title: Expression data of enterotoxigenic (ETEC) isolate E24377A

status: Public on Mar 01 2012

city: Baltimore

first: Jason

last: Sahl

address: 801 West Baltimore St.

department: School of Medicine

institute: University of Maryland

summary:
ETEC is an important human pathogen.  Although the mechanism of diarrhea is known in ETEC, the regulatory networks are less understood.  This study was conducted to understand the global expression of ETEC isolate E24377A under different growth and environemental conditions.
ETEC isolate E24377A was grown in the presence of several chemical signals, including bile salts, glucose, and pre-conditioned media (PCM) from other enteric pathogens.  E24377A was also grown to different densities, to see if a quorum sensing mechanism was in place

platform_organism:
Escherichia coli
Shigella

overall_design: The isolate was grown in different types of media, with different ammendments, and at different growth densities.  The overall goal was to determine how expression gene expression changes in the presence of chemical signals; a special emphasis was placed on the expression of known and suspected virulence and colonization factors

first: David

last: Rasko


title: Rhesus macaque cerebral cortex  DNA methylation profiling by MeDIP-Chip

city: Los Angeles

first: Jinkai

last: Wang

state: CA

address: 650 Charles E. Young Drive South, CHS 33-228

country: USA

institute: University of California, Los Angeles

type: Methylation profiling by genome tiling array

summary: The highly improved cognitive function is the most significant change in human evolutionary history. Recently, several large-scale studies reported the evolutionary roles of DNA methylation; however, the role of DNA methylation on brain evolution is largely unknown. To test if DNA methylation has contributed to the evolution of human brain, with the use of MeDIP-Chip and SEQUENOM MassARRAY, we conducted a genome-wide analysis to identify differentially methylated regions (DMRs) in the brain between humans and rhesus macaques. We first identified a total of 150 candidate DMRs by the MeDIP-Chip method, among which 4DMRs were confirmed by the MassARRAY analysis. All 4 DMRs are within or close to the CpG islands, and a MIR3 repeat element was identified in one DMR, but no repeat sequence was observed in the other 3 DMRs. For the 4 DMR genes, their proteins tend to be conserved and two genes have neural related functions. Bisulfite sequencing and phylogenetic comparison among human, chimpanzee, rhesus macaque and rat suggested several regions of lineage specific DNA methylation, including a human specific hypomethylated region in the promoter of K6IRS2 gene. Our study provides a new angle of studying human brain evolution and understanding the evolutionary role of DNA methylation in the central nervous system. The results suggest that the patterns of DNA methylation in the brain are in general similar between humans and non-human primates, and only a few DMRs were identified.

overall_design: Compare the DNA methylation levels between human and rhesus macaque

first: Xiangyu

last: Cao

first: Yanfeng

last: Zhang

first: Bing

last: Su


title: The effect of zinc limitation on transcriptome expression in Pseudomonas protegens Pf-5

status: Public on Oct 13 2011

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

summary: Transcriptomic profiling of Pseudomonas protegens Pf-5 comparing zinc-limited culture against zinc-amended culture in M9 minimal media

overall_design: Two-condition experiment, non-zinc treated culture versus zinc sulphate supplemented culture. 3 biological replicates including 3 technical replicates for one of the biological replicate and 2 technical replicates for another biological replicate. Swap-dye experiments were performed

first: Chee

middle: K

first: Karl

middle: A

last: Hassan

first: Anahit

last: Penesyan

first: Joyce

middle: E

last: Loper

first: Ian

middle: T

last: Paulsen


title: Gene expression of a Photorhabdus M-form variant relative to the wild type P-form cells

status: Public on Sep 15 2011

city: East Lansing

first: Todd

last: Ciche

state: MI

address: 2215 MMG, BPS Building, MSU

institute: Michigan State University

summary: Photorhabdus luminescens bacteria alternate lifestyles between its pathogenic insect host and its mutualistic nematode host. We found that Photorhabdus changes radically from the insect pathogenic form (P-form) to slow growing small cells when initiating mutualism (M-form). Here we characterize the gene expression of the M-form relative to the P-form.

sample_organism: Photorhabdus laumondii subsp. laumondii TTO1

overall_design: RNA was extracted from mid-exponential phase bacterial cultures of genetically locked P-form and M-form cells in LB media supplemented with 1 g/liter sodium pyruvate at 28 degree celcius. M-form gene expression was calculated relative to P-form. Three replicates were performed for each biological sample.

first: Vishal

middle: S

last: Somvanshi


title: Expression analysis of protein production in the filamentous fungus Trichoderma reesei (Hypocrea jecorina)

status: Public on Dec 22 2011

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

summary:
Comparison of T. reesei grown on lactose fed chemostat cultivations in different growth rates and cell densities
The analysis is further described in paper Correlation of gene expression and protein production rate - a system wide study. Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivistoinen, Paula Jouhten, Erno Lindfors, Marilyn Wiebe, Merja Penttilä and Markku Saloheimo, Submitted.
Abstract:
Background:Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Saccharomyces cerevisiae chemostat cultivations provided the
first analysis on genome wide effects of growth rate. In this work we
study the filamentous fungus Trichoderma reesei (Hypocrea
jecorina) that is an industrial protein production host known for its
exceptional protein secretion capability. Interestingly, it exhibits a
low growth rate protein production phenotype.
Results: We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat
cultivations of T. reesei. Use of chemostat allowed control of
growth rate and exact estimation of the extracellular specific protein
production rate (SPPR). We find that major biosynthetic activities are
all negatively correlated with SPPR.  We also find that expression of
many genes of secreted proteins and secondary metabolism, as well as various
lineage specific, mostly unknown genes are positively correlated with SPPR.
Finally, we enumerate possible regulators and regulatory mechanisms,
arising from the data, for this response.
Conclusions: Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein
production.  Also, we propose that flux through early glycolysis or
the TCA cycle is a more fundamental determining factor than growth rate
for low growth rate protein production and we propose a novel
eukaryotic response to this i.e. the lineage specific response (LSR).

overall_design: A nine chip study using total RNA recovered from three separate cultures of T. reesei RutC-30 grown with growth rate 0.03, three separate cultures grown with growth rate 0.06 and three separate cultures grown with growth rate 0.03 in high cell density.

first: Bart

last: Smith

first: Jari

last: Rautio


title: Long non-coding RNAs and mRNAs expression analysis of HCC

status: Public on Sep 05 2011

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

country: China

institute: Second Military Medical University

type: Non-coding RNA profiling by genome tiling array

summary: Although many protein-coding genes have been identified to be aberrantly expressed in hepatocellular carcinoma (HCC), the mechanisms that account for development and progression of HCC remain unclear. In recent years, long noncoding RNAs (lncRNAs) have been shown to have critical regulatory roles in mammalian cell biology. Many lncRNAs can result in aberrant expression of gene products that may contribute to cancer biology. In this study, we first identified non-overlapping signatures of a small number of lncRNAs that are aberrantly expressed in human HCC compared with paired peritumoral tissues. Then we used real-time PCR to validate five lncRNAs whose expression was altered in HCC compared with paired peritumoral tissues. Using loss-of-function and gain-of-function approaches, we found that an lncRNA (termed lncRNA-HEIH) plays a key role in cell cycle regulation. We further demonstrated that lncRNA-HEIH bound to enhancer of zeste homolog 2 (EZH2) and that this interaction was required for the repression of EZH2 target genes. Together, these results reveal insights into the molecular regulation mechanisms of HCC cell cycle regulation and lead us to propose that lncRNAs may serve as key regulatory hubs in cancer biology.

overall_design: A ten chip study using total RNA recovered from five separate HCC tissues and five corresponding paired non-tumor samples.

first: Fu

last: Yang

first: Ling

first: Xi-song

last: Huo

first: Dan

last: Xu

first: Sheng-xian

last: Yuan

first: Ji-hang

last: Zhu

first: Wei-ping

last: Zhou

first: Guang-shun

first: Chun-fang

last: Gao

first: Feng-rui

first: Fang

first: Shu-han

last: Sun


title: Gene expression profiling of Chinese Hamster Ovary production cell lines

status: Public on Jul 28 2011

city: Dublin

first: Colin

last: Clarke

address: Collin's Av.

department: NICB

country: Ireland

institute: Dublin City University

summary: The dataset set consists of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that varied in terms of seeding density, temperature, medium, feed medium, culture duration and product type. Cells were sampled for gene expression analysis at various stages of the culture and bioprocess-relevant characteristics including cell density, growth rate, viability, lactate, ammonium and cell specific productivity (Qp) were determined

overall_design: A total of 295 microarray samples were assayed. In addition 9 continous bioprocess variables were also measured.

first: Padraig

last: Doolan

first: Niall

last: Barron

first: Paula

last: Meleady

first: Finbarr

last: O'Sullivan

first: Patrick

last: Gammell

first: Mark

last: Melville

last: Leonard

first: Martin

last: Clynes


title: Novel male-biased expression in paralogs of the aphid slilmfast nutrient amino acid transporter expansion

status: Public on Sep 14 2011

city: Coral Gables

first: Rebecca

last: Duncan

state: FL

address: 1301 Memorial Dr.

