title: Molecular Dissection of Pea Shoot Apical Meristem

city: Parkville

first: Chui

last: WONG

state: Victoria

address: University of Melbourne

department: Land and Food

institute: University of Melbourne

summary: Knowledge about an organism’s cell and tissue-specific transcriptional repertoire is essential for understanding the gene regulatory circuits that control key developmental events.  The shoot apical meristem (SAM) is responsible for development of all the above ground parts of plants.  Our understanding of SAM at the molecular level is far from complete.  The present work investigates the global gene expression repertoire of SAMs in the garden pea (Pisum sativum).  To this end, 10,346 EST sequences representing 7611 unique genes were generated from pea SAM cDNA libraries.  These sequences, together with previously reported ESTs, were used to construct a 12K oligonucleotide array used to identify genes exhibiting differential SAM expression, as compared to the axillary meristem, root apical meristem, and non-meristematic tissues.  We identified a number of genes that are predominantly expressed in specific cell layers or domains of the SAM, and thus are likely components of the gene networks involved in stem cell maintenance and initiation of lateral organ primordial cells.  In situ hybridization confirmed the spatial localisation of some of these key genes within the SAM.  Our data also indicate the diversification of some gene expression patterns and functions in legume crop plants.

overall_design:
RNA samples were hybridized to two-colour Combimatrix arrays manufactured with a custom library of 11958 probes.
The limma software package for R (Smyth, 2005) was used in subsequent statistical analysis of the data generated.  On examination of the data during quality control assessment, it became evident that the Cy3 channel showed little dynamic range and background correction and normalisation could not correct for this.  Therefore only the Cy5 channel was used in the subsequent analysis. This resulted in somewhat unbalanced sample sizes with six replicates of SAM and one each of RAM, AM and NM.
Nevertheless, linear modelling and empirical Bayes moderated t-statistics (Smyth, 2004) used in the statistical analysis allows variance information to be borrowed across both samples and genes, resulting in reliable statistical inference even for the groups with only one sample.

first: Dacheng

last: Liang

last: Wong

first: Mohan

middle: B

last: Singh

first: Belinda

last: Phipson

first: Gordon

last: Smyth

first: Prem

last: Bhalla


title: StpA prevents RpoS-dependent transcription during mid-exponential growth in S. Typhimurium

status: Public on Oct 28 2009

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

summary: StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: To test the hypothesis that stpA prevents Sigma38-dependent transcription during mid-exponential growth in S. Typhimurium, we analysed the effect of the stpA deletion on transcription in the presence and absence of rpoS. Three biological replicates were performed for each strain. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

first: Paul

last: Mcdermott

first: Arthur

last: Thompson

first: Jay

middle: C

last: Hinton


title: Inflammation and degeneration of the olfactory epithelium in an immuno-deficient zebrafish

city: Singapore

first: Suresh

last: Jesuthasan

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

summary:
Vertebrates are protected from pathogens by an adaptive and an innate immune system. In mammals, loss of the adaptive immune system severely compromises viability. Zebrafish, in contrast, can survive for relatively long without adaptive immunity, as demonstrated by the immuno-deficient Rag1 mutant. Here, we examine whether the innate immune system is activated in the mutant, and ask whether this has any effect on the nervous system, given the finding that inflammation is linked to neurodegeneration in higher vertebrates. Using microarray analysis of the olfactory epithelium, we show that innate immune responses are upregulated. Neuronal genes are down-regulated, and immunofluorescence for the neural marker HuC shows a progressive loss of olfactory sensory neurons in mutants. Propodium iodide uptake indicates a corresponding increase in cell death. Rag1 mutant fish progressively lose their sensitivity to an olfactory cue, the alarm pheromone Schreckstoff, indicating that neuro-degeneration has a behavioral significance. Taken together, these data establish that immuno-deficiency in the zebrafish is accompanied by neuro-inflammation and loss of neurons. The microarray data document transcriptional changes associated with activation of innate immunity in the context of immunodeficiency and also identify novel genes that are potentially related to function of the olfactory system.
Keywords: analysis of mutant

overall_design: A total of 6 RNA samples were used for hybridization. 3 were from the olfactory rosettes of wild type adult zebrafish and 3 were from Rag1 mutants.

first: Bo

last: Feng

first: Ajay

middle: S

last: Mathuru

middle: J


title: Deinococcus radiodurans R1:  rpob 9-bp-deletion vs. wild-type

status: Public on Oct 22 2009

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

country: China

institute: Zhejiang University

summary: Transcriptional profiling of  comparing wildtype strains with rpob 9-bp-deletion strains under normal growth contidions.

overall_design: One-condition experiment, rpob 9-bp-deletion vs. wild-type.  Two biological replicates were carried out.

first: Xiaoting

first: Hu

last: Wang


title: Profiling of liver tissue from the F2 M16xICR mouse cross.

status: Public on Oct 26 2009

city: Seattle

first: Radu

last: Dobrin

state: WA

address: 401 Terry Ave N

country: USA

institute: Merck and Co. Inc.

summary:
We profiled gene expression in liver tissue from F2 progeny from a cross between the outbred M16 (selectively bred for rapid weight gain) and ICR (control) mouse strains. We developed a framework for reconstructing tissue-to-tissue coexpression networks between genes in hypothalamus, liver or liver tissues that are independent of networks constructed from single tissue analyses. The subnetworks we identify as specific to tissue-to-tissue interactions associate with multiple obesity-relevant biological functions like circadian rhythm, energy balance, stress response, or immune response.

Keywords: Tissue profiling in a mouse F2 cross.

overall_design: We analyzed 302 liver samples.

first: Jun

last: Zhu

first: Cliona

last: Molony

first: Carmen

last: Argman

first: Mark

middle: E

last: Parrish

first: Sonia

last: Carlson

middle: F

last: Allan

first: Daniel

last: Pomp

first: Eric

last: Schadt


title: Profiling of adipose tissue from the F2 M16xICR mouse cross.

summary:
We profiled gene expression in adipose tissue from F2 progeny from a cross between the outbred M16 (selectively bred for rapid weight gain) and ICR (control) mouse strains. We developed a framework for reconstructing tissue-to-tissue coexpression networks between genes in hypothalamus, adipose or adipose tissues that are independent of networks constructed from single tissue analyses. The subnetworks we identify as specific to tissue-to-tissue interactions associate with multiple obesity-relevant biological functions like circadian rhythm, energy balance, stress response, or immune response.

Keywords: Tissue profiling in a mouse F2 cross.

overall_design: We analyzed 308 adipose samples.


title: Profiling of hypothalamus tissue from the F2 M16xICR mouse cross.

summary:
We profiled gene expression in hypothalamus tissue from F2 progeny from a cross between the outbred M16 (selectively bred for rapid weight gain) and ICR (control) mouse strains. We developed a framework for reconstructing tissue-to-tissue coexpression networks between genes in hypothalamus, liver or hypothalamus tissues that are independent of networks constructed from single tissue analyses. The subnetworks we identify as specific to tissue-to-tissue interactions associate with multiple obesity-relevant biological functions like circadian rhythm, energy balance, stress response, or immune response.

