title: Identification of stress response and recovery mechanisms by  multi-scale analyses of drought effect in the maize leaf growth zone.

status: Public on Aug 28 2015

city: Antwerpen

first: Gerrit

middle: TS

last: Beemster

state: Antwerpen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary: We use  the gowth zone of the maize leaf as a model system to study the growth reduction in response to drought stress. The spatial gradient and the relatively large size of the maize leaf allowed us to sample at a subzonal rezolution and to examine different developmental stages at the same time. We compared the response to different levels of drought stress (mild and severe) of proliferating (meristem), expanding (elongation zone) and differentiated (mature zone) tissue.

overall_design: Three separate loop designs were used for the three zones of the maize leaf (meristem, elongation zone, and mature zone). In each loop three treatments were contrasted (control, mild stress, and severe stress). Four biological replicates were used for each zone/condition (4 replicates x 3 zones x 3 conditions = 36 samples).

first: Viktoriya

last: Avramova

first: Hamada

last: AbdElgawad

first: Zhengfeng

last: Zhang

first: Bartosz

last: Fotschki

first: Romina

last: Casadevall

first: Lucia

last: Vergauwen

first: Dries

last: Knapen

first: Edith

last: Taleisnik

first: Yves

last: Guisez

first: Han

last: Asard

middle: T


title: Gene expression analyses of SMAD4 knockdown in pancreatic cell line

status: Public on Aug 20 2015

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

summary: The transforming growth factor β (TGF-β) signaling protein SMAD4 is lost in 60% of PDAC, and this has been associated with poorer prognosis. We expressed SMAD4 in human PDAC cell lines BxPC3, by selection of stable clones containing an inducible SMAD4 Tet-ON construct. After 24h of SMAD4 expression, TGF-β signaling-dependent G1-arrest was observed in BxPC3 cells with an increase in the G1-phase fraction from 48.9% to 71.5%. Microarray analysis of gene expression at 8h, 24h, and 48h after SMAD4 expression characterized the regulatory impact of SMAD4 expression in a SMAD4-null PDAC cell line and identified novel targets of TGF-β signaling.

overall_design: We used BxPC3 cells infected by pINDCUER-SMAD4-Puro virus. After 24h, 1µg/ml doxycycline was added to experimental wells. We profiled the gene expression after 8hr, 24hr and 48hr treatment with doxycycline as well as control at 8hr.

first: Martin

last: Matzuk

first: Paul

last: Fullerton

first: Fengju

last: Chen


title: Gene expression in human pediatric T-acute lymphoblastic leukemia (T-ALL) diagnostic samples

status: Public on Aug 25 2015

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: Comparative expression between T-ALL samples with short or long engraftment kinetics in immunodeficient mice

overall_design: Frozen diagnostic samples

first: Françoise

last: Pflumio


title: Changes in eutopic endometrial gene expression during the progression of experimental endometriosis in the baboon, Papio anubis

status: Public on Aug 27 2015

city: Basel

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

summary:
Endometriosis is associated with aberrant gene expression in the eutopic endometrium of women with disease. To determine if the development of endometriotic lesions directly impacts eutopic endometrial gene expression, we sequentially analyzed the eutopic endometrium across the time course of disease progression in a baboon model of induced disease. Endometriosis was induced in baboons by intraperitoneal inoculation of autologous menstrual endometrium. Eutopic endometria were collected at 9-11 days postovulation) in five time points: 1, 3, 6-7, 10-12, and 15-16 months after disease induction and compared with tissue from disease-free baboons.
We used microarrays to identify differentially expressed genes between time points. Sequential analysis of the same animals during disease progression demonstrated an early disease insult and a transitory dominance of an estrogenic phenotype. However, as the disease progressed, a progesterone-resistant phenotype became evident.

overall_design: Endometriosis was experimentally induced in Papio anubis female baboons (n = 4) by intraperitoneal inoculation with menstrual endometrium on two consecutive menstrual cycles. Baboons with spontaneous endometriosis (n = 2) were also included in this study with an unknown duration of disease. Control endometrium was similarly harvested from animals (n = 4) with no previous surgeries and with no visible disease. The progression of disease was monitored in each animal by consecutive laparoscopies and video recording at 1 (n = 2), 3 (n = 4), 6-7 (n = 4), 10-12, (n = 4), and 15-16 (n = 3) months after inoculation during a window of 9-11 days postovulation. Eutopic endometrial tissues were harvested and were snap frozen in liquid nitrogen for RNA extraction. Additionally, menstrual endometrium was harvested on Days 1-2 of menses using a Unimar Pipelle (Cooper Surgical Inc., Shelton, CT) immediately prior to laparoscopy. Blood samples were collected daily from days 7 through 16 postmenstruation of menstrual cycles.

first: Asgerally

last: Fazleabas

first: Yalda

last: Afshar


title: Malva sylvestris anti-inflammatory activity in oral human cells

city: Piracicaba

first: Bruna

last: Benso

department: Physiological Sciences

country: Brazil

institute: UNICAMP

summary:
Real-time quantitative PCR analysis of human epithelial cells
The activity of Malva sylvestris extract and fractions infected by A. actinomycetemcomitans were investigated using an adapted dual chamber model, oral human epithelial cells were used in the co-culture model. One microgram of RNA was converted in cDNA using RT2 First Strand Kit. 84 genes were analyzed using inflammatory response & Autoimmunity Array RT2 profiler (Qiagen Sabiosciences, Valencia, CA, USA) with buffers supplied by the manufacturer

overall_design: qPCR gene expression profiling. Oral human epithelial cells were infected by A. Actinomycetemcomintans and treated with Malva sylvestris extract and fractions prior to gene expression analysis.

first: Pedro

middle: L

last: Rosalen

first: SeverIno

middle: M

last: Alencar

first: Ramiro

last: Murata


title: Post-vaccination serum anti-glycan IgG antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:50)

status: Public on Aug 26 2015

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

institute: NCI

summary:
Purpose: There is evidence that therapeutic cancer vaccines can lengthen survival for some cancer patients, but responses vary widely from one person to another.  Methods to predict clinical outcomes will advance the field and provide new insights into critical determinants of in vivo efficacy.  This study uses a high-throughput glycan microarray to assess correlations between a subject's overall survival after receiving PROSTVAC-VF and his anti-glycan humoral responses occuring in the first months after treatment with PROSTVAC-VF.
Results:  Humoral responses to the terminal Forssman disaccharide (Fsdi) were found to have a statistically significant correlation with survival.  Long-term survival was approximately doubled in subjects with four-fold or larger anti-Fsdi responses relative to subjects with little or no anti-Fsdi response.  This survival correlation was specific to vaccine treatment, as no correlation was observed in control patients immunized with wild-type poxviruses lacking the key tumor antigen, prostate specific antigen (PSA).  Moreover, anti-Fsdi humoral responses were not correlated with general measures of disease severity, such as PSA levels, Gleason score, or Halabi predicted survival.
Conclusion: In addition to reporting a new biomarker for monitoring benefical responses to PROSTVAC-VF, this study highlights the potential of glycan microarray technology for personalized medicine.

platform_organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Pandalus borealis
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgG levels for the training set measured at serum dilution of 1:50 are detailed here.  The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

first: James

last: Gulley

first: Oyindasola

last: Oyelaran

middle: W

last: Hodge

first: Jeffrey

last: Schlom

middle: C

last: Gildersleeve


title: MeDIP chip from ZOS and ZOSM osteosarcoma cell lines

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre, University of Toronto

type: Methylation profiling by genome tiling array

summary:
Epigenetic change of genes expression, including hypomethylation-linked activation of oncogenes and hypermethylation-associated inactivation of tumor suppressor genes, can affect almost all the cellular signaling pathways that participate in cancer initiation and progression. Unlike genetic alterations, epigenetic changes are potentially reversible, making them attractive and promising targets for therapeutic intervention.
Studies indicated that abnormal DNA methylation is involved in dysregulation of cell cycle, apoptosis, proliferation and differentiation of osteosarcoma. However, epigenetic mechanisms of osteosarcoma metastasis remain largely unknown.

overall_design: MeDIP chips are performed in ZOS and ZOSM—two syngeneic primary human osteosarcoma cell lines with low and high metastatic potential which are established in our lab

first: Jin

last: Wang


title: Re-establishment of desiccation tolerance by PEG in germinated Arabidopsis thaliana seeds

city: Wageningen

first: Maria

middle: Cecilia

last: Costa

state: The Netherlands

address: Droevendaalsesteeg, 1

department: Plant Physiology

country: Netherlands

institute: Wageningen University

summary:
Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose DT while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with polyethylene glycol (PEG).
We used microarrays to identify relevant genes in the re-establishment of desiccation tolerance by PEG.

overall_design: Germinated Arabidopsis seeds at the stage of radicle protrusion incubated in PEG for 72h and non-treated seeds at the same developmental stage were used for for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates represented by pools of seeds bulk-harvested from at least two plants were used.

first: Julio

last: Maia

middle: D

first: Wilco

last: Ligterink

first: Henk

last: Hilhorst


title: Transcriptomic and Proteomic Analysis of Saccharomyces cerevisiae with Secretion of Cellobiohydrolases

