title: nup42-delta cells pretreated with NaCl lose the altered gene expression in response to H2O2

status: Public on Sep 18 2011

city: Madison

first: Suraiya

middle: Ruma

last: Haroon

address: 425 Henry Mall

department: Genetics

institute: University of Wisconsin - Madison

summary: BY4741 (S288c haploid) cells have different gene expression in response to 0.4mM H2O2 when pretreated with 0.7M NaCl compared to cells that are not pretreated with NaCl (mock cells). Cells lacking Nup42p do not exhibit a different gene expression in response to H2O2 between naive cells and cells pretreated with 0.7M NaCl

overall_design: BY4741 and nup42-delta cells were independently grown in log phase for at least 7 doublings (T0) and then the genomic expression of "mock" cells to 0.4mM H2O2 was assessed every 10 mins for 20 mins. To study the effects of NaCl treatment on H2O2 response, cells were grown in log phase at least 7 doublings (T0) and then the genomic expression of cells was measured in response to 0.7M NaCl at 30 mins and the treatment continued for 60 minutes. The cells were then removed from stress and grown in stress free media for four hours (memory t0). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 20 minutes.

first: Guan

last: Qiaoning

first: James

last: Hose

first: Audrey

middle: P

last: Gasch


title: Genome profile of human rectal tumors and response to neoadjuvant chemoradiotherapy

status: Public on Nov 17 2011

city: Meldola

first: Chiara

last: Molinari

state: FC

address: via Maroncelli 40

department: Bioscience Laboratories

country: Italy

institute: IRST(Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori)

type: Genome variation profiling by genome tiling array

summary: Background: Neoadjuvant chemoradiotherapy (NCRT) is the treatment of choice in advanced rectal cancer, even though there are many patients who will not benefit from it. There are still no effective methods for predicting which patients will respond or not. The present study aimed to define the genomic profile of rectal tumors and to identify alterations that are predictive of response in order to optimize therapeutic strategies. Methods: Forty-eight candidates for NCRT were recruited and their pretherapy biopsies analyzed by array Comparative Genomic Hybridization (aCGH).  Pathologic response was evaluated by tumor regression grade (TRG).Results: Both Smoothing and Hidden Markov Model (HMM) approaches identified similar alterations, with a prevalence of DNA gains.  Non responsive patients had a different alteration profile from responsive ones, with a higher number of genome changes mainly located on  2q21, 7q21, 7q36, 13q12, 13q32-34, 16p13, 17p12 chromosomal regions. Conclusion: This exploratory study suggests that an in depth characterization of chromosomal alterations by aCGH would provide useful predictive information about response to NCRT and help to optimize therapy in rectal cancer patients.

overall_design:
48 samples included in the study were analyzed on whole genome BAC arrays with the aim to characterize genomic alterations and correlate them with the tumor response to therapy. The case series was composed by 15%,81% and 4% of uT2, uT3 and uT4 tumors, respectively. At the diagnosis 56% of patients had uN0 tumors and 44% uN+.  30%,13%, 23% and 34% of patients reached/mantained respectively ypT0, ypT1, ypT2 and ypT3. With regard to response to NCRT, according to TRG criteria proposed by Dworak, two group were defined: non responders (TRG0-2= 56%) and responders (TRG3-4=44%).

Clinical and pathological parameters:
uT: pre-therapy stage determined by ultrasounds techniques
uN: pre-therapy lymph node status determined by ultrasounds techniques
ypT: pathologic stage after a neoadjuvant treatment
ypN: pathologic lymph node status after a neoadjuvant treatment

first: Daniele

last: Calistri


title: Gene expression profiling of retinoic acid (RA)-treated embryoid bodies (EBs) derived from Elongin A+/+ and Elongin A-/- ES cells.

status: Public on Jul 26 2011

city: Nankoku

first: Takashi

last: yasukawa

state: Kochi

address: Kohasu, Oko-cho

department: Functional Genomics

country: Japan

institute: Kochi Medical School

summary: To identify potential Elongin A targets during neuronal differentiation of ES cells, a cDNA microarray analysis comparing embryoid bodies (EBs) derived from Elongin A+/+ ES cells and Elongin A-/- ES cells was performed.

overall_design: Gene expression in EBs derived from Elongin A+/+ and Elongin A-/- ES cells was measured at day 4 after retinoic acid treatment (2 μM).

