title: Transcritome in the absence of FUN30

status: Public on Jun 15 2012

city: marseille

first: bertrand

last: llorente

address: 31 chemin josephh aiguier

institute: cnrs

summary: Analysis of the Saccharomyces cerevisiae transcriptome in the absence of the chromatin remodeler Fun30

overall_design: A wild type and a fun30 null strain were grown in rich medium. Each culture was divided in two before RNA extraction. Two hybridizations were performed, both using independent RNA preparations from WT and the fun30 null mutant.

first: Bertrand

last: Llorente


title: NanoString miRNA profiling of peripheral blood sorted CD14+CD16- monocytes from amyotrophic lateral sclerosis, multiple sclerosis and healthy control subjects

status: Public on Jul 26 2012

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

summary:
We investigated the innate immune system in the SOD1 ALS model. We found that splenic Ly6CHi monocytes were activated and their progressive recruitment to the spinal cord, but not brain, correlated with neuronal loss. We found a decrease in resident microglia in the spinal cord with disease progression. Two months prior to disease onset, splenic Ly6CHi monocytes had an M1 signature which included increased CCR2. At one month prior to disease onset, microglia expressed increased CCL2 and other chemotaxis-associated molecules. Microglia derived from the spinal cord of SOD1 mice recruited Ly6C+ monocytes to the CNS. Treatment with anti-Ly6C mAb modulated the Ly6CHi monocyte cytokine profile, reduced monocyte recruitment to the spinal cord, diminished neuronal loss and extended survival. In humans with ALS, CD14+/CD16- monocytes (analogue of Ly6CHi monocytes) exhibited an ALS specific microRNA inflammatory signature similar to that observed in the SOD1 mouse providing a direct link between the animal model and the human disease. Thus, the SOD1-like profile of monocytes in ALS subjects may serve as a biomarker for disease stage or progression. Our results suggest that recruitment of inflammatory monocytes plays an important role in disease progression and that modulation of these cells is a potential therapeutic approach.
This study used the NanoString nCounter hybridization system and nCounter miRNA expression assays to identify and quantitate miRNAs in blood CD14+CD16- monocytes from ALS, MS and HC subjects

overall_design: Total RNA was isolated from FACS sorted CD14+CD16- blood-derived monocytes from sporadic ALS (n=8), MS (n=8) and HC (n=8) subjects. RNA was profiled using the NanoString nCounter miRNA expression assay


title: plasmid-based BIR screen in S. cerevisiae

country: France

summary: We used a plamsid-based assay to identify novel S. cerevisiae mutants with abnormal Break Induced Replication (BIR) efficiencies. We pooled the ca. 5000 yeast deletion mutants from the systematic deletion library and compared the relative tranformation efficiencies of a circular versus linear truncated minichromosome using tag arrays. Our main result is the identification of Fun30 as a novel chromatin remodelr facilitating DNA end resection.

overall_design: A pool of ca. 5000 yeast deletion mutants from the systematic deletion library was transformed with a circular minichromosome on one hand, and with a linear truncated minichromosome on the other hand. Transformants were recovered, DNA was extracted and the systematic tags were PCR amplified with complementary dyes for the two transformations. Amplified tags were mixed and hybridized on a tag array. The overall experiment was done twice.


title: Expression analysis of Streptococcus pyogenes MGAS315 induced with XIP pheromone

status: Public on Jun 01 2012

city: Chicago

first: Michael

middle: J

last: Federle

state: IL

address: 900 S Ashland Ave. MC870

department: Microbiology & Imm. / Cntr Pharm Biotech

institute: University of Illinois at Chicago

type: Expression profiling by genome tiling array

summary:
Whole genome expression profile comparing MGAS315 treated with XIP pheromone versus vehicle-treated cells
Interpretations are described further in the manuscript to be submitted: authors Mashburn-Warren, Morrison, and Federle. Title: The Cryptic Competence Pathway in Streptococcus pyogenes is Controlled by a Peptide Pheromone.

overall_design: A two chip study using total RNA recovered from three separate cultures of Streptococcus pyogenes MGAS315, each treated with either XIP pheromone or with vehicle; RNA preparation of cultures receiving same type of treatment were pooled using equivalent amounts of RNA from each culture. RNA pools were fluorescently labeled and hybridized to arrays designed to the S. pyogenes NZ131 genome.

first: Lauren

last: Mashburn-Warren

first: Donald

last: Morrison


title: Antisense Transcripts in Mutant Strains

status: Public on May 08 2012

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: The positioning of the nucleosome by ATP-dependent nucleosome remodelers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Here, we report that the fission yeast CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in the production of antisense transcripts and perturbation of the nucleosome in an ATPase mutant of Hrp3 was also associated with destabilization of the DNA-histone interaction. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome is important for the spatial-temporal control of transcription-associated processes, and show that this is accomplished by the chromatin remodeler, Hrp3, in fission yeast.

overall_design: Two-condition experiment, Mutant vs Wild-type (control)

first: Yunjeong

first: Keunsoo

last: Kang


title: Analysis of the sigS regulon

status: Public on Feb 01 2012

city: Tampa

first: Ronan

middle: Kevin

last: Carroll

address: 4202 E Fowler Ave

department: CMMB

institute: University of South Florida

summary:
The sigS gene in S. aureus encodes an ECF sigma factor.  ECF sigma factors bind to core-RNA polymerase and redirecting promoter recognition to coordinate gene expression.
To determine all of the genes in S. aureus whose expression is SigS dependent we preformed a microarray analysis of a wild type and sigS mutant strain.  Genes showing altered expression levels in the sigS mutant versus the wild type were deemed SigS dependent.

overall_design: Two strains of S. aureus were used, the wild type RN4220 strain, and RN4220 containing a sigS mutation.  Each strain was grown in triplicate, in TSB broth, at 37°C with shaking.  The RN4220 sigS mutant has an increased lag phase.  Therefore to synchronize cultures and isolate RNA from cells in the same phase of growth samples for microarray analysis were taken following 3 h growth of the wild type (which corresponds to a timepoint when sigS expression is at its highest) and 5 h growth of the sigS mutant.

middle: K

first: Halie

last: Miller


title: E. coli O157:H7 phage type 21/28 & 32 CGH analysis

status: Public on Apr 21 2012

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Six isolates of PT21/28 and six of PT32 were analysed by CGH using UBECarray3 microarrays (containing probes for E. coli K-12 str. MG1655 and O157:H7 str. EDL933 and Sakai) to define genotypic differences between phage types. gDNA from E.coli O157 str. Sakai was hybridised to all arrays to provide a universal control channel on all arrays.

sample_organism:
Escherichia coli O157:H7
Escherichia coli O157:H7 str. Sakai

overall_design: gDNA from 12 PT 21/28 & 32 isolates were labelled with Cy5 and control gDNA from str. Sakai was labelled with Cy3. Test and control gDNA was hybridised to UBECarray3 microarrays. The LOWESS normalised relative signal to the Sakai control channel was used to compare between samples.

first: Xuefang

last: Xu


title: Dietary soyasaponin supplementation to pea protein concentrate reveals nutrigenomic interactions underlying enteropathy in Atlantic salmon

status: Public on Dec 21 2011

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Atlantic salmon was fed with diets based on five plant protein sources combined with soyabean saponins. Diets with corn gluten, sunflower, rapeseed and horsebean produced minor effects while combination of saponins with pea protein concentrate caused enteritis and major transcriptome changes in the distal intestine.

overall_design: Microarray analyses were perfromed in distant intestine. Individual samples from fish that received saponing were hybridized to pools from salmon fed with the same feeds without saponins.

first: T

middle: M

last: Kortner

first: Skugor

last: Stanko


title: Transcriptional profiling of Vitis vinifera during grapevine-downy mildew interaction using cDNA microarrays

status: Public on Apr 06 2012

city: Lisboa

first: Andreia

last: Figueiredo

address: Campo Grande

department: UMBPB

country: Portugal

institute: ICAT/FCUL

summary:
Study of gene expression during Plasmopara viticola infection in the resistant Vitis vinifera cultivar 'Regent'.
The oomycete fungus Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is responsible for grapevine downy mildew disease. Most of the cultivated grapevines are sensitive to this pathogen, thus requiring intensive fungicide treatments. The molecular basis of resistance to this pathogen is poorly understood. We have carried out a cDNA microarray transcriptome analysis to identify grapevine genes associated with resistance traits.
Early transcriptional changes associated with downy mildew infection in the resistant Vitis vinifera cultivar ‘Regent’, when compared to the susceptible cultivar ‘Trincadeira’, were analyzed. Transcript levels were measured at three time-points: 0, 6 and 12 hours post inoculation (hpi). Our data indicate that resistance in V. vinifera ‘Regent’ is induced after infection. This study provides the identification of several candidate genes that may be related to ‘Regent’ defense mechanisms, allowing a better understanding of this cultivar's resistance traits.

overall_design: 3 time points: 0, 6 and 12 hours post inoculation by P. viticola. Two cultivars: control (Trinacedira) and test (Regent). Two biological replicates were performed at 0 hpi, and 3 biological replicates at 6 and 12hpi. At 12hpi, three technical replicates also were performed.

first: Filipa

last: Monteiro

first: Ana

last: Fortes

first: Lisete

last: Sousa

first: Martina

last: Rex

first: Reinhard

last: Töpfer

first: Eva

last: Zyprian

first: Maria

middle: S

last: Pais


title: VALIDATION STUDY TO VERIFY DIAGNOSTIC MARKERS FOR LUNG CANCER IN ENDOBRONCHIAL LINING FLUID

status: Public on Dec 31 2011

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: We investigated whether biomarker analysis in endobronchial epithelial lining fluid (ELF) collected by bronchoscopic microsampling may be useful for a definitive preoperative diagnosis. Therefore we compared ELF samples close to nodule and from the contralateral site from patients with malignant or benign diagnosis.

