title: Oxidative stress alters miRNA and gene expression profiles in villous first trimester trophoblasts

status: Public on Dec 31 2015

city: Cairo

first: Mai

last: Tolba

state: Non-US/Non-Canadian

address: Abbasya

department: Pharmacology and Toxicology

country: Egypt

institute: Faculty of Pharmacy, Ain Shams University

summary: Oxidative stress plays a crucial role in preeclampsia (PE) pathogenesis. Evidence indicates altered microRNAs (miRNAs) expression in PE, however, the relationship between oxidative stress and miRNA changes in placenta as a potential mechanism involved in PE is not fully elucidated. In the present study, we investigate the impact of increased oxidative stress on miRNA and mRNA expression profiles of genes known to be associated with PE in villous 3A first trimester trophoblast cells. Cells were exposed to H2O2 at 10 different concentrations (0-1 mM) for 0.5, 4, 24, and 48 h. Cytotoxicity was determined using the SRB assay and data was used to calculate the IC50 of H2O2. Total RNA was extracted after short-term exposure (4 h) to H2O2 for miRNA expression profiling. H2O2 exerted a concentration and time-dependent cytotoxicity on 3A trophoblast cells. Short-term exposure of 3A cells to low concentration of H2O2 (5% of IC50) significantly altered miRNA profile as evidenced by significant changes in 195 out of 595 evaluatable miRNAs. Short-term exposure of villous first trimester trophoblasts to low concentrations of H2O2 significantly alters miRNA profile.    Oxidative stress plays a crucial role in preeclampsia (PE) pathogenesis. Evidence indicates altered microRNAs (miRNAs) expression in PE, however, the relationship between oxidative stress and miRNA changes in placenta as a potential mechanism involved in PE is not fully elucidated. In the present study, we investigate the impact of increased oxidative stress on miRNA and mRNA expression profiles of genes known to be associated with PE in villous 3A first trimester trophoblast cells. Cells were exposed to H2O2 at 10 different concentrations (0-1 mM) for 0.5, 4, 24, and 48 h. Cytotoxicity was determined using the SRB assay and data was used to calculate the IC50 of H2O2. Total RNA was extracted after short-term exposure (4 h) to H2O2 for miRNA expression profiling. H2O2 exerted a concentration and time-dependent cytotoxicity on 3A trophoblast cells. Short-term exposure of 3A cells to low concentration of H2O2 (5% of IC50) significantly altered miRNA profile as evidenced by significant changes in 195 out of 595 evaluatable miRNAs. Short-term exposure of villous first trimester trophoblasts to low concentrations of H2O2 significantly alters miRNA profile.

overall_design: Cells were grown to 90% confluency in 75 cm2 flasks and exposed to 25 µM H2O2 in complete medium for 4 h.  Total RNA was isolated using the Qiagen miRNEasy Mini Kit and quality/quantity measured in the Molecular Genomics Core at UTMB. RNA was quantitated spectrophotometrically using a NanoDrop ND-1000 (NanoDrop Techniologies, DE). Quality of the purified RNA was assessed by visualization of 18S and 28S RNA bands using an Agilent BioAnalyzer 2100 (Agilent Technologies, CA). Resulting electroperograms were used in the calculation of the 28S/18S ratio and the RNA Integrity Number. Reverse transcription was carried out using either the miScript II RT kit or RT2 First Strand and subsequent SYBR green based real-time PCR on a BioRad Chromo4 Real-Time PCR Detector per manufacturer’s recommendation. The miRNA profile screening was performed using miScript Human miRNome PCR Array (MIHS-3216Z, Qiagen, Valencia, CA). Data was analyzed using the ΔΔCT method with  the miScript miRNA PCR Array Data Analysis version 3.5 (SABiosciences, Valencia CA).


title: Cumulative low doses of the organic pesticide rotenone in the adult rat substantia nigra pars compacta

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Adult male Sprague Dawley rats (5 month-old at the beginning of the study) were subcutaneously exposed to 0.5 mg.kg/d rotenone or the corresponding solvent (PEG/DMSO, 1/1) for 28 days. At the end of the experiment, animals were sacrificed by decapitation and brains were rapidly taken out within 30-40 s. Total RNA was prepared from laser-capture microdissected rat substantia nigra pars compacta (Snpc). Changes in transcript abundance within SNpc were analyzed on samples from solvent and rotenone-exposed groups (n = 3 per group) using CodeLink™ Rat Whole Genome bioarrays containing 34,000 transcripts and EST probes (GE Healthcare, Amersham, Saclay, France).

overall_design: Two groups of rats were exposed either to rotenone (CR rats) or to solvents (CS rats) in order to analyse pesticides impact on gene expression.

first: Christel

middle: C

last: Vanbesien-Mailliot


title: Expression data from Amacr knock-out mouse intestine

status: Public on Dec 22 2015

city: University of Oulu

first: Kaija

middle: J

last: Autio

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

summary: Bile acids play multiple roles in vertebrate metabolism by facilitating lipid absorption in the intestine and acting as a signaling molecule in lipid and carbohydrate metabolism. Bile acids are also the main route to excrete excess cholesterol out of the body. Alpha-methyl-Coa racemase (Amacr) is one of the enzymes needed to produce bile acids from cholesterol. The mouse model lacking Amacr can produce only minor (less than 10%) amounts of bile acids, but still they are symptomless in normal laboratory conditions.

overall_design: Cholesterol absorption occurs in the jejunum part of the intestine. In this experiment, the intestines from Amacr-/- and wild-type mice were divided into four equal segments and the endothelial layer was collected by scraping. The RNA from these samples was isolated and the gene expression levels in each segment were compared. 3 biological replicates per genotype/segment combination.

first: Ari

middle: P

last: Kvist


title: Blood gene expression at 3 months post-transplantation predicts 1-year histologic features in renal transplantation

status: Public on Dec 24 2015

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Histological analysis of biopsy is the gold standard to assess renal allograft status. Furthermore, 1-year protocol biopsy is often performed to evaluated graft outcome. However, since biopsy cannot be performed in a time serial basis, we decided to investigate whether blood can be a good compartment to predict allograft outcome. Gene expression microarrays and a large phenotype have been performed in peripheral blood mononuclear cells from 79 renal transplanted patients taken 3 months after transplantation. We evaluated the association of biological parameters with 4 histological groups defined on renal biopsy taken at 1-year post-transplantation: patients which display normal biopsy (n=45), patients with signs of tubular atrophy and interstitial fibrosis (IFTA) (n=14), with IFTA with inflammation (i-IFTA) (n=14) and patients with alloimmune lesions (n=6)

overall_design: Transcriptomic profile using PBMC from patients showing normal biopsy (n=45), patients with signs of tubular atrophy and interstitial fibrosis (IFTA) (n=14), with IFTA with inflammation (i-IFTA) (n=14) and patients with alloimmune lesions (n=6).

first: R

last: Danger

first: C

last: Paul

first: G

last: Couvrat-Desvergnes

first: J

last: Soulillou

first: S

last: Brouard


title: The homing receptor CD44 is involved in the progression of precancerous gastric lesions in patients infected with Helicobacter pylori and in development of mucous metaplasia in mice (human)

status: Public on Dec 17 2015

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

country: USA

institute: LSUHSC

summary: Gastric cancer continues to be one of the most common cancers, with the third highest cancer-related mortality in the world. After infection with Helicobacter pylori, a cascade of inflammatory events that can lead to gastric cancer is triggered. This inflammatory response to the infection is characterized by the infiltration of mononuclear and polymorphonuclear cells into the infected mucosa. The transition of these cells from the circulation to the tissues is mediated through the interaction of receptors on the immune cells and their ligands in the endothelial compartment. CD44 is the receptor for hyaluronan, but it also interacts with osteopontin and collagen, among other molecules. Previous reports have shown that CD44 expression is increased in advanced gastric lesions. However, the association of this molecule with the progression of these lesions over time has not been investigated. In addition, there is a lack of understanding of the CD44-dependent cellular processes that lead to gastritis, and possibly to gastric cancer. Here we studied a subset of subjects from a cohort of individuals with various degrees of gastric inflammation to determine gene expression changes associated with disease progression over a period of six years. We report that CD44 expression is significantly increased in individuals whose gastric lesions progressed over time (from multifocal atrophic gastritis to intestinal metaplasia or from intestinal metaplasia to dysplasia) along the gastric precancerous cascade. We also show that CD44-/- mice develop less severe and less extensive Helicobacter pylori-induced metaplasia, and show fewer infiltrating Gr1+ cells compared to wild type mice. Thus, we present data suggesting that CD44 is associated with disease progression. Mechanisms associated with these effects include induction of interferon gamma responses.

overall_design: A cohort of individuals having at least  Multifocal Atrophic Gastritis (MAG) was follwed for 6 six years to study the evolution of the gastric lesions over time. The gene CD44 was found to be significantly different between the baseline and follow-up samples of individuals with progression to more advanced gastric lesion. Mouse models of H. pylori infection in wild type and CD44-/- mice showed that the KO mice had reduced levels of gastric itestinal metaplasia than their wild type counterparts after infection. The lesions were associated with differential immune responses and infiltration of GR1 positive cells

first: Jone

last: Garay

first: M

middle: B

last: Piazuelo

first: Sumana

last: Majumdar

first: Li

last: Li

first: Jimena

last: Trillo-Tinoco

first: Luis

last: del Valle

first: Barbara

middle: G

last: Schneider

first: Alberto

last: Delgado

first: Keith

middle: T

last: Wilson

first: Pelayo

last: Correa


title: TB disease classification

status: Public on Dec 21 2015

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

summary: Validation of gene expression levels to assess classification of TB patients and healthy controls

overall_design: qPCR gene expression profiling.  Whole blood gene expression from TB patients (positive in GenXpert assay) and healthy controls; both tuberculin skin test positive (TSTpos) and -negative (TSTneg).

first: Gayle

last: McEwen

first: Eric

last: Lader

first: John

last: Kenneth

first: Stefan

middle: H

last: Kaufmann


title: Expression data from Amacr knock-out mouse liver

first: Kaija

last: Autio

overall_design: Bile acid synthesis occurs in liver. In this experiment, liver samples from Amacr-/- and wild-type mice were collected and their gene expression levels were compared. 4 biological replicates per genotype.

