white, caffeine did not cause upregulation of Rlm1-dependent genes encoding cell wall remodeling enzymes. Interestingly, this global expression analysis revealed a striking resemblance of the transcriptomic responses to caffeine with those of rapamycin, a potent inhibitor of the TOR1 and TOR2 kinases. Consistent with this analysis, we found that the caffeine-induced phosphorylation of Mpk1 was lost in a tor1(delta) mutant but it was conserved in a TOR1-1 strain bearing a rapamycin-insensitive Tor1 kinase. Also, and contrary to the mechanism by which rapamycin led to activation of the PKC pathway, the caffeine-dependent process did not necessitate cell wall sensors and was completely abolished upon deletion of ROM2 encoding a GDP/GTP exchange factor of the Rho1-PKC pathway. Moreover, addition of caffeine to yeast cells resulted in a transient drop in intracellular cAMP, and this effect was not observed in a rom2(delta) mutant. In summary, our results revealed that Tor1 is a potential direct target of caffeine in yeast, whose inhibition leads to activation of the Pkc1-Mpk1 kinase cascade and inhibition of the Ras/cAMP pathway, and that for this specific case, the cross-talk between these signaling pathways is mediated by Rom2. These results may have broad implication for our understanding of caffeine effects in analogous regulatory networks in mammalian cells.

Key words: caffeine, antifungal drugs, cell wall, transcript profiling, TOR, PKC1, RAS/cAMP.
Keywords: time course, dose response

overall_design: At every time point a treated and non treated yeast samples are put on a slide. There are two biological replicates that are labeled in dye-switch way (sometimes called biological dye-swap).

first: Klaudia

last: Kuranda

first: Veronique

last: Le Berre

first: Grazyna

last: Palamarczyk

first: Jean

last: François


title: Array CGH in mentally retarded patients

status: Public on Oct 22 2006

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

summary:
This series represents the data set described in the publication “Impact of low copy repeats on the generation of balanced and unbalanced chromosomal aberrations in mental retardation” by Erdogan et al. (Cytogenetics and Genome Research, accepted).
Keywords: array CGH

overall_design: This study aimed at defining the impact of low copy repeats on the generation of balanced and unbalanced chromosomal rearrangements in mentally retarded patients.  A cohort of 22 patients, pre-selected for the presence of sub-microscopic imbalances, was analysed by sub-megabase resolution tiling path array CGH and results were compared with a set of 41 patients with balanced translocations and breakpoints mapped to the BAC level by FISH.

first: Fikret

last: Erdogan

first: Wei

last: Chen

first: Maria

last: Kirchhoff

first: Vera

last: Kalscheuer

first: Claus

last: Hultschig

first: Ines

last: Mueller

first: Ralph

last: Schulz

first: Corinna

last: Menzel

first: Thue

last: Bryndorf

first: Hilger

last: Ropers


title: 300 ppm Citrinin treatment for 2 h (GPL4399)

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

summary:
The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity. This system possesses the benefit of the essential volume of yeast cultures, the high reproducibility of expression profiles, and the massive functional information. Because small amount of biological sample cultures are required for this analysis, toxicity test for rare chemical such as mycotoxins which is a natural compound and difficult to be artificially synthesized. Citrinin [518-75-2], 4,6-dihydro-8-hydroxy-3,4,5-trimethyl-6-oxo-3H-2-benzopyran-7-crboxylic acid, is the one of the popular mycotoxicin produced by Penicillium and Aspergillus family possibly spread all over the world. This natural chemicals is one of the well characterized mycotoxin but the information especially mechanism of toxic action is limited.
We used two types of microarrays, one have ORF (Open reading Frame) fragment on the surface of the glass as probes and the other have probes as oligonucleotide probes on the microarray with 3 dimensions. We compared data properties and studied the toxicity of citrinin to yeast cells.
Keywords: stress response

overall_design: Biological samples were prepared from 3 independent experiments. Hybridization were done triplicate in each sample-control set. Sample labeling were swapped between 1st hybridization (control = Cy5, sample = Cy3) and 2nd and 3rd hybridization (control = Cy3, sample = Cy5).

first: YoungKyung

last: Kim

first: Yoshiteru

last: Suzuki

first: Hitoshi

last: iwahashi


title: H3K4me3  vs input DNA ChIP chip in Ctk1deletion

first: Jason

last: Lieb

summary:
ChIP-chip experiments were done to analyze the global distribution of H3K4me3 in Ctk1del
Keywords: ChIP-chip

first: Rao

last: Bhargavi


title: H3  vs input DNA ChIP chip in Ctk1deletion

summary:
ChIP-chip experiments were done to analyze the global distribution of H3 in Ctk1del
Keywords: ChIP-chip

overall_design: We analyzed 3 independent replicates of each

first: Bhargavi

last: Rao


title: Loss of the RNA-binding protein Kep1 leads to cytokinesis defects and behavioural abnormalities in male Drosophila.

