title: Investigation of archived formalin-fixed paraffin-embedded (FFPE) pancreatic tissue with whole-genome gene expression microarray.

status: Public on Sep 30 2012

city: Odense C

first: Nete

middle: Vinstrup

last: Michelsen

address: Sdr Boulevard 29

department: Dept of Clinical Genetics

institute: Odense University Hospital

summary: In recent years, the use of FFPE tissue in gene expression microarray (GEM) studies has become a topic of increased interest, because pathology departments worldwide contain an invaluable source of biological disease-specific FFPE- tissue material. Thus far, some published studies on FFPE tissue consider the processed tissue amenable, whereas other studies assert that the tissue is not useful in GEM.  In general, pancreatic tissue is known to contain large amounts of nucleases, leading to high turnover rates and degradation of RNA in the tissue. This characteristic, in combination with FFPE processing time and its effect on the tissue, does not make FFPE pancreatic tissue the obvious choice for GEM. The basis for using FFPE pancreatic tissue in RNA-based assays seems suboptimal.   Previous GEM studies have used different FFPE tissue types, but GEM studies on FFPE pancreatic tissue have not been published. In most studies, the tissue was specially processed for use with GEMs. Here we demonstrate the usefulness of randomly archived FFPE pancreatic tissues for GEMs. For this purpose we included FFPE pancreatic tissue from patients with congenital hyperinsulinism or insulinoma; In these patients, pancreas resection is performed when medical treatment is not adequate to prevent hyperinsulinemic hypoglycemia or when patients do not respond to medical treatment.  Although ribonuclease-rich, we obtained biologically relevant and disease-specific, significant genes; cancer-related genes and genes involved in a) the regulation of insulin secretion and synthesis, b) amino acid metabolism, and c) calcium ion homeostasis. This application may extend the possibilities of gene expression studies to many tissue types, especially in rare diseases, for which fresh frozen tissue is not readily available.

overall_design: A total of 15 samples were included in this study using a 58K chip. 29,134 human 60mer oligonucleotide targets were arrayed on the chips in duplicates. Each chip is hybridized with sample material (labelled with Cy5) from one patient and reference material (labelled with Cy3). Reference material contains pooled RNA from four different cancer cell lines; HeLa (cervical epithelium), SK-BR-3 (mammary gland), HT29 (colon) and A431 (skin) cells. Seven patients with congenital hyperinsulinism (five FFPE  and two frozen samples), one patient with insulinoma and five controls were included in the study. Inclusion criteria for controls was that their cause of death was not pancreas-related. Samples were obtained from archived FFPE pancreatic material. The insulinoma sample was included in the study, because the biopsy was originally divided with one part being frozen and the other part being routinely formalin-fixed and paraffin-embedded. In the study we therefore include a frozen insulinoma sample and a FFPE insulinoma sample that was processed in duplicate.

first: Klaus

last: Brusgaard

first: Qihua

last: Tan

first: Mads

last: Thomassen

first: Khalid

last: Hussain

first: Henrik

last: Christesen


title: Differential gene expression analysis of U87MG EGFRvA cells vs. U87MG EGFR cells

city: Shanghai

first: Min

last: Zhou

address: No.25/Ln2200, XieTu Road

country: China

institute: Medical School of Shanghai Jiao Tong University

summary: EGFRvA is a novel and widely-expressed EGFR isoform, whose upregulation is positively related to glioma grades. Intriguingly, it is the upregulation of EGFRvA but not EGFR that significantly correlates with a poor prognosis in glioma patients. Cancer cells expressing EGFRvA (relative to EGFR) display a higher invasive capacity and a lower sensitivity to EGFR tyrosine kinase inhibitors (TKIs). To investigate the significant differently expressed genes between U87MG EGFRvA cells and U87MG EGFR cells，microarray experiments were conducted.

overall_design: Gene-expression profiling was performed on the CapitalBio 35k human Genome Array microchips (Beijing, China).

first: Zonghai

last: Li


title: Tobacco smoke exposure-related pathway gene expression signature in the bronchial airway epithelium

status: Public on Sep 27 2012

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

country: USA

institute: Boston University Medical Center

summary:
Using primary human bronchial epithelial cells collected at bronchoscopy, we have perturbed signaling pathways important in regulation of response to tobacco smoke exposure and cancer development: ATM, BCL2, GPX1, NOS2, IKBKB, and SIRT1
Using gene expression profiles generated for each pathway and four independent gene expression datasets, we show that SIRT1 activity is significantly up-regulated in cytologically normal airway epithelial cells from active smokers compared to non-smokers; and in contrast, this activity is strikingly down-regulated in non-small cell lung cancer.

overall_design: 52 samples were run on Affymetrix Human Exon 1.0 ST microarrays (n=7 for ATM, n=8 for GPX1, n=7 for SIRT1, n=7 for NOS2, n=7 for IKBKB, n=8 for BCL2, and n=8 for GFP).  The CEL files were processed using RMA and the ENTREZ Gene CDF file. 13 samples were removed either because of a low Pearson correlation between samples (n=1 SIRT1 sample) or a strong batch effect (n=2 ATM, n=2 BCL2, n=2 GFP, n=2 GPX1, n=1 IKBKB, n=2 NOS2, n=1 SIRT1 samples) as determined by PCA.

first: Jennifer

last: Beane

first: Andrea

last: Bild


title: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray)

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: FUS/TLS and TDP-43 are RNA/DNA-binding proteins integrally involved in amyotrophic lateral sclerosis (ALS) and frontal temporal dementia. FUS/TLS is shown to bind RNAs from >5,500 genes in mouse and human brain, primarily through a GUGGU binding motif. A characteristic sawtooth-like binding pattern is identified, supporting co-transcriptional deposition of FUS/TLS. Depletion of FUS/TLS from the adult nervous system is shown to alter levels or splicing of >970 mRNAs, most of which are distinct from the RNAs whose maturation is dependent on TDP-43. Nonetheless, only 55 RNAs are reduced upon depletion of either TDP-43 or FUS/TLS from mouse brain and human neurons differentiated from pluripotent stem cells, including mRNAs transcribed from genes with exceptionally long introns and that encode proteins essential for neuronal integrity. A subset of these is significantly lowered in FUS/TLSR521G and TDP-43G298S mutant fibroblasts and in TDP-43 aggregate-containing motor neurons in sporadic ALS, evidence pointing to a common loss-of-function pathway as one component underlying motor neuron death from misregulation of TDP-43 or FUS/TLS.

overall_design:
Microarray of Fus/Tls in 8 week mouse brain

*Addendum
Depending on the analysis software used, these CEL files may not load correctly using default parameters. This is due to the custom chip type of MJAY not being used during the array scanning step. There are three workarounds known for this problem so far.
1) If using APT, use multiple --chip-type parameters. Specifically, --chip-type mjay --chip-type MJAY --chip-type MoEx-1_0-st-v1.1sq
2) Edit the CEL file by converting to text using the APT command apt-cel-convert, then replacing the MoEx-1_0-st-v1.1sq in the DatHeader line with MJAY (all caps).
3) Edit the .pgf, .clf, and antigenomics.bmp files to use the MoEx-1_0-st-v1.1sq array instead of MJAY for the chip_type and lib_set_name options. (works on AltAnalyze software)

middle: W

first: Don

last: Cleveland


title: SH-SY5Y cells: DMSO vs. clioquinol

status: Public on Oct 01 2012

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Transcriptional profiling of human SH-SY5Y neuroblastoma cells comparing DMSO-treated control cells with those treated with 50 microM clioquinol (CQ) for 24 h.

overall_design: Two-condition experiment, DMSO vs. CQ . Biological replicates: 1DMSO, 1 CQ. One replicate per array.

first: Masato

last: Katsuyama


title: Complement C3 deposition on nucleic acids is characteristic of immune complex initiated classical pathway overdrive in lupus erythematosus

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

summary: Systemic lupus erythematosus is progressive, immune complex-mediated autoimmune disease targeting numerous organs. A central feature of the disease is the development of antibodies against nuclear components, including DNA. Antibodies against double-stranded DNA are so characteristic of this disease that their detection constitutes one of the criteria for diagnosis. We examined the formation of immune complexes on the surface of autoantigen microarrays incubated in the sera of 39 inactive and 22 active lupus patients and of 31 control subjects. Three different kinds of nucleic acids, dsDNA, ssDNA and RNA were used as antigens, along with chromatin (nucleosomal extract) and several other reference molecules. The composition with respect to IgG, IgM and complement components C3 and C4 was determined. We find that while IgM and C4 are physiological components of immune complexes formed from nucleic acids, both IgG and C3 are extremely characteristic of lupus patients. Complement C4 deposition changes were not consistent: these increased on ssDNA and RNA, decreased on chromatin and did not change significantly on dsDNA. The presence of IgG and C3 in the immune complexes formed from different nucleic acids was characteristic for both active and inactive lupus patients. Receiver-operating curve statistics indicate that C3 deposition measurements can improve the efficiency of identification of inactive lupus patients. These observations reveal the complexity of immune profile changes accompanying SLE.

platform_organism:
Homo sapiens
Sus scrofa
Bos taurus
Capra hircus
Oryctolagus cuniculus

overall_design: C3, IgM, C4 and IgG binding in 92 human serum samples were examined using custom-made protein arrays

first: Péter

last: Végh

first: Zoltán

last: Szittner

first: László

last: Czirják

first: Renáta

last: Hóbor

last: Korányi

first: József

last: Prechl


title: Genome-wide profiling of methylation identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes.

status: Public on Sep 28 2012

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events [array component]

status: Public on Sep 26 2012

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and 3 lung tumor/normal pairs (provisional dbGaP accession number; phs000299.v2.p1). Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers.

overall_design: Nineteen non-small cell lung cancer cell lines were assayed for genotype, copy number and LOH using Illumina Omni2.5-4 arrays, GenomeStudio V2011.1, and a modified version of the PICNIC (PMID 19837654) algorithm.

