title: Global gene expression profiling in PPAR-γ agonist-treated kidneys in an orthologous rat model of human autosomal recessive polycystic kidney disease

status: Public on Mar 22 2012

city: Toyoake

first: Kugita

last: Masanori

state: Aichi

address: kutsukake-cho Denngakugakubo 1-98

department: Center of Animal Models for Human Diseases

institute: Fujita Health University

summary: Kidneys are enlarged by aberrant proliferation of tubule epithelial cells leading to the formation of numerous cysts, nephron loss, and interstitial fibrosis in polycystic kidney disease (PKD). Pioglitazone (PIO), a PPAR-γ agonist, decreased cell proliferation, interstitial fibrosis and inflammation, and ameliorated PKD progression in PCK rats.  To examine the genetic mechanisms in this efficacy, we analyzed changes in global gene expression.  By Gene Set Enrichment Analysis of 30655 genes, 13 of the top 20 down-regulated gene ontology biological process gene sets, and six of the top 20 curated gene set canonical pathways identified to be down-regulated by PIO-treatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways.  Their relevant pathways were identified using the Kyoto Encyclopedia of Gene and Genomes database.  Stearoyl-Coenzyme A desaturase 1 is a key enzyme in fatty acid metabolism found in the top 5 genes down-regulated by PIO treatment. Immunohistochemical analysis revealed that the gene product of this enzyme was highly expressed in PCK kidneys, and decreased by PIO.  These data show that PIO alters the expression of genes involved in cell cycle progression, cell proliferation, and fatty acid metabolism.

overall_design: RNA was extracted from kidneys of rats with or without PIO treatment using a monophasic solution of phenol/guanidine isothiocyanate and TRIzol reagent (Invitrogen Co., Carlsbad, CA, USA) in accordance with their manual, and the samples were incubated with RNase-free DNase I (Ambion, TX, USA).  The quality and concentration of each sample was confirmed by spectrophotometry (NanoDropTM ND-1000; Asahi glass Co. Ltd., Tokyo, Japan).  Total RNA obtained from five females were pooled in each PIO-treated or control vehicle-treated (CONT) group. Briefly, 500 ng aliquots of total RNA obtained from kidneys of three rats were labeled using an Quick Amp Labeling Kit, one-color (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.  The pooled renal RNA of PIO- or vehicle-treated rats were labeled with the Cy3-fluorescence dye.  After determination of labeling efficiency, 1.65 μg aliquots of Cy3-labeled RNA were hybridized using the Gene Expression hybridization kit (Agilent Technologies) onto Rat Oligo Microarrays (Agilent Technologies, product no. G4130A) according to the manufacturer’s hybridization protocol.  The microarray slides were examined with an Agilent microarray scanner and software.  Data analysis was performed with Agilent Feature Extraction software (version 10.7.3.1).

first: Daisuke

last: Yoshihara

first: Masanori

last: Kugita

first: Tamio

last: Yamaguchi

first: Harold

last: Aukema

first: Hiroki

last: Kurahashi

first: Miwa

last: Morita

first: Yoshiyuki

last: Hiki

first: James

last: Calvet

first: Darren

last: Wallace

first: Takafumi

last: Toyohara

first: Takaaki

last: Abe

first: Shizuko

last: Nagao


title: Tea tree oil induced transcriptional alterations in Staphylococcus aureus

status: Public on Apr 26 2012

city: Las Cruces

first: John

middle: Eric

last: Gustafson

state: NM

department: Biology and Molecular Biology Program

country: USA

institute: New Mexico State University

summary: S. aureus and MRSA are susceptible to TTO and are therefore targeted in nascent TTO clinical trails. We now report the alterations in the transcriptome of a S. aureus exposed to a growth inhibitory concentration of TTO. These efforts have uncovered additional mechanisms by which this membrane active antimicrobial substance inhibits bacterial growth.

overall_design: Four hybridizations, including a biological replicate and a dye-swap experiment for each replicate was carried out. LOWESS normalization was performed on the raw data to correct for dye-bias. Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast. A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

first: Jesus

last: Cuaron


title: Calvarial osteoblast transcriptome analysis identifies genetic targets and extracellular matrix-mediated focal adhesion as potential biomarkers for single-suture craniosynostosis

status: Public on Mar 04 2012

city: Seattle

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Craniosynostosis is a disease defined by premature fusion of one or more cranial sutures. The mechanistic pathology of isolated single-suture craniosynostosis is complex and while a number of genetic biomarkers and environmental predispositions have been identified, in many cases the causes remain controversial and inconclusive at best.  After controlling for variables contributing to potential bias, FGF7, SFRP4, and VCAM1 emerged as potential genetic biomarkers for single-suture craniosynostosis due to their significantly large changes in gene expression compared to the control population.  Furthermore, pathway analysis implicated focal adhesion and extracellular matrix (ECM)-receptor interaction as differentially regulated gene networks when comparing all cases of single-suture synostosis and controls.  Lastly, overall gene expression was found to be highly conserved between coronal and metopic cases, as evidenced by the fact that WNT2 and IGFBP2 were the only differentially regulated genes identified in a direct comparison.  These results not only confirm the roles of previously reported craniosynostosis-related targets but also introduce novel genetic biomarkers and pathways that may play critical roles in its pathogenesis.

overall_design: In this study, gene expression data from 199 patients with isolated sagittal (n= 100), unilateral coronal (n = 50), and metopic (n = 49) synostosis are compared against both a control population (n = 50), as well as each other.

first: Richard

middle: P

last: Beyer

first: Theodore

middle: K

last: Bammler

first: Michael

middle: L

last: Cunningham

first: Brendan

middle: D

last: Stamper

first: Sarah

middle: S

last: Park

first: Brig

last: Mecham


title: Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma

status: Public on Mar 08 2012

city: Amsterdam

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFβ pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.

overall_design: 88 human Neuroblastoma samples were analyzed.

first: Rogier

last: Versteeg


title: Long RNA-seq from ENCODE/Cold Spring Harbor Lab

status: Public on Apr 02 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

type: Expression profiling by high throughput sequencing

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:davisc@cshl.edu (experimental), Roderic Guigo mailto:rguigo@imim.es and lab (data processing) and Tom Gingeras mailto:gingeras@cshl.edu (primary investigator)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

These tracks were generated by the ENCODE Consortia. They contain information about mouse RNAs > 200 nucleotides in length obtained as short reads off the Illumina platform. Data are available from biological replicates.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Tissue Samples: Individual tissues were harvested from mouse strain C57BL/6NJ at different timepoints according to ENCODE cell culture protocols. Whenever possible biological replicates from litermates.
Library Preparation: The published cDNA sequencing protocol was used. This protocol generates directional libraries and reports the transcripts' strand of origin. Exogenous RNA spike-ins were added to each endogenous RNA isolate and carried through library construction and sequencing. The spike-in sequence and the concentrations are available for download in the supplemental directory.
Sequencing and Mapping: The libraries were sequenced on the Illumina platform (either GAIIx or Hi-Seq) in mate-pair fashion (either pair-end 76 or pair-end 101) to an average depth of 100 million mate-pairs. The data were mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information about STAR, including the parameters used for these data, is available from the Gingeras lab.
Verification: FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated for annotated exons and Spearman correlation coefficients were computed. In general, Rho values are > .90 between biological replicates.

first: Carrie

last: Davis

first: Roderic

last: Guigo

first: Tom

last: Gingeras


title: Sorghum gene expression using Agilent custom 4x44K Microarray

status: Public on Apr 08 2012

city: Singapore

first: Shu-Ye

last: Jiang

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory, National University of Singapore

summary: As no commercial array is available for sorghum microarray analysis, we designed an array based on the annotation of Sbi1.4 gene set  and the available 209,835 sorghum ESTs from the NCBI EST database. The array will be used for investigating the expression divergence between grain and sweet sorghum lines under normal and sucrose treatments

overall_design: The expression analysis was carried out using 14-day old whole seedlings from both grain and sweet sorghum lines. Three samples from sucrose treatment (0h, 2h and 6h) for each line were collected for the analysis . Two biological replicates were carried out for both control and sucrose treatments, resulting in a dataset of 12 microarrays.

first: Zhigang

last: Ma

first: Jeevanandam

last: Vanitha

first: Srinivasan

last: Ramachandran


title: Expression data from germinating conidia of Aspergillus niger in the presence of the polyene antibiotic natamycin.

status: Public on Mar 13 2012

city: Utrecht

first: Martin

middle: Richard

last: van Leeuwen

address: Uppsalalaan 8

department: Applied and Industrial Mycology

institute: CBS-KNAW/Fungal Biodiversity Centre

summary: The impact of natamycin on Aspergillus niger was analysed during 8 h of germination of conidia. Polarization, germ tube formation, and mitosis were inhibited in the presence of 3 µM and 10 µM of the anti fungal compound natamycin, while at 10 µM also isotropic growth was affected. Natamycin did not have an effect on the decrease of internal microviscosity and the concomitant reduction on mannitol and trehalose levels. However, it did abolish the increase of intracellular levels of glycerol and glucose during the 8 h period of germination. Natamycin hardly affected the changes that occur in the RNA profile during the first 2 h of germination. During this time period, genes related to transcription, protein synthesis, energy and cell cycle and DNA processing were particularly up regulated. On the other hand, when 8 h old germlings were compared, genes involved in ergosterol biosynthesis were down regulated while genes related to endocytosis and metabolism of compatible solutes, and genes encoding protective proteins were up regulated.

overall_design: Samples of germinating conidia of Aspergillus niger N402 were taken in triplo at 0h (dormant), 2h, and 8h after inoculation in CM. These were compared with conidia that germinated in the presence of either 3 µM or 10 µM natamycin.