last: Yasukawa

first: Teijiro

last: Aso


title: The design and validation of a Dehalococcoides genus microarray and its application to two newly isolated Dehalococcoides strains for comparative genomics

status: Public on Aug 18 2011

city: Berkeley

first: Patrick

last: Lee

state: CA

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

country: USA

institute: University of California, Berkeley

summary: The chlorinated ethene-respiring bacteria of the genus Dehalococcoides are important for bioremediation. A microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus was designed with 4305 probe sets to target 98.6% of all genes from strains 195, CBDB1, BAV1, and VS. The microarrays were validated with genomic DNA (gDNA) of strains 195 and BAV1 and satisfactory analytical reproducibility, quantitative response and gene detection accuracy were obtained. These microarrays were applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2. Strains ANAS1 and ANAS2 can both couple the reduction of TCE, cDCE and 1,1-DCE but not PCE and tDCE with growth while only strain ANAS2 couples VC reduction to growth. Analysis of the respective gDNA using the microarrays showed that the genomes of both strains are similar to each other and to strain 195, except for genes that are within the previously defined integrated elements (IEs) or high plasticity regions (HPRs). Similar results to the combined isolates were obtained when gDNA of ANAS, the enrichment culture from which the two Dehalococcoides isolates originated, was applied to the microarrays. The genome similarities, together with the distinct chlorinated ethene usage of strains ANAS1, ANAS2 and 195 demonstrate that closely phylogenetically related strains can be physiologically different. This incongruence between physiology and core genome phylogeny appears to be driven by the presence of distinct reductive dehalogenase (RDase)-encoding genes with characterized chlorinated ethene functions (pceA, tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Genes encoding central metabolic functions of strain 195 were all detected in strains ANAS1 and ANAS2, while interestingly, the tryptophan operon of these strains is similar to that of strain VS. Overall, the microarrays are a valuable high-throughput tool for comparative genomics of un-sequenced Dehalococcoides-containing samples.

sample_organism:
Dehalococcoides
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Anaeromyxobacter dehalogenans 2CP-C
Dehalococcoides sp. ANAS1
Dehalococcoides sp. ANAS2

platform_organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Dehalococcoides mccartyi CBDB1
Dehalococcoides mccartyi VS

overall_design: The genomic DNA (gDNA) of each culture was analyzed in triplicate. gDNA from strain 195 and strain BAV1 was used as positive control, while gDNA from Anaeromyxobacter dehalogenans strain 2CP-C served as negative control in validating the microarray. gDNA from the two newly isolated strains ANAS1 and ANAS2 as well as the enrichment culture (ANAS) where the two strains originated was also analyzed.

middle: K

first: Dan

last: Cheng

first: Ping

last: Hu

first: Kimberlee

middle: A

last: West

first: Gregory

middle: J

last: Dick

first: Eoin

middle: L

last: Brodie

first: Gary

last: Andersen

first: Stephen

middle: H

last: Zinder

first: Jianzhong

last: He

first: Lisa

last: Alvarez-Cohen


title: HIV Infection and Antiretroviral Therapy Have Divergent Effects on Mitochondria in Adipose Tissue

status: Public on Jul 07 2011

city: Frederick

first: Richard

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

summary: Exploratory microarray analysis identified significant changes in gene expression in adipose tissue.  These included changes in genes regulating lipid and steroid metabolic processes and electron carrier activity in HIV-infected patients receiving antiretroviral therapy (ART).  Additional genes involved in metabolic processes and mitochondrial function were found to be up-regulated in the adipose tissue of HIV-positive patients compared with HIV-negative controls.

overall_design: To identify differential gene expression in different tissues (PBMC, muscle, adipose tissue) between HIV patient groups (HIV negative, HIV positive with ART, HIV positive without ART).

first: Caryn

middle: G

last: Morse

first: Joachim

last: Voss

first: Goran

last: Rakocevic

first: Mary

last: McLaughlin

first: Carol

last: Vinton

first: Charles

last: Huber

first: Xiaojun

first: Jun

last: Yang

first: Da

middle: W

last: Huang

first: Carolea

last: Logun

first: Robert

last: Danner

first: Zoila

last: Rangel

first: Peter

last: Munson

first: Jan

middle: M

last: Orenstein

first: Elisabeth

last: Rushing

first: Marinos

middle: C

last: Dalakas

first: Joseph

last: Kovacs


title: Androgen regulation of genes in rat forebrain, prostate, ovary, and skin

status: Public on Jun 03 2011

city: Duarte

first: jeremy

last: jones

address: 1500 E Duarte Rd

institute: City of Hope

summary: The goal of this study was to identify androgen regulated genes in the forebrain, prostate, ovary, and skin. The results of this study will be used to make comparisons between androgen regulation of gene expression in different androgen-receptor expressing tissues, and will contribute to our understanding of tissue-selective androgen activity.

overall_design: RNA was extracted from tissues castrate male rodents after 16 hours of treatment of either vehicle (Ctrl) or DHT.  The 4 tissues of extraction are Forebrain (ForeB.Ctrl & ForeB.DHT), Ovary (Ovary.Ctrl & Ovary.DHT), Prostate (Prost.Ctrl & Prost.DHT), and Skin (Skin.Ctrl & Skin.DHT).  There are 3 biological replicates per group for a total of 24 samples.

