title: Analysis of MicroRNA Expression in Embryonic Developmental Toxicity Induced by microcystin arginine arginine (MC-RR).

status: Public on Sep 17 2012

city: Wuhan

first: Yanyan

last: Zhao

address: Donghu South Road 7

country: China

institute: Institute of Hydrobiology

summary: In this study, we used zebrafish embryos as a model system to investigate the toxic effects of MC-RR on early development and try to elucidate the underlying developmental toxicological mechanisms in a global view at posttranscriptional level. Altered expression pattern of miRNAs in embryos treated with MC-RR was detected by miRNA microarray.

overall_design: We examined microRNA expression profiling in paired MC-RR treated and control embroys of zebrafish. There are 4 biological replicates in MC-RR treated group and control group, respectively.

first: Y

middle: Y

first: Q

last: Xiong

first: P

last: Xie


title: Identification of a FOXO3/IRF7 circuit that limits inflammatory sequelae of antiviral responses (expression)

status: Public on Sep 19 2012

city: Seattle

first: Ayush

last: Raman

state: WA

address: 401 Terry Avenue North

department: Computational Dept.

country: USA

institute: Institute for Systems Biology

summary: We have used an unbiased systems approach to predict that a member of the forkhead family of transcription factors, FOXO3, is a negative regulator of a subset of antiviral genes. This prediction was validated using macrophages isolated from Foxo3-null mice. We detected significantly increased transcription of a subset of interferon-stimulated genes (ISGs) under basal conditions in Foxo3-null macrophages when compared to their wild type (WT) counterparts, suggesting that FOXO3 functions as a repressor of these genes. Stimulation of Foxo3-null macrophages with poly-IC (PIC) further increased the levels of this subset of ISGs, and also revealed the transcription of additional ISGs.

overall_design:
C57BL/6 mice were obtained from Jackson Laboratories. Foxo3-/- mice in the FVB background were obtained from MMRRC and were backcrossed to C57BL/6 mice at least 5 times to generate congenic mice. C57BL/6 Foxo3+/- heterozygotes were intercrossed to generate Foxo3-/- mice. Mice were maintained at the animal facility of the Institute for Systems Biology and used at 8-12 weeks of age. All animals were housed and handled according to the approved protocols of the University of Washington and Institute for Systems Biology's Institutional Animal Care and Use Committees.

Bone marrow macrophages from wildtype and Foxo3 knock-out mice were stimulated with PIC or left untreated. 3 replicates per group.

first: Vladimir

last: Litvak


title: Expression analysis of HepG2, HepG2-slug and HepG2-slug on Matrigel

status: Public on Sep 21 2012

city: Tianjin

first: baocun

last: sun

address: Qixiangtai Road No.22, Heping District

institute: Tianjin Medical University

summary:
Investigation of whole genome gene expression level changes in hepatocellular carcinoma cell line hepG2 in regular culture, hepG2-slug in regular culture and hepG2-slug on Matrigel.
Whole genome gene expression level changes have been compared in hepatocellular carcinoma cell line hepG2 in regular culture, hepG2-slug in regular culture and hepG2-slug on Matrigel.

overall_design: Roche NimbleGen micro-array analysis was employed to assess global genome expression in HepG2 in regular culture, HepG2-slug in regular culture and HepG2-slug on Matrigel. The results demonstrated that the up-regulated genes and the down-regulated genes increased significantly when HepG2-slug cells with VM forming ablity were cultured on Matrigel and formed VM.

first: Dan

last: Sun

first: Baocun


title: Ixr1 and the Saccharomyces cerevisiae hypoxic response

status: Public on Sep 13 2012

city: A Coruña

first: M Esperanza

last: Cerdan

state: A Coruña

address: Campus de A Zapateira

department: Biología Celular y Molecular

country: Spain

institute: Universidad de A Coruña

summary: Analysis of the transcriptome of the wild-type strain BY4741 and its isogenic derivative ixr1 null, grown in aerobic, hypoxic conditions and after a hypoxic shift

overall_design: Two biological replicates in two technical replicates for each growth condition

first: Angel

last: Vizoso-Vázquez

first: Mónica

last: Lamas-Maceiras

first: Manuel

last: Becerra

first: M

middle: I

last: González-Siso

first: Esther

last: Rodríguez-Belmonte

middle: E

last: Cerdán


title: Cooperativity of Rb, Brca1, and p53 and malignant breast cancer evolution (MFT121 p53f/f Brca1f/f)

status: Public on Sep 18 2012

city: Worcester

first: Karl

last: Simin

state: MA

address: 364 Plantation St.

institute: UMass Medical School

summary: Breast cancers that are “triple-negative” for the clinical markers ESR1, PGR, and HER2 typically belong to the Basal-like molecular subtype. Defective Rb, p53, and Brca1 pathways are each associated with triple-negative and Basal-like subtypes. Our mouse genetic studies demonstrate that the combined inactivation of Rb and p53 pathways is sufficient to suppress the physiological cell death of mammary involution. Furthermore, concomitant inactivation of all three pathways in mammary epithelium has an additive effect on tumor latency and predisposes highly penetrant, metastatic adenocarcinomas. The tumors are poorly differentiated and have histologic features that are common among human Brca1-mutated tumors, including heterogeneous morphology, metaplasia, and necrosis. Gene expression analyses demonstrate that the tumors share attributes of both Basal-like and Claudin-low signatures, two molecular subtypes encompassed by the broader, triple-negative class defined by clinical markers. These studies establish a unique animal model of aggressive forms of breast cancer for which there are no effective, targeted treatments. Rb, p53, and Brca1 are associated with inherited forms of cancer, but defects in these pathways are also found together in a subset of breast cancer patients without a family history of the disease. Simultaneous inactivation of all three pathways causes more aggressive disease than do pair-wise combinations, indicating that the pathways play non-overlapping roles in tumor prevention.

overall_design: We investigated the effect of perturbation of Rb family pathways, p53, and/or Brca1 in mouse mammary epithelium. Eighteen tumors were compared to normal spleen DNA.


title: SBRI_AB Host response in primary mouse tracheal epitelial cells (mTEC)  to influenza infection with PR8, VN or X31 at MOI of 0.015 at 12 hours

status: Public on Sep 26 2012

first: Aderem

last: Lab

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: Array analysis of total RNA from mTECs 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (MOI 0.015)

overall_design: Time Point: 12 h post infection (Mock, PR8, X31, VN) MOI 0.015; in biological triplicates. Total samples: 12.

first: Alan

last: Aderem


title: SBRI_AA Host response in the lung to influenza infection with PR8, VN or X31 strain at 12 hours.

summary: Array analysis of total lung RNA obtained from mice 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (1x10^5pfu)

overall_design: Time Point: 12 h post infection (Mock, PR8, X31, VN); Mock group has four biological replicates, virally infected groups have five replicates. Total samples: 19.


title: Temperature stress differentially modulates transcription in meiotic anthers of tolerant and sensitive tomato plants

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

country: Italy

institute: University of Verona

summary: We have used cDNA-AFLP and microarray analyses to profile the response of the tomato meiotic anther transcriptome to moderate heat stress condition in Moneymaker or Falcorosso and HeatSet1 tomato genotype.

overall_design: Combimatrix microarray technology were applied to obtain a general overview of the gene expression in meiotic anthers of a tolerant and a sensitive tomato genotype. We analyzed three time points (0,2,and 6h) for each genotype. For each sample we performed three biological replicates.

first: Craita

last: Bita


title: The Membrane Stress Response Buffers Lethal Effects of Lipid Disequilibrium by Reprogramming the Protein Homeostasis Network

status: Public on Sep 25 2012

city: Singapore

first: Guillaume

last: Thibault

address: 1 Research Link, National University of Singapore

department: Cell Stress and Homeostasis

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: Lipid composition can differ widely among organelles and even between leaflets of a membrane. Lipid homeostasis is critical because disequilibrium can have disease outcomes. Despite their importance, mechanisms maintaining lipid homeostasis remain poorly understood. Here, we establish a model system to study the global effects of lipid imbalance. Quantitative lipid profiling was integral to monitor changes to lipid composition and for system validation. Applying global transcriptional and proteomic analyses, a dramatically altered biochemical landscape was revealed from adaptive cells. The resulting composite regulation we term the ?membrane stress response? (MSR) confers compensation, not through restoration of lipid composition, but by remodeling the protein homeostasis network. To validate its physiological significance, we analyzed the unfolded protein response (UPR), one facet of the MSR and a key regulator of protein homeostasis. We demonstrate that the UPR maintains protein biogenesis, quality control, and membrane integrity?functions otherwise lethally compromised in lipid dysregulated cells.

overall_design:
Genes expression from early log phase of CHO2, OPI3, and PAH1 knockout cell and untreated and DTT-treated WT cells. RNA was prepared from independent triplicate samples.

