title: Identification of immediate early transcriptional targets of ephrin-B1 forward signaling

status: Public on Sep 21 2010

city: New York

first: Jeffrey

middle: Ohmann

last: Bush

state: NY

address: One Gustave Levy Place, Box 1020

department: Developmental and Regenerative Biology

institute: Mount Sinai School of Medicine

summary:
The goal of this study was to identify immediate early transcriptional targets of ephrin-B1 forward signaling that are relevant to palatogenesis.
The Ephs compose a family of receptor tyrosine kinase signaling molecules that can be activated by their cognate ligands, the ephrins.  Despite the importance of Eph/ephrin signaling in a wide variety of developmental and cell biological processes, a potential downstream transcriptional response has not been explored.  To understand the role of ephrin-B1 signaling in palatogenesis, we examined transcriptional response to ephrin-B1 in a primary mouse embryonic palatal shelf cell culture system.  We find an immediate early signature of gene expression that reflects the activation of Erk/MAPK signaling by ephrin-B1 signaling in the palatal shelves.

overall_design: Induction of primary palate cells with 2 ug/ml of pre-clustered ephrin-B1 for one hour. Uninduced primary palate cells are the control. Four replicates each.

middle: O

first: Philippe

last: Soriano


title: High fat diet effects on mammary epithelium of OP and OR rats

status: Public on Sep 25 2010

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

country: USA

institute: University of Cincinnati

summary:
Background: Post-menopausal obesity is an established risk factor for breast cancer. Consumption of diets high in fat is known to be highly correlated with obesity.  In this, we sought to evaluate the interaction(s) between high fat diet, weight gain and mammary carcinogenesis using an obese-resistant and obese-prone rat model with direct correlates to human disease.
Methods: Female obese-prone (OP) and obese-resistant (OR) weanling rats were placed on either a low fat (10% kcal) or a high fat (39% kcal) n-6 polyunsaturated (PUFA) safflower diet for 30 days. At post natal day (PND) 50,  global gene expression profiling was performed on microdissected mammary epithlelium from one cohort of rats and another cohort of rats were given a single oral gavage of either 7,12-dimethylbenz[a]anthracene (DMBA at 14 mg/kg) or vehicle. Rats were then maintained on the diets and body weights, food consumption and development of mammary lesions were monitored weekly.
Results: The DMBA-treated OR rats on the 39% safflower diet had significantly greater incidence of ductal carcinoma-in-situ (DCIS) lesions and significantly greater DCIS multiplicity than DMBA-treated OR rats on the 10% safflower diet. These differences were not seen in the OP strain. Gene expression analysis of mammary ductal epithelium from OR rats on the high fat diet showed significant upregulation of proliferation-related genes compared to those consuming the low fat safflower diet.  Again, these differences were not seen in the OP strain.
Conclusion: Our findings indicate that consumption of high fat safflower diet enhances mammary carcinogenesis in an OR rat strain through increased proliferation of mammary epithelium at the time of exposure, but not in the OP rat strain. Thus, the diet-induced increase in sensitivity was strain-specific and independent of weight gain or obesity level.


title: Comparative analysis of ependymal cells from the lateral ventricular wall and the spinal cord of adult mice

status: Public on Oct 01 2010

city: Lund

first: Ulrike

middle: A.

last: Nuber

address: Klinikgatan 26

country: Sweden

institute: Lund University

summary:
In contrast to ependymal cells in the lateral ventricle wall (LVW), spinal cord (SC) ependymal cells possess certain neural stem cell characteristics. Isolated CD133+/CD24+/CD45-/CD34- ependymal cells from the SC displayed in vitro self renewal and differentiation capacity, whereas those from the LVW did not.
The molecular basis of this difference is unknown. In this study, antibodies against multiple surface markers were applied to isolate SC and LVW ependymal cells which allowed a direct comparison of their in vitro behavior and gene expression profile.

overall_design: cRNA samples of three independent biological replicates of CD133+/CD24+/CD45-/CD34- LVW ependymal cells, CD133+/CD24+/CD45-/CD34- SC ependymal cells, CD133+/CD24-/CD45-/CD34- radial glial cells, and SC ependymal cell-derived NSPs were hybridized onto Illumina MouseWG-6 v1.1 gene expression arrays

first: Cosima

middle: V

last: Pfenninger

middle: A


title: Investigation of a patient with a partial 16q trisomy

status: Public on Sep 10 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary: A female patient with a partial trisomy 16q was described previously. Her clinical characteristics included obesity, severe anisomastia, moderate to severe mental retardation, dysmorphic facies, and contractions of the small joints. In this paper, we describe a more detailed analysis of the genetic anomaly in this patient. We were particularly interested in the involvement of the fat mass and obesity associated gene (FTO) in her duplication. Single nucleotide polymorphisms in FTO have recently been associated with obesity. We have precisely mapped the breakpoints of the duplication using high resolution oligonucleotide array comparative genome hybridization (CGH). We found that the duplication spans 11.45 Mb on 16q11.2 to 16q13 and it includes FTO. The increased copy number of FTO was confirmed with a qPCR on genomic DNA of the patient and healthy controls. We investigated the influence of the increased FTO copy number on FTO gene expression in immortalized lymphocytes from the using qPCR. We found no evidence of increased FTO expression in the patient. This observation could be explained by maternal imprinting. We found evidence supporting this hypothesis in a database of imprinted genes. In addition, our results generated new candidate genes for the mental retardation, dysmorphic facies, small joints contractions, small teeth, and anisomastia of the patient.

overall_design:
We used a high density oligonucleotide microarray to delineate the borders of the duplication with high resolution. This analysis enabled us to confirm the inclusion of FTO in the duplication. This was confirmed with quantitative real-time PCR (qPCR) at the level of genomic DNA. To further investigate the role of FTO in the obese phenotype of the patient, we used qPCR to study the expression of FTO in immortalized lymphocytes of the patient. Remarkably, the increased FTO copy number in the patient’s genomic DNA did not give rise to an increased copy number of FTO mRNA molecules. We think this may be the result of maternal imprinting of the gene.

The CGH results also allowed us to generate new hypotheses regarding the etiology of the other clinical problems of the patient. We propose candidate genes for her mental retardation, dysmorphic facies, joint contractures, small teeth, and anisomastia.

first: Linda

last: van den Berg

first: Henriette

last: Delemarre-van de Waal

first: Joan

middle: C

last: Han

first: Bauke

last: Ylstra

first: Paul

last: Eijk

first: Maria

last: Nesterova

first: Peter

last: Heutink

first: Constantine

last: Stratakis


title: Role of miR-210 in late stages of lung cancer: mitochondrial alterations associated with a modulation of HIF1 activity

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

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

summary:
Recent studies have identified miR-210 among a set of hypoxia-regulated miRNAs, and shown the central regulatory role played by HIF to control transcription of this miRNA. Contradictory data exist concerning the regulation and roles of miR-210 during cancer progression. miR-210 appears at the same time over-expressed in some solid tumors (breast, pancreas, head and neck carcinomas, gliomas) while often deleted in ovarian carcinoma. It has been shown that depending on the tissue type or cellular model, miR-210 was indeed able to either promote entry into the cell cycle and to inhibit apoptosis or rather repress tumor initiation.
We show here deregulation of several miRNAs in human lung cancer biopsies, including an over-expression of miR-210 which appears specific of late-stages of the tumor (>stage 2). MiR-210 function was then analyzed in the lung adenocarcinoma cell line A549. We found that miR-210 induced a delayed inhibition of proliferation associated with an induction of cell death. We also observed that mir-210 induces a loss of mitochondrial membrane potential and the apparition of an aberrant mitochondrial phenotype. mRNA expression profiling of cells overexpressing mir-210 revealed a specific signature characterized by an enrichment in mir-210 predicted targets among the downregulated transcripts (57 out of 243, p<10-12). Functional annotation of this set of mir-210-regulated transcripts, which includes several subunits of Electron Transport Chain (ETC) complex I and complex II revealed enrichment for terms such as 'cell death' and 'mitochondrial dysfunction'. Two of these ETC subunits, predicted to be targets of mir-210 by several bioinformatics prediction tools, were experimentally confirmed after cloning of their respective 3'UTR in a luciferase reporter vector. Finally, we provide experimental evidence indicating that these mitochondrial alterations could modulate HIF via a positive regulatory loop.
Overall, our data strongly suggest that mir-210 could mediate two apparently opposite functions: i) apoptosis through targeting of specific mitochondrial components ii) a modulation of HIF through a positive regulatory loop. We propose that this dual behavior can explain the contradictory data regarding the impact of miR-210 during cancer progression.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Global analysis of the impact of environmental perturbation on cis-regulation of gene expression

city: Montreal

first: Elin

last: Grundberg

address: 740 Dr Penfield Avenue

country: Canada

institute: McGill University

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

overall_design: Refer to individual Series


title: Gene expression in endometrium and extra-embryonic membrane at the gravid and non-gravid horn in uterus

status: Public on Sep 07 2010

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

summary: Endometrial remodeling is required for implantation in all mammalian species. To identify the factors that promote cell proliferation at the implantation site were explored in bovine endometrium and extra-embryonic membrane during the peri-implantation period. Microarray analysis showed that the expression levels of various trophoblast specific genes were higher in the extra-embryonic membrane at gravid horn than in the extra-embryonic membrane at non-gravid horn namely, CSH1, PRPs, PAGs, AIF, Muc-1, etc. Furthermore, EGFR, INHBA and INHBB expression were higher in endometrium of gravid horn.

overall_design: Gene expression profiles were analyzed in the gravid and non-gravid extra-embryonic membrane and endometrium at around Day 30 of gestation

first: Kazuyoshi

last: Hashizume


title: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY)

status: Public on Sep 01 2010

city: Santa Clara

first: Jason

middle: Wray

last: Hubbard

state: CA

address: 3380 Central Expressway

institute: Affymetrix Inc

summary: To gain global insights into the role of the well-known repressive splicing regulator PTB we analyzed the consequences of PTB knockdown in HeLa cells using high-density oliogonucleotide splice-sensitive microarrays. The major class of identified PTB-regulated splicing event was PTB-repressed cassette exons, but there was also a substantial number of PTB-activated splicing events. PTB repressed and activated exons showed a distinct arrangement of motifs with pyrimidine-rich motif enrichment within and upstream of repressed exons, but downstream of activated exons. The N-terminal half of PTB was sufficient to activate splicing when recruited downstream of a PTB-activated exon. Moreover, insertion of an upstream pyrimidine tract was sufficient to convert a PTBactivated to a PTB-repressed exon. Our results demonstrate that PTB, an archetypal splicing repressor, has variable splicing activity that predictably depends upon its binding location with respect to target exons.