overall_design:
ELF samples have been derived from early stage NSCLC patients and controls. Wilcox Test was performed to identify differentially expressed genes associated to a malignant diagnosis.
key words: disease subtype analysis

first: Holger

last: Sueltmann

first: Marc

last: Johannes

first: Michael

last: Meister

first: Nicolas

last: Kahn

first: Thomas

last: Muley


status: Public on Sep 01 2011

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: Gene expression profiling of Mycobacterium tuberculosis H37Rv in response to compound CDRI-5g (Saquib, M. et al. Eur. J. Med. Chem. 46 (2011) 2217-2223) was studied by administration of compound at 10 µg/ml in broth culture. RNA was extracted at two time points 12 h and 24 h of growth from replicating phase and compound added culture. Replicating phase culture was incubated for the same time and used as a control. Experiment was repeated three times and for each time points triplicate culture was pelleted to isolate total RNA using Qiagen RNA isolation kit.

overall_design: One-color experiment,Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-019943)

first: Ranjana

last: Srivastava

first: Ravi

last: Gupta


title: miRNA expression profile in PCa And BPH tissue from Chinese patients

status: Public on Feb 28 2012

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: To study the miRNA modulating network and different expressed miRNA lists in prostate cancer, we use high-throughout method to genomically detect the expression profile of miRNA, mRNA and protein.

overall_design: Agilent microarray products for miRNA and mRNA expression profile were chose. With GE Ettan DIGE System, the differentiated expression proteins are detected. As possible as we can to use the same sample for miRNA, mRNA and protein experiment. 4 prostate cancer tissues and 4 normal tissues are applied to mRNA microarray experiment. The mRNA microarray experiment service are supplied by ShanghaiBio Corporation (Shanghai,China).

first: Weide

last: Zhong

first: Huichan

last: He

first: Xingyin

last: Liu

first: Qishan

last: Dai

first: Funeng

last: Jiang

first: Jin

last: Zhao

first: Dongjiang

last: Liao

first: Xinpeng

last: Lu


title: S. aureus expression properties of exponential ISP794 and isogenic norG mutant cells

status: Public on Sep 02 2011

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary: The GntR-like protein NorG has been shown to affect Staphylococcus aureus genes involved in the resistance to quinolones and beta-lactams such as those encoding the NorB and AbcA transporters. To identify the target genes regulated by NorG, we carried out transcriptional profiling assays using S. aureus RN6390 and its isogenic norG::cat mutant. Our data showed that NorG positively affected the transcription of global regulators mgrA, arlS, and sarZ.   The three putative drug efflux pump genes most positively affected by NorG were the NorB efflux pump (5.1-fold), the MmpL-like protein SACOL2566 (5.2-fold), and the BcrA-like drug transporter SACOL2525 (5.7-fold).  The S. aureus predicted MmpL protein showed 53% homology with the MmpL lipid transporter of Mycobacterium tuberculosis, and the putative SACOL2525 protein showed 87% homology with the bacitracin drug transporter BcrA of Staphylococcus hominis. Two pump genes most negatively affected by NorG were NorC (4-fold) and AbcA (6-fold). Other categories of genes such as those participating in amino acid, inorganic ion, or nucleotide transporters and metabolism, were also affected by NorG. Real-time RT-PCR assays for mgrA, arlS, sarZ, norB, norC, abcA, mmpL, and bcrA-like were carried out to verify microarray data and showed the same level of up- or down regulation by NorG. The norG mutant showed a twofold increase in the resistance to norfloxacin and rhodamine, both substrates of the NorC transporter, which is consistent with the resistance phenotype conferred by overexpression of norC on a plasmid. These data indicate that NorG has broad regulatory function in S. aureus.

overall_design: The goal of this study was to define the transcriptional response of S. aureus norG mutant cells.  To do so, commercially available S. aureus Affymetrix GeneChips (Santa Clara, CA) were used to compare the expression properties of wild type (ISP794) and isogenic norG (QT11) mutant cells.  S. aureus strains ISP794 and QT11 were grown to mid exponential phase growth, lysed , total bacterial RNA was extracted, labeled and hybridized to commerically available S. aureus Affymetrix GeneChips.  In total three biological replicates were compared for each strain background.

first: Quechi

last: Truong-Bolduc

first: Tess

last: Eidem

first: David

middle: C

last: Hooper


title: CGH analysis of haploid ES cells

status: Public on Jul 23 2011

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

type: Genome variation profiling by genome tiling array

summary:
DNA samples of haploid ES cells and control DNA were compared to genomic DNA of the C57B/6 inbred mouse strain on a NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9), (GPL10989)
DNA samples of haploid ES cells and control DNA were compared to genomic DNA of the 129/Sv inbred mouse strain on a NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9), (GPL10989)

overall_design:
this analysis was performed to analyse copy number variations in haploid mouse ES cells from different genetic backgrounds. Male C57/B6 DNA was used as control. To identify CNVs based on the different genetic background control experiments comparing DNA from the inbred CBA and a mixed transgeneic mouse strain were performed.
this analysis was performed to analyse copy number variations in haploid mouse ES cells from different genetic backgrounds. Male 129/Sv kidney DNA was used as reference.

first: Anton

last: Wutz

first: Austin

last: Smith


title: Inhibition of VCAM-1 expression by CORM-3: the role of the ubiquitin proteasome system, p38 and mitochondrial respiration

status: Public on Jul 11 2011

city: Mannheim

first: Benito

last: Yard

address: Theodor-Kutzer-Ufer 1-3

institute: University hospital Mannheim

summary: Carbon monoxide (CO) abrogates TNF-alpha mediated inflammatory responses in endothelial cells, yet, the underlying mechanism hereof is still elusive. We sought to explore potential mechanisms by which CO down-regulates VCAM-1 expression on TNF-alpha stimulated human umbilical vein endothelial cells (HUVEC).  By genome-wide gene expression profiling and pathway analysis we studied the relevance of particular pathways for the anti-inflammatory effect of CO.   In CO-releasing molecules-3 (CORM-3) stimulated HUVEC, significant changes in gene expression were found for genes implicated in the proteasome and porphyrine pathways. Although proteasome activities were increased by CORM-3, proteasome inhibitors did not abolish CORM-3‘s effect. Likewise, HO-1 inhibitors did not abrogate the ability of CORM-3 to down-regulate VCAM-1 expression. MAPK p38 was inhibited by CORM-3. Accordingly, VCAM-1 expression was down-regulated by the p38 inhibitor SB203580. Down-regulation of VCAM-1 by CORM-3 only occurred at concentrations that partly inhibit ATP production. Sodium azide and oligomycin paralleled the effect of CORM-3 in this regard.  In conclusion, down-regulation of VCAM-1 by CORM-3 seems to be mediated via inhibition of p38 and mitochondrial respiration. Although CORM-3 up-regulates several genes in the ubiquitin proteasome sytem (UPS) or porphyrin pathway, there is no evidence that these changes are involved in the anti-inflammatory properties of CORM-3.

overall_design: In this study we focused on the potential of CORM-3 to downregulate the expression of TNF-alpha mediated inflammataroy genes

first: Claudia

last: Bergstrasser

first: Neysan

last: Rafat

first: Simone

last: Höger

first: Hui

last: Song

first: Linda

last: Ermantraut

first: Maxi

last: Hottenrot

first: Tobias

last: Czymai

first: Marc

last: Schmidt

first: Matthias

last: Goebeler

first: Norbert

last: Ponelies

first: Carsten

last: Sticht

first: Ralf

last: Loesel

first: Grietje

last: Molema

last: Seelen

first: Willem

last: van Son

middle: A


title: A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence

status: Public on Aug 03 2011

first: Levi

last: Waldron

address: 655 Huntington Avenue

department: Biostatistics

institute: Harvard School of Publich Health

summary: Samples were prospectively collected from patients with histologically normal surgical resection margins. 96 tissue samples (histologically normal margins, oral carcinoma and adjacent normal tissues) from 24 patients comprised the training set. Our study design was guided by the hypothesis that the expression of genes present in oral squamous cell carcinoma (OSCC) but not in healthy oral tissues would be indicative of recurrence in advance of histological alteration. We used meta-analysis of five published microarray data sets (GEO accession GDS2520, Kuriakose et al. 2004; GDS1584, Toruner et al. 2004; GSE6791, Pyeon et al. 2007; GSE9844, Ye et al. 2008; and GSE10121, Sticht et al. 2008), in conjunction with the current training set, to identify genes reliably over-expressed in OSCC. This reduced gene set was used to train a risk model to predict recurrence based on over-expression of a subset of these genes in histologically normal surgical resection margins. Validation of the risk signature was performed using quantitative real-time reverse-transcription PCR in an independent set of 136 samples from an independent cohort of 30 patients.

overall_design: This was a case-only design involving a training set of 23 tumors and 73 margins from 24 patients with squamous cell carcinoma of the tongue.

first: Patricia

middle: P

last: Reis

first: Bayardo

last: Perez-Ordonez

first: Melania

last: Pintilie

first: Natalie

middle: N

last: Galloni

first: Yali

last: Xuan

first: Nilva

last: Cervigne

first: Giles

last: Warner

first: Antti

last: Makitie

first: Colleen

last: Simpson

first: David

last: Goldstein

first: Dale

last: Brown

first: Ralph

last: Gilbert

first: Patrick

last: Gullane

first: Jonathan

last: Irish

first: Igor

last: Jurisica

first: Suzanne

last: Kamel-Reid


title: Low dose human APAP exposure

status: Public on Jul 07 2011

city: Maastricht

first: marlon

last: jetten

address: universiteitssingel 50

country: Netherlands

institute: maastricht university

summary:
Acetaminophen is the primary cause of acute liver toxicity in Europe/USA. Therefore, the FDA reconsiders recommendations concerning safe acetaminophen dosage/use. Current tests for liver toxicity are no ideal predictive markers for liver injury. Here, ‘omics techniques (global analysis of metabolomic/gene expression responses) may provide additional insight.
To better understand acetaminophen-induced responses at low dose, we evaluated effects of (sub-)therapeutic acetaminophen doses on metabolite formation/global gene-expression changes (including, for the first time, miRNA) in blood/urine samples from healthy human volunteers.

