title: Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains

status: Public on Mar 31 2015

city: Paterna

first: Estéfani

last: García-Ríos

state: Valencia

address: Avenue Agustín Escardino, 7

department: Biotechnology

country: Spain

institute: Institute of Agrochemistry and Food Technology (IATA-CSIC)

summary: The aim of this study is to phenotype a collection of 27 S. cerevisiae commercial wine strains growing within temperatures (4-45ºC) in both minimal media (SD) and synthetic must (SM) and, taking into account µmax value, to select two strains with divergent phenotype in their capacity to grow at low temperature. To confirm this differential phenotype, we design a competition between both strains during wine fermentations. As expected, at low temperature fermentation, the strain showing a good performance out-competes to the strain growing badly in cold. Finally we aimed to decipher the molecular basis underlying this divergent phenotype by analyzing the genomic, proteomic and transcriptomic differences between both strains at low temperature (15ºC) and optimum temperature (28ºC).

overall_design: Two Saccharomyces cerevisiae strains with divergent phenotype in their capacity to grow and ferment at low temperature were analyzed (P5 strain as a candidate with a good performance in fermentations at low temperature (15ºC) and P24 as a candidate with a worse behavior at low temperature). All experiments were performed using triplicates arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

first: María

last: López-Malo

first: José

middle: M

last: Guillamón


title: Transcript analysis of nitrogen response in rice

status: Public on Mar 25 2015

city: Guelph

first: JOSE

middle: A

last: CASARETTO

state: ON

address: 50 Stone Road E

department: MCB

country: Canada

institute: University of Guelph

summary:
Understanding gene expression re-programming in response to limiting nitrogen (N) conditions is crucial for ongoing progress towards the development of crop varieties with improved nitrogen use efficiency.
We analyzed expression data obtained from leaves and roots of rice plants adapted to sufficient and limiting nitrate as well as after shifting them to low (reduction) and sufficient (induction) nitrate conditions.

overall_design: Rice plants were grown under sufficient (HN, 3 mM) and limiting (LN, 0.3 mM) nitrate (N) conditions or switched from HN to LN (reduction) or LN to HN (induction). Total RNA was extracted from leaves and roots and used for cDNA synthesis to profile the transcriptome using custom-designed Affimetrix microarrays

first: Jose

last: Casaretto

first: Viktoriya

last: Coneva

first: Ashraf

last: El-kereamy

first: Jonathan

last: Cohn

first: Tong

last: Zhu

first: Yong-Mei

last: Bi

first: Steven

middle: J

last: Rothstein


title: Early vanadium stress induced transcriptional changes in the root of Oryza sativa

status: Public on Mar 23 2015

city: Tainan City

first: Chung-Yi

last: Lin

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

summary:
Whole genome arrays have been used to analyze the transcriptomic response to vanadium stress in rice root.
Identify genes and pathways that would respond to vanadium stress

overall_design: Comparison of mock control and  rice seedlings treated with 1 mM vanadium; Biological replicates: 3 control replicates, 3 V-treated replicates

first: Hao-Jen

last: Huang


title: Gene expression of conventional and unconventional T cell subsets

city: London

first: Lucie

last: Abeler-Dörner

address: Great Maze Pond

department: Immunobiology

country: United Kingdom

institute: King's College London

summary: The experiments were designed to gain insight into the gene expression of conventional and unconventional murine T cell subsets in the steady state and upon activation

overall_design: TCRαβ and TCRγδ intraepithelial lymphocytes (IEL) isolated from murine gut, naïve and virus-induced memory splenocytes, activated dendritic epidermal T cells (DETC)

first: John

last: Shires

first: Efstathios

last: Theodoridis

first: Vicki

last: Giuggio

first: Emma

last: Wise

first: Adrian

middle: C

last: Hayday


title: Characteristic DNA methylation profiles in peripheral blood monocytes are associated with inflammatory phenotypes of asthma

status: Public on Mar 18 2015

city: Callaghan

first: Katherine

last: Baines

state: NSW

address: University drive

country: Australia

institute: The University of Newcastle

summary: Epigenetic changes including DNA methylation caused by environmental exposures may contribute to the heterogeneous inflammatory response in asthma. Here we investigate alterations in DNA methylation of purified blood monocytes that are associated with inflammatory phenotypes of asthma.

overall_design: Peripheral blood was collected from adults with eosinophilic asthma (EA; n=21), paucigranulocytic asthma (PGA; n=22), neutrophilic asthma (NA; n=9), and healthy controls (n =10). Blood monocytes were isolated using ficoll density gradient and immuno-magnetic cell separation. Bisulfite converted genomic DNA was hybridised to Illumina Infinium Methylation27 arrays, and analysed for differential methylation using R/Bioconductor packages

first: Lakshitha

middle: P

last: Gunawardhana

first: Peter

middle: G

last: Gibson

first: Jodie

last: Simpson

first: Miles

last: Benton

first: Rodney

last: Lea


title: Dehong chicken blood samples vs. 22 different chicken blood samples belonging to 11 breeds

status: Public on Mar 13 2015

city: Beijing

first: ming

last: tian

state: Beijing

address: No.2, Yuan Ming Yuan West Road, Haidian District

country: China

institute: China Agricultural University

type: Genome variation profiling by genome tiling array

summary: Copy number variation profiles comparing control female Dehong chiken blood DNA with 11 different chicken breeds(Silkie, Tibetan Chicken, Gallus gallus spadiceus, Bearded Chicken, Jinhu Chicken, Anak Chicken, Beijing Fatty Chicken, Langshan Chicken, Qingyuan partridge Chicken, Shek-Ki Chicken, Wenchang Chicken) blood DNA. Each test breeds had one male and one female sample, totally 22 test DNA samples.Goal is to get the golbal copy number variation profile between chicken breeds.

sample_organism:
Gallus gallus
Gallus gallus spadiceus

overall_design: Female Dehong chicken DNA as reference DNA vs 22 test chicken DNA samples

first: M

last: Tian

first: Y

last: Wang

first: X

last: Hu

first: N

last: Li


title: Cyptophyte gene regulation in the kleptoplastidic ciliate Mesodinium rubrum

status: Public on Mar 11 2015

city: Kongju

first: Jong Won

last: Han

state: Chungnam

address: Sinkwandong

department: Biology

country: South Korea

institute: Kongju National University

summary: Time series microarray analysis on the photosynthetic ciliate was conducted using an oligochip containing 15,654 genes designed from Teleaulax amphioxeia ESTs

sample_organism:
Teleaulax amphioxeia
Mesodinium rubrum

overall_design: To identify the gene expression patterns that occur during the sequesteration of the plastid, a total of 15,654 unique genes from cryptophyte were designed. Gene expression was compared in a free-living cryptophyte and in its sequestered state (in Mesodinium cells).

first: Gwang

middle: H

last: Kim

first: Jihee

first: Jong

middle: W


title: Expression analysis of liver tissues from LPS or LPS/GalN treated mice

city: Tianjin

first: chang

last: antao

address: 94 Weijin Road

department: School of Medicine

institute: Nankai university

summary:
Investigation of whole genome gene expression level changes in the liver tissue from LPS/GalN treated mice, compared to LPS treated mice
Treatment of mice with LPS and the liver-specific transcriptional inhibitor D-(+)-galactosamine (GalN) induces fatal hepatitis, which is mediated by TNFα and characterized by massive hepatic apoptosis. Previous studies suggest that GalN increases the sensitivity to LPS/TNFα probably by blocking the transcription of protective factors, but the identity of most of these factors is still unclear. This analysis is performed to indentify these protective factors.

overall_design: A six chip study using total RNA extracted from liver tissues of three separate LPS treated mice and three separate LPS/GalN treated mice. Each chip measures the expression level of 44,170 genes from C57 BL/6 mice with three 60-mer probe pairs per gene.

first: Antao

last: Chang

first: Yanan

last: Chen

first: Chenghu

last: Liu

first: Rong

last: Xiang


title: Validation of chicken array for gene expression analysis in turkey

city: Saint Paul

first: Sunantha

last: Kosonsiriluk

state: Minnesota

address: 495 AnSci/VetMed 1988 Fitch Ave

department: Animal Science

country: USA

institute: University of Minnesota

summary: To validate the use of chicken array for turkey, the ability of species-specific hybridization (SSH, chicken samples-chicken arrays) and cross-species hybridization (CSH, turkey samples-chicken arrays) were compared in the same biological conditions. Reproductively active laying chickens and reproductively inactive non-laying pullets were used to generate the results for SSH. Similarly, reproductively active laying turkeys and reproductively inactive non-laying photorefractory turkeys were used to generate the results for CSH.

sample_organism:
Gallus gallus
Meleagris gallopavo

overall_design: Four-condition experiments, reproductively active laying chickens vs. reproductively inactive non-laying pullets and reproductively active laying turkeys vs. reproductively inactive non-laying photorefractory turkeys. Four biological replicates with dye swap.

first: Laura

last: Mauro

first: Mohamed

middle: E

last: Elhalawani


title: A role of regulatory T cells in brown adipose tissue physiology

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: The presence of different types of immune cells in adipose tissue has been demonstrated in numerous studies. Whereas cells of the immune system in white adipose tissue contribute to the low-grade chronic inflammation under obese conditions, their function in brown adipose tissue (BAT) remains largely elusive. Here we report a role of regulatory T (Treg) cells in BAT physiology.Ablation of Treg cells resulted in massive invasion of macrophages into BAT concordant with rearrangement of BAT morphology. Treg ablated animals displayed reduced energy expenditure. Our results for the first time demonstrate a functional role of Treg cells in the regulation of energy homeostasis.

overall_design: Two experimental conditions: PBS injected mice as a control vs. diphtheria toxin (DT) injected. 3 biological replicates were used.

first: Stephan

last: Herzig

first: Dasa

last: Medrikova


title: Radiation-induced genes expressed in six murine tumors.

city: Chiba

first: Kazunori

last: Nojiri

address: 4-9-1, Anagawa, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

summary:
Gene expression profiling  was used to identify genes that display radiation-induced transcriptional change over tumor histopathology.

