title: Microarray Analysis of Differentially Expressed Genes in human bronchial cells(BEAS-2B) treated MTX

status: Public on Dec 06 2008

city: seoul

first: mee

last: song

address: P.O. Box 131, cheongryang

institute: KIST

summary:
Methotrexate (MTX) has been widely used for the treatment of a variety of tumors as well as for inflammatory diseases and rheumatoid arthritis (RA). MTX-induced toxicity has been a serious unpredictable side effect of the treatment and an important clinical problem. Possible causes include allergic, cytotoxic or immunologic reactions to this agent. We examined the consequences of the mechanism of MTX-induced pulmonary toxicity gene expression in BEAS-2B cells, huma bronchial cell line, by microarray.  The expression of these genes are potential biomarker of methotrexate-induced pulmonary toxicity. Also, We provide a clue about mechanism of pulmonary toxic action by these clinical chemotherapeutic agents.
Keywords: 48h treatment, 0.144uM (dose), MTX

overall_design: BEAS-2B cells were seeded and after incubation for 24 h at 37C, the cells were treated with 0.144 μM(IC20) MTX for 48 h. And after total RNA isolation, gene expression analysis was conducted using a 44-k whole human genome microarray. Labeling and hybridization were performed using a FairPlay microarray labeling kit, followed by the coupling of Cy3 (controls) or Cy5 (treated samples) dye. The hybridized slides were scanned using a GenePix 4000B microarray scanner, and the images were analyzed using GenePix 4.1 software to obtain gene expression ratios. The fluorescence intensity of each spot was calculated by local median background subtraction. We then used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000. A significance analysis of microarray (SAM) was performed for genes with significant changes in expression.

first: Ryu

last: jae-Chun

first: Kim

last: Youn-Jung

first: Song

last: Mee


title: Swine Profiling of longissimus dorsi muscle and backfat

status: Public on Dec 16 2008

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

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

overall_design: Refer to individual Series

first: Xuewei

first: Li

last: Zhu

first: Yujiao

last: Guo

first: Lei

last: Chen

first: Qiang

first: Surong

last: Shuai

first: Anan

last: Jiang

first: Guangxi

last: Yang

first: Guoqing

last: Tang

first: Yanzhi


title: Comparison Ezh1 and Ezh2 binding by ChIP on chip in F9 mouse cells

status: Public on Dec 01 2008

city: New York

first: Raphael

middle: F

last: Margueron

state: NY

address: 522 first Ave

department: Biochemistry

country: USA

institute: NYU Langone medical center

type: Genome binding/occupancy profiling by genome tiling array

summary: Comparison of Ezh2 and Ezh1 promoter binding in F9 mouse teratoma cell line.

overall_design: Undifferentiated F9 cells were used for this experiment. Antibodies specificity were checked using a stable cell lines overexpressing a GAl4-Ezh1 or a Gal4-Ezh2 in an inducible manner followed by conventional ChIP at Gal4 responsive transgene.

first: Danny

last: Reinberg


title: Modulation of PrfA activity in Listeria monocytogenes upon growth in different culture media

city: Würzburg

first: Regina

last: Stoll

address: Biozentrum, Am Hubland

country: Germany

institute: Lehrstuhl für Mikrobiologie

summary:
PrfA activity was studied in L. monocytogenes strain EGD and in an isogenic prfA deletion mutant (EGDΔprfA) carrying multiple copies of the wild-type prfA or the mutant prfA* gene (strains EGDΔprfApPrfA and EGDΔprfApPrfA*) after growth in brain heart infusion (BHI), Luria-Bertani broth (LB) or a defined minimal medium (MM) supplemented either with one of the three PTS-carbohydrates, glucose, mannose and cellobiose, or the non-PTS carbon source glycerol. Low PrfA activity was observed in the wild-type EGD strain in BHI and LB with either of these carbon sources, while PrfA activity was high in minimal medium in presence of glycerol but significantly reduced in presence of cellobiose. The strains expressing the prfA and prfA* gene under the prfA promoters, P1 and P2, produced equally large amounts of PrfA protein and high PrfA activity was observed in strain EGDΔprfApPrfA* under all growth conditions. In contrast, high PrfA activity in strain EGDΔprfApPrfA was only observed when this strain was cultured in BHI but not in LB or MM (in presence of either carbon source). A ptsH mutant (lacking a functional HPr) was able to grow in BHI suggesting that growth of L. monocytogenes in this culture medium is supported by carbon sources whose uptake and metabolism are independent of the PTS pathway. However, this mutant was unable to grow in LB and MM regardless which of the four carbon sources was added, suggesting that uptake of the used carbohydrates and the catabolism of glycerol depend fully on the functional common PTS pathway. Furthermore, the growth rates of L. monocytogenes are strongly reduced in presence of large amounts of PrfA protein when growing MM but less in LB and only slightly in BHI. The expression profiles of the genes encoding PTS permeases were determined in the three strains under various growth conditions. The data suggest that PrfA activity correlates with the expression level and the phosphorylation state of specific PTS permeases.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Listeria monocytogenes
Listeria monocytogenes EGD-e

overall_design: Refer to individual Series.


title: Time Course of Individuals Vaccinated with YF-17D

status: Public on Nov 23 2008

city: Atlanta

first: Troy

middle: D

last: Querec

state: GA

address: 954 Gatewood Rd

department: Emory Vaccine Rearch Center

institute: Emory University


title: Peripheral WBC from Brahman and Holstein-Friesian cattle infested with the cattle tick Rhipicephalus microplus

status: Public on Nov 26 2008

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 trial was undertaken to examine the perhipheral cellular and antibody response of cattle following infestation with the cattle tick, Rhipicephalus microplus. The information from the Affymetrix gene expression data is used to complement other measurements of immune function such as cellular subset composition and antibody response in cattle of high (Brahman) and low (Holstein-Friesian) resistance to the cattle tick.

Keywords: Disease state analysis

sample_organism:
Bos taurus
Bos indicus

overall_design: RNA was extracted from white blood cells during a period of successive, heavy infestations with R. microplus. RNA samples from 3 Holstein-Friesian and 3 Brahman animals were analysed on individual slides.

middle: K

first: Nicholas

middle: N

last: Jonsson

first: Louise

middle: A

last: Jackson

first: Ala

middle: E

last: Lew

first: Cedric

last: Gondro


title: Changes in colon gene expression assoc. with increased colon inflam. in IL-10-/- mice inoculated with Enterococcus sp.

city: Palmerston North

first: Matthew

last: Barnett

address: Grasslands Research Centre, Tennent Drive

country: New Zealand

institute: AgResearch

summary:
Inappropriate response to normal intestinal bacteria is involved in the development of Inflammatory Bowel Diseases (IBD, e.g. Crohn’s Disease (CD), ulcerative colitis (UC)) and variations in the host genome may mediate this process. IL-10-/- mice develop CD-like colitis mainly in the colon, in part due to inappropriate responses to normal intestinal bacteria including Enterococcus strains. Comprehensive characterization of changes in gene expression associated with the observed inflammation in the IL-10-/- mouse model has yet to be reported. Our aim was to characterize changes in colonic gene expression in IL-10-/- and C57BL/6J (C57; control) mice resulting from oral bacterial inoculation with 12 Enterococcus faecalis and faecium (EF) strains isolated from calves or poultry, complex intestinal flora (CIF) collected from healthy control mice, or a mixture of the two (EF•CIF). At 12 weeks of age, total RNA extracted from intact colon was hybridized to Agilent 44k mouse arrays. Lists of differentially expressed genes were generated using linear models for microarray analysis (Bioconductor), and genes clustered using GeneSpring GX and Ingenuity Pathways Analysis software. Intestinal inflammation was increased in IL-10-/- mice as a result of inoculation, with the strongest effect being in the EF and EF.CIF groups; expression of >4,000 gene probes was altered in colon tissue compared with similarly inoculated C57 mice. Genes differentially expressed in IL-10-/- mice as a result of EF or EF.CIF inoculation were associated with the following pathways: inflammatory disease (111 genes differentially expressed), immune response (209 genes), antigen presentation (11 genes, particularly major histocompatability complex Class II), fatty acid metabolism (30 genes) and detoxification (31 genes). Our results suggest that the colonic inflammation in EF and EF.CIF-inoculated IL-10-/- mice is mediated by mechanisms similar to those of human IBD, in particular CD.

Example logFC calculation

This example describes the calculation of the fold-change value (logFC) for a single spot (in this case, spot 27222) for a single comparison. This calculation method was applied to generate all of the comparison data shown in the supplementary data files.

The comparison in question is for:
colon tissue from C57BL/6J mouse with EF.CIF treatment (represented by duplicate samples GSM307282 (Title: C57BL/6J_Colon_EF.CIF_Rep1_(Pool17)) and GSM307283 (Title: C57BL/6J_Colon_EF.CIF_Rep2_(Pool18))
vs.
colon tissue from C57BL/6J mouse under conventional conditions (represented by duplicate samples GSM307270 (Title: C57BL/6J_Colon_Conventional_Rep1_(Pool5)) and GSM307271 (Title: C57BL/6J_Colon_Conventional_Rep2_(Pool6))

Important Note: Limma analysis maps the treatments on each slide to the M values which are by convention always log2(R) - log2(G). Because this experiment is a reference design, with the reference RNA always Cy5 (i.e. red, channel 2) and the treatment sample Cy3 (i.e. green, channel 1), and we are interested in the values of the treatment samples compared with the reference, the M values in the data files are displayed as log2(G) - log2(R)

The average expression is what is important here, which is calculated from the normalized M values for the appropriate comparison of interest as follows:

[1] Mean value for Spot 27222, for each treatment:
C57BL/6J mouse, EF.CIF: = mean (0.26363587 (GSM307282), 0.05084283 (GSM307283)) = 0.15723935 C57BL/6J mouse, conventional = mean (1.42951674 (GSM307270),1.15444106 (GSM307271)) = 1.2919789

[2] Calculation of LogFC for the comparison of interest:
The contrast of interest is C57BL/6J: EF.CIF vs Conventional, so by performing a subtraction of these values for the comparison of interest (i.e. (mean for EF.CIF) - (mean for Conventional), the common reference is cancelled out, thus:

C57BL/6J: EF.CIF vs Conventional = 0.15723935  -  1.2919789  =   -1.13473955

So, the fold-change value (logFC) for spot 27222 for the comparison in question (C57BL/6J: EF.CIF vs. Conventional) is: -1.13473955

overall_design:
Animals. Twenty five male IL-10-/- (C57BL/6J background, formal designation B6.129P2-IL-10<tm1Cgn>/J) mice and twenty five male C57BL/6J (C57) control mice were received from The Jackson Laboratory (Bar Harbor, Maine, USA) at approximately five weeks of age. Mice were housed either in pairs or groups of three (5 mice per treatment) in shoebox-style cages containing untreated wood shavings and a plastic tube for environmental enrichment. The animal room was maintained at a temperature of ~22°C and humidity of ~50% with a 12 hour light/dark cycle. All mice had ad libitum access to water, which was refreshed twice a week. An AIN-76A powdered diet was supplied twice a week, with sufficient provided to meet the daily intake of IL-10-/- mice, as determined in a previous feeding trial (data not shown). The diet for all groups was sterilized by gamma irradiation (Schering-Plough, Wellington, New Zealand) to a level required for SPF conditions, to minimize the possibility of bacterial introduction to the SPF group of animals. All mice were weighed three times weekly and carefully monitored for disease symptoms (weight loss, soft faeces and inactivity).

