title: Current smoking-specific gene expression signature in bronchial epithelium is enhanced in squamous cell lung cancer

status: Public on Oct 01 2008

city: Groningen

first: Mirjam

last: Boelens

address: Hanzeplein 1

institute: UMCG

summary: Cigarette smoking is the main risk factor for the development of squamous cell lung carcinoma (SCC). However, the smoking-related molecular changes in SCC have not been studied. We wanted to identify genes in both histologically normal bronchial epithelium and SCC samples that are differentially expressed between current and ex-smokers. In addition, to analyze the levels of the smoking-related genes identified in normal bronchial epithelium with the levels in SCC. Gene expression profiles were generated using Agilent whole human genome microarrays in 28 laser microdissected normal bronchus epithelial samples and in 35 laser microdissected SCC samples of current and ex-smokers. Levels of 246 genes, mainly related to oxidative stress response, were significantly different between normal bronchial epithelium of current and ex-smokers. No significant differences were associated with the smoking status in SCC samples. Analysis of the 246 smoking specific genes in SSC from current and ex-smokers also revealed no differences. As a next step, we compared the levels of the smoking-specific gene signature between normal bronchial epithelium from ex- and current smokers to all 34 SCC samples. Twenty-two percent of the upregulated genes are further upregulated in SCC as compared to current smokers. Expression of the downregulated genes was even further downregulated for 79% of the genes in SCC as compared to bronchus epithelium of current smokers. The downregulated genes included several tumour suppressor genes. This study shows that genes upregulated in normal bronchial epithelium of current smokers are expressed at similar levels in SCC samples, while levels of downregulated genes were significantly further reduced in SCC. This indicates that these downregulated genes play a role in SCC oncogenesis.

overall_design:
PATIENTS AND TISSUE SPECIMENS
For each patient, the number of packyears and current smoking status was assessed. Individuals were divided in ex-smokers, who quitted smoking at least two years before surgery, or current smokers, who continued smoking until surgery. We collected cartilaginous bronchial tissues (diameter >2mm) from 28 patients during thoracotomy for a lung tumour (NSCLC) (n=21) or during lung transplantation (n=7). Tumour samples were obtained from 35 patients with primary SCC. For two cases, the bronchus and tumour sample were derived from the same patient. We excluded patients using inhaled, intravenous or oral steroids before surgery. Patients who were treated with chemotherapy and patients with alpha-1-antitrypsin deficiency were also excluded. All tissue samples were snap frozen and stored at -80ºC. The study protocol was consistent with national ethical and professional guidelines (“Code of Good Conduct; Dutch Federation of Biomedical Scientific Societies”).

LASER DISSECTION MICROSCOPY
Histologically normal bronchial epithelial cells (consisting of basal, ciliated and goblet cells) were microdissected from central bronchus sections and vital tumour cells from SCC sections. An area of approximately 20 - 25 x106 μm2 was collected from 8 μm frozen sections using P.A.L.M. Microlaser Technology system (P.A.L.M., Bernried, Germany) in lysis buffer (Macherey-Nagel, Düren, Germany).

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

MICROARRAY APPROACH
Agilent Whole Human Genome Oligo Microarrays, design number 012391 (GPL1708) (Agilent, Palo Alto, CA) were used. Briefly, 150 ng of total RNA was amplified for one round using MessageAmp II (Ambion, Austin, USA). mRNA amplification, ULS labeling, Cy-dye coupling, hybridisation and data extraction were performed at ServiceXS (Leiden, the Netherlands) according to manufacturer’s instructions. A dye-swap was included and samples were hybridised using a randomized approach (scheme available as supplementary table in manuscript), based on the non-competitive conditions of a two-colour array.

T22 failed quality test

first: Anke

last: van den Berg

first: Rudolf

middle: S

last: Fehrmann

first: Marie

last: Geerlings

first: Wouter

last: de Jong

first: Gerard

middle: J

last: te Meerman

first: Hannie

last: Sietsma

first: Wim

last: Timens

first: Dirkje

last: Postma

first: Harry

last: Groen


title: Discovery of the targets of the immune response to chronic lymphocytic and myeloid leukemia

status: Public on May 31 2008

city: Cleveland

first: Ovidiu

last: Marina

state: OH

address: 10900 Euclid Ave

department: School of Medicine

country: USA

institute: Case Western Reserve University

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

overall_design: Refer to individual Series


title: Comparison of fire ant adult workers with different Gp-9 (BB and Bb) genotypes and from monogyne and polygyne colonies.

status: Public on Jun 06 2008

city: Lausanne

first: John

last: Wang

address: Batiment Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

summary:
In fire ants, a complex colony level phenotype, colony queen number, is completely associated with a single Mendelian factor marked by the gene Gp-9. The first aim of this study was to investigate whether variation in the genomic region marked by Gp-9 is associated with differences in patterns of expression of genes other than Gp-9 in workers. The second aim was to study how the social environment (i.e., presence or absence of nestmate workers with the b allele) can alter individual gene expression patterns.

Keywords: Genotype comparison and social form comparison

overall_design: Three-condition experiment: Gp-9 BB monogyne, Gp-9 BB polygyne, and Gp-9 Bb polygyne. Biological replicates: 8 of each sample type from 2004 compared to common reference RNA batch 2004, and 12 of each sample type from 2006 compared to common reference RNA batch 2006. A fourth condition, Gp-9 bb polygyne with 1 biological replicate from 2004 and 1 from 2006, was compared to the respective reference RNA batch. One replicate per array.

first: Ken

middle: G

last: Ross

first: Laurent

last: Keller


title: Montastraea faveolata bleaching study

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

institute: UC San Francisco


title: Role of M. tuberculosis in CO sensing

status: Public on May 29 2008

last: Shiloh

institute: University of California at San Francisco

first: Jeffery

last: Cox


title: Gene expression profiling distinguishes JAK2V617F-negative from JAK2V617F-positive patients in essential thrombocythemia

status: Public on May 19 2008

city: BARCELONA

first: EULÀLIA

last: PUIGDECANET

state: BARCELONA

address: Passeig Marítim, 25-29

department: Patologia

country: Spain

institute: HOSPITAL DEL MAR

summary:
In order to explore the gene expression signature in essential thrombocythemia (ET) patients in relation to JAK2V617F mutational status, expression profiling in circulating granulocytes was performed. Twenty ET were studied by microarray analysis and the results were confirmed by real-time quantitative RT-PCR in 40 ET patients, not receiving cytoreductive treatment. A heterogeneous molecular signature characterized by two main gene expression patterns was found: one with an up-regulation of inflammatory genes related to neutrophil activation and thrombosis, and the other one with significantly lower expression of these genes. Supervised clustering analysis showed 30 genes differentially expressed between JAK2V617F-negative and JAK2V617F-positive ET patients. Among the JAK2V617F-negative, a set of 14 genes (CISH, C13orf18, CCL3, PIM1, MAFF, SOCS3, ID2, GADD45B, KLF5, TNF, LAMB3, HRH4, TAGAP and TRIB1) showed an abnormal expression pattern. In this group of patients CISH, SOCS2, SOCS3 and PIM1 genes, all involved in JAK-STAT signaling pathway, presented a lower expression,. A two-gene predictor model was built comprising FOSB and CISH genes, which were the best discriminators of JAK2V617F status. In conclusion, JAK2V617F-negative ET patients present a characteristic gene expression profile, different from JAK2V617F-positive patients. Other pathways besides JAK-STAT might be implicated in the pathophysiology of JAK2V617F-negative ET patients.
Keywords: Disease state analysis

overall_design: Twenty ET were studied by microarray analysis and the results were confirmed by real-time quantitative RT-PCR in 40 ET patients. Microarray expression profiles were obtained using Whole Human Genome oligonucleotide microarrays (G4112A, Agilent Technologies, Palo Alto, CA). In each microarray experiment, RNA obtained from granulocytes from a single ET patient was compared with a pool of granulocyte RNAs from 10 healthy individuals. Duplicate hybridizations were performed for each comparison with dye-swapping to control.

first: Eulàlia

last: Puigdecanet

first: Blanca

last: Espinet

first: Juanjo

last: Lozano

first: Lauro

last: Sumoy

first: Beatriz

last: Bellosillo

first: Leonor

last: Arenillas

first: Alberto

last: Álvarez-Larrán

first: Francesc

last: Solé

first: Sergi

last: Serrano

first: Carles

last: Besses

first: Lourdes

last: Florensa


title: Regulation of granulosa and theca cell transcriptomes during ovarian antral follicle development.

status: Public on May 20 2008

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
Coordinated interactions between ovarian granulosa and theca cells are required for female endocrine function and fertility. To elucidate these interactions the regulation of the granulosa and theca cell transcriptomes during bovine antral follicle development were investigated. Granulosa cells and theca cells were isolated from small (<5 mm), medium (5-10 mm), and large (>10 mm) antral bovine follicles. A microarray analysis of 24,000 bovine genes revealed that granulosa cells and theca cells each had gene sets specific to small, medium and large follicle cells. Transcripts regulated (i.e., minimally changed 1.5-fold) during antral follicle development for the granulosa cells involved 446 genes and for theca cells 248 genes. Only 28 regulated genes were common to both granulosa and theca cells. Regulated genes were functionally categorized with a focus on growth factors and cytokines expressed and regulated by the two cell types. Candidate regulatory growth factor proteins mediating both paracrine and autocrine cell-cell interactions include macrophage inflammatory protein (MIP1 beta), teratocarcinoma-derived growth factor 1 (TDGF1), stromal derived growth factor 1 (SDF1; i.e., CXCL12), growth differentiation factor 8 (GDF8), glia maturation factor gamma (GMFG), osteopontin (SPP1), angiopoietin 4 (ANGPT4), and chemokine ligands (CCL 2, 3, 5, and 8). The current study examined granulosa cell and theca cell regulated genes associated with bovine antral follicle development and identified candidate growth factors potentially involved in the regulation of cell-cell interactions required for ovarian function.