Keywords: mouse squamous cell carcinoma, fibrosarcoma and mammary carcinoma, gamma-irradiation,  resected sample, transplanted tissues

overall_design: C3H/HeMs male mice were irradiated by gamma-rays as local irradiation in single doses to hind legs where each tumor was transplanted. The animals were sacrificed up to 42 days after irradiation and recurrent point. Non-irradiated mice served as the controls. Each tumor sample was dissected and used for expression analysis.

first: Mayumi

last: Iwakawa


title: Gene Expression profile of Sox9 sorted cells from Vertebral column of E12.5 wildtype (WT) and Homozygous (HOMO) mouse embryos

status: Public on Mar 19 2015

city: Potsdam

first: Thomas

last: Lufkin

state: NY

address: 8 Clarkson Avenue

institute: Clarkson University

summary: This study aims to look at gene expresion profiles between wildtype and Sox9 knockout cells of the vertebral column in a E12.5 mouse embryo. Instead of looking at the whole vertebral column, only cells expressing Sox9 were sorted by Fluroscent Activated Cell Sorting (FACS) and subjected to expression profiling by microarray.

overall_design: EGFP was knocked into the Sox9 locus by homologous recombination in mESC followed by generation of chimaeric and stable mice line. Heterozygous embryos expressing EGFP was was used to dissected out the vertebral column and Fluroscent activated cell sorting was used to sort out cell expressing Sox9 as marked by EGFP. For Homozygous geneotype chimaeric embryos were used as Sox9 homozygotes die at E11.5. Total RNA was extracted and hybidized to an Illumina WG6 v1.1 mouse array.

first: Sumantra

last: Chatterjee


title: Vitamin A and arachidonic acid altered the skeletal mineralization in Atlantic cod larvae (Gadus morhua) without any interactions on the transcriptional level

status: Public on Mar 17 2015

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

summary: The main object of this study was to evaluate the impact of different levels of vitamin A (VA) and arachidonic acid (ARA) in relation to eicosapentaenoic acid (EPA) on mineralization and gene expression in Atlantic cod larvae (Gadus morhua). A two-way factorial design was used to identify possible interactions between the nutrients. First-feeding larvae were fed enriched rotifers from start-feeding until 29 days post hatch (dph). Larvae in four tanks were fed one of the following diets: control (EPA/ARA ratio: 15.8, 0.9 µg VA g-1 wet wt.), control+VA (EPA/ARA ratio: 15.8, 7.8 µg VA g-1 wet wt.), High ARA (EPA/ARA ratio: 0.9, 1.5 µg VA g-1 wet wt.) or High ARA +VA (EPA/ARA ratio: 0.9, 12.0 µg VA g-1 wet wt.). There was no difference in survival (33-40%) between the groups. Larvae fed High ARA+VA were shorter at 29 dph. The larvae fed High ARA+VA had significantly less mineralized bones, showing significant interaction effects between VA and ARA.  Although transcriptomic analysis using a custom-made microarray did not reveal any interaction effects, it was found that high ARA diets altered the transcription of more genes than control +VA diets. Furthermore, blgap1 , blgap2 and col10a1 were all down-regulated in larvae fed High ARA-diets and to a lesser extent by Control +VA diet. Lower expression in the High ARA+VA diets compared to ARA and VA diets indicated an additive effect on mineralization. In conclusion, this study showed that the dietary increase in ARA and VA altered the skeletal metabolism during larval A. cod development, most likely through signaling pathways specific for each nutrient rather than an interaction.  The present study also demonstrates that VA could affect the larval response to ARA, even within the accepted non-toxic/non-deficient range.

overall_design: Four different experimental groups in a two way factorial design were analyzed with different combination of arachidonic acid enrichement (ARA) and vitamin A (VA) supplement. Two oil mixtures were made, named Control and High ARA. Control contained 90% EPAX4510 and 10% EPAX5010, while High ARA contained 65% Cargill ARA oil, 5% EPAX4510 and 30%EPAX5010. The mixtures were then divided in two fractions. VA in the form of retinylpalmitate (Sigma-Aldrich, Oslo, Norway) was added to one fraction from each oil mixture (5 g retinylpalmitate L-1 oil). This gave four different mixtures, namely Control, Control+VA, High ARA and High ARA+VA. These mixtrures were used to enriched rotifers which in turn were subsequently fed to Atlantic cod larvae from 4 days post hatch (dph) to 29 dph. Four tanks per experimental group was used in the factorial design.  Atlantic cod larvae were sampled at 17 dph and 29 dph for microarray analysis. RNA from pooled whole animals were reverse transcribed and Cy3-labled and hybridized.

middle: K

first: Karen

last: Kvalheim

first: Josef

middle: D

last: Rasinger

first: Torstein

last: Harboe

first: Andreas

last: Nordgreen

first: Mari

last: Moren


title: Cervical cancer samples in NIRS

first: Shuhei

last: Noda

state: Chiba

address: Anagawa 4-9-1

department: Frontier research center

institute: National institute of radiological sciences

summary:
cervical cancer samples to test radiosensitivity

Keywords: comparison between pre-irradiation and mid-irradiation status, correlation to prognosis

overall_design:
Patients Characteristics and Biopsy Samples

The subjects were 63 patients with uterine cervix tumors who had been treated after pretreatment sampling. All provided informed consent in accordance with the Institutional Ethical Review Committee at National Institute of Radiological Sciences. Clinical stages and histological classification were based on criteria of the International Federation of Gynecology and Obstetrics. Twenty-five patients received conventional radiotherapy (RT) consisting of 30.6 Gy to the whole pelvis, plus an additional dose to parametria with central shielding to complete 50.6 Gy, along with 192Ir high dose-rate intracavitary brachytherapy. The other 28 patients received radiotherapy as same as RT and chemotherapy consisting of five weekly administrations of CDDP (40mg/m2). The other 10 patients received carbon-ion radiotherapy (HIMAC) for local tumor consisting of 25 GyE to the whole pelvis plus an additional dose to parametria and tumors to complete 45 GyE.
A second biopsy was taken one week after the start of therapy as described elsewhere (14). At that point, patients in CRT and RT groups had received 9 Gy of whole pelvic irradiation and CRT group had received a single dose of CDDP, but brachytherapy had not started yet. HIMAC group had received 12 GyE. One half of each sample was placed immediately in RNAlater (Ambion, Austin, TX, USA) at half volume of specimen, and the other half was fixed in 10% formalin and embedded in paraffin.
A CT scan at 6 months, 1, and 2 years was used to diagnose a response of therapy as complete remission (CR), partial remission (PR), or progressive disease (PD). The prognosis was followed up for more than 2 years in 60 patients. Patients, who did not develop any evidence of disease, were defined as good responders, and patients, who were alive with recurred tumor or newly developed metastasis, or died of them, were defined as poor responders.
From 63 cases, 10 CRT who were diagnosed as FIGO stage IIIB with squamous cell carcinoma (SCC) and 14 RT cases with SCC were selected as training set, and the rest of cases were used for test samples (Table 1).

Extraction of Total RNA, Probe Preparation and Microarray Hybridization

We purified total RNA using ISOGEN (Nippon gene, Tokyo, Japan) followed by the RNeasy Total RNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturers' recommendations. The quality of RNA samples was verified by examining the integrity of 28S and 18S rRNA using 2100 Bioanalyzer (Agilent Technologies, Palp Alto, CA, USA). Double-stranded cDNA and subsequent cRNA was synthesized from 2 micrograms of total RNA using the CodeLink Expression Assay Kit (GE Healthcare, Piscataway, NJ, USA) according to manufacturer's instructions. Bioarrays were stained with Cy5-streptavidin (Amersham Biosciences, Piscataway, NJ, USA) and scanned using the Agilent dual-laser Microarray Scanner (Agilent Technologies, Palo Alto, CA, USA).

Analysis of Microarray Data

We examined all data from multiple arrays for each sample, using statistical correlation as a means of checking quality. Spot signals were quantified using CodeLink Expression Analysis Software (Ver4.0； GE Healthcare). We averaged scan data from 3-4 replicate experiments using an error-weighted algorithm. An output data was further analyzed by the Resolver version 4.0, a gene expression analysis software (Rosetta Biosoftware, Seattle, WA, USA). This software employs an error-modeling approach for the analysis of microarray data. All non-detection calls were filtered prior to performing analysis. We averaged scan data from 3-4 replicate experiments using an error-weighted algorithm.

first: Kaori

last: Imadome

first: Takashi

last: Imai


title: Site-specific methylation of Notch1 controls the amplitude and duration of the Notch1 response

status: Public on Mar 26 2015

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary:
Physiologically, Notch signal transduction plays a pivotal role in differentiation; pathologically, Notch signaling contributes to the development of cancer. Transcriptional activation of Notch target genes involves cleavage of the Notch receptor in response to ligand binding, production of the Notch intracellular domain (NICD), and NICD migration into the nucleus and assembly of a coactivator complex. Posttranslational modifications of the NICD are important for its transcriptional activity and protein turnover. Deregulation of Notch signaling and stabilizing mutations of Notch1 have been linked to leukemia development. We found that the methyltransferase CARM1 (coactivator-associated arginine methyltransferase 1; also known as PRMT4) methylated NICD at five conserved arginine residues within the C-terminal transactivation domain. CARM1 physically and functionally interacted with the NICD-coactivator complex and was found at gene enhancers in a Notch-dependent manner. Although a methylation-defective NICD mutant was biochemically more stable, this mutant was biologically less active as measured with Notch assays in embryos of Xenopus laevis and Danio rerio. Mathematical modeling indicated that full but short and transient Notch signaling required methylation of NICD.
Analysis of gene expression upon inactivation and activation of Notch signaling in Beko cells.

overall_design: Beko cells were treated with DAPT or DMSO for 24h. Or Beko cells were infected with a DNMAML-ER or Notch1-ER fusion protein. After Selection cells were treated with 4-OHT (Tamoxifen) or Ethanol for 48h.

first: Kerstin

last: Hein

first: Gerhard

last: Mittler

first: Wiebke

last: Cizelsky

first: Michael

last: Kühl

first: Francesca

last: Ferrante

first: Ina

last: Berger

first: Steffen

last: Just

first: Jan

last: Sträng

first: Hans

last: Kestler

first: Franz

last: Oswald

first: Tilman

last: Borggrefe


title: Gene expression profiles of parental and chemotherapy-resistant colon cancer cell lines.

status: Public on Mar 15 2015

city: Frederiksberg C

first: Niels

middle: Frank

last: Jensen

address: Dyrlaegevej 88, 1.