middle: R

first: Pauline

last: Krijgsheld

first: Timon

middle: T

last: Wyatt

first: Elena

middle: A

last: Golovina

first: Hildegard

last: Menke

first: Angelina

last: Dekker

first: Jacques

last: Stark

first: Hein

last: Stam

first: Robert

middle: J

last: Bleichrodt

first: Han

last: Wösten

first: Jan

last: Dijksterhuis


title: The temporal dynamics of differential gene expression in human alveolar epithelial and endothelial cells interacting with the human pathogenic mould Aspergillus fumigatus in vitro

status: Public on Apr 17 2012

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

summary: Aspergillus fumigatus is the most relevant pathogenic mould in immunocompromised patients. Spores of A. fumigatus are inhaled and reach the lung alveoli, where they interact with the human immune system. In this set of experiments, we co-cultured with defined morphologies of Aspergillus fumigatus (Af293) for 0h, 3h and 6h with either cells representing human alveolar epithelium (A549) or human alveolar endothelium (HPAEC). We included either monocyte-derived or myeloid dendritic cells from volunteer donor blood to the epithelial layer to examine their effect on gene expression.  RNA was extracted from both cell lines at each time point and hybridised to microarrays.  Microarrays contain probes for approximately 110 selected human immune-relevant genes, including cytokine and chemokine genes, their receptors and downstream innate immunity genes.

overall_design: We used microarrays to detail the gene expression of human alveloar epithelial and endothelials cells after 3h and 6h of co-cultivation with Aspergillus fumigatus and monocyte-derived or myeloid dendritic cells

first: Juergen

last: Loeffler

first: Oliver

last: Morton

first: Helga

last: Sennefelder

first: Ruth

last: Bauer

first: Jasmin

last: Kungl


title: Comparing gene expression in untransfected and transfected mouse neuronal (Neuro2A) cell line

status: Public on Feb 29 2012

city: New Delhi

first: Rohini

last: Muthuswami

address: Room# 333, School of Life Sciences, JNU

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

summary: We compared the gene expression in untransfected Neuro2A cells and in pCDNA3.1myc/his vector transfected Neuro2A cells

overall_design: 1 sample each of untransfected and transfected Neuro2A cells were analyzed


title: cis-Expression QTL Analysis of Established Risk Variants for Colorectal Cancer

status: Public on Jan 31 2012

city: Honolulu

first: Lenora

middle: WM

last: Loo

state: HI

address: 1236 Lauhala St #407

department: Epidemiology Program

institute: University of Hawaii Cancer Center

summary: Genome-wide association studies (GWAS) have identified 19 risk variants associated with colorectal cancer.  As most of these risk variants reside outside the coding regions of genes, we conducted cis-expression quantitative trait loci (cis-eQTL) analyses to investigate possible regulatory functions on the expression of neighboring genes.

overall_design:
Forty microsatellite stable and CpG island methylator phenotype-negative colorectal tumors and paired adjacent-normal colon tissues were used for genome-wide SNP and gene expression profiling in our cis-eQTL analyses.

This submission represents transcriptome component of study.

middle: W

first: Iona

last: Cheng

first: Maarit

last: Tiirikainen

first: Annette

last: Lum-Jones

first: Ann

last: Seifried

first: Lucas

middle: M

last: Dunklee

first: James

last: Church

last: Gryfe

first: Daniel

last: Weisenberger

last: Haile

first: Steven

last: Gallinger

first: David

last: Duggan

first: Stephen

middle: N

last: Thibodeau

first: Graham

last: Casey

first: Loic

last: Marchand


title: Genome-wide gene expression analysis of HL60 cells and its alpha particle-resistant derivative RA11, gamma resistant-derivative RG8, and vincristine resistant-derivative RV+ at baseline and following 8Gy gamma IR and ~2Gy alpha IR

status: Public on Jan 28 2012

city: New York

first: Kurtis

last: Haro

state: NY

address: 1275 York Ave

institute: MSKCC

summary: The purpose of this study was to identify genes that were differentially expressed in radiation-sensitive, naïve HL60 cells, and the derivatives created in our laboratory as indicated in the 'sample title'.  We wanted to identify genes that were differentially expressed both before and after ionizing radiation (IR) exposure, from both a single dose of gamma rays and a single dose of alpha particles, at 4h following IR exposure.  The data were used to identify genes that could be driving radioresistance in each respective cell line.

overall_design: The four cell lines, HL60, RA11, RG8, and RV+ were all analyzed at control (0Gy) radiation dose, 8Gy gamma rays, and ~2Gy alpha particles.  Samples were collected from each cell line, for each dose, 4h following radiation exposure.  The samples were collected from three independent experiments from three consecutive days in cell culture.

last: Scheinberg


title: Gene expression of Pseudomonas aeruginosa (Pae) delta PA1006/nbvF mutant in the absence and presence of nitrate

status: Public on Dec 20 2011

city: Rochester

first: Barbara

middle: H.

last: Iglewski

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

summary: The Pae PA1006/nbvF gene was found to be essential for nitrate utilization, biofilm maturation, and virulence. Microarrays were employed to assess global gene expression changes in response to NO3 compared to wild-type.

overall_design: Cells were grown aerobically in the absence or presence of nitrate and the effect on global gene expression was determined; two to three biological replicates for each condition were analyzed.

first: Melanie

last: Filiatrault

first: Gregory

last: Tombline

first: Victoria

middle: E

last: Wagner

first: Nadine

last: VanAlst

first: Kendra

last: Rumbaugh

first: Pam

last: Sokol

middle: H


title: The mtDNA Amerindian Haplogroup B2 enhances the risk for Cervical Cancer of HPV: de-regulation of mitochondrial genes may be involved.

city: Mexico City

first: Mariano

last: Guardado-Estrada

state: Cuauhtémoc

address: Dr. Bálmis 148 Col. Doctores

department: Medicina Genómica

country: Mexico

institute: Hospital General de México O.D.

summary: Although Human papillomavirus infection is the main causal factor for cervical cancer (CC), there is data suggesting genetic factors could modulate the risk and progression of CC. Sibling studies suggest that maternally inherited factors could be involved in CC. To assess whether mitochondrial DNA (mtDNA) polymorphisms are associated to cervical cancer, HPV infection and HPV types, a case-control study was performed in the Mexican mestizo population. The polymorphism of mtDNA D-Loop was investigated in 187 cervical cancer patients and 270 healthy controls. D-loop was amplified from a blood DNA sample and analyzed by sequencing. HPV was detected and typed in cervical scrapes from both groups. mtDNA polymorphisms were compared in the whole samples and stratified by HPV types. The expression of 29 mitochondrial genes was analyzed in a subset of 45 tumor biopsies using the expression microarray ST1.0. The Amerindian haplogroup B2 increased the risk for CC (OR=1.6, 95% CI: 1.05-2.58) and showed an additive effect of 36% over the risk conferred by the HPV (OR=153, 95% CI: 65.4-357.5). The frequency of HPV 16, 18, 31 and 45 in cancer samples was similar in all haplogroups but one (D1). It showed a very low frequency of HPV16, any HPV18 and high frequency of HPVs 31, 45 and other types. Two mtDNA genes (MT-TD, MTTK) could be involved in the increased risk conferred by the haplogroup B2, since they were up-regulated exclusively in B2 tumors (p<0.05, t-test). These findings will contribute to clarify the importance of genetic factors in CC.

overall_design: 45 cases and 17 controls

first: Ingrid

last: Medina-Martinez

first: Jaime

last: Berumen


title: Expression data form EhCPBF1 gene silenced strain.

status: Public on Dec 13 2011

city: Tokyo

first: Kumiko

last: Nakada-Tsukui

address: 1-23-1, Toyama, Shinjyuku-ku

country: Japan

institute: National Institute of Infectious Diseases

summary:
Enteric protozoan parasite Entamoeba histolytica is a causative agent of amebiasis. One of the major virulence factors of this parasite is cysteine protease (CP). To understand the molecular basis of intracellular trafficking of CP, we identified CP5 binding protein and named cysteine protease binding protein family 1 (CPBF1).
To study the function of CPBF1, we generate CPBF1 gene silenced strain and analyzed the expression profile by custom made microarray.

overall_design: E. histolytica G3 strain was transfected with pSAP2 vector or pSAP2-CPBF1 and established the transformats by selecting the transfected cells with G418. After confirm the gene silencing of CPBF1 by RT-PCR, we performed the transcriptome analysis of pSAP2 (mock) and pSAP2-CPBF1 (gene silenced) cells.

first: Atsushi

last: Furukawa

first: Tomoyoshi

last: Nozaki


title: Expression data of pachytene spermatocytes and round spermatids from young and aged Brown Norway rats

status: Public on Jan 06 2012

city: Montreal

first: Bernard

last: Robaire

state: Quebec

address: 3655 Promenade Sir William Osler

country: Canada

institute: McGill University

summary:
Male fertility and testis function changes with age and so it was sought to determine if these changes are accompanied by changes in gene expression.
A full genome microarray was used to determine if distinct pathways of genes were altered in expression in germ cells (pachytene spermatocytes or round spermatids) with age.

overall_design:
PACH: Testes from young (4 months) and aged (18 months) Brown Norway rats were subjected to a density gradient cell separation to isolate pachytene spermatocytes. RNA was isolated from these cells for hybridization on affymetrix miroarrays.

ROU: Testes from young (4 months) and aged (18 months) Brown Norway rats were subjected to a density gradient cell separation to isolate round spermatids. RNA was isolated from these cells for hybridization on affymetrix miroarrays.

first: Catriona

last: Paul


title: Fetal programming of hepatic transcriptome in response to gestational dietary protein levels in the pig (AP data set)

status: Public on Nov 30 2011

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
German landrace gilts were fed an adequate protein diet (AP, 12% CP) throughout their whole pregnancy. Subsequently hepatic transcriptome profiles of the offspring were analysed at prenatal (94 dpc) and postnatal stages (1, 28, 188 dpn).