first: Ari

last: Kvist


title: RNA-Seq between Proteus mirabilis HI4320 and an rcsB mutant

status: Public on Dec 25 2015

city: Atlanta

first: Philip

last: Rather

state: GA

address: 3001 Rollins Research Bldg

department: Microbiology

institute: Emory University

type: Expression profiling by high throughput sequencing

summary: We report a comparison of the transcriptional profiles between a wild-type P. mirabilis strain and an isogenic rcsB mutant

overall_design: Three replicate pairs of RNA were analyzed between wild-type HI4320 and an rcsB mutant

first: Kristen

last: Howery

first: Katy

last: Clemmer


title: Gene expression profiling for 4 Zebrafish samples

city: Wuhan

first: Xin-ying

last: Zhou

state: Hubei

address: Luoshi South Road

country: China

institute: Huazhong Agriculture University

summary: In our previous study, by microarray detection, we illuminated the gene expression profiling in copper-exposed embryos. We found that genes of hematopoiesis,  hemoglobin genes exhibited  significant increase in copper-exposed embryos.  In addition, copper-exposed embryos presented relatively high levels of reactive oxygen species (ROS), while the oxygen binding and oxygen transporter activities were also up-regulated in the embryos. Moreover, the scavengers NAC, GSH, and DMTU not only inhibited in vivo ROS levels induced by copper, but also significantly rescued expression of hemoglobin genes back to almost normal levels, and also helped with copper excretion from the copper-exposed embryos. Our data first demonstrated that ROS mediated copper induced increased expression of hemoglobin genes in vertebrates, and copper excretion was blocked by its induced ROS.

overall_design:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression pattern among samples.
4 samples in two pairs were analyzed by gene microarray analysis. In each pair, there were control group and disposed group as compared samples. Replicates were normalized by Fisher’s exact test.
KangChen Inc.

first: Jingxia

last: Liu


title: Genome-wide tissue gene expression profiling in 1 year old Göttingen Minipigs with customized NimbleGen microarrays

status: Public on Dec 16 2015

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

summary:
Minipigs resemble many features of human anatomy, physiology, and biochemistry and represent an animal model for drug efficacy and safety testing. To evaluate at the molecular level the expression of drug targets, drug metabolism pathways or general features of organ transcriptomes in minipigs, we used Customized NimbleGen Microarrays (Design-ID:  120229_MiniPig_TH_expr_HX12) for genome-wide gene expression profiling on 18 different tissues from 6 male and 6 female Göttingen minipigs.
The gene expression results analyzed in this study are further described in Heckel T. et al. (2015) Functional analysis and transcriptional output of the Göttingen minipig genome. under submission

overall_design: A NimbleGen customized 12x135K Gene Expression Array [design ID: 120229_MiniPig_TH_expr_HX12] study using total RNA recovered from drug-naive minipig tissues. Each microarray measures the expression level of 24,499 probe sets covering 17,261 genes with five 60-mer probes (PM) per probe set. The number of replicates is 1 - i.e., only one set of probes on the array. The design includes 16,642 random GC probes for the estimation of the signal threshold and 1536 ERCC control probes.

first: Matthew

last: Rodesch

first: Ulrich

last: Certa


title: Beyond acid suppression: Novel therapeutic targets for gastro-esophageal reflux disease based on a murine model

city: Bonn

first: Gudrun

last: Ulrich-Merzenich

address: Sigmund-Freudstr. 25

department: Medical Clinic III

institute: University Clinic Centre UKB, Bonn University

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

overall_design: Refer to individual Series


title: TRANSCRIPTIONAL CHANGES IN HARD CLAM (MERCENARIA MERCENARIA) IN RESPONSE TO QPX DISEASE AND TEMPERATURE

status: Public on Dec 20 2015

city: Stony Brook

first: Kailai

last: Wang

address: Stony Brook University

institute: Stony Brook University

summary:
Transcriptional profiling of different clam tissues (hemolymph and mantle) in response to QPX disease and temperautre
Quahog Parasite Unknown (QPX) is a fatal protistan parasite that causes severe losses in the hard clam (Mercenaria mercenaria) fisheries along the northeastern coast of the US. Field and laboratory studies of QPX disease have demonstrated a major role for water temperature and M. mercenaria genetic origin in disease development. Infections are more likely to occur at cold temperatures, with clam stocks originating from southern states being more susceptible than clams from northern origin where disease is enzootic. Even though the influence of temperature on QPX infection have been examined in susceptible and resistant M. mercenaria at physiological and cellular scales, the underlying molecular mechanisms associated with host-pathogen interactions remain largely unknown. This study was carried out to explore the molecular changes in M. mercenaria in response to temperature and QPX infection on the transcriptomic level, and also to compare molecular responses between susceptible and resistant clam stocks. A M. mercenaria oligoarray (15K Agilent) platform was produced based on our previously generated transcriptomic data and was used to compare gene expression profiles in naive and QPX-infected susceptible (Florida stock) and resistant (Massachusetts) clams maintained at temperatures favoring disease development (13 °C) or clam healing (21 °C). In addition, transcriptomic changes reflecting focal (the site of infection, mantle) and systemic (circulating hemocytes) responses were also assessed using the oligoarray platform. Results revealed significant regulation of multiple biological pathways by temperature and QPX infection, mainly associated with immune recognition, microbial killing, protein synthesis, oxidative protection and metabolism. Alterations were widely systemic with most changes in gene expression revealed in hemocytes, highlighting the role of circulating hemocytes as the first line of defense against pathogenic stress. A large number of complement-related recognition molecules with fibrinogen or C1q domains were shown to be specially induced following QPX challenge, and the expression of these molecules was significantly higher in resistant clams as compared to susceptible ones. These highly variable immune proteins may be potent candidate molecular markers for future study of M. mercenaria resistance against QPX. Beyond the specific case of clam response to QPX, this study also provides insights into the primitive complement-like system in the hard clam.

overall_design: Three-condition interaction experiment (Temperature x clam/infection type x tissue type), 2 temperatures, 3 clam/infection types, 2 tissues, 3 biological replicates for each condition

first: Bassem

last: Allam


title: Genome-wide tissue gene expression profiling in Juvenile Göttingen Minipigs with customized Agilent microarrays

summary:
Minipigs have favorable biological characteristics for juvenile toxicity studies to assess efficacy and safety of pediatric drug products. To evaluate at the molecular level the expression of drug targets, drug metabolism pathways or general maturation of organ transcriptomes in minipigs, we used Customized Agilent Micoarrays (Design-ID 050244) for genome-wide gene expression profiling on 9 different tissues from male and female juvenile Göttingen minipigs aged 1 week to 24 months.
The gene expression results analyzed in this study are further described in Heckel T. et al. (2015) Functional analysis and transcriptional output of the Göttingen minipig genome. under submission

overall_design: Data of 72 different tissue samples from 9 tissues (cerebral cortex, hypothalamus, cerebellum, liver, kidney, spleen, bone marrow, testis, ovary) and 4 age groups in female (1 week, 4 weeks, 2 months, 4 months) and 5 age groups in male (1 week, 4 weeks, 2 months, 4 months, 2 years) Goettingen minipigs (Ellegaard) were measured. One tissue was measured in 8 technical replicates. The combination of data of female and male pigs could be seen as a kind of biological replicate for most genes.

first: Stephan

last: Ringshandl


title: Transcriptional response to diets varying in phosphor content in pigs (low-intake; medium intake; high-intake)

status: Public on Dec 30 2015

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: in vivo microarray study of transcriptional changes in porcine peripheral blood mononuclear cells (PBMCs) due to dietary intake of phosphor

overall_design: per dietary group 6-7 pigs were collected for expression profiling at 2 time points

first: Eduard

last: Muráni

first: Siriluck

last: Ponsuksili

first: Michael

last: Oster


title: Analysis of mRNA of leukocytes before and after exercise in 3 warmblood horses

city: Seoul

first: Hang Ah

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

summary:
Capacity of exercise and performance is the most valuable in the horses. They have been selected for strength, speed, and indurance trait.
Athletic pheno types are influenced markedly by environment, management, and training. However, it has long been accepted that there are underlying genetic factors. To determine altered mRNA expression in circulating leukocytes of horses induced by exercise. Healthy neutered male warmblood horses were subjected to indoor exercise (trotting with alternative cantering for 6o minutes). Peripheral blood was collected from the jugular vein before and after the exercise, and subsequently buffy coat leukocytes were isolated by centrifugation. Total RNAs was isolated. Cyanine 3-labeled cRNA (complementary RNA) was generated from Agilent’s Low RNA Input Linear Amplification kit with 500 ng total RNA. Labeled cRNA was applied microarray (Agilent technologies, 8x60K) using Agilent’s Gene Expression Hybridization Kit. The present study revealed a subset of mRNAs in equine peripheral blood leukocytes affected by exercise, providing background information for genes associated with exercise in warm-blood horses.

overall_design: Three healthy, gelding warmblood horses between 9 and 17 yr were selected. 6 samples were collected containing 3 samples before exercise and 3 samples after exercise

first: Hang

middle: A

first: Yongbaek


title: Beyond acid suppression: Novel therapeutic targets for gastro-esophageal reflux disease based on a murine model (whole blood)

summary: Background & Aims: Because the pathophysiology of GERD is not fully understood, presently used drug target only one or more of the known underlying mechanisms but are not fully effective in all patients. 1Identifying novel central targets may pave the way to develop more effective agents. Methods: A surgical model of sub-chronic reflux esophagitis was developed. Wistar rats were pretreated for 7days with omeprazole (standard proton pump inhibitor) or STW5 (herbal preparation of established efficacy in gastro-intestinal disorders). Treatment was continued for 10days after surgery, rats were sacrificed and esophagi excised. Histological, proteomic and transcriptomic methods were applied to identify reflux induced changes and treatment responses. Results: Protection against reflux induced inflammation was achieved by both test drugs. Both reduced macroscopic and microscopic lesions of the esophagi as well as most measured pro-inflammatory cytokines without significantly affecting NF-kB activity. Proteomic and transcriptomic analysis identified CINC1-3, MIP-1/3α, MIG, RANTES and IL-1β as highly relevant mediators in GERD. Other highly regulated genes were those of IL-6, CCL3, CCL7 and LOX-1. Many affected cyto-/chemokines were involved in the TREM-1 signaling pathway. The fatty acid receptor GPR84 was highly up-regulated in esophagitis but down-regulated by both drugs. This was confirmed by Western blot and immune-histochemical staining, showing for the first time expression of this receptor in esophageal tissue and its possible involvement in GERD. Conclusion: STW5 and omeprazole target a broad spectrum of molecules involved in immunological and inflammatory processes, of which IL-8 (CINC1-3), TREM-1 pathway and GPR84 are proposed to be most promising novel targets for the treatment of GERD.