status: Public on Oct 21 2006

city: Sherbrooke

first: Marco

last: Di Fruscio

state: Quebec

address: 2500 boul. Université

department: Biologie

institute: Université de Sherbrooke

summary:
The kep1 gene encodes an RNA-binding protein containing a single maxi-KH domain. We have previously demonstrated that loss of the kep1 gene results in Drosophila females displaying a reduction in fertility and wished to further characterize the kep1 mutation in Drosophila males. Wild-type females mated to homozygous kep1- males resulted in 6% of the eggs laid hatching. This reduced reproductive success is due in part to a meiosis defect during spermatogenesis with approximately 10 % of sperm demonstrating a defect in cytokinesis.  Utilizing indirect immunohistochemistry we found that the Kep1 protein is present in the nucleus of adult brain neuronal cells, suggesting a behavioural component contributing to the almost complete male sterility phenotype. We report that homozygote kep1- males display almost no courtship behaviour with a measured median courtship index of 0.005 relative to a median index of 0.77 for OreR wild-type controls.  In order to better understand the behavioural role of kep1, we carried out gene profiling experiments to identify transcripts whose steady-state levels are altered in the kep1- homozygote males.  Our gene profiling studies identified 61 transcripts whose steady-state levels are altered by at least 2 fold or more comparing RNA isolated from w1118 and kep1-/kep1- male heads. A large percentage of transcripts identified whose steady-state expression levels are depleted in kep1-/kep1- heads (10 out of 44) encode for proteins involved in some aspect of proteolysis.  Our results show that the Kep1 protein has a pleiotropic effect in Drosophila males leading to cytokinesis defects and behavioural abnormalities.
Keywords: Mutant vs wild-type compairson

overall_design: RNA was isolated from heads of 3-4 day old wild-type or homozygote mutant males. Three indepentent RNA samples were utilized to complete experiment.

first: Judy-Ann

last: Poitras

first: Cécile

last: Robard

first: Bill

last: Shipley


title: E. coli MG1655 transcriptome inferred from a tiled microarray

status: Public on Oct 19 2006

city: Boston

first: Nikos

last: Reppas

address: 77 Avenue Louis Pasteur

institute: Harvard University

summary:
These data were used to infer transcription fragments (transfrags) for the study "The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate-limiting" (Reppas et al. 2006). This study analyzes transfrags with respect to the ChIP profile of the sigma70 and the beta subunit of RNA polymerase.
Keywords: Tiled analysis of mRNA expression; ChIP-chip

overall_design: RNA was isolated from duplicate cell cultures, which were also used for chromatin immunoprecipitation (ChIP) of sigma70- and RNA polymerase beta-crosslinked DNA.

middle: B

first: Joseph

last: Wade

first: George

last: Church

first: Kevin

last: Struhl


title: ChIP-chip of Sigma70 and RNAP Beta in vivo in E. coli MG1655

summary:
These data were used to infer the genome-wide localization of sigma70 and core RNAP beta subunit for the study "The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate-limiting" (Reppas et al. 2006). This study analyzes transfrags with respect to the ChIP profile of the sigma70 and the beta subunit of RNA polymerase.
Keywords: ChIP-chip; tiled analysis of mRNA expression


title: H3K9K14Ac vs H3K36me2 ChIP chip

status: Public on Nov 01 2006

summary:
ChIP-chip experiments were done to analyze the global distribution of H3K9K14Ac in yeast
Keywords: ChIP-chip

overall_design: We analyzed 3 independent replicates


title: RNAi analysis of the FBP transactivator family

status: Public on Oct 17 2006

city: Bethesda

first: David

last: Levens

address: 10 Center Drive

department: NCI/CCR

institute: NIH

summary:
The FBP (FUSE Binding Protein) transcription factor family is composed of three highly related members; FBP/FBP1, FBP2, and FBP3. While they all share distinct modular protein structures and nucleic acid-binding specificities, their transactivator strength is graded and they also differ in their interaction with their protein partners. Especially from the extensive nuclear co-localization of these molecules, we anticipated that they co-regulate a set of common target genes. Thus we knocked down the level of each FBP using specific siRNA and obtained an initial assessment of the degree to which these factors act concertedly or independently.
Keywords: binding site identification design

overall_design: Each FBP family member was knocked down by transiently transfecting siRNAs, and the total RNA was compared after two days against the control RNA from the negative control transfection. Six arrays were hybridized and analyzed for human primary skin fibroblast samples; two independent experimental sets, each for the three different FBPs.