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: The aim of present study is to understand the impact of genetic engineering event, integration of ClCBH2 gene into yeast genome, as well as the subsequent biological process, such as expression and secretion of CBH2 protein. Further, the ‘dosage’ of genetic engineering event, the copy number inserted ClCBH2 gene, is also of particular interest. In parallel, the relationship between the copy number of ClCBH2 gene and the condition of yeast culture during CBH2 production, as well as the effect of these two factors towards yeast metabolism are investigated. Extensive transcriptomics analysis and comparison were conducted for three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates

overall_design: A twenty-four array study using total RNA recovered from three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates

first: Steven

last: Brown

first: Courtney

last: Johnson


title: Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum [HIGH PARASITEMIA ANALYSIS]

city: Bangalore

first: Sanjeev

last: Kumar

state: Karnataka

address: 526/A,19th Main,3-sect,Ganesh Complex (2nd Floor) HSR Layout

department: R&D

country: India

institute: BioCOS Life Sciences Pvt Ltd

summary:
In our global differential gene expression analyses,ETRAMP14.1, an ETRAMP family member was found to be highly transcribed in vivo in severe
Malaria patients from highly endemic Indian region. This study for the first time reports the interaction of ETRAMP14.1 with PfEMP1, EXP2 and Hsp70-1.
Therefore, we propose that ETRAMP14.1 facilitate PfEMP1 to cross the PVM via transcolon machinery component EXP2.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Peripheral blood samples containing ring forms of the P.falciparum from mild and severe malaria patients were used for RNA extraction, CDNA synthesis and hybridization on Affymetrix microarrays. In vitro ring stage P.falciparum cultures were used for normalization.

first: M

middle: V

last: Kirthana

first: S

middle: K

last: Ghosh

first: Namita

last: Surolia


title: Post-vaccination serum anti-glycan total Ig antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:200)

first: Christopher

last: Campbell

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  Total immunoglobin (IgM + IgG + IgA) levels for the training set measured at serum dilution of 1:200 are detailed here.  The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

last: Gulley

last: Oyelaran


title: Post-vaccination serum anti-glycan total Ig antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:50)

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  Total immunoglobin (IgM + IgG + IgA) levels for the training set measured at serum dilution of 1:50 are detailed here.  The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

first: James

last: Hodge

last: Schlom

last: Gildersleeve


title: Characterization of a Lactococcus lactis high-temperature mutant with increased glycolytic flux

city: Kgs. Lyngby

first: Jun

last: Chen

state: Denmark

address: Søltofts Plads Building 221

department: Food

country: Denmark

institute: The Technical University of Denmark

summary: Temperature is an important factor affecting biological organisms. We characterize a Lactococcus lactis (L. lactis) ssp. cremoris MG1363 mutant (CS3527) capable of growing better at a higher temperature than its parent. The transcriptomic analysis also revealed widespread down-regulation of genes encoding membrane transport proteins in the wild-type at 38°C. A fatty acid composition analysis revealed that the mutant has substantially more straight chained saturated and less cyclopropane fatty acids at 30°C and 38°C compared with the wild-type.

platform_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: MG1363 versus CS3527 at two different growth temperatures

first: Christian

last: Solem

first: Lars

last: Hellgren

first: Peter

middle: R

last: Jensen


title: Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum

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

overall_design: Refer to individual Series


title: Effect of PNB-028 on Global gene expression in MAC-16 xenograft

status: Public on Aug 17 2015

city: Memphis

first: Ramesh

last: Narayanan

state: Tennessee

address: 19 S. Manassas, Room 120

department: Medicine

institute: University of Tennessee Health Science Center

summary: Microarray studies were conducted with RNA isolated from vehicle- or PNB-028- treated MAC-16 colon cancer xenograft tumors (n=3/group). PNB-028 significantly regulated over 1400 genes compared to vehicle-treated samples with approximately 450 genes up-regulated and 1100 genes down-regulated by 1.5 fold or greater.

overall_design: All xenograft animal protocols were approved by The University of Tennessee Animal Care and Use Research Committee. MAC-16 cells were harvested, counted under microscope using trypan blue exclusion, and a suspension in growth medium was prepared. The cell suspension (5 million cells/mouse) was implanted subcutaneously in NSG mice. Once the tumors reached 100-200 mm3, the animals were randomized within the respective cell line and treated orally at 50 mg/kg/day. PNB-028 was dissolved in 20% DMSO+80% PEG-300 and administered by oral gavage. Body weight and tumor volumes were measured thrice weekly. Animals were sacrificed (6 hrs after the last dose) when tumors reached 1500 mm3 or when the animals lost over 20% body weight. Tumors were excised, weighed, and stored for further analysis (two parts snap frozen and stored at -80°C and one part stored in formalin for histology). RNA was isolated from MAC-16 tumors (n=3/group) using Qiagen RNAeasy kit. RNA was quantified using nanodrop and diluted to equal concentrations of 100 ng/µl. RNA quality was determined using Agilent Bioanalyzer and RNA samples with RNA Integrity Number (RIN) greater than 7 were used for microarray experiments (ST 2.0 mouse array from Affymetrix). Results from microarray studies were analyzed using Affymetrix software (Transcriptome Analysis Console (TAC)). Pathways differentially regulated by PNB-028 were identified using Ingenuity Pathway Analysis software.


title: Expression profiling in ductus arteriosus and aorta of Brown-Norway and Fischer344 rats

status: Public on Aug 29 2015

city: Tokyo

first: Yi-Ting

middle: Emma

last: Hsieh

address: 2-2Wakamatsu-cho, Shinjuku

country: Japan

institute: Waseda University

summary:
Comparison of gene expression levels in ductus arteriosus (DA) and aorta in full-term (21 days) neonates of Brown-Norway (BN) and Fischer344 (F344) rats
We analyzed the fold difference between BN and F344 rats in ductus arteriosus in order to identify the down-regulated and up-regulated genes specifically in BN rat's DA. The differences in aorta was also examined for additional comparison.

overall_design: Total RNA was extracted from aorta and DA tissues from BN and F344 rat neonates one hour after delivery, and converted to biotin-labeled cRNAs that were hybridized to Affymetrix Rat Gene 1.0 ST Array.

middle: E

first: Susumu

last: Minamisawa


title: Transcriptomic analysis of wild-type, spn-E and aub mutant 0-2h- and 2-4h-embryos

status: Public on Aug 19 2015

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

institute: Institut de Genetique Humaine - CNRS

summary: We used microarrays to identify unstable mRNAs in wild-type embryos by comparing the transcriptomes derived from 0-2h- and 2-4h-embryos. We then analyzed which of these unstable mRNAs are stabilized in embryos from aub or spn-E mutant mothers (aub or spn-E mutant embryos) by comparing mutant and wild-type embryonic transcriptomes

overall_design: Transcriptomic analysis of 0-2 h and 2-4 h-embryos from wild-type, aubHN2/aubQC42 or spn-Ehls-03987/spn-E1 females crossed with wild-type males. Three biological replicates were prepared per condition. A technical replicate of each sample led to 36 hybridizations. Each sample was compared to a common reference made of an equimolar mix of all 18 samples.

first: Bridlin

last: Barckmann

first: Stéphanie

last: Pierson

first: Jérémy

last: Dufourt

first: Martine

last: Simonelig


title: Baseline serum anti-glycan IgM antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:50)

last: Campbell

platform_organism:
Quercus alba
Gossypium hirsutum
Medicago sativa
Rhodotorula
Pandalus borealis
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgM levels for the validation set measured at serum dilution of 1:50 are detailed here.  The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

last: Gulley

first: Oyindasola

first: Jeffrey


title: The inhibition of N2O production by ocean acidification in cold temperate and polar waters

status: Public on Aug 15 2015

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

summary: The effects of ocean acidification (OA) on nitrous oxide (N2O) production and on the community composition of ammonium oxidising archaea (AOA) were examined in the northern and southern sub-polar and polar Atlantic Ocean. Two research cruises were performed during June 2012 between the North Sea and Arctic Greenland and Barent Seas, and in January-February 2013 to the Antarctic Scotia Sea. Seven stations were occupied in all during which shipboard experimental manipulations of the carbonate chemistry were performed through additions of NaHCO3- + HCl in order to examine the impact of short- term (48 hour for N2O and between 96 and 168 hour for AOA) exposure to control and elevated conditions of OA. During each experiment, triplicate incubations were performed at ambient conditions and at 3 lowered levels of pH which varied between 0.06 and 0.4 units according to the total scale and which were targeted at CO2 partial pressures of ~500, 750 and 1000 μatm. The AOA assemblage in both Arctic and Antarctic regions was dominated by two major archetypes that represent the marine AOA clades most often detected in seawater. There were no significant changes in AOA assemblage composition between the beginning and end of the incubation experiments. N2O production was sensitive to decreasing pHT at all stations and decreased by between 2.4 and 44% with reduced pHT values of between 0.06 and 0.4. The reduction in N2O yield from nitrification was directly related to a decrease of between 28 and 67% in available NH3 as a result of the pH driven shift in the NH3:NH4+ equilibrium. The maximum reduction in N2O production at conditions projected for the end of the 21st century was estimated to be 0.82 Tg N y-1.

sample_organism:
synthetic construct
seawater metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5. Two replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: Andrew

last: Rees

first: Ian

last: Brown

first: Amal

last: Jayakumar


title: Integrative analysis of the biodegradation of acetone/isopropanol by Cupriavidus metallidurans CH34: proposal of a metabolic pathway

status: Public on Aug 31 2015

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

institute: SCK-CEN

summary: Various environmental bacteria were adapted to the presence of toxic and recalcitrant organic solvents.  Cupriavidus metallidurans CH34, a β-proteobacterium that was found in industrial environments is known as a bacterial model to study heavy metal resistance. Interestingly, genome screening of CH34 also reveals the existence of genes involved in the degradation of recalcitrant organic solvents, such acetone and aromatic compounds.  Here, we showed that this bacterium could resist a large variety of organic solvents, and was also able to metabolize some of them. In particular, investigations were focused on acetone and isopropanol catabolism.  Integrative studies based on transcriptomic (DNA microarrays), proteomic (2D-DIGE and Isotope-Coded Protein Label technology) and biochemical analyses (enzyme purification and characterization) showed a similar catabolic pathway for both molecules which involved the AcxABC acetone carboxylase.  First, isopropanol is oxidized into acetone by the Adh alcohol dehydrogenase. Acetoacetate production from acetone is then catalyzed by the acetone carboxylase. The generated acetoacetate molecules are then transformed by the PacIJ 3-oxoacid CoA-transferase, to acetoacetyl-CoA and succinate. Finally, an acetyl-CoA acetyltransferase catalyses the hydrolysis of acetoacetyl-CoA into 2 acetyl-CoA that are introduced into the glyoxylate cycle. As demonstrated, key enzymes of the acetone/isopropanol catabolism (encoded by acx and ald genes) are under the control of a σ54-dependent RNA polymerase. Moreover, the catabolic pathway involved in acetone and isopropanol consumption was repressed when gluconate was given as alternative carbon substrate, displaying a new example of diauxie. The results presented here provide a comprehensive picture of acetone and isopropanol biodegradation in Cupriavidus metallidurans CH34 and strongly support the fact that CH34 can be considered as a solvent tolerant bacterium.

