title: Expression in the dorsal telencephalon of E13.5 conditional Dicer KO mice

status: Public on Aug 30 2012

city: Leipzig

first: Wolfgang

last: Enard

address: Deutscher Platz 6

country: Germany

institute: Max Planck Institute for evolutionary anthropology

summary: To study the effect of miRNA depletion in the embryonic forebrain, we isolated RNA from E13.5 dorsal telencephalon of mice homozygous for a floxed Dicer allele and hemizygous for the forebrain expressed Emx1Cre (Dicer KO mice). These samples were compared to littermates heterozygous for the floxed allele and hemizygous for Emx1Cre.

overall_design: 5 Dicerko mice and 4 controls, partly littermates, no technical replicates

first: Davide

last: De Pietri Tonelli


title: PCR array of inflammatory cytokines and receptors in mouse lungs with NF-kappaB RelA mutant in alveolar epithelial cells during LPS stimulation

status: Public on Aug 03 2012

city: Boston

first: Kazuko

last: Yamamoto

state: MA

address: 72 East Concord Street

department: Pulmonary Center

country: USA

institute: Boston University School of Medicine

summary: A murine model of RelA mutated throughout the alveolar epithelium was generated. Mice were anesthetized and intratracheally instilled with 50μg LPS into the left lung lobe. Mice were euthanized after 6 hours after instillation, and left lung lobes were collected to isolate RNA.  We used SABioscience Mouse Inflammatory Cytokines and Receptors PCR Array to evaluate whether the expressions of lung cytokines and receptors during LPS stimulation are dependent on alveolar epithelial NF-κB RelA or not.

overall_design: qPCR gene expression profiling. RNA were collected from six different mouse lungs in each genotype (wild-type and alveolar epithelial RelA mutant). Equal amount of RNA (200ng) was pooled from six different mouse lungs, and 1μg of total RNA (1.2μg) was used to the PCR array.

first: Joseph

middle: P

last: Mizgerd


title: RosR is a haloarchaeal-specific transcription factor required for the response to extreme oxidative stress in Halobacterium salinarum NRC-1.

status: Public on Aug 13 2012

city: Durham

first: Nicholas

middle: A

last: Gillum

state: North Carolina

institute: Duke University

summary:
Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV and gamma radiation.  Genome-wide dynamics alteration of gene the GRN has been implicated in such resistance. However, the molecular function of transcription regulatory proteins involved in this response remains unknown. Here we have leveraged several existing GRN and systems biology datasets for H. salinarum to identify and characterize a novel winged helix-turn-helix transcription factor, VNG0258H, as a regulator required for reactive oxygen species resistance in this organism. This protein appears to be unique to the haloarchaea at the primary sequence level. Quantitative growth assays in a deletion mutant strain implicate VNG0258H in extreme oxidative stress resistance. According to time course gene expression analyses, this transcription factor is required for the appropriate dynamic response of nearly 300 genes to reactive oxygen species damage from paraquat and hydrogen peroxide. These genes are predicted to function in repair of oxidative damage to proteins and DNA. in vivo DNA binding assays (ChIP-qPCR) demonstrate that VNG0258H binds DNA to mediate gene regulation. Together these results suggest that VNG0258H is a novel archaeal transcription regulatory protein that regulates gene expression to enable adaptation to the extremely oxidative, hypersaline niche of H. salinarum. We have therefore renamed VNG0258H as RosR, for reactive oxygen species regulator.
Data in this archive are linked to the publication Sharma KS, Gillum NA, Schmid AK 2012

overall_design: The Δura3 and ΔrosR strains were grown to mid-logarithmic phase (OD600 ~ 0.5) in CM supplemented with uracil. For the H2O2 time courses, 4 ML culture aliquots were removed for RNA extraction at three time points prior to the addition of H2O2 (-40 min, -20 min, 0min) and five time points following H2O2 addition (10 min, 20 min, 40 min, 60 min, 80 min). Paraquat time courses were prepared similarly with the exception that additional time points were taken at 2h, 8h, and 24 h after the addition of paraquat. RNA from two biological replicate time courses were prepared, along with a dye filip.

first: Kriti

last: Sharma

first: Amy

last: Schmid


title: affy_zeawall_ril2_maize: ZeaWall Project, defavorable parent F271

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary: affy_zeawall_ril2_maize - affy_zeawall_ril2_maize - Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). The defavorable parent F271 was studied in complement and is the object of this last array. Expression studies will be investigated in ear internode at two stages (emerging tassel and early silking).-Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). The defavorable parent F271 was also studied in complement and is the object of this last array.Expression study will be investigated in ear internode at two stages emerging tassel and early silking stages with two replicates. Plants were cropped at INRA Lusignan (Vienne, France) in 2009 in a bloc design with two four-row replicates. Below-ear internodes of five representative RIL plants of one row in each replicate were harvested at the two stages and pooled.

overall_design: 4 arrays - maize; time course

first: Stephanie

last: Huguet

first: Yves

last: Barrière

first: Audrey

last: Courtial

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Difference expression analyses before and after human fucosyltransferase gene 1 transfection into ovarian  cancer clear cell line (Human cancer array)

status: Public on Aug 02 2012

city: Shenyang

first: Ziwei

last: Feng

address: Sanhao street

country: China

institute: China Medical University

summary: 75% ovarian epithelial tumor overexpresses Lewis y antigen, which notably strenthen such malignant biological behaviors as metastasis, drug resistance and proliferation. The key enzyme of Lewis y synthesis is human fucosyltransferase gene 1(hfut1).  Through transfecting hfut1 into Lewis y low expressing cell line RMG-I, we got a pair of cell lines. We hypothesized that Lewis y antigen plays a major role in ovarian canceration . Using gene arrays, we comprehensively profiled mRNA differential expression between fut1-pretransfected and posttransfected clear cell of human epithelial OvCa. We expected that over-expression of lewis y antigen would lead to higher expression of genes associated with growth, metastasis,proliferation and so on.

overall_design: we established ovarian tumor cell line RMG-I-H by stably transfecting  human fucosyltransferase gene 1 into cell line RMG-I. RMG-I-H overexpresses Lewis y antigen, which is known as a cancer-related tetrasaccharide antigen. We profiled for tumor-associated gene expression both cells pretransfected and posttransfected.

first: Z

first: L

last: Zhu

first: B

last: Lin


title: CcpA, a Pleiotropic Key Regulator in Butanol-producing Clostridium acetobutylicum ATCC 824

city: Shanghai

first: Cong

last: Ren

address: 300 Feng Lin Road

institute: Institute of Plant Physiology and Ecology, SIBS, CAS.

summary: Clostridium acetobutylicum is a typical bacterium of major importance to industrial butanol production. In order to dissect the regulatory network pertaining to the industrial application of this bacterium, catabolite control protein A (CcpA) was investigated for its global function by DNA microarray.It showed that CcpA of C. acetobutylicum controls hundreds of genes, not only carbon metabolism, but also solvent production and sporulation in the life cycle.The results here demonstrated that CcpA is an important pleiotropic regulator related to some specific physiological and biochemical process in butanol-producing C. acetobutylicum.

overall_design: In order to enable a global understanding of the regulatory roles of CcpA when fermenting mixed sugars, which is of great significance in utilization of lignocellulosic hydrolysates, D-glucose plus D-xylose were used as the carbon sources in fermentation for microarray analysis. Microarray analysis was performed at four time points:the time point M and L were chosen both in acidogenic phase, while the time point T and S were chosen in shift phase (from acidogenesis to solventogenesis) and solventogenic phase, respectively.One-color microarray assays were performed.Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The ratio of transcript level between wildtype and mutant can been achieved using the formula: 2^(value of wildtype)/2^(value of ccpA mutant).

first: Yang

last: Gu

first: Shiyuan

last: Hu

first: Yan

last: Wu

first: Sheng

last: Yang

first: Weihong

last: Jiang


title: Genome Haploidisation with Chromosome 7 Retention in Oncocytic Follicular Thyroid Carcinoma

status: Public on Aug 29 2012

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

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

summary:
Recurrent non-medullary thyroid carcinoma (NMTC) is a rare disease. We initially characterized 27 recurrent NMTC: 13 papillary thyroid cancers (PTC), 10 oncocytic follicular carcinomas (FTC-OV), and 4 non-oncocytic follicular carcinomas (FTC). A validation cohort composed of benign and malignant (both recurrent and non-recurrent) thyroid tumours was subsequently analysed (n = 20).

Methods
Data from genome-wide SNP arrays and flow cytometry were combined to determine the chromosomal dosage (allelic state) in these tumours, including mutation analysis of components of PIK3CA/AKT and MAPK pathways.

Results
All FTC-OVs showed a very distinct pattern of genomic alterations. Ten out of 10 FTC-OV cases showed near-haploidisation with or without subsequent genome endoreduplication. Near-haploidisation was seen in 5/10 as extensive chromosome-wide monosomy (allelic state [A]) with near-haploid DNA indices and retention of especially chromosome 7 (seen as a heterozygous allelic state [AB]). In the remaining 5/10 chromosomal allelic states AA with near diploid DNA indices were seen with allelic state AABB of chromosome 7, suggesting endoreduplication after preceding haploidisation. The latter was supported by the presence of both near-haploid and endoreduplicated tumour fractions in some of the cases. Results were confirmed using FISH analysis. Relatively to FTC-OV limited numbers of genomic alterations were identified in other types of recurrent NMTC studied, except for chromosome 22q which showed alterations in 6 of 13 PTCs. Only two HRAS, but no mutations of EGFR or BRAF were found in FTC-OV. The validation cohort showed two additional tumours with the distinct pattern of genomic alterations (both with oncocytic features and recurrent).