overall_design: Refluxesophagitis was surgically induced. Wistar rats were pretreated for 7 days with omeprazole or STW5. Treatment was continued for 10days after surgery, rats were sacrificed and esophagi exiced. The study had 5 groups. Group 1: sham operated, Group 2: esophagitis group, untreated, Group3: esophagitis treated with STW5 0.5ml/kg. Group 4: esophagitis treated with STW5 2ml/kg. Group 5: esophagitis treated with Omeprazole (30mg/kg). 4 microarrays from esophageal tissue and blood from 4 animals of each group were performed.

first: Heba

last: Abdel-Aziz


title: Functional splicing network reveals extensive regulatory plasticity of the core  Spliceosomal machinery

first: Juan

last: Valcarcel

state: Barcelona

address: Dr Aiguader 88

department: Gene regulation stem cells and cancer

institute: CRG

summary: Pre-mRNA splicing relies on the still poorly understood dynamic interplay between  more than 150 protein components of the Spliceosome, and the steps at which splicing  can be regulated remain largely unknown. Here we systematically analyze the effect of  knocking down the components of the splicing machinery on alternative splicing events  relevant for cell proliferation and apoptosis and use this information to reconstruct a  network of functional interactions. The network accurately captures well-established  physical and functional associations and identifies new, revealing remarkable  regulatory potential of core spliceosomal components, related to the order and duration  of their recruitment during Spliceosome assembly. In contrast with standard models of  regulation at early events of splice site recognition, factors involved in catalytic  activation of the Spliceosome display regulatory properties. The network also sheds  light on the antagonism between hnRNP C and U2AF and on targets of anti-tumor  drugs, and can be widely used to identify mechanisms of splicing regulation.

overall_design: RNA from 3 biological replicates of 72 hours knockdowns of human IK or SMU1 and a control set were used. Changes between the control and knockdowns were measured based on using a splice-junction array (Affymetrix HJAY).

first: Panagiotis

last: Papasaikas

middle: R

last: Tejedor


title: mRNA expression profile of MCF7 cells with retroviral inducible expression of ΔNp63α [total RNA]

status: Public on Dec 28 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: MCF7 is a breast adenocarcinoma cell line which exhibits properties of differentiated luminal epithelial cells. ΔNp63α, an N-terminally truncated isoform of p51/p63 protein, plays a critical role in mammary gland development. Here, we inducibly express ΔNp63α in MCF7 cells and studied its role in stemness of breast cancer cells.

overall_design: Expression of ΔNp63α was induced in MCF7 cells with Doxycycline (Dox) for 48 hours. Total RNAs containing microRNAs were isolated. Microarray analysis was performed in Dox- (MCF7-PTO-ΔNp63α-Dox-) and Dox+ (MCF7-PTO-ΔNp63α-Dox+) samples.

first: Ruhul

last: Amin

first: Yuiko-Morita

last: Fujimura

first: Shuntaro

last: Ikawa


title: Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an heat shock

city: Evora

first: Marta

last: Laranjo

address: Apartado 94

department: ICAAM

country: Portugal

institute: Universidade de Evora

summary: Expression profiling of a total of 7281 transcripts was compared between control and heat shock conditions.

overall_design: In the present study, RNA was extracted from three independent cell cultures for each treatment (control and heat shock).

first: Ana

last: Alexandre

first: Solange

last: Oliveira


title: Mechanisms of phenanthrene toxicity in the soil invertebrate Enchytraeus crypticus

status: Public on Dec 18 2015

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

summary: Polycyclic Aromatic Hydrocarbons (PAHs) continue to cause environmental challenges due to their release in the environment by a great variety of anthropogenic activities and their accumulation in soil ecosystems. Here we studied the toxicological effect of the model PAH phenanthrene (Phe) on the soil invertebrate model Enchytraeus crypticus at the individual, tissue and molecular level. Organisms were exposed to Phe for 2 and 21 days to the (previously estimated) EC10 and EC50 (population reproduction over 3 weeks). Gene expression profiling did not reveal a typical Phe-induced biotransfor-mation signature, as it usually does in arthropods and vertebrates. Instead, we observed only general metabolic processes to be affected after 2 days of exposure, such as translation and ATP synthesis-coupled electron transport. Histological sections of tissues of 2-day exposed animals did not show any deviations from the control situation. In contrast, prolonged exposure up to 21 days showed histopathological effects: chloragogenous cells were highly vacuolated and hypertrophic. This was corroborated by differential expression of genes related to immune response and oxidative stress at the transcriptomic level. The data exemplify the complexity and species-specific features of PAH toxicity among soil invertebrate communities, which restricts read-across and extrapolation in the context of soil ecological risk assessment.

overall_design: The data presented in our manuscript is an exposure experiment where E. cryticus is exposed to phenanthrene EC10 and EC50 on reproduction for 2 and 21 days. A single channel, interwoven loop design was used to test animals. 4 biological replicates per condition were used containing 25 grams of soil and 5 - 7, adult old animals per replicate. The platform is a 4*180k Agilent platform containing some 86k E. crypticus probes in duplicate. However, only a subset of the probes (23k) was used for the analysis. To see which probes were used in the analysis see the raw data files control type column, only probes which are denoted with a 0 were used.

first: Dick

last: Roelofs

first: Rita

last: Bicho

last: Castro-Ferreira

middle: E

first: Kora

last: Montagne-Wajer

first: Cornelis

last: van Gestel

first: Nico

middle: M

last: van Straalen

first: Amadeu

last: Soares

first: Mónica

last: Amorim


title: Transcriptional Response to Ciprofloxacin in Enteropathogenic Escherichia coli Deng

status: Public on Dec 15 2015

city: Shenzhen

first: zhong

last: chen

address: No 89, Taoyuan Road, Nanshan district, Shenzhen 518052, China.

institute: the Affiliated Shenzhen Nanshan Hospital, Guangdong Medical College

summary: We employed a genome-wide microarray approach to obtain a profile of the transcriptional events in ciprofloxacin-treated EPEC shedding light on how ciprofloxacin affects EPEC transcriptional events and growth, aside from resistance mechanisms, and how this bacterium tolerates antibiotic stress.

overall_design: Sample of each culture immediately after the addition of ciprofloxacin  (t0), 45 min (t45), 90 min (t90), 135 min (t135), and 180 min (t180), ciprofloxacin induced gene expression in EPEC Deng strain were measure by microarray statistical analysis

first: Zhong

last: Chen

first: Zhijian

last: Yu

first: Qiwen

last: Deng


title: Expression profile of deletion strain of yeast Mitochondrial Transcription factor 1 (mtf1∆)

city: Bangalore

first: Malathi

last: Srinivasan

state: Karnataka

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

country: India

institute: Central Food Technological Research Institute

summary: Expression profile of mtf1∆ showed change in expression of many mitochondrial genes comapre to WT(BY4741)

overall_design: Organism : Saccharomyces cerevisiae , Custom Saccharomyces cerevisiae 8x15k Gene expresssion Microarray (AMADID: 016333) designed by Genotypic Technology Private Limited

first: Priya

last: Kumari

first: Ram

last: Rajasekharan


title: Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

type: Methylation profiling by genome tiling array

summary: The human liver contains multiple cell types whose epigenetic patterns are undetermined. We examined the promoter methylome of purified and uncultured hepatic stellate cells (HSCs), hepatocytes (HEPs) and liver sinusoidal endothelial cells (LSECs), by methylated DNA immunoprecipitation (MeDIP) and array hybridization. Uncultured HSCs, LSECs and Heps show ~7000-8000 methylated promoters, with 60-70% similarity between all cell types. GO analysis for commonly methylated genes reveals involvement in germ cell development, segregating germ-line from somatic lineage methylation. HSCs, LSECs and HEPs also contain ~500-1000 uniquely methylated promoters; these are implicated in signaling and biosynthetic processes (HSCs), lipid transport and metabolism (LSECs), and chromatin assembly (HEPs). The promoter methylome of culture-activated HSCs deviates from that of their uncultured (quiescent) counterparts. HSC culture-induced activation also enhances methylation differences between individual donors; however this does not necessarily relate to changes in gene expression. HSc activation results in a net gain of promoter DNA methylation, despite the demethylation and de novo methylation of thousands of promoters. Our data provide to our knowledge the first genome-wide maps of promoter DNA methylation in human purified and uncultured liver cell types. Although methylation profiles are largely similar between HSCs, LSECs and hepatocytes, the detection of cell type-specific methylation patterns suggests a differential epigenetic programming of these cell types in the liver.

overall_design: Determine the promoter DNA methylation pattern of 3 uncultured, reshly isolated, human healthy liver cell types (hepatocytes (HEPs), liver sinusoidal endothelial cells (LSECs) and haptic stellate cells (HSCs), and of HSCs after a 24-h culture-induced activation.

first: Anita

middle: L

last: Sørensen

first: Andrew

last: Reiner

first: Adil

last: El Taghdouini

first: Leo

last: van Grunsveen


title: Expression data from Amacr knock-out mouse liver and intestine

city: University of Oulu

first: Kaija

last: Autio

institute: University of Oulu


title: Gene expression of Listeria monocytogenes-infected HepG2  hepatocellular carcinoma in the presense of IL-17Aand IL-22

first: Satoshi

last: Kondo

summary: IL-17A and IL-22 induced several inflammation-induced genes and anti-microbial molecules including Pla2g2a and Lcn2 on HepG2 cells when the cells were treated with the cytokines before Listeria monocytogenes infection.

overall_design: HepG2 cells were treated with 50 ng/ml IL-17A and 10 ng/ml IL-22 before L. monocytogenes in vitro infection at MOI 10. Reference cells were not treated with the cytokines before the infection. Two independent experiments were carried out.

first: Masayuki

last: Umemura

first: Takeru

last: Shiono

first: Goro

last: Matsuzaki


title: Investigating pathogen defense mechanisms of porcine mammary epithelial cells in vitro.

first: Klaus

last: Wimmers

summary: Porcine mammary epithelial cell (PMEC) cultures of three lactating sows were treated with potential mastitis-causing pathogens E. coli and S. aureus in vitro. Subsequently transcriptome profiles were analysed after 3 h and 24 h post-challenge, respectively.

overall_design: per experimental group 3 PMEC cultures were sampled in triplicate for expression profiling.