overall_design: Target was prepared from 3 biological replicates of PTB/nPTB knockdown and 3 control mock knockdowns from HeLa S3 cell line and hybridized to a custom Affymetrix array containing exon and exon-junction probes for more than 30,000 human genes

first: Miriam

last: Llorian

first: Schraga

last: Schwartz

first: Tyson

last: Clark

first: Dror

last: Hollander

first: Lit-Yeen

last: Tan

first: Rachel

last: Spellman

first: Adele

last: Gordon

first: Anthony

last: Schweitzer

first: Pierre

last: de la Grange

first: Gil

last: Ast

first: Christopher

middle: W

last: Smith


title: Myocardial contractile response to physiological stress improves with high saturated fat feeding in heart failure

city: Birmingham

first: Molly

middle: Bray

last: Bray

state: AL

address: 720 20th Street S

department: Genetics

institute: Univ of Alabama at Birmingham

summary: Impaired myocardial contractile function is a hallmark of heart failure (HF) which may present under resting conditions and/or during physiological stress.  Previous studies reported that high fat feeding in HF is associated with improved myocardial contractile function at baseline.  Our goal was to determine whether myocardial function is compromised in response to physiological stress and to evaluate the global gene expression profile of rats fed high dietary fat following infarction.   Male Wistar rats underwent ligation or sham surgery and were fed normal (10% kcal fat) (SHAM+NC, HF+NC) or high fat (60% kcal saturated fat) (SHAM+SAT, HF+SAT) for 8 weeks.  Myocardial contractile function was assessed using a Millar pressure-volume (PV) conductance catheter at baseline, during inferior vena caval occlusions and dobutamine (DOB) stress.  Steady state indices of systolic function, left ventricular (LV)+dP/dtmax, stroke work and maximal power were increased in HF+SAT vs HF+NC; HF+NC were reduced vs SHAM+NC.  Preload-recruitable measures of contractility [end systolic PV relationship, maximal elastance, preload recruitable SW and peak+dP/dtmax to end diastolic volume] were decreased in HF+NC but not HF+SAT.  β-adrenergic responsiveness (delta-LV+dP/dtmax and delta-cardiac output DOB 0-10 µg•kg-1•min-1) was reduced in HF, but high fat feeding did not further impact contractile reserve in HF.  Contractile reserve was reduced by high fat in SHAM+SAT.  Microarray gene expression analysis reveals the majority of significantly altered pathways identified to contain multiple gene targets correspond to cell signaling pathways and energy metabolism.  These findings suggest that high saturated fat improves myocardial function at rest and during physiological stress in infarcted hearts, but may negatively impact contractile reserve under non-pathological conditions.  Furthermore, high fat feeding-induced alterations in gene expression related to energy metabolism and specific signaling pathways reveal promising targets through which high saturated fat potentially mediates cardioprotection in heart failure/LV dysfunction.

overall_design:
Comparison of gene expression in heart failure or sham surgery hearts exposed to saturated or normal diets.
Male Wistar rats (300-350g) were maintained on a reverse light-dark cycle and all procedures were done 3-6 hours into the dark phase cycle to synchronize with the normal active state of the rodents.  Rats were randomly assigned to receive either a sham-operation (SH) or coronary ligation to induce cardiac dysfunction (HF).  Heart failure was induced by ligating the left main coronary artery.  Following surgery, rats were immediately fed either a normal rodent chow (NC) or a high saturated fat chow (SAT) with 60% caloric content derived from fat (25% palmitic, 33% stearic, 33% oleic acid, Research Diets).

first: Jessica

middle: M

last: Berthiaume

middle: S

first: Tracy

last: McElfresh

first: Xiaoqin

last: Chen

first: Salman

last: Azam

first: Martin

middle: E

last: Young

first: Brian

middle: D

last: Hoit

first: Margaret

middle: P

last: Chandler


title: Differential gene expression profile in skin of Hoxc13 gene-targeted mice

status: Public on Aug 25 2010

city: Bar Harbor

middle: S.

last: Potter

state: ME

address: 600 Main St.

institute: The Jackson Laboratory

summary: Hoxc13 has been shown to be essential for proper hair shaft differentiation as Hoxc13 gene-targeted (Hoxc13tm1Mrc) mice completely lack external hair. Because of the phenotypic parallels to the Foxn1nu (nude) mutant mice, we tested whether Hoxc13 and Foxn1 act in a common pathway of hair follicle (HF) differentiation. We show that the alopecia exhibited by both the Hoxc13tm1Mrc and Foxn1nu mice is due to strikingly similar defects in hair shaft differentiation and that both mutants suffer from a severe nail dystrophy. These similarities are consistent with the overlap of Hoxc13 and Foxn1 expression patterns in the HF and nail matrix. DNA microarray analysis of scapular skin from Hoxc13tm1Mrc mutant (mut) compared to wild type (wt) mice identified Foxn1 as significantly down-regulated along with numerous hair keratin genes. This Foxn1 down-regulation apparently reflects the loss of direct transcriptional control by HOXC13 as indicated by our results obtained through co-tranfection and chromatin immunoprecipitation (ChIP) assays.

overall_design: Total number of samples was 6. The experiment was perfomed in triplicate involving 3 indendent wild type skin samples (sample 1, 2, and 3) and 3 independent mutant skin samples (sample 4, 5, and 6).

first: Alexander

last: Awgulewitsch

first: John

last: Sundberg

first: Alan

last: Godwin


title: SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle

status: Public on Aug 26 2010

city: Ghent

first: Stijn

last: Dhondt

address: Technolgiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB

summary: SHORT-ROOT (SHR) and SCARECROW (SCR) are required for stem cell maintenance in the Arabidopsis thaliana root meristem, ensuring its indeterminate growth. Mutation of SHR and SCR genes results in disorganization of the quiescent center and loss of stem cell activity, resulting in the cessation of root growth. This manuscript reports on the role of SHR and SCR in the development of leaves, which, in contrast to the root, have a determinate growth pattern and lack a persistent stem-cell niche. Our results demonstrate that inhibition of leaf growth in shr and scr mutants is not a secondary effect of the compromised root development, but is caused by a direct effect on cell division in the leaves: a reduced cell division rate and early exit of proliferation phase. Consistent with the observed cell division phenotype, the expression of SHR and SCR genes in leaves is closely associated with cell division activity in most cell types. The increased cell cycle duration is due to a prolonged S-phase duration, which is mediated by up-regulation of cell cycle inhibitors known to restrain the activity of the transcription factor, E2Fa. Therefore, we conclude that, in contrast to their specific role in cortex/endodermis differentiation and stem cell maintenance in the root, SHR and SCR primarily function as general regulators of cell proliferation in leaves.

overall_design: Total RNAs were extracted using RNeasy plant mini kit (Qiagen) from vegetative part of seedlings at stage 1.04 grown in vitro. RNAs from three biological repeats of wild type (wt, control) and scr and shr mutants were submitted to ATH1 array hybridization.

first: Frederik

last: Coppens

first: Freya

last: De Winter

first: Kamal

last: Swarup

first: Roeland

last: Merks

first: Dirk

last: Inzé

first: Malcolm

middle: J

last: Bennett

first: Gerrit

middle: T

last: Beemster


title: Peripheral blood gene-expression in depressed subjects with bipolar disorder vs healthy controls.

status: Public on Aug 27 2010

city: New Haven

first: Robert

last: Beech

state: CT

address: 34 Park St

department: Psychiatry

institute: Yale University

summary: Analysis of gene-expression changes in depressed subjects with bipolar disorder compared to healthy controls. Results provide information on pathways that may be involved in the pathogenesis of bipolar depression.

overall_design: Total RNA isolated from PAXgene blood RNA tubes from 20 depressed subjects with bipolar disorder and 15 healthy controls.


title: An ESRP-regulated splicing program is abrogated during the Epithelial Mesenchymal Transition

status: Public on Aug 23 2010

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

summary:
Alternative splicing achieves coordinated changes in post-transcriptional gene expression programs through the activities of diverse RNA binding proteins.  Epithelial Splicing Regulatory Proteins 1 and 2 (ESRP1 and ESRP2) are cell type-specific regulators of transcripts that switch splicing during the Epithelial Mesenchymal Transition (EMT).  To define a comprehensive program of alternative splicing that is regulated during the EMT, we identified an extensive ESRP-regulated splicing network of hundreds of alternative splicing events within numerous genes with roles in cell-cell adhesion, polarity, and migration.  Loss of this global ESRP-regulated epithelial splicing program induces the phenotypic changes in cell morphology that are observed during the EMT.  Components of this splicing signature provide novel molecular markers that can be used to characterize the EMT.  Bioinformatics and experimental approaches revealed a high affinity ESRP binding motif and a predictive RNA map that governs their activity.  This work establishes the ESRPs as coordinators of a complex alternative splicing network that adds an important post-transcriptional layer to the changes in gene expression that underlie epithelial-mesenchymal transitions during development and disease.

Keywords: control / knockdown comparison and control / ectopic expression comparison

overall_design: siRNA knockdown of ESRP1 and ESRP2 in human prostate epithelial cells PNT2 and ectopic expression of mEsrp1 in human breast cancer cells MDA-MB-231 as described before (Warzecha et al., 2009, Molecular Cell 33:591 - 601).  The efficiency of ESRP knockdown and ectopic expression was monitored by western blot using a monoclonal antibody which recognizes both proteins (Clone 23A7) prepared by Rockland Immunochemicals, Inc. (Gilbertsville, PA) using our GST-Esrp1 recombinant protein.  We conducted HJAY exon and exon junction array profiling on RNAs from four siESRP1 + siESRP2 treated PNT2 samples vs. four siGFP treated PNT2 samples and four samples of MDA-MB-231 cells transduced with retrovirus expressing a cDNA for mEsrp1 vs. four samples of MDA-MB-231 cells transduced with retrovirus expressing a control empty vector.

first: Claude

last: Warzecha

first: Shihao

last: Shen

first: Russ

last: Carstens


title: The male sterility 8 mutation of maize disrupts the temporal progression of the transcriptome and results in the mis-regulation of metabolic functions

status: Public on Aug 20 2010

city: Stanford

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
Phenotypes of maize male sterile 8 plants are small anthers, meiotic failure, shorter epidermal cells, and non-secreting tapetal cells.  Excess callose accumulates around meiotic cells, which later abort. Thousands of transcriptome changes occur including ectopic activation of genes not expressed in fertile siblings, failure to express genes, and differential expression of genes shared with fertile siblings. Sixty-three differentially expressed proteins were identified after 2-D DIGE followed by LC/MS/MS, including those involved in metabolism and cell division. The majority were not identified by differential RNA expression.