Conclusions
We demonstrate that recurrent FTC-OV is frequently characterised by genome-wide DNA haploidisation, heterozygous retention of chromosome 7, and endoreduplication of a near-haploid genome. Whether normal gene dosage on especially chromosome 7 (containing EGFR, BRAF, cMET) is crucial for FTC-OV tumour survival is an important topic for future research.

overall_design: 28 thyroid tumors from 27 patients were profiled by SNP array. Comparisons between different types were made.

first: Oosting

last: Jan

first: Corver

middle: E

last: Willem

first: vanWezel

last: Tom

first: Morreau

last: Hans


title: Muscleblind-Like 2 Mediated Alternative Splicing in the Developing Brain

status: Public on Aug 16 2012

city: Santa Cruz

first: Lily

last: Shiue

state: CA

address: 1156 High Street

department: MCD Biology

institute: UCSC

summary: We have characterized the MBNL2-dependent changes in expression and alternative splicing by comparing hippocampi from MBNL2 deltaE2/deltaE2 and WT mouse brains.

overall_design: 6 total samples were analyzed: brains from 3 WT and 3 MBNL2 deltaE2/deltaE2 female mice, all 2-3 months of age.

first: Charizanis

last: Konstantinos

first: Swanson

last: Maurice


title: Cell cycle motif decoy oligos

status: Public on Aug 23 2012

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Single-stranded oligos listed below (and the corresponding reverse compliment) were synthesized and annealed:
E2F: CTAGATTTCCCGCGGATC (decoy); CTAGACTCTGCTCGGATC (scrambled)
KTGGYRSGAA: CTAGATTCCCGCCAAGGATC (decoy); CTAGACAGCTACTCCGGATC (scrambled)
TGCGCANK: CTAGACATGCGCAGGATC (decoy); CTAGATCACAGGCGGATC (scrambled)
CCAATNNSNNNGCG: CTAGACGCCCTCCGATTGGGGATC (decoy); CTAGATGCACGCTCGGTCCGGATC (scrambled)
ACTWSNACTNY: CTAGAGGAGTTGTAGTGGATC (decoy); CTAGAGATAGTGTGTGGGATC (scrambled)
HeLa cells were propagated in DMEM (Invitrogen) plus 10% FBS and transfected with 0.5 uM of double-stranded DNA. Total RNA was extracted with TRIzol (Invitrogen) from HeLa cells 2 d after transfection of the indicated decoy oligo or scrambled oligo in duplicate. RNA was amplified using the Ambion Amino Allyl MessageAmp II aRNA kit. For each motif, decoy oligo transfected samples (labeled with Cy5) and the corresponding scrambled oligo transfected samples (labeled with Cy3) were competitively hybridized to HEEBO microarrays as described (http://www.microarray.org/sfgf/heebo.do).

first: Adam

last: Adler


title: Mutation Mapping of 31 Streptococcus suis strains

status: Public on Aug 09 2012

city: Beijing

first: Xiao

last: Zheng

address: Liuzi five hao

institute: China CDC

type: Genome variation profiling by genome tiling array

summary:
Identification of Genes and Genomic Islands Correlated with High Pathogenicity through Tilling Microarray-Based Comparative Genomics in S. suis.

Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. S. suis isolates have been categorized into groups of different levels of pathogenicity, with sequence type (ST) ST1 clonal complex strains having a higher degree of virulence than other STs. However, the genetic basis of the differences in pathogenicity is still poorly understood. In this study, a comprehensive genomic comparison of 31 S. suis strains from different clinical sources with the genome sequence of the high pathogenicity (HP) strain GZ1 was conducted using NimbleGen’s tilling microarray platform.

overall_design: Comparative genomic analysis on the 31 S. suis strains of different serotypes and ST types through tilling arrays.

first: Han

first: Changyun

last: Ye

first: Jianguo

last: Xu


title: PCR array of inflammatory cytokines and receptors in mouse lungs with NF-kappaB RelA mutant in alveolar epithelial cells during pneumococcal pneumonia

first: Kazuko

last: Yamamoto

summary: A murine model of RelA mutated throughout the alveolar epithelium was generated. Mice were anesthetized and intratracheally instilled with 106 CFU of Streptococcus pneumoniae serotype 3 into the left lung lobe. Mice were euthanized after 15 hours after instillation, and left lung lobes were collected to isolate RNA.  We used SABioscience Mouse Inflammatory Cytokines and Receptors PCR Array to evaluate whether the expressions of lung cytokines and receptors during pneumococcal pneumonia are dependent on alveolar epithelial NF-κB RelA or not.

first: Joseph

last: Mizgerd


title: Functional control of the Candida albicans cell wall by catalytic protein kinase A subunit Tpk1

status: Public on Aug 07 2012

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

summary: The cyclic AMP-protein kinase A pathway has a central role in the biology of Candida albicans, a prominent fungal pathogen of humans. The two catalytic subunits for cyclic AMP-dependent protein kinase, Tpk1 (orf19.4892) and Tpk2 (orf19.2277), have divergent roles, and most studies indicate a more pronounced role for Tpk2. Here we dissect two Tpk1-responsive properties: adherence and cell wall integrity. Homozygous tpk1/tpk1 mutants are hyperadherent, and a Tpk1 defect enables biofilm formation in the absence of Bcr1, a central transcriptional regulator of biofilm adhesins. Microarray analysis revealed an enrichment for cell wall and surface functions among Tpk1-repressed genes, and overexpression of individual target genes indicates that cell surface proteins Als1, Als2, Als4, Csh1, and Csp37 contribute to Tpk1-regulated adherence. Tpk1 is also required for cell wall integrity, but has no role in the cell wall integrity gene expression response. Interestingly, increased expression of the adhesin gene ALS2 conferred a cell wall defect, as manifested in hypersensitivity to the cell wall inhibitor caspofungin and a shallow cell wall structure. Our findings indicate that Tpk1 has a central role in C. albicans cell wall properties that is exerted through repression of select cell surface protein genes.

overall_design: Two-color microarrays using a closed-loop experimental design to determine the effects of a ∆tpk1 deletion in the absence or presence of the antifungal Caspofungin (CF)

first: Saranna

last: Fanning

first: W

first: Cecile

last: Beaurepaire

first: JP

last: Suhan

first: Aaron

last: Mitchell


title: Gene expression changes in testes from Abcg8 knockout mice compared to wild-type mice or to Abcg8 knockout mice where plant sterol entry was blocked by ezetimibe

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: Abcg8 knockout mice, fed chow, are infertile. These mice also are susceptible to absorption and retention of xenosterols contained in the diet. Ezetimibe, a blocker of dieary sterol entry, can reverse the fertility in Abcg8 knockout mice. In order to identify if the xenosterols resulted in disruption of a specific set of genes in the testes, we compared wild-type testes, Abcg8 knockout testes, or testes from Abcg8 knockout mice fed chow supplemented with 0.005% ezetimibe. To identify genes of interest, we reasoned that any causative gene expression changes seen in Abcg8 knockout mice fed chow, resulting in xenosterol exposure and accumulation, leading to infertilty, would be reveresed back to a pattern seen in the wild-type mice, when Abcg8 knockout mice are raised on chow containing ezetimibe (which prevents xenosterol absorption in the intestine). The target of this drug, Npc1l1, is not expressed in the testes.

overall_design: Testes from wild-type mice, Abcg8 knockout mice, and Abcg8 knockout mice fed chow supplemented with ezetimibe were analyzed.

first: Shailendra

middle: B

last: Patel

first: Curzio

last: Solca


title: Effect of obacunone on Salmonella Typhimurium transcriptome

status: Public on Aug 21 2012

city: College Station

first: Bhimanagouda

middle: S

last: Patil

state: TX

address: 1500 Research Pkwy, Ste A120

institute: Texas A&M University

summary:
Obacunone is a limonoids present in Citrus species. We previously reported that obacunone was inhibitory to the cell-cell signaling in Vibrio harveyi and Escherichia coli O157:H7. In the present work we evaluated the effect of obacunone on the food borne pathogen Salmonella Typhimurium LT2 using cDNA microarray.
The results demonstrate that obacunone exerts an antivirulence effect on S. Typhimurium LT2 by repressing SPI1 and SPI2. Furthermore, the effect of obacunone seems to be dependent upon EnvZ.

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

platform_organism: Salmonella enterica subsp. enterica serovar Typhi str. Ty2

platform_organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18

overall_design: One condition experiment, obacunone treated versus DMSO treated. Biological replicates: 3 control, 3 treatment, hybridized in dye-swapped design

first: Amit

last: Vikram

first: G

middle: K

last: Jayaprakasha

first: Palmy

middle: R

last: Jesudhasan

first: Suresh

middle: D

last: Pillai


title: Benzo[a]pyrene-induced changes in microRNA-mRNA networks

city: Maastricht

first: Daneida

last: Lizarraga

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

summary: The microarray contains 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs. The other 8024 reporters represent microRNAs from other species. cDNA was generated using 1 μg of total RNA per sample. RNA was labeled only with Hy3 containing dye using the microRNACURY LNA™ microRNA Hy3 Power labeling kit (Exiqon, Denmark) according to the manufacturer’s protocol in a total volume of 25 μl. To adjust the volume to 100 μl, a hybridization buffer provided in miRCURY LNA™ microRNA Array, 5th generation kit (Exiqon, Denmark) was used.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: For each biological experiment, one hybridization per time point was conducted and one sample per array. In total, 24 arrays were used for 8 different conditions (BaP or control, at 6, 12, 24 and 48 hours).

first: Stan

last: Gaj

first: Karen

last: Brauers

first: Jos

middle: C

last: Kleinjans

first: Joost

middle: H

last: van Delft


title: LncRNA expression profiles of 59 tumorous liver tissues derived from patients with hepatocellular carcinoma (HCC)

first: Wei

last: Li

address: 136 Yi Xue Yuan Road

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University;

summary: Long noncoding RNAs (lncRNAs) are a class of non-coding RNAs longer than 200 nt that function in endogenous gene regulation and tumorigenesis. Hepatocellular carcinoma (HCC) is a heterogeneous disease with different treatment outcome. It is a challenge to develop a prognostic marker to identify HCC patients who are at greatest risk for recurrence or death. In this study, we try to screen lncRNAs whose expression levels are associated with recurrence or death of HCC patients through an extensive lncRNA profiling study on a cohort of 59 HCC patients.

overall_design: For these experiments, we used RNA extracted from 59 HCC tissues and 20 normal livers. Total RNAs from the 20 normal livers were pooled and used as a reference for all microarray experiments. For each microarray experiment, Cy5-labeled probes derived from the DNase-treated total RNA from each HCC sample was hybridized against Cy3-labeled probes derived from common reference on Arraystar Human LncRNA Microarray (Arraystar, Rockville, USA).   LncRNAs whose expression was significantly associated with disease-specific survival and time to recurrence were selected based on microarray data. The univariate Cox proportional hazards model was used to assess the association of lncRNAs with survival. We computed a statistical significance level (P value) for two endpoints—the time to cancer-related death and time to recurrence, based on univariate Cox proportional hazards models in BRB-ArrayTools version 4.2.0.