first: Eduard

last: Murani

first: Alexandra

last: Jaeger

first: Michael

last: Oster

first: Danielo

last: Bardehle

first: Juliane

last: Günther

first: Siriluck

last: Ponsuksili

first: Nicole

last: Kemper


title: Effects of retene, an AhR agonistic PAH, on the transcriptome of the rainbow trout (Oncorhynchus mykiss) embryo heart

city: Jyväskylä

first: Eeva-Riikka

last: Vehniäinen

address: Survontie 9, POB 35

institute: University of Jyväskylä

summary: Retene is an aryl hydrocarbon receptor (AhR) activating PAH that causes dioxin-like developmental toxicity in fish embryos. The cardiovascular tissues seem to be the target tissues. To explore the effect of retene exposure on the hearts of developing rainbow trout embryos, a microarray study was conducted. The results serve as a basis for developing further hypothesis in the search for the candidate genes behind the physiological changes.  Expression of eight genes was quantified by qPCR, confirming the results of the microarray.

overall_design: Gene expression was measured in the hearts of rainbow trout embryos after 1, 3, 7 and 14 days of exposure to 0 and 32 µg/l retene. Samples were pooled from 15 or 45 hearts, and there were three biological replicates for each exposure at each time point.

first: Jason

last: Scott

first: Katharina

last: Bremer

first: Sini

last: Junttila

first: Asta

last: Laiho

first: Attila

last: Gyenesei

first: Peter

last: Hodson

first: Aimo

middle: O

last: Oikari


title: Probing the regulatory effects of specific mutations in three major binding domains of the pleiotropic regulator CcpA of Bacillus subtilis

city: Groningen

first: Ruud

last: Detert Oude Weme

state: Groningen

address: Nijenborgh 7

institute: University of Groningen

summary: Study the effect of single amino acid point mutations in CcpA at the transcriptome level. Cells were grown in LB with or without 1% glucose and harvested at an OD600 of 0.3 (early exponential phase).

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Bacillus subtilis strain ccpA::spec carrying pHT304 (empty plasmid), pWH_ccpA_M17R, pWH_ccpA_T62H, or pWH_ccpA_R304W were grown in LB with or without 1% glucose. The control in the microarray study was the strain Bacillus subtilis ccpA::spec carrying pWH_ccpA-wt. All Bacillus subtilis cultures were harvested in the early exponential growth phase at an OD600 of 0.3 from 100 ml culture. Two independent cultures of each strain per growth condition (+/- glucose) and a technical replicate (dye-swap) were used.
Please note that '[A}' and '{B}' channels (in the raw data *slide.txt files) correspond to Cy3 (Ch1) and Cy5 (Ch2) in each sample record.

first: Gerald

last: Seidel

first: Oscar

last: Kuipers


title: MicroRNA-29c is down-regulated in basal-like breast cancers and regulates invasion and chemosensitivity

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: While the basal-like subtype accounts for only a small subset of all breast cancer cases, it is associated with the worst prognosis. The majority of basal-like tumors are triple-negative (ER-, PR-, and HER2-negative), and thus lack molecular targets for therapy. To identify potential molecular markers and/or pathways that are critical to the basal-like tumor phenotype, we investigated the deregulation of microRNAs in primary breast tumors from an ethnically diverse cohort of patients.  Forty-four microRNAs were identified as down-regulated in basal-like tumors compared to luminal-A tumors. MicroRNA-29c (miR-29c) was the most significantly down-regulated microRNA.  In breast cancer cells in vitro, miR-29c was capable of regulating phenotypes associated with basal-like tumors such as cell invasion and drug sensitivity. Exogenous expression of miR-29c sensitizes UACC 3199 to doxorubicin-induced killing, while its inhibition leads to resistance to doxorubicin-induced killing. In addition, miR-29c decreases invasiveness of UACC-3199 cells, along with down-regulation of extracellular matrix (ECM) genes (LAMC1 and COL5A2) and ECM modifying enzyme LOXL2. In addition, miR-29c directly regulates B-MYB, an oncogene over expressed in basal-like tumors and co-expression of miR-29c and B-MYB abolishes UACC 3199 sensitivity to doxorubicin. Furthermore, our work demonstrates a regulatory role for the transcription factor GATA3 in miR-29c expression in breast cancer. Our findings support a role for miR-29c in basal-like breast tumorigenesis that is linked to drug resistance.

overall_design: reference VS sample

first: Huiping

last: Liu

first: Aleix

last: Prat


title: IRF4, a master transcription factor, regulates genes involved in BCR signaling, antigen processing and presentation, and GC development

city: New Haven

first: Yasuhiro

last: Nakayama

state: CT

address: 1 Gilbert St

department: Genetics

institute: Yale University

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Effect of floT and floA mutations on the global transcriptome of Bacillus subtilis NCIB3610

city: Jena

first: Akos

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary: To compare the altered transcript levels in the floT, floA single and floTfloA double mutants of Bacillus subtilis, cells were grown in MSgg medium until the late exponential phase and their transcriptome was compared to the wild type, NCIB3610 strain.

overall_design: Bacillus subtilis NCIB3610 wild type and its floT, floA, and floTfloA mutants strain were grown in MSgg medium and cells were harvested at late exponential (OD600 ~1.0-1,2) phase. 3 biological replicates were used, resulting 3 slides for each mutant strain. Dye swaps are included in both experiments.


title: Gene expression of FACC canine cancer cell line panel (Affymetrix Canine 2.0 array)

city: Fort Collins

first: Daniel

last: Gustafson

state: CO

address: 300 West Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Cancer cell line panels that incorporate genomic and pharmacologic screening data have become powerful tools for investigating the relationship between gene expression and drug response in human cancer research.  Similar cell line panels of such a scale as the NCI60, CCLE, or GDSC do not currently exist in canine cancer research.  Here we have assembled a canine cancer cell line panel of 29 cell lines representing multiple tumor types that have undergone gene expression profiling and have begun to be used for pharmacologic screening.

overall_design: RNA was extracted from drug naïve canine cancer cell lines and subjected to microarray analysis.

first: Jared

middle: S

last: Fowles


title: Upstream regulators of human T cell-associated diseases (dataset 4)

status: Public on Dec 12 2015

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

summary: Medical research focuses on disease-specific genes. By contrast, here we systematically examined the roles of shared genes for disease susceptibility and as therapeutic and diagnostic targets. Meta-analysis of all published disease-related genome-wide association studies (GWAS) showed that T helper (Th) cell differentiation was the most shared pathway. Expression profiling data from highly diverse CD4+ T cell-associated diseases revealed shared disease-associated genes, which were enriched for Th cell differentiation, but also metabolic and proliferative pathways. This pleiotropy suggested that altered functions of shared genes could generally increase disease susceptibility. Indeed, compared to specific genes, the shared genes were enriched for disease-associated SNPs identified by all published disease-related GWAS. To examine if the shared genes induced disease-relevant pathways, we focused on transcription factors (TFs) that induced Th differentiation. Those TFs were enriched among the shared genes, as well as for disease-associated SNPs identified by GWAS, and disease-phenotypes in mice knock-out studies. Original GWAS and profiling data from patients with multiple sclerosis and allergy confirmed enrichment of disease-associated SNPs in the TFs, and that the TFs were differentially expressed at early disease stages, and their targets increased in parallel with disease development. From a clinical perspective, the shared genes were significantly enriched for known diagnostic and therapeutic targets. Prospective clinical studies of multiple sclerosis and allergy showed that shared or specific genes could be used to stratify patients for individualized medicine. Our findings show that shared disease genes generally increase disease susceptibility and are important therapeutic and diagnostic targets.

overall_design: Peripheral blood mononuclear cells (PBMCs) from 10 patients with seasonal allergic rhinitis (SAR) and 10 healthy controls were challenged with diluent and allergen for 17 hours. Total CD4+ T cells were enriched for the gene expression microarray analysis.

first: Mika

last: Gustafsson

first: Måns

last: Edström

first: Fredrik

last: Barrenäs

first: Sören

last: Bruhn

first: Ingrid

last: Kockum

first: Tomas

last: Olsson

first: Colm

last: Nestor

first: Jan

last: Ernerudh

first: Mikael

last: Benson


title: Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Sphyracephala beccarii

status: Public on Dec 11 2015

city: New York

first: Richard

last: Baker

state: NY

address: 79th at Central Park West

department: Sackler Institute for Comparative Genomics

institute: American Museum of Natural History

summary: We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Sphyracephala beccarii. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

overall_design: Two-condition experiment, female vs. male DNA, for one species with 3 biological replicates

first: R

first: J

last: Reinhardt

first: G

last: Wilkinson


title: Analysis of Molecular Cytogenetic Alteration in Rhabdomyosarcoma by Array Comparative Genomic Hybridization

city: shihezi

first: chunxia

last: liu

address: 2nd North Road

department: Pathology

institute: Shihezi University School of Medicine

type: Genome variation profiling by genome tiling array

summary: The tumor-associated copy number variations and genes in rhabdomyosarcoma. Functional annotation clustering in rhabdomyosarcoma.

overall_design: 20 formalin-fixed, paraffin-embedded (FFPE) rhabdomyosarcoma tumors and two cell lines

first: Chunxia

last: Liu

first: Feng

last: Li


title: Beyond acid suppression: Novel therapeutic targets for gastro-esophageal reflux disease based on a murine model (esophageal tissue)

city: Bonn

first: Gudrun

last: Ulrich-Merzenich

address: Sigmund-Freudstr. 25

institute: University Clinic Centre UKB, Bonn University

summary: Background & Aims: Because the pathophysiology of GERD is not fully understood, presently used drug target only one or more of the known underlying mechanisms but are not fully effective in all patients. 1Identifying novel central targets may pave the way to develop more effective agents. Methods: A surgical model of sub-chronic reflux esophagitis was developed. Wistar rats were pretreated for 7days with omeprazole (standard proton pump inhibitor) or STW5 (herbal preparation of established efficacy in gastro-intestinal disorders). Treatment was continued for 10days after surgery, rats were sacrificed and esophagi excised. Histological, proteomic and transcriptomic methods were applied to identify reflux induced changes and treatment responses. Results: Protection against reflux induced inflammation was achieved by both test drugs. Both reduced macroscopic and microscopic lesions of the esophagi as well as most measured pro-inflammatory cytokines without significantly affecting NF-kB activity. Proteomic and transcriptomic analysis identified CINC1-3, MIP-1/3α, MIG, RANTES and IL-1β as highly relevant mediators in GERD. Other highly regulated genes were those of IL-6, CCL3, CCL7 and LOX-1. Many affected cyto-/chemokines were involved in the TREM-1 signaling pathway. The fatty acid receptor GPR84 was highly up-regulated in esophagitis but down-regulated by both drugs. This was confirmed by Western blot and immune-histochemical staining, showing for the first time expression of this receptor in esophageal tissue and its possible involvement in GERD. Conclusion: STW5 and omeprazole target a broad spectrum of molecules involved in immunological and inflammatory processes, of which IL-8 (CINC1-3), TREM-1 pathway and GPR84 are proposed to be most promising novel targets for the treatment of GERD.