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

summary: The aim of this study was to identify biomarkers of drug response and investigate mechanisms of drug resistance to the two chemotherapeutic drugs oxaliplatin and irinotecan (active metabolite SN-38) in colorectal cancer, using a cell-based model system of drug-sensitive parental colon cancer cell lines and sub-cell lines with acquired drug resistance.

overall_design:
Three human colon cancer cell lines (HCT116, HT29 and LoVo) were exposed in vitro to gradually increasing drug (oxaliplatin or SN-38) concentrations for about nine months, generating sub-cell lines with acquired resistance.
Gene expression profiles of the parental and resistant cell lines cultured in drug-free medium for two to three weeks were obtained (each in triplicate) and compared to identify gene expression changes associated to chemotherapy resistance.

middle: F

last: Stenvang

first: Kirstine

last: Belling

first: Khoa

middle: N

last: Do

first: Ramneek

last: Gupta

first: Maria

middle: U

last: Rømer

first: Nils

last: Brünner


title: The Aspergillus nidulans metZ gene encodes a transcription factor involved in regulation of sulfur metabolism in this fungus and other Eurotiales

city: Warszawa

first: Marek

last: Skoneczny

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

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

summary: In Aspergillus nidulans, expression of sulfur metabolism genes is activated by the MetR transcription factor containing a basic region and leucine zipper domain (bZIP). Here we identified and characterized MetZ, a new transcriptional regulator in Aspergillus nidulans and other Eurotiales. It contains a bZIP domain similar to the corresponding region in MetR and this similarity suggests that MetZ could potentially complement the MetR deficiency. The metR and metZ genes are interrupted by unusually long introns. Transcription of metZ, unlike that of metR, is controlled by the sulfur metabolite repression system (SMR) dependent on the MetR protein. Overexpression of metZ from a MetR-independent promoter in a metR strain, activates transcription of genes encoding sulfate permease, homocysteine synthase and methionine permease, partially complementing the phenotype of the metR mutation. Thus, MetZ appears to be a second transcription factor involved in regulation of sulfur metabolism genes.

overall_design: Comparison of transcriptomes of the filamentous fungus Aspergillus nidulans two congenic strains, K1 (delmetR,pyr-4+) and TZ12(delmetR,trpCpr::metZ,pyr-4+). Four biological replicates of K1 vs TZ12  were performed. Each biological replicate had two technical replicates with dye swapping.

first: Sebastian

last: Pilsyk

first: Renata

last: Natorff

first: Marzena

last: Sieńko

first: Andrzej

last: Paszewski

first: Jerzy

last: Brzywczy


title: Gene expression analysis in the adult carotid body stem cell niche

city: Seville

first: Ricardo

last: Pardal

address: Avda. Manuel Siurot, s/n.

department: Medical Physiology and Biophysics

institute: University of Seville

summary:
The carotid body (CB) is a peripheral chemoreceptor organ that suffers a profound angiogenic and neurogenic process in response to hypoxemia, to contribute to physiological adaptation of the organism.
We have previously described a subpopulation of neural crest-derived stem cells residing in the organ. These cells are responsible for hypoxia-induced neurogenesis. Little is known about the molecular mechanisms underlying this neurogenic process.

overall_design: We have used neuronal cell-enriched neurosphere (NS) cultures vs. undifferentiated cell-enriched NS to study molecular pathways involved in the biology of these CB different cell types.

first: Aida

last: Platero-Luengo


title: Patient-derived primary xenografts in the preclinical development of novel targeted therapies for bladder cancer

status: Public on Mar 27 2015

city: vancouver

first: Mohammed

last: Alshalalfa

state: bc

address: water st

institute: GenomeDx

summary: Purpose: While molecular targeted therapy has revolutionized the treatment of many cancers, little progress has been made in the development of novel therapies for muscle invasive bladder cancer (MIBC). Here we report on the establishment and characterization of patient-derived primary MIBC xenografts

overall_design: Tumor fragments derived from 7 patients with MIBC were grafted under the renal capsule of NOD-SCID mice and subsequently transplanted to further mice over multiple generations. Patient tumor and xenograft tissue were processed for analysis of , gene expression by microarray, and expression of select potential target pathways by immunohistochemistry (IHC).

first: Wolfgang

last: Jager

first: Hui

last: Xue

first: Tetsutaro

last: Hayashi

first: Claudia

last: Janssen

first: Shannon

last: Awrey

first: Shawn

last: Anderson

first: Ann

last: Haegert

first: Nicholas

last: Erho

first: Ladan

last: Fazli

first: Estelle

last: Li

first: Elai

last: Davicioni

first: Yuzhuo

middle: Z

last: Wang

first: Peter

last: Black


title: Transcriptional profile of muscle following acute induction of symptoms in a mouse model of Kennedy's disease/SBMA

status: Public on Mar 22 2015

city: Mississauga

first: Ashley

last: Monks

state: Ontario

address: 3359 Mississauga Road

department: Dept. of Psychology

institute: University of Toronto

summary: Kennedy’s disease/Spinobulbar muscular atrophy (KD/SBMA) is a degenerative neuromuscular disease affecting males. This disease is caused by polyglutamine expansion mutations of the androgen receptor (AR) gene. Although KD/SBMA has been traditionally considered a motor neuron disease, emerging evidence points to a central etiological role of muscle. We previously reported a microarray study of genes regulated in muscle of three genetically unique mouse models of KD/SBMA but were unable to those which are androgen-dependent or are associated with onset of symptoms. Methodology/principal findings: In the current study we examined the time course and androgen-dependence of transcriptional changes in the HSA-AR transgenic (Tg) mouse model, in which females have a severe phenotype after acute testosterone treatment. Using microarray analysis we identified regulated genes at the onset and peak of muscle weakness in testosterone-treated Tg females. We found both transient and persistent groups of regulated genes and analysis of gene function indicated functional groups such as mitochondrion, ion and nucleotide binding, muscle development, and sarcomere maintenance. By comparing the current results with those from the three previously reported models we were able to identify KD/SBMA candidate genes that are androgen dependent, and occur early in the disease process, properties which are promising for targeted therapeutics.

overall_design: We used microarray (38.5K oligo mouse array, which contain 35,302 of 70mer oligonucleotide probes largely derived from constitutively expressed exons and 3,482 of controls) to analyze gene expression in limb muscles of transgenic mice. Five sample groups of 3 animals each were performed: Tg female 3 days testosterone treatment; Tg female 7d T treatment; WT untreated; WT 3d T treatment; and WT 7d T treatment. We additionally used microarray data from HSA-AR males to compare with HSA-AR females. A universal RNA reference sample made from WT (C57BL/6J) mice was utilized on each array. Triplicate arrays using RNA  samples from the different experimental animals (i.e., 3 of Tg female with 3d T treatment, 3 of Tg female with 7d T treatment, 3 of untreated WT females, 3 of WT female with 3d T treatment, 3 of WT female with 7d T treatment) were performed. Log2 ratios of experimental samples (Cy5) versus reference RNA (Cy3) were obtained. The log2 ratios of Tg mice samples were then subtracted from log2 ratios of WT to find differentially regulated genes (3d T-treated Tg subtracted from 3d T-treated WT, 7d T-treated Tg subtracted from 7d T-treated WT). log2 ratios of T-treated WT were subtracted from log2 ratio of untreated WT.

first: Katherine

last: Halievski

first: Kaiguo

last: Mo

first: J

middle: T

last: Westwood

first: Douglas


title: Functional diversity and convergence of small non-coding RNAs in male germ cell differentiation and fertilization (mRNA analysis)

city: Madrid

first: Jesus

last: Garcia Lopez

address: C/Ramiro de Maeztu 9

department: Cellular and Molecular Biology

institute: Cib (CSIC)

summary: The small non-coding RNAs (sncRNAs) are considered as postranscriptional key regulators of male germ cell development. In addition to microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), other sncRNAs generated from small nucleolar RNAs (snoRNAs), tRNAs or rRNAs processing may also play important regulatory roles in spermatogenesis. By next generation sequencing (NGS), we characterized the different sncRNA populations detected at three milestone stages in male germ differentiation: primordial germ cells (PGCs) at 13.5 dpc, pubertal spermatogonia cells, and mature spermatozoa. In order to assess the potential transmission of the sncRNAs through the mature spermatozoa during fertilization, the sncRNA population detected in male germ cells was also compared with sncRNAs detected in unfertilized mouse oocytes and zygotes. Combining the data obtained by NGS and microarrays from whole PGC and spermatogonia transcriptome, we defined the potential regulatory roles of specific miRNAs and their validated targets. Similar to miRNAs, both the small RNAs derived from snoRNAs and the piRNAs, could be involved in the postranscriptional regulation of mRNA transcripts during the male germ development. Finally, our results strongly suggest that the small RNAs-derived from tRNAs and rRNAs are interacting with PIWI proteins, and specifically with MILI. These new classes of piRNAs are not generated by the ping-pong pathway and could be the source of primary piRNAs.

overall_design: mRNA analysis of Primordial Germ Cells (PGCs), Spermatogonia cells (SPG), adult testis (AdT) and Gonad-less (GL) embryos. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

last: García-López

first: D

last: Cárdenas

first: L

last: Alonso

first: H

last: Artaza

last: Hourcade

first: S

last: Martínez

first: M

middle: A

last: Brieño

last: del Mazo


title: A. baumannii Cells:  1/2MIC chloramphenicol (Cm) tretment vs. 1/2MIC 4-hydroxybenzaldehyde (HBA) treatment vs. 1/4MIC combination of  Cm and HBA treatment vs. Ethanol treatment

status: Public on Mar 24 2015

city: seoul

first: BORA

last: SHIN

state: 성북구 안암로

institute: Korea university

summary: Transcriptional profiling of Acinetobacter baumannii ATCC17978 cells comparing each treated 1/2MIC Cm, 1/2MIC HBA and combination of 1/4MIC Cm and HBA cells with same volume of ethanol treated. Based on the gene expression, we analyzed results to confirm the relation between Cm and HBA to antibacterial synergism against A. baumannii. (Concentrations treated respectivly in all samples were adjusted to add same volume of Cm, HBA and combination)

overall_design: We performed a transcriptome anaylsis of 4 samples that are ethanol, Cm, HBA and combination treatment, respectively.

first: Bora

last: Shin

first: Park

last: Woojun


title: Cell cycle-independent phospho-regulation of Fkh2 during hyphal growth regulates Candida albicans pathogenesis.