overall_design: Three dose rounds with 6 individuals were performed with 0.5, 2 or 4 g APAP. In the 0.5 and 2 g dose-rounds T0(control) T1, T7 and T25 samples were collected in the 4g round only T0(control) and T25 samples are available.

first: Marlon

last: Jetten

first: Stan

last: Gaj

first: Ainhoa

last: Ruiz-Aracama

first: Theo

last: de Kok

first: Joost

last: van Delft

first: Arjen

last: Lommen

first: Eugene

last: van Someren

first: Danyel

last: Jennen

first: Sandra

last: Claessen

first: Ad

last: Peijnenburg

first: Rob

last: Stierum

first: Jos

last: Kleinjans


title: Changes in the transcriptome of Entamoeba histolytica accompany the epigenetic silencing of the amoebapore gene.

status: Public on Aug 31 2011

city: Charlottesville

first: Carol

last: Gilchrist

state: VA

address: Dept. of Medicine/Division of Infectious Diseases, Building MR4, Rm 2126,PO Box 801365

department: Medicine

institute: University of Virginia

summary: We previously showed that epigenetic transcriptional silencing of the amoebapore gene (Ehap-a) in E. histolytica G3 trophozoites was accompanied by the down-regulation of two other members of the saposin-like gene family (Ehap-b, and EhSaplip1).  Comparison of the transcriptomes of G3 trophozoites with those of the parent HM-1:IMSS strain revealed 72 additional transcripts that were either down- or up-regulated at least 7 fold. One of the polyA+, up-regulated (>200) transcripts (459.m00030), had the potential to encode a 66 amino acid protein.  Antibodies raised against a synthetic N-terminal peptide of the gene did not recognize any such protein in trophozoite lysates. Trophozoite cultures grown with the proteasome inhibitor MG-132 to prevent protein degradation, also did not have any detectable protein. Transfections with a plasmid in which the Ehactin gene promoter elements were used to flank the 459.m gene, significantly increased their level transcript but again, no protein was detected. Transfectants in which the 459.m ORF was placed downstream to the GST gene, expressed a fused protein which reacted with the antibody against the m.459 peptide. Constructs with the CAT reporter gene placed under the 459.m gene promoter element or fused to the C-terminal sequence of the 459.m ORF were prepared to determine if the higher levels of 459.m transcript found in the G3 trophozoites were due to changes in the stability of the transcript or increased transcription. No difference was observed in the very weak expressions seen in both G3 and HM-1:IMSS transfectants. Similarly, transfectants with a plasmid construct in which the 459.m gene was placed under its regulatory elements, did not induce an increase in the transcript levels. Our conclusions are that the transcript of the 459.m gene is an mRNA-like ncRNA and that modulations of transcript levels, especially of hypothetical genes, may not correlate with changes in the proteome.

overall_design: Samples include two replicates of the HM-1:IMSS strain and the amoebapore a silenced G3 strain (G3(A))

first: Rivka

last: Bracha

first: David

last: Mirelman


title: Expression data from day 17 bovine endometrium

status: Public on Jan 20 2012

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

summary:
The potential for dietary supplementation with n-3 polyunsaturated fatty acids (n-3 PUFA) to improve reproductive efficiency in cattle has received much interest. The mechanisms by which n-3 PUFA may affect physiological and biochemical processes in key reproductive tissues are likely to be mediated by significant alterations in gene expression.
We used microarrays to assess endometrial gene expression on day 17 of the estrous cycle in n-3 PUFA compared with control fed heifers.

overall_design: Beef heifers were supplemented with a rumen protected source of either a saturated fatty acid (CON; palmitic acid) or high n-3 PUFA (n-3 PUFA; 275 g) diet per animal per day for 45 days and global gene expression was determined in uterine endometrial tissue using an Affymetrix® oligonucleotide bovine array.

first: Gerard

last: Coyne

last: Kenny

last: McHugh

first: Sinead

last: Waters


title: The Adaptive Response of Endothelial Cells to Increased Shear Stress

status: Public on Dec 01 2011

city: Durham

first: Ji

last: Zhang

state: NC

address: Room 136 Hudson Hall

department: Department of Biomedical Engineering

institute: Duke University

summary: In this study, we characterized the adaptive response of arterial endothelial cells to acute increases in shear stress magnitude in well-defined in vitro settings. Porcine endothelial cells were preconditioned by a basal level shear stress of 15 ± 15 dynes/cm2 at 1 Hz for 24 hours, and an acute increase in shear stress magnitude (30 ± 15 dynes/cm2) was then applied. The transcriptomics studies using microarray identified  genes that were sensitive to the elevated shear magnitude. A significant number of the identified genes in our study are previously unknown as sensitive to shear stress.

overall_design: Porcine endothelial cells were preconditioned by a basal level shear stress of 15 ± 15 dynes/cm2 at 1 Hz for 24 hours, and an acute increase in shear stress magnitude (30 ± 15 dynes/cm2) was then applied. Gene expression at multiple time points was measured using microarray.

first: Morton

middle: H

last: Friedman


title: Asymmetric cancer cell division regulated by AKT, Reactive Oxygen Species (ROS) high versus ROS low mRNA

status: Public on Jul 15 2011

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Human tumors often contain slowly proliferating cancer cells that resist treatment but we do not know precisely how these cells arise. We show that rapidly proliferating cancer cells can divide asymmetrically to produce slowly proliferating “G0-like” progeny that are enriched following chemotherapy in breast cancer patients. Asymmetric cancer cell division results from asymmetric suppression of AKT/PKB kinase signaling in one daughter cell during telophase of mitosis. Moreover, inhibition of AKT signaling with small molecule drugs can induce asymmetric cancer cell division and the production of slow proliferators. Cancer cells therefore appear to continuously flux between symmetric and asymmetric division depending on the precise state of their AKT signaling network. This model may have significant implications for understanding how tumors grow, evade treatment, and recur.

overall_design: 3 replicates each of MCF7 Reactive Oxygen Species (ROS) high, HCT116 ROS high, MCF7 ROS low, and HCT116 ROS low.

first: Ipsita

last: Dey-Guha

first: Anita

last: Wolfer

first: Albert

last: Yeh

first: John

last: Albeck

first: Revati

last: Darp

first: Eduardo

last: Leon

first: Julia

middle: D

last: Wulfkuhle

first: Emanuel

middle: F

last: Petricoin

first: Sridhar

last: Ramaswamy


title: Whole blood microRNA expression profiles in human non-small cell lung adenocarcinoma

status: Public on May 20 2011

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

summary: Fifth generation Exiqon® locked nucleic acid miRCURY™ LNA microarrays were used to profile the expression of microRNAs in whole blood of patients with non-small cell lung adenocarcinoma and of clinically relevant controls without the disease.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
Total RNA was isolated from whole blood of 22 cases and 23 controls. Sample RNA was labeled with the Cy3-like Hy3™ dye, mixed with a human universal reference RNA labeled with the Cy5-like Hy5™ dye, and hybridized to two-color miRCURY™ arrays from Exiqon®.

- Disease: Lung adenocarcinoma: samples 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 23, 24, 25

- Disease: No cancer: samples 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49


title: Expression data from  mouse primary brown preadipocytes

status: Public on May 02 2011

city: Cambridge

first: Bingbing

last: Yuan

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Brown adipocytes are specialized for heat generation and energy expenditure as a defense against cold and obesity. Recent studies demonstrate that brown adipocytes arise in vivo from a Myf5-positive, myoblastic progenitor by the action of PRDM16. Here, we identified a brown fat-enriched miRNA cluster mir-193b-365 as a key regulator of brown fat development. Blocking miR-193b and/or miR-365 in primary brown preadipocytes dramatically impaired brown adipocyte adipogenesis whereas myogenic markers were significantly induced. Forced expression of miR-193b and/or miR-365 in C2C12 myoblasts blocked the entire program of myogenesis, and miR-193b induced myoblasts to differentiate into brown adipocytes. Mir-193b-365 was upregulated by PRDM16. Our results demonstrate that mir-193b-365 serves as an essential regulator for brown fat differentiation, in part by repressing myogenesis.

overall_design: To study if miR-193b-365 is required for brown adipocyte adipogenesis, mRNAs from cultured primary brown adipocytes (Day 4) transfected with each locked nucleic acid (LNA) miRNA inhibitor or Control inhibitor were analyzed by microarray analysis.

first: Lei

last: Sun


title: Expression data from low fluid shear cultured Staphylococcus aureus

status: Public on May 31 2011

city: Galveston

first: Sarah

middle: L

last: Castro

state: TX

address: 301 University Blvd

institute: University of Texas Medical Branch

summary: The opportunistic pathogen, Staphylococcus aureus, encounters a wide variety of fluid shear levels within the human host, which may play a key role in dictating whether this organism adopts a commensal interaction with the host or transitions to cause disease.  Using rotating-wall vessel bioreactors to create a physiologically-relevant, low fluid shear environment, S. aureus was evaluated for cellular responses that could impact its colonization and virulence.  S. aureus cells grown in a low fluid shear environment initiated a novel attachment-independent biofilm phenotype and were completely encased in extracellular polymeric substances.  Compared to controls, low-shear cultured cells displayed slower growth and repressed virulence characteristics, including decreased carotenoid production,  increased susceptibility to oxidative stress, and reduced survival in whole blood.  Transcriptional whole genome microarray profiling suggested alterations in metabolic pathways.  Further genetic expression analysis revealed the down-regulation of the RNA chaperone Hfq, which parallels low fluid shear responses of certain Gram negative organisms.  This is the first study to report an Hfq association to fluid shear in a Gram positive organism, suggesting an evolutionarily conserved response to fluid shear among structurally diverse prokaryotes.  Collectively, our results suggest S. aureus responds to a low fluid shear environment by initiating a biofilm/colonization phenotype with diminished virulence characteristics, which could lead to insight into key factors influencing the divergence between infection and colonization during initial host pathogen interaction.