overall_design: Refluxesophagitis was surgically induced. Wistar rats were pretreated for 7 days with omeprazole or STW5. Treatment was continued for 10days after surgery, rats were sacrificed and esophagi exiced. The study had 5 groups. Group 1: sham operated, Group 2: esophagitis group, untreated, Group3: esophagitis treated with STW5 0.5ml/kg. Group 4: esophagitis treated with STW5 2ml/kg. Group 5: esophagitis treated with Omeprazole (30mg/kg). 4 microarrays from esophageal tissue and blood from 4 animals of each group were performed.

first: Heba

last: Abdel-Aziz


title: IRF4, a master transcription factor, regulates genes involved in BCR signaling, antigen processing and presentation, and GC development [ChIP-chip]

first: Yasuhiro

last: Nakayama

summary: Interferon regulatory factor 4 (IRF4) is a master transcription factor required for the maturation of germinal center B cells that eventually develop into antibody secreting plasma cells and memory B cells. IRF4-deficient mice exhibit a profound reduction in serum immunoglobulin levels.  In spite of wealth of the information relating to IRF4 and B cell biology, little is known about the intricate molecular details of the role of this transcription factor during B cell development. We therefore examined the genome-wide targets of IRF4 by ChIP-chip analysis in GC derived BL2 Burkitt’s lymphoma cells.  ChIP studies were further supplemented by whole genome expression analysis after shRNA-mediated knockdown of IRF4. Our study revealed that IRF4 regulates expression of genes important for a) BCR signaling b) antigen processing and presentation by MHC. In addition we found that IRF4 possibly in some way involved to regulate LTA, LTB and CXCR5 those involved in immune system development, particularly light zone development related genes such as FDC clustering regulating and IL21R and IL10 who are involved in B cell development.. On the other hand, IRF4 suppressesd genes in the oxidative phosphorylation pathway. Our findings illuminate hitherto unexplored roles of IRF4 in GC B cell development.

overall_design: ChIP-chip was performed following the protocols described before [Lian Z, et al.,Genome Res. 18: 1224, 2008] with slight modifications. Briefly, 3X10^8 BL2 cells were cross-linked in 1% formaldehyde for 10 mins at room temperature and then the cells were lysed in RIPA buffer(0.1% SDS) containing protease inhibitors(Roche Inc) . Cell suspensions were sonicated under ice-cold conditions using a Branson 250 Sonifier (Branson, Danbury, CT) with a power setting 60%, fifteen 30-sec pulses on ice to shear the chromatin to a size of approximately 300-500b. Anti-IRF4 antibody (sc6059 Santa Cruz Biotechnology, Santa Cruz, CA) or normal pre-immune mouse serum IgG as a control were added to the suspensions. The suspension was incubated at 4C rotating overnight to allow the antibodies to bind to DNA fragments. Protein G beads were added next day and incubated at 4C with gentle agitation for 1 hr.  The antibody–DNA complexes were eluted from the beads by 1% SDS in TE incubated at 65°C. The beads were sedemented by centrifugation, and the supernatants were incubated overnight at 65°C to reverse the cross-linking in the chromatin-protein complex. RNA contamination was eliminated by incubating the samples with 200 mg of Rnase for 1 hour at 37°C. Finally, proteinase K (400 μg of proteinase K/mL, 1X TE) was added, and the samples were incubated for 2 h at 45°C, followed by a phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation to recover the DNA. Immunoprecipitated DNA was analyzed by PCR for the enriched factor binding at target sequences. In some cases we did LM-PCR, about 20-100ng of the ChIP-DNA was blunt-ended by T4 DNA polymerase (New England Biolabs, Boston MA), then ligated with pre-annealed oligonucleotide linkers (oligo-1: GCGGTGACCCGGGAGATCTGAATTC, oligo-2: GAATTCAGATC) using T4 DNA ligase (New England Biolabs) at 16°C overnight.  The ligated DNA was further amplified by PCR with oligo-1 as a PCR primer, followed by purification using the Qiaquick PCR purification kit (Qiagen).   We used Nimblegen high density promoter arrays based on human genome HG17 (Nimblegen System INC. Reykjavik Iceland).Taq Mastermix (QIAGEN) was used for PCR amplification under the following reaction conditions: 5 min at 94°C, 30 cycles of 30 sec at 94°C, 30 sec at 53°C, 30 sec at 72°C, and 10 min at 72°C. PCR products were analyzed by gel electrophoresis.  DNA samples to be hybridized to microarrays were labeled by random priming with nonamer oligonucleotides attached to Cy3 or Cy5 dyes. Control samples for the chromatin immunoprecipitation experiments were total genomic DNA prepared from chromatin cross-linked and precipitated by the same procedure as the test sample but with non-specific IgG.. Test samples were labeled with Cy5 and applied to the same chip as the Cy3-labeled control sample.   ChIP DNA samples were randomly primed with Cy3 and Cy5 random nonomers or septamers and the labeled fragments were hybridized to the promoter arrays. Data analysis was carried out by Tilescope [Lian Z, et al.,Genome Res. 18: 1224, 2008] and Integrated Genome Browser (IGB). Nimblegen ChIP-chip data were processed by automated Tilescope analysis [Zhang ZD, et al., Genome Biol. 8: R81, 2007].  The program normalizes Cy3 and Cy5 files of the tiling array results and identifies regions with statistically significant binding enrichment.  Visualization and further analysis of the data were carried out using the IGB program (http://www.affymetrix.com/partners_programs/programs/developer/tools/download_igb.affx) and Database for Annotation, Visualization and Integrated Discovery (http://david.abcc.ncifcrf.gov/summary.jsp).

first: Subhradip

last: Karmakar

first: Vincent

last: Schulz

first: Brian

last: Reed

first: David

last: Tuck

first: Milind

last: Mahajan

first: Michael

last: Snyder

first: Sherman

last: Weissman

first: Yujiro

last: Tanaka


title: Snf5F/Fp53L/LGFAP-Cre tumors and human AT/RT show similar gene expression signatures

city: Philadelphia

first: Jessica

middle: Mei Y.

last: Ng

state: PA

address: Colket Translational Research Bldg (Rm 4059) 3501 Civic Center Blvd

department: Pathology and Laboratory Medicine

institute: The Children's Hopsital of Philadelphia

summary: Human medulloblastoma (MB) can be segregated into four major categories based on gene expression patterns: Hedgehog (HH) subtype, Wnt subtype, Group 3, and Group 4. However, they all exhibit strikingly different gene expression profiles from Atypical Teratoid/Rhabdoid Tumor (AT/RT). We re-analyzed published gene expression microarray dataset of pediatric brain tumors to identify a gene expression profile that clearly distinguished human AT/RT from human MB. We used this profile, choosing only genes that have clear murine orthologs, to compare tumors from Snf5F/Fp53L/LGFAP-Cre mice (in C57Bl/6 strain background) with MB from Ptc1+/- mice (in mixed C57Bl/6 and 129Sv strain background). Snf5F/Fp53L/LGFAP-Cre tumors are clearly very different from mouse MB and the markers that distinguish human AT/RT from human MB also distinguish the mouse tumors.

overall_design: RNA extracted from 5 AT/RT and 5 medulloblastoma mouse tumors were analyzed using the Affymetrix Mouse Genome 430 2.0 microarray platform.

first: Zhe

last: Zhang

first: Eric

last: Rappaport

first: Tom

last: Curran


title: Expression analysis of Acacia koa in response to mechanical stimuli

status: Public on Dec 14 2015

city: Honolulu

first: Kazue

last: Ishihara

state: HI

address: 1955 East-West Rd AgSci 218

department: Molecular Biosciences and Bioengineering

institute: University of Hawaii at Manoa

summary:
The genes induced by mechanical stimuli may be also involved in disease resistance and wood formation and development in Acacia koa.  If so, mechanically stressed A. koa may be used as a model to study disease resistance and wood formation and development.
Microarray analysis was performed to determine expression levels of 4,000 genes related to disease resistance and wood development in Acacia koa in response to mechanical stimuli (touch).

overall_design: RNA was extracted from two groups of A. koa seedlings, (1) mechanically stressed and (2) unstressed koa seedlings. Each group had two biological replicates (n=2), where n represents pools of approcimately 20 individuals.

first: Dulal

last: Borthakur


title: Expression profile analysis of macrosclereid cell development in Medicago truncatula

city: West Lafayette

first: Fuyou

last: Fu

state: INDIANA

address: 915 W. State Street

institute: Fuyou Fu

summary:
Macrosclereid cells, which form a layer in the seed coat of Medicago truncatula, accumulate large amounts of phytochemicals during their development.
To characterize these phytochemicals and provide a broad analysis of gene expression in developing M. truncatula macrosclereid cells, we produced microarrays that displayed approximately 4861 differentially expressed probe sets (absolute fold-change of ≥3.0; LogRatio p-value of ≤0.001) between at least two time points in macrosclereid cell development, inculding 6DPP, 10DPP, 13DPP, 16DPP, 20DPP, 27DPP.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Randomly selected flowers were tagged (using small different colored tags with different colored strings) on the day after pollination. Whole pods were collected at various days post pollination (DPP; from 6 to 27 DPP).

first: Hongli

last: Wang


title: Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae)

first: Richard

last: Baker

sample_organism:
Teleopsis quinqueguttata
Sphyracephala beccarii


title: Cdk5 regulates activity-dependent gene expression and dendrite development [cultured cortical neurons]

city: Hong Kong

first: Nancy

middle: Y.