Keywords: anther development, maize, male-sterile, ms8

overall_design: 4 replicates of ms8 mutant and 4 replicates of ms8 fertile siblings at 3 anther stages.  Spike-in controls were included.

first: DongXue

last: Wang

first: Virginia

last: Walbot


title: Gene Expression Profiles Characterize Inflammation Stages in the Acute Respiratory Distress Syndrome in Mice

city: Marseille

first: Isabelle

last: Lesur Kupin

address: 163 av. de Luminy - case 928

department: Bioinformatics

institute: INSERM U928

summary: Acute respiratory distress syndrome (ARDS) carries about a 50 percent mortality and is frequently associated with an infection (sepsis). Life-support treatment with assisted ventilation rescues many patients, although superimposed infection or multiple organ failure can result in death. The outcome of a patient developing sepsis highly depends on the degree of pre-existing inflammation prior to the infection. In this study, we describe each stage of the inflammation process using a transcriptomic approach. Female C57BL6/J mice received an intra-veinous oleic acid injection to induce an acute lung injury and lung expression patterns have been analyzed using a 9900 cDNA mouse microarray (MusV29K). Our gene-expression analysis revealed maked changes in the immune and inflammatory response metabolic pathways, notably lipid metabolism and transcription. The early pro-inflammatory stage (1H-1H30) is characterized by the release of immune response and activation of inflammatory mechanisms. Later (3H-4H), the immune cells migrate into inflamed tissues through interaction with vascular endothelial cells. Finally, at late stages of inflammation (18H-24H), metabolism is deeply disturbed. Highly expressed pro-inflammatory cytokines activate transcription of many genes as well as lipid metabolism. This global overview of critical events occuring during lung inflammation is essential to understand infectious pathologies such as sepsis where inflammation and infection are interwined. From now on, it becomes possible to isolate the impact of a pathogen at the transcriptomic level from the global gene expression modifications resulting from the infection associated with the inflammation. Also, our work allowed to identify genes involved in the response to inflammation. Among those, several may be candidate fro gene therapy.

overall_design: Wild-type female C57Bl/6J mice, 7 weeks old, were obtained from Charles River and housed in a specific pathogen-free animal facility. We studied 36 mice divided into 6 groups. Each group included one or two mice administered with physiological serum and 3 to 7 mice administered with OA. Each group can be distinguished given the incubation time: 1H, 1H30, 3H, 4H, 18H and 24H. All experimental procedures involving animals were approved by the veterinary office of the Ministry of Agriculture, France (authorization number: 13-27). 16 mRNA samples extracted from an individual organ were run on a single microarray. In addition, 22 samples were run on two microarrays, and were considered as technical replicates. This corresponds to a total of 60 microarrays. 9 microarrays were hybridized with mice administered with physiological serum and 51  were hybridized with mice administered with oleic acid.

first: Catherine

last: Nguyen


title: Gene expression study in choroid plexus

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: The choroid plexus (CP) constitutes one of the blood–brain barriers – the blood cerebrospinal fluid barrier. It is formed by a monolayer of epithelial cells located within the brain ventricles and in addition to be responsible for the formation of the cerebrospinal fluid (CSF) is ideally positioned to transmit signals into and out of the brain. Specifically, here, we evaluated the overall kinetic response of the mouse CP to peripheral administration of lipopolysaccharide (LPS) that is the Gram-negative bacteria cell wall. This study shows that as soon as 1h after the injection, the CP responds by altering the expression of several genes. This response reaches a maximum at 3h and returns to the basal profile for most of the transcripts at 72h. To do this analysis we compared the CP transcriptome of LPS injected animals with the CP transcriptome of saline injected animals and using this we also dissect the CP basal transcriptome. From this analysis we confirm that the genes most highly expressed were those implicated in energy metabolism (oxidative phosphorylation, glycolysis/gluconeogenesis) and in ribosomal function, which is in agreement with the secretory nature of the CP. Finally, we also describe genes not previously identified as being expressed in the basal CP.

overall_design: Gene expression study in choroid plexus. Time series after acute LPS treatment

first: Fernanda

last: Marques

first: João

last: Sousa

first: Fuying

last: Gao

first: Renato

last: Puga

first: Helena

last: Brentani

first: Daniel

last: Geschwind

first: Nuno

first: Margarida

last: Correia-Neves

first: Joana

last: Palha


title: Host pathogen interaction between Staphylococcus aureus ATCC25923 and murine RAW264.7 macrophage-like cells

status: Public on Aug 11 2010

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Macrophages infected with S. aureus were subjected to gene expression profiling to undertake a complete understanding of the interaction induced gene expression changes in both, S.aureus and the RAW macrophages.

sample_organism:
Staphylococcus aureus
Mus musculus

platform_organism:
Staphylococcus aureus
Mus musculus

overall_design: Agilent one-color experiment, Agilent-021933 Genotypic designed Custom Staphylococcus aureus and Mus musculus 8x15k

first: T

middle: K

last: Ananthalakshmi

first: C

last: Dipshikha


title: Study the role of miRNAs in metastasis progression of RCC cell lines

status: Public on Aug 19 2010

city: New York

first: Venkata

last: Thodima

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

summary: This study investigates for the miRNAs that drive or regulates Renal Cell Carcinoma (RCC) metastatic progression using two different RCC cell lines, the metastatic (LM2 and LM1) and non-metastatic (SN12C).

overall_design: The experiment is designed with three RCC cell lines one non-metastatic (SN12C) and two metastatic (LM1 and LM2). Each cell line has two biological replicates (exception SN12C has 3 replicates)

first: Miguel

last: Lopez-Lago


title: Transforming properties of 8p11-12 amplified genes in human breast cancer

status: Public on Aug 21 2010

city: Detroit

first: Zeng-Quan

last: Yang

state: MI

address: 4100 John R HWCRC 815

department: Oncology

institute: Karmanos Cancer Institute

summary: MCF10A cells was transduced with WHSC1L1 short isoform lentiviral expression vector.  Expression profiling of  MCF10A-WHSC1L1 cells, and breast cancer SUM-44 cells were performed

overall_design: To identify genes most likely to be regulated by over expression of WHSC1L1 and relevant to human breast cancer, we determined which genes are differentially expressed in MCF10A-WHSC1L1 cells relative to parental MCF10A cells, and then determined which of those genes are also differentially expressed in SUM-44 cells compared to MCF10A cells.


title: Hepatic gene expression profiling during Genistein and Quercetin treatments

city: Lucknow

first: Prabhat

last: Singh

state: Uttar Pradesh

address: MG Marg

department: Toxicology

institute: Central Drug Research Institute

summary: Differential gene expression in mice liver after Quercetin administration. Gene expression from control mice were compared with Quercetin treated mice at different dose level

overall_design: 2-color experiment. The normalization was done using channel split method as biological replicates were hybridized to the same microarray.

first: Srikanta

last: Rath


title: Germfree C57BL/6J mice are resistant to high fat diet-induced insulin resistance and have altered cholesterol metabolism

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: Germfree (GF) mice have been used as a model to study the contribution of the intestinal microbiota to metabolic energy balance of the host. Despite a wealth of knowledge accumulated since the 1940’s, the response of GF mice to a high fat diet is largely unknown. In the present study, we compared the metabolic consequences of a high fat (HF) diet on GF and conventional (Conv) C57BL/6J mice. As expected, Conv mice developed obesity and glucose intolerance with a HF diet. In contrast, GF mice remained lean and resisted the HF diet-induced insulin resistance. The anti-obesity phenotype of GF/HF mice was accompanied by reduced caloric intake, diminished food efficiency, and excessive fecal lipid excretion contributed to the reduced food efficiency. In addition, HF diet-induced hypercholesterolemia was ameliorated, which was partially due to an increase in fecal cholesterol excretion. However, hepatic cholesterols were increased in GF/HF mice. Elevated nuclear SREBP2 proteins and the up-regulation of cholesterol biosynthesis genes support the increased liver cholesterol biosynthesis in GF/HF mice. The resistance to HF diet-induced metabolic abnormalities in GF mice was also associated with a reduced immune response, indicated by low plasma pro-inflammatory and anti-inflammatory markers. These data suggest that the gut microbiota of Conv mice contributes to HF diet-induced obesity, insulin resistance, dyslipidemia and hepatic steatosis in mice. Thus, results of the present study describe the metabolic responses of GF mice to a HF diet and further our understandings of the relationship between the gut microbiota and the host.

overall_design: Germfree and conventional C57BL/6J mice were fed with a high fat diet for 11 weeks. Then, all mice were sacrified under 10-h food deprevation, and liver samples of germfree (n=14) and conventional (n=16) were examined.

first: Chieh

last: Chou

first: Robert

last: Mansourian


title: HUMAN ENDOMETRIAL SIDE POPULATION CELLS EXHIBIT GENOTYPIC, PHENOTYPIC AND FUNCTIONAL FEATURES OF SOMATIC STEM CELLS

status: Public on Aug 15 2010

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

summary: During reproductive life, the human endometrium undergoes around 480 cycles of growth, breakdown and regeneration should pregnancy not be achieved. This outstanding regenerative capacity is the basis for women’s cycling and its dysfunction may be involved in the etiology of pathological disorders. Therefore, the human endometrial tissue must rely on a remarkable endometrial somatic stem cells (SSC) population. Here we explore the hypothesis that human endometrial side population (SP) cells correspond to somatic stem cells. We isolated, identified and characterized the SP corresponding to the stromal and epithelial compartments using endometrial SP genes signature, immunophenotyping and characteristic telomerase pattern. We analyzed the clonogenic activity of SP cells under hypoxic conditions and the differentiation capacity in vitro to adipogenic and osteogenic lineages. Finally, we demonstrated the functional capability of endometrial SP to develop human endometrium after subcutaneous injection in NOD-SCID mice. Briefly, SP cells of human endometrium from epithelial and stromal compartments display genotypic, phenotypic and functional features of SSC.

overall_design:
Human tissue collection:
Human endometrial biopsies were taken using a Pipelle catheter under sterile conditions (from 18 to 48 years) throughout the menstrual cycle.

Epithelial and stromal separation:
Epithelial and stromal fractions were isolated using an established protocol with modifications. Briefly, samples were carefully dissected and minced into 1-2mm fragments, and enzymatically digested in DMEM containing 10 mg/ml collagenase type IA. Stromal cells (single cells or small aggregates) and epithelial glands were separated on a size basis using gravity sedimentation and membrane filtration.
Cell suspensions were treated with erythrocyte lysis solution and evaluation of cell viability was performed with Propidium Iodide (PI; 5 μg/ml).

