title: Identification and Correction of Amplification Protocol Bias in Microarray Studies

city: Toronto

first: Rui

last: Yan

address: 101 College Street

department: Informatics and Bio-computing Platform

institute: Ontario Institute for Cancer Research

summary: mRNA abundance microarrays are the most widely used high-throughput technology for functional genomics. But despite this extensive characterization, and despite their wide-spread adoption in discovery research, the uptake of microarrays as clinical diagnostic tools remains relatively limited due to sample degradation. Recently, the NuGEN WT-Ovation Pico kit was developed to resolve this problem. Here, we comprehensively evaluate its utility on two separate biological problems. First, we evaluate its effect on 12 malignant and 2 normal cervix samples. Second, we evaluate its effect on 2 normal kidney samples. In each case, we directly compare aliquots of the same RNA sample that are prepared by standard and low-input/low-RIN protocols to address three key questions. First, does the use of a low-input/degraded-sample protocol alter transcriptional profiles either globally or of specific genes? Second, do these changes alter biological conclusions drawn from the dataset? Third, are these changes biased towards specific classes of genes, either in terms of their sequence characteristics (e.g. length, GC-content) or their biological function?

overall_design: To achieve these goals, we selected 12 frozen cervix cancers and 2 unmatched normal samples. RNA was extracted and was split into two aliquots: one was prepared using the Nugen WT-Ovation Pico kit and the other using the standard Affymetrix Express array method. This approach allows us to directly assess the effect of sample preparation, in isolation of any other effects. These data were then pre-processed  and the filtered genes were subject to linear-modeling to evaluate technical and biological variability. The resulting gene sets were then subject to pathway and sequence analysis, and LTR analysis. Lastly, to generalize these conclusions we repeated this experimental approach identically in two normal kidney samples and one RNA mixture control sample.

first: Christine

last: How

first: Sheshadrie

last: Saha

first: Syed

last: Haider

first: Angela

last: Hui

first: Daryl

last: Waggott

first: Lauren

last: Chong

first: Nickolas

last: Harding

first: Arek

last: Kasprzyk

first: Blaise

last: Clarke

first: Anthony

last: Fyles

first: Heather

middle: N

last: Reich

first: Fei-Fei

last: Liu

first: Paul

last: Boutros


title: DamID profiling of proneural transcription factor binding in Drosophila melanogaster wing imaginal discs

status: Public on Jan 01 2014

city: Paris

first: francois

last: schweisguth

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

type: Genome binding/occupancy profiling by genome tiling array

summary: Genome-wide identification of the binding sites of the Drosophila transcription factors Achaete, Asense, E(spl)m3-HLH and Senseless in wing imaginal cells using DamID profiling.

overall_design: Each Dam-fusion-derived sample is compared to a control Dam-only sample. Two biological replicates were performed for sca-Asense, neur-Asense, sca-Achaete, neur-Achaete, neur-Sens and sca-E(spl)m3-HLH.

first: K

last: Mazouni

first: F

last: Bernard

first: H

last: Rouault

first: C

last: Besson

first: L

last: Couturier

last: Schweisguth.


title: Study of poplar shoot apex transcriptomic response to variations in soil water avaialbility

city: Uppsala

first: Clement

last: Lafon-Placette

address: Almas Allé 5

country: Sweden

institute: SLU

summary: In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, gene expression patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides × P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Methylome response was also studied and is another GEO submission. Several gene clusters with expression patterns specific to SAM drought response as well as specific to the rewatering condition could be identified. Among them, genes involved in phytohormone pathways like brassinosteroids were found.

overall_design: Populus deltoides × P. nigra 'Carpaccio' hybrid cuttings were submitted to 3 water conditions: non-limiting, water deficit and water deficit/rewatering cycle (14 days treatment). At the end of the experiment, buds were collected and SAM maually isolated for 6 individuals per condition. Total RNA were independently extracted from 3 individuals per condition and used for microarray analyses.

first: Clément

first: Alain

last: Delaunay

first: Irène

last: Hummel

first: Béline

last: Jesson

first: Marie-Béatrice

last: Bogeat-Triboulot

first: Franck

last: Brignolas

first: Stéphane

last: Maury


title: Gene expression during head development in a sexually monomorphic stalk-eyed fly

city: College Park

first: Gerald

middle: S

last: Wilkinson

state: MD

address: Bldg 144, 4094 Campus Dr

department: Biology

country: USA

institute: University of Maryland

summary: Stalk-eyed flies (family Diopsidae) are a model system for studying sexual selection due to the elongated and sexually dimorphic eye-stalks found in some species. These flies are of additional interest because their X chromosome is derived largely from an autosomal arm in other flies. To investigate how sex-biased expression arose on the novel X we compared gene expression between males and females using oligonucleotide microarrays and RNA from developing eyestalk tissue in the sexually monomorphic diopsid, Teleopsis quinqueguttata. We use probe sequence divergence to evaluate cross-species ascertainment bias and chromosome assignment to determine if sex linkage influence expression.  Microarray analysis revealed sex-biased expression for only 1.9% of 3,748 genes expressed in eye-antennal imaginal discs. Analysis of probe sequences between species indicates that the lack of sex-biased expression is not due to ascertainment bias.  These findings indicate that the the majority of sex-biased gene expression observed in developing heads of the dimorphic species, T. dalmanni, is causally related to development of dimorphic head shape.

overall_design: Two-condition experiment, female vs. male RNA using larval eye discs and adult heads for one species (Teleopsis quinqueguttata)


title: Escherichia coli K-12: 1% hydrogen peroxide treatment under anaerobic condition

city: Singapore

first: Aram

last: Kang

state: Singapore

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

summary: Transcripitonal profiling of Escherichia coli K-12 W3110 comparing cells with and without hydrogen peroxide treatment, two biological replicates each

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

overall_design: One-condition experiment, cells with or without hydrogen peroxide treatment for 10min

first: Hua

last: Ling

first: Matthew

middle: W

last: Chang


title: Effect of selection on residual feed intake on gene expression in porcine liver (20 kg body weight)

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

institute: INRA

summary: Transcriptional profiling in liver of 16 pigs of 20 kg body weight from lines divergently selected for residual feed intake (RFI): low-RFI pigs (RFIneg), high-RFI pigs (RFIpl) .

overall_design: Two conditions experiment: low-RFI (RFIneg), high-RFI (RFIpl) . 8 pigs in RFIneg stain and 8 pigs in RFIpl stain . One replicate per array.

first: Isabelle

last: Louveau


title: Effect of selection on residual feed intake on gene expression in porcine liver  (115 kg body weight)

summary: Transcriptional profiling in liver of 24 pigs of 115 kg body weight from lines divergently selected for residual feed intake (RFI): low-RFI pigs fed ad libitum (RFIneg), high-RFI pigs fed ad libitum (RFIpl) and high-RFI pigs restricted at RFIneg feeding level (RFIplR) to investigate the impact of feeding independently of selection.

overall_design: Three experimental conditions: low-RFI (RFIneg), high-RFI (RFIpl) and restricted-high RFI (RFIplR). 8 pigs per condition. One replicate per array.


title: Expression data from Burkholderia cenocepacia J2315 hfq and hfq2 mutants

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

summary: Hfq proteins are RNA chaperones that play a critical role in post-transcription regulation of gene expression. Bacteria of the Burkholderia cepacia complex harbor two distinct and functional Hfq proteins, the Hfq and Hfq2. We have previously performed the functional analysis of Hfq and Hfq2 in the pathogen Burkholderia cenocepacia J2315. In order to examine the impacts of each RNA chaperone on the global transcriptome of B. cenocepacia J2315, we performed comparative transcriptome profile of mutants on the hfq and hfq2 genes, using as reference the wild-type strain.

platform_organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616

overall_design: For expression profiling, over-night cultures of the Burkholderia cenocepacia J2315 wild-type strain and the isogenic mutants hfq::Tp and Δhfq2 grown in LB medium were diluted to an initial OD640 nm of 0.25 into  LB medium. Triplicate samples were cultured at 37ºC with 250 r.p.m. agitation for 16 h and RNA extracted from the three bacterial isolates.

first: Christian

middle: G

last: Ramos

first: Jorge

middle: H

last: Leitão

first: Jorg

middle: D

last: Becker

middle: M


title: BORG analysis

city: Santa Cruz

first: Manny

last: Ares

state: CA

address: 1125 High St

department: Molecular and Cellular Biology

institute: UCSC

summary: A long intergenic non-protein-coding RNA , BORG, is almost exclusively expressed in neurons and is induced during the differentiation of human and mouse pluripotent cells and neuronal progenitors into neurons.

overall_design: shRNA knockdown was used to examine the effects of BORG expression

first: Saba

last: Valadkhan

first: Fereshteh

last: Jahaniani

first: Lily

last: Shiue

first: Bing

last: Zhang

first: John

middle: P

last: Donohue


title: Comparison of transcriptional profiling between insecticide-resistant (SP) and -susceptible (SMK) strains of Aedes aegypti

city: Shinjukuku

first: Shinji

last: Kasai

state: Tokyo

address: 1-23-1 Toyama

department: Department of Medical Entomology

country: Japan

institute: National Institute of Infectious Diseases

summary:
Aedes aegypti SP strain vs. SMK strain.
Aedes aegypti is the major vector of yellow fever and dengue/dengue hemorrhagic fever. Starting with a population collected from Singapore, we established a pyrethroid-resistant A. aegypti strain (SP) and investigated three major possible mechanisms of insecticide resistance. After 10 generations of adult selection, an A. aegypti strain developed 1650-fold resistance to permethrin, which is one of the most widely used pyrethroid insecticides for mosquito control. SP larvae also developed 8790-fold resistance following selection of the adults. Prior to the selections, the frequencies of V1016G and F1534C mutations in domains II and III, respectively, of voltage-sensitive sodium channel genes (Vssc) were 0.44 and 0.56, respectively. In contrast, only G1016 alleles were present after two permethrin selections, indicating that G1016 can contribute more to the insensitivity of Vssc than C1534. In vivo metabolism studies showed that the SP strain excreted permethrin metabolites more rapidly than the susceptible SMK strain. Pretreatment with piperonyl butoxide caused strong inhibition of excretion of permethrin metabolites, suggesting that cytochrome P450 monooxygenases (P450s) play an important role in resistance development. In vitro metabolism studies also indicated an association of P450s with resistance. Microarray analysis showed that multiple P450 genes were over-expressed during the larval and adult stages in the SP strain. Following quantitative real time PCR, we focused on two P450 isoforms, CYP9M6 and CYP6BB2, and confirmed that they were capable of detoxifying permethrin to 4'-HO-permethrin. Over-expression of CYP9M6 was partially due to gene amplification. Association analysis demonstrated that CYP9M6 and CYP6BB2 complementarily conferred permethrin resistance. Two other P450s (CYP9J26 and CYP9J28), which are capable of metabolizing permethrin, were also over-expressed in the SP strain, indicating that at least four P450 isoforms are likely involved in resistance development. Our data show that it is unlikely that reduced cuticle penetration of permethrin contributes to resistance.

