title: Identification of skin-expressed genes possibly associated with wool growth regulation in Aohan fine wool sheep

status: Public on Dec 31 2014

city: Qingdao

first: Hegang

last: Li

state: Shandong

address: 149 Xiazhuang Road, Licang District

department: Animal Reproduction and Breeding

country: China

institute: Qingdao Institute of Animal Science and Veterinary Medicine

summary:
Background: Sheep are valuable resources for the animal fibre industry. Therefore, identifying genes which regulate wool growth would offer strategies for improving the quality of fine wool. In this study, we employed Agilent sheep gene expression microarray and proteomic technology to compare the gene expression patterns of the  body side (hair-rich) and groin (hairless) skins of Aohan fine wool sheep (a Chinese indigenous breed).
Results: Comparing the body side to the groin skins (S/G) of Aohan fine wool sheep, the microarray study revealed that 1494 probes were differentially expressed, including 602 more highly expressed and 892 less highly expressed probes. The microarray results were verified by means of quantitative PCR. Cluster analysis could distinguish the body side skin and the groin skin. Based on the Database for Annotation, Visualization and Integrated Discovery (DAVID), 38 of the differentially expressed genes were classified into four categories, namely regulation of receptor binding, multicellular organismal process, protein binding and macromolecular complex. Proteomic study revealed that 187 protein spots showed significant (p < 0.05) differences in their respective expression levels. Among them, 46 protein entries were further identified by MALDI-TOF/MS analyses.
Conclusions: Microarray analysis revealed thousands of differentially expressed genes, many of which were possibly associated with wool growth. Several potential gene families might participate in hair growth regulation. Proteomic analysis also indentified hundreds of differentially expressed proteins.

overall_design: One ram and two ewes of 16-month-old Aohan fine wool sheep were used in the microarray study. These animals were half sibs (sharing the same father). In December 2010, two areas of full-thickness skin were sampled from the same animal under local anaesthesia: body side skin (wool bearing) and groin skin (non-wool bearing) for microarray and proteomic experiments. The area of each sample was about 1 cm2. All samples were immediately put into collection tubes and stored in liquid nitrogen for RNA and protein extraction. A total of 15, 208 probes were spotted on this Agilent Sheep Gene Expression Microarray (Santa Clara, CA, USA).

last: Liu

first: Kaidong

first: Juanjuan

last: Yu

first: Ran

last: Bu

first: Ming

last: Cheng

first: Wei

last: De

first: Jifeng

first: Guangling

last: He

first: Jinshan

last: Zhao


city: Heverlee

first: Hans

last: Steenackers

address: Kasteelpark Arenberg 20, box 2460

country: Belgium

institute: KU Leuven

type: Genome binding/occupancy profiling by genome tiling array

summary: FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged FabR (IP samples) and wildtype strain (mock IP samples)

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: IP sample (using anti-Myc antibody against Salmonella Typhimurium SL1344 strain encoding chromosomally 9Myc-tagged FabR) and control mock IP sample (using anti-Myc antibody against Salmonella Typhimurium SL1344 wildtype strain) were labeled with Cy5 and hybridized against a common genomic DNA reference, labeled with Cy3, on 2 S. Typhimurium LT2 whole genome tiling arrays

first: Kim

last: Hermans

first: Inge

last: Thijs

first: Marchal

last: Kathleen

first: Sigrid

last: De Keersmaecker


city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: The aim of our study was to assess miRNA expression of canine mammary cancer stem cells.  Three canine mammary cancer cell lines (CMT-U27, CMT-U309 and P114) were stained using  Anti-Sca1 (Stem cell antigen 1) antibodies. The FACS analysis showed 0,3-1% of Sca1+ cells in  each of the cell line. The cells were sorted (using FACS Aria II) as Sca1+ and Sca1- and subjected  to further analysis of miRNA expression (using Agilent custom miRNA microarray).

overall_design: Canine mammary cancer cell lines were stained using Stem Cell Antigen 1 antibodies and then sorted using FACS Aria II as Sca-1 positive (cancer stem cells) and Sca-1 negative (control). Then, total RNA was isolated and hybridized at miRNA microarrays.

last: Krol

first: Agata

last: Homa

first: J

last: Mucha


title: Early Leptin Intervention Reverses Perturbed Energy Balance Regulating Hypothalamic Neuropeptides in the Pre- and Postnatal Calorie Restricted Offspring

city: Los Angeles

first: William

middle: Alexander

last: Freije

state: CA

address: 650 Charles Young Drive, South CHS B8-127

department: Obstetrics and Gynecology

country: USA

institute: UCLA

summary: Pre- and postnatal calorie restriction is associated with postnatal growth restriction,  reduced circulating leptin concentrations and perturbed energy balance. Hypothalamic  regulation of energy balance demonstrates enhanced orexigenic (NPY, AgRP) and  diminished anorexigenic (POMC, CART) neuropeptide expression (PN21) setting the  stage for subsequent development of obesity. Leptin replenishment during the early  postnatal period (PN2-PN8) led to reversing the hypothalamic orexigenic:anorexigenic  neuropeptide ratio at PN21 by only reducing the orexigenic (NPY, AgRP) without  affecting the anorexigenic (POMC, CART) neuropeptide expression. This hypothalamic  effect was mediated via enhanced leptin receptor (ObRb) signaling that involved  increased pSTAT3 but reduced PTP1B. This was further confirmed by an increase in  body weight at PN21 in response to intracerebroventricular administration of antisense  ObRb oligonucleotides (PN2-PN8). The change in the hypothalamic neuropeptide  balance in response to leptin administration caused increased oxygen consumption,  carbon dioxide production and physical activity which resulted in increased milk intake  (PN14) with no change in body weight. This is in contrast to the reduction in milk intake  with no effect on energy expenditure and physical activity observed in controls. We  conclude that pre- and postnatal calorie restriction perturbs hypothalamic neuropeptide  regulation of energy balance setting the stage for hyperphagia and reduced energy  expenditure, hallmarks of obesity. Leptin in turn reverses this phenotype by increasing  hypothalamic ObRb signaling (sensitivity) and affecting only the orexigenic arm of the  neuropeptide balance.

overall_design: Transcriptional studies have been performed using Affymetrix Rat Gene 1.0 arrays for the following treatment groups, with each group run in duplicate: Day 21 Control saline treatment (Con-s), Day 21 Control leptin treatment (Con-r), Day 21 calorie restriction saline treatment (CR-s), and  Day 21 calorie restriction leptin treatment (CR-l).

first: Sherin

last: Devaskar


title: A DNA hypermethylation profile reveals new potential biomarkers for prostate cancer diagnosis and prognosis

city: Alcala de Henares

first: Nadia

last: Ashour

address: S/N

department: Biochemistry

country: Spain

institute: Universidad de Alcala

summary: Detection of DNA hypermethylation has emerged as a novel molecular biomarker for the evaluation of prostate cancer diagnosis and prognosis, but the use of single gene hypermethylation could produce unspecific results. Defining the specific gene hypermethylation profile for prostate cancer could provide groups of genes that specifically discriminate the patients with indolent and aggressive tumors. To compare the methylation profile of normal and malignant prostate we performed Genome-wide methylation analysis on 83 tumor samples, that included all clinical stages of the disease, 10 normal prostate samples and LNCaP, DU145 and PC3 prostate cancer cell lines using the GoldenGate Methylation Cancer Panel I (Illumina, Inc.) that interrogate for 1505 CpGs. We found 41 genes significantly hypermethylated in more than 20% of the tumors analyzed (p<0.01). Of these we identified GSTM2 and PENK as novel hypermethylated genes in prostate cancer that were simultaneously methylated in 40.9% of the tumors analyzed. We also identified panels of genes more frequently methylated in tumor samples with clinico-pathological indicators of poor prognosis: high Gleason score, elevated Ki-67 or advanced disease. Of these, we found that simultaneous hypermethylation of CFTR and HTR1B is common in patients with high Gleason score and high ki-67 levels and might signal the population at higher risk of therapeutic failure. DNA hypermethylation profile was associated with cancer-specific mortality (log-rank, p=0.007) and biochemical recurrence-free survival (log-rank, p=0.0008). In conclusion, our data strongly indicate that epigenetic silencing of GSTM2 and PENK is a common event in prostate cancer that could be used as a molecular marker for prostate cancer diagnosis. In addition, simultaneous HTR1B and CFTR hypermethylation could help discriminate aggressive from indolent prostate tumors.A DNA hypermethylation profile associated with cancer-specific mortality and biochemical recurrence in patients receiving radical prostatectomy is presented. GST2 and PENK are new hipermethylated genes identified. Simultaneous hypermethylation of CFTR and HTR1B could help discriminate aggressive disease.

overall_design: Total DNA isolated by standard procedures from prostate tumors and prostate cancer cell lines  cultured under standard conditions

first: Javier

middle: C

last: Angulo

first: Guillermo

last: Andrés

first: Raúl

last: Alelú

first: Ana

last: González-Corpas

first: María

middle: V

last: Toledo

first: José

middle: M

last: Rodríguez-Barbero

middle: I

last: López

first: Manuel

last: Sánchez-Chapado

first: Santiago

last: Ropero


title: Variation in embryonic mortality and maternal transcript expression among Atlantic cod (Gadus morhua) females: a functional genomics study

city: St. John's

first: Matthew

last: Rise

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: Early life stage mortality is an important issue for Atlantic cod aquaculture.  The impact of the cod maternal (egg) transcriptome on egg quality and mortality during embryonic development is poorly understood.  In the present work we studied embryonic mortality and maternal transcript expression using 15 females within an Atlantic cod broodstock development program.  Cumulative mortality at 7 days post-fertilization (segmentation stage) and percent hatch were used to assess embryonic survival as an indicator of egg quality.  A 20,000 probe (20K) microarray experiment compared the 7 hour post-fertilization (7 hpf, ~ 2-cell stage) egg transcriptome of the two lowest quality females (both with less than 1 percent hatch) to that of the highest quality female (greater than 50 percent hatch).

