title: Genes differentially expressed upon CHD8 knockdown

status: Public on May 01 2009

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

summary:
CHD8 is a putative chromatin remodeling ATPase of the SNF2 family. We found that depletion of CHD8 impairs cell proliferation. In order to identify CHD8 target genes, we performed a transcriptomic analysis of CHD8-depleted cells. CHD8 was knockdown by doxycyclin-dependent expression of a shRNA that target the CHD8 mRNA.
Keywords: CHD8 knockdown analysis

overall_design: C33KD2 is a stable cell line where expression of a shRNA, that targets the CHD8 mRNA, is dependent on doxycycline. Addition of doxyclycin provokes a significant reduction in the level of CHD8 protein. Total RNA samples coming from C33KD2 cells cultured for 48 hours either with or without 2 µg/ml doxycycline were used to generate complementary RNA labelled with Cy5 with the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The reference sample was Stratagene human universal reference and was amplified at the same time as the sample RNA using the same method. Reference samples were labeled using Cy3.

first: Manuel

last: Rodríguez-Paredes

first: Maria

last: Ceballos-Chávez

first: Manel

last: Esteller

first: Mario

last: García-Domínguez

middle: C


title: Serum amyloid and serum amyloid P are not induced in response to diesel exhaust particles or carbon black

status: Public on Apr 27 2009

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

summary:
W evaluated an experimental particle exposure model, including markers of the acute phase system assessed as the hepatic mRNA expression of Sap, the murine homologue of CRP, and Saa1 and Saa3.
Keywords: Toxicology, disease state analysis, stress response, nanoparticles, air pollution

overall_design: 12-13 weeks old Apoe knockout mice (C57BL/6-Apoe tm1) mice were injected intraperitoneally with varying doses of SRM 2975. In a parallel experiment C57BL mice were exposed by inhalation for 90 minutes to four consecutive doses of 20mg/m3 of filtered air, NIST 2975 or Ptintex 90. Livers and aortic tissue were collected.

first: Anne

middle: T

last: Saber

first: Sabina

last: Halappanavar

first: Janne

middle: K

last: Folkmann

first: Jette

last: Bornholdt

middle: M

last: Boisen

first: Peter

last: Møller

first: Carole

last: Yauk

first: Ulla

last: Vogel

first: Steffen

last: Loft

first: Håkan

last: Wallin


title: Gene Expression in Adipose Tissue during Weight Loss

status: Public on May 12 2009

city: Toulouse

first: Frederic

last: Capel

address: 1 Av Jean Poulhes

department: INSERM UPS U858

country: France

institute: INSERM

summary: We investigated the regulation of adipose tissue (AT) gene expression during different phases of a dietary weight loss program and its relationship with insulin sensitivity. Obese women followed a weight reduction program composed of an energy restriction phase (ER) with a 4-week very-low-calorie diet and a weight stabilization period (WS) composed of a 2-month low-calorie diet followed by 3 to 4 months of a weight maintenance diet. At each time point, body composition, plasma parameters and glucose disposal rate were assessed and subcutaneous AT biopsies were performed. Variations in mRNA levels were determined using DNA microarrays and reverse transcription-quantitative PCR. Distinct sets of AT genes are regulated during calorie restriction and weight stabilization revealing an unexpected temporal pattern in the link between AT and insulin sensitivity during weight loss.

overall_design: Fifteen obese premenopausal women were recruited at the Third Faculty of Medicine of Charles University and at the Institute for Mother and Child Care in Prague, Czech Republic. During the first four weeks of the dietary intervention program, the subjects received an energy restricted diet of 800 kcal/day (liquid formula diet, Redita, Promil). During the next two months, a low-calorie diet was designed to provide 600 kcal/day less than the individually estimated energy requirement based on an initial resting metabolic rate multiplied by 1.3. Following this, subjects entered a weight maintenance phase for a period of 3 to 4 months, during which the patients were instructed to keep their weight stable. A complete clinical investigation in the fasting state was realized before and at the end of each phase. Needle microbiopsy of subcutaneous AT was performed under local anesthesia (1% Xylocaine) from the abdominal region (14–20 cm lateral to the umbilicus). Total RNA were isolated from AT samples with Qiagen RNeasy kit. RNA quantity and quality were checked with the Experion automated electrophoresis system (BioRad laboratories). We performed a whole transcriptome analysis comparing 1) before vs. after the initial 4 weeks severe energy restriction (ER), 2) after energy restriction vs. after weight stabilization (WS) and 3) before dietary intervention vs. after weight stabilization (DI). Eight subjects representative of the cohort were selected, matched for high quality of total RNA samples, insulin sensitivity and weight changes during the study. Targets for microarray experiments were generated from 500 ng of total RNA with Agilent low RNA input amplification kit (Agilent Technologies) and hybridized to whole genome 44k oligonucleotide arrays (Agilent Technologies). Each combination of samples was analyzed twice using a dye swap design (i.e., a total of 48 hybridizations). Data acquisition from microarrays was obtained with a GenePix 4000B scanner (Axon instruments) and image processing was performed with Feature Extraction 8.5 (Agilent Technologies). Raw data were normalized with a global Lowess procedure and filtered with R package LIMMA (Bioconductor). Outlier replicates and spots with a signal to noise ratio lesser than 2 on both red and green channel were eliminated from our analyses. Mean log ratios were calculated from paired duplicates before normalization. Differentially expressed genes were identified with Significance Analysis of Microarray (SAM) procedure.

first: Nathalie

last: Viguerie

first: Eva

last: Klimcakova

first: Balbine

last: Roussel

first: Vladimir

last: Stich

first: Dominique

last: Langin


title: Establishing a set of genes differentially expressed in benign versus malignant adrenocortical cells

status: Public on Dec 31 2011

city: Grenoble

first: Michaël

last: Thomas

address: 17 rue des martyrs

department: iRTSV/BCI

institute: Inserm U1036

summary: Models for tumorigenesis can be made by transforming normal cells with defined genetic elements. This allows us to determine that adrenocortical tumor development and progression follows a multistep model. Morever, we demonstrated that the order of genetic events has a great consequence on the phenotype of the resultant tumor. We performed transcriptomic analysis using cDNA microarrays to identify the molecular signature that might explain the distinctive in vivo phenotypes observed in response to both orders of the mutational events.

overall_design: Two p53+Ras two pBabe +pLNCX2 (control for the p53+Ras cells), three Ras+p53 and two pLNCX2+pBabe (control for Ras+p53 cells) cell populations were prepared and used for microarray analysis;


title: Mechanisms that specify promoter nucleosome location and identity

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Biochemistry and Biophysics

country: USA

institute: University of California, San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary: The chromatin architecture of eukaryotic gene promoters is generally characterized by a nucleosome-free region (NFR) flanked by at least one H2A.Z variant nucleosome.  Computational predictions of nucleosome positions based on thermodynamic properties of DNA-histone interactions have met with limited success.  Here we show that the action of the essential RSC remodeling complex in S. cerevisiae helps explain the discrepancy between theory and experiment.  In RSC-depleted cells, NFRs shrink such that the average positions of flanking nucleosomes move toward predicted sites.  Nucleosome positioning at distinct subsets of promoters additionally requires the essential Myb family proteins Abf1 and Reb1, whose binding sites are enriched in NFRs.  In contrast, H2A.Z deposition is dispensable for nucleosome positioning.  By regulating H2A.Z deposition using a steroid-inducible protein splicing strategy, we show that NFR establishment is necessary for H2A.Z deposition.  These studies suggest an ordered pathway for the assembly of promoter chromatin architecture.

overall_design:
Nucleosome positions were mapped in a variety of strains under a variety of conditions to determine how several proteins are involved in nucleosome positioning.  All replicates are biological replicates.  Each set of replicates is balanced in terms of Cy3:Cy5 such that there are equal numbers of Cy3:Cy5 and Cy5:Cy3 arrays (format:  mononucleosomal DNA:reference DNA).

Changes in gene expression in a strain carrying either the Sth1-degron or Abf1-Reb1-degron under degron-inducing conditions were profiled by hybridizing labeled cDNA derived from the degron strain against labeled cDNA derived from a control strain lacking the degron, but grown under the same conditions.  Four biological replicates for each experiment were done using a balanced dye-swap design.

first: Paul

middle: D

last: Hartley


title: Arabidopsis gene expression profile : Col-0 wild-type vs. pif3pif4pil5pil6 (pifQ) mutant

status: Public on Apr 23 2009

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

department: Biological Sciences

country: South Korea

institute: KAIST

summary:
Transcriptional profiling of 60h-old Arabidopsis whole seedlings comparing control Col-0 wild-type plants with pifQ mutant plants
The expression profile of dark-grown pifQ mutant shows similar pattern of Rc-grown Col-0 wild-type

Keywords: Genetic modification

overall_design: In all cases, 60h-old dark-grown Col-0 wild-type was used as background. 2-condition experiment, Rc-grown Col-0 vs. dark-grown pifQ. Biological replicates : 3 each, was independently grown and harvested. One replicate per array.


title: PTEN-deficiency in luminal MMTV-ErbB-2 mouse model results in dramatic acceleration in mammary tumorigenesis/metastasis

status: Public on Jun 29 2009

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

summary: Overexpression and/or amplification of the ErbB-2 oncogene, as well as inactivation of the tumor suppressor PTEN, are two important genetic events in human breast carcinogenesis.  To address the biological impact of conditional inactivation of PTEN on ErbB-2-induced mammary tumorigenesis, we generated a novel transgenic mouse model that utilizes the MMTV promoter to directly couple expression of activated ErbB-2 and Cre recombinase to the same mammary epithelial cell (MMTV-NIC).  Disruption of PTEN in the mammary epithelium of the MMTV-NIC model system dramatically accelerated the formation of multifocal and highly metastatic mammary tumors, which exhibit homogenous pathology.  PTEN-deficient/NIC tumorigenesis was associated with an increase in angiogenesis. Moreover, inactivation of PTEN in the MMTV-NIC mouse model resulted in hyperactivation of the PI3K/Akt signalling pathway. However, like the parental strain, tumors obtained from PTEN-deficient/NIC mice displayed histopathological and molecular features of the luminal-like subtype of breast cancer.  Taken together, our findings provide important implications in understanding the molecular determinants of mammary tumorigenesis driven by PTEN deficiency and ErbB-2 activation, and could provide a valuable tool for testing the efficacy of therapeutic strategies that target these critical signalling pathways.

overall_design: Common reference design. 9 samples (including 2 normal tissue and 7 tumor tissue samples) replicated twice as dye swaps, generating a total of 18 arrays.