overall_design: One-color experiment with two strains (SP, SMK) and 3 developmental stages/genders (larvae, adult males, and adult females), 4 biological replicates each.

first: Osamu

last: Komagata

first: Kentaro

last: Itokawa

first: Takashi

last: Tomita


title: Lack of genetic heterogeneity at high-resolution aCGH between primary breast  cancers and their paired lymph node metastases

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: Netherlands

institute: Genentech

type: Genome variation profiling by genome tiling array

summary: Lymph-node (LN) metastases predict for high recurrence rates in breast cancer patients. Eradication of micro-metastatic tumor cells is the primary goal of adjuvant systemic treatment. Decisions regarding systemic treatment depend largely on primary tumor characteristics rather than on characteristics of their LN metastases. However, it remains unclear to what extent LN metastases, having already metastasized locally, resemble their primary breast tumors and as such will be eradicated by the systemic therapy chosen. In this study we investigated the genetic differences between primary breast cancers and their paired LN metastases using array comparative genomic hybridization analyses on a high resolution 720K Nimblegen platform. Thus far, no metastasis-specific genomic aberrations have been identified. We hypothesized that this is due to low-resolution platforms and lack of stratification on breast cancer subtypes (specifically, triple-negative (TN) versus luminal). Furthermore, we speculated that as TN tumours are known to be more genetically unstable, their LN metastases would show an increase in random copy number aberrations (CNAs). Therefore, we studied 10 primary TN breast tumour–LN pairs and 10 luminal pairs and found that all LN metastases clustered nearest to their matched tumour except for two. These two were explained by poor hybridization quality and, interestingly, the presence of two histological components in one tumour. We found no significantly altered CNAs between pairs in the whole group, nor when subdivided over subtypes; neither did we find a CNA increase in LN metastases compared to primary tumours within the TN subgroup, suggesting most CNAs are functional and not random. Our findings suggest a strong clonal relationship between primary breast tumours and its LN metastases and support the use of the primary tumor characteristics to guide adjuvant systemic chemotherapy in breast cancer patients, since primary tumors and their subsequent LN metastases seem remarkably similar, at least prior to treatment.

overall_design: The experiment contains 20 paired primary breast cancer samples with their lymph node metastases, analysed on a 720 whole genome CGH array. Additionally, for one sample its two distinct histological subpopulations were analysed on the same platform.

first: Christaan

first: Marieke

last: Vollebergh


title: Copy Number Variation in Neuroblastoma

city: Rio de Janeiro

first: Tatiana

middle: Vaz de

last: Carvalho

state: Rio de Janeiro

address: Andre Cavalcanti 37

department: Genetica

country: Brazil

institute: INCA

summary: Neuroblastoma is a tumour of the sympathetic nervous system, with a clinical phenotype resulting from complex patterns of genetic abnormalities, accounting for the most common extracranial neoplasia in childhood. Here we report 44 copy number variations, validated by qPCR, in paired tumour and blood samples of seven patients with neuroblastoma. Thirty four genes were included in altered regions while 11 altered regions did not apparently contain known genes. Five changes were present both in tumour and blood DNA samples in four patients, suggesting presence of germline and/or somatic changes maintained throughout tumorigenesis. Furthermore, some similar or identical changes were observed in different patients. The X chromosome showed the largest number of alterations.

overall_design: DNA from peripheral blood and tumour samples was isolated following using Qiagen DNA Blood Mini Kit. Microarray assays were performed in an Affymetrix platform with Cytogenetics Whole-Genome 2.7 M Array® (Affymetrix, Inc., Santa Clara, CA) for detecting copy number variation across coverage of the whole genome with the highest density of markers for superior resolution. Assays were performed following the procedure of Cytogenetics Copy Number Assay User Guide (Affymetrix®) and analysed with the Affymetrix® Chromosome Analysis Suite (ChAS) software. Gains and losses in tumour and blood samples from each patient were estimated with 95% confidence intervals.


title: Changes in the expression of miRs in the aorta after 3 and 10 months of a high fat diet compared with normal diet

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

summary: We tried to identify miRs that are differentially expresssed during atherogenesis. Aortic miRs expression profile in female apoe-/- mice after 3 and 10 months of a high fat diet were compared with female apoe-/- mice on normal diet.

overall_design: 4 Female apoe-/- mice (6-8 weeks) were fed on high fat diet for 3 months.  3 female apoe-/- mice (6-8 weeks) were fed on high fat diet for 10 months. 4 female apoe-/- mice (6-8 weeks) on normal diet served as controls. Total RNA was isolated from whole aortic tissue. RNA samples with RIN>8 were used for array. The aortic miRs expression profile after 3 months of a high fat diet was compared with the control group. Biological replicates: 4 per group. One replicate per array.

first: Malihe

last: Jahantigh


title: Genomic analyses of Loc1, Puf6, and Khd1 binding patterns and transcriptional effects

city: Boston

first: Suzanne

last: Komili

state: MA

address: 44 Binney St.

institute: Harvard University

type: Genome binding/occupancy profiling by array

summary: We performed ChIP-chip of Loc1, Puf6, and Khd1 in order to determine the genetic loci they bind.  We repeated these experiments with lighter fixation in the presence and absence of RNase to determine whether these associations are via DNA or RNA (analysis shows that they associate with the loci via the RNA).  We also performed transcriptional profiling of knd1- and puf6- cells to determine if the binding of each factor has significant effects on the mRNA abundances of its targets (no significant transcriptional effects were observed).

overall_design: Each analyzed dataset comes from independently-produced triplicate samples, with one dye-swap performed for each dataset.

middle: K

first: Frederick

last: Roth

first: Pamela

middle: A

last: Silver

first: Dale

last: Muzzey

first: Jonathan

last: Weissman


title: Genomic profiling of splenic marginal zone lymphoma (SMZL)

city: Pierre Benite

first: Laurent

last: JALLADES

address: 165 Chemin du Grand Revoyet

institute: Hospices Civils de Lyon

summary: Array-based comparative genomic hybridization comparing splenic marginal zone lymphoma (SMZL) specimens with control DNA

overall_design: A custom high-definition oligonucleotide microarray (4x44K, Agilent) was designed for aCGH from the online application tool eArray (version 5.3) and HD-CGH probe library (sequence source UCSC hg18 / NCBI Build 36). This custom microarray combines the capability to scan human genome-wide with an average resolution of approximately 100 Kb and to focus on regions of interest for highest resolution tiling (11 Kb-resolution for either chromosomes 3q and 7q). The array contains about 8,500 and 9,000 oligonucleotides spanning 97 Mb and 105 Mb of the 7q and the 3q chromosomes respectively. Twenty-seven SMZL specimens (9 males, 18 females) were analyzed using a dye-swap methodology to confirm the copy number variations. Two samples (one male, one female, namely M-CTRL and F-CTRL) collected from healthy volunteers blood from national Etablissement Français du Sang were used as DNA reference for aCGH experiments.

first: L

last: Jallades


title: Specific Lineage differentiation of proepicardial explant cultures

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

summary:
The HH16/17 chicken proepicardium (PE) gives rise to the embryonic epicardium (Epi) which significantly contributes formation of the coronary vasculature during cardiac development. In contrast to explanted Epi cells, explanted PE cells can undergo differentiation into a cardiac myocyte phenotype.
In order to assess which genes are associated with PE differentiation into distinc cellular lineages, three interconnented microarray gene-expression time series were performed at time 0, 24, 72 and 120h after incubation with specific growth conditions:
1: Bmp2 + U0126: differentiation towards a cardiomyocyte phenotype
2: F2f2 + Vegf: differentiation towards a vascular epithelial phenotype
3: Fgf2: differentiation towards a epicardial phenotype

overall_design: Gene-expression profiles were determined by hybridizing Cy3 and Cy5 labelled amplified RNA to the ArkGen 20K oligo arrays in a 2-color looped experiment design, i.e., hybridization of successive time-points per array, including dye swaps, resulting in four technical replicates for each time point.

first: Bram

last: van Wijk

first: Maurice

middle: J

last: van den Hoff

first: Peter-Bram

last: 't Hoen


title: The effect of milk accumulation on gene expression in bovine mammary gland

city: Burlington

first: Emma

middle: Hull

last: Wall

state: VT

address: 89 Beaumont Ave

department: Medicine

institute: University of Vermont

summary: We hypothesized that accumulation of milk would influence gene expression in the mammary gland of lactating dairy cows.  To test this hypothesis, we enrolled 4 multiparous Holstein cows (150 ± 10 DIM) in a half-udder milk stasis experiment.  On day 1 of the experiment, cows were milked at 0430 h and at 1430 h, only right udder halves were milked.  Mammary biopsies were obtained from both udder halves on day 2 of the experiment at 0500 h, immediately after right udder halves were milked and 12 h since left udder halves had last been milked.  Using Affymetrix GeneChip® Bovine Genome Arrays, we identified 32 genes that were differentially expressed between left (full) and right (empty) udder halves (fold change > 1.5; P < 0.05).  Four of the genes were downregulated in response to milk stasis, whereas 28 were upregulated.  Differentially expressed genes were associated with extracellular matrix remodeling, tight junction formation, regulation of blood flow, and apoptosis.  In addition, four of the differentially expressed genes had been previously identified as candidates for local regulation of milk production in dairy cows.  Expression of two of these candidates, early growth response-1 (EGR-1) and thrombospondin-1 (THBS-1), was validated using real-time quantitative RT-PCR.  Consistent with microarray results, both genes were upregulated in response to 24-h of milk stasis (P < 0.03).  Immunofluorescence was used to localize expression of EGR-1 protein, which was restricted to epithelia and was uniformly distributed.  We conclude that accumulation of milk alters gene expression in the bovine mammary gland.  In particular, EGR-1 and THBS-1 have emerged as strong candidates for local regulation of milk production in dairy cows.