first: Jeremy

middle: O

last: Jones

first: Rebecca

last: Barbeau


title: Expression data from human healthy EPCs/CACs

status: Public on Apr 13 2011

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary:
Systemic lupus erythematosus (SLE) is characterized by increased vascular risk due to premature atherosclerosis independent of traditional risk factors. We previously proposed that interferon-α plays a crucial role in premature vascular damage in SLE. IFN-α alters the balance between endothelial cell apoptosis and vascular repair mediated by endothelial progenitor cells (EPCs) and myeloid circulating angiogenic cells (CACs). Here we demonstrate that IFN-α promotes an antiangiogenic signature in SLE and control EPCs/CACs, characterized by transcriptional repression of IL-1α and β, IL-1 receptor 1 and vascular endothelial growth factor A (VEGF-A) and upregulation of IL-1 receptor antagonist (IL-1RN) and the decoy receptor IL1-R2. IL-1β promotes significant improvement in the functional capacity of lupus EPCs/CACs, therefore abrogating the deleterious effects of IFN-α.
We used microarrays to analyze the effect of IFNα on peripheral blood EPCs/CACs and on bone marrow EPCs exposed to proangiogenic stimulation.

overall_design: Human healthy EPCs and CACs from PBMCs were isolated and cultured under proangiogenic stimulation; after IFNa incubation or not, RNA was extracted and processed for hybridization on Affymetrix microarrays.

first: Seth

last: Thacker

first: Deborah

last: Mattinzoli

first: Maria

last: Rastaldi

first: Matthias

last: Kretzler

first: Mariana

last: Kaplan


title: Expression data from human lupus EPCs/CACs

overall_design: Human lupus EPCs and CACs from PBMCs were isolated and cultured under proangiogenic stimulation; after IFNa incubation or not, RNA was extracted and processed for hybridization on Affymetrix microarrays.


title: Expression data from human healthy CD133+ bone marrow EPCs

overall_design: Human healthy EPCs from bone marrow were isolated and cultured under proangiogenic stimulation; after IFNa incubation or not, RNA was extracted and processed for hybridization on Affymetrix microarrays.


title: Custom array CGH validation of de novo CNVs in asthma samples

status: Public on Sep 01 2010

city: Seattle

first: Andy

last: Itsara

state: WA

address: Foege Building S-250, Box 355065, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

summary: This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent.

overall_design: We attempted to validate 9 de novo CNVs in the same number of trios. In 3 cases, paternal DNA was not available leaving a total of 24 distinct samples for hybridization. All samples were hybridized against a previously well-characterized reference (NA15510; see Tuzun et al., Nat Genet 2005).

first: Evan

last: Eichler


title: stationary phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl

status: Public on Jun 10 2010

city: Nagaoka

first: Toju

last: Iino

state: Niigata

address: 1603-1 Kamitomioka

department: Dept. Bioengineering

institute: Nagaoka University of Technology

summary: Transcriptomic analysis of the cells grown on biphenyl to stationary phase and those grown on biphenyl to mid-exponential phase

overall_design: 3x dual channel slides.

last: IINO

first: Keisuke

last: MIYAUCHI

first: Daisuke

last: KASAI

first: Eiji

last: MASAI

first: Masao

last: FUKUDA


title: Rhododoccus jostii RHA1 was grown in the sterilized soil with pyruvate

summary: Transcroptomic analysis of the cells grown on pyruvate in the sterilized soil and those grown on pyruvate to mid-exponenyial phase in a liquid medium

overall_design: 4x dual channel slides.

first: Yong

last: WANG

first: Takeshi

last: FUJII

first: Naoto

last: OGAWA


title: Rhododoccus jostii RHA1 was grown in the sterilized soil with biphenyl

summary: Transcriptomic analysis of the cells grown on biphenyl in the sterilized soil and those grown on biphenyl to mid-exponential phase in a liquid medium


title: solid-support dependent genes, Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal 2%-agar solid medium with vapor of biphenyl

summary: Transcriptomic analysis of the cells grown on biphenyl on a filter placed on a minimal agar medium and those grown on biphenyl to mid-exponential phase in a liquid medium


title: microRNA profiling in primary clear cell renal cell carcinoma

status: Public on Jul 22 2010

city: Toronto

first: George

last: Yousef

state: ON

address: 30 Bond Street

department: Pathology

country: Canada

institute: St.Michael's Hospital

summary: Renal cell carcinoma (RCC) is the most common neoplasm of the adult kidney.  Currently, there are no biomarkers for the diagnostic, prognostic, or predictive applications in RCC.  MicroRNAs (miRNAs) are short non protein-coding RNAs that negatively regulate gene expression and have been shown to be involved in cancer.  We analyzed a total of 70 matched pairs of clear cell RCC (ccRCC) and normal kidney tissues from the same patients by microarray analysis and validated our results by quantitative real time PCR. We identified 166 miRNAs significantly dysregulated in ccRCC.  MiR-122, miR-155 and miR-210 had the highest fold changes of overexpression while miR-200c, miR-335, and miR-218 were the most downregulated.  We performed extensive bioinformatics analysis including a combinatorial analysis of previously reported miRNAs dysregulated in RCC and extensive target prediction analysis. Many miRNAs were predicted to target a number of genes involved in RCC pathogenesis.  Our results showed that miRNA dysregulation in RCC can be attributed in part, to chromosomal aberrations, the co-regulation of miRNA clusters, and co-expression with host genes.  We also correlated miRNA expression with clinical characteristics and found miR-155 expression was correlated with ccRCC tumor size. In conclusion, our analysis showed that a number of miRNAs are dysregulated in ccRCC and may contribute to kidney cancer pathogenesis by targeting more than one key molecule. We identified mechanisms that may contribute to miRNA dysregulation in ccRCC.   Dysregulated miRNAs represent potential biomarkers for kidney cancer.