overall_design: At 7 hours post-fertilization, 3 batches of 0.25 ml eggs were collected from each of the two lowest quality females (females 12 and 13) and the highest quality female (female 2). For each female, total RNA was isolated from each of the three batches separately, and pooled before microarray analysis. Two 4-array direct comparison experiments were performed. For each 4-array experiment, one of the ‘low quality’ females was compared to the ‘high quality’ female, and each RNA was labeled in 4 labeling reactions: two with AlexaFluor 647 and two with AlexaFluor 555. Each 4-array experiment consisted of four technical replicates: two duplicates and two dye-swaps. Females 12 and 13 are two biological replicates.

middle: L

first: Gordon

middle: W

last: Nash

first: Jennifer

middle: R

last: Hall

first: A

middle: K

last: Gamperl

first: Marije

last: Booman

first: Tiago

middle: S

last: Hori

first: Edward

middle: A

last: Trippel


title: Genome-wide transcriptional profiling of Clostridium perfringens SM101 during sporulation

city: Wageningen

first: Yinghua

last: Xiao

address: Bornse Weilanden 9

country: Netherlands

institute: Wageningen University

summary: In this study we focus on the identification of new genes tentatively involved in sporulation and those that influence properties of spores and their ability to germinate. To this end, the sporulation stages of C. perfringens enterotoxic strain SM101 were characterized based on morphological characteristics and biological indicators. Subsequently, whole genome expression profiling during key stages of the sporulation process was performed using DNA microarrays, and genes were clustered based on their time-course expression profiles during sporulation. The majority of previously characterized C. perfringens germination genes showed upregulated expression profiles in time during sporulation and mainly belonged to two clusters of genes.

overall_design: Loop design for two indepedantly perfromed experiments (biological replicates, A or B), each of which contains five time points (T1-T5). Cy3- and Cy5-labeled cDNA of the same RNA sample were hybridized 2 to 3 times (techical replicates) on Agilent custom microarrays.

first: Sacha

last: van Hijum

first: Tjakko

last: Abee

first: Marjon

middle: H

last: Wells-Bennik


title: CbGRiTS: Cerebellar Gene Regulation in Time and Space

city: Vancouver

first: Thomas

last: Ha

state: British Columbia

address: 950 West 28th Avenue

department: CMMT

institute: University of British Columbia

summary: This dataset is populated with transcriptome data across embryonic and postnatal development from two standard mouse strains, C57BL/6J and DBA/2J. Users can evaluate expression profiles across cerebellar development in a deep time series.

overall_design: We performed microarray analysis on whole cerebellar tissues from two inbred strains of mouse [C57BL/6J (B6) and DBA/2J (D2)] at 24-hour intervals in embryonic development from embryonic day 12 (E12) to postnatal day 0 (P0), and at 3-day intervals from P0 to P9 in the postnatal period and most time point samples include 3 biological replicates each for both strains.

first: Doug

last: Swanson

first: Dan

last: Goldowitz


title: Effect of calcium depletion on cold induced gene expression in barley

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

summary: Agilent 44k barley microarray was used to screen calcium dependent cold induced genes. Calcium chelator (EGTA) or calcium channel blocker (lanthanum) or phospholipase C activator (mastoparan) pretreatments were performed to block/enhance calcium response in barley seedlings. Calcium depleted and control plants were cold treated and the difference in the gene expression was investigated.

overall_design: Hordeum vulgare, L. cv. Nure / lower part (~1.5 cm) of the stem (hypocotyl and cotyledons) of 4-day-old seedlings / sampling: at 24 hours after the beginning of cold treatment, 2 biological replications per treatment, 15 individual plants per replication

first: Ildikó

last: Vashegyi

first: Vilmos

last: Soós

first: Zsuzsa

last: Marozsán-Tóth

first: Balázs

last: Tóth


title: Gene profiling during symbiosis between the actinorhizal tree Casuarina glauca and the actinobacteria Frankia CcI3 after treatment with 1-naphtoxy acetic acid, an auxin influx inhibitor.

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

country: France

institute: IRD

summary:
Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to study the role of the plant growth regulator auxin during actinorhizal symbiosis and to identify  key plant genes that are involved in auxin signaling during symbiosis in C. glauca.
Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen (N2) which favors the induction of nitrogen fixing symbiosis. For auxin role study, plant were treated with 25µM 1-naphtoxy acetic acid (1-NOA) all along nodulation time. Nodule were harvested 3 weeks after inoculation. For this study we considered two stages:  -  21 days old nodules obtained on plants not treated with 1-NOA (control condition)    - 21 days old nodules obtained on plants supplemented with 25µM of 1-NOA.   Three biological replicates were used for each condition, however due to non valid staistics, two of the replicates (one for control condition, one for treated condition were removed.

overall_design: Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for C. glauca, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent.

last: Hocher

first: Laurent

last: Laplaze


title: Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RT-PCR

city: Manchester

first: Ged

last: Brady

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Rd

department: Clinical and Experimental Pharmacology

country: United Kingdom

institute: Caner Research UK Manchester Institute

summary: Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. The approach was tested by comparing expression profiles of amplified single MCF7 and MCF10A cells to profiles generated from unamplified RNA. The expression profiles were compared by Affymetrix-U133 arrays, RNA-Seq and high-density qPCR.  There were strong cross-platform correlations of >80% and concordance between single cell and unamplified material of >70%. We exemplify the approach through analysis of rare sorted cancer initiating cells (CICs) derived from a NSCLC patient-derived xenograft. Populations of 10 cells from total tumour and two distinct subsets of CIC, putatively involved in primary tumor maintenance or metastasis formation were FACS sorted then directly amplified. CIC expression profiles strongly correlated with published stem-cell and epithelial-mesenchymal transition (EMT) signatures. Our results confirm the utility of the amplification system and our methodology to detect and distinguish RNA profiles in rare cell populations that inform on EMT and stem-cell characteristics. This GEO dataset comprises the RT-qPCR data for MCF7 and MCF10A unamplified cDNA from 1μg RNA, RNA-AMP cDNA from 1ng RNA and RNA-AMP cDNA from single cell samples.

overall_design: 22 samples. 3 biological replicates each for MCF7 cDNA generated from 1ng amplified RNA, MCF10A cDNA generated from 1ng amplified RNA, MCF7 cDNA generated from 1 μg unamplified RNA and MCF10A cDNA generated from 1 μg unamplified RNA. 5 biological replicates each for MCF7 cDNA generated from RNA amplified from a single cell and MCF10A cDNA generated from RNA amplified from a single cell. Expression of genes in MCF7 and MCF10A was compared in each of the sample types, and these results from each sample type were compared.

first: Dominic

middle: G

last: Rothwell

first: Yaotong

last: Li

first: Gillian

last: Newton

first: Yvonne

last: Hey

first: Mahmood

last: Ayub

first: Catriona

last: Tate

first: Louise

last: Carter

first: Suzanne

last: Faulkner

first: Stuart

last: Pepper

first: Crispin

last: Miller

first: Fiona

last: Blackhall

first: Giulia

last: Bertolini

first: Luca

last: Roz

first: Caroline

last: Dive


title: Expression data from lupus NZB/W and NZW/BXSB mouse prenephritic kidneys

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary: We defined the shared and unique features of systemic lupus erythematosus (SLE) nephritis in 2 mouse models of proliferative renal disease. We identified shared inflammatory mechanisms of SLE nephritis that can be therapeutically targeted. Some common mechanisms are shared with non-immune-mediated renal diseases, suggesting that new strategies to prevent tissue hypoxia and remodeling may be useful in SLE nephritis.

overall_design: RNA from whole kidneys was extracted and processed for hybridization on Affymetrix microarrays.

first: Ramalingam

last: Bethunaickan

first: Weija

last: Zhang

first: Matthias

last: Kretzler

first: Anne

last: Davidson


title: A jasmonate ZIM-domain protein NaJAZd regulates floral jasmonic acid levels and counteracts flower abscission in Nicotiana attenuata plants

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of transcripts that change expression in Nicotiana attenuata plants with reduced expression of JAZd after elicitation with oral secretions of Manduca sexta larvae.

overall_design: Gene expression in leaves of Nicotiana attenuata wild type and irJAZd plants was measured at 2 hour after elicitation with oral secretions of Manduca sexta larvae. Three independent experiments were performed with wild type plants and three independent experiments were performed with irJAZd plants. A total of  503 genes were identified as more the 2 fold differentially regulated in irJAZd plants compared to wild type plants.

first: Youngjoo

last: Oh

first: Ivan

last: Galis


title: Gene expression of immune-related genes in peripheral blood of children with Down syndrome

city: São José do Rio Preto

first: Érika

middle: Cristina

last: Pavarino

state: São Paulo

address: Avenida Brigadeiro Faria Lima, nº 5416 - UPGEM/Bloco U-6

department: Departamento de Biologia Molecular

country: Brazil

institute: Faculdade de Medicina de São José do Rio Preto (FAMERP)

summary: To identify differentially expressed genes that might be of pathogenetic importance for the development of the immunological alterations observed in individuals with Down syndrome (DS) we profiled the expression pattern of 92 immune-related genes in peripheral blood mononuclear cells (PBMC) of two different groups, children with DS and control children.

overall_design: Peripheral blood mononuclear cells  samples were obtained from six healthy individuals with karyotypically confirmed full trisomy 21 and six healthy control individuals (ages 2-6 years). Gene expression was profiled in duplicate according to the manufacturer’s instructions provided by commercially available TaqMan® Human Immune Array representing 92 immune function genes and four reference genes on a 96-plex gene card.

first: Bruna

last: Zampieri

first: Joice

last: Biselli-Périco

first: Matheus

last: Bürger

first: Jorge

middle: E

last: de Souza

first: Wilson

last: da Silva Júnior

first: Eny

last: Goloni-Bertollo


title: Leishmania infantum: Alba20 null mutant Vs wild type

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

institute: Université Laval

summary: Transcriptome analysis of an LiAlba20 (LinJ.34.2410) null mutant strain versus Wild type. Experiments were run with promastigotes and axenic amastigotes independently. Null mutant was produced by homologous recombination, replacing both alleles with Hygromycin phosphotransferase and Puromycin.

overall_design: Two independent experiments, each samples were used as triplicates

first: Aurélien

last: Dupé

first: Éric

last: Madore

first: Frédéric

first: Carole

last: Dumas

first: Barbara

last: Papadopoulou


title: Oral squamous cell carcinoma cells: microRNA-34a transfected vs. the control

city: Wuhan

first: YU

last: WANG

address: No.237 Luoyu Road

institute: Wuhan University

summary: To compare the differential gene expression  between oral squamous cancer cells stably  overexpression of miR-34a and cells transfected with control vectors.