Experimental design. Both IL-10-/- and C57 mice were randomly divided into five treatment groups with five animals per group.

SPF. Housed in Specific Pathogen Free (SPF) conditions (isolator cages supplied with HEPA filtered air (Tecniplast SpA, Buguggiate, Italy)).

C. Maintained under conventional conditions.

EF. Maintained under conventional conditions and orally inoculated (200 microlitres) with a solutions containing 12 pure strains of Enterococcus (1.2 x 10^8 colony forming units (CFU)).

CIF. Maintained under conventional conditions and orally inoculated with conventional intestinal flora (CIF) derived from healthy age-matched C57BL/6 mice which had been raised under conventional conditions. The CIF inoculation protocol was included to better mimic the complete microbiota associated with the mouse gastrointestinal tract.

EF•CIF. Maintained under conventional conditions and orally inoculated with a combination of the EF and CIF inoculation solutions (6.0 x 10^7 CFU from the EF inoculum).

All mice were euthanised via CO2 asphyxiation and cervical dislocation at 12 weeks of age. Blood was collected from euthanised mice by cardiac puncture. Plasma was separated from red blood cells by centrifugation (2000 g, 10 min, 4 ºC), frozen in liquid nitrogen and stored at - 80 ºC. The intestine was removed, cut open lengthwise and flushed with 0•9 % NaCl to remove digesta residues. The proximal half of the colon was cut in two pieces, one for histological evaluation and other for gene expression studies. Samples of the colon tissue for gene expression analysis were frozen in liquid nitrogen and stored at - 80 ºC. Samples for histological analysis were stored in formalin solution (10 % neutral buffered) at room temperature.

Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

The Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., Palo Alto, California, USA) was used to synthesize cDNA and fluorescent cRNA. Labelled cRNA was made on the same day for all sample pools, including the reference sample. cDNA was synthesized from 500 ng of purified total RNA from each pool using T7 promotor primer and Moloney Murine Leukemia Virus Reverse Transcriptase according to the manufacturer’s protocol. Cy3 (PerkinElmer, Waltham, Massachusetts 02451, USA) was used to label sample groups, while the reference RNA was labeled with Cy5 (PerkinElmer, Waltham, Massachusetts 02451, USA).

HYBRIDIZATION
Microarray hybridization was performed according to a reference design without dye swap. The in situ hybridization kit-plus (Agilent Technologies Inc., Palo Alto, California, USA) was used to hybridize cRNA samples to Agilent Technologies Mouse G4121A - 44k 60mer oligonucleotide arrays. Cy3-labelled cRNA (sample, 0.75 µg) and Cy5-labelled cRNA (reference, 0.75 µg) were hybridised onto the microarray according to the manufacturer’s protocol. Following hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

SCAN PROTOCOL
Slides were scanned using a GenePix 4200A scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at a photomultiplier tube (PMT) setting of 450 V. Spot identification and quantification were performed using GenePix 6.0 software (Molecular Devices Corporation, Sunnyvale, CA, USA). Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices). All slides were individually checked and manually flagged for abnormalities.

DATA PROCESSING
Statistical analysis was performed using linear models for microarray analysis (limma) within the Bioconductor framework. Before analysis, poor quality spots were manually flagged and filtered out. Quality of the microarray data was assessed on diagnostic plots (boxplots and density plots) and spatial images generated from the raw (non-processed) data. All twenty arrays passed these strict criteria and were included in the analyses. Intensity ratio values for all microarray spots were normalized using a within-slide global Locally Weighted Scatterplot Smoothing (Loess) procedure to remove the effect of systematic variation in the microarrays; no background correction was necessary due to homogeneous hybridization. The normalized data from the arrays of each treatment group were averaged. For each comparison, differentially expressed genes were identified using false discovery rate (FDR) control with a threshold of q < 0.05. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe using an empirical Bayes approach.
The probability values were then corrected for multiple testing using the Benjamini and Hochberg correction, and a false discovery rate (FDR) calculated. Probes that had an FDR of less than 5 % (q<0*05) were considered to be differentially expressed between treatment.

middle: P

first: Warren

middle: C

last: McNabb

first: Adrian

middle: L

last: Cookson

first: Shuotun

first: Marcus

last: Davy

first: Bianca

last: Knoch

first: Katia

last: Nones

first: Alison

middle: J

last: Hodgkinson

first: Nicole

last: Roy


title: Screening bone marrow derived murine mesenchymal stem cells for tumourigenicity

status: Public on Aug 13 2009

city: Leiden

first: Alex

middle: B

last: Mohseny

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

type: Genome variation profiling by genome tiling array

summary: To study early events in osteosarcoma genesis murine bone marrow derived mesenchymal stem cells (mMSCs) were studied which generated osteosarcoma-like tumours upon injection into nude mice. The process of transformation was studied in a step-wise manner by culturing the MSCs in vitro for 28 passages. Subsequently the transformed passage 28 MSCs were compared to their normal passage 12 originator cells in a number of experiments to identify underlying events prior to malignant transformation. In addition both low and high passage MSCs were shown to still have the phenotypical and functional characteristics of normal MSCs.

overall_design: Previously reported tumourigenic MSCs (TmMSCs) and tumours derived from these cells (T1 and RT2) as well as two new bone marrow derived MSCs cultures from C57BL/6 and BALB/c mice (B6-mMSCs and Bc-mMSCs respectively) were cultured. To characterize the cells FACS analysis and multi-lineage differentiation analysis were performed. To screen for genetic alternations genome wide high resolution arrayCGH (all 7 samples) and COBRA-FISH (for 5 samples) were performed and validated at the gene expression level by qRT-PCR. To look for the clinical relevance of the findings an osteosarcoma tissue array containing human osteosarcoma samples from 88 well-characterized patients was constructed and stained for the relevant proteins by IHC. Correlations with the survival of the patient and other characteristics were analyzed by using SPSS software.

first: Karoly

last: Szuhai

first: Salvatore

last: Romeo

first: Emilie

last: Buddingh

first: Inge

last: Briaire-de Bruin

first: Daniëlle

last: de Jong

first: Melissa

last: van Pel

first: Pancras

last: Hogendoorn

first: Anne-Marie

last: Cleton-Jansen


title: A study of the transcriptional response to a single double-strand break in Bacillus subtilis

status: Public on Nov 21 2008

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT


title: Transcriptional profiles of adult Schistosoma japonicum in response to insulin

status: Public on Dec 12 2008

first: Hong

last: You

state: QLD

address: 300 Herston Road

institute: Queensland Institute of Medical Reaseach

summary: To define the differential gene regulation of adult Schistosoma japonicum in response to host insulin, we utilised a parasite microarray with 38,444 probes representing 19,222 genes. We cultured male and female adult worms were exposed to insulin and glucose; and then parasites were collected at three time-points. There were 1,437 probes (1101 genes) up or down regulated (±1.5 fold change) by insulin after 0.5, 3, 24 hours, with the majority, 712 probes (577 genes) and 623 probes (486 genes) were up-regulated at 24 hour of adding insulin in males and females respectively compared with the control (without insulin).

platform_organism:
Schistosoma japonicum
Schistosoma mansoni

overall_design: Single colour microarray, insulin treated adult Schistosoma japonicum with technical replicates in duplicate: Separate male and female worms exposed to insulin at 0, 0.5, 3, 24 hours. This study includes 6 control samples for separate male and female worms cultured without insulin at 0, 0.5, 3, 24 hours.

first: Wenbao

last: Zhang

first: Luke

last: Moertel

first: Don

last: McManus

first: Geoffrey

last: Gobert


title: Transformants of some rice full-length cDNAs vs wild-type Col-0

city: Yokohama

first: Minami

last: Matsui

address: Suyehirocho 1-7-22 , Tsurumiku

department: Plant Science Center

country: Japan

institute: RIKEN

summary: We generated more than 23,000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt-tolerance, UV signaling, high light tolerance, and heat stress tolerance. Since we isolated 6 genes (AK069096, AK073112, AK073675, AK065297, AK102323 and AK073210) causing an increase in the abundance of metabolites or pigments detected by absorption data, we investigated the expression profiles in transgenic plants by using microarray analysis. Expression of the genes encoding chalcone synthase and dihydroflavonol-4-reductase was increased in all 6 cDNA transformants. These results indicate that an increase in expression of the genes encoding flavonoid biosynthesis enzymes caused an accumulation of pigments in these 6 transformants.

overall_design: Total RNA was isolated from aerial parts of re-transformants of some rice cDNAs and wild type using an RNAqueous Kit (Ambion, Inc, USA).

first: Kondou

last: Youichi

first: Mika

last: Kawashima


title: Profile of estrogen-responsive genes in an estrogen-specific mammary gland outgrowth model

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Both ovarian and pituitary hormones are required for the pubertal development of the mouse mammary gland. Estradiol directs ductal elongation and branching within the adipose stroma of the adolescent mouse mammary gland, while progesterone leads to tertiary branching and alveolar development. The purpose of this investigation was to identify the estrogen-responsive genes that are associated with estrogen-stimulated ductal elongation and branching in the mouse mammary gland in the absence of other ovarian hormones. We also wanted to determine if estrogen-responsive gene regulation at early stages of ductal elongation (ie. when ductal growth was minimal) was similar to those regulated after significant ductal elongation had occurred. To identify estrogen-regulated genes, ovariectomized prepubertal mice were exposed to 17beta-estradiol for four weeks, and mammary gland global gene expression analyzed by microarray analysis at various points during this time course. We determined that while many genes are regulated in all weeks of treatment, there remained a subset of genes that was uniquely regulated at each time-point. This observation was reflected in the biological functions of these genes; some categories were represented in all weeks of treatment while others were specific to only certain time-points. We have also identified estradiol-responsive genes in the mouse mammary gland that co-express with Estrogen Receptor alpha in human breast cancer, which may represent novel effectors of estrogen action and/or biomarkers for the progression of estrogen-dependent cancers and other estrogen-driven diseases.