title: Transcriptome Analysis of the Lates calcarifer Immune Response Towards Cryptocaryon irritans Infection

status: Public on Aug 08 2012

city: Bangi

first: Abdul Munir

last: Abdul Murad

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: Cryptocaryon irritans is the causative agent of white spot disease that infects virtually all marine teleost including Lates calcarifer. We undertook to gain an informative snapshot of the host’s transcriptomic response during the course of infection. Liver and spleen cDNA libraries-based L. calcarifer cDNA microarray were used as a tool to oversee the infection response. Parasites infection was carried out on juvenile fish for four days, and total RNA was extracted from the daily harvested infected liver. cDNAs synthesized from respective daily pooled total RNA were labelled and hybridized onto the L. calcarifer chip. The majority of infection-induced genes are acute phase proteins (APP) with hepcidin, C-type lectin and serum amyloid A being the most up-regulated products.

overall_design: Two-condition experiment: Control vs. Infected. Time series experiment: 4 time points (Day 1-Day 4 post infection). Biological replicates: 3 control, 3 infected per day. Two-color arrays (Cy3=daily control, Cy5=daily infected). Six arrays (including 3 dye-swap arrays) per each time series.

first: Choon

last: Khoo

first: Abdul

middle: M

last: Murad

first: Adura

last: Mohd-Adnan


title: BRE silencing effect on gene expression profile of human umbilical cord perivascular (HUCPV) progenitor cells

city: Hong Kong

first: Ka Ho Kenneth

last: Lee

email: kaholee@cuhk.edu.hk, elve@cuhk.edu.hk

address: 126 Lo Kwee Seong Integrated Biomedical Science Building, CUHK, Shatin, N.T.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Analysis of HUCPV progenitor cells following BRE silencing using BRE-siRNA. BRE (Brain and reproductive organ-expressed) protein is also known as TNFRSF1A (tumor necrosis factor receptor superfamily, member 1A) modulator and BRCC45 (BRCA-1 containing complex subunit 45). Results identify gene targets of BRE.

overall_design: Total RNA extracted from 3 separate cell cultures that have been transfected with BRE-siRNA and 3 separate cell cultures that have been transfected with ctl (scrambled)-siRNA.

first: Ka

first: Elve

last: Chen


title: Expression data of spleens from chickens infected with different Newcastle Disease Viruses

status: Public on Aug 15 2012

city: yangzhou

first: Zenglei

last: Hu

address: 12 East Wenhui Road

institute: Yangzhou University

summary:
Genotype VIId NDV is characterized by severe tissue damage in chicken lymphoid organs compared to other virulent strains. However, biological basis of this unusual pathological phenotype is unknown. Host response is associated with pathogenicity of Newcastle Disease Virus (NDV). We aim to determine the contribution of host response to the severe tissue destruction in the lymphoid system caused by genotype VIId NDV.
We used microarray analysis to evaluate the global transcriptional response in the spleen of chickens infected with genotype VIId NDV strain JS5/05 and genotype IV NDV Herts/33.

overall_design: Chickens were inoculated with JS5/05 or Herts/33 or mock-infected. At day 2 post infection, spleens were isolated from three chickens per group for RNA extraction and hybridization on Affymetrix microarrays. Samples were named as follows: JS5/05 (I4_1_NS,I4_2_NS,I4_3_NS), Herts/33 (H1_NS,H2_NS, H3_NS), control (C1_NS, C2_NS, C3_NS).

first: Jiao


title: Genome-wide expression profiling in a Fusarium graminearum lacking FgVelB, a velvet complex gene

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary:
Using a 3'-tiling microarray covering the whole F. graminearum genes, we carried out genome-wide expression analyses of both a wild type and a FgVelB deletion strainn of F. graminearum  at a sexual stage (3 days after perithecial induction on carrot agar)
Our study is the first report elucidating regulatory pathways controlled by FgVelB in Fusarium graminearum.

overall_design: A total of 4 chips were used for microarray. Total RNAs were extracted from perithecia and/or ground mycelia formed on carrot agar cultures of a self-fertile wild-type and a self-sterile FgVelB-deleted strain of F. graminearum with two biological replicates.

first: Jungkwan

first: Kilseon

last: Myong

first: Jung-Eun

first: Hee-Kyoung

first: Sung-Hwan

last: Yun

first: Yin-Won


title: Identification of candidate genes affecting juvenile wood density in Pinus radiata

city: Canberra

first: Xinguo

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

country: Australia

institute: CSIRO

summary: Wood density is a foundamental quality trait for structural timber, bioenergy and pulp industries. We investigated genes differentially transcribed in radiate pine juvneile trees with distinct wood density using cDNA microarrays.

overall_design: Radiata pine trees were selected from a progeny trial planted at Flynn, Australia. Based on the gravitical measurement of wood cores, 12 families with highest and lowest density each were selected, representing two groups of trees with contrasting wood density. One individual with higher or lower density were further sampled in each selected family. Developing xylem tissues of selected trees were sampled in autumn (April) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. Wood cores of the sampled trees were further measured using SilviScan 2. Total RNA extracted from ten developing xylem tissues with confirmed distinct density in each tree group were pooled into two bulks (five trees each), and the two bulks of HD were compared with two LD bulks in the microarray experiment (named the bulk experiment). Six developing xylem tissues with the most distinct density from each tree group were further chosen. Six xylem tissues with HD were individually compared with bulked six xylem tissues with LD in the second microarray experiment (named individual experiment). These two different pooling strategies can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.

first: Harry

middle: X

last: Wu

first: Simon

middle: G

last: Southerton


title: Gene expression changes in Dhcr7 knockout brain, lung and liver at E18.5 compared to wild-type embryos

first: Michael

last: Falduto

summary:
The genetic defect underlying the human Smith-Lemli-Opitz dysmorphological disorder is loss-of-function mutations affecting the cholesterol synthesis enzyme dehydrocholesterol delta7 reductase, DHCR7. Dhcr7 knockout mice recapitulate the biochemical characteristics, but all knockout pups die within 14h of birth. Tissues of knockout mice accumulate the precursor sterol, 7-dehydrocholesterol, and show reduced levels of cholesterol (J. Clin. Invest. (2001) 108: 905-915). We compared the global gene expression changes in lung, liver and brain from knockout mice to those seen from organs harvested from same-pregnancy wild-type embryos, harvested before birth (E18.5). Since the P0 knockout pups die, we expected that there would be significant changes in gene expression between knockout and wild-type organs, and further comparing the altered genes in common to brain, lung and liver would point to a common mechanistic pathway where disruption of normal sterol synthesis in all cells leads to pathophysiology.
Remarkably, these data show that the global gene expression between knockout and wild-type organs is hardly altered, despite the complete loss of cholesterol synthesis. There are so few genes that are altered, and furthermore, those that are altered are very limited in sharing similarities in all three tissues. This suggests that disorganized gene expression is not the cause of the early neonatal lethality.

overall_design: Dhcr7+/- females were mated with Dhcr+/- males, and timed pregnancy obtained. At E18.5, pregnant dams were sacrificed, and embryos harvested, organs removed and RNA extracted, and all embryos were genotyped. Matching wild-type and knockout embryos were taken from each pregnancy, and two females yielded all genotypes used herein.

first: Shailendra

last: Patel

first: Hongwei

last: Yu


title: MicroRNA expression in thioglycollate and alternatively activated

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

summary: Macrophage activation must be tightly controlled to prevent overzealous responses that cause self-damage. MicroRNAs have been shown to promote classical macrophage activation by blocking concomitant anti-inflammatory signals and transcription factors, but can also place restraints on activation by preventing excessive TLR-signalling. In contrast, the microRNA profile associated with alternatively activated macrophages and their role in regulating wound-healing or anti-helminthic responses has not yet been described. Utilizing an in vivo model of alternative activation, in which adult Brugia malayi nematodes are surgically implanted in the peritoneal cavity of mice, we examined the profile of microRNA expression in these alternatively activated macrophages and compared this to alternatively activated IL-4 receptor knockout macrophages and thioglycollate elicited macrophages.

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

overall_design: Peritoneal macrophages from BALB/c wild type or IL-4 receptor knockout mice were elicited with thioglycollate or using nemtodes (peritoneal implant of Brugia malayi). The latter leads to a population of alternatively activated macrophages. Microarray analysis was used to examine the microRNA profile of WT alternatively activated macrophages (n = 4), IL-4 receptor knockout alternatively activated macrophages (n = 4), WT thioglycollate elicited macrophages (n = 3) and IL-4 receptor knockout thioglycollate elicited macrophages (n = 3).

middle: J


title: Effects of a diet high in monounsaturated fat and a full Mediterranean diet on PBMC whole genome gene expression and plasma proteins

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: This study aimed to identify the effects of replacement of saturated fat (SFA) by monunsaturated fat (MUFA) in a western-type diet and the effects of a full Mediterranean (MED) diet on whole genome PBMC gene expression and plasma protein profiles. Abdominally overweight subjects were randomized to a 8 wk completely controlled SFA-rich diet, a SFA-by-MUFA-replaced diet (MUFA diet) or a MED diet. Concentrations of 124 plasma proteins and PBMCs whole genome transcriptional profiles were assessed. Consumption of the MUFA and MED diet, compared with the SFA diet, decreased expression of oxidative phosphorylation (OXPHOS) genes, serum lipids and plasma Connective Tissue Growth Factor, myoglobin and Apo B concentrations. The MED diet additional lowered plasma α-2-macroglobulin concentration compared with the SFA diet. Within the MED diet group concentrations of several pro-inflammatory proteins were lowered. We conclude that MUFA as replacement of SFA in a western-type diet or in a MED diet had similar effects on lowering expression of OXPHOS genes. We hypothesize that replacement of SFA by MUFA increased metabolic health as reflected by lowered serum lipids and certain plasma proteins, thereby reducing metabolic stress and OXPHOS activity in PBMCs. The MED diet may have additional anti-atherogenic effects by lowering concentrations of pro-inflammatory plasma proteins.

overall_design: Expression profiling by array

first: Susan

last: van Dijk

first: Edith

last: Feskens

first: Marieke

last: Bos

first: Lisette

last: de Groot

first: Jeanne

last: de Vries

last: Müller

first: Lydia

last: Afman


title: Expression data from Maize leaves post inoculation of Sporisorium reilianum.