overall_design: Two head and neck squamous cell carcinoma  cell lines( FADU and UM-SCC-23) transfected with control Lentivirus pCDH-CMV-MCS-EF1-eGFP and Lenti‐ pCDH-CMV-MCS-EF1-eGFP-miR‐34a respectively were analyzed. The dual channel method was used to detect the hybridization of fadu-miR-34a vs Fadu control and um-scc-23-miR-34a vs control.

first: Jiali

last: Zhang

first: Yu

last: Wang


title: MicroRNA expression in human colon: Crohn's disease versus ulcerative colitis

city: Houston

first: Jeremy

last: Schaefer

state: TX

address: 1941 East Rd

department: Diagnostic Sciences

institute: The University of Texas Health Science Center at Houston School of Dentistry

summary: Analysis of miRNA expression in colon biopsies from Crohn's disease (CD), ulcerative colitis (UC), and non-inflammatory bowel disease (IBD) control subjects.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two Crohn's disease colon biopsies and two ulcerative colitis colon biopsies were compared to a single non-IBD control colon biopsy to ascertain differences in miRNA expression.

first: John

last: Klein

first: David

middle: Y

last: Graham

first: Taraq

last: Attumi

first: Antone

last: Opekun

first: Bincy

last: Abraham

first: Jason

last: Hou

first: Harold

last: Shelby

first: Charles

last: Streckfus


title: A Ten-microRNA signature identified from a genome-wide microRNA expression profiling in human epithelial ovarian cancer

city: Shanghai

first: Ruo-Ying

last: Tan

address: 2nd Floor, 1st Building, 2140 Xietu Road,

institute: Biovue Technology (China) Ltd

summary: Human Ovarian tissue samples  including 15 normal tissue samples  and 48 malignant ovarian tissue  were collected at Zhongshan Hospital of Fudan University. All tissue samples were immediately frozen in liquid nitrogen after being removed from body and stored at -80°C. Biovue's Sharpvue miRNA qPCR array panels (A-E) including 1721 unique assays were used to quantitate genome-wide miRNA gene expression from the collected ovarian tissue samples.

overall_design: qPCR genome-wide miRNA gene expression profiling for ovarian tissue samples from clinical hosptial.  Equal amount total RNA from each sample was used in gene expression analysis. Normal (n=14) and (n=45) samples.

first: Lin

first: Ai-Min

last: Ren

first: Rui-Qin

last: Tu

first: Miao-Jun

last: Zhu

first: Hong-Fei

last: Wu

first: Wu-Mei

last: Hang


title: Amoebal endosymbiont Neochlamydia S13 gene expression in host amoebae when Leginella infected

city: Sapporo

first: Hiroyuki

last: Yamaguchi

address: N5 K12 Jo Kita-ku

country: Japan

institute: Hokkaido University

summary: To further development of our gene expression approch to intracellular pathogenic bacterial controlling, we have employed castamized Neochlamydia S13 genomic microarray  as a discovery platform to identy genes with the potential to inhibit Legionella growth into hoat amoebae , based on our data that the the amoebae haboring amoebal endosymbiont Neochlamydia S13 (an environmental chlamydia) could evade Legionella infection.

overall_design: Neochlamydia S13 gene experssions in host ameobae  with or without Legionella infection (24h pi, MOI1) was measured. Single experiment was performed; a probe against each of the genes was arrayed quintuply. Avaraged values were used for analysis.

first: Junji

last: Matsuo


title: Phenotypic and genotypic stability in a preclinical model of renal cell carcinoma

city: Paris

first: Anne

last: Janin

address: 1 Av C Vellefaux

institute: University Paris 7, INSERM, APHP

type: Genome variation profiling by genome tiling array

summary: Renal cell carcinomas are often resistant to conventional cytotoxic agents. Xenograft models are used for in vivo preclinical studies and drug development. The validity of these studies is highly dependent on the phenotypic and genotypic stability of the models.  We evaluated the stability of six kidney tumors xenografted in nude/NMRI mice. We compared the initial sample (P0), 1st (P1) and 5th (P5) passages for the following criteria: histopathological analysis, immunohistochemistry for CK7, CD10, vimentin and p53, and DNA analysis with 10 microsatellites. We also performed CGH-array and we compared the sensitivity to sunitinib with tumor response in patients.  The six xenografted tumors showed no difference between the morphology of the primary tumor and that of the xenografted tumor at P1 and P5 but we observed differences for CK7 expression in one case and for p53 expression in another.   Out of 44 P0-P1-P5 groups with fully available microsatellite data, 29 (66%) showed no significant difference from P0 to P5 while 15 (34%) showed new or lost alleles. In CGH-array, genomic alterations at P5 were close to those already present in the initial tumor. We also observed similarity between the models and the patients for response to antiangiogenic treatment.  We showed that the six xenograft models were phenotypically and genotypically stable across passages and showed similarity with response to treatment in patients.

overall_design: CGH-arrays are realized on samples at P0 (samples K8-614_P0 and K9-162_P0) and their corresponding xenografted tumors at P5 (samples K8-614_P5 and K9-162_P5)

first: Mariana

last: Varna

first: Guilhem

last: Bousquet

first: Irmine

last: Ferreira

first: Marie

last: Goulard

first: Morad

last: El-Bouchtaoui

first: Pierre

last: Artus

first: Jerome

last: Verine

first: Eric

last: de Kerviler

first: Lucie

last: Hernandez

first: Christophe

last: Leboeuf

first: Bernard

last: Escudier

first: Luc

last: Legrès

first: Niclas

last: Setterblad

first: Hany

last: Soliman

first: Jean-Paul

last: Feugeas

first: Philippe

last: Bertheau


title: Gene expression profiles in juvenile hormone biosynthetic organ compared to other tissues in Bombyx mori

city: Tokyo

first: Toru

last: Togawa

address: Sakurajyosui 3-25-40, Setagaya-ku

department: Integrated Sciences in Physics and Biology

institute: Nihon University

summary: Juvenile hormone (JH) is produced and secreted by corpora allata (CA) during larval stages.  JH biosynthesis from acetyl-CoA includes 13 enzymatic steps.  Genes for 10 of those enzymes have been identified from Bombyx mori.  It was also reported that they are basically expressed selectively in CA.  Genes for the other 3 enzymes were recently reported from other insects, i.e., farnesyl diphosphate pyrophosphatase (FPPP) from Drosophila and farnesol dehydrogenase (FolD) and farnesal dehydrogenase (FalD) from Aedes.  In order to reveal the expression profiles of these genes in Bombyx CA and to find other candidate genes involved in JH biosynthesis, we performed a transcriptomic analysis in corpora cardiaca-CA (CC-CA) complexes using a custom-made DNA microarray on which sequences from CC-CA EST libraries and genome-widely predicted genes are loaded.  CC-CA complexes vigorously expressed JH-biosynthetic genes identified in Bombyx as well as genes involved in methyl-group metabolism and ribosomal protein genes; this is suitable for JH production.  Bombyx counterparts of Drosophila FPPP and Aedes FolD genes, however, showed quite low level of expression.  On the other hand, some other genes probably encoding oxidoreductases were expressed highly and selectively in CC-CA complex.  Their products might function as FolD and/or FalD in Bombyx.

overall_design: Microarray experiments were performed for RNA samples isolated from 2 batches of CC-CA complexes (CCCA1 and CCCA2, independent experiments), prothoracic glands (PG), brains (Br), fat bodies (FB), mid guts (MG), epidermis (Ep), Malpighan tubules (MT), salivary glands (SalG) of day-2 4th instar; testes (W3Ts) and ovaries (W3Ov) of day-10 5th instar (3 days after the beginning of wandering); and CC-CA complexes (V4CCCA) of day-4 5th instar larvae.

first: Yuki

last: Nakamura

first: Tetsuro

last: Shinoda


title: Experimental selection of long-term intracellular mycobacteria

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Some intracellular bacteria are known to cause long-term infections for periods of time that last decades without compromising the viability of the host. Although of critical importance, the changes that intracellular bacteria suffer during this long process of residence in a host cell environment remain obscure. Here, we report an experimental approach to study the adaptations of intracellular mycobacteria forced by a long-term intracellular lifestyle. Long-term infection of host macrophages with mycobacteria was maintained for a period of years. Mycobacteria in the long-term infected macrophages underwent an adaptation process leading to impaired phenolic glycolipids (PGL) synthesis, preference for glucose as a carbon source and neutral lipids accumulation. These changes correlated with increased survival of mycobacteria in macrophages and mice during re-infection and specific expression of stress- and survival-related genes. Our findings identify bacterial traits implicated in the establishment of long-term cellular infections and represent a tool for understanding the physiological states of bacteria living in fluctuating intracellular environments.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: We investigated the genes differentially expressed during re-infection that might contribute to the improved survival. Using a microarray, we identified a clear and distinct pattern of gene expression after re-infection comparing ancestral (BCGanc) and selected bacteria (BCGevo)

first: G

last: Gutierrez

first: R


title: Salmonella enterica serovar Typhimurium SL1344 cells: wildtype vs. ΔfabR mutant

city: Heverlee

first: Hans

last: Steenackers

address: Kasteelpark Arenberg 20, box 2460

institute: KU Leuven

summary: Transcriptional profiling of Salmonella enterica serovar Typhimurium SL1344 cells comparing wildtype with ΔfabR mutant. Salmonella strains were cultured under free-living TSB conditions (TSB 1/20, 200 rpm, 25 °C) for 6h (ca. 2 x 108 cells/ml).

overall_design: two strain experiment. One biological repeat for each strain. Hybridizations were performed in color flip.