Keywords: Tissue profiling in a mouse F2 cross.

overall_design: We analyzed 308 hypothalamus samples.


title: Cardiac gene expression and systemic cytokine profile are complementary in a murine model of post ischemic heart failure

status: Public on Oct 24 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: After myocardial infarction (MI) activation of the immune system and inflammatory mechanisms, among others, can lead to ventricular remodeling and heart failure (HF). Interaction between these systemic alterations and corresponding changes in the heart has not been extensively examined in the setting of chronic ischemia. The main purpose of this study was to investigate alterations in cardiac gene and systemic cytokine profile in mice with post-ischemic HF. Plasma was tested for IgM and IgG anti-heart reactive repertoire and inflammatory cytokines. Heart samples were assayed for gene expression. Ischemic HF significantly increased the levels of serum IgM (by 5.2 fold) and IgG (by 3.6 fold) associated with remarkable content of anti-heart specificity. Comparable increase was observed in levels of circulating pro-inflammatory cytokines, such as IL-1β (3.8x) and TNF-α (6.0x). IFN-gamma was also increased in the MI group by 3.1x. However, IL-4 and IL-10 showed no significant difference between MI and sham groups. Chemokines such as MCP-1 and IL-8 were enhanced in the plasma of infarcted mice. We identified 2079 well annotated unigenes that were significantly regulated by the post-ischemic HF. Complement activation and immune response was among the most up-regulated processes. Interestingly, 21 out of the 101 quantified unigenes involved in inflammatory response were significantly up-regulated and none were down-regulated. These data indicate that post-ischemic heart remodeling is accompanied by immune mediated mechanisms that act both systemically and locally.

overall_design: We compared RNA samples extracted from whole hearts of control and infarcted mice samples by analyzing hybridization to AECOM 32k mouse microarrays (http://microarray1k.aecom.yu.edu/) spotted with Operon version 3.0 70-mer oligonucleotides. The hybridization protocol, the slide type and the scanner settings were uniform throughout the entire experiment to minimize the technical noise. Control (sham) and infarcted red-labeled heart samples were hybridized against an in-house prepared green-labeled universal mouse reference.

first: S

last: Lachtermacher

first: B

middle: L

last: Esporcatte

first: F

last: Montalvão

first: P

last: Costa

first: D

last: Rodrigues

first: L

last: Belem

first: A

last: Rabischoffisky

first: H

last: Faria Neto

first: R

last: Vasconcellos

middle: A

last: Dohmann

last: Spray

last: Goldenberg

last: Campos de Carvalho


title: Differentiation of human monocytes to macrophages in the presence of GM-CSF +/- forskolin (FSK)

first: Joseph

last: Beavo

address: 1959 NE Pacific St

department: Pharmacology

institute: University of Washington

summary: Macrophages are central mediators of the innate immune system that can be differentiated from monocytes upon exposure to cytokines. While increased cyclic adenosine monophosphate (cAMP) levels inhibit many lipopolysaccharide (LPS) -elicited macrophage inflammatory responses, the effects of elevated cAMP on macrophage differentiation are not well understood. We have differentiated monocytes to macrophages in the presence of GM-CSF or GM-CSF + FSK to elevate cAMP levels and determine its effects on differentiation.

overall_design: Microarray analysis was performed separately on samples from 3 human donors: 3 control and 3 forskolin-treated samples.

first: Angie

last: Hertz


title: Radical prostatectomy specimens with and without TMPRSS2:ERG fusion from 139 patients with prostate in a Toronto cohort

status: Public on Oct 23 2009

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: Prostate tumors with the gene fusion TMPRSS2:ERG have been reported to have a significantly higher risk of recurrence compared with tumors lacking the fusion. Tumors from 139 patients who underwent radical prostatectomy were analyzed for the expression of 502 cancer-related genes to identify genes differentially regulated in TMPRSS2:ERG fusion tumors as well as identify biomarkers of biochemical recurrence.

overall_design: 139 prostate fresh-frozen tumors from radical prostatectomy surgery where profiled on the Illumina Human Cancer DASL Panel. 69 tumors were positive for the gene fusion TMPRSS2:ERG while 70 where not. 33 of the 139 patients experienced biochemical recurrence. Data was analyzed for differential genes in TMPRSS2:ERG fusion positive tumors as well as clinical and molecular biomarkers of recurrence.

first: Arun

last: Seth

first: Brian

middle: R

last: Leyland-Jones

last: Abramovitz


title: MicroRNA Expression in Kidney Development Comparing E14.5 and P1

city: New Orleans

first: Oliver

last: Wessely

state: LA

address: 1901 Perdido Street

department: Cell Biology & Anatomy

institute: LSU Health Sciences Center

summary: This study was performed to identify miRNAs that are differentially regulated during mouse kidney development. Two stages (E14.5 and P1) were analyzed. Differential expression was verified using qPCR and/or in situ hybridization.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Multiple kidneys were dissected, pooled and processed for total mRNA isolation. Probe labeling, hybridization and data analysis were performed by Exiqon. The three submitted sample files are technical replicas using the same mRNAs.

first: Raman

last: Agrawal

first: Uyen

last: Tran


title: Genome-wide analysis of maltose utilization and regulation in aspergilla

city: Gothenburg

first: wanwipa

last: vongsangnak

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary:
Comparative genomics and transcriptomics of the filamentous fungi Aspergillus oryzae and Aspergillus niger have opened possibilities for investigating the cellular metabolism and regulation of these fungi on a systemic level. The aim of this work was to understand how metabolism is regulated and to identify common regulatory responses between A. oryzae and A. niger. We therefore conducted batch fermentations with A. oryzae and A. niger grown on three different carbon sources (glucose, maltose, and xylose) in order to investigate their genome-wide transcription response

Keywords: Two Aspergillus species and different carbon sources

sample_organism:
Aspergillus niger
Aspergillus oryzae

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Three conditions (glucose, maltose and xylose) with three biological replicates for A. oryzae and A. niger

first: W

last: Vongsangnak

first: M

middle: P

last: Salazar

first: K

last: Hansen

first: J

last: Nielsen


title: Taura Syndrome Virus or Yellow Head Virus infection in two strains of L. vannamei different in their resistance to TSV

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

summary:
The transcriptomic response of two strains of the Pacific whiteleg shrimp, different in their resistance to Taura Syndrome Virus (TSV), in response to infection with TSV and Yellow Head Virus (YHV). Changes in gene expression in the shrimp’s hepatopancreas were assessed using a cDNA microarray containing 2,469 putative unigenes. The patterns of gene expression between the shrimp strains were considerably similar, except for the more advanced stages of Taura Syndrome. Between the different treatments approximately 250 genes were differently expressed. The most advanced stages of YHV infection showed the highest number of differently expressed genes. During infection there were profound changes in the expression of genes related to lipid and protein metabolism, cellular trafficking, immune defense and stress response.

Keywords: Disease state analysis, disease resistance

overall_design: There were 5 biological replicates for each of the groups in this experiment.  Also, two strains of Litopenaeus vannamei were used: a strain resistant to TSV and a strain susceptible to TSV (Kona line).  The treatments consisted of injecting both strains with 60mL of a shrimp extract made from shrimp previously injected with either a SPF shrimp extract (1x10-4), Taura Syndrome Virus (1x10-5) or Yellow Head Virus (1x10-4).  The 2 initial control groups were composed of hepatopancreas samples from both strains prior the injections.  Samples were also collected from at days 1 and 2 from both strains from the 3 different treatments (control, TSV and YHV).