sample_organism: Staphylococcus aureus subsp. aureus N315

overall_design: Genetic expression profiles of Staphylococcus aureus cultured under low fluid shear conditions was compared to control cultures of S. aureus which was cultured in identical hardware in an orientation disrupting the low fluid shear effect.  Samples from the same date of culture were compared (control 21:low 21 and control 30: low 30).  S. aureus  was cultured for 20 hours in either the low fluid shear or control orientated rotating wall vessel (RWV) bioreactor at which point the cells were removed and RNA extracted.  At 20 hours, both cultures were in the same stage of growth (stationary phase) and at this point phenotypic differences between control and low fluid shear cultures were noted.

first: Mayra

last: Nelman-Gonzalez

first: Cheryl

last: Nicerson

first: C

last: Ott


title: Expression data from 42 prostate cancer samples - 16 recurrent and 26 recurrence-free

status: Public on Jun 15 2011

city: Sao Paulo

first: Yuri

middle: Barros

last: Moreira

state: SP

address: Av. Prof. Lineu Prestes 748 sala 1200

department: Biochemistry

country: Brazil

institute: Universidade de Sao Paulo

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

summary:
We analyzed the protein-coding and non-coding gene expression profiles of 64 samples of prostate cancer primary tumors. All samples were collected between 1998 and 2001 with informed consent from patients subjected to radical prostatectomy at Hospital Sirio-Libanes in São Paulo. Selected patients were identified with clinical Stage T1-2 prostate cancer and no lymph node involvement, and received no adjuvant treatment after surgery as long as they remained recurrence-free. Biochemical recurrence was defined as an increase in patient blood PSA level to 0.2 ng per mL of blood at any time during the 5-year follow-up after prostatectomy.

For this kind of experiment, also called self-self hybridization, the microarrays were cohybridized with each of Cy3- and Cy5-labeled cRNA replicates.  This strategy has been used to derive intensity-dependent cutoffs to classify a gene as differentially expressed  or divergent in comparative genomic hybridization (CGH) studies. The comparative analysis of constant fold change cutoffs and intensity-dependent ones has been extensively discussed, showing a superior performance of the intensity-dependent strategy.

overall_design: Here we describe a gene expression profile comprised of 32 protein-coding mRNAs and 6 intronic noncoding RNAs (ncRNAs) that effectively classified a set of 42 prostate cancer samples according to the patients’ biochemical recurrence status within a 5-year follow-up after radical prostatectomy.

middle: B

first: Egidio

last: Camila

first: Miguel

last: Srougi

first: Katia

last: Leite

first: Luiz

last: Camara-Lopes

last: Reis

first: Sergio

last: Verjovski-Almeida


title: Global MicroRNA Expression Profiling Identifies MiR-210 Associated with Tumor Proliferation, Invasion and Poor Clinical Outcome in Breast Cancer

status: Public on Jul 01 2011

city: brussels

first: Françoise

last: Rothé

address: boulevard de waterloo 127

country: Belgium

institute: Jules Bordet Institute

summary: In order to improve our understanding of breast cancer (BC) biology and its prognostication, global miRNA expression profiling was performed using microarray technology on systemically untreated BC patients with long-term follow up.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, global miRNA expression profiling using microarray technology was conducted on 56 systemically untreated BC patients with long-term follow up. The arrays used for miRNAs expression profiling comprise a total of 640 probes targeting 328 human miRNAs (hsa-miRs), as well as mouse and rat miRNAs, from the miRBase Sequence Database version 8.0.

first: Christos

last: Sotiriou


title: Expression data from 22 prostate cancer samples - 6 recurrent and 16 recurrence-free from the validation dataset

summary:
We analyzed the protein-coding and non-coding gene expression profiles of 64 samples of prostate cancer primary tumors. All samples were collected between 1998 and 2001 with informed consent from patients subjected to radical prostatectomy at Hospital Sirio-Libanes in São Paulo. Selected patients were identified with clinical Stage T1-2 prostate cancer and no lymph node involvement, and received no adjuvant treatment after surgery as long as they remained recurrence-free. Biochemical recurrence was defined as an increase in patient blood PSA level to 0.2 ng per mL of blood at any time during the 5-year follow-up after prostatectomy.

For this kind of experiment, also called self-self hybridization, the microarrays were cohybridized with each of Cy3- and Cy5-labeled cRNA replicates.  This strategy has been used to derive intensity-dependent cutoffs to classify a gene as differentially expressed  or divergent in comparative genomic hybridization (CGH) studies. The comparative analysis of constant fold change cutoffs and intensity-dependent ones has been extensively discussed, showing a superior performance of the intensity-dependent strategy. For the validation dataset processing, reference values obtained with the training dataset processin were applied to normalize the validation dataset. These values were: Average ranked intensities (quantile normalization), batch information (batch adjustment), and gene average and standard deviations (z-score transformation.

overall_design: Here we describe the validation of the gene expression profile comprised of 32 protein-coding mRNAs and 6 intronic non-coding RNAs (ncRNAs) in an independent set of 22 samples, 16 from recurrence-free patients and 6 recurrent patients. In order to compare the expression levels of training and independent validation samples, gene intensity levels of samples in the validation dataset were transformed using normalization factors that had been generated with the training dataset.

first: Eduardo


title: Transcriptional profiling during pollination in Ophrys fusca, through cDNA microarrays

status: Public on Mar 31 2011

city: Lisboa

first: Filipa

middle: Isabel de Almeida

last: Monteiro

address: Ed. ICAT, Faculty of Sciences, Rua Ernesto Vasconcelos, Campo Grande

department: BioFIG

institute: Plant Systems Biology Lab

summary: Survey of post pollination events in a sexually deceptive orchid (Ophrys fusca): a transcriptional approach  Pollination through deception is a widespread phenomenon in angiosperm, and is extremely common in Orchidaceae family. One of the most striking pollination mechanism in orchids is known as sexual deception, in which flowers lure pollinators by foraging chemical (sex pheromones), visual (e.g. labellum colour and/or shape) and tactile (e.g. labellum pilosity) cues of the female insect pollinator. Ophrys has been used as a model genus to study sexual deception mechanism, mainly regarding chemical analysis in plant-insect association. Study was focused on Ophrys fusca, a species widely distributed in Mediterranean Basin. The main objective rely on Ophrys fusca gene expression study after pollination, through a transcriptional approach using cDNA microarrays.   In order to evaluate pollination enhanced events, two different time points were selected: 2 days and 4 days after pollination. Ophrys fusca plants were sampled from a Portuguese natural occurring population. Plants were covered with a white and inert net, built specially for preventing pollinator’s visits in both pollinated and unpollinated flowers. Cross- pollination was performed manually with a sterile plastic stick.  Five biological replicates (5 plants in each replicate) from each condition (pollinated and unpollinated) were collected in each time-point    Flowers that demonstrate strict pollination regulation, as orchids, provide an excellent model system to unravel pollination- elicited mechanisms (i.e. petal senescence, pigmentation changes, ovary growth). Therefore, this study aims to contribute to the overall knowledge on orchid pollination biology, which is still lacking.

overall_design: 2 time points: 2 days and 4 days after pollination.Two-samples accessed: control (nonpollinated labella) and test (pollinated labella). 5 Biological replicates and 2 technical replicates (repeats of labelling and hybridization using randomly chosen biological replicates) in each time point were made.

first: Mónica

last: Sebastiana

first: Andreia

last: Figueiredo

first: Lisete

last: Sousa

first: Helena

last: Cotrim

first: Maria

last: Pais


title: Effect of Continuous Suppression of Heparan Sulfate during Flow on Arterial Endothelial Function

status: Public on Jul 22 2011

first: Charles

last: Wallace

state: North Carolina

address: 100 Science Drive

department: Biomedical Engineering

summary: The arterial endothelium’s response to its flow environment is critical to vascular homeostasis. The endothelial glycocalyx has been shown to play a major role in mechanotransduction, but the extent to which the components of the glycocalyx affect the overall function of the endothelium remains unclear. The objective of this study was to further elucidate the role of heparan sulfate as a mechanosensor on the surface of the arterial endothelium, by (1) expanding the variety of shear waveforms investigated, (2) continuously suppressing heparan sulfate expression rather than using a pre-flow batch treatment, and (3) performing microarray analysis on post-flow samples. Porcine aortic endothelial cells were exposed to non-reversing, reversing, and oscillatory shear waveforms for 24 hours with or without continuous heparan sulfate suppression with heparinase. All shear waveforms significantly increased the amount of heparan sulfate on the surface of the endothelium. Suppression of heparan sulfate to less than 25% of control levels did not inhibit shear-induced cell alignment or nitric oxide production, or alter gene expression, for any of the shear waveforms investigated. We infer that heparan sulfate on the surface of porcine aortic endothelial cells is not the primary mechanosensor for many shear-responsive endothelial cell functions in this species.

overall_design: Porcine aortic endothelial cells were exposed to 3 different shear waveforms for 24 hours with or without the addition of 300 mU/ml heparinase III to the flow media. The shear waveforms inculded Non-reversing (15 ± 15 dyne/cm2, 1 Hz), Steady (15 dyne/cm2), or Oscillatory (0 ± 15 dyne/cm2, 1 Hz) shear. Four replicates of each condition were performed for a total of 24 experiments. Each experimental sample was hybridized to an oligonucleotide array along with a standard reference sample (static cells).

first: Morton

last: Friedman


title: Analysis of gene expression in QKI knockdown CG-4 cells

status: Public on Jan 20 2011

city: Worcester

first: Sean

last: Ryder

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: UMass Medical School

summary:
QKI is required for myelin formation in the verterbrate brain.  It functions by binding RNA and regulating its stability, translation, and/or aternative splicing.
We have used Affymetrix exon arrays to assess changes in gene expression in response to QKI knockdown on an exon level in rat CG-4 oligodendrocyte precursor cells.

overall_design: Knockdown cells were compared to control cells.  Knockdown groups included QKI siRNA transfection, QKI shRNA stable transfection, and hnRNP A1 transient transfection.  Control groups consisted of untransfected, control siRNA transfection, control shRNA stable transfection. Each group was analyzed in triplicate.