Hoechst 33342 labeling:
Cells isolated from the endometrial epithelial and stromal fractions were resuspended in DMEM prewarmed at 37ºC and supplemented with 2% FBS and 10mM HEPES. The cell suspension was labeled in the same media with 5 μg/ml of Hoechst 33342 dye (Ho-33342), either alone or in combination with 100 μM verapamil (Vp), in a water bath at 37ºC for 90-120 minutes. Then, cells were centrifuged for 6 minutes at 4ºC, and were resuspended in cold HBSS supplemented with 2%FBS and 10mM HEPES. PI permits to exclude dead cells prior to the flow cytometric analysis and sorting.

Isolation of human endometrial SP cells:
Cells were analyzed and sorted by a MoFlo® jet-in-air high speed sorter. Excitation was performed with a water cooled Enterprise II ion laser which operated at the 351 nm and 488 nm wavelengths, and worked at 30 mW. Hoechst 33342 blue and red fluorescences were detected through 405/30 and 670/20 nm band-pass filters respectively, by measuring the signals on a linear scale. PI fluorescence was detected through a band-pass filter of 613/20 on a logarithmic scale. The gates for cell sorting were defined to collect live cells with a low Hoechst 33342 fluorescence (SP fraction), as well as live cells with a high Hoechst 33342 fluorescence (NSP fraction).

Microarrays experiments:
Endometrial tissue consisted in a total of 8 endometrial biopsies (epithelial (n=8) and stromal (n=8) endometrial cell suspensions, epithelial SP fraction (n=8) and stromal SP fractions (n=8) separately) which were pooled in pairs at the RNA levels. Four microarrays were analyzed per group.

first: Irene

last: Cervelló

first: Claudia

last: Gil-Sanchis

first: Aymara

last: Mas

first: Francisco

last: Delgado-Rosas

first: Amparo

last: Galán

first: Alicia

last: Martínez-Romero

first: Sebastian

last: Martinez

first: Ismael

last: Navarro

first: Jaime

last: Ferro

last: Horcajadas

last: Esteban

last: O'Connor

first: Antonio

last: Pellicer

first: Carlos

last: Simón


title: Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 25mg/kg DMNQ

status: Public on Aug 06 2010

city: Leicester

first: Amy

last: Pointon

address: Lancaster Road

department: Systems Toxicology Group

country: United Kingdom

institute: MRC Toxicology Unit

summary: Translational profiling of mouse cardiac tissue treated with 25mg/kg DMNQ in 10 ml/kg arachis oil over an acute time course (0.5-120 hours) compared to time matched control animals treated with 10ml/kg saline

overall_design: Two colour microarrays with time matched controls vs 25mg/kg DMNQ cardiac tissue. Before microarray analysis RNA separated on a sucrose density gradient into those mRNAs activitly undergoing translation (polysomes) and those not (monosomes) with control monosomes and treated monosomes on one set of arrays, and polysome control and polysome treated on another set of microarrays. The normalized Log2 of the monosomes was subtracted from the respective Log2 of the polysomes (on Series record). Time points studied were 0.5, 1, 2, 12, 24 and 120 hours following dosing, biological replicates n=3 independent animals at each time point, technical replicates (reverse labelling) n<1. One array printed onto two slides (A and B), one replicate per array.


title: Global comparison of mouse ES cell lines derived from blastocysts and preblastocysts.

status: Public on Aug 04 2010

city: Storrs

first: Mark

middle: Gerald

last: Carter

address: 1392 Storrs Road

department: Center for Regenerative Biology

institute: University of Connecticut

summary:
Standard mouse ES cell derivation protocols use blastocysts at 3.5 dpc, but the efficiency of successful line derivation is low in commonly-used inbred strains, and much lower in other mouse strains. By using 2-cell zona pellucida-free embryos, culturing them on embryonic feeder cells, and passaging the outgrowths in several different media formulations, we have dramatically improved mouse ES cell line derivation efficiency.
Mouse ES cell lines derived from blastocyst outgrowths using standard procedures were compared to preblastocyst (2-cell outgrowth)-derived lines, each derived in three different media formulations, using the genome-scale MEEBO gene expression oligo probe set.
The overall goal of this microarray study is to determine the overall similarity between cell lines derived using the two methods, in terms of gene expression, as well as to identify important differences. Additionally, we hope to identify effects of the media formulation on gene expression in the cell lines.

overall_design: Seven-condition experiment (two cell types, three derivation conditions, plus one control cell line). 2 biological replicates for each cell line, independently grown and harvested. One dye-swapped pair of arrays per replicate, one probe replicate per array.

first: Chul

last: Kim

first: Joonghoon

last: Park

first: Tomokazu

last: Amano

first: Ge

last: Lin

first: Ren-He

last: Xu

first: Xiuchun

last: Tian

first: Xiangzhong

last: Yang

middle: G


title: Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 15mg/kg doxorubicin

summary: Translational profiling of mouse cardiac tissue treated with 15mg/kg doxorubicin in 10 ml/kg saline over an acute time course (0.5-120 hours) compared to time matched control animals treated with 10ml/kg saline.

overall_design: Two colour microarrays with time matched controls vs 15mg/kg doxorubicin cardiac tissue.  Before microarray analysis, RNA is separated on a sucrose density gradient into those mRNAs activity undergoing translation (polysomes) and those not (monosomes) with control monosomes and treated monosomes on one set of arrays, and polysome control and polysome treated on another set of microarrays.  Thealized Log2 of the monosomes was subtracted from the respective Log2 of the polysomes (on Series record).  Time points studied were 0.5, 1, 2, 12, 24 and 120 hours following dosing, biological replicates n=3 independent animals at each time point, technical replicates (reverse labelling) n<1.  One array printed onto two slides (A and B), one replicate per array.


title: hERK1 with Mitochondria

status: Public on Aug 01 2010

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) are members of the MAPK family and participate in the transduction of stimuli in cellular responses. Their long-term actions are accomplished by promoting the expression of specific genes whereas faster responses are achieved by direct phosphorylation of downstream effectors located throughout the cell. Here, we determined that hERK1 translocates into the mitochondria of HeLa cells upon a proliferative stimulus. In that environment, hERK1 physically associates with (i) at least 5 known mitochondrial proteins with functions related to transport, signalling, and metabolism; (ii) histones H2A and H4; and (iii) other cytosolic proteins. This work indicates for the first time the presence of diverse ERKcomplexes in mitochondria and thus provides a new perspective for assessing the functions of ERK1 in the regulation of cellular signalling and trafficking. We propose that ERK may act as a carrier protein, bringing histones into close proximity with mitochondrial enriched ATP surroundings and assisting their translocation to the nucleus, where ERK-histone complexes may act upon gene transcription. Furthermore, histones may sense the status of energetic metabolism and relay the information to the nuclei so as to influence cell division.

overall_design: Dye-Swap Design ERK vs. Control (3+3 Replicates)

first: Soledad

last: Galli

first: Olaf

last: Jahn

first: Reiner

last: Hitt

first: Doerte

last: Hesse

first: Lennart

last: Opitz

first: Uwe

last: Plessmann

first: Henning

last: Urlaub

first: Juan

last: Puderoso

first: Elizabeth

last: Jares-Erijman

first: Thomas

last: Jovin


title: Expression profile of HCT116 p53+/+ and P53-/- cells treated with Leptomycin B

status: Public on Jul 31 2010

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

country: Singapore

institute: Experimental Therapeutics Centre

summary: HCT116 wild type cells express p53. The isogenic HCT116 p53KO cells have the p53 gene knocked out. Cells were treated for 16 hours. Dosages for leptomycin B treatment was 2 nM and 20 nM.

overall_design: Measuring the gene expression profile of the isogenic cell lines when the cells were treated with leptomycin B at different concentrations

first: Meng-Ling

first: May-Ann

last: Lee

first: David

last: Lane


title: Developmental time-course study of Drosophila melanogaster, D. sechellia, D. simulans, and D. sim x D.s sec hybrids

status: Public on Aug 03 2010

city: Hamilton

first: Rama

last: Singh

state: Ontario

address: 1280 Main Street West

department: Biology Department

institute: McMaster University

summary: In order to test the hypothesis that adult hybrid misexpression results from the cascading effect of earlier-expressed developmentally important improperly regulated genes, as well as address whether Von Baer’s 3rd law (suggesting that earlier stages of development should be more similar between species than later stages) holds at the level of gene expression, we conducted whole-transcriptome Drosophila melanogaster cDNA microarray-based expression profiling of males of D. melanogaster, D. sechellia, and D. simulans, at four synchronized developmental time-points (3rd instar larval [larval], early pupal, late pupal, and newly-emerged adult [adult]). D. simulans and D. sechellia shared a most recent common ancestor (MRCA) ~0.5 to 1.0 million years ago (MYA) and form a clade that shared an MRCA with D. melanogaster approximately 5.4 MYA. In addition, we also performed the same analysis on the male interspecific F1 hybrids of the D. simulans (♀) × D. sechellia (♂) cross.

sample_organism: Drosophila sechellia x Drosophila simulans

overall_design: Males from each species and hybrids were synchronized within a 2h window (1.5h for adults) at the beginning of the stage during which they were collected (larval, early pupal, late pupal and adult) and 25 staged individuals were collected and their RNA extracted and amplified twice according to the protocols associated with each array. For the three pure species, 3 technical replicates were performed for each stage; however, in the case of the D. simulans x D. sechellia F1 hybrids, three separate extractions of 25 individuals were performed at each stage, such that they acted as biological as well as technical replicates. Arrays were scanned and analyzed as indicated in the descriptions of each array with the intent of profiling how gene expression changes over development within species as well as comparing how expression levels evolve during development between species. The hybrids were used in order to analyze how mechanisms of gene regulation diverge between species as manifested as misexpression of genes in the hybrids relative to their parents.

first: Carlo

last: Artieri


title: Mouse cardiac tissue: Vehicle treated control vs. 15mg/kg doxorubicin

first: Amy

last: Pointon

summary: Transcriptional profiling of mouse cardiac tissue treated with 15mg/kg doxorubicin in 10 ml/kg saline over an acute time course (0.5-120 hours) compared to time matched control animals treated with 10ml/kg saline.

overall_design: Two colour microarrays with time matched controls against 15mg/kg doxorubicin cardiac tissue.  Time points studied were 0.5, 1, 2, 12, 24 and 120 hours following dosing, biological replicates n=>3 independent animals at each time point, technical replicate n>1 with reverse labelling at each time point.  One array printed onto two slides (A and B), one replicate per array.