Array sets performed and collected on different dates are as follows:
Array 1, Day 1:
WT_rep1
pah1_rep1
cho2_rep1
opi3_rep1

Array 2, Day 2:
WT_rep2
WT_rep3
WT_Tm_rep1
WT_DTT_rep1

Array 3, Day 2:
WT_DTT_rep2
WT_DTT_rep3
cho2_rep2
cho2_rep3

Array 4, Day 2:
pah1_rep2
pah1_rep3
opi3_rep2
opi3_rep3

first: Davis

middle: T

last: Ng


title: Genomic Library Enrichment for n-Butanol tolerance in E. coli. Samples vs Reference

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

summary: Genomic Library Enrichment to determine the n-Butanol Tolerant related genes in E. coli.  The samples involves a series of batch transfers to increasing concentrations of n-butanol and controls (always grew in absence of the solvent)

overall_design: Two technical replicas.  Samples 1, 3, 5, and 7 are the serial transfers (samples 15, 13, 11, and 9 are their respective replicas).  Samples 2, 4, 6 and 8 are the controls grown in absence of n-butanol (samples 16, 14, 12 and 10 are their respective replicas)

first: Luis

middle: H

last: Reyes

first: Katy

middle: C

last: Kao

middle: D


title: Methylation profiling of Low-Risk Myelodysplastic Syndromes (MDSs)

status: Public on Sep 28 2012

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

institute: Cancer Research Center (CiC-IBMCC)

type: Methylation profiling by genome tiling array

summary:
Genome-wide expression and methylation profiling identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes (MDSs).
Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. Gene expression and methylation status were measured using high-density microarrays. A total of 552 differentially methylated CpG loci were identified as being present in low-risk MDS; hypermethylated genes were more frequent than hypomethylated genes. In addition, mRNA expression profiling identified 1005 genes that significantly differed between low-risk MDS and the control group. Integrative analysis of the epigenetic and expression profiles revealed that 66.7% of the hypermethylated genes were underexpressed in low-risk MDS cases. Gene network analysis revealed molecular mechanisms associated with the low-risk MDS group, including altered apoptosis pathways. The two key apoptotic genes BCL2 and ETS1 were identified as silenced genes. In addition, the immune response and micro RNA biogenesis were affected by the hypermethylation and underexpression of IL27RA and DICER1. Our integrative analysis revealed that aberrant epigenetic regulation is a hallmark of low-risk MDS patients and could have a central role in these diseases.

overall_design: Low-risk MDS patients and age-matched controls without haematological malignancies were included in the study. Mononuclear cells were isolated from bone marrow samples of low-risk MDS patients and controls by density gradient (Ficoll). A cohort of 18 patients with low-risk MDS and seven controls were included in a simultaneous integrative study of methylation (using Methylated CpG Island Amplification and Microarrays, MCAM) and expression (using Affymetrix microarrays HG-U133 Plus 2), while the whole series was used as a control group of expression data.

first: Monica

last: Del Rey

first: Kathleen

last: O’Hagan

first: Margaret

last: Dellett

last: Aibar

first: Hilary

middle: A

last: Colyer

first: MariaEugenia

last: Alonso

first: Maria

last: Diez-Campelo

first: Richard

middle: N

last: Armstrong

first: Daniel

middle: J

last: Sharpe

first: Norma

last: Gutierrez

first: JuanLuis

last: García

last: DeLasRivas

first: Ken

last: Mills

first: Jesus

middle: M

last: Hernández-Rivas


title: ENCODE SUNY RNA Binding Protein Tiling Data for K562 and GM12878

status: Public on Sep 24 2012

city: Albany

first: Frank

last: Doyle

state: NY

address: 257 Fuller Rd

department: Nanobiology

institute: UAlbany CNSE

type: Expression profiling by genome tiling array

summary:
RNA Binding Protein immunoprecipitation study for multiple target proteins in K562 & GM12878 cell lines as part of the ENCODE consortium.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: Three sample replicates per sample type.  Total input RNA and Negative target RIP (antibody for bacteriophage coat protein) are provided as controls.  Individual samples reflect  reflect biological replicates defined as separate RIP runs (as opposed to technical replicate defined as multiple arrays run with same RIP sample as starting material).

first: Scott

last: Tenenbaum

first: Francis


title: Grape flesh and skin ripening transcriptomic profiling

status: Public on Sep 27 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: The experiment was aimed at describing similarities and differences between grapevine flesh and skin ripening at the transcriptome level. Transcriptional profiles throughout flesh and skin ripening were followed in three biological replicas during two consecutive growing seasons in a table grape cultivar ‘Muscat Hamburg’. Berries were weekly picked off bunches (one bunch per vine from each selected vine) from june to august. For each sampling, berries were classified in five ripening stages based on monitoring developmental stages instead of a simple chronological sampling. They corresponded to pre-véraison (P), 50% véraison (V1), 100% véraison (V2), ripe 1 (R1), and ripe 2 R2). P samples were harvested as green, hard berries of at least 15 mm in size, according to touch-assessed hardiness. Véraison berries with half or full coloured skin surface corresponded to V1 and V2 samples. After véraison, ripening berries were classified according to their floatability in solutions with different NaCl densities, as an indication of the internal sugar concentration. At this stage berries were sampled with densities between 110-130 g NaCl/L for R1 and between 130-150 g NaCl/L for R2, which corresponded to commercially ripen table grape berries. On each of the five samples, frozen berries were dissected and RNA from flesh and skin was obtained and processed for Grapegen Genechip microarray hybridizations.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Pablo Carbonell-Bejerano.  The equivalent experiment is VV33 at PLEXdb.]

overall_design: tissue type name: Flesh - developmental stage name: P(6-replications);  tissue type name: Flesh - developmental stage name: V1(6-replications);  tissue type name: Flesh - developmental stage name: V2(6-replications);  tissue type name: Flesh - developmental stage name: R1(6-replications);  tissue type name: Flesh - developmental stage name: R2(6-replications);  tissue type name: Skin - developmental stage name: P(6-replications);  tissue type name: Skin - developmental stage name: V1(6-replications);  tissue type name: Skin - developmental stage name: V2(6-replications);  tissue type name: Skin - developmental stage name: R1(6-replications);  tissue type name: Skin - developmental stage name: R2(6-replications)

first: Pablo

last: Carbonell-Bejerano

first: José

last: Martínez-Zapater


title: Leishmania major: Sir2rp3 overexpressor vs wild-type

status: Public on Sep 10 2012

city: Ribeirão Preto

first: Nilmar

middle: Silvio

last: Moretti

state: Sao Paulo

address: Av. Bandeirantes, 3900

department: Molecular and Cellular Biology

country: Brazil

institute: Sao Paulo University

summary: Transcriptional profiling of Leishmania major parasites overexpressing LmSir2rp3 protein compared with wild-type cell line transfected with empty vector in normal growth conditions. Goal of this experiment was to evaluate the possible effect of LmSir2rp3 in the control of gene expression in this protozoan parasite that has a polycistronic transcription.

overall_design: Two-condition experiment, LmSir2rp3 overexpressor vs. Wild-type cell line bearing empty vector. Biological replicates, 3 LmSir2rp3 overexpressor replicates and 3 wild-type cell line bearing empty-vector

first: N

middle: S

first: E

last: Madore

first: B

last: Papadopoulou

first: L

middle: R

last: Tosie


title: Chip-chip from HepG2 cells and HepG2 cells with slug overexpression

first: baocun

last: sun

type: Genome binding/occupancy profiling by array

summary:
The transcription factor slug represses genes with E-box and then activates cancer stem cell related pathway: Wnt, Notch and Hedgehog pathway.
Chromatin immunoprecipitation (ChIP) of slug by ChIP-on-chip analysis demonstrated that slug indirectly activates cancer stem cell related pathway and thus promotes vasculogenic mimicry formation.

overall_design: Comparison of HepG2-control in regular culture, HepG2-slug in regular culture and HepG2-slug on Matrigel.

first: Dan

last: Sun

first: Baocun


title: Uranium extremophily is an adaptive, rather than intrinsic, feature for extremely thermoacidophilic Metallosphaera species

city: Raleigh

first: Arpan

last: Mukherjee

state: NC

address: 840 Main Campus Dr. Rm 3304

department: Chemical Engineering

institute: North Carolina State University

summary: Thermoacidophilic archaea are found in heavy metal-rich environments and, in some cases, these microorganisms are causative agents of metal mobilization through cellular processes related to their bioenergetics. Given the nature of their habitats, these microorganisms must deal with the potentially toxic effect of heavy metals.  Here, we show that two thermoacidophilic Metallosphaera species with nearly identical (99.99%) genomes differed significantly in their sensitivity and reactivity to uranium. M. prunae, isolated from a smoldering heap on a uranium mine in Thuringen, Germany, could be viewed as a “spontaneous mutant” of M. sedula, an isolate from Pisciarelli solfatara near Naples, Italy. M. prunae tolerated U3O8 and U(VI) to a much greater extent than M. sedula. Within 15 minutes following exposure to “U(VI) shock”, M. sedula, and not M. prunae, exhibited transcriptomic features associated with severe stress response. Furthermore, within 15 minutes post-U(VI) shock, M. prunae, and not M. sedula, showed evidence of substantial degradation of cellular RNA. This suggested that transcriptional and translational processes were aborted as a dynamic mechanism for resisting U toxicity; by 60 minutes post-U(VI) shock, RNA integrity in M. prunae recovered, and known modes for heavy metal resistance were activated. In addition, M. sedula rapidly oxidized solid U3O8 to soluble U(VI) for bioenergetic purposes, a chemolithoautotrophic feature not previously reported. M. prunae, however, did not solubilize solid U3O8 to any significant extent, thereby not exacerbating U(VI) toxicity. These results point to uranium extremophily as an adaptive, rather than intrinsic, feature for Metallosphaera species, driven by environmental factors.

sample_organism:
Metallosphaera sedula
Metallosphaera sedula DSM 5348

overall_design:
The study comprises 9 Samples, described in detail below.
MprAU_MseAU: Transcriptional analysis of the response of Metallosphaera prunae (Mpr) and Metallosphaera sedula(Mse) to chemolithoautotrophic conditions (0.1 wt% Uranium octaoxide with CO2 supplementation in headspace). This experiment was done to identify the key terminal oxidases which responded to a Uranium oxide while doing inter-species comparison between Mpr and Mse. Transcriptional response of the terminal oxidase clusters proved that certain key genes play a role in the vastly different physiologies of these two species.

MprN_MprU60: Transcriptional analysis of the response of Metallosphaera prunae (Mpr) to 60 min of Uranium shock. This experiment was done to analyze the differential transcription of Mpr cells challenged with 1 mM uranyl acetate shock (U shock) compared to normal growth. The Uranium cultures were harvested 60 min after the shock.

MprN_MseN: Differential transcription of Metallosphaera species under normal growth conditions. This experiment was done to analyze the differential transcription of Mpr cells compared with Mse cells at mid log phase.

MprN_MprU3h: Transcriptional response of Metallosphaera prunae (Mpr) to 3h of Uranium shock compared to normal growth. This experiment was done to analyze the differential transcription of Mpr cells challenged with 1 mM uranyl acetate shock (U shock) . The Uranium cultures were harvested 3 h after the shock.

MseN_MseU15: Transcriptional response of Metallosphaera sedula (Mse) to 15 min of Uranium shock. This experiment was done to analyze the differential transcription of Mse cells challenged with 1 mM uranyl acetate shock (U shock) compared to normal growth. The Uranium cultures were harvested 15 min after the shock.