first: Jinfeng

last: Liu

first: William

last: Lee

first: Zhongqiang

last: Chen

first: Zhaoshi

last: Jiang

first: Suchit

last: Jhunjhunwala

middle: M

first: Florian

last: Gnad

first: Yinghui

last: Guan

first: Houston

last: Gilbert

first: Jeremy

last: Stinson

first: Christiaan

last: Klijn

first: Joseph

last: Guillory

first: Deepali

last: Bhatt

first: Steffan

last: Vartanian

first: Kim

last: Walter

first: Jocelyn

last: Chan

last: Dijkgraaf

first: Stephanie

last: Johnson

first: Julie

last: Koeman

first: Adi

last: Gazdar

first: Howard

last: Stern

first: Klaus

middle: P

last: Hoeflich

first: Thomas

middle: D

last: Wu

first: Frederic

middle: J

last: de Sauvage

first: Robert

middle: C

last: Gentleman

first: Richard

last: Neve

first: David

last: Stokoe

first: Zora

last: Modrusan

first: Somasekar

last: Seshagiri

middle: S

last: Shames

first: Zemin

last: Zhang


title: Expression profiling of Low-Risk Myelodysplastic Syndromes (MDSs)

status: Public on Sep 25 2012

first: Javier

last: De Las Rivas

summary:
Genome-wide expression and methylation profiling identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes (MDSs).
Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. Gene expression and methylation status were measured using high-density microarrays. A total of 552 differentially methylated CpG loci were identified as being present in low-risk MDS; hypermethylated genes were more frequent than hypomethylated genes. In addition, mRNA expression profiling identified 1005 genes that significantly differed between low-risk MDS and the control group. Integrative analysis of the epigenetic and expression profiles revealed that 66.7% of the hypermethylated genes were underexpressed in low-risk MDS cases. Gene network analysis revealed molecular mechanisms associated with the low-risk MDS group, including altered apoptosis pathways. The two key apoptotic genes BCL2 and ETS1 were identified as silenced genes. In addition, the immune response and micro RNA biogenesis were affected by the hypermethylation and underexpression of IL27RA and DICER1. Our integrative analysis revealed that aberrant epigenetic regulation is a hallmark of low-risk MDS patients and could have a central role in these diseases.

overall_design: Low-risk MDS patients and age-matched controls without haematological malignancies were included in the study. Mononuclear cells were isolated from bone marrow samples of low-risk MDS patients and controls by density gradient (Ficoll). A cohort of 18 patients with low-risk MDS and seven controls were included in a simultaneous integrative study of methylation (using Methylated CpG Island Amplification and Microarrays, MCAM) and expression (using Affymetrix microarrays HG-U133 Plus 2), while the whole series was used as a control group of expression data.

first: Monica

last: Del Rey

first: Kathleen

last: O’Hagan

first: Margaret

last: Dellett

first: Sara

last: Aibar

first: Hilary

middle: A

last: Colyer

first: MariaEugenia

last: Alonso

first: Maria

last: Diez-Campelo

middle: N

last: Armstrong

first: Daniel

last: Sharpe

first: Norma

last: Gutierrez

first: JuanLuis

last: García

last: DeLasRivas

first: Ken

middle: I

last: Mills

first: Jesus

last: Hernández-Rivas


title: Identification of an intrahepatic transcriptional signature associated with self-limiting infection in the woodchuck model of hepatitis B

status: Public on Sep 22 2012

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

summary: The woodchuck model of hepatitis B virus (HBV) infection displays many characteristics of human infection and has particular value for characterizing the host immune responses during the development of chronic infection. Using the newly developed custom woodchuck microarray platform, we compared the intrahepatic transcriptional responses of neonatal woodchucks with self-limiting and progressing persistent infection with woodchuck hepatitis virus (WHV). This revealed that WHV does not induce intrahepatic gene expression during the early acute stage of infection (8 weeks), suggesting it is a “stealth” virus. At the mid-acute phase of infection (14 weeks), resolution was associated with induction of a prominent cytotoxic T cell signature, with perforin and other markers of immune-mediated cytotolytic response being strongly expressed. Strikingly, this was accompanied by high level expression of PD-1 and various other inhibitory T cell receptors, which likely act to minimize liver damage by cytotoxic T cells during viral clearance. Conversely, self-limiting infection was not associated with a strong interferon-α/β (IFN-α/β) transcriptional response, while the IFN-γ signaling response (as measured by expression of CXCL9) in the mid-acute phase was comparable to that in chronically infected adult animals. Nevertheless, viperin and other antiviral genes were differentially expressed during resolving infection, suggesting that a subset of interferon-stimulated genes (ISGs) may play a role in the control of WHV replication. Conclusion: This study identifies new immune pathways associated with the clearance of hepadnavirus infection and reveals novel targets with potential for the treatment of chronic hepatitis B.

overall_design: Neonatal woodchucks of both genders were infected at 3 days of age with the same WHV7P1 inoculum containing 5 x 106 WID50 of WHV strain WHV7-11. Custom microarrays were generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, and were used to examine liver gene expression in animals which eventually become chronically infected with WHV (8 weeks, n=5; 14 weeks, n=9), animals that  eventually resolve WHV infection (8 weeks, n=10;14 weeks, n=7) and uninfected animals (8 weeks, n=5;14 weeks,n=5).

first: Simon

last: Fletcher

last: Chin

middle: T

first: Palanikumar

last: Ravindran

first: Hans

last: Bitter

first: Lore

last: Gruenbaum

first: Paul

last: Cote

first: Han

last: Ma

first: Klaus

last: Klumpp

first: Stephan

last: Menne


title: A Short-Term Study Investigating the Estrogenic Potency of Diethylstilbesterol in the Fathead Minnow (Pimephales promelas): Recovery phase

status: Public on Sep 20 2012

city: Duluth

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

summary:
Diethylstilbestrol (DES) is a synthetic estrogen that has been banned for use in humans, but still is employed in livestock and aquaculture operations in some parts of the world.  Detectable concentrations of DES in effluent and surface waters have been reported to range from slightly below 1 to greater than 10 ng/L.  Little is known, however, concerning the toxicological potency of DES in fish.  In this study, sexually-mature fathead minnows (Pimephales promelas) of both sexes were exposed to 1, 10 or 100 ng DES/L water in a flow-through system.  Tissue concentrations of DES and changes in a number of estrogen-responsive endpoints, including alterations to the hepatic transcriptome in females, were measured in the fish at the end of a 4-d exposure, and after a 4-d depuration/recovery period in clean water. The objectives of the study were to measure accumulation of DES in fish tissues, characterize effects of the chemical on physiological endpoints related to reproductive performance, and to evaluate DES's potency relative to concentrations reported in aquatic environments.
The current series includes n=11 microarrays associated with recovery-phase samples (collected from fish exposed continuously for 4 d, and then held in control water for an additional 4 days before tissues were collected).

overall_design: Fish were exposed to 0, 1, 10, or 100 ng DES/L delivered in a continuous flow (45 ml/min) of sand filtered, UV treated, Lake Superior Water, without the use of carrier solvents. Flow of DES into the test system was initiated without fish present and continued for 1 d.  Exposures then were started by placing three male and three female sexually-mature fathead minnows into each tank. There were eight replicate tanks for the control and 100 ng/L treatments, and six replicate tanks for the 1 and 10 ng/L groups.  The fish were held at 25+1ºC under a 16:8 L:D photoperiod and were fed frozen adult brine shrimp twice daily (San Francisco Bay Brand, Newark, CA, USA).  Fish used for the experiment were from an on-site culture, and all procedures involving animals conformed to guidelines approved by the local Animal Care and Use Committee. After the 4-d exposure, fish from three tanks from each treatment (n=9 per sex) were sampled for determination of various biological endpoints.  At this time fish from two additional tanks from the control and 100 ng/L treatments also were sampled for determination of DES tissue residues (n=6 per sex).  Delivery of DES to the test system was subsequently stopped, and fish from the remaining three tanks per treatment group were sampled 4 d later (n= 9 per sex). The fathead minnows were euthanized with buffered MS-222 (Argent, Redmond, VA, USA) and weighed.  Fish were scored for occurrence and relative expression of nuptial tubercles, which in males can be reduced by ER agonists.  Blood was collected from the caudal vein/artery with a microhematocrit tube, and plasma was separated by centrifugation and stored at -80ºC.  Gonads were removed from males and a subsample (8.5±3.0 mg; mean±SD) was immediately immersed in tissue culture media for determination of ex vivo steroid production. Livers were removed from both sexes and flash-frozen for gene expression analyses using microarray (females) or real-time QPCR (males). Hepatic transcripts from three females per treatment group, in each phase of the experiment (except n=2 from recovery phase 10 ng/L) were analyzed using a custom 15,000 feature microarray (GEO Platform Accession GPL9248). Data sets for the exposure phase (n=12 microarrays) and recovery phase (n=11) were normalized independently using Fastlo (Ballman et al., 2004) implemented in R (http://www.r-project.org/), but analyzed using parallel approaches.

middle: L

first: Natalia

last: Garcia-Reyero

first: Olufemi

middle: B

last: Adedeji

first: Elizabeth

last: Durhan

first: Michael

last: Kahl

first: Kathleen

last: Jensen

first: Carlie

last: LaLone

last: Makynen

first: Edward

last: Perkins

first: Linnea

last: Thomas

first: Gerald

last: Ankley


title: A Short-Term Study Investigating the Estrogenic Potency of Diethylstilbesterol in the Fathead Minnow (Pimephales promelas): Exposure Phase

first: Daniel

summary:
Diethylstilbestrol (DES) is a synthetic estrogen that has been banned for use in humans, but still is employed in livestock and aquaculture operations in some parts of the world.  Detectable concentrations of DES in effluent and surface waters have been reported to range from slightly below 1 to greater than 10 ng/L.  Little is known, however, concerning the toxicological potency of DES in fish.  In this study, sexually-mature fathead minnows (Pimephales promelas) of both sexes were exposed to 1, 10 or 100 ng DES/L water in a flow-through system.  Tissue concentrations of DES and changes in a number of estrogen-responsive endpoints, including alterations to the hepatic transcriptome in females, were measured in the fish at the end of a 4-d exposure, and after a 4-d depuration/recovery period in clean water. The objectives of the study were to measure accumulation of DES in fish tissues, characterize effects of the chemical on physiological endpoints related to reproductive performance, and to evaluate DES's potency relative to concentrations reported in aquatic environments.
The current series includes n=12 microarrays associated with exposure-phase samples (collected from fish exposed continuously for 4 d).


title: A radiation-induced gene expression signature as a tool to predict acute radiotherapy-induced adverse side effects

status: Public on Sep 06 2012

city: Heidelberg

first: Peter

last: Schmezer

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: The majority of patients tolerate radiotherapy well, but some of them suffer from severe side effects. To find genes possibly predictive for radiosensitivity, mRNA profiles were generated before and 6 h after in vitro irradiation with 5 Gy. We analyzed lymphocytes from four head and neck and eight breast cancer patients with strong acute radiation toxicity and from 12 matching normal reacting patients in a blind study. In peripheral blood lymphocytes of all patients, 153 genes were identified which were statistically significantly altered by a fold change of more than 50% by irradiation. Pathway analysis revealed genes involved in p53 signalling, cell cycle control and apoptosis in response to radiation in primary lymphocytes. In these cells, a set of 67 radiation-induced genes was identified capable of differentiating between severe radiosensitive and normal reacting patients. More than one third of such classifying genes belong to the group of apoptosis or cell cycle regulating genes.