first: Kim

last: Hermans

first: Kathleen

last: Marchal

first: Sigrid

last: De Keersmaecker


title: The Effect of Camelina Oil-Containing Diets on the Expression of Genes Involved in the Innate Anti-Viral Immune Response in Atlantic Cod (Gadus Morhua)

city: St. John's

first: Marije

last: Booman

address: 1 Marine Lab Road

department: Ocean Sciences

institute: Memorial University of Newfoundland

summary: This study was performed to investigate the effect of camelina oil-based diets on the immune function of Atlantic cod, as measured by gene expression in spleen. Atlantic cod were fed with one of three practical diets (three tanks per diet): a control diet using herring oil as a lipid source (FO diet), and two experimental diets using vegetable oil from Camelina sativa to replace 40% or 80% of herring oil (40CO and 80CO diets). We studied both the effect of the diet alone on basal spleen gene expression levels, as well as the effect of the diet after fish were injected with the synthetic double-stranded RNA polyriboinosinic polyribocytidylic acid (pIC), which mimics a viral immune stimulus.

overall_design: Atlantic cod were fed for 67 days with the FO, 40CO or 80CO diet (three tanks per diet). Then the fish from each tank were divided over two separate tanks and after 6 days of acclimation they were injected intra-peritoneally with either pIC (3 tanks per diet) or PBS (three tanks per diet). Spleen samples were taken from 6 fish from each tank at 0h (pre-injection), 6 hours post injection (HPI), and 24HPI. A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual spleens of fish from the following 9 treatment groups: FO 0h, 40CO 0h, 80CO 0h, FO 24HPI PBS, FO 24HPI pIC, 40CO 24HPI PBS, 40CO 24HPI pIC, 80CO 24HPI PBS, and 80CO 24HPI pIC. For each 0h group we used 12 biological replicates (2 fish from each of 6 tanks), and for each 24HPI group we used 9 biological replicates (3 fish from each of 3 tanks). All test samples were labeled with AlexaFluor 647. The common reference was a pool of 259 RNA samples from spleens of fish from all tanks, representing all 3 diets, both PBS and pIC treatments, and all 3 time points. The common reference was labeled with Alexafluor 555. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 90 microarrays

first: Qingheng

last: Xu

first: Matthew

last: Rise


title: Evaluation of MicroRNA Expression Profiles for Form-Deprivation Myopia in Mouse

city: Durham

first: Terri

last: Young

state: NC

address: LaSale St.

department: Ophthalmology

institute: Duke University

summary: The study aim was to determine microRNA (miRNA) expression profiles of ocular tissues in form-deprivation induced myopia (FDM) mice. Form-deprivation myopia was induced in C57BL/6Jmice over the right eye; the contralateral left eyes were used as controls. Whole genome microRNA expression profiles in myopic whole eye, retina, and sclera were determined using the Agilent mouse miRNA microarray. The normalized microarray data were performed ANOVA test to identify differences in miRNA expression between myopic and control eyes. The differential expression for selected miRNAs was validated by quantitative real time PCR (qRT-PCR).

overall_design: Fifteen C57BL/6J mice were used in this study.  Form-deprivation myopia was induced over the right eyes; the contralateral left eyes were used as controls. Total RNA was isolated from the whole eye (6 mice), retina (9 mice), and sclera (9 mice) and was used for miRNA expression profiling with the Agilent Mouse miRNA v.15 Microarray.

first: Xiaoyan

last: Luo

first: Tatiana

last: Tkatchenko

first: Andrei

first: Pedro

last: Gonzalez


title: Effect of cigarette smoke extract, cisplatin, nicotine and/or ionizing radiation on microRNA expression in the NCI-H460 human lung large cell carcinoma cell line

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

summary: To understand the effect of nicotine on sensitivity of cancer cells to radiation or anti-cancer drugs, NCI-H460 human lung large cell carcinoma cells were treated with 6 Gy ionizing radiation or 1 uM cisplatin after exposure to 0.5 uM nicotine or cigarette smoke extract. MicroRNA expression in total RNA extracted from the treated cells was quantified using the 7th generation miRCURY™ locked nucleic acid microarray platform from Exiqon® (Vedbaek, Denmark).

platform_organism:
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Cells were subjected to one of nine types of treatment in triplicate and harvested for RNA extraction after 2 or 24 hours. Thus, 54 RNA samples representing biological triplicates for nine types of treatments and two time-points were obtained and analyzed using microarrays. Three RNA samples were assayed in duplicate (thus, 3 sets of technical duplicates: samples 5 & 55, 7 & 56, and 28 & 57). Reference RNA created by pooling the 54 unique RNA samples (at equal concentrations) was used in the reference channel (channel 2) of all microarrays. The reference RNA was also assessed in the test channel (channel 1) of one microarray (i.e., both test and reference channels had the pooled RNA).

first: Michelle

last: Romano

first: Samantha

last: Sobus

first: Krista

last: Pundt

first: Sai

last: Yendamuri

first: Graham

last: Warren


title: Chip-chip from budding yeast cells with Set3 complex

city: MIAOLI COUNTY

first: GUNN-GUANG

last: LIOU

state: TAIWAN

address: 35 KEYAN ROAD, JHUNAN TOWN

department: INSTITUTE OF MOLECULAR AND GENOMIC MEDICINE

country: Taiwan

institute: NATIONAL HEALTH RESEARCH INSTITUTES

summary: Chromatin immunoprecipitation of Set3 complex applied with tilling array chip ( ChIP on chip of either Set3-TAP or Snt1-TAP) analysis demonstrated that the genome-wide localization of Set3 complex in Saccharomyces cerevisiae

overall_design: Comparison the genome-wide localization of Set3-TAP with that of Snt1-TAP to map the majority of genome-wide localization of Set3 complex

first: Gunn-Guang

last: Liou

first: Shu-Yun

last: Tung


title: MicroRNA expression in epithelial and stromal compartments of stage I human non-small cell lung cancer tumors

summary: To identify tumor compartment-specific microRNA expression in stage I non-small cell lung cancer in humans, surgically resected and formalin-fixed tumor tissues were used in laser capture microdissection to isolate tumor epithelia and stroma. Total RNA extracted from the microdissectates was analyzed for microRNA expression using the 7th generation miRCURY™ locked nucleic acid microarray platform (Exiqon®, Vedbaek, Denmark).

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

overall_design: 69 pairs of RNA from epithelia or stroma microdissected from tumors of 68 patients were obtained. Not all samples yielded microarray data of good quality (thus, excluded here). The tumor component (E=epithelia, S=stroma), individuality of patients, the histology (AC=adenocarcinoma, BAC=bronchioloalveolar carcinoma, AS=adenosquamous carcinoma, SCC=squamous cell carcinoma) and pathologic stage of tumors, patients' age (at surgey, in years), gender (M=male), race, history of smoking at time of surgery, status of recurrence of cancer during post-surgery follow-up (N=no recurrence; at least 36 months to denote non-recurrence), time in months to recurrence (or death if time to recurrence is unknown), and time in months to death or censorship are noted for the samples. Six RNA samples were assayed in duplicate (thus, 6 sets of technical duplicates: samples 1 & 7, 2 & 27, 3 & 59, 4 & 91, 5 & 127, and 6 & 143). One tumor (patient ID 62) was microdissected twice; thus, samples 127 & 143, and 128 & 144 can be considered as pairs of biological duplicates. The reference RNA, a human 'universal reference total RNA,' was obtained by Exiqon® from Ambion® (catalog# AM6000; Austin, TX), and was used in the reference channel (channel 2) of all microarrays. Microdissections and RNA extractions were performed over a period of about 18 months. All RNA samples were analyzed by microarrays within a period of about a month, with samples 1-6 analyzed first, in a batch separate from the other samples. Data from a total of 136 microarrays obtained using 130 unique RNA samples from 68 tumors of 68 patients is used here.

first: Eric

last: Kannisto


title: Toxicogenomics and the circadian clock: Impact of time of day of exposure on the hepatic transcriptome of cyclophosphamide exposed mice

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary:
Nowadays, many innovative omics-based technologies are used in toxicogenomic and risk assessment studies to investigate and identify changes in gene expression and protein levels. Recently, it became clear that the biological response for many compounds might depend on the moment of exposure (time-of-day), a phenomenon referred to as chronotoxicity. However, in most toxicogenomic and risk assessment studies, the temporal variations in gene expression caused by the circadian clock are neglected. These temporal variations can influence the outcome of omics- based experiments.
In the present study, we investigated the impact of the circadian clock on the response of the liver transcriptome and acute toxicity of mice exposed to the chemotherapeutic agent cyclophosphamide at defined time points during the day.

overall_design: Male C57BL/6 mice received a single injection (i.p) of cyclophosphamide at two different timepoints during the day, ZT8 and ZT20 ( 8 and 20 hours after light on, respectively). Animals (n=4 per time point) were sacrificed by cervical dislocation at 0.5, 1, 2 and 4 hours after CP injection (T0.5, T1, T2 and T4), and at 0 and 4 hours after vehicle injection (C0 and C4).

first: Kirsten

last: Van Dycke

first: Romana

last: Nijman

first: Paul

middle: F

last: Wackers

middle: J

first: Wendy

last: Rodenburg

first: Conny

middle: T

last: van Oostrom

first: Timo

last: Breit

first: Harry

last: van Steeg

first: Mirjam

last: Luijten

first: Gijsbertus

last: van der Horst


title: FabR regulates Salmonella biofilm formation via its direct target FabB

first: Hans

last: Steenackers

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

overall_design: Refer to individual Series


title: Characterization of Nicotiana attenuata stems with reduced expression of calcium dependent protein kinase 4/5 (ir-CDPK4/5 plants).

first: Klaus

last: Gase

summary: Identification of transcripts that change expression in Nicotiana attenuata plants with reduced expression of calcium dependent protein kinase 4/5 compared to WT.

overall_design: Gene expression in leaves of Nicotiana attenuata wild type and ir-CDPK4/5 stems was measured at an age of 41 days.Three independent experiments were performed with ir-CDPk4/5 plants.

first: Maria

last: Heinrich

first: Jianqiang

last: Wu

first: Jyotasana

last: Gulati


title: Transcriptional and Functional Characterization of genetic elements involved in galacto-oligosaccharide utilisation by Bifidobacterium breve UCC2003