title: Sub-adult RDX Exposure, Whole Body Tissue Investigation

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: We investigated ecotoxicological effects and toxicogenomic responses in fathead minnows (Pimephales promelas) exposed to an environmentally-relevant concentration (0.83 mg/L) of the munitions compound cyclotrimethylenetrinitramine (RDX) in one year and multi-generational assays.  In the one year assay, RDX effects were discerned by comparing breeding groups reared in control or RDX-exposure conditions for one year.  RDX had no detectable effect on gonad-somatic index, or condition factor in females assayed at 1 day and at 1, 3, 6, 9, and 12 months, however the liver-somatic index was significantly increased versus controls only at the 12 month time point.  RDX had no effect on live-prey capture rates at all time points assayed and no significant impacts on egg production, fertilization or hatch success in the 1-year exposure trial.  Genomic analyses indicated that RDX exposure caused limited differential expression of transcripts within time points and no functional conservation of effects indicative of RDX exposure among time points for either brain or liver tissues in the one year exposure.  In the multi-generational assay, the effects of acute (96h) exposure to RDX were compared in fish reared to the F2 generation in either control or RDX-exposure conditions.  The RDX-reared fish were not observed to have appreciably enhanced RDX tolerance versus the control-reared fish.  However, significant differences in gene expression were observed among the control and RDX-reared fish related to neuro-excitatory glutamate metabolism, sensory signaling and processes in neurological development.  In total, our results indicate that exposure to an RDX concentration approximating maximum levels observed in the field (0.83 mg/L) caused limited impacts in fathead minnows in a one year exposure, however caused altered expression in genes involved in neural function in a multi-generational exposure.

overall_design: P.  promelas larvae produced in the original one year exposure were collected and grown out to sexual maturity while being maintained in the same treatment (control or 0.83 mg/L RDX) as their respective F0 parental generation.  Once the fish reached sexual maturity, they were placed into eight experimental units for both control and RDX treatment consisting of four females and two males and were maintained with the same experimental conditions as the F0 generation.  To determine if the chronic, multi-generational exposure to RDX resulted in any change in sensitivity to RDX, 90 dph progeny (F2 or sub-adults) of the control and RDX-exposed F1 generation were subjected to a challenge experiment where the fish were exposed to RDX at 5 mg/L.

first: Sandra

last: Brasfield

first: Jacob

last: Stanley

first: Mitchell

last: Wilbanks

first: Pornsawan

last: Chappell

first: Edward

last: Perkins

first: Guilherme

middle: R

last: Lotufo

first: Richard

last: Lance


title: Mouse cardiac tissue: Vehicle treated control vs. 25mg/kg DMNQ

summary: Transcriptional profiling of mouse cardiac tissue treated with 25mg/kg DMNQ in 10 ml/kg arachis oil over an acute time course (5 minutes-120 hours) compared to time matached control animals treated with 10ml/kg arachis oil

overall_design: Two colour microarrays with time matched controls against 25mg/kg DMNQ cardiac tissue.  Time points studied were 5, 10, 15, 20, 30, 45 minutes and 1, 1.5, 2, 5, 12, 24, 120 hours following dosing, biological replicates n=>2 independent animals at each time point, technical replicate n>1 with reverse labelling at each time point.  One array printed onto two slides (A and B), one replicate per array.


title: Stress-induced activation of heterochromatic transcription

status: Public on Jul 29 2010

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

type: Expression profiling by genome tiling array

summary: Constitutive heterochromatin comprising the centromeric and telomeric parts of chromosomes includes DNA marked by high levels of methylation associated with histones modified by repressive marks. These epigenetic modifications silence transcription and ensure stable inheritance of this inert state. Although, environmental cues can alter epigenetic marks and lead to modulation of the transcription of genes located in euchromatic parts of the chromosomes, there is no evidence that external stimuli can globally destabilize silencing of constitutive heterochromatin. We have found that heterochromatin-associated silencing in Arabidopsis plants subjected to a particular temperature regime is released in a genome-wide manner. This occurs without alteration of repressive epigenetic modifications and does not involve common epigenetic mechanisms. Such induced release of silencing is mostly transient and rapid restoration of the silent state occurs without the involvement of factors known to be required for silencing initiation. Thus, our results reveal new regulatory aspects of transcriptional repression in constitutive heterochromatin and open up possibilities to identify the molecular mechanisms involved.

overall_design: 4 samples: CTS, ITS, CTS+2d, IST+2d with 3 replicates each

first: Mireille

last: Tittel-Elmer

first: Larissa

last: Broger

first: Olivier

last: Mathieu

first: Jerzy

last: Paszkowski

first: Isabelle

last: Vaillant


title: CAST x C57 QTLs Effect on Gene Expression for Chromosomes 2, 11, and 17

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary:
Three congenic mouse strains were profiled with microarrays and were analyzed using a QTL/Microarray approach to identify candidate genes that regulate biometric phenotypes: HG2D (HG.CAST-(D2Mit329-D2Mit457)), HG11 (HG.CAST-(D11Mit260-D11Mit255, MGI reference: 3771218), and HG17 (HG.CAST-(D17Mit196-D17Mit190); MGI reference: 3771215). All these congenic strains isolate CAST/EiJ (CAST) alleles in a C57BL/6Jhg/hg (C57) background and bare the hg deletion in the high growth locus on chromosome 10. F2 animals from intercrossing congenic males and C57 control females were profiled for gene expresion on brain, liver and gonadal white fat.
To detect differential expression produced by allelic effects of biometric QTLs on chromosomes 2, 11, and 17.

overall_design: Three strains were profiled: HG2D, HG11, and HG17, isolating CAST alleles in a high growth (HG) background on chromosomes 2, 11, and 17 respectively. Four biological replicates were assayed per strain for brain, liver and gonadal white adipose tissue. Experiments for each chromosomes were done independently. Only genotype comparisons within tissue in each strain were performed.

first: Craig

middle: H

last: Warden

first: Juan

last: Medrano


title: Differentially expressed genes at molting and metamorphosis stages in Bombyx fat body

status: Public on Aug 05 2010

city: Shanghai

first: Ling

last: Tian

address: Fenglin Road 300

department: Institute of Plant Physiology and Ecology

country: China

institute: Chinese Academy of Sciences

summary: In the silkworm, Bombyx mori, juvenile hormone (JH) and 20-hydroxyecdysone (20E) levels are high during the final larval molt (4M) but both absent during the feeding stage of 5th instar (5F), while JH level is low and 20E level is high during the prepupal stage (PP). Fat body is the important organs in insect, we want to find out differentially expressed genes which are respectively regulated by the two hormones.

overall_design: Total RNA from 4th molting,5th feeding and prepupa stages Bombyx fat body were used to generate target cDNA, and then hybridized to 48k Bombyx genome Array Genechips, representing about 23000 characterized genes

first: Sheng

last: Li


title: C. elegans : Control vs. Chlorpyrifos (0.5mg/ml) + Diazinon (1 mg/ml) treatment

status: Public on Jul 22 2010

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

institute: King's College London

summary: Transcriptional profile of C. elegans comparing control vs. nematodes treated with 0.5 mg/ml of Chlorpyrifos and 1mg/ml of Diazinon (DZN) at 16°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.

overall_design: One condition experiment with six biological replicates in a dye swap design.

first: Jan

last: Kammenga


title: Application of blood transcriptomics to identify three novel biomarkers for monitoring anti-TGFbeta therapy

status: Public on Jul 20 2010

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Background: Development of target specific therapeutics greatly benefits from simultaneous identification of biomarkers to determine aspects of bioactivity, drug safety and efficacy or even treatment outcome. This is particularly important when targeting pleiotropic factors such as the TGFbeta system. TGFbeta has become a prime target for cancer therapeutics since inhibition of TGFbeta signaling simultaneously attacks the tumor and its microenvironment.   Methods: Here we introduce blood transcriptomics followed by a defined set of validation assays as a promising approach to identify novel biomarkers for monitoring TGFbeta therapy.   Findings: Our initial genome-wide analysis of transcription in peripheral blood revealed 12 candidate genes specifically regulated in peripheral blood by the TGFbeta receptor I kinase inhibitor LY2109761. In subsequent in vitro and in vivo molecular and immunological analyses, the combined monitoring of gene regulation of three genes, namely TMEPAI, OCIAD2, and SMAD7 was established as novel biomarkers for anti-TGFbeta based therapies.   Interpretation: Overall, the proposed algorithm of biomarker identification is easily adapted towards other drug candidates for which gene regulation can be established in peripheral blood.

overall_design: CD4+ T cells were serum-deprived for 12 hours followed by 8 hours incubation with the indicated compounds, total of 22 samples.

first: S

last: Classen

first: C

last: Muth

first: J

first: A

last: Staratschek-Jox


title: C. elegans : Control vs. Chlorpyrifos (0.5mg/ml) treatment

summary: Transcriptional profile of C. elegans comparing control vs. nematodes treated with 0.5mg/ml of Chorpyrifos (CPF) at 16°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.


title: Mouse cardiac tissues treated with doxorubicin and DMNQ

first: Amy

last: Pointon

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

overall_design: Refer to individual Series


title: C. elegans : Control vs.Chlorpyrifos and Diazinon treatments


title: Expression data from Toxoplasma gondii mutants and wild-type during bradyzoite differentiation in vitro

status: Public on Jul 27 2010

city: Burlington

first: Mariana

last: Matrajt

address: 95 Carrigan Drive

institute: University of Vermont

summary: Toxoplasma gondii pathogenesis includes the invasion of host cells by extracellular parasites (tachyzoites), replication of intracellular tachyzoites, and differentiation to a latent bradyzoite stage. Whole genome expression profiling was carried out using the newly developed Affymetrix ToxoGeneChip (GeneChip Tgondiia520372) in order to analyze the ~8,000 predicted genes in the T. gondii genome of mutants and wild-type, allowing for full-scale expression profiling during bradyzoite differentiation in vitro.

overall_design: RNA from mutant and wild-type parasites was extracted and hybridized to the ToxoGeneChip. We harvested extracellular tachyzoites from freshly lysed fibroblasts (ET, 0h), intracellular tachyzoites (IT, 24h post-invasion) and parasites subjected to bradyzoite growth conditions for 72h (B72, 72h of induction).  Extracellular parasites from freshly lysed fibroblasts were harvested for the seven mutant parasite lines (12K, 13P, B7, 11P, 11K, 7K and P11) and mutant parasites subjected to bradyzoite differentiation conditions for 72h. For a few samples we also harvested parasites 11h post egress of host cells. A time course was carried out with wild-type: parasites subjected to bradyzoite growth conditions for 24h, 36h and 48h.