status: Public on Oct 31 2006

city: Philadelphia

first: Xiangxi

last: Xu

state: PA

address: 333 Cottman Ave

department: Ovarian Cancer and Tumor Cell Biology

institute: Fox Chase Cancer Center

summary:
Alteration of differentiation potentials by modulating GATA transcription factors in murine embryonic stem cells
Keywords: retinoic acid-induced differentiation in GATA4,5,6 (-/-) cell lines

overall_design: RW-4 ES cells of [1] wild-type, [2] GATA4 (-/-), [3]  GATA5 (-/-), [4] GATA6 (-/-) were treated (experimental) or not (control) with retinoic acid to induce differentiation.

first: Callinice

last: Capo-chichi

first: Jennifer

middle: L

last: Smedberg

first: Malgorzata

last: Rula

first: Emmanuelle

last: Nicolas

first: Anthony

last: Yeung

first: Richard

last: Adamo

first: Andrey

last: Frolov

first: Andrew

middle: k

last: Godwin

first: Xiang-Xi


title: Role of E2F3 expression in human bladder and prostate cancer cells

city: Sutton

first: Ian

last: Giddings

summary:
Amplification and overexpression of the E2F3 gene at  6p22 in human bladder cancer is associated with increased  tumour stage, grade and proliferation index, and in  prostate cancer E2F3 overexpression is linked to tumour  aggressiveness. We first used small interfering RNA  technology to confirm the potential importance of E2F3  overexpression in bladder cancer development. Knockdown  of E2F3 expression in bladder cells containing the  6p22 amplicon strongly reduced the extent of bromodeoxyuridine  (BrdU) incorporation and the rate of cellular  proliferation. In contrast, knockdown of CDKAL1/  FLJ20342, another proposed oncogene, from this amplicon  had no effect. Expression cDNA microarray analysis  on bladder cancer cells following E2F3 knockdown was  then used to identify genes regulated by E2F3, leading to  the identification of known E2F3 targets such as Cyclin A  and CDC2 and novel targets including pituitary tumour  transforming gene 1, Polo-like kinase 1 (PLK1) and  Caveolin-2. For both bladder and prostate cancer, we have  proposed that E2F3 protein overexpression may cooperate  with removal of the E2F inhibitor retinoblastoma tumor  suppressor protein (pRB) to drive cellular proliferation. In  support of this model, we found that ectopic expression of  E2F3a enhanced the BrdU incorporation, a marker of  cellular proliferation rate, of prostate cancer DU145 cells,  which lack pRB, but had no effect on the proliferation rate  of PC3 prostate cancer cells that express wild-type pRB.  BrdU incorporation in PC3 cells could, however, be  increased by overexpressing E2F3a in cells depleted of  pRB. When taken together, these observations indicate  that E2F3 levels have a critical role in modifying cellular  proliferation rate in human bladder and prostate cancer.
Keywords: siRNA knock down

overall_design: 3 samples  - siRNA treated versus scambled siRNA control microarrays

first: A

middle: Y

last: Olsson

last: Feber

first: S

last: Edwards

first: R

last: te Poele

first: I

last: Merson

first: C

middle: S

last: Cooper


title: MMASS: an optimised array-based method for assessing CpG island

first: Ashraf

last: Ibrahim

address: Hills Road

department: Pathology

institute: Univeristy of Cambridge

type: Methylation profiling by genome tiling array

summary:
We describe an optimized microarray method for identifying genome-wide CpG island methylation called Microarray-based Methylation Assessment of Single Samples (MMASS) which directly compares methylated to unmethylated sequences within a single sample. To improve previous methods we used bioinformatic analysis to predict an optimised combination of methylation-sensitive enzymes that had the highest utility for CpG-island probes and different methods to produce unmethylated representations of test DNA for more sensitive detection of differential methylation by hybridization. Subtraction or methylation-dependent digestion with McrBC was used with optimized (MMASS-v2) or previously described (MMASS-v1, MMASS-sub) methylation-sensitive enzyme combinations and compared to a published McrBC method. Comparison was performed using DNA from the cell line HCT116. We show that the distribution of methylation microarray data is inherently skewed and requires exogenous spiked controls for normalization and that analysis of digestion of methylated and unmethylated control sequences together with linear fit models of replicate data showed superior statistical power for the MMASS-v2 method. Comparison to previous
methylation data for HCT116 and validation of CpG islands from PXMP4, SFRP2, DCC, RARB and TSEN2 confirmed the accuracy of MMASS-v2 results. The MMASS-v2 method offers improved sensitivity and statistical power for high-throughput microarray identification of differential methylation.
Keywords: Methylation genomic hybridizations.