overall_design:
For each time-course experiment, one frozen #4 mammary gland was individually pulverized from four to five animals per treatment group, then homogenized in 3mL Trizol (Invitrogen, Carlsbad, CA) and RNA was prepared according to the manufacturer’s protocol. The RNA from individual animals was then pooled for each treatment group (four to five animals per group) and further purified using the QIAGEN (Valencia, CA) RNeasy Mini kit (Cat. No. 74104) clean-up protocol.
Gene expression analysis was conducted using Agilent Mouse Oligo arrays (pattern number 011978) (Agilent Technologies, Palo Alto, CA). 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. In each case, samples from estradiol-treated animals were co-hybridized with the day 7 placebo sample. Due to the rapid increase in adiposity in the mammary fat pad in the ovariectomized placebo-treated mice in days 14 and 28, the day 7 placebo sample was used as a control for all estradiol treated samples to avoid any variation due to this biological difference. 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 was obtained using 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 (version 7.1) (Rosetta Biosoftware, Kirkland, WA).

first: Bonnie

last: Deroo

first: Sylvia

last: Hewitt

first: Jennifer

last: Collins

first: Sherry

last: Grissom

first: Katherine

last: Hamilton

first: Kenneth

middle: S

last: Korach


title: Transcriptional Regulation of HL60 Neutrophil Differentiation: Promyelocyte trajectory vs. Neutrophil trajectory

status: Public on Nov 20 2008

city: St. Louis

first: Michael

last: Diamond

state: MO

address: McDonnell Pediatric Research Building, Room 7264

department: Division of Infectious Diseases

institute: Washington University in St. Louis

summary:
Using the HL60 multipotent promyelocytic leukemia cell line, we performed experiments that lead to two different cell fate attractors by treatments of varying dosage and duration of the differentiation agent all-trans-retinoic acid (ATRA). The dosage and duration combinations corresponding to the two treatments were chosen by means of of cytometric measurements of CD11b, a well-known early differentiation marker, such that the two populations are poised at the same stage of differentiation. Using the selected treatment combinations, one population proceeds toward the terminally differentiated neutrophil attractor while the other population reverts back toward the undifferentiated promyelocytic attractor. We monitored the gene expression changes in the two populations after their respective treatments over a period of five days and identified a set of genes that diverged in their expression; a subset of which promotes neutrophil differentiation while the other represses cell cycle progression. By employing promoter based transcription factor binding site analysis, we found enrichment of transcription factors functionally linked to tumor progression, cell cycle, and development.

Keywords: Time course, dose response

overall_design: Untreated HL60 cells are hybrized on the channel 1 with Cy3, ATRA-Treated HL60 cells are hybridized on channel 2 with Cy5. HK60 cells were treated with high dosage/short duration and low dosage/long duration to achieve 55% of CD11b+ cells. These positive cells were then isolated and culture in fresh media and total RNA were isolated for comparison. Cells treated with high dosage/short duration treatment proceed toward the neutrophil attractor while cells treated with the low dosage/long duration treatment revert back toward the promyelocyte attractor.

first: Albert

last: Huang


title: Genome-Wide profile of c-Myc binding in HL60 cells

status: Public on Nov 01 2008

city: Toronto

first: Paul

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
Analysis of technical variance of ChIP-on-Chip studies by characterization of Myc-binding in HL60 cells.
Keywords: ChIP, c-Myc

overall_design: ChIP-on-chip against c-Myc, each array is one biological replicate

first: Romina

last: Ponzielli

first: Christina

last: Bros

first: Igor

last: Jurisica

first: Linda

middle: Z

last: Penn


title: Expression profiling of C. albicans and C. dubliniensis in reconstituted human epithelium

status: Public on Nov 14 2008

city: Rockville

first: Martin

last: Spiering

state: MD

address: 9600 Gudelsky Dr

department: UMBI

institute: University of Maryland

sample_organism:
Candida albicans
Candida dubliniensis


title: Expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation in vivo

status: Public on Oct 27 2008

city: Berlin

first: Smita

last: Sudheer

email: sudheer@molgen.mpg.de, adjaye@molgen.mpg.de, kues@tzv.fal.de, niemann@tzv.fal.de

address: Ihnestr. 63-73

institute: Max Planck Institute for Molecular Genetics

summary:
This study provides the first comprehensive analysis of gene expression and transcriptome dynamics of bovine metaphase II oocytes and in vivo developing bovine embryos.
For this study, Affymetrix GeneChip Bovine Genome Array which covers ~23,000 transcripts was used, which revealed several distinct clusters of genes regulated during various stages of bovine preimplantation development.

Keywords: Time course

overall_design: In vivo matured oocytes were aspirated from the pre-ovulatory follicles of 9 animals on day 0 (=day of standing estrous). For embryo collection, donor animals were inseminated with frozen/thawed semen samples from one Holstein-Friesian bull with proven 270 fertility. Zygotes, 2-cell, 4-cell and 8-to 16-cell stages were recovered by oviductal flushing using a minimally invasive endoscopic approach (24 cows) 1-4 days after artificial insemination (AI). These oviductal stages were collected in pre-warmed phosphate buffered saline (PBS) containing 0.5% bovine serum albumin (BSA) (44). Morulae and blastocysts 12 were collected by uterine flushing at day 7 or 8 after AI (7 animals) using routine nonsurgical 275 procedures. All embryos were carefully evaluated under a stereo microscope and only morphologically intact embryos meeting established criteria (Manual of the International Embryo Transfer Society, IETS) were used. Embryos were pooled in groups of 5, in the case at blastocysts, or 10 embryos for the other stages, washed in PBS + 0.1% PVA, frozen in a minimum amount of medium in siliconised 0.6 ml cups and stored at -80°C. Typically, the 280 time period between flushing and freezing was less than 30 minutes. Animal treatments were conducted according to the German animal welfare guidelines.

first: Wilfried

last: Kues

first: Heiner

last: Niemann

first: James

last: Adjaye


title: Predicting Outcome in Follicular Lymphoma by Using Interactive Gene Pairs

status: Public on Oct 15 2008

city: Kingston

first: Harriet

last: Feilotter

address: 88 Stuart St

department: Pathology and molecular department

institute: Queen's University

summary:
Purpose: Follicular lymphoma is a common lymphoma of adults. Although its course is often indolent, a substantial proportion of patients have a poor prognosis, often due to rapid progression or transformation to a more aggressive lymphoma. Currently available clinical prognostic scores, such as the follicular lymphoma international prognostic index, are not able to optimally predict transformation or poor outcome. Experimental Design: Gene expression profiling was done on primary lymphoma biopsy samples.  Results: Using a statistically conservative approach, predictive interaction analysis, we have identified pairs of interacting genes that predict poor outcome, measured as death within 5 years of diagnosis. The best gene pair performs >1,000-fold better than any single gene or the follicular lymphoma international prognostic index in our data set. Many gene pairs achieve outcome prediction accuracies exceeding 85% in extensive cross-validation and noise sensitivity computational analyses.Many genes repeatedly appear in top-ranking pairs, suggesting that they reproducibly provide predictive capability. Conclusions:The evidence reported here may provide the basis for an expression-based, multigene test for predicting poor follicular lymphoma outcomes.

Keywords: Comparative genomics

overall_design: 41 frozen follicular lymphoma tissues were profiled, then correlated to 5 year follow up survival data.

first: David

last: LeBrun

first: Tara

last: Baetz

first: Cheryl

last: Foster

first: Patricia

last: Farmer

first: Roger

last: Sidhu

first: Hong

last: Guo

first: Karen

last: Harrison

first: Roland

last: Somogyi

first: Larry

last: Greller


title: Endomyocardial biopsies with different acute rejection gradings

status: Public on Oct 18 2008

city: Stanford

first: Cecile

last: Holweg

state: CA

address: 300 Pasteur Drive

department: Cardiovascular Medicine

institute: Stanford University

summary:
Our goals were to determine whether (i) gene expression patterns in biopsies grouped by acute rejection grade (AR) would be consistent; (ii) a characteristic gene expression profile would be associated with ISHLT Grade 0, 1A & 1B (equivalent to 1R on recently revised criteria) and ISHLT grade 3A & 3B (equivalent to 2R & 3R on recently revised criteria); (iii) gene expression patterns emerging from the analysis would provide insights into mechanisms of AR.
The samples used for gene expression profiling were endomyocardial biopsies (EMB) with different acute rejection gradings. The EMB (n=2726) were obtained from the right site of the interventricular septum of heart transplant recipients (n=2423) and graded according to the guidelines of the International Society for Heart and Lung Transplantation (ISHLT, grade 0, n=9; grade1A, n=5; 1B, n=5; 3A, n=4; 3B, n=43). Selection criteria for inclusion of patients in this analysis required the availability of appropriately stored EMB samples for RNA extraction; absence of any infection that required treatment with an antimicrobial drug at anytime during the posttransplant course of the patient; absence of prior AR rejection of any grade; absence of hemodynamic compromise at the time of EMB; use of standard immunosuppressive regimen; and the absence of HLA antibodies prior to transplant.