department: Department of Biology

institute: University of Miami

summary: A major goal of molecular evolutionary biology is to understand the fate and consequences of duplicated genes. In this context, aphids are particularly intriguing because the newly sequenced pea aphid genome is characterized by extraordinarily high levels of lineage-specific gene duplication relative to other insect genomes. While analyzing the results of a microarray comparing gene expression between male, sexual female and asexual female Myzus persicae aphids, we unexpectedly found duplicated nutrient amino acid transporters highly upregulated in males. These transporters, homologous to the Drosophila slimfast, belong to an aphid-specific gene family expansion in which other paralogs are thought to have functionally diverged to fill a role in mediating interactions between aphids and their nutrititonally required bacterial symbiont. The lack of a known male role for slimfast in other insects suggests that aphid slimfast paralogs have been retained as a result of functional divergence to fill multiple novel functional roles in symbiosis and in males.

overall_design: Two biological replicates, four treatments (males, asexual females at long day, asexual females at short day, sexual females), dye flip

middle: P

first: Lubov

last: Nathanson

first: Alex

middle: C

last: Wilson


title: MiRNA microarray analysis of human bicuspid and tricuspid aortic valve leaflet tissues

status: Public on Jun 24 2011

city: Toronto

first: Bobby

last: Yanagawa

state: ONT

address: 306-25 The Esplanade

department: Cardiac Surgery

country: Canada

institute: University of Toronto

summary: Bicuspid aortic valve (BAV) is a common congenital cardiac anomaly, with an estimated incidence of 1-2%.  It is responsible for the greatest burden of aortic valve disease in patients younger than 70 years in North America.  We performed microRNA profiling in end-stage valve leaflets with BAV and TAV.

overall_design: Patients undergoing elective aortic valve replacement for aortic stenosis at St. Michael’s Hospital, University of Toronto, between June 2010 and June 2011 were enrolled.  Aortic valve leaflets were obtained intraoperatively from patients with congenital bicuspid (BAV; N=10) and tricuspid aortic valves (TAV; N=10) at the time of valve replacement.  Leaflets were flash frozen in liquid nitrogen.  MiRNA was isolated using the miRNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer`s instructions.  For miRNA microarray analysis, total RNA was directly labeled with biotin and hybridized to the GenoExplorer microRNA human array containing 1583 human miRNA probes (Genosensor, Tempe, AZ) and the fluorescent signals were then scanned using a GenePix 4000b Biochip.  The average of 3 mean fluorescence signal intensities for each miRNA probe was normalized to that for tRNAmet.  Precursor miRNAs detected at 2-fold greater than background were considered to be expressed.  Data were analyzed with GenePix 5.0 software, provided by GenoSensor Corp.


title: Glycemic index differences of high-fat diets modulate primarily lipid metabolism in murine adipose tissue

status: Public on Sep 13 2011

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: We previously reported that a low versus high glycemic index (GI) diet on a high fat (30% kcal fat) background (LGI and HGI, respectively) significantly retarded adverse health effects in C57BL/6J male mice. The LGI diet enhanced whole body insulin sensitivity and repressed high fat diet-induced body and adipose tissue weight gain, resulting in reduced serum leptin and resistin levels (Faseb J 2009; 23: 1092-1101). How white adipose tissue (WAT) is effected is examined in the present study. We characterized the molecular mechanisms underlying the GI-mediated effects in WAT using whole genome transcriptomics technology. We show that a LGI vs. HGI diet mainly exerts its beneficial effects on substrate metabolism, especially insulin signaling of fatty acid metabolism. In addition, cell adhesion and cytoskeleton remodeling showed reduced expression in line with lower WAT mass, but it might also be due to altered insulin sensitivity. An important transcription factor showing enhanced expression is PPARgamma. Furthermore, serum levels of triglycerides, total cholesterol, HDL- and LDL-cholesterol were significantly reduced by a LGI vs. HGI diet, and muscle insulin sensitivity was significantly increased as analyzed by PKB/Akt phosphorylation. Cumulatively, even though these mice were fed a high fat diet, the low versus high GI induced significantly favorable changes in metabolism in WAT. These effects suggest a partial overlap with pharmacological approaches by thiazolidinediones (TZDs) to treat insulin resistance and statins and plantsterols/stanols for hypercholesterolemia. It is therefore tempting to speculate that such a dietary approach might beneficially support pharmacological treatment of insulin resistance or hypercholesterolemia in humans.

overall_design: We analyzed 19 epididymal whie adipose tissue (epiWAT) samples from a 13 week High fat diet, Low glycemic index dietary group (LGI, n=9) versus a High fat diet, High glycemic index dietary group (HGI, n=10) after 13 weeks of feeding wildtype C57BL/6J male adult mice. Of the 19 arrays, we excluded 2 arrays for downstream analysis based on quality control (total final set contains 8 LGI and 9 HGI samples).

middle: M

first: Annelies

last: Bunschoten

first: Eline

last: Verlinde

last: Schrauwen

first: Jaap

last: Keijer


title: Yarrowia lipolytica fed-batch biolipid production.

status: Public on May 15 2011

city: Thiverval-Grignon

first: Nicolas

last: Morin

address: Av. Lucien Bretignières

department: UMR 1319 Micalis

country: France

institute: INRA

summary: Time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, during a controlled fed-batch. A nitrogen limitation was applied during the course of the fed-batch to initiate de novo biolipid synthesis.

overall_design: Dual staining, one replicate per slide. On each slide, a time point sample and a reference sample are spotted. Reference samples were obtained by pooling the RNAs from the time-course samples.

first: Julien

last: Cescut

first: Gaelle

last: Lelandais

first: Véronique

last: Leberre

first: Jean-Louis

last: Uribelarrea

first: Carole

last: Molina-Jouve

first: Jean-Marc

last: Nicaud


title: Transcription factor profiling of T cells containing stably integrated or transiently transfected HTLV-1 LTR.

status: Public on Nov 12 2011

city: Doylestown

first: Saifur

last: Rahman

state: PA

address: 3805 Old Easton Rd

department: Microbiology and Immunology

institute: Drexel University

overall_design: Nuclear extract from one million stably or transiently transfected Jurkat (CD4 T cell) cell line was extracted and labeled with TransSignal Probe mix (Panomics) and then hybridized to the array.

first: Kevin

last: Quann

first: Devanshi

last: Pandya

first: Shruti

last: Singh

first: Zafar

last: Khan

first: Pooja

last: Jain


title: Differential miRNA expression in gingival epithelial cells infected with Porphyromonas gingivalis

status: Public on Apr 15 2011

city: Louisville

first: Richard

middle: J

last: Lamont

state: KY

address: 570 South Preston Street

department: Oral Biology

institute: University of Louisville

summary: Porphyromonas gingivalis is a pathogen in severe periodontal disease. Able to exploit an intracellular lifestyle within primary gingival epithelial cells (GECs), a reservoir of P. gingivalis can persist within the gingival epithelia.  This process is facilitated by manipulation of the host cell signal transduction cascades which can impact cell cycle, cell death and cytokine responses.  Using microarrays, we investigated the ability of P. gingivalis 33277 to regulate microRNA (miRNA) expression in GECs. One of several miRNAs differentially regulated by GECs in the presence of P. gingivalis was miR-203, which was upregulated 4-fold compared with uninfected controls.  Differential regulation of miR-203 was confirmed by qRT-PCR.  Putative targets of miR-203, suppressors of cytokine signaling (SOCS) 3 and 6, were evaluated by qRT-PCR. SOCS3 and SOCS6 mRNA levels were reduced >5-fold and >2-fold, respectively, in P. gingivalis-infected GECs compared with controls.  Silencing miR-203 using a si-RNA construct reversed the inhibition of SOCS3 expression.  A dual luciferase assay confirmed binding of miR-203 to the putative target binding site of SOCS3 3’ UTR. Western blot analysis demonstrated that activation of Stat3, a downstream target of SOCS, was diminished following miR-203 silencing.  This study shows that induction of miRNAs by P. gingivalis can modulate important host signaling responses.

overall_design:
MicroRNAs differentially expressed in human gingival epithelial cells in response to P. gingivalis infection were identified.
P. gingivalis were reacted with primary gingival epithelial cells at an MOI of 100 for 6 hours at 37C in 5% CO2. Co-cultures were carried out in triplicate. The GECs were lysed with Trizol (Invitrogen) prior to RNA extraction and total RNA isolation.  The microarray assay was performed using a service provider (LC Sciences).  The assay started from 4 to 8 µg total RNA sample which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Cy3 dyes were circulated through the microfluidic chip for dye staining. Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).  Microarray data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).  For a transcript to be listed as detectable it had a signal intensity higher than 3×(background standard deviation) and spot coefficient of variance (CV) < 0.5.  CV was calculated by (standard deviation)/(signal intensity).  When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level. t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric. This experiment includes a total of 6 samples which are divided in to 2 groups, each with 3 biological repeats: 3 untreated normal samples as controls and 3 infected samples as the treated condition.

first: Catherine

last: Moffatt


title: Human cerebral cortex DNA methylation by MeDIP-Chip

first: Jinkai

last: Wang

first: Xiangyu

last: Cao

first: Yanfeng

last: Zhang

first: Bing

last: Su


title: Strome Pol II, H3K36me3  and CENP-A in met-1 EEMB

status: Public on Jan 24 2012

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip of Pol II, H3K36me3 and CENP-A in met-1 C. elegans early embryo

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: met-1(n4337); Developmental Stage: Early Embryo; Genotype: met-1(n4337); Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS:  temperature 20