MseN_MseU60: Transcriptional response of Metallosphaera sedula to 60 min of Uranium shock. Mse cells were grown upto mid log phase after which the cells were subjected to U shock and harvested 60 min later. Biological repeats were done for both experimental conditions.

MseN_MseU3h: Transcriptional response of Metallosphaera sedula (Mse) to 3h of Uranium shock compared to normal growth. This experiment was done to analyze the differential transcription of Mse cells challenged with 1 mM uranyl acetate shock (U shock) . The Uranium cultures were harvested 3 h after the shock.

MseU15_MseU60: Transcriptional response of Metallosphaera sedula to 15 min of Uranium shock compared with 60 min of Uranium shock. This experiment was done to analyze the differential transcription of Mse cells challenged with 1 mM uranyl acetate shock (U shock) . The Uranium cultures were harvested 15 min and 60 min after the shock.

MprU3h_MseU3h: Differential transcription of Metallosphaera cells under Uranium shock. This experiment was done to analyze the differential transcription of Metallosphaera sedula (Mse) and Metallosphaera prunae (Mpr) challenged with 1 mM uranyl acetate.

first: Garrett

last: Wheaton

first: Paul

last: Blum

first: Robert

last: Kelly


title: Integrative Transcriptomic Profiling reveals Hepatic Stem-like Phenotype and Interplay of EMT and miR-200c in Intrahepatic Cholangiocarcinoma [miRNA]

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary:
We compared transcriptomic profiles of ICC tumor specimens to hepatocellular carcinoma (HCC) specimens using Affymetrix mRNA array and the miRNA array platforms to search for unique gene signatures linked to patient prognosis.
ICC and HCC share common stem-like molecular characteristics and stem-like tumor features associated with poor prognosis.

overall_design: Gene expression profiling of 16 intrahepatic cholangiocarcinoma (ICC), 7 mixed type of combined hepatocellular cholangiocarcinoma (CHC), 2 Hepatic adenoma, 3 focal nodular hyperplasia (FNH), 5 non-tumor liver tissues, and 2 CCA cell lines were performed.

first: Naoki

last: Oishi

middle: W


title: Differential gene expression profile of Streptococcus pneumoniae early biofilm cells and planktonic cells

city: Goyang

first: Jae-Jun

last: Song

state: Gyeonggi

department: Department of Otorhinolaryngology-Head & Neck Surgery

country: South Korea

institute: Dongguk University Medical center

summary: Otitis media, pneumonia, sinusitis and as well as severe diseases such as meningitis and bacteraemia are related to biofilm-like diseases, in which Streptococcus pneumoniae demonstrated differential and tissue specific gene expressions. In this study, we reported the differential gene expression profile of early in vitro biofilm and planktonic cell in c-DNA microarray analysis. The microarray analysis was performed on total RNA extracted from biofilms grown in 24-well microtiter plate and mid-log grown planktonic cells. To validate the results of microarray, real-time RT-PCR was performed on 13 differentially expressed genes and one constitutively expressed gene from six different functional groups. cDNA-microarray analyses indicated 89 genes that were significantly differentially expressed in biofilm and planktonic cells. Among total differentially expressed gene, almost 50% were hypothetical genes. Of the 46 protein coding genes, 34 showed up-regulation and 16 showed down-regulation in biofilm. The functional annotation showed that many functional categories were differentially regulated in biofilm and planktonic cells, such as genes involve in purine, pyrimidine nucleotide metabolism, RNA/DNA metabolism, amino acid transport and metabolism, translation, transporter protein, carbohydrate transport and metabolism, cell wall biosynthesis, isoprenoid biosynthesis, transcription regulator and cellular process.

overall_design: Streptococcus pneumoniae R6 strain used in this is an unencapsulated and avirulent strain derived from encapsulated serotype 2 pathogenic strain D39. In vitro biofilm formation was carried out in 24-well, flat-bottom, polystyrene microtiter plate (BD falcon, MD, USA) in static model. S. pneumoniae grown up to mid-logarithmic phase in TSB medium was diluted 1:100 with fresh sterile TSB medium supplied with 1% glucose, inoculated 1.5 mL in 24-well microtiter plate and, incubated for 15 hours at 37°C in 5% CO2. After incubation medium was discarded, and the plates were gently washed three times with 1.5 mL sterile, cold phosphate buffer saline (PBS). Adherent cell were scraped and immediately processed for RNA extraction. For planktonic cells RNA extraction, five ml of mid-logarithmic phase cell suspension was pelleted by centrifugation and wash three times with sterile PBS and immediately processed for RNA extraction. All experiments were performed in triplicate (3 independent biological replicates)

first: Mukesh

middle: K

last: Yadav


title: Transcription differences of Micrococcus luteus at late-exponential and stationary phase

city: Emeryville

first: Ee-Been

last: Goh

state: CA

address: 5885 Hollis St, 4th Floor

department: Fuels Synthesis Division

institute: Joint BioEnergy Institute

summary:
Investigation of transcriptomic changes in M.luteus at 12hrs and 24hrs.  Differences in fatty acid profiles of M. luteus at exponential and stationary phase is attributed to transcriptional changes of branched amino acid biosynthesis and degradation genes.
This study is described by Pereira, J.H., E.B. Goh, J.D. Keasling, H.R. Beller and P.A. Adams in Crystal structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus, which has been submitted to Acta Crystallographica Section D

overall_design: A 6 microarray study using total RNA recovered from six separate control cultures of Micrococcus luteus NCTC2665 strain with 3 harvested after 12hrs of growth and the other 3 after 24hrs of growth.  Each chip measures the expression level of 2,374 ORF based on the draft genome sequence of Micrococcus luteus with ten 60-mer probe pairs (PM/MM) per gene, with 3-fold technical redundancy.

first: Harry

last: Beller


title: Differentially Expressed Genes Regulating the Progression of Ductal Carcinoma In Situ to Invasive Breast Cancer (Group 4 stroma)

status: Public on Sep 29 2012

city: St Louis

first: Sangjun

last: Lee

state: MO

address: 4940 Parkview Place

department: Pathology

institute: Washington University at St. Louis

summary: We used gene expression profiling of human DCIS and IBC to discover uniquely expressed genes that may also regulate progression.

overall_design: RNA from human samples were extracted, purified, amplified, and evaluated for gene expression using Affymetrix U133-X3P gene expression arrays.

first: D

last: Allred


title: Differentially Expressed Genes Regulating the Progression of Ductal Carcinoma In Situ to Invasive Breast Cancer (Group 4 Epithelial)


title: microRNA-146b improves intestinal injury in mouse colitis by activating NF-kB and improving epithelial barrier function

city: Asahikawa-city

first: Mikihiro

last: Fujiya

state: Hokkaido

address: 1-1-1, Higashi 2-jou, Midorigaoka

department: Department of Medicine

country: Japan

institute: Asahikawa Medical University

summary:
Aim: The precise role of microRNAs in inflammatory disease has been less clear. The present study investigated the effect of microRNA (miR-146b) on improving intestinal inflammation.

Methods: The microRNA profile in IL-10-deficient mice was examined using microRNA arrays and miR-146b was selected for the following experiments. The expression vectors containing either the whole sequence of miR-146b or its siRNA were intraperitoneally administered to the dextran sulfate sodium (DSS)-induced colitis mouse.

Results: The overexpression of miR-146b activated the NF-kB pathway, improved the epithelial barrier function, relieved intestinal inflammation in the DSS-induced colitis mice, and improved the survival rate of mice with lethal colitis. Furthermore, this amelioration of the intestinal inflammation by miR-146b was negated by the inhibitor for NF-kB pathway.

Conclusion: The modulation of miR-146b expression is a potentially useful therapy for the treatment of intestinal inflammation through the activation of the NF-kB pathway.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
Mice: The present studies were approved by the Institutional Animal Care and Use Committee of the Asahikawa Medical College. C57BL/6 and IL-10-/- mice were purchased from Sankyo Labo Service Co., Inc. (Tokyo, Japan) and Jackson Laboratories (Bar Harbor, ME), respectively. Large intestines with or without treatments were removed, rinsed with saline, and the epithelium was gently sheared off with glass slides for protein determination.
microRNA arrays: RNA was extracted from the large intestines of mice with Trizol and then was immediately frozen in liquid nitrogen. Next, the microRNA expression profiles of large intestine in wild-type and IL-10-deficient mouse were investigated using the mirVanaTM miRNA bioarray (Filgene, Inc., Japan). Any more than 2-fold differences were considered to indicate a significant change.


title: Expression analysis of C. elegans genes kin-1 and crh-1 mutant

city: Kunming

first: Cheng Gang

last: Zou

state: Yunnan

address: No. 2,North of Cuihu Road

institute: Yunnan University

summary:
Investigation of whole genome gene expression level changes in C. elegans genes kin-1 and crh-1 mutant, compared to the wild-type strain.
NimbleScan software’s implementation of RMA offers quantile normalization and background correction. There are three steps of RMA: Firstly, background subtraction was performed using a local background estimator. Secondly, quantile normalization (Bioinformatics 2003; 19:185) at probe level was done to make the expression distributions the same for all arrays. Last, probe set summarization was performed using Robust Multichip Average (RMA) algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249).

overall_design: A nine chip study using total RNA recovered from three separate wild-type cultures of C. elegans and three separate cultures of kin-1 mutant, and three separate cultures of crh-1 mutant. The C. elegans 12 x 135K Gene Expression Array was manufactured by Roche NimbleGen. This array enables you to conveniently and simultaneously hybridize 12 samples on each slide. About 13,187 genes are collected from the authoritative data source including Wormbase.

first: Yi

last: Xiao

first: Cheng-Gang


title: Gene expression profiling analysis of nasopharyngeal carcinoma cell CNE1/MTA1-si cells and CNE1 cells

status: Public on Sep 14 2012

city: Guangzhou

first: Xiaoxia

last: Zhu

address: Department of Radiation Oncology,Nanfang Hospital, Southern Medical University

department: Department of Radiation Oncology

summary: Investigation of whole genome gene expression level changes in MTA1-silencing CNE1 cells, compared to the wild-type CNE1 cell.