overall_design: Two-condition experiments. Comparing samples after induction with acetone versus non-induced samples. Biological triplicate. Each array contains 3 technical replicates.

first: Caroline

last: Rosier

first: Rudy

last: Wattiez

first: Ann

last: Janssen

first: Pieter

last: Monsieurs

first: Ilse

last: Coninx

first: Max

last: Mergeay

first: Natalie

last: Leys


title: Post-vaccination serum anti-glycan IgM antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:50)

first: Christopher

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgM levels for the training set measured at serum dilution of 1:50 are detailed here.  The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

first: James

last: Oyelaran

last: Hodge

last: Schlom

last: Gildersleeve


title: Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum [LOW PARASITEMIA ANALYSIS]

first: Sanjeev

last: Kumar

first: M

last: Kirthana

first: S

last: Ghosh

first: Namita

last: Surolia


title: Expression profiling of 143B-shCtrl and 143B-shIRX1 stable osteosarcoma cell lines

first: Jinchang

last: Lu

summary:
Pulmonary metastasis is the main cause of medical failure and death of osteosarcoma patients. Our recent study identified IRX1 as a potential metastasis-driving gene in osteosarcoma. Studies showed that IRX1 can promote the migration, invasion and anoikis resistance of osteosarcoma cells.
We generated 143B stable IRX1 knockdown and control cell lines, and found that IRX1 knockdown can inhibit the pulmonary metastasis of 143B cells in orthotopic mouse osteosarcoma model.

overall_design: Expression microarrays are performed in143B-shCtrl and 143B-shIRX1 cells to study the mechanism of IRX1 on promoting metastasis of osteosarcoma

first: Jin

last: Wang


title: Transcriptome analysis of Streptococcus gordonii strain Challis DL1 indicates a role for the biofilm-associated fruRBA operon in response to Candida albicans hyphae formation

city: Buffalo

last: Vickerman

state: NY

address: 3435 Main St.

department: Periodontics and Endodontics

institute: University at Buffalo

summary: Multiple levels of interkingdom signaling have been implicated in maintaining the ecological balance between Candida albicans and commensal streptococci to assure a state of oral health. To better understand the molecular mechanisms involved in the initial streptococcal response to the presence of C. albicans that can initiate oral surface colonization and biofilm formation, hypha-forming cells were incubated with Streptococcus gordonii cells for 30 minutes to assess the streptococcal transcriptome response. A genome wide microarray analysis and quantitative PCR validation of S. gordonii transcripts identified a number of genes, the majority of which were involved in metabolic functions, that were differentially expressed in the presence of hyphae.  The fruR, fruB and fruA genes encoding the transcriptional regulator, fructose-1-phosphate kinase, and fructose-specific permease, respectively, of the phosphoenolpyruvate-dependent fructose phosphotransferase system, were consistently up-regulated. An S. gordonii mutant in which these genes were deleted by allelic replacement, formed an architecturally-distinct, less robust biofilm with C. albicans than did parental strain cells. Complementing the mutant with plasmid borne fruR, fruB and fruA genes caused phenotype reversion, indicating that the genes in this operon played a role in dual species biofilm formation. This genome wide analysis of the S. gordonii transcriptional response to C. albicans has identified several genes that have potential roles in interkingdom signaling and responses.

overall_design: This set includes 2076 oligonucleotides, has 16416 spots distributed in 48 blocks. (GPL10584)

first: Amy

last: Jesionowski

first: Jane

last: Brittan

first: Jillian

last: Mansfield

first: Howard

middle: F

last: Jenkinson


title: Integrating tumor and stromal gene expression signatures with clinical indices for survival stratification of early-stage non-small cell lung cancer

status: Public on Aug 24 2015

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

type:
Third-party reanalysis
Expression profiling by array

summary: Background: Accurate survival stratification in early-stage NSCLC could inform the use of adjuvant therapy. We developed a clinically-implementable mortality risk score incorporating distinct tumor microenvironmental gene expression signatures and clinical variables.    Methods: Gene expression profiles from 1106 non-squamous NSCLCs were used for generation and internal validation of a 9-gene molecular prognostic index (MPI). Expression of the MPI genes was determined within sorted tumor cell subpopulations. A quantitative PCR (qPCR) assay was developed and validated on an independent cohort of FFPE tissues. A prognostic score using clinical variables was generated using Surveillance Epidemiology and End Results (SEER) data and combined with the MPI.    Results: The MPI stratified stage I patients into prognostic categories in four independent validation datasets, including three microarray and one FFPE qPCR cohorts (HR=2.4, 95% CI, 1.8-3.3, P=7x10-9 in the largest microarray cohort; and HR=2.5, 95% CI 1.1-6.0, P=.03 in stage I patients of the qPCR validation cohort). Prognostic genes were expressed in distinct tumor cell subpopulations and expression of genes implicated in cellular proliferation and stem cells portended poor outcomes, while expression of genes involved in normal lung differentiation and immune infiltration was associated with superior survival. Integrating the MPI with clinical variables conferred greatest prognostic power (HR=3.3, 95% CI 2.4-4.6; P=2x10-15 in the largest microarray cohort; and HR=3.6, 95% CI 1.5-8.8, P=.003 in stage I patients of the qPCR validation cohort). Finally, the MPI was prognostic irrespective of somatic alterations in EGFR, KRAS, TP53, and ALK.    Conclusion: The MPI incorporates genes expressed in the tumor and its microenvironment, and designates risk of death for patients with early-stage non-squamous NSCLC. The MPI can be implemented clinically using qPCR assays on FFPE tissues and a composite model integrating the MPI with clinical variables provides the most accurate risk stratification.

relation:
Affiliated with: GSE31210
Affiliated with: GSE13213
Affiliated with: GSE5843

overall_design:
Third part re-analysis of GSE31210, GSE13213, GSE5843, NCI caArray (https://wiki.nci.nih.gov/display/caArray2/caArray+Directory) accessions ca00153, ca00182, ca00191 (now retired), Roepman et al. PMID 19118056. Where applicable, raw Affymetrix CEL files were renormalized using MAS5 and Custom CDF probe mappings to Entrez Gene IDs. Within each dataset, each gene was standardized so that it had mean zero and variance 1 across stage 1 adenocarcinoma patients. Datasets were then merged into one meta-cohort of 1106 samples.
The custom CDF link is
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.asp


title: Post-vaccination serum anti-glycan IgG antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:50)

last: Campbell

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgG levels for the validation set measured at serum dilution of 1:50 are detailed here.  The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

last: Gulley

first: Oyindasola

first: Jeffrey


title: Post-vaccination serum anti-glycan total Ig antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:200)

summary:
Purpose: There is evidence that therapeutic cancer vaccines can lengthen survival for some cancer patients, but responses vary widely from one person to another. Methods to predict clinical outcomes will advance the field and provide new insights into critical determinants of in vivo efficacy. This study uses a high-throughput glycan microarray to assess correlations between a subject's overall survival after receiving PROSTVAC-VF and his anti-glycan humoral responses occuring in the first months after treatment with PROSTVAC-VF.
Results: Humoral responses to the terminal Forssman disaccharide (Fsdi) were found to have a statistically significant correlation with survival. Long-term survival was approximately doubled in subjects with four-fold or larger anti-Fsdi responses relative to subjects with little or no anti-Fsdi response. This survival correlation was specific to vaccine treatment, as no correlation was observed in control patients immunized with wild-type poxviruses lacking the key tumor antigen, prostate specific antigen (PSA). Moreover, anti-Fsdi humoral responses were not correlated with general measures of disease severity, such as PSA levels, Gleason score, or Halabi predicted survival.
Conclusion: In addition to reporting a new biomarker for monitoring benefical responses to PROSTVAC-VF, this study highlights the potential of glycan microarray technology for personalized medicine.