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

summary: The opportunistic human fungal pathogen, Candida albicans, undergoes morphological and transcriptional adaptation in the switch from commensalism to pathogenicity. Although previous gene-knockout studies have identified many factors involved in this transformation, it remains unclear how these factors are regulated to coordinate the switch. Investigating morphogenetic control by post-translational phosphorylation has generated important regulatory insights into this process, especially focusing on coordinated control by the cyclin-dependent kinase Cdc28. Here we have identified the Fkh2 transcription factor as a regulatory target of both Cdc28 and the cell wall biosynthesis kinase Cbk1, in a role distinct from its conserved function in cell cycle progression. Transcript profiling of Fkh2 deletion and non-phosphrylatable mutants in yeast and hypae revealed that the the hyphal-specific shift in the phosphorylation profile is required for the expression of genes involved in pathogenesis, host interaction and biofilm formation. We confirmed that these changes in gene expression resulted in corresponding defects in pathogenic processes

overall_design: Two colour arrays comparing both non-phosphylatable Fkh2 and double deletion mutants to their respective wildtypes in both yeast and hyphal C. albicans.

middle: M

first: Jamie

last: Greig

first: Jonathan

last: Richardson

first: Julian

last: Naglik

first: Yue

last: Wang


title: Expression of Autophagy Genes in Myeloproliferative Disorders

city: New York

first: Mike

last: Harr

address: 1275 York Ave.

institute: Memorial Sloan-Ketering Cancer Center

summary: Comparison of ATG gene family members in MPN pattients with normal controls

overall_design: One-Way ANOVA while contrasting ATG gene family members in 11 Normal (Control) with either 1) 13 PV samples 2)  24 ET samples or 3) 18 PMF samples

first: B

last: Ebert

first: R

last: Levine


title: Molecular pathogenetic study of Fusarium head blight in highly resistant, resistant and susceptible common wheat (Triticum aestivum L.)

status: Public on Mar 14 2015

city: Yokohama

first: Alagu

last: Manickavelu

state: Kanagawa

address: Maioka 641-12

institute: Yokohama City University

summary: Fusarium graminearum (F.g) is responsible for Fusarium head blight (FHB), which is a destructive disease of wheat that accumulates mycotoxin such as deoxynivalenol (DON) and makes its quality unsuitable for end use. Several FHB resistant varieties development is going on world-wide. However the complete understanding of wheat defence response, pathogen (Fusarium graminearum) disease development mechanism and the gene crosstalk between organisms is still unclear.  In our study focused to analyse pathogen (F. graminearum) molecular action in different Fusarium head blight resistance cultivars during the disease development. To understand the Fusarium graminearum pathogen molecular reaction, microarray gene expression analysis was carried out by using Fusarium graminearum (8 x 15k) Agilent arrays at two time points (3 & 7 days after infection) on three wheat genotypes (Japanese landrace cv. Nobeokabouzu-komugi - highly resistant, Chinese cv. Sumai 3 - resistant and Australian cv. Gamenya - susceptible), which spikes infected by Fusarium graminearum ‘H-3’strain. During the disease development the pathogen biomass as well as the expression of Trichothecene biosynthesis involved genes (Tri genes) in three wheat cultivars was determined. In our material no relation between fungus biomass and the disease symptoms were observed, however, it showed relation with fungus virulence factors expression (Tri genes).   For the first time, we report the nature of Fusarium graminearum gene expression in the FHB-highly resistant cv. Nobeokabouzu-komugi during the disease development stage and the possible underlying molecular response.

overall_design: F. graminearum inoculated (3 and 7 days after inoculation) and water inoculated Mock samples were used for cRNA synthesis and further hybridization with 3 biological replications. Total 12 samples per genotype

first: Ayumi

last: Kosaka


title: The premammillary nucleus (PMM) of the mediobasal hypothalamus: Photosensitive vs. Photorefractory

first: Sunantha

last: Kosonsiriluk

institute: University of Minnesota

summary: Gene expression profiling of the premammillary nucleus comparing short day photosensitive, long day photosensitive, and long day photorefractory turkey hens

overall_design: Three-condition experiment, short day photosensitive vs. long day photosensitive vs. long day photorefractory. Loop design with 4 biological replicates.

first: Laura

middle: J

last: Mauro

first: Mohamed

last: El Halawani


title: The Gene Expression Profile of Peripheral Blood Mononuclear Cells from CA16-Infected Rhesus Neonates

status: Public on Mar 10 2015

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

summary: The present work focuses on global gene expression of peripheral blood mononuclear cells in rhesus monkey infants with HFMD induced by CA16 infection at different time points. Genome-wide expression and analysis were performed by using Agilent whole genome microarrays and established bioinformatics tools. 931   signiﬁcantly differentially expressed genes associated with 5 gene ontology categories, including cell communication, cell cycle, immune system process, regulation of transcription and metabolic process were identified. Subsequently, by mapping genes related to immune system process on KEGG pathways, the predominance of inflammation mediate by chemokine and cytokine signaling pathway and interleukin signaling pathway emerged. Ultimately, co-expression genes and their networks were analysised.

overall_design: Coxsackievirus A16 infection induced gene expression in rhesus monkey peripheral blood mononuclear cells was measured at 7-1st dpi, 3-2nd dpi, 7-2nd dpi, 14-2nd dpi.  Three samples from two experiment donors and one control donor were performed at each time. To exclude the individual difference, mix the two experiment samples at each time, and mix the two control samples.

first: Longding

last: Liu

first: Qihan

last: Li


title: Role of AcsR in expression of the acetly-CoA synthetase gene in Vibrio vulnificus

city: Seoul

first: Juri

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Environmental Medical Biology

institute: Yonsei University

summary: VarS/A is one of the global factors regulating diverse aspects of metabolism and virulence of bacteria including pathogenic Vibrio spp. An experiment to identify VarS/A-regulon in V. vulnificus revealed that a putative LuxR-type transcriptional regulator was down-regulated in ΔvarA mutant. To investigate the roles of this regulatory cascade from VarS/A to a LuxR-type regulator in V. vulnificus, the target gene regulated by a LuxR-regulator was identified and its expression was characterized.

overall_design:
Four-condition experiment, Mo6 vs acsR, Mo6 vs VarA. Biological replicates: 9 wild-type strain, 4 acsR deletion mutant strain, 5 varA deletion mutant strain, independently grown and harvested.
Please note that 'wild-type Mo6 vs acsR mutant replicate 1' sample was hybridized to the 30K platform chip while the others were hybridized to the 15K platform Therefore, the 'MO6 vs acsR_1.gpr' has 30,755 data rows (while  the other files have 16,355). The 30K platform chip is made of duplication of the 15K platform chip with the same probes.

first: Soon-Jung

last: Park


title: Rat ventral prostate gland gene profile after androgen deprivation

status: Public on Mar 28 2015

city: Campinas

first: Rafaela

middle: da Rosa

last: Ribeiro

address: Charles Dawin st, bl.N room 10

department: Structural and functional biology department

country: Brazil

institute: State University of Campinas

summary:
Androgens are required for prostate development, growth and physiology, by activating the androgen receptor (AR) upon activation by testosterone and dihydrotestosterone (DHT), the AR undergoes conformational changes, dimerizes and translocates to the cell nucleus regulation important genes releted to cell survival. Understanding the mechanisms of androgen regulation in the prostate gland is important, because the prostate is affected by several different diseases, in particular prostate cancer (PCa). Several ways exist to treat prostate cancer and promote epithelial cell death. Treatments involving androgen manipulation include surgical castration (bilateral orchiectomy), antiandrogens (usually AR antagonists), or substances that inhibit androgen synthesis (5 alpha-reductase inhibitors, gonadotrophin-releasing hormone blockers). 17 beta-estradiol exerts anti-androgen effects by blocking the hypothalamic production of gonadotropin-releasing hormone and thereby inhibiting the production of testosterone by the testes , but also acts locally via interactions with either of the estrogen receptors found in the gland. It is known that the kinetics of apoptosis are different in the rat ventral prostate (VP) of castrated rats (Cas group) and in rats subjected to 17 beta-estradiol high dose (group E2) or their combination (group Cas+E2), with an evident additive effect in the latter situation (Garcia-Florez et al, 2005).
The microarray approach was done to figure out what genes are expressed and how the cells of ventral prostate gland responses when the androgen is not available comparing three diferent androgen deprivation methods (sirurgical castration, high dose of 17-beta estradiol and both treatment combined).

overall_design: Forty-eight 21-day-old male Wistar rats were obtained from the Multidisciplinary Center for Biological Research (CEMIB), University of Campinas. The animals were kept under normal light conditions (12-h light:dark cycle) and received filtered tap water and Purina rodent chow ad libitum.  On the 90th day after birth, the rats were divided in four groups (n=3) and assigned to different treatment groups. To cause androgen deprivation, we utilized three different procedures with different effects on epithelial cell apoptosis. Animals in the first group were castrated (Cas) by orchiectomy via scrotal incision under ketamine (150 mg/Kg body weight) and xylazin (10 mg/kg body weight) anesthesia. Animals in the second group received a 25 mg/Kg body weight dose of 17β-estradiol diluted in corn oil (E2 group). The third group received a combination of both treatments (Cas+E2 group) (combined orchiectomy and 17β-estradiol). In the control group (Ct; normal androgen and estrogen), the animals received only the vehicle. Three days after the treatments, the rats were killed by anesthetic overdose, and the ventral prostate was dissected out for the microarray and immunohistochemistry analyses.

last: Rosa-Ribeiro

first: Hernandes

last: Carvalho


title: Arabidopsis Wild-type vs. Gcn2 GT8350 mutant line.