overall_design: 8 samples from 4 cows

first: E

first: J

last: Bond

first: T

middle: B

last: McFadden


title: MiR expression profile in M1-polarized bone marrow derived macrophage cells compared with normal mouse aortic tissue.

first: Andreas

summary: The global change of the miR expression profile during atherosclerosis is due to the infiltration of different types of leukocytes into the arterail vessel wall in addition to disease-specific regulation in vascular cells. Monocyte-derived macrophage accumulation in the subintimal region is critical in the formation of atherosclerotic plaques. It is currently unknown which miRs are involved in the atherogenic macrophage response. The comparison of the miR expression profile in LPS/Interferon-gamma activated mouse macrophages with the miR expression in the normal aortic vessel wall was performed to detect macrophage-enriched miRs. This screening may help to identify macrophage-enriched miRs in atherosclerotic vessels that may play a role in the macrophage function during atherogenesis.

overall_design: Bone marrow cells were harvested from femura of 6-8 week old female C57BL/6 mice, re-suspended in DMEM-F12/10% FCS/10% L929-conditioned medium, and cultured for 7 days to differentiate into primary macrophages. F4/80 and CD11b expression was determined by flow cytometry to confirm the macrophage phenotype. Macrophages were stimulated with LPS (100ng/ml, 14 hours) and INF-g (10ng/ml, 6 hours) and the M1 polarization was verified by quantification of mannose receptor C type 1 (MRC1), arginase II (ArgII), inducible nitric oxide synthase (iNOS), and arginase I (ArgI) by qRT-PCR. Total RNA (M1-type macrophages and aorta tissue) was isolated using mirVana microRNA Isolation Kit.

first: Yuanyuan

last: Wie


title: Miniature pigs tooth germ tissue: four different types of teeth in three different developing stages

status: Public on Dec 31 2013

city: xian

first: Ang

last: Li

address: Xi wu Road98#

country: China

institute: Stomatological Hospital of Xi’an Jiao-Tong University

summary: The miRNAs expression profile of three different types of teeth include deciduous incisor (QY), deciduous canine (JY) , deciduous premolar (QMY) ,and deciduous molar (MY) in three typical stages of tooth development embryonic day 40 , 50, and 60, which cover the major morphological and physiological changes in pig tooth germ growth and development throughout pregnancy including the bud, cap, and bell stages.

overall_design: twelve-condition experiment, QY40 vs.QY50 vs.QY60 vs. JY40 vs. JY50vs. JY60 vs.QMY40 vs.QMY50 vs.QMY60  vs.MY40.vs.MY50.vs.MY60. Biological replicates: 1 , independently removed under a microscope. Four replicate per array.

first: Songlin

last: Wang


title: Regulation involved in difference in nitrogen requirements of Saccharomyces cerevisiae wine yeasts in alcoholic fermentation

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

summary: The objective of this work is to identify, in enological condition, differences in transcriptomic regulation that may explain the differences in strains fermentation properties. For this, we compared the global expression patterns of 8 Saccharomyces cerevisiae strains with different nitrogen requirement (L2868, 4CAR1, Fermiflor, Zymasil, MTF1782, 7013, K1M, EC1118). The transcriptome was analyzed on cells fermenting in a nitrogen limited medium containing 100mg.l-1 assimilable nitrogen (SM100) and harvested at stationary phase (45g/L of CO2 produced and corresponding to 6% ethanol). At this stage the strains exhibited differences in fermentation rates. Moreover, the transcriptome was shown to be rather stable at this stage since growth was stopped for all cells and nutrients have been depleted (Rossignol et al. 2003).

overall_design: Eight strains with different nitrogen requirement were analyzed (L2868, 4CAR1, Fermiflor, Zymasil, MTF1782, 7013, K1M, EC1118). This analysis includes two biological replicates for each strain.

first: Claire

last: Brice


title: Psychosocial stress reflected by the liver transcriptome in the pig

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: Unfamiliar individuals (German Landrace pigs) with different aggressiveness were mixed. Subsequently hepatic transcriptome profiles were analysed at postnatal stage (190 dpn)

overall_design: per psychosocial group 6 pigs were collected for expression profiling

first: Eduard

last: Murani

first: Michael

last: Oster


title: Recipe for a busy bee: MicroRNAs in honey bee caste determination (microRNA array)

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

summary:
Social caste determination in the honey bee is assumed to be determined by the dietary status of the young larvae and translated into physiological and epigenetic changes through nutrient-sensing pathways. We have employed microRNA gene-microarray, and observed that both worker jelly and royal jelly showed dynamic changes in miRNA content during the 4th to 6th day of larval development .
Adding specific miRNAs to royal jelly elicited significant changes in queen larval mRNA expression and in morphological characters of the emerging adult queen bee. We propose that miRNAs in the nurse bee secretions constitute an additional element in the regulatory control of caste determination in the honey bee.

overall_design: We collected worker and royal jelly of the Italian honeybee (ZND No.1, Apis mellifera ligustica) at 73~90 hours (4th-day larvae), 97~114 hours (5th-day larvae), and 121~138 hours (6th-day larvae) after hatching. After total RNA was extracted  and quantified , equal amounts of total RNAs from each of the three sampling days were analyzed on the LC Science miRNA-array to observe the expression variation of miRNAs between worker jelly and royal jelly along with the development time points (4th-day, 5th-day and 6th-day).

first: Songkun

last: Su

first: Geir

last: Skogerbø

first: Aung

last: Si

first: Shuanjin

last: Dai

first: Wenfeng

first: Zhiguo

first: Fang

last: Liu

first: Ruifeng

last: Ni

first: Yu

first: Shenglu

last: Chen

first: Shaowu

last: Zhang

first: Runsheng


title: The genes upregulated in WRKY45-ox rice relative to Nipponbare

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

summary: WRKY45-overexpressing (WRKY45-ox) rice plants are extremely resistant to rice blast and bacterial leaf-blight diseases. To search for the genes that are potentially responsible for the strong resistance, we performed genome-wide gene expression analysis in WRKY45-ox rice. A microarray analysis using Agilent rice oligo microarray for approximately 42,000 rice genes identified 1,664 genes that are upregulated in WRKY45-ox rice compared with non-transformant rice cv. Nipponbare (NB). Analysis of the genes with altered expression in WRKY45-ox rice by a Gene ontology program (Agri GO; http://bioinfo.cau.edu.cn/agriGO/) revealed that several genes in the biosynthetic pathway for diterpenoid phytoalexins, for which anti-blast fungus activities have been reported, were upregulated in WRKY45-ox rice.

overall_design: Nipponbare rice (Oryza sativa) and WRKY45-ox rice were analyzed in three biological replicates.

first: Aya

last: Akagi


title: Different miRNA expression profiles of CRC with or without lymph node metastasis

city: beijing

first: jie

last: ma

address: No17, panjiayuan nanli

institute: cancer hospital

summary: Identifying the exact molecules associated with CRC metastasis may be crucial to understand the process, which might also be translated to the diagnosis and treatment of CRC. In this study, we investigate the association of microRNA expression patterns with the lymph node metastasis of colorectal cancer.

overall_design: To investigate the association of microRNA expression patterns with the lymph node metastasis of colorectal cancer, eight primary colorectal cancer tissues derived from stage II–III colorectal cancer patients with (n = 4) or without (n = 4) lymph node metastasis were collected and the miRNA expression profiles of them were determined using Agilent miRNA microarray.  Different miRNA expression profiles were identified in CRC tissues between lymph node metastasis positive and negative group.

first: W

last: Yuan

first: J

last: Ma


title: Profiling transcriptomic response of Enchytraeus albidus to Cu and Ni: Comparison with Cd and Zn

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

institute: CESAM & University of Aveiro

summary: Metals, including copper (Cu) and nickel (Ni) are among the most common contaminants in soils in Europe. Although their effects are relatively well known regarding survival and reproduction of soil invertebrates, their modes of action in these organisms are still poorly studied. Enchytraeus albidus has been used in soil ecotoxicology for many years, and more recently has a gene library and an oligonucleotide microarray for this species which allowed gene expression studies. This has potentiated the means to study further in depth the mechanisms of response to stressors. The main aim of this study is to understand the mechanisms of response of E. albidus to Cu and Ni. For that we have 1) assessed and compared the transcriptomic profile of E. albidus in response to Cu and Ni and 2) compared the Cu, Ni, Cd and Zn transcriptomic profiles. For the microarray hybridizations, E. albidus were exposed to the reproduction effect concentrations EC50 and EC90 of Cu and Ni during 4 days. Results indicate that Cu and Ni have to some extent, similar mechanisms of toxicity and that have already been identified in other species, indicating cross-species conserved mechanisms. Based on hierarchical clustering, it was possible to observe a clear separation of Cd treatments from all other metals. This separation strongly correlates with the available information regarding the toxicokinetics of the tested metals, in which Ni shows properties similar to essential metals.

overall_design: Gene expression in E.albidus was measured  4 days after exposure to Copper, Nickel, Cadmium and Zinc at 2 concentrations of effect on reprocduction (EC50 and EC90). Three biological replicates per exposure condition and 6 biological replicates of control conditions were used.

middle: I

first: Sara

middle: C

last: Novais

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: Aberrant promoter methylation and gene amplification in colorectal cancer

city: Heidelberg

first: Odilia

last: Popanda

address: Im Neuenheimer Feld 280

department: Epigenomics and Cancer Risk Factors

institute: German Cancer Research Center (DKFZ)

type: Methylation profiling by genome tiling array

summary:
To identify new markers for colorectal cancer we scrutinized the methylation status by methyl-CpG immunoprecipitation followed by global methylation profiling on a CpG island microarray, as altered expression could drive genomic and chromosomal instability observed in these tumors. We show for the first time hypermethylation of MMP9, DNMT3A, and LIG4 in CRC which was confirmed in two independent ethnic CRC patients groups.
Hypermethylation of the LIG4 promoter is a new mechanism to control ligase IV expression. It may represent a new epigenetic marker for colorectal cancer independent of known markers.

overall_design: Methylation profiling in 16 tumors of colorectal cancer patients compared to matched normal tissue of these patients

first: Tsun

middle: L

last: Chan


title: Comparative genomic hybridization of strains of Leishmania infantum wild-type and five independent 5-fluorouracil resistant mutant.