Keywords: expression analysis, follicle assembly, ovary granulosa cell

overall_design: Granulosacell RNA samples from three groups of follicles different in size - small, medium, and large (pooled untreated ovaries) are compared between each other. Each group has 2 separate biological replicas; each replica contained pooled RNA from 20-40 ovaries from 6-10 different animals.

first: Michelle

last: Schmidt

first: Marina

last: Savenkova

first: Ingrid

last: Sadler-Riggleman

first: Eric

last: Nilsson


title: Molecular Profiling of Small and Large Retinal Ganglion Cells

status: Public on May 17 2008

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Ave

institute: University of Miami

summary:
Different sub-types of ganglion cells existing in mammalian retinas possessing distinct function in processing the visual information. In primates, RGC are commonly divided into midget cells, which are relatively small, and parasol cells, with a larger soma size. Rodents also possess morphologically distinct populations, but their physiological properties are less characterized. The two types of mammalian RGCs differ in their response to pathological conditions such as retinal ischemia, diabetic retinopathy and glaucoma. In this work, we compared gene expression profiles of large (LRGCs) and small (SRGCs) ganglion cells isolated from rat retina in attempt to identify molecular determinants underlying differences in function and tolerance to stress.
Keywords: comparative hybridization

overall_design: Rat RGCs retrogradely labeled with 4DI-10ASP were purified from freshly dissected retinas and subjected to fluorescent-activated cell sorting (FACS) in order to separate the SRGC and LRGC sub-populations. Actinomycin D was added to prevent new transcription during experimental procedures. Purified cells were used for RNA isolation. Following two rounds of linear amplification aRNA probes were hybridized with two-color Agilent Rat Genomic Oligo Arrays. We utilized the dye swap experimental design to eliminate the dye bias effects and make data from different experiments available for the cross-comparison.

first: Val

last: Shestopalov


title: Expression QTL mapping of Toxoplasma gondii genes

status: Public on May 22 2008

city: Stanford

first: Jon

last: Boyle

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University School of Medicine

sample_organism:
Toxoplasma gondii
synthetic construct


title: Transcriptome analysis of mouse muscle

status: Public on Aug 08 2008

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

institute: University of Berne


title: AdHBx UV vs AdEasy UV vs HepG2

status: Public on Jul 01 2008

city: Singapore

first: Wah Heng

last: Lee

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary:
Transcriptional profiling of HepG2 cells treated with UVC (254 nm) for 30 seconds and transduced with Adenoviral vector carrying the Hepatitis B Virus HBx gene vs Adenoviral vector control  under UV treatment
Keywords: Over-expression

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

first: Caroline


title: Gene expression profiling of the periovulatory follicle

status: Public on May 03 2008

city: Bangalore

first: jyotsna

middle: U

last: rao

state: Karnataka

address: C.V. Raman Road

department: MRDG

country: India

institute: Indian Institute of Science

summary:
Gonadotropin surge acts on the preovulatory follicle of the ovary to induce luteinization of follicular cells, oocyte meiotic maturation, cumulus expansion and follicular rupture leading to ovulation. These processes are brought about by spatial and temporal changes in transcriptional regulation of genes in the follicular cells in response to the gonadotropin surge. Analysis of gene expression changes in the periovulatory follicular cells will help in delineating the signal transduction pathways involved in the above mentioned processes. In monoovulatory species like bovines, the time interval of 24-28 hours between gonadotropin surge and ovulation provides distinct advantage for studying the temporal changes in the gene expression pattern. Thus, in the present study, we attempt to identify the temporal changes in the global gene expression profile in the periovulatory follicle of buffalo cows in response to gonadotropin surge and the results suggest the involvement of Insulin-like Growth Factor 1 and cytokine signaling pathways in the periovulatory events.
Keywords: Time course

overall_design: To study the periovulatory gene expression changes in buffalo cows, an induced-ovulation model system involving sequential treatment with PGF2alpha and GnRH was standardized. The follicular wave containing at least one large follicle of ~7mm size was determined by ultrasonography on day 7 of the estrous cycle before administering exogenous PGF2alpha to induce luteolysis and follicular growth. Exogenous GnRH (100µg i.m) was administered 36h post PGF2alpha to induce LH surge. The time course of increase in LH levels post GnRH injection was monitored. Since peak LH levels are attained 2 h post GnRH administration, the time intervals of 3 h post GnRH (corresponding to1 h post LH surge) and 24 h post GnRH (corresponding to 22 h post LH surge) were chosen to identify the gene expression profile associated with immediate early and delayed changes in periovulatory follicle respectively. Thus ovaries were collected before, 1 h and 22 h post LH surge and follicle wall and granulosa cells were isolated from the ovaries and snap frozen for the purpose of RNA isolation.

first: Jyotsna

last: Rao

first: Satheesha

last: Mahalingappa

first: Jayaram

last: Puttaiah

first: Medhamurthy

last: Rudraiah


title: OsGLK1 regulated genes in rice

status: Public on Jun 15 2008

city: Bunkyo-ku

first: Hidemitsu

last: Nakamura

state: Tokyo

address: 1-1-1 Yayoi

department: Department of Applied Biological Chemistry

country: Japan

institute: The University of Tokyo

summary:
Transcription factors encoded by GLK genes are putative positive regulators of chloroplast development. To identify the potential downstream genes regulated by OsGLK1, we performed the rice 44k oligo microarray analysis.
Keywords: over-expression of full-length cDNAs

overall_design: Total RNA was extracted from calluses derived from T1 seeds of the OsGLK1 full length cDNA overexpression line and the control line grown on the N6D medium with 30 mg/l of Hyg for 14 days at 30˚C, and subjected to 44k oligo-DNA microarray with 4 biological replicates.

first: Makoto

last: Hakata

first: Masayuki

last: Muramatsu

first: Yoshiaki

last: Nagamura

first: Hirohiko

last: Hirochika

first: Hiroaki

last: Ichikawa


title: Identification of Tmem10/Opalin as a novel marker for oligodendrocytes using gene expression profiling

status: Public on May 07 2008

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary:
Background
During the development of the central nervous system, oligodendrocytes generate large amounts of myelin, a multilayered insulating membrane that ensheathes axons, thereby allowing the fast conduction of the action potential and maintaining axonal integrity. Differentiation of oligodendrocytes to myelin-forming cells requires the downregulation of RhoA GTPase activity.

Results
To gain insights into the molecular mechanisms of oligodendrocyte differentiation, we performed microarray expression profiling of the oligodendroglial cell line, Oli-neu, treated with the Rho kinase (ROCK) inhibitor, Y-27632 or with conditioned neuronal medium. This resulted in the identification of the transmembrane protein 10 (Tmem10/Opalin), a novel type I transmembrane protein enriched in differentiating oligodendrocytes. In primary cultures, Tmem10 was abundantly expressed in O4-positive oligodendrocytes, but not in oligodendroglial precursor cells, astrocytes, microglia or neurons. In mature oligodendrocytes Tmem10 was enriched in the rims and processes of the cells and was only found to a lesser extent in the membrane sheets.

Conclusions
Together, our results demonstrate that Tmem10 is a novel marker for in vitro generated oligodendrocytes.
Keywords: gene expression profiling for oligodendrocytes, olineu, oligodendrocyte differentiation

overall_design:
2 Subexperiments:
1. olineu in absence of neurons (control) vs. olineu in presence of neurons
including dye swap design with 6 technical replicates
2. olineu in presence of neurons (control) vs. Y27631 treated olineu in presence of neurons

first: Angelika

last: Kippert

first: Katarina

last: Trajkovic

first: Dirk

last: Fitzner

first: Lennart

last: Opitz

first: Mikael

last: Simons


title: Microarray analysis of rice plants fumigated with ozone

status: Public on Apr 24 2008

city: Tsukuba

first: Randeep

last: Rakwal

state: Ibaraki

address: AIST WEST, Onagawa 16-1

institute: AIST

summary:
In this study, integrated transcriptomics, proteomics and metabolomics approaches were applied to investigate the molecular responses of O3 in the leaves of two-weeks old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O3 for a period of 24 h.  Based on the morphological alteration of O3-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that O3 triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice.
Also investigated were the molecular responses in the leaves of two-weeks old rice (cv. Nipponbare) seedlings under continuous light and pure air (as a positive control for ozone exposure experiments) for a period of 24 h. Transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that continuous light and growth for 24 h also triggers a chain reaction of altered gene expressions involved in multiple cellular processes in rice, but different from those against ozone, in general.
Keywords: Ozone fumigation response

overall_design:
Ozone-treated Samples: An in vivo 14-days-old rice seedling model system was used, where whole seedlings were used for exposure/fumigation to the ozone (0.2 ppm). Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a GenePix microarray scanner followed by the Gene Pix 4000 analysis application program for image analysis and data extraction processes. The GeneSpring Ver. 4 software was used for normalization.
Control Samples: An in vivo 14-days-old rice seedling model system was used, where whole seedlings were used for exposure to continuous light and pure air. Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) 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.


title: Female adult to male adult comparison and 1st instar larvae to adult comparisons

status: Public on Jun 19 2008

city: Lubbock

first: Scot

last: Dowd

state: TX

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

middle: E

first: Felix

last: Guerrero


title: Microarray analysis of rice plants exposed to jasmonic acid (JA)

status: Public on Apr 15 2008

summary:
In this study, integrated transcriptomics and proteomics approaches were applied to investigate the molecular responses of JA in the shoots of 7-days old rice (cv. Nipponbare) seedlings exposed to 5 micromolar JA for a period of 7 days. Based on the morphological alteration of JA-exposed rice seedlings, transcript profiling of rice genes was performed in seedlings using rice DNA microarray chip, and proteomics by 2-DGE. This systematic survey showed that JA triggers a chain reaction of altered gene and protein expressions involved in multiple cellular processes in rice growth and development and defense.
Keywords: JA exposure response

overall_design: An in vivo 7-days-old rice seedling model system was used, where whole seedlings were used for exposure to the JA (5 micromolar). Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a GenePix microarray scanner followed by the Gene Pix 4000 analysis application program for image analysis and data extraction processes. The GeneSpring Ver. 4 software was used for normalization.