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

summary: Transcriptomic profiling of  seedlings comparing Arabidopsis wild-type (Ler) versus gcn2 mutant line

overall_design: Two-condition experiment, WT vs. Gcn2 seedlings. Biological replicates: 3, randomly paired


title: Transcriptional regulation of the sialic acid utilization gene cluster of Bifidobacterium breve UCC2003 by a GntR-type transcriptional repressor.

status: Public on Mar 05 2015

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: Members of the genus Bifidobacterium are typically found in the gastrointestinal tract (GIT) of humans and other mammals. Bifidobacterium breve strains are numerically prevalent among the gut microbiota of healthy, breast-fed infants. The metabolism of sialic acid, a ubiquitous monosaccharide in the infant and adult gut, by B. breve UCC2003 is dependent on a large gene cluster, designated the nan/nag cluster. This study describes the transcriptional regulation of the nan/nag cluster and thus sialic acid metabolism in B. breve UCC2003. Insertion mutagenesis and transcriptome analysis revealed that the nan/nag cluster is regulated by a GntR family transcriptional repressor, designated NanR. NanR was shown to bind to two promoter regions within this cluster, each of which containing an imperfect inverted repeat that is believed to act as the NanR operator sequence. Formation of the DNA-NanR complex is prevented in the presence of sialic acid, which we had previously shown to induce transcription of this gene cluster. NanR represents the first GntR-type transcriptional regulator to be characterised from bifidobacteria.

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


title: Wash regulates lamin-dependent nuclear genome organization [Chromatin Accessibility]

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by genome tiling array

summary:
The cytoplasmic functions of Wiskott-Aldrich Syndrome family (WASP) proteins are well known and include roles in cytoskeleton reorganization and membrane-cytoskeletal interactions important for membrane/vesicle trafficking, morphogenesis, immune response and signal transduction. Mis-regulation of these proteins is associated with immune deficiency and metastasis. Cytoplasmic WASP proteins act as effectors of Rho family GTPases and polymerize branched actin through the Arp2/3 complex. However, recent evidence has revealed that this classically cytoplasmic protein family also functions in the nucleus. Previously, we identified Drosophila washout (wash) as a new member of the WASP family with essential cytoplasmic roles in early development. Here we show that Wash is also present in the nucleus and plays a key role in nuclear organization via its interaction with Lamin Dm0 at the nuclear envelope. Wash and Lamin Dm0 occupy similar genomic regions that overlap with transcriptionally silent chromatin including constitutive heterochromatin. Strikingly, wash mutant and knockdown nuclei exhibit the same abnormal wrinkled morphology observed in diverse laminopathies, including the Hutchinson-Gilford progeria syndrome, and consistent with disruption of the nuclear organization of several sub-nuclear structures including cajal bodies and the chromocenter in salivary glands. We also found that Wash and Lamin knockdown disrupt chromatin accessibility of repressive compartments in agreement with an observed global redistribution of repressive histone modifications. Functional genetic approaches show wash mutants exhibit similar phenotypes to lamin Dm0 mutants, suggesting they participate in similar regulatory networks. Our results reveal a novel role for Wash in modulating nuclear organization via its interaction with the nuclear envelope protein Lamin Dm0. These findings highlight the functional complexity of WASP family proteins and provide new venues to understand their molecular roles in cell biology and disease.
We evaluated the effect of Wash knockdown in S2R+ cells on chromatin accessibility using an M.SssI-based approach.

overall_design: To establish the effects of Wash and Lamin depletion on chromatin organization, we performed a M.SssI-based chromatin accessibility assay. Upon knockdown, nuclei were isolated and incubated with the bacterial methylase M.SssI for 20 min. Genomic DNA was recovered and sonicated in order to obtain 300-1000 bp fragments. DNA was denatured and incubated with anti-5 methylcytosine (clone 33A3; Cat. No. 39649; Active Motif) to immunoprecipitate methylated DNA. M.SssI methylated DNA was amplified, labeled and hybridized on arrays.

first: H

first: J

last: Verboon

first: T

middle: R

last: Werwie

last: Delrow

first: D

last: Scalzo

first: M

last: Groudine

first: S

last: Parkhurst


title: Expression profiles of microRNA in bovine raw milk exosome and supernatant without exosome [miRNA array]

status: Public on Mar 09 2015

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

institute: Morinaga Milk Industry Co., Ltd.

summary: We have reported that microRNAs are present in human, bovine, and rat milk whey. Milk whey miRNAs were resistant to acidic condition and to RNase. Thus, milk miRNAs were thought to be present packaged into membrane vesicles like exosome. However, body fluid miRNAs have been reported that there are in different forms. To clarify which miRNAs species are exist in exosome and which species are exist in another form, we used bovine raw milk and purified total RNA from exosome fraction and ultracentrifugated supernatant fraction, and analyzed by miRNA microarray.

overall_design: Three bovine raw milk samples were prepared and mixed equally. These raw milks are usually used for R&D in our laboratory. For example, trial manufacturing.


title: The role of BPTF in melanoma progression and in response to BRAF-targeted therapy

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

summary: These studies demonstrate multiple pro-tumorigenic functions for BPTF, and identify it as a novel target for anti-cancer therapy. They also suggest the combination of BPTF targeting with BRAF inhibitors as a novel therapeutic strategy for melanomas with mutant BRAF.

overall_design: Parental B16 cells transfected with a control or anti-BPTF shRNAs consitute the comparative arms of this study.Five replicates of each condition was performed.

first: Altaf

last: Dar

first: Mohammed

last: Kashani-Sabet


title: microRNA profile of human intrahepatic cholangiocarcinoma: intrahepatic cholangiocarcinoma vs. normal intrahepatic bile duct tissue

status: Public on Mar 06 2015

city: Guangzhou

first: Mei-Yin

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

summary: MicroRNA expression profiles were sucessfully contructed in 63 patients with ICC and 9 normal intrahepatic bile ducts using a custom microarray containing probes for 1094 miRNAs and an outcome prediction of miRNA signature was successfully identified for predicting prognosis in ICC.

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 63 ICC cases, followed up more than three years, was used to acquire miRNA expression profiles of 1094 miRNAs and identify a miRNA signature, leading to the successfully for predicting prognosis in ICC.

first: Meiyin

first: Shengping

last: Li

first: Huiyun

last: Wang


title: Diurnal variation for rice leaves in a growth chamber

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary:
Time-course transcriptional profiling to compare progression of subjective time with that in the field. The subjective time was inferred from expressions of multiple circadian clock-related genes.
24-h time series with 2-h interval were sampled for 2 developmental stage with no replicate. Two more varieties were sampled only at 3 time points for plants of 28 days past sown (DPS).

overall_design: Jun, Matsuzaki

first: Yoshihiro

last: Kawahara


title: Wash regulates lamin-dependent nuclear genome organization [DamID]

first: Hector

summary:
The cytoplasmic functions of Wiskott-Aldrich Syndrome family (WASP) proteins are well known and include roles in cytoskeleton reorganization and membrane-cytoskeletal interactions important for membrane/vesicle trafficking, morphogenesis, immune response and signal transduction. Mis-regulation of these proteins is associated with immune deficiency and metastasis. Cytoplasmic WASP proteins act as effectors of Rho family GTPases and polymerize branched actin through the Arp2/3 complex. However, recent evidence has revealed that this classically cytoplasmic protein family also functions in the nucleus. Previously, we identified Drosophila washout (wash) as a new member of the WASP family with essential cytoplasmic roles in early development. Here we show that Wash is also present in the nucleus and plays a key role in nuclear organization via its interaction with Lamin Dm0 at the nuclear envelope. Wash and Lamin Dm0 occupy similar genomic regions that overlap with transcriptionally silent chromatin including constitutive heterochromatin. Strikingly, wash mutant and knockdown nuclei exhibit the same abnormal wrinkled morphology observed in diverse laminopathies, including the Hutchinson-Gilford progeria syndrome, and consistent with disruption of the nuclear organization of several sub-nuclear structures including cajal bodies and the chromocenter in salivary glands. We also found that Wash and Lamin knockdown disrupt chromatin accessibility of repressive compartments in agreement with an observed global redistribution of repressive histone modifications. Functional genetic approaches show wash mutants exhibit similar phenotypes to lamin Dm0 mutants, suggesting they participate in similar regulatory networks. Our results reveal a novel role for Wash in modulating nuclear organization via its interaction with the nuclear envelope protein Lamin Dm0. These findings highlight the functional complexity of WASP family proteins and provide new venues to understand their molecular roles in cell biology and disease.
DamID chromatin profiling demostrate that Wash binds similar regions to those bound by Lamin Dm0, in particular transcriptional silent chromatin

overall_design: To establish Wash and Lamin chromatin profiles, Kc167 cells were transfected with the Dam methylase fused to Wash or Lamin cDNAs and compared to the Dam methylase alone. Experiments were performed triplicates (Biological replicates). 10e6 cells were electroporated and incubated for 48 h at 250C. Genomic DNA was recovered and digested with DpnI overnight at 37C. A 5-30% sucrose gradient was used to recover a DNA fragments range between 0.3-2.5Kb.


title: Expression data of lungs from chickens infected with different H5N1 Avian Influenza Viruses [24 hours post infection]

status: Public on Mar 04 2015

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

institute: Yangzhou University

summary:
Recently, a novel protein in the influenza virus segment 3 has been identified, namely PA-X. This small protein has been reported to play a role in modulating host response of the 1918 H1N1 pandemic virus-infected mice. However, poteinal role of this protein in the pathogenicity and regulating host response of the highly pathogenic H5N1 virus in a chicken animal model is completely unknown.
We used microarray analysis to evaluate the global transcriptional response in the lungs of the chickens infected with the parental strain (CK10) and PA-X deficiency mutant strain (CK-PAX3).