overall_design: We preformed a miRNA microarray on 20 pairs of matched primary clear cell renal cell carcinoma (ccRCC) and normal kidney tissue from the same patient (St. Michael's Hospital, Toronto, Canada).   One matched pair was used per array for a total of 20 arrays.  Microarray results were validated by quantitative real time PCR using an independent set of 50 matched pairs of ccRCC and normal kidney tissue from the same patient.

first: Nicole

last: White

first: Tian

middle: T

last: Bao

first: Joerg

last: Grigull


title: Custom array CGH validation of de novo CNVs in CEU HapMap samples

summary: This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459.

overall_design: 12 samples were hybridized in each of the three pedigrees (36 samples total) against a previously well-characterized reference (GM15510; see Tuzun et al., Nat Genet 2005).


title: Human Mammary Epithelial Cell Response to EGF, microarray analysis

status: Public on Apr 14 2010

city: Richland

first: Katrina

last: Waters

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary:
To understand how integration of multiple data types can help decipher cellular responses at the systems level, we analyzed the mitogenic response of human mammary epithelial cells to epidermal growth factor (EGF) using whole genome microarrays, mass spectrometry-based proteomics and large-scale western blots with over 1000 antibodies.  A time course analysis revealed significant differences in the expression of 3172 genes and 596 proteins, including protein phosphorylation changes measured by western blot. Integration of these disparate data types showed that each contributed qualitatively different components to the observed cell response to EGF and that varying degrees of concordance in gene expression and protein abundance measurements could be linked to specific biological processes.  Networks inferred from individual data types were relatively limited, whereas networks derived from the integrated data recapitulated the known major cellular responses to EGF and exhibited more highly connected signaling nodes than networks derived from any individual dataset.  While cell cycle regulatory pathways were altered as anticipated, we found the most robust response to mitogenic concentrations of EGF was induction of matrix metalloprotease cascades, highlighting the importance of the EGFR system as a regulator of the extracellular environment.  These results demonstrate the value of integrating multiple levels of biological information to more accurately reconstruct networks of cellular response.

Keywords: time-course analysis

overall_design: Synchronized human mammary epithelial cells were stimulated into mitosis using epidermal growth factor and samples were harvested at 1, 4, 8, 13, 18 and 24hrs for parallel analysis by microarray, global proteomics and western blot analysis.

first: H

middle: S

last: Wiley

first: Brian

middle: D

last: Thrall


title: Copy number profiling of gastric cancer cell lines and gastric tumor tissues

status: Public on Dec 31 2010

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

summary: Copy number profiling of 27 gastric cancer cell lines and 105 gastric tumor tissues. we hypothesized that a detailed fine-scale survey of genomic CNAs might reveal potential genes disrupted by fusion events in gastric cancer. We inferred the locations of likely chromosomal breakpoints by identifying regions where closely-spaced microarray probes exhibited striking transitions in copy number.

overall_design: 27 gastric cancer cell lines and 105 gastric tumor tissues were profiled by Agilent 244K microarray.


title: Vascular Permeability and Apoptosis are Separable Processes in Retinal Ischemia-Reperfusion Injury

status: Public on Jun 01 2010

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary:
Effects of Ischemic Preconditioning, Bevacizumab and Etanercept
Ischemia and reperfusion injury provides an acute model of ischemic retinopathy that includes neurodegeneration and VEGF-dependent vascular permeability and is amenable to rapid drug testing.  The distinct effects of ischemic preconditioning and bevacizumab demonstrate that the apoptotic and vascular responses to ischemia may be separated and that VEGF expression is not neuroprotective following ischemic-reperfusion.

overall_design:
Using transient ischemia followed by reperfusion (IR) to model ischemic retinal disease, this study compares the effects of ischemic preconditioning (IPC) and therapies targeting vascular endothelial growth factor (VEGF) and tumor necrosis factor α (TNFα) on retinal apoptosis, vascular permeability and mRNA biomarker expression.
Only the Ischemic Preconditioning (not Bevacizumab and Etanercept treated samples) were hybridized to arrays.  Study contains 6 replicates of control and 6 IP treated retinal samples.