first: Artur

last: Veloso

first: Gregory

middle: W

last: Warr

first: Craig

last: Browdy

first: Robert

last: Chapman


title: Regulation of the microRNA processor DGCR8 by the tumor suppressor ING1

status: Public on Oct 21 2009

city: Madrid

first: Sergio

last: Callejas

address: Melchor Fernández Almagro, 3

department: Genomics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: The ING familiy of tumor suppressor proteins control several cellular functions relevant to anti-tumor protection, like cell-cycle control, apoptosis, senescence or migration.  ING proteins are functionally linked to the p53 pathway, and they participate in transcriptional control via the recognisition of histone marks and recruitment of protein complexes with chromatin-modifying activity to specific promoters.  Here, we have investigated the global impact of ING1 in gene regulation through genome-wide analysis of expression profiles in primary embryonic fibroblasts deficient for the Ing1 locus.  We find that Ing1 has a predominant role as transcriptional repressor in this setting, affecting the expression of genes involved in a variety of cellular functions.  Within the subset of genes showing differential expression, we have identified DGCR8, a protein involved in the early steps of microRNA biogenesis.  We show that ING1 binds to the DGCR8 promoter and controls its transcription through chromatin regulation at its promoter.  We also find that ING1 and DGCR8 can cooperate in restraining proliferation.  In summary, this study reveals a novel connection between ING1 and a regulator of microRNA biogenesis, and identifies new links between tumor suppressor proteins and the microRNA machinery

sample_organism:
Homo sapiens
Mus musculus

overall_design:
For MEFs, two replicates were used for each genotype (wild-type or Ing1-deficient).  Wild type MEFs were used as reference.
For EMG cells [a cell line generated in our laboratory], two replicates were used for each condition (cells where ING1 was induced by doxycycline or uninduced cells).  Uninduced cells were used as reference.

first: Daniel

last: Gómez-Cabello

first: Alberto

last: Benguría

first: A

last: Moreno

first: Javier

last: Alonso

first: Ignacio

last: Palmero


title: Differential gene expression in brain of the Cin85-/- mutant mouse line

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
Cin85 is an adaptor protein independently identified as Cbl-interactin protein of 85kDA, SETA and SH3KBP1. The protein control the spatial and temporal assembly of multiprotein complexes that transmit intracellular signals that eventually controll physiological or pathological processes. Cin85 interacts with components of the synaptic vesicles. The Cin85 knock out could be a model for neuronal defects related to impaird neurotransmitter release line mental retardation, abnormal behaviour and cognitive function. The role of Cin85 in EGFR internalization might be a model for different kind of cancer. Detection of changes in gene expression levels in brain of Cin85 k.o. have been done. About 77 significantly regulated genes in brain have been found. Several of the differentially regulated genes are transcription factors, are involved in tumorigenesis, associated with neuronal functions and neurodegenerative diseases or have functions in splicing processes.
Keywords: genome-wide molecular phenotying, Cin85-/-, brain

overall_design: Brain of five Cin85-/- mice in two replicates including one dye swap experiment  have been performed for each individual mice (in total 10 chip experiments), reference: Pool of 5 wildtype mice

first: Marion

last: Horsch

first: Johannes

last: Beckers


title: Expression data from batch cultivations with A. niger, A. oryzae and  A. nidulans grown on glucose and glycerol

city: Göteborg

first: Margarita

last: Salazar Peña

address: Kemigården 4

department: Chemical and Biological Engineering

summary:
Conserved transcriptional regulation of glycerol metabolism was investigated in three Aspergillus species, A. nidulans, A. oryzae and A. niger. For this purpose, batch cultivations under well controlled conditions were performed with the three Aspergilli. Samples for RNA extraction were collected
and further processed for hybridization in custom designed Affymetrix microarrays containing probes for the three Aspergillus species. Protein comparisons and cross analysis with gene expression data of all three species resulted in the identification of 88 genes having a conserved response across the three Aspergillus species. A promoter analysis of the up-regulated genes led to the identification of a conserved binding site for a putative regulator.

sample_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Triplicate batch fermentations with each of the three Aspergillus species were carried out and transcriptome analysis was performed. Biomass from each Aspergillus species was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.

last: Salazar

first: Wanwipa

last: Vongsangnak

first: Gianni

last: Panagiotou

first: Mikael

last: Andersen

first: Jens


title: Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries

status: Public on Oct 20 2009

city: Vancouver

first: Marianne

middle: D.

last: Sadar

state: British Columbia

address: 675 W. 10th Ave

department: Genome Sciences Centre

country: Canada

institute: British Columbia Cancer Agency

summary: Background: The development and maintenance of the prostate is dependent on androgens and the androgen receptor. The androgen pathway continues to be important in prostate cancer. Here, we evaluated the transcriptome of prostate cancer cells in response to androgen using long serial analysis of gene expression (LongSAGE) libraries. Results: There were 131 tags (87 genes) that displayed statistically significant (p=<0.001) differences in expression in response to androgen. Many of the genes identified by LongSAGE (35/87) have not been previously reported to change expression in the direction or sense observed. In regulatory regions of the promoter and/or enhancer regions of some of these genes there are confirmed or potential androgen response elements (AREs). The expression trends of 24 novel genes were validated using quantitative real time-polymerase chain reaction (qRT-PCR). These genes were: ARL6IP5, BLVRB, C19orf48, C1orf122, C6orf66, CAMK2N1, CCNI, DERA, ERRFI1, GLUL, GOLPH3, HM13, HSP90B1, MANEA, NANS, NIPSNAP3A, SLC41A1, SOD1, SVIP, TAOK3, TCP1, TMEM66, USP33, and VTA1. The physiological relevance of these expression trends was evaluated in vivo using the LNCaP Hollow Fibre model. Novel androgen-responsive genes identified here participate in protein synthesis and trafficking, response to oxidative stress, transcription, proliferation, apoptosis, and differentiation. Conclusions: These processes may represent the molecular mechanisms of androgen-dependency of the prostate. Genes that participate in these pathways may be targets for therapies or biomarkers of prostate cancer.

overall_design: There are 2 samples. R1881 is the androgen/test sample. Vehicle is the ethanol/control sample.

first: Tammy

last: Romanuik

first: Gang

last: Wang

last: Holt

first: Steven

last: Jones

first: Marco

last: Marra

middle: D


title: RNA  validation of LAB 2k v2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
To study their metabolic potential in natural ecosystems, we developed a species-independent LAB microarray, containing 2,269 30-mer oligonucleotides, and targeting 406 genes that play a key role in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response. Also, genes linked to negative traits such as antibiotic resistance and virulence are represented.  This experiment is a validation experiment, where we hybridized labelled RNA from 20 LAB strains, covering 86% of all oligos.
Keywords: Platform validation experiment

sample_organism:
Leuconostoc mesenteroides
Enterococcus faecalis
Enterococcus faecium
Lactococcus lactis
Lactobacillus acidophilus
Lactobacillus delbrueckii
Lactiplantibacillus plantarum
Latilactobacillus sakei
Limosilactobacillus fermentum
Fructilactobacillus sanfranciscensis
Latilactobacillus curvatus
Lactobacillus johnsonii
Limosilactobacillus pontis
Companilactobacillus paralimentarius

platform_organism:
Leuconostoc mesenteroides
Oenococcus oeni
Pediococcus acidilactici
Pediococcus pentosaceus
Staphylococcus aureus
Streptococcus thermophilus
Enterococcus faecalis
Enterococcus faecium
Enterococcus hirae
Lactococcus lactis
Lactobacillus acidophilus
Levilactobacillus brevis
Lentilactobacillus buchneri
Lacticaseibacillus casei
Weissella confusa
Lactobacillus delbrueckii
Lactobacillus helveticus
Lentilactobacillus hilgardii
Lactiplantibacillus pentosus
Lactiplantibacillus plantarum
Lactobacillus gasseri
Lacticaseibacillus paracasei
Limosilactobacillus reuteri
Latilactobacillus sakei
Companilactobacillus alimentarius
Lactobacillus amylovorus
Companilactobacillus farciminis
Limosilactobacillus fermentum
Fructilactobacillus fructivorans
Fructilactobacillus sanfranciscensis
Bifidobacterium
Brevibacterium linens
Latilactobacillus curvatus
Lactobacillus johnsonii
Leuconostoc citreum
Leuconostoc pseudomesenteroides
Limosilactobacillus pontis
Enterococcus casseliflavus
Mammaliicoccus lentus
Limosilactobacillus panis
Lacticaseibacillus rhamnosus
Lactobacillus crispatus
Enterococcus mundtii
Lactiplantibacillus paraplantarum
Companilactobacillus paralimentarius
Limosilactobacillus frumenti
Lentilactobacillus parabuchneri
Companilactobacillus mindensis
Furfurilactobacillus rossiae

overall_design: Loop design, hence all RNA samples were hybridized once in each colour (Cy3 and Cy5).