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: It is increasingly recognised that the gastrointestinal microbiota plays a critical role in human health and promising evidence is accumulating that with dietary strategies, of prebiotic intervention, microbiota imbalances can be corrected and host health improved. Several prebiotics are widely used commercially in foods including inulin, fructo-oligosaccharides, galacto-oligosaccharides and resistant starches and there is convincing evidence, in particular for galacto-oligosaccharides, that prebiotics can modulate the microbiota and promote the growth of bifidobacteria in the intestinal tract of infants and adults. In this study we describe the identification and functional characterisation of the genetic loci responsible for the transport and metabolism of purified galacto-oligosaccharides (PGOS) by our model bifidobacterial strain, B. breve UCC2003. We further demonstrate that the extracellular endogalactanase specified by several B. breve strains, including B. breve UCC2003, is essential for metabolism of PGOS components with a long retention time and high degree of polymerisation. These PGOS components are transported into the bifidobacterial cell via various ABC transport systems and sugar permeases where they are further metabolised to galactose and glucose monomers that feed into the bifid shunt. This research described here advances our understanding of GOS metabolism by bifidobacteria and for the future there is great potential for exploiting bifidobacterial beta-galactosidase to create targeted prebiotics that can enrich for selected Bifiobacteria sp. and other beneficial microbes among the gut microbiota.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.


title: Phylogenetic footprinting and transcriptome profiling reveal new roles for two Bacillus cereus two-component systems

city: Wageningen

first: Mark

middle: de

last: Been

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

institute: Wageningen UR

summary: Members of the Bacillus cereus group can adapt to a wide range of environmental challenges. In bacteria, these challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). We have previously developed a phylogenetic footprinting approach that was successfully implemented to predict specific binding sites (operators) and target genes for the RRs of B. cereus and related species. In this study, this footprinting approach was integrated with transcriptome analyses of two B. cereus TCS deletion mutants, involving the TCSs YvrHG and YufLM. Comparison of mutant versus wild-type transcriptomes revealed that the respective TCSs were significantly active during the exponential growth phase in rich medium and that the footprinting-based predictions were accurate for the two TCSs. Moreover, the predicted specific operators were used in combination with the transcriptome data to guide the identification of more extended TCS regulons. This revealed new roles for the respective TCSs, including the participation in an intricate transcriptional network involved in antibiotic resistance, including the confirmed resistance to oxolinic acid (YvrHG) and the confirmed uptake and metabolism of fumarate and the repression of fermentative pathways (YufLM).

overall_design:
Two different comparisons were performed (both in duplo and Cy5-Cy3 dye-swapped):

(1) B. cereus WT 30°C (mid-exponential) versus B. cereus delta-yufLM 30°C (mid-exponential)
(2) B. cereus WT 30°C (mid-exponential) versus B. cereus delta-yvrHG 30°C (mid-exponential)

last: de Been

first: Julien

last: Brillard

first: Véronique

last: Brousolle

first: Tjakko

last: Abee


title: ChIP-chip analysis of Ring1B in thymocytes

status: Public on Dec 26 2014

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Genome binding/occupancy profiling by array

summary: During ontogeny, totipotent progenitors undergo stepwise lineage-determination to give rise to progenitors with narrower potential and eventually to unipotent progenitors. Status of the progenitors with restricted potential is determined by transcription factors, and by epigenetic mechanisms. It is generally conceived that transcription factors primarily determine the commitment status of progenitors and epigenetic mechanisms follow to fix the status. In line with this idea is that, whereas many cases are known where the loss or over-expression of a certain single transcription factor bring about the cell fate conversion, no cases have ever been reported where alteration of epigenetic status solely leads to convert the determined cell lineage. Here we provide such a case where the inactivation of polycomb-medicated epigenetic regulation resulted in conversion of T lineage progenitors to B cell fate. In mice in which epigenetic repressor Ring1A and B are conditionally deleted in T cell lineage, T cell development was severely blocked at around T cell lineage determination step. Such developmental block was partially rescued by the additional deletion of Cdkn2a, one of cell cycle inhibitors, allowing the generation of T cell lineage progenitors that bear rearranged TCRβ chain gene. We found that these T cell progenitors co-express B cell lineage associated genes, and furthermore, these T cell progenitors were able to give rise to IgM+ mature B cells with normal function upon transfer to immuno-deficient mouse. These results indicate that T and B cell lineages are asymmetric in requirement of epigenetic regulation for the maintenance of respective lineages.

overall_design: ChIP samples of H3K4me3, H3K27me3 and Ring1B

first: Mitsuhiro

last: Endoh

first: Tomokatsu

last: Ikawa


title: Pseudomonas-derived Ceramidase Induces Production of Inflammatory Mediators from Human Keratinocytes via Sphingosine-1-Phosphate

status: Public on Dec 25 2014

city: Urayasu

first: Kazuhisa

last: Iwabuchi

state: Chiba

address: 2-1-1 Tomioka

department: Institute for Environmental and Gender-specific Medicine

institute: Juntendo University Graduate School of Medicine

summary: A Pseudomonas aeruginosa-derived neutral ceramidase (PaCDase) isolated from a patient with atopic dermatitis was shown to effectively degrade ceramide in the presence of Staphylococcus aureus-derived lipids or neutral detergents. To understand the effect of ceramide metabolites on the functions of differentiating keratinocytes, we have conducted genes expressions analysis from PaCDase-, sphingosine-1-phosphate (S1P)-treated or untreated three-dimensionally cultured human primary keratinocytes, which form a stratum corneum, in the presence of Triton X-100 using high resolution DNA microarray.

overall_design: To evaluate the effects of PaCDase and S1P on keratinocyte functions, we applied an epicutaneous 24-h patch test on the EPI-Model in keratinocyte serum-free medium (keratinocyte-SFM) (Invitrogen; Carlsbad, CA, USA) by the method of Spiekstra et al. [25] with some modification. The Triton X-100 treated samples were labeled using Cy5, and the PaCDase or S1P samples were labeled with Cy3.

first: Ami

last: Oizumi

first: Hitoshi

last: Nakayama

first: Chihiro

last: Iwahara

first: Katsunari

last: Kina

first: Ryo

last: Matsumoto

first: Nozomu

last: Okino

first: Makoto

last: Ito

first: Hideoki

last: Ogawa

first: Kenji

last: Takamori

first: Yasushi

last: Suga


title: Identification of the genes differently expressed after Edwardsiella tarda FKC and Streptococcus iniae FKC treatment in Japanese flounder, Paralichthys olivaceus

status: Public on Dec 24 2014

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

summary: 3,484 genes showed more than 2-fold up or down-regulated expressions by the E. tarda and S. iniae FKC treatments.

overall_design: Fish were treated with E. tarda FKC, S. iniae FKC and PBS (control) and isolation of total RNA from kidney of the fish at 6 hours and 12 hours after the treatments.

first: Yuriko

last: Kawana

first: Ikuo

last: Hirono


title: Transcriptional profiling of apolipoprotein-O-overexpressing H9c2 cardiomyoblasts

status: Public on Dec 30 2014

city: Toulouse

first: Philippe

middle: V

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

institute: INSERM U1048

summary: Mitochondrial dysfunction and excessive lipid accumulation in non-adipose tissues have been proposed widely as the roots for comorbidities generated by the growing epidemia of type 2 diabetes mellitus. Mouse models of lipotoxic cardiomyopathy have underlined this detrimental situation, but so far the proteins involved in diabetic patients’s induced mitochondrial dysfunction remain unknown. Apolipoprotein O (ApoO), originally found overexpressed in human diabetics hearts (Lamant et al. JBC 2006), is a candidate that was investigated here at the transcriptome level using H9c2 cardiomyoblasts after stable integration of an expression vector (pTT-ApoO) constitutively expressing ApoO.

overall_design: Two-condition experiment (pTT-transfected vs. pTT-ApoO-transfected H9c2 cells). Pools of transfectants are compared.


title: Genome wide profiling of buffalo (Bubalus bubalis) sperm DNA methylation in relation to bull fertility

city: KARNAL

first: TIRTHA

middle: KUMAR

last: DATTA

state: HARYANA

address: NDRI

department: ANIMAL BIOTECHNOLOGY

country: India

institute: NATIONAL DAIRY RESEARCH INSTITUTE

summary: Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and histone modifications. During spermatogenesis, the DNA of sperm undergoes overall methylation changes and this could have some role to play in fertilizing ability of the sperm. Many of the studies have shown that the altered methylation can cause sub fertility. In the present study we report the development of first comprehensive 4X180K buffalo (Bubalus bubalis) CpG island/promoter microarray for studying the global DNA methylation profile of buffalo sperm. The array has been developed by employing microarray based comparative genomic hybridization (aCGH) technique with bovine and buffalo DNA using bovine genome sequence as reference. The array represents 157084 features assembled from CDS, Promotor and CpG regions covering  2,967 unique genes. We also report the comparison of genome wide methylation differences in buffalo sperm from high fertile and sub fertile bulls which indicated profound discrepancies in their methylation status. A total of 96 individual genes along with another 55 genes covered under CpG islands  were found differentially methylated and and were associated with different cellular functions and biological processes affecting germ cell development, spermatogenesis, capacitation and embryonic development.

overall_design: Agilent two-color Methylation experiment, Organism: Bos taurus , 4X180K buffalo (Bubalus bubalis) CpG island/promoter microarray designed  by Genotypic Technology Private Limited (AMADID-037258). To see the differential DNA methylation pattern between high and sub fertile buffalo bull sperm, the cryopreserved semen samples from the identified bulls were procured. The DNA was isolated from all the samples, sheared, immunoprecipitated for methylated DNA (meDIP) and hybdidized on array to get information for all the probes printed on the array. The data was analyzed and the differentially methylated genes between the two group were identified.

first: Arpana

last: Verma

first: Tirtha

last: Datta


title: The effects of simazine, a chlorotriazine herbicide, on expression of genes in developing male Xenopus laevis

city: jinan

first: sai

middle: lin

last: lin

state: shandong

address: 18877Jingshi Road

department: Toxicology

institute: Shandong Academy of Occupational Health and Occupational Medicine

summary: Numerous studies have shown simazine produces adverse effects on growth, development, immune and endocrine system functions in a wide range of species, few describe gene expression changes concurrent with simazine-induced changes in phenotype during development. In this report, developing Xenopus laevis tadpoles were chronically exposed to simazine for 90 days at dosages of 0.1, 1, 10 and 100µg/L. Affymetrix microarrays and Taqman RT-PCR were used to define gene expression changes in male tadpoles exposed to 100µg/L atrazine.