city: Harbin

first: Tao

address: mucai street

institute: Northeast Agricultural University

summary: Head smut of maize, which is caused by the Sporisorium reilianum f. sp. Zeae (Kühn), has been a serious disease in maize. In order to find head smut resistant candidate genes, microarrays were used to monitor the gene expression profiles between disease resistant near isogenic lines (NIL) L282 and L43, highly resistant inbred line Q319 and highly susceptible inbred line Huangzao4 after 0 to7 days post inoculation of S.reiliana by artificial inoculation method.

overall_design: Maize leaves were selected at 0d, 1d, 2d, 4d, 7d post inoculation for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain different expression genes of different varieties at each inoculation stage in order to find head smut resistant candidate genes.

first: Z

last: Wang


title: MeDIP-chip from clinical cervical tissues in promoters

status: Public on Aug 06 2012

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

type: Methylation profiling by genome tiling array

summary: Utilizing methylation DNA immunoprecipitation (MeDIP) coupled with promoter tiling arrays, we analyzed the methylation profiles of pooled DNA from human cervical carcinoma and normal cervix

overall_design: Cervical carcinoma compaire with normal cervix

first: Rui-Lan

last: Huang

first: Yu-Zhi

last: Chan

first: Yu-Ping

last: Laio

first: Hui-Chen

first: Yi-Te

last: Yo

first: Tai-Kuang

last: Chao

first: Shin-Ping

last: Lin

first: Ya-Wen

first: Hsuan-Cheng


title: Expression analysis of the starvation and recovery response of Nitrosomonas europaea ATCC 19718

city: Cambridge

first: Paul

last: Berube

address: 15 Vassar Street

department: Civil and Environmental Engineering

institute: Massachusetts Institute of Technology

summary:
Investigation of the whole genome gene expression level changes relative to exponential phase growth in Nitrosomonas europaea ATCC19718 after 12 hours ammonia starvation, 144 hours ammonia starvation, and 20 minutes following ammonia addition to starved cells.
The ammonia monooxygenase of chemolithotrophic ammonia oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine.  The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB1,2).  Several AOB, including N. europaea, also posess a divergent monocistronic copy of amoC (amoC3) of unknown function.  Previous work suggested a possible functional role for amoC3 in N. europaea during recovery from extended ammonia starvation as part of the σE- stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation.  We here used global transcription analysis to show that expression of amoC3 is part of a general post-starvation cellular response system in N. europaea.  We also found that amoC3 is required for efficient exit from prolonged ammonia starvation, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions.  Deletion of the σ32 global stress response regulator demonstrated that the heat shock regulon also plays a significant role in mediating the recovery of N. europaea from starvation.  These findings provide the first described phenotype associated with the divergent AmoC3 subunit which appears to function as a stress responsive subunit capable of maintaining ammonia oxidation activity under stress conditions.

overall_design: A twelve chip study using total RNA recovered from four timepoints for each of three biological replicates of wild-type cultures of Nitrosomonas europaea ATCC 19718.  Total RNA was obtained from each biological culture replicate during exponential growth, following 12 hours ammonia starvation, 144 hours ammonia starvations, and 20 minutes following ammonia addition to starved cells.

first: David

last: Stahl


title: Discovery of a phenotypic switch regulating sexual mating in the opportunistic fungal pathogen Candida tropicalis

status: Public on Aug 28 2012

city: Providence

first: Richard

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

summary: Sexual reproduction can promote genetic diversity in eukaryotes, and yet many pathogenic fungi have been labeled as obligate asexual species. It is becoming increasingly clear, however, that cryptic sexual programs may exist in some species, and that efficient mating requires the necessary developmental switch to be triggered. In this study we investigate Candida tropicalis, an important human fungal pathogen that has been reported to be asexual. Significantly, we demonstrate that C. tropicalis uses a phenotypic switch to regulate a cryptic program of sexual mating. Thus, diploid a and α cells must undergo a developmental transition to the mating-competent form, and only then does efficient cell-cell conjugation take place resulting in the formation of stable a/α tetraploids. We show that both the phenotypic switch and sexual mating depend on the conserved transcriptional regulator Wor1, which is regulated by temperature in other fungal species. In contrast, C. tropicalis mating occurs efficiently at both 25 °C and 37 °C, suggesting that it could occur in the mammalian host and have direct consequences for the outcome of an infection. Transcriptional profiling further reveals that ≈400 genes are differentially expressed between the two phenotypic states, including the regulatory factor Wor1. Taken together, our results demonstrate that C. tropicalis has a unique sexual program, and that entry to this program is controlled via a Wor1-mediated, metastable switch. These observations have direct implications for the regulation and evolution of cryptic sexual programs in related fungal pathogens.

overall_design: 4 biological replicates of both the white (CAY1504) and opaque (CAY2275) states of C. tropicalis a cells are included on this array. All are hybridized against a universal reference sample, which consists of the combined RNA from all 8 replicates used on this array.

first: Allison

last: Porman

first: Kevin

last: Alby

first: Matthew

last: Hirakawa


title: Gene expression profiles in black soybean sprouts: 0.5 cm long vs 5 cm long

status: Public on Aug 10 2012

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

summary: To explore the mechanism underlying antioxidant activity of extracts from black soybean sprouts 0.5 cm long, Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K was used to compare mRNA expression between the black soybean sprouts 0.5 cm long (n=4) and the black soybean sprouts 5 cm long (n=4). GO term enrichment analysis showed ten up-regulated genes (BE823689.1_567, GMFL01-02-F14-R_381, GMFL01-03-G22-R_364, GMFL01-14-M12-R_553, GMFL01-51-M23-R_265, AW757007.1_297, AW761420.1_260, BI788389.1_501, BQ273202.1_332 and GMFL01-10-I14-F_701) in the 0.5 cm seedlings were associated with response to oxidative stress. qRT-PCR assay confirmed the up-regulation of these ten genes in sprouts 0.5 cm long. In conclusion, these ten genes may contribute to antioxidant activity of sprout extract.

overall_design: Gene expressions in black soybean sprouts were measured using Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K. Four independent experiments were performed in each group using different sprout sample.

first: Jixiang

first: Congfen

last: He

first: Yinmao

last: Dong

first: Yuanhong

last: Zhuang

first: Shaomin

last: Wei


title: Toxicogenomic Responses of Nanotoxicity in Daphnia magna Exposed to Silver Nitrate and Coated Silver Nanoparticles

status: Public on Aug 05 2012

city: Boston

first: Helen

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

summary: Applications for silver nanomaterials in consumer products are rapidly expanding, creating an urgent need for toxicological examination of the exposure potential and ecological effects of silver nanoparticles (AgNPs).   The integration of genomic techniques into environmental toxicology has presented new avenues to develop exposure biomarkers and investigate the mode of toxicity of novel chemicals.  In the present study we used a 15k oligonucleotide microarray for Daphnia magna, a freshwater crustacean and common indicator species for toxicity, to differentiate between particle specific and ionic silver toxicity and to develop exposure biomarkers for citrate-coated and PVP-coated AgNPs.  Gene expression profiles revealed that AgNO3 and AgNPs have distinct expression profiles suggesting different modes of toxicity.  However, the gene expression profiles of the different coated AgNPs were similar revealing similarities in the cellular effects of these two particles.  Major biological processes disrupted by the AgNPs include protein metabolism and signal transduction.  In contrast, AgNO3 caused a downregulation of developmental processes, particularly in sensory development.  Metal responsive and DNA damage repair genes were induced by the PVP AgNPs, but not the other treatments.  In addition, two specific biomarkers were developed for the environmental detection of PVP AgNPs; although further verification under different environmental conditions is needed.

overall_design: We exposed Daphnia magna to the 1/10 LC50 and LC25 of citrate coated and PVP-coated Ag nanoparticles and Ag+ as AgNO3 for 24-h.  For each exposure condition, we performed 6 replicate exposures with 5 individuals in each.  All exposures were compared to a unexposed laboratory control.

first: James

last: Lazorchak

first: Christopher

last: Impellitteri

first: Bonnie

last: Blalock

first: Kim

last: Rogers

first: H

last: Allen

first: Alexandre

last: Loguinov

first: J

last: Heckman

first: Shekar

last: Govindasmawy


title: Interaction between gibberellins and brassinosteroids during etiolated growth in Arabidopsis.

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

summary: The proper transition between the skotomorphogenic and photomorphogenic developmental programs is key for seedling survival and it is therefore tightly regulated. Besides light, which is the major cue that triggers this transition, several hormone pathways participate in this control, mainly antagonizing the light effect. Two of these hormones are gibberellins (GA) and brassinosteroids (BR). Both hormones promote the skotomorphogenesis and prevent photomorphogenesis, as evidenced by the partially de-etiolated phenotype caused by GA or BR deficiency, or by a blockage in the respective signaling pathways. We have previously shown that BR mediate GA activity in the control of this transition. For instance, treatment of dark-grown, GA-deficient seedlings with BRs was able to partially restore morphological phenotypes such as hypocotyl growth, and importantly to restore completely the molecular phenotype of CAB2 and RbcS gene expression. On the contrary, GA-treatment did not alter the same phenotypes in the BR deficient det2 mutant. Thus, the aim of this study was to investigate to what extent BRs mediate GA activity in dark-grown seedlings, and for that purpose we have the examined global changes in gene expression caused by treatment with GA and BRs in BR- and GA-deficient seedlings, respectively.

overall_design: We performed two sets of experiments, each one including three different samples. The first experiment included dark-grown, WT Col-0 mock-treated seedlings, or seedlings treated with either the GA biosynthesis inhibitor paclobutrazol (PAC) or with PAC+epibrassinolide (EBR). In this experiment, PAC samples were labelled with Cy3 and compared to WT and PAC+EBR samples, which were labelled with Cy5. Two biological repeast were performed. The second experiment included dark-grown, WT Col-0 seedlings and the det2-1 mutant, which was either mock-treated or treated with GA3. Two biological replicates were performed, in the first one the WT and det2-1+GA3 were labelled with Cy3 and the det2-1 sample with Cy5. The reverse labelling was used in the second replicate.