first: Stefan

last: Weckx

first: Joke

last: Allemeersch

first: Roel

last: Van der Meulen

first: Gino

last: Vrancken

first: Luc

last: De Vuyst

first: Paul

last: Van Hummelen


title: Direct calibration of PICKY-designed microarrays

city: Ames

first: Hui-Hsien

last: Chou

state: IA

address: 503 Science II

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary:
Picky is an optimal microarray design software which designed the NSF Rice 45K Array. A series of microarray experiments using a one-chip version of this array were conducted to validate as well as to develop a calibration method for Picky designed microarrays. Synthesized samples with known content were used in the validation. PICKY designed microarrays were found to be highly reliable. The PICKY predicted closest nontarget information was used to quantitatively calibrate the best microarray hybridization conditions using the same microarrays and synthesized samples. Because this method works under most microarray protocols, it is generally applicable in any lab that uses PICKY as their microarray design tool. The associate publication provides more details about the experiment design and discussions about its results.

Keywords: Microarray Calibration

overall_design: 20 probes on the NSF Rice Oligonucleotide 45K Array grouped into two sets were chosen for microarray calibration. 40 antisense oligonucleotides were synthesized based on the target and closest nontarget gene sequences for each of the chosen probes. 5 different experiments were designed with varied concentrations and dye labeling schemes for the 40 antisense oligos. Two hybridizations were conducted for each experiment at each calibration temperature. 7 sets of experiments were conducted at 70, 60, 55, 53, 50, 48 and 45 degree C using a total of 70 microarrays. Each microarray is scanned at multiple PMT settings to obtain multiple data files. After inspection, weak signal results at 70 degree C and a few contaminated microarray results were discarded. Altogether, 165 valid GenePix GPR files were produced and included in this series.

first: Arunee

last: Trisiriroj

first: Sunyoung

last: Park

first: Yue-Ie

last: Hsing

first: Pamela

last: Ronald

first: Patrick

last: Schnable


title: Rearrangement of CRLF2 in B-progenitor and Down syndrome associated acute lymphoblastic leukemia

status: Public on Oct 18 2009

city: Memphis

first: Charles

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

type: Genome variation profiling by genome tiling array

summary: Chromosomal aneuploidy and translocations are hallmarks of acute lymphoblastic leukemia (ALL), but many patients lack a recurring chromosomal alteration. Here we report a recurring interstitial deletion of the pseudoautosomal region 1 of chromosomes X and Y in B-progenitor ALL that results in the expression of a novel fusion that juxtaposes the first non-coding exon of P2RY8 to the coding region of the CRLF2  (cytokine receptor like factor 2, or thymic stromal lymphopoietin receptor) gene. The P2RY8-CRLF2 fusion was identified in 7% of B-ALL cases, and was very common in ALL associated with Down syndrome (55% of cases) and was associated with the presence of JAK mutations. The P2RY8-CRLF2 fusion results in increased expression of CRLF2, a lymphoid signaling molecule that forms a heterodimeric complex with interleukin receptor 7 alpha. These findings identify a novel recurring chromosomal alteration in B-ALL, and suggest that perturbed CRLF2-mediated signaling is a key event in leukemogenesis in these cases.

overall_design: Profiling of tumor acquired DNA copy number alterations in 2 patients with Down syndrome associated B-progenitor acute lymphoblastic leukemia. Matched tumor and normal DNA was used for each array hybridization in each case.


title: DNA  validation of LAB 2k v2

summary:
To study their metabolic potential in natural ecosystems, we developed a species-independent LAB microarray, containing 2,269 30-mer oligonucleotides, and targeting 406 genes that play a key role in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response. Also, genes linked to negative traits such as antibiotic resistance and virulence are represented.  This experiment is a validation experiment, where we hybridized labelled DNA from 20 LAB strains, covering 86% of all oligos.
Keywords: Platform validation experiment

overall_design: All sampels were hybridized twice in the Cy3 channel. In the Cy5 channel no sample was hybridized.


title: ChIP of ICEBs1 induced Bacillus subtilis

status: Public on Oct 16 2009

city: Cambridge

first: Alan

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

type: Genome binding/occupancy profiling by array

summary: Examine possible association of Ssb, PolC, DnaC, PcrA with ICEBs1 in RapI-induced Bacillus subtilis

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Samples submitted are representative

first: Catherine

last: Lee


title: Characterization of the autoaggregation response of Fusobacterium nucleatum

status: Public on Oct 15 2009

city: Oklahoma City

first: Justin

last: Merritt

state: OK

address: 975 NE 10th St BRC364

department: Oral Biology

institute: University of Oklahoma Health Sciences Center

summary: Fusobacterium nucleatum is a Gram negative oral bacterial species associated with periodontal disease progression. This species is perhaps best known for its ability to adhere to a vast array of other bacteria and eukaryotic cells. Numerous studies of F. nucleatum have examined various coaggregation partners and inhibitors, but it is largely unknown whether these interactions induce a particular genetic response. We tested coaggregation between F. nucleatum ATCC strain 25586 and various species of Streptococcus in the presence of a semi-defined growth medium containing saliva. We found that this condition could support efficient coaggregation, but surprisingly also stimulated a similar degree of autoaggregation. We further characterized the autoaggregation response, since few reports have examined this in F. nucleatum. After screening several common coaggregation inhibitors, we identified L-lysine as a competitive inhibitor of autoaggregation. We performed a microarray analysis of the planktonic vs. autoaggregated cells and found nearly 100 genes that were affected after only about 60 min. of aggregation. We tested a subset of these genes via real-time RT-PCR and confirmed the validity of the microarray results. Some of these genes were also found to be inducible in cell pellets created by centrifugation. Based upon these data, it appears that autoaggregation activates a genetic program that may be utilized for growth in a high cell density environment, such as the oral biofilm.

overall_design: The study aims to determine the effect of autoaggregation upon the transcriptome.  The study contains 2 separate experiments that both measure dispersed (i.e. non-aggregated) vs. aggregated cells and each experiment was performed in duplicate.  Samples with no added components other than medium were dispersed, samples containing 25% saliva were aggregated, and samples containing 25% saliva + 50mM L-lysine remained dispersed.


title: E coli MG1655 biofilm and planktonic gene expression

status: Public on Oct 17 2009

city: San Marcos

first: Robert

middle: JC

last: McLean

address: 601 University Drive

institute: Texas State University-San Marcos

summary: Bacteria growing as surface-adherent biofilms are better able to withstand chemical and physical stresses than their unattached, planktonic counterparts. Using transcriptional profiling and quantitative PCR, we observed a previously uncharacterized gene, yjfO, to be upregulated during Escherichia coli MG1655 biofilm growth in a chemostat on serine-limited defined medium. A yjfO mutant, developed through targeted insertion mutagenesis, and a yjfO-complemented strain, were obtained for further characterization. While bacterial surface colonization levels (CFU/cm2) were similar in all three strains, the mutant strain exhibited reduced microcolony formation when observed in flow cells, and greatly enhanced flagellar motility on soft (0.3%) agar. Complementation of yjfO restored microcolony formation and flagellar motility to wild type levels. Cell surface hydrophobicity and twitching motility were unaffected by the presence or absence of yjfO. In contrast to the parent strain, biofilms from the mutant strain were less able to resist acid and peroxide stresses. yjfO had no significant effect on E. coli biofilm susceptibility to alkali or heat stress. Planktonic cultures from all three strains showed similar responses to these stresses. Regardless of the presence of yjfO, planktonic E. coli withstood alkali stress better than biofilm populations. Complementation of yjfO restored viability following exposure to peroxide stress, but did not restore acid resistance. Based on its influence on biofilm formation, stress response, and effects on motility, we propose renaming the uncharacterized gene, yjfO, as bsmA (biofilm stress and motility).