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner


title: Transcriptional response of susceptible and tolerant citrus to infection with Candidatus Liberibacter asiaticus

status: Public on Oct 04 2011

city: Fort Pierce

first: Ute

last: Albrecht

address: 2001 South Rock Road

institute: USDA, ARS, US Horticultural Research Laboratory

summary:
Candidatus Liberibacter asiaticus (Las), a non-culturable phloem-limited bacterium, is the suspected causal agent of Huanglongbing (HLB) in Florida.  HLB is one of the most devastating diseases of citrus and no resistant cultivars have been identified to date, though tolerance has been suggested in the genus Poncirus.  A recent study conducted in our laboratory demonstrated tolerance of US-897, a hybrid of Poncirus trifoliata (L. Raf.) and the susceptible ‘Cleopatra’ mandarin (Citrus reticulata Blanco), to Ca. L. asiaticus, the presumed causal agent of HLB in Florida (Albrecht & Bowman, HortScience 46 (2011) 16-22).
This study compares transcriptional changes in tolerant US-897 and susceptible ‘Cleopatra’ mandarin seedlings in response to infection with Las using the Affymetrix GeneChip citrus array with the main objective of identifying genes associated with tolerance to HLB.  Such genes may be suitable as potential targets for biotechnology approaches, providing one strategy to possibly control this destructive disease of citrus.

sample_organism:
Citrus reticulata
Citrus reticulata x Citrus trifoliata

overall_design: Fifteen months-old seedlings of the genotypes 'Cleopatra' mandarin and US-897 were graft-inoculated with non-infected (control) or Las-infected tissue from greenhouse-grown 'Valencia' (C. sinensis L.) plants.  Six non-infected control plants each from 'Cleopatra' (MC)  and US-897 (TC) and six infected plants each from Cleopatra (MI) and US-897 (TI) were used.  Four to six leaves per plant were excised at 32 weeks after inoculation (wai) and immediately frozen in liquid nitrogen. Total RNA was extracted from all 24 plants.  Equal amounts of RNA from two samples were pooled to obtain three biological replicates per genotype and treatment and used for hybridization on Affymetrix citrus microarrays.

first: Kim

middle: D

last: Bowman


title: Modulation of Androgen Receptor Signaling in Hormonal Therapy-Resistant Prostate Cancer Cell Lines

status: Public on Aug 05 2011

city: Rotterdam

first: Rute

last: Marques

address: Dr Molewaterplein 50

institute: Erasmus MC

summary:
Prostate epithelial cells depend on androgens for survival and function. In early prostate cancer, besides survival, androgens also regulated tumor growth, which is exploited by androgen ablation/ blockade therapies in metastatic disease. The aim of the present study was to characterize the role of the androgen receptor pathway in prostate cancer progression and to identify potential disease markers.
Microarray analysis was used to establish the androgen-regulated gene expression profile, upon stimulation with the synthetic androgen R1881 or the antiandrogen hydroxyflutamide, of the androgen-responsive PC346C cell line and its derivative castration-resistant sublines: PC346DCC (vestigial AR levels), PC346Flu1 (AR overexpression) and PC346Flu2 (T877A mutated AR)

overall_design: PC346C, PC346DCC, PC346Flu1 and PC346Flu2 were stimulated with 1 nM R1881, 1uM hydroxyflutamide or vehicle control, following a 4, 8 and 16h time-course. Each condition was performed in dye-swap, using biological duplicates. PC346DCC was only stimulated with R1881, not hydroxyflutamide.

middle: B

first: Guido

last: Jenster


title: Effects of low and high doses of bisphenol A on mouse liver transcriptome

status: Public on Sep 21 2011

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

summary: Bisphenol A (BPA) is used in the plastic industry as the monomer of polycarbonates and epoxy resins. Heat and changes in pH conditions lead to its leakage from the plastics in which it is incorporated. This largely contributes to the widespread exposure of the general population to this environmental contaminant. The exposure levels in humans are likely below the Tolerable Daily Intake (TDI: 50 µg/kg/day) and well below the No Observable Adverse Effect Level (NOAEL: 5000 µg/kg/day) defined from reprotoxicity studies. However, several studies suggest that BPA could induce deleterious effects specifically at low, environmentally relevant, doses. BPA has been described as an endocrine disruptor with estrogenic activity. Recently, it has been shown that BPA exposure has an impact on metabolic functions including stimulation of adipogenesis and of insulin production by the pancreas. Here, we investigated the effects of oral exposure to low (TDI) and high (NOAEL) doses of BPA on mouse liver transcriptome.

overall_design: Liver gene expression was measured from CD-1 mice (6 mice/group) exposed for 28 days to bisphenol A at doses 0 (controls), 50 (TDI or low dose) or 5000 µg/kg/day (NOAEL or high dose) via food contamination.

middle: G

first: Arnaud

last: Polizzi

first: Alice

last: Marmugi

first: Hervé

last: Guillou

first: Laila

last: Lakhal

first: Nathalie

last: Priymenko

first: Alain

last: Paris


title: Affymetrix Human Exon 1.0 ST array analysis of lymphoblastoid cell lines

status: Public on May 23 2011

city: Paris

first: Claire

last: Vandiedonck

address: 10 avenue de Verdun

department: Faculte de Medicine Villemin

institute: Inserm U958, Universite Paris Denis Diderot - Paris 7

summary: This experiment accompanies the main analysis using a custom MHC array to define the first high-resolution, strand-specific transcriptional map of the MHC, defining differences in gene expression for three common haplotypes associated with autoimmune disease. Unstimulated samples for each haplotype were hybridised to Affymetrix Human Exon 1.0 ST arrays as well the custom MHC array. Exon array data were used to assess the concordance of signal obtained from the two platforms and to investigate the extent of alternative splicing in the MHC, and how it compares to the rest of the genome.

overall_design: Lymphoblastoid cell lines carrying three common autoimmunity haplotypes (COX, PGF, QBL) were analysed in triplicate using the Affymetrix Human Exon 1.0 ST Array.

first: Martin

last: Taylor

first: Helen

last: Lockstone

first: Katharine

last: Plant

first: Jennifer

first: Caroline

last: Durrant

first: John

last: Broxholme

first: Benjamin

last: Fairfax

first: Julian

last: Knight


title: Allele-specific expression between Arabidopsis genus

status: Public on Jul 27 2011

city: Münster

first: Fei

last: He

address: Hüfferstr. 1

department: Münster University

country: Germany

institute: Institute for Evolution and Biodiversity

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

summary: We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1).

sample_organism: Arabidopsis thaliana x Arabidopsis lyrata

overall_design: 24 sampes, 12 DNA samples from parents and hybrids, 12 RNA sample from leaf and flowers of hybrids

first: Juliette

last: demeaux


title: Comparative Genomic Hybridization of E. coli and Shigella species to determine the relatedness of isolates from Neobladders

status: Public on Jul 25 2011

city: Baltimore

first: David

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: Using comparative genomic hybridization we examined the genome content of 30 isolates of E. coli and Shigella to determine the relative location of E. coli isolates from the human neobladder

sample_organism:
Escherichia coli
Shigella boydii
Shigella dysenteriae
Shigella flexneri
Shigella sonnei

overall_design: Isolates were included in the study that represent the prototype strains of multiple pathovars.  No replicates were included in the final comparisons


title: Lieb SDQ3891_LEM2_SP646_MXEMB

status: Public on Mar 09 2011

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3389
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.  We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: SP646; Developmental Stage: Mixed Embryo; Genotype: mnT12(IV;X).; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody SDQ3891 LEM2 (target is LEM-2); Strain SP646

first: Ikegami

last: Kohta

first: Jason

last: Lieb


title: GAS M49: wild type vs Δralp3 mutant

status: Public on Jul 05 2011

city: Rostock

first: Nikolai

last: Siemens

state: MV

address: Schillingallee 70

department: IMIKRO

institute: University of Rostock

summary:
GAS is a highly virulent Gram-positive bacterium. For the successful infection GAS express many virulence factors, which are clustered together with transcriptional regulators in distinct genomic regions. Ralp3 is a central regulator of the ERES region. In this study, we investigated the role of Ralp3 in GAS pathogenesis.
To characterize the Ralp3 regulatory function on the whole genome level, GAS M49 wild type and Äralp3 mutant strains were comprehensively compared by two colour microarray analysis. Samples were taken from cultures in the transition phase.

overall_design: One condition experiment, wild type vs Δralp3. Biological replicates: 4 wild type and 4 mutant replicates per array.

first: Tomas

last: Fiedler

first: Jana

last: Normann

first: Johannes

last: Klein

first: Richard

last: Münch

first: Nadja

last: Patenge

first: Bernd

last: Kreikemeyer


title: Dehong chicken blood samples: Control vs. 6 chicken blood samples belonging to 3 different breeds

status: Public on Apr 12 2011

city: Columbus

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

institute: The Ohio State University

type: Genome variation profiling by genome tiling array

summary: Copy number variation profiles comparing control female Dehong chicken blood DNA with 3 different chicken breeds (white Leghorn, Cobb broiler, and Dou chicken) blood DNA. Each test breed had one male and one female sample, for a total of 6 test DNA samples. The goal is to determine the global copy number variation profiles between chicken breeds.

overall_design: Female Dehong chicken DNA as reference DNA vs. 6 test chicken DNA samples.

first: Xiaoxiang

last: Hu

first: Ning

last: Li


title: Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.).

status: Public on Aug 04 2011

city: Athens

first: Adam

middle: W.

last: Barb

state: GA

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.

