title: 4PEHz-treated P.falciparum parasites vs. untreated extracted at timepoints t1 (12 Hours post invasion or HPI), t2 (24 HPI) and t3 (36 HPI)

status: Public on Feb 28 2014

city: Pretoria

first: Shaun

last: Reeksting

state: Gauteng

address: Lunnon Rd.

department: Biochemistry

country: South Africa

institute: University of Pretoria

summary:
Plasmodium falciparum parasites were treated with the PfPdx1 inhibitor 4PEHz and the transcriptional responses of three different timepoints throughout the intraerythrocyic developmental cycle of the parasite were compared to untreated parasites.
The goal was to determine the functional consequences of attenuating vitamin B6 metabolism in the parasites using 4PEHz (4-phospho-D-erythronhydrazide)

overall_design: Two color array with reference pool design, at least 2 biological replicates from each timepoint of treated and untreated parasites.

middle: B

first: Nicky

last: Olivier


title: Methylation profiling of the chimpanzee CNTNAP2 gene in brain using high-resolution tiling arrays.

status: Public on Feb 20 2014

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

type: Methylation profiling by genome tiling array

summary:
Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the chimpanzee genome, encompassing 2.5 Mb. It encodes a neurexin with essential roles in the vertebrate nervous system. The aim of our study was to compare the methylation patterns of CNTNAP2 in human and chimpanzee brains, assuming that epigenetic regulation is essential for brain development and human language abilities. To this end, we designed a NimbleGen tiling array covering the entire chimpanzee CNTNAP2 gene plus 0.1 Mb up- and downstream flanking sequence with an average resolution of 13 bp.
Methylated DNA ImmunoPreciptation (MeDIP) was used to enrich cytosine-methylated DNA fragments for downstream analysis with high-resolution tiling arrays.

overall_design: MeDIP-based CNTNAP2 methylation profiling

first: Eberhard

last: Schneider

first: Nady

last: el Hajj

middle: J

first: Thomas

last: Haaf


title: miRNA profiling in hPASMC isolated from normal and PAH patients

city: Chicago

first: Guofei

last: Zhou

state: IL

address: 840 S Wood St, ste 1206, MC856

department: Pediatrics

country: USA

institute: University of Illinois at Chicago

summary: To identify dysregulated miRNAs in PAH HPASMC, we compared the miRNA expression profiles between normal and PAH HPASMC using the RT2 miRNA PCR Array System.

overall_design: Total RNA was isolated using a miRNeasy Mini Kit (Qiagen, Valencia, CA) and treated with an RNase-Free DNase Set (Qiagen). After quantification with Nanodrop 2000 spectrophotometer (ThermoScientific, Rockford, IL), miRNAs were reversely transcribed using a RT2 miRNA First Strand Kit (SABiosciences, Frederick, MD). The RT2 miRNA PCR Array System (SABiosciences) was used to study miRNA profiling in normal and PAH HPASMC. U6, SNORD44, SNORD47 and SNORD48 were used as internal controls for the profiling. HPASMC isolated from oe normal donor (C128, as control), one IPAH patient (B157), one PAH patient with Eisenmenger’s syndrome (CC-008) and one PAH patient with Scleroderma (CCF-004) were used for miRNA PCR array study. Data is normalized to the control sample.  Three independent sample preparations were used for this study.

first: Tianji

last: Chen

first: Usha

last: Raj


title: Transcriptome profiling of alkaloid biosynthesis induced opium poppy

status: Public on Feb 21 2014

city: Çankırı

first: tugba

last: gurkok

address: Uluyazı

department: biology

country: Turkey

institute: Çankırı Karatekin University

summary: To identify the molecular basis of genome-wide transcriptome analysis in induced opium poppy capsule tissues NimbleGen microarray (12X135 K element) analysis was performed. Fungal elicitor methyl jasmonate (MeJa) treatment was applied on capsules of opium poppy during 0, 3, and 12 h.

overall_design: Four sample sets were prepared for array analyses:  i) control ii) 0 hour after treatment iii) 3 hour after treatment iv) 12 h after treatment

first: Tugba

last: Gurkok

first: Mine

last: Turktas

first: İskender

last: Parmaksız

first: Turgay

last: Unver


title: DGAT1 Inhibitor-Induced Gene Expression in Mouse Skin

city: Boston

first: eric

last: muise

state: MA

address: 33 Ave Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

summary: Inhibition of Diacylglycerol O-acyltransferase 1 (DGAT1) has been a mechanism of interest for metabolic disorders. DGAT1 inhibition has been shown to be a key regulator in an array of metabolic pathways; however, based on the DGAT1 KO mouse phenotype the anticipation is that pharmacological inhibition of DGAT1 could potentially lead to skin related adverse effects. One of the aims in developing small molecule DGAT1 inhibitors that target key metabolic tissues is to avoid activity on skin-localized DGAT1 enzyme. In this report we describe a modeling-based approach to identify molecules with physical properties leading to differential exposure distribution. In addition, we demonstrate histological and RNA based biomarker approaches that can detect sebaceous gland atrophy pre-clinically that could be used as potential biomarkers in a clinical setting.

overall_design: Mice were treated with DGAT1 inhibitors for 14 days and dorsal skin biopsies (3-5 mm^2) were taken. RNA was profiled on custom Affymetrix microarrays. The primary goal was to identify robust and consistent biomarkers of DGAT1 inibition in skin.

first: Eric

last: Muise


title: Transcriptome comparison of bat (Miniopterus natalensis) forelimb and hindlimb autopods at developmental stages CS16 and CS17 and E13.5 mouse forelimb autopods

status: Public on Feb 15 2014

city: Rondebosch

first: Nicola

last: Illing

state: Western Cape

address: Chemistry Rd

department: Molecular and Cell Biology

institute: University of Cape Town

summary: The bat offers an alternative paradigm to the standard mouse and chick model of limb development as it has extremely divergent forelimbs (long digits supporting a wing) and hindlimbs (short digits and claws) due the distinct requirements of both aerial and terrestrial locomotion. We used a cross-species microarray approach to identify differentially expressed (DE) genes between the bat (Minniopterus natalensis) forelimb and hindlimb autopods at Carollia developmental stages (CS) 16 and CS17, and between the bat (CS17) and mouse (E13.5) forelimb autopods. Several DE genes were identified, including two homeobox genes, Meis2, a proximal limb-patterning gene, and Hoxd11, a gene involved in digit elongation. Both genes are significantly over-expressed in the developing bat forelimb as compared to the hindlimb and equivalently staged mouse forelimbs.

sample_organism:
Mus musculus
Miniopterus natalensis

overall_design: A reference design was used in this microarray experiment. A pool of left and right mouse forelimb autopods from 24 embryos was used as the reference sample. This sample was directly compared to individual CS16 and CS17 bat fore- and hindlimbs (left and right of one individual pooled) that were classified as the test conditions. Four experimental sessions were performed using an independently amplified mouse reference pool and 4 biological repeats for the bat limbs. These samples were co-hybridised to OPERON Mouse OpArray (ver. 4.0) spotted oligonucleotide slides to perform a competitive Cross-Species Hybridisation experiment. The bat aRNA (test) samples were labelled with Cy3 dye (green signal), the mouse aRNA (reference) sample was labelled with Cy5 dye (red signal).

first: Mandy

middle: K

last: Mason

first: David

middle: S

last: Jacobs


title: Influence of Cochliobolus miyabeanus and silicon on gene expression in rice leaves (Oryza sativa L.)

status: Public on Feb 25 2014

city: Gent

first: Jonas

last: Van Bockhaven

state: Oost-Vlaanderen

address: Coupure-Links 653

department: Crop protection

country: Belgium

institute: Ghent University

summary: Although Cochliobolus miyabeanus is an important fungal leaf pathogen on rice plants worldwide, it is largely neglected by molecular plant phytopathologists. To shed new light on the molecular and genetic basis of the rice – C. miyabeanus interaction, we compared the transcriptome of rice leaves 12h post inoculation to uninfected leaves. Even though usable sources of resistance against brown spot disease caused by C. miyabeanus are scarce, silicon application emerges as a sustainable protection strategy. Many articles report the beneficial effect of silicon on brown spot resistance. however the underlying mechanisms remain largely unclear. The influence of silicon application on the transcriptome of healthy and infected rice leaves 12hpi was compared as well in an attempt to disentangle the modulation of silicon-induced brown spot resistance.

overall_design: Comparison between C. miyabeanus- and mock-infected rice leaves 12h post inoculation. This study consist of a 2 x 2 factorial design (infected and non-infected; untreated and silicon-treated) in three biological replicates.

last: De Vleesschauwer

first: Shoshi

last: Kikuchi

first: Monica

last: Höfte


title: Transcription profiling of stigmas after pollination and after pollen coat adhesion

status: Public on Feb 26 2014

city: Ikoma

first: Megumi

last: Iwano

state: Nara

address: 8916-5 Takayama

department: Biological Sciences

country: Japan

institute: NAIST

summary:
Transcriptional analysis of stigmas was performed to identify molecules functioning in compatible pollination.  Stigmas of A. thaliana Col-0 were collected (i) at 0 min or 15 min after pollination and (ii) before or at 15 min after pollen coat adhesion, and used for microarray analysis. Genes up-regulated after pollination and after pollen coat adhesion were identified.
.

overall_design: Four-condition experiment, stigmas at 0 min vs. 15 min after pollination; stigmas before vs. at 15 min after pollen coat adhesion.