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.


title: Comparison of the transcriptomes of hmgb1 vs Col-0

status: Public on Nov 24 2008

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 chromatin-associated HMGB1 protein on the transcriptome in Arabidopsis.
Keywords: Comparison of mutant and wildtype samples.

overall_design:
Four replicate RNA extractions were performed of each genotype using independent pools of plants.
hmgb1#1 (Cy5) vs. Col-0#1 (Cy3)
Col-0#2 (Cy5) vs. hmgb1#2 (Cy3) dye-swap
hmgb1#3 (Cy5) vs. Col-0#3 (Cy3)
Col-0#5 (Cy5) vs. hmgb1#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: Dorte

last: Lildballe

first: Klaus

last: Grasser


title: Wild type H37Rv vs HtpX mutant strain

city: Boston

first: Kevin

last: Conlon

address: 300 Longwood avenue

department: Infectious Disease

institute: Childrens Hospital Boston


title: Technical Analysis of Fundulus heteroclitus cDNA Microarrays

city: Miami

first: Cinda

last: Scott

state: FL

address: 4600 Rickenbacker Cswy

department: Marine Biology and Fisheries

institute: University of Miami


title: Intestinal epithelial FHs 74 cell response to 30 minutes and 4 hours treatment with 500 uM Na2S

status: Public on Oct 10 2008

city: Urbana

first: H

middle: Rex

last: Gaskins

state: IL

address: 1207 W Gregory dr

department: Institute for Genomic Biology

institute: University of Illinois


title: Peripheral Blood Cell Gene Expression Profiling in Patients with Coronary Artery Disease (Homo sapiens)

status: Public on Oct 08 2008

city: CA

first: James

middle: A.

last: Wingrove

address: 2500 Faber Place

institute: CardioDx, Inc.

summary:
Expression profiling of peripheral blood mononuclear cells isolated from patients piror to undergoing cardiac catheterization
Disease: NonStenotic: 17-0711, 17-0889, 17-0920, 17-0810, 17-0985, 17-0948, 17-0933, 17-0929, 17-0828, 17-0813, 17-1068, 17-0842, 17-0967, 17-0750
Disease: Stentotic: 17-0736, 17-0727, 17-0915, 17-0913, 17-0866, 17-1043, 17-1037, 17-0994, 17-0924, 17-0921, 17-0917, 17-0916, 17-0808, 17-0758, 17-0963, 17-0958, 17-0951, 17-0822, 17-0815, 17-1089, 17-1083, 17-1077, 17-0954, 17-1086, 17-1057, 17-0748, 17-0722
biological repeat: 17-0711, 17-0889, 17-0920, 17-0810, 17-0985, 17-0948, 17-0933, 17-0929, 17-0828, 17-0813, 17-1068, 17-0842, 17-0967, 17-0750
biological repeat: 17-0736, 17-0727, 17-0915, 17-0913, 17-0866, 17-1043, 17-1037, 17-0994, 17-0924, 17-0921, 17-0917, 17-0916, 17-0808, 17-0758, 17-0963, 17-0958, 17-0951, 17-0822, 17-0815, 17-1089, 17-1083, 17-1077, 17-0954, 17-1086, 17-1057, 17-0748, 17-0722
Keywords: disease state analysis

overall_design: 2 condition experiment: Cases are patients with  ≥70% stenosis in >1 major vessel or ≥50% stenosis in >2 arteries, controls have luminal stenosis of 0%

first: Amy

last: Sehnert

first: Michael

last: Elashoff

first: Susan

last: Daniels

first: Whittemore

last: Tingley

first: Eberhard

last: Grube

first: Geoffrey

last: Ginsburg

first: Kristin

last: Newby

first: Lutz

last: Buellesfeld

first: Steven

last: Rosenberg

first: William

last: Kraus


title: Mouse Chromosome 17 Mapping in Two MEF Cell Lines

city: Vienna

first: Florian

middle: M

last: Pauler

state: Vienna

address: Dr Bohrgasse 9/4

country: Austria

institute: CeMM

type: Genome binding/occupancy profiling by high throughput sequencing


title: Transcriptomics of Rat Striata 16 h after Gamma Knife Surgery: Distinct Bilateral Effects in the Un-irradiated Striatum

city: Tsukuba

first: Randeep

last: Rakwal

state: Ibaraki

address: AIST WEST, Onagawa 16-1

institute: AIST

summary: Gamma knife surgery (GKS) is used for treatment of various brain disorders.  The effects of gamma  irradiation to targeted and un-targeted regions were evaluated by monitoring gene expression changes in the unilateral irradiated (60 Gy) and contralateral un-irradiated striata in the rat. Striata of irradiated and control brains were dissected 16 h post-irradiation for analysis by rat whole genome 44K DNA oligo microarray. Results revealed 230 induced and 144 repressed genes in the irradiated striatum and 432 induced and 239 repressed genes in the un-irradiated striatum. The number of altered genes in un-irradiated striatum was more than that in irradiated striatum. Results of RT-PCR and western analyses suggested that gamma-irradiation caused cellular damage, including oxidative stress, in both striata of both hemispheres. Our present results indicate that unilateral irradiation during GKS produce bilateral effects as early as 16 h, the time-period analyzed, and these molecular changes in the un-irradiated striatum are ample proof.

overall_design: For the experiment, a total of four adult male Wistar rats were housed in acrylic cage at 24 ºC with tap water and laboratory chow ad libitum. The rats were anesthetized with pentobarbital (40 mg/kg intraperitoneally) and fixed in the Regis-Valliccioni frame (Neurospace, Neuilly, France).  A central maximum dose of 60 Gy was administered (for 30 min) to the unilateral striatum with the Leksell gamma knife model C (Elekta Instrument AB) unit by means of 4-mm collimator.  At 16 h post-irradiation, whole brains were rapidly removed and left and right striata were separated on ice according to the method of Glowinski and Iversen with some modifications. The irradiated and un-irradiated striata from irradiated rats and the ipsilateral and contralateral striata from control rats, respectively, were dissected from individual male rats and used for extraction of total RNA. Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4131A) were scanned using a Standard protocol of Agilent DNA Microarray Scanner and data processing was done by Feature Extraction software Version 8.1 from Agilent Technologies.

first: Misato

last: Hirano

first: Junko

last: Shibato

first: Nobuo

last: Kouyama

first: Yoko

last: Katayama

first: Motohiro

last: Hayashi

first: Yoshinori

last: Masuo


title: Quantification of vascular lineage-specific differentiation

status: Public on Oct 04 2008

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

summary:
Angiogenesis and lymphangiogenesis have important roles in cancer progression and chronic inflammatory diseases, but efficient therapies against these diseases have been hampered by the lack of identified vascular lineage-specific markers and growth factors. Using transcriptional profiling of matched pairs of human dermal blood vascular and lymphatic endothelial cells, we first identified 236 lymphatic and 342 blood vascular signature genes. In silico analyses of the biologic pathways associated with these genes revealed lineage-specific functions for each cell type. Using a selection of 85 identified vascular lineage-specific genes, we developed a TaqMan RT-PCR-based, microfluidic card-formatted low-density microvascular differentiation array (LD-MDA) that was used to reliably identify and quantify the degree of lineage-specific differentiation in different types of endothelial cells, and to detect admixture of lymphatic endothelial cells in commercial preparations of microvascular endothelial cells. Application of Prediction Relevance Ranking and analysis of variance of LD-MDA expression profiles of 43 lesional skin samples obtained from patients with the chronic inflammatory disease psoriasis led to identification of cytokines which are significantly associated with angiogenesis or lymphangiogenesis in vivo. In particular, interleukin-7 and fibroblast growth factor-12 were identified as novel (lymph)angiogenic factors. This technology provides a novel tool to quantify lineage-specific vascular differentiation and to characterize (lymph)angiogenesis in clinical samples obtained from angiogenic diseases.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptomes from Longissimus dorsi samples of Korean Native Cattle (Hanwoo)

status: Public on Oct 06 2008

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

summary: To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture.

overall_design: Gene expression profiles were correlated with beef traits measured at the same cattle.

first: Hyun-Jung

last: Kee


title: Human_IPAH_LMM_Arteries

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

institute: Uniklinikum Giessen

summary:
Idiopathic pulmonary arterial hypertension (iPAH) is a fatal disease that is associated with increased vascular resistance due to sustained contraction and enhanced proliferation of pulmonary vascular cells. The current treatment however is still not satisfactory. A better understanding of the involved molecular mechanisms may lead to new therapeutical strategies.

Pulmonary arterial walls of healthy human lung tissue and of iPAH lungs were laser-microdissected. The extracted RNA was pooled and subjected to SMART-based RNA preamplification and fluorescence labeling. Gene expressions between iPAH and donors were compared using dual-channel microarrays.
Keywords: disease characterization

overall_design: For this study, fresh lung samples from 6 iPAH patients and from 6 healthy donors were available. Laser-microdissected arteries of 3 individuals each were pooled. Dual-color hybridizations were carried out comparing iPAH versus donor including dye-swaps as technical replicates.

first: Isabel

last: Laumanns

first: Ludger

last: Fink

first: Rita

last: Mittnach-Kraus

first: Jens

last: Wolff

first: Sabine

last: Gräf-Höchst

first: Maria

last: Stein

first: Walter

last: Klepetko

first: Ralph

middle: T

last: Schermuly

first: Friedrich

last: Grimminger

first: Werner

last: Seeger

first: Robert

last: Voswinckel


title: Chromosomal aberrations in benign and malignant salivary gland myoepitheliomas

status: Public on Oct 01 2008

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

summary: Salivary gland myoepithelial tumors are relatively uncommon tumors with an unpredictable clinical course. More knowledge about their genetic profiles is necessary to identify novel predictors of disease. In this study, we subjected 27 primary tumors (15 myoepitheliomas and 12 myoepithelial carcinomas) to genome-wide microarray-based comparative genomic hybridization (array CGH). We set out to delineate known chromosomal aberrations in more detail and to unravel chromosomal differences between benign myoepitheliomas and myoepithelial carcinomas. Patterns of DNA copy number aberrations were analyzed by unsupervised hierarchical cluster analysis. Both benign and malignant tumors revealed a limited amount of chromosomal alterations (median of 5 and 7.5 respectively). In both tumor groups, high frequency gains (≥20%) were found mainly at loci of growth factors and growth factor receptors (e.g. PDGF, FGF(R)s, and EGFR). In myoepitheliomas, high frequency losses (≥20%) were detected at regions of proto-cadherins. Cluster analysis of the array CGH data identified three clusters. Differential copy numbers on chromosome arm 8q and chromosome 17 set the clusters apart. Cluster 1 contained a mixture of the two phenotypes (n=10), cluster 2 included mostly benign tumors (n=10), and cluster 3 only contained carcinomas (n=7). Supervised analysis between malignant and benign tumors revealed a 36 Mbp-region at 8q being more frequently gained in malignant tumors (p=0.007, FDR=0.05). This is the first study investigating genomic differences between benign and malignant myoepithelial tumors of the salivary glands at a genomic level. Both unsupervised and supervised analysis of the genomic profiles revealed chromosome arm 8q to be involved in the malignant phenotype of salivary gland myoepitheliomas.