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer. The subjects were divided into a training set (n=28) and a validation set (n=113). A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF. For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200). Total immunoglobin (IgM + IgG + IgA) levels for the validation set measured at serum dilution of 1:200 are detailed here. The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

last: Oyelaran

last: Hodge


title: Baseline serum anti-glycan total Ig antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine. (Dilution = 1:50)

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination and post-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  Total immunoglobin (IgM + IgG + IgA) levels for the validation set measured at serum dilution of 1:50 are detailed here.  The screen for response biomarkers identified anti-glycan humoral responses that consistently stratified subjects into groups with different Kaplan Meier survival estimates.
Raw data on SuperSeries GSE50410 record.

last: Schlom

last: Gildersleeve


title: Differential Gene Expression Profiles of PASMCs Induced by Quercetin under Hypoxia

city: wuhan

first: he

middle: yuan

last: zhou

address: Huazhong University of Science and Technology,

country: China

institute: Tongji Hospital of Tongji Medical College

summary: As the critical step of pathogenesis during hypoxic pulmonary arterial hypertension (PAH) vascular remodeling is closely associated with pulmonary arterial smooth muscle cell (PASMC) alterations induced by hypoxia that include persistent vasoconstriction, abnormal proliferation and PASMC resistance to apoptosis. Quercetin is a flavonoid compound extracted from green plants that inhibits proliferation, induces apoptosis, arrests the cell cycle, and rescues the constriction of PASMCs, but the underlying mechanisms remain poorly understood. In this study, we used a commercial Agilent Whole Rat Genome Oligo Microarray to determine the overall transcriptional response of PASMCs in response to exposure to hypoxia and the optimal concentration of quercetin. Hypoxia induced the upregulation of 1694 genes and the downregulation of 2091 genes compared with the normoxia group. Quercetin treatment resulted in 1790 upregulated genes and 1450 downregulated genes. Quercetin is known to cause differential expression of several of these genes that are known to promote proliferation, induce apoptosis (Cycs, Ppp3ca, Prkar2b, Akt3, Ppp3cc, Il1rap, Ntrk1), arrest the cell cycle (Chek2, Cdkn1c, Gadd45b, Stag2, Anapc7, Orc1, Ccne1, Myc3, Skp1, Espl1, Cdc45, Mcm4), and rescue PASMC constriction (Ramp1, Ramp3, Adcy5, Gnas, Prkcd, Itpr3, Adra1d, Calm1, Npr1, Avpr1a, Ednra, Adcy8). Real-time quantitative RT-PCR was performed to verify the microarray results. In conclusion, quercetin altered the expression profile of many genes regulated by hypoxia in PASMCs, which helps to further explore the mechanism of the effects of quercetin treatment on hypoxic PAH.

overall_design: G1(normoxia1,normoxia2,normoxia3),G2(hypoxia1,hypoxia2,hypoxia3)and G3(hypoxia+quercetin 1,hypoxia+quercetin 2,hypoxia+quercetin 3)

first: Yuanzhou

last: He

first: Xiansheng

last: Liu


title: Whole C57BL/6 mouse esophagus: embryonic day 15.5 (E15.5) vs. postnatal day 2 (P2)

status: Public on Aug 14 2015

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

summary: Gene expression profiling was performed using the total RNA isolated from pooled esophagi (plural of esophagus) of embryonic day 15.5 (E15.5) C57BL/6 mouse embryos and total RNA isolated from pooled esophagi of postnatal day 2 (P2) C57BL/6 pups. The goal was to identify differentially regulated genes in these two separate developmental stages.

overall_design: Single replicate two-color experiment.

first: David

middle: H


title: Anti-glycan humoral responses after vaccination with PROSTVAC-VF

first: Christopher


title: Expression data of MACS sorted cells (SSEA-1+ and SSEA-1-) from porcine fetal fibroblast cell line

status: Public on Aug 13 2015

city: Frederiksberg C

first: Vanessa

last: Hall

address: Grønnegårdsvej 7

institute: University of Copenhagen

summary: A subset of cells in cellular populations may be preferentially reprogrammed into pluripotent stem cells due to their innate gene expression characteristics. SSEA-1+ sorted cells were shown to be more amenable to reprogramming than other cells in porcine fetal fibroblast cell lines. This microarray data reveals which genes are unique to the SSEA1+ sorted cells and helps to give them an identity.

overall_design: Porcine fetal fibroblasts were subjected to Magnetic Activated Cell Sorting using anti-SSEA-1. Five biological replicates were performed resulting in 5 SSEA-1 positive fractions and 5 SSEA-1 negative fractions which were analyzed.

first: Dong

last: Li

first: Kaveh

last: Mashayekhi-Nezamabadi

first: Kristine

last: Freude

first: Poul

last: Hyttel


title: The pH-sensing receptor OGR1 improves barrier function of CaCo-2 cells and inhibits migration in an acidic environment

city: Zurich

first: Cheryl

last: de Valliere

address: Steinwartstrasse 14

institute: University Hospital Zurich

summary:
OGR1 is a pH-sensing G-protein coupled receptor involved in intestinal homeostasis and inflammation
Proton activation of OGR1 increases barrier function in Caco2 cells

overall_design: Microarray profiling was performed on OGR1 stable overexpressing Caco-2 cells during acidic pH shift

last: de Vallière

first: Gerhard

last: Rogler

first: Klaus

last: Seuwen


title: Targeting β-catenin overcomes resistance to MEK inhibitor in PIK3CA mutant colon cancer

city: Seoul

first: Dong-Hoon

last: Jin

address: 88 Olympicro-43gil, Songpa-gu

country: South Korea

institute: Asan Medical Center

summary: Mitogen-activated protein kinases (MEK 1/2) are central components of the RAS signaling pathway and attractive targets for cancer therapy. However, PIK3CA mutation, which commonly co-occurs with KRAS mutation, offered resistance to MEK inhibitor through activation of PI3K-AKT signaling. We identified a gene that cooperates with MEK inhibitors to forcefully treat PIK3CA mutant colon cancer cells. -catenin, a key molecule of the WNT pathway, emerged as a candidate by protein/Ab Chip array. MEK inhibitor treatment led to a decrease in -catenin in PIK3CA wild-type colon cancer cells but not in PIK3CA mutant colon cancer cells. Tumor regression was promoted by a combination of MEK inhibitor and NVP-TNS656, which targets the WNT pathway. Furthermore, combined inhibition of MEK and -catenin by NVP-TNS656 promoted tumor regression in colon cancer patient-derived xenograft (PDX) models expressing mutant PIK3CA. Taken together, we propose that inhibition of the WNT pathway, particularly -catenin, may bypass resistance to MEK inhibitor in human PIK3CA mutant colon cancer. Additionally, -catenin is a potential PD marker of MEK inhibitor resistance.

overall_design: In the study, we identified and evaluated biomarker for response to MEK inhibitor on colon cancer cells.


title: Cytomegalovirus promotes maintenance and growth of glioblastoma stem cells [HCMV gene expression]

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary:
Primary human GBM stem like cells were infected with HCMV TR strain (MOI=1) and treated with IE siRNA (a combination of oligos targeting IE1 and IE2 HCMV genes)
72 hours following siRNA treatment, RNA was harvested using Qiagen and divided equally for profiling using Affymetrix arrays and HCMV arrays.

overall_design: Primary human glioma stem cells were maintained in neurosphere growth conditions, treated with IE1 and control siRNA for 48-72h prior to RNA harvesting. RNA was hybridized to HCMV spotted arrays.

first: Liliana

last: Soroceanu


title: miRNA array data of human ESCC tissues and normal controls

status: Public on Aug 07 2015

city: Nanjing

first: rui

middle: hua

last: shi

state: jiangsu

address: guangzhou road 300#

department: gastroenterology

institute: the First Affiliated Hospital of Nanjing Medical University

summary: The human miRNA profiles of esophageal squamous cell carcinoma are rarely reported. Surgically removed human ESCC tissues and matched normal esophageal epithelial tissues (5cm away from tumor) were collected to make an Agilent microarray.

overall_design: Three paired of human ESCC tissues and normal controls were collected. All patients have no radiotherapy or chemotherapy before surgery. None of these three patients have distant metastasis.

first: Ruihua

last: Shi


title: Transcriptome profile on epileptogenic zones of patients with neocortical epilepsy

city: Hualien

first: Ingrid

address: E411, 701, Section 3 Chung Yang Road

department: Molecular Biology and Human Genetics

country: Taiwan

institute: Tzu Chi University

summary:
In the present study, we used expression microarray to establish a transcriptome on epileptogenic zone versus irritative zone from removed brain tissues of patients affected with intractable neocortical epilepsies.
Our results showed that expression profiling of a total of 30,968 human genes in 10 patients brain samples.

overall_design: A total of 10 patients were recruited in this study. Mean age and period of intractable neocortical epilepsy were 19.8±2.5 and 13.7±2.3 years, respectively. After clinical evaluatng by EEG, SPEC, MRI, and v-EEG, patients were performed with surgical removal of epileptogenic zone and irritative zone. Removed surgical samples were obtained snap-frozen on dry ice for total RNA extraction commissined to Phalanx Biotech Group, Taiwan. RNA samples were evaluated using Human OneArray TM with 30,968 human genome probes.

first: Yu-Loong

last: Hsin

first: Hsiao-Lin

last: Tsen

first: Tomor

last: Harnod

middle: Y


title: Diurnal Gene Variation in Mouse Eye

status: Public on Aug 09 2015

first: David

last: Strick

address: 300 Pasteur Dr

summary:
The purpose of this study was to explore diurnal gene expression changes that occur in the RPE/Choroid/Sclera. Mice C57BL/6J were purchased from the Jackson Laboratory (Bar Harbor, ME) and raised to approximately 2 months of age and entrained to a 12hr/12hr light/dark cycle for two weeks. Eye cups from male mice were rapidly dissected and RPE/ choroid/sclera tissues were collected over three consecutive diurnal cycles at Zeitgeber time (ZT) 0.5, 1, 1.5, 4, 11, 13, 16, and 23 hrs, for a total of 24 time points. Three mice were used for each time point and dissections for dark time points were done under dim-red light. To generate a reference RNA for microarray hybridization, whole eyes from equal numbers of male and female mice were collected at ZT6 and ZT7.
Time: Samples were collected at the indicated Zeitgeber time points

overall_design: time series design

first: Mitra

last: Alizadeh


title: Transcriptional changes in Atlantic salmon (Salmo salar) after embryonic exposure to road salt (NaCl)

status: Public on Aug 05 2015

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

summary: The present study aimed to identify the persistent molecular changes occurring in Atlantic Salmon salmon (Salmo salar) eggs after 24h exposure to high concentrations (5000 mg/L) of road salt at fertilization.

overall_design: Atlantic Salmon (Salmo salar) eggs after fertilization were exposed to high concentrations (5000 mg/L) of road salt for 24 h and used for gene expression analysis.