first: Babette

last: Schade

first: Trisha

last: Rao

last: Dourdin

first: Michael

last: Hallett

last: Cardiff

first: William

middle: J

last: Muller


title: Magnaporthe oryzae Gene Expression During Biotrophic Invasion of Rice (Agilent Array, G4137B)

status: Public on Apr 08 2009

city: Manhattan

first: Barbara

last: Valent

state: KS

address: 4024 Throckmorton Plant Sciences

department: Department of Plant Pathology

institute: Kansas State University

summary:
The hemibiotrophic fungus Magnaporthe oryzae produces specialized biotrophic invasive hyphae (IH) that alter membrane structure and defense responses in invaded rice cells.  IH successively invade live neighbor cells, apparently through plasmodesmata.  Understanding fungal and rice genes that contribute to biotrophic invasion has been a challenge because so few plant cells have encountered IH at the earliest infection stages.  Using a rice sheath inoculation method, we successfully enriched for infected tissue RNA that contained ~20% fungal RNA at a point when most IH were still growing in first-invaded rice cells.  The RNAs were analyzed using the whole-genome M. oryzae oligoarray and a rice oligoarray.  Rice genes that were induced >50-fold during infection were enriched for genes involved in transferring information from sensors to cellular responses.  Fungal genes that were induced >50-fold in IH included the PWL2 avirulence gene and genes encoding hypothetical secreted proteins.  The IH-specific secreted proteins are candidate effectors, proteins that the fungus secretes into live host cells to control cellular processes.  Gene knock-out analyses of three putative effector genes failed to show major effects on pathogenicity.  Details of the blast interaction transcriptome will provide insights on the mechanisms of biotrophic plant disease.
Keywords: Disease state analysis

sample_organism:
Oryza sativa
Pyricularia oryzae

overall_design: Our goal was to compare expression in biotrophic IH to expression in mycelium grown in nutrient medium, and to compare expression in infected rice sheath to expression in mock inoculated rice.  Using version 2 of the fungal whole genome microarray (Agilent Technologies), we analyzed samples from three biological replicates of rice leaf sheath at 36 hours after inoculation with the rice blast fungus M. oryzae. The same samples were used with the Agilent rice microarray (see series GSE8518). To estimate the ratio of fungal to rice RNAs in the infected sheaths, we compared RT-PCR amplification of fungal genes in infected tissue to amplification in standards produced by mixing known ratios of pure mycelial RNA with mock-inoculated rice RNA. Using this assay, fungal RNA content in infected tissues were approximately 20% of the total RNAs. We prepared control mixtures by pooling 20% mycelial RNA and 80% RNA from mock-inoculated rice sheath. Complementary RNAs from infected tissues were labeled with Cy3 or Cy5 and hybridized together with the control mixture RNA labeled with the other dye.  Three independent biological replications were performed, with separate hybridizations for 2 technical replications and corresponding dye swap experiments.  Data were analyzed by Rosetta Resolver® and showed a correlation of over 80% between biological replications.

first: Gloria

last: Mosquera

first: Sean

last: Coughlan


title: Rice Gene Expression During Biotrophic Invasion by Magnaporthe oryzae (Agilent Array G4138A)

overall_design: Our goal was to compare expression in infected rice sheath to expression in mock inoculated rice, and to compare expression in biotrophic IH to expression in mycelium grown in nutrient medium. Using the rice microarray (Agilent Technologies), we analyzed samples from three biological replicates of rice leaf sheath at 36 hours after inoculation with the rice blast fungus M. oryzae. The same samples were used with the Agilent M. oryzae microarray (see series GSE8517). To estimate the ratio of fungal to rice RNAs in the infected sheaths, we compared RT-PCR amplification of fungal genes in infected tissue to amplification in standards produced by mixing known ratios of pure mycelial RNA with mock-inoculated rice RNA. Using this assay, fungal RNA content in infected tissues were approximately 20% of the total RNAs. We prepared control mixtures by pooling 20% mycelial RNA and 80% RNA from mock-inoculated rice sheath. Complementary RNAs from infected tissues were labeled with Cy3 or Cy5 and hybridized together with the control mixture RNA labeled with the other dye.  Three independent biological replications were performed, with separate hybridizations for 2 technical replications and corresponding dye swap experiments.  Data were analyzed by Rosetta Resolver® and showed a correlation of over 80% between biological replications.


title: microRNA expression profiling among human embryonic stem cells, differerentiated EBs and adult cells

status: Public on Apr 17 2009

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary:
Human embryonic stem (hES) cells have unique features: self-renewal ability and pluripotency. They can be continuously cultured in undifferentiated state and give rise to cells and tissues of all three germ layers. Thus hES cells provide a resource not only for cell replacement therapy but also for studying human developmental biology. We aimed to identify the unique signature of miRNAs in human embryonic stem cells.

Keywords: cell type comparison design

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Betapolyomavirus macacae

overall_design: We performed microRNA expression profiling on 3 passages from 2 different hES cell lines (WA09 (H9) and BG01v) and 4 passages from 1 hES cell line (TE06 (I6)), EBs samples derived from WA09 cells at 4 different time points with replicates, and 5 types of adult cells (HUVEC, HMVEC, UASMC NHA, and LFB).


title: Comparison of the transcriptomes of tfIIs vs Col-0

status: Public on Mar 24 2009

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Testing the consequences of the absence of the transcript elongation factor TFIIS on the transcriptome in Arabidopsis.
Keywords: Comparison of mutant and wildtype

overall_design:
Four replicate RNA extractions were performed of each genotype using independent pools of plants. Samples were hybridized in two dye-swaps.
tfIIs1#1 (Cy5) vs. Col-0#1 (Cy3)
Col-0#2 (Cy5) vs. tfIIs1#2 (Cy3) dye-swap
tfIIs1#3 (Cy5) vs. Col-0#3 (Cy3)
Col-0#5 (Cy5) vs. tfIIs1#4 (Cy3) dye-swap
Samples were hybridized in two dye-swaps.
The data were normalized over all 4 hybridizations to obtain one, single log-ratio(Sample/Reference).
The raw data files of all four of the hybridizations are attached to the Sample.

first: Marion

last: Grasser

first: Klaus


title: Granulosa cell gene expression in gonadotropin-treated ERbeta-het and ERbeta-null mice

status: Public on Mar 31 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The aim of this study was to determine the role of ERβ in the response of mouse granulosa cells to PMSG (an FSH analog) by comparing the gene expression profiles of ERβ-het and ERβ-null animals treated with this compound.

overall_design: ERβ-het and ERβ-null mice were treated with PMSG for 48h and granulosa cells isolated and pooled according to gentoype, resulting in the production of two RNA samples (one biological replicate per gentoype). There were two hyb replicates for the comparison. Two slides were hybridized for the sample pairing to allow for dye reversals (technical replicates).

first: Kenneth

middle: S

last: Korach

first: Bonnie

last: Deroo

first: John

middle: F

last: Couse

first: Katherine

last: Hamilton

first: Jennifer

middle: B

last: Collins

first: Sherry

last: Grissom


title: Microarray analysis of strain EG4 vs. Nipponbare

city: Athens

first: Ken

last: Naito

state: GA

address: 4505 Miller Plant Sciences Building

department: Plant Biology

institute: University of Georgia

summary: In the japonica rice strain Gimbozu EG4, the DNA transposon mPing is actively transposing to attain over 1,000 copies, whereas in Nipponbare, where this element is virtually silent and has only 50 copies. To analyze the impact of such a massive amplification of transposable element on gene regulation, we performed the rice 44k oligo microarray analysis.

overall_design: Total RNA was extracted from 7-day-old seedlings of EG4 and Nipponbare plants, grown in a greenhouse at at 26˚C and subjected to 44k oligo-DNA microarray with 4 biological replicates.

first: Feng

last: Zhang

first: Takuji

last: Tsukiyama

first: Hiroki

last: Saito

first: Yutaka

last: Okumoto

first: Takatoshi

last: Tanisaka


title: Microarray analysis of gene expression in the skin of tick-naïve and tick-infested Holstein-Friesian and Brahman cattle

status: Public on Apr 03 2009

city: Brisbane

first: Emily

middle: Kate

last: Piper

address: Seddon Buildings (Bldg 82)

department: School of Veterinary Science

country: Australia

institute: University of Queensland

summary:
This experiment was undertaken to document changes in gene expression in the skin of tick-resistant Brahman (Bos indicus) and tick-susceptible Holstein-Friesian (Bos taurus) cattle prior to, and following, infestation with the cattle tick Rhipicephalus (Boophilus) microplus

Keywords: Disease state analysis

sample_organism:
Bos taurus
Bos indicus

overall_design: RNA was extracted from skin samples of tick-naïve cattle (animals with no previous R.microplus exposure) and tick-infested cattle after a period of successive, heavy infestations with R. microplus. Skin samples taken from tick-infested animals were taken at sites where tick larvae (approximately 24 h old) were attached to the skin sample. Skin samples were of 8 mm diameter and full skin thickness (approximately 10 mm). RNA samples from 12 animals (3 tick-naive Holstein-Friesian, 3 tick-naive Brahman, 3 tick-infested Holstein-Friesian and 3 tick-infested Brahman) were processed and hybridised to individual slides.

first: Nicholas

middle: N

last: Jonsson

first: Louise

middle: A

last: Jackson

first: Ala

middle: E

last: Lew

first: Cedric

last: Gondro


title: Acute effects of particulate matter (EHC-93) inhalation in mice with chronic lung inflammation

status: Public on Mar 23 2009

first: Andrew

last: Williams

summary:
We examined the impact of chronic lung inflammation on the pulmonary transcriptional response to inhaled urban particles.  Transcript levels were measured using high density microarrays in total RNA isolated from whole lungs of wildtype and TNF-α overexpressing mice exposed by inhalation to particulate matter and euthanized immediately or 24 h post-exposure.
Keywords: Toxicology, disease state analysis, stress response

overall_design: Transgenic SP-C/TNF-α mice and their wildtype littermates were exposed by inhalation to particulate matter (0, 42 mg/m3 EHC-93) for 4 h and euthanized immediately or 24 h post-exposure (n=5 per treatment per time point, 40 animals total).  Agilent 22K oligonucleotide microarrays were used to examine transcript levels in whole lung RNA.  Stratagene Universal Mouse RNA was used as a reference.

first: Errol

last: Thomson

first: Carole

middle: L

last: Yauk

first: Renaud

last: Vincent


title: Genome-Wide Promoter Analysis of Epigenetic Regulation by Cocaine

status: Public on May 20 2009

city: Dallas

first: guanghua

last: xiao

state: TX

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: University of Texas Southwestern Medical Center