overall_design: Transcriptional profiling of duplicate biofilm and planktonic cultures of E. coli MG1655 grown in serine-limited MOPS minimal media.

first: Deborah

last: Siegele


title: Genomic microarrays of RapI-induced Bacillus subtilis

summary: Examine increase in gene copy number after induction of ICEBs1 by RapI expression

overall_design: Samples are done in independent duplicates


title: Histone H1 binding is restricted by histone variant H3.3 (Expression)

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary:
Linker histones are involved in the formation of higher-order chromatin structure. Although linker histones have been implicated in the regulation of specific genes, it still remains unclear what their principal binding determinants are and how their repressive function in vitro can be reconciled with presumed broad binding in vivo.  We generated a full genome, high resolution binding map of linker histone H1 in Drosophila Kc cells, using DamID. H1 binds at similar levels across much of the genome, both in classical euchromatin and heterochromatin. Strikingly, there are pronounced dips of low H1 occupancy around transcription start sites of active genes and at many distant cis-regulatory sites. H1 dips are not due to lack of nucleosomes. Rather, all regions with low binding of H1 show enrichment of the histone variant H3.3 which itself has been linked to high nucleosome turnover. Upon knockdown of H3.3, we find that H1 levels increase at sites previously not covered with H1 with a concomitant increase in nucleosome repeat length. These changes are independent of transcriptional changes. Our results show that the H3.3 protein counteracts association of H1 at genomic sites with high rates of histone turnover. This antagonism provides a mechanism to keep diverse genomic sites in an open chromatin conformation.
For this study, we generated DamID profiles of histone H1 and RpII18 in Drosophila Kc167 cells. Additionally, we generated H1 profiles in cells treated with RNAi against white, H3.3B, or H3.3A and H3.3B. Nucleosome positioning profiles were generated in untreated cells and cells treated with RNAi against white, H3.3B, or H3.3A and H3.3B. Profiles of expression changes were generated for H3.3B RNAi and H3.3A and H3.3B RNAi.

overall_design: DamID experiments for H1 and RpII18 were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Formaldehyde-assisted isolation of regulatotry elements (FAIRE) was performed in Drosophila Kc167 cells. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing over non-crosslinked genomic DNA. Nucleosome positioning profiles were made by hybridizing mononucleosomal DNA over MNase digested purified genomic DNA on 380k NimbleGen arrays with 10 bp probe spacing. Expression profiles were made as H3.3 RNAi over white RNAi cohybridizations on spotted INDAC long oligo arrays. Every experiment was done in duplicate in the reverse dye orientation.

first: Ulrich

last: Braunschweig

first: Greg

last: Hogan

first: Ludo

last: Pagie


title: Genomic microarrays of RapI-induced Bacillus subtilis effect of pcrA

overall_design: Samples are independent triplicates or duplicates


title: ChIP-chip with antibodies for histone 3 lysine 4 trimethylation in Mll3+/+ and Mll3-/- MEFs and Ptip+/+ and Ptip-/- MEFs

city: Kansas City

first: Pengfei

last: Wang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute

summary:
Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II

A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions.  The Set1/COMPASS was the founding member and the only H3K4 methylases in S. cerevisiae, however, in mammals at least six H3K4 methylases Set1A/B and MLL1-4 are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation pattern in wild-type Mll1+/+ and Mll1-/- mouse fibroblasts (MEFs).  We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters   carrying this modification.  Many of these genes, which include developmental regulators such as Hox genes show decreased levels of RNA polymerase II recruitment and   expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, Menin, a component of the Mll1   and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci.  However, the loss of MLL3/4 and/or the Set1 complexes have little to no effect   on the Hox loci H3K4 methylation or expression levels in these MEFs.  Together these data provide insight into redundancy and specialization of COMPASS-like complexes in   mammals and provide evidence on a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation.

overall_design: Chromatin Immunoprecipitation was performed with antibodies for histone 3 lysine 4 trimethylation in Mll3+/+ and Mll3-/- mouse embryonic fibroblasts and Ptip+/+ and Ptip-/- mouse embryonic fibroblasts. DNA was hybridized to a custom Agilent tiling array (4x44k format) that covers three of the hox regions (A,B,D) and a collection of other genes (array is identical to array 018680 except for e_ on the ids due to an error with custom array submission to agilent).

first: Chengqi

last: Lin

first: Edwin

last: Smith

first: Hong

last: Guo

first: Brian

last: Sanderson

first: Min

last: Wu

first: Madelaine

last: Gogol

first: Tara

last: Alexander

first: Christopher

last: Seidel

first: Leanne

middle: M

last: Wiedemann

first: Kai

last: Ge

first: Robb

last: Krumlauf

first: Ali

last: Shilatifard


title: Histone H1 binding is restricted by histone variant H3.3 (Nucleosome)

first: Bas

last: van Steensel

type: Genome binding/occupancy profiling by genome tiling array

summary:
Linker histones are involved in the formation of higher-order chromatin structure. Although linker histones have been implicated in the regulation of specific genes, it still remains unclear what their principal binding determinants are and how their repressive function in vitro can be reconciled with presumed broad binding in vivo.  We generated a full genome, high resolution binding map of linker histone H1 in Drosophila Kc cells, using DamID. H1 binds at similar levels across much of the genome, both in classical euchromatin and heterochromatin. Strikingly, there are pronounced dips of low H1 occupancy around transcription start sites of active genes and at many distant cis-regulatory sites. H1 dips are not due to lack of nucleosomes. Rather, all regions with low binding of H1 show enrichment of the histone variant H3.3 which itself has been linked to high nucleosome turnover. Upon knockdown of H3.3, we find that H1 levels increase at sites previously not covered with H1 with a concomitant increase in nucleosome repeat length. These changes are independent of transcriptional changes. Our results show that the H3.3 protein counteracts association of H1 at genomic sites with high rates of histone turnover. This antagonism provides a mechanism to keep diverse genomic sites in an open chromatin conformation.
For this study, we generated DamID profiles of histone H1 and RpII18 in Drosophila Kc167 cells. Additionally, we generated H1 profiles in cells treated with RNAi against white, H3.3B, or H3.3A and H3.3B. Nucleosome occupancy profiles were generated in untreated cells and cells treated with RNAi against white or H3.3A and H3.3B. Profiles of expression changes were generated for H3.3B RNAi and H3.3A and H3.3B RNAi.

overall_design: DamID experiments for H1 and RpII18 were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Formaldehyde-assisted isolation of regulatotry elements (FAIRE) was performed in Drosophila Kc167 cells. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing over non-crosslinked genomic DNA. Nucleosome positioning profiles were made by hybridizing mononucleosomal DNA over MNase digested purified genomic DNA  on 380k NimbleGen arrays with 10 bp probe spacing. Expression profiles were made as H3.3 RNAi over white RNAi cohybridizations on spotted INDAC long oligo arrays. Every experiment was done in duplicate in the reverse dye orientation.