overall_design: Reference design. Three condition experiment, each compared to a common reference. Biological replicates: 4 well-watered (control), 4 drought-stressed, 4 drought-stressed + recovery. cDNA synthesized on three occassions (A, B, and C) and 2 replicates were performed for each synthesis for a total of 6 technical replicates for each biological replicate. 72 slides total

first: W

middle: W

last: Lorenz

first: Rob

last: Alba

first: Yuan-Sheng

last: Yu

first: John

last: Bordeaux

first: Marta

last: Simoes

first: Jeffrey

middle: F

last: Dean


title: Lieb JL00006_ZFP1_RB774_MXEMB

first: DCC

last: modENCODE

summary:
modENCODE_submission_3361
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.  We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 1;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody JL00006 ZFP1 (target is ZFP-1); Strain N2

first: Morten

last: Jensen

first: Jason

last: Lieb


title: Screening for altered plasma miRNAs in traumatic brain injured patients

status: Public on Apr 06 2011

city: Houston

last: Redell

state: TX

institute: University of Texas Health Science Center at Houston

summary: In this study, we examined if the composition of plasma miRNAs is altered in patients with traumatic brain injury (TBI), and if these changes can be used as diagnostic markers.  A microarray containing 875 human miRNAs was used to compare the miRNA profile of plasma collected from severe TBI patients (GCS ≤ 8) to that of age-, gender-, and race-matched healthy volunteers.  This screen identified 108 miRNAs in the plasma of healthy volunteers. Of these, 52 were found to be altered in plasma samples from persons with severe TBI, and an additional 8 miRNAs were detected only in the plasma of TBI patients.

overall_design: Plasma samples from 10 patients from either severe TBI (experimental group) or healthy volunteers (reference group; age-, gender-, and race-matched ) were pooled, the total RNA extracted in parallel, eluted in 100ul, and dried to 30 ul.  Equal volumes of extracted plasma RNAs were assayed for global miRNA content using a service provider (LC Sciences, Houston, TX).  There were no replicates performed for this screen.  Healthy volunteer group served as the reference.

first: Pramod

middle: K

last: Dash


title: Genome-wide analysis of pluripotency marker expression of ESKM-iPS cells

status: Public on Apr 14 2011

city: Berlin

first: Torben

last: Redmer

address: Robert-Roessle Str. 10

department: Signaling in embryonic stem cells

institute: Max-Delbrueck-Center (MDC)

summary: iPS cells, produced in in presence of exogeneously expressed E-cadherin and abcence of viral Oct4 were compared with conventional produced OSKM-iPS cells and murine embryonic stem cells (mESCs) or MEFs

overall_design: Total RNA was isolated from iPSCs and mESCs grown in presence of LIF on gelatin-coated plates for 4 days and from murine embryonic fibroblasts grown in standard medium (DMEM-Glutamax, high-glucose, 10 % FBS, 1X non-essential amino acids, penicillin/ streptomycin

first: Daniel

last: Besser


title: Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development

status: Public on Dec 31 2010

city: St. Catharines

first: Ping

last: Liang

address: 500 Glenridge Ave

department: Department of Biological Sciences

institute: Brock University

summary:
To further our understanding of the role of DNA methylation in development, Methylated DNA Immunoprecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis.  Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). Almost 5,000 adult T-DMRs and 10,000 DS-DMRs were identified. Surprisingly, almost all DS-DMRs were tissue specific (i.e., methylated and ummenthylated in one or more non-overlapping tissues), indicating that the vast majority of unique sequence DNA methylation has tissue specificity. Also, many DS-DMRs were methylated at early development stages (E15 and NB) but unmethylated in adult, indicating “demethylation” has a prominent role in tissue differentiation.
The pattern of DNA methylation in adult testis was dramatically different from somatic tissues in many aspects, mostly notably with a very strong bias of methylation in non-CpGi (CpG island) promoter regions (94%). Although the majority of T-DMRs and DS-DMRs tended to be in non-CpGi promoter regions, a relatively large number were also located in CpGi in promoter, intra-genic and inter-genic regions (>15% of all CpGi). Gene Ontology analysis of genes with methylation in non-CpGi promoters indicates enrichment of genes related to membrane proteins and G-protein coupled receptors. Our data also suggest regulatory roles of DNA methylation outside of promoter regions and in alternative promoter selection. Overall, our studies indicate that change in DNA methylation during development is a dynamic, widespread and tissue-specific process involving both DNA methylation and demethylation.

overall_design: Comparison of DNA methylation across 3 developmental stages (15 day embryo, newborn, and adult) for four tissues (brain, heart, liver and testis)

first: Fei

last: Song

first: Srimoyee

last: Ghosh

first: Evan

last: Morien

first: Maoqun

last: Qin

first: Saleh

last: Mahmood

first: Kyoko

last: Fujiwara

first: Jun

last: Igarashi

first: Hiroki

last: Nagase

first: William

middle: A

last: Held


title: Novel aspects of the transcriptional stress response in the paraventricular nucleus of the mouse strains DBA/2J and C57BL/6J

status: Public on Oct 20 2010

city: München

first: Benno

last: Pütz

address: Kraepelinstr. 2

department: Statistical Genetics

institute: MPI of Psychiatry

summary:
The pivotal role of stress in the precipitation of psychiatric diseases is generally accepted. To further elucidate the underlying molecular mechanisms, gene networks and signalling cascades, we investigated the impact of an acute stressor, forced swimming, on the gene expression profile in the hypothalamic paraventricular nucleus (PVN). We performed this study in C57BL/6J and DBA/2J mice, which are known to differ in their reaction to stress. Mice were exposed to forced swimming as stressor, brains were dissected 4h and 8h after stress, both from stressed and unstressed animals, and the RNA profiles from the PVN were evaluated by microarray analysis.

Keywords: time course, treatment response, strain differences

overall_design: RNAs from unstressed animals (basal) were compared to RNAs from stressed animals (either 4h or 8h after stress) for both mouse strains (DBA/2J and C57BL/6). In addition, RNA from the two strains were compared under basal conditions. Technical replicates: 10 for each time point, including dye-swap each with 5 replicates

first: Amalia

last: Tsolakidou

first: Ludwig

last: Czibere

first: Dietrich

last: Trümbach

first: Markus

last: Panhuysen

first: Jan

last: Deussing

first: Wolfgang

last: Wurst

first: Inge

last: Sillaber

first: Rainer

last: Landgraf

first: Florian

last: Holsboer

first: Theo

last: Rein


title: Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors DASL Cancer Panel

status: Public on Dec 20 2010

city: Rochester

first: Keith

last: Anderson

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: HER2-positive and HER2-negative samples are compared within this DASL Cancer Panel Platform

overall_design: Two-class comparison

first: Monica

last: Reinholz

first: Jeanette

middle: E

last: Eckel-Passow

first: S

first: Yan

last: Asmann

first: Michael

last: Zschunke

first: Ann

middle: L

last: Oberg

last: McCullough

first: Amylou

last: Dueck

first: Beiyun

last: Chen

first: Craig

last: April

first: Eliza

last: Wickham-Garcia

first: Robert

last: Jenkins

first: Julie

last: Cunningham

first: Jin

last: Jen

first: Edith

last: Perez

first: Jian-Bing

last: Fan

first: Wilma

last: Lingle


title: Gene expression profiling of BHDS-associated renal tumors

status: Public on Dec 21 2010

city: Grand Rapids

first: Jeff

last: Klomp

address: 333 Bostwick Ave, NE

institute: Van Andel Research Institute

summary: Renal tumors that arise in individuals with BHD Syndrome represent a molecularly distinct form of renal cancer.  In addition, BHD syndrome is due to a mutation the folliculin gene (FLCN). While the folliculin gene is an important tumor suppressor gene, the molecular function of this gene is not well defined.  By analyzing tumor samples that contain FLCN mutations, we demonstrate that the FLCN gene is an important regulator of mitochondrial function.

overall_design: Gene expression profiling of BHDS tumors and normal kidney tissues


title: Drosophila U6atac snRNA mutant

status: Public on Oct 11 2010

city: Helsinki

first: Heli

last: Pessa

address: Haartmaninkatu 8

department: Faculty of Medicine; Research Programme in Translational Immunology

institute: University of Helsinki

summary:
A Drosophila line (l(2)k01105) with a P-element insertion in U6atac snRNA, an essential component of the U12-type spliceosome, was used to investigate the impact of disrupted U12-dependent splicing during larval development.
A custom-designed exon array was used to study the expression of genes containing U12-type introns and genes involved in downstream pathways affected by deficient U12-dependent splicing.
Flies homozygous for the U6atac mutation (U6atac/U6atac) were compared to heterozygotes (U6atac/CyO-GFP) which have a normal phenotype.

overall_design:
Samples from homozygous and heterozygous U6atac mutant larvae at 1st, 2nd and 3rd larval instar were labelled with three colours and hybridized three samples per array. Three independently harvested biological replicates were made, with dye swap, except only two replicates for 3rd stage heterozygous control.  This study presents exon-level data.