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

summary:
The genomic DNAs of strains 263 of L. infantum and five derived independent resistant mutants to 5-fluorouracil were used in comparative genomic hybridizations to reveal the deletion and/or amplification events occured by drug resistance mechanisms.
The human protozoan parasites Leishmania are prototrophic for pyrimidines and de novo pyrimidine biosynthesis is necessary for their growth. Five independent L. infantum mutants were selected for resistance to the pyrimidine analogue 5-fluorouracil (5-FU) in the hope to better understand the metabolism of pyrimidine in Leishmania. Analysis of the 5-FU mutants by comparative genomic hybridization and whole genome sequencing revealed amplification and deletion events as well as point mutations in metabolic genes involved in either the uridine salvage, folate or dTMP biosynthesis pathways. In particular, a dhfr-ts containing amplicon was observed in two mutants and a deletion of part of chromosome 10 was detected in one mutant. Point mutations in uridine phosphorybosyl transferase (UPRT), thymidine kinase (TK) and uridine phosphorylase (UP) were also discovered. Transfection experiments confirmed that these molecular alterations were responsible for the 5-FU resistance phenotype. Transport studies revealed that one resistant mutant was defective for uracil and 5-FU import although the identity of the transporter remains elusive. This study provided further insights in pyrimidine metabolism in Leishmania and confirmed that multiple mutations can co-exist in a cell to lead to resistance.

overall_design: Each independent resistant mutant to 5-fluorouracil was hybridizated with the wild-type L. infantum 263 to 10 microarrays, each with three biological replicates (independent cultures).


title: Genomic Array Footprinting of Shewanella oneidensis grown under aerobic conditions

city: Hangzhou

first: haichun

last: gao

address: 388 Yuhangtang Rd.

institute: Zhejiang University

summary: We undertook a genomic array footprinting to identify genes important for aerobic growth of S. oneidensis. The data revealed that removal of 96 genes resulted in significant impacts on aerobic growth.

overall_design: Experimental cells collected 5 days after competition started; Control cells collected 1 day after competition started. In total, 6 samples were studied (3 for 5 days and 3 for 1 day, 3 replicates).

first: Haichun

last: Gao


title: Subtracted Diversity Array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

summary: Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationships within the species of this genus are unclear, which makes difficult the authentication of the species used for the medicinal industry. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences.

sample_organism: Echinacea angustifolia var. angustifolia

overall_design: In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes, including four that were not used in the array construction, could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic sequences. Five out of the eleven most discriminatory features matched to known retrotransposons.

first: Alexandra

last: Olarte

first: Edwin

last: Pang


title: Reduced Treg suppressive function and HIF-1α expression in hypoxia

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

institute: Universitaetsmedizin Goettingen

summary: Recently, hypoxia via the transcription factor HIF-1a has been implicated to play an important role for the fate of the adaptive immune response by regulatory T cells (Treg) and T helper 17 cells (TH17) in the mouse model. However, the reports on the effect of HIF-1a are conflicting and so far no functional data in the human system are available. Therefore, we analyzed the effect of hypoxia and HIF-1a on Treg and TH17 in the human system. FACS, western blot and reporter assays clearly demonstrated that hypoxia does not up-regulate the level of HIF-1a in CD4+ T cells (THC) and microarray analysis revealed no change of the transcriptome comparing normoxia vs. hypoxia. Furthermore, we could show that HIF-1a is almost exclusively regulated via NF-kB and NFAT, whereas hydroxylation and subsequent degradation of HIF-1a had little to no effect. In addition, we showed that HIF-1a is essential for nTreg mediated suppression and for IL-17A secretion of TH17, but not for TH17 lineage commitment measured by RORγt expression. In conclusion, our results demonstrated that THC have a distinct regulation of HIF-1a protein levels, which was absolutely essential for Treg and TH17 function.

overall_design: 3 patients, 2 cell type, 2 treatments = 12 arrays

first: Thomas

last: Bollinger

first: Sydney

last: Gies

first: Julius

last: Naujoks

first: Werner

last: Solbach

first: Jan

last: Rupp


title: A Novel Osteoclastic Network Determines Niche for Mouse Hematopoietic Stem Cells In Vitro

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

institute: University of Montreal

summary: The importance of extrinsic regulation of hematopoietic stem cell activity is increasingly acknowledged. Here we report the generation of a new niche system, which supports expansion of mouse hematopoietic stem cells in vitro. Characterization of this niche revealed a transcriptional regulatory network including four critical factors, namely FOS, SPI1, KLF10 and TFEC. Interestingly, these factors are essential for osteoclastogenesis, thus revealing an osteoclastic network that supports hematopoietic stem cell self-renewal.

overall_design: Lentiviral vectors containing putative transcription factors regulating HSC expansion were transfected into GPE cells and gene expression values were compared to empty vector controls.

first: Eric

last: Deneault

middle: T

first: Anne

last: Bergeron

first: Frédéric

last: Barabé

first: Guy

last: Sauvageau


title: Circadian transcriptional profile of Synechococcus under the kaiA overexpression

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

summary:
In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression in kaiA-overexpressor (Ptrc::[GTG]kaiA) strains under LL.
KaiC has been proposed to globally activate gene expression, our analysis revealed that dawn expressing genes were downregulated by kaiA-overexpression, such that the clock was arrested at subjective dawn.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design:
IPTG-inducible kaiA-overexpressor (oxA) S. elongatus PCC 7942 strains were analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: a single experiment in oxA under LL in the presence or absence of an inducer, IPTG, from hour 24 to 48 in LL
timecourse data (24~48 hours under continuous light) from Synechococcus elongatus PCC 7942 (inducible kaiA-overexpressor) strains

first: Miki

last: Umetani


title: Expression data from vegetative tissues of grain, sweet and bioenergy sorghums

city: Chicago

first: Nadia

last: Shakoor

state: Illinois

address: 10 South LaSalle Street, Suite 2100

institute: Chromatin, Inc.

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

summary: We developed a commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) and generated this dataset to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes.  Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design.

platform_organism:
Sorghum bicolor
Saccharum hybrid cultivar
Zea mays subsp. mays

overall_design: 78 samples were analyzed from four different tissue types (shoot, seedling, leaves and stem), two dissected stem tissues (pith and rind) and six diverse genotypes (PI455230, Atlas, PI152611, AR2400, R159, and Fremont)

first: Alex

last: Feltus

first: Stephen

last: Kresovich


title: Costimulation through costimulatory molecules (CD40 or CD86) Synergizes with TLR-2 in the Activation of Resting B Cells: A Novel BCR Independent Approach of B Cell Stimulation

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary:
Resting B cells were isolated from mice splenocytes. Briefly, single cell suspension was prepared and treated with B cell enrichment cocktail supplemented with biotinylated anti-CD43 Abs. The cells were then treated with same volume of streptavidin-magnetic beads and negatively selected on BD IMagnet. The purity of RB cells obtained was >98%, as established by flow cytometry (CD45R^+ CD19^+ CD43^- CD4^- CD8^- ).  Purified  cells were cross linked with anti-CD86 Abs or anti-CD40 Abs, washed and cultured for 4 hours in the presence or absence of Pam2CSK4.  Cells were harvested and washed and treated with RNAlater and subjected to microarray analysis.

Microarray was performed by Genotypic Technology Pvt. Ltd. (Bangalore, India; www.genotypic.co.in <http://www.genotypic.co.in/>). The samples for gene expression were labeled using Agilent Quick-Amp labelling kit (p/n5190-0442). The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Mouse 8x60k (AMADID No: 26986). Cy3-labeled samples (800 ng) were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the gene expression hybridization kit of Agilent. Hybridization was carried out in Agilent's Surehyb Chambers at 65 C for 16h. The hybridized slides were washed using Agilent gene expression wash buffers and scanned using the Agilent microarray scanner, G2505C at 3 resolution. Data extraction from images was done using Feature extraction software v 10.5.1.1 of Agilent. Feature extracted data were analyzed using GeneSpring GX v 11 software from Agilent. Genes were classified based on the functional category and pathways using GeneSpringGX Software and Genotypic Biointerpreter-Biological Analysis Software.

overall_design: One-color experiment; Organism: Mus musculus; Custom Whole Genome Mouse 8x60k designed by Genotypic Technology Pvt. Ltd. (Agilent-026986); Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Shweta

last: Jain

first: Sathi

last: Chodisetti

first: Javed

middle: N

last: Agrewala


title: B31 vs rrp1 mutant

city: Dallas

first: zhiming

last: ouyang

state: TX

address: 6000 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwestern Medical Center

summary:
Transcriptional profiling of gene expression between parental strain B31 and rrp1 mutant.