overall_design: Developing tadpoles (NF stage 46) were treated with concentrations (ranging from ecologically relevant to very great) of simazine for 90 days. Then three testis from Simazine group and two testis from control group were chose for microarray analysis.

first: Sai

middle: L

last: Lin

first: Liu

last: Zhong

first: Li

middle: X

last: Xin


title: SCID mouse thymic lymphoma transduced with Early Growth Response transcriptional regulator

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

summary: Gradations in ERK signaling have been implicated in essentially every developmental checkpoint or differentiation process encountered by lymphocytes. Yet, despite intensive effort, the molecular basis by which differences in ERK activation specify alternative cell fates remains poorly understood. We report here that differential ERK signaling controls lymphoid fate specification through an alternative mode of action. While ERK phosphorylates most substrates, such as Rsk, by targeting them through its D-domain, this well-studied mode of ERK action was dispensable for development of gamma-delta T cells. Instead, development of gamma-delta T cells was dependent upon an alternative mode of action mediated by the DEF-binding pocket (DBP) of ERK. This domain enabled ERK to bind a distinct and select set of proteins required for specification of the gamma-delta fate. These data provide the first in vivo demonstration for the role of DBP-mediated interactions in orchestrating alternate ERK-dependent developmental outcomes.

overall_design:
RNA profiles of a scid thymic lymphoma (Scid.adh) transduced with either EGR1, EGR2, EGR3, EGR4 or stimulated through a chimeric receptor, “TAC:E stimulated,” were hybed against a reference pool RNA derived from non transduced Scid.adh.  This series contains one pair of samples, Scid.adh transduced with EGR1 hybed against non-transduced Scid.adh.  Samples were hybed on 2-color Agilent arrays with dye swaps.  There are no replicate samples.

Additional data has been requested by the GEO staff in order to complete this submission. Please contact the submitter (contact details below) for additional information or to ascertain when the missing data will be uploaded to GEO.


title: Global Transcript Profiles of Maize Seedling Roots in the Presence and Absence of Nitrate

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

summary:
The following study was conducted to better understand the genetic response of maize roots to nitrate availability. To do so, an array was designed and created by the Plant Sciences Institute at Iowa State University. This custom array contained 7,888 informative spots of cDNA obtained from NSF Plant Genome EST projects led by Ginny Walbot and Pat Schnable. RNA was collected from root tissue at two time points: 30 minutes and 24 hours. At each time point, transcript profiles were compared between root tissues treated with 5mM calcium nitrate and controls treated with 5mM calcium sulfate.

Keywords: Nutrient response in maize roots

overall_design: For each comparison, 6 replicates and multiple power settings were considered. Dye-swaps were performed between replicates.

middle: S


title: Analyses of long-range interactions of the NR0B1 (DAX1) promoter using chromosome conformation capture-on-chip

city: Warsaw

first: Marta

last: Smyk

address: Kasprzaka 17A

department: Medical Genetics

institute: Intitute of Mother and Child

summary:
Heterozygous point mutations or genomic deletions of NR0B1 in Xp21.2 result in congenital adrenal hypoplasia and hypogonadotropic hypogonadism, whereas the NR0B1 locus duplications in XY individuals lead to gonadal dysgenesis and a male-to-female dosage-sensitive sex reversal. We previously reported an ~ 257 kb deletion mapping 11 kb upstream to NR0B1 in a XY female with primary amenorrhea, small immature uterus, and gonadal dysgenesis pointing to an alteration of its regulatory region. To identify the potential regulatory elements of NR0B1, we have analyzed its 2 Mb flanking regions using chromosome conformation capture-on-chip (4C) in Sertoli cells and lymphoblasts.
We confirm the involvement of the previously proposed regulatory region in the control of NR0B1 expression and describe several novel potential chromatin interactions within the NR0B1 locus that may be involved in sex differentiation.

overall_design: Custom designed 3x720K tiling microarrays covering 4 Mb region (chrX:28,082,100-32,087,100) flanking NR0B1 gene of interest

first: Michał

last: Startek

first: Anna

last: Gambin

first: Paweł

last: Stankiewicz

first: Przemyslaw

last: Szafranski


title: Parp-1 wildtype and deficient mouse embryonic stem cells

city: Tokyo

first: Hiroaki

last: Fujimori

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

type: Methylation profiling by genome tiling array

summary: Genome-wide methylation analysis was performed by methylated DNA immunoprecipitation (MeDIP)-CpG island (CGI) microarray analysis to identify the CpG methylation levels of Parp-1 wildtype, Parp-1 deficient or Parp inhibitor treated mouse embryonic stem cells.

overall_design: Two samples were analyzed by MeDIP-CGI microarray. One is a whole genomic DNA and another is the MeDIP DNA. The whole DNA samples were used as reference.

first: Mitsuko

last: Masutani


title: Expression data from early diphyodont morphogenesis in minature pig

status: Public on Dec 23 2014

city: Beijing

first: Fu

last: Wang

address: Tian Tan Xi Li No.4, P. R. China

institute: Capital Medical University

summary:
The miniature pig is diphyodont, making it a valuable alternative model for understanding human tooth development and replacement.  However, little is known about gene expression and function during swine odontogenesis.
The goal of this study is to undertake the survey of differential gene expression profiling with Affymetrix Porcine GeneChip and functional network analysis during morphogenesis of diphyodont dentition in miniature pigs. The identification of genes related to diphyodont development should lead to a better understanding of morphogenetic patterns and the mechanisms of diphyodont replacement in large animal models and humans.

overall_design: The staged miniature pig embryos and fetuses were obtained by cesarean section at E40, E50, and E60.  The last deciduous molar germs, including the dental lamina in mandibles from the same litter were isolated and pooled. The gestational age of embryos used in our study just cover 3 characteristic stages: Dm3 in cap stage without secondary dental lamina (E40); Dm3 in bell stage with secondary dental lamina initiation (E50); Dm3 in secretory stage without evidence of morphological changes in the secondary dental lamina.

first: Jing

last: Xiao

first: Wei

last: Cong

first: Ang

last: Li

first: Fulan

last: Wei

first: Junji

last: Xu

first: Chunmei

last: Zhang

first: Zhipeng

last: Fan

first: Junqi

last: He

first: Songlin


title: Plant root transcriptome profiling of Azospirillum-rice cooperation

status: Public on Dec 22 2014

city: Villeurbanne

first: Benoît

last: DROGUE

state: Rhône-Alpes

address: Boulevard du 11 novembre

department: Université Lyon 1

institute: Université de Lyon

summary: Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defense and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. In this context, this study aimed at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyses of root gene expression of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post inoculation with A. lipoferum 4B (isolated from Cigalon roots) or Azospirillum sp. B510 (isolated from Nipponbare) and compared to the respective non-inoculated condition.

overall_design: For each of the four condition, three replicates were analysed on an oligo microarray produced by NimbleGenTM (Madison, WI, USA). The microarray was derived of the one previously described in Yuan et al. 2005 . This microarray is composed of about 385,000 60mer probes selected for their GC content, Tm and number of cycles needed to synthesize the oligo. This chip contains 90,000 probes representing 45,000 genes (two probes per gene) of rice Oryza sativa ssp. japonica, based on the TIGR rice genome annotation version 3.1 genes (Chaparro et al. 2007) and 201 691 oligomers corresponding to previously described copies of LTR retrotranposons available on the retrOryza database (www.retroryza.fr). Probes represent 1,000 bp of the LTR-retrotransposon flanking regions at the 3’ and 5’ side. The oligonucleotides have been designed at the 3’ end of the genes to detect the readings of reverse transcriptase. On the other hand, the LTR-retrotransposons are represented throughout their length at the rate of a probe every 500 bp.

last: Drogue

first: Hervé

last: Sanguin

first: Amel

last: Chamam

first: Michael

last: Mozar

first: Christel

last: Llauro

first: Olivier

last: Panaud

first: Claire

last: Prigent-Combaret

first: Nathalie

last: Picault

first: Florence

last: Wisniewski-Dyé


title: Genome wide differential H3K4me2 and H3K27me3 profile of spermatozoa from high and sub-fertility buffalo bulls

first: TIRTHA

last: DATTA

summary: Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and Histone modifications. During spermatogenesis the chromatin of sperm undergoes wide level of modifications and histone proteins are replaced by Protamine proteins. But some modified Histone forms still remain and they carry epigenetic codes essential for fertility and embryo development. Through this work we are trying to see the difference between H3K4me2 and H3K27me3 kind of histone modifications in spermatozoa of high and low fertility buffalo bulls.

overall_design: Agilent two-color ChIP-on-Chip, 4X180K Microarray designed by Genotypic Technology Private Limited. (AMADID-040096). To see the differential H3K4me2 and H3K27me3 pattern between high and low fertile buffalo bull spermatozoa, the cryopreserved semen samples from the identified bulls were procured. The chromatin was isolated from all the samples, sheared with micrococcal nuclease treatment (NEB, Cat no. MO247S), immunoprecipitated and hybdidized on array to get information for all the probes printed on the array. The data was analyzed and the differentially enriched genes between the two group were identified for both kinds of histone modifications.

first: Arpana

last: Verma

first: Tirtha

middle: K

last: Datta


title: Gene expression profile of ‘heat stress’ in the Red Sea coral Stylophora pistillata

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

summary: Over the past several decades, corals worldwide have been affected by global warming, experiencing severe bleaching events that have often lead to coral death. The symbiotic Red Sea coral Stylophora pistillata is considered an opportunistic ‘r’ strategist, thriving in relatively unstable and unpredictable environments, and it is considered a stress-tolerant species. This study aimed to examine S. pistillata gene expression and to clarify the cellular pathways that are active during short-term heat stress caused by an increase from 24°C to 34°C over a 10-day period. Total RNA was extracted from heat-stressed coral fragments, labeled and hybridized against a designated S. pistillata custom microarray containing approximately 12,000 genes. Our results show that the heat stress reaction was sighted from 32°C and intensified significantly after 34°C treatment. Protein interaction networks of up- and down-regulated genes were constructed. The main clustering groups of up-regulated genes were ER stress and ER protein folding, cell cycle, ubiquitin-mediated proteolysis, cell death and cell death regulation and cellular stress response genes. These genes were enriched in cellular pathways related to the unfolded protein response (UPR) in the ER, ER-associated degradation (ERAD) and ubiquitin-mediated proteolysis. An analysis of the down-regulated genes yielded different clusters of genes related to extracellular matrix and actin organization, collagen, negative regulation of cell death and the Notch and Wnt signaling pathways. Genes encoding redox regulation proteins and molecular chaperones may be considered accurate “early warning genes”, while genes related to sensing and repairing DNA damage are severe heat-related genes. Here, we suggest that during short-term heat stress, S. pistillata might divert cellular energy into mechanisms such as UPR and ERAD at the expense of growth and biomineralization processes in an effort to recover from the stress.