first: Motoko

last: Igarashi

first: Yoshiaki

last: Tarutani

first: Pulla

last: Kaothien-Nakayama

first: Hideki

last: Nakayama

last: Moriyama

first: Ryo

last: Yakabe

first: Tetsuyuki

last: Entani

first: Hiroko

last: Shimosato-Asano

first: Masao

last: Ueki

first: Gen

last: Tamiya

first: Seiji

last: Takayama


title: Methylation profiling of the human CNTNAP2 gene in brain using high-resolution tiling arrays.

first: Claus

last: Scholz

summary:
Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the human genome, encompassing 2.3 Mb. It encodes a neurexin with essential roles in the vertebrate nervous system. The aim of our study was to compare the methylation patterns of CNTNAP2 in human and chimpanzee brains, assuming that epigenetic regulation is essential for brain development and human language abilities. To this end, we designed a NimbleGen tiling array covering the entire human CNTNAP2 gene plus 0.1 Mb up- and downstream flanking sequence with an average resolution of 13 bp.
Methylated DNA ImmunoPreciptation (MeDIP) was used to enrich cytosine-methylated DNA fragments for downstream analysis with high-resolution tiling arrays.

first: Eberhard

last: Schneider

first: Nady

last: el Hajj

first: Thomas

last: Haaf


title: Whole transcription data for mouse spermatogonial cells

status: Public on Feb 27 2014

city: Shatin

first: Tin-Lap

last: Lee

address: Area 39

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Expression profiling by genome tiling array

summary: Spermatogenesis is a multi-step yet tightly regulated developmental process to produce male gemetes for reproduction. In mouse spermatogenesis, a sub-group of type A spermatogonia (Spga) known as spermatogonial stem cells (SSCs) maintain their population by self-renewal, and differentiate through mitosis and meiosis to form tetraploid (4n) pacchytene spermatocytes (Spcy) and haploid (n) round spermatids (Sptd), which further differentiate into functional sperms. In this study, we selected three representative stages of mouse spermatogenesis, namely Spga, Spcy and Sptd, to study their transcriptomic charteristics using whole genome tiling microarray.

overall_design: Three biological replicates of each selected stage. Spga were isolated from 6-day-old Balb/c mice, Spcy and Sptd from 60-day-old Balb/c mice. Transcriptomic landscapes of these three cell types were analysed with whole genome tiling array.

first: Owen

middle: M

last: Rennert

first: Wai-Yee

last: Chan


title: Comparison of the expression profiles of the 630E JIR8094 strain and sporulation sigma factor mutants (sigE, sigF, sigG, sigK, spoIIID) in MS

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

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

overall_design: Refer to individual Series


title: Genome-wide analysis of small intestinal gene expression of control and villinCre:Shp2fl mutant mice

status: Public on Feb 24 2014

city: Berlin

first: Jingjing

last: Qi

state: Outside the US or Canada

address: Robert-Roessle-str. 10

institute: Max-Delbrueck-Center for Molecular Medicine

summary: Analysis of genes regulated by Shp2 mediated signaling in the small intestine

overall_design: Total RNA from small intestine of 6 villinCre;Shp2fl conditional mutant mice  was compared to 6 control mice

first: Julian

last: Heuberger

first: Walter

last: Birchmeier


title: Comparison of the expression profiles of the 630E strain and a sigE mutant after 14h of growth

summary:
Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG.

Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigE mutant after 14h of growth in MS is performed.

overall_design: Two-condition experiment: 630E strain 14h vs. sigE mutant 14h. 4 biological replicates for each condition, including dye-swaps.

first: Laure

last: Saujet

first: Marc

last: Monot


title: Evaluation of chronic sublethal effects effects of the organophosphate flame retardant Tris(2-butoxyethyl)phosphate (TBEP) using Daphni magna transcriptomic response

status: Public on Feb 19 2014

city: Montreal

first: Maeva

last: Giraudo

state: Quebec

address: 105 McGill street

department: Water Science and Technology Directorate

country: Canada

institute: Environment Canada

summary: The aim of this study was to measure chronic sublethal effects of the flame retardant Tris(2-butoxyethyl)phosphate (TBEP) on gene expression, associated protein activity and life-history endpoints (reproduction, development) in the freshwater crustacean Daphnia magna. We exposed <24h old D. magna neonates for 21 days to culture medium (control) and to 3 sublethal doses of TBEP: 14.7, 147 and 1470 µg/L. Exposure doses were chosen from 48h acute toxicity testing and represent 1/10000, 1/1000 and 1/100 of the LC50, respectively. Each condition (control and the 3 different doses) were performed on 3 independant biological replicates, with 10 individuals each. We used a custom 15000 sequences D. magna microarray to measure transcriptional effect of each of the TBEP doses in comparison to unexposed controls.

overall_design: We exposed <24h old Daphnia magna to culture medium (unexposed controls) and 3 sublethal doses of TBEP (14.7µg/L, 147µg/L and 1470µg/L) for 21 days. We used 3 biological replicates of 10 individuals for each condition.

first: Mélanie

last: Douville

first: Magali

last: Houde


title: affy_med_2011_10- Comparison of plant responses upon Aphanomyces euteiches infection in wild type (A17) line and in the lyr3-1 and lyr3-2 mutants

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_med_2011_10 - affy_med_2011_10 -   LYR3 encodes a lysin motif-receptor-like kinase (LysM-RLK) that consists of an extracellular ligand-binding domain composed of three LysM domains, a single transmembrane domain and a cytoplasmic serine/threonine kinase domain. A reverse genetic approach was undertaken to study the role of this gene in the pathosystem Medicago truncatula – Aphanomyces euteiches (Ae). Results suggest that lyr3-1 and lyr3-2 mutants are more susceptible to the root pathogen Aphanomyces euteiches than the A17 wild type (WT) line.  In this study, we want to compare the early plant responses, 3 days post inoculation (dpi), between WT and the lyr3-1 and lyr3-2 mutants, in order to identify LYR3-dependent gene networks during infection.-Fourteen days old A17, lyr3-1 or lyr3-2 plants were grown in vitro on M medium. The entire roots were then inoculated (or not = controls) with A. euteiches zoospores (105/ml) and harvested three days after inoculation. Three independent repeats were performed.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 18 arrays - Medicago; normal vs mutant comparison,near isogenic lines (hif)

first: Christophe

last: Jacquet

first: Stephanie

last: Huguet

first: DELPHINE

last: PITORRE

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Expression profiling of various colony phenotypes of wild Saccharomyces cerevisiae strain

city: Prague

first: Vratislav

last: Stovicek

address: Vinicna 5

department: Genetics and Microbiology

country: Czech Republic

institute: Faculty of Science, Charles University in Prague

summary: Transcriptome comparison of cells from 4 and 7 day-old microcolonies of wild Saccharomyces cerevisiae BR-F strain, 4 and 7 day-old microcolonies of feral BR-RF strain and 4- and 7 day-old microcolonies of domesticated BR-S strain. All colonies grown on solid complex media with glycerol as carbon source. The aim of the study was to identify genes required for fluffy (structured) colony formation as well as the genes specific for certain phenotypic variant. BR-F is wild strain isolated from natural habitat and forms structured colonies when grown on media with non-fermentable carbon source. BR-S strain arose by phenotypic switch from the original wild BR-F strain during the cultivation of BR-F strain under rich and favourable conditions (process of so-called domestication), forms smooth colonies. BR-RF strain is derived from the domesticated BR-S strain under adverse conditions and restores the formation of structured colonies and other properties of original wild BR-F strain.

overall_design: Comparison of transcriptomes of cells from BR-F colonies vs cells from BR-RF colonies (see samples BR-FxBR-RF...), comparison of transcriptomes of cells from BR-F colonies vs cells from BR-S colonies (see samples BR-FxBR-S...) and comparison of transcriptomes of cells from BR-RF colonies vs cells from BR-S colonies (see samples BR-RFxBR-S...). Comparison of each couple performed with 4 day-old colonies and with 7 day-old colonies. 2 biological replicates for each time point from total 3 technical replicates (for first biological replicate see ...rep1, ...rep2 files, second biological replicate ...rep3 file). Dye-swap was performed between first two replicates (...rep1, ...rep2). In total six samples for each couple. Spotted ORFs microarray slides contain double genome of S. cerevisiae.

first: Zdena

last: Palkova


title: A genetic atlas of human admixture history

status: Public on Feb 14 2014

city: Oxford

first: George

last: Busby

state: OXON

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

overall_design: 158 indviduals of Eurasian descent included as part of a global analysis of admixture

first: Garrett

last: Hellenthal

first: Gavin

last: Band

first: James

middle: F

last: Wilson

first: Cristian

last: Capelli

first: Daniel

last: Falush

first: Simon

last: Myers


title: Comparison of the expression profiles of the Clostridium difficile 630E strain and a spoIIID mutant after 15h of growth

first: Monot

last: Marc

summary: Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. We also performed a transcriptome experiment of the spoIIID mutant compared to the 630E strain and showed that SpoIIID represses the expression of SigE target genes and activates the expression of sigK.

overall_design: Transcriptional profiling of the C. difficile 630E strain vs. a spoIIID mutant after 15h of growth in MS. Two-condition experiment: 630E strain 15h vs. spoIIID mutant 15h. 2 biological replicates for each condition.

first: Laure

last: Saujet

first: Marc

last: Monot


title: Reverse phase protein array based protein profiling of breast cancer specimens (2)

status: Public on Feb 18 2014

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

summary: Expression levels of proteins and phosphoproteins, covering major cancer signaling pathways with a special focus on breast cancer biology, were obtained for a series of 164 breast cancer tumor specimens with positive estrogen receptor status.