overall_design: Chickens were inoculated with CK10 or CK-PAX3 or mock-infected. At 24 hours post infection, lungs were isolated from three chickens per group for RNA extraction and hybridization on Affymetrix microarrays. Samples were named as follows: CK10 (CK10-1,CK10-2,CK10-3), CK-PAX3 (CK-PAX3-1,CK-PAX3-2, CK-PAX3-3), Control (C-1, C-2, C-3).

first: Zenglei


title: Wash regulates lamin-dependent nuclear genome organization

last: Rincon-Arano

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

overall_design: Refer to individual Series


title: Microarray analysis of Indian mustard plants subjected to arsenate stress

city: Varanasi

first: Sudhakar

last: Srivastava

address: Lanka

department: INSTT. OF ENV.  AND SUST. DEV.

country: India

institute: Banaras Hindu University

summary: In this study, time dependent (4 h to 96 h) transcriptome changes in roots and shoots of Brassica juncea were analyzed under arsenate (AsV) stress by using Agilent platform.    A total of 1285 genes showed significant change in expression pattern upon arsenate (AsV) exposure. The genes belonged to various signaling pathways including hormones   (jasmonate, abscisic acid (ABA), auxin and ethylene) and kinases. Significant effects were also noticed on genes of sulfur, nitrogen, CHO, and lipid metabolisms along with photosynthesis.  These studies indicated interconnections among sulfur metabolism, jasmonate and kinase signaling pathways. Transcriptome results and biochemical analyses highlight that signaling and   metabolic pathways work in a dynamic coordination to perceive and respond to the stress.

overall_design: A set of 53939 sequences, which include EST and nucleotide sequences of Brassica sp., were downloaded from GenBank. These sequences were subjected to clustering and analyzed using  CAP3/tgicl program and other in-house tools. A set of 26881 non-redundant sequences was created, which was used for probe design. This set included 1720 Brassica juncea, 15259 Brassica   napus and 5075 Brassica rapa sequences; and 6456 from other species. Probes were designed for the non-redundant sequences using Agilent eArray tool. Best probe composition algorithm with   the option to design multiple probes for each sequence was the main criteria used for the probe design. Agilent’s 4x44 array was selected to print the oligos. A set of positive and negative controls   were also added on to the microarray chip. A set of replicate probes were also added for calculating the intra-array reproducibility. The quantity and purity of the RNA was determined by absorbance   at 260 nm and 260/280 absorbance ratio respectively.  Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and RIN measured on an   Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit .With the use of Agilent’s 1-Color Quick Amp Labeling Kit, 500 ng of high quality total RNA was denatured in the presence of   a T7 promoter primer and a 1-Color RNA Spike-In Kit. Reverse transcriptase was used to reverse-transcribe the mRNA. cDNA was used as a template for in vitro transcription where a T7 RNA polymerase   simultaneously amplified target material and incorporated cyanine 3-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity   and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.    With the use of Agilent’s Gene Expression Hybridization Kit, 1.65 µg of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented. The hybridization   cocktail was then dispensed into the wells of gasket slides on top of which a Brassica 4x44K Gene Expression Microarray was placed. This microarray “sandwich” was then sealed in a hybridization chamber.   The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours. Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer specifications.   The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Agilent Technologies Feature Extraction software version 10.7.3.1.Microarray data   quality was evaluated by reviewing ten standard QC metrics generated by the Feature Extraction Software [Consult the Agilent Technologies Feature Extraction Software version 10.7.3.1 reference guide   for a full explanation of the QC metrics]. To determine if there was a large hybridization, staining, or wash artifacts, a visual examination of each array was   performed by loading the array image into Feature Extraction Software. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the   quality of the data.

first: Ashish

first: Tejaswini

last: Deshpande

first: Penna

last: Suprasanna


title: Study of microRNA associated with metformin’s anti-tumor effect [Huh7 cells]

status: Public on Mar 01 2015

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The miRNAs expression was markedly altered with the treatment of metformin in vitro and in vivo and various miRNAs induced by metformin also may contribute to tumor growth in vitro and in vivo.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 985 human miRNA probes in the cell lines in vitro and tumorous tissues in vivo that were treated with and without metformin.

first: Hisaaki

last: Miyoshi

first: Tsutomu

last: Masaki


title: Gene expression of rat uterine endometrial stromal cells treated with ethanol (vehicle) or 0.1 nM progestin R5020

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Although non-genomic steroid receptor pathways have been studied over the past decade, little is known about the direct gene expression changes that take place as a consequence of their activation. Progesterone controls proliferation of rat endometrial stromal cells during the peri-implantation phase of pregnancy. We showed that picomolar concentration of progestin R5020 mimics this control in UIII endometrial stromal cells via ERK1-2 and AKT activation mediated by interaction of Progesterone Receptor (PR) with Estrogen Receptor beta (ERb) and without transcriptional activity of endogenous PR and ER. Here we identify early downstream targets of cytoplasmic PR signaling and their possible role in endometrial stromal cell proliferation. Microarray analysis of global gene expression changes in UIII cells treated for 45 min with progestin identified 97 up- and 341 down-regulated genes. The most over-represented molecular functions were transcription factors and regulatory factors associated with cell proliferation and cell cycle, a large fraction of which were repressors down-regulated by hormone. Further analysis verified that progestins regulate Ccnd1, JunD, Usf1, Gfi1, Cyr61, and Cdkn1b through PR-mediated activation of ligand-free ER, ERK1-2 or AKT, in the absence of genomic PR binding. ChIP experiments show that progestin promoted the interaction of USF1 with the proximal promoter of the Cdc2 gene, and Usf1 knockdown abrogated Cdc2 progestin-dependent transcriptional regulation providing a mechanism for direct regulation of its expression. Finally, Cdc2 knockdown blocked R5020 induced UIII cell proliferation. We conclude that progestin induced proliferation of endometrial stromal cells requires ERK1-2 and AKT mediated early regulation of USF1, that induces Cdc2. To our knowledge, this is the first description of early target genes of progestin-activated classical PR via crosstalk with protein kinases and independently of hormone receptor binding to the genomic targets.

overall_design: Two-condition experiment, OH vs. 0.1 nM R5020 treated UIII cells during 45 minutes. Biological replicates:3 ethanol (vehicle control) independent replicates, 3 R5020 independent replicates, 1 dye swap.

first: Patricia

last: Saragüeta

first: Griselda

last: Vallejo

first: Alejandro

last: La Greca

first: Inti

middle: C

last: Tarifa-Reischle

first: Ana

last: Mestre-Citrinovitz

first: Cecilia

last: Ballaré

first: Miguel

last: Beato

first: Juanjo

last: Lozano


title: Studies of wax genes in cotton (Gossypium arboreum)

status: Public on Mar 08 2015

city: Lahore

first: Muhammad

middle: Younas

last: khan

state: Punjab

address: Thokar Niaz Baig

department: Molecular biology

country: Pakistan

institute: National centre of Excellence in Molecular biology

summary: The aim of the present study is to list the genes involved in cotton (G. arboreum) leaf epicuticular wax production and deposition. For this purpose differentially expressed genes (especially, down-regulated in wax deficient mutant plant) in wild and epicuticular wax mutant (Gawm3) plants were founded through cDNA microarray, developed from the wild plant leaves.

overall_design:
3× (wild cotton leaf labeled with Cy3/ epicuticular wax mutant cotton leaf (Gawm3) labeled with Cy5)
3× (wild cotton leaf labeled with Cy5/ epicuticular wax mutant cotton leaf (Gawm3) labeled with Cy3)

first: MuhammedYounas

last: KhanBarozai

first: Tayyab

last: Hussnain


title: Arabidopsis Wild-type vs. Gcn2 GT8350 mutant line. Glyphosate-treated

first: Jose

last: Gadea

country: Spain

summary: Transcriptomic profiling of glyphosate-treated seedlings comparing Arabidopsis wild-type (Ler) versus gcn2 mutant line

overall_design: Two-condition experiment, WT-glyphosate vs. Gcn2-glyphosate seedlings. Biological replicates: 3, randomly paired


title: Identification of pathogenic microRNAs in Helicobacter pylori-associated gastric cancer

city: Hong Kong

first: Jing

last: Shen

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, cuhk, Shatin NT

department: sbs

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: To identify dysregulated miRNA(s) upon infection with H. pylori during different pre-malignant and malignant stages of gastric cancer in a mouse model

overall_design: miRNA expression in pre-neoplastic and neoplastic lesions in murine stomachs induced by H. pylori and N-methyl-N-nitrosourea (MNU) after 12 months was profiled by miRNA expression array.

first: William

last: Wu


title: Expression data of lungs from chickens infected with different H5N1 Avian Influenza Viruses

first: Jiao

last: Hu


title: Dynamic profiling of the protein life cycle in response to pathogens (protein)

city: Boston

first: Catherine

state: MA

address: 450 Brookline Ave.

institute: Dana Farber Cancer Institute

summary: Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle.

overall_design: Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

first: Marko

last: Jovanovic

first: Michael

middle: S

last: Rooney

first: Nir

last: Hacohen

first: Aviv

last: Regev


title: miRNA expression data in 3rd mammary gland and mammary flank region at embryonic day 13.5

first: Eun-Jung

last: Kim

address: 50 Yonsei-ro

department: Department of Oral Biology

institute: Yonsei Universiry

summary: miRNAs are not well known their expression and function in mammary gland development. To identify the miRNAs expression during mammary gland development, mammary bud were dissected at E13.5

overall_design: miRNA-chip expression analysis was performed with RNAs of the 3rd mammary gland and mammary flank region between 3rd and 4th mammary gland from embryos of pregnant mice at emrbryonic day 13.5, using Agilent's miRNA microarray.