first: Steven

middle: F

last: Abcouwer

first: Cheng-mao

last: Lin

first: Ellen

middle: B

last: Wolpert

first: Sumathi

last: Shanmugan

first: Eric

last: Schaefer

first: Willard

last: Freeman

first: Alistair

last: Barber

first: David

last: Antonetti


title: Transcriptomic differences between E. coli B REL606 and K-12 MG1655

status: Public on Sep 28 2009

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

summary:
Transcriptome profiles were analyzed using the samples taken at the exponential and stationary phases during the cultivation of REL606 and MG1655 in LB medium. At the exponential growth phase, most highly expressed genes of B were those for replication, translation, or nucleotide transport and metabolism, while many of the K-12 genes were involved in cell motility, transcription, carbohydrate transport, or energy production. At the stationary phase, many of the genes highly expressed in B were for transport and metabolism of various amino acids and carbohydrates, whereas those in K-12 had functions related to cell motility, ribosomal subunit protein production, or energy generation.
Many genes in REL606 and MG1655 showed highly distinct expression levels irrespective of growth conditions. Highly expressed genes in REL606 included those encoding enzymes for biosynthesis of L-arginine (argAGDECBHI) and branched-chain amino acid (ilvGMEDA), and those encoding a subunit of the L-arginine transporter (artJ), cytochrome b562 (cybC), subunits of the histidine ABC transporter (hisPJ), cytotoxins (hokED), outer membrane porin (ompF), L-arginine decarboxylase (speA), and cell division inhibitor (sulA). Highly expressed genes in MG1655 included those for chemotaxis (cheZYRWA, tap, trg, tsr), Lon protease (lon), C4-dicarboxylate-sensing histidine kinase (dcuS), chaperones (clpB, dnaK, groES, htpG, ibpA), the major subunit of type 1 fimbriae (fimA), a regulator of flagellar biosynthesis (flhC), glycerol-3-phosphate-dehydrogenase (glpABCD), glycerophosphoryl diester phosphodiesterase (glpQ), glycerol-3-phosphate transporter (glpT), hydrogenase 2 (hybCBO), outer membrane porins (nmpC, ompA, ompC), and galactitol transport and metabolism (gatYZC).

overall_design:
All microarray experiments were performed in duplicate with dye-swapping. The probes were spotted in duplicate onto the microarray.
Thus, the log2 of the intensity ratio with the two dyes for each spot was calculated from up to four values from the duplicated spot on the microarray and the dye-swap experiment.

first: SungHo

first: Jihyun

last: Kim


title: Gene expression analysis of zebrafish embryos depleted of arrb1 and/or arrb2 at 12 hpf

status: Public on Oct 30 2009

city: Shanghai

first: Rui

last: Yue

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: To comprehensively understand the genes affected by beta-arrestin1 depletion in zebrafish fish embryos at 12 hpf, microarray analysis was performed. As controls, zebrafish embryos depleted of beta-arrestin2 and double depletion of beta-arrestin1 and beta-arrestin2 were also analyzed.

overall_design: Briefly, 50 AB/WT zebrafish embryos injected with 4ng control MO, 4ng arrb1 MO, 4ng arrb2 MO and 4ng arrb1+ 4ng arrb2 MO were lyzed in Trizol reagent at 12 hpf. Total RNAs were extracted, and subsequent operation was performed according to Agilent "One-Color Microarray-Based Gene Expression Analysis" protocol, version 5.5.

first: Xiaosong

last: Liu

first: Cong

last: Zhao

first: Jiuhong

last: Kang

first: Gang

last: Pei


title: Transcriptional response of Leptospira interrogans to iron limitation and characterization of putative Fur-like protein

status: Public on Mar 22 2010

city: Clayton

first: Miranda

last: Lo

address: Wellington Road

country: Australia

institute: Monash University

summary: Leptospirosis is a globally significant zoonotic disease caused by Leptospira spp. Iron is essential for growth of most bacterial species. Since availability of iron is low in the host, pathogens have evolved complex iron acquisition mechanisms to survive and establish infection. Virulence genes in some bacteria have been shown to be iron-regulated. In many bacteria, expression of iron-uptake and storage proteins is regulated by Fur. L. interrogans encodes four predicted Fur homologs; we have constructed a mutant in one of these, la1857. We conducted microarray analysis to identify differentially expressed genes in L. interrogans serovar Manilae grown under low iron compared with normal iron conditions found in EMJH medium. We also compared the transcriptional profile of the la1857 mutant versus wild-type Manilae under normal and low iron conditions.

overall_design: Analysis used RNA derived from L. interrogans serovar Manilae grown under low iron (EMJH medium + 40 µM 2,2-dipyridyl) and normal iron as experimental and control samples, respectively.  We have a serovar Manilae mutant in la1857, one of four predicted fur homologs. The mutant was also grown under low iron and normal iron conditions and compared with wild-type Manilae grown under low and normal iron conditions respectively. Three independent RNA samples (biological replicates) from parent and mutant strains grown with or without 2,2-dipyridyl were compared in a loop design resulting in 12 arrays. The orientation of Cy3 to Cy5 labeling was the same for replicates 1 and 3, while replicate 2 was a dye swap. Direct comparisons were made between arrays of experimental and control samples using raw data pulled from two different channels for data analysis. Data from wild-type Manilae grown under low iron versus normal iron and mutant versus wild-type under normal iron conditions is reported in the manuscript.