overall_design: Tumor specimens from patients diagnosed with primary invasive breast carcinoma were collected at the time of surgery between 2005 and 2011 and provided by the NCT Tissue Bank Heidelberg as well as by the Department of Gynecology and Obstetrics / National Center for Tumor Diseases Heidelberg. None of the patients had received neoadjuvant therapy.Tumor specimens were processed within 20 min after surgery. Samples were stored snap frozen at -80°C until further use. Only tumor samples with > 70% tumour cells and positive estrogen receptor status (immunoreactive score ≥ 3) as assessed by routine immunohistochemistry were selected for this study (n = 164). Tumor lysates were printed on a series of nitrocellulose coated glass slides and probed with with differnt primary antibodies directed against proteins and phosphoproteins of interest. Primary antibodies were selected to recognize proteins involved in major cancer signaling pathways with a special focus on breast cancer biology.

first: Johanna

last: Sonntag

first: Christian

last: Bender

first: Sebastian

last: Aulmann

first: Silvia

last: von der Heyde

first: Manuel

last: Nietert

first: Barbara

last: Burwinkel

first: Stefan

last: Wiemann

first: Tim

last: Beißbarth

first: Hans-Peter

last: Sinn

first: Andreas

last: Schneeweiss


title: Reverse phase protein array based protein profiling of breast cancer specimens

summary: Expression levels of proteins and phosphoproteins, covering major cancer signaling pathways with a special focus on breast cancer biology, were obtained for a series of 109 breast cancer tumor specimens with positive estrogen receptor status.

overall_design: Tumor specimens from patients diagnosed with primary invasive breast carcinoma were collected at the time of surgery between 2008 and 2010 at the Department of Gynecology and Obstetrics / National Center for Tumor Diseases Heidelberg. None of the patients had received neoadjuvant therapy. Institutional Review Board approval was received as ethics vote no. S039/2008 and informed consent was obtained from all patients. Tumor specimens were processed within 20 min after surgery. Samples were stored snap frozen at -80°C until further use. Only tumor samples with > 70% tumour cells and positive estrogen receptor status (immunoreactive score ≥ 3) as assessed by routine immunohistochemistry were selected for this study (n = 109). Tumor lysates were printed on a series of nitrocellulose coated glass slides and probed with 128 different primary antibodies directed against proteins and phosphoproteins of interest. Primary antibodies were selected to recognize proteins involved in major cancer signaling pathways with a special focus on breast cancer biology.

last: Beibarth


title: Comparison of the expression profiles of the 630E strain and a sigG mutant after 19h of growth

summary:
Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG.

Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigG mutant after 19h of growth in MS is performed.

overall_design: Two-condition experiment: 630E strain 19h vs. sigG mutant 19h. 4 biological replicates for each condition, including dye-swaps.


title: Identification of genes expressed during ROL barrier formation in rice root

city: Chikusa

first: Takaki

last: Yamauchi

address: Furo-cho

institute: Nagoya University

summary:
Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restricted by the formation of a suberized exodermis and/or lignified sclerenchyma in the outer part of the root.
To characterize reorganization of primary carbon metabolism in rice roots during the ROL barrier formation, we obtained the profiles of polar metabolites and the profiles of fatty acids of different zones of rice roots from plants growing in stagnant (anaerobic) and in well aerated medium. Biochemical data are combined with the results of microarray analysis.

overall_design: Nine days after germination, the seedlings were transferred to well aerated nutrient solution or stagnant deoxygenated nutrient solution. Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen, <0.5 mg l–1) prior to use by flushing with N2 gas. After 14 d (23 d old), adventitious roots, 100-150 mm long, were harvested from rice plants grown either in aerated or stagnant conditions and RNA was extracted from 10 mm segments from the regions 0-10 mm, 10-20 mm and 20-30 mm from the root apex have been cut with sterile razor blade and collected and processed separately. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (825 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.

first: Konstantin

last: KULICHIKHIN

last: YAMAUCHI

first: Kohtaro

last: WATANABE

first: Mikio

last: NAKAZONO


title: Time dependent expression profiles of microRNAs in rat milk

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

institute: Morinaga Milk Industry Co., Ltd.

summary: We have reported that microRNAs are present in human and bovine milk. But, it is unknown the roles of milk miRNAs. To clarify the roles of milk miRNAs, experimental animal such as rat study would be needed. However, it is unclear whether rat milk also contains miRNAs. Thus, we have employed microarray to show that rat milk also contains miRNAs.

overall_design: Milk samples were obtained at day 2, 9, and 16 postpartum from 3 rats. And serum samples were obtained from dam rats (n=3) at day 21 postpartum.


title: Comparison of the expression profiles of the 630E strain and a sigK mutant after 24h of growth

first: Monot

last: Marc

summary:
Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG.

Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigE mutant after 24h of growth in MS is performed.

overall_design: Two-conditions experiments, 630E strain 24h vs sigK mutant 24h, 4 biological replicates for each condition

first: Laure

last: Saujet

first: Marc

last: Monot


title: Comparison of the expression profiles of the 630E strain and a sigF mutant after 14h of growth

overall_design: Two-condition experiment: 630E strain 14h vs. sigF mutant 14h. 4 biological replicates for each condition, including dye-swaps.


title: KO comR vs. KO comX comparison

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Place Croix du Sud 5

department: Institut des Sciences de la Vie

institute: Université catholique de louvain

summary: Transcriptional profiling of mutant Streptococcus thermophilus LMD-9 comR::lox72 (strain LF148) compared to mutant S. thermophilus LMD-9 DcomX (strain CB003) for the identification of the ComR regulon. Cells were grown in CDM medium supplemented with lactose 1% (CDML) and sampled at OD600 = 0.3~0.4 for mRNA extraction.

overall_design: 2 LF148 biological replicates (one used as a technical replicate for a dye swap), 2 CB003 biological replicates (one used as a technical replicate for a dye swap).

first: Laetitia

last: Fontaine

first: André

last: Clippe


title: Expression Profiles of HepG2 cells treated with 22 compounds and solvent controls

city: Maastricht

first: Wim

last: Van den Hof

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: The transcriptomics changes induced in the human liver cell line HepG2 by 17 hepatotoxic compounds, 5 non-hepatotoxic compounds and solvent controls after treatment for 24h

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 24 hours of exposure to 17 hepatotoxic compounds, 5 non-hepatotoxic compounds and solvent controls. Three biological replicates per compound/solvent. In total 105 arrays .


title: Gene expression profiles in the bacterial pustule-resistant soybean cultivars(2)

status: Public on Feb 12 2014

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

summary:
To investigate the differential action between resistance and susceptible cultivars, we examined genome wide expression levels at five time points after Xag-inoculation using microarray.
The soybean microarray was designed using the server-based eArray platform (http://earray.chem.agilent.com/earray/) from Agilent Technologies (Wolber et al., 2006). The current slide layout consists of four arrays of >44,000 features, including a set of Agilent's positive and negative control features.

overall_design: An oligonucleotide microarray containing 42,564 unique probes (60-mer) was created from 33,574 unigenes from Glycine max database (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3847) (May 2009) as templates for probe design.

first: Jung

first: Seong-yun

first: In-soo

last: Choi


title: Regulatory Mutations Affecting Sulfur Metabolism Induce Environmental Stress Response in Aspergillus nidulas

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

summary: Mutations in the cysB, sconB and sconC genes affect sulfur metabolism in Aspergillus nidulans in different ways. Mutation of cysB blocks synthesis of cysteine by the main pathway leaving only the less effective alternative route. Mutations of sconB or sconC affect subunits of the SCF ubiquitin ligase complex, a negative controller of METR transcription factor, resulting in specific activation of a number of sulfur assimilation and metabolism genes, ultimately leading to elevated levels of cysteine and glutathione in scon mutants. We compared transcriptomes of these three mutants with that of a wild type strain finding that expression of a few hundred genes is altered at least twofold indicating a major reorganization of cellular metabolism. Despite the different effects of the cysB and scon mutations on sulfur metabolism they affect expression of overlapping sets of genes.  We identified categories of the Functional Catalogue assigned to the differentially expressed genes and selected categories most enriched among the up- and down-regulated gene groups. Besides those involved in sulfur metabolism, many up-regulated genes are related to stress responses. The two-component signal transduction system is most enriched in genes up-regulated in the cysB, sconB and sconC mutants. This category contains histidine kinases that sense and transduce environmental signals to a cascade of protein kinases. Genes encoding heat shock proteins are also up-regulated, as are genes of the glutamate degradation pathway. The latter, also known as the GABA shunt, is induced by oxidative stress.  A large group of up-regulated genes are involved in carbohydrate and energy metabolism, including genes coding for enzymes of trehalose and glycerol synthesis. Genes coding for enzymes of alcohol fermentation, which are induced in response to anaerobic stress, are also up-regulated in the mutants studied. The altered expression of the carbohydrate metabolism genes is accompanied by changes in sugar accumulation in mycelia and conidia of the mutants.  Among the down-regulated genes the most numerous are those encoding membrane proteins and enzymes involved in secondary metabolism, including the penicillin biosynthesis cluster. Genes coding for lysozyme are down-regulated too. As secondary metabolites often inhibit growth of other organisms, lowered expression of genes responsible for their synthesis suggests a decreased response to biotic stress in the mutants studied.