overall_design: Total RNA obtained from lymphocytes of cancer patients with strong acute radiation toxicity and from matching normal reacting patients were compared 6 hours after in vitro irradiation with 5 Gy.

first: Odilia

last: Popanda


title: A Short-Term Study Investigating the Estrogenic Potency of Diethylstilbesterol in the Fathead Minnow


title: Mapping of the HUWE1 duplication at Xp11.22 in eight unrelated XLID patients

status: Public on Sep 03 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

type: Genome variation profiling by genome tiling array

summary: In a study to elucidate the genetic defects in patients with X-linked intellectual disability (XLID) we performed X chromosome-specific BAC-array-CGH and identified 0.33 to 1.0 Mb nonrecurrent copy number gains at Xp11.22 in affected males of unrelated XLID families. All aberrations segregate with the disease in the families and the carrier mothers show a nonrandom X-inactivation. Affected males suffered from mild to moderate ID. Tiling Xp11.22 region-specific oligo-array (ChrX:52.50 - 54.50 Mb) revealed that all aberrations had different start and stop sites. The twofold copy number gain included up to 20 genes but only the HUWE1 gene is located in the minimal common region of overlap in these  families. Moreover, expression analysis revealed about twofold increased HUWE1 mRNA levels in affected patients when compared to control individuals. Breakpoint analysis revealed Non-homologous end-joining (4 cases), serial replication slippage (1 case) and non-allelic homologous recmbination (one case) as the potential recombination mechanism.

overall_design: For duplication mapping and exact copy number analysis in all four families, differentially-labeled patient versus male control DNA samples were hybridized onto a custom designed 4x44k oligo-array (Agilent Technologies) that covers the repeat-masked region 52.50 Mb to 54.50 Mb at tiling resolution.

first: Joke

last: Vandewalle

first: Matthias

last: Declercq

first: Karen

last: Govaerts

first: Francisco

last: Martinez

first: Sonia

last: Mayo

first: Monica

last: Rosello

first: Annabel

last: Whibley

first: Lucy

last: Raymond

first: Siren

last: Berland

first: Randi

last: Hovland

first: Tulika

last: Bose

first: Leslie

last: Sheffield

first: Mark

last: Corbett

first: Stefanie

last: Belet

first: Jelle

last: Verbeeck

last: Marynen

first: Guy

last: Froyen


title: Gene expression analysis of granulosa cells from Fzd1 WT and KO mice

status: Public on Sep 01 2012

city: Saint-Hyacinthe

first: Derek

last: Boerboom

address: 3200 rue Sicotte

country: Canada

institute: Centre de recherche en reproduction animale

summary: WNT4 is required for normal ovarian follicle development and female fertility in mice, but how its signal is transduced remains unknown.  Fzd1 encodes a WNT receptor whose expression is markedly induced in both mural granulosa cells and cumulus cells during the preovulatory period, in a manner similar to Wnt4.  To study the physiological roles of FZD1 in ovarian physiology and to determine if it serves as receptor for WNT4, Fzd1-null mice were created by gene targeting.  Whereas rare Fzd1-/- females were sterile due to uterine fibrosis and ovarian tubulostromal hyperplasia, the majority were subfertile, producing ≈1 less pup per litter on average relative to controls.  Unlike WNT4-deficient mice, ovaries from Fzd1-/- mice had normal weights, numbers of follicles, steroid hormone production and WNT4 target gene expression levels.  Microarray analyses of granulosa cells from periovulatory follicles revealed few genes whose expression was altered in Fzd1-/- mice.  However, gene expression analyses of cumulus-oocyte complexes (COCs) revealed a blunted response of both oocyte (Zp3, Dppa3, Nlrp5, Bmp15) and cumulus (Btc, Ptgs2, Sema3a, Ptx3, Il6, Nts, Alcam, Cspg2) genes to the ovulatory signal, whereas the expression of these genes was not altered in WNT4-deficient COCs from Wnt4tm1.1Boer/tm1.1Boer;Tg(CYP19A1-cre)1Jri mice.  Despite altered gene expression, cumulus expansion appeared normal in Fzd1-/- COCs both in vitro and in vivo.  Together, these results indicate that Fzd1 is required for normal female fertility and may act in part to regulate oocyte maturation and cumulus cell function, but is unlikely to function as the sole ovarian WNT4 receptor.

overall_design: Triplicate RNA samples from granulosa cells of Fzd1 KO mice are compared to triplicate RNA samples from granulosa cells of control Fzd1 WT mice

first: Alexandre

last: Boyer

first: Charlène

last: Ricco

first: Marilène

last: Paquet

first: Heather

last: Franco

first: Jan

last: Gossen

first: Francesco

last: DeMayo

first: JoAnne

last: Richards


title: Deregulated sex chromosome gene expression with male germ cell-specific loss of Dicer1

status: Public on Sep 10 2012

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

type:
Expression profiling by array
Non-coding RNA profiling by array


title: A non-coding mutation implicates HCFC1 in non-syndromic intellectual disability

city: Adelaide

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

summary: Human disease mutation discovery has so far been biased towards protein coding regions. Having excluded all annotated coding regions, we performed targeted massively parallel re-sequencing of the non-repetitive genomic linkage interval of the MRX3 family at Xq28. We identified a regulatory mutation in the YY1 transcription factor binding site, which leads to overexpression of the chromatin-associated transcriptional regulator, HCFC1. When tested on embryonic murine neural stem cells (NSCs) and embryonic hippocampal neurons, HCFC1 overexpression led to a significant increase of the production of astrocytes and considerable reduction in neurite growth. Two other non-synonymous, potentially deleterious changes have been identified by X-exome sequencing in individuals with intellectual disability, implicating HCFC1 in normal brain function.

overall_design: Total RNA was extracted from LCL derived from four unrelated male controls, five unrelated female controls and two affected male cousins from the MRX3 family.

first: Lingli

last: Huang

first: Lachlan

last: Jolly

first: Saffron

last: Willis-Owen

first: Alison

last: Gardner

first: Raman

last: Kumar

first: Evelyn

last: Douglas

first: Cheryl

last: Shoubridge

first: Dagmar

last: Wieczorek

first: Andreas

last: Tzschach

first: Monika

last: Cohen

first: Anna

last: Hackett

first: Michael

last: Field

first: Hao

last: Hu

first: Stefan

last: Haas

first: Hans-Hilger

last: Ropers

first: Vera

last: Kalscheuer

first: Jozef

last: Gecz


title: Identification of copy number alterations associated with the progression of DCIS to Invasive Ductal Carcinoma

status: Public on Sep 04 2012

city: East Melbourne

first: Kylie

last: Gorringe

state: Victoria

address: St Andrew's Pl

department: Research Division

institute: Peter MacCallum Cancer Centre

summary: Ductal carcinoma in situ (DCIS) is a non-obligate precursor to invasive ductal carcinoma (IDC).  Annotation of the genetic differences between the two lesions may assist in the identification of genes that promote the invasive phenotype. Matched IDC and DCIS showed highly similar copy number profiles (average of 83% of the genome shared) indicating a common clonal orgin although there is evidence that the DCIS continues to evolve in parallel with the co-existing IDC. Four chromosomal regions of loss (3q, 6q, 8p and 11q) and four regions of gain (5q, 16p, 19q and 20) were recurrently affected in IDC but not in DCIS. CCND1 and MYC showed increased amplitude of gain in IDC. One region of loss (17p11.2) was specific to DCIS.

overall_design: 21 cases of synchronous DCIS and IDC were microdissected from FFPE tissue and analysed by molecular inversion probe (MIP) copy number arrays. The arrays were early release OncoScan arrays and the data in this submission are CN values for the ~300,000 probes common to two batches performed. Raw data is retained by Affymetrix.

first: Ella

middle: R

last: Thompson


title: TGF-beta/Smad3-dependent gene expression analysis in naive CD4 T cells

status: Public on Aug 31 2012

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Qc

address: 5415 de L'Assomption

institute: CR-HMR

summary: Investigation of transcript level modulation in unstimulated and TGF-beta treated (with or without superimposed T-cell receptor and CD28 stimulation) naive CD4 T cells from wild type or Smad3-deficient littermate mice. Smad3 is a critical signaling molecule and transcription factor downstream of TGF-beta and mediates several of the TGF-beta dependent tolerogenic effects in T cells. This study was undertaken to unveil the transcriptionnal program controled by the TGF-b/Smad3 axis.

overall_design: Microarray study using RNA recovered after 6 hours of culture in either serum free media, serum-free media + TGF-beta (2.5ng/ml) or serum-free media + TGF-beta and anti-CD3e and anti-CD28 stimulation (3 conditions). Naive CD4 T cells (TCRb+, CD4+, CD62L+ and CD44-) were sorted from either wild type or Smad3 deficient littermates and submitted to the 3 culture conditions. Three biological replicates were obtained (each from at least 2 different mice). Thus a total of 18 Nimblegen 365K chip were used.

first: Martin

last: Giroux

first: Claude

last: Perreault

first: Genevieve

last: Boucher

first: Josette-Renée

last: Landry


title: Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region

status: Public on Aug 30 2012

city: Cambridge

first: Ben

last: Skinner

address: Tennis Court Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

summary:
Background
Sex chromosomes are subject to evolutionary pressures distinct from the remainder of the genome, shaping their structure and sequence content. We are interested in the sex chromosomes of domestic pigs (Sus scrofa), how their structure and gene content compares and contrasts with other mammalian species, and the role of gonosomal genes in fertility. This requires an understanding of the XY-homologous sequence on these chromosomes.

To this end, we performed microarray-based comparative genomic hybridisation (array-CGH) with male and female Duroc genomic DNA on a pig X-chromosome BAC tiling-path microarray. Putative XY-homologous BACs from regions of interest were subsequently FISH mapped.

Results
We show that the porcine PAR is approximately 6.5-6.9Mb at the beginning of the short arm of the X, with gene content reflective of the artiodactyl common ancestor. Our array-CGH data also shows an XY-homologous region close to the end of the X long arm, spanning three X BACs. These BACs were FISH mapped, and paint the entire long arm of SSCY. Further clones of interest revealed X-autosomal homology or regions containing repetitive content.