title: Differential gene expression profiles of human promyelocytic leukemia cell lines exposed to benzene and its metabolites

status: Public on Jul 24 2010

city: Seoul

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

country: South Korea

institute: Korea Institute of Science and Technology

summary:
The gene expression profiles of HL-60 cells were determined with IC50 doses of 3 chemicals (benzene, hydroquinone and benzoquinone) at a 3 h time point. Assays were performed in triplicate for each chemical/dose, and individual gene-expression profiles were determined for each chemical at the tested concentration doses.
SUBMITTER_CITATION: http://www.sciencedirect.com/science/article/pii/S1382668911001049, DOI: doi:10.1016/j.etap.2011.06.001, Reference: ENVTOX 1446

overall_design: Three independent experiments were performed for each chemical (N = 6), simultaneously. Labeling and hybridization were performed using the instructions of the Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). This was followed by the coupling of the Cy3 dye for the controls (DMSO) and Cy5 dye for the treated samples. Hybridization was performed in a hybridization oven at 62 oC for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58 oC, 1× SSC for 2 min at RT and 0.2× SSC for 3 min at RT), the slide was dried by centrifugation at 800 rpm for 3 min at RT. Hybridization images on the slides were scanned by ScanArray Lite (PerkinElmer Life Sciences, USA). Scanned images were analyzed with GenePix 3.0 software (Axon Instruments, USA) to obtain gene expression ratios.

middle: N

first: Youn-Jung

last: Kim

first: Jae-Chun

last: Ryu


title: C. elegans : Control vs. Diazinon (1 mg/ml) treatment

summary: Transcriptional profile of C. elegans comparing control vs. nematodes treated with 1mg/ml of Diazinon (DZN) at 16°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.

middle: E


title: Systemic transcriptome alternation under mtDNA depletion in 143B TK- osteosarcoma cells

status: Public on Jul 17 2010

city: seoul

first: hyun-jung

last: koo

address: hoegi-dong,dongdaemun-gu

institute: Kyung Hee University

summary: The mitochondrial protein repertoire varies depending on cellular states, tissue type, species, and disease state. However, little is known about how this repertoire changes under different cellular or disease states. To gain a better understanding of dynamic mitochondrial proteomic changes, we compared alterations of mitochondrial proteome with transcriptome under mitochondrial DNA depletion.

overall_design: Total RNA obtained from 143B TK- osteosarcoma ρ+ cells or 143B TK- osteosarcoma ρ° cells

first: Hyun-Jung

last: Koo

first: Youngmi

last: Pak


title: PF4-Cre mediated deletion of SRF in murine megakaryocytes.

status: Public on Jul 13 2010

city: New Haven

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: Srf is a MADS-box transcription factor that is critical for muscle differentiation. Its function in hematopoiesis has not yet been revealed. Mkl1, a cofactor of Srf, is part of the t(1;22) translocation in acute megakaryoblastic leukemia, and plays a critical role in megakaryopoiesis. In order to test the role of Srf in megakaryocyte development, we crossed Pf4-Cre mice, which express Cre recombinase in cells committed to the megakaryocytic lineage, to SrfF/F mice in which functional Srf is no longer expressed after Cre-mediated excision. Pf4-Cre/SrfF/F (KO) mice are born with normal mendelian frequency, but have significant macrothrombocytopenia with approximately 50% reduction in platelet count. In contrast, the BM has increased numbers and percentages of CD41+ megakaryocytes (WT: 0.41+/-0.06%; KO: 1.92+/-0.12%) with significantly reduced ploidy. KO mice show significantly increased megakaryocyte progenitors in the BM by both FACS analysis and CFU-Mk. Megakaryocytes lacking Srf have abnormal stress fiber and demarcation membrane formation and platelets lacking Srf have abnormal actin distribution. In vitro and in vivo assays reveal platelet function defects in KO mice. Critical actin cytoskeletal genes are downregulated in KO megakaryocytes. Thus, Srf is required for normal megakaryocyte maturation and platelet production, due at least in part, to regulation of cytoskeletal genes.

overall_design: C-kit+CD41+ megakaryocyte progenitors from PF4-Cre/SRF C57BL/6 SRF WT (3) and C57BL/6 SRF KO (3) mice were sorted by flow cytometry and cultured for three days in thrombopoietin.

first: Stephanie

last: Halene

first: Vincent

first: Diane

last: Krause


title: Atf1-mediated active gene response to H2O2 challenge.

status: Public on Jul 19 2010

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by genome tiling array

summary:
Here we present the study on ChIP-chip mapping of the genomic binding sites for Sty1, Atf1, and the Atf1's binding partner Pcr1; the genome-wide transcriptional profiling of the atf1 and pcr1 strains in response to H2O2; and the phenotypic assessment of ~90 Atf1/Pcr1-bound or unbound genes for growth fitness under H2O2 conditions. ChIP-chip analysis shows that Atf1 and Pcr1 binding sites are overlapped in the genome and constitutively present before H2O2 stress. On the other hand, Sty1 recruitment primarily occurs at the Atf1/Pcr1 binding sites and is induced by H2O2. We found that Atf1/Pcr1 is clearly responsible for the high-level transcriptional response to H2O2. Furthermore, phenotypic assessment indicates that among the H2O2-induced genes, Atf1/Pcr1-bound genes exhibit a higher likelihood of functional requirement for growth fitness under the stress condition than the Atf1/Pcr1-unbound genes do. Notably, we found that the Atf1/Pcr1-bound genes regardless of their responsiveness to H2O2 show a high probability of requirement for growth fitness.

.

overall_design: Expression level of genes in triplicates at 0min (without stress) is compared with that at 10, 30, 60, and 120min after stress treatment. ChIP-chip analyses is done for Atf1-HA, pcr1-HA, sty1-HA, Sty1-HA allele in the atf1D or pcr1D background without and with H2O2 (0.5mM for 30min).

first: Jianhua

last: Liu


title: Expression data from Anopheles gambiae females blood fed twice within a gonotrophic cycle

status: Public on Jul 08 2010

city: Irvine

first: Osvaldo

last: Marinotti

address: University of California, Irvine

department: Molecular Biology & Biochemistry

institute: University of California, Irvine

summary: Anopheline mosquitoes frequently take multiple blood meals in a single gonotrophic cycle. In this study we determined patterns of gene expression in Anopheles gambiae females blood fed twice within the first gonotrophic cycle.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: 1 condition, 3 replicates per condition, Affymetrix internal controls

first: Anthony

last: James


title: Wild type vs. Nova2 KO mouse E14.5 cortex RNA

status: Public on Jul 07 2010

city: New York

first: Masato

last: Yano

state: NY

address: 1230 York Avenue

department: Molecular Neuro-Oncology

institute: The Rockefeller University

summary:
To assess the requirement of Nova2 for alternative processing of RNA in the developping brain.
Neuronal migration leads to a highly organized laminar structure in the mammalian brain and its mis-regulation causes lissencephaly, behavioral and cognitive defects. Reelin signaling, mediated in part by a key adaptor, disabled-1 (Dab1), plays a critical but incompletely understood role in this process.  We found that the neuron-specific RNA binding protein Nova2 regulates neuronal migration in late-generated cortical and Purkinje neurons.  An unbiased HITS-CLIP and exon junction array search for Nova-dependent RNAs at E14.5 focused on components of the reelin pathway revealed only one candidate—an alternatively spliced isoform of Dab1 (Dab1.7bc).  In utero electroporation demonstrated that Dab1.7bc was sufficient to induce neuronal migration defects in wild-type mice and exacerbate defects when Dab1 levels were reduced, while Dab1 overexpression mitigates defects in Nova2-null mice. Thus Nova2 regulates an RNA switch controlling the ability of Dab1 to mediate neuronal responsiveness to reelin signaling and neuronal migration, suggesting new links between splicing regulation, brain disease and development.

Keywords: Comparative analysis

overall_design: RNA from the cortex of 3 wild type and 3 Nova2 KO E14.5 cortex.  One array per biological replicate.

first: Robert

middle: B

last: Darnell


title: Candida albicans DOPA-grown cells

city: Aberdeen

first: Frank

middle: C

last: Odds

address: Institute of Medical Sciences

department: School of Medical Sciences

institute: University of Aberdeen

summary: The fungal pathogen Candida albicans produces dark-pigmented melanin when grown in a basal medium containing 1 mM l-DOPA as melanin substrate.  In the widely used C. albicans strain SC5314, melanin appeared after 3-4 days of incubation in l-DOPA medium.  The experiment was designed to reveal cadidate genes associated with melanin biosynthesis by expression profiling at different times of growth with and without L-DOPA added to the medium.  Expression profiling of C. albicans revealed very few genes significantly up- or down-regulated by growth in l-DOPA.

overall_design: Sixteen paired samples were submitted to dual channel analysis.  Four biological replicate samples of RNA were prepared from cells of C. albicans strain SC5314 at four time points, from cultures grown with and without addition of 1 mM L-DOPA, thus generating an initial total of 32 samples for analysis: four experimental and four control samples made after 6 h, 24 h, 48 h and 72 h of growth.  For each time point the control (no L-DOPA) samples were pooled and labelled with Cy3-dUTP by reverse transcription.  The four individual biological replicates for each time point were separately labelled with Cy5-dUTP by reverse transcription and independently hybridized against the pooled controls on the microarray chips.  Results were read with a ScanArray 4000 Microarray Analysis System.


title: Dissociated avian utricle sensory epithelia treated with one of various siRNAs or small molecule inhibitors

status: Public on Jul 02 2010

city: St. Louis

first: David

middle: Michael

last: Alvarado

state: MO

address: 4565 Scott Ave

department: Genetics

institute: Washington University in St. Louis

summary: The inner ear utilizes sensory hair cells as mechano-electric transducers for sensing sound and balance. In mammals, these sensory hair cells lack the capacity for regeneration and if damaged lead to hearing or balance disorders. However, non-mammalian vertebrates such as birds maintain their regenerative abilities throughout their life. In a previous study we conducted a gene expression profiling time course of regenerating sensory epithelia (SE) in avian cochlea and utricle on a custom transcription factor microarray following damage by both laser and chemical ablation. We identified several known signaling cascades such as The Pax-Eya-Six-Dach pathway, Ap-1 pathway, the Tgf-β pathway and sonic hedgehog signaling that are differentially expressed during SE regeneration. In this study we selected 27 of these genes for knockdown by siRNA or small molecule inhibition to determine their requirement for SE regeneration and identify downstream targets. We assessed phenotypes using a 96 well proliferation assay and expression profiled each knockdown on a custom transcription factor microarray. Using these techniques we have determined several genes that are required for SE proliferation and identified novel epistatic relationships between many of these genes.