overall_design: For each of the methods we obtained four microarray hybridisations, using replicate biological preparations in a balanced dye-swap design and compared the results to the published method of Nouzova et al. DNA from the colorectal cancer cell line HCT116 was used for all experiments as methylation patterns have been well characterized in this cell lin

first: Natalie

last: Thorne

first: Nuno

last: Morais

first: Mark

middle: J

last: Arends

first: James

last: Brenton


title: Lmo0688 (GmaR) regulon at room temperature

first: Aimee

last: Shen

state: MA

address: Armenise Building, rm 313, 200 Longwood Avenue

department: Microbiology and Molecular Genetics

summary:
Microarray analyses comparing the transcriptional profile of wild-type EGDe relative to ∆lmo0688 (L. monocytogenes) during standing growth at RT in BHI broth. These analyses revealed that Lmo0688 is required for expression of flagellar motility genes during growth at RT.
In this study, we identify an additional component of the molecular circuitry governing temperature-dependent flagellar gene expression. At low temperatures (30˚C and below), MogR repression activity is specifically inhibited by an anti-repressor, GmaR. We demonstrate that GmaR forms a stable complex with MogR, preventing MogR from binding its DNA target sites. GmaR anti-repression activity is temperature-dependent due to DegU-dependent transcriptional activation of gmaR at low temperatures. Thus, GmaR production represents the first committed step for flagella production in L. monocytogenes. Interestingly, GmaR also functions as a glycosyltransferase exhibiting O-linked N-acetylglucosamine transferase (OGT) activity for flagellin (FlaA). GmaR is the first OGT to be identified and characterized in prokaryotes. Unlike the well-characterized, highly conserved OGT regulatory protein in eukaryotes, the catalytic activity of GmaR is functionally separable from its anti-repression function.

Keywords: EGDe vs ∆688, Temperature, Growth condition

overall_design: Oligonucleotide spotted arrays obtained from the Pathogen Functional Genomic Resource Center at TIGR were used for competitive hybridization studies comparing the transcriptional profile of wild-type EGDe to ∆lmo0688 (L. monocytogenes). Two technical replicates with associated dye swaps was performed for each growth condition.

first: Darren

last: Higgins

first: Heather

last: Kamp

first: Angelika

last: Grundling


title: Fire ant adult vs brood comparison for microarray quality control

status: Public on Oct 14 2006

city: Lausanne

first: John

last: Wang

address: Batiment Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

summary:
Ants display a range of fascinating behaviors, a remarkable level of intra-species phenotypic plasticity and many other interesting characteristics. Here we present a new tool to study the molecular mechanisms underlying these traits: a tentatively annotated expressed sequence tag (EST) resource for the fire ant Solenopsis invicta. From a normalized cDNA library we obtained 21,715 ESTs, which represent 11,864 putatively different transcripts with very diverse molecular functions. All ESTs were used to construct a cDNA microarray. We compared mixed adults to mixed brood to test the quality of the microarrays.
Keywords: microarray quality control

overall_design: We compared RNA from 1 biological replicate of each mixed adults and mixed brood. We generated amplified adult and brood RNA 2 and 3 independent times, respectively. Amplified and labeled RNA was hybridized to a total of 4 microarrays. Two microarrays were brood vs adult and two were dye swaps.

first: Stephanie

last: Jemielity

first: Paolo

last: Uva

first: Yannick

last: Wurm

first: Johannes

last: Gräff

first: Laurent

last: Keller


title: Gene expression profiling reveals stromal genes expressed in common between Barrett's esophagus and adenocarcinoma.