first: M

last: Blazquez

first: D


title: Transcriptional responses of normal human dermal fibroblasts (NHDF) induced by Borrelia burgdorferi sensu stricto

city: Strasbourg

first: Frédéric

last: Schramm

address: 3, rue Koeberlé

institute: EA4438 Physiopathologie et médecine translationnelle, Groupe borréliose de Lyme

summary: The aim of the study was to compare the global transcriptional responses elicited in NHDF cells by three different strains of Borrelia burgdorferi ss (the  agent of Lyme borreliosis), representative of different stages in the life cycle of Borrelia: one reference strain isolated from a tick (strain N40), and two invasive strains isolated from skin biopsy of erythema migrans (strain Pbre c4) and acrodermatitis chronica atrophians skin lesions (strain 1408 c1).

overall_design: Three different experimental conditions have been tested: (1) unstimulated NHDF vs NHDF stimulated by Borrelia strain N40 / (2) unstimulated NHDF vs NHDF stimulated by Borrelia strain Pbre c4 / (3) unstimulated NHDF vs NHDF stimulated by Borrelia strain 1408 c1. There is 2 biological replicates for each condition. All NHDF stimulation have been performed in independent experiments.

first: Sophie

last: Nadau

first: Nicolas

last: Meyer


title: Genes involved in synthesis of lipoteichoic acids are induced when  Bifidobacterium animalis subsp. lactis BB12 is incubated with Human Enterocyte-Like Caco-2 Cells

status: Public on Aug 01 2012

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

summary: Bifidobacterium animalis subsp. lactis BB12 is a widely used probiotic bacterium. However the molecular mechanism by which this bacterium confers positive health effects to the host is largely unknown. The importance of lipoteichoic acids (LTA) in the cross-talk between the bacteria and human enterocyte-like Caco-2 cells was investigated in the present study. A microarray-based analysis of gene expression revealed induction of genes encoding enzymes involved in the synthesis of lipoteichoic acids of BB12. This observation was confirmed in phenotypic experiments, where a specific galactofuranosyl carbohydrate epitope present in the structure of lipoteichoic acids of BB12 was used as a detection marker. An exopolysaccharide EPS/LTA extract isolated from BB12 and commercially available pure LTAs from the human pathogen S. pyogenes were tested in competitive adhesion experiments. The adhesion of B. animalis subsp. lactis BB12 to Caco-2 cells was inhibited in presence of LTA. The strongest inhibition was observed in the concentration range 0.5-10 ug/ml for LTAs from S. pyogenes and 5-10 ug/ml for EPS/LTA extract from BB12. The inhibitory concentrations in both cases likely reflect the physico-chemical properties of LTAs with the highest efficacy below the critical micelle concentration, and therefore we ascribe the main inhibitory effect to LTAs for the BB12 isolated EPS/LTA extract as well. In conclusion we present increased biosynthesis of lipoteichoic acids of BB12 co-incubated with human Caco-2 cells and evidence that LTA serve as important cell wall factors involved in adhesion to these human enterocyte-like cells.

sample_organism: Bifidobacterium animalis subsp. lactis BB-12

overall_design: The experimental design is described under the single sample. Data desribed in the manuscript (as briefly described under Summary/Abstract) were validated by qPCR.

first: Ondrej

last: Valina

first: Christel

last: Garrigues

first: Karsten

last: Kristiansen

first: Thomas

last: Leser


title: An Emerging Threat to Honey Bees from the Parasitic Phorid Fly Apocephalus borealis

city: San Francisco

first: Charles

last: Runckel

department: Biochemistry

institute: UCSF

summary:
Pathogen detection microarrays analyzing honeybee samples taken after parasitization with a predatory fly, oligos correspond to specific pathogens or pathogen families of viruses, bacteria, fungi, protists, and other parasites
Samples were analyzed with the E-Predict analysis package.

platform_organism:
Fungi
unidentified entomopoxvirus
unidentified baculovirus
Iridovirus
Cypovirus
Birnaviridae
Luteovirus
Black beetle virus
unclassified viruses
Densovirinae
Ascovirus
Betabaculovirus
Gammabaculovirus

overall_design: Honey bees parasitized with the phorid fly Apocephalus borealis were screened for viral and non-viral pathogens by microarray.

first: Core

last: Andy

first: Runckel

last: Charles


title: Response to dexamethasone in A549, U2OS, and Nalm6

status: Public on Jul 31 2012

first: Samantha

middle: B.

last: Cooper

department: Cellular and Molecular Pharmacology

institute: UC San Francisco

summary: Transcriptional profiling of A549, U2OS, and Nalm6 comparing dexamethason with vehicle control, 3 hour timepoint

overall_design: Two conditions (treated and untreated), three cell types. Biological replicates: 3 treated and 3 vehicle controls for each cell type. Each array is a two-color hyb of treated vs control in a single cell type (9 arrays total). One dye swap for each condition


title: Regulatory element copy number differences shape primate expression profiles

last: Lee

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

summary: Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.

sample_organism:
Macaca mulatta
Pan troglodytes
Pongo abelii
Homo sapiens
Gorilla beringei

overall_design: 17 primate samples were run on a custom Agilent arrayCGH platform against a single human reference (HapMap sample, NA10851). The array is designed based on human genome build hg18. All probes on the array have 100% identity to the human, chimpanzee, and rhesus macaque reference genomes. Thus, hybridization bias between the human reference and nonhuman primate samples should be minimized. These arrayCGH runs were used to determine copy number differences between species in order to study their role on gene expression differences between the same species.

first: Rebecca

last: Iskow

first: Omer

last: Gokcumen

first: Alexej

last: Abyzov

first: Joanna

last: Malukiewicz

first: Qihui

last: Zhu

first: Ann

middle: T

last: Sukumar

first: Athma

last: Pai

first: Ryan

last: Mills

first: Lukas

last: Habegger

first: Darren

last: Cusanovich

first: Meagan

last: Rubel

first: George

last: Perry

first: Mark

last: Gerstein

first: Anne

last: Stone

first: Yoav

last: Gilad


title: Comparison of Ets2-null and control ES cell derived lineages

status: Public on Jul 01 2012

city: Houston Road

first: Robert

middle: Joel

last: Schwartz

state: Texas

address: 4800 Calhoun

department: Biology and Biochemistry

institute: University of Houston

summary: Ets2-null ES cells are defective in differentiating into cardiac myocytes, evidenced by the lack of spontaneous beating, cardiac transcription factors and structural proteins. With the Phalanx mouse Onearray v2, we compared the gene expression profiles of cells derived from Ets2-null and wildtype ES cells.

overall_design: Standard embryoid body culture protocol was used to induce differentiation of murine ES cells. On the 10th day, replicates of either Ets2-null or control wildtype EB culture were collected in Trizol for total RNA extraction. Microarray was preformed by Phalanx.

first: Yu

last: Liu

first: John

last: Harger


title: Expression Data from Brucella abortus strain 2308 and isogenic abcR1 abcR2 mutant cells

status: Public on Jun 15 2012

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
abcR1 and abcR2 produce two regulatory RNA molecules, that are produced during stationary phase growth.
We used custom-made Affymetrix B. abortus strain 2308 derived GeneChips to compare the gene expression properties of wild type and isogenic abcR1 abcR2 double mutant cells.

overall_design: B. abortus strain 2308 or abcR1 abcR2 double mutant cells were grown to stationary phase growth, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of abcR1 and abcR2 RNA species.

first: R

last: Roop


title: Expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes or control M199 medium.

city: Dublin

first: Graham

middle: P

last: Pidgeon

address: St. James' Hospital

country: Ireland

institute: Trinity College Dublin

summary:
Obesity is linked to increased mortality from many cancer types, and oesophageal adenocarcinoma displays one of the strongest epidemiological associations.
The aim of this study was to dissect molecular pathways linking obesity with oesophageal adenocarcinoma and to determine if obesity is linked to increased aggressiveness of this disease.

overall_design: Affymetrix microarrays were used to identify altered signaling pathways in an oesophageal adenocarcinoma cell line following co-culture with isolated adipocytes from viscerally obese oesophageal adenocarcinoma patients (n=6).

first: Emma

last: Allott

first: Melissa

last: Morine


title: Expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants or control M199 medium.

overall_design: Affymetrix microarrays were used to identify altered signaling pathways in an oesophageal adenocarcinoma cell line following co-culture with visceral adipose tissue from viscerally obese oesophageal adenocarcinoma patients (n=6).


title: Gene expression profiles of spontaneous gastric tumors in the antrum of the stomach of 30,60, and 90 day old CEA424-SV40 -T antigen transgenic mice.

status: Public on Aug 02 2012

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

institute: University of Bonn

summary: Analysis of global gene expression in the antral portion of the stomach in control  and mice with a developing tumor to get further insight into the exact tumor type and the influence of local gene expression.

overall_design: Total RNA obtained from tissue samples from the antrum. Follow up of gene expression over the time of the tumor development

first: Georg

last: Enders


title: The transcriptional response to the inactivation of the PaMpk1 and PaMpk2 MAP kinase pathways in Podospora anserina

status: Public on Jun 12 2012

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

institute: Institut de Génétique et Microbiologie UMR 8621

summary: To gain insight into the targets of the PaMpk1 and PaMpk2 MAPK, we here determine the transcription profile of the mutants inactivated for PaMpk1, PaMpk2 and PaNox1 during vegetative growth at stages where they are required for proper development, in comparison with wild type. Microarrays representing 10556 coding sequences (CDS) predicted by the P. anserina genome project were used to estimate the transcription profiles (transcriptomes) during vegetative growth of three-day-old homokaryotic cultures of ∆PaMpk1, ∆PaMpk2 and the IDC343 PaNox1 mutants in comparison to wild type. Three zones corresponding to three developmental stages can be defined in such wild-type culture. From the growing edge the colony, the first five milimeters (zone 1) are constituted of hyphae lacking pigment and growing on the substrate. In this zone, very few hyphae are aerial and appressorium-like structures are not differentiated. In the second intermediate zone (zone 2), profuse aerial hyphae and appressorium-like structures are differentiated. This zone is about 7 mm wide and corresponds to the area where most perithecia are differentiated during sexual development of heterokaryotic mycelia. The zone that is most distal from the edge lack aerial hyphae (zone 3) accumulates a larger amount of pigment and differentiates few perithecia during sexual reproduction. It is about 1 cm wide. These three zones are easily visualized by the naked eye for sample recovery. The ∆PaMpk1, ∆PaMpk2  and the IDC343 PaNox1 mutants lack a clear zonation, since the three genes are involved in the signalling of stationary phase . Materials from these mutants were nonetheless recovered as three samples corresponding to the same zones, based mostly on the distance from the growing edge but also from subtle morphological differences.