Keywords: ANOVA

overall_design: per stage offspring of 8 gilts were collected for expression profiling

first: Siriluck

last: Ponsuksili

first: Michael

last: Oster


title: Gene Expression Analysis of Stage I Endometrial Cancers

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: Global gene expression patterns associated with early stage endometrial cancer have been reported, but changes in molecular expression associated with tumor grade, depth of myometrial invasion, and non-endometrioid histology have not been previously elucidated.  Our group hypothesized there are unique genetic events underlying early endometrial carcinogenesis.  Ninety-two samples of pathologically reviewed stage I endometrial cancers (80 endometrioid and 12 serous) with a heterogeneous distribution of grade and depth of myometrial invasion (i.e. 9 IAG1, 14 IAG2, 7 IAG3, 14 IBG1, 12 IBG2, 13 IBG3, 7 ICG1, 10 ICG2, and 6 ICG3)  were examined in relation to 12 samples of atrophic endometrium from postmenopausal women.  Specimens were analyzed using oligonucleotide microarray analysis and a subset of the differentially expressed transcripts was validated using quantitative PCR.  Comparison of early stage cancers with normal endometrium samples by the univariate t-test with 10,000 permutations identified 900 genes that were differentially regulated by at least 4-fold at a p value of <0.001.   Unsupervised analysis revealed that when compared to normal endometrium, serous and endometrioid stage I cancers appeared to have similar expression patterns.  However, when compared in the absence of normal controls, they were distinct.   Differential expression analysis revealed a number of transcripts that were common as well as unique to both histologic types.  This data uncovers previously unrecognized, novel pathways involved in early stage endometrial cancers and identifys targets for prevention strategies that are inclusive of both endometrioid and serous histologic subtypes.

overall_design: Ninety-one samples of pathologically reviewed stage I endometrial cancers (79 endometrioid and 12 serous) with a heterogeneous distribution of grade and depth of myometrial invasion (i.e. 9 IAG1, 14 IAG2, 7 IAG3, 14 IBG1, 12 IBG2, 13 IBG3, 7 ICG1, 10 ICG2, and 6 ICG3) were examined in relation to 12 samples of atrophic endometrium from postmenopausal women. Specimens were analyzed using oligonucleotide array analysis.

first: John

last: Risinger

first: Jay

last: Allard

first: Caela

last: Miller

first: Mark

last: Sherman

first: Chris

last: Zahn

first: Julie

last: Oliver

first: Subhadra

last: Banerjee

first: Tracy

last: Litzi

last: Carlson

last: Farley

first: Scott

last: Rose

first: Andrew

last: Berchuck

first: Elise

last: Kohn

first: Roger

last: Day

first: Tom

last: Conrads

first: Ron

last: Herberman

first: G

last: Maxwell


title: Study for evaluating the effect of cold ischemic time and RNA stabilization method on RNA integrity and gene expression measurements

status: Public on Nov 02 2011

city: Woburn

first: Christos

last: Hatzis

state: MA

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

summary:
Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision.
A different 2x2 factorial within this study evaluated the effect of stabilization method (RNAlater vs snap freezing) and stablization delay (0 and 40 min) at room temperature.

overall_design: Tissue samples were collected at surgery, cut into 1-2 mm pieces and divided into 8 portions.  Portions were put in RNAlater or fresh frozen at baseline, 20, 40, 60, 120, and 180 minutes thereafter, or snap frozen in dry ice in a pre-chilled sample vial at baseline and 40 minutes thereafter.

first: W

middle: F

last: Symmans

first: Hongxia

last: Sun


title: Effect of EWS/FLI1 and DAX1 silencing on the gene expression profile of the A673 Ewing cell line

status: Public on Feb 23 2012

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

country: Spain

institute: INSTITUTO DE SALUD CARLOS III - IIER

summary: The molecular hallmark of the Ewing family of tumors is the presence of balanced chromosomal translocations leading to the formation of chimerical transcription factors (i.e. EWS/FLI1) that play a pivotal role in the pathogenesis of Ewing tumors by deregulating gene expression. We have recently demonstrated that DAX1 (NR0B1), an orphan nuclear receptor which was not previously implicated in cancer, is induced by the EWS/FLI1 oncoprotein and is highly expressed in Ewing tumors, suggesting that DAX1 is a biologically relevant target of EWS/FLI1-mediated oncogenesis. In this work we demonstrate that DAX1 is a direct transcriptional target of the EWS/FLI1 oncoprotein through its binding to a GGA-rich region in the DAX1 promoter and show that DAX1 is a key player of EWS/FLI1-mediated oncogenesis. DAX1 silencing using an inducible model of RNA interference induces growth arrest in the A673 Ewing cell line and severely impairs its capability to grow in semisolid medium and form tumors in immunodeficient mice. Gene expression profile analysis demonstrated that about ten percent of the genes regulated by EWS/FLI1 in Ewing cells are DAX1 targets, confirming the importance of DAX1 in Ewing oncogenesis. These findings indicate that DAX1 is an important player in the pathogenesis of the Ewing family of tumors, identify new functions for DAX1 as a cell cycle progression regulator and open the possibility to new therapeutic approaches based on DAX1 function interference.

overall_design: A673 cells derived from Ewing sarcoma were genetically enginereed to express specific shRNAs against GFP (control), EWS/FLI1 and DAX1 upon doxycycline stimulation. Three independent clones and a polyclonal population from each enginereed cell were analyzed. Cells were stimulated with doxycycline for 72 hours to induce the expression of the corresponding shRNA and whole gene expression profile performed. Gene expression profile in A673 cells in which EWS/FLI1 or DAX1 were silenced were compared to the control cells.


title: Characterization of the small RNA population in Human spermatozoa

status: Public on Oct 16 2011

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock, CS Mott Center

department: Obstetrics and Gynecology

institute: Wayne State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small noncoding RNAs (sncRNA) are becoming recognized for their participation in a diverse range of cellular functions. In this study, their global characterization in human spermatozoa from donors with proven fertility was undertaken. Reads were analyzed in two classes, those mapping to unique locations and those that could be aligned to up to 10 genomic locations.  All libraries showed comparable distribution of reads between intergenic, intronic and exonic genomic regions.   Analysis of the sequences revealed the presence of multiple small RNA classes. The miRNAs retained in spermatozoa were found to be associated with promoter regions, suggestive of a role at the transcriptional level.  Piwi-interacting sncRNAs as well as repeat-associated small RNAs were identified for the first time in mature spermatozoa from a mammalian species. Human spermatozoa retain a multifaceted population of small non-coding RNAs. Their presence is consistent with the view that they may function to stabilize the genome as part of the confrontation and consolidation of the genomes at fertilization.

overall_design: Examination of sperm samples from 3 individuals, sequenced individually

first: Claudia

last: Lalancette

first: Adéle

last: Kruger

first: Adrian

last: Platts

first: Michael

middle: P

last: Diamond


title: Gene expression profiling in HCV associated liver disease

status: Public on Nov 21 2011

city: Lahore

first: Sajida

last: Hassan

address: 87-West Canal bank Road

department: CEMB

country: Pakistan

institute: University of the Punjab

summary: Expression of human genes was compared in liver fibrosis stage F1, F2, F3, and F4 to find markers that can differentiate among each fibrosis stages and cirrhosis.

overall_design: Four- condition experiment, F1 vs. F2 vs. F3 vs. F4. Biological replicates: 3 Normal, 3 F1, 3 F2, 3 F3 and 3 F4 stage samples.

first: Bushra

last: Ijaz

first: Wagar

last: Ahmad


title: A gene expression database for retinal neuron subtypes

city: Cambridge

first: Jeremy

last: Kay

address: 52 Oxford Street

institute: Harvard University

summary: The goal of this experiment was to define gene expression patterns of thirteen mouse retinal neuron subsets, labeled by expression of fluorescent proteins in transgenic mice.

overall_design: Neurons expressing xFPs were purified by flow cytometry. Thirteen different neuron subtypes were compared. Two biological replicates, originating from different litters, were collected for each cell type. RNA was extracted from sorted cells and prepared for hybridization to Affymetrix microarrays.

first: Joshua

last: Sanes


title: Microglia infection of Listeria monocytogenes is regulated by ActA virulence factor and TNF-α.

status: Public on Oct 03 2011

city: Liencres

first: carmen

last: alvarez-dominguez

state: Cantabria

address: Barrio de las Mazas, 17

department: Immunology Department-HUMV

institute: fundación marqués de valdecilla-IFIMAV

summary:
Cerebral listeriosis is characterized by neuronal apoptosis and microglial cell activation, but little is known about the bacterial virulence factors involved in this process and how bacterial dissemination is controlled.   Here, we show that the cellular target of Listeria monocytogenes (LM) in murine hippocampal cultures is microglia rather than neurons or other glial cells, which are rarely infected. This in vitro model served to demonstrate that infected microglial cells release a soluble factor to the medium responsible for neuronal apoptosis. We investigated the production of this factor in a well-established murine microglia cell model BV2 cells, and compared with J-774 macrophage cells after infection with different LM bacterial mutants. Our purpose was to study in both cell types parameters such as the listericidal capacities, pro-inflammatory cytokines released, and bacterial factors involved in the intracellular cycle.
Our data reveal that microglia shows unique features to handle a LM infection. Microglia is three times more permissive for LM intracellular growth than murine macrophages; while producing five times higher levels of pro-inflammatory cytokines IL-6, MCP-1 and TNF-α than macrophages. Using different LM mutants (i.e., LMWT, LM∆LLO, LM∆ActA or LM∆plcB) we conclude that LLO and ActA are not involved in LM proliferation within microglia cells, while they are required for survival within macrophages. Moreover, ActA controls TNF-α production, a cytokine involved in neural apoptosis. Transcriptional differential response of microglia infected with different LM mutants reflected ActA controls the TNF-a signaling pathway through out molecules and chemokines involved in this pathway such as NFkβ, MAPK-1, Ccl2, Ccl3, Ccl4 and CxCl10.

overall_design:
The project implies the analysis of two replicates from three different conditions, in total 6 samples: microglia cells non-infected, microglia cells infected with Listeria monocytogenes (LM) wild type (LLO+), microglia cells infected with LM deficient in listeriolysin O (LLO-) and microglia cells infected with LM deficient in ActA (1942). References samples were microglia cells non-infected (NT). Infection with LM was performed for 1 hour, followed by 24 hours in medium with antibiotics to avoid bacterial extracellular growth.
Gene expression analysis was performed using Partek Genomics Suite software (version 6.11.0801; Partek). GeneChip data were filtered to remove those probe sets with an intensity raw value close to background levels. Probe sets for each array are pre-processed using RMA. Also, probe sets whose expression change under all experimental conditions was below a threshold, based on the standard desviation of the normalised intensity values, were filtered.