Conclusions
This study has identified regions of XY homology in the pig genome, and defined the boundary of the PAR on the X chromosome. This adds to our understanding of the evolution of the sex chromosomes in different mammalian lineages, and will prove valuable for future comparative genomic work in suids and for the construction and annotation of the genome sequence for the sex chromosomes. Our finding that the SSCYq repetitive content has corresponding sequence on the X chromosome gives further insight into structure of SSCY, and suggests further functionally important sequences remain to be discovered on the X and Y.

overall_design: Genomic DNA from male and female Duroc pigs were competitively hybridised to an X-chromosome BAC tiling-path microarray. Male DNA came from the animal used for Y chromosome sequencing at the Wellcome Trust Sanger Institute. Female DNA came from a fibroblast cell line. 4 hybridisations were performed. Clones with successful hybridisation in 2 or more of these replicates were used for analysis and detection of potential regions of XY homology.

first: Benjamin

first: Kim

last: Lachani

first: Carole

last: Sargent

first: Nabeel

last: Affara


title: Deregulated sex chromosome gene expression with male germ cell-specific loss of Dicer1 (gene array data)

first: Timothy

last: Stearns

summary: MicroRNAs (miRNAs) are a class of endogenous, non-coding RNAs that mediate post-transcriptional gene silencing by inhibiting mRNA translation and promoting mRNA decay. DICER1, an RNAse III endonuclease encoded by Dicer1, is required for processing short 21-22 nucleotide miRNAs from longer double-stranded RNA precursors. Here, we investigate the loss of Dicer1 in mouse postnatal male germ cells to determine how disruptions in the miRNA biogenesis pathway may contribute to infertility. Reduced levels of Dicer1 transcripts and DICER1 were confirmed in germ cell knock-out (GCKO) testes by postnatal day 18 (P18). Compared to wild-type (WT) at 8 weeks, GCKO males had no change in body weight, yet showed significant reductions in testis mass and sperm number. Histology and fertility tests confirmed spermatogenic failure in GCKO males. Array analyses at P18 showed 96% of miRNA genes were down-regulated and 37% of protein-coding genes were differentially expressed in GCKO testes. Interestingly, we observed preferential overexpression of genes on the sex chromosomes in GCKO testes, with more than 80% of the genes overlapping those proposed to undergo meiotic sex chromosome inactivation (MSCI) in the germ cells. Compared to WT, GCKO mice showed higher percentages of cells at early meiotic stages (leptotene and zygotene) but lower percentages at later stages (pachytene, diplotene and metaphase I), providing evidence that deletion of Dicer1 leads to disruptions in meiotic progression. Furthermore, we observed fewer elongating spermatids with proper translational activation of transition protein 2 (Tnp2), protamine 1 and 2 (Prm1 and Prm2) in GCKO testes after step 12-14. Therefore, deleting Dicer1 in early postnatal germ cells causes misregulation of transcripts encoded by genes on the sex chromosomes, impairs meiotic progression and post-meiotic translational control and results in spermatogenic failure and infertility.

overall_design: Total RNA, including miRNAs, were purified from a total of six individual mouse samples. The tissue collected was obtained from wild-type (control; n=3) and Dicer1 germ cell knockout (mutant; n=3) testes on P18.

first: Anne

last: Greenlee

first: Meng

last: Shiao

first: Elizabeth

last: Snyder

first: F

last: Buass

first: Tongjun

last: Gu

first: Manju

last: Sharma

last: Murchison

first: Gabriella

last: Puenta

first: Robert

middle: E

last: Braun


title: The expression of inflammatory genes in endothelial cells is inhibited by N-octanoyl dopamine via modulation of the NFkB pathway

city: Mannheim

first: Benito

last: Yard

address: Theodor-Kutzer-Ufer 1-3

institute: University hospital Mannheim

summary:
Background: Dopamine has intrinsic receptor-independent anti-inflammatory properties when used at high concentrations. Since cellular uptake of N-octanoyl dopamine (NOD) is far better than of dopamine, NOD might display anti-inflammatory effects already at relative low concentrations. The present study was conducted to assess the anti-inflammatory potential of NOD and to elucidate how this was mediated.

Methods: Human umbilical vein endothelial cells (HUVECs) were stimulated with TNF-α in the presence of various NOD concentrations. Affymetrix gene expression profiling (GEP), Western blotting, adhesion of peripheral blood mononuclear cells (PBMC) to endothelial cells and NFκB activation was studied. Compounds that were structurally related to NOD were used to address the molecular entities within NOD that were required for its anti-inflammatory properties.

Results: GEP revealed that NOD down-regulates a wide range of pro-inflammatory mediators. Down-regulation of adhesion molecules was confirmed at the protein level and resulted in a decreased adhesion of PBMC to endothelial cells under static and flow conditions. NOD inhibited NFκB independently of IκBα degradation. Inhibition was associated with an overall decrease in p65 expression and a significant decrease in p65 phosphorylation at Ser276. De novo protein synthesis was not required for inhibition and was not mediated via HO-1. Redox activity and hydrophobicity of NOD seemed to be important entities for its anti-inflammatory properties.

Conclusion: Our data demonstrate that NOD has potent anti-inflammatory effects through its action on NFκB. Unlike dopamine, NOD has no adverse effects on blood pressure, making it a promising candidate drug to reduce excessive inflammation occurring under various pathological conditions.

overall_design: A total of 6 different HUVEC lines were used, n=3 for each group (TNF or TNF+ NOD).

first: Maximilia

last: Hottenrott

first: Linda

last: Mandel

first: Tinejke

last: Kraaij

first: Johannes

last: Wedel

first: Claudia

last: Bergstraesser

first: Ralf

last: Lösel

first: Carsten

last: Sticht

first: Simone

last: Hoeger

first: Mathias

last: Hafner

first: Charalambos

last: Tsagogiorgas


title: INS1-EGFP-L10a stable cell lines treated with Thapsigargin

city: San Francisco

first: Feroz

last: Papa

address: 1700 4th Street

department: Medicine

institute: University of California, San Francisco

summary:
INS1-EGFP-L10a stable cell lines were induced with Doxycycline (Dox) for 24 hours, then either untreated or treated for 30 minutes with 1uM Thapsigargin to induce ER stress. Total RNA was purified with Trizol, and RIP RNA  samples were extracted by immunoaffinity purification using an EGFP antibody
We aimed to determine which genes are enriched under ER stress at the polyribosomal level. To do this we compared expression profiles of Total RNA with and without ER stress, and Immunoaffinity purified RNA (RIP) with and without ER stress. Microarray results of INS-1 EGFP-L10a cells either untreated or treated with 1uM Thapsigargin (Tg) in triplicate. Both Total RNA and RNA isolated from ribosomal Immunoprecipitation (RIP)
When unfolded proteins accumulate to irremediably high levels within the endoplasmic reticulum (ER), intracellular signaling pathways called the unfolded protein response (UPR) become hyperactivated to cause programmed cell death.  We discovered that thioredoxin-interacting protein (TXNIP) is a critical node in this “Terminal UPR”. TXNIP becomes rapidly induced by hyperactivated IRE1a, an ER bifunctional kinase/endoribonuclease (RNase). IRE1a controls TXNIP mRNA stability by reducing levels of a TXNIP destabilizing micro-RNA, miR-17. In turn, elevated TXNIP protein activates the NLRP3 inflammasome, causing Caspase-1 cleavage and interleukin 1b (IL-1b) secretion. Txnip gene deletion reduces pancreatic b-cell death during ER stress, and suppresses diabetes caused by proinsulin misfolding in the Akita mouse. Finally, small molecule IRE1a RNase inhibitors suppress TXNIP production to block IL-1b secretion. In summary, the IRE1a-TXNIP pathway is used in the terminal UPR to promote sterile inflammation and programmed cell death, and may be targeted to develop new treatments for degenerative diseases driven by ER stress.

overall_design: There are 12 samples total all in INS-1 EGFP L10a cells- 3 untreated total RNA (reference sample), 3 treated with 1uM Tg 30 min total RNA, 3 untreated RIP RNA (reference sample), 3 treated with 1uM for 30 min RIP RNA

first: Alana

middle: G

last: Lerner


title: Molecular alterations in prostate carcinomas that associate with in vivo exposure to chemotherapy

status: Public on Aug 29 2012

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Patients with high-risk localized prostate cancer (tumor-node-metastasis ≥ T2b or prostate-specific antigen ≥ 15 ng/mL or Gleason glade ≥ 4+3) were enrolled into a phase II clinical trial of neoadjuvant chemotherapy with docetaxel and mitoxantrone followed by prostatectomy. Pretreatment prostate tissue was acquired by needle biopsy and posttreatment tissue was acquired by prostatectomy. Prostate epithelium was captured by microdissection, and transcript levels were quantitated by cDNA microarray hybridization.

overall_design: To evaluate gene expression alterations after chemotherapy, neoplastic epithelium from pretreated biopsy and posttreated prostatectomy specimens were laser captured separately (∼3,000 cells per sample). cDNA synthesized from amplified total RNA of pre-treated biopsy samples and post-treatment surgical samples were hybridized head-to-head, alternating Cy3 and Cy5 to custom-made microarrays composed of 6,200 clones derived from the Prostate Expression Database.

first: Chung-Ying

last: Huang

first: Tomasz

middle: M

last: Beer

first: Celestia

last: Higano

first: Lawrence

last: True

last: Vessella

first: Paul

middle: H

last: Lange

first: Mark

last: Garzotto

first: Peter

last: Nelson


title: Prostate Cancer–Associated Gene Expression Alterations Determined from Needle Biopsies

status: Public on Aug 24 2012

summary: To accurately identify gene expression alterations that differentiate neoplastic from normal prostate epithelium using an approach that avoids contamination by unwanted cellular components and is not compromised by acute gene expression changes associated with tumor devascularization and resulting ischemia.

overall_design: Approximately 3,000 neoplastic and benign prostate epithelial cells were isolated using laser capture microdissection from snap-frozen prostate biopsy specimens provided by 31 patients who subsequently participated in a clinical trial of preoperative chemotherapy.  To eliminate potential dye bias, we randomly alternated Cy3 and Cy5 labeling to neoplastic and benign epithelium across 31 samples. Labeled cDNA probes were hybridized in a head-to-head fashion, normal versus neoplastic from the same individual, to custom-made microarrays composed of 6,200 clones derived from the Prostate Expression Database.