first: Knut

last: Tollefsen

first: Merete

last: Kleiven

first: Urma

last: Mahrosh

first: Sondre

last: Meland

first: Bjørn

middle: O

last: Rosseland

first: Hans-Christian

last: Teien


title: Transcriptional profiling analysis of Bacillus subtilis in response to high levels of iron (Fe3+)

city: shanghai

first: wenbang

last: yu

address: meilong road 130, east china university of science and technology, shanghai, china

summary: Transcriptional profiling analysis was used to reveral the genetic changes of B.subtilis after addition of high levels of iron. This study is to reveal the effect of high levels of iron on B.subtilis' metabolism and identify the potential resistance mechanism to high levels of iron.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: 1_1 is the independent biological replicate of sample 2_1, while sample 1_2 is the independent biological replicate of sample 2_2. Bacteria collected from each B.subtilis culture at 0min were mixed and used as ch2 source for each sample. The ch1 sources of sample 1_1 and 2_1 are bacteria collected from cultures without addition of Fe3+ at 20min, while the ch1 sources of sample 2_1 and 2_2 are bacteria collected from cultures with addition of 4mM Fe3+ at 20min.

first: Wen-Bang

last: Yu

first: Bang-Ce

last: Ye


title: The regulation of miRNA expression by DNA methylation in hepatocellular carcinoma

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

institute: Tongji Hospital

summary:
Emerging evidences indicate that microRNAs (miRNAs) are often deregulated and have fundamental roles in hepatocellular carcinoma (HCC). However, the mechanism underlying miRNA dysregulation in HCC is still elusive. In this report, we used an integrated analysis strategy combining methylated DNA immunoprecipitation chip (MeDIP-chip) and miRNA expression microarray data to study the correlation between aberrant methylation and dysregulation of miRNA in HCC.
In all, we showed that global miRNA methylation profiles were significantly different between cancerous and normal hepatocytes, and abnormal methylation was an important mechanism governing miRNA expression in HCC.

overall_design: MeDIP-chip was processed in cancerous hepatocytes SK-HEP-1, HepG2, MHCC97-H and normal hepatocytes PHHC-4-1, PHHC-4-2, PHHC-4-3 (3 technical repeat of PHHC-4). MiRNA microarray were processed for cancerous hepatocytes SK-HEP-1, HepG2, Hep3B, Huh7, MHCC97-H, MHCC97-L, SMMC-7721 and normal hepatocytes PHHC-1, PHHC-2, PHHC-3. Then an integrated analysis strategy combining MeDIP-chip and miRNA expression microarray [GSE20077] were used to study the correlation of aberrant DNA methylation and dysregulation of miRNAs.

first: Shu-Zhen

last: Kuang

first: Ju-Sheng

last: Lin

first: An-Yuan

last: Guo

first: Ying

last: Chang


title: MicroRNA Profile in CD8+ T-lymphocytes from HIV-Infected Individuals: Relationship with Disease Progression

status: Public on Aug 04 2015

city: Barcelona

first: Mireia

last: Arnedo

state: Other

address: Casanovas, 143. CELLEX, A41

department: AIDS Unit

country: Spain

institute: Institut Investigacions Biomediques Agusti Pi i Sunyer (IDIBAPS)

summary: The relationship between host microRNAs (miRNA), viral control and immune response has not been elucidated in the field of HIV yet. The aim of this study was to assess the differential miRNA profile in CD8+ T-cells between HIV-infected individuals who differ in terms of disease progression.

overall_design: A total of 136 RNAs (miRNAs) were analyzed: 68 RNAs from resting CD8+ T-cells and the respective 68 RNAs from stimulated CD8+ T-cells from Elite Controllers (EC, n=15), Viremic Controllers (VC, n=15), Viremic Progressors (VP, n=13), Treated Patients (ART, n=14) and Uninfect Donors (HIV-, n=11).

first: Lander

last: Egaña-Gorroño

first: Alberto

last: Crespo Guardo

first: Manel

last: Bargalló Marès

first: Elisenda

last: Vilaplana

first: Tuixent

last: Escribà

first: Iñaki

last: Pérez

first: José

last: Gatell

first: Felipe

last: García

first: Montserrat

last: Plana


title: Molecular Mechanisms Associated with Primary Open-angle Glaucoma with MicroRNA Microarray Data

city: Shanghai，China

first: Xiangmei

last: Kong

address: 83 Fenyang Road, Xuhui District

department: Department of Ophthalmology

institute: Eye & ENT Hospital of Fudan University

summary: This study aimed to investigate the molecular mechanism responsible for primary open-angle glaucoma (POAG) progression. We analyzed microRNAs (miRNAs) expression profiling in aqueous humor (AH) of both POAG patients and normal controls, using a microarray-based approach. Subsequently, differentially expressed miRNAs (DEmiRNAs) were identified using Bayes moderated t-test. Next, DEmiRNAs target genes were predicted based on miRNA databases, followed by GO analysis and pathway analysis using DAVID. Furthermore, OAG-related genes analysis for target genes was carried out using CTD database, respectively. Finally, verification of DEmiRNAs expression levels was performed by RT-qPCR. A total of 40 significant DEmiRNAs were identified between control and POAG groups, including 24 up-regulated miRNAs and 16 down-regulated miRNAs. Further, the target genes of hsa-miR-206, including BMP2, SMAD4, ID2, and TNF, were mainly enriched in transforming growth factor-β (TGF-β) signaling pathway. While, target genes of hsa-miR-184, hsa-miR-34c-5p, hsa-miR-7-2-3p and hsa-miR-20b-3p, including BCL2, EPHB2, VEGFA, COL4A1, APC, and TGFBR1, were enriched in eye development. Moreover, FNDC3B, CAV2 and VEGF, target genes of hsa-miR-206 or hsa-miR-34c-5p, were the OAG-related genes. Ultimately, RT-qPCR analysis confirmed that mRNA levels of hsa-miR-206, hsa-miR-7-2-3p, and hsa-miR-20b-3p were increased, while those of hsa-miR-184 and hsa-miR-34c-5p were decreased in POAG compared with normal groups (P < 0.05). Hsa-miR-206, hsa-miR-184, hsa-miR-34c-5p, hsa-miR-7-2-3p and hsa-miR-20b-3p might play a significant role in the pathogenesis of POAG and hsa-miR-206 might be associated with the development of POAG by regulating TGF-β signaling pathway. These results might provide insight toward a better understanding of the pathogenesis of POAG.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Fifteen patients with ocular hypertensive POAG, who needed glaucoma filtrating surgeries, were enrolled in this studydisease group:PA group,PB group,PC group;each group of five patients). Fifteen patients with cataract undergoing cataract surgery were recruited as normal group (normal group:NA group,NB group,NC group;each group of five patients).

first: Huan

last: Xu

first: Jiajian

last: Wang

first: Xinghuai

last: Sun


title: Identification of recurrence related microRNAs from bone marrow in hepatocellular carcinoma (HCC) patients

status: Public on Aug 06 2015

city: Beppu

first: Shotaro

last: Sakimura

address: 4546 Tsurumihara Tsurumi

department: Department of surgeryy

institute: Kyushu University Beppu Hospital

summary: To identify the role of miRNAs in patient bone marrow (BM) and explore the function of these molecules during HCC progression, we employed microarray-based profiling to analyze miRNA expression in the BM of patients with HCC.

overall_design: MicroRNA expression in the BW of HCC patients was measured by using microarray-based profiling. BM cells were separated into 3fraction by cell surface markers as follows: CD45+(macrophage), CD14-/CD45+(lymphocyte) and CD14-/CD45-/EpCAM+(epithelial cell).

first: Keishi

last: Sugimachi

first: Koshi

last: Mimori


title: Transcriptional analysis between Streptomyces clavuligerus ATCC 27064 and a mutant altered in antibiotic production

city: León

first: Paloma

last: Liras

state: León, Spain

address: Facultad de Biología. Campus de Vegazana

department: Molecular Biology

institute: Universidad de León

summary: The objective was to analyze the differential expression between the wild strain and the Streptomyces clavuligerus  ΔclaR::aac mutant

overall_design: Six experimental conditions were assayed, two strains (Streptomyces clavuligerus ATCC 27064, S. clavuligerus  ΔclaR::aac) in three culture times (22.5h, 46.5h and 60 h). Two biological replicates for each condition.

first: Y

last: Martínez-Burgo

first: R

last: Álvarez-Álvarez

first: A

last: Rodríguez-García

first: P


title: Human Esophageal cells: Normal epithelial vs squamous cancer cell line

city: Baltimore

first: James

middle: M

last: Donahue

address: 10 North Greene

department: Surgery

institute: University of Maryland

summary: Micro RNA expression profiling of human esophageal normal epithelial (hESO) cells comparing two human esophageal squamous cancer cell lines (TE7 and TE10).

overall_design: Two-condition experiment, Normal epithelial vs. tumor cells. Biological replicates: 2 normal epithelial  and 2 tumor cells replicates each respectively, independently grown and harvested. One replicate per array.

first: Pornima

last: Phatak


title: The sunflower transcription factor HaHB11 improves yield, biomass and flood tolerance via the quiescent response in transgenic plants

status: Public on Aug 03 2015

city: Santa Fe

first: Jorge

middle: Ignacio

last: Giacomelli

state: Santa Fe

address: Ciudad Universitaria

department: LBV

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

summary: HaHB11 is a divergent member of the sunflower homeodomain-leucine zipper I subfamily of transcription factors. A sunflower microarray was hybridized with RNA from HaHB11-transformed leaf-disks and its analysis indicated the regulation of many genes encoding enzymes from fermentative pathways. A 1300 bp sequence exhibiting flooding-responsive cis-acting elements, upstream the transcription initiation site, was isolated and Arabidopsis plants transformed with a construct in which this promoter directs GUS expression. GUS expression was induced after flooding treatments and, in the same sense, HaHB11 expression was induced by flooding stress in sunflower. Furthermore, Arabidopsis plants were transformed with different constructs, varying in the promoter used, able to express HaHB11 cDNA. These transgenic plants exhibited differential phenotypes which the more remarkable traits were a significant increase in the rosette biomass and seeds yield. Moreover these plants exhibited an enhanced tolerance to flooding stress, both to submergence and waterlogging. Starch, sucrose and glucose contents were higher in the transgenics compared to WT and decreased less after submergence treatments. Finally, transcript levels of selected genes, involved in fermentative pathways, and the corresponding enzymatic activities were assessed both in sunflower and transgenic Arabidopsis plants after submergence indicating a general repression of the fermentative pathway which suggested that tolerance occurs via the quiescent strategy. Altogether the results indicated a role for HaHB11 in the flooding response and allowed us to propose this gene as a biotechnological tool to improve crops for increased yield and biomass and flooding tolerance.

overall_design: Transient sunflower discs (Manavella and Chan, Nature Protocols 2009) 35S Promoter::GUS vs. 35S Promoter::HaHB11. Three biological replicates each.

first: J

last: Cabello

middle: I

first: C

last: Piattoni

middle: A

last: Iglesias

middle: L

last: Chan


title: Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth [gene expression]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

type:
Expression profiling by array
Third-party reanalysis

summary:
The goal of this study was to identify YAP/TAZ direct transcriptional targets and transcriptional partners, through ChIP-sequencing and gene expression profiling.