first: Gerald

last: Murray

first: Chen

last: Khoo

last: Haake

first: Richard

last: Zuerner

first: Ben

last: Adler


title: Raloxifene Attenuates Gas6 and Apoptosis in Experimental Aortic Valve Disease in Renal Failure

status: Public on May 11 2010

city: Jerusalem

first: Mony

last: Shuvy

address: Ein-Karem

department: Cardiology

country: Israel

institute: Hadassah Hospital

summary: Introduction: Renal failure is associated with aortic valve calcification. Using our rat model of uraemia-induced reversible aortic valve calcification, we assessed the role of apoptosis and survival pathways in aortic valve calcification. We also explored the effects of raloxifene - an estrogen receptor modulator on valvular calcification.  Methods: Gene array analysis was performed in aortic valves obtained from 3 groups of rats (n=7 each): calcified valves from rats fed with uremic diet -high-adenine (0.75%), high-phosphate diet (1.5%), valves after calcification resolution following diet cessation (reversibility) and control. In addition, four groups of rats (n=10 each) were used in order to evaluate the effect of raloxifene in aortic valve calcification: three groups as mentioned above and a fourth group fed with the uremic diet which also received daily raloxifene.  Evaluation of these groups included imaging, histology and antigen expression analysis.   Results: Gene array results showed that the majority of the expressed genes that were altered were from the diet group valves. Most apoptosis-related genes were changed in a pro-apoptotic direction in calcified valves. Apoptosis and decrease in several survival pathways were confirmed in calcified valves. Resolution of aortic valve calcification was accompanied by decreased apoptosis and upregulation of these ant-apoptotic pathways. Imaging and histology demonstrated that raloxifene significantly decreased aortic valve calcification.   Conclusion: Downregulation of several survival pathways and apoptosis are involved in the pathogenesis of aortic valve calcification. The beneficial effect of raloxifene in valve calcification is related to apoptosis modulation. This novel observation is important for developing remedies for aortic valve calcification in patients with renal failure.  Introduction: Renal failure is associated with aortic valve calcification. Using our rat model of uraemia-induced reversible aortic valve calcification, we assessed the role of apoptosis and survival pathways in aortic valve calcification. We also explored the effects of raloxifene - an estrogen receptor modulator on valvular calcification.  Methods: Gene array analysis was performed in aortic valves obtained from 3 groups of rats (n=7 each): calcified valves from rats fed with uremic diet -high-adenine (0.75%), high-phosphate diet (1.5%), valves after calcification resolution following diet cessation (reversibility) and control. In addition, four groups of rats (n=10 each) were used in order to evaluate the effect of raloxifene in aortic valve calcification: three groups as mentioned above and a fourth group fed with the uremic diet which also received daily raloxifene.  Evaluation of these groups included imaging, histology and antigen expression analysis.   Results: Gene array results showed that the majority of the expressed genes that were altered were from the diet group valves. Most apoptosis-related genes were changed in a pro-apoptotic direction in calcified valves. Apoptosis and decrease in several survival pathways were confirmed in calcified valves. Resolution of aortic valve calcification was accompanied by decreased apoptosis and upregulation of these ant-apoptotic pathways. Imaging and histology demonstrated that raloxifene significantly decreased aortic valve calcification.   Conclusion: Downregulation of several survival pathways and apoptosis are involved in the pathogenesis of aortic valve calcification. The beneficial effect of raloxifene in valve calcification is related to apoptosis modulation. This novel observation is important for developing remedies for aortic valve calcification in patients with renal failure.

overall_design: Three-condition experiment,  Uremic-Diet, Reversibility and Control rats. Biological replicates: 7 in each group pooled together.