Cyclic-di-GMP is a bacterial second messenger that modulates many biological processes.  Although its role in bacterial pathogenesis during mammalian infection has been widely recognized, the role of c-di-GMP in pathogen's life cycle in vector hosts is less understood. The enzootic cycle of the Lyme disease pathogen Borrelia burgdorferi involves both a mammalian host and an Ixodes tick vector.  The B. burgdorferi genome encodes a single copy of the diguanylate cyclase gene (rrp1), which is responsible for the production of c-di-GMP. To determine the role of c-di-GMP in the life cycle of B. burgdorferi, an Rrp1-deficient B. burgdorferi strain was generated. The rrp1 mutant remains infectious in the mammalian host, but could not survive in the tick vector. To identify the mechanisms of Rrp1 contributing to B. burgdorferi pathogenesis and gene regulation, microarray was employed to compare gene expression profiles between the parental strain B31 and the rrp1 mutant.

overall_design: Two-condition experiment, B31 vs. rrp1 mutant. Biological replicates: 3 B31, 3 rrp1 mutant, independently grown and harvested. One replicate (dye-swap) per array.

first: Zhiming

last: Ouyang

first: Ming

last: He

first: Xiaofeng

last: Yang


title: Cross-species meta-analysis of regulatory networks of the Pax5 transcription factor

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

institute: Karolinska Institutet

summary:
Transcription profiling of chicken Pax5 deficient DT40 B cell line to investigate the targets of Pax5 which is required for B-cell differentiation
Used in cross-species comparison to investigate evolutionarily conserved regulatory circuits in B cell development

overall_design: Pax5 deficient DT40 B cells (3 biological replicates) were compared to DT40 wild-type cells (3 biological replicates).

first: Jukka

last: Alinikula

first: Kalle-Pekka

last: Nera

first: Olli

last: Lassila


title: Global miRNA transcriptomic profiling of permanent focal ischemia in an in vivo rat model

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

institute: Menzies Research Institute

summary: Focal ischemia is triggered by the sudden significant reduction of blood supply to the brain, as a result of either the rupture or occlusion by thrombus/embolism of a blood vessel in the brain. Permanent focal ischemia occurred when blood supply to a specific part of the brain is impeded without reperfusion. Despite major steps achieved in the elucidation of the patho-physiology of cerebral ischemia, the available therapeutic avenues for acute ischemic stroke remain scarce. Cell cycle re-activation has been revealed as a novel signaling pathway during permanent focal ischemia. As such, non-specific aurora kinase inhibitor ZM447439, has been injected intracranial-ventricularly 30min post-ischemia induction to determine its efficacy in reduction of neuronal damage in terms of infarct volume.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
miRNA microarray analysis was performed on Exiqon 5th generation - hsa, mmu & rno (Product no: 208300-A) to compliment our existing gene expression microarray data [GSE23651]. Arrays were run as dual colour (Hy3: Sample, and Hy5: Common sample reference pool). Right cortex RNA samples were collected at two time-points (8h and 24h )respectively for all three experimental conditions: Sham (n=4), vehicle (i.e. ischemic injury with i.c.v. injection 80% DMSO; n=4) and treatment (injury plus i.c.v.injection of 30mM ZM447439 in 80% DMSO; n=4).
Supplementary file: Project_Summary_Report.txt
The percentages listed in the top row are present-call rates, i.e. number of identified miRNAs compared to number of miRNAs on array.

first: Nam

middle: S

last: Cheung

first: Minghui

first: Peter

last: Wong

first: Jayapal

last: Manikandan


title: INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and its receptors HAE/HSL2 are  required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana (part 1)

status: Public on Dec 30 2013

city: Oslo

first: Reidunn

middle: B.

last: Aalen

address: P.O.Box 1066 Blindern

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: Plants have the ability to shed organs that are no longer in use. In Arabidopsis thaliana abscission of floral organs involves cell wall remodeling and cell expansion prior to cell wall dissolution.  IDA encodes a secreted peptide that signals through the leucine-rich repeat receptor-like kinases (LRR-RLKs) HAESA (HAE) (At4g28490) and HASEA-LIKE2 (HSL2) (At5g65710).

overall_design: Arabidopsis thaliana (ecotype Colombia-0)  plants were kept in growth chambers with a 16/8 h (light/dark) photoperiod at 22 °C, and 100 mE m-2 s-1 light intensity. 4 biological replicates were prepared from each sample, each containing abscission zone regions of siliques position 4 to 8 (when counting from the flowe at anthesis at the top of the inflorescence) from  plants with at least 20 siliques. Differences in transcriptional responses were measured by comparing genes expression in abscission zones of hae hsl2  plants  (SALK_021905 x SALK_030520) against abscission zones from control plants.

first: Bin

last: Liu

first: Melinka

last: Butenko

first: Tore

last: Brembu

first: Grethe-Elisabeth

last: Stenvik

first: Torfinn

last: Sparstad

first: Ane

last: Vie

first: Chun-Lin

last: Shi

first: Per

last: Winge

first: Atle

middle: M

last: Bones


title: Intermittent suckling does not influence the gene expression of Day 9 embryos during early gestation in primiparous sows

status: Public on Dec 23 2013

city: Edmonton

first: Stephen

last: Tsoi

address: 4-32G Agriculture/Forestry Centre

department: AFNS

institute: University of Alberta

summary: Primiparous sows were randomly allocated to two treatments and were separated from piglets 8h daily from Day 21 of lactation companied with daily boar exposure for oestrus detection until weaning (Day 28). Gene expression of Day 9 embryos were compared between control sows (FE; sows artificially inseminated when  in heat during lactation ) and Skip-a-Heat sows (SE; sows in heat during lactation and artificially inseminated on the following oestrus cycle).

overall_design: Stimulating lactational oestrus then two mating strategies were applied to primiparous sows; 1)FE; sows were in heat during lactation and received artificial insemination) and Skip-a-Heat sows (SE; sows were in heat during lactation and received artificial insemination at fallowing oestrus cycle).

first: Tai

middle: Y

first: Michael

last: Dyck


title: House Dust Mediates Gut Microbiome Lactobacillus johnsonii Enrichment and Immune Defense Against Airway Allergens [Set3]

status: Public on Dec 20 2013

city: San Francisco

first: Susan

last: Lynch

address: 513 Parnassus Ave

department: GI

institute: UCSF

summary:
Exposure to dogs in early infancy has been shown to reduce the risk of childhood allergic disease development and dog-ownership is associated with a distinct house dust microbial exposure. Here we demonstrate, using murine models, that exposure of mice to dog-associated house dust protects against ovalbumin or cockroach allergen mediated airway pathology.
Protected animals exhibited significant reductions in the total number of airway T cells, down-regulation of Th2-related airway responses as well as mucin secretion. Following house dust exposure, the cecal microbiome of protected animals was extensively restructured with significant enrichment of, amongst others, Lactobacillus johnsonii.
Supplementation of wild type animals with L. johnsonii protected them against both airway allergen challenge or infection with respiratory syncytial virus. L. johnsonii mediated protection was associated with significant reductions in the total number and proportion of activated CD11c+/CD11b+ and CD11c+/CD8+ cells, as well as significantly reduced airway Th2 cytokine expression.
Our results reveal that exposure to dog-associated household dust results in protection against airway allergen challenge and a distinct GI microbiome composition.
Moreover the study identifies L. johnsonii as a pivotal species within the gastrointestinal tract capable of influencing adaptive immunity at remote mucosal surfaces in a manner that is protective against a variety of respiratory insults.

platform_organism: Bacteria Archaea

overall_design: The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile cecal gut bacteria from 29 mice: 7 controls, 5 gavaged with dust from homes with pets, 5 gavaged with dust from homes with no pets, 4 CRA-challenged, 4 gavaged with L. johnsonii, and 4 gavaged with L. johnsonii prior to CRA challenge. The PhyloChip was also used to profile 1 house dust sample collected from a home with dogs

first: Kei

middle: E

last: Fujimura

first: Tine

last: Demoor

first: Marcus

last: Rauch

first: Ali

last: Faruqi

first: Christine

last: Johnson

first: Homer

last: Boushey

first: Edward

last: Zoratti

first: Dennis

last: Ownby

first: Nick

last: Lukacs

middle: V


title: Gene expressions with nisin A or nukacin ISK-1 treatment of nsrRS deletion mutant or lcrRS deletion mutant in Streptococcus mutans UA159

city: Kagoshima

first: Kawada-matsuo

last: Miki

department: oral microbiology

institute: Kagoshima University

summary: The two-component system (TCS) is a specific regulatory system in bacteria and plays an important role in sensing and adapting to the environment. In this study, we evaluated the roles of TCSs in the major cariogenic pathogen Streptococcus mutans in resistance to several types of bacteriocin. In a comprehensive analysis using individual TCS mutants, we found that two novel TCSs were associated with resistance against distinct lantibiotics nisin A (class I type A[I]) and nukacin ISK-1(class I type A[II]). One TCS, SMU.659-660 (designated as NsrRS), was related to resistance against nisin A produced by Lactococcus lactis ATCC 11454. The other TCS, SMU.1146-1145 (designated as LcrRS), was related to resistance against nukacin ISK-1 produced by Staphylococcus warneri ISK-1. NsrRS induced the expression of SMU.658 (designated as NsrX), which constitutes an operon with nsrRS, in response to nisin A. Inactivation of nsrX increased susceptibility to nisin A. Additionally, NsrX expression in S. mutans increased the binding affinity to nisin A compared to a no-expression strain. LcrRS induced the expression of SMU.1148-50 (lctFEG), which encodes an ABC transporter and is located upstream of lcrRS, in response to nukacin ISK-1. Inactivation of lctFEG significantly increased susceptibility to nukacin ISK-1. Electrophoretic mobility shift assay analysis revealed that NsrR and LcrR bound directly to regions upstream of nsrX and lctFEG, respectively. This is the first report that two distinct TCSs, NsrRS and LcrRS, are independently involved in resistance to nisin A and nukacin ISK-1 in S. mutans.

overall_design: Total of 14 samples were analyzed. Total RNA from each test strain and control described below were labeled with Alexa Fluor® 555 and Alexa Fluor® 647, respectively, and were cohybridized on a single array. Labeling and hybridization were performed once or twice independently. UA159 wild type as control vs. UA159 with nisinA or nukacin ISK-1, UA159 wild type with nisinA or nukacin ISK-1 vs. nsrRS or lcrRS deletion mutant in UA159 with nisinA or nukacin ISK-1.

first: M

last: Kawada-Matsuo

first: Y

last: Oogai

last: Ogura

first: T

last: Hayashi

first: H

last: Komatsuzawa


title: House Dust Mediates Gut Microbiome Lactobacillus johnsonii Enrichment and Immune Defense Against Airway Allergens