Keywords: Expression profiling by array

overall_design: MDA-MB-231 cells growing at low confluence in standard growth conditions were transfected with the indicated siRNAs (Dupont et al., Nature 2011). The following day, growth medium was renewed and cells were incubated for 24 more hours, and then harvested for total RNA extraction. 4 independent biological replicates were plated, transfected and harvested in parallel for each siRNA. Raw .CEL files are the same as in GSE59230 (Enzo et al., EMBO J 2015), but gene expression levels have been quantified using Brainarray HGU133Plus2_Hs_ENTREZG_v17 custom chip definition files.

first: Mattia

last: Forcato

first: Francesca

last: Zanconato

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Sliding of Bacillus subtilis Natto

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University of Jena

summary: Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions.

overall_design: B subtilis Natto wild type cells were grown on the top of LB solid medium with 1.5% and 0.7% agar concentration (samples 1-4). B subtilis Natto wild type and spo0A derivative were grown on top of LB solid medium with 0.7% agar concentration (Sample 5-7). In first experiment, 4 biological replicates were used, while in the second experiment 3 biological replicates included. Dye swaps are included in both experiments.

first: Tamara

last: Spalding

first: Roberto

last: Grau

first: Oscar

middle: P

last: Kuipers


title: Off-target effects of VEGF-A regulation by shRNAs

city: Kuopio

first: Mikko

middle: Petri

last: Turunen

address: Neulaniementie 2

department: AIVI

country: Finland

institute: University of Eastern Finland

summary:
The aim of this project was to investigate how genome-wide gene expression patterns change when the expression of VEGF-A is modulated using different lentivirally delivered shRNA molecules that are complementary to VEGF-A promoter region.
To study these changes, 12 gene expression array experiments were conducted with mouse endothelial cell line (C166).

overall_design: The C166 cells were transduced (20% confluency, MOI 10) with lentiviral vectors that all express GFP marker gene and two of them express additional shRNA molecule that is complementary to different regions in the VEGF-A promoter and either up-regulate (VEGF-up) or downregulate (VEGF-down) VEGF-A expression. Fresh medium was changed 72h after transduction. Cells were collected at day 7.

first: Tiia

last: Husso


title: Expression Data from Brucella abortus strain 2308 and isogenic vtlR mutant cells

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

country: USA

institute: University of Rochester

summary:
VtlR (virulence-associated transcriptional LysR-family regulator) is thought to be a transcriptional regulator of B. abortus virulence determinants
We used custom-made Affymetrix B. abortus strain 2308 derived GeneChips to compare the gene expression properties of wild type and isogenic vtlR mutant cells.

overall_design: B. abortus strain 2308 or vltR mutant cells were grown to late exponential phase growth, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of VtlR.

first: Clayton

last: Caswell


title: An Automated, High Platform for Induced Pluripotent Stem Cell Derivation, Characterization and Differentiation

city: Bethesda

first: Thierry

last: Vilboux

address: 10 Center drive

department: NHGRI

institute: NIH

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

summary: Induced pluripotent stem cells (iPSCs) have become an essential tool for both modeling how causal genetic variants impact cellular function in disease, as well as being an emerging source of tissue for transplantation medicine. Unfortunately the preparation of somatic cells, their reprogramming and the subsequent verification of iPSC pluripotency are laborious, manual processes that limit the scale and level of reproducibility of this technology. Here we describe a modular, robotic platform for iPSC reprogramming that enables automated, high-throughput conversion of skin biopsies into iPSCs and differentiated cells with minimal manual intervention. Using this platform, we demonstrate that automated reprogramming and the pooled selection of pluripotent cells results in high quality, stable, iPSCs. These lines display less line-to-line variation than either manually produced lines or lines produced through automation followed by single colony-subcloning. The robotic platform we describe will enable the application of iPSCs to population-scale biomedical problems including the study of complex genetic diseases and the development of personalized medicines.

overall_design: Two independent human fibroblast lines were reprogrammed, using modified mRNA, into induced pluripotent stem cells (iPSCs). The genomic stability of several cell lines was evaluated using SNP arrays. Three iPSCs originating from one fibroblast line were tested at passages 8 and 20, with two of these derived as picked (clonal) lines and the third being a pooled population. Five iPSCs originating from a second fibroblast line were tested at passages 8 and 20, with three of these derives derived as picked (clonal) lines and two derived as pooled populations. The iPSCs were compared against the original parental fibroblasts.

first: Daniel

last: Paull

first: Ana

last: Sevilla

first: Hongyan

last: Zhou

first: Aana

middle: K

last: Hahn

first: Hesed

last: Kim

first: Christopher

last: Napolitano

first: Alexander

last: Tsankov

first: Linshan

last: Shang

first: Katie

last: Krumholz

first: Premlatha

last: Jagadeesan

first: Chris

last: Woodard

first: Bruce

last: Sun

first: Matthew

last: Zimmer

first: Eliana

last: Forero

first: Dorota

middle: N

last: Moroziewicz

first: Hector

last: Martinez

first: May

middle: C

last: Malicdan

first: Keren

last: Weiss

first: Lauren

last: Vensand

first: Carmen

middle: R

last: Dusenberry

first: Hannah

last: Polus

first: Reese

last: Sy

first: David

last: Kahler

first: William

last: Gahl

first: Susan

last: Solomon

first: Stephen

last: Chang

last: Meissner

first: Kevin

last: Eggan

first: Scott

last: Noggle


title: Methionine starvation of M. tuberculosis H37Rv ΔmetA

city: Bronx

first: Michael

last: Berney

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔmetA during methionine starvation

overall_design: Two-condition experiment, before starvation vs. either 2 days, 4days or 6days after starvation. Biological replicates: 3, one dye swap


title: Expression profiles of allopolyploids and their parents lines during allopolyploidization

status: Public on Aug 01 2015

city: Yokohama

first: Yeonju

last: Jung

state: Kanagawa

address: Maioka-cho 641-12

department: Yokohama City University

institute: Kihara Institute for Biological Research

summary: We profiled genome-wide gene expression changes in newly hybridized triploids (ABD), its genome-duplicated hexaploid (AABBDD), stable synthetic hexaploid (AABBDD) and T. turgidum (AABB) and Ae. tauschii (DD) parental lines of two independent crosses to reconstruct the events of allopolyploidization and genome stabilization.

sample_organism: Triticum dicoccon x Aegilops tauschii subsp. strangulata

sample_organism: Triticum turgidum subsp. durum x Aegilops tauschii subsp. strangulata

overall_design: Gene expression levels of newly hybridized triploids (ABD), its chromosome-doubled hexaploids (AABBDD), stable synthetic hexaploid (AABBDD) which were selfed during 4 and 13 generations, and their parents, Triticum turgidum (AABB) and Aegilops tauschii (DD) were compared. Total RNA of each line was extracted from three biological replicates of two leaves seedlings except for triploids.For newly hybridized triploids, biological duplicates of two leaves seedlings were used.

first: Kanako

last: Kawaura


title: Expression profiles of allopolyploids and their parents lines during allopolyploidization (Chines Spring and hexaploid)

summary: We profiled genome-wide gene expression levels in natural hexaploid. Chinese spring and three accessions were used.

overall_design: Total RNA of each line was extracted from three biological replicates.


title: Hepatic miRNA profiles and thyroid hormone homeostasis in rats exposed to dietary potassium perfluorooctanesulfonate (PFOS) [miRNA]

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

institute: health canada

summary: Perfluorooctanesulfonate (PFOS) has been widely used in a variety of industrial and commercial applications as a surfactant and stain repellent. PFOS causes liver damage (including liver tumors) in experimental animals, primarily via interaction with PPARa and CAR/PXR. We investigated the involvement of microRNAs (miRNAs) in PFOS-induced hepatotoxicity, and mechanisms involved in abnormal TH homeostasis, in the livers of adult male rats exposed in feed to 50 mg PFOS/kg diet for 28 days. PFOS-treated rats exhibited expected histopathological and clinical chemistry changes. Global gene expression changes were consistent with the involvement of PPARα and CAR/PXR in PFOS-induced effects. Thirty-eight miRNAs were significantly altered. Three members of the miR-200 family were the most increased, while miR-122 and miR-21 were the most decreased, in PFOS-treated relative to control rats. Expression of the miR-23b/27b/24 cluster also decreased in PFOS-treated animals. Pathway analysis of miRNAs and associated gene expression changes demonstrated enrichment of transcripts involved in epithelial to mesenchymal transition (EMT), which is a primary process involved in tumor cell motility and cancer metastasis. Liver expression analysis revealed transcripts that may mediate PFOS effects on thyroid hormone (TH) homeostasis including: activation of the CAR/PXR pathway, phase II/III enzymes, and deiodinase. These changes are consistent with low serum TH due to enhanced metabolic clearance of TH. However, most TH hepatic target genes were not altered in a manner consistent with reduced TH signalling; suggesting that PFOS exposure did not induce functional hypothyroidism. Collectively, PFOS-induced miRNA perturbations were strongly associated with EMT suggesting an important role for miRNAs in PFOS-induced hepatotoxicity. The work also provides novel insights into the effects of PFOS on TH homeostasis.