title: Gene Expression in Response to excess Copper Stress in Rice Leaves

status: Public on Apr 30 2008

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

institute: RIKEN

summary:
Gene expression in response to Cu stress in rice leaves was quantified using DNA microarray (Agilent 22K Rice Oligo Microarray) and real-time PCR technology. Rice plants were grown in hydroponic solutions containing 0.3 (control), 10, 45 or 130 µM of CuCl2, and Cu accumulation and photosynthesis inhibition were observed in leaves within 1 day of the start of treatment. Microarray analysis flagged 305 Cu-responsive genes, and their expression profile showed that a large proportion of general and defense stress response genes are up-regulated under excess Cu conditions, whereas photosynthesis and transport-related genes are down-regulated. The Cu sensitivity of each Cu-responsive gene was estimated by the median effective concentration value (EC50) and the range of fold-changes (F) under the highest (130 µM) Cu conditions (|log2F|130). Defense-related genes involved in phytoalexin and lignin biosynthesis were the most sensitive to Cu. Our results indicate that plant management of abiotic and pathogen stresses has overlapping components, possibly including signal transduction.
Keywords: dose response, stress response

overall_design: Rice plants were treated with hydroponic solutions containing 10 µM, 45 µM, or 130 µM CuCl2. Treatment with the standard rice hydroponic solution containing 0.3 µM CuCl2 was performed simultaneously as a control. Each experiment was triplicated. Thus, 9 array chips were used.

first: Emi

last: Sudo

first: Misao

last: Itouga

first: Kayo

last: Yoshida-Hatanaka

first: Yoshiro

last: Ono


title: Phosphate stimulates parathyroid cell proliferation and PTH release in organ cultures of hyperparathyroidism

status: Public on May 13 2008

city: Shinjuku-ku

first: Kanji

last: Sato

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

institute: Tokyo Women's Medical University

summary:
The pathogenesis of primary hyperparathyroidism (I-HPT) and secondary hyperparathyroidism (II-PTH) remains to be elucidated. To characterize their pathophysiology, we investigated the effects of calcium and phosphate on cell proliferation and PTH release in an organ culture of parathyroid tissues. Dissected parathyroid tissues obtained from patients with I-HPT (adenoma) or II-PTH (nodular hyperplasia) were precultured on a collagen-coated membrane for 1-4 week. After exchanging the medium for one containing various concentrations of phosphate, PTH release and [3H]thymidine incorporation were studied. In contrast to dispersed parathyroid cells cultured in a monolayer, calcium decreased PTH release in a concentration-dependent manner in parathyroid tissues. Furthermore, when parathyroid tissues obtained from II-PTH were precultured for 1-4 weeks, PTH release and parathyroid cell proliferation were significantly increased in high-phosphate medium. These phosphate effects were also observed to a lesser extent in parathyroid tissues obtained from I-HPT, but there was no significant difference between I-HPT and II-HPT. Microarray analyses revealed that mRNA levels of PTH, CaSR, and VDR were well preserved, and several growth factors (e.g. TGF-beta1-induced protein) were abundantly expressed in II-PTH. Using organ cultures of hyperparathyroid tissues, in which PTH release and CaSR are well preserved for a prolonged period, we have demonstrated that phosphate stimulates parathyroid cell proliferation not only in II-PTH but also in I-HPT. Although the mechanism responsible for phosphate-induced cell proliferation remains to be elucidated, our in vitro findings suggest that both parathyroid tissues preserve to some extent a physiological response system to hyperphosphatemia as observed in normal parathyroid cells. These data will be published in Journal of Bone & Mineral Metabolism.
Keywords: Organ culture experiments, dultured in low vs.high phosphate medium

overall_design: Two conditioned experimets, low vs. high phosphate medium, cultured for 1 and 4 days

first: Yoshiaki

last: Azuma


title: Differential gene expression between individuals exposed to different levels of air pollution

status: Public on Apr 17 2008

city: Maastricht

first: Danitsja

middle: Maria

last: van Leeuwen

address: PO Box 616

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

summary:
Comparison of genome-wide gene expression between humans living in areas of high levels of air pollution and less polluted areas.
Keywords: Comparison of genome-wide gene expression between different conditions

overall_design: The study investigated differential gene expression in peripheral blood from 23 children and 12 adults from a region of residence with high levels of air pollution as compared to 24 children and 12 adults from a less-polluted area.Two conditions: living in the polluted or in the less-polluted area. One individual per array, hybridized against a common reference sample

middle: M

first: Marie

last: Pedersen

first: Peter

last: Hendriksen

first: Andre

last: Boorsma

first: Marcel

middle: H

last: van Herwijnen

first: Ralph

middle: W

last: Gottschalk

first: Micheline

last: Kirsch-Volders

first: Lisbeth

last: Knudsen

first: Radim

last: Sram

first: E

last: Bajak

first: Joost

last: van Delft

first: Jos

middle: C

last: Kleinjans


title: Effects of dietary curcumin and rutin on colonic inflammation and gene expression in mdr1a-/- mice, a model of IBD

status: Public on Apr 10 2008

city: Palmerston North

first: Katia

last: Nones

address: Private Bag 11-600

country: New Zealand

institute: Crop & Food Research

summary:
Damage of the intestinal epithelial barrier by xenobiotics or reactive oxygen species and a dysregulated immune response are both factors involved in the pathogenesis of inflammatory bowel diseases (IBD). Curcumin and rutin are polyphenolic compounds known to have anti-oxidant and anti-inflammatory activities, but their mechanism(s) of action are yet to be fully elucidated. Mdr1a-/- mice spontaneously develop intestinal inflammation, predominantly in the colon, with pathology similar to IBD, so this mouse model is relevant for studying diet-gene interactions and potential effects of foods on remission or development of IBD. This study tested whether the addition of curcumin or rutin to the diet would alleviate colonic inflammation in mdr1a-/- mice. Using whole-genome microarrays, the effect of dietary curcumin on gene expression in colon tissue was also investigated. Twelve mice were randomly assigned to each of three diets; control (AIN-76A), control + 0.2% curcumin or control + 0.1% rutin and monitored from the age of 7 to 24 weeks. Curcumin, but not rutin, significantly reduced histological signs of colonic inflammation in mdr1a-/- mice. Microarray and pathway analyses suggested that the effect of dietary curcumin on colon inflammation could be via an up-regulation of xenobiotic metabolism and a down-regulation of pro-inflammatory pathways probably mediated by PXR and PPARalpha activation of RXR. These results reveal the potential of global gene expression and pathway analyses to study and better understand the effect of foods in colonic inflammation.
Keywords: Colonic inflammation, gene expression, curcumin, rutin, genome-wide microarrays

overall_design: Twelve mice were randomly assigned to each of three diets; control (AIN-76A), control + 0.2% curcumin or control + 0.1% rutin and monitored from the age of 7 to 24 weeks. As only curcumin significantly reduced colonic HIS, comparison of the gene expression levels in colon was carried out using total RNA from colon tissue of four mdr1a-/- mice from the control group (high HIS) and four mdr1a-/- mice from the curcumin group (low HIS). A reference design with eight arrays was used for this comparison, where each individual RNA sample was hybridized in the array with the reference RNA, totalizing 4 biological replicates per treatment.

first: Yvonne

last: Dommels

first: Sheridan

last: Martell

first: Christine

last: Butts

first: Warren

last: McNabb

first: Zaneta

middle: A

last: Park

first: Shotun

last: Zhu

first: Duncan

last: Hedderly

first: Matthew

middle: P

last: Barnett

first: Nicole

last: Roy


title: Ino80 chromatin remodeling complex promotes recovery of stalled replication forks

city: Sendai

first: Yukako

last: Oma

address: Tsutsumidori-Amamiyamachi 1-1, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

type: Genome binding/occupancy profiling by genome tiling array

first: Kenji

last: Shimada

first: Thomas

last: Schleker

first: Kazuto

last: Kugou

first: Kunihiro

last: Ohta

first: Masahiko

last: Harata

first: Susan

last: Gasser


title: Identification of Genes and Gene Ontology Process Critical to Skin Papilloma Development in Tg.AC Transgenic Mice

status: Public on Apr 11 2008

city: RTP

first: Hong

last: Dang

state: NC

address: 111 TW. Alexander Dr

institute: NIEHS

summary:
This study analyzes gene expression associated with papilloma development in Tg.AC v-Ha-ras transgenic mice and identifies novel genes and biological processes that may be critical to skin carcinogenesis in these mice.  Epidermal abrasion was used to synchronously induce epidermal regeneration in FVB/N wild type and transgenic Tg.AC mice.  Skin papillomagenesis was uniquely induced in Tg.AC mice, and gene expression profiling was carried out using a 22,000 element mouse DNA microarray.  Histological analysis showed that papillomas developed at a high rate by day 30 after abrasion in transgenic animals, while no papilloma developed in wild type mice.  Transgene specific differentially expressed genes were identified at day 30 post-abrasion and these genes were annotated using EASE software and literature mining.  Annotated and non-annotated genes associated with papilloma development were identified and clustering analysis revealed groups of genes that are coordinately expressed.  A number of genes associated with differentiation and development were also physically clustered on mouse chromosome 16, including 16B3 that contains several Stefins and stefin-like genes, and 16A1 containing a number of keratin associated protein genes.  Additional analyses presented here yield novel insights into the genes and processes involved in papilloma development in Tg.AC mice.
Keywords: Time course of papilloma tumorigenesis between genetically modified strains after skin abrasion.

overall_design: Strains: Tg.AC vs FVB/N; Treatment: epidermal abrasion vs sham treatment, samples collected 3, 5, 9, 18, and 30 days post treatment; Microarray: 2-channel, pooled total RNA from 5 animals, 2 technical replicate arrays with dye-swaps.

first: Carol

last: Trempus

first: David

last: Malarkey

first: Sung-Jen

last: Wei

first: Margaret

last: Humble

first: Rebecca

last: Morris

first: Raymond

last: Tennant


title: Transcript Analysis of Human Mammary Cell Subsets

status: Public on May 10 2008

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

type:
Expression profiling by array
Expression profiling by SAGE


title: Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance

status: Public on Apr 08 2008

first: Daniel

last: Hogan

address: 279 Campus Dr B439

institute: Stanford University


title: Microarray assay of the genetic response of Picea abies to Heterobasidion annosum infection (Loops 1 and 2)

city: Raleigh

first: Chris

last: Smith

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU

summary:
The hypothesis of the experiment is that infected trees of high resistance express a wider variety of resistance genes than infected trees of low resistance, and that the level of expression of these resistance genes differs between infected and healthy branches. Also, some genes highly expressed in the infected state not expressed in the healthy state may be in response to the wounding rather than the actual infection. By comparing these expressions to that of wounded, uninfected branches, this could also be clarified.