first: Carmen

last: Alvarez


title: Mouse ischemic tolerance genomic analysis of the brain and blood.

status: Public on Oct 05 2011

city: Portland

first: Susan

middle: L

last: Stevens

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Molecular Microbiology & Immunology

institute: Oregon Health & Science University

summary:
Ischemic tolerance can be induced by numerous preconditioning stimuli, including various Toll-like receptor (TLR) ligands. We have shown previously that systemic administration of the TLR4 ligand, lipopolysaccharide (LPS) or the TLR9 ligand, unmethylated CpG ODNs prior to transient brain ischemia in mice confers substantial protection against ischemic damage. To elucidate the molecular mechanisms of preconditioning, we compared brain and blood genomic profiles in response to preconditioning with these TLR ligands and to preconditioning via exposure to brief ischemia.
The experiment is a comparison of multiple treatment groups with sampling at multiple time points. The objective is to identify differentially regulated genes associated with preconditioning. Time points are examined both following preconditioning alone and following subsequent ischemic challenge (middle cerebral artery occlusion (MCAO)).
Brain ipsilateral cortex tissue and blood were collected and processed from each animal.

overall_design: 6 experimental conditions: (n=3-4 mice/condition)  LPS treated  (i.p. 0.2mg/kg) + ischemic challenge (45min MCAO)     CpG treated  (i.p. 0.8mg/kg) + ischemic challenge (45min MCAO)   Saline treated (i.p.) + ischemic challenge (45min MCAO)     brief ischemia (12 min MCAO) + ischemic challenge (45min MCAO)  Sham of brief ischemia (12 min)  + ischemic challenge (45min MCAO)   Non-treated  + ischemic challenge (45min MCAO)      Time points:  Pre-ischemic challenge   3hr 24hr 72hr  Post-ischemic challenge  3hr 24hr  Unhandled (6 mice)-BASELINE

first: Mary

last: Stenzel-Poore


title: Polyhedral microcompartments in Clostridium phytofermentans

status: Public on Sep 01 2011

city: Amherst

first: Jeffrey

last: Blanchard

address: 203 Morrill Science Center IVN

department: Biology

institute: University of Massachusetts Amherst

summary: Clostridium phytofermentans ferments all major component of the plant cell wall to alcohols and is an emerging model organism for understanding the direct conversion of plant biomass into biofuels.  Encoded in the genome of C. phytofermentans are three large genetic loci for the production of polyhedral microcompartments (PMCs) that may function as metabolic centers for the dissimilation of plant cell wall components into primary alcohols.  We demonstrate that the PMC encoded by one of these loci acts in the fermentation of fucose and rhamnose to propanol and propionate.  The PMC contains a propanediol dehydratase that is part of a new superfamily of enzymes that utilizes S-adenosylmethionine in place of adenosylcobalamin to catalyze radical reactions.    Analysis of the C. phytofermentans genome sequence data indicated that the fucose and rhamnose pathways might converge at the point of the enzymes encoded by the PMC loci.  When C. phytofermentans is grown on fucose, a 100-200 nm polyhedral body is apparent in electron micrographs, and ethanol and propanol are produced.  Microarray experiments revealed that during growth on fucose, three fucose-related operons coding for (i) the PMC shell and metabolic proteins, (ii) cytoplasmic fucose dissimilatory enzymes, and (iii) an ABC transporter system become the dominant transcripts in the cell.   Similarly when C. phytofermentans is grown on rhamnose, three rhamnose-related operons coding for (i) the PMC shell and metabolic proteins, (ii) cytoplasmic rhamnose dissimilatory enzymes, and (iii) an ABC transporter system become the dominant transcripts in the cell.  Quite surprisingly, growth on fucose or rhamnose also led to the expression of a broader plant degradative transcriptional response.  The expression of cellulose degrading enzymes on fucose and rhamnose is a fundamental difference between C. phytofermentans and its closest relatives, the human gut commensals.

overall_design: C. phytofermentans ISDg was cultured in anaerobic medium GS-2CB [20].  Growth on single carbon-source utilized anaerobic medium derived from GS-2CB and containing the following (g l-1): yeast extract, 6.0; urea, 2.1; KH2PO4, 4.0; Na2HPO4, 6.5; trisodium citrate dihydrate, 3.0; L-cysteine hydrochloride monohydrate, 2.0; resazurin, 1; with pH adjusted to 7.0 using KOH.  This medium was supplemented with 0.3% (wt/vol) of the specific substrate (glucose, fucose and rhamnose) added as a filter-sterilized solution to the sterile medium.  Broth cultures were incubated at 30˚C under anaerobic conditions (100% N2) as described in by Hungate [30].  Growth was determined spectrophotometrically by monitoring changes in optical density at 660 nm.  RNA was purified from mid-exponential phase cultures at 27 hr for glucose and 62 hrs for fucose and rhamnose.

first: Elsa

last: Petit

first: William

middle: G

last: Latouf

first: Thomas

last: Warnick

first: Supriya

last: Deshpande

first: Devin

last: Currie

first: Igor

last: Romashko

first: Danny

last: Schnell

middle: B

last: Leschine


title: Gene expression signature-based novel prognostic risk score in gastric cancer

status: Public on Jul 19 2011

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Despite continual efforts to establish pre-operative prognostic model of gastric cancer by using clinical and pathological parameters, a staging system that reliably separates patients with early and advanced gastric cancer into homogeneous groups with respect to prognosis does not exist. With use of microarray and quantitative RT-PCR technologies, we exploited series of experiments in combination with complementary data analyses on tumor specimens from 161 gastric cancer patients. Various statistical analyses were applied to gene expression data to uncover subgroups of gastric cancer, to identify potential biomarkers associated with prognosis, and to construct molecular predictor of risk from identified prognostic biomarkers.Two subgroups of gastric cancer with strong association with prognosis were uncovered. The robustness of prognostic gene expression signature was validated in independent patient cohort with use of support vector machines prediction model. For easy translation of our finding to clinics, we develop scoring system based on expression of six genes that can predict the likelihood of recurrence after curative resection of tumors. In multivariate analysis, our novel risk score was an independent predictor of recurrence (P=0.004) in cohort of 96 patients, and its robustness was validated in two other independent cohorts. We identified novel prognostic subgroups of gastric cancer that are distinctive in gene expression patterns. Six-gene signature and risk score derived from them has been validated for predicting the likelihood of survival at diagnosis.

overall_design:
65 primary gastric adenocarcinoma,  6 GIST and 19 surrounding normal fresh frozen tissues were used for microarray. All the tissues were obtained after curative resection after pathologic confirm at Yonsei cancer center(Seoul, Korea). Microarray experiment and data analysis were done at Dept. of systems biology, MDACC
DNA microarray (Illumina human V3)

first: JaeYong

last: Cho

first: HoGeun

first: SungHoon

last: Noh

first: Jaffer

last: Ajani

first: Ju-Seog

last: Lee


title: Expression data from  Ad-atrogin-1-GFP or Ad-GFP infected cardiomyocytes

status: Public on Aug 03 2011

city: Beijing

first: junjie

last: li

address: #5 Dong Dan San Tiao

country: China

institute: PUMC

summary:
Cardiomyocyte cell death and renewal are the pivotal events in the pathogenesis of heart failure .Atrogin-1/MAFbx is an ubiquitin E3 ligase that regulates myocardial structure and function through the cellular mechanism of protein degradation.
We used DNA microarrays to detail the global trends in gene expression underlying atrogin-1- overexpressed cardiomyocytes and identified distinct classes of up-regulated genes during this process. Our findings suggest that atrogin-1 plays a critical role in regulating cardiac dysfunction at transcriptional level and may provide novel insight into how atrogin-1 modulates the programming of cardiac muscle gene expression.

overall_design: Cardiomyocytes were infected with GFP control or atrogin-1 adenoviruses for RNA extraction and hybridization on Affymetrix microarrays. We sought to define the effects of atrogin-1 on the global programme of gene expression in primary cardiomyocytes. To that end, neonatal rat cardiomyocytes were infected with GFP control (G) or atrogin-1 adenovirus (A) for 24 hours.

first: Jun

last: Li

first: Hui


title: L. plantarum grown in a variety of different fermentation conditions

status: Public on Oct 01 2011

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: Lactobacillus plantarum WCFS1 was differentially fermented in 29 different fermentations according to a factorial, combinatorial scheme that included variations in growth temperature (28 or 37C), NaCl concentration (0 or 0.3M), pH (5.2, 5.8, 6.4), as well as oxygen (N2 or air) and amino acid availability (1.1 or 2x concentration).

overall_design: Samples were hybridized in a star design using five samples in the center all connected to each other. The remaining samples were linked (evenly distributed) to the samples in the inner circle in a loop design with additional links (shortcuts) to the center sample. All samples were hybridized in duplicate (at minimum) using each of the two dyes (Cy3/Cy5) at least once per sample.

first: Peter

last: Bron

first: Roger

last: Bongers

first: Anne

last: Wiersma

first: Lex

last: Overmars

first: Maria

last: Marco

last: Kleerebezem


title: IL13 and CCL2 drive disease in an inflammatory subset of Scleroderma [IL13]

status: Public on Jun 30 2011

city: Hanover

first: Jennifer

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

institute: Dartmouth Medical School

summary: Scleroderma is a lethal and currently irreversible autoimmune disease characterized by widespread tissue fibrosis and vasculopathy. Using cross-species comparative gene expression profiling we show that murine sclerodematous graft-versus-host disease (sclGVHD) approximates an “inflammatory” subset of human scleroderma and that both diseases demonstrate activation of the IL13 cytokine pathway. We report that both host myeloid cells expressing type I and II activated macrophage markers and graft T-cells produce IL13 and that host mice deficient in either IL13 or IL4Ra, an IL13 signal transducer, are protected from disease. This signaling pathway converges on a single gene, CCL2, which is coordinately upregulated in sclGVHD, in the human inflammatory scleroderma subset and in IL13 treated human dermal fibroblasts. Accordingly, treatment with antibodies to CCL2, and its murine homolog CCL12, prevent sclGVHD.  Lastly, we provide evidence that IL13 pathway activation in early scleroderma patients correlates with modified Rodnan skin scores (mRSS).  These data indicate that an inflammatory subset of scleroderma is driven by IL13 and may benefit from IL13 or CCL2 blockade.