overall_design: Comparison of transcriptomes of the filamentous fungus Aspergillus nidulans strains bearing mutations in the cysB, sconB or sconC genes, affecting sulfur metabolism in different ways, with that of the wild type (WT) strain. Three biological replicates of WT vs cysB and WT vs sconC comparisons were performed and four biological replicates of WT vs sconB comparison were done. Each biological replicate had two technical replicates with dye swapping. A total of twenty individual hybridizations were made.

first: Marzena

last: Sieńko

first: Renata

last: Natorff

first: Joanna

last: Kruszewska

first: Andrzej

last: Paszewski

first: Jerzy

last: Brzywczy


title: Profiling of Islet, Lim3, Hb9 and Eve genomic binding in Drosophila with DamID

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

type: Genome binding/occupancy profiling by genome tiling array

summary: While developmental processes such as axon pathfinding and synapse formation have been characterized in detail, comparatively less is known of the intrinsic developmental mechanisms that regulate transcription of ion channel genes in embryonic neurons. Early decisions, including motoneuron axon targeting, are orchestrated by a cohort of transcription factors that act together in a combinatorial manner. These transcription factors include Even-skipped (Eve), Islet, Lim3 and Hb9. The perdurance of these factors in late embryonic neurons is, however, indicative that they might also regulate additional aspects of neuron development, including the acquisition of electrical properties. We have shown that Eve binds and regulates both voltage- and ligand-gated currents in motoneurons (Pym et al., 2006). We have also shown that Islet is sufficient to repress a Shaker-mediated A-type K(+) current, most likely due to a direct transcriptional effect (Wolfram et al., 2012). Finally, we have shown that Islet and Lim3 act in a combinatorial fashion to regulate Shaker-mediated A-type K(+) current (Wolfram et al., 2014).

overall_design: 3 biological relicates were performed for Islet, Lim3 and Hb9 (with one dye-swap). 2 biological relicates were performed for Eve.

middle: D

first: Richard

middle: A

last: Baines

first: Andrea

middle: H

last: Brand


title: Analysis of DNA methylation changes in normal human hematopoietic stem and progenitor cells

status: Public on Feb 07 2014

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary:
DNA methylation analysis on purified human long-term and short-term hematopoietic stem cells (LT-HSC, ST-HSC), common myeloid and megakaryocyte-erythrocyte progenitor cells (CMP, MEP) using HELP arrays.
FACS-purified hematopoietic stem and progenitor cell (HSPC) subsets were analyzed for changes in DNA methylation using NimbleGen HELP microarrays.

overall_design: Analysis of DNA methylation of bone marrow-derived HSPC subsets of healthy human donors.

first: Ulrich

last: Steidl

first: Amit

last: Verma

first: Maximilian

last: Christopeit

first: Britta

last: Will

first: Yongkai

last: Mo

first: Laura

last: Barreyro

first: Yiting

last: Yu

first: Tushar

last: Bhagat

first: Ujunwa

middle: C

last: Okoye-Okafor

first: Tihomira

middle: I

last: Todorova

first: John

last: Greally

first: Ross

middle: L

last: Levine

first: Ari

last: Melnick


title: Analysis of RNA expression and DNA cytosine methylation in healthy human hematopoietic stem and progenitor cells

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

overall_design: Refer to individual Series


title: Effects of antagonist of retinoid X receptor (UVI3003) on morphology and gene profile of Xenopus tropicalis embryos

status: Public on Feb 13 2014

city: Shanghai

first: jingmin

last: zhu

address: Room 501,State Key Laboratory of Estuarine and Coastal Research,No.3663,ZhongShan North Road, PuTuo District

country: China

institute: East China Normal University

summary:
Retinoid X receptor (RXR) plays an important role in the development of vertebrates, and the agonists of RXR are well-known to induce featured malformations in vertebrate embryos. However, there is no information about the teratogenicity of antagonists of RXR in vertebrate embryos.
We exposed embryos of amphibian (Xenopus tropicalis) at stages 10/11 to a highly selective antagonist of RXR (UVI3003).

overall_design: The experiments were initiated when embryos reached stage 10/11, the embryos were exposed to 250, 500, 750 µg/L UVI3003 for 0-24 and 24-48 for microarray analysis (n=24).

first: Jingmin

last: Zhu

first: Huahong

last: Shi


title: Human umbilical vascular endothelial cells: control vs. safrole oxide treatment

city: Jinan

first: Jing

last: Zhao

address: Shanda nan road 27#

institute: Shandong University

summary: Safrole oxide (SFO) at 50 μg/ml could most effectively induce EndoMT within 12 h. Transcriptional profiling of control and SFO-treated Human umbilical vascular endothelial cells was analyzed to understand the underlying molecular mechanism

overall_design: Two groups were used. One is control group, the other is SFO treatment group. 6 dishes of cells in each group  were used for microarray analysis.

first: Junying

last: Miao


title: Analysis of RNA expression changes in normal human hematopoietic stem and progenitor cells

first: Boris

last: Bartholdy

summary:
RNA expression analysis on purified human long-term and short-term hematopoietic stem cells (LT-HSC, ST-HSC), common myeloid and megakaryocyte-erythrocyte progenitor cells (CMP, MEP) using microarrays.
FACS-purified hematopoietic stem and progenitor cell (HSPC) subsets were analyzed for changes in RNA expression using NimbleGen gene expression microarrays.

overall_design: Analysis of RNA expression of bone marrow-derived HSPC subsets of healthy human donors.

first: Ulrich

last: Steidl

first: Amit

last: Verma


title: Comparison of mouse genes from the lungs of chronic, acute, tolerant, and non-asthmatic mouse models

city: Denver

first: Rafeul

last: Alam

state: CO

address: 1400 Jackson St. K609

institute: National Jewish Health

summary:
Microarray analysis of whole lung tissue from three mouse models of asthma
Acute asthma was produced by immunization twice, one week apart, of Balb/C mice 8-12 weeks of age with Aspergillus species (5 μg) in adjuvant (1:1 vol/vol). Adjuvant was aluminum and magnesium hydroxide (Pierce). Asthma was initiated by three consecutive intranasal exposures to Aspergillus species (5μg in 15μL saline) and asthma was evaluated 72 hours after the final exposure. Tolerant asthma was produced by intranasal delivery of Aspergillus species (5μg in 15μL saline) twice a week for six consecutive weeks to Balb/C mice 8-12 weeks of age. Asthma was evaluated after mice were rested for an additional three weeks. Chronic asthma was produced by intranasal delivery of the Dustmite/ Ragweed/ Aspergillus (5,50,5ug in 15ul saline) mixture twice a week for six consecutive weeks in female mice Balb/C mice 8-12 weeks of age. Asthma was evaluated 3 weeks after cessation of allergen exposure. Saline control mice were treated intransally with 15ul of saline twice a week for 6 weeks. Asthma was assesed 3 weeks after the final exposure.

overall_design: n=3 samples/ mouse model.


title: MicroRNAs and their target genes in gingival tissues.

status: Public on Feb 05 2014

city: New York

first: Paolo

last: Guarnieri

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

summary: To gain insights into the in vivo function of miRNAs in the context of periodontitis, we examined the occurrence of miRNAs in healthy and diseased gingival tissues and validated their in silico-predicted targets through mRNA profiling using whole-genome microarrays in the same specimens. Eighty-six individuals with periodontitis contributed 198 gingival papillae: 158 'diseased' (bleeding-on-probing, PD > 4 mm, and AL ≥ 3 mm) and 40 'healthy' (no bleeding, PD ≤ 4 mm, and AL ≤ 2 mm). Expression of 1,205 miRNAs was assessed by microarrays, followed by selected confirmation by quantitative RT-PCR. Predicted miRNA targets were identified and tested for enrichment by Gene Set Enrichment Analysis (GSEA). Enriched gene sets were grouped in functional categories by DAVID and Ingenuity Pathway Analysis. One hundred fifty-nine miRNAs were significantly differentially expressed between healthy and diseased gingiva. Four miRNAs (hsa-miR-451, hsa-miR-223, hsa-miR-486-5p, hsa-miR-3917) were significantly overexpressed, and 7 (hsa-miR-1246, hsa-miR-1260, hsa-miR-141, hsa-miR-1260b, hsa-miR-203, hsa-miR-210, hsa-miR-205*) were underexpressed by > 2-fold in diseased vs. healthy gingiva. GSEA and additional filtering identified 60 enriched miRNA gene sets with target genes involved in immune/inflammatory responses and tissue homeostasis. This is the first study that concurrently examined miRNA and mRNA expression in gingival tissues and will inform mechanistic experimentation to dissect the role of miRNAs in periodontal tissue homeostasis and pathology.

overall_design: The dataset comprise 200 gingival tissue samples from 86 patients with periodontitis. All samples are included in this series, but 2 where not included in the study, as they did not pass our QC. Each patient has one or more healthy and disease sample and samples can be of chronic or aggressive periodontitis type.

first: C

last: Stoecklin-Wasmer

first: P

first: R

last: Celenti

middle: T

last: Demmer

first: M

last: Kebschull

middle: N

last: Papapanou


title: Time series of gene expression in murine ES cells with different sex chromosome complement during EpiSC differentiation

status: Public on Feb 11 2014

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

summary: Mouse ES-cells with different sex chromosome compliment were differentiated into EpiSC, samples were taken  every 4-12 hours for 84 hours in total. The original data for the XX-cells is also available as GSE34243, but normalisation of these differs.