first: S

first: N

middle: R

last: Zearfoss


title: Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis

status: Public on Nov 01 2010

first: Carol

last: Gilchrist

summary:
Entamoeba histolytica contains a large and novel family of transmembrane kinases (TMK) with proposed roles that include both amebic response to the environment and immune evasion. In the later case, the process requires several elements --these include a large gene family encoding antigenically distinct surface proteins and the expression of one variant antigen at a time by a single pathogen.
Laser-capture microdissection was used in conjunction with microarray analysis to demonstrate that single trophozoites express more than one TMK gene.  Overall, our data indicates that multiple members of the novel E. histolytica TMK family are utilized for non-redundant functions by the parasite.

overall_design: For laser capture microdissection analysis, harvested trophozoites were allowed to adhere to metal framed PEN membrane slides (Molecular Devices, Sunnyvale, CA) for 15 mins at 37°C in TYI-S-33 media.  Subsequently, single cells were captured from the PEN slides using a Pix Cell II laser capture microdissection system equipped with an Olympus microscope (Arcturus Engineering, Mountain View, CA).

first: Sarah

last: Buss

first: Shinjiro

last: Hamano

first: Alda

last: Vidrich

first: Clive

last: Evans

first: Yan

last: Zhang

first: Oswald

last: Crasta

first: Bruno

middle: W

last: Sobral

first: William

last: Petri Jr


title: Endothelial transcriptional profiles of porcine coronary and iliac arteries passages 1 through 4

status: Public on Dec 18 2010

first: Kelley

last: Burridge

address: Rm 136 Hudson Hall

summary: Atherosclerotic plaques tend to form in the major arteries at certain predictable locations.  As these arteries vary in atherosusceptibility, inter-arterial differences in endothelial cell (EC) biology are of considerable interest.  To explore the origin of differences observed between typical atheroprone and atheroresistant arteries, we used DNA microarrays to compare gene expression profiles of harvested porcine coronary (CECs) and iliac (IECs) artery ECs grown in static culture out to passage four.  Fewer differences were observed between the transcriptional profiles of CECs and IECs in culture compared to in vivo, suggesting that most differences observed in vivo were due to distinct environmental cues in the two arteries.   One-class significance of microarrays revealed that most in vivo interarterial differences disappeared in culture, as fold differences after passaging were not significant for 85% of genes identified as differentially expressed in vivo at a 5% false discovery rate.   However, the three homeobox genes HOXA9, HOXA10, and HOXD3 remained under-expressed in coronary endothelium for all passages by at least 9, 8, and 2-fold, respectively.  Continued differential expression despite removal from the in vivo environment suggests that primarily heritable or epigenetic mechanism(s) influence transcription of these three genes.  Quantitative real-time polymerase chain reaction confirmed expression ratios for seven genes associated with atherogenesis and over- or under-expressed by 3-fold in CECs relative to IECs. The present study provides evidence that both local environment and vascular bed origin modulate gene expression in arterial endothelium.  The transcriptional differences observed here may provide new insights into pathways responsible for coronary artery susceptibility.

overall_design: Endothelial cells were freshly harvested from right coronary and iliac arteries from four pigs. Cells were cultured out to passage four.  RNA was isolated after each passage and expression profiles were obtained using oligo microarrays.


title: Sural nerve of progressive and non-progressive diabetic neuropathy patients

status: Public on Sep 24 2010

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Diabetic neuropathy (DN) is a common complication of diabetes.  While multiple pathways are implicated in the pathophysiology of DN, there are no specific treatments for DN and currently it is not possible to predict DN onset or progression. To examine gene expression signatures related to DN, microarray experiments were performed on a subset of human sural nerves collected during a 52-week clinical trial of acetyl-L-carnitine. A series of bioinformatics analyses analyzed differential gene expression and identified gene networks and pathways potentially responsible for the progression of DN. We identified 532 differentially expressed genes (DEGs) between patient samples with progressing or non-progressing DN, which were functionally enriched in pathways involving defense and inflammatory responses and lipid metabolism. A literature-derived co-citation network of the DEGs revealed gene sub-networks centered on apolipoprotein E (APOE), jun oncogene (JUN), leptin (LEP), serpin peptidase inhibitor E Type 1 (SERPINE1) and peroxisome proliferator-activated receptor gamma (PPARG). DEGs were used to predict DN progression in a test set of patients. Ridge-regression classification models with 14 DEGs achieved an overall accuracy of 92%, correctly classifying the progression status of 11 out of 12 patients. To our knowledge, this is the first study to identify transcriptional changes associated with DN progression in human sural nerves biopsies and describe their potential utility for molecular prediction of DN. Our results identifying the unique gene signature of patients with progressive DN will facilitate the development of new mechanism-based diagnostics and therapies.

overall_design: 18 progressor and 17 non-progressor at 52 weeks


title: Expression data from parental MDA-MB-231 cells and MDA-MB-231(SA) variant

status: Public on Apr 19 2010

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: Since bone metastatic breast cancer is an incurable disease, causing significant morbidity and mortality, understanding of the underlying molecular mechanisms would be highly valuable. Here, we describe in vitro and in vivo evidence for the importance of serine biosynthesis in the metastasis of breast cancer to bone. We first characterized the bone metastatic propensity of the MDA-MB-231(SA) cell line variant as compared to the parental MDA-MB-231 cells by radiographic and histological observations in the inoculated mice. Genome-wide gene expression profiling of this isogenic cell line pair revealed that all the three genes involved in the L-serine biosynthesis pathway, phosphoglycerate dehydrogenase (PHGDH), phosphoserine aminotransferase 1 (PSAT1), and phosphoserine phosphatase (PSPH) were upregulated in the highly metastatic variant. This pathway is the primary endogenous source for L-serine in mammalian tissues. Consistently, we observed that the proliferation of MDA-MB-231(SA) cells in serine-free conditions was dependent on PSAT1 expression. In addition, we observed that L-serine is essential for the formation of bone resorbing human osteoclasts and may thus contribute to the vicious cycle of osteolytic bone metastasis. High expression of PHGDH and PSAT1 in primary breast cancer was significantly associated with decreased relapse-free and overall survival of patients and malignant phenotypic features of breast cancer. In conclusion, high expression of serine biosynthesis genes in metastatic breast cancer cells and the stimulating effect of L-serine on osteoclastogenesis and cancer cell proliferation indicate a functionally critical role for serine biosynthesis in bone metastatic breast cancer and thereby an opportunity for targeted therapeutic interventions.

overall_design: Parental MDA-MB-231 cells and MDA-MB-231(SA) cells were cultured in cell culture flasks. RNA was isolated in order to compare the gene expression profiles of these cell variants. Total of two samples. No replicates.

first: Sirkku

last: Pollari


title: Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown in a rich medium (labeling:Affymetrix)

status: Public on Oct 15 2010

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

country: Japan

institute: RIKEN Harima Institute

summary: In order to observe altered expression profile of wild-type T. thermophilus HB8 strain grown in a rich (TT) medium at 70°C. we analyzed time-dependent mRNA expression profile of the total mRNA from the strain, which corresponds the logarithmic phase to the early stationary phase.

overall_design: Three wild-type T. thermophilus HB8 strains were pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 180, 240, 300, 360, 420, 480, 540, 600, 680, and 760 min, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.

first: Aiko

last: Kashihara

first: Emi

last: Nakai

first: Noriko

last: Nakagawa

first: Yoshihiro

last: Agari

first: Shigeyuki

last: Yokoyama

first: Seiki

last: Kuramitsu


title: A Transcriptional Signature and Common Gene Networks Link Cancer with Metabolic Syndrome and Auto-immune Diseases

first: Kevin

last: Struhl

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharamcology

institute: Harvard Medical School

summary:
Epidemiological studies have revealed concurrence of specific cancers with other disease states such as metabolic syndrome, inflammatory disease and autoimmune disease. Patients with these chronic conditions have a higher incidence of various cancers, more aggressive tumors, and a higher mortality rate. It has been proposed that obesity, inflammation and chronic disease should be correlated with cancer at the molecular level, but common gene signatures or networks have yet to be described. Here, we identify genes regulated during the process of cellular transformation in both a breast epithelial cell line and a set of isogenic fibroblastic cell lines.
The resulting gene signature strongly mimics those of many different cancer types, thereby validating these experimental systems as models of oncogenesis. Furthermore, it uncovers transcriptional factors and common gene regulatory networks linking cancer with other disease states such as atheroscelorsis, type II diabetes, obesity, lupus, and cardiomyopathy. We suggest that this common transcriptional program can contribute to the concurrence of different diseases, and that the interplay between this program and cell-type specific factors can give rise to a variety of human diseases.

overall_design: Two isogenic cell lines were used to model transformation.  The first employed an inducible oncogene: src fused to the ligand binding domain of the estrogen receptor.  ER-src and pBABE control cells were dosed with Tamoxifen or Etoh control across several time points to monitor gene expression during transformation.  The other model consists of three isogenic cell lines derived from primary fibroblasts in a serial manner.  The first is immortalized by overexpression of telomerase (hTERT), and exhibits normal fibroblast morphology.  The second expresses hTERT along with both large and small T antigens of Simian virus 40, and it displays an altered morphology but is not transformed.  The third cell line expresses hTERT, T antigens, and an oncogenic derivative of Ras (H-RasV12); it is morphologically transformed and has tumorigenic potential in soft agar and nude mice.  Thus, three stages of transformation are represented by these cells.

first: Heather

last: Hirsch

first: Dimitrios

last: Iliopoulos

first: Amita

last: Joshi

first: Yong

first: Savina

last: Jaeger

first: Martha

last: Bulyk

first: Shirley

middle: X

last: Liu


title: Expression data from Staphylococcus aureus ATCC 25923 (antibiotic sensitive) and ATCC 33591 (MRSA)

status: Public on Sep 15 2010

city: Seoul

first: Taehoen

last: Lee

address: Gwanangno, Gwanak-gu

institute: SNU

summary: S. aureus ATCC 25923 is performance standard for antimicrobial susceptibility testing. S. aureus ATCC 33591 showed resistance against erytrhromycin, penicillin, and streptomycin. We used microarray to compare RNA expression between sensitive and resistant strain of S. aureus as a preliminary research for MRSA inhibition.