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

summary: To investigate the molecular mechanism underlying activity-dependent dendrite development regulated by Cdk5, an unbiased microarray analysis was performed to identify activity-dependent genes differentially regulated in cortical neurons from E18 Cdk5-knockout embryos.

overall_design: Cortical neurons were cultured from E18 Cdk5-knockout embryos and littermates. RNA was extracted and analyzed at 5 days in vitro (DIV) by the GeneChip® WT PLUS Reagent Kit (WT PLUS Kit, Affymetrix) according to the manufacturer’s instructions.

first: Zhuoyi

last: Liang

first: Tao

last: Ye

first: Xiaopu

last: Zhou

first: Kwok-On

last: Lai

first: Amy

middle: Y


title: IRF4, a master transcription factor, regulates genes involved in BCR signaling, antigen processing and presentation, and GC development [expression array]

first: Yasuhiro

last: Nakayama

overall_design: BL2 Burkitt's lymphoma-derived B cells  were infected with lentivirus expressing shRNA for IRF4 or control, and total RNA was subjected to Illumina BeadsExpression Arrays analysis.

first: Subhradip

last: Karmakar

first: Vincent

last: Schulz

first: Brian

last: Reed

first: David

last: Tuck

first: Milind

middle: C

last: Mahajan

first: Michael

last: Snyder

first: Sherman


title: Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Teleopsis quinqueguttata

summary: We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

first: R

first: J

last: Reinhardt

first: G

last: Wilkinson


title: Elevated MTSS1 mRNA Expression Is Associated with Metastasis and Poor Prognosis of Residual Hepatitis B-related Hepatocellular Carcinoma

city: shanghai

first: xin

last: ge

address: xietu road

institute: xybiotech

summary: Hepatectomy generally offers the best chance of long-term survival for patients with hepatocellular carcinoma (HCC). Many studies have shown that hepatectomy accelerates tumor metastasis, but the mechanism remains unclear. In this study, palliative hepatectomy was performed in an orthotopic nude mice model of HCC (MHCC97H) with high metastatic potential. Using Human Tumor Metastasis Microarray, we screened the metastasis-related genes in tumor tissues following palliative resection, and found that Metastasis suppressor 1 (MTSS1) located in the central position of gene function net of residual HCC; MTSS1 was up-regulated in residual tumor after palliative resection. Further studies found that MTSS1 enhanced the metastasis of residual HCC. In hepatitis B-related HCC patients undergone palliative hepatectomy, those with higher MTSS1 mRNA expression accompanied by the activation of matrix metalloproteinase 2 (MMP2) in residual HCC, had earlier residual HCC detection after hepatectomy and poorer survival when compared to those with lower MTSS1 level. In different cell lines, the levels of MTSS1 mRNA increased in parallel with metastatic potential. MTSS1 down regulation via siRNA decreased MMP2 activity, reduced invasive potentials of HCC by 28.9% in vitro, and averted the deteriorated lung metastatic extent in vivo. In conclusion, the poor prognosis of hepatitis B-related HCC patients following palliative hepatectomy associates with elevated MTSS1 mRNA expression; therefore, MTSS1 may provide a new research field for HCC diagnosis and treatment.

overall_design: Eighteen nude mice bearing HCC xenografts were randomized into three groups 14 days after orthotopic implantation: palliative resection group (mice received partial HCC resection with preservation of 2 mm tumor pedicles), sham operation group (mice only undergone an exposure of liver but without resection), and blank control group (mice without further surgical intervention). All mice were sacrificed by cervical dislocation 14 days following palliative resection based on pre-experimental results. The first time surgically removed HCC tissues were named tumor tissues T1;  the second time surgically removed HCC tissues from sham operation group were named tumor tissues T2; Tissues from blank control group were named tumor tissues T3; Tissues from palliative resection group were named tumor tissues T4 that was residual HCC. Randomly selected 5 tumor specimens from each group were used for the screen of genes related to metastasis by microarray techniques.

first: Xiu-yan

last: Huang


title: Identification of potassium and chloride channels in eccrine sweat glands

status: Public on Dec 09 2015

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: K and Cl channels play critical role for sweat secretion, however, individual K or Cl channels and their functions are largely unknown. By comparing expreession profilings between wild-type and Eda mutant Tabby footpads we identified 4 K and 2 Cl channels highly expressed in mouse eccrine sweat glands.

overall_design: Total RNAs isolated from microdissected wild-type and Tabby footpads were profiled with Agilent 44K NIA mouse microarrays.

first: Makoto

last: Kunisada

first: Changyi

last: Cui


title: ECSTASY (MDMA) ALTERS CARDIAC GENE EXPRESSION AND DNA METHYLATION: IMPLICATIONS FOR CIRCADIAN RHYTHM DYSFUNCTION IN THE HEART (methylation)

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

institute: Emory University

summary:
MDMA (ecstasy) is an illicit drug that stimulates monoamine neurotransmitter release and inhibits reuptake.  MDMA’s acute cardiotoxicity includes tachycardia and arrhythmia which are associated with cardiomyopathy (CM). MDMA acute cardiotoxicity has been explored, but neither long-term MDMA cardiac pathological changes nor epigenetic changes have been evaluated.  Microarray analyses were employed to identify cardiac gene expression changes and epigenetic DNA methylation changes. To identify permanent MDMA-induced pathogenetic changes, mice received daily 10d or 35d MDMA , or daily 10d MDMA followed by 25d saline washout (10+25d).  MDMA treatment (10d) caused differentially gene expression (p<0.05, fold change >1.5), with 752 genes 558 genes following 35d MDMA, and 113 genes following 10d treatment +25d washout.  Changes in MAPK and circadian rhythm gene expression were identified following 10d administration.  After 35d, circadian rhythm genes (Per3, CLOCK, ARNTL, and NPAS2) remained differentially expressed.  MDMA caused DNA hypermethylation and hypomethylation that was independent of gene expression; hypermethylation of genes was 71% at 10d, 68% at 35d, and 91% at 10+25d.  Differential gene expression that corresponded directly with DNA methylation changes occurred in 22% of genes at 10d, 17% at 35d, and 48% at 10d+25d washout.  MDMA treatment resulted in epigenetic changes in cardiac DNA methylation. Hypermethylation was the predominant effect.  MDMA induced gene expression of key elements of circadian rhythm regulatory genes and suggest a fundamental mechanism for MDMA dysfunction in the heart.
This study addresses how MDMA (ecstasy) affects cardiac (left ventricle) gene expression and epigenetic nuclear DNA methylation.

overall_design: Each sample was fluorescently labeled and hybridized to Roche Nimblegen 2.1M Deluxe Promoter Arrays.

first: Christopher

last: Koczor


title: Molecular characterization of chronic antibody mediated rejection in kidney transplantation (microRNA)

status: Public on Dec 10 2015

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

summary:
Chronic antibody-mediated rejection (CAMR) represents the main cause of kidney graft loss, but its pathogenesis is unclear. In order to uncover the molecular mechanisms underlying this condition, we characterized the molecular signature of circulating peripheral blood mononuclear cells and, separately, of CD4+ T lymphocytes isolated from CAMR patients compared to kidney transplant recipients with normal graft function and histology.
In total peripheral lympho-monocytes, forty-five genes resulted differentially expressed between the two groups, most of them were up-regulated in CAMR and were involved in type I interferon signaling. In addition, in the same set of patients, 16 microRNAs resulted down-regulated in CAMR subjects compared to controls: 4 were predicted modulators of 6 mRNAs identified in the transcriptional analysis. In silico functional analysis supported the involvement of type I interferon signaling. To further confirm this hypothesis, we investigated the transcriptomic profiles of CD4+ T lymphocytes in an independent group of patients and we observed that the activation of type I interferon signaling was a specific hallmark of CAMR. In addition, in CAMR patients we detected a reduction of circulating BDCA2+ dendritic cells, the natural type I interferon- producing cells and their recruitment into the graft along with an increased expression of MXA, a type I interferon-induced protein, at tubulointerstitial and vascular level.
In conclusion, our data suggest that type I interferon signaling may represent the molecular signature of CAMR.

overall_design: For microarray analysis, we studied 5 patients included into the control-group and 4 included into the study group. The control group was represented by renal transplant recipients undergoing protocol graft biopsies, with normal renal function and histology, in the absence of circulating anti-HLA antibodies. Study group patients showed clinical and histological evidence of CAMR according to Banff 2011 criteria.

first: Federica

last: Rascio

first: Matteo

last: Accetturo

first: Annarita

last: Oranger

first: Margherita

last: Gigante

first: Giuseppe

last: Castellano

first: Maddalena

first: Anna

last: Zito

first: Gianluigi

last: Zaza

first: Antonio

last: Lupo

first: Elena

last: Ranieri

first: Giovanni

last: Stallone

first: Loreto

last: Gesualdo

last: Grandaliano


title: Expression data from primary isolated colonic epithelial cells from ChopIEC Tg/Tg mice and Chopflox/flox mice as wild-type controls

city: Freising

first: Nadine

last: Waldschmitt

address: Gregor-Mendel Str. 2

institute: Technische Universität München

summary: BACKGROUND AND AIMS: Loss of epithelial cell homeostasis and apoptosis highly con-tribute to intestinal inflammation. While endoplasmic reticulum unfolded protein response (UPR) has been implicated in chronic intestinal inflammation, functional correlation between UPR-related C/EBP homologous protein (CHOP) expression and CHOP-mediated programming towards inflammation-related disease susceptibility remains unclear. In this study, we generated the new mouse model ChopIEC Tg/Tg to investigate consequences of intestinal epithelial cell (IEC)-specific CHOP overexpression. Transcriptional profiling of transgenic mice identified a set of CHOP-dependent target genes related to inflammatory and microbial defense program in the intestinal epithelium.

overall_design:
Effect of CHOP overexpression in intestial epithelial cells was investigated on epithelial homeostasis using transgenic mice
Disease-free mice do not show enhanced apoptotic signaling
Intestinal epithelial cells were isolated from 12 week old females

first: Dirk

last: Haller

first: Michael

last: Müller


title: Dynamic interplay between the transcriptome and methylome in response to oxidative and alkylating stress

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

institute: Maastricht University

summary: Methyl radicals are not able to form 5'methylcytosine directly. However, tert-butylhydroperoxide-induced responses in the transcriptome are partly regulated by the methylome to restore normal cellular function

overall_design: Cells were exposed to tert-butylhydroperoxide (TBH, Sigma) at a concentrations of 200 µM for 1, 8 and 24 hours


title: Identification of a genomic signature in BRCA1-mutated triple negative breast cancer by Comparative Genomic Hybridization

city: GOSSELIES

first: SEBASTIEN

last: TOFFOLI

address: AVENUE GEORGES LEMAITRE 25

country: Belgium

institute: IPG

summary: Determination of recurrent chromosomal aberrations in Luninal A, Luminal B, HER2-positve, and triple negative breast cancers

overall_design: 131 samples, Tumour DNA vs Normal DNA

first: Sébastien

last: Toffoli

first: Isabelle

last: Bar

first: Fadi

last: Abdulsater

first: Paul

last: Delrée

first: Jean-Luc

last: Canon


title: MntR(Rv2788): a transcriptional regulator that controls manganese homeostasis in Mycobacterium tuberculosis.