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus

overall_design:
Pure sensory epithelia was isolated from avian utricles. Sensory epithelia was physically dissociated and grown in 96 well cultures for 3 days.  Prior to confluency, dissociated sensory epithelia were transfected with siRNAs (12 pmol/well) or small molecule inhibitor in 0.1% DMSO. RNA was isolated 24 hrs post transfection and assayed on a custom oligonucleotide transcription factor microarray compared to controls (GFP siRNA or 0.1% DMSO only).

siRNA: CEBPG, JunD, BTAF1, LRP5, PAX2, PAX5, PAX7, Wnt4, BCL11A, CBX3, CBX4, CTNNB1, CUTL1, MYT1L, RARA, TIMELESS, TRIP15, PAX3, EZH2, HES1, ID1, CDKN1B, and PPARGC1

small molecule inhibition: IGF, MAPK, SHH, and JNK

middle: M

last: Hawkins

first: Stavros

last: Bashiardes

first: Rose

last: Veile

first: Kara

last: Powder

first: Judith

last: Speck

first: Mark

last: Warchol

first: Michael

last: Lovett


title: Analysis of gene expression in different T cell clones

status: Public on Jul 01 2010

city: Naples

first: gabriella

last: rodolico

address: Via Costantinopoli 16

country: Italy

institute: Second University of Naples

summary:
The aim was to analyze the expression of genes in Th17 cell clones derived from a patient affected by multiple sclerosis before and after activation with anti-CD3 and anti-CD28.

Keywords: Gene expression, T cell clones, Th17 characterisation

overall_design: The T cell clones were derived according to well known protocol, using different cytokines, and classified on the basis of their ability to produce cytokines. Once characterized for their production of different cytokines, they were stimulated with anti-CD23 and anti-CD28 and used to prepare microarray experiments comparing the stimulated clones against the unstimulated ones.

first: Gabriella

last: Rodolico

first: Lorenzo

last: Cosmi

first: Francesco

last: Annunziato

first: Raffaele

last: De Palma


title: Expression Differences in Ethanol Stress Response Between  Saccharomyces cerevisiae Parent W303-1A Strain and its Two Ethanol Tolerant Mutants

city: East Geelong

first: Dragana

last: Stanley

state: Victoria

address: 5 Portarlington Rd

department: AAHL

country: Australia

institute: CSIRO

summary: Saccharomyces spp. are widely used for ethanol production however fermentation productivity is negatively affected by the impact of ethanol accumulation on yeast metabolic rate and viability. This study used microarray and statistical two-way ANOVA analysis to compare and evaluate gene expression profiles of two previously generated ethanol-tolerant mutants, CM1 and SM1, with their parent, S. cerevisiae W303-1A, in the presence and absence of ethanol stress.  Although sharing the same parentage, the mutants were created differently; SM1 by adaptive evolution involving long-term exposure to ethanol stress, and CM1 using chemical mutagenesis followed by adaptive evolution-based screening.  Compared to the parent, differences in the expression levels of genes associated with a number of GO categories in the mutants suggest that their improved ethanol stress response is a consequence of increased mitochondrial and NADH oxidation activities, stimulating glycolysis and energy production.  This leads to increased activity of energy-demanding processes associated with the production of proteins and plasma membrane components, which are necessary for acclimation to ethanol stress.  It is suggested that a key function of the ethanol stress response is restoration of the NAD+/NADH redox balance, which increases glyceraldehyde-3-phosphate dehydrogenase activity, and higher glycolytic flux in the ethanol-stressed cell.  Both mutants achieved this by a constitutive increase in carbon flux in the glycerol pathway as a means of increasing NADH oxidation.

overall_design: Two conditions: 0% and 6.5 % (v/v) ethanol added to the culture growth medium for each strain. One set of triplicates with one dye swap for each condition. Each triplicate was prepared from different biological replicate (i.e. different culture).

first: Paul

middle: J

last: Chambers

first: Grant

last: Borneman

first: Sarah

last: Fraser


title: Human BJ fibroblasts containing control vs. BRD7 shRNA

city: Boston

first: Anna

last: Burrows

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard Medical School

summary: Transcriptional profiling of human BJ fibroblasts comparing control FF shRNA expressing cells vs. BRD7 shRNA expressing cells under two conditions, either untreated or treated with 8uM nutln-3a for 8 hours. This experiment was done using two independent shRNAs targeting BRD7. Nutlin-3a was used to stabilize p53 and induce its transcriptional activity.

overall_design: Two-condition experiment, FF shRNA cells vs. BRD7 shRNAs cells in two experimental conditions, either untreated or treated with nutlin-3a.


title: Global gene expression profile of stomach from wild-type and NHE4-knockout mice.

city: Cincinnati

first: Gary

last: Shull

state: OH

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

summary: The objective of this study was to identify changes in gene expression levels between wild-type and NHE4-knockout stomach.

overall_design: 6 wild-type and 6 NHE4-knockout stomach RNA samples were compared.  Total RNA was collected from both male and female adult (between 8 and 12 weeks of age) wild-type and NHE4-null mice on a mixed 129 Black Swiss background. With the exception of one, all comparisons were done between wild-type and NHE4-null samples from littermate age- and gender-matched siblings.

first: Emily

last: Bradford

first: Lara

last: Gawenis


title: Genes Differentially Expressed as a Result of Enforced EDAG Expression In 32D Cells

city: Beijing

first: changyan

last: li

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

summary: Erythroid differentiation-associated gene (EDAG), a hematopoietic tissue-specific transcription regulator, plays a key role in maintaining the homeostasis of hematopoietic lineage commitment. However, the mechanism and genes regulated by EDAG remain unknown.Here, we performed genome-wide parallel expression analyses of 32D cells stably transfected with EDAG.

overall_design: Total RNA from the control 32D cells and 32D/EDAG cells were used to generate target cDNA, and then hybridized to 36k Mouse Genome Array Genechips, representing about 25000 characterized murine genes.

first: Yali

last: Ding

first: Changyan

last: Li

first: Xiaoming

last: Yang


title: Morphological and molecular evidence that the zebrafish intestine is organized into a small and large intestine

status: Public on Jun 29 2010

city: Singapore

first: zhengyuan

last: wang

address: 14 Science Drive 4

department: Biological Sciences

institute: National University of Singapore

summary: Our genome-wide gene expression data indicate that, despite the lack of crypts, the rostral, mid, and caudal portions of the zebrafish intestine have distinct functions analogous to the mammalian small and large intestine, respectively. Organization of ridge structures represents a unique feature of zebrafish intestine, though they produce similar cross sections to mammalian intestines. Evolutionary lack of stomach, crypts, Paneth cells and submucosal glands has shaped the zebrafish intestine into a simpler but unique organ in vertebrate intestinal biology.

overall_design: We analyzed gene expressions in wildtype adult zebrafish (Danio rerio) intestine by dividing it into seven segments s1 to s7 (rostral to caudal). 3 to 5 replicates. 30 samples total.

first: Zhengyuan

last: Wang

first: Jianguo

last: Du

first: Siew

last: Lam

first: Sinnakarupan

last: Mathavan

middle: T

last: Matsudaira

first: Zhiyuan

last: Gong


title: Comparisons of the global gene profile between C-CPE treated- and untreated- SKOV-3 ovarian cancer cells.

status: Public on Jun 23 2010

first: Zhijian

last: Gao

address: Longwood 221

institute: BWH, Harvard Medical School

summary: A microarray analysis was performed to compare the global gene expression profile between C-CPE treated- and untreated- SKOV-3 ovarian cancer cells.

overall_design: SKOV-3 cells were treated with or without C-CPE for 72 hours, and total RNA was extracted and microarray was perfomed to compare the gene profiling changes between C-CPE treated- and untreated- cells. The experiment was  performed in triplicate.


title: Identification of differentially expressed genes in equine endometrium at day 8 and 12 of pregnancy

status: Public on Jun 30 2010

city: Lindau

first: Stefan

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

institute: University of Zurich

summary: In order to systematically analyze the maternal, i.e. the endometrial, changes in the equine endometrium underlying the complex embryo-maternal dialogue during early pregnancy, a transcriptome study of endometrium samples from five mares at day 8 and six mares at day 12 of early pregnancy and the corresponding non-pregnant stage was performed.

overall_design:
Endometrial biopsies were taken from six warmblood mares at day 12 of early pregnancy after embryo recovery and at the corresponding non-pregnant stage. 12 samples were analyzed: one pregnant sample and the corresponding control sample of every mare each at a time.
Endometrial biopsies were taken from five warmblood mares at day 8 of early pregnancy after embryo recovery and at the corresponding non-pregnant stage. 10 samples were analyzed: one pregnant sample and the corresponding control sample of every mare each at a time.

Two experimental groups: 8 and 12 days

first: Maximiliane

last: Merkl

first: Johannes

last: Handler


title: Homozygous BUB1B mutation and susceptibility to multi-site gastrointestinal neoplasia

status: Public on Jun 09 2010

city: Montreal

first: Thomas

last: Rio Frio

state: QC

address: 1625 Pine Avenue

department: Human Genetics

institute: McGill University

summary: We investigated the cause of gastrointestinal neoplasia in a man who developed adenocarcinoma of the ampulla of Vater at the age of 34, followed almost three decades later by adenomatous polyps and invasive adenocarcinomas of both the colon and stomach. Premature chromatid separation, mosaic variegated aneuploidy (MVA), combined with structural chromosome abnormalities were detected in his cells. We identified a homozygous intronic mutation, c.2386-11A>G in BUB1B which creates a de novo splice site that is favored over the authentic site. This study expands the phenotype of BUB1B mutations and MVA to include common adult-onset cancers and provides evidence for the interdependency of APC and BUBR1 proteins in humans.

overall_design: 2 biological replicates of 7 samples (lymphoblastoid cell line (LCL) of the affected proband, fibroblasts of the affected proband, LCLs from 2 relatives of the proband, LCLs from 2 unaffected controls, fibroblasts from 1 control) were processed at the same time.