first: David

middle: Z

last: Qian

first: Catherine

last: O'Brien

middle: D

first: Robert


title: Genome-wide anyalysis of gene expression during prolonged endotoxin tolerance in Aoah -/- mice

status: Public on Aug 17 2012

city: Bethesda

first: Mingfang

last: Lu

state: MD

address: 9000 Rockville Pike

department: LCID

institute: NIH/NIAID

summary:
Analysis of gene expression in explanted peritoneal macrophages from  Aoah -/- and Aoah +/+ mice treated with LPS 21 days prior to harvest. Explanted peritoneal machrophages were challenged with LPS or control (PBS).
The study seeks to characterize global gene expression in the state of prolonged LPS tolerance induced in mice lacking the LPS-inactivating enzyme Aoah.

overall_design: Groups of 9 C57BL/6 Aoah+/+ or Aoah-/- mice were given i.p. injections of 10 µg E. coli LPS/mouse.  Twenty-one days later (when Aoah-/- mice remain tolerant and Aoah+/+ mice have recovered), peritoneal macrophages were harvested and the yields from three mice were pooled to form 3 samples per group (i.e., three samples of Aoah+/+ and Aoah-/- mice, with each sample comprised of peritoneal macrophages from 3 mice). Next day, cells were challenged with LPS or PBS and whole RNA was isolated 2 hours later and used for microarray experiments.

first: A

middle: W

last: Varley

last: Munford


title: affy_tour_2010_21-Assessing drought stress transcriptomics in Helianthus annus in field cultures

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary: affy_tour_2010_21 - affy_tour_2010_21 - The aim of this project is to assess the possibility of implementing transcriptomic studies on sunflower plants grown in field assays. Data obtained from plants under drought in the glasshouse have already obtained. We intend to use these results as a template and see if the field offers the possibility of carrying these studies. In order to do so, treatment-effect as well as intra and inter-plot variability will be assessed.-Plants were grown in the field. The assay was arranged in plots with one genotype per plot. The assay was divided in two identically seized parts, containing the same number of plots. Starting from the capitule, flower # -3 was harvested in every plant. In some cases, several plants from the same plot were harvested. In other, plants from different plots were harvested. We expect that this sampling will allow us to assess intra- as well as inter-plot variability in the analysis of drought-driven gene expression modulation.

overall_design: 24 arrays - SUNFLOWER; treated vs untreated comparison

first: Stephanie

last: Huguet

last: Rengel

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Effect of unilateral naris occlusion on gene profile in mouse olfactory mucosa.

status: Public on Aug 22 2012

city: Ashland

last: Coppola

state: Virginia

address: 304 Caroline

department: Biology

institute: Randolph Macon College

summary:
Unilateral naris occlusion was performed the day after birth in three FVB strain mice. At 25 days of age olfactory mucosa was collected from open nasal fossa, the occluded nasal fossa and from three untreated mice. Total RNA was extracted and gene profiles among these three treatment conditions were compared.
The goal of the study was to determine the effect of stimulus deprivation on the genetic profile of olfactory mucosa.

overall_design: There were three treatment conditions: open mucosa, occluded mucosa, and untreated mucosa. Each of these conditions had three biological replicates. Open and occluded however were repeated measures i.e. from the same individuals.

first: Chris

last: Waggener


title: Human breast cancer cells: control vs treated with breast cancer patients' sera

status: Public on Aug 15 2012

city: Beijing

first: sp

last: zhang

address: 18 Shuangqing Road, Haidian District

institute: RCEES, CAS

summary: To investigate the significant differently expressed genes upon the stimulation of breast cancer patients' sera.

overall_design: Cells were untreated or treated with 10% breast cancer patients' sera for 24h followed by isolation of total RNA using TRIZOL. Gene-expression profiling was performed on the CapitalBio 35k human Genome Array microchips  (Beijing, China).

first: Shuping

last: Zhang

first: Yue

last: Chen

first: Sijin

last: Liu


title: Array-Painting with Hoolock sorted chromosomes

status: Public on Aug 10 2012

city: Beaverton

first: Lucia

last: Carbone

state: Oregon

address: 505 NW 185th ave

institute: Oregon Health & Science University

summary: Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH and selective sequencing in two of the four karyomorphs, has shown that high resolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n=50), and Hoolock (2n=38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome.  Bioinformatics analyses of the human-gibbon synteny breakpoints revealed association with transposable elements and segmental duplications providing some insight into the mechanisms that might have promoted rearrangements in small apes.  In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning event presented here will facilitate genome sequence assembly for these close relatives of humans.

sample_organism:
Homo sapiens
Hoolock leuconedys

overall_design: FACS sorted chromosomes from Hoolock leuconedys were labelled, pooled, and hybridized on the array platform. Five pools were hybridized totally

first: Pieter

last: deJong


title: Disomic yeast response to heat shock

status: Public on Aug 14 2012

first: Ana

last: Oromendia

address: 500 Main St

institute: MIT- Koch Institute

summary: These experiments were done to compare the transcriptional response to high temperature of disomic yeast to that of WT yeast.

overall_design: Total RNA from strains and timepoints specified was labeled by Cy3- this was compared to WT total RNA in all cases.

first: Angelika

last: Amon


title: Transcriptomic analysis of the effect of CT16 (PAGE5) silencing by RNAi in A2058 melanoma cells

city: Turku

first: Jyrki

last: Heino

address: Vatselankatu 2

department: Biochemistry

country: Finland

institute: University of Turku

summary: The cellular gene expression profiles were investigated after CT16 (PAGE5) silencing in CT16 positive A2058 melanoma cells. Control siRNA treated A2058 cells was used as a negative control.

overall_design: Total RNA from three individual cultures of A2058 cells treated with CT16 siRNA and from three individual cultures of A2058 cells treated with control siRNA.

first: Camilla

last: Nylund


title: Chromosomal aberration of asbestos-induced malignant mesothelioma in rats

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary: Exposure to asbestos is a risk for malignant mesothelioma in humans. We carried out array comparative genomic hybridization (CGH) analysis in a rat model by repeated intraperitoneal injections of three types of asbestos including chrysotile, crocidolite and amosite. We found a common chromosomal deletion mapped to the chromosome 5q32 locus, containing the genes encoding tumour suppressor genes CDKN2A/2B/ARF.  Homozygous deletion of CDKN2A/2B/ARF was observed in the majority (92.6%) of the rat MM samples.

overall_design: Carcinogenesis protocol was performed using specific pathogen-free male and female F1 hybrid rats between Fischer344 and Brown-Norway strains. A total of 27 tumor samples were profiled on Agilent 244A aCGH arrays according to manufacturer's instructions for the screening purpose.

first: Toyokuni

last: Shinya

first: Jiang

last: Li

first: Akatsuka


title: GC424 tumor cells and gastric tumors

status: Public on Aug 02 2012

city: Bonn

first: Joachim

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

institute: University of Bonn

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

overall_design: Refer to individual Series


title: Transcriptomic analyis of the response of porcine PBMC to stimulation with concanavalin A

status: Public on Aug 01 2012

city: Edmonton

first: James

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

institute: University of Alberta

summary: One of the top priorities of the swine industry worldwide is to decrease the susceptibility of its animals to infectious diseases. There is therefore now an increased focus on the production of more “robust” animals, which have lower susceptibility to a broad range of infectious diseases. One general measure of immune competence is the proliferative response of peripheral blood mononuclear cells (PBMC) to mitogenic stimulation. Concanavalin A (ConA) is a mitogen that predominantly stimulates T lymphocytes within the PBMC fraction of blood. T cells play a crucial role in both cell-mediated and humoral immunity. Variation between individuals in the magnitude of the proliferative response to ConA has been estimated to have moderate heritability, and quantitative trait loci (QTL) for this trait have been identified. However, detailed knowledge of the genomic pathways which coordinate this process in swine PBMC is currently lacking. The recent development of a high density oligonucleotide microarray for the pig research community means that it is now possible to study simultaneously the expression of a large proportion of genes from the pig genome. The objective of this research project was to profile gene expression in ConA-stimulated PBMC to identify the gene networks that control the cellular response to this mitogen.

overall_design: Peripheral Blood Mononuclear Cells (PBMC) from 4 individual biological replicates were used for this experiment. Separate cell aliquots from these animals were grown in culture with the mitogen concanavalin A for 4 different times: 0, 3, 20, and 68 hours. For the hybridization experiment, 3 separate direct comparisons of gene expression were made (0 v 3 hr, 0 v 20 hr and 0 vs 68 hr). Time-point samples from the same individual were always compared on the same array. Each comparison consisted of 8 hybridizations (4 biological replicates; 2 dye-swap technical replicates), making a total of 24 hybridizations.

first: Jamie

first: Mike

middle: K

last: Dyck

first: Walter

last: Dixon

first: George

last: Foxcroft

first: Shrijana

last: Dhakal

first: John

middle: C

last: Harding


title: The effects of oxygen treatments on angiogenesis and lymphangiogenesis in mouse embryoid bodies

status: Public on Aug 12 2012

city: College Station

first: Mariappan

last: Muthuchamy

state: TX

address: 346A Reynolds Medical Building

department: Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

summary: This study investigates the processes of angiogenesis and lymphangiogenesis in an in vitro mouse Embryoid Body (EB) model while maintaining as closely as possible an in vivo environment that is observed in human and murine placental development. Several studies have documented that human placental development is profoundly influenced by oxygen tension. Further the developing murine embryo also experiences hypoxic conditions prior to parturition, which regulates early organogenesis and embryonic blood vessel formation in vivo.  Embryonic stem (ES) cells derived from 129/SvJ mice were differentiated into embryoid bodies (EBs) and were subjected to two oxygen treatments: normoxia (21% O2) and hypoxia (2.6%). Hypoxia was achieved in a humidified chamber flushed with 95% N2/5% CO2 until the oxygen level was stably maintained at 2.6%. EBs were transferred on days E8, E12, E15 and E18 to hypoxia or maintained in normoxia. After 2 days of differential oxygen treatments, these EBs were analyzed at E10, E14, E17 and E20 respectively.

overall_design: A 4 x 2, reference-based, experimental design was utilized consisting of 4 timepoints (E10, E14, E17 and E20) subjected to 2 oxygen treatments (normoxia, hypoxia)  with n=4 biological replicates present in each group. All EB samples were handled in parallel through all experimental steps. Each EB RNA sample was amplified, labeled with Cy5, and compared to the same Mouse Universal Reference RNA sample (Stratagene, La Jolla, CA) that was amplified and labeled with Cy3 dye. No dye swaps were utilized.

first: Andrea

last: Foskett

first: Uthayashanker

last: Ezekiel

first: Jerome

middle: P

last: Trzeciakowski

first: David

last: Zawieja


title: Comparison of human Rheumatoid arthritis patient peripheral whole blood mRNAs just before and after Leukocytapheresis