overall_design: A double chip study using total RNA recovered from two cell lines, CNE1/MTA1-si cells and CNE1 cells.  Each chip measures the expression level of 45,033 genes from human.


title: Transcriptome analysis of the WalKR regulon in Staphylococcus aureus

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

summary: The WalKR regulon was studied by comparing genes expression in a strain producing a constitutively active WalR regulator (WalRc) versus the wild type strain carrying the empty expression vector. Hybridizations were performed with three independent biological replicates. Our data allowed to identify 165 genes differentially expressed in the walRc expressing strain with a P-value ≤ 0.05 using Z-test and a threshold value of two-fold change in transcriptional levels. Among them, 108 genes are activated, and 57 genes are repressed. About 10% of these results were confirmed by quantitative real time PCR, revealing the high reliability of this overall study. Beyond the major effect of the WalKR system on genes expressing cell wall hydrolases, we have shown that it activates a large number of genes involved in virulence, and probably through its positive impact on the SaeRS two-component system, is a major activator of S. aureus virulence.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Cells were grown in TSB rich medium added with 0.25 µM CdCl2 to allow walRc expression until OD600nm of 1. Gene expression was compared between the HG001 wild type reference strain carrying the pCN51 empty vector (HG001/pCN51) and the HG001 strain carrying a pCN51 derivative with the walRc allele under the control of the Pcad inducible promoter (HG001/pSD3-12). Each condition was done in triplicate and the data were analyzed using the Arraystat software. Genes were considered as differentially expressed if their transcriptional level differed by at least two-fold with a Z-test P-value ≤ 0.05 in at least two of the replicates.

first: Aurélia

last: Delauné

first: Sarah

last: Dubrac

first: Olivier

last: Poupel

first: Pierre

last: Nicolas

first: Aurelie

last: Leduc

first: Tarek

last: Msadek


title: Chip-chip from Mouse E10.5 anterior and posterior immortalised limb cell lines and limb tissue for H3K27me3 antibody and from Mouse E10.5 anterior and posterior limb tissue for Ring1B antibody.

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

type: Genome binding/occupancy profiling by genome tiling array

summary:
Anterior-posterior differences in H3K27me3 and Ring1B enrichment over the 5 prime Hoxd genes in E10.5 murine distal forelimbs.
Chromatin immunoprecipitation (ChIP) of H3K27me3 together with Ring1B and by ChIP-on-chip analysis demonstrated that over the 5 prime HoxD locus H3K27me3 enrichment is decreased and Ring1B enrichment is sparse in limb cells derived from the distal posterior forelimb bud of E10.5 mouse embryos.

overall_design: Array design includes 2 biological replicates for H3K27me3 in the cell lines and Ring1B in the limb tissue, and 2 biological replicates and 2 dye swap replicates for H3K27me3 in the limb tissue.

first: Graeme

last: Grimes

first: Wendy

last: Bickmore


title: SBRI_AC Host response in primary mouse tracheal epitelial cells (mTEC)  to influenza infection with PR8, VN or X31 at MOI of 3 at 12 hours

city: Seattle

first: Aderem

last: Lab

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: Array analysis of total RNA from mTECs 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (MOI 3)

overall_design: Time Point: 12 h post infection (Mock, PR8, X31, VN) MOI 3.0; in biological triplicates. Total samples: 12.

first: Alan

last: Aderem


title: TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Background: Gene expression profiling of breast carcinomas has increased our understanding of the heterogeneous biology of this disease and promises to impact clinical care. The aim of this study was to evaluate the prognostic value of gene expression-based classification along with established prognostic markers and mutation status of the TP53 gene, in a group of breast cancer patients with long-term (12-16 years) follow-up.
Methods: The clinical and histopathological parameters of 200 breast cancer patients were studied for their effects on clinical outcome using univariate/multivariate Cox regression. The prognostic impact of mutations in the TP53 gene, identified using TTGE and sequencing, was also evaluated. Eighty of the samples were analyzed for gene expression using 42K cDNA microarrays and the patients were assigned to five previously defined molecular expression groups. The strength of the gene expression based classification versus standard markers was evaluated by adding this variable to the Cox regression model used to analyze all samples.
Results: Both univariate and multivariate analysis showed that TP53 mutation status, tumor size and lymph node status were the strongest predictors of breast cancer survival for the whole group of patients. Analyses of the patients with gene expression data showed that TP53 mutation status, gene expression based classification, tumor size and lymph node status were significant predictors of survival. The TP53 mutation status showed strong association with the ?basal-like? and ?ERBB2+? gene expression subgroups, and tumors with mutation had a characteristic gene expression pattern.
Conclusions: TP53 mutation status and gene-expression based groups are important survival markers of breast cancer, and these molecular markers may provide prognostic information that complements clinical variables. The study adds experience and knowledge to an ongoing characterization and classification of the disease.

overall_design: Experiment set consisting of 80 primary breast carcinomas collected at Ulleval University Hospital (ULL-samples), Oslo, Norway from 1990-94, and one normal sample from breast reduction surgery.

first: Anita

last: Langerod

first: Hongjuan

last: Zhao


title: LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (splicing array)

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: LIN28 is a conserved RNA binding protein implicated in pluripotency, reprogramming and oncogenesis. Previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) targets. Through cross-linking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells and somatic cells expressing exogenous LIN28, we have defined discrete LIN28 binding sites in a quarter of human transcripts. These sites revealed that LIN28 binds to GGAGA sequences enriched within loop structures in mRNAs, reminiscent of its interaction with let-7 miRNA precursors. Among LIN28 mRNA targets, we found evidence for LIN28 autoregulation and also direct but differing effects on the protein abundance of splicing regulators in somatic and pluripotent stem cells. Splicing-sensitive microarrays demonstrated that exogenous LIN28 expression causes widespread downstream alternative splicing changes. These findings identify important regulatory functions of LIN28 via direct mRNA interactions.

overall_design: In triplicate, polyA-selected RNA was extracted from untreated Flp-In-293 cells, stable LIN28V5 293 cells, TDP-43 over-expressed Flp-In-293 cells, control over-expressed Flp-In-293 cells, LIN28 depleted hES cells, and control depleted hES cells, and hybridized to custom human splicing sensitive microarrays

first: Stephanie

last: Huelga

first: Melissa

middle: L

last: Wilbert


title: Comparative genome hybridization profiles of six strains of Lactococcus lactis

status: Public on Sep 07 2012

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

summary: The intra sub-species diversity of six strains of Lactococcus lactis subsp. lactis was investigated at the genomic level and in terms of phenotypic and transcriptomic profiles in UF-cheese model. Six strains were isolated from various sources, but all are exhibiting a dairy phenotype. Our results showed that, the six strains exhibited small phenotypic differences since similar behaviour in terms of growth was obtained during cheese ripening while only different acidification capability was detected. Even if all strains displayed high genomic similarities, sharing a high core genome of almost two thousands genes, the expression of this core genome directly in the cheese matrix revealed major strain-specific differences. This strains with the same dairy origin.

overall_design: Strains were cultured on M17. At least three independent cultures of the six strains were performed. Genomic DNA was extracted from cells grown overnight on M17 and radiolabelled cDNA were prepared and hybridized on nylon arrays. 1948 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. 3 independent repetitions were performed.

first: Punthip

last: Tan-a-ram

first: Tamara

last: Cardoso

first: Marie-Line

last: Daveran-Mingot

first: Sunthorn

last: Kanchanatawee

first: Pascal

last: Loubiere

first: Laurence

last: Girbal


title: H3Cit26 ChIP-chip from MCF-7 cells

status: Public on Sep 04 2012

city: Ithaca

first: Xuesen

last: Zhang

address: Hungerford Hill RD

institute: Cornell Univ.

summary: Estrogen receptor α (ER), a member of the nuclear hormone receptor superfamily, regulates transcriptional activity by ligand-dependent recruitment of cofactors which, in turn, locally alter chromatin structure. It is generally believed that co-factor activity at target promoters leads to a more open, transcriptionally permissive chromatin structure, however, these mechanisms remain to be fully established. Peptidylarginine deiminases (PADIs) catalyze the conversion of positively charged arginine and methylarginine residues to neutrally charged citrulline and this activity has been linked to the gene regulation. Here, we found that PADI2 citrullinate H3 Arginine 26 (H3R26) in vitro and, using a specific H3R26 citrulline (H3Cit26) antibody, we demonstrate that H3Cit26 occurs in vivo following 17β-estradiol (E2) stimulation and this unique and pronounced global activation of H3Cit26 is ER-dependent. Using a mammalian-based promoter chromosomal array system, we observed that citrullination at H3R26 is robust and co-localizes with ER at decondensed chromatin loci. Additionally, this histone modification is specifically enriched at ER bound regions of target promoters, forming a permissive chromatin environment for gene transactivation. Interestingly, we have shown in a reciprocal way, that either depletion of PADI2 or inhibition of ER not only dramatically abolished E2-induced activation of H3Cit26 on gene promoters but also affect ER recruitment. Collectively, our results demonstrate that citrullination of H3R26 by PADI2 following estrogen stimulation plays a role in ER target gene activation, likely via decondensation of the local chromatin architecture.

overall_design: Two H3Cit26 ChIP-chip biological replicates under vehicle treatment and two H3Cit26 ChIP-chip biological replicates under E2 stimulation from MCF-7 human breast cancer cells are included.

first: Scott

last: Coonrod


title: Transcriptomic profiles of six strains of Lactococcus lactis in ultrafiltration-cheese model

overall_design: Strains were cultured on skimmed raw milk ultrafiltration (UF) retentate. The UF retentate was pre-incubated overnight at 4 °C, then 45 minutes at 50 °C and homogenized during 1.5 minutes at 24 000 rpm with an ultra-turax (Imlab, France). After addition of rennet (0.3 µl ml-1), 400 g UF retentate was inoculated at 2 106 CFU/g with L. lactis subsp. lactis strains. After incubation for 8 hours at 30 °C, the cheeses were transferred at 12° C until 7 days for ripening simulation. At least three independent cultures of the six strains were performed. Total RNA was extracted from cells grown 24 hours in UF-cheese and radiolabelled cDNA were prepared and hybridized on nylon arrays. 1948 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. 3 independent repetitions were performed.