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Head and neck squamous cell carcinomas

status: Public on Mar 12 2009

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

first: Serge

last: Smeets

first: Boudewijn

last: Braakhuis

first: Saman

last: Abbas

first: Peter

last: Snijders

first: Bauke

last: Ylstra

first: Mark

last: van de Wiel

first: Gerrit

last: Meijer

first: Rene

last: Leemans

first: Ruud

middle: H

last: Brakenhoff


title: PLN tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice.

status: Public on Mar 10 2009

city: Stanford

first: Keiichi

last: Kodama

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

summary: 41K whole genome oligo-microarrays (Agilent Technologies) were used to characterize age-dependent changes in gene expression in pancreatic lymph nodes (PLN) obtained from up to 7 individual NOD mice at 6 different time points (10 days (n=7), and 4 weeks (n=6), 8 weeks (n=4), 12 weeks (n=7), 16 weeks (n=6), and 20 weeks of age (n=5)), compared to NOD.B10 tissue controls. "Milestone Genes" are genes whose expression was significantly changed (approximately 3 fold) as the result of splicing or changes in transcript level. Milestone Genes were identified among genes within type one diabetes (T1D) susceptibility regions (Idd). Milestone Genes showing uniform patterns of changes in expression at various time points were identified. Potential T1D candidate genes were identified among Milestone Genes within Idd regions and/or hierarchical clusters. These studies identified tissue- and age-specific changes in gene expression that may play an important role in the inductive or destructive events of T1D.

overall_design:
NOD/LtJ (NOD), NOD.B10Sn-H2b/J (NOD.B10) female mice of multiple ages were used for this study.
Six Groups of NOD mice were sacrificed at 10 days, and 4, 8, 12, 16, and 20 weeks of age and pancreatic lymph nodes (PLN) were removed and prepared for mRNA analysis.  Two Groups of 10 NOD.B10 mice [10 days (n=10) + 20 weeks of age (n=10)] were used as a tissue specific control.  Gene (mRNA) expression was analyzed using the 41K Whole Mouse Genome Oligo Microarray Kit (Agilent Technologies), and gene expression data are processed (cy3: NOD, cy5: NOD.B10) and reported as normalized expression ratios: Log 10 (NOD processed signal / NOD.B10 processed signal) (Log ratio).
10days of age; PLN_10d (n=7), 4 weeks of age; PLN_4w (n=6), 8 weeks of age; PLN_8w (n=4), 12 weeks of age; PLN_12w (n=7), 16 weeks of age; PLN_16w (n=6), 20 weeks of age; PLN_20w (n=5)

first: Atul

last: Butte

first: Remi

last: Creusot

first: Leon

last: Su

first: Deqiao

last: Sheng

last: Hartnett

first: Hideyuki

last: Iwai

first: Luis

middle: R

last: Soares

first: Garrison

last: Fathman


title: H1 hESC Exposed to Butyrate

status: Public on Mar 05 2009

city: Seattle

first: Brig

last: Mecham

state: WA

address: 1100 Fairview Ave N

institute: University of Washington

summary: To assess the effect of sodium butyrate exposure on human ESC grown without culture support for self-renewal (I.e. without conditioned medium and added bFGF) - three groups were compared - H1 culture in feeder conditioned medium vs without conditioned medium in 0.2 mM sodium butyrate vs. grown in sodium butyrate for 4 passages followed by return to conditioned medium conditions for 3 passages.  The three groups were grown in triplicate and compared on Agilent whole human genome array

overall_design: H1 hESC were grown under 3 conditions: A.  48 passages total, the last 9 passages off of feeders on Matrigel in feeder conditioned medium B.  48 passages total, within the last 9 passges, #39-41 were in conditioned medium and #42-48 were without conditioned medium and added bFGF but with 0.2 mM sodium butyrate on Matrigel C. 49 passages total, within the last 10 passages #39-41 were in conditioned medium, #42-46 in 0.2 mM sodium butyrate (without feeder of bFGF support) and #47-49 back to conditioned medium + bFGF.  The RNA from these cells were compared via Agilent whole human genome array.

first: Carol

last: Ware

first: Anthony

last: Balu

first: Brigham


title: Cellulose-induced and Nutrient limitation-induced regulation of Phanaerochaete chrysosporium genes

status: Public on Mar 30 2009

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL


title: Effects of trans-10, cis-12-Conjugated Linoleic Acid on Hepatic Gene Expression in a Polygenic Obese Line of Mice

status: Public on Mar 01 2009

city: Raleigh

first: Melissa

last: Ashwell

address: Campus Box 7621

institute: North Carolina State University

summary:
The trans-10, cis-12-isomer of conjugated linoleic acid (CLA) causes a rapid reduction of body and adipose mass in mice by decreasing adipocyte size and number. In addition to changes in adipose tissue, numerous studies have reported alterations in hepatic lipid metabolism. Livers of CLA fed mice gain mass due to lipid accumulation; however, the precise molecular mechanisms are unknown. To elucidate these mechanisms, we examined fatty acid composition and gene expression profiles of livers from a polygenic obese line of mice fed 1% trans-10, cis-12 CLA. Following examination of the fatty acid profile it was concluded that stearoyl CoA desaturase (SCD) activity was unaffected by CLA. Analysis of gene expression data led to the identification of 1393 genes differentially expressed in the liver of CLA fed mice at a nominal P-value of 0.01 and 775 were considered significant using a false discovery rate threshold of 0.05. Following Bonferroni correction and excluding lowly expressed transcripts, 198 genes were identified as being differentially expressed with 17 genes having ≥ 2-fold change. Pathway analysis of the 775 genes considered significant using FDR found that 38 of these genes are controlled by Hepatocyte Nuclear Factor 4α, a transcription factor thought to be important in controlling liver metabolic status.
Keywords: obesity, conjugated linoleic acid, polygenic obese mice, liver, lipid metabolism

The list of significant differentially expressed genes found in the liver of mice fed CLA vs. LA is linked below as a supplementary file.

overall_design: Functional genomic analysis of liver tissue extracted from polygenic obese male mice fed either a control (1% linoleic acid) or treatment (1% trans 10, cis 12 conjugated linoleic acid) diet after fourteen days. Four or five mice were pooled for each labeling. There is 1 replicate for each experiment, for a total of 4 microarrays.

first: Ryan

middle: P

last: Ceddia

first: Ralph

last: House

first: Joseph

last: Cassady

first: Eugene

last: Eisen

first: Thomas

last: Eling

first: Jennifer

last: Collins

first: Sherry

last: Grissom

first: Jack

last: Odle


title: Down syndrome study

status: Public on Feb 23 2009

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

institute: INSERM U675


title: Study of Drosophila cell lines

status: Public on Mar 20 2009

city: Bloomington

first: Lucy

last: Cherbas

state: IN

department: CGB

institute: Indiana University


title: Effects of Black Raspberry diet on N-Nitrosomethylbenzylamine-altered gene expression in Rat Esophagus

city: Columbus

first: Gary

last: Stoner

state: OH

address: 2001 Polaris Pkwy

department: The Ohio State University

institute: Department of Internal Medicine

summary:
Our recent study (Reen et al., Cancer Res 2007;67:6484-92) identified 2261 dysregulated genes in the esophagi of rats that received a one week exposure to the carcinogen, N-Nitrosomethylbenzylamine (NMBA). We further reported that 1323 of these genes were positively modulated in the esophagus of NMBA-treated animals that also consumed dietary phenethyl isothiocyanate (PEITC), a constituent of cruciferous vegetables. Herein, we report our companion study wherein litter mate rats either received regular chow or chow with 5% freeze-dried black raspberries (BRB) for three weeks.  During the third week one-half of these animals received three subcutaneous injections of NMBA (0.5 mg/kg body weight). All animals were sacrificed 24h after the last dose of NMBA, and their esophagi excised and processed for histological grading and RNA microarray profiling. Two hundred and fifty nine of the 2261 genes that were dysregulated by NMBA-alone were expressed at control levels in the esophagus of  BRB-fed rats. Overall, the data indicate that a BRB diet has a genome-wide modulating effect on NMBA-caused dysregulation of gene expression in rat esophagus, including genes involved in phase I and phase II metabolism, oxidative damage, inflammation, differentiation, chromosome partitioning, cell adhesion, motility and cytoskeleton formation, and genes known to act as oncogenes and tumor suppressor genes regulating apoptosis, cell-cycling and proliferation, and angiogenesis.
Keywords: Toxicogenomics, reference design.

overall_design: For each treatment we used a pooling strategy to enable the inclusion of samples from numerous animals. Three replicate microarrays were completed for each of the four treatments (control, BRB, NMBA and NMBA+BRB) for a total of twelve microarrays. Each microarray was hybridized using a pooled RNA sample, and each pool was created from equal amounts of total RNA from two or three independent RNA samples, representing individual animals. Each of these samples was obtained from a different animal, and no sample was included in more than one pool.  In total, samples from nine animals per group were pooled for control, NMBA, BRB and NMBA+BRB microarrays. To facilitate comparisons of gene expression across all treatments, we utilized a reference design in which each microarray was co-hybridized with a common reference sample labeled with Cy3, and RNA from the treatment pool was labeled with Cy5. Stratagene’s Universal Rat reference RNA (Stratagene, La Jolla, CA) was used as the common reference in all microarrays.

first: Rashmeet

last: Reen

first: Alan

last: Dombkowski

first: Laura

last: Kresty

first: Daniela

last: Cukovic

last: Mele

first: Sridevi

last: Salagrama

first: Ronald

last: Nines


title: DNA methylation profiling of ductal carcinoma in situ (DCIS)

status: Public on Feb 18 2009

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Methylation profiling by genome tiling array

summary:
Methylated genomic fragments from tumor DNA and matching normal control were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. MIRA enriched samples from tumor were labeled with Cy5 while MIRA enriched DNA samples from normal tissue were labeled with Cy3.