overall_design: Total RNAs from liver samples (4 animals from each group) were labelled using the miRNA Complete Labelling and Hybridization kit (Agilent Technologies). Labelled RNA was hybridized on 8 X 15K Agilent rat miRNA microarray slides. Arrays were scanned using an Agilent G2505B scanner (5 μm resolution). Agilent Feature Extraction (version 10.7.3.1) was used to acquire the fluorescence intensity of each probe. The quality of the microarray data was evaluated using Agilent Feature Extraction quality control metrics. Data were normalized in R using cyclic-lowess (Bolstad et al., 2003). Ratio-intensity plots, boxplots and cluster analyses were used to identify potential outliers. One control sample failed the quality control tests and was eliminated for subsequent analyses. Statistically significantly altered miRNAs were identified using the methods described above for gene expression.

first: Hongyan

last: Dong

first: Ivan

last: Curran

first: Andrew

last: Williams

first: Genevieve

last: Bondy

first: Carole

last: Yauk

middle: G

last: Wade


title: Hepatic miRNA profiles and thyroid hormone homeostasis in rats exposed to dietary potassium perfluorooctanesulfonate (PFOS) [mRNA]

overall_design: Four RNA samples from control and four from PFOS treated rats were labelled with Cyanine 5-CTP (Cy5) using Low Input Quick Amp Labelling kits (Agilent Technologies Inc.) following the manufacturer’s instruction. Universal rat reference total RNA (Agilent Technologies Inc.) was labelled with Cyanine 3-CTP (Cy3). Cy5-sample cRNA and Cy3-reference cRNA were hybridized to Agilent G4853A SurePrint G3 Rat GE 8 X 60K microarrays (Agilent Technologies Inc.) at 65°C overnight with Agilent hybridization solution. Slides were washed and scanned on an Agilent G2505B microarray scanner at 5 μm resolution, and the data were acquired with Agilent Feature Extraction software version 10.7.3.1. Microarray data quality was confirmed using Agilent Feature Extraction quality control metrics and in-house metrics (boxplots, cluster analyses, and MA plots to identify poor quality outlier arrays). All samples passed the quality control tests and were used for subsequent analyses.

middle: H


title: Effects of SUV39H1 depletion on gene expression in HeLa cells

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
HeLa cells were transiently transfected with siRNA against SUV39H1, a histone H3K9 methyltransferase.
Several genes were significantly up- or down-regulated.

overall_design: HeLa cells were transiently transfected with siRNA against SUV39H1 or negative control siRNA. Then total RNA was extracted.

first: Miki

last: Hieda


title: Gene expression analysis compared myxoid liposarcoma tissue with normal fat tissue

summary: To identify molecular biomakers that are useful for diagnosis and its targeting treatment, we compared the gene expression profile of myxiod liposarcoma with that of normal fat tissue.

overall_design: In the present study, we studied about gene expression profiles comparing 6 non-preoperative myxoid liposarcoma with 3 normal fat tissue.

first: Kunio

last: Iura

first: Yoshinao

last: Oda


title: Hepatic miRNA profiles and thyroid hormone homeostasis in rats exposed to dietary potassium perfluorooctanesulfonate (PFOS)

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

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

overall_design: Refer to individual Series


title: Microarray Analysis Reveals a Role of the Notch System in Ciona Siphon Regeneration

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

summary: Microarray analysis indicated many changes in gene expression, including genes related the the Notch signaling system, during oral siphon regeneration in adult Ciona. Subsequent qPCR gene expression and inhibitor of experiments confirm a role of the Notch system, probably in the formation of a regeneration blastema.

overall_design: To identify the genes defferentially expressed in degenerating siphone, gene expressions in intact siphones and excised siphones (after 3 days, 6 days and 9 days) were examined.

first: William

last: Jeffery

first: Spela

last: Goricki

first: Mardi

last: Byerly

first: Nori

last: Satoh


title: Gene expression profile of hemocytes from Manila clam (Venerupis philippinarum) after a Perkinsus olseni challenge using an immune-enriched oligo-microarray

status: Public on Jul 31 2015

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

summary: Parasites of the genus Perkinsus spp. cause high mortalities and economic losses to the most noticeable bivalves produced in the worldwide aquaculture. In this study, we analyze how P. olseni influences the gene expression profiles of hemocytes from Manila clam (Venerupis philippinarum) using experimental infections along a temporal series and a Manila clam immune-enriched DNA microarray.

overall_design: Healthy and Perkinsus-infected clams (V. philippinarum) were obtained from Carril and Pontevedra shellfish farms, respectively (Galicia, NW Spain). The presence-absence of P. olseni was confirmed using the Ray`s fluid thioglycollate medium assay (RFTM) (Ray, 1966). Healthy clams were maintained in an open circuit filtered sea water tanks at 15°C with aeration. Natural infected animals were maintained in the same conditions using closed circuit sea water. All animals were fed daily with a mixture of microalgae containing Phaeodactylum tricornutum, Isochrysis galbana and Rhodomonas lens. Clams were acclimatized to the aquarium conditions for one week before the experiments were conducted. Perkinsus trophozoites were isolated from naturally infected animals following the protocol established by Ford et al., (2002). The concentration was adjusted to 5x104 trophozoites /ml in filtered sea water (FSW). Healthy clams (P. olseni free animals) (n=100) with a weight of 2.25 ± 0.64 g soft tissue, were notched in the shell and intramuscularly injected with 100 µl of the trophozoites suspension. Control animals (n=100) were injected with 100 µl of FSW. After infection, clams were maintained in 50 l tanks with aeration.Twenty animals from each experimental group and time point were sampled at 5, 10, 14, and 31 days post infection (pi).Hemolymph were extracted to perform microarrays experiments. In each condition hemolymph from three five individuals was pooled. Total RNA isolation was conducted following the manufacturer’s specifications. Isolated RNAs were treated with DNase I and purified again using the RNeasy Mini kit (Qiagen). A 8x15K Agilent 60-mer oligo-microarray (GPL16450) was used to compare gene expression profiles of clams after P. olseni infection with uninfected animals. The Agilent Feature Extraction Software (version 9.5.1) was used for the data extraction and background subtraction following standard procedures. The GeneSpring software (Agilent) was used to normalize and analyze the microarray fluorescence data.

first: Luca

last: Bargelloni

first: Rebeca

last: Moreira

first: Romero

last: Alejandro

first: Antonio

last: Figueras

first: Beatriz

last: Novoa


title: Decoding NF1 intragenic copy number changes

status: Public on Jul 30 2015

city: Gdansk

first: Arkadiusz

last: Piotrowski

address: Hallera 107

department: Biology and Pharmaceutical Botany

country: Poland

institute: Medical University of Gdansk

summary: Genomic rearrangements may cause both Mendelian and complex disorders. Currently, several major mechanisms causing genomic rearrangements have been proposed such as non-allelic homologous recombination (NAHR), non-homologous end joining (NHEJ), fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR). However, to what extent these mechanisms contribute to gene-specific pathogenic copy-number changes (CNCs) remains understudied. Furthermore, only few studies resolved these pathogenic alterations at nucleotide-level resolution. Accordingly, our aim is to explore which mechanisms contribute to a large, unique set of locus-specific non-recurrent genomic rearrangements causing the genetic neurocutaneous disorder neurofibromatosis type 1 (NF1). Through breakpoint-spanning PCR as well as array Comparative Genomic Hybridization (aCGH), we have identified the breakpoints and characterized the likely rearrangement mechanism of the NF1 intragenic CNCs in 78 unrelated patients. Unlike the most typical recurrent rearrangements mediated by flanking low copy repeats (LCRs), NF1 intragenic CNCs have diverse breakpoint locations, and are characterized by different rearrangement mechanisms. We propose the DNA replication-based mechanisms comprising FoSTeS/MMBIR and serial replication stalling to be the predominant mechanism leading to NF1 intragenic CNCs. In addition to the loop of a 197-bp palindrome located in intron 40, four Alu elements located in intron 1, 2, 3 and 50 were also identified as significant intragenic rearrangement hotspots within the NF1 gene. However, no clear genotype-phenotype correlations could be identified among the NF1 patients carrying NF1 intragenic CNCs.

overall_design:
Patient DNA samples with non-overlapping CNCs, as estimated by MLPA,  were labeled with Cy3 and Cy5 fluorophores respectively, and hybridized onto the microarray. Alternatively, patient DNA was hybridized versus unrelated individual blood DNA. No hybridizations using biological replicates were performed. In total 6 samples were included.