Supplementary files:
Raw data (.gpr) files.
Series variables and repeats information.

first: Dario

last: Greco

first: Jouni

last: Kvist

first: Gudrun

last: Wahlstrom

first: Tapio

middle: I

last: Heino

first: Petri

last: Auvinen

first: Mikko

last: Frilander


title: Effects of estrogen and progesterone on glycosyltransferase expression in mice

status: Public on Mar 02 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
This laboratory studies the structural basis of carbohydrate function in terms of adhesion and other biological processes.
The Fisher lab is testing the hypothesis that the mucin-coated oral and uterine cavities present similar carbohydrate receptors that specify the bacterial ecology of both regions and the repertoire of these oligosaccharide species is hormonally regulated. This theory also suggests that certain individuals express carbohydrate receptors that make them susceptible to both periodontal disease and preterm labor.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Experimental procedure: 40 mature female mice were ovariectomize . The mice were allowed to rest for two weeks to eliminate any remaining endogenous estrogen (E2) and progesterone (P4). Then the mice were separated into four groups (10 each) that received the treatment indicated. Group 1: ovariectomized mice with no supplement, only sesame oil vehicle. Group 2: ovariectomized mice with only P4 supplement (2 mg/day/mouse). Group 3: ovariectomized mice with E2 supplement (100 ng/day/mouse). Group 4: ovariectomized mice with both P4 (2 mg/day/mouse) and E2 (100 ng/day/mouse) supplement. The treatment lasted for 4 days; the steroids were dissolved in sesame oil and injected subcutaneously. After treatment, salivary glands (parotid, submandibular, and sublingual gland), submandibular lymph nodes and uterine horns with cervix were collected. Total RNA was extracted from these samples using Trizol.

first: Susan

last: Fisher

middle: R


title: Aging and MicroRNA Expression in Human Skeletal Muscle

status: Public on Oct 01 2010

city: Galveston

first: micah

last: Drummond

address: 301 University Boulevard

institute: University of Texas Medical Branch

summary: A common characteristic of aging is the loss of skeletal muscle (sarcopenia) which can lead to falls and fractures.  MicroRNAs (miRNA) are novel post-transcriptional modulators of gene expression with a potential role as a regulator of skeletal muscle mass and function.  The purpose of this study was to profile miRNA expression patterns in aging human skeletal muscle using a miRNA array followed by in-depth functional and network analysis.  Muscle biopsy samples from 36 men (young: 31±2; n=19; older: 73±3; n=17) were: 1) analyzed for the expression of miRNAs using a microRNA array 2) validated with Taqman quantitative real-time PCR assays, and 3) identified (and later validated) for potential gene targets using the bioinformatics knowledge base software, Ingenuity Pathways Analysis. We found that 18 miRNAs were differentially expressed in older humans (P<0.05 and >500 expression level).  The Let-7 family members, Let-7b and Let-7e, were significantly elevated and further validated in older subjects (P<0.05).  Functional and network analysis from Ingenuity determined that gene targets of the Let-7’s were associated with molecular networks involved in cell cycle control such as cellular proliferation and differentiation. We confirmed with real-time PCR that the mRNA expression of the cell cycle regulators, CDK6, CDC25A and CDC34 were downregulated in older subjects compared to the young (P<0.05).  These data suggest that aging is characterized by an increased expression of Let-7 family members which may downregulate genes related to cellular proliferation.  We propose that the increased Let-7 expression in older human muscle may be an indicator of impaired cell cycle function.

overall_design:
We analyzed skeletal muscle biopsy samples from 19 young and 17 older male subjects that have participated in our previous and current research experiments.  The subjects were not engaged in any regular exercise training at the time of the enrollment; however they were physically independent and overall healthy. Screening of subjects were performed with clinical history, physical exam, and laboratory tests including complete blood count with differential, liver and kidney function tests, coagulation profile, fasting blood glucose and oral glucose tolerance test, hepatitis B and C screening, HIV test, TSH,  urinalysis, and drug screening.  All subjects gave informed written consent before participating in the study, which was approved by the Institutional Review Board of the University of Texas Medical Branch (which is in compliance with the Declaration of Helsinki).  Once recruited, a dual-energy X-ray absorptiometry (DEXA) scan (Hologic QDR 4500W, Bedford, MA) was performed to measure body composition and lean mass.
Study design. All subjects were admitted to the Clinical Research Center the day prior to the experiment, were provided a standardized dinner and were studied following an overnight fast under basal conditions.  Subjects were studied during the same time of day to avoid potential circadian changes and refrained from exercise 48h prior to study participation.  A muscle biopsy was obtained from the vastus lateralis of the leg. The biopsy was performed using a 5 mm Bergström biopsy needle, under sterile procedure and local anesthesia (1% lidocaine). Muscle biopsy sample was immediately blotted and frozen in liquid nitrogen and stored at -80oC until analysis. The muscle biopsy sample was used for microRNA and gene analysis.

first: Micah

first: John

last: McCarthy

first: Mala

last: Sinha

first: Heidi

last: Spratt

first: Elena

last: Volpi

first: Karyn

last: Esser

first: Blake

last: Rasmussen


title: Whole genome analysis of p38 SAPK-mediated gene expression upon stress

status: Public on Sep 29 2010

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

country: Spain

institute: CNIO (Spanish National Cancer Center)

summary:
Cells have the ability to respond and adapt to environmental changes through the activation of stress-activated protein kinases (SAPKs). Although it has been shown that p38 SAPK signalling participates in the regulation of gene transcription, there is not a comprehensive genome-wide transcription study reported to date describing neither the role of the p38 SAPK on the immediate response to stress and its kinetics nor a comparative vision of the genes that respond to different stimuli that activate the p38 SAPK.
Here, we report a whole genome microarray analyses on wild type mouse embryonic fibroblasts (MEFs) treated with different p38 SAPK activators, namely the physiological cytokine TNF alpha, the protein synthesis inhibitor antibiotic anisomycin and osmostress. In addition, we have analysed the contribution of p38 alpha the major isoform of p38 present in MEF cells, in the overall transcription in response to those stimuli by both, the inhibition of p38 SAPK by using a chemical inhibitor (SB203580) and the use of p38 alpha knock out MEFs. Furthermore, we have analysed the kinetics of the gene expression response to osmostress by the p38 SAPK.

overall_design: Two samples have been analysed; wild type Mouse embryonic fibroblast (WT-MEFs) and MAPK p38alfa knock out MEFs (KO-MEFs) respectively treated with 11 and 4 different treatments. Each experiment was performed in duplicate and referenced to a pool of two non-treated WT MEFs.

first: Isabel

last: Ferreiro

first: Manel

last: Joaquin

first: Montserrat

last: Barragan

last: Lombardia

first: Orlando

last: Dominguez

first: Angel

last: Nebreda

first: Francesc

last: Posas


title: Expression of miRNAs in HOZOT, a line of multifunctional Treg cells

status: Public on Jun 03 2010

city: Okayama

first: Mayuko

last: Yamamoto

address: 675-1, Fujisaki, Naka-ku

department: Cell Biology Institute, Research Center

country: Japan

institute: Hayashibara Biochemical Laboratories Inc.

summary: We used microarray analysis to compare miRNA expression profiles of novel type of Treg cell line, termed HOZOT, with those of activated T cells, so called conventional CD4+ T (Tconv) cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: HOZOT-17, a representative HOZOT cell line, was used for profiling.  Tconv cells were prepared from the same UCB source as HOZOT-17.  CD4+ cells were activated with anti-CD3 antibody plus anti-CD28 antibody (CD3/CD28) and cultured for at least seven days in the presence of IL-2. The chip used for this analysis was a mirVanaTM miRNA Bioarray system.

first: Shuji

last: Nakamura

first: Eisaku

last: Kondo


title: Desai OD00079_HCP3_N2_MXEMB

status: Public on Jul 07 2010

city: Toronto

first: DCC

last: modENCODE

summary:
modENCODE_submission_2446
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Developmental Stage Mixed Embryo; temperature 20; Antibody OD00079 HCP3 (target is HCP-3); Strain N2

first: Reto

last: Gassmann

first: Arshad

last: Desai


title: Nucleoredoxin is required for the maintenance of Wnt/β-catenin signaling in mice embryo

status: Public on Oct 26 2010

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We previously showed that nucleoredoxin (NRX) suppresses Wnt/β-catenin signaling through its binding to Dishevelled (Dvl) (Nat Cell Biol 8, 501-508 (2006)). To clarify the in vivo role of NRX in mammals, we here generate NRX gene-knockout mice (NRX-/- mice) by homologous recombination. NRX-/- mice die around birth. Therefore, we performed microarray analyses with NRX+/+ and NRX-/- embryos of E9.5 and E11.5 stages. Surprisingly, in the genes commonly upregulated at both stages, we could not observe Wnt/β-catenin targets. Rather, several target genes for Wnt/β-catenin pathway, such as Frizzled2 and Occludin, are downregulated in NRX-/- whole embryos. Frizzled2 is a gene reportedly expressed in developmental heart. Indeed, by RT-PCR analyses we confirmed that the expression of Frizzled2, as well as other Wnt/β-catenin target genes, was downregulated in embryonic heart of NRX-/- mice. We also found that the amount of unphosphorylated (i.e. activated) form of β-catenin was downregulated in NRX-/- embryonic heart. These results reveal that NRX plays another role which was unidentified in culture cell studies; it is required for the maintenance of Wnt/β-catenin signaling activity.

overall_design: Total RNAs were extracted from E9.5 and E11.5 embryos derived from NRX+/+ and NRX-/- C57BL/6J mice using RNeasy extraction kit (Qiagen). Two dye-swapped experiments were performed by hybridizing complimentary RNA (cRNA) labeled with either Cyanine (Cy) -3 or Cy-5 (Perkin-Elmer) onto Whole Mouse Genome Oligo Microarray (G4122A; Agilent Technologies). The signature genes with mean fold changes > +2.0 or < -2.0 at both stages were subjected for further evaluation.

first: Yosuke

last: Funato

first: Hiroshi

last: Nojima

first: Hiroaki

last: Miki


title: Transcriptional Response to Iron Limitation in Pelagibacter ubique

status: Public on May 05 2010

city: Corvallis

first: Daniel

middle: Patrick

last: Smith

state: OR

address: 220 Nash Hall

department: Microbiology Department

institute: Oregon State University

summary:
We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation.
Differential expression was observed for genes in iron acquisition and incorporation operons. SfuC in particular was 16 times higher in iron-limited cultures and encodes a periplasmic iron-binding protein.

platform_organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

overall_design: Six natural seawater cultures were amended with minimal nutrients and inoculated with P. ubique. Close to maximum cell density, all carboys were supplemented with 100 nM ferrichrome (an iron-chelating siderophore) and three carboys were additionally supplemented with 1 µM FeCl3. Each of the six carboys was sampled for microarray analyses one, two, and eleven days after the ferrichrome addition.

middle: P

first: Michael

middle: S

last: Schwalbach

first: Laura

last: Steindler

first: Stephen

last: Giovannoni


title: Gene Expression in Prokaryotic Microbial Assemblages Across Salinity Gradients in the Columbia River Coastal Margin

status: Public on Sep 10 2010

city: Beaverton

first: Maria

last: Smit

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

institute: Oregon Health and Science University

summary:
Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation.
Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212).

platform_organism: Bacteria Archaea

overall_design:
Total RNA was isolated from 64 filtered environmental water samples collected in the Columbia River coastal margin during 4 research cruises (14 from August, 2007; 17 from November, 2007; 18 from April, 2008; and 16 from June, 2008), and analyzed using microarray hybridization with the CombiMatrix 4X2K format. Microarray targets were prepared by reverse transcription of total RNA into fluorescently labeled cDNA. All samples were hybridized in duplicate, except samples 212 and 310 (hybridized in triplicate) and samples 336, 339, 50, 152, 157, and 199 (hybridized once).