Keywords: Cancer

overall_design: Methylation patterns of tumors; six patients with early stage breast cancer (DCIS)

first: Stella

last: Tommasi

first: Gerd

last: Pfeifer


title: Transcriptional analysis of E12.5 telencephalon from 152F7 transgenic mouse

summary: The molecular mechanisms that lead to the cognitive defects characteristic of Down syndrome (DS), the most frequent cause of mental retardation, have remained elusive. Here we use a transgenic DS mouse model to show that DYRK1A gene dosage imbalance deregulates chromosomal clusters of genes located near neuron-restrictive silencer factor (REST/NRSF) binding sites. We found that DYRK1A binds the SWI/SNF-complex known to interact with REST/NRSF. Mutation of a REST/NRSF binding site in the promoter of the REST/NRSF target gene L1cam modifies the transcriptional effect of Dyrk1A-dosage imbalance on L1cam. DyrkA dosage imbalance perturbs Rest/Nrsf levels with decreased Rest/Nrsf expression in embryonic neurons and increased expression in adult neurons. We identified a coordinated deregulation of multiple genes that are responsible for the cellular phenotypic traits present in DS such as dendritic growth impairment and microcephaly during prenatal cortex development. Dyrk1a overexpression in primary mouse cortical neurons reduced the neuritic complexity. In the postnatal hippocampus, DYRK1A overexpression suppresses a form of synaptic plasticity that may be sufficient to cause DS cognitive defects. We propose that DYRK1A overexpression-related neuronal gene deregulation generates the brain phenotypic changes that characterize DS, with an accessory role for the gene dosage imbalance of other chromosome 21 genes.

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL2872, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Of 44,290 spots, 2756 are controls. The remaining 41,534 spots represent 33,661 unique transcripts which correspond to 20,202 unique human genes. Four dependent (152F7, one series of pooled samples) measurements were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dye-swapping experiments).

first: Aude-Marie

last: Lepagnol-Bestel

first: Agnes

last: Zvara

first: Frédérique

last: Quignon

first: Bedel

last: Ngimbous

first: Nicolas

last: Ramoz

first: Sandrine

last: Imbeaud

first: Yann

last: Loe-Mie

first: Karim

last: Benihoud

last: Agier

first: Paul

last: Salin

first: Ana

last: Cardona

first: Suonavy

last: Khung-Savatovsky

first: Pekka

last: Kallunki

first: Jean-Maurice

last: Delabar

first: Laszlo

middle: G

last: Puskas

first: Hervé

last: Delacroix

first: Lawrence

last: Aggerbeck

first: Anne-Lise

last: Delezoide

first: Olivier

last: Delattre

first: Philip

last: Gorwood

first: Jean-Marie

last: Moalic

first: Michel

last: Simonneau


title: Genome-wide binding of the insulator factors CTCF and CP190

status: Public on Feb 20 2009

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen


title: Effects of single or 35 days oral exposure of adult Sprague-Dawley rats to p-tert-octylphenol on uterine gene expression

city: Laval

first: Patrick

last: Devine

state: QC

address: 531 boulevard des Prairies

department: INRS-Institut Armand-Frappier

institute: Institut national de la recherche scientifique

summary:
Contamination of the environment with endocrine disrupting chemicals (EDCs) has raised concerns about potential health hazards for humans and wildlife. P-tert-octylphenol (OP) is one such ubiquitous chemical reported to bind to the estrogen receptor (ER) and alter expression of estrogen-responsive genes. Human and wildlife exposure to OP are likely, due to its persistence in the environment and its presence in food, water and items of daily use. Detrimental effects of OP exposures on the reproductive system have been observed in some, but not all, in vivo experiments. This study compared estrogenic effects of OP in vitro with those in vivo in adult female rats, attempting to better mimic real-life exposures in adults. In vitro, OP bound to human ER weakly and accelerated proliferation of MCF-7 cells.  Adult Sprague-Dawley rats were given OP by gavage either once or daily for 35 days (125 mg/kg body weight).  Body and organ weights and ovarian follicle populations were unaltered in OP-exposed adult rats after either time point, despite detectable levels of OP in reproductive organs. Toxicity of OP was demonstrated by a slightly reduced growth rate and slightly altered estrous cycle, but there were no significant estrogen-like changes in histomorphology or microarray analyses of gene expression of uterine tissue.  Prepubertal rats exposed by gavage to 125 or 250 mg/kg OP for three days failed to show any uterotrophic effects, although E2 caused a 3-fold increase in uterine weight. Results do not support a dose-dependent, estrogenic mode of action for OP.

This SuperSeries is composed of the SubSeries listed below.


title: Transcriptional analysis of murine neurobastoma N18 cell line transfected with a pAd-Dyrk1a vector

first: Gilles

last: Maussion

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL2872, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Of 44,290 spots, 2756 are controls. The remaining 41,534 spots represent 33,661 unique transcripts which correspond to 20,202 unique human genes. Five independent (Dyrk1A overexpression, five individual samples) measurements were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dye-swapping experiments).

first: Aude-Marie

last: Lepagnol-Bestel

first: Agnes

last: Zvara

first: Frédérique

last: Quignon

first: Bedel

last: Ngimbous

first: Nicolas

last: Ramoz

first: Sandrine

last: Imbeaud

first: Yann

last: Loe-Mie

last: Benihoud


title: Changes in gene expression in MKK2 and MKKKC5 mutants

status: Public on Feb 15 2009

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary:
The mkkkC5 mutant, a knockout line of MAPKKKC5, shows changes in growth and development, as well as an altered Alternaria sensitivity. It was shown by Brader and Djamei et al.(2007) that Alternaria brassicicola sensitivity is also influenced by MKK2-activity. Aim of this experiment is to access the transcriptional changes in the mkkkc5plants as well as in plants overexpressing a constitutively active MKK2-version (MKK2EE). The second part of the experiment addresses transcriptional changes in these plants after Alternaria brassicicola infection.

This SuperSeries is composed of the SubSeries listed below.

first: Jean-Pierre

last: Renou

first: Heribert

last: Hirt

first: Sarah-

last: Himbert

first: Marie-Laure

last: Martin-Magniette


title: Time course gene expression profiling of T-cell (CD40L+) induced, anti-CD40-siRNA treated, HUVECs

status: Public on Feb 10 2009

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary:
The CD40-CD40L dyad seems to play a prominent role fostering the immune-inflammatory response triggered by endothelial cell (EC)-T cell interaction. To comprehensively delineate the involvement of CD40 (TNFRSF5) in EC activation, we combined RNAi-mediated CD40 knock-down with comparative genome-wide transcriptional profiling of EC in response to T cell. We report the initiation of a profound stress response in ECs upon CD40-CD40L engagement through early up-regulation, among others, of the major pro-inflammatory NFkB and MAPK/SAPK pathways and their associated transcription factors. Moreover, we have identified novel genes regulated through the CD40-CD40L interaction, and pathways previously unrecognized to be induced by CD40 signaling in ECs. Thus, we document a strong down-regulation of endothelial APLN by CD40-CD40L interaction, which could lead to vascular tone dysfunction in atherosclerotic lesions. Conversely, CD40-mediated up-regulation of the viral immune surveillance system, notably TLR3, IFIH1, RIG-I, and RNASEL, establishes a reverse link from adaptive to innate immunity in ECs. Moreover, systematic enrichment analysis substantiates endothelial CD40 involvement in the transcriptional regulation of gene networks associated with adhesion and motility, immunity, cell fate control, hemostasis and metabolism. Our study also highlights the potency and specificity of CD40 siRNA mediated inhibition, and the relevance of CD40 signaling pathways for anti-inflammatory therapeutic intervention.
Keywords: treated vs. untreated comparison, time course

overall_design: Time course experiment comparing endothelial gene expression profiling of CD40-silenced versus non-silenced cultured cells using RNA interference. Two independent experiments were performed where HUVECs were siRNA-transfected and co-cultured with Jurkat D1.1 for 4, 10, 16 h and harvested for RNA extraction. Technical dye swap duplicates were performed for each of the two biological replicates in all three time points.

first: Raquel

last: Pluvinet

first: Josep

last: Aran


title: Whole genome microarray analysis of the Drosophila morphogenetic process

status: Public on Feb 11 2009

city: Los Angeles

first: Matthew

last: Lebo

address: 1040 Child's Way

department: Molecular and Copmutational Biology

institute: University of Southern California


title: The distinct response of gd T cells to the Nod2 agonist muramyl dipeptide

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

summary:
We have begun to approach gd T cells more as prospective innate cells than as conventional T cells.  Recent results indicated that purified gd T cells are primed directly in response to pathogen associated molecular patterns (PAMPs) to better respond to secondary signals and increase expression of chemokine and activation-related genes.  In microarray and real time PCR analyses of RNA derived from bovine and human gd T cells, transcripts encoding Nod2 were repeatedly amplified.  Nod2 is the intracellular receptor for muramyl dipeptide (MDP), a subunit of PGN, functions in regulating innate activities, and was thought to be expressed primarily in APCs.  Given our repeated detection of Nod2 transcripts in gd T cells, the specific direct response of gd T cells to MDP was analyzed by microarray, real time PCR, proteome array and in a functional priming assay.  The results indicate a subtle activation in response to MDP akin to priming, and suggest a unique mechanism for differential gene expression.
Keywords: Comparison of genes expressed after stimulation of bovine gd T cells with either PBS or MDP

overall_design: PBLs from calf 129 were stained with GD3.8 directly conjugated to FITC, washed, and sorted on a Vantage SE cell sorter (BD Immunocytometry Systems) as previously described.  PBLs from calves 150 and 151 were stained with GD3.8, and anti-Mouse IgG magnetic beads and sorted with MACS magnetic bead system (Miltenyi Biotec) as previously described to a purity of >98%.  Sorted cells were rested overnight, stimulated for 4 hours then lysed in Buffer RLT and genomic DNA sheared using Qiashredder columns then frozen at -80oC.  RNA was extracted following the manufacturer’s protocol for RNeasy (Qiagen) column purification, assessed on a Bioanalyzer 2100 (Agilent Technologies), and amplified using the Affymetrix One-cycle protocol with approximately 1.7micrograms of total RNA as described in the GeneChip® Expression Analysis Technical Manual (June 2004).  Hybridizations to Genechip® Bovine Genome Arrays (Affymetrix) were performed with 15 mg biotin labeled cRNA.  Washing and staining was performed in the GeneChip® Fluidics Station 450 using the Midi_euk2v3 protocol.  Chip scans were performed on the Affymetrix GeneChip® Scanner 3000.  GeneChip® Operating Software (GCOS v.1.1, Affymetrix) 19;20 was used for data collection.

first: Mark

last: Jutila

first: Hannah

last: Kerns


title: Secondary NS from Cortex and spinal cord

first: Terry

last: Kelly

address: 700 Westwood Blvd

institute: UCLA

summary:
Neural stem cells (NSCs) can be isolated from different regions of the central nervous system. There has been controversy whether regional differences amongst stem and progenitor cells are cell intrinsic and whether these differences are maintained during expansion in culture. The identification of inherent regional differences has important implications for the use of these cells in neural repair. Here, we compared neural stem cells derived from the spinal cord and embryonic cortex. We found that while cultured cortical and spinal cord derived neural stem cells respond similarly to mitogens and are equally neuronogenic, they retain and maintain through multiple passages gene expression patterns indicative of the region from which they were isolated. Further microarray analysis identified 229 genes that were differentially expressed between cortical and spinal cord derived neurospheres.
Keywords: stem cell comparison

overall_design: Cortex and and spinal cords were isolated from embryonic day 14 cd1 mice and cultured ad neurospheres for 2 passages in EGF and bFGF. 3 independent sets of cultures serve as biological replicates with a dye flip control for each hybridization, for a total of 6 arrays.