This SuperSeries is composed of the SubSeries listed below.


title: Expression study of 'hemocyte minus vs hemocyte plus, and wounded vs unwounded hemocyte deficient' drosophila embryos

status: Public on Apr 01 2008

city: Bristol

first: Mark

middle: Owen

last: Winfield

address: Woodland Road

department: Biological Sciences

country: United Kingdom

institute: Bristol University

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


title: Transcriptional and polysomal profile of poliovirus-infected HUVECs

status: Public on Mar 27 2009

city: Salt Lake City

first: Douglas

middle: I.

last: Schmid

state: UT

department: HMBG

institute: University of Utah

summary: Translation initiation of eukaryotic mRNAs mostly occurs by the cap-dependent ribosome scanning mechanism.  However, certain mRNAs are translated by ribosome assembly at internal ribosome entry sites (IRES), a mechanism that allows the synthesis of certain proteins when cap-dependent translation is inhibited by cellular stress.  Whether IRES-mediated translation occurs in stressed human endothelial cells (EC) is unknown.  We performed whole genome microarray analysis of polyribosomal mRNA (43,203 sequences) from virus-infected EC to identify IRES-containing mRNAs.

overall_design: RNA from polysome fractions or total RNA were isolated from control or PV-infected HUVECs using Trizol LS (Invitrogen, Carlsbad, CA) and then subjected to the whole human genome-wide microarray analysis (43,203 transcripts, Agilent, Santa Clara, CA) to obtain the translational profile.

first: Huimiao

last: Jiang

first: Brandt

last: Jones

first: John

last: Kriesel

last: Martinez

first: Andrew

last: Weyrich

first: Guy

last: Zimmerman

first: Larry

last: Kraiss


title: Gene expression profiles of various tissues under different physiological conditions

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

summary:
Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892).
1: reproducibility of labeling:
mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples.
Keywords: variety among tissues

platform_organism:
Oryza sativa
Oryza sativa Japonica Group

overall_design:
organisms: Oryza sativa ssp. japonica (Nipponbare)
tissue: shoot, root, germinated seed, panicle, callus derived from more than 100 plants
treatement1: cold stress (10 degreeC)
time course1: 24, 48, 72 hours
tissue1: shoot
treatment2: drought stress (25% polyethylene glycol 6000)
time course2: 1, 9, 24 hours
tissue: shoot
treatment3: flood and lay-down stress
time course3: 1, 6, 24, 48 hours
tissue3: shoot
treatment4: flood stress
time course4: 1, 24, 48, 72 hours
tissue4: shoot
treatment5: osmotic stress (260mM mannitol) for 24 hours
tissue5: shoot
treatment6: 150mM NaCl for 24 hours
tissue6: shoot
hybridization : two dye method
hybridization: self-hybridization
replication: Hybridization of shoot replicated 11 times, and germinated seed was twice. Other samples did not replicated.
array: 1 array per 1 experiment (total 39 arrays)

first: Hisako

last: Ooka

first: Kimihisa

last: Tasaki

first: Hitomi

last: Yamada-Akiyama

first: J

last: Lee

first: Shoshi

last: Kikuchi


title: Microarray analysis of rice plants irradiated with carbon ion beams (HIMAC)

status: Public on Mar 29 2008

first: Randeep

last: Rakwal

summary:
In this study, carbon-ion beams generated via the heavy-ion medical accelerator in Chiba (HIMAC) were targeted to growing rice seedlings (7-days-old) to examine their effect on this genome model. Both physiological parameters, such as growth, and molecular events, specially the gene expression profiles were examined immediately after irradiation (at 270 Gy dose) by rice oligo (22K) DNA microarrays. Genome-wide transcriptional profiling of radiation-response genes in rice provides us with first report on how our radioactive environment affects a plant species.
Keywords: Irradiation response

overall_design: An in vivo 7-days-old rice seedling model system was used, where whole seedlings were used for exposure to the emitted radiation from HIMAC (carbon ion beams). Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a GenePix microarray scanner followed by the Gene Pix 4000 analysis application program for image analysis and data extraction processes. The GeneSpring Ver. 4 software was used for normalization.

first: Junko

last: Shibato

first: Kumie

last: Nojima

first: Yeon-Ki

last: Kim

first: Baek

last: Nahm

first: Nam-Soo

last: Jwa

first: Satoru

last: Endo

first: Kenichi

last: Tanaka

first: Hitoshi

last: Iwahashi


title: Toxicogenomic Analysis of Caenorhabditis elegans Reveals Genes Involved in the Resistance to Cadmium Toxicity

status: Public on Mar 26 2008

city: Research Triangle Park

first: Yuxia

last: Cui

address: 111 TW Alexander Dr.

department: ETP, DIR

summary:
Exposure to cadmium is associated with a variety of human diseases.  At low concentrations, cadmium activates the transcription of stress-responsive genes, which can prevent or repair the adverse effects caused by this metal.  Using C. elegans, 290 genes were identified that are differentially expressed (≥1.5-fold) following a 4 or 24 hour exposure to cadmium.  Several of these genes are known to be involved in metal detoxification, including mtl-1, mtl-2, cdr-1 and ttm-1, confirming the efficacy of the study.  The majority, however, were not previously associated with metal-responsiveness and are novel.  Gene Ontology analysis mapped these genes to cellular/ion trafficking, metabolic enzymes and proteolysis categories.  RNAi-mediated inhibition of 50 cadmium-responsive genes resulted in an increased sensitivity to cadmium toxicity, demonstrating that these genes are involved in the resistance to cadmium toxicity.  Several functional protein interacting networks were identified by interactome analysis.  Within one network, the signaling protein KEL-8 was identified.  Kel-8 protects C. elegans from cadmium toxicity in a mek-1 (MAPKK)-dependent manner.  Because many C. elegans genes and signal transduction pathways are evolutionarily conserved, these results may contribute to the understanding of the functional roles of various genes in cadmium toxicity in higher organisms.
Keywords: gene expression time course

overall_design: Total RNA was prepared from non-treated control nematodes and those exposed to 100 μM cadmium for 4 h and 24 h.  For each condition, RNA samples were prepared from three independent cultures of C. elegans, and the RNA was isolated in triplicate.  This generated nine replicates per treatment.  RNA samples from cadmium-treated and control C. elegans were labeled using Low RNA Input Fluorescent Linear Amplification Kits following the manufacture’s protocols (Agilent Technologies).  Labeled cRNAs were hybridization to Agilent C. elegans oligonucleotide microarrays.  These microarrays contain target probes for the entire C. elegans genome, ~20,000 ORFs (Agilent Technologies).  Dye-flips were performed for each pair of hybridizations resulting in a total of 36 hybridizations.  Data was extracted from the microarrays using Agilent’s DNA microarray scanner and Feature Extraction Software (Agilent Technologies).

first: Sandra

last: McBride

first: Windy

last: Boyd

first: Scott

last: Alper

first: Jonathan

last: Freedman


title: Array-comparative genomic hybridization by using DualChip® human cancer 1.1 arrays

status: Public on Apr 22 2008

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

type: Genome variation profiling by genome tiling array

summary:
Tumors often harbor several genetic aberrations at both RNA and DNA level. Integration of expression data with copy number changes represents a powerful strategy to investigate genes involved in tumorigenesis. Here we describe a fluorescent array-based Comparative Genomic Hybridization protocol to be used on a commercial microarray platform optimized to detect cancer-related gene expression. This method will be valuable to use a single low-density array platform monitoring gene expression and copy number assessment in parallel.
Keywords: Comparative genomic hybridization, neuroblastoma

overall_design:
Here we describe a fluorescent array-based Comparative Genomic Hybridization (aCGH) protocol to be used on DualChip® (Eppendorf, Hamburg, Germany) arrays, in view of an application of cancer-specific DualChip® platforms for both gene expression profiling and copy number assessment.
Since we previously analyzed #501 and #2270 neuroblastoma samples by Agilent Human Genome CGH 44A microarrays (Scaruffi, P. Coco, S., Cifuentes, F., Albino, D., Nair, M., Defferrari, R., Mazzocco, K., and G.P. Tonini. 2007. Identification and characterization of DNA imbalances in neuroblastoma by high-resolution oligonucleotide array comparative genomic hybridization. Cancer Genetics and Cytogenetics. 177(1): 20-29) and all 294 genes contained in DualChip® human cancer 1.1 arrays were present also in Agilent arrays, it has been possible to compare results obtained by the two different platforms. We assumed aCGH performed by Agilent slides as reference method to assess gene gains and losses in neuroblastoma samples. This approach allowed us to select 120 genes printed on DualChip® arrays as invariant genes (ABI2, ADAM9, ANGPT1, AREG, BAK1, BIK, BARD1, BCL2A1, BCL2L2, BMP1, CASP3, CASP8, CDH12, CFLAR, CTNNA1, CD34, CLK1, CGRRF1, COL6A1, CSF1R, CSPG2, CTGF, CXCL9, CCNA2, CCNB1, CCNG1, CCNH, CDKN1A, CDKN1C, CDKN2A, CDKN2B, CDKL1, DSP, E2F3, E2F5, EFNA1, EGF, EGR1, FASTK, FGF1, FGF2, FGFR1, FGR, FN1, GAS1, HGFAC, HMMR, IGF1R, IGFBP2, IK, IFNAR1, IFNGR1, ILK, IRF1, ITGA1, ITGA4, IL10, IL13, IL15, IL1A, IL2, IL3, IL4, IL5, IL6R, IL8, KDR, KISS1, LIF, MIF, MMP11, MMP14,
MDH1, MAP2K1, MAP2K5, MAPK10, MAPK14, MCL1, NF2, NID1, NINJ1, NRG1, NTRK1, PGF, PDGFB, PDGFRA, PLAT, PLG, PDCD2, PPBP, PRODH, PTGES, PCDH1, PTK2, PURA, QSCN6, RIPK1, RRM1, ARHGDIA, SFRP2, SOD1, STAT1, TEK, TERT, THBS1, TIAM1, TNC, TANK, TGFA, TGFB2, XRCC6, TGFB3, TGFBR1, TMED10, TPBG, TYRO3, ERBB4, FLT4, FOS, VIL2).