first: Jong-Min

last: Lee

first: Kyoung-Won

last: Cho

first: Qinghuang

last: Tang

first: Kye-Seong

first: Cheryll

last: Tickle

first: Han-Sung

last: Jung


title: cDNA-Shigella flexnerri- Furazolidone

city: Beijing

first: Hua

last: Fu

address: 6#, Rongjing East Street

institute: Institute of pathogen biology

summary:
Shigella flexneri is a facultative intracellular pathogen which is mainly responsible for endemic shigellosis in developing countries. In the present study, we demonstrated S.flexnerri was susceptible to furazolidone, a nitrofuran derivative that has been used as therapeutic regimen against a variety of gastro-intestinal bacterial infections. To identify the global transcriptional responses of S.flexnerri in response to furazolidone treatment, S.flexnrri was exposed to both subinhibitory and inhibitory concentrations of furazolidone and microarray analysis was used to examine gene expressions after both short and long period of incubation. Analysis of microarray data revealed that genes involved in soxRS and oxyR regulons, iron metabolism, DNA replication and repair and lipid peroxidation were induced by the drug, while a large percentage of genes involved in energy production, carbohydrate metabolism, amino acid metabolism, and lipid metabolism were significantly repressed after the drug treatment. In addition, many genes related to preventing against injuries of iron-sulfur clusters known to be caused by superoxide radicals were also up-regulated. These data establish potential for furazolidone to enhance free radical reactions through its reductive activation, which indicates oxidative damages may be implicated in antibacterial effect of the drug.
Keywords: drug expressional profiles

overall_design: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 0.25× ,0.5× or 1× minimum inhibitory concentration (MIC). Thus the final concentration of solvent (DMSO) in every test was 0.25% (vol/vol). Meanwhile, DMSO without the antimicrobial was added to control cultures at a final concentration of 0.25% (vol/vol) .At 30 and 90 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation. Therefore, we established six test conditions altogether. In order to prepare biological replicates for RNA isolation, the experiment was independently performed three times. Altogether, there are  18 samples in our study.


title: RPPA_RATHER_ILC

status: Public on Mar 07 2015

city: Paris

first: Leanne

last: de Koning

address: 26 rue d'Ulm

department: Department of translational research

country: France

institute: Institut Curie

summary: Invasive lobular carcinoma (ILC) is the second most frequent histological breast cancer subtype after invasive ductal carcinoma (IDC), accounting for 5-15% of all breast cancers. Although clinical outcomes of ILC and IDC seem similar, the molecular processes underlying ILC are still largely unknown. To explore this, we have performed a comprehensive proteomics analysis of a large ILC patient cohort. These data are generated in the context of the RATHER consortium (http://www.ratherproject.com/)

overall_design: Fresh frozen tissue sections from 118 ILCs with a median clinical follow-up of 6.8 years were lysed and printed on protein arrays. Each sample was printed in 5 serial dilutions and each dilution was printed twice on the arrays. Arrays were hybridized with 168 specific primary antibodies against the kinome and cancer-related proteins.

first: Thierry

last: Dubois

first: Beilei

last: He

first: Caroline

last: Lecerf

first: Floriane

last: Bard

first: Aurélie

last: Barbet


title: Expression data of lungs from chickens infected with different H5N1 Avian Influenza Viruses [12 hours post infection]

first: Jiao

last: Hu

overall_design: Chickens were inoculated with CK10 or CK-PAX3 or mock-infected. At 12 hours post infection, lungs were isolated from three chickens per group for RNA extraction and hybridization on Affymetrix microarrays. Samples were named as follows: CK10 (CK10-1,CK10-2,CK10-3), CK-PAX3 (CK-PAX3-1,CK-PAX3-2, CK-PAX3-3), Control (C-1, C-2, C-3).

first: Zenglei


title: Androgen receptor gene aberrations in circulating cell-free DNA: biomarkers of therapeutic resistance and response in castration-resistant prostate cancer

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

summary: aCGH experiment on cell-free DNA collected from the plasma of patients with castration-resistant prostate cancer. No replicates.

overall_design: castration-resistant prostate cancer vs male reference DNA

first: S

middle: V

last: Volik

first: A

middle: W

last: Wyatt

first: C

last: Collins


title: Recurrent copy number alterations are associated with poor prognosis and HPV infection in penile carcinomas

status: Public on Feb 20 2015

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

institute: ICESP

summary: Array-based comparative genomic hybridization (aCGH) was used to evaluate DNA copy number alterations related and non related to HPV infection status aiming to identify potential molecular markers in penile cancer (PC).

overall_design: DNA was extracted from thirty-eight fresh frozen PC samples and submitted to HPV genotyping and array-CGH. Commercial male reference samples (Promega) were used as normal controls. Specific genomic alterations were investigated by qPCR and FISH methodologies.

first: Ariane

last: Busso

first: Fábio


title: Artemisinin mimics calorie restriction to trigger mitochondrial biogenesis and compromise telomere shortening in mice

status: Public on Feb 18 2015

first: Qing-Ping

last: Zeng

address: No. 12, Airport Rd.

department: Tropical Medicine Institute

institute: Guangzhou University of Chinese Medicine

summary: Calorie restriction is known to extend lifespan among organisms by a debating mechanism underlying nitric oxide-driven mitochondrial biogenesis. We report here that nitric oxide generators including artemisinin, sodium nitroprusside, and L-arginine mimics calorie restriction and resembles hydrogen peroxide to initiate the nitric oxide signaling cascades and to elicit the global antioxidative responses in mice. The large quantities of antioxidant enzymes are correlated with the low levels of reactive oxygen species, which allow the down-regulation of tumor suppressors and accessory DNA repair partners, eventually leading to the compromise of telomere shortening. Accompanying with the up-regulation of kinases, acetylases, and biomarkers, mitochondrial biogenesis occurs with the elevation of adenosine triphosphate levels upon exposure of mouse skeletal muscles to the mimetics of calorie restriction. In conclusion, calorie restriction-triggered nitric oxide provides antioxidative protection and alleviates telomere attrition via mitochondrial biogenesis, thereby maintaining chromosomal stability and integrity, which are the hallmarks of longevity.

overall_design: Six samples were analyzed, in which a control sample was included.


title: Transcript profiling of Mungbean yellow mosaic India virus (MYMIV) infected Glycine max

city: New Delhi

first: rajiv

middle: kumar

last: yadav

address: Aruna Asaf Ali Marg

institute: National Institute of Plant Genome Research

summary: Transcript profiling of control vs Mungbean yellow mosaic India virus infected Glycine max variety JS335. RNA samples were collected at 2 dpi to study change in transcript profile at early infection.

overall_design: Two-condition experiment, control vs. MYMIV infected.

first: Rajiv

middle: K

last: Yadav

first: Debasis

last: Chattopadhyay


title: Evaluation of DNA-binding preferences of C2H2 zinc finger domains by PBM

status: Public on Feb 17 2015

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

institute: McGill University

summary: The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site.  Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution.  Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA.  Using the bacterial 1-hybrid (B1H) system, we determined DNA-binding motifs for thousands of individual natural C2H2-ZFs, and correlated them with C2H2-ZF specificity residues. The data reported here includes results of protein-binding microarray (PBM) assays for 146 of these natural C2H2-ZFs, performed in order to validate B1H assays and to explore the DNA-binding specificity of C2H2-ZFs.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 185 variants of mouse Egr1 in which the third zinc finger was replaced by different C2H2-ZFs from different organisms. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006. Among the 185 variants examined, 146 variants yielded motifs in PBMs, which are included here.

first: Sanie

last: Mnaimneh

first: Ally

last: Yang

first: Mihai

last: Albu

first: Timothy

last: Hughes


title: Screening the target genes of IRF10 in Japanese flounder, Paralichthys olivaceus

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

summary: In previous study, we revealed that IRF10 is involved in the immune-reponse against bacteria and virus in Paralichthys olivaceus. However, the target genes of IRF10 is still unknown in teleosts. We searched the target genes of IRF10 by microarray in IRF10 over expressed HINAE cell

overall_design: HINAE cells were culured in 24-well plate. HINAE cells were transfected using lipofectamine2000 (Invitrogen, USA) with 7.2nM IRF10 expression plasmid vector (pcDNA3.1-IRF10) or empty-vector (pcDNA3.1). The equal volume of sterile water was used as a control. On other hands, the 1μg/ml of poly I:C also transfected to HINAE cells using lipofectamine2000 with each plasmid and vehicles (sterile water). After 48 hours from the transfection, we harvested the two samples of the control and poly I:C only and the three samples of plasmids or plasmids with poly I:C transfected cells (16 hybridization).

first: Yoshiaki

last: Suzuki

first: Takashi

last: Aoki

first: Ikuo

last: Hirono


title: Human induced Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

status: Public on Feb 16 2015

city: New York

first: Eirini

last: Papapetrou

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Mapping deletions of Chr7 in human iPSC derived from patients cells through reprogramming

overall_design: Two-condition experiment, normal diploid iPSCs vs del7q-iPSCs


title: Human Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

summary: Mapping deletions of Chr7 in human iPSC and ESCs derived from patients cells through reprogramming or chromosome engineering

overall_design: Two-condition experiment, normal diploid hPSCs vs del7q-hPSCs


title: Molecular mechanisms vascular smooth muscle cell (VSMC) acquisition of macrophage features in response to cholesterol loading

status: Public on Feb 06 2015

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

summary: In this study, murine primary aortic smooth muscle cells (SMCs) were transcriptionally profiled at baseline, after 3 d of cholesterol loading, and after 3 d of subsequent cholesterol unloading with HDL treatment, to identify vascular SMC genes that are transcripionally dysregulated in response to cholesterol loading and/or unloading.