first: Theresa

middle: K

first: Harley

middle: I

last: Kornblum

first: Daniel

last: Geschwind

first: Stanislav

last: Karsten


title: Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas

first: Daoud

last: Sie

summary:
Cervical cancer develops from pre-cancerous high-grade cervical intraepithelial neoplasia (CIN) lesions harbouring a transforming infection with high-risk human papillomavirus (hrHPV), which is characterised by p16INK4a overexpression. Since it takes one or more decades for these pre-cancerous lesions to progress to invasive squamous cell carcinomas (SCCs), it is obvious that they are heterogeneous in terms of duration of existence and progression risk.
We performed array-based comparative genomic hybridisation (array CGH) of 46 p16INK4a immuno-positive CIN2/3 lesions to determine whether this heterogeneity is reflected in their chromosomal profiles. Chromosomal profiles of CIN2/3 lesions were related to those of invasive cervical squamous cell carcinomas (SCCs) and promoter methylation of the CADM1 gene, a tumour suppressor gene known to be functionally involved in the tumorigenic phenotype of cervical cancer cells.
Frequent alterations found in CIN2/3 lesions included gains located at chromosome 1, 3, 7 and 20 and losses located at 4, 11, 16, 17 and 19. Unsupervised hierarchical clustering identified two subsets of CIN2/3 lesions, chromosomal profiles of one of which closely resembled invasive SCCs. Gains of 1, 3q and 20 were characteristic for CIN2/3 lesions with chromosomal signatures resembling carcinomas. In addition, dense promoter methylation of the CADM1 gene was significantly more frequent in these CIN2/3 lesions (p=0.004). No chromosomal alterations were detected in one p16INK4a positive and five p16INK4a negative CIN1 lesions.
These findings suggest that biomarkers associated with gains at chromosomes 1, 3q and 20 are potential hallmarks of advanced p16INK4a positive CIN2/3 lesions with a high short-term risk of progression.

overall_design:
Genomic DNA of 46 high-grade cervical lesions was hybridised to 5K CGH BAC microarrays (5K) produced at the Microarray facility of the VU Medical Center. In total 4632 BAC clones with known chromosomal location were spotted in triplicate, which included the 1Mb resolution Sanger BAC clone set and a subset of clones from the Children’s Hospital Oakland Research Institute (CHORI). All samples were labelled with Cy3 and hybridised together with a pool of normal male reference DNA labelled with Cy5. Hybridisations were essentially performed as described by Snijders et al (Nature Genetics 2001). Both pre-hybridisation and hybridisation were performed in a hybridisation station (HybStation12 – Perkin Elmer Life Sciences). Hybridised arrays were scanned using a G2505B scanner (Agilent, Wilmington, DE, USA). Spots were quantified using ImaGene 5.6.1 software (BioDiscovery Ltd, Marina del Rey, CA, USA) with default settings for the flagging of bad quality spots.
Genomic DNA of 6 CIN1 lesions was hybridised on CGH oligo microarrays (44K) produced by Agilent following the manufacturer’s protocol against the same normal reference pool. Hybridised arrays were scanned using the same scanner (G2505B, Agilent). Quantification of these arrays was done using Feature Extraction software version 9.5.1 (Agilent).


title: Mismatch oligonucleotides in human and yeast

city: New Haven, BASS 437

first: Michael

last: Seringhaus

state: CT

address: 266 Whitney Ave

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary:
Background
Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM) structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S.cerevisiae and H.sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions.
Results
We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C->A, C->G and T->A (yielding purine-purine mispairs) are most disruptive, whereas A->X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa). This skew is small in highly-expressed regions (±0.5% of total intensity range) and large (±2% or more) elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM).

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens


title: Sclerotinia infected vs Mock infected controls in B. napus Westar and Zhong You 821

status: Public on Feb 01 2009

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary:
The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus.  To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray.
For each cultivar, a two-dye experiment was run comparing infected to mock-infected stem tissue.  For each time point, 6 microarray slides were done (3 biological replicates, with a dye swap for each biological replicate).

This SuperSeries is composed of the SubSeries listed below.

first: Jianwei

last: Zhao

first: Lone

last: Buchwaldt

first: Roger

last: Rimmer

first: Andrew

last: Sharpe

first: Linda

last: McGregor

first: Diana

last: Bekkaoui


title: FFPE study using MIP copy number platform

city: Santa Clara

first: Yuker

last: Wang

address: 3380 Central Expressway

institute: Affymetrix

overall_design: Refer to individual Series, GSE14856_quartets.txt contains list of matched samples


title: Rabbit heart gene expression in global ischemia and cardioplegia

status: Public on Jan 28 2009

city: Boston

first: James

middle: D

last: McCully

state: MA

address: 77 Avenue Louis Pasteur

department: Cardiothoracic Surgery

institute: BIDMC/Harvard Medical School

summary: The mechanisms through which cardioplegia affords cardioprotection is complex and  can not be investigated as a single entity but rather must be investigated as a  system. In order to improve understanding of the molecular processes modulating the effects of global ischemia and the cardioprotection afforded by cardioplegia  we have constructed rabbit heart cDNA libraries and have isolated, sequenced and identified a compendium of non-redundant cDNAs for use in microarray analysis.   Methods: New Zealand White rabbits were used for Langendorff perfusion consisting of 30 minutes global ischemia (GI)and 120 minutes reperfusion. Cardioplegia hearts received cardioplegia prior to GI. Control hearts were perfused without GI. The effects of RNA and protein synthesis on the cardioprotection afforded by cardioplegia were investigated separately by pre-perfusion with either alpha-amanitin or cycloheximide. Rabbit heart cDNA libraries were constructed and cDNAs isolated and identified by 5’ sequencing to create a compendium of non-redundant cDNAs for microarray analysis coupled with proteomic analysis.  Results and Conclusion: Our studies demonstrate that the cardioprotection afforded by cardioplegia is modulated by RNA and protein dependent mechanisms. Microarray and proteomic enrichment analysis indicated that cardioplegia significantly increases differentially expressed genes/proteins associated with the mitochondrion and mitochondrial function and significantly up-regulates the biological processes of muscle contraction, involuntary muscle contraction, carboxylic acid and fatty acid catabolic processes, fatty acid beta-oxidation and fatty acid metabolic processes.

overall_design:
Rabbit heart (atria and ventricles):control vs. global ischemia; control vs. cardioplegia; cardioplegia vs. global ischemia

GSM364554 Rabbit slide 56 550_600_33 Raw data for Control vs. Global Ischemia (GI). Control+ Cy3; GI + Cy5.
GSM364554 Rabbit slide 56 530_650_33 Raw data for Control vs. Global Ischemia (GI)-- Control= Cy3; GI=Cy5
GSM364555 Rabbit slide 58 550_600_33 Raw data for Control vs. KMg+DZX (cardioplegia)   Control=Cy3;  KMg+DZX (cardioplegia)=Cy5.
GSM364554 Rabbit slide 60 550_600_33 Raw data for Control vs GI   Control =Cy3; GI=Cy5.
GSM364555 Rabbit slide 62 520_680_33 Raw data for Control vs. KMg+DZX (Cardioplegia). Control Cy5; KMg+DZX (Cardioplegia)= Cy3.
GSM364556 Rabbit slide 70 505_590_33 Raw data for Global Ischemia (GI) vs. KMg+DZX (Cardioplegia). GI +Cy3;  KMg+DZX (Cardioplegia)= Cy5
GSM364556 Rabbit slide 71 505_590_33 Raw data for Global Ischemia (GI) vs. KMg+DZX (Cardioplegia). GI +Cy5;  KMg+DZX (Cardioplegia)= Cy3


title: Gene expression profiling of C. elegans under various thermal conditions

status: Public on Feb 28 2009

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

country: Japan

institute: Japan Aerospace Exploration Agency

summary: To realistically evaluate the effects of the environment in space, it is necessary to understand the effects of external factors during sample transport from Earth to space. The present study focused on temperature, profiling the altered gene expression that develops under low cultivation temperatures in C. elegans, used as a space life science model. The 7903 genes were selected as differentially expressed genes, and divided into five sets with similar expression patterns using k-means clustering. Results from Gene Ontology analysis are significantly indicated that the cell cycle related genes, and the TGFβ/insulin-like signal pathway related genes changed. The TGFβ/insulin-like signal pathway is expected to be activated due to low temperatures, as well as by other stressors.

overall_design: To determine the genes whose expression changed four thermal conditions (10, 15, 20, and 25 °C), DNA microarray analysis was performed. The data consisted of 12 samples, consisting of three biological replicates at each temperature.

first: Toko

last: Hashizume

first: Noriaki

last: Ishioka


title: Hypoxia alters gene expression in the gonads of zebrafish

status: Public on Feb 02 2009

city: Duluth

first: Dalma

last: Martinovic

state: MN

address: 6201 Congdon Blvd

department: ORD-NHEERL

institute: U.S. EPA

summary:
The objectives of this study were to characterize gene expression responses to hypoxia in gonads of mature zebrafish (Danio rerio), and to start characterizing modes of action by which hypoxia could potentially alter reproduction. Adult male and female zebrafish were maintained under normoxia (7 mg O2/L), moderate hypoxia (3 mg O2/L) and severe hypoxia (1 mg O2/L) for 4 and 14 days (n = 5 per treatment) and changes in gene expression in gonadal tissues were evaluated using a commercial 21,000 gene zebrafish oligonucleotide microarray. Differentially expressed genes were determined using ANOVA (p < 0.01), and enriched gene ontology (GO) categories (p < 0.05) identified using GeneSpring GX software (Agilent, USA). Short-term (4 d) exposure to hypoxia affected expression of genes associated with the initial adaptive responses such as: metabolism of carbohydrates and proteins, nucleotide metabolism, haemoglobin synthesis, reactive oxygen species metabolism and locomotion. More prolonged (14 d) hypoxia affected a suite of genes belonging to different GO categories: lipid metabolism, reproduction (e.g., steroid hormone synthesis), and immune responses (cytokine synthesis). The results of the present study demonstrate that reproduction likely would be affected by hypoxia via multiple modes of action. These include previously hypothesized mechanisms such as inhibition of steroidogenesis via modulation of expression of steroidogenic genes, and downregulation of serotonergic pathway. But, in addition to these, we propose that there are multiple other points of disruption of reproductive system function linked, for example, to reorganization of lipid transport and other mechanisms involved in responding to hypoxia (e.g., hydroxysteroid dehydrogenase alterations, downregulation of contractile elements etc.).
Keywords: time course and dose response

overall_design: Reproductively mature zebrafish (Danio rerio; ab wild-type strain; 7 months old) were obtained from an on-site culture unit. Mixed groups of four males and four females were randomly loaded into 10 L tanks, receiving a continuous flow of Lake Superior water. Zebrafish were exposed to hypoxia for duration of 4 and 14 days. There were three oxygen treatments: normoxia (6.5 mg dissolved O2/L), moderate hypoxia (3 mg dissolved O2/L) and severe hypoxia (1 mg dissolved O2/L). Each exposure tank contained four males and four females, and each time and oxygen content treatment combination was replicated twice (i.e., fish were held in two separate exposure tanks). The 4 and 14 d exposures were conducted concurrently. Aliquots of gonadal RNA from male and female fish exposed to hypoxia for 4 and 14 days (five biological replicates from each of the three oxygen treatment groups) were submitted to an Agilent certified facility, MOgene, LC (St. Louis, MO), for gene expression profiling.