overall_design: FFPE material was used throughout the study. 15 primary myoepitheliomas and 12 malignant myoepitheliomas were analyzed on two different BAC platforms, both with 1 Mb spatial resolution. To investigate amplified regions in more detail, a 44k oligo platform was employed on a malignant myoepithelioma. After extraction, DNA quality was assessed by isothermal amplification (Buffart et al., 2007). Only DNAs which scored as excellent, good, or intermediate were used for array CGH analysis. Genomic DNA (600 ng) from both the test and reference sample was labeled and hybridizations were essentially performed according to Snijders et al. (Snijders et al., 2001) without the prehybridization step. Spot analysis and quality control for the BAC arrays were fully automated using Bluefuse 3.4 edition software (BlueGnome, Cambridge, UK). Spots with Quality flag <1 or Confidence value <0.3 were excluded. Log2ratios (tumor signal divided by normal reference signal) of spots that were not excluded after quality flagging and mapping were normalized to their block median value. For the array analysis, BAC clones were positioned along the genome using the March 2006 freeze of the UCSC database. For each clone the average of the triplicate spots was calculated and ratios were normalized by subtraction of the median value of all BAC clones on chromosomes 1-22. The sex chromosomes were discarded from the analysis, since all tumor samples were hybridized to reference DNA of the opposite gender.

first: H

last: Vekony

first: K

last: Roeser

first: T

last: Loening

first: B

last: Ylstra

first: GA

last: Meijer

first: W

last: Van Wieringen

first: M

last: Van de Wiel

last: Carvalho

last: Kok

first: CR

last: Leemans

first: I

last: Van der Waal

first: E

last: Bloemena


title: Transcriptome analysis of transgenics overexpressing SIBA(At3g56710) and SA treated plants.

status: Public on Oct 23 2008

city: Kaga-gun, Okayama

first: Yoshihiro

last: Narusaka

address: 7549-1, Kibityuo-town Yoshikawa

institute: Research Institute for Biological Sciences

summary:
We found SIBA gene which rapidly increased with a peak at 2 h after SA treatments. Analysis of the transcriptional profiling of Arabidopsis palnts which were treated salicilic acid (SA) and SIBA overexpressed plant.
Keywords: Dose response and analysis of SIBA gene

overall_design: The experiment is done using Agilent Arabidopsis 2 Oligo Microarray. We analyzed gene expression patterns using oligonucleotide arrays at 2, 5, 10 and 24 hours after treated with 5mM SA and we identified genes which were induced by overexpressing SIBA plant.

first: Mari


title: The function of CERK1 receptor-like kinase in the chitin elicitor signaling in Arabidopsis

city: Kawasaki

first: Hanae

last: Kaku

state: Kanagawa

address: 1-1-1, Higashi-Mita, Tama-ku

department: Life Sciences

institute: Meiji University

summary:
To see the function of CERK1 receptor-like kinase in the chitin elicitor signaling in Arabidopsis, we compared the gene expression profiles in the chitin oligosaccharide treated seedlings of wild type A. thaliana and CERK1 knock-out mutant.
Keywords: Defense response

overall_design: 1,Chitin oligosaccharide treatment (wild type), 2,Chitin oligosaccharide treatment (wild type) color swap, 3,Chitin oligosaccharide treatment (cerk1), 4,Chitin oligosaccharide treatment (cerk1) color swap

first: Ayako

last: Miya

first: Premkumar

last: Albert

first: Tomonori

last: Shinya

first: Yoshitake

last: Desaki

first: Kazuya

last: Ichimura

first: Ken

last: Shirasu

first: Naoto

last: Kawakami

last: Shibuya


title: CGH analysis of two components of carcinosarcoma

first: Daoud

last: Sie

summary: In this study, we present a case of parotid gland de novo carcinosarcoma. Salivary gland carcinosarcoma (or true malignant mixed tumor) is a rare biphasic neoplasm, composed of both malignant epithelial and malignant mesenchymal components. It is yet unclear whether these two phenotypes occur by collision of two independent tumors or if they are of clonal origin. To analyze the clonality of the different morphologic tumor components, oligonucleotide microarray-based comparative genomic hybridization (oaCGH) was performed on the carcinoma and the sarcoma entity separately. This technique enables a high-resolution, genome-wide overview of the chromosomal alterations in the distinct tumor elements. Analysis of both fractions showed a high number of DNA copy number changes. Losses were more prevalent than gains (82 and 49, respectively). The carcinomatous element displayed more chromosomal aberrations than the sarcomatous component.  Specific amplifications of MUC20 (in mesenchymal element) and BMI-1 (in both elements) loci were observed. Overall homology between the two genomic profiles was 75%. DNA copy number profiles of the epithelial and mesenchymal components in this salivary gland carcinosarcoma displayed extensive overlap, indicating a monoclonal origin. Since losses are shared to a larger extent than gains, they seem to be more essential for initial oncogenic events. Furthermore, specific amplifications of a mucin and a Polycomb group gene imply these proteins in the tumorigenesis of carcinosarcomas.

overall_design: We investigated 1 FFPE salivary gland carcinosarcoma, of which we macrodissected the two components separately before DNA extraction. To explore the genomic profiles of the two distinct cellular components of the carcinosarcoma, we employed a 4x44k array CGH platform including 45.214 60-mer oligonucleotides. This allowed us a genome-wide survey and molecular karyotyping of genomic aberrations with an average resolution of 75 kb.18 Labeling of tumor and reference DNA was performed using the ENZO BioArray™ CGH Labeling System (Farmingdale, NY, USA). 500 ng genomic DNA of tumor was labeled in Cy3 and mixed with a normal human reference pool of ten healthy individuals (labeled with Cy5) prior to hybridization on a 4x44K Agilent slide (Amstelveen, The Netherlands) using the Agilent hybridization oven (G2545A) overnight at 20 rpm. The oligo CGH-microarray slide was scanned using a DNA microarray scanner G2565AB (Agilent Technologies Netherlands B.V., Amstelveen, The Netherlands).Washing, scanning and feature selection (Feature extraction software v.9.1) were furthermore performed using standard Agilent procedures. In order to determine exact breakpoints in the generated array CGH profiles, we segmented the obtained log2 ratios by DNAcopy. Sex chromosomes were discarded from the analysis, since all tumor samples were hybridized to a pool of reference DNA of the opposite gender. In the downstream analysis, only clones with no missing values were included. Segmented log2 ratios were converted to four levels of categorized data (i.e. losses, normals, gains, and amplifications) by CGHCall,20 implemented using the statistical software environment R [R Development Core Team (2006)].

first: H.

last: Vekony

first: CR.

first: B.

last: Ylstra

last: Meijer


title: Molecular alterations following myocardial infarction in mice

status: Public on Sep 25 2008

city: Oslo

first: Cathrine

last: Husberg

address: Kirkeveien 166

country: Norway

institute: Institute for experimental medical research

summary:
Background and Aims: It is known that inflammatory processes are activated in heart failure, but the regulation of cytokines and their role in the pathogenesis of the disease are not well understood. To address this issue, we have performed microarray analysis of non-infarcted left ventricular tissue from mice at various time-points after myocardial infarction.
Methods: Molecular alterations in myocardial tissue were measured 3, 5, 7 and 14 days after induced infarction by using cDNA microarrays. Sham operated mice served as controls. Altered gene transcriptions were verified by real-time polymerase chain reaction. Attention focused on genes encoding cytokines which had not previously been assigned a role in heart failure development.
Results: The highest number of regulated genes was found at day 5 post myocardial infarction, and 22 genes encoding cytokines were identified as being regulated. Several of the identified genes encoding cytokines have not previously been associated with HF, and among those fractalkine showed strongest up-regulation.
Keywords: Disease state analysis, time course

overall_design: A time-serie where 4 male sham mice or post infarction mice were sacrificed at time-points 3,5,7 and 14 days after surgery. Including one dye-swap there were a total of 5 arrays at each time-point.

first: Geir

last: Christensen

first: Pål

last: Aukrust

first: Jan

middle: K

last: Damås

first: Alexandra

middle: V

last: Finsen

first: Arnoldo

last: Frigessi

first: Lars

last: Gullestad

first: Ståle

last: Nygård

first: Arne

last: Yndestad

first: Erik

last: Øye


title: trx regulatory gene network in D. melanogaster

status: Public on Sep 26 2008

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

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


title: Gene profiling of mouse brain infected with scrapie strain 22A_End-point analysis

status: Public on Sep 30 2008

city: Winnipeg

first: Reuben

last: Saba

state: Manitoba

address: 1015 Arligton Street

department: Medical Microbiology

institute: University of Manitoba: Public Health agency of Canada


title: The impact of glycerol on the metabolism of Lactobacillus reuteri

status: Public on Sep 15 2008

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

institute: Vrije Universiteit Amsterdam

sample_organism: Limosilactobacillus reuteri subsp. reuteri F275


title: Expression profiling of prion accumulating ovine microglia

status: Public on Sep 06 2008

city: Pullman

first: James

last: Stanton

state: WA

institute: Washington State University

summary:
Sheep scrapie (Sc) is the classical transmissible spongiform encephalopathy (prion disease).  The conversion of normal cellular prion protein (PrPC) to disease-associated prion protein (PrPSc) is a fundamental component of prion disease pathogenesis.  The molecular mechanisms contributing to prion diseases and the impact of PrPSc accumulation on cellular biology are not fully understood.  To define the molecular changes associated with PrPSc accumulation, primary sheep microglia were inoculated with PrPSc and then the transcriptional profile of these PrPSc-accumulating microglial cells was compared to the profile of PrPSc-lacking microglial cells using the Affymetrix Bovine Genome Array.  The experimental design included three biological replicates, each with three technical replicates, and samples that were collected at the point of maximal PrPSc accumulation levels as measured by ELISA.  The array analysis revealed 19 upregulated genes and 30 downregulated genes in PrPSc-accumulating microglia.  Three transcripts (CCL2, SGK1, and AASDHPPT) were differentially regulated in a direction similar to previous reports from mouse or human models, whereas the response of three other transcripts (MT1E, NR4A1, PKP2) conflicted with previous reports.  Overall, the results demonstrated a limited transcriptional response to PrPSc accumulation, when compared to microglia and macrophage cultures infected with other agents such as viruses and bacteria.  This is the first microarray-based analysis of prion accumulation in primary cells derived from a natural TSE-host.