overall_design: sample vs reference. Total RNA isolated from a time course of primary adult dermal fibroblasts treated with 50nM recombinant IL13 over 24 hours

first: Antonios

middle: O

last: Aliprantis

first: Matthew

last: Greenblatt

first: Giuseppina

last: Farina

first: Robert

last: Lafyatis

first: Kelly

last: Tsang

first: Laurie

last: Glimcher

first: Michael

last: Whitfield


title: IL13 and CCL2 Drive Disease in an Inflammatory Subset of Scleroderma [cGVHD]

summary: Scleroderma is a lethal and currently irreversible autoimmune disease characterized by widespread tissue fibrosis and vasculopathy. Using cross-species comparative gene expression profiling we show that murine sclerodematous graft-versus-host disease (sclGVHD) approximates an “inflammatory” subset of human scleroderma and that both diseases demonstrate activation of the IL13 cytokine pathway. We report that both host myeloid cells expressing type I and II activated macrophage markers and graft T-cells produce IL13 and that host mice deficient in either IL13 or IL4Rα, an IL13 signal transducer, are protected from disease. This signaling pathway converges on a single gene, CCL2, which is coordinately upregulated in sclGVHD, in the human inflammatory scleroderma subset and in IL13 treated human dermal fibroblasts. Accordingly, treatment with antibodies to CCL2, and its murine homolog CCL12, prevent sclGVHD.  Lastly, we provide evidence that IL13 pathway activation in early scleroderma patients correlates with modified Rodnan skin scores (mRSS).  These data indicate that an inflammatory subset of scleroderma is driven by IL13 and may benefit from IL13 or CCL2 blockade.

overall_design: Sample vs reference. Total RNA isolated from skin of the following mice:  B10->balb/c; balb/c->balb/c;  B10->balb/c IL13-/-; balb/c->balb/c IL13-/-; B10->balb/c IL4Ra -/-; balb/c->balb/c IL4Ra -/-


title: Dihydrotestosterone induced changes in gene expression in immortalized human conjunctival epithelial cells

status: Public on Mar 31 2011

city: Boston

first: David

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in immortalized human conjunctival epithelial cells.

Analysis of regulation of immortalized human conjunctival epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like conjunctival cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation of numerous genes in response to dihydrotestosterone incubation of immortalized human conjunctival epithelial cells.

overall_design: Total RNA was obtained from immortalized human conjunctival epithelial cells treated for 96 hours with 10 nM dihydrotestosterone (n=3) or vehicle (n=3).  The RNA was then used with Illumina HumanHT-12 v3 Expression BeadChips to determine the effect of DHT on gene expression in an immortalized human conjunctival epithelial cell line developed in Dr. Rheinwald's laboratory [Rheinwald et al. MCB, 22 (14): 5157. (2002)] and charecterized in Dr. Ilene Gibson's laboratory [Gipson et al. IOVS, 44 (6): 2496. (2003)].

first: Payal

last: Khandelwal


title: IL13 and CCL2 drive disease in an inflammatory subset of Scleroderma [IL4]

overall_design: sample vs reference. Total RNA isolated from a time course of primary adult dermal fibroblasts treated with 50nM recombinant IL4 over 24 hours


title: Genome-wide analysis of poly(I:C)-responsive gene expression by primary human keratinocytes with and without episomal human papillomavirus

status: Public on Mar 14 2011

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

institute: Prinses Maxima Centrum

summary: Analysis of the effect of high-risk human papillomaviruses HPV16 and HPV18 in keratinocytes at gene expression level. The hypothesis tested in the present study was that HPVs inhibit the function of pathogen recognition receptors (PRRs), thereby evading the immune system. Results show that HPV-positive keratinocytes have a weaker response to poly(I:C), a synthetic double strand RNA agonist of viral PRRs, with IL1B as a central hub in a gene expression network of relative downregulation.

overall_design: Total RNA from eight primary undifferentiated keratinocyte cultures, four uninfected and four HPV-positive, that were either left unstimulated, or stimulated for 4 or 24 hrs with 25 ug/ml poly(I:C).

first: Rezaul

last: Karim


title: Gene expression profiling of dendritic cells in different physiological stages under Cordyceps sinensis treatment

status: Public on Sep 09 2011

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

summary: Cordyceps sinensis (CS) has been commonly used as a herbal medicine as well as a health supplement in China for over two thousand years. Although previous studies demonstrated that CS has benefit in immunoregulation and anti-inflammation, the precise mechanism by which CS affects immunomodulation is still unclear. In this study, we adopted duplicate sets of loop-design microarray experiments to examine two different batches of CS and analyzed the effects of CS on dendritic cells (DCs) in different physiology stages, naïve stage and inflammatory stage.

overall_design: We used duplicate sets of loop-design microarray in this study. Each loop experiment consisted of 4 RNA samples, including untreated samples, CS 1μg/ml, LPS  1μg/ml, and LPS  1μg/ml+ CS 1μg/ml.

first: ChiaYang

last: Li

first: ChiShiun

last: Chiang

first: WeiChung

last: Cheng

first: HonZu

first: ChaangRay

last: Chen

first: WunYi

last: Shu

first: MinLung

last: Tsai

first: ChingLung

last: Huang

first: RueyShyang

last: Hseu

first: ChaoYing

first: ShihHua

last: Fang

first: Ian

middle: C

last: Hsu


title: MOYO-S and MOYO-R responsive genes to dengue-2 infection at 3hr and 18hr post-infection times

status: Public on Sep 30 2011

city: NOTRE DAME

first: David

last: Severson

state: IN

address: Galvin Life Science

department: Dept. of Biological Sciences

institute: University of Notre Dame

summary: We conducted a genome-wide survey of genes in Ae. aegypti females that are transcriptionally responsive upon challenge with dengue virus (serotype-2). The array was designed with 60-mer oligos specific to 16,092 gene transcripts of gene build AaegL1.1 (www. vectorbase.org). The hybridizations were performed at NimbleGen. We provided total RNA purified from the infected and control samples to NimbleGen. To identify dengue-specific transcription response (DTR) genes of MS and MR females upon infection with DENV2-JAM1409, a total of 15 independent samples (12 test samples and 3 control samples) were used for array hybridizations. These consisted of four DENV2 infected samples (MS-3hr, MR-3hr, MS-18hr and MR-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling.  Three independent biological replicates were prepared for each of the above five samples were used for hybridizations.

overall_design:
The Ae. aegypti genes responsive to dengue infection were identified in MOYO-S (MS) and MOYO-R (MR) females, upon challenging them with DENV serotype-2, by a genome-wide transcriptome analysis carried out using the NimbleGen oligonucleotide microarray format. We profiled gene expressions of Aedes aegypti mosquitoes, strain MOYO-S (MS, susceptible to dengue virus) and MOYO-R (MR, refractory to dengue virus) at 3 hr and 18 hr after infection with dengue virus (seroptype-2). The test samples were prepared in parallel to the control samples. The control samples were derived from females fed with normal blood that was not mixed with dengue (mock infection). The test samples were prepared from females that were fed with blood mixed with dengue virus (infectious meal). A total of 12 test samples were prepared that represented three biological replicates of dengue infected MS females at 3hr and 18 post-infection times; and MR females at 3hr and 18hr post-infection times. The test samples were compared to a common uninfected control that was prepared by pooling equal amount RNA of the individual control of both strains and both post-infection time points (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr). The control-pool strategy ensured  us to identify genes that were responsive in response to dengue infection but not due to genetic differences between the two strains or developmental changes between the two post-infection time points.

A total of 3 control pools were used in our array expression studies. Control-1 was prepared from RNA isolated from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the first biological replication. Similarly, control-2 was prepared from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the second biological replication. And control-3 was prepared from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the third biological replication. Thus, the three control pools represented three biological replicates corresponding to the three biological replicates of the test samples.

first: Susanta

middle: K

last: Behura


title: Gene expression-based analysis of neural tube closure for the posterior neuropore of Fkbp8 embryos at E9.5

status: Public on Dec 10 2010

city: Austin

first: Robert

last: Cabrera

address: 1400 Barbara Jordan Blvd

institute: DPRI

summary: Three wildtype and three nullizygous embryonic posterior neural tube tissues were collected at embryonic day 9.5 and the gene expression patterns were profiled on CodeLink Mouse Whole Genome Bioarrays.

overall_design: Wild type versus nullizygous Fkbp8 embryonic tissues were compared individually and as separate groups to determine classifiers and differences in expression due to the nullizygous mutation.

first: Bogdan

middle: J

last: Wlodarczyk


title: Gene expression-based analysis of neural tube closure for the posterior neuropore of Splotch embryos at E9.5

overall_design: Wild type versus nullizygous Splotch embryonic tissues were compared individually and as separate groups to determine classifiers and differences in expression due to the nullizygous mutation.


title: Gene expression signatures differ with extent of atherosclerosis in monkey iliac artery

status: Public on Jul 06 2011

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary:
Goal of the experiment:  To examine differential gene expression in the iliac arteries of cynomolgous monkeys in the presence of small, medium, or large atherosclerotic plaque.