last: Villeneuve

last: Kahl

first: Jeffrey

last: Brodin

first: Lindsey

last: Blake

first: Gerald

last: Ankley


title: Toxicogenomic response of Mycobacterium bovis to disinfectant treatments

status: Public on Jan 20 2009

city: ft. meade

first: Hyeung-Jin

last: Jang

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2


title: Analysis of the Interaction Transcriptome During Biotrophic Invasion of Rice by the Blast Fungus, Magnaporthe oryzae

status: Public on Apr 08 2009

city: Manhattan

first: Barbara

last: Valent

state: KS

address: 4024 Throckmorton Plant Sciences

department: Department of Plant Pathology

institute: Kansas State University

platform_organism:
Oryza sativa Japonica Group
Pyricularia grisea

first: Gloria

last: Mosquera

first: Martha

middle: C

last: Giraldo

first: Chang-Hyun

last: Khang

first: Sean

last: Coughlan


title: Pearl millet seedlings infected with rust, or treated with MeJA or SA

status: Public on Jan 01 2009

city: Pretoria

first: Bridget

middle: Genevieve

last: Crampton

address: PO Box 395

country: South Africa

institute: CSIR Biosciences


title: Acetaminophen-induced gene expression profiles in sandwich-cultured primary rat hepatoctyes

city: Bilthoven

first: Anne

middle: Susan

last: Kienhuis

address: A. van Leeuwenhoeklaan 9

institute: RIVM

summary:
The frequent use of rodent hepatic in vitro systems in pharmacological and toxicological investigations challenges extrapolation of in vitro results to the situation in vivo and interspecies extrapolation from rodents to humans. The toxicogenomics approach may aid in evaluating relevance of these model systems for human risk assessment by direct comparison of toxicant-induced gene expression profiles and infers mechanisms between several systems. In the present study, acetaminophen (APAP) was used as a model compound to compare gene expression responses between rat and human using in vitro cellular models, hepatocytes, and between rat in vitro and in vivo. Comparison at the level of modulated biochemical pathways and biological processes rather than at that of individual genes appears preferable as it increases the overlap between various systems. Pathway analysis by T-profiler revealed similar biochemical pathways and biological processes repressed in rat and human hepatocytes in vitro, as well as in rat liver in vitro and in vivo. Repressed pathways comprised energy-consuming biochemical pathways, mitochondrial function, and oxidoreductase activity. Conclusion: the present study is the first that used a toxicogenomics-based parallelogram approach, extrapolating in vitro to in vivo and interspecies, to reveal relevant mechanisms indicative of APAP-induced liver toxicity in humans in vivo.

Gene expression profiles of sandwich-cutlured primary rat hepatocytes exposed to 5 mM and 10 mM acetaminophen were used in a parallelogram approach in order to compare gene expression responses between rat and human using in vitro cellular models, heaptocytes, and between rat in vitro and in vivo

Keywords: Toxicogenomics, dose response

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Samples were retrieved from acetaminophen treated rat hepatocyte cultures from 3 rats (3 biological replicates). Rat hepatocytes from each replicate were cultured in two culture conditions, each treated with 0, 5, and 10 mM acetaminophen for 24 h. This resulted in (3 rats x 2 culture conditions x 3 doses) 18 dual channel arrays on which control (0 mM acetaminophen) and reference samples (0, 5, and 10 mM acetaminophen) were hybridized

middle: S

first: Heleen

middle: M

last: Wortelboer

first: Marcel

last: van Herwijnen

first: Ralph

last: Gottschalk

first: Jos

last: Kleinjans

first: Rob

last: Stierum

first: Joost

last: van Delft


title: Acetaminophen-induced gene expression profiles in sandwich-cultured primary human hepatocytes

summary:
The frequent use of rodent hepatic in vitro systems in pharmacological and toxicological investigations challenges extrapolation of in vitro results to the situation in vivo and interspecies extrapolation from rodents to humans. The toxicogenomics approach may aid in evaluating relevance of these model systems for human risk assessment by direct comparison of toxicant-induced gene expression profiles and infers mechanisms between several systems. In the present study, acetaminophen (APAP) was used as a model compound to compare gene expression responses between rat and human using in vitro cellular models, hepatocytes, and between rat in vitro and in vivo. Comparison at the level of modulated biochemical pathways and biological processes rather than at that of individual genes appears preferable as it increases the overlap between various systems. Pathway analysis by T-profiler revealed similar biochemical pathways and biological processes repressed in rat and human hepatocytes in vitro, as well as in rat liver in vitro and in vivo. Repressed pathways comprised energy-consuming biochemical pathways, mitochondrial function, and oxidoreductase activity. Conclusion: the present study is the first that used a toxicogenomics-based parallelogram approach, extrapolating in vitro to in vivo and interspecies, to reveal relevant mechanisms indicative of APAP-induced liver toxicity in humans in vivo.

expression profiles of sandwich-cultured primary human hepatocytes exposed to 5 mM and 10 mM acetaminophen were used in a parallelogram approach in order to compare gene expression responses between rat and human using in vitro cellular models, hepatocytes, and between rat in vitro and in vivo.

Keywords: Toxicogenomics, dose response

overall_design:
Samples were retrieved from acetaminophen treated human hepatocyte cultures from 5 individuals (5 biological replicates).
Human hepatocytes from each replicate were treated with 0, 5, and 10 mM acetaminophen for 24 h.
This resulted in (3x5) 15 dual channel arrays on which control (0 mM acetaminophen) and reference samples (0, 5, and 10 mM acetaminophen) were hybridized.

last: van de Poll

first: Cornelis

last: Dejong


title: Array Comparative Genomic Hybridization of Merkel Cell Carcinoma Tumors

city: Seattle

first: Bianca

middle: Durando

last: Lemos

address: 815 Mercer St.

department: Medicine/Dermatology

institute: University of Washington

summary:
Array-CGH profiles of Merkel cell carcinoma tumors

Keywords: fresh frozen and formalin fixed paraffin embedded primary tumor, nodal and metastasis merkel cell carcinoma tumor samples

overall_design:
We perfromed array-CGH on 25 Merkel cell carcinoma tumor samples (2 primary/metastasis pairs) looking for recurrent gains/losses among the cohort of tumors.

Results from the Analysis of Copy Errors (ACE) may be found in GSE13239_MccACEAnalyzedData.txt.

The overall profiles of the primary/metastasis pairs are similar.  These metastases samples, 1m and 3m, were excluded from the ACE analysis.

first: Paul

last: Nghiem

first: Kelly

last: Paulson


title: Transcriptional profiling of FeHm effects on Haemophilus influenzae

status: Public on Jan 21 2009

city: Oklahoma City

first: Timothy

last: VanWagoner

state: OK

address: 940 SL Young Blvd, BMS340

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

summary:
Background: Haemophilus influenzae has an absolute aerobic growth requirement for heme and has developed multiple complex mechanisms to obtain this essential nutrient.  Although an understanding of the heme acquisition mechanisms of H. influenzae is emerging, significant gaps remain to be elucidated.  In a previous study we utilized H. influenzae strain Rd KW20 to demonstrate the utility of transcriptional profiling in defining the genes exhibiting altered transcription in response to environmental iron and heme levels. The current study expands upon those initial observations by determining the iron/heme regulons of two additional H. influenzae clinical isolates, i.e. the type b isolate 10810 and the nontypeable isolate R2866, to characterize the core iron/heme regulon of the species.
Results: A microarray chip was designed to incorporate probes for all of the genes of H. influenzae isolates 10810 and R2866, and microarray studies were performed to compare gene expression under iron/heme-replete and iron/heme-restricted conditions for each isolate.  Of 1820 ORFs on the array corresponding to R2866 genes, 363 were significantly differentially expressed.  Of these 363 genes, 233 were maximally transcribed under iron/heme-replete conditions and 130 were preferentially transcribed in iron/heme-restricted conditions.  Of the 1883 ORFs representing genes of strain10810, 351 were significantly differentially transcribed, 150 of these were preferentially transcribed in iron/heme-replete conditions and 201 were preferentially transcribed in iron/heme-restricted conditions.  Comparison of the data sets indicated that 163 genes were similarly regulated in both isolates and that 74 of these also exhibited similar patterns of regulation in strain Rd KW20.
Conclusion: This study provides evidence for a core of H. influenzae genes that are regulated by the availability of iron and/or heme in the growth environment.  Elucidation of this core regulon provides targets for investigation of genes with an unrecognized role in iron and heme homeostasis, as well as other potential virulence determinants. In addition, the set of core genes potentially provides targets for therapeutic and vaccine designs since these products of these genes are likely to be preferentially expressed during growth in iron/heme restricted sites of the human body.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Haemophilus influenzae
Haemophilus influenzae R2866

overall_design: Refer to individual Series

middle: W

last: Whitby

first: Thomas

last: Seale

first: Daniel

middle: J

last: Morton

first: Terrence

last: Stull


title: Interleukin-1-induced gene expression in mouse dermal fibroblasts

city: Charlestown

first: Jin Mo

last: Park

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary:
Interleukin-1 (IL-1) is produced from immune-activated cells upon infection and tissue injury, and stimulates a variety of cells expressing its receptor. IL-1 receptor activation results in intracellular signaling cascades that culminate in the activation of transcription factors such as NF-kappaB, AP-1, and C/EBPbeta. To identify genes whose expression is induced in response to IL-1, we performed DNA microarray analysis of IL-1-treated murine dermal fibroblasts (DFs). The gene expression patterns in control, untreated DFs and in DFs treated with IL-1 were compared.