overall_design: Mouse Pgk12.1 ES cells or E14 cells with different sex chromosome compliment were differentiated into EpiSC, samples were taken  every 4-12 hours for 84 hours in total

first: E

middle: G

last: Schulz

first: J

last: Meisig

first: N

last: Heard


title: Detection of aberrant DNA methylation in undifferentiated and differentiated mouse ES cells compared to normal tissues

city: Jerusalem

first: guy

last: ludwig

address: Ein Kerem

country: Israel

institute: Hebrew University

summary: Embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. We have employed the mDIP method combined with hybridization to a CpG islend microarray . We show that this differentiation is accompanied by an intrinsic process of extensive aberrant CpG island de novo methylation that includes developmental and cancer target genes.

overall_design: CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

first: Howard

last: Cedar


title: Gene expression data from malignant gliomas

city: Houston

first: Roel

last: Verhaak

state: TX

address: 1400 Pressler street

institute: UT MD Anderson Cancer Center

summary:
Formalin-fixed, paraffin-embedded (FFPE) samples of varying grade (II-IV) malignant gliomas were measured by Illumina cDNA-mediated Annealing, Selection, extension and ligration (DASL) platform.
DASL platform was selected for its specialized design for partially degraded RNA.

overall_design: Overall mRNA was extracted from FFPE samples using the GoldenGate Assay protocol and hybridized to Illumina BeadChips.

first: John

last: deGroot


title: Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

summary: Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose

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

overall_design: E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide. Data for wild type controls are GSM389302, GSM389303, and GSM389304.

first: Byung-Kwan

last: Cho

first: Bernhard

middle: O

last: Palsson


title: Investigation of endothelial cell gene dysregulation in early pulmonary arterial hypertension disease model

status: Public on Feb 06 2014

city: Baltimore

first: Molong

last: Li

state: MD

address: 733 N. Broadway

department: School of Medicine

institute: Johns Hopkins University

summary: Endothelial cell (EC) dysfunction plays a key role in the pathogenesis of pulmonary arterial hypertension (PAH). To avoid cell cultures and whole lung tissue samples, we have, for the first time, used CD31 antibody coated magnetic beads in conjunction with genome scale RNA expression microarrays to profile ECs in vivo at any stage of PAH. We hypothesized that targeting early stages of the disease would identify novel mediators of PAH and genes linked to bone morphogenetic protein receptor 2 (BMPR2) signaling.

overall_design: Rats were treated with either monocrotaline (60mg/kg) or saline as control with 4 animals in each experimental group. Gene expression profiling was performed on primary pulmonary endothelial cells directly after isolation from whole lung tissue 5 days after treatment.

first: Sanna

last: Vattulainen

first: Tero-Pekka

last: Alastalo


title: Transcriptome analysis of a Ustilago maydis ust1 deletion mutant

status: Public on Feb 04 2014

city: ATHENS

first: Scott

middle: E

last: Gold

state: GA

address: 950 COLLEGE STATION RD

department: Toxicology and Mycotoxin Research

institute: USDA ARS

summary: Ustilago maydis, the causal agent of corn smut disease, is a dimorphic fungus alternating between a saprobic haploid budding form, and an obligate pathogenic filamentous dikaryon. Maize responds to U. maydis colonization by producing highly modified tumorous structures and it is only within these plant galls that the fungus sporulates giving rise to melanized sexual spores, the teliospores. Previously we identified a regulatory protein from the APSES family of transcription factors, which we named Ust1, whose absence in yeast cells led to filamentous growth and the production of highly pigmented spore-like structures in culture. In this study, we analyzed the transcriptome of a ∆ust1  deletion mutant.

overall_design: To identify genes potentially involved in the sporulation program, we carried out microarray analysis comparing a haploid U. maydis WT strain (1/2) and ust1 (14/25) in vitro.  Wild-type and ∆ust1 strains were grown in potato dextrose broth (PDB) for 48 h at 30oC. To allow effective comparison with other array data generated by U. maydis researchers, cells were then transferred to liquid array medium (6.25% Holiday salt solution, 30mM L-glutamine, 1% glucose, pH7.0, filter sterilized) at 30 C. Total RNA samples from WT 1/2  and ∆ust1 mutant strains grown in array medium for 24 h (mutant’s filamentous phase), and 48 h (mutant’s spore-like structure formation phase) were extracted and purified (Sigma Spectrum Plant Total RNA Kit, Cat.No.STRN50). RNA was sent to NimbleGen, where it was reverse transcribed to cDNA and Cy3 labeled. The cDNA samples were hybridized, microarray chips scanned, and raw data normalized with appropriate controls.

first: Emir

last: Islamovic


title: Genome-wide analysis of gene expression and intron retention during deveopment in a U12-type splicing-deficient zebrafish mutant [microarray]

city: Parkville

first: Joan

middle: Kathleen

last: Heath

state: Victoria

address: 1G Royal Parade

department: Development and Cancer

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: To determine the global impact of the clbn mutation on gene expression and efficiency of U2- and U12-type splicing, we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2-type and U12-type intron on a genome-wide scale to confirm that rnpc3 deficiency specifically impairs U12-type splicing. RNAseq and microarray data were combined to yield high-confidence lists of differentially expressed genes which show that impaired U12-type splicing has a wide-ranging effect on the developing transcriptome.

overall_design: Total RNA was prepared from pools consisting of approx. 20 individually genotyped homozygous wildtype or mutant larvae, respectively. Three biologically independent replicate pools were generated and analyzed for each condition.

first: Sebastian

last: Markmiller

first: Nicole

last: Cloonan

first: Rea

last: Lardelli

first: Karen

last: Doggett

first: Maria-Cristina

last: Keightley

first: Yeliz

last: Boglev

first: Andrew

middle: J

last: Trotter

first: Annie

middle: Y

last: Ng

first: Simon

last: Wilkins

first: Heather

last: Verkade

first: Elke

last: Ober

first: Holly

last: Field

first: Sean

last: Grimmond

first: Graham

last: Lieschke

first: Didier

last: Stainier


title: MicroRNA expression changes associated with specific STAT3 activation

city: Boston

first: Michael

last: Xiang

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Signal transducer and activator of transcription 3 (STAT3) is a critical transcription factor in cancer. However, while the protein-coding target genes of STAT3 have been extensively studied, the microRNA target genes of STAT3 are less understood. MicroRNAs are short, non-coding RNAs that regulate messenger RNAs through translational inhibition and transcript degradation. They have been found to be involved in all aspects of cancer biology. Given the roles of both STAT3 and miRNAs in cancer, the function of STAT3 as a transcription factor, and the dearth of known STAT3 miRNA targets, our goal was to identify novel STAT3 miRNA targets relevant to cancer. To do so, we engineered MCF-10A cells with doxycycline-inducible expression of STAT3C. STAT3C is a constitutively-active mutant version of STAT3. Although STAT3 can be activated by various growth factors and kinases, other pathways can be activated as well, which would confound analysis of the results. Thus, the advantage of STAT3C is that it allowed specific and focused activation of STAT3 alone, and this screen represents the first genome-wide survey of miRNA expression changes associated specifically with STAT3 activity. MCF-10A, a non-transformed breast epithelial cell line, was chosen because STAT3C has been reported to be sufficient to cause their neoplastic transformation. Therefore, we reasoned that analysis of STAT3C’s effects in MCF-10A cells would be especially informative for STAT3-regulated miRNAs relevant to cancer. As a result of our study, we identified previously-known as well as novel miRNA targets of STAT3.

overall_design: Doxycycline-inducible MCF-10A cells were seeded, and then untreated (grown in standard growth media alone) or treated with 2μg/ml doxycycline for 48hr. Each condition was performed in biological triplicate (labeled A, B, and C), for a total of 6 samples. Total RNA was harvested and submitted to the Dana-Farber Cancer Institute Molecular Diagnostics Laboratory. MicroRNA expression profiling was performed using TaqMan Low-Density Arrays (TLDA), human miRNA version 2.0A and version 3.0B cards (Applied Biosystems).

first: David

last: Frank


title: Fkh1 and Fkh2 Bind Multiple Chromosomal Elements in the S. cerevisiae Genome with Distinct Specificities and Cell Cycle Dynamics

city: Los Angeles

middle: Zachary

last: Ostrow

state: California

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

summary: Forkhead box (FOX) transcription factors regulate a wide variety of cellular functions in higher eukaryotes, including cell cycle control and developmental regulation. In Saccharomyces cerevisiae, Forkhead proteins Fkh1 and Fkh2 perform analogous functions, regulating genes involved in cell cycle control, while also regulating matingtype silencing and switching involved in gamete development. Recently, we revealed a novel role for Fkh1 and Fkh2 in the regulation of replication origin initiation timing, which, like donor preference in mating-type switching, appears to involve long-range chromosomal interactions, suggesting roles for Fkh1 and Fkh2 in chromatin architecture and organization. To elucidate how Fkh1 and Fkh2 regulate their target DNA elements and potentially regulate the spatial organization of the genome, we undertook a genome-wide analysis of Fkh1 and Fkh2 chromatin binding by ChIP-chip using tiling DNA microarrays. Our results confirm and extend previous findings showing that Fkh1 and Fkh2 control the expression of cell cycle-regulated genes. In addition, the data reveal hundreds of novel loci that bind Fkh1 only and exhibit a distinct chromatin structure from loci that bind both Fkh1 and Fkh2. The findings also show that Fkh1 plays the predominant role in the regulation of a subset of replication origins that initiate replication early, and that Fkh1/2 binding to these loci is cell cycleregulated. Finally, we demonstrate that Fkh1 and Fkh2 bind proximally to a variety of genetic elements, including centromeres and Pol III-transcribed snoRNAs and tRNAs, greatly expanding their potential repertoire of functional targets, consistent with their recently suggested role in mediating the spatial organization of the genome.