first: Paola

last: Scaruffi

first: Stefano

last: Moretti

first: Caterina

last: Cremonesi

last: Bonassi

first: GianPaolo

last: Tonini


title: High-throughput sequencing of small RNAs: Caenorhabditis elegans

status: Public on Jun 16 2008

city: San Francisco

first: James

middle: Graham

last: Ruby

address: 1700 4th Street QB3 s404

department: Biochemistry

institute: UCSF

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Mouse embryonic stem cell line R1 differentiation study

status: Public on Mar 28 2008

city: Santiago

first: Dario

last: Sepulveda

state: RM

address: Beacuhef 861

department: Chemical Engineering and Biotechnology

country: Chile

institute: Universidad de Chile

summary:
Cell line R1 (Mouse embryonic stem cell line) was cultured on 3 different conditions for differentiation study. The experiment ran for 7 days and samples were taken every 24hrs. Afterward, samples on days 0,3,5 and 7 were processed for microarray analysis.

The conditions were the differentiation of the stem cells for 7 days through a)formation of embryoid bodies, b)culture on a gelatin coated surface and c) culture on a matrigel coated surface.
Keywords: Time course

overall_design: 10 samples, considering: days 3, 5 and 7 for each of the 3 differentiating conditions and one for day zero. Technical replicates were made every three sample points. 3 Complete biological replicates were performed.

first: Eleftherios

middle: T

last: Papoutsakis

first: Juan

last: Asenjo


title: Gene expression variation increase in trisomy 21 tissues

status: Public on Mar 18 2008

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

country: Taiwan

institute: National Taiwan University

summary:
Congenital development disorders with variable severity occur in trisomy 21. However, how these phenotypic abnormalities develop with variations remains elusive. We hypothesize that the difference in euploidy gene expression variation among trisomy 21 tissues are perturbed by the presence of an extra copy of chromosome 21 and this may contribute to the phenotypic variations in Down syndrome.
Keywords: Disease state analysis

overall_design: We used DNA microarray to measure the differences in gene expression variance (representing variation) between four human trisomy 21 amniocytes and six human euploid amniocytes.

first: Hsieh

last: Fon Jou

first: Chou

last: Ching Yu

first: Chen

last: Chien Yu

first: Tsai

last: Cheng Hsien

first: Hwa

last: Hsiao Lin

first: Chang

last: Li Yun

first: Lin

last: Yi Shing


title: Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids II

status: Public on Mar 13 2008

city: Los Angeles

first: Christopher

last: Park

address: 23-151 CHS, 650 Charles E. Young Drive

department: Molecular and Medical Pharmacology

institute: UCLA

summary:
We have mapped regulatory loci for nearly all protein coding genes in the mammalian genome using microarray measurements from a panel of mouse/hamster radiation hybrids.
Proof of principle transfection experiment.  Pcdh7 (a gene identified as being a regulator of many genes) is transfected into A23 and HEK cells and compared to A23 and HEK cells transfected with an empty vector.  Upregulated genes predicted by our approach are compared with the transfection experiments
Keywords: tranfection, regulation of gene expression

sample_organism:
Homo sapiens
Cricetulus griseus

overall_design: There are 4 microarrays.  The first two are biological replicates of A23 (transfected with Pcdh7, labeled with cy5) / A23 (tranfected with empty vector, labeled with cy3).  The second two are biological replicates of HEK (transfected with Pcdh7, labeled with cy5) / HEK (tranfected with empty vector, labeled with cy3).

first: Desmond

last: Smith


title: Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids (control II)

summary:
We have mapped regulatory loci for nearly all protein coding genes in the mammalian genome using microarray measurements from a panel of mouse/hamster radiation hybrids.
Keywords: regulation of gene expression

overall_design: A control array to examine the copy number of the A23 Hamster fibroblast cell line vs. Chinese Hamster Kidney Genomic DNA


title: Comprehensive Microarray Transcriptome Profiling of CD34-Enriched Mouse Keratinocyte Stem Cells

status: Public on Apr 21 2008

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

summary:
Recent developments in animal models (Morris et al., 2004; Tumbar et al., 2004) as well as the discovery of cell surface markers (Jones and Watt, 1993; Tani et al., 2000; Trempus et al., 2003; Nijhof et al., 2006) have made it possible to isolate living epidermal hair follicle stem cells (HFSCs) from mouse skin, facilitating the study of the biological and molecular features inherent to HFSCs.  A complexity of stem and progenitor cell populations within the hair follicle has been revealed. Here, we report comprehensive profiling of mouse CD34-expressing HFSCs using the Agilent mouse oligo microarray platform in order to extend and enrich the existing HFSC databases.
Keywords: gene expression, cell characterization

overall_design: Total RNA was prepared from CD34(+) and CD34(-) keratinocytes obtained from three biological replicates, labeled with 2 different fluorescent dyes, and hybridized to the Agilent oligo-microarrays containing ~22,000 mouse genes and Expression Sequence Tag (EST) probes (supplemental methods).  The experiment contained technical dye-flips of each pairwise comparison.

first: Carol

middle: S

last: Trempus

first: Hong

last: Dang

first: Margaret

last: Humble

first: Sung-Jen

last: Wei

first: Michael

last: Gerdes

first: Rebecca

last: Morris

first: Carl

middle: D

last: Bortner

first: George

last: Cotsarelis

first: Raymond

last: Tennant


title: Differentially expressed genes under different stress conditions in rice

first: Kouji

last: Satoh

summary:
Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892).
2: reproducibility of hybridization-2:
We made a dye-swap experiment to validate dye-effect and data reproducibility between arrays. We hybridized shoot (as control) and stress-treated shoot. This data also indicated the diversity of gene expression profile among stress response. In addition, array data of samples treated for 24 hours have been already published on NCBI-GEO (GSE2415)
Keywords: variety among tissues

overall_design:
organisms: Oryza sativa ssp. japonica (Nipponbare)
tissue: shoot derived from more than 100 plants
treatement1: cold stress (10 degreeC)
time course1: 48, 72 hours
tissue1: shoot
treatment2: drought stress (25% polyethylene glycol 6000)
time course2: 1, 9 hours
tissue: shoot
treatment3: flood and lay-down stress
time course3: 1, 6, 24, 48 hours
tissue3: shoot
treatment4: flood stress
time course4: 1, 24, 48, 72 hours
tissue4: shoot
treatment5: lay-down stress for 24 hours
tissue5: shoot
hybridization : two dye method
hybridization: Dye-swap experiment
replication: samples were not replicated.
array: 2 array per 1 experiment (total 26 arrays)

first: Hisako

last: Ooka

first: Kimihisa

last: Tasaki

first: Hitomi

last: Yamada-Akiyama

first: J

last: Lee

first: Shoshi

last: Kikuchi


title: Differentially expressed genes from different developmantal stages in rice

summary:
Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892).
2: reproducibility of hybridization-1:
We made a dye-swap experiment to validate dye-effect and data reproducibility between arrays. We hybridized shoot (as control) and other developmental stage tissues. This data also indicated the diversity of gene expression profile among developmental stages.
Keywords: variety among tissues

overall_design:
organisms: Oryza sativa ssp. japonica (Nipponbare)
tissue: shoot, root, germinated seed, panicle, callus derived from more than 100 plants
hybridization : two dye method
hybridization: dye-swap experiment
replication: germinated seed, panicle, and propagated callus were replicated twice, others were not replicated.
array: 2 array per 1 experiment (total 26 arrays)


title: Human epithelial cell line (HL) infected with Chlamydia pneumoniae

status: Public on Mar 30 2008

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary:
Transcriptional profiling of human epithelial cell line (HL) infected with Chlamydia penumoniae compared to control cells at time points 12h, 24h, 48h, 72h after the infection.
Keywords: Chlamydia peneumoniae infection

overall_design: Two-condition experiment over the time. Biological replicates: 2 infected, 2 controls at each time point (12h, 24h, 48h, and 72h), independently grown.

first: Joni

last: Alvesalo

first: Maija

last: Leinonen

first: Tuomas

last: Raitila

first: Pia

last: Vuorela

first: Petri

last: Auvinen


title: Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids (control I)

first: Christopher

last: Park

overall_design: Five replicas of RNA from the A23 cell line vs. itself.  These arrays serve as a control to determine the power to detect cis ceQTLs in this experiment.

first: Desmond

middle: J

last: Smith


title: Tumor-associated stroma derived from primary clinical breast cancer samples

city: Montreal

first: Greg

last: Finak

state: QC

address: 3775 University

department: Mcgill Center For Bioinformatics

institute: McGill University

summary:
Tumor-associated breast stroma was laser-capture microdissected from IDC breast cancer cases. The goal of the study was to characterize the heterogeneity of breast tumor-assocaited stroma and identify gene expression signatures predictive of clinical outcome.
Keywords: disease state analysis

overall_design: Common reference design, 53 samples, with dye-swap replicates. Some samples replicated three or four times, a total of 111 arrays.

first: Nicholas

last: Bertos

first: Francois

last: Pepin

first: Svetlana

last: Sadekova

first: Margarita

last: Souleimanova

first: Hong

last: Zhao

first: Haiying

last: Chen

first: Gulbeyaz

last: Omeroglu

first: Sarkis

last: Meterissian

first: Atilla

first: Michael

last: Hallett

first: Morag


title: Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids Ia

state: CA

sample_organism:
Cricetulus griseus
Mus musculus

overall_design: 99 RH cells with biological replicates (198 total) and biological replicates of mouse brain RNA vs. hamster brain RNA and mouse liver RNA vs. hamster liver RNA (4 total)


title: Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids Ib

overall_design: We have performed a copy number analysis on 99 cell lines of the T31 Radiation Hybrid Panel using CGH microarrays.  Cell line 67 is not present.