Keywords: Time course

overall_design: Total RNAs from untreated DFs (0 h) vs. IL-1-treated DFs (1 h, 2 h, or 4 h after IL-1 treatment) were isolated and analyzed using an Agilent DNA microarray platform. Hybridization was performed in duplicate for dye swapping.

first: Jin

first: Hirofumi

last: Aoki


title: Transgenic inhibition of astroglial NF-kappaB in experimental autoimmune encephalomyelitis

city: Miami

first: Roberta

last: Brambilla

state: FL

address: 1095 NW 14th Terrace

institute: Miller School of Medicine University of Miami

summary:
In the central nervous system (CNS) the transcription factor NF-kappaB is a key regulator of inflammation and secondary injury processes. Following trauma or disease, the expression of NF-kappaB-dependent genes is activated, leading to both protective and detrimental effects on CNS recovery. Here we show that transgenic inactivation of astroglial NF-kappaB in mice (GFAP-IkappaBalpha-dn mice) resulted in dramatic reduction of disease severity and improvement in functional recovery following EAE. This coincided with a higher presence of leukocytes in the cord and brain of transgenic mice at the chronic phase of the disease, when the functional recovery over WT mice was the most significant. We observed that expression of proinflammatory genes in both spinal cord and cerebellum was delayed and reduced, while the loss of neuronal-specific molecules essential for synaptic transmission was limited compared to WT mice. Furthermore, death of retinal ganglion cells in affected retinas was almost abolished, suggesting the activation of neuroprotective mechanisms. Our data indicate that inhibiting NF-kappaB in astrocytes results in neuroprotective effects following EAE, directly implicating astrocytes in the pathophysiology of this disease.
Keywords: time course, EAE, transgenic mice, astrocytes, inflammation, cytokines, chemokines

overall_design:
All mice used were 2-4 months old obtained by breeding heterozygous GFAP-IkappaBalpha-dn males with WT females. WT littermates were used as controls. Spinal cords from WT and GFAP-IkappaBalpha-dn transgenic mice (1), naive or induced with experimental autoimmune encephalomyelitis (EAE) at 10, 17 and 80 days post-induction (dpi) were used to isolate RNA. 3 animals were used for each time point.

To identify significantly expressed genes across all replicate arrays we used R software package LIMMA. Each individual array was normalized within the array using global loess normalization. “Between array” normalization was carried out using the “quantile” algorithm also found in the LIMMA package. Differential expression and False Discovery Rate were assessed by using linear model and empirical Bayes moderated F statistics.

first: Trikaldarshi

last: Persaud

first: Xianchen

last: Hu

first: Shaffiat

last: Karmally

first: Valery

last: Shestopalov

first: Galina

last: Dvoriantchikova

first: Dimitry

last: Ivanov

first: Lubov

last: Nathanson

first: Scott

last: Barnum

first: John

last: Bethea


title: Mouse CD8+CD122+ regulatory T cells

status: Public on Dec 31 2008

city: Nagoya

first: Haruhiko

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: Immunology

institute: Nagoya University Graduate School of Medicine

summary: Gene expression profile was compared between CD8+CD122+ T cells and CD8+CD122- T cells.

overall_design: mRNA taken from CD8+CD122+ cells or CD8+CD122- cells collected by cell sorting from C57BL/6 mice spleen was amplified and analyzed by using gene chip of Agilent.

first: Zhe

last: Shi


title: Hybrid_Poplar_H11-11_Leaves_Local_Stress_Response

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

institute: University of British Columbia


title: Changes in gene expression in kidneys from Glis2-deficient mice

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Glis2 is a member of the Gli-similar (Glis) subfamily of Kruppel-like zinc finger transcription factors. To obtain insights into the physiological functions of Glis2, mice deficient in Glis2 expression were generated. These mutant mice develop progressive renal disease associated with fibrosis and inflammation. Gene expression profiles were examined to identify changes in gene expression at early stages of progressive renal disease in Glis2 mutant mice.
Keywords: Glis2, kidney, fibrosis, nephropathy, inflammation

overall_design:
To analyze changes in gene expression, microarray analysis was performed using RNA from kidneys of PND25 and PND60 wild type and Glis2-mutant mice.
Gene expression profiles were compared between kidneys of PND25 wt and Glis2 mutant mice and between PND60 wt and Glis2 mutants. RNA from three kidneys were pooled. RNA from two independent experiments was used and each microarray analysis was performed in duplicate.

first: Yong-Sik

last: Kim

first: HongSoon

last: Kang

first: JuYoun

last: Beak

first: Ronald

last: Herbert

first: Jennifer

middle: B

last: Collins

first: Sherry

middle: F

last: Grissom

first: Anton

last: Jetten


title: Agilent _CRUK_platform_comparison

status: Public on Dec 30 2008

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

summary:
HepG2 cells were exposed to similar concentrations of BaP in two different laboratories (2.5 uM at Institute of Cancer Research and 3 uM at Maastricht University)for 6 and 24 h. Gene expression was analysed by Agilent oligonucleotide microarrays and Cancer Research UK (CR-UK) cDNA microarrays. An inter-laboratory and inter-platform comparison were performed on the data.
Keywords: other

overall_design: 1 samples  - cells exposed to benzo(a)pyrene dissolved in DMSO were compared to cells exposed to DMSO alone


title: Oligonucleotide array CGH in high-risk neuroblastoma tumors

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

summary: We performed array CGH in high-risk neuroblastoma tumors in order to compare genome aberrations with expression of small non-coding RNAs.

overall_design: We analyzed 33 NB primary tumors collected at the onset of disease. All patients were classified as stage 4 according to the International Neuroblastoma Staging System (Brodeur GM, Pritchard J, Berthold F, et al. Revision of the international criteria for neuroblastoma diagnosis, staging and response to treatment. J Clin Oncol. 1993; 11: 1466-1477) and they were older than 1 year of age at time of diagnosis. Regarding clinical course, patients were categorized into two subgroups: “good-outcome” (n = 16, neither relapse nor progression), and “poor-outcome” (n = 17, died due to the disease).

first: Paola

last: Scaruffi

first: Sara

last: Stigliani

first: Simona

last: Coco

first: Carla

last: De Vecchi

first: Francesca

last: Valdora

first: GianPaolo

last: Tonini


title: Transcriptional profiling of Escherichia coli

status: Public on Dec 22 2008

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield


title: Methylation of Polycomb target genes in intestinal cancer is mediated by inflammation

city: Duarte

first: Maria

last: Hahn

state: CA

address: 1500 E. Duarte Rd

department: Biology

institute: City of Hope, Beckman Research Institute

summary: Using glutathione peroxidase, Gpx1 and Gpx2, double knockout (Gpx1/2-KO) mice as a model of inflammatory bowel disease predisposing to intestinal cancer, we analyzed genome-wide DNA methylation and chromatin changing’s in the mouse ileum during chronic inflammation, aging and cancer. We found that inflammation leads to aberrant DNA methylation in Polycomb target genes, with 70% of the ~250 genes methylated in the inflamed tissue being PcG targets in embryonic stem cells and 58% of the methylated genes being marked by H3K27 trimethylation in the ileum of adult wildtype mice. Acquisition of DNA methylation at CpG islands in the ileum of Gpx-1/2-KO mice frequently correlated with loss of H3K27 trimethylation at the same loci. Inflammation-associated DNA methylation occurs preferentially in tissue-specific silent genes and, importantly, is much more frequently represented in tumors than is age-dependent DNA methylation. 60% of aberrant methylation found in tumors is also present in the inflamed tissue. In summary, inflammation creates a signature of aberrant DNA methylation, which is observed later in the malignant tissue and is directed by the PcG complex.

overall_design: In our study we used mice Gpx1/2-ko with B6 and B6.129 genetic background which are characterized by different level of inflammation in ileum and different tumor susceptibility. DNA methylation was analyzed by using MIRA-assisted Microarrays approach. Changing of the DNA methylation in intestinal epithelium during inflammation and tumorgenesis in Gpx1/2-KO mice were compared to healthy control mice with matching age. Aged dependent DNA methylation was study by comparing DNA methylation between 28-days-old healthy control mice with 8-month-old mice. To detect DKO-specific DNA methylation, we compared the changing DNA methylation in liver from Gpx1/2-KO mice with liver from control mice at age 28 days and 8 month. Association of the inflammation dependent DNA methylation with Polycomb targets and loss of H3K27me3 were verified by ChIp-on-ChIp experiments using H3K27me3 antibodies.

middle: A

first: Torsten

first: Lee

last: Dong-Hyun

first: Arthur

last: Riggs

first: Steven

middle: R

last: Esworthy

first: Byung-wook

first: Fong-Fong

last: Chu

first: Gerd

last: Pfeifer


title: Characterization of Primary Melanomas Using High-Resolution Array Based CGH Technology

city: Madrid

first: Juan

last: Cigudosa

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

institute: Centro Nacional de Investigaciones Oncologicas - CNIO

summary:
Malignant melanoma is an aggressive heterogeneous disease for which new biomarkers for diagnosis and clinical outcome are needed. We investigated by array-CGH the presence of DNA gains and losses to provide better genomic profile of primary malignant melanoma and to explore the possibility to distinguish metastatic from non metastatic melanomas using this technology. High resolution array-CGH (Agilent Technologies, Palo Alto, CA), with more than 40.000 probes, has been used to analyze 20 frozen tissues of vertical growth phase primary melanoma with a minimum follow-up time of 36 months. Eight patients developed nodal metastatic disease and twelve did not. For results validation, 83 additional melanoma samples with similar clinical characteristics were analysed by FISH. DNA copy number aberrations (CNA) were observed in 19 out of 20 cases. The most frequent changes were complete or partial losses in chromosomes 9 (12 cases, 60%) and 10 (9 cases, 45%), partial gains or trisomies of chromosome 7 (10 cases, 50%); and monosomy of chromosome 19 (7 cases, 35%). Sixty-four recurrent aberrant regions (SORIs) were precisely delimited and used as variables for clustering. Unsupervised Cluster analysis allowed the segregation of samples into two genomic groups that naturally fitted with the metastatic condition of the cases. Four of these aberrant regions were chosen for their biological interest and were confirmed as aberrant using FISH technique on fixed paraffin embedded tissues. Conclusion: Supervised classification allowed obtaining aberrations useful to separate samples with different clinical outcome. Obtained results are useful to improve the knowledge about melanoma tumorigenesis but unfortunately cannot be used as a marker for metastatic progression.
Keywords: Comparative Genomic Hybridization - array; Genomic Instability

overall_design: Comparative experiment: pheripheral blood pool of ten healthy female donors: CONTROL vs. 20 Primary Vertigal Growth Phase Melanoma samples.