overall_design:
Mouse aortic SMCs were isolated from thoracic aortas of 8 week-old C57BL/6 mice (as described in Rong et al., Proc Nat Acad Sci USA, v100, pp13531–13536, 2003) and subconfluent cell preparations were harvested and transcriptionally profiled (baseline group) or treated with 10 μg/mL cholesterol:methyl-β-cyclodextrin complex (1:6 molar ratio) for 72 h for cholesterol loading. Of the cholesterol-loaded cells, samples were transcriptionally profiled (cholesterol samples) or treated for an additional 72 h with 100 μg/mL human HDL and then transcriptionally profiled (HDL treatment). For all transcriptional profiling, RNA was isolated from cells using TRIzol, and labeled aRNA was prepared for hybridization to Affymetrix Mouse Genome 430 2.0 microarrays according to the manufacturer's protocol. Probe-level intensities were background-adjusted and normalized (in two separate analyses, one with baseline and cholesterol-treated samples, and the other analysis with all three sample groups) using Robust Multichip Average and combined into probesets using probe-to-probeset mappings from the University of Michigan CustomCDF project based on Ensembl Gene identifiers (release 59). Using the data from the analysis that combined the baseline and cholesterol-loaded samples, log2 probeset intensities were compared the between baseline and cholesterol sample groups using a one-way ANOVA with a P value cutoff determined by a Benjamini-Hochberg false discovery rate threshold of 0.05.
Analysis (I): baseline and cholesterol-treated sample groups.
Analysis (II): all three sample groups.

first: Yuliya

last: Vengrenyuk

first: Elizabeth

last: Gold

first: Alan

last: Aderem

first: Edward

last: Fisher


title: Development of a Fluorescence-Activated Cell Sorting Method Coupled with Whole Genome Amplification To Analyze Minority and Trace Dehalococcoides Genomes in Microbial Communities

status: Public on Jan 31 2015

city: Berkeley

first: Patrick

last: Lee

state: CA

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

summary: Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ~1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ~10% and ~1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

platform_organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Dehalococcoides mccartyi CBDB1
Dehalococcoides mccartyi VS

overall_design: The genomic DNA (gDNA) of each culture or sorted and amplifed DNA was analyzed in triplicate.

first: Yujie

last: Men

first: Shanquan

last: Wang

first: Jianzhong

last: He

first: Lisa

last: Alvarez-Cohen


title: Genome-wide miRNA turnover profile in various cell types after transcription inhibition

status: Public on Feb 05 2015

city: New Haven

first: Yanwen

last: Guo

state: CT

address: 214K 10 Amistad St

department: Genetics

institute: Yale University

summary: We measured miRNA turnover rates in 8 mammalian cell types post transcription inhibitors ActinomycinD (ActD) or 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) treatment with miRNA expression profiling, generating 218 expression profiles on 528 endogenous miRNAs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus
human gammaherpesvirus 4

overall_design: Cells were plated in six-well plates at around 200,000 cells/well. A media change was performed one day after plating. ActD and DRB treatment were started after confluency (around two days after plating) for 0, 2, 4, 6, 12, and 24 hours post treatment with biological duplicate (ActD treatment) or biological triplicate (DRB treatment). The concentration of ActD and DRB for different cell lines were titrated to achieve rapid c-myc down-regulation after 2 hours of ActD and DRB treatment. After treatment at indicated time points, cells were washed with PBS once and lysed in TriZol reagent immediately (Invitrogen). RNA extraction was performed following the manufacturer’s protocol. miRNA profiling was performed using a Luminex bead-based method.

first: Jun

last: Lu


title: Differential Gene Expression in Uterine Endometrium during Implantation in Pigs

status: Public on Jan 26 2015

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

summary: This study provide an opportunity to elucidate the genetic control of fetal implantation and improve our understanding of fetal implantation and gestation maintenance, thus make further improvement for litter size of pigs.

overall_design: Nine pregnant sows were slaughtered by electrical on day 13, day 18 and day 24 after insemination (the pregnant group, three sows every period). The non-pregnant sows were slaughtered on day 13 after inseminated (n=3).In pregnant sows, samples of the endometrium attachment sites and inter-sites were taken. Samples from the endometrium of the non-pregnant sows were taken from comparable locations.


title: The effects of herb-partitioned moxibustion on miRNA expression profiling in the colons of CD rats

city: Shanghai

first: Kai

last: Wei

address: 130 Dong'an Road, Xuhui District, Shanghai, China

institute: Shanghai Medical College of Fudan University

summary: Using the highly sensitive miRNA microarray, we screened differentially-expressed miRNAs in colons of normal control (NC) rats, model control (MC) rats and herb-partitioned moxibustion (HPM) rats. We found 40 miRNAs differentially expressed in CD rats’ colons compared with the NC rats, and HPM significantly regulated 26 miRNAs in colon tissues compared with the MC group. Furthermore, the quantitative real-time polymerase chain reaction results showed that down-regulated miR-147 and miR-205 in CD rats’ colons were both significantly up-regulated by HPM, with 2.64- and 3.72-folds increased respectively, indicating that miR-147 and miR-205 are the target genes of HPM in treating CD rats.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the study presented here, four samples from each group were used to screen the differentially-expressed miRNAs in colons of experimental CD rats and the target genes of HPM. Six colons from each group were further used to verify the target genes of HPM. Finally, miR-147 and miR-205 were experimentally validated to be target genes of HPM.

first: Dan

last: Zhang


title: Identification of hsa-miR-135a target genes in the HeLa cell line

status: Public on Mar 18 2015

city: Lyon Cedex 07

first: Nathalie

last: ALLIOLI

address: 46 Allée d'Italie

department: Institut de Génomique Fonctionnelle de Lyon (IGFL)

institute: Ecole Normale Supérieure de Lyon (ENS)

summary: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs. They act as negative regulators of protein-coding gene expression at the post-transcriptional level via sequence-specific interaction with the 3' UTR of targeted mRNAs. A miR-135a dysregulation has been observed in various cancers, where a dual role of oncomiR or of tumor suppressor has been reported for the cancers profiled to date; however, knowledge is limited to explain these contentious data. In the present study, we investigate the regulation and mechanism of action of miR-135a, including identification of functionally targets that contributes to its actions, in prostate cancer progression. We demonstrate that the expression of miR-135a is regulated by androgens, in a time- and dose-dependent manner and identify miR-135a as a direct target gene of the androgen receptor AR. A functional androgen response element (ARE) is identified in the promoter region of the miR-135a gene and ChIP assay reveal AR protein binding to. Anti-androgen treatment and AR-targeted siRNA knockdown strategy suggest a novel function for miR-135a in AR signaling. In silico prediction, transcriptomic and proteomic combined analyses lead to identify ROCK-1/-2 as two miR-135a-targeted genes. Luciferase reporter assays indicate that these two proteins are miR-135a's direct targets. We finally demonstrate that miR-135a acts through ROCK-1/-2 pathways to affect migration and invasion cellular processes. MiR-135a expression level was lower in surgical cancerous samples compared to paired adjacent non-tumoral tissues and was gradually diminished consistent with cancer progression, suggesting the significance of miR-135a-mediated prostate cancer transformation. Our findings define miR-135a as a candidate tumor suppressor and potential prognostic marker in human prostate cancer.

overall_design:
Transcriptional profiling of the HeLa cell line that over-expressed hsa-miR-135a.
HeLa cells were transfected with the hsa-miR-135a mimic (Ambion) and compared to control cells transfected with the negative control.

last: Allioli

first: Auriane

last: Kroiss

first: Séverine

last: Vincent

first: Jacques

last: Samarut


title: Transcriptional expression patterns triggered by chemically distinct neuroprotective molecules

status: Public on Jan 01 2015

city: San Francisco

first: Derek

last: Pappas

address: 675 Nelson Rising Lane, RM 240

department: Neurology

institute: University of California, San Francisco

summary:
To increase our understanding of the mechanisms that underlie neuroprotection following glutamate receptor-induced excitotoxicity, we treated primary CD-1 mouse cortical neurons with NMDA in the presence of absence of neuroprotective compounds. The results indicate a convergence at the level of whole genome expression, despite the divergent chemistries and purported mechanisms of action.
While more arrays were performed than published, only the extreme arrays were used in subsequent analyses.

overall_design: CD-1 Mouse cortical neurons were exposed to NMDA, in the presence or absence of neuroprotective molecules, followed by a recovery period (16hr) and total RNA extraction.


title: Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion

status: Public on Jan 12 2015

city: Tsukuba

first: Bei-Wen

last: Ying

address: 1-1-1 Tennoudai

institute: University of Tsukuba

type: Expression profiling by genome tiling array

summary: An assortment of genetically engineered Escherichia coli strains of the rewired gene regulation were used to study whether the cells could adapt to the environmental changes without the evolved gene regulatory machinaries. These E. coli strains had a synthetic gene circuit comprising a rewried gene that natively located within the His opeon. The cells growing under histidine supplied or depleted conditions were subjected to the macrioarray analysis. Multilevel analyses were performed to evaluate the global reorganization of gene expression in response to histidine depletion. A common pattern in transcriptome was observed in the adpative cells, indicating a survival strategy of "stochastic adaptation with regular transcriptome reorganization".

overall_design: The genetically engineered strains of rewired genes and the control strain of the native gene regulation were grown in the presence and absence of histidine, and the cells within the exponetially growing phase were collected for the microarray analysis. Temproal changes in response to histidine depletion were also investigated. Every 3 biological replications for each condition were performed. Total 90 array assays were reported here.

first: Yoshie

last: Murakami

first: Tetsuya

last: Yomo


title: Disruption of transkingdom communication by antibiotics leads to immune and mitochondrial dysfunction in the gut

first: Natalia

last: Shulzhenko

state: Oregon

address: 700 SW 30th St, 105 Dryden Hall

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

We analyzed the effects of antibiotics using a popular model of gut microbiota depletion in mice by a cocktail of antibiotics. We combined intestinal transcriptome together with metagenomic analysis of the gut microbiota to develop a new bioinformatics approach that probes the links between microbial components and host functions. We found that most antibiotic-induced alterations can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues; and the effects of remaining antibiotic-resistant microbes. While microbe depletion led to down-regulation of immunity, the two other factors primarily inhibited mitochondrial gene expression and amounts of active mitochondria, and induced cell death. By reconstructing and analyzing a transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria.

overall_design: Refer to individual Series