title: Dengue patients whole blood

status: Public on Sep 06 2012

summary: Whole blood RNA (PAXgene tubes) was collected from 14 Dengue patients after hospital admission.  Additional samples were collected at later time points from 6 of the patients, and single samples were also collected from 4 healthy donors.  RNA was amplified using the MessageAmp kit (Ambion), and reverse transcribed.  Each sample was labelled with Cy5, and hybridized to a Lymphochip cDNA array along with amplified human reference RNA labelled with Cy3(Universal Human Reference RNA, Stratagene).  Analysis was restricted to those array elements (LUIDs) with signal intensity/background of at least 2.5 in either channel for at least 80% (28/34) of the samples, and a regression correlation of 0.6.  We characterized gene expression patterns associated with acute dengue infection, and identified a set of transcripts associated with diagnosis of Dengue Shock Syndrome.

first: Stephen

last: Popper


title: A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: This work reports on the identification and molecular characterization of a two-component regulatory system (2CRS), encoded by phoRP in Bifidobacterium breve UCC2003, which controls the response to phosphate (Pi) starvation. The response regulator PhoP was shown to bind to the promoter region of pstSCAB, specifying a predicted Pi transporter system, as well as that of phoU, which specifies a putative Pi-responsive regulatory protein. This interaction is assumed to cause transcriptional activation under conditions of Pi limitation. The phoRP genes appear to be subject to positive auto-regulation, and with pstSCAB and phoU, represent the complete regulon controlled by the phoRP-encoded 2CRS in B. breve UCC2003. Determination of the minimal PhoP binding region combined with bioinformatic analysis revealed the probable recognition sequence of PhoP, designated here as the PHO box, which together with phoRP is conserved among many high GC-content Gram+ bacteria. The importance of the phoRP 2CRS in the response of B. breve to Pi starvation conditions was confirmed by generating a B. breve::phoP insertion mutant which exhibited decreased growth under phosphate-limiting conditions as compared to its parent strain UCC2003.

overall_design: In order to investigate differences in global gene expression upon growth of B. breve UCC2003 under low phosphate conditions compared to normal growing cells, DNA microarray experiments were performed in CDM. Total RNA was isolated from B. breve UCC2003 cultures under normal conditions and cultures grown under low phosphate conditions. Starvation experiments with wildtype and overexpression strains were performed in triplicate, while knockout array experiments where performed as single experiments and targets were confirmed with QRT-PCR.

first: Douwe

last: van Sinderen


title: LMN-1-DamID in N2 and set-25(n5021) met-2(n4256) mutant early C. elegans embryos

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: We asked if the perinuclear position of chromosome arms in C. elegans depends on the histone methyltransferases MET-2 and SET-25. To this end, we performed LMN-1-DamID in wild-type (N2) and mutant (set-25 met-2) strains. LMN-1-DamID signal on chromosome arms was significantly reduced in the mutant.

overall_design: Three biological replicas were performed for each genotype. For one replica dyes were swapped. For each replica methylated DNA amplified from a strain expressing LMN-1-Dam was competitively hybridized against DNA amplified from a strain expressing GFP-Dam.

first: Benjamin

last: Towbin

first: Cristina

last: González-Aguilera

first: Peter

last: Askjaer

first: Susan

last: Gasser

first: Leslie

last: Hoerner


title: Expression analysis of Drosophila yakuba, D. santomea and hybrids to evaluate the large-X effect using Nimblegen 60-mer custom made arrays

status: Public on Sep 05 2012

city: Iowa City

first: Ana

last: Llopart

address: 469 Biology Building

institute: University of Iowa

summary: The X chromosome has a large effect on hybrid dysfunction, particularly hybrid male sterility.  Although the evidence for this so-called large-X effect is clear, its molecular causes are not yet fully understood.  One possibility is that, under certain conditions, evolution proceeds faster in X-linked loci than in their autosomal counterparts due to both natural selection and their hemizygosity in males (i.e. Faster-X effect), an effect that is expected to be greatest in genes with male-biased expression.  Here I studied variation in transcript abundance within and between species in Drosophila yakuba, D. santomea and their hybrid males to evaluate both the faster-X and large-X effects at the level of genome-wide gene expression.  I found that expression in X-linked male-biased genes evolves faster than in their autosomal counterparts, an effect that is accompanied by a unique reduction in gene expression polymorphism.  Although we do not know the precise relationship between nucleotide and gene expression changes, elevated divergence to polymorphism ratios are consistent with Darwinian selection driving expression differences between species in X-linked male-biased genes, likely enhanced by male hemizygosity.  Abundant changes in both cis- and trans-regulatory elements underlie regulatory gene expression divergence in the majority of the genes analyzed despite the recent split of the two sister species.  I detected a large-X effect on regulation of expression in hybrid males, affecting mostly male-biased genes but also, to a lesser degree, nonsex-biased genes.  Interestingly this misexpression is concentrated mostly in autosomal genes, likely facilitated by the rapid evolution of sex-linked trans-acting factors. I conclude that the faster evolution of X-linked male-biased genes, at both protein and expression levels, can contribute to explain the large effect of the X chromosome on hybrid male sterility, possibly mediating autosomal misexpression through cis-trans interactions.

sample_organism:
Drosophila yakuba
Drosophila santomea
Drosophila yakuba x Drosophila santomea

overall_design: 18 array study using total RNA (cDNA retranscribed with Oligo-dT) recovered from 1-day old adult males of three Drosophila yakuba and three D. santomea isofemale lines and the two reciprocal F1 hybrid males, with three-fold technical redundancy.  Gene expression was estimated from a total of 12,442 protein-coding genes using 60-mer probes and an average of 10 probes per gene.


title: Global transcriptional profiles response to strain variation and medium change for validamycin overproduction

status: Public on Sep 01 2012

city: shanghai

first: hang

last: wu

address: Huashan Road

institute: sjtu

summary: To explore the molecular basis of validamycin overproduction at the transcriptional level, the transcriptomes of strain 5008 and TL01 cultivated in Yeast extract-Malt extract-Glucose (YMG) and rice-peanut cake based industrial (IND) fermentation medium were compared by microarray analysis.

sample_organism: Streptomyces hygroscopicus subsp. jinggangensis 5008

sample_organism: Streptomyces hygroscopicus subsp. jinggangensis TL01

overall_design: Global gene expressions in the strain 5008 and TL01 were measured in fermentation medium YMG and IND, respectively. Three independent experiments were performed at each condition.

first: Hang

last: Wu


title: Biological replicates of Ruditapes philippinarum digestive gland pools

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

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

institute: University of Padova

summary: Four pools of digestive glands were treated as biological replicates in order to evaluate the repeatability of Ruditapes philippinarum oligo microarray platform.

overall_design: In this study, we analyzed four (4) independent pools of Ruditapes philippinarum digestive glands. Gene expression profiling was performed using the Agilent-027304 Ruditapes philippinarum Oligo Microarray platform (1 arrays) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Milan

last: Massimo

first: Bargelloni

last: Luca


title: Comparison of gene expression profile of Ruditapes philippinarum gills and digestive glands.

summary: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills and digestive gland of R. philippinarum. For each tissue, total RNA was extracted from three (3) independent biological replicates of digestive gland and gills, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified 8,257 probes differentially expressed between the two different tissues.

overall_design: In this study, we analyzed six (6) samples, three (3) pools of digestive gland and three (3) pools of gills. Gene expression profiling was performed using the Agilent-019810 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni


title: In vivo and in vitro investigations of heterozygous nebulin knock-out mice reveal similarities with mild human form of nemaline myopathy [mRNA]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: In the present study, we used a multimodal approach including protein and gene expression analysis and combined in vivo and in vitro measurements of force production. Overall, we aimed at investigating the functional impact of the expression of a single nebulin allele.

overall_design: Comparison of the mRNA expression profile of quadriceps in 3 nebulin wild type mice with 3 nebulin heterozygous mice.

first: C

last: Gineste

first: J

last: De Winter

last: Kohl


title: Vibrio campbellii bioluminescence and its effect on gene expression and virulence

status: Public on Aug 31 2012

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary: The selective advantage of bioluminescence in bacterial cells that do not form symbiotic relationships with aquatic animals is still not known. Some evidence suggests that bioluminescence plays a role in DNA repair by a photoreactivation process (Czyz 2000) and that non-bioluminescent strains are less virulent than their bioluminescent isogenic counterparts (Ruwandeepika 2010). All hypotheses to date suggest bioluminescence associated or mediated changes in gene expression, yet the evidence for this does not exist. In this study, we generated an in-frame luxAB deletion mutant (the two contiguous genes that encode for bacterial luciferase) and compared its mid-log phase gene expression profile with that of the wild type spontaneous streptomycin resistant (STR) V. campbellii BAA-1116 parental strain from which it was derived. Both mid-log phase transcriptomes were elucidated using custom designed whole genome microarrays (520694F, Affymetrix) to determine the effect luciferase has on V. campbellii gene expression. The virulence phenotypes of both strains were also subsequently tested in Artemia franciscana challenge experiments.

platform_organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

overall_design: Three biological replicates of the wild type (STR) and luxAB deletion mutant of V. campbellii BAA-1116 were grown to mid-log phase (15 h, 200 rpm, 30°C, in 25 mL autoinducer bioassay medium) and total RNA was extracted from 1.0E+9 cells. Messenger RNA was isolated from the total RNA extracts treated with DNase, labeled with biotin, fragmented and hybridized to V. campbellii BAA-1116 whole genome microarrays (520694F, Affymetrix).

first: Zheng

last: Wang

first: Robert

last: Rubin

first: Tom

last: Defoirdt

last: Bossier

first: Gary

last: Vora


title: X-chromosome inactivation in monkey embryos and pluripotent stem cells

city: Beaverton

first: Shoukhrat

last: Mitalipov

address: 505 N.W. 185th Avenue

institute: Oregon National Primate Research Center

summary:
In this study, we explored x-inactivation in monkey embryos (ICM and TE separately) and pluripotent stem cells (IVF derived ES, SCNT-derived ES and monkey iPS)
To elucidate x-inactivation in experimentally reprogrammed pluripotent cells, we derived pluripotent stem cells by both SCNT and iPS approaches from same parental skin fibroblasts. We also compared gene patterns of those cells to IVF-derived counterpart.