Brief description of the experiment:
Objective:  To examine global gene expression patterns in the iliac arteries of monkeys containing small, medium, or large atherosclerotic plaque.
Design:  The left iliac artery of 12 ovariectomized cynomolgous monkeys on a high fat diet for 8 years was biopsied.  Gene expression was analyzed by DNA microarray and real time RT-PCR.
Results:  Significant up- or down-regulation of 986 genes was observed in monkey iliac arteries in the presence of atherosclerotic plaque.  Changes in gene expression with atherosclerosis ranged from 0.1-151.9-fold.  Differentially expressed genes included many cytokines, chemokines, components of signal transduction pathways, and transcriptional activators and repressors, among others.  Real time RT-PCR confirmed down-regulation of estrogen receptor 1 (ESR1), claudin 11, BH protocadherin 7 (PCDH7), and the up-regulation of apolipoprotein E (ApoE), growth differentiation factor 15 (GDF15), superoxide dismutase 2 (SOD2), SET domain, bifurcated 2 (SETDB2), phospholipase A2 group IIA (PLA2IIA), phospholipase A2 group VII (PLA2VII), and ring finger protein 149 (RNF149).
Conclusions:  The gene expression environment in arteries containing atherosclerotic plaque is profoundly different from that of arteries without atherosclerosis.  The data suggest that the changes in gene expression contribute to the disease process in diseased arteries.

overall_design:
Experimental factors:  presence of disease (atherosclerosis)

Experimental design:  Female cynomolgous monkeys had been ovariectomized for 4 years and on a high fat diet for 8 years. The left iliac artery was removed at surgical biopsy.  The presence and size of atherosclerotic plaque was quantified in the iliac arteries.  Samples were divided categories based on plaque size; categories were small (0-0.113mm2, n=4), medium (0.30-0.542 mm2, n=5), and large (0.61-1.003 mm2, n=3) atherosclerotic plaques.  Arterial tissue from the iliac arteries was used for DNA microarray analysis of gene expression.

Quality control steps:  The cRNA that was synthesized from each iliac artery was used for hybridization to a single CodeLink (Amersham/GE) whole human microarray.  Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary.  Bacterial control spikes were used as per manufacturer's instructions.

Samples used, extract preparation and labelling:
The origin of each biological sample:  The samples were iliac arterial tissue from cynomolgous monkeys.

Manipulations of biological samples and protocols used:  Cynomolgous monkeys were placed on a high fat diet 8 years before the experiment and ovariectomized 4 years prior to the experiment to induce a surgical menopause.  The left iliac artery was surgically removed from each animal in the study.  The presence and size of atherosclerotic plaque was quantified in the iliac arteries

Experimental factor:  size of atherosclerotic plaque

Technical protocols:  The iliac arteries were homogenized in TRI reagent, bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

	Labelled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  0.275 microgram of total iliac artery RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator.  The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNeasy columns (Qiagen).  The concentration of cRNA was determined by spectrophotometry.

Hybridization procedures and parameters:  10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.
	The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

Keywords:  nonhuman primate, disease state analysis

first: Susan

last: Appt

first: Connie

last: Mark-Kappeler

first: Abha

last: Chalpe

first: Thomas

last: Register

last: Clarkson


title: Molecular Characterization of Breast Cancer Subtypes Derived from Joint Analysis of High Throughput miRNA and mRNA Data

status: Public on Dec 01 2010

city: Oslo

first: Hilde

last: Johnsen

address: Montebello

country: Norway

institute: Norwegian Radium Hospital

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

summary: MicroRNAs (miRNAs) are a class of short, single-stranded widely expressed noncoding RNAs that regulate the stability or translational efficiency of target messenger RNAs. Date derived from expression profiling of 489 miRNAs in 101 human primary breast tumor samples, along with genome-wide matched mRNA profiling and extensive clinical information were investigated in this study. miRNA and mRNA expression were analyzed using correlations and enrichments analyses. The results show that particular cellular processes such as proliferation, cell adhesion, and immune response are significantly enriched among genes with strong positive or negative correlation to individual or groups of miRNAs. Functional analyses were performed to validate the influence of miRNAs on proliferation. A group of miRNAs was identified that is associated to breast cancer disease free survival. This study provides a comprehensive dataset that can be used as groundwork for further studies of the involvement of miRNA in breast cancer.

overall_design:
miRNA profiling from 101 breast cancer samples was performed. Experiments were mostly performed using duplicate hybridizations (99 samples) on different arrays and time points. Two samples were profiled only once. miRNA signal intensities for replicate probes were averaged across the platform, log2 transformed and normalized to the 75 percentile. miRNA expression status was scored as present or absent for each gene in each sample by default settings in FE v9.5. miRNAs in samples that were run in replicates were considered present if scored in one of the two arrays.
mRNA profiling from 114 breast cancer samples was performed. Replicates not included. Final processed mRNA data (quantile-normalized and averaged per Gene Symbol) is represented in the supplementary file at the foot of this record.

first: Espen

last: Enerly

first: Israel

last: Steinfeld

first: Kristine

last: Kleivi

first: Suvi

last: Leivonen

first: Hege

last: Russnes

first: Jo

middle: A

last: Rønneberg

first: Roy

last: Navon

first: Einar

last: Rødland

first: Miriam

middle: R

last: Aure

first: Rami

last: Mäkelä

first: Bjørn

last: Naume

first: Merja

last: Perälä

first: Olli

last: Kallioniemi

first: Vessela

last: Kristensen

first: Anne-Lise

last: Børresen-Dale

first: Zohar

last: Yakhini


title: Gene expression-based analysis of neural tube closure for the posterior neuropore

first: Robert

last: Cabrera

summary:
Background:
Spina bifida is one of the most common and life threatening human congenital defects. Despite considerable effort and investigations, the causes and mechanisms underlying this malformation remain poorly characterized. In order to better understand pathogenesis of this abnormality, we conducted a microarray study to compare gene expression profiles between two mouse models, CLX-Splotch and Fkbp8Gt(neo),  that both have spina bifida.
Results:
To compare the gene expression profiles in these two mouse models we performed microarray analysis using Mouse Whole Genome CodeLink Bioarray. We compared the level of gene expression between wildtype and homozygous mutant embryos in Fkbp8Gt(neo) and CXL-Splotch separately. A total of 54 genes were determined to be differentially expressed (25 down, 29 up) in the posterior neural tube of Fkbp8Gt(neo) mice embryos; while 73 genes were differentially expressed (56 down, 17 up) in the CXL-Splotch mouse. The only two genes that showed decreased expression in both mutants were v-ski sarcoma viral oncogene homolog (Ski) and Zic1, a transcription factor member of the zinc finger family. Interestingly, when Gene Ontology (GO) analysis was performed on all of the differentially expressed genes, there was a striking enrichment of genes associated with mesoderm development and central nervous system development in CLX-Splotch, whereas in Fkbp8Gt(neo) genes involved in dorsal/ventral pattern formation, cell fate specification, and positive regulation of cell differentiation were distinguished.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Time course of gene expression profiling in the liver of experimental mice infected with Echinococcus multilocularis

status: Public on Sep 28 2010

city: Urumqi

first: guo

middle: dong

last: lv

state: Xinjiang

address: liyushan

department: clinical cases reserch center

institute: Xinjiang medical hospital

summary:
For Samples GSM601017-28: The aim of this study was to use expression profiling to define transcriptional patterns and regulatory pathways that characterize the host liver response to E. multilocularis infection in the experimental model of secondary infection, to compare gene expression in this model to those described in the model of "primary infection", and to follow the changes in gene expression and in the expression of a cell proliferation marker over time during the complete chronic phase of E.multilocularis infection, following early and middle stages.
For Samples GSM601029-40: The aim of this study was to use expression profiling to define transcriptional patterns and regulatory pathways that characterize the host liver response to E. multilocularis infection in the experimental model of secondary infection, to compare gene expression in this model to those described in the model of "primary infection", and to follow the changes in gene expression and in the expression of a cell proliferation marker over time during the complete chronic phase of E.multilocularis infection, following its middle and late stages.

overall_design:
For Samples GSM601017-28: The anterior liver tissue sample of control mice group and alveolar echinococcosis mice group were obtained at each time point(1 month and 3 month). Biological replicates is 3. Then, total RNA from anterior liver of both groups were used as test sample, which labelled cy5 fluorescein, and the pool RNA of healthy BALB/c mice anterior liver was used as reference sample, which labelled cy3 fluorescein, and then hybridized to 32K Mouse Genome Array Genechips, representing about 25000 characterized murine genes.
For Samples GSM601029-40: The anterior liver tissue sample of control mice group and alveolar echinococcosis mice group were obtained at each time point(2 month and 6 month). Biological replicates is 3. Then, total RNA from anterior liver of both groups were used as test sample, which labelled cy5 fluorescein, and the pool RNA of healthy BALB/c mice anterior liver was used as reference sample, which labelled cy3 fluorescein, and then hybridized to 36K Mouse Genome Array Genechips, representing about 25000 characterized murine genes.

first: Renyong

last: Lin

first: Guodong

last: Lv


title: Expression data of germinating Arabidopsis seeds

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

summary:
In depth temporal profiling of transcript changes at 10 time points during germination in Arabidopsis seed was carried out. The time course utilised, encompassed seed maturation, stratification, germination and post-germination and provided a global investigation into the tightly regulated, phasic changes that define seed germination.
A previously unidentified transient expression pattern was identified for a group of genes, whereby a significant rise in abundance was observed at the end of stratification and significantly lower expression observed up to 6 hours later.

overall_design: Total RNA extraction was carried out on 80 mg of Arabidopsis seeds at 10 time points during germination in triplicate. The time points selected were: freshly harvested seed (H), seeds following 15 days of ripening (0 h), seeds after; 1 h of stratification (1 h S), 12 h of stratification (12 h S), 48 h of stratification (48 h S), followed by seed collected 1 hour into the light (1 h SL), 6 hours into the light (6 h SL), 12 hours into the light (12 h SL), 24 hours into the light (24 h SL) and 48 hours into the light (48 h SL).