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Leukocytapheresis((LCAP) is a safe, unique therapy prevalent for intractable rheumatoid arthritis even in case of drug allergy or infectious state. To investigate how to improve LCAP efficacy, we have conducted genes expressions analysis from peripheral blood of Rheumatoid arthritis patients using high resolution DNA microarray just before and after LCAP procedure.

overall_design: 8 Rheurmatoid arthritis patients have been compared just before and after Leukocytapheresis treatment (overall 16 samples). The Pre-LCAP samples were labeled using Cy5, and the Post-LCAP labeled with Cy3.

first: Makio

last: Kusaoi

first: Ken

last: Yamaji

first: Go

last: Murayama

first: Misa

last: Yasui

first: Risa

last: Yamada

first: Ruka

last: Hishinuma

first: Takuya

last: Nemoto

first: Katsura

last: Hohtatsu

first: Michiaki

last: Kageyama

first: Kaoru

last: Sugimoto

first: Michihiro

last: Ogasawara

first: Kazuo

last: Kempe

first: Hiroshi

last: Tsuda

first: Yoshinari

last: Takasaki


title: Differential gene expression analysis of murine liver and kidney following exposure to malarial parasite

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Global changes in murine liver and kidney transcriptome were analyzed following different levels of malarial  parasite infection.Known levels of parasites were injected in mice and transcriptomic changes were recorded with comparison to control non infected healthy mice.

overall_design: Two color ,Organism: Mus Musculus, Genotypic Technology designed "Custom Agilent Mus Musculus  8x15k GE Microarray (AMADID-016270) "

first: Shrawan

last: Mishra

first: Srikanta

last: Rath

first: Prabhat

last: Singh


title: Molecular characteristics and metastasis predictor genes of triple-negative breast cancer

status: Public on Nov 01 2012

city: Taipei

first: King-Jen

last: Chang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Surgery

country: Taiwan

institute: National Taiwan University Hospital

type:
Expression profiling by array
Third-party reanalysis

summary:
This microarray dataset contains 51 triple-negative breast cancers with clinical and recurrence information for at least 3 years of follow-up and 106 luminal breast cancers (reanalyzed data from Series GSE24124, GSE9309, and GSE17040).
A novel set of 45-gene signature that was statistically predictive of distant metastasis recurrence for triple-negative breast cancer was identified in this study.

overall_design: Specimens of breast cancer tissue were collected and snap-frozen from breast cancer patients who had surgery between 1995 and 2008 at National Taiwan University Hospital (NTUH, Taipei, Taiwan). Clinicopathological information was obtained for all breast cancer patients along with informed consent. The AJCC/UICC TNM system was used for breast cancer staging classification.

first: Wen-Hung

last: Kuo


title: Gene expression profiles of control GC424 tumor cell lines and after downregulation of the SV40 large T-antigen

first: Joachim

last: Schultze

summary: Analysis of global gene expression in a tumor cell line established from a CEA424-Tag mouse and comparison with the expressed gene profile after downregulating the expression of the large T antigen

overall_design: Total RNA obtained from cultured control  cell lines and after siRNA mediated downregulation of the SV40 large T antigen

first: Georg

last: Enders


title: B. pseudomallei K96243 genome: Control vs. B. pseudomallei environmental or clinical isolates

status: Public on Jul 31 2012

city: Maung

first: THANATCHAPORN

last: BARTPHO

state: Khon Kaen

address: 123 Mitthaphap

department: Microbiology

country: Thailand

institute: Meliodosis Research Center, Faculty of Medicine, Khon Kaen University

summary:
To use whole genome microarrays to compare the differences in genome contents of 5 B. pseudomallei isolated from clinical specimens and environmental sample with B. pseudomallei K96243 reference strain and reveals variable patterns of Genomic Islands (GIs)

Keywords: Comparative genomic hybridization

platform_organism:
Burkholderia mallei
Burkholderia pseudomallei

overall_design: DNA microarrays were used to compare genome of clinical and environmental B. pseudomallei isolates with B. pseudomallei K96243 reference strain (B. pseudomallei K96243 vs. B. pseudmallei isolates). Each hybridization was used for comparison between B. pseudomallei K96243 as a reference strain with environmental isolate BP45s, environmental isolate BP28L, clinical isolate H307, clinical isolate P54, clinical isolate P82. Two replicate per array. Multiple hits with 90-99.99 % identity correspond to other locus are replicate of their genes were averaged and analyzed.

first: Thanatchaporn

last: Bartpho

first: Thidathip

last: Wongsurawat

first: Surasakdi

last: Wongratanacheewin

first: Adel

last: Talaat

first: Nitsara

last: Karoonuthaisiri

first: Rasana

last: Sermswan


title: LAP2beta-induced change in gene expression in gastric cancer cells

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Knock-down or overexpression of LAP2beta regulated migration and invasion of gastric cancer cells in vivo and in vitro studies. To investigate the underlying mechanism for LAP2beta-regulated migration and invasion, we compared the gene expression changes between the mock cells and the stable cells.

overall_design: Total RNA was purified from the mock cells and the stable cells overexpressing LAP2beta

first: Sae-Ock

last: Oh


title: Comparing genome-wide H3K36me3 levels in WT vs. dKDM4A mutant

status: Public on Jul 10 2012

city: Kansas City

first: Ariel

last: Paulson

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

type: Genome binding/occupancy profiling by genome tiling array

summary: dKDM4A is a Drosophila H3 K9/K36 me2/me3 demethylase, which has been disrupted here by P-element insertion.  We compare whole-genome ChIP-chip in mutant and WT to look for target genes of dKDM4A.

overall_design: Two samples, WT and dkDM4A mutant. 2 biological replicates each. 2 arrays.


title: affy_sunyfuel_drought_sunflower-Sunyfuel

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary: affy_sunyfuel_drought_sunflower - Drought is the main cause or crop loss around the globe and it is expected to be more so in years to come. Helianthus genus comprises species that are able to grow in harsh environments suffering from severe water shortage. Cultivated H.annuus, i.e. sunflower, is a highly valuable oil crop due to, among other features, its ability to grow under low input conditions. The aim of our project is to unravel the transcriptional regulation underpinning drought tolerance in sunflower, with the ultimate goal of improving crop yield. Ninety six individual pots were arranged in six blocks of 16 plants each, which were sown in individual pots. Each block contained 2 plants of 8 different genotypes, one of which was used as control and the other one as treated plant. Plants within each block were randomly arranged. At the right developmental stage, treated plants were water-deprived and their water status was monitored as compared to the untreated control. Three out of the six blocks were harvested on a given date, so water stress among genotypes varied. The plants in the other three blocks were harvested when the treated plant reached a given water stress.

overall_design: 96 arrays - SUNFLOWER; treated vs untreated comparison

first: Sandrine

last: Arribat

last: Balzergue

first: David

last: Rengel

first: Marie-Laure

last: Martin-Magniette


title: Senescence-correlated gene expression programs of human prostate stromal cells in response to multiple proliferation-arresting stress and their potential in driving prostate neoplasia

status: Public on Jul 23 2012

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

institute: Fred Hutchinson Cancer Center

summary: As an age-related process, cellular senescence is cell cycle arrest and it safeguards against incidental oncogenic activation by playing antiproliferative roles. Despite the establishment that senescence is a beneficial anticancer mechanism, increasing evidence indicates its deleterious effects that might contribute to age-related pathologies. We applied a group of methods that causes typical senescence to PSC27, a primary normal human prostate stromal cell line, and compared their capacity in influencing the expression of senescence- and proliferation-related genes.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile PSC27 prostate fibroblast cells treated with agents to induce senescence (oxidative stress, DNA damage, and radiation.)  Total RNA was isolated and amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Yu

last: Sun

first: Peter

middle: S

last: Nelson


title: NaJAZh regulates a subset of defense responses against herbivores and counteracts developmental necrosis in Nicotiana attenuata plants

status: Public on Jul 12 2012

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of transcripts that change expression in Nicotiana attenuata plants with reduced expression of JAZh after elicitation with oral secretions of Manduca sexta larvae.

overall_design: Gene expression in leaves of Nicotiana attenuata wild type and irJAZh plants was measured at 2 hour after elicitation with oral secretions of Manduca sexta larvae. Three independent experiments were performed with wild type plants and three independent experiments were performed with irJAZh plants. A total of 480 genes were identified as more the 2 fold differentially regulated in irJAZh plants compared to wild type plants.

first: Youngjoo

first: Ivan

last: Galis


title: DDX20 knockdown effect on hepatocellular carcinoma cells

status: Public on Jul 15 2012

first: Satoshi

last: Kondo

state: Kanagawa

summary: Analysis of DDX20 knockdown - hepatocellular carcinoma cells. The expression levels of genes driven by NF-kB and related with carcinogenesis, were significantly enhanced in DDX20-knockdown cells.

overall_design: One condition experiment, HepG2 vs. HepG2-DDX20 knockdown cells

first: Akemi

last: Takata

first: Motoyuki

last: Otsuka

first: Kentaro

last: Kojima

first: Takeshi

last: Yoshikawa

first: Takahiro

last: Kishikawa

first: Yohko

last: Hikiba

first: Shin

last: Maeda

first: Yotaro

last: Kudo

first: Shuntaro

last: Obi

first: Young

middle: J

last: Kang

first: Hiroshi

last: Asahara

first: Jiahuai

last: Han

first: Haruhiko

last: Yoshida

first: Masao

last: Omata

first: Kazuhiko

last: Koike


title: Hypoxia triggers meiotic fate acquisition in maize

status: Public on Jul 05 2012

city: Stanford

first: Timothy

last: Kelliher

state: Ca

address: 385 Serra Mall

institute: Stanford University

summary:
Evidence from confocal microscopic reconstruction of maize anther development in fertile, mac1 (excess germ cells) and msca1 (no germ cells) flowers indicates that the male germ line is multiclonal and uses the MAC1 protein to organize the somatic niche. Furthermore, we identified redox status as a determinant of germ cell fate, defining a mechanism distinct from the animal germ cell lineage. Decreasing oxygen or H2O2 increases germ cell numbers, stimulates superficial germ cell formation, and rescues germinal differentiation in msca1 flowers. Conversly, oxidizing environments inhibit germ cell specification and cause ectopic differentiation in deeper tissues. We propose that hypoxia, arising naturally within growing anther tissue, acts as a positional cue to set germ cell fate.
key words: anther development, maize, male-sterile

overall_design: Two replicates of laser microdissected pre-meiotic cells were compared to two replicates of whole anthers, which contains pre-meiotic cells and somatic cells, from the same developmental stage and individual wild type plants.  In another experiment, laser microdissected pre-meiotic cells from wild type (mac1-heterozygous) anthers were compared to laser microdissected pre-meiotic cells from mac1 (mutant) anthers.