overall_design: 30 total ChIP-chip samples were analyzed in triplicate. Two antibodies were used, and samples lacking epitopes were processed as controls.

first: A

middle: Z

first: Tittu

last: Nellimoottil

middle: R

last: Knott

first: Catherine

last: Fox

last: Tavaré

first: Oscar

middle: M

last: Aparicio


title: Age-associated bidirectional modulation of gene expression in single identified R15 neuron of Aplysia

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Research

summary: Despite the advances in our understanding of aging-associated behavioral decline, we know relatively little about how aging affect neural circuits that underlie specific behaviors. Specifically, we know little about how aging affect expression of genes in specific neural circuits. We have now addressed this problem by exploring a cholinergic neuron R15, an identified neuron of marine snail Aplysia. R15 is characterized by bursting action potentials and is implicated in reproduction, osmoregulation and locomotion.

overall_design: We examined changes in gene expression in R15 neurons during aging by microarray analyses of RNAs prepared from two different age groups, mature and old animals. Specifically we find that 1083 ESTs are differentially regulated in mature and old R15 neurons.  Bioinformatics analyses of these genes have identified specific biological pathways and molecular processes that are up or down regulated in mature and old neurons. Comparison with human signaling networks using pathway analyses have identified three major networks that are altered in old R15 neurons. Furthermore, by single neuron qRTPCR we examined expression levels of candidate regulators involved in transcription (CREB1) and translation (S6 kinase) and find that aging is associated with a decrease in expression of these regulators. We next studied expression of CREB1 and S6 kinase in two different motor neurons (L7 and L11) and another cholinergic neuron R2 and find that these neurons have characteristic changes in gene expression during aging

first: Beena

last: Kadakkuzha

first: Mohammad

last: Fallahi


title: Genome-Wide Molecular Signature of Cholangiocarcinoma and Its Trandifferentation-Related Genes

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: Cholangiocarcinoma (CC) is an aggressive tumor that shows a poor survival rate even after resection. The present study aimed at identification of the genome-wide expressed genes related to CC oncogenesis and its sarcomatous transdifferentiation using DNA microarray technology. The differentially expressed genes in 9 cholangiocarcinoma cell lines (Choi.CK, Cho.CK, J.CK, S.CK, CK.L1, CK.L2, CK.P1, CK.P2 and CK.Y1) were analyzed in comparison with 4 kinds of cultured biliary epithelial cells (ND.1, ND.2, ND.3 and ND.4) using the Illumina Human-6 v2 BeadChip (48 K). Unsupervised hierachical clustering analysis perfectively classified the 13 cell samples into two groups, normal biliary epithelial (N) and immortalized biliary epithelial cells and CC (T) cells. We identified 120 commonly upregulated ( > 2.5 fold) genes and 340 commonly downregulated ( < 0.4-fold) genes in the two groups. Hierachical clustering analysis of sarcomatoid CC cells (S.CK) revealed 316 differentially upregulated genes (> 4-fold) and 335 downregulated genes (< 0.25-fold).) compared with 3 CC cell lines (Choi.CK, Cho.CK, and J.CK). In conclusion, these data will contribute to better understand the molecular mechanisms of oncogenesis and transdifferentiation in CC and provide the molecular targets for CC diagnosis and therapy.

overall_design: Total RNA was extracted from each sample. Five-hundred nanograms of total RNA were used for labeling and hybridization, according to the manufacturer’s protocols (Illumina). After the bead chips were scanned with an Illumina BeadArray Reader (Illumina), the microarray data were normalized using the quantile normalization method in the Linear Models for Microarray Data package in the R language environment. The expression level of each gene was transformed into a log 2 base before further analysis.

first: SH

last: Leem

first: DG

first: SK

first: IS

last: Chu


title: Platelet-secreted microRNA-223 promotes endothelial cell apoptosis induced by advanced glycation end products via targeting the insulin-like growth factor 1 receptor

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: Platelets contain abundant miRNAs, however, the biogenesis pathway of miRNAs in anucleate platelets is unclear.

overall_design: Platelet-rich plasma was diluted in washing buffer and the platelet suspension was centrifuged to isolated pure platelets.Finally, platelets were recovered in suspension buffer at the concentration of 4–5×10^8 platelets/ml. Aliquots of the platelet suspensions were activated in the presence of 2.5 mM CaCl2 with 0ng/ml or 1 ng/ml thrombopoietin (TPO)

first: Yi

last: Pan

first: Hongwei

last: Liang


title: ChIP-chip of E. coli K-12 MG1655 with antibody against RNA polymerase subunits, RpoB, RpoD, RpoS,RpoH, RpoN, FliA, and FecI

first: Donghyuk

summary: We investigate sigma factor binding regions for each sigma factor under various enviromental and/or genetic conditions. To measure sigma factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of  E. coli K-12 MG1655 wild type and its isogenic rpoS and rpoN knock-out strains under various conditions.

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

overall_design: A 45 ChIP-chip study under 4 separate culture conditions.  The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome.

first: Byung-Kwan

last: Cho

first: Bernhard

last: Palsson


title: Gene expression in extra-embryonic tissues flushed out at D18 from heifers, early and late lactating cows

city: Carrières sur Seine

first: Damien

last: VALOUR

state: Île-de-France

address: 34, rue Victor HUGO (Bât D)

department: PHASE

institute: INRA

summary:
Evaluate the influence of maternal metabolism on gene expression profiles from extra-embryonic tissues at D18
Keyword: Holstein Heifers and Postpartum dairy cows, metabolism and energy status, elongation and gastrulation, extra-embryonic tissues, transcriptome, correlations between genes & metabolites?

overall_design: 8 replicates in GH, 11 replicates in ELC and 10 replicates in LLC (extra-embryonic tissues) per group of female (N=3) were hybridized (total N=29) against a placental reference that hybridized itself to 99% of the array. Hybridization design: 6 microarrays per experiment (N=5) were randomly hybridized to the EET from 2 conceptuses originating either from development in heifers, ELC or LLC. Extra-embryonic tissues were systematically labelled with Cy3 and Reference in Cy5.

last: Valour

first: Severine

last: Degrelle

first: Benedicte

last: Grimard

first: Isabelle

last: Hue


title: Expression and differential expression analysis in colorectal carcinoma cells

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Expression and differential expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway.  In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. Colorectal carcinoma cells with defunct TP53 compared to colorectal carcinoma cells with induced TP53.

overall_design: We analyzed three arrays each for colorectal carcinoma cells with defunct TP53 and with induced TP53 expression

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller

first: Kurt

last: Engeland


title: Transcriptional analysis reveals the molecular details of atrophic gastritis in Helicobacter pylori infected corpus mucosa

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary:
The majority of gastric cancer cases are believed to be caused by chronic infection with the bacterium Helicobacter pylori, and atrophic corpus gastritis is a predisposing condition to gastric cancer development. We aimed to increase understanding of the molecular details of atrophy by performing a global transcriptome analysis of stomach tissue.
Biopsies from patients with different stages of H. pylori infection were taken from both the antrum and corpus mucosa and analyzed on microarrays. The stages included patients without current H. pylori infection, H. pylori-infected without corpus atrophy and patients with current or past H. pylori-infection with corpus-predominant atrophic gastritis.Using clustering and integrated analysis, we found firm evidence for antralization of the corpus mucosa of atrophy patients. This antralization harbored gain of gastrin expression, as well as loss of expression of corpus-related genes, such as genes associated with acid production, energy metabolism and blood clotting. The analyses provided detailed molecular evidence for simultaneous intestinal metaplasia (IM) and spasmolytic polypeptide expressing metaplasia (SPEM) in atrophic corpus tissue. Finally, acidic mammalian chitinase, a chitin-degrading enzyme produced by chief cells, was shown to be strongly down-regulated in corpus atrophy.Transcriptome analysis revealed several gene groups which are related to development of corpus atrophy, some of which were increased also in H. pylori-infected non-atrophic patients. Furthermore, loss of acidic chitinase expression is a promising marker for corpus atrophy.

overall_design: Biopsies from well classified patients with different stages of H. pylori infection were taken from both the antrum and corpus mucosa. These stages included H. pylori un-infected, H. pylori-infected without corpus atrophy and H. pylori-infected with corpus-predominant atrophic gastritis.

first: Kaisa

last: Thorell

first: Kuntal

last: Worah

first: Shugui

last: Wang

first: Sven

last: Pettersson

first: Henrik

last: Sjövall

first: Jens

last: Nielsen

first: Samuel

middle: B

last: Lundin


title: Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro

status: Public on Feb 03 2014

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: To investigate the time-dependent and coordinated sequence of inflammation-related events, and the dynamic features of macrophage polarisation/activation, we build and validated an in vitro model based on primary human monocytes

overall_design: Monocytes were sequentially exposed to relevant stimuli: hrCCL2 (10 ng/ml; 0-2 h), LPS (5 ng/ml; 2-14 h) hrTNF-α (10 ng/ml; 3-14 h), hrIFN-γ (25 ng/ml; 7-14 h), hrIL-10 (20 ng/ml; 14-24 h), hrTGF-β (10 ng/ml; 24-48 h). The temperature was raised to 39 °C from 2 h to 14 h. Fresh monocytes were taken as time 0. Samples were collected at different time points and processed for total RNA extraction and hybridization on Affymetrix microarrays. Nine donors (A, B, C, D, E, F, G, H, L) were used for each of the 5 conditions (0, 4, 14, 24, 48 h) for a total of 45 samples, and 3 donors (M, N, O) were used for the following time-points: 0, 2, 2,5, 3, 3,5 h.