overall_design: With GPL10116 : reference design, 4 strains (WT, ∆PaMpk1, ∆PaMpk2  and IDC343 PaNox1 with 3 growth conditions (zone1,2 and 3) each with four biological replicates, the 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: Evelyne

last: Coppin

first: Philippe

last: Silar


title: ZBTB32 Is an Early Repressor of the CIITA MHC Class II Gene Expression during B Cell Differentiation to Plasma Cells

city: Atlanta

first: Jeremy

last: Boss

state: GA

address: 1510 Clifton Rd

department: Micobiology and Immunology

institute: Emory University

summary: Primary murine B cells were stimulated with IL2, IL5, LPS to induce B cell differentiation for 24 hours. RNA was extracted from control and differentiated B cell to compare gene expression.

overall_design: Murine B cells (CD43-) were purfied from 5 weeks old mice splenocytes. And purified B cells were stimulated with IL2, IL5, LPS for 24 hours.

first: Hyesuk

last: Yoon


title: Gene expression data from phosphinothricin (PPT) treated Medicago truncatula root nodules

status: Public on May 09 2012

city: Porto

first: Helena

last: Carvalho

address: Rua do Campo Alegre,823

department: MBNA

country: Portugal

institute: Instituto de Biologia Molecular e Celular

summary:
Nitrogen assimilation in plants is a tightly regulated process that integrates developmental and environmental signals. The legume-rhizobial symbiosis results in the formation of a specialized organ called root nodule, where the rhizobia fixes atmospheric nitrogen into ammonia. Ammonia is assimilated by the plant enzyme glutamine synthetase, which is specifically inhibited by PPT. The expression of key genes related to the regulation of root nodule metabolism will likely be affected by glutamine synthetase inhibition.
We used microarrays to detail the global programme of gene expression in response to Glutamine synthetase inhibition in root nodules and identified genes differentially expressed over a time course.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Medicago truncatula nodulated plants (20 days post inoculation) were treated with 0.25 mM of PPT. Root nodules were harvested at 4, 8 and 24 hours after PPT application. As a control, root nodules collected just before PPT application were used (PPT 0h). Three biological replicates consisting of pools of root nodules harvested from five distinct plants were used for RNA extraction and hybridization on Affymetrix GeneChips.

first: Ana

last: Seabra

first: Patrícia

last: Pereira

first: Jörg

last: Becker


title: Association of microRNAs with CD68 and NOS2 in IBD tissues.

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary:
We analyzed the association of CD68 and NOS2 mRNA expression with microRNAs in IBD tissues.  For this analysis, data was LOESS normalized in R.  Data was then imported into Partek Genomics Suite and Batch effects caused by day to day variability (Dategroup of array charateristic) were corrected.  We did not have mRNA expression data for CD68 and NOS2 for all of the samples, therefore those samples were not used for analysis.
We identified several microRNAs associated with CD68 and NOS2 expression.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total mRNA was extracted from colon tissue that was flash frozen immediately after surgery.  A total of 114 tissues were used for microarray analysis.  Briefly, 5 ug of RNA were biotin labeled and hybridized to OSU-CCC microRNA microarrays version 2.0.  We then analyzed associations with CD68 and NOS2 mRNA expression.

first: Jane

last: Sohn

first: Curtis

last: Harris


title: Chicken neural crest and neural plate

status: Public on Jun 01 2012

first: Yukinori

last: Endo

address: 30 Convent Drive, MSC 4370, Room 402

department: Laboratory of Cell and Developmental Biology

institute: NIDCR, NIH

summary: Neural cest cells are a transient stem cell-like population appearing during vertebrate embryonic development. Generation of the cranial neural crest is known to require a balanced combination of FGF and BMP levels. However, it is poorly understood how the functions of such growth factors are controlled in the extracellular spaces. Anosmin is an extracellular matrix protein implicated in FGF signaling and mutated in Kallmann syndrome. Here, we demonstrate that anosmin  (Gga.14976.1.S1_at, clone ChEST132d10) is synthesized locally in the cranial neural crest of chicken embryos and is essential for cranial neural crest formation. Anosmin upregulates FGF8 and BMP5 gene expression; it also enhances FGF8 activity while inhibiting BMP5 and WNT3a signaling. Taken together, our data establish that the matrix protein anosmin is required for cranial neural crest formation, with funtional modulation of FGF, BMP, and WNT.

overall_design: Cranial neural folds (NF) and ventral neural plates (NP) were dissected from Hamburger & Hamilton stage 8 (HH8) embryos (80 to 114 embryos, n=4), and total RNA was analyzed using a GeneChip chicken genome arrays (Affymetrix)

first: Hiroko

last: Ishiwata-Endo

first: Kenneth

last: Yamada


title: Human Tissues: pancreatic cancer vs. pancreatic non-tumoral tissues

city: Cordoba

first: German

middle: Alexis

last: Gonzalez

state: Cordoba

address: Av. Armada Argentina 3555

department: School of Engineering

country: Argentina

institute: Catholic University of Cordoba

summary: Transcriptional profiling of pancreatic tumors comparing to adjacent non-tumoral pancreatic tissue by two strategies. The first strategy implies a traditional microarray assay, while the second involves a previous Suppression Subtractive Hybridization (SSH) and then the traditional microarray assay. Goal was to determine differences in gene expression profile in tumor samples by both strategies.

overall_design: Two-condition experiment, tumoral vs. non-tumoral tissues. Biological replicates: 6 tumoral replicates, 6 non-tumoral replicates. The same replicates for both strategies.

first: Jaime

last: Espinoza

first: Carolina

last: Bizama

first: Felipe

last: Benavente

first: Edgardo

last: Salvatierra

last: Gutiérrez

first: Elmer

last: Fernández

first: Iván

last: Roa

first: Osvaldo

last: Podhajcer

first: Manuel

last: Gidekel


title: Immune response of germline-ablated P. pacificus exposed to S. marcescens

status: Public on Apr 18 2012

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

summary: Transcriptional profiling of germline-ablated P. pacificus worms exposed to S. marcescens for 8 hours versus germline-ablated P. pacificus exposed to the control E. coli OP50. First goal was to identify genes that are involved in immune response of germline-ablated P. pacificus when exposed to S. marcescens. Second, this was compared to longevity-regulating genes in germline-deficient animals (see series GSE37331).

overall_design:
One-condition experiments.
Germline ablated P. pacificus worms exposed to S. marcescens for 8 hours versus germline-ablated P. pacificus exposed to the control E. coli OP50. 4 biological replicates for each condition, including 2 dye-swaps.

first: Robbie

last: Rae

first: Ralf

last: Sommer


title: Exposure of microaerobic Campylobacter jejuni to 10 micromolar NOC-5 & NOC-7

status: Public on May 23 2012

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

summary: Two batch cultures of Wild-type C. jejuni NCTC 11168 were grown in 100 ml volumes of Mueller-Hinton broth in 250 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % Oxygen, 10 % Carbon dioxide, 80 % Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ºC. When mid-exponential phase was reached 0.010 mM NOC-5 & NOC-7 was added to one of the cultures. After a 15 minute exposure samples of both treated and untreated cells were harvested into phenol/ethanol to stabilize the RNA and total RNA was purified using Qiagen’s RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design:
Batch cultures of Wild-type C. jejuni NCTC 11168 were grown in 100 ml volumes of Mueller-Hinton broth in 250 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % Oxygen, 10 % Carbon dioxide, 80 % Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ºC. When mid-exponential phase was reached 0.25 mM GSNO was added to half of the cultures. After a 10 minute exposure, 30 ml samples of both treated and untreated cells were mixed immediately on ice with 3.56 ml 100% ethanol and 185 µl phenol to stabilize the RNA. The cells were subsequently harvested by centrifugation. Total RNA was purified by using a Qiagen RNeasy Mini kit as recommended by the supplier.    Equivalent amounts of RNA (15 μg) from control and test cultures were used as template for synthesis of labelled cDNA. Labelling was done by using dCTP nucleotide analogues containing either Cy3 or Cy5 fluorescent dyes.  RNA was primed with 9 μg pd(N)6 random hexamers (Amersham Biosciences).  For annealing, the mixture was incubated for 10 min at 65oC and then 10 min at room temperature.  Each reaction mixture (0.5 mM dATP, dTTP and dGTP, 0.2 mM dCTP, 0.1 mM DTT (Invitrogen) and 1 mM Cy3-dCTP or Cy5-dCTP, total volume 25ul) was incubated for 3 h at 42 oC with 200 U of Superscript III RNase-H Reverse Transcriptase (Invitrogen). The reaction was terminated by the addition of 5u1 mM NaOH and heating the tube to 65 oC for 10 min to hydrolyse the RNA.  Then it was neutralised with 5ul 1M HCl and 1 M TE (pH 8). Purification of cDNA was done with a PCR purification kit (Qiagen).  The cDNA was eluted and resuspended in 30 μl elution buffer (Qiagen, supplied in kit).

Each slide set (control slide and dye-swap) was prepared as follows: For control slide Cy3-dCTP labelled control cDNA was mixed with Cy5-dCTP labelled test cDNA. For   dye-swap slide Cy5-dCTP labelled control cDNA was mixed with Cy3-dCTP labelled test cDNA. This is made for compensate possible differences in the labelled nucleotides incorporation. The slides used were C. jejuni OciChip® arrays from Ocimum Biosolutions.  The cDNA mixture for each slide was dried by evaporation for approximately 35 min in a SPD 121P SpeedVac® (Thermo Savant, Waltham, MA, USA)  The dry cDNA was resuspended in pre-warmed (42ºC) salt-based hybridisation buffer (Ocimum Biosolutions) and was heated to 95 °C for 3 min and then placed on ice for 3 min.  The spoted area of the slide (located with an array finder) was enclosed within a gene frame (MWG/Ocimum).  The cDNA suspension was distributed through the inner space of the gene frame and enclosed with an air-tight coverslip.  The slides were incubated for 16-24 hours at 42º C in sealed MWG hybridisation chambers shaken in a water bath. After incubation, gene frames and coverslips were removed and slides washed sequentially in 2x, 1x, 0.2x y 0.1x SSC buffer, by shaking for 5 minutes at 80 rpm at 37º C pre-warmed buffer. (2x buffer was supplemented with 1% SDS). Then the slides were dried by centrifugation at 250 x g for 5 min.  Slides were scanned using an Affymetrix 428 scanner.