overall_design: Three-condition experiment, 28°C, 32°C and 34°C vs. 24°C short-term heat stress on Red Sea coral Stylophora pistillata. Data from three biological replicates and two to four technical replicates were used for each temperaure treatment.

first: Keren

last: Maor-Landaw

first: Sarit

last: Karako-Lampert

first: Stefano

last: Goffredo

first: Giuseppe

last: Falini

first: Zvy

last: Dubinsky

first: Oren

last: Levy


title: Gene expression profiles of vaccinated fish using a long-term efficiency mixed vaccine against Edwardsiella tarda performed by a new designed oligo DNA microarray in Japanese flounder Paralichthys olivaceus

first: Hidehiro

last: Kondo

summary: Gene expression profiles by microarray have contributed for a elucidation of an immune-response and a determination of efficiency in vaccination. Recent day, edwardsielosis have caused a fatal damage in the aquaculture of Japanese flounder, Paralichthys olivaceus. However the formalin killed-cell vaccines made from Edwardsiella tarda isolated same fish species were not efficient. Recent our study revealed the mixed FKC vaccine made from the two different type of E. tarda protected Japanese flounder against Edwardsiella tarda infection for long-term. In this study, we analyzed the immune-response of a vaccinated fish kidney using the mixed FKC vaccine against Edwardsiella tarda with an Agilent custom-oligo DNA microarray on 9,573 probes of Japanese flounder. Our study revealed that the mixed FKC vaccine confered a strong immune-response and keeped a efficient for long-term on Japanese flounder.

overall_design: The kidney were isolated from the vaccinated Japanese flounder using the three formalin-killed vaccines, 1st is a typical type of E. tarda strain UH6 isolated from Japanese flounder, Paralichthys olivaceus, 2nd is a atypical type of E. tarda strain UT1 isolated from Red seabream, Pagrus major and 3rd is an equal (1:1) mixture FKC with these two type E. tarda. Fishes were vaccinated by intramuscular injection using the 1.0 x 10^8 cell of FKC vaccines. After 3 and 7 days from a vaccination, fish kidney was isolated. We also isolated non-vaccinated fish kidney as a control. We analyzed a four of individual fish kidney vaccinated using mixed FKC on day 7. We also analyze the three samples which are the two of the pooled total RNA from a two fish and the one of the one fish total RNA in typical FKC and atypical FKC vaccinated fish after 3 and 7 days from a vaccination, mixed FKC vaccinated fish after day 3 from a vaccination and a control (22 hybridization).

first: Yoshiaki

last: Suzuki

first: Yukinori

last: Takahashi

first: Kouhei

last: Fukuda

first: Kei

last: Kawamura

first: Masakazu

first: Takashi

last: Aoki

first: Ikuo

last: Hirono


title: Transcriptomic effects of GLUT2 knock-down in zebrafish embryos

city: Barcelona

first: Josep

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

institute: Universitat de Barcelona

summary: Glucose transporter 2 (GLUT2) is a key player in the regulation of glucose dynamics in organs central to metabolism, namely the liver, pancreas and intestine In humans, mutations of the GLUT2 gene (Fanconi-Bickel syndrome) cause important defects in glucose homeostasis. Although GLUT2 has been studied in the context of its participation in peripheral and central glucose sensing, to date it is still unclear which role it plays in the brain. In this regard, in order to shed some light on the function of GLUT2 in the vertebrate brain, we have knocked down the functional ortholog of human GLUT2 in zebrafish. Our results show that abrogation of glut2 in vivo leads to defective brain organogenesis coinciding with reduced glucose uptake and increased programmed cell death in the brain region. Interestingly, coinciding with the observed localization of glut2 expression in the hindbrain, glut2 deficiency affected the development of neural progenitor cells expressing the proneural genes atoh1b and ptf1a that are the source of glutamatergic and GABAergic neurons, respectively. In addition, progenitor cells expressing neurod, a marker for immature and mature granule cells, were not affected by the lack of glut2. Furthermore, transcriptome analysis of glut2 knockdown embryos supports the notion that the lack of glut2 impacts brain development. Overall, the results of this study highlight the physiological relevance of glut2 in glucose uptake and availability during brain development, supporting the important role of glut2 in brain glucose sensing, and demonstrate the usefulness of a novel in vivo model of GLUT2 deficiency.

overall_design: Control and ATG morphant embryos were harvested at 72 hpf and RNA samples were obtained from pools of 20 embryos per condition and three pooled biological replicates of control and ATG morphants were analyzed.


title: Exercise promotes growth and vascularization of fast skeletal muscle by activating myogenic and angiogenic transcriptional programs in adult zebrafish

summary: The adult skeletal muscle is a plastic tissue with a remarkable ability to adapt to different levels of activity by altering its excitability, its contractile and metabolic phenotype and its mass. Knowledge on the mechanisms responsible for muscle mass comes primarily from models of muscle inactivity or denervation or from genetic models of muscle diseases. Given that the underlying exercise-induced transcriptional mechanisms regulating muscle mass are not fully understood, here we investigated the cellular and molecular adaptive mechanisms taking place in fast skeletal muscle of adult zebrafish in response to swimming. Fish were trained at low swimming speed (0.1 m/s; non-exercised) or at their optimal swimming speed (0.4 m/s; exercised). A significant increase in fibre cross-sectional area (1,290 ± 88 vs. 1,665 ± 106 μm2) and vascularization (298 ± 23 vs. 458 ± 38 capillaries/mm2) was found in exercised over non-exercised fish. Gene expression profiling evidenced the transcriptional activation of a series of complex networks of extracellular and intracellular signaling molecules and pathways involved in the regulation of muscle mass, myogenesis and angiogenesis, many (e.g. BMP, TGF, FGF, Notch, Wnt, MEF2, Shh, EphrinB2) not previously associated with exercise-induced contractile activity, and that recapitulate in part the transcriptional events occurring during skeletal muscle regeneration. These results demonstrate that fibre hypertrophy is responsible for the growth-promoting effects of exercise accompanied by a switch to a more oxidative capacity of white muscle fibres to fuel the increased energy demands. Importantly, our study identified novel molecular mechanisms regulating muscle mass and function in vertebrates.

overall_design: Adult zebrafish were subjected or not to a swim training regime consisting of swimming at the optimal swimming speed for this species for 6 h/day, 5 days/week for a total of 4 weeks (20 experimental days). Total RNA of fast muscle from individual non-exercised (n = 8) and exercised (n = 8) zebrafish was analyzed.


title: System responses to equal doses of photosynthetically usable radiation of blue, green, and red light in the marine diatom Phaeodactylum tricornutum.

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: We have studied the transcriptional, metabolic and photo-physiological responses to light of different spectral quality in the marine diatom Phaeodactylum tricornutum through time-series studies of cultures exposed to equal doses of photosynthetically usable radiation of blue, green and red light. The experiments showed that short-term differences in gene expression and profiles are mainly light quality-dependent. Transcription of photosynthesis-associated nuclear genes was activated mainly through a light quality-independent mechanism likely to rely on chloroplast-to-nucleus signaling. In contrast, genes encoding proteins important for photoprotection and PSII repair were highly dependent on a blue light receptor-mediated signal. Changes in energy transfer efficiency by light-harvesting pigments were spectrally dependent; furthermore, a declining trend in photosynthetic efficiency was observed in red light. The combined results suggest that diatoms possess a light quality-dependent ability to activate photoprotection and efficient repair of photodamaged PSII. In spite of approximately equal numbers of PSII-absorbed quanta in blue, green and red light, the spectral quality of light is important for diatom responses to ambient light conditions.

overall_design: Continuous, axenic culturing of P. tricornutum was done as described in Nymark et al. (2009). The cultures were incubated at 15°C under cool white fluorescent light (Philips TLD 36W/96) providing a scalar irradiance (EPAR) of 100 μmol m-2 s-1 under continuous white light (CWL) conditions. Upon the onset of the experiment the cultures were synchronized by 48 h dark-treatment (D48). Thereafter the algae were exposed to blue light (BL), green light (GL) or red light (RL) provided by a waveband specific LED panel (SL3500, Photon Systems Instruments). The algae were exposed to 0.5 h, 6 h or 24 h of: 1) 230 μmol m-2 s-1 of RL, 2) 100 μmol m-2 s-1 of GL, 3) 50 μmol m-2 s-1 of BL or 4) 100 μmol m-2 s-1 of WL respectively. Three biological replicas for each of the treatments were harvested. Data for the white light exposure and 48h dark treatment is described in GSE42039, PMID: 23520530.

first: Marianne

last: Nymark

first: Kristin

middle: C

last: Valle

first: Tore

last: Brembu

first: Atle

middle: M

last: Bones

first: Torfinn

last: Sparstad


title: Transcriptional Profiling of rat hypothalamic response to TCDD

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

summary: In many mammals, halogenated aromatic hydrocarbon (HAH) exposure causes wasting syndrome, defined as lethal weight loss as a result of severe and persistent hypophagia. The most potent HAH in causing wasting is 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), which exerts its toxic effects through the aryl hydrocarbon receptor (AHR) – a transcription factor. Because TCDD toxicity is thought to predominantly arise from dysregulation of AHR-transcribed genes, we hypothesized that wasting syndrome is due to TCDD-induced dysregulation of genes involved in regulation of food-intake. We therefore focused on the hypothalamus, as it is the regulatory center of food-intake and energy balance in the central nervous system. We profiled mRNA abundance in hypothalamic tissue from two rat strains with widely differing sensitivities to wasting syndrome: TCDD-sensitive Long-Evans rats and TCDD-resistant Han/Wistar rats, 23 hours after exposure to TCDD (100 μg/kg) or corn oil vehicle. We found that TCDD exposure caused minimal transcriptional dysregulation effects in the hypothalamus, with only 6 genes changed in Long-Evans rats and 15 genes in Han/Wistar rats. Two of the most dysregulated genes were Cyp1a1 and Nqo1, which are induced by TCDD across a wide range of tissues and are considered sensitive markers of TCDD exposure. The minimal response of the hypothalamic transcriptome to a lethal dose of TCDD at an early time-point suggests that the hypothalamus is not the predominant site of initial events leading to hypophagia and associated wasting. TCDD may affect feeding behaviour via events upstream or downstream of the hypothalamus, and further work is required to evaluate this at the level of individual hypothalamic nuclei and subregions.