status: Public on Dec 08 2015

city: Newark

first: G

middle: Marcela

last: Rodriguez

state: NJ

address: 225 Warren St

department: Public Health Research Institute

institute: Rutgers University

summary: Transcriptional profiling of SirR and manganese regulated expression of genes in Mycobacterium tuberculosis strains comparing high manganese vs. low manganese in Rv (wild type Mycobacterium tuberculosis) and ST70 (mntR mutant strain of Mycobacterium tuberculosis)

overall_design: Two strains each with two conditions experiment, Rv (Mycobacterium tuberculosis wild type strain) high manganese vs. low manganese and ST70 (mntR mutant strain of Mycobacterium tuberculosis) high manganese vs. low manganese.  Number of biological replicates is 3 for each condition for each strain.

first: Marcela

first: Ruchi

last: Pandey


title: Expression data from Day 15 bovine conceptuses

city: Raleigh

first: Callie

middle: Virginia

last: Barnwell

address: North Carolina State University

department: Animal Science

institute: North Carolina State University

summary:
The majority of pregnancy loss in cattle occurs between days 8 and 16 of gestation coincident with the initiation of conceptus elongation and the onset of maternal recognition of pregnancy. Differences in conceptus lengths on the same day of gestation may be related to an inherent lack of developmental competency or may simply be a consequence of asynchrony with the maternal environment. The primary objective of this work was to characterize differential patterns of mRNA expression between short and long bovine conceptuses recovered on Day 15 of gestation.
Embryo selection is an important factor that contributes to pregnancy success following transfer of embryos produced in vivo or in vitro. Morphological evaluation of embryos for stage of development and quality grade is the most widely used method for predicting embryo viability in cattle. Multiple studies have demonstrated that there are significant differences in pregnancy rates across different morphological grades. However, morphological evaluation is not always the best predictor of pregnancy success. Therefore, it is of interest to develop an objective and highly predictive method of pre-transfer embryo screening. A secondary objective of this experiment was to characterize differential patterns of mRNA expression between Day 15 bovine conceptuses derived from Grade 1 (excellent)  and Grade 3 (poor) embryos.

overall_design: In Experiment 1, gene expression was compared between Day 15 conceptuses derived from the transfer of Grade 1 (n=4) versus Grade 3 (n=3) embryos. In Experiment 2, gene expression was compared between Grade 1-derived Day 15 conceptuses classified as either short (n=5) or long (n=5) in length.

middle: V

first: Peter

middle: W

last: Farin

first: Christopher

last: Ashwell

first: William

last: Farmer

first: Samuel

last: Galphin

first: Charlotte


title: MELK-T1, a small molecule inhibitor of protein kinase MELK, decreases DNA damage tolerance in highly proliferating cancer cells

city: Beerse

first: Steven

last: Osselaer

address: Turnhoutseweg 30

institute: Janssen Pharmaceutica NV

summary:
Maternal Embryonic Leucine Zipper Kinase (MELK), a Ser/Thr protein kinase, is highly over expressed in stem and cancer cells. The oncogenic role of MELK is attributed to its capacity to disable critical cell cycle checkpoints and to enhance replication. Most functional studies have relied on the use of siRNA/shRNA-mediated gene silencing, but this is often compromised by off target effects. Here we present the cellular validation of a novel, potent and selective small molecule MELK inhibitor, MELK-T1, which has enabled us to explore the biological function of MELK.  Strikingly, the binding of MELK-T1 to endogenous MELK triggers a rapid and proteasome dependent degradation of the MELK protein. Treatment of MCF-7 breast adenocarcinoma cells with MELK-T1 leads to an accumulation of stalled replication forks and double strand breaks, followed by a replicative senescence phenotype. This phenotype correlates with a rapid and long-lasting ATM activation and phosphorylation of CHK2. Furthermore, MELK-T1 induces strong phosphorylation of p53 and prolonged up-regulation of p21.
Our data generated with MELK-T1 indicate that MELK is a key stimulator of proliferation by its ability to increase the threshold for DNA damage tolerance. Thus, targeting MELK by combined inhibition of its catalytic function and inhibitor-induced degradation might sensitize tumors to DNA-damaging agents or radiation therapy, by lowering the DNA damage threshold.

overall_design: This study includes 18 samples. There are 4 treatments considered, each with at least three biological replicates.

first: Lijs

last: Beke

first: Joannes

middle: T

last: Linders

first: Cenk

last: Kig

first: An

last: Boeckx

first: Erika

last: van Heerde

first: Marc

last: Parade

last: De Bondt

first: Ilse

last: Van den Wyngaert

first: Tarig

last: Bashir

first: Souichi

last: Ogata

first: Lieven

last: Meerpoel

middle: N

last: Johnson

first: Monique

last: Beullens

first: Mathieu

last: Bollen

first: Dirk

last: Brehmer


title: Expression data from lung tissues of minipig with left lung ischemia-reperfusion

status: Public on Dec 07 2015

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

summary:
Lung ischemia-reperfusion (I/R) injury remains one of the common complications after various cardiopulmonary surgeries. I-R injury represents one potentially maladaptive response of the innate immune system which is featured by an exacerbated sterile inflammatory response triggered by tissue damage.
Thus, understanding the key components and processes involved in sterile inflammation during lung I-R injury is critical to alter care and extend survival for patients with acute lung injury.

overall_design: We constructed a minipig surgical model of transient unilateral left pulmonary artery occlusion without bronchial involvement to create ventilated lung I-R injury. Lung tissues from minipig with sham operation (one sample), left side lung tissues (the operated side)(one sample) and right side lung tissues (the non-operated side)(one sample) from minipig with lung ischemia-reperfusion were submitted for gene expression array analysis.

first: Hao

last: Cao

first: Zhongmin

last: Liu

first: Huimin

last: Fan


title: DNA methylation profiles across different brain regions in APP/PSEN1 mice

status: Public on Dec 05 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: Genome wide DNA methylation profiling of normal and APP/PSEN1 mice.  A custom Illumina Golden Gate DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 800 CpGs.

overall_design: Bisulphite converted DNA from the 96 samples were hybridised to the Illumina custom golden gate DNA methylation array.

first: Jose

last: Sanchez-Mut


title: Identification of Copy Number Variants in Patients with Hypoplastic Left Heart Syndrome and Other Congenital Heart Defects

city: Aurora

first: Mark

last: Geraci

address: Mail Stop C272, 12700 E 19th Ave

department: Division of Pulmonary Sciences and Critical Care Medicine

institute: University of Colorado Anschutz Medical Campus

summary: Hypoplastic left heart syndrome (HLHS) is a heterogeneous, lethal combination of congenital malformations that result in a heart unable to sustain systemic circulation. The genetic determinants of this disorder are largely unknown. Evidence of copy number variants (CNVs) contributing to the genetic etiology of HLHS and other congenital heart defects (CHDs) has been mounting. However, the functional effects of such CNVs have not been examined, particularly in cases where the variant of interest is found in only a single patient. Initially whole-genome SNP microarrays were employed to detect CNVs in two patient cohorts (N = 70 total) predominantly diagnosed with some form of nonsyndromic HLHS. We discovered 16 rare variants adjacent to or overlapping 20 genes associated with cardiovascular or premature lethality phenotypes in mouse knockout models. Fifteen of the 16 variants were identified in separate patients, suggestive of a private mutation model of disease. We evaluated the impact of selected variants on the expression of nine of these genes through quantitative PCR on cDNA derived from patient heart tissue. Four genes displayed significantly altered expression in patients with an overlapping or proximal CNV verses patients without such CNVs. Thus, rare and private genomic imbalances perturb transcription of genes affecting cardiogenesis in a subset of nonsyndromic HLHS patients. Some of these genes influence extracellular matrix structure, cardiac neural crest development, and coronary vascularization.

overall_design: A total of 70 samples from CHD patients, mostly with nonsyndromic HLHS, yielded SNP genotypes and probe intensity ratios of sufficient quality for CNV identification. Two classes of CNV detection algorithms (HMM and CBS) were employed. After identification, concordant entries were subjected to selection criteria based on rarity and gene content, which produced putative candidate genes for follow-up experiments.

first: Steven

last: Glidewell


title: ECSTASY (MDMA) ALTERS CARDIAC GENE EXPRESSION AND DNA METHYLATION: IMPLICATIONS FOR CIRCADIAN RHYTHM DYSFUNCTION IN THE HEART (expression)

first: William

last: Lewis

overall_design: Each sample was fluorescently labeled and hybridized to Roche Nimblegen 12X135kb MM9 Gene Expression Arrays.

first: Christopher

middle: A

last: Koczor


title: Cpeb4-mediated Translational Regulatory Circuitry Controls Terminal Erythroid Differentiation

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary:
Erythropoiesis is essential to mammals and is regulated at multiple steps by both extracellular and intracellular factors. Many transcriptional regulatory networks in erythroid differentiation have been well characterized. However, our understanding of post-transcriptional regulatory circuitries in this developmental process is still limited. Using genomic approaches, we identified a sequence-specific RNA-binding protein, Cpeb4, which is dramatically induced in terminal erythroid differentiation (TED) by two erythroid important transcription factors, Gata1/Tal1. Cpeb4 belongs to the cytoplasmic polyadenylation element binding (CPEB) protein family that regulates translation of target mRNAs in early embryonic development, neuronal synapse, and cancer. Using primary mouse fetal liver erythroblasts, we found that Cpeb4 is required for terminal erythropoiesis by repressing the translation of a set of mRNAs highly expressed in progenitor cells. This translational repression occurs by the interaction with a general translational initiation factor, eIF3. Interestingly, Cpeb4 also binds its own mRNA and represses its translation, thus forming a negative regulatory circuitry to limit Cpeb4 protein level. This mechanism ensures that the translation repressor, Cpeb4, does not interfere with the translation of other mRNAs in differentiating erythroblasts. Our study characterized a translational regulatorycircuitry that controls TED and revealed that Cpeb4 is required for somatic cell differentiation.
We used microarray to identify mRNAs associated with Cpeb4 in mouse fetal liver erythroblasts.

overall_design: Cpeb4 associated mRNAs were isolated from mouse fetal liver erythroblasts using anti-Cpeb4 antibody for immunoprecipitation followed by RNA extraction. Then Affymetrix microarrays were used to identify and quantify the mRNAs associated with Cpeb4.