first: Ingrid

last: Cifola

first: Cristina

last: Battaglia

first: Paola

last: Italiani

first: Diana

last: Boraschi

first: Emilia

last: Mazza


title: In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts

city: Raleigh

first: Pete

last: Pascuzzi

state: NC

address: 851 Main Campus Drive

institute: North Carolina State University

summary:
Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context
of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression.
Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/
MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4
(chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been
studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features,
suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the
transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is
particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns
show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the
majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to
begin evaluating genome-scale models for S/MAR function.

overall_design: Contrast between DNA bound to nuclear scaffold/matrix and total genomic DNA in Arabidopsis Chr4 excluding the constitutive heterochromatin.  Total of three biological replicates with two independent hybridizations on custom-designed NimbleGen high-density microarrays that include duplicate spots for each probe.

first: Miguel

middle: A

last: Flores-Vergara

first: Tae-Jin

last: Lee

first: Bryon

last: Sosinski

first: Matthew

middle: W

last: Vaughn

first: Linda

last: Hanley-Bowdoin

first: William

middle: F

last: Thompson

first: George

middle: C

last: Allen


title: Tibialis anterior muscle of myostatin null mice treated with clenbuterol

city: Urbana

first: Anna

last: Dilger

state: IL

address: Meat Science Lab 1503 S Maryland Drive

department: Animal Science

institute: University of Illinois

summary: Transcription profiling of skeletal muscle (tibialis anterior) of 5-week-old male wild type and myostatin null mice given ad libitum access to 20ppm clenbuterol hydrochloride in drinking water or plain tap water for 2 weeks. The objective of the study was to determine overlap in the mechanisms of muscle hypertrophy of the two models.

overall_design: 2x2 factorial arrangement of genotype (wild type and myostatin null) and clenbuterol treatment (control and clenbuterol at 20 ppm) with 4 replicates.

first: Savannah

last: Gabriel

first: John

last: Killefer


title: Social odors conveying dominance and reproductive information induce rapid physiological and neuromolecular changes in a cichlid fish.

status: Public on Feb 01 2014

city: Lisboa

first: José Miguel

last: Simões

address: Rua Jardim do Tabaco 34

department: Eco-Ethology Research Unit

country: Portugal

institute: ISPA - Instituto Universitário

summary: Social plasticity is a pervasive feature of animal behavior. Animals adjust the expression of their social behavior to the daily changes in social life and to transitions between life-history stages, and the ability to change in these ways impacts their Darwinian fitness. This behavioral plasticity may be achieved either by rewiring or by biochemically switching nodes of the neural network underlying the social behavior in response to perceived social information. Independent of the proximate mechanisms, at the neuromolecular level social plasticity relies on the regulation of gene expression, such that different neurogenomic states emerge in response to different social stimuli and the switches between states are orchestrated by signaling pathways that interface the social environment and the genotype. Here, we test this hypothesis by characterizing the changes in the brain profile of gene expression in response to social odors in the Mozambique Tilapia, Oreochromis mossambicus. This species has a rich repertoire of social behaviors during which both visual and chemical information are conveyed to conspecifics. Specifically, dominant males increase their urination frequency during agonist encounters and during courtship to convey chemical information reflecting their dominance status. We recorded electro-olfactograms to test the extent to which the olfactory epithelium can discriminate between olfactory information from dominant and subordinate males as well as from pre- and post-spawning females. We then performed a genome-scale gene expression analysis of the olfactory bulb and the olfactory cortex homolog in order to identify the neuromolecular systems involved in processing these social stimuli. Our results show that different olfactory stimuli from conspecifics’ have a major impact in the brain transcriptome, with different chemical social cues eliciting specific patterns of gene expression in the brain. These results confirm the role of rapid changes in gene expression in the brain as a genomic mechanism underlying behavioural plasticity and reinforce the idea of an extensive transcriptional plasticity of cichlid genomes, especially in response to rapid changes in their social environment.

overall_design: Brain samples from 40 African cichlid males, Oreochromis mossambicus were collected after stimulation with different social olfactory stimuli. Samples were collected from 2 brain areas: BO and Dp after males were exposed to dominant (DOM) and subordinate (SUB) male urine and pre- (PRE) and post-ovulatory (POST) female scent. In OB 5 replicates were collected from males exposed to DOM and 6 to the other stimuli. For Dp 5 replicates were collected from males exposed to DOM and POST, 4 to SUB and 6 to PRE.

first: J

first: Eduardo

middle: N

last: Barata

first: Rayna

last: Harris

first: Lauren

last: O'Connell

first: Rui

last: Oliveira

first: Hans

middle: H

last: Hofmann


title: Gene Expression Profile of Moraxella catarrhalis Grown in Pooled Human Sputum

status: Public on Feb 02 2014

city: Dallas

first: Todd

middle: C.

last: Hoopman

address: 5323 Harry Hines Blvd.

department: Microbiology

country: USA

institute: University of Texas Southwestern Medical Center

summary: Comparison of the gene expression profile of Moraxella catarrhalis grown in the presence of 20% pooled human sputum in chemically-defined medium relative to Moraxella catarrhalis grown in chemically-defined medium alone.

overall_design: Moraxella catarrhalis ATCC43617 was grown to mid-logarithmic phase either in the presence of 20% pooled human sputum in chemically-defined medium or in chemically-defined medium alone.  Total RNA was extracted from bacterial cells exposed to each of these conditions and cDNA was generated for CyDye labelling.  3 biologic replicates were generated and each replicate underwent a dye swap (total of 6 experimental data collections).  The gene expression profile reported is that of Moraxella catarrhalis grown in the presence of pooled human sputum in a chemically-defined medium relative to Moraxella catarrhalis grown only in the presence of the chemically-defined medium.

first: Timothy

last: Murphy

first: Aimee

last: Brauer


title: Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to Shenzhou-8 spaceflight based on comparative transcriptomics.

city: Beijing

first: Huang

last: Bing

state: Chaoyang district

address: NO.1 Beichen West Road

department: State Key Laboratory of Microbial Resources

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: In order to gain a better understanding of the effects of Streptomyces coelicolor A3(2) wild type strain exposed to spaceflight condition, we constructed a whole genome microarray to screen simulated microgravity sensitive genes using the Agilent eArray 5.0 program. The genechip was custom designed according to the manufacturer’s recommendations (Agilent, 8*15K). The genome sequences were downloaded from: http://www.ncbi.nlm.nih.gov/genome?Db =genome&Cmd = Search&Term = NC_003888, NC_003903.1, NC_003904.1. Each gene was represented by one 60-nt oligonucleotide probe, and 680 genes associated with morphological differentiation and secondary metabolism out of the total 8116 genes were replicated 9 times each.

overall_design: Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 23±0.5°C for 16.5 days in spaceflight experiments. Total RNA was extracted to conduct the microarray experiments. The samples labeled in SP12_1 were from the “μg-position” and C07_1 from the “simulated 1g-position” inside the BIOBOX for spaceflight during Shenzhou-8 space mission. The samples labeled in DB3_1 were from static 1g position on gound as the control. SP12_1 was test sample; C07_1 and DB3_1 were both samples for control.

last: Ying


title: Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to simulated microgravity based on comparative transcriptomics (2-color)

summary: In order to gain a better understanding of the effects of Streptomyces coelicolor A3(2) wild type strain exposed to simulated microgravity condition by clinorotation, we constructed a whole genome microarray to screen simulated microgravity sensitive genes using the Agilent eArray 5.0 program. The genechip was custom designed according to the manufacturer’s recommendations (Agilent, 8*15K). The genome sequences were downloaded from: http://www.ncbi.nlm.nih.gov/genome?Db =genome&Cmd = Search&Term = NC_003888, NC_003903.1, NC_003904.1. Each gene was represented by one 60-nt oligonucleotide probe, and 680 genes associated with morphological differentiation and secondary metabolism out of the total 8116 genes were replicated 9 times each.

overall_design: Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 28°C for 144h (6d) under simulated microgravity (by a rotating clinostat) and 1g control conditions respectively. Total RNA was extracted to conduct the microarray hybridization experiments for two color (Cy3/Cy5).


title: col-0 vs cyp715a1-Genome-wide transcriptional analysis of cyp715A1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: rs12-08_cyp715a1 - col-0 vs cyp715a1 - The microarray analysis is part of a project aimed at characterizing the function of the cytochrome P450 CYP715A1 in Arabidopsis thaliana. - Flower buds of Arabidopsis Col-0 (wild-type) and cyp715A1 mutant were harvested for a comparative analysis of their transcriptomes.