overall_design: Two strains, each with drug-treated vs vehicle-control

first: Kathleen

middle: E

last: Houlahan

middle: D

first: Ivy

last: Moffat

first: Jere

last: Lindén

first: Sanna

last: Lensu

first: Allan

middle: B

last: Okey

first: Raimo

last: Pohjanvirta

first: Paul

last: Boutros


title: Microarray analysis of murine kidney treated with Amodiaquine and Sulfodoxine-Pyrimethamine

city: Lucknow

first: Shrawan

middle: Kumar

last: Mishra

address: MG Marg,Chattar Manzil Palace

institute: CDRI

summary: Differential gene expression in mice kidney after Amodiaquine and Sulfodoxine-Pyrimethamine anti-malaria treatments were evaluated. Dosages were decided based on standard malaria therapy in human.

overall_design: Mice (Mus musculus) belonging to control and Amodiaquine and Sulfodoxine-Pyrimethamine administered groups (n=4) were sacrificed. The kidneys were snap frozen in liquid nitrogen, and subsequently stored at -80ºC till further use. Kidney samples were homogenized and total RNA was extracted with TRI reagent. 25 ug of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit. The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer containing 10ug/ml sheared Salmon sperm DNA and 10ug/ml Yeast tRNA. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42ºC. Fluorescent array images were collected for both Cy3 and Cy5 with Molecular Dynamics III scanner supported with ImageQuant v5.0. Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background-corrected data was LOWESS normalized and log ratios were calculated using Avadis v4. Further, mean log ratios were calculated for duplicate spots. Duplicate experiments were carried out for all the dosages.

first: Prabhat

last: Singh

first: Srikanta

last: Rath


title: Functional genomics in perinatal asphyxia and fetal asphyctic preconditioning in the brain

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Fetal asphyctic (FA) preconditioning is effective in attenuating brain damage incurred by a subsequent perinatal asphyctic insult. Unraveling mechanisms of this endogenous neuroprotection, activated by FA preconditioning, is an important step towards new clinical strategies for asphyctic neonates. Genomic reprogramming is thought to be, at least in part, responsible for the protective effect of preconditioning. Therefore, we investigated whole genome differential expression in the preconditioned rat brain.

overall_design: FA preconditioning was induced on embryonic day 17 (E17) by reversibly clamping the uterine circulation. Perinatal asphyxia (PA) was induced while pups were being born by caesarean section; the uterine horns, including pups, were placed in a water bath for 19 minutes. FAPA pups underwent both procedures. Control (C) pups did not undergo FA or PA procedures, but were born by caesarean section. Pups were sacrificed at 3 time-points: 96 hours after FA (E21), 6 hours after birth/PA (P0), and 96 hours after birth/PA (P4).

first: Kimberly

last: Cox

first: Johan

last: Vles

first: Jana

last: Schlechter

first: Luc

middle: J

last: Zimmermann

first: Eveline

last: Strackx

first: Antonio

middle: W

last: Gavilanes


title: Transcriptome of a malO deletion mutant of Clostridium perfringens during stationary phase growth.

city: Clayton

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

summary: The MalNO is a putative two-component signal transduction system, previously known as the VirJI sytem.  MalO is the putative cognate response regulator of the MalN sensor histidine kinase.  Based on previous evidence that suggested the plc gene, encoding α-toxin, was upregulated during stationary phase in the malO mutant, microarrays were used to analyse the transcriptome of a malO mutant during stationary phase growth.

overall_design: Total RNA was isolated from stationary phase cells of the malO mutant and the wild-type control.  Gene expression levels were compared between the malO mutant and wild-type strain 13

first: Thomas

last: Hiscox

first: Kaori

last: Ohtani

first: Anjana

last: Chakravorty

first: Jocelyn

last: Choo

first: Tohru

last: Shimizu

first: Jackie

last: Cheung


city: San Francisco

first: Feroz

last: Papa

state: CA

address: 1700 4th Street

department: Medicine

country: USA

institute: University of California, San Francisco

summary: Transcriptional profiling of INS1 CAT cells treated with 1μM thapsigargin vs control.

overall_design: All arrays are hybed pairwise with treated against untreated


title: The overall response of Paenibacillus larvae to bodily fluids of honeybee larvae (Apis mellifera).

summary: Paenibacillus larvae, the causal agent of American Foulbrood disease (AFB), affects honeybee health worldwide. The present study investigates the transcriptional response of this Gram-positive, endospore-forming bacterium to bodily fluids from honeybee larvae. Four different conditions were evaluated with a loop design: sampling of in vitro grown P. larvae cultures one or four hours after addition of larval fluids or BHIT-broth (C1, T1, C4, T4).

overall_design: total of 16 samples, 4 independent samples per group, 4 groups (C1, C4, T1 and T4), loopdesign, dye swap

first: Dieter

last: De Koker

first: Lina

last: De Smet

first: Alyse

last: Hawley

first: Leonard

last: Foster

first: Paul

last: De Vos

first: Dirk

last: de Graaf


title: Engineered Methylobacterium methanol

city: Cambridge

first: HSIN-HUNG

last: CHOU

address: 16 Divinity Avenue, Biolab 3079

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: Engineered Methylobacterium methanol batch exponential

overall_design: strain CM702 vs. strain CM502


title: WT MEFs or IRE1α-/- MEFs treated with 1μM thapsigargin vs control

summary: Transcriptional profiling of WT MEFs or IRE1α-/- MEFs treated with 1μM thapsigargin for 12hrs compared with their corresponding non-treated cells.


title: INS1 cells expressing either WT IRE1α, I642G IRE1α, N906A IRE1α, or spliced XBP1 treated with  dox and 1NMPP1

summary: Transcriptional profiling of INS1 cells expressing either WT IRE1α, I642G IRE1α, N906A IRE1α, or spliced XBP1 comparing 1μg/mL dox and 5μM 1NMPP1 treated vs control.

overall_design: All arrays are hybed pairwise with treated hybed against untreated


title: T-REx 293 cells expressiong either WT or I642G IRE1α: 1μg/mL dox and 5μM 1NMPP1 treated vs control at two time points

summary: Transcriptional profiling of 1μg/mL dox and 5μM 1NMPP1 treatedT-REx 293 cells expressing either WT or I642G IRE1α  vs control.

overall_design: TREx 293_WT_8h_03 and TREx 293_WT_NT_03 are hybed against a universal control sample;TREx 293_WT_24h_01and TREx 293_WT_NT_01 are hybed against a universal control smaple;TREx 293_WT_24h_02 and TREx 293_WT_NT_02 are hybed against a universal control smaple;TREx 293_IG_24h_01 and TREx 293_IG_NT_01 are hybed against a universal control sample;TREx 293_IG_24h_02 and TREx 293_IG_NT_02 are hybed against a universal control sample. The rest arrays are hybed pairwise with treated vs untreated on the same array.


title: Akita cells  vs its wildtype counterpart (ct14 cells).

summary: Transcriptional profiling of Akita cells vs ct14 cells .

overall_design: All arrays are hybed pairwise with Akita against ct14.


title: Transcriptomic analysis of Vibrio vulnificus in response to iron concentration and Fur protein

status: Public on Dec 20 2014

city: Burjassot

first: David

last: Pajuelo Gámez

state: Valencia

address: Doctor Moliner, 50.

department: Microbiology and Ecology

country: Spain

institute: University of Valencia

summary: V. vulnificus is a marine bacteria that causes diseases in both mammals and fish. In both hosts, the iron concentration represents a key factor that greatly influences the virulence of this bacterium. To further define the gene repertoire that is regulated by iron concentration and Fur protein (the main transcriptional regulator in response to iron concentration) in V. vulnificus, we obtained a mutant in Fur and used DNA microarray technology to monitor the expression of the entire gene repertoire in response to iron.  Global transcriptomic response was reconstructed by comparing the transcriptional profiles of the wild-type (R99) and Fur mutant strains in poor and rich iron conditions.

overall_design: To identify the genes that were under control of Fur, we compared the transcriptomic profile of the wild-type strain with the profile of a mutant strain in Fur protein; in contrast, to identify the genes that were under control of iron, we compared the transcriptomic profile of the wild-type strain grown in iron-rich conditions with the profile of the wild-type strain grown in iron-restricted conditions. For each one of the four samples, three replicates were performed, and RNA was sampled in the mid-log phase of growth (wild-type, 6h; Fur mutant, 6h; wild-type+iron, 5h; wild-type-iron,9h).

last: Pajuelo

first: Carmen

last: Amaro

first: Simon

last: Mackenzie

first: Sebastian

last: Boltaña


title: Cross-feeding by Bifidobacterium breve UCC2003 during Bifidobacterium bifidum PRL2010 growth on a mucin-based medium.

status: Public on Dec 17 2014

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

institute: University College Cork

summary: Bifidobacteria constitute commensal bacteria that commonly inhabit the mammalian gastro intestinal tract. The gut commensal Bifidobacterium breve UCC2003 was previously shown to utilise a variety of plant/diet-derived carbohydrates, including cellodextrin, starch and galactan. In the current study, we investigated the ability of this strain to utilize (parts of) a host-derived source of carbohydrate, namely the mucin glycoprotein. Here, we demonstrate that B. breve UCC2003 exhibits growth properties in a mucin-based medium, but only when in the presence of Bifidobacterium bifidum PRL2010, which is known to metabolize mucin. Based on HPAEC analysis, transcriptome data and insertion mutagenesis, it appears that B. breve UCC2003 sustains this improved survival in co-culture by cross-feeding on a combination of fucose, sialic acid and galactose-containing oligosaccharides.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003  (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Muireann

last: Egan