Please note that our experimental setup included a hybridization in which two DNA samples with non-overlapping deletions, from two NF1 patients, were hybridized in one experiment (sample codes: 1253 and 1403). In this specific case, assigning test or reference function to the samples was a matter of arbitrary choice. However, if needed, sample 1253 can be denoted as test, and sample 1403 can be denoted as reference in this experiment.

first: Piotr

last: Madanecki

first: Meng-Chang

last: Hsiao

first: Ludwine

last: Messiaen


title: Identification of genes regulated by GIGANTEA (GI), the CYCLING DOF FACTORS (CDFs) and the GI-CDF module

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

institute: Max Planck Institute

type: Expression profiling by genome tiling array

summary: Plants monitor and integrate temperature, photoperiod and light quality signals to respond to continuous changes in their environment. The GIGANTEA (GI) protein is central in diverse signaling pathways, including photoperiodic, sugar and light signaling pathways, stress responses and circadian clock regulation. Previously, GI was shown to activate expression of the key floral regulators CONSTANS (CO) and FLOWERING LOCUS T (FT) by facilitating degradation of a family of CYCLING DOF FACTOR (CDF) transcriptional repressors. However, whether CDFs are implicated in other processes regulated by GI remains unclear. We investigated the contribution of the GI-CDF module to traits that depend on GI. Transcriptome profiling indicated that mutations in GI and the CDFs have antagonistic effects on expression of a wider set of genes than CO and FT, whilst other genes are regulated by GI independently of the CDFs. Detailed expression studies followed by phenotypic assays showed that the CDFs function downstream of GI to control responses to freezing temperatures and growth, but are not necessary for proper clock function. Thus GI-mediated regulation of CDFs contributes to several processes in addition to flowering, but is not implicated in all of the phenotypes influenced by GI.

overall_design: Seedlings of Col-0, the cdf1-R cdf2-1 cdf3-1 cdf5-1 quadruple mutant, gi-100 and gi-100 cdf1-R cdf2-1 cdf3-1 cdf5-1 quintuple mutant were grown for 10 days under LD conditions (16h light/8h dark). The aerial part of the seedlings was collected at ZT12 and RNA was prepared from three biological replicas

first: Fabio

last: Fornara

first: George

last: Coupland


title: Concurrent DNA copy number alterations and mutations in genes related to maintenance of genome stability in uninvolved glandular tissue from breast cancer patients

type: Genome variation profiling by genome tiling array

summary: Somatic mosaicism for DNA copy number alterations (SMC-CNA) is defined as gain or loss of chromosomal segments in mitotic cells within a single organism. As cells harboring SMC-CNA have the potential to undergo clonal expansion, SMC-CNA may be present in a substantial portion of cells in differentiated human tissues and may contribute to the predisposition of these cells to genetic disease including cancer. We characterized gross genomic alterations (>500 kbp) in uninvolved glandular tissue from 59 breast cancer patients and matched samples of primary tumors and lymph node metastases. Array based comparative genomic hybridization experiments showed 10% (6/59) of patients harbored 1 - 359 large SMC-CNA (mean: 1328 kbp; median: 961 kbp) in uninvolved glandular tissue. SMC-CNA were partially recurrent in tumors, albeit with considerable contribution of stochastic SMC-can, indicating genomic destabilization. Therefore, we hypothesized that the observed genomic destabilization is predetermined by mutations in genes related to maintenance of genomic integrity. Targeted resequencing of 301 known predisposition and somatic driver loci revealed mutations in the following genes: BRCA1 (p.Gln1756Profs*74, p.Arg504Cys), BRCA2 (p.Asn3124Ile), NCOR1 (p.Pro1570Glnfs*45), PALB2 (p.Ser500Pro) and TP53 (p.Arg306*). We demonstrated that gross SMC-CNA may be present in a substantial portion of glandular tissue cells, which are  distant from that of the tumor cells, and may co-occur with point mutations in crucial cancer predisposing or somatic driver genes. Taken together, this highlights temporal and spatial neoplastic potential of uninvolved glandular tissue from breast cancer patients.

overall_design: Characterization of gross genomic alterations (>500 kbp) in uninvolved glandular tissue from 59 breast cancer patients and in the matched samples of primary tumors and lymph node metastases. Corresponding peripheral blood lekocyte DNA, a pool of female DNA (Promega), or uninvolved glandular tissue DNA was used as reference. No biological replicates are included.

first: Anna

last: Ronowicz


title: Genomic evidence for the Pleistocene and Recent population history of Native Americans

status: Public on Jul 20 2015

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

summary: How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Native Americans diversified into two basal genetic branches around 13 KYA, one in North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians and Australo-Melanesians, the latter possibly through the ancestors of Aleutian Islanders. Putative relict populations in South America, including the historical Pericúes and Fuego-Patagonians, are not directly related to modern Australo-Melanesians.

overall_design: 3 samples were analysed with the Illumina HumanOmni1-Quad Genotyping BeadChip and are described herein.

first: Richard

last: Villems

first: Eske

last: Willerslev

first: Maanasa

last: Raghavan


title: miR-130a activates apoptotic signaling through activation of caspase-8 in taxane-resistant prostate cancer cells [miRNA]

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary:
Background: The acquisition of drug resistance is one of the most malignant phenotypes of cancer. MicroRNAs (miRNAs) have been implicated in various types of cancers, but its role in taxane-resistance of prostate cancer remains poorly understood.
Methods: In order to identify miRNAs related to taxane-resistance, miRNA profiling was performed using prostate cancer PC3 cells and paclitaxel-resistant PC3 cell lines established from PC3 cells. Microarray analysis of mRNA expression was also conducted to search for potential target genes of miRNA. The effects of ectopic expression of miRNA on cell growth, tubulin polymerization, drug sensitivity and apoptotic signaling pathway were investigated in a paclitaxel-resistant PC3 cell line.
Results: The expression of miR-130a was down-regulated in all paclitaxel-resistant cell lines compared with parental PC3 cells. Based on mRNA microarray analysis, we identified SLAIN1 and CAV2 as potential target genes for miR-130a. Transfection with a miR-130a precursor into a paclitaxel-resistant cell line suppressed cell growth and increased the sensitivity to paclitaxel. Lastly, ectopic expression of miR-130a did not affect the polymerized tubulin level, but activated apoptotic signaling through activation of caspase-8.
Conclusion: These results suggested that miR-130a may be involved in the paclitaxel-resistance and could be a therapeutic target for taxane-resistant prostate cancer.

overall_design: Human hormone-refractory prostate cancer PC3 cells were cultured in RPMI1640 medium supplemented with 10 % of fetal bovine serum, 100 units/ml of penicillin and 100 ug/ml of streptomycin. Paclitaxel-resistant PC3PR20, PC3PR70 and PC3PR200 cells, which respectively could proliferate in the presence of 20, 70 and 200 nM of paclitaxel (Sigma-Aldrich, St. Louis, MO, USA), were previously established from PC3 cells by a stepwise increase of paclitaxel in the culture medium (Kojima et al, 2010, Prostate 70: 1501-12).

first: Yasunori

last: Fujita

first: Kyojiro

last: Kawakami

first: Kosuke

last: Mizutani

first: Taku

last: Kato

first: Takashi

last: Deguchi

first: Masafumi

last: Ito


title: MicroRNA expression profiling of the prostate biopsy samples from African American and European American prostate cancer patients

status: Public on Jul 27 2015

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

summary: Prostate cancer (PCa) tends to be more aggressive and lethal in African Americans (AA) compared to European Americans (EA). To further understand the thebiological risk factors associated with PCa disparities observed in AA and EA patients, we performed microRNA profiling using Agilent Human miRNA arrays to identify the differentially expressed microRNAs beween: 1) AA and EA PCa patients; 2) AA PCa vs. AA normal; and 3) EA PCa vs. EA normal.

overall_design: 54 prostate biopsy specimens (tumor and adjacent normal tissues) were collected from 14 African American and 13 European American prostate cancer patients. 54 RNA samples, purified from the collected biopy specimens using Qiagen miRNeasy kit, were process and applied to Agilent human miRNA arrays. Array data was normalized and analyzed using Agilent GeneSpring program.

first: Norman

last: Lee


title: Stimulation of cell elongation by tetraploidy in hypocotyls of dark-grown Arabidopsis seedlings

status: Public on Jul 16 2015

city: Sendai

first: Kazuhiko

last: Nishitani

state: Miyagi

address: 6-3 Aramaki a2a Aoba Aoba-ku

department: Life Sciences

institute: Tohoku University

summary: Transcriptional profiling of diploid and tetraploid Arabidopsis dark-grown hypocotyls. The aim of this study was to identify ploidy-related genes involved in the determination of cell size. This study showed that a group of genes involved in lipid transport/localization/binding were downregulated in a defined region of the tetraploid hypocotyl when compared to the diploid hypocotyl.

overall_design: Comparison of tetraploid vs diploid Arabidopsis thaliana (L.) Heynh. Col-0. Three biological replicates of 80 hypocotyl-segments each derived from the apical 4 mm region of 7-day-old dark-grown hypocotyls; the same tetraploid line was used.

first: Hideki

last: Narukawa

first: Ryusuke

last: Yokoyama


title: cAMP treated rat DRGs

status: Public on Jul 06 2015

city: Piscataway

first: Ronald

middle: P.

last: Hart

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: To identify potential regeneration-associated genes, rat cultures of dissociated dorsal root ganglia (DRG) cells were treated with dbcAMP for 0,3,6,12, or 18 hours.

overall_design:
A total of 15 paired samples were examined in 5 time points with 3 replicates each.  For each array, dbcAMP-treated and control samples were run in a two-color experiment.
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submitters of this record cannot locate the raw data

first: Jason

middle: B

last: Carmel


title: Transcriptome analysis of FSH response in bovine cumulus cells

status: Public on Jul 01 2015

city: Quebec

first: Daulat Raheem

last: Khan

state: QC

address: 2425, rue de l'Agriculture, Pavillon Paul-Comtois

department: Sciences Animales

country: Canada

institute: Université Laval

summary: Study the effect of recombinant human FSH supplementation in the in vitro maturation medium for an incubation of 6 hrs on the transcriptomics of bovine cumulus cells.

overall_design: 3 biological replicates of cumulus cells derived from cumulus oocyte complexes (COCs) supplemented with FSH (CC-FSH) vs. cumulus cells without FSH (Ct-6H, REFERENCE) were contrasted. Each replicate was subjected to a dye-swap procedure.

first: Daulat

first: Christine

last: Guillemette

first: Marc-André

last: Sirard

first: François

middle: J

last: Richard