first: Francesco

last: Acquadro


title: Identification of transcripts regulated by RNA helicase A (RHA)

status: Public on Dec 20 2008

city: Columbus

first: Kathleen

last: Boris-Lawrie

state: OH

address: 1925 Coffey Rd

department: Department of Veterinary Biosciences

institute: The Ohio State University

type:
Expression profiling by array
Other


title: A COPD-related gene expression signature in squamous cell lung cancer

city: Groningen

first: Mirjam

last: Boelens

address: Hanzeplein 1

institute: UMCG

summary: Chronic obstructive pulmonary disease (COPD) and squamous cell lung carcinoma (SCC) are both smoking-related diseases. Interestingly, COPD itself is a risk factor for SCC, and this is independent of smoking history. Inferring from this knowledge, it is plausible to assume that patients with COPD may have a different gene expression profile in normal bronchial epithelium and in SCC. To test this hypothesis, we compared gene expression profiles in bronchial epithelium and in SCC from patients with and without COPD. Gene expression profiles were generated using whole human genome oligo microarrays for 28 laser microdissected histologically normal bronchial epithelium samples (10 without COPD, 18 with COPD) and 35 laser microdissected SCC samples (17 without COPD, 18 with COPD). We found no significant differences in gene expression levels between normal bronchial epithelium from patients with and without COPD. Remarkably, 374 genes were differentially expressed in SCC obtained from patients with or without COPD; 295 showed a higher expression level in SCC from patients with COPD and 79 genes showed higher expression levels in SCC from patients without COPD. Genes related to mitochondrial localization (n=44) and genes located on chromosomal arm 5q (n=34) were significantly overrepresented. For both categories, all genes showed a higher expression level in SCC from patients with COPD than from those without COPD. In conclusion, SCC from patients with COPD show a different gene expression profile compared to SCC from patients without COPD. This suggests that COPD related factors affect the gene expression signature in SCC.

overall_design:
PATIENTS AND TISSUE SPECIMENS
We collected resected bronchial tissues of the larger airways (bronchus diameter > 2 mm, surrounded by cartilage) from 10 individuals without COPD (“no COPD”) and 18 patients with COPD (“COPD”). We collected centrally located primary squamous cell lung carcinoma (SCC) from 35 patients; 17 patients without COPD (“no COPD”) and 18 patients with COPD (“COPD”). COPD stages were assessed according the Global initiative for chronic Obstructive Lung Disease (GOLD) classification. Briefly, individuals with a normal spirometry (FEV1/FVC greater than or equal to 70%) are classified as “no COPD”. Patients with FEV1/FVC < 70% are classified as “COPD”. For every patient, the most recent (post-bronchodilator) spirometric results before surgery were used to assess the GOLD stage. Bronchial tissues from 10 individuals without COPD were obtained during thoracotomy for non-small cell lung carcinoma (NSCLC); bronchial tissues from 18 patients with COPD were obtained during thoracotomy for NSCLC (n=11) or lung transplantation (n=7). Bronchus samples of patients with or without COPD were matched for current smoking status and packyears. Patients with SCC who were treated with chemotherapy, used intravenous and/or oral steroids before surgery, and patients with COPD due to alpha-1-antitrypsin deficiency were excluded. All tissue samples were snap frozen in liquid isopentane, and stored at -80 ºC until further processing. The study protocol was consistent with national ethical and professional guidelines (“Code of Conduct; Dutch Federation of Biomedical Scientific Societies”).

LASER MICRODISSECTION MICROSCOPY
For bronchus samples, only histologically normal bronchial epithelium that consists of basal epithelial, ciliated epithelial and goblet cells was laser microdissected. For SCC samples, only vital tumour cells without apparent admixture of inflammatory cells through the tumour fields were isolated using laser microdissection. Areas containing hyperplastic, metaplastic or dysplastic epithelial cells were excluded. An area of approximately 20 – 25 x106 μm2 was microdissected from frozen sections of 8 μm by the P.A.L.M. Microlaser Technology system, according to the manufacturer’s instructions (P.A.L.M., Bernried, Germany). Microdissected cells were immediately collected in lysis buffer (Macherey-Nagel, Düren, Germany).

RNA ISOLATION
Total RNA was isolated and purified from the laser-dissected cells with a Nucleospin RNA II kit (Macherey-Nagel), according to the manufacturer’s instructions, including DNase treatment. The quantity of DNA-free total RNA was measured using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed with RNA 6000 PicoChip (Agilent, Palo Alto, CA) on the 2100 bioanalyzer (Agilent) by the ratio of the 18S and 28S rRNA bands combined with a low baseline.

MICROARRAY APPROACH
Agilent Whole Human Genome (WHG) Oligo Microarrays (GPL1708) (Agilent, Palo Alto, CA), containing 44K 60-mer oligonucleotides representing over 41,000 human genes and transcripts, were used to determine gene expression levels in laser microdissected bronchial epithelial cells. 150 ng of total RNA was amplified for one round using MessageAmp II (Ambion, Austin, USA). mRNA amplification, ULS labelling, Cy-dye coupling, hybridization and data extraction were performed at ServiceXS (Leiden, the Netherlands) according to manufacturer’s instructions. A total of 63 samples (28 bronchus, 35 SCC) were hybridized randomly, including a dye-swap, on 63 Agilent WHG arrays resulting in data from 126 individual hybridizations, based on the non-competitive conditions of a two-colour array (table of randomization will be added to this series as a supplementary table).

first: Adam

last: Gustafson

first: Dirkje

last: Postma

first: Avrum

last: Spira

first: Marc

middle: E

last: Lenburg

first: Marie

last: Geerlings

first: Hannie

last: Sietsma

first: Wim

last: Timens

first: Anke

last: van den Berg

first: Harry

last: Groen


title: TATA-Binding Protein Variants that Bypass the Requirement for Mot1 In Vivo

status: Public on Dec 17 2008

first: NIEHS

last: Microarray Core

summary: Mot1 is an essential TATA-binding protein (TBP)-associated factor and Snf2/Swi2 ATPase that both represses and activates transcription.  Biochemical and structural results support a model in which ATP binding and hydrolysis induce a conformational change in Mot1 that drives local translocation along DNA, thus removing TBP.  While this activity explains transcriptional repression, it does not as easily explain Mot1-mediated transcriptional activation, and several different models have been proposed to explain how Mot1 activates transcription.  To better understand the function of Mot1 in yeast cells in vivo, particularly with regard to gene activation, TBP mutants were identified that bypass the requirement for Mot1 in vivo.  Although TBP has been extensively mutated and analyzed previously, this screen uncovered two novel TBP variants that are unique in their ability to bypass the requirement for Mot1.  Surprisingly, in vitro analyses reveal that rather than having acquired an improved biochemical activity, one of the TBPs was defective for interaction with Pol II preinitiation complex (PIC) components and other regulators of TBP function.  The other mutant was defective for DNA binding in vitro, yet was still recruited to chromatin in vivo.  These results suggest that Mot1-mediated dissociation of TBP (or TBP-containing complexes) from chromatin can explain the Mot1 activation mechanism at some promoters.  The results also suggest that PICs can be dynamically unstable, and that appropriate PIC instability is critical for the regulation of transcription in vivo.

overall_design: Poly (A)+ mRNA was harvested from WT MOT1, mot1-14, and the bypass strains TBP-Y185C and TBP-F207L to determine the effect of the mutant TBP alleles on transcription.  The reference sample for each of the three mutants (mot1-14, TBP-Y185C, and TBP-F207L) was from WT MOT1 cells.  The genes misregulated by TBP-Y185C and TBP-F207L were compared to those misregulated by mot1-14 to determine which Mot1-regulated genes were restored to WT expression levels in the bypass strains, and also to determine the subset of genes that were newly misregulated by each of the bypass mutants.  Each comparison was conducted in duplicate, employing a fluor reversal.  For each array, the data shown is the ratio of Mutant/WT for each probe.

first: Rebekka

middle: O

last: Sprouse

first: Melissa

middle: N

last: Wells

first: David

middle: T

last: Auble


title: Physiological functions of the RORs in brown adipose tissue

status: Public on Dec 18 2008

summary:
To determine the physiological targets of the RORs in brown adipose tissue.
Keywords: Nuclear receptors, RORs, adipose

overall_design: Gene expression analysis was conducted using Agilent whole mouse genome arrays (012694). The analysis was perfomed in duplicate, employing a fluor reversal. RNA was isolated from interscapular brown adipose tissue from C57BL/6 male WT or DKO (RORa-/- and RORg-/-) 8-12 week old mice around circadian time 20. Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Data were retrieved with the Agilent Feature Extraction software (v7.5), using defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.  The resulting data were processed using the Rosetta Resolver® system (Rosetta Biosoftware, Kirkland, WA).

first: Martin

last: Angers

first: HongSoon

last: Kang

first: Jennifer

last: Collins

first: Anton

last: Jetten


title: Pancreatic islet expression profiling in diabetes prone C57BLKS/J mice vs C57BL6/J mice.

city: Thousand Oaks

first: Dan

last: Baker

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

summary:
C57BLKS/J mice are susceptible to diabetes, because of islet dysfunction, whereas C57BL6/J mice are not. Differences in gene expression between the two strains may account for this sensitivity. Furthermore these differences may only be evident in the hyperstimulated (diabetic or hyperglycemic) state. To this end profiling islets from these two strains cultured in both low and high glucose may reveal the underlying mechanism.
Keywords: Mouse strain comparison under different culture conditions

overall_design: In the study presented here, pancreatic islets from 20 mice grown in low and high glucose conditions were assayed for differences in gene expression.  (five C57BLKS/J low glucose, four C57BLKS/J high glucose, six C57BL6/J low glucose, five C57BL6/J high glucose).  Technical replicates are achieved by labeling each sample with both Cy3 and Cy5, and combining the values for each hybridization.

first: Abraham

last: Anderson

first: Joan

last: Helmering

first: Todd

last: Juan

first: Jocelyn

last: McCormick

last: Graham

first: Russ

last: Cattley

first: Daniel

first: Michael

last: Damore

first: Murielle

last: Véniant

last: Lloyd


title: Gene Expression Profiles of PBMC Subsets in Acute GVHD Following Cord Blood Transplantation

city: Minato-ku

first: Naoyuki

last: Takahashi

state: Tokyo

address: 4-6-1, Shirokanedai

department: Research Hospital

institute: The Institute of Medical Science, The University of Tokyo

summary: This SuperSeries is composed of the SubSeries listed below.