status: Public on Oct 18 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
samples contain normal, Barrett and duodenum and adenocarcinoma
BACKGROUND & AIMS: Barrett's esophagus is a precursor of esophageal adenocarcinoma. DNA microarrays that enable a genome-wide assessment of gene expression enhance the identification of specific genes as well as gene expression patterns that are expressed by Barrett's esophagus and adenocarcinoma compared with normal tissues. Barrett's esophagus length has also been identified as a risk factor for progression to adenocarcinoma, but whether there are intrinsic biological differences between short-segment and long-segment Barrett's esophagus can be explored with microarrays. METHODS: Gene expression profiles for endoscopically obtained biopsy specimens of Barrett's esophagus or esophageal adenocarcinoma and associated normal esophagus and duodenum were identified for 17 patients using DNA microarrays. Unsupervised and supervised approaches for data analysis defined similarities and differences between the tissues as well as correlations with clinical phenotypes. RESULTS: Each tissue displays a unique expression profile that distinguishes it from others. Barrett's esophagus and esophageal adenocarcinoma express a unique set of stromal genes that is distinct from normal tissues but similar to other cancers. Adenocarcinoma also showed lower and higher expression for many genes compared with Barrett's esophagus. No difference in gene expression was found between short-segment and long-segment Barrett's esophagus. CONCLUSIONS: The genome-wide assessment provided by current DNA microarrays reveals many candidate genes and patterns not previously identified. Stromal gene expression in Barrett's esophagus and adenocarcinoma is similar, indicating that these changes precede malignant transformation.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

overall_design: Computed

first: Ying

last: Hao


title: Comparison of miRNA profile of natural T reg cells with conventional CD4+CD25- T cells

city: Cambridge

last: Smith

address: Tennis Court Road

institute: Cambridge University

summary:
Low molecular weight RNA from conventional T cells and T reg cells was hybridised to microarrays containing oligonucleotide probes corresponding to known miRNA sequences.
Keywords: cell type comparison

overall_design: Six arrays representing three biological replicates and dyeswaps of each.

first: Bradley

last: Cobb

first: Arnulf

last: Hertweck

first: Frederick

last: Livesey

first: Matthias

last: Merkenschlager


title: Altered expression of a limited number of genes contributes to cardiac decompensation during chronic pacing in dogs

status: Public on Oct 13 2006

city: Valhalla

first: Caroline

last: Ojaimi

state: NY

institute: New York Medical College

summary:
We have used chronic cardiac pacing in conscious dogs to study mechanism related to the development of dilated cardiomyopathy and the transition from compensated dysfunction (CD) to decompensated heart failure (HF).  This occurs from the 3rd to 4th week of pacing with end-stage HF at 30?1 days.
Keywords: disease state analysis

overall_design: In this study we used the Affymetrix Canine Array to determine differential expression of potential target genes during the progression to decompensation. Cardiac RNA was extracted at control, 3 and 4 weeks of pacing (n=4).

first: Khaled

last: Qanud

first: Thomas

middle: H

last: Hintze

first: Fabio

last: Recchia


title: DIP-chip:  Rapid and accurate determination of DNA-binding specificity

first: Jason

last: Lieb

state: NC

address: CB# 3280, 202 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

summary:
Validation of DNA ImmunoPrecipitation with microarray analysis (DIP-chip) technique using the Leu3 DNA binding domain.
Keywords: DIP-chip, Leu3

overall_design: Detected in vitro Leu3 DBD binding with 4 replicates at 40nM Leu3 DBD.  Detected in vitro Leu3 DBD binding with 3 replicates at 4nM Leu3 DBD.  Determined in vivo binding of Leu3DB with 5 ChIP-chip replicates.  Determined in vivo binding of Leu3AD with 7 ChIP-chip replicates

first: X

last: Liu

first: D

middle: M

last: Noll

first: J

first: N

last: Clarke


title: High-resolution comparative genome hybridization survey of healthy individuals (chromosome 22)

status: Public on Oct 12 2006

city: New Haven

first: Jan

middle: Oliver

last: Korbel

state: CT

address: 266 Whitney Avenue

institute: Yale University

summary:
HighRes-CGH arrays that utilize ≈385,000 distinct oligonucleotide probes to cover chromosome 22 at 85 bp resolution (tiling path step size) were designed and synthesized as previously described (Urban et al., Proc Natl Acad Sci U S A. 2006;103(12):4534-9; see also GSE4240 record). Here, two healthy individuals were studied using the same experimental protocols as in Urban et al.
Keywords: high-resolution comparative genome hybridization using oligonucleotides

overall_design:
See above, same as in Urban et al., Proc Natl Acad Sci U S A. 2006;103(12):4534-9; see also GSE4240 record.
	The overall goal of the study was the detection of the precise boundaries of deletions and amplifications. Maskless array synthesis was used to construct custom isothermal arrays containing up to 385,000 oligonucleotides, tiling the non-repetitive regions of chromosome 22. Genomic DNA isolated from patients (Cy3) was co-hybridized with a reference DNA pool (Promega; Cy5).

middle: O

first: Alexander

last: Urban

first: Fabian

last: Grubert

first: Beverly

last: Emanuel

first: Sherman

last: Weissman

first: Michael

last: Snyder

first: Mark

last: Gerstein