overall_design: 3 dye-swap - gene knock out,genotype comparaison

first: Daniele

last: Werck

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Increased expression of c-Jun in nonalcoholic fatty liver disease

city: Regensburg

first: Julia

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

country: Germany

institute: University of Regensburg

summary:
Background & Aims: Overnutrition is one of the major causes of non-alcoholic fatty liver disease (NAFLD) and its advanced form non-alcoholic steatohepatitis (NASH). Besides the quantity of consumed calories, distinct dietary components are increasingly recognized as important contributor to the pathogenesis of NASH. We aimed to develop and characterize a hitherto missing murine model which resembles both the pathology and nutritional situation of NASH-patients in Western societies.
Methods: We developed a NASH-inducing diet (ND) enriched with sucrose, cholesterol and a high concentration of fats rich in saturated fatty acids in a composition which mimics Western food. C57Bl6/N mice were fed with the ND or control chow for 12 weeks. Biochemical, real-time polymerase chain reaction, Western Blot and immunohistochemical analyses were performed to characterize systemic and hepatic changes induced by ND-feeding. Immunohistochemistry was used to assess c-Jun levels and activation in 110 human NAFLD and control liver specimens applying tissue micro array technology.
Results: ND-fed mice showed significant body weight gain, impaired glucose tolerance, elevated fasting blood glucose levels as well as decreased adiponectin and increased leptin serum levels compared to control mice. In the liver, ND-feeding led to marked steatosis, enhanced cholesterol levels, distinct signs of oxidative stress, hepatocellular damage, inflammation, activation of hepatic stellate cells, and beginning fibrosis. Transcriptome-wide hepatic gene expression analysis comparing ND-fed mice and control mice indicated main alterations in lipid metabolism and inflammatory processes. Search for over-represented transcription factor target sites among the differentially expressed genes identified AP-1 as the most likely factor to cause the transcriptional changes in ND-livers. Combining differentially expressed gene and protein-protein interaction network analysis identified c-Jun (a component of the AP-1 complex) as hub in the largest connected deregulated sub-network in ND-livers. In accordance, ND-livers revealed c-Jun-phosphorylation and nuclear translocation. Moreover, hepatic c-Jun RNA and protein expression was enhanced in ND-fed compared to control mice. Also NAFLD-patients showed enhanced hepatic c-Jun levels, which correlated with inflammation, and notably, with the degree of hepatic steatosis.
Conclusions: The new dietary mouse-model shows important pathological changes also found in human NASH and indicates c-jun/AP-1 activation as critical regulator of hepatic alterations. Abundance of c-jun in NAFLD likely facilitates development and progression of NASH, and thus, c-jun appears as attractive prognostic and therapeutic target of NAFLD progression.

overall_design: 14-weeks old male C57BL/6N mice were fed with either regular diet or a newly designed NASH-inducing diet for 12 weeks. Hepatic gene expression levels were measured thereafter.

first: Christoph

last: Dorn

first: Michael

last: Saugspier

first: Andreas

last: Koch

first: Arndt

last: Hartmann

first: Martina

last: Müller

first: Rainer

last: Spang

first: Anja

last: Bosserhoff

first: Claus

last: Hellerbrand


title: Transcriptional Profiling of the sexual life cycle of Candida lusitaniae.

city: Providence

first: Christine

last: Scaduto

state: RI

address: 171 Meeting Street

department: Molecular Microbiology and Immunology

institute: Brown University

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

overall_design: Refer to individual Series


title: Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to simulated microgravity based on comparative transcriptomics.

overall_design: Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 28°C for 96h (4d) under simulated microgravity and 1g control conditions. Total RNA was extracted to conduct the microarray hybridization experiments. Three independent experiments were performed in which ASM_1A, ASM_2A, ASM_3A were the test group samples and ANG_1A, ANG_2A, ANG_3A were the control group samples. Differentially expressed genes were selected with P＜0.05, FC≥2.0 by T-test methods using the independent three sets data.


title: Phenotype heterogeneity and maturation of alveolar macrophages in the domestic pig

city: St Lucia

first: ronan

last: kapetanovic

state: QLD

address: The University of Queensland

institute: Institute for Molecular Bioscience

summary: The macrophages of the airways are the first line of innate immune defense against inhaled pathogens. We showed that pig bronchoalveolar cells are composed of an heterogeneous alveolar macrophage (AM) population. The adherent AM non-adherent produce more TNF when stimulated with bacterial compound and are more efficient at phagocytosis than the non-adherent AM.The micro-array analysis revealed two different gene expression and would suggest that the non-adherent population would be more adapted to anti-viral responses.

overall_design: 5 Affymetrix Snowball microarray were analyzed from 1 pig breed (HAMSHIRE). Gene expression from non-adherent AM was compared to previous Array of Adherent AM from the same individuals (Series GSE45145). Cells were left untreated.

first: R

last: Kapetanovic

first: L

last: Fairbairn

last: Moffat

first: AE

last: Karagianni

first: A

last: Downing

first: RH

last: Fleming

first: AL

last: Archibald

first: DA

last: Hume


title: INTEGRATING TRANSCRIPTOMICS INTO TRIAD-BASED SOIL QUALITY ASSESSMENT

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

summary: This study examined how transcriptomics tools can be included in a Triad-based soil quality assessment to assess the toxicity of soils from river banks polluted by metals. To that end we measured chemical soil properties and used the standardized ISO guideline for ecotoxicological tests and a newly developed microarray for gene expression in the indicator soil arthropod, Folsomia candida. Microarray analysis revealed that the oxidative stress response pathway was significantly affected in all soils except one. The data indicate that changes in cell redox homeostasis are a significant signature of metal stress. Finally, 32 genes showed significant dose-dependent expression with metal concentrations. They are promising genetic markers providing an early indication of the need for higher tier testing in soil quality. One of the least polluted soils showed toxicity in the bioassay that could be removed by sterilization. The gene expression profile for this soil did not show a metal-related signature, confirming that another factor than metals (most likely of biological origin) caused the toxicity. This study demonstrates the feasibility and advantages of integrating transcriptomics into Triad-based soil quality assessment. Combining molecular and organismal life-history trait’s stress responses helps identifying causes of adverse effect in bioassays. Further validation is needed for verifying the set of genes with dose-dependent expression patterns linked with toxic stress.

overall_design: We used a one-color microarray design where each sample was hybridized to a single array

first: Guangquan

last: Chen

middle: E

first: Marlea

last: Wagelmans

first: Cornelis

last: van Gestel

first: Nico

last: van Straalen

first: Dick

last: Roelofs


title: Candida lusitaniae mating

summary: Transcriptional profiling of C. lusitaniae a and alpha cells mixed on 0.37% PDA (potato dextrose agar) for 0 hours (h) ,4h, and 12n  hybridized against WT cells on YPD for 4 hours and also  a and alpha ime2 deletion mutants mixed on 0.37% PDA for 4 hours hybridized against WT cells on YPD (yeast peptone dextrose) for 4h

overall_design: Two condition experiment: WT a and alpha cells on 0.37% PDA and a and alpha ime2 deletion mutants mixed on 0.37% PDA. Three biological replicates

first: Racquel

last: Sherwood

first: Richard

last: Bennett


title: Gene expression profiling of FFPE breast cancer samples

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: We implemented an optimized processing, using alternative Chip Description Files (CDFs) and fRMA normalization, which improve the quality of downstream analysis.

overall_design: We profiled 44 FFPE primary breast cancer samples using Affymetrix HG-U133 Plus 2.0 microarray platform after RNA amplification with the Nugen WT-Ovation FFPE System

first: Valeria

last: Musella

first: Vera

last: Cappelletti

first: Antonio

last: Lembo

first: Paolo

last: Provero

first: Giampaolo

last: Bianchini

first: Luca

last: Gianni

first: Maria

middle: G

last: Daidone


title: Differential gene expression in notochord and nerve-cord fate segregation in the Ciona intestinalis embryo

city: Toba

first: Lixy

last: Yamada

state: Mie

address: 429-63 Sugashima

department: Graduate School of Science,

institute: Nagoya University

summary: Fertilized eggs are plulipotent and during early embryogenesis, embryonic cells gradually restrict their developmental potential and are eventually destined to give rise to one type of cells. Molecular mechanism underlying developmental fate restriction is one of the major research subjects of developmental biology. Here we address this question by combining a classical technique of blastomere isolation with a modern technique of microarray analysis. During the 6th cleavage of the Ciona intestinalis embryo, from the 32-cell to the 64-cell stage, four mother cells divide into daughter cells with two distinct fates, one giving rise to notochord and the other to nerve-cord precursor cells.  Nearly 500 notochord or nerve-cord precursor cells each were isolated, and difference in the quality of mRNAs between them was compared by microarray. This analysis identified 111 and 69 genes that are differentially expressed in the notochord and nerve-cord precursor cells, respectively. These included not only genes for transcription factors and signalling molecules but also those with functions that many kinds of cells used. In addition, whole-mount in situ hybridization showed complex and dynamic profiles of spatial expression of these genes during the segregation of the two fates. The process is accomplished by that transcripts that have been already present in the mother cell are properly partitioned into either type of cells and that new and preferential expression of genes in either type of cells.

overall_design: Two kinds of sample, Dye Swap design with 2 arrays

first: Kenji

last: Kobayashi

first: Yutaka

last: Satou

first: Nori

last: Satoh


title: Candida lusitaniae a/alpha WT meiosis

first: Christine

last: Scaduto

summary: Transcriptional profiling of C. lusitaniae a/alpha WT cells on 0.37% PDA (potato dextrose agar) for 30 minutes (m), 2 hours (h), 4h, 8h, 12h, 18h, 24, and 30h hybridized against WT a/alpha cells in non-meiosis inducing conditions YPD (yeast peptone dextrose) for 2h

overall_design: Two condition experiment: a/alpha WT on PDA vs. a/alpha WT on YPD, 4 biological replicates

middle: J


title: Candida lusitaniae STE12 meiosis

summary: Transcriptional profiling of C. lusitaniae a/alpha ste12Δ/ste12Δ  deletion mutants on .37% PDA (potato dextrose agar) media for 0 hours (h), 12h, 28h, and 24 hours hybridized against WT a/alpha cells on YPD (yeast peptone dextrose) media for 2h

overall_design: Two condition experiment: 2N (a/alpha) ste12Δ/ste12Δ  (CAY4240) on PDA vs. 2N WT (RSY432) on YPD, 1 biological replicate