title: Salmonella enterica Typhimurium grown with and without glucose

city: Dallas

first: Palmy

last: Jesudhasan

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary:
Cell to cell communication in bacteria to regulate various cellular processes with respect to their population density is termed quorum sensing and is achieved using signaling molecules called autoinducers. LuxS, which is involved in the synthesis of the autoinducer molecule-2 (AI-2), is conserved in several Gram-positive and Gram-negative bacteria including the enteric pathogen Salmonella Typhimurium. Genes that are regulated by luxS in S. Typhimurium were identified using microarrays and RNA samples from wild type S. Typhimurium  and its isogenic luxS mutant, in two growth conditions (presence and absence of glucose), and at two different time points (mid-log and early-stationary phases).  Minimal differential gene expression was observed in the presence of glucose.  In the absence of both luxS and glucose, a total of 1560 genes were differentially expressed and 1361 genes were identified as luxS/AI-2-regulated at the mid-log phase and 199 genes at the early-stationary phase. Quantitative real-time PCR was performed on selected genes to validate the microarray results. These results suggest that although the expression of the luxS gene in S. Typhimurium is independent of the growth condition, its role in the production of AI-2 depends on the growth condition. It was found that luxS/AI-2 plays a vital role in a variety of processes such as metabolism, virulence gene expression, motility, transcription and translation.
Keywords: Salmonella Typhimurium, quorum sensing, luxS mutant, autoinducer-2

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

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

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

overall_design: Purified cDNAs from the wild type and mutant were each labeled with Cy-3 mono-Reactive Dye and Cy-5 mono-Reactive Dye (GE Health Care) and were processed using a dye-swapping design.

first: James

last: Zhu

first: Suresh

last: Pillai


title: ChIP-chip with antibodies for histone 3 lysine 4 trimethylation, histone 3, and PolII in Mll1+/+ and Mll1-/- MEFs

first: Pengfei

last: Wang

overall_design: Chromatin Immunoprecipitation was performed with antibodies for histone 3 lysine 4 trimethylation, histone 3, and PolII in Mll1+/+ and Mll1-/- mouse embryonic fibroblasts. DNA was hybridized to a custom Agilent tiling array (4x44k format) that covers three of the hox regions (A,B,D) and a collection of other genes.


title: Equine skeletal muscle: pre versus post-exercise

status: Public on Oct 14 2009

city: Dublin

first: Beatrice

middle: Ann

last: McGivney

state: Dublin

address: Belfield

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary: Unconditioned thoroughbred geldings were exercised to maximal heart rate or fatigue on an equine high-speed treadmill. Skeletal muscle biopsies were taken from the middle gluteal muscle before, immediately after and four hours after exercise.

overall_design: Three-condition experiment, Pre exercise (T0), Immediately post exercise (T1),  4 hours post exercise (T2). Hybridisations: T0 vs T1, T0 vs T2  Biological replicates: 8 Technical replication Dye swap

first: Suzanne

last: Eivers

first: David

last: MacHugh

last: MacLeod

first: Stephen

last: Park

first: Lisa

last: Katz

first: Emmeline

last: Hill


title: Cwc23, an essential J-protein critical for pre-mRNA splicing with a dispensable J-domain

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary: J-proteins are structurally diverse, obligatory co-chaperones of Hsp70s, each with a highly conserved J-domain that plays a critical role in stimulation of Hsp70’s ATPase activity. The essential protein, Cwc23, is one of 13 J-proteins found in the cytosol and/or nucleus of Saccharomyces cerevisiae. We report that a partial loss-of-function CWC23 mutant has severe, global defects in pre-mRNA splicing. This mutation leads to accumulation of the excised, lariat form of the intron, as well as unspliced pre-mRNA, suggesting a role for Cwc23 in spliceosome disassembly. Such a role is further supported by the observation that this mutation results in reduced interaction between Cwc23 and Ntr1 (SPP382), a known component of the disassembly pathway. However, Cwc23 is a very atypical J-protein. Its J-domain, although functional, is dispensable for both cell viability and pre-mRNA splicing. Nevertheless, strong genetic interactions were uncovered between point mutations encoding alterations in Cwc23’s J-domain and either Ntr1 or Prp43, a DExD/H-box helicase essential for spliceosome disassembly. These genetic interactions suggest that Hsp70-based chaperone machinery does play a role in the disassembly process. Cwc23 provides a unique example of a J-protein; its partnership with Hsp70 plays an auxiliary, rather than a central, role in its essential cellular function.

overall_design: Splicing-sensitive microarrays were used to probe the defects seen when the C-terminal or N-terminal regions of Cwc23 were disrupted.

first: Chandan

last: Sahi

first: Thomas

last: Lee

first: Maki

last: Inada

first: Elizabeth

last: Craig


title: Chondrocyte Gene Expression in Proliferative and Hypertrophic Chondrocytes of Chick

city: University Park

first: Paul

last: Bartell

state: PA

address: 205 Henning Bldg.

department: Poultry Science

institute: Penn State University

summary:
Longitudinal bone growth depends upon the execution of an intricate series of cellular activities by epiphyseal growth plate chondrocytes. In order to better understand these coordinated events, microarray analysis was used to compare gene expression in chondrocytes isolated from the proliferative and hypertrophic zones of the avian growth plate.
In this experiment we compared pooled samples of proliferative and hypertrophic chondrocytes isolated from the chick growth plate. The expression of 745 genes was found to differ 3-fold or greater at the 0.05 level of probability.

overall_design: We examined 8 samples using arrays: 4 from proliferative and 4 from hypertrophic chondrocytes.

first: Maria

last: Horvat-Gordon

first: Craig

last: Praul

first: Ramesh

last: Ramachandran

first: Roland

last: Leach


title: Expression profiling of hypoxic HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells: time course

status: Public on Oct 09 2009

city: Boston

first: Xiaobo

last: Xia

address: 44 Binney St, Mayer 649

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Analysis of expression changes of cultured HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells subjected to hypoxia (0.5% O2) for 0, 4, 8, 12 hours . Results provide insight to cell type-specific response to hypoxia.

overall_design: HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells were collected under normoxic conditions (~19% O2, 0 hours) and after 4, 8 and 12 hours of hypoxia treatment (0.5% O2). For each cell line, three replicates of total RNA at each time point were prepared using Trizol and submitted to the DFCI Microarray Core for labeling, hybridization to Affymetrix HG-U133Plus2 oligonucleotide arrays and image scanning.

first: Andrew

last: Kung


title: High-density gene expression analysis of tumor-associated macrophages from mouse mammary tumors

status: Public on Oct 10 2009

city: Bronx

first: Laureen

last: Ojalvo

address: Chanin 607, 1300 Morris Park Avenue

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

summary: Clinical and experimental evidence indicates that tumor-associated macrophages (TAMs) promote malignant progression. In breast cancer, TAMs enhance tumor angiogenesis, tumor cell invasion, matrix remodeling, and immune suppression against the tumor. In this study, we examined late-stage mammary tumors from a transgenic mouse model of breast cancer. We used flow cytometry under conditions that minimized gene expression changes to isolate a rigorously defined TAM population previously shown to be associated with invasive carcinoma cells. The gene expression signature of this population was compared with a similar population derived from spleens of non-tumor-bearing mice using high-density oligonucleotide arrays. Using stringent selection criteria, transcript abundance of 460 genes was shown to be differentially regulated between the two populations. Bioinformatic analyses of known functions of these genes indicated that formerly ascribed TAM functions, including suppression of immune activation and matrix remodeling, as well as multiple mediators of tumor angiogenesis, were elevated in TAMs. Further bioinformatic analyses confirmed that a pure and valid TAM gene expression signature in mouse tumors could be used to assess expression of TAMs in human breast cancer. The data derived from these more physiologically relevant autochthonous tumors compared with previous studies in tumor xenografts suggest tactics by which TAMs may regulate tumor angiogenesis and thus provide a basis for exploring other transcriptional mediators of TAM trophic functions within the tumor microenvironment.