first: Kelliher

last: Timothy

first: Virginia

last: Walbot


title: Role of MXD3 in DAOY cell proliferation

status: Public on Jul 13 2012

city: Sacramento

first: Gustavo

middle: A.

last: Barisone

state: CA

department: Internal Medicine

institute: University of California Davis Health System

middle: A

first: Elva

last: Díaz


title: Pla2g12b and Hpn are Genes Identified by Mouse ENU Mutagenesis that affect HDL cholesterol

status: Public on Jul 01 2012

city: Williamsville

first: Rachael

middle: Hageman

last: Blair

state: NY

address: 70 Woodlee Road

institute: University at Buffalo

summary: Despite considerable progress understanding genes that affect the HDL particle, its function, and cholesterol content, genes identified to date explain only a small percentage of the genetic variation. We used N-ethyl-N-nitrosourea mutagenesis in mice to discover novel genes that affect HDL cholesterol levels. Two mutant lines (Hlb218 and Hlb320) with low HDL cholesterol levels were established. Causal mutations in these lines were mapped using linkage analysis: For line Hlb218 within a 12 Mbp region on Chr 10; and for line Hlb320 within a 17 Mbp region on Chr 7. High-throughput sequencing of Hlb218 liver RNA identified a mutation in Pla2g12b. The transition of G to A leads to a cysteine to tyrosine change and most likely causes a loss of a disulfide bridge. Microarray analysis of Hlb320 liver RNA showed a 7-fold downregulation of Hpn; sequencing identified a mutation in the 3′ splice site of exon 8. Northern blot confirmed lower mRNA expression level in Hlb320 and did not show a difference in splicing, suggesting that the mutation only affects the splicing rate. In addition to affecting HDL cholesterol, the mutated genes also lead to reduction in serum non-HDL cholesterol and triglyceride levels. Despite low HDL cholesterol levels, the mice from both mutant lines show similar atherosclerotic lesion sizes compared to control mice. These new mutant mouse models are valuable tools to further study the role of these genes, their affect on HDL cholesterol levels, and metabolism.

overall_design: Mutant mice were generated as part of The Jackson Laboratory’s Heart, Lung, Blood, and Sleep Disorder Mutagenesis Program by treating male C57BL/6J (B6) mice with N-ethyl-N-nitrosourea (ENU). Third generation (G3) mice were phenotyped to ensure capture of both dominant and recessive mutations. Two unique G3 animals with low HDL cholesterol levels were then used to establish new inbred lines (Hlb218 and Hlb320) by mating them with B6 mice and intercrossing the offspring with low HDL cholesterol for 7 generations. Livers from 3 Hlb218, 3 Hlb320 males, and 6 B6 male controls were obtained for gene expression analysis. The samples were randomized over Illumina Mouse-6 Expression 1.1 BeadChips .

first: Aleksandra

last: Aljakna

first: Seungbum

last: Choi

first: Holly

last: Savage

first: Tonjun

last: Gu

first: Karen

last: Svenson

first: Matt

last: Hibbs

first: Gary

last: Churhill

first: Ron

last: Korstanje


title: Transciptome analysis of Salmonella enterica serovar Typhimurium UK1 delta-raoN at oxidative stress

city: Seoul

first: Yong Keun

last: Park

address: Anam-dong 5Ga, Seoungbuk-Gu

department: School of Life Sciences and Biotechnology

institute: Korea University

summary: Salmonella has various mechanisms of small RNA-mediated gene regulation. In Salmonella enterica serovar Typhimurium, a novel intergenic transcript RaoN is involved in oxidative stress response which functions as one of the powerful antimicrobials in macrophage innate immunity. We note that the ∆raoN mutant is sensitive to hydrogen peroxide (5.0 mM). This finding provides insights into the function of RaoN as a regulator of oxidative stress response.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: UK1 wild-type and ∆raoN strains were grown in LB medium at 37℃ to an OD600 of 0.6, and then subjected to oxidative stress (5.0 mM hydroperoxide) for 30 min. Total RNA was extracted from three biological replicates of wild-type and ∆raoN mutant.

first: Sinyeon

last: Kim

first: YongHeon

last: Lee

first: YongKeun


title: Expression profiling of MXD3 stable cell lines

summary:
A subset of medulloblastomas, the most common brain tumor in children, is hypothesized to originate from granule neuron precursors (GNPs) in which the sonic hedgehog (SHH) pathway is over-activated. MXD3, a basic helix-look-helix zipper transcription factor of the MAD family, has been reported to be upregulated during postnatal cerebellar development and to promote GNP proliferation and MYCN expression. Mxd3 is upregulated in mouse models of medulloblastoma as well as in human medulloblastomas. Therefore, we hypothesize that MXD3 plays a role in the cellular events that lead to medulloblastoma biogenesis.
The purpose of this study was to identify changes in gene expression in response to MXD3.

overall_design: RNA from MXD3 stable cell lines compared to vector-only cell lines and to parental (DAOY) cell line.


title: Drosophila the 3rd instar larvae testis: Control vs. Wolbachia-infected

city: Wuhan

first: Jialin

last: Wang

address: no.152 Luoyu Road

institute: Central China Normal University

summary: Transcriptional profiling of Drosophila melanogaster larval testes with and without the wMel strain of Wolbachia and found that 296 genes had at least a 1.5 fold change [q-value (%)<5%] in transcript levels, with 167 genes up-regulated and 129 genes down-regulated when comparing Wolbachia-infected flies to uninfected ones. Differential expression of genes related to metabolism, immunity, reproduction and other  functions were observed.

overall_design: Two-condition experiment, Wolbachia-infected vs. Wolbachia-uninfected testes. Biological replicates: 3 control, 3 infected, independently grown and dissected. One replicate per array.

first: Ya

last: Zheng

first: Jia-Lin

first: Chen

last: Liu

first: Cui-Ping

first: Yu-Feng


title: Lung Adenocarcinoma derived from Normal Bronchial Epithelial Cells Co-cultured with HPV-Positive Peripheral Blood lymphocyte from Lung Cancer Patient

status: Public on Jun 28 2012

city: Taichung

first: YAWEN

last: CHENG

address: No. 110, Sec. 1, Jianguo N. Rd.

institute: Chung Shan Medical University

summary: Microarray and bioinformatics analysis indicated that Wnt/β-catenin pathway activation may play a crucial role in HPV-infected lung adenocarcinomas derived from NHBE cells.

overall_design: Microarray and bioinformatic analysis were used to understand what is the most important pathway involved in HPV-induced lung tumorigenesis.

first: Ya-Wen

last: Cheng

first: Huei


title: Study of transcriptional expression in HCM

status: Public on Jun 30 2012

city: Umeå

first: Nina

last: Gennebäck

address: NUS 6M

department: Public health and clinical medicin/medicin

country: Sweden

institute: Umeå University

summary: The transcriptional expression patterns in the myocardium of HCM patients may contribute to the understanding of the mechanisms that drive and stabilize the hypertrophy.

overall_design: Cardiac myectomies/biopsies from 8 patients with hypertrophic obstructive cardiomyopathy (HOCM) (3 men) and 5 controls without cardiac disease were studied

first: Gerhard

last: Wikström

first: Urban

last: Hellman

first: Jane-Lise

last: Samuel

first: Anders

last: Waldenström

first: Stellan

last: Mörner


title: Novel Transcriptome Profiling Analyses Demonstrate that Selective PPARg Modulators Display Attenuated and Selective Gene Regulatory Activity in Comparison with PPARg Full Agonists

city: Rahway

first: Yejun

last: Tan

state: NJ

address: 126 E. Lincoln Ave, POBox 2000

department: Molecular Profiling

institute: Merck & Co.

summary: We conducted extensive transcriptome profiling studies to characterize 70 SPPARgMs and seven PPARg full agonists in 3T3-L1 adipocytes, and a subset of these ligands in adipose tissue of diabetic db/db mice. In both cases, the SPPARgMs generated attenuated gene regulatory responses, and their gene expression signatures were more enriched in metabolic pathways that are likely to mediate anti-diabetic efficacy than those of PPARg full agonists. More importantly, our profiling results demonstrated that in both 3T3-L1 adipocytes and db/db mice, SPPARgMs regulate the expression of anti-diabetic efficacy-associated genes to a greater extent than that of adverse effect-associated genes, while PPARg full agonists regulate both gene sets proportionally.

overall_design: We conducted 10 independent batches of profiling experiments. Within each batch, drug treatment and pool of vehicle controls were hybridized to the Agilent two channel microarray. Generally 2-3 biological replicates for each condition.

first: Eric

last: Muise

first: Hongyue

last: Dai

first: Richard

last: Raubertas

first: Kenny

last: Wong

first: Marie

last: Thompson

first: Harold

middle: B

last: Wood

first: Peter

middle: T

last: Meinke

first: Pek

middle: Y

last: Lum

first: John

first: Joel

last: Berger


title: Gene expression profiling of Plasmodium falciparum after co-culture with NK cells

city: Tuebingen

first: Evelyn

last: Boettger

address: Wilhelmstrasse 27

institute: Institute of Tropical Medicine

summary: The aim of the study was to determine the effect of natural killer (NK) cells on the global gene expression in Plasmodium falciparum.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: FCR3-CSA-infected red blood cells (RBCs) were co-cultured for 24h with NK92. Prior to RNA extraction, the parasitized RBCs were separated via Ficoll from the lymphocyte fraction. Control cultures of parasites without NK cells were cultivated in parallel. In addition, the effect of the separation method was determined via a Ficoll control culture of FCR3-CSA that was passed over a Ficoll gradient. All three treatments were performed in triplicate. The RNA was reverse-transcribed and hybridized onto microarrays.


title: Genomic characterization of osteoblastic differentiation of MC-3T3E1 cells

city: Charleston

first: Louis

last: Luttrell

address: 173 Ashley Ave

institute: MUSC

summary: Gene expression analysis of murine MC3T3-E1 cells induced to undergo synchronized osteoblastic differentiation in vitro.

overall_design: MC3T3-E1 cells were cultured in vitro for up to 28 days in the presence of 8-glycerol phosphate and ascorbic acid to induce osteoblastic differentiation.  Total RNA was isolated after 2, 5, 10 and 28 days in culture to sample proliferating preosteoblasts (Day 2), growth arrested preosteoblasts (Day 5), differentiating osteoblasts (Day 10), and mature osteoblasts (Day 28).  Timing of sample collection was based on direct measurements of cell number, alkaline phosphatase expression, type 1A collagen synthesis, and matrix mineralization in parallel cultures.  Triplicate samples from each time point were hybridized to slide arrays printed with the Operon Mouse Oligo set, version 2.0.