first: Reena

last: Narsai

first: Chris

last: Carrie

first: Lin

last: Xiu

first: Jim

last: Whelan


title: Spatio-temporal transcriptome of the human brain

status: Public on Oct 27 2011

city: New Haven

first: Feng

last: Cheng

state: CT

address: 333 Cedar Street SHM C338

department: Neurobiology

institute: Yale University

summary: The development of the human brain is a complex and precisely regulated process that unfolds over a protracted period of time. Human-specific features of this process, especially the ways in which highly complex neural circuits of the cerebral cortex form, are likely to be important factors in the evolution of human specializations. However, in addition to giving us remarkable cognitive and motor abilities, the formation of intricate neural circuits may have also increased our susceptibility to psychiatric and neurodegenerative disorders. Furthermore, substantial evidence suggests that the symptoms and progression of many brain disorders are dramatically influenced by genetic and developmental processes that define regional cell phenotypes and connectivity. Sex differences also play an important role in brain development and function and are a risk factor for several brain disorders, such as autism spectrum disorders (ASD) and depression. Thus understanding the spatiotemporal dynamics and functional organization of the brain transcriptome is essential to teasing out the keys to human neurodevelopment, sexual dimorphism, and evolution as well as our increased susceptibility to certain brain disorders.  Most transcriptome studies of the developing brain have been restricted to rodents, and those performed in humans and nonhuman primates have included relatively small sample sizes and predominantly focused on few regions or developmental time points. Because many prominent features of human brain development significantly diverge from those of well-characterized model organisms, the translation of knowledge across species is difficult, and it is likely that many underlying genetic processes have gone undetected. In this study, we have taken a genome-wide approach to analyze the human transcriptome at single-exon resolution with ~1.4 million exon-level probe sets in 16 brain regions from donors representing both sexes and multiple ethnicities, across pre and postnatal development, including adolescence, and adulthood. We also generated genome-wide genotype data for 2.5 million single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) for each specimen. Our analyses of the data revealed several features of the human brain transcriptome: spatiotemporal expression dynamics of individual and functionally related groups of genes, differential exon usage, sex-specific expression patterns and exon usage, and organization of the transcriptome into functional modules. We also profiled developmental trajectories of genes important for neurobiological themes and genes associated with ASD and schizophrenia. Finally, we present associations between specific SNPs and gene expression levels in different brain regions across development. The dataset presented here provides research opportunities and a wealth of information not previously available to the scientific community.

overall_design:
Here we report the generation and analysis of genome-wide exon-level transcriptome data from 16 brain regions comprising the cerebellar cortex, mediodorsal nucleus of the thalamus, striatum, amygdala, hippocampus, and 11 areas of the neocortex. The dataset was generated from 1,340 samples collected from both hemispheres of 57 postmortem human brains, spanning from embryonic development to late adulthood and representing males and females of multiple ethnicities. We also performed genome-wide genotyping of 2.5 million single nucleotide polymorphisms (SNPs) and assessed copy number variations for all donors. We found that approximately 86% of protein-coding genes are expressed above background, and over 90% of these are differentially regulated at the whole transcript or exon level across regions and/or time. The majority of these spatiotemporal differences occur before birth, followed by a progressive increase in the similarity among regional transcriptome during the postnatal lifespan. Distinctive transcriptional patterns were also identified among neocortical areas, including an alternative isoform of ANKRD32 that is transiently upregulated in the late midfetal frontal cortex of human but not mouse. Developmentally and regionally regulated differences in gene expression and exon usage were also identified between males and females, including IGF2, an imprinted gene implicated in brain growth and cognitive function, and NLGN4X, a candidate gene for autism spectrum disorders. We found that the developing transcriptome is organized into functionally distinct large-scale networks of co-regulated transcripts. We also observed marked differences in expression trajectories of genes associated with specific neurodevelopmental processes, neural cell types, neurotransmitter systems, autism spectrum disorders, and schizophrenia. Association analysis of the SNP genotypes and transcriptome revealed potential polymorphic regulators of gene expression in different regions across development. This study provides a comprehensive, publicly available dataset on the spatiotemporal human brain transcriptome and new insights into the transcriptional foundations of brain development and evolution.

This submission represents the transcriptome component of the study.
Submitter did not submit SNP and CNV data due to privacy issue of patients.

first: Hyojung

last: Kang

first: Yuka

middle: I

last: Kawasawa

first: Ying

last: Zhu

first: Xuming

last: Xu

first: Mingfeng

last: Li

first: André

middle: M

last: Sousa

first: Mihovil

last: Pletikos

first: Kyle

last: Meyer

first: Goran

last: Sedmak

first: Tobias

last: Guennel

first: Yurae

last: Shin

first: Matthew

last: Johnson

first: Zeljka

last: Krsnik

first: Simone

last: Mayer

first: Sofia

last: Fertuzinhos

first: Sheila

last: Umlauf

first: Alexander

last: Vortmeyer

first: Daniel

last: Weinberger

first: Shrikant

last: Mane

first: Thomas

last: Hyde

first: Anita

last: Huttner

first: Mark

last: Reimers

first: Joel

last: Kleinman

first: Nenad

last: Sestan


title: Gene profiling: U87 IRE1 dominant negative cells vs. U87ctrl cells in culture

status: Public on Aug 08 2010

city: Talence

first: Michel

last: Moenner

address: Avenue des Facultés

department: Université Bordeaux 1

country: France

institute: Inserm U920

summary: Transcriptome analysis was performed from human U87 glioblastoma cell clones: U87 IRE1.NCK DN (U87dn, IRE1 dominant negative) and U87 control  (U87ctrl, empty plasmid). Cells were  grown in DMEM supplemented with 10% FBS and glutamine for 16 hours in culture prior mRNA isolation and analyses

overall_design: U87dn cells expressing a dominant negative transgene of IRE1alpha were compared to U87ctrl cells transfected with the corresponding empty plamid to identify genes associated to tumor invasion and angiogenesis.

first: Gregor

last: Auf

first: Arnaud

last: Jabouille

first: Marion

last: Bouchecareilh

first: Eric

last: Chevet

first: Andreas

last: Bikfalvi


title: Influence of elevated atmospheric carbon dioxide on transcriptional responses of Bradyrhizobium japonicum in the soybean rhizosphere

status: Public on Jul 29 2010

city: Saint Paul

first: Masayuki

last: Sugawara

state: MN

address: 250 Borloug Hall, 1991 Upper Buford Circle

department: Soil, Water, and Climate

institute: University of Minnesota

summary:
Elevated atmospheric CO2 can influence the structure and function of rhizosphere microorganisms by altering root growth and the quality and quantity of compounds released into the rhizosphere via root exudation. In these studies we investigated the transcriptional responses of Bradyrhizobium japonicum cells growing in the rhizosphere of soybean plants exposed to elevated atmospheric CO2. The results of microarray analyses indicated that atmospheric elevated CO2 concentration indirectly influences on expression of large number of Bradyrhizobium genes through soybean roots. In addition, genes involved in C1 metabolism, denitrification and FixK2-associated genes, including those involved in nitrogen fixation, microanaerobic respiration, respiratory nitrite reductase, and heme biosynthesis, were significantly up-regulated under conditions of elevated CO2 in the rhizosphere, relative to plants and bacteria grown under ambient CO2 growth conditions.
The expression profile of genes involved in lipochitinoligosaccharide Nod factor biosynthesis and negative transcriptional regulators of nodulation genes, nolA and nodD2, were also influenced by plant growth under conditions of elevated CO2. Taken together, results of these studies indicate that growth of soybeans under conditions of elevated atmospheric CO2 influences gene expressions in B. japonicum in the soybean rhizosphere, resulting in changes to carbon/nitrogen metabolism, respiration, and nodulation efficiency.

overall_design: Bradyrhizobium japonicum strains were grown in the soybean rhizosphere under two different CO2 concentrations. Transcriptional profiling of B. japonicum was compared between cells grown under elevated CO2 and ambient conditions. Four biological replicates of each treatment were prepared, and four microarray slides were used for each strain.

first: Michael

last: Sadowsky

first: Johan

last: Six


title: Dihydrotestosterone induced changes in gene expression in immortalized human meibomian gland epithelial cells

first: David

last: Sullivan

summary:
Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in immortalized human meibomian gland epithelial cells.

Analysis of regulation of immortalized human meibomian gland epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like meibomian gland cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation of numerous genes in response to dihydrotestosterone incubation of immortalized human meibomian gland epithelial cells.

overall_design: Total RNA was obtained from immortalized human meibomian gland epithelial cells treated for 72 hours with 10 nM dihydrotestosterone (n=3) or vehicle (n=3).  The RNA was then used with Illumina HumanHT-12 v3 Expression BeadChips to determine the effect of DHT on gene expression in an immortalized human meibomian epithelial cell line developed in our laboratory.

first: Payal

last: Khandelwal


title: PPARg and IL-4-induced gene expression data from wild-type and STAT6 knockout mouse bone marrow-derived macrophages

status: Public on Nov 18 2010

first: Attila

last: Szanto

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

summary: C57Bl/6 wild-type and STAT6 KO mice were used to study PPARg and IL-4 signaling. Bone marrow of 3 mice per group was isolated and differentiated to macrophages with M-CSF (20 ng/ml). 20 ng/ml IL-4 was used to induce alternative macrophage activation and 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF, 2. M-CSF+RSG, 3. IL-4 and 4. IL-4+RSG. All compounds were added throughout the whole differentiation process, and frech media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 10 days, RNA was isolated and gene expression profiles were analyzed using Mouse Genome 430 2.0 microarrays from Affymetrix.

overall_design: 3 C57Bl/6 wild-type and 3 STAT6 KO mice were used to isolate bone marrow and from each macrophages were differentiated with or without IL-4 and simultaneously treated with vehicle or RSG. Altogether we analyzed 24 samples with 3 biological replicates as below.

first: Laszlo

last: Nagy


title: Discrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during Helper T Cell Differentiation  (ChIP-Seq)

status: Public on Jun 18 2010

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Signal transducer and activator of transcription 4 (STAT4) and STAT6 are key factors in the specification of helper T cells; however, their direct roles in driving differentiation are not well understood.  Using chromatin immunoprecipitation and massive parallel sequencing, we quantitated the full complement of STAT-bound genes, concurrently assessing global STAT-dependent epigenetic modifications and gene transcription using cells from cognate STAT-deficient mice. STAT4 and STAT6 each bound over 4000 genes with distinct binding motifs.  Both played critical roles in maintaining chromatin configuration and transcription of a core subset of genes through the combination of different epigenetic patterns. Globally, STAT4 had a more dominant role in promoting active epigenetic marks, whereas STAT6 had a more prominent role in antagonizing repressive marks. Clusters of genes negatively regulated by STATs were also identified, highlighting previously unappreciated repressive roles. Therefore, STAT4 and STAT6 play wide regulatory roles in T helper specification.

overall_design: The roles of STAT proteins to shape T helper cell phenotype was investigated by comparing DNA binding profiles of STAT4 and STAT6 in Th1 and Th2 conditions. The functional outcome of STAT bindings was further evaluated by profiling histone epigenetic marks and gene expression changes between WT and STAT-deficient T cells in Th1 and Th2 conditions.

first: Lai

last: Wei

first: Hong-Wei

last: Sun

first: Wendy

middle: T

last: Watford

first: Hiroaki

last: Takatori

first: Haydee

last: Ramos

first: Hayato

last: Takahashi

first: Jonathan

last: Liang

first: Gustavo

last: Gutierrez-Cruz

first: Chongzhi

last: Zang

first: Weiqun

last: Peng

first: John

last: O’Shea

first: Yuka

last: Kanno


title: Analysis of Promoter Methylation in Breast Cancer

status: Public on Mar 07 2011

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

type:
Methylation profiling by array
Expression profiling by array

summary:
Promoter methylation was assayed in a number of breast cancer and control normal samples along with the effects of 5'-aza-2'-deoxycytidine on breast cancer cell line transcriptomes.