title: Energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough

status: Public on Apr 05 2008

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough


title: CD133+ and CD133- cells

status: Public on Mar 01 2008

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research


title: Expression Profiling of Severed Rat Medial Collateral Ligament Following Injury

status: Public on Mar 05 2008

city: San Antonio

first: Xinyu

last: Wang

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

institute: US Army Institute of Surgical Research

summary:
Gene Expression Profiling of Severed Rat Medial Collateral Ligament at 1, 2, 4, 7,1 0, and 14 days Following Injury with Control and Cultured Ligament Fibroblasts and Rat Universal Reference RNA

The aim of this study was to assess the genes involved in the repair of the the dense connective tissue of the a rat ligament in order to provide targets for improvement in healing.
Rat whole genome microarrays (Agilent) were used in this study and Cy3 and Cy5 labeled total RNA was extracted and labeled with Cy3 or Cy5 prior to fragmentation and hybridization.
Keywords: Time course of changes in gene expression in the healing of the rat medial collateral ligament.

overall_design: To conserve microarrays to allow maximum replicates, two samples either Cy3 or Cy5 labeled were hybridized to each microarry.  Total RNA from each rat medial collateral ligament was labeled and hybrided to a microarray.  The fluorescence intensity for each column minus the background was extracted from each microarray for submission to BRB Array tools for statistical analysis.

first: Brett

last: Owens

first: Joseph

last: Wenke

first: James

last: Bynum

first: Phillip

last: Bowman

first: J

last: Estep


title: Chronic LPS Exposure

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health


title: Chronic Inhaled LPS Exposure

summary:
Chronic LPS inhalation causes submucosal thickening and airway narrowing. To address the hypothesis that environmental airway disease is, in part, a fibroproliferative lung disease, we exposed C57BL/6 mice daily to LPS by inhalation for up to two months followed by one month of recovery. C57BL/6 mice exposed to daily inhaled LPS had significantly enhanced mRNA expression of TGF-beta1, TIMP-1, fibronectin-1, and pro-collagen types I, III, and IV and show prominent submucosal expression of the myofibroblast markers desmin and alpha-smooth muscle actin. To identify novel candidate genes that contribute to airway fibroproliferation, we performed microarray analysis on total lung RNA from mice exposed to LPS for one week. This analysis revealed a distinct subset of genes known to regulate ECM homeostasis. To further identify candidate genes specifically involved in generic fibroproliferation we interrogated this analysis with genes induced in C57BL/6 mouse lung by bleomycin. This analysis yielded a list of 212 genes in common. Prominent among which are genes know to be important in maintenance of bone homeostasis and which may play a central role in ECM homeostasis in the lung. These results suggest that there is a common subset of genes that regulate fibroproliferation in the lung independent of etiologic agent and site of injury.
Keywords: mouse model of environmental airway disease; chronic LPS exposure

overall_design: 4 RNA pools of 3 animals each exposed to aerosolized LPS and 4 RNA pools of 3 animals each exposed to air only were co-hybridized with the Stratagene Universal Mouse Reference RNA. Each sample was assayed in duplicate with Cy3 and Cy5 dyes swapped.

first: David

last: Brass

first: Marcus

last: Kennedy

first: Gregory

last: Whitehead

first: Holly

last: Rutledge

first: Lauranell

last: Burch

last: Schwartz


title: Gene expression in Maize root

city: Columbia

first: William

middle: G.

last: Spollen

state: MO

address: 113 Bond Life Sciences Center

department: Informatics Research Core Facility

institute: University of Missouri-Columbia

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


title: A Link between the N363S Glucocorticoid Receptor Polymorphism and Altered Gene Expression Related to Human Disease

status: Public on Mar 10 2008

city: RTP

first: NIEHS

last: Microarray Core

institute: NIEHS

summary:
A single nucleotide polymorphism (SNP) in the human glucocorticoid receptor (GR), N363S, has been the focus of several clinical studies, and some epidemiological data link this SNP to increased glucocorticoid sensitivity, coronary artery disease and increased body mass index (BMI).  However, molecular studies in vitro using reporter gene expression systems have failed to define a link between this polymorphism and altered glucocorticoid receptor function.  To address the biological relevancy of N363S in glucocorticoid receptor mechanisms and function, we established stable U-2 OS (human osteosarcoma) cell lines expressing wild type hGR or N363S using a tetracycline-regulated expression system.  Functional assays with reporter gene systems revealed only minor differences between the wild type hGR and N363S receptors under a variety of conditions that probe for GR function.  However, examination of this polymorphism by human gene microarray analysis showed, for the first time, that there are significant differences between wild type hGR and the N363S SNP in their ability to selectively regulate gene expression.  Several of these genes may define the link between the N363S SNP and human disease.
Keywords: human glucocorticoid receptor, N363S single nucleotide polymorphism, microarray gene analysis

overall_design:
U-2 OS cells were transfected with the BD Clontech pTET-OFF regulatory plasmid to establish the U-OFF parental cell line.  MluI and EcoRV ends were generated onto the coding region of hGRa using PCR amplification of the pCMVhGRa plasmid.  The pTRE2hyg vector was digested with MluI and EcoRV and the two DNAs were ligated to form the pTRE2hGRa plasmid (Lu and Cidlowski).  Site-directed mutagenesis was then performed to make pTRE2N363S.  The wild type hGR and the N363S mutant were individually transfected into the U-OFF cells and clones were selected which stably expressed either hGRa or N363S using 200 mg/ml of geneticin and 500 mg/ml of hygromycin. Several clones were obtained for each receptor, and the receptor levels were compared using western blot analyses. In these cell lines, the expression of hGR can be repressed by the addition of tetracycline or the derivative doxycycline to the media. U-2 OS (human osteosarcoma) cells were maintained in DMEM/F-12 supplemented with 10% FCS:CS, 2 mM glutamine and pen-strep and selected clones were maintained in the same media with the addition of 200 mg/ml Geneticin and 200 mg/ml hygromycin. All cells were maintained in a humidified, 5% CO2 atmosphere.  For the Microarray:  U-2 OS cells stably expressing either wild type hGR or N363S were treated for six hours with 10 nM dexamethasone or vehicle, and total RNA was isolated using the Qiagen RNeasy midi kit (Qiagen, Valencia, CA).
Gene expression analysis was conducted using Agilent Human1Av2 arrays (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.  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.  For each comparison, two biological replicates were used, each with a dye reversal (totaling four arrays per comparison).

first: Christine

last: Jewell

first: John

last: Cidlowski

first: Jennifer

middle: B

last: Collins

first: Danica

last: Ducharme


title: Gene expression in early stage cervical cancer

city: Amsterdam

first: Petra

last: Biewenga

address: Meibergdreef 9

department: Department Gynaecologic Oncology

institute: Academic Medical Centre

summary:
Gene expression profiling of early stage cervical cancer tumours with and without lymph node metastasis, in order to predict lymph node metastasis before treatment.
Subsequently, comparing gene expression profiles between healthy cervical tissue and early stage cervical cancer tissue.
Keywords: Disease stage analysis

overall_design: All patients had clinical FIGO stage IB-IIA cervical cancer, the low-risk group (N) included 19 patients without unfavourable prognostic factors (positive lymph nodes, parametrial invasion, positive margins or a combination of unfavourable prognostic factors); the high risk group (P) consisted of 16 patients with lymph node metastasis, who were treated with adjuvant radiation therapy with or without chemotherapy. Healthy cervical tissue biopsies (H) were collected from 5 non-cervical carcinoma patients who underwent hysterectomy for benign reasons. RNA pooled from all tumour tissue samples was used as reference sample. Log-ratios of five technical replicates were used for normalization.

first: P

first: E

last: Ver Loren van Themaat


title: Farnesol-induced apoptosis in human lung carcinoma cells is coupled to the endoplasmic reticulum (ER) stress response

status: Public on Feb 26 2008

summary:
Farnesol (FOH) and other isoprenoid alcohols induce apoptosis in various carcinoma cells and inhibit tumorigenesis in several in vivo models. However, the mechanisms by which these isoprenoids mediate their effects are not yet fully understood. In this study, we show that FOH is effective inducer of apoptosis in several lung carcinoma cells, including H460 cells. This induction is associated with activation of caspase-3, -9, and -12, and cleavage of PARP. To obtain insight into the mechanism involved in FOH-induced apoptosis, we compared the gene expression profiles of FOH-treated and control H460 cells using microarray analysis. This analysis revealed that many of the genes implicated in endoplasmic reticulum (ER) stress, including ATF3, CHOP/GADD153, HERPUD1, BIP (GRP78), XBP1, PDIA4, and TDAG51, were highly up-regulated within 4 hr of FOH treatment suggesting that FOH-induced apoptosis involves an ER-stress response. This was supported by observations showing that treatment with FOH induces phosphorylation of eIF2alpha. FOH induces activation of several MAPK pathways, including p38, MEK-ERK, and JNK. Inhibition of MEK1/2 by U0126 inhibited the induction of ER stress-response genes. In addition, knockdown of the MEK1/2 and JNK1/2 expression by short interfering RNA (siRNA) effectively inhibited the induction of apoptosis and activation of caspase-3 and cleavage of PARP by FOH. However, only MEK1/2 siRNAs reduced the expression of ER stress-related genes and inhibited phosphorylation of eIF2alpha. Our results demonstrate that FOH-induced apoptosis is coupled to ER stress and that activation of MEK1/2 is an upstream event in the FOH-induced ER stress signaling cascade.