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

sample_organism:
Mus musculus
dust metagenome

overall_design: Refer to individual Series

middle: A


title: House Dust Mediates Gut Microbiome Lactobacillus johnsonii Enrichment and Immune Defense Against Airway Allergens [Set1]


title: House Dust Mediates Gut Microbiome Lactobacillus johnsonii Enrichment and Immune Defense Against Airway Allergens [Set2]


title: Identification of alternative splicing events regulated by the splicing factor SRSF1 using data from exon-junction microarray technologies

status: Public on Dec 18 2013

city: San Sebastian

first: Ravi

middle: Datta

last: Sharma

state: Gipuzkoa

address: Parque Tecnológico de San Sebastián, Paseo Mikeletegi, Nº 48,

department: Biomedical Engineering

country: Spain

institute: CEIT

summary: Analysis to identify genome-wide differential alternative splicing events in A549 cells in which the levels of the gene SRSF1 were down-regulated with a specific siRNA

overall_design: 9 samples from three independent experiments using A549 cells transfected with lipofectamine alone, scramble siRNA or SRSF1 siRNA

first: Fernando

last: de Miguel

middle: D

first: Maria

middle: J

last: Pajares

first: Luis

last: Montuenga

first: Angel

last: Rubio

first: Ruben

last: Pio


title: Characterization of the Quality of Imbibed Soybean at an Early Stage of Pre-Germination for the Development of a New Protein Food Item

status: Public on Dec 13 2013

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

institute: Tokyo University of Agriculture

summary: Global analyses on gene expression profiles in short-term imbibition (0, 8, and 16 h) was performed using DNA microarray technique to look at changes of expression of genes coding for components that may determine food protein quality. DNA microarray analysis followed by gene ontology statistics revealed that, prior to 16 h, (i) genes for carbohydrate metabolism giving rise to nutrients as the primary metabolism were up-regulated; (ii) genes response to water-, temperature-, and light-stimulation which may not be related to soybean protein properties were down-regulated; and (iii) gene associated with lipid metabolism and secondary metabolite production which can be activated during germination showed indistinct up- and down-regulations.

overall_design: Soybean seeds were selected at 0, 8, and 16 h imbibition for RNA extraction and hybridization on Agilent microarrays.

last: Tamura

first: Asuka

last: Kamei

first: Reiko

last: Ueda

first: Soichi

last: Arai

first: Kiyoshi

last: Mura


title: Differential miroRNA expression in myostatin knockout mice

status: Public on Dec 17 2013

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: To identify microRNAs involved in myostatin-deficient muscular hypertrophy, we compared miRNA expression in wild-type and myostatin knockout mice.

overall_design: Total RNA, isolated from three wild-type or myostatin knockout mice, was pooled and then used for microarray analysis.

first: Keisuke

last: Hitachi


title: Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21 [CGH]

status: Public on Dec 01 2013

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

summary: Down syndrome (trisomy 21) is the most common viable chromosomal disorder with intellectual impairment and several other developmental abnormalities. Here, we report the generation and characterization of induced pluripotent stem cells (iPSCs) derived from monozygotic twins discordant for trisomy 21 in order to eliminate the effects of the variability of genomic background. The alterations observed by genetic analysis at the iPSC level and at first approximation in early development illustrate the developmental disease transcriptional signature of Down syndrome. Moreover, we observed an abnormal neural differentiation of Down syndrome iPSCs in vivo when formed teratoma in NOD-SCID mice, and in vitro when differentiated into neuroprogenitors and neurons. These defects were associated with changes in the architecture and density of neurons, astroglial and oligodendroglial cells together with misexpression of genes involved in neurogenesis, lineage specification and differentiation. Furthermore, we provide novel evidence that dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A) on chromosome 21 likely contribute to these defects. Importantly, we found that targeting DYRK1A pharmacologically or by shRNA results in a considerable correction of these defects.

overall_design: aCGH profiling of iPS cells derived from fibroblasts of monozygotic twins discordant for trisomy 21

first: Youssef

last: Hibaoui

first: Iwona

last: Grad

last: Sailani

first: Sophie

last: Dahoun

first: Federico

last: Santoni

first: Stefania

last: Gimelli

first: Michel

last: Guipponi

first: Marie

middle: F

last: Pelte

first: Frédérique

last: Béna

first: Stylianos

last: Antonarakis

first: Anis

last: Feki


title: The conserved DNA-binding protein WhiA is involved in cell division in Bacillus subtilis

status: Public on Nov 28 2013

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary: One of the first steps in bacterial cell division is the polymerization of the tubulin-like protein FtsZ at midcell. The dynamics of FtsZ polymerization is regulated by a set of proteins among which ZapA. A zapA mutation does not result in a clear phenotype in Bacillus subtilis. In this study we used a synthetic-lethal screen to find genes that become essential when ZapA is absent. Three transposon insertions were found in yvcL. Deletion of yvcL in a wild type background had only a mild effect on growth, but a yvcL zapA double mutant is very filamentous and sick. This filamentation is caused by a strong reduction in FtsZ polymerization, suggesting that YvcL is involved in an early stage of cell division. YvcL is 25 % identical and 50 % similar to the Streptomyces coelicolor transcription factor WhiA. WhiA is required for septation of aerial hyphae during sporulation. Using GFP fusions, we show that YvcL localizes at the nucleoid. Surprisingly, transcriptome analyses in combination with a ChIP on chip assay did not provide clear evidence that YvcL functions as a transcription factor. To gain more insight into the function of YvcL, we searched for suppressors of the filamentous phenotype of a ∆yvcL ∆zapA mutant. Transposon insertions in gtaB and pgcA restored normal cell division of the double mutant. The corresponding proteins have been implemented in the metabolic sensing of cell division. We conclude that YvcL (WhiA) is involved in cell division in B. subtilis through an as yet unknown mechanism.

overall_design: Comparing wild tpe Bascillus subtilus (n=3) with Bascillus Subtilis KS400 (n=2) and Bascillus subtilis KS696 (n=2)

first: Katarina

last: Surdova

first: Dennis

last: Claessen

first: Tjalling

last: Siersma

first: Jeff

last: Errington

first: Leendert

middle: W

last: Hamoen


title: ERα gene expression profile in MCF7 cells

city: Houston

first: Anne

middle: Chinenye

last: Katchy

state: Texas

address: 3605 Cullen Blvd, Room 3021

department: CNRCS, Biology and Biochemistry

institute: University of Houston

summary: This submission is a part of two separate studies: a study of estrogen receptor-alpha (ERalpha)-mediated gene expression in response to different ligands and a study examining the roles of ERalpha and ERbeta in gene regulation in breast cancer cells.

overall_design: Comparison of estrogen-treated versus vehicle-treated MCF7 parental cells. Each comparison was performed in biological duplicate, with dye swapping.

first: Cecilia

last: Williams


title: Genome wide gene-expression analysis of facultative reproductive diapause in the two-spotted spider mite Tetranychus urticae

status: Public on Nov 29 2013

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
Investigating essential physiological processes in diapausing mites by analyzing genome wide gene expression changes using custom-built microarray.
We investigated the molecular biology of facultative reproductive diapause in the chelicerate Tetranychus urticae (Acari: Tetranychidae) by analyzing genome-wide gene expression differences in diapausing and non diapausing T. urticae, using an Agilent custom-built two color gene expression microarray. Analysis of this dataset showed that a remarkable number, 11% of the total number of predicted T. urticae genes, were differentially expressed. Gene Ontology analysis revealed that many metabolic pathways were affected in diapausing females. Genes related to digestion and detoxification, cryo-protection, carotenoid synthesis and the organization of the cytoskeleton were profoundly influenced by the state of diapause. We also further confirmed the importance of horizontally transferred carotenoid synthesis genes in diapause and different color morphs of T. urticae.

overall_design: We made one comparison: diapausing mites (DIA) vs non-diapausing mites (NON-DIA), in 4 replicates. Both types of mites belonged to the T. urticae LS-VL strain. In this strain, approximately 30% of mites enter diapause under the experimental conditions applied. Hence, we were able to sample RNA of mites with similar genetic background that were reared under identical environmental conditions. The labeled cRNA samples were pooled and hybdrized to a custom Sureprint genome wide G3 Gene Expression 8x60K microarray. Data was normalized by Agilent Feature Extraction software (using protocol GE2_107_SEP09). Genespring software (Agilent technologies) was used for the statistical analysis of the data.

first: Astrid

last: Bryon

first: Wannes

last: Dermauw

first: Luc

last: Tirry

first: Thomas

last: Van Leeuwen


title: Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
S. aureus biofilms are associated with the organism's ability to cause disease.  Biofilm associated bacteria must cope with the host's innate immune system.
We used commercially available Affymetrix S. aureus GeneChips to compare the gene expression properties of 4 and 6 day established biofilms following short (1 hr)- and long (24 hr)- term exposure to macrophages and neutrophils.

overall_design: S. aureus strain USA300 LAC biofilms where formed for 4 or 6 days.  Established biofilms were then exposed to macrophages for 1 or 24 hr.  Alternatively, biofilms were exposed to neutrophils for 1 or 4 hr.  Total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of Macrophages and Neutrophils on established S. aureus biofilms.

first: Tammy

middle: L

last: Kielian


title: Expression analysis of HCT116 cells transfected using Tip60 or p400-targetting siRNA

status: Public on Nov 22 2013

city: TOULOUSE Cedex 9

first: Fabrice

last: ESCAFFIT

address: 118, route de Narbonne

department: LBCMCP UMR5088

country: France

institute: CNRS

type: Expression profiling by genome tiling array

summary:
Investigation of whole genome gene expression level changes in HCT116 cells upon knockdown of Tip60 or p400, compared to control siRNA-transfected cells.
Two different siRNA directed against Tip60 were used and experiments were done in duplicate. Same for p400-targetting or control siRNA.

overall_design: Hybridization experiment using total RNA recovered from independent cell cultures of HCT116 transfected using control, Tip60-targetting or p400-targetting siRNA.

last: Escaffit

first: Martine

last: Chevillard-Briet

first: Muriel

last: Quaranta


title: Chip-chip from HCT116 cells with p400 antibody

summary:
The chromatin remodeller p400 has oncogenic properties that promote early steps of colon cancer.
Chromatin immunoprecipitation (ChIP) of p400 together with chromatin profiling by ChIP-on-chip analysis demonstrated that p400 directly binds the chromatin at promoters of p400 target genes.