overall_design: Tumor-associated macrophages from late-stage mouse mammary tumors compared to splenic macrophages from non-tumor-bearing littermate controls. 4 biological replicates of each population were compared via gene expression arrays.

first: William

last: King

first: Dianne

last: Cox

last: Pollard


title: Histone H1 binding is restricted by histone variant H3.3 (DamID)

first: Bas

last: van Steensel

first: Ulrich

last: Braunschweig

first: Greg

last: Hogan

first: Ludo

last: Pagie


title: Identification of changes in gene expression in inflorescences of the ashh2/sdg8 Arabidopsis mutant

city: Oslo

first: Reidunn

middle: B.

last: Aalen

address: P.O.Box 1066 Blindern

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: Mutation of the ASHH2 gene has pleiotropic developmental effects. We have focused on the role of ASHH2 in plant reproduction.The aim of the study was to identify changes in gene expression in inflorescences of the ashh2-1/sdg8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) compared to wt Arabidopsis thaliana (ecotype Colombia) inflorescences. On the female side, close to 80% of mature ovules lack embryo sac. On the male side, anthers frequently develop without pollen sacs or with specific defects in the tapetum layer, resulting in reduction in the number of functional pollen per anther by up to ~90%. ashh2 mutations also result in homeotic changes in floral organ identity. Transcriptional profiling identified more than 300 up-regulated and 600 down-regulated genes in ashh2 mutant inflorescences, whereof the latter included genes involved in determination of floral organ identity, embryo sac and anther/pollen development. This was confirmed by real-time PCR. In the chromatin of such genes (AP1, AtDMC1 and MYB99) we observed a reduction of H3K36 trimethylation (me3), but not H3K4me3 or H3K36me2.

overall_design: Five biological replicates with 12 plants each both of Arabidopsis thaliana wild type (ecotype Colombia-0) and ashh2-1/sgd8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) were sown out on soil and grown under the following conditions; 22oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 μmol/m2/sek in light intensity. The inflorescences of each biological replikate were harvested in bulk from 30-36 days old plants at same time of the day (between 12:45 and 13:45) and at the same developmental stage in bulk.

first: Vibeke

last: Alm

first: Tage

last: Thorstensen

first: Tommy

last: Jørstad

middle: B


title: Addition of Exogenous AI-2 to C. jejuni 11168 Wild Type and LuxS01.

status: Public on Oct 08 2009

first: Kathryn

last: Holmes

address: Trinity Centre for Health Science, Adelaide and Meath Hospital

department: Clinical Medicine

institute: Trinity College Dublin

summary: Transcriptional profiling of Campylobacter jejuni NCTC 11168 wild type and LuxS01 mutant strains comparing the effects of exogenously added in vitro-produced autoinducer 2 (AI-2) versus a control buffer to both strains.

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

overall_design: Two-condition experiment, addition of exogenous AI-2 to both the parent and mutant 11168 strains. Control microarrays included comparing 11168 with AI-2 free buffer vs 11168 with AI-2-free buffer and mutant with AI-2 free buffer versus mutant with AI-2 free buffer used for analyses. 3 biological replicates for each, independently grown and harvested.

first: Kate

first: Klaus

last: Winzer

first: Kim

last: Hardie

first: Timothy

last: Tavender

first: Jerry

last: Wells


title: Wild Type 11168 versus LuxS01 Mutant Cultured in MHB and MEM- α media

summary: Transcriptional profiling of Campylobacter jejuni NCTC 11168 wild type versus LuxS01 mutant strain grown in a minimal culture medium (MEM- α ) versus complex culture medium (MHB).

overall_design: Two-condition experiment, the parent versus the mutant 11168 strains were grown in 2 types of culture medium for comparison. Control microarrays included comparing wild type vs wild type in the same culture medium. 4 biological replicates for each test microarray and 2 biological replicates for each control microarray, independently grown and harvested.


title: Diet Synergistically Affects Helicobacter pylori-Induced Gastric Carcinogenesis in Nonhuman Primates

status: Public on Oct 07 2009

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
BACKGROUND & AIMS: Gastric cancer results from a combination of Helicobacter pylori (H pylori) infection, exposure to dietary carcinogens, and predisposing genetic make-up. Because the role of these factors in gastric carcinogenesis cannot be determined readily in human beings, the present study examined the role of an oral carcinogen and H pylori infection in rhesus monkeys.
METHODS: Gastroscopies were performed in 23 monkeys assigned to 4 groups: controls; nitrosating carcinogen ethyl-nitro-nitrosoguanidine administration alone; and inoculation of a virulent H pylori strain alone (H), or in combination with ethyl-nitro-nitrosoguanidine (EH). Follow-up gastroscopies and biopsies were performed at 3-month intervals for 5 years for pathologic and molecular studies.
RESULTS: Postinoculation, H and EH groups showed persistent infection and antral gastritis. Starting at 2 and 5 years, respectively, gastric intestinal metaplasia and intraepithelial neoplasia developed in 3 EH monkeys but in no other groups. Transcriptional analysis of biopsies at 5 years revealed group-specific expression profiles, with striking changes in EH monkeys, plus a neoplasia-specific expression profile characterized by changes in multiple cancer-associated genes. Importantly, this neoplastic profile was evident in nonneoplastic mucosa, suggesting that the identified genes may represent markers preceding cancer.
CONCLUSIONS: Gastric intraglandular neoplasia is induced in primates when H pylori infection is associated with consumption of a carcinogen similar to the nitrosaminesfound in pickled vegetables, suggesting that H pylori and the carcinogen synergistically induce gastric neoplasia in primates. Monkey arrays used for analysis of the affect of Helicobacter pylori and diet on development of gastric cancer.  Each RNA was hybridized against a common reference.  Biopsy numbers represent the following in terms of descriptions used in publication of the paper... Each set of numbers/descriptions is organized in the following order:

Biopsy#; Monkey#; Group Code on Fig 5
Biopsy #4674; AB24; E; E1
Biopsy #4684; 16G; E; E2
Biopsy #4716; 89G; H; H1
Biopsy #4724; 54H; H; H2
Biopsy #4720; 20G; H; H3
Biopsy #4710; 92F; C; C1
Biopsy #4714; 26G; C; C2
Biopsy #4712; 92G; C; C3
Biopsy #4726; 08G; H; H4
Biopsy #4722; 57G; H; H5
Biopsy #4718; 85G; H; H6
Biopsy #4694; 48H; HE NON; HE1
Biopsy #4686; 59H; HE NON; HE2
Biopsy #4690; 81G; HE NEO; HE3
Biopsy #4696; 36G; HE NEO; HE4
Biopsy #4692; 63G; HE NEO; HE5
Biopsy #4680; 76G; E; E3
Biopsy #4682; 52G; E; E4
Biopsy #4678; 15G; E; E5
Biopsy #4676; 93G; E; E6
Biopsy #4688; 47H; HE NON; HE6
A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
Infection: Rhesus monkeys were infected with H. pylori (+/-)
Compound Based Treatment: Rhesus monkeys were treated with ENNG (N-ethyl-N-nitrosoguanidine) (+/-)

first: Douglas

middle: S

last: Merrell


title: Evolution of Gene Expression  in Spruce (Genus Picea)

city: Vancouver

first: Dr. Kermit

last: Ritland

state: BC

address: 2424 Main Mall

department: Forest Sciences

institute: University of British Columbia

summary:
Diversification of defense-related compounds is a plant defense mechanism against the diverse array of natural enemies in the course of evolution, and is known to involve various sources of tissue. Here a large-scale survey of gene expression is conducted from three different sources of tissue; needles, phloem with the attached bark, and xylem, with an emphasis on the expression of the secondary metabolites of the core phenylpropanoid pathway and derivative pathways, taken together as phenolic defense-related compounds. Five species of spruce; P. abies, P. glauca, P. jezoensis, P. mariana, and P. omorika, spanning much of their known phylogeny, are chosen for cross-species microarray hybridizations.
The objectives are: first) to explore the tissue-related differences in the expression of phenolic genes and their coherent role in tree defense; second) to describe the diversification trends in the expression of phenolic gene families with respect to their position in the pathway; and third) to infer the mode of evolution underlying the expression of the selected genes.