overall_design: S. aureus strains were cultivated in tryptic soy broth at 37℃ for 18hrs and harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun-Sang

last: Ham

first: Heebal

last: Kim


title: Expression profiling of microRNAs in primary melanocytes

status: Public on Apr 15 2010

city: San Francisco

first: Jun

middle: S

last: Song

state: CA

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

summary: DICER is a central regulator of microRNA maturation.  However little is known about mechanisms regulating its expression in development or disease. While profiling miRNA expression in differentiating melanocytes, two populations were observed: some upregulated at the pre-miRNA stage, and others upregulated as “mature” miRNAs (with stable pre-miRNA levels). Conversion of pre-miRNAs to fully processed miRNAs appeared to be dependent upon stimulation of DICER expression—an event found to occur via direct transcriptional targeting of DICER by the melanocyte master transcriptional regulator MITF.  MITF binds and activates a conserved regulatory element upstream of DICER’s transcriptional start site upon melanocyte differentiation. Targeted knockout of DICER is lethal to melanocytes, at least partly via DICER-dependent processing of the pre-miRNA-17~92 cluster thus targeting BIM, a known pro-apoptotic regulator of melanocyte survival. These observations highlight a central mechanism underlying miRNA regulation which could exist for other cell types during development.

overall_design: Primary melanocytes were obtained from 7 independent donors.  Mature-miRNA levels were detected using Applied Biosystem's TaqMan PCR assay.

first: Carmit

last: Levy

first: David

middle: E

last: Fisher


title: Endothelial Gene Expression in Regions of Defined Shear Exposure in the Porcine Iliac Arteries

status: Public on Mar 31 2009

first: Ji

last: Zhang

address: Room 136 Hudson Hall

summary:
The effect of hemodynamic shear stress on endothelial gene expression was investigated in the porcine iliac arteries. Computational fluid dynamics simulations identified three anatomical regions likely to experience high, medium, and low shear stress. The expression of genes in endothelial cells recovered from these regions were assessed using microarray.
Keywords: shear stress, endothelial cell gene expression, in vivo

overall_design: 11 iliac arteries were obtained from 6 animals, total RNA were extracted from high, medium and low shear region. The expression profiles were compared with a reference RNA using dual channel arrays. Samples with low original RNA quality and low hybridization quality were not included.

first: Jeffrey

middle: A

last: LaMack

last: Himburg

first: Morton

last: Friedman


status: Public on Dec 19 2009

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

summary: Expression profiles of AhR mutant vs N2 wild-type C.elegans, in L1 larval stage compared by using 23232 feature WUSTL microarray

overall_design: 4 ahr-mutant worm samples compared to 3 wild-type samples. Total RNAs purified and reverse transcribed to cDNA and labeled with Cy3-dUTP, and then hybridized on microarray.

first: Vuokko

last: Aarnio

first: Marko

last: Lehtonen

first: James

last: Callaway

first: Martina

last: Rudgalvyte

first: Merja

last: Lakso

first: Garry

last: Wong


title: Renal gene expression analysis: exon-level data

status: Public on Aug 25 2009

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

summary: This is a SubSeries of GSE12672

overall_design: 48 samples: 4 strains (F, L, FL, LF) x 3 time points (0, 7, 10 day induction) x 4 biological replicates each


title: The Aryl Hydrocarbon Receptor Regulates Tissue-Specific Dioxin-Dependent and Dioxin-Independent Gene Batteries: Kidney

status: Public on Sep 21 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary: The aryl hydrocarbon receptor (AHR) is a widely-expressed ligand-dependent transcription-factor that mediates cellular responses to dioxins and other planar aromatic hydrocarbons. Indeed, AHR-null mice are refractory to the physiological effects of dioxin-exposure. Although some mechanistic aspects of AHR activity are well understood, the tissue-specificity of AHR effects remains unclear, both during development and following administration of exogenous ligands. Previously we employed studied the transcriptional responses of wild-type and AHR-null C57BL/6J mice to dioxin-exposure. We found that essentially all hepatic effects of dioxin were mediated by the AHR, and that large numbers of genes were affected by dioxin exposure. Surprisingly, we also identified a large effect of AHR genotype, even in the absence of dioxin-exposure. To help assess the tissue-specificity of AHR activity we replicated that prior study in the kidney from the same animals previously studied, and extensively compared the hepatic and renal transcriptional profiles. We find that dioxin-exposure causes essentially no transcriptional effects in the absence of a functional AHR in either liver or kidney. Surprisingly, aside from a number of well-established AHR target genes, dioxin-exposure has few effects in animals harbouring a wild-type AHR. By contrast, AHR genotype profoundly remodels the renal transcriptome, and is associated with perturbation of specific functional pathways and with specific DNA motifs. Our results demonstrate the importance of inter-tissue comparisons and highlight the basal role of AHR activity in renal and hepatic development or normal physiology.

overall_design: Two-Factor, Two-Level. AHRnull and wildtype mice were treated with dioxin (TCDD) or corn oil vehicle. 3 replicates per treatment for AHRnull mice, and 6 replicates per treatment for wildtype mice.

first: Margaret

last: Miller

first: Kirsten

last: Bielefeld

first: Raimo

last: Pohjanvirta

first: Patricia

last: Harper


title: The Aryl Hydrocarbon Receptor Regulates Tissue-Specific Dioxin-Dependent and Dioxin-Independent Gene Batteries: Liver

overall_design: Two-Factor, Two-Level. AHRnull and wildtype mice were treated with dioxin (TCDD) or corn oil vehicle. 3 replicates per treatment for AHRnull mice, 6 replicates of dioxin treatment for wildtype mice, and 5 replicates of corn oil treatment for wildtype mice.


title: Staphylococcus aureus nonribosomal peptide secondary metabolites regulate virulence

status: Public on Jul 01 2010

city: Omaha

middle: M

last: Dunman

state: NE

address: 986495 Nebraska Medical Center

department: Pathology and Microbiology

country: USA

institute: University of Nebraska Medical Center

summary: Staphylococcus aureus is a major human pathogen and resistant to numerous clinically used antibiotics. The first antibiotic developed for S. aureus infections was the nonribosomal petide secondary metabolite penicillin.  We discovered cryptic nonribosomal peptide secondary metabolites, the aureusimines, made by S. aureus itself that are not antibiotics, but function as small molecule regulators of virulence factor expression.  Using established rules and codes for nonribosomal peptide assembly we predicted these nonribosomal peptides, and used these predictions to identify them from S. aureus culture broths.  Functional studies using global microarray and mouse bacteremia models established that the aureusimines control virulence factor expression and are necessary for productive infections.  This is the first report of the aureusimines and has important implications for the treatment of drug resistant S. aureus.  Targeting aureusimine synthesis may provide novel anti-infectives.

overall_design: Commerically available S. aureus GeneChips (Affymetrix) were used to compare biological replicates of early and late exponential phase wild type (Newman) and aureusimine defective (ausA) organisms.

first: Aubrey-Bailey

last: Wyatt

first: Wenliang

last: Wang

first: Christelle

last: Roux

first: Frederico

last: Beasley

first: David

last: Heinrichs

first: Nathan

last: Magarvey


title: Profiling downregulation of the mevalonate pathway in Staphylococcus aureus

status: Public on Feb 20 2009

first: Carl

middle: J.

last: Balibar

address: 500 Technology Sq.

department: Infectious Diseases

institute: Novartis Institutes for BioMedical Research

summary:
Isoprenoids are a class of ubiquitous organic molecules synthesized from the five-carbon starter unit isopentenyl pyrophosphate (IPP). Comprising more than 30,000 known natural products, isoprenoids serve various important biological functions in many organisms. In bacteria, undecaprenyl pyrophosphate is absolutely required for the formation of cell wall peptidoglycan and other cell surface structures, while ubiquinones and menaquinones, both containing an essential prenyl moiety, are key electron carriers in respiratory energy generation. There is scant knowledge on the nature and regulation of bacterial isoprenoid pathways. In order to explore the cellular responses to perturbations in the mevalonate pathway, responsible for producing the isoprenoid precursor IPP in many Gram-positive bacteria and eukaryotes, we constructed three strains of Staphylococcus aureus in which each of the mevalonate pathway genes is regulated by an IPTG inducible promoter. We used DNA microarrays to profile the transcriptional effects of downregulating the components of the mevalonate pathway in S. aureus and demonstrate that decreased expression of the mevalonate pathway leads to widespread downregulation of primary metabolism genes, an upregulation in virulence factors and cell wall biosynthetic determinants, and surprisingly little compensatory expression in other isoprenoid biosynthetic genes. We subsequently correlate these transcriptional changes with downstream metabolic consequences.
We used microarrays to profile the transcriptional changes incurred when downregulating mvaS, mvaA, or mvaK in S. aureus.