Keywords: disease state analysis

overall_design:
Primary sheep microglial cells were either inoculated with PrPSc (Inoc) or sham-inoculated (Mock)
Three biological replicates per treatment.
Three technical replicates per biological replicate.
biological replicate: Inoc12A, Inoc12B.2, Inoc12C
biological replicate: Mock12A, Mock12B.2, Mock12C
technical replicate - extract: Inoc12A.1, Inoc12A.2, Inoc12A.3
technical replicate - extract: Inoc12B.2.1, Inoc12B.2.2, Inoc12B.2.3
technical replicate - extract: Inoc12C.1, Inoc12C.2, Inoc12C.3
technical replicate - extract: Mock12A.1, Mock12A.2, Mock12A.3
technical replicate - extract: Mock12B.2.1, Mock12B.2.2, Mock12B.2.3
technical replicate - extract: Mock12C.1, Mock12C.2, Mock12C.3

first: Donald

last: Knowles

first: Douglas

middle: R

last: Call

first: Bruce

middle: A

last: Mathison

first: Timothy

last: Baszler


title: Chromosomal changes in aggressive breast cancers with basal-like features

status: Public on Sep 04 2008

city: Baltimore

first: Wayne

last: Yu

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

summary:
Chromosomal changes in human aggressive breast cancer samples with basal-like features were detected using 44K oligo array CGH

Keywords: DNA copy number change

overall_design: Each of cancer samples was co-hybridized with a commercial pooled normal human female genomic DNA in two-color array CGH

first: Edward

last: Gabrielson


title: Global mRNA expression analysis in myo1 delta strains of the budding yeast Saccharomyces cerevisiae

status: Public on Sep 18 2008

city: San Juan

first: José

last: Rodríguez-Medina

state: PR

department: Biochemistry

institute: University of Puerto Rico Medical Sciences Campus

summary:
The Saccharomyces cerevisiae MYO1 gene encodes the myosin type II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Deletion of the MYO1 gene prevents actomyosin-driven cytokinesis thereby activating an alternative mechanism that involves the synthesis of a remedial septum. Myo1p deficiency in yeast (myo1) also causes the formation of attached cells, abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, and increased chitin synthesis.  To determine how the differential expression of genes is related to these diverse phenotypes, we analyzed the global mRNA expression profile of myo1 strains. Global mRNA expression profiles of myo1 strains and their corresponding wild type controls were obtained by hybridization to yeast oligonucleotide microarrays. Results for selected genes were confirmed by real time RT-PCR. A total of 547 differentially expressed genes  were identified with 263 up-regulated and 284 down regulated genes in the myo1 strains.  Gene set enrichment analysis revealed the significant over-representation of genes in the protein biosynthesis and stress response categories.
Genes involved in cell wall assembly (GAS1, PSA1, CIS3, FIT1, WSC2), MAP kinase activity (SLT2), Rho1p Guanine Exchange Factor (ROM1), and regulation of cell proliferation (RAS1) were also differentially expressed in myo1 strains.
Conclusions:
We have presented a global mRNA expression analysis of yeast myo1 strains and hypothesized about possible correlations with morphological and biochemical phenotypes observed in these strains. We report 547 differentially regulated genes in the myo1 mutant strains. Genes involved in the control of cell proliferation, protein synthesis and maturation, DNA replication, and cell division processes were largely down regulated, suggesting a mechanism for delayed cell cycle progression and growth that involves coordinated regulation of these processes in myo1 strains. Other genes involved in the cellular response to cell wall stress and cell wall organization were largely up-regulated suggesting that cell wall biogenesis is important for the completion of cytokinesis and cell wall morphogenetic processes that may also be affected by myosin II deficiency. Gene set enrichment analysis indicates that stress response and protein biosynthesis gene categories are inversely correlated in this mutant.
Keywords: Comparative genomic hybridization

overall_design: All the experiments were performed using Saccharomyces cerevisiae wild type and myo1 strains.  Six biological replicates were performed for this experiment, three arrays comparing myo1 vs. wild type from (MGD353-46D vs.YJR6) and three from (YJR12 vs.YJR13).  YJR6 is a myo1::HIS5 strain generated by homologous recombination in the parental haploid wild type strain, MGD-353-46D using a PCR based method.  YJR12 (wild type) and YJR13 (myo1∆) strains were obtained as haploid segregants from a cross between YJR6 and BY4741 (obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) or histidine dropout media (CSM-HIS-) with continuous shaking at 200 rpm. Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of strains MGD343-56D, YJR6, YJR12, and YJR13 using the RNeasy Mini Kit for isolation of total RNA following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions. 1.0 ug of total RNA from each sample was amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies).  The amplified cRNA was labeled with 10mM Cyanine 5-CTP (Cy5) or Cyanine 3-CTP (Cy3) (Perkin Elmer Life Sciences).  Labeled cRNA’s were purified with Qiagen RNeasy mini spin columns and dye incorporation was monitored on an Agilent Bioanalyzer.  Hybridization of Cy5 and Cy3 labeled cRNA’s were performed using Yeast Oligo Microarray slides and hybridization kit from Agilent Technologies in 1012AG hybridization chambers (Sheldon Manufacturing) at 60ºC for 17 hours. Slides were washed at high stringency and scanned with a VersArray Chip Reader system (BioRad, Hercules, CA) at a resolution of 5um with detector sensitivity values between 704-800 and laser power at 85%. Scanned images were transferred to the Imagene 3.0 software  (Biodiscovery) for further analysis to locate spots, adjust the appropriate grid, and obtain the Cy3 and Cy5 TIFF files.  The microarrays raw data generated with Imagene 3.0 were analyzed using Limma software (Bioconductor Package 1.7). The data was prepared for analysis by correcting for background intensity.  The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array.  After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated.  The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change after background correction and normalization.  An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed by Limma. Genes with a p-value ≤ 0.01 were established as a cutoff for differential expression. In addition, a false discovery rate (FDR) test was performed by Limma program.

middle: F

last: Rodríguez-Quiñones

first: Rafael

last: Irizarry

first: Diana

last: Gómez-Garzón

first: Félix

middle: E

last: Rivera-Molina


title: Expression data from Magnaporthe oryzae (M. grisea) in response to darkness

status: Public on Aug 29 2008

city: Camden

first: Kwangwon

last: Lee

state: NJ

address: 315 Penn Street

department: Department of Biology, Center for Computational & Integrative Biology

institute: Rutgers University

summary:
The dark-phase in light/dark cycle plays an important role in successful disease development in M. oryzae-Oryza sativa. We used microarrays to detail the global programme of gene expression in response to light-to-dark transition. We identified different groups of genes (based on GO categories) that are up- or down-regulated in response to light-to-dark transition.

Keywords: time course

overall_design: We performed a microarray experiment using microarray chips manufactured by Agilent Technologies Inc.  This chip contains more than 13,000 M. oryzae probes and 7,000 rice probes.  Our mycelial samples were grown in liquid media under constant white-light and then moved to constant darkness for 0.5, 2, 12, or 24 hours.  Three biological samples per data point were collected in two separate experiments.  Total RNA was extracted from the mycelial samples and labeled with Cy-3 dye.  For normalization between slides we used a control RNA, which was prepared by pooling RNA samples from all of the time points.  The control RNA was labeled with Cy-5.  Hybridization and all the subsequent procedures were performed following the manufacturer’s recommendations.

first: Joshua

last: Ash

first: Tian

last: Zheng

first: Qi

last: Sun


title: hog1, slt2, rlm1, and msn2/4 mutants exposed to zymolyase

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

institute: Facultad de Farmacia (UCM)

overall_design: S. cerevisiae wild type (BY4741) and mutants were grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T. Cells were collected at 3 hours of growth, frozen at -80 °C and processed for RNA extraction. The total RNA from one culture was analyzed, and, in addition, for this sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to two DNA microarrays analyzed.

first: Raul

last: Garcia

first: Clara

last: Bermejo

first: Rodriguez-Peña

last: Jose

first: Nombela

last: Cesar

first: Arroyo

last: Javier


title: Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains

status: Public on Sep 05 2008

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

type:
Expression profiling by array
Genome variation profiling by array


title: Developmental gene expression profiles of the human pathogen Schistosoma japonicum

status: Public on Sep 12 2008

city: Herston

first: Dr Geoffrey

middle: N

last: Gobert

state: QLD

address: 300 Herston road

department: Infectious Diseases / Molecular Parasitology

institute: Queensland Institute of Medical Research

summary: The life cycle of schistosomes is complex, being characterised by a series of distinct parasitic and free-living phases involving an invertebrate snail host, water and a mammalian host. A custom designed oligonucleotide microarray was utilized to profile developmental gene expression in the Asian blood fluke, Schistosoma japonicum during these parasitic and free-living transitions. Total RNAs were isolated from lung schistosomula, juvenile females and males (paired but little or no egg production), adult males and females (paired with full scale egg production), eggs, miracidia, sporocysts and cercariae. We focused on the three distinct environmental phases of the lifecycle - aquatic/snail (eggs, miracidia, sporocysts, cercariae), juvenile (lung schistosomula and paired pre-egg laying adults) and adult (paired males and females, both examined separately) stages.

overall_design: Single colour schistosome life cycle with technical replicates in triplicate: Separate adult female and male worms at 4, 6, 6.5 and 7 weeks; cercariae; eggs; miracidia; schistosomula; and sporocysts.  This study includes 6 adult male biological replicates.

first: Geoffrey

first: Luke

last: Moertel

first: Donald

middle: P

last: McManus


title: Gene expression profiling of GABAergic neurons isolated from different brain regions

status: Public on Aug 12 2008

city: Cologne

first: Olaf

last: Hardt

state: NRW

address: Stöckheimer Weg 1

department: MACSmolecular Business Unit, Research and Development

institute: Miltenyi Biotec GmbH

summary:
The main goal of the experiment was to analize the transcriptome of GABAergic neurons in general and compare their expression profiles among different brain regions
Keywords: GABAergic neurons; expression profiling; rare cell

overall_design: We used transgenic GAD67-eGFP mice to isolate early postnatal GABAergic neurons by flow cytometric cell sorting from whole mouse brains as well as from the olfactory bulb, the cortex, the striatum, and the cerebellum. Subsequently, microarray analysis was performed from amplified RNA of the isolated cells. Biological replicates: 4 for whole brain, 3 for each brain region. One replicate per array.

first: Corinna

last: Scholz

first: Yuchio

last: Yanagawa

first: Sandra

last: Pennartz

first: Harold

last: Cremer

first: Andreas

last: Bosio


title: Phenobarbital and TCPOBOP effects on CAR and PXR regulated genes involved in drug metabolism and cholesterol homeostasis

status: Public on Aug 23 2008

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

first: Viola

last: Tamasi

first: Markus

last: Beer

first: Damjana

last: Rozman

first: Urs

last: Meyer


title: Dietary folate depletion and repletion

status: Public on Aug 27 2008

city: Cleveleand

first: Joseph

last: Nadeau

state: OH

address: 10900 Euclid Avenue

department: Genetics

institute: Case Western Reserve University


title: Profiles and ChIP on chip experiments with dl1500 virus (expressing WT small e1a), R2G and deltaCR2 mutant viruses

status: Public on Aug 26 2008

city: Los Angeles

first: Siavash

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary:
Adenovirus e1a induces quiescent human cells to divide. We found that e1a causes global relocalization of the RB-proteins (RB, p130, p107) and p300/CBP histone acetyltransferases on promoters that restricts H3K18ac to a limited set of genes to stimulate cell cycling and inhibit antiviral responses and cellular differentiation. Soon after expression, e1a binds transiently to cell cycle/growth genes, causing enrichment of p300/CBP, PCAF, H3K18ac, depletion of RB-proteins, and transcriptional activation. e1a also associates transiently with antiviral genes, causing enrichment for RB, p130, H4K16ac, increased nucleosome density, and repression. At later times, e1a and p107 bind mainly to development/differentiation genes, repressing transcription. The temporal order of e1a binding required its interactions with p300/CBP and RB-proteins. Our data uncover a defined transcriptional and epigenetic reprogramming leading to cellular transformation.