Vehicle vs. 4h FOH Signature Gene lists (Replicates 1 & 2) are linked as supplementary files to the Series record.
Keywords: gene expression

overall_design: H460 cells were treated for 4 hours with 250 micromolar FOH or vehicle (DMSO) in duplicate experiments.  Each FOH treated sample was compared to its matched Vehicle and dye-flips were performed, resulting in 4 arrays (2 replicate sets x 2 technical replicates).

first: JoungHyuck

last: Joo

first: Grace

last: Liao

first: Sherry

middle: F

last: Grissom

first: Anton

last: Jetten


title: Hepatic response to ischemia and reperfusion: young and adult mice

city: Cincinnati

first: Bhuvaneswari

last: Sakthivel

state: OH

address: 3333 Burnet Ave

department: Biomedical Informatics

institute: CCHMC

overall_design: Refer to individual Series


title: Azaspiracid_jurkat_time series experiment

status: Public on Feb 19 2008

city: Charleston

first: Mike

last: Twiner

state: SC

address: 219 Fort Johnson Rd

department: Marine Biotoxins

institute: NOAA/NOS

summary:
Azaspiracid-1 (AZA-1) is a marine phycotoxin that accumulates in shellfish and known to cause severe gastrointestinal intoxications in humans. As the mechanism of action of AZA-1 is currently unknown, human DNA microarrays were used to profile gene expression in human lymphocyte T cells following AZA-1 exposure. Highly significant early (1 hr) genes consisted of a T cell specific transcription factor, membrane proteins, receptors, and inflammatory genes. At 4 hr, responding genes included transcription factors and cell growth genes, in addition to 16 genes involved in fatty acid and cholesterol synthesis. Similarly, at 24 hr, 17 of the top 35 signature genes were involved in fatty acid and cholesterol synthesis. Gene Map Annotator and Pathway Profiler software confirmed cell signaling effects targeted toward lipid biosynthesis pathways. The transcriptional profile induced by AZA-1 shared high similarity to expression profiles of in vitro cholesterol synthesis inhibitor studies and in vitro and in vivo cholesterol synthesis gene knockout studies, suggesting a common transcriptional response and possible mechanism of action.
Keywords: Time course; AZA treatment vs. vehicle control

overall_design:
Time course experiment comparing AZA treatment gene expression to vehicle control.  Parallel cultures of cells (n=2) were exposed to AZA or vehicle control for 1, 4, 24hr and harvested for RNA extraction.  dye swaps were used for the replicate time points.
Log Ratio data are listed as Log10.


title: Equine Laminitis vs Control.

status: Public on Mar 22 2008

city: Philadelphia

first: Murat

last: Budak

state: PA

institute: University of Pennsylvania

summary:
Equine lameller tissues were collected to compare normal vs laminitis generated differences in transcriptom level.
Keywords: Laminitis, Equine, Diseased foot

overall_design:
Three Laminitis generated vs three normal Equine hoof tissues were subjected to comparison analysis in transcriptom level by using the Affymetrix Bovine GeneChip.
The reasons for Bovine chip were; 1) Genetic similarity to Equine.
2) More transcriptom was search at that Affymetrix platform comparing the Equine GeneChip at the time of the study.

first: Neal

last: Rubinstein

first: James

last: Orsini

first: C

last: Pollitt


title: Tissue specific profiling 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

country: Australia

institute: Queensland Institute of Medical Research

summary: Key tissues of the adult female parasite involved in nutritional uptake and reproduction were examined using a novel gene discovery approach that combined laser microdissection microscopy and microarray analyses. Gastrodermis, vitelline glands and ovary were microdissected from unfixed, frozen sections of the Asian species, Schistosoma japonicum.  Total RNA was isolated from the enriched tissue preparations and microarray analyses undertaken to generate tissue specific gene expression profiles.

platform_organism:
Schistosoma japonicum
Schistosoma mansoni

overall_design: Single colour adult female schistosome laser microdissection microarray data with technical replicates in duplicate: Gastrodermis (gut); vitelline glands (vitelline); ovary; and whole section (control).

first: Geoffrey

first: Donald

last: McManus

first: Sujeevi

last: Nawaratna

first: Luke

last: Moertel

first: Malcolm

middle: K

last: Jones


title: ChIP-chip of mouse ES cells using Ring1B antibody

status: Public on Feb 16 2008

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary:
The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2).  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC1. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.
Keywords: ChIP-chip

overall_design: Comprehensive location mapping of Ring1B binding regions was carried out using Mouse promoter Chip-on-chip 244k slide 2 (Agilent, G4495A＃014717), which covers chromosomes 9 to 19, sex chromosomes and mitochondrial genome of mice. 5x107 ES cells were grown on a 10cm dish. After removal from culture dish using cell scraper, cells were fixed in 1% formaldehyde/PBS for 10 minutes at room temperature with rocking, washed twice in PBS, suspended to 3ml TE [10mM Tris-HCl (pH 8.0), 1mM EDTA], and sonicated with microtip attached to Digital Sonifier 450 (Branson) 30 seconds, five times with maximum output power. Insoluble material was removed by centrifugation and NaCl and NP-40 were added to the supernatants to 100mM and 0.4% respectively. After preclearing with 10% volume of 50% protein A Sepharose beads slurry, lysate was incubated with 10% volume of monoclonal anti-Ring1b culture soup overnight. Immune complexes were captured bu incubating for 1 hour with 500ml of 50% Protein A Sepharose beads slurry. DNA was purified from immunoprecipitant and a small aliquot of precleared lysate was used to estimate yield as described previously12. Blunting of DNA ends, ligation with linker oligo DNA, amplification of DNA via linker mediated PCR (LM-PCR), labeling, hybridization and washing were performed following Agilent mammalian ChIP-on-chip protocol. Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

first: Mitsuhiro

last: Endoh

first: Yuichi

last: Fujimura

first: Osamu

last: Ohara

first: Tetsuro

last: Toyoda

first: Arie

last: Otte

first: Masaki

last: Okano

first: Hitoshi

last: Niwa

first: Neil

last: Brockdorff

first: Miguel

last: Vidal

first: Haruhiko

last: Koseki


title: Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids

first: Christopher

last: Park

type:
Expression profiling by array
Genome variation profiling by array

sample_organism:
Homo sapiens
Cricetulus griseus
Mus musculus


title: Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation

status: Public on Mar 14 2008

first: Hugo

last: Lavoie

state: Quebec

address: 6100 Royalmount

department: Genetics

institute: CNRC-IRB

summary:
Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. These two factors bind both the promoters of RP genes and the rDNA locus; Tbf1 activates transcription at these loci and is essential. Orthologs of Tbf1 bind TTAGGG telomeric repeats in most eukaryotes, and TTAGGG cis-elements are present upstream of RP genes in plants and fungi, suggesting that Tbf1 was involved in both functions in ancestral eukaryotes. In all Hemiascomycetes, Rap1 substituted Tbf1 at telomeres and in the S. cerevisiae lineage this substitution also occurred independently at RP genes, illustrating the extreme adaptability and flexibility of transcriptional regulatory networks.

This SuperSeries is composed of the SubSeries listed below.


title: The effects of artificial tethering of chromosomes to the nuclear periphery using LacI/lap2b anchorage constructs

status: Public on Mar 04 2008

city: Edinburgh

first: Lee

middle: Edward

last: Finlan

state: Lothian

address: Crewe Road South

department: Chromosomes & Gene Expression Laboratory

institute: MRC Human Genetics Unit

summary:
Background: The spatial organisation of the genome in the nucleus has a role in the regulation of gene expression.
In mammals, chromosomal regions with low gene-density are located close to the nuclear periphery.
Correlations have also been made between the transcriptional state of some genes and their location near the nuclear periphery.
However, a crucial issue is whether this level of nuclear organisation directly affects gene function, rather than merely reflecting it.
Methodology: To directly investigate whether proximity to the nuclear periphery can influence gene expression in mammalian cells.
here we relocate specific human chromosomes to the nuclear periphery by tethering them to a protein of the inner nuclear membrane.
Principal findings: We show that this can reversibly suppress the expression of some endogenous human genes located near the tethering sites, and even genes further away.
However, the expression of many other genes is not detectably reduced and we show that location at the nuclear periphery is not incompatible with active transcription.
The dampening of gene expression around the nuclear periphery is dependent on the activity of histone deacetylases.
Significance: Our data show that the radial position within the nucleus can influence the expression of some, but not all, genes.
This is compatible with the suggestion that re-localisation of genes to the peripheral zone of the nucleus could be used by metazoans to modulate the expression of selected genes during development and differentiation.

This SuperSeries is composed of the SubSeries listed below.

first: Duncan

last: Sproul


title: Down-stream effects in demyelinating neuropathies

first: Marcel

last: Kwa

email: m.s.kwa@amc.uva.nl, m.s.kwa@wxs.nl

department: Neurology

institute: Academic Medical Center, Univ. Amsterdam

summary:
Hereditary Motor and Sensory Neuropathies (HMSN) are the most common inherited peripheral neuropathies and comprise a group of genetically heterogeneous diseases.
We study the genetic defects causing three demyelinating disorders: HMSN1A, HMSN-LOM and congenital cateracts facial dysmophism neuropathy (CCFDN) syndrome, which are caused by mutations in PMP22, NDRG1 and CTDP1, respectively. The function and patho-mechanisms of these genes is still unknown. To identify effects downstream of the mutations, thereby possibly involved in the disease process, we used Serial expression of gene expression (SAGE) and microarray analysis. We analyzed human Schwann cell lines from three normal subjects, one HMSN-LOM patient, two HMSN-1A patients and two CCFDN patients and compared our data to a recent dataset of human Schwann cells (4 normal subjects passage 1 vs. 3, GDS1869/GSE4030 M.B. Bunge, 2006). We excluded genes that were not consistently regulated between biological and technical replicates and genes that were found to be influenced by passage number (p<0.05). Comparing expression profiles of demyelinating neuropathies with different mutations we identified: 1. expression signatures specific for each genotype. 2. Genes commonly (dys)regulated in all screened neuropathies. Interestingly, these include genes that play a role in reorganization of sodium channels in central and peripheral nerves (S100A10, CD90), or extracellular matrix remodeling (e.g. TGFBI, SERPINE1, THBS1). We also found high up-regulation of genes involved in Schwann cell lineage and in particular, genes that are associated with an immature or pre-myelinating Schwann cell phenotype (i.e. Sox2, Sox10, COL18A1, TFAP2A, Pax3, CDH19). Our study shows that many genes, possibly contributing to nerve pathology can be identified by this approach.
Keywords: disease state analysis, genotype down-stream effects analysis

overall_design: Experimental design: in total 12 (two-color) arrays were run. All neuropathy samples were in duplicate (technical replicates). Two CCFDN and two HMSN1A patients were also analyzed as biological replicates. Three healthy subjects were included from which one was in duplicate. All samples (Cy3) were compared to a common reference pool (Cy5) which consisted of a mix of all samples.