overall_design: The transcriptomes of rhesus monkey embryonic stem cell lines derived by both SCNT (CRES) and iPS (RiPS) from same monkey skin fibroblasts were compared each other. Both experimentally reprogrammed cells were also compared with IVF-derived counterpart (ORMES23). Finally, the adult somatic skin fibroblasts were analyzed. Three biological replicates of each cell line (A, B, C) were analyzed.

first: Masahito

last: Tachibana

first: Hong

last: Ma

first: Hathaitip

last: Sritanaudomchai


title: Comparison of gene expression profile of Ruditapes philippinarum sampled in Marghera and Alberoni

status: Public on Aug 25 2012

last: Milan

summary:
Digestive Gland Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of digestive gland for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed.
Gills Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of gills for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed.

overall_design:
Digestive Gland Samples: In this study, we analyzed six (6) samples, three (3) pools of digestive gland of Manila clam sampled in Marghera and three(3) pools of digestive gland of Manila clam sampled in Alberoni. Gene expression profiling was performed using the Agilent-019810 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
Gills Samples: In this study, we analyzed six (6) samples, three (3) pools of gills of Manila clam sampled in Marghera and three(3) pools of gills of Manila clam sampled in Alberoni. Gene expression profiling was performed using the Agilent-019810 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.


title: Genomic profiles of oxidative stress-induced rat renal cell carcinomas

status: Public on Aug 30 2012

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

institute: Nagoya University

summary: Intraperitoneal administration of ferric nitrilotriacetate (Fe-NTA) initiates Fenton reaction in the renal proximal tubules of rodents that ultimately leads to a high incidence of renal cell carcinoma (RCC) after repeated treatment. We performed high-resolution microarray comparative genomic hybridization to identify characteristics in the genomic profiles of oxidative stress-induced rat RCCs. The results revealed extensive large-scale genomic alterations with a preference for deletion.

overall_design: Carcinogenesis protocol was performed using male F1 hybrid rats between Fischer344 and Brown-Norway strains. 13 primary tumors and 2 cell lines of Fe-NTA induced RCCs were profiled on Agilent 185K rat genome CGH microarrays. One RCC sample of a female Eker rat was also analyzed with the same Agilent 185K rat genome CGH microarray.

first: Toyokuni

last: Shinya

first: Akatsuka


title: miRNA gene expression profiles from osteosarcoma samples and cell lines

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Although the introduction of combined neoadjuvant chemotherapy has significantly prolonged the survival, the outcome of OS patients with poor response to chemotherapy is still unfavorable. To develop new therapeutics the elucidation of the entire molecular pathway regulating OS cell proliferation is warranted.
We analysed the expression levels of 933 miRNA probes in surgical 24 samples and 8 cell lines of osteosarcoma with 3D-Gene human miRNA oligo chips.

overall_design: Total RNA was extracted from 24 fresh frozen tumour specimens and 8 OS cell lines. We analysed the global miRNA exprssion profiles of these osteosarcoma cases in order to find new novel potential targets for the development of therapeutic targeting OS.

first: Eisuke

last: Kobayashi

last: Nakayama

first: Hitoshi

last: Ichikawa

first: Tesshi

last: Yamada


title: EST sequencing and microarray analysis of the floral transcriptome of Eustoma grandiflorum

city: Bunkyo-ku

first: Saneyuki

last: Kawabata

state: Tokyo

address: 1-1-1 Yayoi

institute: University of Tokyo

summary: Genome-wide DNA sequence resources are expected to enhance our understanding of the molecular basis of plant development and lead to improvements in desirable traits in horticultural crops. In this study, we sequenced 643,366 ESTs from Eustoma grandiflorum flowers using a normalised cDNA library constructed for several different flower development stages, times of day, and pollinated stamens. The sequences were assembled into 63,401 contigs and 242,212 singletons. BlastX searches for all of the contigs in the GenBank database matched 65% of the contigs to registered sequences, while 35% presented no hits. GO mapping assigned 48% of the 63,401 contigs to GO terms. Microarray analysis showed that subsets of genes were up- or downregulated as the flower developed. The downregulated genes were enriched for GO terms related to 1) oligopeptide transport, 2) response to jasmonic acid stimulus, and 3) cell wall modification, whereas the upregulated genes were enriched for GO terms involved in 1) secondary metabolism, such as the flavonoid biosynthetic process and the terpenoid biosynthetic process, and 2) epidermal cell modification.

overall_design: Two-condition experiment, loop-design among 4 developmental stages. Biological replicates: 4.

first: Yuhua

last: Li

first: Kentaro

last: Miyamoto


title: Sense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type

status: Public on Jul 25 2012

city: Kansas City

first: Swaminathan

last: Venkatesh

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary: Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in K36A, K56R and K36AK56R mutant yeast strain compared to wildtype.

overall_design: Two color experiment. Mutant/WT. Biological replicates=3. Hybridisation of same samples to strand-specific gene expression arrays.

first: Madelaine

last: Gogol

first: Hua

first: Jerry

last: Workman

first: Michaela

last: Smolle


title: Isw1 and Chd1 maintain chromatin organization during transcription [isw1 chd1 mutant expression]

state: Missouri

summary: Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in an isw1 chd1 mutant yeast strain.


title: Transcriptome Profiling of Surgical Myectomy Tissue from Patients with Hypertrophic Cardiomyopathy

city: Rochester

first: Virginia

middle: Bartleson

last: Hebl

state: MN

address: 200 1st St. SW

institute: Mayo Clinic

summary: Using a high-throughput gene expression profiling technology, we have been able to develop new hypotheses regarding the molecular pathogenic mechanisms of human hypertrophic cardiomyopathy (HCM). It is hoped that these hypotheses, among others generated by this data, will fuel future research endeavors that will uncover novel biomarkers, prognostic indicators, and therapeutic targets to improve our ability to diagnose, counsel, and treat patients with this highly heterogeneous and potentially life-threatening condition.

overall_design: Case-control study comparing the messenger RNA transcriptome of cardiac tissues from patients with hypertrophic cardiomyopathy to the transcriptome of control donor cardiac tissues.

middle: B

first: J

last: Bos

first: Ann

last: Oberg

first: Zhifu

last: Sun

first: Daniel

last: Herman

first: Polakit

last: Teekakirikul

middle: G

last: Seidman

first: Christine

middle: E

first: Cristobal

last: dos Remedios

first: Hartzell

middle: V

last: Schaff

first: Joseph

last: Dearani

first: Steve

last: Ommen

first: Frank

last: Brozovich

first: Michael

last: Ackerman


title: Insights into the transcriptomics of polyphagy: Bemisia tabaci adaptability to phenylpropanoids involves coordinated expression of defense and metabolic genes

city: Rehovot

first: Michal

last: Alon

address: Herzel St.

department: Department of Entomology

country: Israel

institute: Hebrew University of Jerusalem

summary:
Background: The whitefly Bemisia tabaci is a major generalist agricultural pest of field and horticultural crops world-wide. Despite its importance, the molecular bases of defense mechanisms in B. tabaci against major plant secondary defense compounds, such as the phenylpropanoids, remain unknown.
Results: Our experimental system utilized transgenic Nicotiana tabacum plants constitutively expressing the PAP1 ⁄ AtMYB75 transcription factor which activates specifically the phenylpropanoid / flavonoids biosynthetic pathway. Our study used suppression subtractive hybridization (SSH) and cDNA microarray approaches to compare gene expression between B. tabaci adults subjected to wild-type or transgenic plants for six hours. A total of 2880 clones from the SSH libraries were sequenced. Both the SSH and cDNA microarray analyses indicated a complex interaction between B. tabaci and secondary defense metabolites produced by the phenylproapnoids / flavonoids pathway, involving enhanced expression of detoxification, immunity, oxidative stress and general stress related genes as well as general metabolism and ribosomal genes. Quantitative PCR revealed significant changes in the expression of several of these genes in response to feeding on artificial diet containing the flavonol quercetin. The elevated transcriptional activity was not accompanied by reduced reproductive performance, indicating high adaptability of B. tabaci to this large group of plant secondary defense metabolites.
Conclusion: Results of this study allows first insight into the molecular mechanisms underlining polyphagy in B. tabaci. Our analyses revealed many candidate genes related to the insect's various defense systems capable of neutralizing a broad range of plant toxins. Future technological developments allowing silencing or over-expression of selected target genes in B. tabaci, will enable determining a specific linkage between gene expression and host related performance in this species.

overall_design: 3 hybridizations were performed for RNA extracted from Bemisia tabaci adults that fed on PAP Purple transgenic tobacco plants for 6hr, labeled with Cy5 and directly hybridized against 3 samples from B. tabaci adults that fed on wild type plants as a control and labeled with Cy3. Another 3 swap dye hybridizations were performed in which adults that fed on wild type plants for 6hr were coupled with the Cy5 and adults that fed on PAP Purple transgenic plants were coupled with Cy3.

first: Moshe

last: Elbaz

last: Ben-Zvi

first: Ester

last: Feldmesser

first: Alexander

last: Vainstein

first: Shai

last: Morin


title: Characterizing gene regulatory networks in the brain of largemouth bass inhabiting rivers containing high levels of methyl-mercury (field study)