first: Suzan

last: Abedat

first: Ronen

last: Beeri

first: Michael

last: Valitsky

first: Sameh

last: Daher

first: Miriam

last: Kott-Gutkowski

first: Anca

last: Gal-Moscovici

first: Nalini

last: Rajamannan

first: Chaim

last: Lotan


title: Mechanism for hepatic tumor promotion by PFOA in rainbow trout

status: Public on Aug 31 2007

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary:
Perfluorooctanoic acid (PFOA) is a potent hepatocarcinogen and peroxisome proliferator (PP) in rodents.  Humans are not susceptible to peroxisome proliferation and are thought to be refractory to carcinogenesis by PFOA and other PPs.  However, previous studies with rainbow trout have shown that they are also insensitive to peroxisome proliferation by the PP, dehydroepiandrosterone (DHEA), but are still susceptible to enhanced hepatocarcinogenesis after chronic exposure.  In this study, we determined whether PFOA is also a tumor promotor in trout and then examined hepatic gene expression profiles to further investigate possible mechanisms of action.  Trout were initiated as fry to the hepatocarcinogen, aflatoxin B1, and then fed 200-1800 ppm PFOA in the diet for 30 weeks.  Two structurally diverse PPs, clofibrate (CLOF) and DHEA, were included for comparison.  Hepatic gene expression profiles were subsequently examined in animals exposed to similar doses of PFOA, DHEA and CLOF along with 5 ppm 17β-estradiol (E2; a known tumor promotor) in the diet.  PFOA (1800 ppm) and DHEA treatments resulted in enhanced liver tumor incidence and multiplicity while CLOF showed no effect.  Carcinogenesis seemed independent of peroxisome proliferation as no induction of peroxisomal β-oxidation and catalase activity were observed.  Alternately, plasma VTG was elevated in fish fed PFOA and DHEA suggesting that estrogenic mechanisms may play a role.  Both tumor promotors, PFOA and DHEA, resulted in strong correlation of transcriptional profiles with E2 by Pearson correlation (R=0.81 and 0.78, respectively).  In comparison, CLOF regulated no genes in common with E2.  Overall, these data suggest that the tumor promoting activities of DHEA and PFOA in trout are independent of peroxisome proliferation and may involve estrogenic mechanisms.
Keywords: treatment effect

overall_design: Juvenile trout, 12-18 months old, were fed experimental diets containing 500 or 1800 ppm PFOA, 1800 ppm CLOF, 750 ppm DHEA, 5 ppm E2 or 0.15 % dimethyl sulfoxide vehicle control for 14 days.  Liver samples were collected for microarray analysis.  Hybridizations were performed using standard reference design with dye-swapping. For each sample, equal amounts of RNA (µg) were pooled from five fish per tank for every treatment (n=3 biological replicates per treatment). cDNA from two of the three biological replicates was dye-swapped and hybridized to two slides as technical replicates (5 arrays per treatment).

first: Gayle

last: Orner

first: Abby

last: Benninghoff

first: Jerry

last: Hendricks

first: Cliff

last: Pereira

first: David

middle: E

last: Williams


title: Gene expression profiles after infection of zebrafish with viral haemorrhagic septicemia rhabdovirus (VHSV)

status: Public on Feb 01 2010

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

summary: We describe for the first time transcripts induced after infection of zebrafish with viral haemorrhagic septicemia rhabdovirus (VHSV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in both fins and internal organs (pooled spleen, head kidney and liver).

overall_design: VHSV-induced gene expression in zebrafish fins and organs was measured at 2 days after infection.  Four independent experiments were performed for each treatment and their corresponding controls.


title: whole reference dataset (cell wall chip)

status: Public on Mar 01 2005

first: Javier

last: Arroyo

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

institute: Facultad de Farmacia (UCM)

summary:
Data processing included:

1. Filtering of those bad quality image spots (these includes alterations on the shape or hybridization)

2. Filtering of low intensity which was done flagging with -50 those spots whose feature intensity was lower in any of both channels than the average of the local background in the corresponding channel for all spots. However, those genes whose feature intensity in one channel was under the limit but in the other channel was 5 times over limit were considered as on-off genes and were not filtered.

3. Filtering of low reproducibility intrachip replicated spots. Normal distribution was created with the value obtained from the formula: log2(Rax1/Rb) which means logarithm (two-based) of one ratio multiplied by the inverse of its replicate. This value for each gene shoud keep between the range of average ± 3SD. Those genes out of these range are flagged as -25

4. Normalization of ratios was done by Lowess mathematical method. Correction factor was 0.33

Keywords: other

first: Jose

last: Rodríguez-Peña

first: Rosa

last: Pérez-Díaz

first: Sara

last: Alvarez

first: Clara

last: Bermejo

first: Raúl

last: García

first: Catalina

last: Santiago

first: César

last: Nombela


title: SARST analysis of arctic soil samples

status: Public on Jan 12 2004

city: Vancouver

first: Josh

last: Neufeld

state: BC

address: #300-6174 University Blvd.

department: Department of Microbiology & Immunology

institute: University of British Columbia

summary:
Analysis of microbial community composition in arctic tundra and boreal forest soils using serial analysis of ribosomal sequence tags (SARST).
Keywords: other

first: J

first: W

last: Mohn

first: Z

last: Yu

last: Lam


title: Effects of Fescue Toxins On Hepatic Gene Expression in Mice.