first: Moahad

last: Dar

first: Diane

last: Gesty-Palmer

first: Hesham

last: El-Shewy


title: Parallel selection mapping using artificially selected mice reveals body weight control loci (SNP)

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory

summary:
Understanding how polygenic traits evolve and respond to selection is a major unsolved problem, because challenges exist for identifying genes underlying a complex trait and understanding how multi-locus selection operates in the genome. Here we used artificial selection experiments to study polygenic response to selection. Inbred strains from seven independent long-term selection experiments in mice for extreme bodyweight (“High” lines weigh 77-42g vs. 40-16g in “Controls” lines), were genotyped at 527,572 SNPs to identify genetic variants controlling bodyweight. We identified 67 high-resolution parallel selected regions (PSRs) where multiple High lines share variants rarely found among the Controls. By comparing allele frequencies in one selection experiment against its unselected control, we found classical selective sweep signatures centered on the PSRs. Multiple lines of evidence support two G protein-coupled receptors GPR133 and Prlhr, as positional candidate genes controlling bodyweight. Artificial selection may mimic natural selection in the wild: compared to control loci, we detected reduced heterozygosity in PSRs in wild populations of unusually large mice on islands. Many PSRs overlap loci associated with human height variation, possibly through evolutionary conservation of functional pathways. Our data suggest that parallel selection on complex traits may evoke parallel responses at many genes involved in diverse but relevant pathways.
These samples were used to test the enrichment of certain gene functional categories.

overall_design: Genomic DNA SNP comparison between artificially selected high lines (BEH, DAHi, DUH, MUH, EDH, RAHi, Du6/G154 and Du6i/G80) and unselected control lines.

first: F

last: Jones

first: E

last: McConnell

first: J

last: Bryk

first: L

last: Bunger

first: D

last: Tautz


title: Comparison between liver transcriptomes of newborn male Erhualian and Large White piglets

status: Public on Jun 18 2012

city: Nanjing

first: Runsheng

last: Li

state: Jiangsu

department: Nanjing Agricultural University

country: China

institute: Nanjing Agricultural University

summary:
Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress.To further investigate the different breed-specific metabolic characters, a comparison of gene expression profile in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six niemblegen 135K expression microarrays were used. Among 44,987 pig transcripts investigated, 23,807 transcripts retained for further analysis after removing the probes with poor quality intensities and low dependability.All these qualified transcripts were then annotated by manual blast and by referring to previously developed protein-based annotation for pigs. In total, we observed 9,447 genes expressed in the liver of new born piglets. The microarray data of LW piglets were treated as control in the selection of differentially expressed genes related to EHL piglets. The FDR (False Discovery Rate) and fold change were calculated by SAMR 3.02. With FDR< 5%, after the removal of redundant and unannotated sequences, 53 genes were found to be significantly up-regulated and 200 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. With FDR < 10%, 298 genes were found to be significantly up-regulated and 510 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets.
These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs.

overall_design: Six newborn male piglets were sampled from three litters (2 from each litter) of purebred EHL and LW sows and sacrificed. Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 °C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. Total RNAs of the two littermate piglets were pooled for the microarray analysis. The pooled samples were named as EHL1-3 and LW1-3, representing 3 mixed liver RNA samples each from EHL and LW piglets, respectively. Microarray experiment was performed by a service provider (CapitalBio, Beijing, China). The microarray (Probe length 60-mer, 135K Format) containing 44987 probe sets was provided by Roche-NimbleGen.

first: Ruqian

last: Zhao


title: Human gastric cancer cells SGC7901-NM RIP-Chip result: has-miR-625 lentivirus infected vs. control

status: Public on Jun 20 2012

city: Xi'an

first: sijun

last: Hu

address: Changle Road

institute: Xijing Hospital

summary: Transcriptional profiling of RIP products of human gastric cancer cells SGC7901-NM comparing control with SGC7901-NM infected with has-miR-625 lentivirus

overall_design: Stable transfected cell lines, SGC7901-NM-has-miR-625 vs. SGC7901-NM-NC,  after RNA-binding protein immunoprecipitation with Ago2 antibody, the experimental group (Ago2) vs. the control group (input) per array.

first: Sijun

first: Jun

last: Tie


title: Human Breast Tumor Cored Sample mRNA Array

status: Public on Jun 15 2012

city: Farmington

first: Kevin

last: Claffey

state: CT

address: 263 Farmington Ave

country: USA

institute: UConn Health Center

summary:
An eight sample cohort of primary human breast cancer sample total RNA gene expression analysis.
Illumina HumanRef-8 v2 11223162_B

overall_design: Total RNA was isolated from tumor cell dense regions of fresh frozen primary breast cancer samples.


title: Comparative genomic analysis of human and non-human primate CD34+ MPBSCs exposed to PGE2

status: Public on Jun 25 2012

city: Doha

first: Francesco

middle: Maria

last: Marincola

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

country: Qatar

institute: Sidra Medical and Research Center

summary: Abstract: Hematopoietic stem cells (HSCs) are used in transplantation therapy to reconstitute the hematopoietic system. Human cord blood (hCB) transplantation has emerged as an attractive alternative treatment option when traditional HSC sources are unavailable, however, the absolute number of hCB HSCs transplanted is significantly lower than bone marrow or mobilized peripheral blood stem cells (MPBSCs). We previously demonstrated that dimethyl-prostaglandin E2 (dmPGE2) increased HSCs in vertebrate models. Here, we describe preclinical analyses of the therapeutic potential of dmPGE2-treatment using human and non-human primate HSCs. dmPGE2 significantly increased total human hematopoietic colony formation in vitro and enhanced engraftment of unfractionated and CD34+ hCB following xenotransplantation. In non-human primate autologous transplantation, dmPGE2-treated CD34+ MPBSCs showed stable multilineage engraftment over one year post-infusion. Together, our analyses indicated that dmPGE2 mediates conserved responses in HSCs from human and non-human primates, and provided sufficient preclinical information to support proceeding to an FDA-approved phase 1 clinical trial.

sample_organism:
Macaca mulatta
Homo sapiens

overall_design: In order to identify the potential mechanism of action of dmPGE2 on gene expression and HSC function, and to possibly explain the muted response of rhesus CD34+ MPBSCs to dmPGE2 exposure, microarray gene expression analysis was conducted. Human and rhesus CD34+ MPBSCs were exposed to DMSO control or dmPGE2 at a dose of either 10 and 50 uM as described above, and processed for microarray analysis at 0, 2, 6, 12 and 24 hours post treatment. Four human donors contributed 8 to 10 samples each at varying time points and dosage for a total of 37 samples (2 samples were technical repeats). Six rhesus macaques contributed 3 to 9 samples each at varying time points and dosage for a total of 28 samples (4 samples were technical repeats). Pooled PBMC's from 6 donors aphereses were used as a reference sample.


title: Prenatal Arsenic Exposure Alters Gene Expression in the Adult Liver to a Proinflammatory State Contributing to Accelerated Atherosclerosis

status: Public on Jun 22 2012

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

institute: University of Louisville

summary: Developmental exposures play a role in adult onset chronic disease. The mechanisms by which environmental toxicants alter developmental processes predisposing individuals to chronic disease are not understood. arsenic exposure via drinking water causes cancer and cardiovascular disease. Transplacental arsenic exposure accelerates and exacerbates atherosclerosis in ApoE-knockout mice. The liver plays a central role in the interlinked diseases diabetes, metabolic syndrome and atherosclerosis. The hypothesis that accelerated atherosclerosis is a consequence of altered hepatic development was investigated by microarray profiling of mRNA and microRNA abundance in livers isolated from 10 week old (PND70) and newborn (PND1) mice exposed or not exposed to arsenic from day 8 post-fertilization to birth. The results show that arsenic exposure alters the trajectory of both mRNA and microRNA expression as mice age. A 51-gene signature of arsenic exposure in both PND1 and PND70 mice was identified. Pathway Architect analysis of this signature identified nodes of interaction including Hspa8, IgM and Hnf4a. Gene ontology analysis of arsenic exposure-altered mRNAs indicated that pathways for gluconeogenesis and glycolysis were suppressed in PND1 mice and pathways for protein export, ribosome, antigen processing and presentation, and complement and coagulation cascades were induced in PND70 mice. Analysis of promoters of differentially expressed genes identified enriched transcription factor binding sites and cluster analyses revealed groups of genes sharing sets of transcription factor binding sites suggesting common regulation. Srebp1 binding sites are present in ~1/6 of the genes differentially expressed in PND70 livers. Western blot analyses of PND70 liver proteins showed that the inducible form of heat shock protein 70 (Hspa1, Hsp70) and the active form of Srebp1 were induced in arsenic-exposed mice as were plasma AST and ALT levels. These results suggest that transplacental ar

overall_design:
Samples from three frozen livers from each group (newborn exposed and unexposed, 10 week old exposed and unexposed), and from separate litters, were homogenized and total RNA purified using mirVANA RNA pufification kits (Ambion, Carlsbad, CA). RNA was quantitated and intergrity determined on a Nanochip using a Bioanalyzer (Agilent, Santa Clara, CA). Microarray analyses for miRNAs abundance in total liver RNAs was performed by Exiqon (Woburn, MA) using two-color design against mouse standard total RNA (Ambion, now part of Applied Biosystems) and Exiqon LNA 1500 microarrays. Microarray analyses for mRNA abundance was performed using 2 color design against mouse standard total RNA (Stratgene, LaJolla, CA) and 44k arrays produced at the NIA .
The processed data on Exiqon LNA-1500 are attached as a Series supplementary file. The data are based on the same samples as described in Agilent data submitted here. The supplementary data includes only the murine miRNA data on the array because these are the only data supplied by Exiqon.
The relationship between GEO's sample names here (Agilent data) and column heads of spreadsheets (Exiqon data) are described in the first sheet of supplemental file:
Project_Summary_Report_Heather_Miller_01042009_MTE.xls

first: Christopher

first: Amar

middle: V

last: Singh

first: Thomas

last: Knudsen

first: Eric

last: Rouchka

first: Ntube

middle: O

first: Juliane

middle: I

last: Beier

first: Gavin

middle: E

last: Arteel

first: Heather

last: Miller

first: Yulan

last: Piao

first: Minoru

last: Ko