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Background and Methods: High mercury (Hg) levels are a significant concern in many aquatic environments, and adverse effects of Hg exposure in fish can include altered behavior, reproduction, growth, and increased stress responses. In addition, human health concerns over Hg continue to warrant new research on its mechanisms of action.  The objectives of this study were to investigate the impacts of Hg on the female largemouth bass (LMB) central nervous system transcriptome by conducting a laboratory injection experiment with 2.5 µg/g body weight in addition to sampling LMB from an environment that contains high levels of Hg (St. Mary’s River, Florida, USA).  These animals were compared to LMB that inhibit river systems with lower Hg (Big Wekiva, Santa Fe and St. John’s Rivers Florida, USA).  A LMB 8 x 15 K microarray was used for hypothalamic (laboratory) and whole brain (field) transcriptomics analysis.  Results: Mercury in the blood of LMB collected from St Mary’s River was significantly elevated 3-fold (~ 0.1 ng Hg/ml blood) compared to LMB collected from the other three sites (~ 0.03 ng Hg/ml blood).  In the hypothalamus of Hg injected LMB, there were 937 genes that showed differential expression (raw p = 0.05) but there were no probes that passed an FDR for multiple hypothesis correction. In contrast, in field collected LMB there were 2909 genes that that showed differential expression (raw p = 0.05) of which 38 were significant after correction for multiple hypothesis testing (FDR = 0.05).  These included Hsp90 co-chaperone Cdc37, multicopper oxidase, mismatch repair protein Msh6, and 16 kDa heat shock protein A.  Functional enrichment in whole brains of LMB collected from the field sites revealed that genes involved in the biological processes of protein folding and targeting, regulation of protein metabolic process, and protein degradation (i.e. ubiquitin cycle) were over-represented. Interestingly, gene set enrichment analysis identifed expression targets that were in common between the laboratory experiment  (MeHg injected) and field collected LMB and these consisted of mainly homeobox transcription factors (PROP paired-like homeobox 1, LIM homeobox 3 and paired-like homeodomain 1 and 2). Lastly, prevalent themes emerged in the SNEA expression targets that included neuropeptide receptor signaling, steroid signaling, and structural components, such as beta-actin, integrins, and stress fibres.  Conclusions: This study characterizes novel cell signaling pathways that underlie Hg toxicity in the teleostean central nervous system.

overall_design: field study with methyl mercury

first: Chris

first: Cathy

last: Richter

first: Nancy

middle: D

last: Denslow

first: Don

last: Tillit


title: Characterizing gene regulatory networks in the brain of largemouth bass inhabiting rivers containing high levels of methyl-mercury (lab study)

overall_design: 4 control and 3 treated hypothalami

middle: J


title: Gene expression profiling of RPMI-grown and macrophage-internalized Candida glabrata wild-type, Cgrsc3-a∆ and Cgrtt109∆ cells.

status: Public on Aug 18 2012

city: Hyderabad

first: Rupinder

last: Kaur

state: AP

address: Building 7, Gruhakalpa,Nampally

department: Fungal Pathogenesis

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

summary:
To delineate the interaction of Candida glabrata with host immune cells, we performed genome-wide transcriptional  profiling analysis on  THP-1 macrophage-internalized  wild-type and chromatin remodeling defective mutant (Cgrsc3-a∆ and Cgrtt109∆) yeasts. Genes implicated in ergosterol biosynthesis, and high-affinity iron uptake and homeostasis were found to be down-regulated in C. glabrata wild-type and mutant cells upon macrophage internalization. Additionally, global gene expression profiles of RPMI-grown and macrophage-ingested Cgrsc3-a∆ and Cgrtt109∆ cells revealed down-regulation of genes involved in mitochondrial respiration under normal growth conditions and induction of genes required for generation of precursors of metabolites and energy upon macrophage internalization.
To examine the behavior of Candida glabrata wild-type and chromatin remodeling defective mutants upon internalization by differentiated human monocytic THP-1 cells, we compared the transcript profiles of 10 hour RPMI-grown with those of 10 hour THP-1 macrophage internalized C. glabrata cells. Additionally, early transcriptional response of C. glabrata wild-type cells to macrophage internal milieu was examined post 2 hour THP-1 macrophage infection.

overall_design: Agilent one-color experiment, Organism: Yeast  (Candida glabrata)

first: Maruti

middle: N

last: Rai

first: Sriram

last: Balusu

first: Neelima

last: Gorityala

first: Lakshmi

last: Dandu


title: EGF decreases the abundance of microRNAs that restrain oncogenic transription factors

city: reovot

first: roi

last: avraham

address: hertzel

institute: weizmann

summary: Epidermal growth factor (EGF) stimulates cells by launching gene expression programs that are frequently deregulated in cancer. MicroRNAs, which attenuate gene expression by binding complementary regions in messenger RNAs, are broadly implicated in cancer. Using genome-wide approaches, we showed that EGF stimulation initiates a coordinated transcriptional program of microRNAs and transcription factors. The earliest event involved a decrease in the abundance of a subset of 23 microRNAs. This step permitted rapid induction of oncogenic transcription factors, such as c-FOS, encoded by immediate early genes. In line with roles as suppressors of EGF receptor (EGFR) signaling, we report that the abundance of this early subset of microRNAs is decreased in breast and in brain tumors driven by the EGFR or the closely related HER2. These findings identify specific microRNAs as attenuators of growth factor signaling and oncogenesis

overall_design: 24 conditions: time course of 8 hours of HeLa and MCF10A cells after EGF or SERUM stimulation

first: Roi

last: Avraham

first: Yosef

last: Yarden


title: Antisense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type

first: Swaminathan

last: Venkatesh

first: Madelaine

last: Gogol

first: Hua

last: Li

first: Jerry

last: Workman

first: Michaela

last: Smolle


title: Isw1 and Chd1 maintain chromatin organization during transcription [K56ac data]

summary: ChIP-chip assays to determine the occupancy of acetylated histone H3 K56 in wildtype, isw1, chd1, isw1 chd1 and ISW1[K227R] yeast.

overall_design: Two color experiment. ChIP/Input. K56ac data normalized to histone H3 and plotted as mutant over wildtype. Biological replicates=3. Please note that H3 data for YMS123-125 & YMS127 is part of the AcH4 file.


title: High Glucose (HG) treated morula vs control glucose (CTL) treated morula

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

summary: Early bovine cleavage (day 0 to 3) was treated with high glucose (5mM) or control glucose (0.2mM) then total day 3 embryos were cultured in control condition until day 5 when gene expression was assessed in developping morula by microarray

overall_design: 4 replicates of 10 morulae/rep was produced for high glucose and control treatment. According to a dye swap design, 4 arrays were used, one array for each comparison between HG and control, i.e replicate 1 from HG were compared to replicate 1 from CTL, rep 2 from HG were compared to rep 2 from CTL, rep 3 HG vs rep 3 CTL, rep 4 HG vs rep 4 CTL.


title: Comparative transcription profiling of heritage maize lines

status: Public on Aug 16 2012

city: Peoria

first: Eric

last: Johnson

state: IL

address: 1815 N. University St.

department: Crop Bioprotection Research

institute: USDA ARS

summary: Three different maize lines were assayed for differential gene expression in mature leaf tissue. Leaves from the Oh43 maize line are more resistant to insect larvae damage than the original parents, lines Oh40B and W8. The goal of the project was to discover genes highly expressed in the Oh43 line that potentially contributes to insect resistance.

overall_design: RNA was extracted from a mature leaf (third visible leaf from the top of a 7 leaf plant) of each inbred (Oh43, Oh40B, and W8). cDNA from four biological replicates of each inbred was labeled (indirect method) twice with Cy5 and twice with Cy3. A total of six microarray slides were probed with 12 different labeled cDNAs.

middle: T

first: Patrick

middle: F

last: Dowd


title: Isw1 and Chd1 maintain chromatin organization during transcription [AcH4 data]

summary: ChIP-chip assays to determine the occupancy of acetylated histone H4 in wildtype, isw1 and chd1 yeast.

overall_design: Two color experiment. ChIP/Input. AcH4 data normalized to histone H3 and plotted as mutant over wildtype. Biological replicates=3.


title: The IHF regulon of exponentially growing Pseudomonas putida cells

city: Campus de Cantoblanco

first: Victor

last: de Lorenzo

state: Madrid

address: Darwin 3

department: Systems Biology

institute: CNB-CSIC

summary: Integration host factor (IHF) sites are largely absent from intergenic regions of ORFs encoding central metabolic functions in Pseudomonas putida mt-2. To gain an insight into this unequal distribution of otherwise abundant IHF-binding sequences, the transcriptome of IHF-plus and IHF-minus cells growing exponentially on glucose as sole carbon source was examined. In parallel, the cognate metabolic fluxes of the wild-type P. putida strain and its ihfA derivative were determined by culturing cells to a steady-state physiological regime with (13) C-labelled glucose. While expression of many transcripts was altered by the lack of IHF, flux balance analysis revealed that the ihfA mutation did not influence central carbon metabolism. Identification of multiple IHF sites adjacent to genes responsive to the factor allowed a refinement of the consensus and the mapping of the preferred binding positions for activation or repression of associated promoters. That few (if any) of the genes affected by IHF involved core pathways suggested that the central carbon metabolism tolerates the loss of the factor. Instead, IHF controlled various cell surface-related functions and downregulated genes encoding ribosomal proteins, the alpha subunit of RNA polymerase and components of the ATP synthase. These results were confirmed with lacZ fusions to a suite of promoters detected in the transcriptome as affected by IHF. Taken together, the data suggest that IHF plays a role in the physiological shift that sets P. putida for entering stationary phase.

overall_design: We compared the transcriptional profiles of P. putida mt-2 and the ihfA mutant. Samples were hybridized on a P. putida genome-wide oligonucleotide-based DNA microarray (Progenika Biopharma SA). RNA samples of seven independent biological samples were mixed in three pools. A dye-swap was performed.

first: Rafael

last: Silva-Rocha

first: Max

last: Chavarría

first: Roelco

last: Kleijn

first: Uwe

last: Sauer


title: Merging candidate gene approach with high throughput systems biology technology for the development of xylose utilising S. cerevisiae strains

status: Public on Jul 15 2012

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

summary: Though highly efficient at fermenting hexose sugars, the ethanologenic yeast Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomasses is the five carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars. Here we combined classical candidate gene approach with systems biology to develop xylose-utilising S. cerevisiae strains. The introduction of an exogenous xylose isomerase (XYLA) and an additional copy of the endogenous xylulokinase gene (XKS1) results in the significant improvement of xylose consumption. Microarray studies reveal that the introduction of XYLA and XKS1 results in the dramatic transcriptional remodelling of the cell under both glucose and xylose conditions. To further investigate the cellular processes impacted by the introduction of XYLA and XKS1, using genome-wide chemical and synthetic lethal screens we identified greater than 40 deletion mutants that impact xylose utilization. We identified four genes, ALP1, ISC1, RPL20B and BUD21, that when individually deleted allow S. cerevisiae to utilize xylose as the sole carbon source. When these mutants are combined with XYLA and XKS1, it results in strains with significant improvement in xylose consumption. We have demonstrated that systems biology techniques combined with candidate gene approaches can successfully lead to novel genetic strategies for the improvement of xylose utilization

overall_design: For this experiment samples (2 reference and 2 test samples), consisting of at least 3 biological reps were hybridized. Cy3 one-color labelling was used for each sample.