first: Bingbing

last: Yuan


title: miRNAs Expression of Mexican Patients with Breast Cancer

status: Public on Dec 04 2015

city: Monterrey

first: Hugo

last: Gomez

state: Nuevo Leon

address: Garza Sada

department: Bioinformatics

country: Mexico

institute: ITESM

summary:
miRNAs expression of tumor sample of mexican patients with breast cancer.
Samples obtained from the Hospital San Jose Tec de Monterrey.

overall_design: The experiments were with one color per patient, miRNAs expression profile is from a tumor sample of mexican patients with breast cancer.

first: Victor

last: Trevino


title: Differentially expressed human and viral miRNAs across a panel of B-cell lines, including primary effusion lymphomas

city: London

first: Dan

last: Frampton

address: Gower Street

department: Infection

country: United Kingdom

institute: UCL

summary:
To identify differentially expressed human and viral miRNAs across a panel of B-cell lines, including several primary effusion lymphomas (PEL).
Gammaherpesvirus and host cell microRNAs (miRNAs) together modulate gene expression in normal and malignant cells. Using microRNA microarrays, we determined the expression of mature viral and host cellular miRNAs in a series of B cell tumours that include Kaposi’s Sarcoma-associated herpesvirus (KSHV) infected Primary Effusion Lymphoma (PEL) and Epstein-Barr virus (EBV) infected Burkitt’s lymphoma (BL) cell lines. We show that 35 host miRNAs were constitutively expressed in all the B cell lymphomas and differences in viral miRNA expression were evident between herpesvirus positive tumour types. Furthermore, we show that in PEL, miR-221 and miR-222 expression is defective due to a lack of transcript expression rather than mutation in the miRNA encoding loci. Absence of miR-221 and miR-222 resulted in the enhanced expression of the known target gene p27 (CDKN1B) and reintroduction of miR221 in PEL reduces p27 protein expression.

overall_design: miRNA expression profiling of a panel of 25 B-cell line samples.

first: Eve

last: Coulter

first: Amy

last: Buck

first: Paul

last: Kellam


title: MicroRNA expression data from lung tissue of Idiopathic Pulmonary Fibrosis

city: Beijing

first: Shuhong

last: Li

address: No.8 GongTiNanLu

institute: Beijing Chao-Yang Hospital

summary:
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and usually lethal lung disease characterized by unknown causes and few treatment options
We used microarray to determine the expression of miRNA and 17 miRNAs were differentially expressed in IPF lungs, including 10 upregulated and 7 downregulated miRNAs.

overall_design: Lung tissue was obtained from 4 IPF patients with histological evidence of usual interstitial pneumonia at the time of surgical lung biopsy or lung transplantation. The diagnosis of IPF was derived according to the standards accepted by the American Thoracic Society/European Respiratory Society. Histological normal lung tissues used as controls was obtained from 3 patients with primary spontaneous pneumothorax at the time of thoracoscopy with stapling of any air leak.The miRNA expression profile was determined by Affymetrix microarray, and transcriptome with Affymetrix array

first: Dianhua

last: Jiang

first: Huaping

last: Dai


title: Reconstruction of microRNA/genes transcriptional regulatory networks of multiple myeloma through in silico integrative genomics analysis [PCL, miRNA]

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: The identification of deregulated miRNA in multiple myeloma (MM) has progressively added a further level of complexity to MM biology. In the present study, we take virtue of in silico integrative genomics analysis to generate an unprecedented global view of the transcriptional regulatory networks modulated in MM to define microRNAs impacting in regulatory circuits with potential functional and clinical relevance. miRNA and gene expression profiles in two large representative MM datasets, available from retrospective and prospective clinical trials and encompassing a total of 249 patients at diagnosis, were analyzed by means of two robust computational procedure to identify (i) relevant miRNA/transcription factors/target gene circuits in the disease and (ii) highly modulated miRNA-gene networks in those pathways enriched with miRNA-target gene interactions in specific MM subgroups. The analysis reinforced the pivotal role the miRNA cluster miR-99b/let-7e/miR-125a, specifically deregulated in MM patients with t(4;14) translocation, and disentangled its major relationships with transcriptional relevance. Integrated pathway analyses performed on the expression data of the MM patients stratified according to t(4;14) further allowed to define the pathway composed by the interactions that mainly characterize this MM subset and unravel connected pathways with putative role in the tumor biology.

overall_design:
miRNA and transcripts expression data were analyzed using MAGIA2, to identify mixed circuits (triplets) involving miRNA/gene/transcription factor (TF; http://gencomp.bio.unipd.it/magia2/), as previously described [Bisognin A et al., 2012, Nucl Acid Res]. Specifically, Targetscan was used as target prediction algorithm, and Pearson coefficient was used to measure relationships between microRNA and target mRNA expression profiles. Only the most variable 75% genes according to the coefficient of variation were considered. Lower threshold for absolute correlation coefficients within circuits was set to 0.2; 0.4 was used for miRNA/target binary relationships. Micrographite pipeline allows integrating pathway topologies with predicted and validated miRNA-target interactions, to perform integrated analyses of miRNA and gene expression profiles, for the identification of modulated regulatory circuits involved in the disease in terms of both expression variations and differential strength of inferred interactions [Calura E et al., 2014, Nucl Acid Res]. Micrographite has two steps: i) the extension of pathway annotation using miRNA-target interaction and ii) recursive topological pathway analysis on these networks. We considered network topologies derived from KEGG database by Graphite package [Sales G et al., 2012, BMC Bioinformatics] and miRNA-target gene interactions identified by the above-described MAGIA2 analysis. Specifically, a miRNA was added to a pathway-derived network only if one (or more) of its validated or predicted target genes is a pathway component. Then, a modified recursive version of CliPPER topological pathway analysis [Martini P et al., 2013; Nucl Acid Res] was applied to the composite network, as previously described [Calura E et al., 2014, Nucl Acid Res] in order to identify the most important and non-redundant circuit modulated across groups. Briefly, (i) in the first step, the most significant pathways were selected using P<0.1 as cut-off value for significance; (ii) for each dataset, the upper-scored 10th percentile of the portion of these previously selected pathways (i.e. paths, calculated over a 10,000-permutation step) mostly associated with phenotype were selected; and (iii) for each dataset a meta-pathway was assembled using the paths extracted from previous step and finally re-analyzed.

GSE73452 and GSE73454 Samples with the same patient number represent the same sample, profiled using two different Platforms.

first: Enrica

last: Calura

first: Andrea

last: Bisognin

first: Martina

last: Manzoni

first: Katia

last: Todoerti

first: Gabriele

last: Sales

first: Gareth

middle: J

last: Morgan

first: Antonino

last: Neri

first: Chiara

last: Romualdi

first: Stefania

last: Bortoluzzi

first: Elisa

last: Taiana

first: Nicola

last: Amodio

first: Pierfrancesco

last: Tassone

first: Giovanni

last: Tonon


title: miRNAs classifiers are powerful diagnostic/prognostic tools in ALK, EGFR, KRAS driven lung cancer

status: Public on Dec 03 2015

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

summary: microRNA profiles of NSCLCs driven by ALK, EGFR or KRAS in order to find driver-specific diagnostic and prognostic microRNA signatures.

first: Pierluigi

last: Gasparini

first: Carlo

middle: M

last: Croce


title: Transcriptomic analysis of Mtb H37Rv and MtbΔwhiB3 at pH 4.5

status: Public on Dec 02 2015

city: Bangalore

first: Amit

last: Singh

state: Karnataka

address: CV Raman Road

department: MCBL

institute: Indian Institute of Science

summary: Since WhiB3 expression was shown to be maximally upregulated at pH 4.5 and MtbΔwhiB3 was shown to be defective in survival in Ph 4.5, we did microarray at pH 4.5 so as to study comprehensive role of WhiB3 in regulating gene expression at acidic Ph

overall_design: Mtb H37Rv and MtbΔwhiB3 were grown till early log phase and exposed to 7H9-Tylaxapol at pH 4.5 for 2 hours at 37 degree at 150rpm. Two independent experiments were done for each of the strain.

first: Mansi

last: Mehta


title: Effects of perfluoroethylcyclohexanesulfonate (PFECHS)

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

summary:
Sublethal effects of perfluoroethylcyclohexanesulfonate (PFECHS) on the gene expression and protein activity of Daphnia magna
Reference sample is a composite of equal amounts of total RNA (500 ng each) from n=3 culture media control

overall_design: Two-condition experiment:  control (culture media) and three sublethal doses of PFECHS (0.06 mg/L, 0.6 mg/L, 6 mg/L). Biological replicates:  3 replicates each group.

first: Douville

last: Melanie

first: Carter

last: Barbara

first: Houde

last: Magali


title: The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons [ChIP-chip]

status: Public on Dec 01 2015

city: Madison

first: Patricia

last: Kiley

state: WI

address: 420 Henry Mall, Room 1135 Biochemistry Building

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

summary: As descirbed in the manuscript The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons we performed a control ChIP-chip experiment in an E. coli strain lacking the transcription factor Fur to identify regions Fur-independent enrichment.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
We performed ChIP-chip on E. coli K12  lacking the transcription factor Fur using an affinity purified anti-Fur antibody to identify areas of enrichment (false positives) under anaerobic growth conditions.
Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.

first: Nicole

last: Beauchene

first: Kevin

last: Myers

first: Dongjun

last: Chung

first: Dan

last: Park

first: Allison

last: Weisnicht

first: Sunduz

last: Keles


title: The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons [expression microarray]

type: Expression profiling by genome tiling array

summary: As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we profiled the gene expression of E. coli K12 during aerobic or anaerobic growth and in the presence or absence of the transcription factor Fur and/or the small RNA RyhB.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
We performed tiling microarray analyses to reveal the expression profiles of wild-type E. coli K12 or E. coli K12 lacking the transcription factor Fur and/or the small RNA RyhB during aerobic or ananerobic growth.

Please note that the *PAIR.pair files contain the complete normalized data ('PM' column; 389,307 data rows including controls) while the sample data tables contain 378,238 rows (without control values)


title: MicroRNA-221/222 and keratin 8/18 as potential biomarkers of high-risk cutaneous squamous cell carcinoma

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: In a search for biomarkers for patients with cutaneous squamous cell carcinoma with high risk of metasitasis, a microarray comparison of  miRNA expression profile between a non-metasitatic mouse keratinocyte cell line Pam212 and its metasitatic derivative LY-1 was carried out. Upregulation of the mir-221/222 cluster was the only notable change observed in LY-1 cells.

overall_design: Conluent cultures  (single plate of each cell line) were compared. Signal-to-noise ratio was large enough and variation of duplicate spots were minimal for mir-221/222.

first: Kimiko

last: Takei

first: Ken-ichi

last: Kariya