The processing of images and quantification of the microarrays signal was done using software from Biodiscovery Inc (Imagene, version 4.0 and Genesight, version 4.0). Spots with signal intensity lower than background or other significant blemishes were eliminated from subsequent processing. Mean values from each channel were then log2 transformed and normalised using the Subtract by Mean method to remove intensity-dependent effects in the log2 (ratios) values.  The Cy3/Cy5 fluorescent ratios were calculated from the normalised values. Significance analysis of the data used the Student’s t test to determine the probability that the average of the experimental replicates was significantly different from the average of the control replicates. p-values for the data were calculated by treating each slide as a repeat using Genesight 4.  Genes differentially regulated ≥ 2-fold and displaying a p-value of ≤ 0.05 were defined as being statistically significant and differentially transcribed.

first: Carlos

last: Avila-Ramirez


title: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (CGH)

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

institute: Center for Applied Medical Research (Cima)

summary: Using high-resolution genomic microarray analysis, a distinct genomic profile was defined in 114 samples from patients with splenic marginal zone lymphoma (SMZL). Notably, deletion or uniparental disomy of chromosome 7q were detected in 39% of SMZLs but in only 9 of 170 (5%) mature B-cell lymphomas (p<10-6). The presence of unmutated IgVH genes, genomic complexity, 17p13-P53 deletion and 8q gain including MYC gene, but not 7q deletion, were correlated with shorter overall survival. Extensive mapping analyses narrowed down the commonly deleted region to 2.7 Mb. in 7q32.1-q32.2 from SND1 to COPG2 genes. High-throughput sequencing analysis of the 7q32 deleted segment in SMZL cells did not identify bi-allelic deletions, insertions or clear pathogenic mutations, but detected six single nucleotide changes in IRF5 (n=2), TMEM209 (n=2), CALU (n=1) and ZC3HC1 (n=1). Comparative expression analysis found that IRF5, TMEM209 and CALU genes had down-regulated expression in lymphomas with 7q32 deletion vs. non-deleted tumors. Ectopic expression of IRF5 in marginal-zone lymphoma cells decreased cell proliferation and induced apoptosis. These results indicate that small deletions, insertions and/or point mutations inactivating genes within 7q32 are not common events in SMZL. Further studies are required to evaluate the putative role of IRF5 in SMZL pathogenesis.

overall_design: CGH analysis was performed for 76 Splenic Marginal Zone lymphoma patient samples. Production and validation of the array, hybridization methods and analytical procedures have been described elsewhere: Snijder AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001;29:263-264.

first: Eloy

middle: F

last: Robles

first: Anton

last: Parker

first: Javier

last: Martinez-Useros

first: Maria

last: Mena

first: Raquel

last: Malumbres

first: Lorena

last: Fontan

first: Jose

middle: I

last: Martinez-Ferrandis

first: Xabier

last: Aguirre

first: Susana

last: Catarino

first: David

last: Arteta

first: Lourdes

last: Osaba

first: Manuela

last: Mollejo

first: Jesus

last: Hernandez-Rivas

last: Calasanz

first: Masanori

last: Daibata

first: A

last: Karpas

first: Martin

last: Dyer

last: Prosper

first: Esperanza

last: Vizcarra

first: Miguel

middle: A

last: Piris

last: Oscier

last: Martinez-Climent


title: Gene regulatory networks involved in early embryonic Silurana tropicalis development

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Gene set and sub-network enrichment analysis provides an integrated approach for identifying gene regulatory networks underlying development. Anuran development is a coordinated process, and levels of mRNA are first dominated by maternally deposited genes, followed by active transcription of embryonic genes as the embryo undergoes morphogenesis and organ formation.  The objectives of this study were to characterize early gene regulatory networks underlying Silurana tropicalis development.  A custom Agilent 4 x 44 K microarray was developed to characterize networks during early development (1, 17, 36, 96 hpf).  Cluster analysis revealed that each stage showed unique gene expression profiles and that 1 hpf was most different than the other three stages.  There were > 8000 unique gene probes (p<0.01, FDR = 5%) that were differentially expressed between 1 hpf (2 cell stage) and 17 hpf and > 2000 gene probes differentially expressed between 36 hpf and 96 hpf.  Genes higher in abundance (>100-fold) at 1 hpf compared to 17 hpf included oocyte-specific histone RNA stem-loop-binding protein 2, mitogen-activated protein kinase 14, and cyclin B5, suggesting these transcripts are maternally inherited or actively transcribed at fertilization.  Gene ontology revealed that genes involved in nucleosome assembly, cell division, pattern specification, neurotransmission, and general metabolism were increasingly regulated throughout development, consistent with active development. In the period between 17-36 hpf, gene networks that play a role in organogenesis and organ function, including those related to the heart (heart morphogenesis, central nervous system (olfactory bulb development, dopamine metabolism), and kidney (renal reabsorption, water balance) were activated while between 36-96 hpf, networks involving in gut development, immune responses, lipid metabolism, hormone signaling, and brain development were prevalent. This study increases understanding of the spatiotemporal S. tropicalis embryonic development using gene regulatory networks.

overall_design: Gene expression analysis was performed with four biological replicates for four developmental stages (n = 16). Stages were NF stages 2, 16, 34, and 46.

first: Valerie

middle: S

last: Langlois


title: IL-4 stimulation of Dicer deficient bone-marrow derived macrophages in vitro

status: Public on Mar 17 2012

city: Seattle

first: James

last: Sissons

state: WA

address: 307 Westlake Avenue N # 500

institute: Seattle BioMed

summary: Macrophages were derived from the bone-marrow of 3 x fl/+ Dicer LysCre +/- (wild-type) and 3 x fl/fl Dicer  LysCre +/- mice and stimulated with IL-4 (50ng/mL) for 72h. Total RNA was isolated and analyzed by gene array.

overall_design: In this experiment, we derived Dicer deficient bone-marrow macrophages using Dicer fl/+ LysM-Cre by Dicer fl/+ crossed mice to obtain Dicer fl/fl LysM-cre  progeny (and Dicer deficient macrophages). Next, we studied the effects of IL-4 stimulation in macrophage with a deficiency in Dicer/microRNAs.

first: Alan

last: Aderem


title: Exposure of oxygen limited Campylobacter jejuni to 10 micromolar NOC-5 & NOC-7

first: Robert

last: Poole

summary: Batch cultures of Wild-type C. jejuni NCTC 11168 were grown in 200 ml volumes of Mueller-Hinton broth in 250 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % Oxygen, 10 % Carbon dioxide, 80 % Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ºC. When mid-exponential phase was reached 0.010 mM NOC-5 & NOC-7 was added to one of the cultures. After a 15 minute exposure samples of both treated and untreated cells were harvested into phenol/ethanol to stabilize the RNA and total RNA was purified using Qiagen’s RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.

overall_design:
Batch cultures of Wild-type C. jejuni NCTC 11168 were grown in 200 ml volumes of Mueller-Hinton broth in 250 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % Oxygen, 10 % Carbon dioxide, 80 % Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ºC. When mid-exponential phase was reached 0.25 mM GSNO was added to half of the cultures. After a 10 minute exposure, 30 ml samples of both treated and untreated cells were mixed immediately on ice with 3.56 ml 100% ethanol and 185 µl phenol to stabilize the RNA. The cells were subsequently harvested by centrifugation. Total RNA was purified by using a Qiagen RNeasy Mini kit as recommended by the supplier.    Equivalent amounts of RNA (15 μg) from control and test cultures were used as template for synthesis of labelled cDNA. Labelling was done by using dCTP nucleotide analogues containing either Cy3 or Cy5 fluorescent dyes.  RNA was primed with 9 μg pd(N)6 random hexamers (Amersham Biosciences).  For annealing, the mixture was incubated for 10 min at 65oC and then 10 min at room temperature.  Each reaction mixture (0.5 mM dATP, dTTP and dGTP, 0.2 mM dCTP, 0.1 mM DTT (Invitrogen) and 1 mM Cy3-dCTP or Cy5-dCTP, total volume 25ul) was incubated for 3 h at 42 oC with 200 U of Superscript III RNase-H Reverse Transcriptase (Invitrogen). The reaction was terminated by the addition of 5ul 1 mM NaOH and heating the tube to 65 oC for 10 min to hydrolyse the RNA.  Then it was neutralised with 5ul 1 M HCl and 1 M TE (pH 8). Purification of cDNA was done with a PCR purification kit (Qiagen).  The cDNA was eluted and resuspended in 30 μl elution buffer (Qiagen, supplied in kit).

Each slide set (control slide and dye-swap) was prepared as follows: For control slide Cy3-dCTP labelled control cDNA was mixed with Cy5-dCTP labelled test cDNA. For   dye-swap slide Cy5-dCTP labelled control cDNA was mixed with Cy3-dCTP labelled test cDNA. This is made for compensate possible differences in the labelled nucleotides incorporation. The slides used were C. jejuni OciChip® arrays from Ocimum Biosolutions.  The cDNA mixture for each slide was dried by evaporation for approximately 35 min in a SPD 121P SpeedVac® (Thermo Savant, Waltham, MA, USA)  The dry cDNA was resuspended in pre-warmed (42ºC) salt-based hybridisation buffer (Ocimum Biosolutions) and was heated to 95 °C for 3 min and then placed on ice for 3 min.  The spoted area of the slide (located with an array finder) was enclosed within a gene frame (MWG/Ocimum).  The cDNA suspension was distributed through the inner space of the gene frame and enclosed with an air-tight coverslip.  The slides were incubated for 16-24 hours at 42º C in sealed MWG hybridisation chambers shaken in a water bath. After incubation, gene frames and coverslips were removed and slides washed sequentially in 2x, 1x, 0.2x y 0.1x SSC buffer, by shaking for 5 minutes at 80 rpm at 37º C pre-warmed buffer. (2x buffer was supplemented with 1% SDS). Then the slides were dried by centrifugation at 250 x g for 5 min.  Slides were scanned using an Affymetrix 428 scanner.