status: Public on Jan 26 2005

city: Columbia

first: Sachin

last: Bhusari

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: Univ of Missouri

summary:
Fescue toxicosis is a disease of wild and domestic animals grazing on fescue pasture infected with the endophytic fungus, Neotyphodium Coenophialum. Mice, previously selected for increased sensitivity to endophyte-infected fescue seed diets indicated by slow weight gain, were used to study the effects of fescue toxicosis on hepatic gene expression. Liver genes differentially expressed due to fescue toxins were studied using DNA microarray. A two-stage ANOVA of microarray data identified forty differentially expressed genes between mice fed endophyte-infected (E+) and endophyte-free (E-) fescue seeds. Significant Analysis of Microarray (SAM) analysis identified 9 genes as differentially expressed between treatment groups. Hierarchical clustering with the 40 genes identified by ANOVA clearly separate the mice according to their diets, with 100% confidence as computed by bootstrap analysis. Expressions of eleven genes were verified using quantitative real-time PCR (qPCR). The E+ diet resulted in downregulation of genes involved in sex-steroid metabolism pathway, genes involved in cholesterol and lipid metabolism.
Keywords = Endophyte
Keywords = Fescue Toxicosis
Keywords = microarray
Keywords: repeat sample

first: S.

first: L.

last: Hearne

first: D.

last: Spiers

first: W.

middle: R

last: Lamberson

first: E.

last: Antoniou


title: Zebrafish von Hippel-Lindau (vhl) tumor suppressor mutants compared to siblings at 7 dpf

status: Public on Mar 01 2009

city: Utrecht

first: Ellen

last: van Rooijen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute- KNAW and UMC Utrecht

summary: We have generated two zebrafish lines carrying inactivating germline mutations in the von Hippel-Lindau (VHL) tumor suppressor gene ortholog vhl. Mutant embryos display a general systemic hypoxic response, including the upregulation of hypoxia-induced genes by 1 day post-fertilization and a severe hyperventilation and cardiophysiological response. vhl mutants develop polycythemia with concomitantly increased epo/epor mRNA levels and Epo signaling. In situ hybridizations reveal global up-regulation of both red and white hematopoietic lineages. Hematopoietic tissues are highly proliferative, with enlarged populations of c-myb+ HSCs and circulating erythroid precursors. Chemical activation of Hif-signaling recapitulated aspects of the vhl-/- phenotype. Furthermore, microarray expression analysis confirms the hypoxic response and hematopoietic phenotype observed in vhl-/- embryos. We conclude that Vhl participates in regulating hematopoiesis and erythroid differentiation. Injections with human VHLp30 and R200W mutant mRNA demonstrate functional conservation of VHL between mammals and zebrafish at the amino acid level, indicating that vhl mutants are a powerful new tool to study genotype-phenotype correlations in human disease. Zebrafish mutants are the first congenital embryonic viable systemic vertebrate animal model for VHL, representing the most accurate model for VHL-associated polycythemia to date. They will contribute to our understanding of hypoxic signaling, hematopoiesis and VHL-associated disease progression.

overall_design: We have compared gene expression profiles between pooled zebrafish vhl mutants and siblings from four different transheterozygous (hu2081/+ x hu2117/+) clutches at 7 days post-fertilization. Samples were run in dye-swap. Results were validated by whole mount in situ hybridization.

first: Emile

last: Voest

first: Ive

last: Logister

first: Stefan

last: Schulte-Merker

first: Rachel

last: Giles

first: Freek

last: van Eeden


title: Cynomolgus monkey testicular cDNAs for discovery of novel human genes

status: Public on Jul 16 2003

city: Tokyo

first: Naoki

last: Osada

state: Tokyo

address: 1-23-1, Toyama-cho, Shinjuku-ku

institute: National Institute of Infectious Diseases

summary:
BACKGROUND: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. RESULT: The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl.We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously. CONCLUSIONS: In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies.
Keywords: other

sample_organism:
Macaca fascicularis
Homo sapiens

first: Munetomo

last: Hida

first: Jun

last: Kusuda

first: Reiko

last: Tanuma

first: Makoto

last: Hirata

first: Yumiko

last: Suto

first: Momoki

last: Hirai

first: Keiji

last: Terao

first: Sumko

last: Sugano

first: Katsuyuki

last: Hasihmoto


title: Hog1 mutant 4 hours exposure to congo red (cell wall chip)

first: Javier

last: Arroyo

summary:
S. cerevisiae hog1 mutant strain was grown on YEPD. For Congo Red experiments, yest cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 µg/ml. Cells were collected at 4hours of growth, frozen at -80 °C and processed for RNA extraction.
Keywords: repeat sample

first: Jose

last: Rodríguez-Peña

first: Rosa

last: Pérez-Díaz

first: Sara

last: Alvarez

first: Clara

last: Bermejo

first: Raúl

last: García

first: Catalina

last: Santiago

first: Cesar

last: Nombela


title: Transition phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl

status: Public on Jun 09 2010

first: Toju

last: Iino

summary: Transcriptomic analysis of the cells grown on biphenyl to transition phase and those grown on biphenyl to mid-exponential phase

overall_design: 3x dual channel slides

last: IINO

first: Keisuke

last: MIYAUCHI

first: Daisuke

last: KASAI

first: Eiji

last: MASAI

first: Masao

last: FUKUDA