Sample location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; AST and HAM, Columbia River estuary locations near Astoria (river mile 7-9) and Hammond (river mile 5), respectively; TID, Columbia River estuary locations in the tidal basin (river mile 22-23); BA, river location at Beaver Army Dock (river mile 53) near Quincy, Oregon; UP, river location at mile 74.

first: Holly

middle: M

last: Simon


title: Microarray Analysis of Retinal Endothelial Tip Cells Identifies CXCR4 as a Mediator of Tip Cell Morphology and Branching

status: Public on Mar 17 2010

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

summary: The development of the vertebrate vascular system is mediated by both genetic patterning of vessels and by angiogenic sprouting in response to hypoxia.  Both of these processes depend on the detection of environmental guidance cues by endothelial cells.  A specialized subtype of endothelial cell known as the tip cell is believed to be involved in the detection and response to these cues, but the molecular signaling pathways utilized by tip cells to mediate tissue vascularization remain largely uncharacterized.  To identify genes critical to tip cell function, we have developed a method to isolate them using laser capture microdissection, permitting comparison of RNA extracted from endothelial tip cells to that of endothelial stalk cells using microarray analysis.  Genes enriched in tip cells include ESM-1, Angiopoietin-2, and SLP-76. CXCR4, a receptor for the chemokine SDF-1, was also identified as a tip cell-enriched gene, and we provide evidence for a novel role for this receptor in mediating tip cell morphology and vascular patterning in the neonatal retina.

overall_design: Experiments:  Three non-vasculature control samples 4 stalk only replicates, 6 tip only samples


title: Direct transcriptomics comparison of pre-weaned bovine mammary parenchyma and fat pad

status: Public on Jun 01 2010

first: Massimo

last: Bionaz

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

summary:
Direct transcriptomics comparison corroborated by functional and gene network analyses of pre-weaned bovine mammary parenchyma and fat pad shed light on potential cross-talk between these developing tissues.
Transcriptomic characterization of mammary parenchyma and fat pad and their interaction is still incomplete. In the present experiment, the molecular epithelial-fat pad cross-talk during mammary development was assessed by transcript profiling and functional analyses.
Background: Interactions between bovine mammary parenchyma (PAR) and fat pad (MFP) during neonatal tissue development are still not fully understood.  It is thought that the MFP surrounding the parenchymal tissue exerts proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones.  Main objectives in the present study were to use bioinformatics tools to characterize differences in transcript profiles between mammary PAR and MFP from Holstein heifers at ca. 65 d age and uncover potential cross-talk between the two tissues via the analyses of signaling molecules (e.g., cytokines and growth factors) preferentially expressed in one tissue relative to the other.
Results: Over 9,000 differentially expressed genes (DEG; False discovery rate  ≤ 0.05) were found of which 1,478 had a ≥1.5-fold difference. Within these DEG in PAR vs. MFP (n = 736) we noted enrichment of functions related to cell cycle, structural organization, signaling, and DNA/RNA metabolism.  Few canonical pathways were among DEG and were mostly involved in cell cycle and tissue organization (p53 signaling).  Enriched among DEG more highly-expressed in MFP vs. PAR (n = 742) were genes involved in lipid metabolism, signaling, cell movement, and immune-related functions. Canonical pathways associated with metabolism (fatty acid metabolism) and signaling, particularly immune- (acute phase response) and metabolism-related (cAMP signaling), were significantly enriched. Network analysis uncovered a central role of MYC, TP53, and CTNNB1 in controlling expression of DEG highly-expressed in PAR vs. MFP.  Similar analysis revealed a central role of PPARG, KLF2, EGR2, and EPAS1 in regulating expression of highly-expressed DEG in MFP vs. PAR.  Analyses revealed putative crosstalk between tissues via differential expression of cytokines and growth factors highly-expressed in PAR (angiopoietin-1, osteopontin, interleukin-1β) or in MFP (adiponectin, interleukin-13, fibroblast growth factor-2, leptin) during bovine mammary development.
Conclusions: We uncovered specific transcriptomic signatures characterizing MFP and PAR tissue.  Not surprisingly, the expression profile of the MFP is characteristic of adipose tissue, and the one of PAR is characteristic of an epithelial tissue undergoing expansion and remodeling.  Overall, our data highlighted a large degree of interaction between the two tissues and allowed envisaging a reciprocal influence in determining the biological features (and perhaps the fate) of each of the two tissues during this stage of development. This is strongly suggested by the potential effect that the signaling molecules released preferentially by PAR have on lipid metabolism-related pathways, which from our data was what most distinguished the MFP from PAR.  Similarly, the cytokines and growth factors largely expressed in MFP potentially affect the pathways related to cell cycle, development, and proliferation in PAR, which our data highlighted as the main functions represented among the genes highly expressed in PAR vs. MFP.  Based on the current analysis, the number of cytokines and growth factors that potentially are secreted by each tissue and affect molecules in the other underscores the concept of crosstalk.  Ultimately, these bidirectional interactions might be required to coordinate mammary tissue development under normal circumstances or in response to environmental stimuli, such as nutrition.

overall_design:
Mammary tissues (parenchyma and fat pad) from pre-weaned calves fed one of four diets (HPHF, HPHF+, HPLF, control) were harvested at 65 d of age. A dye-swap reference design (reference =  mixture of RNA from several bovine tissues) was used.

HPHF: high-protein/high-fat milk replacer (280 g/kg crude protein, 280 g/kg crude fat) fed at 951 g DM/d.
HPHF+: high-protein/high-fat milk replacer (280 g/kg crude protein, 280 g/kg crude fat) fed at 1,431 g DM/d.
HPLF: high-protein/low-fat milk replacer (280 g/kg crude protein, 200 g/kg crude fat) fed at 951 g DM/d.
Control: control milk replacer (200 g/kg crude protein, 200 g/kg crude fat) fed at 441 g DM/d.

first: Paola

last: Piantoni

last: Graugnard

first: Kristy

last: Daniels

first: Robin

last: Everts

first: Sandra

last: Rodriguez-Zas

first: Harris

last: Lewin

first: Walter

last: Hurley

last: Akers

first: Juan

middle: J

last: Loor


title: Comparative gene expression analysis in fruits of a tomato introgression line performing higher ascorbic acid content

status: Public on Aug 16 2010

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

country: Italy

institute: University of Naples Federico II

summary: High levels of ascorbic acid (AsA) in tomato fruits provide health benefits for humans and also play an important role in several aspects of the plant life. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. We used an introgression line (IL 12-4) containing a QTL promoting AsA accumulation in the fruit and carried out a comparative transcriptomic analysis of fruit tissue using a parental cultivar (M82) with low AsA levels as a reference. We identified 253 differentially expressed genes, indicating that AsA accumulation in IL 12-4 reflects a combination of increased metabolic flux and reduced utilization of AsA. Evidences coming from the experiment suggest that AsA accumulation in IL 12-4 fruit is mainly achieved by increasing flux through the L-galactonic acid pathway, which is driven by pectin degradation and may be triggered by ethylene.

overall_design: Comparative microarray analysis between a tomato introgression line (IL 12-4) expressing higher level of fruit ascorbic acid and its parental cultivar M82 (reference) was performed. In particular, samples were generated by pooling red-ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Three plant replica were used for each line (IL 12-4 and M82) and the experiment was replicated over two consecutive years.