overall_design: Study of p400 binding on promoters of HCT116 cells

first: Aude

last: Grézy


title: Transcriptional Response of Mycobacterium tuberculosis CDC1551 Rv0516c::Tn to treatment with 140 mM NaCl for 1 hr

status: Public on Nov 15 2013

city: Berkeley, CA

first: Stavroula

last: Hatzios

address: B84 Hildebrand Hall #1460

institute: UC Berkeley

summary: To characterize the role of Rv0516c in the osmotic stress response of Mycobacterium tuberculosis (Mtb), we performed transcriptional profiling of CDC1551 Rv0516c::Tn following treatment with 140 mM NaCl for 1 hr relative to an untreated control.

overall_design: CDC1551 Rv0516c::Tn  was treated with 140 mM NaCl for 1 h and compared to the same strain treated with 0 mM NaCl for 0 h.  4 biological replicates, independently grown and harvested.  One replicate per array.

middle: K

first: Christina

last: Baer

first: Tige

middle: R

last: Rustad

first: Jennifer

last: Pang

first: Corrie

last: Ortega

first: M

last: Siegrist

first: Tom

last: Alber

first: Christoph

last: Grundner

first: David

last: Sherman

first: Carolyn

last: Bertozzi


title: Rapid Transcriptome Changes Induced by Excess Chromium in Rice Roots

status: Public on Oct 31 2013

city: Tainan

first: Tsai-Lien

last: Huang

state: Taiwan

address: No.1, University Raod,

department: Life Sciences

country: Taiwan

institute: National Cheng Kung University

summary:
Chromium (Cr) is a non-essential metal for normal plants and is toxic to plants at high concentration. In spite of many previous studies having been conducted on the effects of Cr stress, the precise molecular mechanisms and signaling pathways of action of Cr remain poorly understood. In this study, the transcriptome at the early of Cr (VI) stress were assayed in rice roots. To gain more insight into these cellular responses, we analyzed whole-genome transcriptome of rice expose to Cr (VI) for 1 and 3 h. Analysis revealed 1,261 and 267 up and down-regulated genes by Cr (VI). Cr (VI) stress triggered changes in transcript levels of genes related to secondary metabolism process, biosynthetic process, specially jasmonic acid biosynthetic process, response to abiotic stress, specially response to toxin, transcription regulator activity, specially transcription factors activity. The most predominant transcription factor families were WRKY, AP2/ERF, NAC, C2H2, MYB. In addition, many protein kinase, including eight MAPKKK, two CDPK, and one MAPK, showed significant increase in transcriptional level under Cr (VI) stress.
Molecular mechanisms for the excess Cr(VI) in rice roots

overall_design: Comparison of mock control and rice seedlings treated with 200 μM Cr(VI); Biological replicates: 3 control replicates, 3 Cr(VI)-treated replicates.

first: Ngoc-Nam

last: Trinh

first: Hao-Jen


title: Transcriptional Response of Mycobacterium tuberculosis CDC1551 to treatment with 140 mM NaCl for 1 hr

country: USA

summary: To identify mediators of the osmotic stress response in Mycobacterium tuberculosis (Mtb), we performed transcriptional profiling of WT CDC1551 following treatment with 140 mM NaCl for 1 hr relative to an untreated control.  140 mM NaCl was chosen to reflect the approximate osmolarity of human plasma (i.e., 280 mOsm/L), which may be relevant during the course of infection.

overall_design: CDC1551 was treated with 140 mM NaCl for 1 h and compared to the same strain treated with 0 mM NaCl for 0 h.  4 biological replicates, independently grown and harvested.  One replicate per array.


title: p400 binding and Tip60/p400 gene expression regulation in HCT116 cells

first: Fabrice

last: ESCAFFIT


title: Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome

status: Public on Oct 28 2013

city: Marseille

first: Abdessamad

last: EL KAOUTARI

state: France

address: 27 boulevard Lei Roure

institute: INSERM

summary: Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a high density custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.

overall_design: Fecal samples were collected from eight female subjects. Three were obese subjects of BMI kg m-2: 35, 46.8 and 51.3, respectively; age: 42, 21 and 65 years old, respectively. Three were anorexic women of BMI kg m-2: 9.8, 10 and 13.7, respectively; age: 19, 23 and 49 years old, respectively. Finally, two fecal samples from lean women of BMI kg m-2: 18.6 and 23.42 were analyzed.

last: El Kaoutari

last: Armougom

first: Quentin

last: Leroy

first: Bernard

last: Vialettes

first: Matthieu

last: Million

first: Didier

last: Raoult

last: Henrissat


title: Association of CREB3L1 with promoters in MDA-MB-435 cells

status: Public on Oct 30 2013

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

institute: University of Saskatchewan

summary:
The unfolded protein response (UPR) is activated in response to hypoxia-induced stress such as in the tumor microenvironment.  This study examined the role of CREB3L1 (cAMP-responsive element-binding protein 3-like protein 1), a member of the UPR, in breast cancer development and metastasis.  Initial experiments identified the loss of CREB3L1 expression in metastatic breast cancer cell lines compared to low- or non-metastatic cell lines.  When metastatic cells were transfected with CREB3L1 they demonstrated reduced invasion and migration in vitro, as well as a significantly decreased ability to survive under non-adherent or hypoxic conditions.  Interestingly, in an in vivo rat mammary tumor model, CREB3L1 expressing cells not only failed to form metastases compared to CREB3L1 null cells but regression of the primary tumors was seen in 70% of the animals as a result of impaired angiogenesis.  Microarray and ChIP on Chip analyses identified changes in the expression of many genes involved in cancer development and metastasis, including a decrease in those involved in angiogenesis.  These data suggest that CREB3L1 plays an important role in suppressing tumorgenesis and loss of expression is required for the development of a metastatic phenotype.
CREB3L1 is a member of the unfolded protein response family of proteins. CREB3L1 expression is lost from metastatic breast cancer cells. We wanted to determine the promoters of genes that CREB3L1 bound to.

overall_design: Idenification of promoters to which CREB3L1 is bound following ChIP with a HA antibody in MDA-MB-435 cells.

first: Paul

last: Mellor


title: Support of a bi-faceted role of ERβ in ERα-positive breast cancer cells

status: Public on Nov 21 2013

first: Philip

last: Jonsson

address: Department of Biology and Biochemistry – NSM Center for Nuclear Receptors and Cell Signaling 3605 Cullen Blvd, Science & Engineering Research Center Bldg 545

summary: Comparison of the basal and estrogen-induced effects on genome-wide transcription in ERα-positive breast cancer cell lines T47D and MCF7 after lentiviral transduction with ERβ.

overall_design: Comparison of ERβ-transduced T47D and MCF7 cells versus respective control-transduced cells, in the presence of vehicle or estrogen. Each comparison in technical and biological duplicate.

first: Anne

last: Katchy

first: Cecilia

last: Williams


title: Association of CREB3L1 with promoters in LN4D6 CREB3L1 cells

overall_design: Idenification of promoters to which CREB3L1 is bound following ChIP with a HA antibody or control.


title: Assignment of unknown contigs to chicken microchromosome 16 (GGA16)

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Trisomy mapping has long been a powerful means for assigning genes to chicken microchromosome 16 (GGA16). The major histocompatibility complex (MHC-Y, MHC-B) and CD1 genes were previously assigned to GGA16 by trisomy mapping.  Here we combined array comparative genomic hybridization (aCGH) with trisomy mapping to investigate unassigned genomic contigs (temporarily assigned to chrUn_random) by the chicken genome sequencing projects for sequences originating from GGA16. We used the Cornell Trisomy chicken line in our study, as this line contains an extra copy of GGA16 and crosses between these individuals generate disomic, trisomic, and tetrasomic GGA16 offspring. Through the analysis of these individuals with aCGH, we compare signal intensities from unknowns to those expected based on copy number, and putatively assign or reject assignment to GGA16 accordingly.

overall_design: A three-condition experiment, where individuals (n=8) are classified based on their GGA16 content, with a total of 24 individuals. Each individual is either disomic (2X), trisomic (3X) or tetrasomic (4X) for GGA16. This 'loop' design also incorporates a dye swap.

first: Huaijun

last: Zhou


title: Real-time quantitative PCR analysis of hormone-receptor-negative primary breast tumors

status: Public on Oct 25 2013

city: Novato

first: Christina

last: Yau

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

summary: Total RNA was extracted from FFPE samples of 139 chemotherapy-naïve hormone-receptor-negative breast cancers pooled from three sample sources and assayed for the expression of 21 genes within two previously reported microarray-derived prognostic signatures in 6 RT-PCR multiplexes.

overall_design: RT-PCR gene expression profiling. Total RNA was extracted from 10 micron FFPE sections, and expression levels of the 21 genes of interest plus two reference genes were quantified with 6 multiplex RT-PCR TaqMan assays.

first: John

last: Sninsky

first: Shirley

last: Kwok

first: Alice

last: Wang

first: Amy

last: Degnim

first: James

middle: N

last: Ingle

first: Cheryl

last: Gillett

first: Andrew

last: Tutt

first: Fred

last: Waldman

first: Dan

last: Moore

first: Laura

last: Esserman

first: Christopher

middle: C

last: Benz


title: Comparison of microRNA Profiling Platforms (NanoString)

status: Public on Oct 22 2013

city: Toronto

last: Tam

state: Ontario

address: 661 University Avenue, Suite 510, MaRS Building, West Tower

department: Genome Technologies

institute: Ontario Institute for Cancer Research

summary: Global miRNA expression profiling of human malignancies is gaining popularity in both basic and clinically driven research. But to date, the majority of such analyses have used microarrays and quantitative real-time PCR.  With the introduction of digital count technologies, such as next-generation sequencing (NGS) and the NanoString nCounter System, we have at our disposal, many more options. To make effective use of these different platforms, the strengths and pitfalls of several miRNA profiling technologies were assessed, including a microarray platform, NGS technologies and the NanoString nCounter System.  These results were compared to gold-standard quantitative real-time PCR.

overall_design: Comparison of non-small cell lung cancer cell lines grown in vitro (n = 5) and in vivo (n = 5) as xenograft models.