This SuperSeries is composed of the SubSeries listed below.

first: Roberto

last: Ferrari

first: Matteo

last: Pellegrini

first: Gregory

last: Horwitz

first: Wei

last: Xei

first: Arnold

last: Berk


title: miRNA Microarray Profiling: multiple tissues and cell lines

status: Public on Aug 19 2008

city: Santa Clara

first: Robert

last: Ach

address: 5301 Stevens Creek Boulevard

department: Agilent Laboratories

institute: Agilent Technologies


title: Iodide Inhibits Vascular Endothelial Growth Factor-A Expression in Cultured Human Thyroid Follicles

status: Public on Aug 01 2008

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

institute: Tokyo Women's Medical University

summary:
A Microarray Search for Effects of Thyrotropin and Iodide on Angiogenesis Factors

Objective: Excess iodide has been administered to hyperthyroid patients before thyroid surgery to reduce intraoperative bleeding and oozing. The purpose of this study was to elucidate the mechanism by which iodide reduces blood flow in the hypervascular thyroid gland.   Design: Human thyroid follicles were cultured in the presence or absence of thyrotropin (TSH), or in medium containing various concentrations of iodide, and TSH- or iodide-regulated gene expression was analyzed by cDNA microarray.  Main outcome: TSH stimulated the expression of thyroglobulin, peroxidase, sodium-iodide symporter, vascular endothelial growth factor (VEGF)-A, VEGF-B, and placental growth factor (PGF) but decreased that of VEGF-C by half. When thyroid follicles were cultured in high-iodide (10-5M) medium, TSH-induced expression of VEGF-A, VEGF-B and PGF was decreased, accompanied by a reduction of VEGF-A release into the medium. Furthermore, expression of putative angiogenesis inhibitors such as urokinase-type plasminogen activator (PLAU) was increased. These findings were confirmed by real-time polymerase chain reaction (PCR) and Northern blot hybridization.  Conclusions: We have demonstrated for the first time that iodide at high concentration decreases the expression of the angiogenic factors VEGF-A, VEGF-B, and PGF, accompanied by an increase in the expression of possible anti-angiogenic factors such as PLAU. These proangiogenic and antiangiogenic factors may at least partly account for the iodide-induced decrease in thyroid blood flow.

overall_design:
One conditioned experiments:
control vs. bovine thyrotropin (bTSH) 30 microUnit/ml
iodide 1x10e-8M vs. iodide 2x10e-5M

first: Emiko

last: Yamada


title: Secreted transcription factor controls Mycobacterium tuberculosis virulence

status: Public on Aug 08 2008

city: San Francisco

first: Paolo

last: Manzanillo

state: CA

department: Microbiology and Immunology

institute: University of California at San Francisco


title: Methotrexate resistant Leishmania strains

city: Québec

first: Marc

last: Ouellette

state: Québec

address: 2705 bd Laurier

department: Département médecine

institute: Université Laval

sample_organism:
Leishmania major
Leishmania infantum

platform_organism:
Leishmania major
Leishmania infantum


title: SuperSeries for the study of expression analysis of the SdrP (TTHA1359) in T. thermophilus HB8

status: Public on Aug 03 2008

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

first: Yoshihiro

last: Agari

first: Aiko

last: Kashihara

first: Emi

last: Nakai

first: Miwa

last: Ohmori

first: Shigeyuki

last: Yokoyama

first: Seiki

last: Kuramitsu


title: Melan-a mouse melanocytes vs. B16 mouse melanoma cells

status: Public on Jul 31 2008

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary:
Gene expression profile of melan-a mouse melanocytes vs. B16 mouse melanoma cells.

Keywords: Cell type comparison

overall_design: Balanced block design with dye swap. Six biological replicates, one replicate per array.

first: Mary

last: Estler

first: Goran

last: Boskovic

first: Sarah

last: Miles

first: Don

last: Primerano

first: Richard

last: Niles


title: EXPRESSION PROFILING IN shlOXL2 AND shSNAIL IN HACA CELLS

first: Gema

last: Moreno-Bueno

address: Arturo Duperier

institute: IIB

summary:
To better understand the implication of LOXL2  AND SNAIL in re-adquisition of epithelial phenotype we performed a gene expression profile comparing the highly malignant control cell line HaCa4shEGFP (interfered with an irrelevant sequence) with the LOXL2 and SNAIL interfered cell lines HaCa4shLOXL2 and HaCa4shSNAIL
Keywords: expression profiling

overall_design: Two different RNA samples obtained from shLoxl2 and shSnail cells were labelled with Cy5-dUTP and from control cells (shGFP) with Cy3-dUTP (Amersham, Uppsala, Sweden). Two additional hybridizations using the reciprocal fluorochrome labeling were performed, making a total of three hybridizations by condition.

first: H

last: Peinado

first: G

first: F

last: Portillo

first: A

last: Cano


title: Aging study

status: Public on Jul 29 2008

city: Stanford

first: Stuart

last: Kim

department: Department of Developmental Biology

institute: Stanford University Medical Center

overall_design: Refer to individual Series


title: Amiodarone effects on cultured human thyroid follicles

status: Public on Jul 19 2008

first: Kanji

last: Sato

summary:
Amiodarone reversibly decreases sodium-iodide symporter mRNA expression at therapeutic concentrations and induces antioxidant responses at supraphysiological concentrations in cultured human thyroid follicles
Amiodarone, a potent antiarrhythmic agent, is a highly active oxidant, exerting cytotoxic effects on thyrocytes at pharmacological concentrations. Patients receiving amiodarone usually remain euthyroid, but occasionally develop thyroid dysfunction, such as amiodarone-associated hypothyroidism or amiodarone-induced thyrotoxicosis.  To elucidate the mechanism by which amiodarone elicits thyroid dysfunction, human thyroid follicles were cultured with TSH and amiodarone at therapeutic (1-2 microM) and pharmacological (10-20microM) concentrations, and the drug-induced effect on whole human gene expression was analyzed by cDNA microarray.  Amiodarone at 1-2microM decreased the expression level of the sodium-iodide symporter (NIS) to nearly half, but did not affect genes participating in thyroid hormonogenesis (thyroid peroxidase, thyroglobulin, pendrin, NADPH oxidase).  Higher concentrations (10-20 microM) decreased the expression of all these genes, accompanied by increased expression of antioxidant proteins such as heme oxygenase 1 and ferritin.  When thyroid follicles obtained from a patient with Graves’ disease who had been treated with amiodarone for 2 months before thyroidectomy were cultured in amiodarone-free medium, TSH-induced thyroid function was intact, suggesting that amiodarone at a maintenance dose did not elicit any cytotoxic effect on thyrocytes. The ultrastructural features of cultured thyroid follicles were compatible with these in vitro findings.     These in vitro and ex vivo findings suggest that patients taking maintenance doses of amiodarone usually remain euthyroid, probably due to escape from the Wolff-Chaikoff effect mediated by decreased expression of NIS mRNA.  Furthermore, amiodarone is not cytotoxic for thyrocytes at therapeutic concentrations but elicits cytotoxicity through oxidant activity at supra-physiological concentrations.

Keywords: Cultured human thyroid follicles

overall_design: Two condition experiment, control vs. Amiodarone 1 and 10 microM, cultured for 5 days

first: Kazuko

last: Yamazaki


title: RIP-Chip analysis of Musashi (Msi1)

city: San Antonio

first: Luiz

last: Penalva

state: TX

address: 8403 Floyd Curl Drive

department: GCCRI

institute: UTHSCSA

summary:
RIP-Chip analysis of Msi1 and identification of preferentially associated mRNAs.

Keywords: RIP-Chip

overall_design: Two experiments with different controls, GFP (Green Fluorescent Protein) and PABP1 (Poly A Binding Protein 1). Each experiment includes 4 microarrays, 2 replicates for each dye orientation.

first: Patricia

middle: C

last: Sanchez-Diaz

first: Raquel

last: Abreu

first: Suzanne

last: Burns

first: Daijin

last: Ko

first: Tarea

middle: L

last: Burton

first: Soudhamini

last: Chennasamudaram

first: Shu-Yu

first: Bruce

last: Shapiro

middle: O


title: Islet cells CD40L_vs_ islet cells CTRL

city: Miami

first: Ricardo

last: Pastori

state: FL

department: Diabetes Research Institute

institute: University of Miami

summary:
 Expression of CD40 in non-hematopoietic cells has been linked to inflammation.  We presented evidence that CD40, a T-cell costimulatory molecule, is expressed in human β-cells and the engagement of CD40 in insulinoma cells activated the NFKB and ERK1/2 pathways. CD40 activation in human islets cells induced secretion of IL-8, MCP-1 and MIP-1 β, which is abrogated by inhibitors of NFkB and ERK1/2 inhibitors. In this study,  we have studied gene expression mediated by CD40-CD40L interaction in islet cells. This approach identified 90 genes and transcripts exhibiting at least a 1.7 fold increase in their expression intensity after treatment with soluble CD40L. A significant number of genes were related to inflammation and oxidative stress. We have a strong overexpression of CXCL1 (Groα), CXCL2 (Mif2) and CXCL3; chemokines belonging to CXC family structurally related to Il-8. 11 genes were selected from this group and further quantified by Real Time PCR, including CXCL1. Activation of islet cells with CD40L induced the secretion of CXCL1 in a NFKB dependent manner. Engagement of CD40 in islet cells did not induce apoptosis, neither β-cell death and did not enhanced TNF-α mediated cell death as observed in insulinoma cells. CD40 activation in insulinoma cells, results in ERK1/2 dependent phsophorylation of synapsin I, a protein associated with the exocytosis machinery in neurons and β-cells.  However, treatment of islets with soluble CD40L did not affect glucose induced insulin secretion.  It has been reported that ductal cells always present in human islet preparations express CD40 constitutively (ref).  We found that CD40-CD40L interaction in ductal cells, unlike in β-cells, induces secretion of diabetogenic cytokines IFNγ and TNF-α.  Furthermore, incubation of islets containing ductal cells with CD40L decreased β-cells viability as assessed by measurement of their mitochondrial membrane potential
Keywords: Pancreas, Islets of Langerhans,  chemokines, cytokines, inflammation, apoptosis, Nuclear Factor-κB(NFκB)

overall_design: We isolated islet cells from three patients. Part of islet cells from each patient has been treated with CD40L. We compared gene expression in treated cells vs untreated for each patient using dye-swap.