first: Jane

last: Usher

first: Anne

last: Johnston

first: Peter

last: Quon

first: Nicholas

last: Gold

first: Vincent

last: Martin

first: Kristin

last: Baetz


summary: Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains.

overall_design: Two color experiment. Deletion mutant vs. WT cells. Biological replicates=3 per IP per cell type.

first: Madelaine

last: Gogol

first: Hua

last: Li

first: Jerry

last: Workman


title: ChIP-on-chip analysis of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells

status: Public on Jun 06 2012

city: Yokohama

first: Takaho

middle: A.

last: Endo

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: ChIP-on-chip analysis was carried out to determine targets of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells.

overall_design: ChIP-on-chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). ESCs were subjected to ChIP assay using specific antibodies. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously (van Bakel et al., 2008). Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

first: Mitsuhiro

last: Endoh

middle: A

first: Haruhiko

last: Koseki


title: cDNA microarray expression profile during fiber elongation between G. hirsutum and G. barbadense

status: Public on May 24 2012

city: Nanjing

first: Tianzhen

last: Zhang

state: Jiangsu

institute: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute

summary: Sea-island cotton (Gossypium barbadense L.) has superior fiber quality properties such as length, fineness and strength, while Upland cotton (Gossypium hirsutum L.) is characterized by high yield. To reveal features of Upland cotton and Sea-island cotton fiber cells, differential genes expression profiles during fiber cell elongation and in secondary wall deposits were established using cDNA microarray technology. This research provides a valuable genomic resource to deepen our understanding of the molecular mechanisms of cotton fiber development, and may ultimately lead to improvements in cotton fiber quality and yield.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: 15 samples were prepared for microarray slides hybridized with three biological replicate samples including a swap-dye experiment for each growth stage. Each spot had a repeat in the microarray slide，therefore, data for six replicate experiments performed with biologically independent samples.

first: Xiangdong

last: Chen


title: Expression analysis of Saccharomyces cerevisiae INVSc1 under accumulation of the bacterial alarmone ppGpp

status: Public on May 31 2012

city: Hiroshima

first: Kozo

last: Ochi

state: Hiroshima

address: 2-1-1 Miyake, Saeki-ku

department: Food Sciences and Biotechnology

institute: Hiroshima Institute of Technology

summary:
ppGpp accumulation caused by ectopic expression of RelA in Saccharomyces cerevisiae gave rise to marked changes in gene expression with both upregulation and downregulation, including changes in mitochondrial gene expression. The most prominent upregulation (38-fold) was detected in the function-unknown hypothetical gene YBR072C-A, followed by many other known stress-responsive genes.
ppGpp acuumulation resulted in enhancement of tolerance against various stress stimuli, such as osmotic stress, ethanol, hydrogen peroxide, and high temperature.

overall_design: A two chip study using total RNA recoverd from the Saccharomyces cerevisiae TN2080 (accumulating ppGpp) and TN2077 (vector control) grown to mid-growth phase (8h) in SC-uracil medium. The plasmid pYC2/CT (V5-epitope tag vector) was used as a vector to express Sj-RSH.

first: Tomoyasu

last: Nishizawa


title: Protein Kinase C Mediated Extraembryonic Endoderm Differentiation of Human Embryonic Stem Cells

status: Public on Jun 01 2012

city: madison

first: James

last: Thomson

state: Wisconsin

address: 425 Henry Mall

department: Regenerative Biology

institute: Mogridge Institute for Research

summary: Unlike mouse embryonic stem (ES) cells, which are closely related to the inner cell mass, human ES cells appear to be more closely related to the later primitive ectoderm.  For example, human ES cells and primitive ectoderm share a common epithelial morphology, growth factor requirements, and the potential to differentiate to all three embryonic germ layers. However, it has previously been shown that human ES cells can also differentiate to cells expressing markers of trophoblast, an extraembryonic lineage formed before the formation of primitive ectoderm. Here we show that phorbol ester 12-O-Tetradecanoylphorbol 13-acetate (TPA) causes human ES cells to undergo an epithelial mesenchymal transition and to differentiate into cells expressing markers of parietal endoderm, another extraembryonic lineage. We further confirmed that this differentiation is through the activation of PKC pathway and demonstrated that a particular PKC subtype, PKC-delta, is most responsible for this transition.

overall_design: This is a time course design. It includes 16 samples.

first: Xuezhu

last: Feng

first: Jiuchun

first: Kim

last: Smuga-Otto

first: Shulan

last: Tian

first: Junying

last: Yu

first: Ron

last: Stewart


title: Transcriptomic profiling of chicken adipose tissue in response to insulin neutralization and fasting

status: Public on Jun 22 2012

city: Knoxville

first: Bo

last: Ji

state: TN

address: 2640 Morgan Circle Drive

department: Animal Science

institute: University of Tennessee

summary: Domestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the suite of rodent models used for studies of obesity and type 2 diabetes in humans. Furthermore, chicken adipose tissue is considered as poorly sensitive to insulin and lipolysis is under glucagon control. Excessive fat accumulation is also an economic and environmental concern for the broiler industry due to the loss of feed efficiency and excessive nitrogen wasting, as well as a negative trait for consumers who are increasingly conscious of dietary fat intake. Understanding the control of avian adipose tissue metabolism would both enhance the utility of chicken as a model organism for human obesity and insulin resistance and highlight new approaches to reduce fat deposition in commercial chickens.

overall_design: In the present study we simultaneously characterized the effects of a short term (5 hours) fast or neutralization of insulin action (5 hours) on adipose tissue of young (16-17 day-old), fed commercial broiler chickens.

first: Suchita

last: Das

first: Arnold

middle: M

last: Saxton

first: Jean

last: Simon

first: Joelle

last: Dupont

first: Sonia

last: Métayer-Coustard

first: Brynn

middle: H

last: Voy


title: Heterologous expression of sahH reveals that biofilm formation is autoinducer-2 independent in Streptococcus sanguinis, but is associated with an intact AMC

status: Public on Apr 04 2012

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

institute: hospital university rostock

summary:
In a transcriptome based trail, we figured out that the deletion of luxS has a massive influence to cell growth and metabolism of Streptococcus sanguinis SK36. The biofilm defective luxS deletion mutant was comlemented by transgenic sahH from Pseudomonas aeruginosa. Thus 209 of 216 influenced genes of the luxS mutant compared to the isogenic wildype were restored in their expression (fold change of n ≥ 3; p ≤ 0.05), including genes involved in cell division processes, stress response and catabolite control. Phenotypically, the reduced biofilm depth of S. sanguinis SR DELTAluxS was elevated to wild type level by the complementation with sahH. Neither the addition of physiological concentrated artificial autoinducer 2 (AI-2) to the culture of S. sanguinis SR DELTAluxS nor the presence of the wild type strain in a trans-well assay had a cumulative effect on biofilm thickness of the luxS mutant. Furthermore, we identified 9 genes in the sahH complemented luxS mutant, which were regulated directly by AI-2 (fold change ≥ 3; p ≤ 0.05), amongst them genes involved in competence development. So we concluded that AI-2 has no influence on biofilm growth, but regulative functions in competence development in S. sanguinis. Further, we figured out the suitability of transgenic sahH for the complementation of the interrupted Pfs/LuxS pathway without restoration of AI-2 release acquiring an essential tool for further investigations on AI-2.
Aim: Is the presence of AI-2 necessary for the biofilm formation of S. sanguinis SK36?  What is the impact of a deletion of luxS, is a disrupted activated methionine cycle the reason for the hampered biofilm depth causes by its inactivation?
Materials and Methods: S. sanguinis SK36, S. sanguinis SR ΔluxS, and S. sanguinis SR ΔluxS/sahH were grown in CDM/sucrose for 24 h anaerobically; biofilm depth was measured by safranine and crystal violet stain. Biofilm morphology was investigated by scanning electron microscopy. The AI-2 release was monitored hourly to identify the time period of its release. For transcriptome analysis total RNA was isolated after 8 hours of growth and used for microarray analysis.

overall_design: The chip study used total RNA recovered from S. sanguinis SK36, its luxS mutant, and the sahH complementated luxS mutant. Gene expression analysis was done with three independent replicates, each. Chip content: 10186 genes (1883 genes of P. gingivalis W83, 1964 genes of F. nucleatum DSMZ 25586, 2244 genes of S. sanguinis SK36, 2168 genes of A. actinomycetemcomitans HK1651, 1927 genes of S. mutans UA159) with up to thirteen 60-mer probes per gene, with three-fold technical redundancy and additionally 3510 random sequence probe. In this study only the S. sanguinis and RANDOM probes were used for analysis.

first: Kerstin

last: Standar

first: Andreas

last: Podbielski

first: Bernd

last: Kreikemeyer


title: Colon tissue of Il10-/- mice monoassociated with Escherichia coli NC101 or Escherichia faecalis OG1RF (PAMM-077 array)

status: Public on Jul 04 2012

city: Chapel Hill

first: Janelle

middle: C

last: Arthur

state: NC

address: 111 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: We observed that interleukin-10 knockout (Il10-/-) mice injected with azoxymethane (AOM) and monoassociated with E. coli NC101, but not E. faecalis OG1RF, develop tumors. Histologic inflammation is not different in mice monoassociated with either bacterium. The goal of this experiment is to assess inflammatory cytokine levels in colonic tissue of these mice.

overall_design: 4 germ-free Il10-/- mice were assayed and used as controls. 4 E. coli and 4 E. faecalis monoassociated mice were experimental samples.

first: Christian

last: Jobin