title: Berry skin development in Norton grape: Distinct patterns of transcriptional regulation and flavonoid biosynthesis

status: Public on Oct 08 2010

city: Mountain Grove

first: Susanne

last: Howard

state: MO

address: 9740 Red Spring Rd

department: William H. Darr School of Agriculture

institute: Missouri State University

summary:
Background: The complex and dynamic changes during grape berry development have been studied in Vitis vinifera, but little is known about these processes in other Vitis species. The grape variety ‘Norton’, with a major portion of its genome derived from Vitis aestivalis, maintains high levels of malic acid and phenolic acids in the ripening berries in comparison with V. vinifera varieties such as Cabernet Sauvignon. Furthermore, Norton berries develop a remarkably high level of resistance to most fungal pathogens while Cabernet Sauvignon berries remain susceptible to those pathogens. The distinct characteristics of Norton and Cabernet Sauvignon merit a comprehensive analysis of transcriptional regulation and metabolite pathways.
Results: A microarray study was conducted on transcriptome changes of Norton berry skin during the period of 37 to 127 days after bloom, which represents berry developmental phases from herbaceous growth to full ripeness. Samples of six berry developmental stages were collected. Analysis of the microarray data revealed that a total of 3,352 probe sets exhibited significant differences at transcript levels, with two-fold changes between at least two developmental stages. Expression profiles of defense-related genes showed a dynamic modulation of nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes and pathogenesis-related (PR) genes during berry development. Transcript levels of PR-1 in Norton berry skin clearly increased during the ripening phase. As in other grapevines, genes of the phenylpropanoid pathway were up-regulated in Norton as the berry developed. The most noticeable was the steady increase of transcript levels of stilbene synthase genes. Transcriptional patterns of six MYB transcription factors and eleven structural genes of the flavonoid pathway and profiles of anthocyanins and proanthocyanidins (PAs) during berry skin development were analyzed comparatively in Norton and Cabernet Sauvignon. Transcriptional patterns of MYB5A and MYB5B were similar during berry development between the two varieties, but those of MYBPA1 and MYBPA2 were strikingly different, demonstrating that the general flavonoid pathways are regulated under different MYB factors. The data showed that there were higher transcript levels of the genes encoding flavonoid-3´-O-hydroxylase (F3´H), flavonoid-3´,5´-hydroxylase (F3´5´H), leucoanthocyanidin dioxygenase (LDOX), UDP-glucose:flavonoid 3´-O-glucosyltransferase (UFGT), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR) 1 and LAR2 in berry skin of Norton than in those of Cabernet Sauvignon. It was also found that the total amount of anthocyanins was markedly higher in Norton than in Cabernet Sauvignon berry skin at harvest, and five anthocyanin derivatives and three PA compounds exhibited distinctive accumulation patterns in Norton berry skin.
Conclusions: This study provides an overview of the transcriptome changes and the flavonoid profiles in the berry skin of Norton, an important North American wine grape, during berry development. The steady increase of transcripts of PR-1 and stilbene synthase genes likely contributes to the developmentally regulated resistance during ripening of Norton berries. More studies are required to address the precise role of each stilbene synthase gene in berry development and disease resistance. Transcriptional regulation of MYBA1, MYBA2, MYB5A and MYBPA1 as well as expression levels of their putative targets F3´H, F3´5´H, LDOX, UFGT, ANR LAR1, and LAR2 are highly correlated with the characteristic anthocyanin and PA profiles of Norton berry skin. These results reveal a unique pattern of the regulation of transcription and biosynthesis pathways underlying the viticultural and enological characteristics of Norton grape, and yield new insights into the understanding of the flavonoid pathway in non-vinifera grape varieties.

overall_design: At each of six developmental stages, three biological replicates of berry samples were collected, each consists of ten randomly selected vines, a total of 18 samples were proccessed for analysis

first: Mohammad

middle: B

last: Ali

first: Shangwu

last: Chen

first: Yechun

last: Wang

first: Oliver

last: Yu

first: Laszlo

last: Kovacs

first: Wenping

last: Qiu


title: A Gene Expression Signature for Insulin Resistance

city: Waurn Ponds

first: Sean

last: McGee

state: Victoria

address: 75 Pigdons Rd

department: Metolic Research Unit, School of Medicine

country: Australia

institute: Deakin University

summary: Insulin resistance is a heterogeneous disorder caused by a range of genetic and environmental factors, and we hypothesise that its aetiology varies considerably between individuals. This heterogeneity provides significant challenges to the development of effective therapeutic regimes for long-term management of type 2 diabetes. We describe a novel strategy, using large-scale gene expression profiling, to develop a gene expression signature (GES) that reflects the overall state of insulin resistance in cells and patients. The GES was developed from 3T3-L1 adipocytes that were made “insulin resistant” by treatment with tumour necrosis factor (TNF-alpha and then reversed with aspirin and troglitazone (“re-sensitized”). The GES consisted of 5 genes whose expression levels best discriminated between the insulin resistant and insulin re-sensitized states. We then used this GES to screen a compound library for agents that affected the GES genes in 3T3-L1 adipocytes in a way that most closely resembled the changes seen when insulin resistance was successfully reversed using aspirin and troglitazone. This screen identified both known and new insulin sensitising compounds including non-steroidal anti-inflammatory agents, beta-adrenergic antagonists, beta-lactams and sodium channel blockers. We tested the biological relevance of this GES in participants in the San Antonio Family Heart Study (n = 1,240) and showed that patients with the lowest GES scores were more insulin resistant (according to HOMA_IR and fasting plasma insulin levels, P < 0.001). These findings show that GES technology can be used for both discovery of insulin sensitising compounds and characterisation of patients into subtypes of insulin resistance according to GES scores, opening the possibility of developing a personalised medicine approach to type 2 diabetes.

overall_design: Three-condition experiment, Vehicle, TNF and TNF+ASA+TGZ with biological replicates: 22 Vehicle, 21 TNF and 21 TNF+ASA+TGZ , independently grown and harvested. One replicate per array.

first: Nicky

last: Konstantopoulos

first: Victoria

middle: C

last: Foletta

first: David

middle: H

last: Segal

first: Katherine

last: Shields

first: Kelly

last: Windmill

first: Andrew

last: Sanigorski

first: Courtney

last: Swinton

first: Tim

last: Connor

first: Stephen

last: Wanyonyi

first: Thomas

middle: D

last: Dyer

first: Joanne

last: Curran

first: Juan-Carlos

last: Molero

first: Guy

last: Krippner

first: Greg

last: Collier

last: James

first: John

last: Blangero

first: Jeremy

last: Jowett

first: Ken

last: Walder


title: PtrA is required for coordinate regulation of gene expression during phosphate depletion in a marine Synechococcus

status: Public on Apr 08 2010

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

institute: Macquarie University

summary: The genome of the marine Synechococcus sp. WH8102 displays a minimal regulatory network yet physiological and molecular responses of this organism are tuned to episodic limitation for nitrogen and phosphorus. Microarray analyses have demonstrated a key role for the two-component regulatory system, PhoBR, in the regulation of P transport and metabolism in this strain. However, there is some evidence that another regulator, SYNW1019 (designated as ptrA), probably under the control of PhoB, is involved in the wider response to P-depletion. PtrA is one of only two genome encoded DNA binding proteins of the CRP family in Synechococcus sp. WH8102, and a potential transcriptional regulator with homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the precise role of this regulator we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-deplete growth conditions. During P-depletion the ptrA mutant failed to up-regulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is directly controlled by PtrA, including two phosphatase genes (SYNW0196, SYNW2390), a predicted phytase (SYNW0762) and a gene of unknown function (SYNW0165) all of which are highly up regulated during P-limitation. This result was confirmed by electrophoretic mobility shift assays which demonstrated binding of over expressed PtrA to promoter sequences upstream of the induced phosphatases (SYNW0165, SYNW0196 and SYNW2390). This work suggests a two-tiered response to P-depletion in this strain, the first being PhoB-dependent induction of high affinity PO4 transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly controlled by PtrA, including those involved in cell surface modification, metal uptake, photosynthesis, stress responses and other metabolic process, which may indicate a wider role for PtrA in cellular organisation. In an environmental context ptrA is found in a number of picocyanobateria isolated from a range of oceanic provinces, including strains that lack a functional phoBR..These results give broader insight into the regulation of physiological responses that may dictate niche adaptation in genetically diverse lineages of marine Synechococcus, and suggest that signalling networks and coordinated responses to nutrient availability are important, even in oligotrophic ocean environments.

overall_design: In this series gene expression of a ptrA mutant has been analyzed under phosphorus deplete conditions just after the onset of induction of phosphatase activity in wild type.  There are six duel-channel slides upon which both ptrA mutant and wild type samples were hybridized.  There are three technical replicates for each of two biological replicates including one flip-dye comparison.  Each slide contains six replicate spots per gene.

first: Martin

last: Ostrowski

first: Sophie

last: Mazard

first: Sasha

middle: G

last: Tetu

last: Phillippy

first: Daniel

last: Johnson

first: Brian

last: Palenik

middle: T

first: Dave

last: Scanlan


title: Benzoate induced transcriptomic response in Bacillus subtilis

status: Public on Dec 01 2009

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

summary: Bacillus subtilis strain AG174 was grown in the presence and absence of  benzoate (30 mM). Benzoate was used in order to equalize the external and internal pH. The cultures were grown at external pH 7.0, and the addition of benzoate did not change the external pH. Microarray analysis was performed on cDNA synthesized from bacterial RNA. Real-time PCR of highly up-regulated genes confirmed the results of the microarray. These data were compared to previous B.subtilis microarray results, where genes regulated by external pH were identified.

overall_design: Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM MOPS at pH 7.0. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 220 rpm, incubated at 37 °C to an optical density at 600 nm of 0.2. Four cultures were grown in the presence of 30 mM benzoate and four cultures were grown without benzoate. One sample was taken from each of four replicate cultures of 0 mM benzoate and 30 mM benzoate. RNA was isolated using 10% saturated phenol-ethanol solution and the RNeasy Kit. Gene expression profiles were obtained with standard Affymetrix procedures.

first: Ryan

last: Kitko

first: Rebecca

last: Cleeton

first: Erin

last: Armentrout

first: Grace

last: Lee

last: Noguchi

first: Melanie

last: Berkmen

last: Jones


title: Transcriptional profiling differences for articular cartilage and repair tissue in equine joint surface lesions.