first: Dagmar

last: Klein

first: Francesca

last: Timoneri

first: Florencia

last: Barbe-Tuana

first: Hirohito

last: Ichii

first: Camillo

last: Ricordi


title: Stimulation of type I Interferon system by double-stranded RNA in cultured human thyroid follicles

status: Public on Jul 18 2008

first: Kanji

summary:
Although viral infection is thought to be associated with subacute thyroiditis and probably with autoimmune thyroid disease, possible changes in thyroid function during the prodromal period of infection or subclinical infection remain largely unknown. Recently, it was shown that pathogen-associated molecular patterns stimulate Toll-like receptors (TLR) and activate innate immune responses by producing type I interferons (IFN).  Using a human thyroid follicle culture system, in which de novo synthesized thyroid hormones are released into the culture medium under physiological concentrations of hTSH, we studied the effects of polyinosinic-polycytidylic acid (Poly(I:C)), a chemical analog of viral double-stranded RNA (dsRNA), on TSH-induced thyroid function.        Thyrocytes expressed ligands for dsRNA (TLR 3, CD14, and RIG-1) comparable to the TSH receptor.  DNA microarray and real-time PCR analyses revealed that dsRNA increased the expression of mRNA for TLR3, IFN-g, interferon-regulating factors, proinflammatory cytokines, and class I MHC, whereas genes associated with thyroid hormonogenesis (NIS, peroxidase, deiodinases) were suppressed. In accordance to these data, Poly(I:C) suppressed TSH-induced 125I uptake and hormone synthesis dose-dependently, accompanied by a decrease in the ratio of 125I-T3/125I-T4 released into the culture medium, whereas peptidoglycan, lipopolysaccharides, or unmethylated CpG DNA, ligands for TLR2, TLR4, and TLR9, respectively, had no significant effect.  These inhibitory effects of Poly(I:C) were not blocked by a neutralizing antibody against TLR3 and an anti-IFN alpha/beta receptor antibody. These in vitro findings suggest that when thyrocytes are infected with certain viruses, dsRNA formed intracellularly in thyrocytes may be a cause for thyroid dysfunction, leading to development of autoimmune thyroiditis.
This data was published in Endocrinology, vol.148, 3226-3235, 2007.

Keywords: Cultured human thyroid follicles

overall_design: Two conditioned experimets, control vs. double-stranded RNA (polyI-C), cultured for 6


title: Murine Atm deficient thymocytes vs. murine wildtype thymocytes

status: Public on Jul 15 2008

city: Heidelberg

first: Hendrik

last: Reuter

department: Moleculare Genetics B060

institute: DKFZ

summary:
genomic profiling of murine thymocytes of Atm deficient mice with and without T-cell lymphoma
Keywords: genetic modification

overall_design: two-condition experiment: Atm ko vs. wildtype. 8 Atm ko with thymic lymphoma, 14 Atm ko w/o thymic lymphoma

first: Peter

last: Lichter


title: SuperSeries for the study of expression analysis of the T. thermophilus sigE (TTHB211) and anti-sigE (TTHB212)

status: Public on Jul 16 2008

first: Akeo

last: Shinkai


title: Heterotrophy, chemoautotrophy, and arabinose supplementation in Bradyrhizobium japonicum

city: Arlington

first: Woo-Suk

last: Chang

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington


title: Modulation of colon inflammation in interleukin-10 gene-deficient mice via dietary polyunsaturated fatty acid

status: Public on Jul 10 2008

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

institute: AgResearch NZ

summary: Dietary n-3 polyunsaturated fatty acids can reduce inflammation via a range of mechanisms. This study tested the effect of dietary eicosapentaenoic acid (EPA) on intestinal inflammation using interleukin-10 gene-deficient (Il10-/-) mice. Methods: At 35 days of age, 12 weaned Il10-/- and 12 C57 mice were randomly assigned to one of two modified AIN-76A diets, supplemented with 3.7% purified ethyl esters of either EPA (n-3) or oleic acid (OA, control). To identify genes relevant to colon inflammation, transcription profiling (microarrays and qRT-PCR) and bioinformatic analyses were used. Results: In this study, dietary EPA reversed the decrease in colon fatty acid β-oxidation gene expression observed in OA-fed Il10-/- compared to C57 mice. Il10-/- mice fed the OA diet showed decreased expression of antioxidant enzyme genes, as well as those involved in detoxification of xenobiotics, compared to C57 mice on the same diet. In contrast, dietary EPA increased the expression of these genes in Il10-/- mice. Conclusions: These data indicate that dietary EPA induced endogenous lipid oxidation which might have a potential anti-inflammatory effect on colon tissue. This is supported by the activation of the Ppara gene that regulates the expression of pro-inflammatory and immunomodulatory genes and proteins.

overall_design:
The diet abbreviations EPA, OA, AA and CO used in the sample records
refer to the following :

CO  :    AIN-76A (control)
OA  :    AIN-76A (fat-free) + 1% corn oil + 3.7% oleic acid
EPA :    AIN-76A (fat-free) + 1% corn oil + 3.7% eicosapentaenoic acid
AA :     AIN-76A (fat-free) + 1% corn oil + 3.7% arachidonic acid

Corn oil was supplemented with purified linoleic and alpha-linolenic acid to meet the nutritional requirements of mice for these essential fatty acids. Diets fed for 6 weeks.

first: Bianca

last: Knoch


title: rge1-1, retarded growth of embryo mutant  vs wild-type Col-0

status: Public on Jul 01 2008

city: Yokohama

first: Minami

last: Matsui

address: Suyehirocho 1-7-22 , Tsurumiku

department: Plant Science Center

institute: RIKEN

summary: The loss-of-function mutation of the RGE1 (retarded growth of embryo) gene, which is expressed during seed development, caused small and shriveled seeds.  The embryo of the loss-of-function mutant showed retarded growth after the heart stage although abnormal morphogenesis and pattern formation of the embryo and endosperm was not observed. RGE1 expression was determined in endosperm cells using the β-glucuronidase reporter gene and RT-PCR.  The differences of expression profile between rge1-1 and wild type Col-0 was examined to know the functions of RGE1.  The result of Microarray analysis showed specific down-regulation of putative GDSL motif lipase genes in the rge1-1 mutant indicating possible involvement of these genes in seed morphology.

overall_design: Total RNA was isolated from siliques of rge1-1 and wild type at 12 DAF using an RNAqueous Kit (Ambion, Inc, USA).

first: Youichi

last: Kondou

first: Miki

last: Nakazawa

first: Mika

last: Kawashima

first: Shu

last: Muto


title: Bacillus subtilis 168 cells: ccpN mutant and ccpN-yqfL double mutant analysis

city: Thiverval-Grignon

first: Thierry

last: Doan

address: INRA

department: Microbiologie

country: France

institute: INRA

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

sample_organism: Bacillus subtilis subsp. subtilis str. 168


title: Glycodelin-induced changes in MCF-7 breast cancer cells

status: Public on Jul 11 2008

city: Helsinki

first: Hannu

last: Koistinen

address: PO Box 63

department: Clinical Chemistry

country: Finland

institute: University of Helsinki

summary:
Recent reports suggest that glycodelin induces epithelial differentiation. Little is known about the mechanisms involved in this process. To elucidate this we transfected glycodelin-negative MCF-7 breast cancer cells with glycodelin cDNA. Cells transfected with a vector in which glycodelin cDNA was in antisense orientation were used as non-glycodelin-producing controls. Oligo microarray was performed to study gene expression changes between glycodelin-transfected and control cells.
Keywords: Cell type comparison, genetic modification

overall_design: Gene expression differences between MCF-7 breast cancer cells transfected  with glycodelin cDNA and the cells transfected with a vector in which glycodelin cDNA was in antisense orientation were studied by oligo microarray.

first: Laura

last: Hautala

first: Riitta

first: Markku

last: Seppala

first: Ralf

last: Butzow

first: Ulf-Hakan

last: Stenman

first: Pirjo

last: Laakkonen


title: IRF4 ChIP-on-chip for Myeloma Cell Lines

status: Public on Jul 07 2008

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary:
To identify IRF4 transcription factor binding on chromatin at 5' regulatory regions of genes in myeloma cell line models.
Keywords: binding site identification design

overall_design: Formaldehyde cross-linked, sonicated chromatin is prepared from cell lines Kms12 (test) and Ly19 (control). Chromatin immunoprecipated with anti-IRF4 antibody is labeled with Cy5 and co-hybridized on Agilent Human Promoter Set arrays with chromatin immunoprecipated with normal sera labeled with Cy3 . Two biological replicates were performed for the Kms12 and Ly19 experiments.


title: Study of HepG2 cells transduced with HBX expressing recombinant Adenoviruses (AdHBx) and treated with UV

city: Singapore

first: Wah Heng

last: Lee

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

overall_design: One-condition experiment, AdHBx (experimental) UV vs AdEasy (vector control) UV.  HepG2 cells were infected with either recombinant HBx adenoviruses (AdHBx) or control adenoviruses (AdEasy). Seventy-two hours later, infected cells were exposed for 30 seconds to UVC (254 nm) irradiation with a germicidal lamp calibrated to deliver 8 or 16 J/m2.  Cells were then harvested for either ChIP-chip profiling or expression microarray profiling.


title: T-cell lymphoblastic lymphomas induced by gamma-irradiation

status: Public on Jun 26 2008

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)


title: Comparison between saprotrophic and biotrophic-like mycelia of cacao WBD causal agent Moniliophthora perniciosa

status: Public on Jun 13 2008

city: Campinas

first: Jorge

middle: Maurício Costa

last: Mondego

state: SP

address: Cidade Universitária Zeferino Vaz s/n

department: Genetics and Evolution

country: Brazil

institute: UNICAMP


title: Heterosis

status: Public on Jun 19 2008

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

country: USA

institute: Iowa State University