Keywords: stress response

sample_organism: Staphylococcus aureus subsp. aureus RN4220

overall_design: S. aureus mutants were generated in which mvaS, mvaA, or mvaK were placed under control of the IPTG-inducible Pspac promoter. These mutants, as well as wildtype RN4220 S. aureus, were grown with or without 1 mM IPTG, harvested in exponential phase, and their total RNA was extracted and hybridized to Affymetrix GeneChips. Experiments were done in triplicate.

first: Balibar

last: Carl J.

first: Shen

last: Xiaoyu

first: Tao

last: Jianshi


title: Mouse_embryoid Body_Retinoic acid treatment

status: Public on Feb 17 2010

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: S6K1 Knockout mice has a lean phenotype and resitant to a High Fat Diet-induced obesity (Um S.H., Nature, 2004). Adipocyte differentiation consists of two step, first, commitment from stem cell to adipocyte progenitors and second, terminal differentiation from adipocyte progenitors to mature adipocyte. We studied S6K1-dependent gene expression regulation in early stage of commitment by employing ES cell(ESC)-Embryoid Bodies(EBs) differentiation model. We established stable ES cell lines infected with either control non-silencing shRNA (shNS) or S6K1 targetting shRNA (shS6K1). Each sample was treated with retinoic acid for 3 days to induce adipogenesis, then gene expression profile was analyzed employing microarrays and up-regulated and down-regulated genes were selected for analysis.

overall_design: Mouse Embryoid Bodies (approximately 1000 EBs per sample) were treated with retinoic acid (1µM) for 3 days then collected for RNA extraction and hybridization on Affimetrix microarray. Two biological replicates were each performed for EBs prepared from either shNS ESCs or shS6K1 ESCs.

first: Larissa

last: Carnevalli

first: Sara

last: Kozma


title: A New Oxidative Sensing and Regulation Pathway Mediated by the MgrA Homologue SarZ in Staphylococcus aureus

status: Public on Dec 01 2008

first: Paul

overall_design: The S. aureus transcriptome was assessed for strains Newman (wild type) and Newman (sarZ) during both exponential (2hr) and early stationary (5hr) cell growth.  The experiment was performed in duplicate or triplicate, and RNA samples labeled/hybridized to independent commercially available Affymetrix GeneChips

first: Peng

last: Chen

first: Satoshi

last: Nishida

first: Catherine

last: Poor

first: Alice

last: Cheng

first: Taeok

last: Bae

first: Lisa

last: Kuechenmeister

first: Dominique

last: Missiakas

first: Chuan

last: He


title: Direct targets of CodY in Staphylococcus aureus

status: Public on Apr 01 2010

last: Dunman

summary: More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the agr locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the agr locus. Since S. aureus CodY was activated in vitro by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence.

overall_design: Affymetrix GeneChips were used to compare the transcript titers of S. aureus strains UAMS-1 (wild type) and corresponding agr- (strain CM18), codY- (strain MS1), and agr- codY- (strain CM19) isogenic mutant strains during exponential and stationary phase growth.  At least two biological replicates were assessed for each strain and each growth phase.

first: Charlotte

middle: D

last: Majerczyk

first: Thanh

middle: T

last: Luong

first: Chia

middle: Y

last: Lee

first: Marat

last: Sadykov

first: Greg

last: Somerville

first: Kip

last: Bodi

first: Abraham

last: Sonenshein


title: Characterization of Calprotectin treated medium

status: Public on Feb 01 2008

summary:
The goal of this study is to correlate the transcriptional response of S. aureus cells grown in Calprotectin treated medium with that of cells grown in Mn or Zn depletion conditions.
Keywords: RNA sample

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: Staphylcoccus aureus strain Newman was grown to mid-log phase in Calprotectin treated medium or medium lacking either Zn or Mn.  RNA was isolated, labeled and hybridized to an S. aureus Affymetrix GeneChip.  Biological replicates are indicated as A, B, or C.

first: Brian

last: Corbin

first: Erin

middle: H

last: Seeley

first: Andrea

last: Raab

first: Joerg

last: Feldmann

first: Michael

last: Miller

first: Victor

middle: J

last: Torres

first: Kelsi

middle: L

last: Anderson

last: Datillo

first: Russell

last: Gerads

first: Richard

last: Caprioli

first: Wolfgang

last: Nacken

first: Walter

last: Chazin

first: Eric

middle: P

last: Skaar


title: The ACME and SCCmec Linkage of Virulence with Resistance in the Community Methicillin Resistant S. aureus USA300 Clone

status: Public on Sep 30 2008

city: Hamilton

first: Amy

last: Palazzolo-Ballance

state: MT

address: 903 S. 4th Street

department: Rocky Mountain Laboratory

institute: NIH/NIAID

summary:
The epidemic character of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA), especially the geographically widespread clone USA300, is poorly understood.  USA300 isolates carry a type IV staphylococcal chromosomal cassette mec (SCCmec) element conferring  -lactam antibiotic class resistance and a putative pathogenicity island, ACME (arginine catabolic mobile element).
Physical linkage between SCCmec and ACME suggests that selection for antibiotic resistance and for pathogenicity may be interconnected.  We constructed isogenic mutants containing deletions of SCCmec and ACME in a USA300 clinical isolate to determine the role of these elements in a rabbit model of bacteremia.  We found that deletion of type IV SCCmec did not affect competitive fitness, whereas deletion of ACME significantly attenuated pathogenicity or fitness of USA300.  These data are consistent with a model in which ACME enhances growth and survival of USA300, allowing for genetic "hitchhiking" of SCCmec.  SCCmec in turn protects against exposure to β -lactams.
Keywords: Wild type control vs mutant

overall_design: Wild type untreated in triplicate is compared to three mutants in triplicate in both exponential and stationary growth phases, totalling 24 samples

first: Binh

last: Diep

first: Gregory

middle: G

last: Stone

first: Li

last: Basuino

first: Christopher

last: Graber

first: Alita

first: Shelly-Ann

last: des Etages

first: Alison

last: Jones

first: Francoise

last: Perdreau-Remington

first: George

middle: F

last: Sensabaugh

first: Frank

middle: R

last: DeLeo

first: Henry

last: Chambers


title: Global transcriptional profiling of Staphylococcus aureus treated with sodium houttuyfonate

status: Public on Oct 22 2008

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

institute: College of Animal Science and Veterinary Medicine, Jilin University

summary:
Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. sodium houttuyfonate has potent antimicrobial activity against S. aureus.
We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with sodium houttuyfonate.

Keywords: gene expression array-based, count

overall_design: Staphylococcus aureus cells were exposed for a certain to sodium houttuyfonate at certain concentration, 6 samples including 3 control samples are analyzed.


title: Bacteroides fragilis oxidative stress

status: Public on Dec 30 2007

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

summary:
The idea was to examine the role of OxyR in control of the oxidative stress response of B. fragilis when exposed to either atmospheric oxygen, 5% oxygen atmosphere, or hydrogen peroxide
Keywords: stress response

overall_design:
The experiment was designed to compare the response of IB397 (wild type) to IB425 (oxyR) under anaerobic conditions, hydrogen peroxide stress, and atmospheric oxygen stress.  In addition, IB397 was subjected to 5% oxygen stress for comparison to full atmospheric oxygen stress.  Samples ultimately compared to Anaerobic IB397 which is considered the baseline state for these bacteria.

Sample replicates are identified according to the following protocol: biological replicates are given a letter designation at the end of the title.  This letter is followed by a number if a technical replicate exists.  In the following example IB397 O2-a is a biological replicate of IB397 O2-c1 and IB397 O2-c2.  IB397 O2-c1 and IB397-c2 are technical replicates.

The following replicates were used:
IB397 Anaerobic - three samples; one biological replicate and one labeled extract technical replicate.
IB397 Atmospheric oxygen - four samples; two biological replicates and one labeled extract technical replicate.
IB397 Hydrogen peroxide - four samples; two biological replicates and one labeled extract technical replicate.
IB397 5% oxygen - four samples; one biological replicate and two labeled extract technical replicates.

IB425 Anaerobic - four samples; one biological replicate and one labeled extract technical replicate.
IB425 Atmospheric oxygen- four samples; one biological replicate and one labeled extract technical replicate.
IB425 Hydrogen peroxide - four samples; one biological replicate and one labeled extract technical replicate.

first: Christian

last: Sund

first: William

last: Wells


title: Microarray Analysis of Toxicogenomic Effects of Ortho-Phenylphenol on Staphylococcus aureus

status: Public on Apr 01 2008

city: ft. meade

first: Hyeung-Jin

last: Jang

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

summary:
In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to Ortho-Phenylphenol, which involved initial growth inhibition and metabolism.
Keywords: Time course

overall_design: We conducted five independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Ortho-Phenylphenol. We calculated fold change as the ratio between the signal averages of five untreated (control) and five ortho-phenylphenol-treated (experimental) cultures for 0, 20 and 60 min exposures.

first: Freshteh

last: Toghrol

last: Bentley


title: S_aureus_&_triclosan

status: Public on Jan 11 2008

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

summary:
A triclosan-ciprofloxacin cross-resistant mutant strain of Staphylococcus aureus displays an alteration in the expression of several cell membrane structural and functional genes.

Triclosan is an antimicrobial agent found in many consumer products.  Several studies have demonstrated that triclosan inhibits the bacterial fatty acid biosynthetic enzyme, enoyl-ACP reductase (FabI).  Studies have also demonstrated that decreased susceptibility to triclosan correlates with ciprofloxacin resistance in several bacteria.  In these bacteria, resistance to both drugs maps to genes encoding multi-drug efflux pumps.  The focus of this study was to determine whether triclosan resistance contributes to ciprofloxacin resistance in Staphylococcus aureus.  Gene expression profiling was performed to compare the gene expression profiles of unexposed and triclosan-exposed wild-type and JJ5 determined that an alteration in global gene expression possibly resulting in a change in cell membrane structure and function is likely responsible for triclosan and ciprofloxacin resistance in JJ5.
Keywords: Treatment response

overall_design: WT and triclosan resistant mutant were treated with triclosan and their gene expression was compared to their untreated conterparts.

first: Marcy

last: Peteroy-Kelly

first: Olga

last: Tkachenko

first: J

last: Shepard

first: A

last: Joy

last: Marku

first: Patricia

last: Soteropoulos


title: Breast Cell Lines: Experimental vs. Mixed Reference

status: Public on Oct 10 2009

city: LA

first: Richard

middle: S

last: Finn

address: 10833 Le Conte, 11-934 Factor Building

department: Medicine-Hem/Onc

institute: UCLA

summary: Transcriptional profiling of breast cell lines comparing breast cell line mixed reference with individual breast cell lines. Goal was to characterize breast cell line subtypes.

overall_design:
Fifty one cell lines profiled against breast cell line mixed reference
Breast cell line mixed reference is a pool of the following 10 breast cell lines selected for their diverse molecular properties:  184B5, CAMA-1, DU4475, MCF-7, MDA-MB-157, MDA-MB-175, MDA-MB-231, MDA-MB-361, MDA-MB-468, and SK-BR-3.

first: Judy

last: Dering

last: Ginther

first: Dennis

last: Slamon


title: Global transcriptional profiling of Staphylococcus aureus treated with magnolol

last: Deng

summary:
Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. magnolol has potent antimicrobial activity against S. aureus.
We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with magnolol.