first: Josée

last: Lavoie

first: Nancy

last: Hamel

first: Felipe

last: Geyer

first: Yael

last: Kushner

first: David

last: Novak

first: Landon

last: Wark

first: Cristian

last: Capelli

first: Jorge

middle: S

last: Reis-Filho

first: Sabine

last: Mai

first: Tomi

last: Pastinen

first: Marc

middle: D

last: Tischkowitz

first: Victoria

last: Marcus

first: William

last: Foulkes


title: Comparative DNA methylation profiling of human monocyte-derived macrophages and dendritic cells

status: Public on Jun 07 2010

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

type: Methylation profiling by genome tiling array

summary:
In mammals, the dynamics of DNA methylation, in particular the regulated, active removal of cytosine methylation has remained a mystery, partly due to the lack of appropriate model systems to study DNA demethylation. Previous work largely focused on proliferating cell types that had been mitotically arrested using pharmacological inhibitors to distinguish between active and passive mechanisms of DNA demethylation. Here, we characterised this epigenetic phenomenon in a natural setting of post-mitotic cells: the differentiation of human peripheral blood monocytes into macrophages or dendritic cells which proceeds without cell division. We identified many novel examples of active DNA demethylation using a global, comparative CpG methylation profiling approach and characterised accompanying transcriptional and epigenetic events at these sites during monocytic differentiation.
Keywords: MCIp-on-Chip; comparative genomic hybridization

overall_design: DNA from monocytes and dendritic cells was separated into methylated and unmethylated pools. Corresponding pools of each cell type were co-hybridized on custom promoter arrays. Methylated and unmethylated pools serve as diametrically oposed technical replicates (mirror image approach). Two biological replicates .

first: Maja

last: Klug


title: miR-122 as a Regulator of Mitochondrial Metabolic Gene Network in Hepatocellular Carcinoma

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

type:
Expression profiling by array
Other

summary: Hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths worldwide, reflecting the need for a better understanding of hepatocarcinogenesis. In this study, we examined the genome-wide expression profiles of both miRNAs and mRNAs from paired tumor and adjacent non-tumor tissues from a cohort of 96 HCC patients in Hong Kong where hepatitis B virus (HBV) is endemic. The comprehensive analysis of the coordinate expression of miRNAs and mRNAs reveals that miR-122 is under-expressed in HCC and that it is an important regulator for normal mitochondrial metabolism. A decreased level of miR-122 leads to an increase in expression of miR-122 seed-matched genes, a loss of mitochondrial metabolic function, and a decrease in the expression of many miR-122 secondary targets. These secondary targets are prognostic markers for HCC patients. Transcriptome profiling data from an additional 180 HCC and 40 liver cirrhotic patients in the same cohort were used to confirm the anti-correlation of miR-122 primary and secondary target gene sets. To test the HCC findings in normal mouse liver, we used an antagomir against miR-122 and identified altered gene expression profiling by microarray analysis in mouse in vivo experiments. The mouse data recapitulated the human HCC findings. Our anti-miR122 data further provided a direct link between increases in the mRNA levels of miR-122 controlled genes and impairments of mitochondrial metabolism. In summary, we find miR-122 loss may be detrimental to mitochondrial-related metabolisms in sustaining critical liver function and contribute to the morbidity and mortality of liver cancer patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Mouse liver profiling:
In one treatment regimen, four animals were given four doses of 100mg ASO/kg body weight, administered every other day, and sacrificed one day after the last dose.  Four animals treated for four weeks were treated twice weekly with 50mg ASO/kg body weight, and sacrificed two days after the last dose.  Mice were sacrificed in the morning, and liver was removed for further analysis.  Samples from oligonucleotide-treated mice were referenced against samples from saline-treated mice in fluor-reversed pairs.

Human liver profiling:
For human HCC patient samples, 192 samples -- 96 resected tumor and 96 adjacent non-tumor liver tissues -- were collected from 96 patients who had undergone hepatectomy for curative treatment of HCC at Queen Mary Hospital, Pokfulam, Hong Kong between 1990 and 2007. Informed consents were obtained from patients regarding the use of the liver specimens for research.  Samples were hybridized to Affymetrix arrays for mRNA profiling and were analyzed by quantitative PCR for microRNA profiling.

first: Chunsheng

last: Zhang

first: Angela

last: Liu

first: Nikki

middle: P

last: Lee

first: Kwong-Fai

last: Wong

first: Ronnie

last: Poon

first: Park

last: Sham

first: Brian

middle: Y

last: Lam

first: Mark

last: Ferguson

first: George

last: Tokiwa

first: Ryan

last: Smith

first: Brendan

last: Leeson

first: Rebecca

last: Beard

first: John

last: Lamb

first: Lee

last: Lim

first: Mao

last: Mao

first: Hongyue

last: Dai

last: Luk


title: Breast cancer MCF-7 Cells and MDA-MB-435 cells: pre-miR-125b Transfected cells vs. pre-control transfected cells

status: Public on Jun 25 2010

city: Guangzhou

first: Li

middle: Xu

last: Yan

state: Guangdong

address: 651# Dong Feng Road East

department: Department of Pathology

institute: Sun Yat-Sen University Cancer Center

summary: Transcriptional profiling of breast cancer cells comparing pre-control transfected cells with cells transfected with pre-miR-125b. We searched for miR-125b targets by systematic screening of mRNA profiling of pre-miR-125b transfected MCF-7 cells and MDA-MB-435 cells.

overall_design: Two-condition experiment, pre-miR-125b Transfected vs. pre-control Transfected MCF-7 cells. One replicate per array.

first: Yan

last: Zhang

first: Li-Xu

first: Qi-Nian

last: Wu


title: Gene expression profile after CCM1 over expression in human umbilical vein endothelial cells

status: Public on Jun 08 2010

city: Mannheim

first: Andreas

last: Fischer

address: Ludolf-Krehl-Str. 13-17

department: Joint Research Division Vascular Biology

institute: German Cancer Research Center and Medical Faculty Mannheim, Heidelberg University

summary: CCM1 (also known as KRIT1) is critical regulator of endothelial cell biology. Mutations in CCM1 can lead to the formation of cerebral cavernous malformations (CCM). CCM lesions are frequent in the human population; however, their pathogenesis is poorly understood. This genome-wide expression analysis is aimed to unravelling novel mechanisms how CCM1 executes its functions in endothelial cells. We used human umbilical vein endothelial cells (HUVEC) as a model system to study CCM1 functions after adenoviral over expression. The results of this experiment suggest that CCM1 is a critical regulator of endothelial cell cycle control and proliferation as well as migration and angiogenesis. This fits well to the roles of CCM1 in HUVEC which indeed acts as a negative regulator of angiogenesis.

overall_design:
Human umbilical vein endothelial cells were transduced with adenovirus expressing CCM1 or GFP as control. 48 hours after transduction total RNA was isolated from duplicates for genome-wide expression analysis
biological replicate: GFP rep1, GFP rep2
biological replicate: CCM1 rep1, CCM1 rep2

first: Joycelyn

last: Wuestehube

first: Sven

last: Liebler

first: Arne

last: Bartol


title: Comparison of gene expression of OT-I CD8 T cells after infection

status: Public on Jun 01 2010

city: Farmington

first: Leo

last: Lefrancois

state: CT

address: 263 Farmington Ave.

institute: UCONN Health Center

summary:
The goal was to examine gene expression after in vivo activation by different vaccine strains of Listeria monocytogenes.
Heat killed LM, irradiated LM and live actA- LM were used to immunize mice after transfer of OT-I cells

overall_design:
5x10e5 OT-I-RAG-/- cells transferred to B6 mice, 24hrs later mice immunized; 24hrs later cells sorted on MHC class II-, CD45.1+, CD8+, CD69+
Two arrays were performed per sample for a total of 8 arrays.  RAW data file (supplementary file on the Series record) contains the data for each array individually.

first: Kamal

last: Khanna


title: Phenotypic and genomic analysis of an exceptional case of enteropathy associated T cell lymphoma

status: Public on Jun 17 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Approximately 2–5% of adult-onset coeliac disease (CD) patients develops refractory coeliac disease (RCD).  In contrast to RCD type I, RCD type II is characterised by the presence of aberrant small intestinal intraepithelial T-lymphocytes (IEL) expressing cytoplasmic CD3 but lacking surface expression of CD3, CD4 and CD8. Development of Enteropathy Associated T-cell Lymphoma (EATL) is directly associated with the presence of >20% aberrant IEL in RCD II patients and has a very poor prognosis. We report on an exceptional case of EATL presenting as leukemic ascites and on the unique opportunity to perform extensive  phenotypic and genomic analysis of this malignancy. Flow cytometric immunophenotyping of the ascitic EATL presentation showed CD30 expression typical for EATL and loss of the above mentioned surface markers similar to the aberrant IEL it originated from, as indicated by an identical monoclonal TCR-gamma rearrangement. In addition, expression of a substantial number of markers, including CD2, CD7, CD11a/CD18, CD52, CD103 and granzyme B was lost, which has not been reported sofar. Expression of proliferation markers Ki-67 en PCNA was clearly detected in the majority of EATL cells. Karyotype and comparative genomic hybridisation (CGH) analyses showed many genomic alterations, including chromosomal gains and losses up to 47Mb not previously reported for EATL. In conclusion, the current exceptional EATL presentation displays both immunophenotypic and genomic alterations not described previously and not included in the current WHO classifications of lymphoid malignancies.

overall_design: Comparative genomic hybridisation (CGH) analyses of an exceptional case of enteropathy associated T cell lymphoma

last: Tack

last: Verbeek

last: van de Water

last: von Blomberg

last: Bhola

first: B.

last: Ylstra

last: Mulder

last: Schreurs


title: Nuclear Matrix Association in Proliferative and Invasive Cytotrophoblasts

status: Public on Jun 22 2010

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 East Hancock, CS Mott Center

institute: Wayne State University

summary: Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy.  The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood.  The aim of this study was to characterize the transcriptome of the HTR-8/SVneo human cytotrophoblast cell line which displays well characterized invasive and non-invasive behaviors, and to correlate the activity of the transcriptome with nuclear matrix attachment and cell phenotype.  Interestingly comparison of the transcriptome did not reveal an obvious significant difference between the transcriptomes of invasive and non-invasive HTR cells.  In contrast, comparison of the MARs on chromosomes 14-18 revealed an increased number of MARs associated with an invasive phenotype.  These attachment areas were more likely to be associated with silent (rather than actively transcribed) genes.

overall_design: DNA extraction with a 2 M NaCl solution followed by restriction digestion with EcoR1 facilitates the separation of matrix bound DNA from non matrix bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of the genome in non-invasive (proliferative) and invasive trophoblasts.  The matrix association was assessed relative to gene expression measured on Illumina expression beadchips.

first: Kathryn

last: Drennan

first: Amelia

middle: K

last: Linnemann

first: Adrian

last: Platts

first: Henry

last: Heng

first: David

middle: R

last: Armant