status: Public on Sep 10 2009

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

summary: Full thickness articular cartilage lesions with penetration into the subchondral bone fill with fibrocartilage-like repair tissue.  However, the repair tissue has compromised structural and biomechanical properties relative to normal articular cartilage.  The objective of this study was to evaluate transcriptome differences between normal articular cartilage and repair tissue.  Bilateral one-cm2 full-thickness lesions were made in the articular surface of the distal femurs of four adult horses followed by subchondral microfracture.  Four months postoperatively, repair tissue from the lesion site and grossly normal articular cartilage from each stifle were collected.  Total RNA was isolated from tissue samples, linearly amplified, and applied to a 9367-probeset equine-specific cDNA microarray.  Eight paired comparisons matched by limb and horse were made with a dye-swap experimental design.  Comparisons were validated by histological analysis and quantitative real-time polymerase chain reaction (qPCR).  Statistical analysis revealed 3,327 (35.2%) differentially expressed probesets.  Biomarkers typically associated with normal articular cartilage and fibrocartilage repair tissue corroborate earlier studies.  Other changes in gene expression previously unassociated with cartilage repair were also revealed and validated by qPCR.  The magnitude of divergence in transcriptional profiles between normal chondrocytes and the cells that populate repair tissue reveal substantial functional differences between these two cell populations.  At the four-month postoperative time point, the relative deficiency within repair tissue of transcripts from genes which typically define articular cartilage indicate that while cells occupying the lesion might be of mesenchymal origin, they have not recapitulated differentiation to the chondrogenic phenotype of normal articular chondrocytes.

overall_design: This is a direct comparison between grossly normal articular cartilage and repair tissue transcriptomes four months postoperatively.  Eight paired comparisons (repair vs. normal) were made from the eight stifles of four horses.  For each comparison of tissues within each limb, a dye-swap was performed.  Thus, a total of 16 slides were analyzed.  Each pair of slides represented a dye-swap comparison of repair tissue and normal cartilage four months postoperatively from each stifle of the 4 horses.

first: Liping

last: Huang

first: David

last: Frisbie

first: C

middle: W

last: McIlwraith

first: Arnold

last: Stromberg

first: Arne

last: Bathke

first: James

middle: N

last: MacLeod


title: Intra- and inter-individual genetic differences in gene expression

status: Public on Dec 31 2009

city: University of New South Wales

first: Mark

last: Cowley

address: School of BABS, Building D26

department: Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary:
Each expressed gene was tested for differential expression in three mouse tissues (Brain, Kidney, Liver) in a direct comparison of SJL/J vs. C57BL/6J
Keywords: direct comparison, multiple tissues

overall_design: Whole RNA from a pool of 5 SJL/J mice was compared to a pool of RNA from C57BL/6J mice with three technical replicates per tissue, no dye swaps.

first: Chris

last: Cotsapas

first: Rohan

last: Williams

first: Eva

middle: K

last: Chan

first: Jeremy

last: Pulvers

middle: Y

last: Liu

first: Oscar

last: Luo

last: Nott

first: Peter

middle: F

last: Little


title: Deciphering the porcine intestinal microRNA transcriptome

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

institute: Freie Universitaet Berlin

summary:
Background

While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy.
Results

Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks.
Conclusions

In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.

overall_design:
RNA isolation from porcine intestinal tissue
Intestinal samples (~ 2 cm circle segments) were taken from duodenum, proximal and distal jejunum, ileum, ascending and transverse colon of four 31 days old healthy piglets (EUROC x Pietrain). The piglets were weaned at the age of 28 days. Samples were quick-frozen in liquid nitrogen and stored at -80 °C. In order to obtain representative measurements in each intestinal locus, three cross sections of approximately 2 mm out of the 2 cm segment of frozen intestine were examined. These 3 sections were pooled and total RNA was isolated from samples using an automated homogenizer (FastPrep Instrument, MP Biomedicals, Heidelberg, Germany) and the mirVana miRNA Isolation Kit (Applied Biosystems, Darmstadt, Germany), according to the manufacturer’s protocol. The RNA quality and quantity of all samples were proven using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kits (Agilent, Waldbronn, Germany) and the Nanodrop 1000 Spectrophotometer (Thermo Scientific, MA, USA).
Microfluidic miRNA microarrays
Microfluidic microarray experiments were performed using customized Geniom biochips (febit). Customized microarrays were synthesized with the Geniom One device (febit) applying febit’s standard shortmer kit for oligonucleotide synthesis.
The light-activated in situ oligonucleotide synthesis using a digital micromirror device was performed within the Geniom One instrument on an activated three-dimensional reaction carrier consisting of a glass-silicon-glass sandwich (biochip). Using standard DNA synthesis reagents and 3’-phosphoramidites carrying 5’-photolabile protective group, oligonucleotides were synthesized in parallel in eight individually accessible microchannels (referred to as microarrays) of one biochip. Prior to synthesis, the glass surface was activated by coating with spacer to facilitate probe-target interaction and to avoid probe-probe interface [37]. Two different microarray designs were used. The first one included only the 399 miRDeep predicted mature miRNAs and their star sequences in seven replicates allowing highly accurate validation of the miRDeep prediction plus 16 spike-in controls. The second design consisted of 1117 features in triplicate, including the identified conserved porcine mature miRNA sequences (18 mapping to the porcine genome and another 124, which did not map), 74 known porcine and 885 human miRNAs from miRBase (13.0) and 16 spike-in controls.
For microarray experiments, intestinal total RNA samples from different loci of four subjects were isolated independently and respective pools of total RNA samples were prepared. All pools underwent a second quality control to determine the quality and quantity using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit according to the manufacturer’s instructions. For each microarray 250 ng of total RNA were suspended in 25 µl of febit’s proprietary miRNA hybridization buffer. The hybridization was performed automatically for 16h at 42°C using the Geniom RT-Analyzer (febit). After stringent washing a microfluidic-based extension assay was performed to label the miRNAs using biotinylated nucleotides. After washing, biotinylated nucleotides were detected by streptavidin-phycoerythrin and signal recognition and calculation were done automatically within milliseconds. The background of the chips was effectively corrected by global background subtraction and inter-array effects were corrected by variance stabilizing normalization.

first: Marc

middle: R

last: Friedländer

first: Jutta

first: Lena

last: Hoeke

first: Wei

last: Chen

first: Andreas

last: Keller

first: Peer

last: Stähler

first: Nikolaus

last: Rajewsky

first: Ralf

last: Einspanier


title: Analysis of the turkey skeletal muscle transcriptome through development within a genetic line (Experiment 1)

status: Public on Feb 01 2010

city: East Lansing

first: Kelly

last: Sporer

state: MI

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

summary: The purpose of Experiment 1 was two-fold:  a) to evaluate a unique set of negative, distance, and mismatch control probes on the newly designed 6K TSKMLO microarray, and b) to identify patterns of gene expression in skeletal muscle during development.  Negative and mismatch controls confirmed specific hybridization using this array, and genes identified as differentially expressed between developmental stages by microarray analysis were confirmed by qRT-PCR.  Novel candidate genes and pathways were identified as playing potentially crucial roles in turkey skeletal muscle development with implications for improving turkey meat quality defects and growth-induced myopathies long-term.

overall_design: This experiment utilized turkeys from two genetic lines: RBC2, a randomly bred control line representative of a 1967 commercial turkey, and F, a subline genetically selected from the RBC2 line for increased 16-week body weight.  Skeletal muscle was collected at three critical developmental stages:  18-day embryo (18de; peak of hyperplasia), 1-day post-hatch (1d; shift from myoblast-mediated growth to satellite cell modulated growth by hypertrophy), and 16-week-old birds (16wk; completion of muscle formation and approximate age of commercial slaughter).  Experiment 1 was designed to directly compare the three stages of skeletal muscle development: 18de vs. 1d, or 1d vs. 16wk, for each of the genetic lines.  Experiment 1 contained 10 arrays per comparison, therefore, it contained 40 arrays total.  Birds were randomly assigned to an array, and hybridizations were performed in random order.

first: Wen

last: Chiang

first: Robert

last: Tempelman

first: Catherine

last: Ernst

first: Kent

last: Reed

first: Sandra

last: Velleman

first: Gale

last: Strasburg


title: Glis3: a critical player in the regulation of pancreatic beta cell development

status: Public on Nov 15 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Glis3 mutant mice (Glis3zf/zf) die within the first week after birth due to overt diabetes, evidenced by hyperglycemia and hypoinsulinemia. Histopathological analysis showed that Glis3zf/zf mice develop a pancreatic phenotype with a dramatic loss of beta- (insulin) and delta- (somatostatin) cells contrasting a smaller relative loss of alpha- (glucagon), PP- (pancreatic polypeptide), and epsilon- (ghrelin) cells. Glis3zf/zf mice develop ductal cysts with decreased number of primary cilia, while the acini are not significantly affected. Gene expression profiling by microarray analysis demonstrated that the expression of terminal hormonal genes and several transcription factors important in endocrine development were significantly deregulated in Glis3zf/zf mice. During pancreatic development, Glis3 mRNA expression is induced during the secondary transition, a stage of cell lineage specification and extensive patterning. Changes in pancreatic development of Glis3zf/zf mice are noted during and after this stage; the number of cells staining positively for Ngn3, MafA, or Pdx-1 is greatly diminished. These observations indicate that Glis3 plays a key role in the development of mature beta cells.

overall_design: RNA samples from 2 pups for each WT or Glis3zf/zf pups were pooled, then analyzed.

first: H.

middle: S

last: Kang

first: J.

last: Beak

first: Y.

last: Kim

first: A.

last: Jetten