The processing of images and quantification of the microarrays signal was done using software from Biodiscovery Inc (Imagene, version 4.0 and Genesight, version 4.0). Spots with signal intensity lower than background or other significant blemishes were eliminated from subsequent processing. Mean values from each channel were then log2 transformed and normalised using the Subtract by Mean method to remove intensity-dependent effects in the log2 (ratios) values.  The Cy3/Cy5 fluorescent ratios were calculated from the normalised values. Significance analysis of the data used the Student’s t test to determine the probability that the average of the experimental replicates was significantly different from the average of the control replicates. p-values for the data were calculated by treating each slide as a repeat using Genesight 4.  Genes differentially regulated ≥ 2-fold and displaying a p-value of ≤ 0.05 were defined as being statistically significant and differentially transcribed.

first: Carlos

last: Avila-Ramirez

middle: K


title: Hierarchical regulation in a KRAS pathway-dependent transcriptional network revealed by a reverse-engineering approach (RAS-ROSE and ROSE with siRNA)

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

summary: RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here we used a reverse-engineering approach in an ovarian cancer model to reconstruct KRAS oncogene-dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT-PCR and Western Blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions we analysed growth parameters and transcriptional deregulation in the KRAS-transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype.

overall_design: RAS-ROSE cells and ROSE cells treated with Scrambled siRNA

first: I

last: Stelniec

first: R

last: Schäfer

first: N


title: Hierarchical regulation in a KRAS pathway-dependent transcriptional network revealed by a reverse-engineering approach (7TF and control)

overall_design: RAS-ROSE cells were treated with siRNA against 7 transcription factors or controls,


title: Transcriptomics of rapid cold-hardening and cold shock recovery in Sarcophaga bullata

status: Public on Mar 14 2012

city: Columbus

first: Nicholas

middle: M

last: Teets

state: OH

address: 300 Aronoff Laboratory, 318 W. 12th Ave.

department: Department of Entomology

country: USA

institute: Ohio State University

summary: The ability to rapidly respond to changes in temperature is critical for insects and other ectotherms living in variable environments. In a physiological process termed rapid cold-hardening (RCH), exposure to non-lethal low temperature allows many insects to significantly increase their cold tolerance in a matter of minutes to hours. Additionally, there are rapid changes in gene expression and cell physiology during recovery from cold injury, and we hypothesize that RCH may modulate some of these processes during recovery. In this study, we used a cDNA microarray to examine the molecular mechanisms of RCH and cold shock (CS) recovery in the flesh fly, Sarcophaga bullata. With our custom 2-color array, we measured expression of ~15,000 ESTs during RCH and during recovery from cold shock. Surprisingly, no transcripts were upregulated during RCH, and likewise, RCH had a minimal effect on the transcript signature during recovery from cold shock. However, during recovery from cold shock, we observed differential expression of ~1,400 ESTs, including a number of heat shock proteins, cytoskeletal components, and genes from several cell signaling pathways. Several gene pathways correlated well with metabolomics data, indicating that coordinated changes in gene expression and metabolism contribute to recovery from cold shock.

overall_design: Four treatment groups (C, RCH, CS+2R, RCH+CS+2R), four biological replicates of four pooled individuals for each treatment. Each phenotype was hybridized with the control, and the CS+2R and RCH+CS+2R groups were also hybridized together.


title: CDK-4 inhibitor P276-00 sensitizes Pancreatic Cancer cells to Gemcitabine induced Apoptosis

status: Public on Mar 23 2012

city: Mumbai

first: Muralidhara

last: Padigaru

state: Maharashtra

address: 1, Nirlon Compex, Off Western Express Highway

department: Translational Research

country: India

institute: Piramal Lifesciences India Limited

summary: Despite advances in molecular pathogenesis, pancreatic cancer remains a major unsolved health problem. It is a rapidly invasive, metastatic tumor that is resistant to standard therapies. The phosphatidylinositol-3-kinase (PI3K)/Akt and mammalian target of rapamycin (mTOR) signaling pathways are frequently dysregulated in pancreatic cancer. Gemcitabine (Gem) is the mainstay treatment for metastatic pancreatic cancer. P276 is a novel CDK inhibitor that induces G2/M arrest and inhibits tumor growth in vivo models. Here, we determined that P276 sensitizes pancreatic cancer cells to Gem induced apoptosis, a mechanism mediated through inhibition of Akt-mTOR signaling. In vitro, the combination of P276 and Gem resulted in a dose- and time-dependent inhibition of proliferation and colony formation of pancreatic cancer cells but not with normal pancreatic ductal cells. This combination also induced apoptosis, as seen by activated caspase 3 and increased Bax/Bcl2 ratio. Gene profiling studies demonstrated that this combination down regulated Akt-mTOR signaling pathway, which was confirmed by western blot analyses. There was also a down regulation of vascular endothelial growth factor (VEGF) and interleukin-8 expression suggesting effects on angiogenesis pathway. In vivo, intraperitoneal administration of the P276-Gem combination significantly suppressed the growth of pancreatic cancer tumor xenografts. There was a reduction in CD31 positive blood vessels, and reduced VEGF expression, again suggesting an effect on angiogenesis. Taken together, these data suggest that P276-Gem combination is a novel potent therapeutic agent that can target the Akt-mTOR signaling pathway to inhibit both tumor growth and angiogenesis.

overall_design: Case control dual channel design

first: Periyasamy

last: Giridharan

first: Debarshi

last: Chakrabarti

first: Urvi

last: Ved

last: Padiagru

first: Arun

last: Balakrishnan

first: Somesh

last: Sharma


title: Impaired Natural Killer Cell Self-Education and 'Missing-Self' Responses in Ly49-Deficient Mice

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

institute: University of Montreal

summary: Nimblegen arrays were used to perform aCGH analysis on 2 mice strains, one which lacks the Ly49 gene cluster and the parent strain which still has the cluster.  A targeted knock-out of the cluster resulted in the rearrangment and deletion of the cluster.  The aCGH experiment was performed to elucidate the extent of the deletion.

overall_design: high resolution aCGH analysis of the Ly49 cluster in deletion strain

first: Simon

last: Bélanger

first: Megan

last: Tu

first: Mir

last: Rahim

first: Ahmad

middle: B

last: Mahmoud

first: Rajen

last: Patel

first: Lee-Hwa

last: Tai

first: Angela

middle: D

last: Troke

first: Josette-Renée

last: Landry

first: Qinzhang

last: Zhu

first: Kenneth

last: Tung

first: David

middle: H

last: Raulet

first: Andrew

last: Makrigiannis


title: Identification of XMRV Infection-Associated microRNAs in Four Cell Types in Culture (Experiment B)

status: Public on May 06 2012

first: Krishna

last: Ketha

address: 8800 Rockville Pike

department: Division of Hematology

institute: CBER/FDA

summary: XMRV is a gammaretrovirus that was thought to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS) in humans until recently. The virus is culturable in various cells of human origin like lymphocytes, NK cells, neuronal cells, and prostate cell lines. MicroRNAs (miRNAs), which regulate gene expression, were so far not identified in cells infected with XMRV in culture. Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection and evaluated for microRNA profile in a microarray. MicroRNA expression profiles of XMRV-infected continuous prostate cancer cell lines differ from that of virus-infected primary cells (PBLs and MDMs). miR-193a-3p and miRPlus-E1245 were observed to be specific to XMRV infection in all 4 cell types. While miR-193a-3p levels were down-regulated, miRPlus-E1245 on the other hand exhibited varied expression among the 4 cell types. The present study demonstrates that cellular microRNAs are expressed during XMRV infection of human cells. This is the first report demonstrating the regulation of miR193a-3p and miRPlus-E1245 during XMRV infection in four different human cell types.

overall_design: Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection in duplicates and evaluated for microRNA profile in a microarray. Each test sample RNA was labeled with Hy3 and the reference pool (made by pooling all 24 test samples in each run) was labeled with Hy5.

first: Ketha

middle: V

last: Mohan

first: Krishnakumar

last: Devadas

first: Shilpakala

last: Rao

first: Indira

last: Hewlett

first: Chintamani

last: Atreya


title: Identification of XMRV Infection-Associated microRNAs in Four Cell Types in Culture (Experiment A)


title: Comparison of DEV infected CEF with control

status: Public on Mar 08 2012

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

summary: Duck enteritis virus (DEV) is an important herpesvirus pathogen of waterfowl associated with an acute, highly contagious lethal disease. Using a deep sequencing approach on RNA from infected chicken embryo fibroblast (CEF) cultures, we determined the global changes in the microRNA (miRNA) expression profiles during DEV infection. In addition to the changes in the expression of a number of host miRNAs as a result of DEV infection, we identified several novel DEV-encoded miRNAs. Unlike most Mardivirus-encoded miRNAs, the majority of the DEV miRNAs were encoded within the unique long region of the viral genome. The precursors of DEV miR-D18 and miR-D19 overlapped with each other suggesting similarities to miRNA-offset RNAs, although only the DEV-miR-D18-3p was functional in reporter assays. Identification of these novel miRNAs will add to the growing list of virus-encoded miRNAs enabling the exploration of their roles in pathogenesis.

overall_design: Each microRNA is spotted on the array 6 times.  We compared expression of duck enteritis virus (DEV)-infected chicken embryo fibroblasts (CEF) with CEF control.

first: Yongxiu

last: Yao

first: Venu

last: Nair


title: Expression analysis of both total and polysomal mRNAs under drought, salt and cold stress conditions

status: Public on Mar 02 2012

city: Yongin

first: Su-Hyun

last: Park

address: 38-2 Nam-dong

institute: Myongji University

summary: Using 3′-tiling microarray covering the rice genes, we carried out genome-wide expression analyses of total and polysome-fractionated samples treated with drought, salt and cold at 2-week-old rice leaves. compared to non-treated negative control (NC) samples. Our study is the first report which elucidated the global alternation of polysome association in response to abiotic stress.

overall_design: A total of 24 chips were used for microarray. At 2h, total and polysomal RNAs were extracted from drought, salt and cold at 2-week-old rice leaves with three biological replicates.

first: Pil

middle: J

last: Chung

first: Piyada

last: Juntawong

first: Julia

last: Bailey-Serres

first: Youn

last: Kim

first: Harin

last: Jung

first: Seung

middle: W

last: Bang

first: Yeon-Ki

first: Yang

last: Choi

first: Ju-Kon