first: Richard

last: de Borja

first: Ming-Sound

last: Tsao

last: McPherson


title: A genetic and functional investigation of the Zn2Cys6 transcription factors RSE2 and RSE3 in Podospora anserina

city: Gif-sur-Yvette

first: Annie

last: Sainsard-Chanet

address: Allée de la Terrasse

department: Régulation et Compartimentation des Fonctions Cellulaires

institute: Centre de Génétique Moléculaire du CNRS UPR 3404

summary: Abstract    In Podospora anserina, the two zinc cluster proteins RSE2 and RSE3 are essential for the expression of the gene encoding the alternative oxidase (aox) when the mitochondrial electron transport chain is impaired. In parallel they activated the expression of gluconeogenic genes encoding phosphoenolpyruvate carboxykinase (pck) and fructose-1,6-biphosphatase (fbp). Orthologues of these transcription factors are present in a wide range of filamentous fungi and no other role than the regulation of these three genes has been evidenced so far. In order to better understand the function and the organisation of RSE2 and RSE3, we conducted a saturated genetic screen based on the constitutive expression of the aox gene. We identified 10 independent mutations in 9 positions in rse2 and 11 in 5 positions in rse3. Deletions were generated at some of these positions and the effects analyzed. This analysis suggests the presence of central regulatory domains and a C-ter activation domain in both proteins. Microarray analysis revealed 598 genes that were differentially expressed in the strains containing gain- or loss-of-function mutations in rse2 or rse3.  It showed that in addition of aox, fbp and pck, RSE2 and RSE3 regulate the expression of genes encoding the alternative NADH dehydrogenase, a Zn2Cys6 transcription factor, a flavohemoglobin and various hydrolases. As a complement to expression data, a metabolome profiling approach revealed that both an rse2 gain-of-function mutation and growth on antimycin result in similar metabolic alterations in amino acids, fatty acids and α-ketoglutarate pools.

overall_design: With GPL10116: 7 conditions each with four biological replicates: wt, rse2Y326D, rse3G642V, rse2Y326D-rse3G642V, Δrse2, Δrse3 and Δrse2-Δrse3; common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5

first: Elodie

last: Bovier

first: Carole

middle: H

last: Sellem

first: Adeline

last: Humbert


title: Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

status: Public on Oct 21 2013

city: Saint Louis

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level.

overall_design:
Phytophthora sojae mycelium small RNAs were sequenced and aligned to the P. sojae genome for analysis.
*Raw data files (fastq) are unavailable for this study.

first: Noah

last: Fahlgren

first: Stephanie

last: Bollmann

first: Kristin

last: Kasschau

first: Josh

middle: T

last: Cuperus

first: Caroline

middle: M

last: Press

last: Sullivan

first: Elisabeth

last: Chapman

first: J

middle: S

last: Hoyer

first: Kerrigan

middle: B

last: Gilbert

first: Niklaus

last: Grünwald


title: Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora ramorum small RNA

first: James

overall_design:
Phytophthora ramorum mycelium small RNAs were sequenced and aligned to the P. ramorum genome for analysis.
*Raw data files (fastq) are unavailable for this study.


title: miR-134/487b/655 Cluster regulates TGF-β-induced epithelial-mesenchymal transition and drug resistance to Gefitinib by targeting MAGI2 in lung adenocarcinoma cells.

city: Tokyo

first: Kazuhiro

last: Kitamura

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Pulmonary Medicine and Oncology, Graduate School of Medicine

institute: Nippon Medical School

summary: Epithelial-mesenchymal transition (EMT) has recently been recognized as a key element of cell invasion, migration, metastasis, and drug resistance in several types of cancer, including non-small cell lung cancer (NSCLC). Our aim was to clarify microRNA (miRNA) -related mechanisms underlying EMT followed by acquired resistance to epidermal growth factor receptor tyrosine-kinase inhibitor (EGFR-TKI) in NSCLC. MiRNA expression profiles were examined before and after transforming growth factor-beta1 (TGF-β1) exposure in four human adenocarcinoma cell lines with or without EMT. Correlation between expressions of EMT-related miRNAs and resistance to EGFR-TKI gefitinib was evaluated. MiRNA array and quantitative RT-PCR revealed that TGF-β1 significantly induced overexpression of miR-134, miR-487b, and miR-655, which belong to the same cluster located on chromosome 14q32, in lung adenocarcinoma cells with EMT. MAGI2 (membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2), a predicted target of these miRNAs and a scaffold protein required for PTEN (phosphatase and tensin homolog), was diminished in A549 cells with EMT after the TGF-β1 stimulation. Overexpression of miR-134 and miR-487b promoted the EMT phenomenon and affected the drug resistance to gefitinib, whereas knockdown of these miRNAs inhibited the EMT process and reversed TGF-β1-induced resistance to gefitinib. Our study demonstrated that the miR-134/487b/655 cluster contributed to the TGF-β1-induced EMT phenomenon and affected the resistance to gefitinib by directly targeting MAGI2, whose suppression subsequently caused loss of PTEN stability in lung cancer cells. The miR-134/miR-487b/miR-655 cluster may be new therapeutic targets in advanced lung adenocarcinoma patients, depending on the EMT phenomenon.

overall_design: miRNA expression profiles before and after TGF-β1 exposure were assessed in the four  lung adenocarcinoma cell lines, A549, LC2/ad, PC3, and, PC9 by TaqMan miRNA arrays. Relative ratios of miRNAs in cells after TGF-β1 exposure were calculated when compared with the cells before TGF-β1 exposure.

first: Masahiro

last: Seike


title: DamID for MBD3 in human breast cancer cell lines

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

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

overall_design: Refer to individual Series


title: Ventral prostate in TRAP rats: Control vs. apocyin treatment

status: Public on Oct 18 2013

city: Nagoya

first: Shugo

last: Suzuki

state: Aichi

address: 1 Kawasumi, Mizuho-Cho, Mizuho-Ku

department: Experimental Pathology and Tumor Biology

institute: Nagoya City University Graduate School of Medical Sciences

summary: The gene expression profling between Control and apocynin 500 mg/L treatment  in ventral prostate lobe of Transgenic Rat for Adenocarcinoma of Prostate (TRAP) rats

overall_design: Two-condition experiment, Control vs. apocynin treatment. Biological replicates: 3 control rats, 3 apocynin-treated rats. Mixed 3 samples from each group on one array


title: Comparison of microRNA Profiling Platforms (RT-PCR)

first: Shirley

last: Tam

first: Richard

last: de Borja

first: Ming-Sound

last: Tsao

first: John

last: McPherson


title: Gene Expression Profile for the identification of miR-126 targets

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

summary:
"The analysis was designed to search for putative seed sequences for miR-126 in the 3’UTR of up-regulated genes. ECs were co-transfected
with anti-miR-126 and a plasmid vector bearing the GFP-coding sequence and three complementary sites for miR-126 downstream. As a consequence of the presence of miR-126 binding sites the GFP expression was under the control of miR-126. Fluorescente cells were the cells transfected with anti-miR-126 oligo. MiR-126 target enrichment analysis was performed on the basis of the Miranda database, as provided by Diana miRGen. Significance was estimated on the basis of hyper geometric distribution p-values comparing the occurrence of miR targets in the signature with respect to the universe, defined as the genes expressed in HUVEC. Frequency of log 2 ratio between the subset of mir-126 targets and the genes which are not targets of miR-126 were plotted, highlighting enrichment of the target of miR in differentially regulated genes. "

overall_design: 3 x biological replicates of transiently trasfected cells with anti miR-126 oligo (LNA), and controls oligo. 2 biological replicates for GFP are included as technical controls.

first: Roberto

last: Sessa

first: Luca

last: Primo

first: Claudio

last: Isella


title: Temporal gene expression analysis of the Brucella melitensis-infected bovine Peyer's patch

status: Public on Oct 15 2013

city: College Station

first: Leslie

middle: Garry

last: Adams

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

summary: In a time course study, we characterized global gene expression profile of B. melitensis-infected bovine Peyer patches in the first 4 h p.i. Microarray analysis revealed that 2,916 bovine genes were detected as differentially expressed (z-score p < 0.025) in loops inoculated with virulent B. melitensis 16M compared with controls between 15 min and 4 h post-infection. From these genes, 2,286 (78%) were up- and 630 (22%) were down-regulated. Specific genes and biological processes identified in this study will further help elucidate how both host and Brucella interact during the early infectious process to the eventual benefit of the pathogen and to the detriment of the naïve host.

overall_design: Microarrays were used to examine the transcriptional profiles of bovine intestinal Peyer patches infected with wild type Brucella melitensis 16M across five time points (15 min, 30 min, 1, 2 and 4 hours). Intestinal loops inoculated with cell culture medium were used as a control.  Experiments were performed in quadruplicate (bovine ligated ileal loops surgeries were performed with four calves), generating a total of 40 arrays.

first: Carlos

middle: A

last: Rossetti

first: Kenneth

last: Drake

first: Prasad

last: Siddavatam

first: Sara

last: Lawhon

first: Jairo

middle: E

last: Nunes

first: Tamara

last: Gull

first: Sangeeta

last: Khare

first: Robin

last: Everts

first: Harris

last: Lewin

first: L

middle: G


title: Taqman Low Density Arrays (TLDA) based microRNAs expression profile of mouse extrahepatic bileducts and gallbladders during a mouse model of biliary atresia.

city: Cincinnati

first: Jorge

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: Newborn Balb/c mice were injected with 1.5x10^6 fluorescent-forming units (ffu) of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth to induce experimental model of biliary atresia. The extrahepatic bile ducts including gallbladder were microdissected en bloc at 3, 7 and 14 days after rhesus rotavirus or saline injection. TaqMan® Array Rodent MicroRNA Card v2.0 (A and B) were used to screen microRNAs whose expression was differently regulated after rhusus rotavirus injection compare to the normal saline controls.

overall_design: microRNA expression profiling.  Each experimental conditon has 3 sets samples . Two to six extrahepatic bileducts were pooled prior to total RNA isolation depending on the size to ensure adequate RNA quantities to perform experiments quantifying microRNA expression.

first: Kazuhiko

last: Bessho

first: Kumar

last: Shanmukhappa

first: Rachel

last: Sheridan

first: Pranavkumar

last: Shivakumar

first: Reena

last: Mourya

first: Stephanie

last: Walters

first: Vivek

last: Kaimal

first: Eric

last: Dilbone

first: Anil

last: Jegga