first: MS

middle: G

first: D

middle: C

last: Chandler

first: R

middle: R

last: De Jonge

first: ALM

middle: A

last: Ten Asbroek

middle: H

last: King

first: L

last: Kalaydjieva

first: F

last: Baas


title: Bleomycin-induced Lung Fibrosis for Comparison with Chronic LPS Exposure

first: Ivana

last: Yang

summary:
Chronic LPS inhalation causes submucosal thickening and airway narrowing.  To address the hypothesis that environmental airway disease is, in part, a fibroproliferative lung disease, we exposed C57BL/6 mice daily to LPS by inhalation for up to two months followed by one month of recovery.  C57BL/6 mice exposed to daily inhaled LPS had significantly enhanced mRNA expression of TGF-beta1, TIMP-1, fibronectin-1, and pro-collagen types I, III, and IV and show prominent submucosal expression of the myofibroblast markers desmin and alpha-smooth muscle actin.  To identify novel candidate genes that contribute to airway fibroproliferation, we performed microarray analysis on total lung RNA from mice exposed to LPS for one week.  This analysis revealed a distinct subset of genes known to regulate ECM homeostasis.  To further identify candidate genes specifically involved in generic fibroproliferation we interrogated this analysis with genes induced in C57BL/6 mouse lung by bleomycin.  This analysis yielded a list of 212 genes in common.  Prominent among which are genes know to be important in maintenance of bone homeostasis and which may play a central role in ECM homeostasis in the lung.  These results suggest that there is a common subset of genes that regulate fibroproliferation in the lung independent of etiologic agent and site of injury.
Keywords: mouse model of pulmonary fibrosis; timecourse

overall_design: For each timepoint (1 week, 2 weeks, 3 weeks), 2 RNA pools of 3 animals each treated intratracheally with bleomycin and 1 RNA pool of 3 animals each treated with saline control were co-hybridized with the Stratagene Universal Mouse Reference RNA.  Each sample was assayed in duplicate with Cy3 and Cy5 dyes swapped.

first: David

middle: M

last: Brass

first: Marcus

middle: P

last: Kennedy

first: Gregory

last: Whitehead

first: Holly

last: Rutledge

first: Lauranell

last: Burch

last: Schwartz


title: A tri-species Aspergillus array

status: Public on Feb 10 2008

city: Kgs. Lyngby

first: Mikael

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

sample_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

first: Wanwipa

last: Vongsangnak

first: Gianni

last: Panagiotou

first: Margarita

last: Salazar

first: Linda

last: Lehmann

first: Jens

last: Nielsen


title: Histone H3 lysine 9 (H3K9) acetylation and RNA mapping in MCF-7 human breast cancer cells

status: Public on Feb 08 2008

first: Takahiro

last: Suzuki

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

type: Expression profiling by genome tiling array


title: Mycobacterium tuberculosis targets DC-SIGN for immunosuppression through the PD-1/PD-Ligand pathway

status: Public on Feb 01 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
The inhibitory axis of PD-1 expressed on T cells and its ligands produced by APCs mediates T cell exhaustion in chronic viral infection. We asked whether temporality of the infectious process is decisive for regulation through PD-1/PD-Ligand and investigated its impact on chronic bacterial infection. Here we show that M. tuberculosis and its lipid compounds induce expression of PD-Ligand on dendritic cells (DC). Upregulation of PD-Ligand depended on signaling through DC-SIGN upon infection. As a counterpart, expression of the PD-1 receptor was increased on T cells from tuberculosis patients and PPD+ donors compared to healthy normal individuals. Moreover, PD-1 expressing T cells were confined to granulomatous lesions in tuberculous lungs. Finally, functional blocking of PD-Ligand rescued antigen-specific T cell responses of tuberculosis patients. Taken together, we demonstrate that the inhibitory axis of PD-1/PD-Ligand is operative in mycobacterial infection and suggest inhibition of inhibition for rescuing exhausted T cells in tuberculosis.
Keywords: Agilent two-color catolog 44K human whole genome microarrays

overall_design: Human PBMC-derived DCs were grown in 6-well plates and stimulated for 18 h with either mycobacterial ManLAM or recombinantly expressed ICAM-3. To ensure complete naïve status of DCs before stimulation, cells were left in wells from the day of PBMC isolation until end of stimulation. Change of medium was performed by carefully removing medium from wells without any manipulation of DCs. After stimulation, total RNA was isolated as described above and labeled with Fluorescent Direct Labeling Kit (Agilent Technologies) following manufacturer’s protocols. Microarray experiments were performed as two-color dye-reversal hybridizations. To compensate for dye-specific effects, a color swap was performed. Labeled RNA was hybridized on Whole Human Genome Oligo Microarray Kit 44k Format and scanned using an Agilent scanner according to manufacturer’s protocol (Agilent Technologies). Image analysis was performed using Feature Extractor software (Agilent Technologies). For data analysis Rosetta Resolver software was used (Rosetta Inpharmatics).

first: Florian

last: Winau

first: Guido

last: Hegasy

first: Stefan

last: Kaufmann

first: Tracey

last: Walker


title: Human Breast Cancer Cell Lines: Control vs. Fn14 or Luciferase siRNA Treated

city: Phoenix

first: Heather

middle: E

last: Cunliffe

state: AZ

address: 445 N 5th Street

department: Cancer and Cell Biology

country: USA

institute: Translational Genomics Research Institute

summary:
We performed gene expression profiling on the MDA-MB-231 and MDA-MB-436 human breast cancer cell lines following siRNA-mediated inhibition of Fn14 expression as an approach to identify the mechanistic basis for Fn14 regulation of invasive capacity.
Keywords: siRNA-mediated inhibition

overall_design: Each cell lines was transfected with etiher an Fn14 or firefly luciferase-specific (GL2) siRNA, with untreated cells used as a reference. 2 biological replicates were performed for each array, independently grown, treated and harvested.

first: Amanda

middle: L

last: Willis


title: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

sample_organism: Xanthomonas oryzae pv. oryzae KACC 10331


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

status: Public on Feb 12 2008

first: Xinyu

last: Wang

state: TX

institute: US Army Institute of Surgical Research

first: Phillip

middle: D

last: Bowman


title: Adult cardiomyocytes treated with fractalkine (CX3CL1)

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. We have identified fractalkine as a possible novel mediator in HF development. To address this issue, we have performed microarray analysis of cardiomyocytes treated with different isoforms of fractalkine.
Methods: Cardiomyocytes isolated from adult rat hearts and treated with different forms of fractalkine for 24 hours. Control cells were treated with BSA. Molecular alterations in myocardial tissue were measured by using cDNA microarrays. Molecular pathways affected were identified by the Ingenuity Pathway Analysis software.
Results: Several molecular pathways were affected upon fractalkine stimulation of adult cardiomyocytes.
Keywords: Fractalkines effect on cardiomyocytes

overall_design: Cardiomyocytes isolated from adult rat hearts at three different timepoints. Five fractalkine treated samples and five control samples were pairwise analyzed. The cells were from three different isolations. Treated and untreated cells from the same isolation were compared on each microarray.

first: Geir

last: Christensen

first: Ståle

last: Nygård


title: Identifying targets of Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells

status: Public on Feb 11 2008

city: Urbana

first: jun

last: cai

state: IL

address: Springfield Ave, DCL

institute: UIUC


title: Azaspiracid exposure to lymphocyte T cells

first: Mike

last: Twiner

summary: Human lymphocyte T cells in vitro were exposed to azaspiracid (1 or 10 nM) for 1, 4, or 24 hours.  Time matched controls (methanol 0.1% v/v) was used.

overall_design: RNA was extracted and gene expression changes observed using Agilents whole genome array.  n =2 at 1 hr and n = 3 at 4 and 24 hr.  At least one array from each time point utilized a dye swap.

first: Michael

middle: J

first: James

last: Ryan

first: Greg

last: Doucette


title: A systems approach to delineate functions of YAP family members

status: Public on Feb 04 2008

city: La Jolla

first: Kai

last: Tan

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary:
Duplication of genes encoding transcription factors plays an essential role in driving phenotypic variation.
Because regulation can occur at multiple levels, it is often difficult to discern how each duplicated factor achieves its regulatory specificity.
In these cases, a systems approach may distinguish the role of each factor by integrating complementary large-scale measurements of the regulatory network.
To explore such an approach, we integrate growth phenotypes, promoter binding profiles, and gene expression patterns to model the DNA damage response network controlled by the Yeast-specific AP-1 (YAP) family of transcription factors.
This analysis reveals that YAP regulatory specificity is achieved by at least three mechanisms: (a) Divergence of DNA-binding sequences into two subfamilies; (b) Condition-specific combinatorial regulation by multiple Yap factors; and (c) Interactions of Yap 1, 4, and 6 with chromatin remodeling proteins.
Additional microarray experiments establish that Yap4 and 6 regulate gene expression through interactions with the histone deacetylase, Hda1.
The data further highlight differences among Yap paralogs in terms of their regulatory mode of action (activation vs. repression).
This study suggests how other large TF families might be disentangled in the future.
Keywords: gene expression microarray and ChIP-chip

overall_design: Gene expression of wild type and single YAP deletion (YAP1/2/4/5/6) strains were profiled in media supplemented with either MMS or CDDP at two different concentrations. ChIP-chip of five YAPs (YAP1/2/4/6/6) were done in duplicate in both drug-treated (MMS or CDDP) or untreated (SC media) conditions.

first: Hoda

last: Feizi

first: Colin

last: Luo

first: Stephanie

last: Fan

first: Timothy

last: Ravasi

first: Trey

last: Ideker