Keywords: gene expression array-based, count

overall_design: Staphylococcus aureus cells were exposed for a certain time to magnolol at a certain concentration, 6 samples including 3 control samples are analyzed.


title: Staphylococcus aureus treated with fosfomycin

status: Public on Mar 26 2009

city: Ljubljana

first: Drago

last: Kuzman

address: Verovskova 57

country: Slovenia

institute: Lek pharmaceuticals d.d.

summary:
Staphylococcus aureus is a highly adaptable human pathogen; therefore a constant search for new effective antibiotic compounds is being preformed. Gene expression profiling can be used to determine potential targets and mechanisms of action (MOA) of known or potential drugs. The goal of our study was a development of a focused transcriptome platform to be used for confirming the MOA of new chemical entities which are designed as inhibitors of Mur ligases. A model transcriptional profile was set up for well described inhibitor of MurA ligase, fosfomycin. Moreover, we wanted to identify the pathways and processes primarily affected by this compound. S. aureus ATCC 29213 cells were treated with low concentrations of fosfomycin (1 and 4 µg/ml, respectively) and harvested at 10, 20 and 40 minutes after treatment, respectively. RNA was isolated, transcribed, labeled and hybridized to S. aureus GeneChips, representing approximately 3000 S. aureus genes.

Using meta-analysis of our results and the results in the S. aureus microarray database, we have confirmed that fosfomycin induces “cell wall stimulon” genes and were able to identify genes and pathways specifically modulated by fosfomycin.

overall_design: Time course, different fosfomycin concentration

first: Marko

last: Petek


title: Global transcriptional profiling of Staphylococcus aureus treated with cryptotanshinone

status: Public on Oct 16 2008

first: Xuming

summary:
Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. Cryptotanshinone, a natural plant product, has potent antimicrobial activity against S. aureus.
We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with cryptotanshinone.

Keywords: gene expression array-based, count

overall_design: Staphylococcus aureus cells were exposed for 45 minutes to cryptotanshinone at concentration of 2 µg/ml (1/2× MIC), 6 samples including 3 control samples are analyzed.


title: Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei

status: Public on Sep 24 2009

city: Seattle

first: Dhileep

last: Sivam

state: WA

address: 307 Westlake Ave N

department: Bioinformatics Core

institute: Seattle Biomedical Research Institute

summary: Whole genome comparison of RNA levels for both protein coding genes and structural RNAs in five different life cycle stages: in vivo slender bloodstream form, in vivo stumpy bloodstream form, cultured bloodstream form, log-phase procyclic culture form and stationary-phase procyclic culture form

overall_design: RNA from three independent biological replicates from five different life cycle stages were hybridized to Nimblegen arrays (Madison,WI USA) that contained 8 probes per open reading frame and 3 probes per structural RNA spotted three times per array

first: Bryan

last: Jensen

first: Charles

last: Kifer

first: Peter

last: Myler

first: Marilyn

last: Parsons


title: In vivo endothelial transcriptional profiles of porcine coronary and iliac arteries

status: Public on Aug 23 2008

city: Durham

first: Ji

last: Zhang

department: Department of Biomedical Engineering

institute: Duke University

summary:
Phenotypic heterogeneity among arterial ECs is particularly relevant to atherosclerosis since the disease occurs predominantly in major arteries, which vary in their atherosusceptibility. To explore EC heterogeneity, we used DNA microarrays to compare gene expression profiles of freshly harvested porcine coronary and iliac artery ECs. We demonstrate that in vivo the endothelial transcriptional profile of a coronary artery (the right coronary artery) is intrinsically different from that of a major conduit vessel (the external iliac artery), and that this difference is consistent with former vessel being more prone to atherosclerosis.
Keywords: coronary atherosclerosis, endothelial heterogeneity, microarray, gene expression

overall_design: Endothelial cells were freshly harvest from right coronary, left and right iliac arteries from four pigs. RNA were isolated and expression profiles were obtained using olig microarrays.

first: Kelley

middle: A

last: Burridge

first: Morton

last: Friedman


title: Comparison of Agr-regulated virulence factor expression in FRI1169 and non-hemolytic variant

status: Public on Sep 01 2007

city: St Paul

first: Jeremy

last: Yarwood

state: MN

department: Corporate Research

summary:
These cultures were grown to examine the differences in Agr-regulated virulence factor gene expression between wild-type S. aureus FRI1169 and a non-hemolytic variant isolated from a biofilm inoculated with FRI1169. The study is described more thoroughly in the paper "Generation of virulence factor variants in Staphylococcus aureus biofilms", Yarwood et al., J. Bacteriol. 2007.
Keywords: Wild-type versus mutant comparison, single time-point

overall_design: Two indepent batch cultures were grown for both the wild-type strain FRI1169 and the non-hemolytic variant on two separate days (4 total experiments).  Transcript levels from FRI1169 and non-hemolytic variant grown in parallel on the same days were compared (FRI1169 replicate #1 versus non-hemolytic variant #1 and FRI1169 replicate #2 versus non-hemolytic variant #2).  Those Agr-regulated virulence factors whose expression was determined as being significantly changed in the non-hemolytic variant in both experiments/comparisons are shown in Table 1 of the paper "Generation of virulence factor variants in Staphylococcus aureus biofilms", Yarwood et al., J. Bacteriol. 2007, in press.  The fold-change values shown in this table represent the average of the two experiments.

first: Kara

last: Paquette

first: Ilya

middle: B

last: Tikh

first: Ester

last: Volper

first: E

last: Greenberg


title: Global transcriptional profiling of Staphylococcus aureus treated with eugenol

status: Public on Aug 10 2007

summary:
Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. eugenol, a natural plant product, has potent antimicrobial activity against S. aureus.
We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with eugenol.
Keywords: gene expression array-based, count

overall_design: Staphylococcus aureus cells were exposed for 45 minutes to eugenol at concentration of 250µg/ml (1/2× MIC), 2 samples including 1 control samples are analyzed.


title: Global transcriptional profiling of Staphylococcus aureus treated with berberine chloride

status: Public on May 30 2007

summary:
Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. Berberine chloride (BBR), a natural plant product, has potent antimicrobial activity against S. aureus.
We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with berberine chloride.
Keywords: gene expression array-based, count

overall_design: Staphylococcus aureus cells were exposed for 45 minutes to berberine chloride at concentration of 64 µg/ml (1/2× MIC), 6 samples including 3 control samples are analyzed.


title: Microarray Analysis of Toxicogenomic Effects of Triclosan on Staphylococcus aureus

status: Public on Aug 25 2007

first: Hyeung-Jin

last: Jang

summary:
In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to triclosan, which involved initial growth inhibition and metabolism.
Keywords: Transcriptome study; antimicrobial response; time course

overall_design: We conducted five independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of triclosan. We calculated fold change as the ratio between the signal averages of five untreated (control) and five triclosan-treated (experimental) cultures for 0, 10 and 60 min exposures.

first: Freshteh

last: Toghrol

first: William

middle: E

last: Bentley


title: Global transcriptional profiling of Staphylococcus aureus treated with rhein

status: Public on Jun 15 2007

first: Xuming

last: Deng

summary:
Staphylococcus aureus is one of the most important pathogens in humans and animals, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. Rhein, a natural plant product, has potential antimicrobial activity against Staphylococcus aureus.
We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with rhein. Results provided insight into mechanisms involved in rhein - Staphylococcus aureus interactions.
Keywords: rhein response

overall_design: Staphylococcus aureus cells were exposed for 45 minutes to rhein at concentration of 8 µg/ml (1/2× MIC), 6 samples including 3 control samples are analyzed.

first: Ximing


title: Toxicogenomic response to chlorination includes induction of major virulence genes in Staphylococcus aureus

status: Public on Aug 01 2007

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

summary:
In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to hypochlorite, which involved initial growth inhibition and subsequent partial recovery.
Keywords: Time course

overall_design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of hypochlorite. We calculated fold change as the ratio between the signal averages of three untreated (control) and three hypochlorite-treated (experimental) cultures for 10 and 20 min exposures.

middle: W


title: Prognostic Gene Expression Signature Associated with Two Molecularly Distinct Subtypes of Colorectal Cancer

status: Public on Jun 20 2011

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

type:
Third-party reanalysis
Expression profiling by array

summary: The aim of this study is to identify prognostic gene expression signatures associated with two molecularly distinct subtypes of colorectal cancer. Samples were taken from colorectal cancers in surgically resected specimens in 96 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. This is a test set for validation of prognostic gene expression signature that was developed from GSE14333. All data were normalized by using the RMA method (affy package in R/Bioconductor).

overall_design:
mRNA from 96 primary colorectal tumor samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. All data were normalized by using RMA method.

This study represents a re-analysis of 96 Samples (listed below) from Series GSE14333. The re-processed data is linked to this record as a supplementary file. The raw data files can be downloaded using the 'Supplementary file' links at the bottom of the Sample records.

first: Ju-Seog

last: Lee


title: Individuality and variation in gene expression patterns in human blood.

status: Public on Nov 23 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
We carried out a survey of the variation in gene expression patterns in the blood of healthy individuals, by using cDNA microarrays.  Our results revealed a surprising consistency in these patterns, but also evidence of distinct patterns of interindividual and temporal variation.  Some features of variation in the expression patterns were associated with differences in the cellular composition of the blood sample, with gender, age, and time of day.  These results expand our understanding of human variation and hematological physiology and provide a genome-wide molecular portrait of a healthy human tissue.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Addie

last: Whitney


title: M74 disorder in Baltic salmon

status: Public on Feb 16 2005

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary:
M74 developmental disorder is characterized with high mortality in salmon fry. Samples are categorized by the onset and stage of disease; analyses were conduced in a dye swap design
Keywords: parallel sample

first: Kristiina

last: Vuori