Aberrant promoter hypermethylation is frequently observed in cancer.
The potential for this to contribute to tumour development depends on whether the genes affected are repressed because of their methylation.
Many aberrantly methylated genes play important roles in development and are bivalently marked in ES cells suggesting that their aberrant methylation may reflect developmental processes. We investigated this possibility by analysing promoter methylation in 19 breast cancer cell lines, 10 normal tissues and 47 primary breast tumours. In order to determine the role of DNA methylation in silencing genes in breast cancer, we also examined the effects of the demethylating agent 5-aza-2?-deoxycytidine on gene expression in 3 breast cancer cell lines and HCT116 cells.  Gene expression changes were also assayed in the DNA methyltransferase deficient HCT116 DKO cell line. Our findings implicate aberrant DNA methylation as a marker of cell lineage rather than tumour progression and suggest that, in most cases, it does not cause the repression with which it is associated.

overall_design: A number of human breast cancer cell lines, breast tumours and normal tissues were analysed on Illumina Infinium Methylation27 Beadchips to assay promoter methylation.  Selected cell lines were analysed on expression arrays before and after treatment with 5-aza-2'-deoxycytidine.


title: Gene expression profiles of caseous human pulmonary TB granulomas derived from TB patients

status: Public on Jun 02 2010

city: Ithaca

first: Mi-Jeong

last: Kim

state: NY

address: C5 104 VMC Cornell University

department: Microbiology and Immunology

institute: Cornell University

summary: Most individuals infected with Mycobacterium tuberculosis can control the infection by forming and maintaining TB granulomas at the local infection foci.  However, when the chronic infection (also known as latency) becomes active, the caseous center of TB granuloma enlarges, and it liquefies and cavitates, ultimately releasing bacilli into airway.  Deciphering how genes are regulated within TB granulomas will help to understand the granuloma biology.  Therefore, we performed genome-wide microarray on caseous human pulmonary TB granulomas and compared with normal lung tissues.

overall_design:
Laser capture microdissection (LCM) was used to dissect out caseous granulomas from TB patients' lung tissues, excluding uninvolved areas.  Total RNA were isolated from LCM-derived materials and used for microarray.  As a control, parenchyma from normal lung tissues was prepared in the same manner as caseous granulomas.

Sample GSM501252, Caseum 2-C, is missing a CEL file.

first: Helen

last: Wainwright

first: Michael

last: Locketz

first: Linda-Gail

last: Bekker

first: Gabriele

last: Walther

first: Corneli

last: Dittrich

first: Annalie

last: Visser

first: Wei

last: Wang

first: Hsu

last: Fong-Fu

first: Ursula

last: Wiehart

first: Liana

last: Tsenova

first: Gilla

last: Kaplan

first: David

last: Russell


status: Public on Apr 01 2010

city: Stevenage

first: Adam

last: Taylor

address: Medicine Research Center

institute: GalxoSmithKline

summary:
Expression Profiling of a Genetic Animal Model of Depression Reveals Novel Molecular Pathways Underlying Depressive-like Behaviours

In this study we have used genome-wide microarray expression profiling of the hippocampus and prefrontal/frontal cortex of Flinders Depression Sensitive (FSL) and control Flinders Depression Resistant (FRL) lines to understand molecular basis for the differences between the two lines.

We profiled two independent cohorts of Flinders animals derived from the same colony six months apart, each cohort statistically powered to allow independent as well as combined analysis. Using this approach, we were able to validate using real-time-PCR a core set of gene expression differences that showed statistical significance in each of the temporally distinct cohorts, representing consistently maintained features of the model.

overall_design: Cohort one was established with 12 FRL and 9 FSL animals, while the second cohort (6 months later) was made up of 10 FRL and 8 FSL animals.

first: Ekaterini

last: Blaveri

first: Fiona

last: Kelly

first: Alessandra

last: Mallei

first: Kriss

last: Harris

first: Juliet

last: Reid

first: Maria

last: Razzoli

first: Lucia

last: Carboni

first: Chiara

last: Piubelli

first: Laura

last: Musazzi

first: Giorgio

last: Racagni

first: Aleksander

last: Mathe

first: Maurizio

last: Popoli

first: Enrico

last: Domenici

first: Stewart

last: Bates


title: Roles of STAT3 and STAT5 in regulation of gene expression under Th17 differentiation

status: Public on Feb 09 2011

first: Golnaz

last: Vahedi

summary: Interleukin 2 (IL-2), a cytokine linked to human autoimmune diseases, limits IL-17 production. We show that deletion of Stat3 in T cells abrogates IL-17 production and attenuates autoimmunity associated with IL-2 deficiency. While STAT3 induces IL-17 and RORγt and inhibits Foxp3, IL-2 inhibited IL-17 independently of Foxp3 and RORγt. We found that STAT3 and STAT5 bound to multiple common sites across the Il17 genetic locus. The induction of STAT5 binding by IL-2 was associated with a reduction in STAT3 binding at these sites and the inhibition of associated active epigenetic marks. Titrating the relative activation of STAT3 and STAT5 modulated TH17 cell specification. Thus, the balance rather than the absolute magnitude of these signals determines the propensity of cells to make a key inflammatory cytokine.

overall_design: The roles of STAT3 and STAT5 in regulation of gene expression under Th17 differentiation was investigated.  Affymetrix Mouse Genome 430 2.0 Arrays were used to evaluate global gene expression.

first: Xiang-Ping

last: Yang

first: Kamran

last: Ghoreschi

first: Scott

last: Steward-Tharp

first: Jaime

last: Rodriguez-Canales

first: Jinfang

last: Zhu

first: John

last: Grainger

first: Kiyoshi

last: Hirahara

first: Hong-Wei

last: Sun

first: Lai

last: Wei

first: Yuka

last: Kanno

last: O’Shea

first: Arian

last: Laurence


title: Analysis of the role of CggR in Lactobacillus plantarum NC8 and WCFS1 by transcriptome analysis

status: Public on Jan 01 2010

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: The level of the Central glycolytic gene regulator (CggR) was engineered in Lactobacillus plantarum NC8 and WCFS1 by over-expression and in-frame mutation of the cggR gene in order to evaluate its regulatory role on the glycolytic gap operon and the glyco

sample_organism:
Lactiplantibacillus plantarum
Lactiplantibacillus plantarum WCFS1

overall_design: The hybridization scheme of the different strains (wild-type, cggRKO mutant, cggR+) in relation to carbon source (glucose or ribose) has a loop design.

first: Ida

last: Rud

first: Kristine

last: Naterstad

first: Roger

middle: S

last: Bongers

first: Douwe

last: Molenaar

last: Kleerebezem

first: Lars

last: Axelsson


title: Gene expression in the human prefrontal cortex during postnatal development

status: Public on Nov 11 2009

city: Cambridge

first: Laura

middle: Wiseman

last: Harris

address: Tennis Court Road

department: Insitute of Chemical Engineering and Biotechnology

institute: University of Cambridge

summary:
Fresh frozen post mortem prefrontal cortex tissue (Brodman area 46) was obtained from 44 individuals varying in age from 0 to 49 years. RNA was extracted from these samples and hybridized to HG133plus2.0 GeneChips. The data was used to examine patterns of gene expression over the course of human postnatal developmental and ageing.

PMI - postmortem interval, DLPFC - dorsolateral prefrontal cortex

overall_design: The dataset consists of 44 individuals varying in age from 0 to 49 years

middle: W

first: Helen

last: Lockstone

first: Phillipp

last: Khaitovich

first: Cynthia

last: Shannon-Weickert

first: Maree

last: Webster

first: Sabine

last: Bahn


title: Murine model of gastrointestinal stromal tumors harboring a germline Kit K641E oncogenic mutant

status: Public on Sep 25 2009

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: Gastrointestinal stromal tumors (GIST) are thought to derive from the interstitial cells of Cajal (ICC) or an ICC precursor. Oncogenic mutations of the receptor tyrosine kinase KIT are present in most GIST. KIT K642E was originally identified in sporadic GIST and later found in the germ line of a familial GIST. A mouse model of harboring a germline Kit K641E mutant was created to model familial GIST. The expression profile was investigated in the gastric antrum in the knock-in Kit K641E murine GIST model by microarray.

overall_design: Microarray analysis was performed on antral tissue from three pairs of KitK641E:Neo/K641E:Neo and KitWT/WT  P14 littermates. Antrum labeled RNAs were hybridized to MEEBO arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US).

first: Petra

last: Gromova

first: Sebastian

last: Ralea

first: Anne

last: Lefort

first: Brian

middle: P

last: Rubin

first: Christophe

last: Erneux

first: Jean-Marie

last: Vanderwinden