sample_organism:
Picea abies
Picea glauca
Picea mariana
Picea omorika
Picea jezoensis

overall_design:
Trees at the arboretum of Kalamalka Research Station, Vernon, BC, Canada (http://www.for.gov.bc.ca/hre/forgen/rstations.htm#Kalamalka_Research_Station) were designated for sampling. Three biological replicates of Black spruce (Picea mariana), Jezo spruce (P. jezoensis), Norway spruce (P. abies), Serbian spruce (P. omorika), and White spruce (P. glauca) were sampled. The bark and the attached phloem were separated from inner layers, and the xylem tissue was scraped off. The fresh current-year needles were  pooled from different aerial branches on the mid-afternoon of Apr. 24, 2007, flash-frozen in liquid nitrogen, and transferred into separate containers.
A modified loop design was decided for gene expression profiling with 15 cross-species hybridizations per each source of tissue (total of 45 slides) using the Treenomix third generation cDNA microarray platform (GEO accession #: GPL5423). Array350 kit (Genisphere, Hatfield, USA) was chosen for the microarray hybridizations of needle and bark/phloem sources of tissue. Due to the lower yield of RNA extraction, microarray hybridization of the xylem tissue used Array900 (Genisphere, Hatfield, USA).
The slides were scanned with a ProScanArray scanner (PerkinElmer, Downers Grove, IL, USA), and the scanned TIF images were processed by ImaGene software (BioDiscovery, Inc., El Segundo, CA, USA)to quantify spot intensities. The spot intensities were normalized with the variance stabilizing (VSN) method, and the normalized log channel intensities were analyzed by fitting a linear mixed effects model.

first: Rokneddin

last: Albouyeh

first: Bjoern

last: Hamberger

first: Richard

last: White

first: Nima

last: Farzaneh

first: Gillian

last: Leung

first: Michelle

last: Tang

first: Leyla

last: Tabanfar

first: Carol

first: Joerg

last: Bohlmann

first: Kermit


title: Characterization of mycobacterial oligopeptide permease system

summary:
M. tuberculosis strain 1254 wild type (WT) and its isogenic delta Rv3662c-Rv3665c KO (opp KO) and complemented opp::opp were cultured in vitro, in liquid 7H9 media supplemented with OADC and 0.05% Tween 80, 0.5% glycerol, in a 150 mL volume, contained in roller bottles, incubated at 37oC.  Growth was monitored as OD600 nm and recorded on a daily basis. In all experiments, the starting OD600 nm was 0.04-0.05. Aliquots were removed at each OD600 nm to make serial dilutions, plate onto 7H10 OADC agar plates for CFU counts. When cells reached OD600 nm of 0.3, 1.0, and 1.5, a 10-30 mL aliquot was taken, centrifuged 3 min at 3000 g, at room temperature, and the supernatant was discarded, with cell pellets being immediately frozen by inclusion into dry ice. Frozen cell pellets were stored at -80oC for later RNA isolation. In all experiments, RNA from WT was labeled with Cy5, and RNA from the opp KO was labeled with Cy3. In all experiments, the microarray comparsion used RNA from cells of the same growth stage, i.e., WT OD 0.3 vs opp KO OD 0.3, WT OD 1.0 vs opp KO OD 1.0, and WT OD 1.5 vs opp KO OD 1.5. When comparing the Complemented opp::opp vs the mutant opp KO, RNA from the later strain was Cy3-labeled.
A cell type comparison design experiment design type compares cells of different type for example different cell lines.

first: Mario

last: Flores-Valdez


title: Expression in larvae fed on resistant or susceptible plants, and in larvae that are at different developmental stages

status: Public on Oct 06 2009

city: Manhattan

first: Ming

last: Chen

state: KS

address: Kansas State University, 123 Waters Hall

department: Entomology

institute: Kansas State University

summary: Genes expressed in the salivary glands and gut of Hessian fly (Mayetiola destructor) larvae are likely involved in interactions with host plants.

overall_design: RNA samples were extracted from whole larvae. The microarray was used to determine the abundance of transcripts in larvae at different developmental stage or larvae that feed on resistant and susceptible host plants.

first: Ming-Shun

first: Shize

last: Zhang


title: Expression in dissected larval tissues including gut, salivary glands, Malpighian tubules, and the remaining cascade

overall_design: Hessian fly larval tissues were derived from three day old larvae that were cultured on susceptible cultivar Newton. Each tissue sample contained 200 individuals dissected from the same stage of insects. The same type of dissected tissues were pooled and total RNA was extracted from development of microarray probes.


title: Development of a novel splice array platform and its application in the identification of alternative splice variants

city: PAMPLONA

first: David

last: Blanco

address: Avda Pio XII, 55

department: Area Oncology

institute: CIMA

summary: Changes in alternative splicing are associated with several pathological conditions, including cancer. Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array platform was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. The array consists of exon probes and thermodynamically balanced junction probes. Suboptimal probes are tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was first validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms for 8000 genes in lung cancer samples compared to matched normal lung tissue. The expression of lung cancer-associated splice isoforms was validated by RT-PCR. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. In conclusion, this highly accurate methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies.

overall_design: 20 normal/tumor paired specimens. Tumor samples are from non-small cell lung cancer (NSCLC) whereas normals are from adjacent normal lung tissue.

first: Ruben

last: Pio

first: Luis

last: Montuenga

first: Elena

last: Aibar


title: Expression data from chicken bursal cells treated with stem cell antigen 2

city: East Lansing

first: Weifeng

last: Mao

state: MI

address: 3606 E. Mount Hope Rd. USDA-ARS

department: Genetics Program

institute: Michigan State University

summary:
The differentiation and proliferation of chicken B cells rely on the antigens on the cell surface of bursal stromal cells. Chicken stem cell antigen 2 (SCA2) is localized on the surface of bursal cortical and medullary epithelial cells. The signals through SCA2 may regulate the expressions critical for the B cell development.
The altered expressions of bursal cells that were induced through SCA2-signaling were detailed via Affemetrix array experiments.

overall_design: Bursa of 3 week old line 0 chickens were collected and manually teased to harvest the bursal cells. The bursal cells were spread on the monolayers of SCA2Flag-DF1 cells or control Vector-DF1 cells in triplicate. After growth in the mixture of Liebovitz’s L-15 and McCoy 5A media (1:1) supplemented with 4% FBS, penicillin, and streptomycin for overnight at 37 ºC in 5% CO2, the bursal cells were recovered by washes (DF1 cells are adhesive) followed by gentle centrifugation at 1000×g for 10 min. Total RNA was isolated using the absolutely RNA microprep kit.

first: Hans

last: Cheng


title: Gene expression in the Atlantic salmon adipose-derived stromal-vascular fraction during differentiation into adipocytes

status: Public on Oct 03 2009

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

institute: Nofima AS

summary: Changes of gene expression in primary cell cultures of salmon adipose-derived stromal-vascular fraction were studied at six time-points that covered the key differentiation events: confluence, clonal expansion, determination and establishment of the mature adipocyte phenotype.

overall_design: Time-course experiment: six developmental stages of stromal-vascular fraction against the pooled reference. Biological replicates: 5 per developmental stage, pooled samples of all 6 stages were used as common reference. One stage per array.

first: Marijana

last: Todorcevic

first: Stanko

last: Skugor

first: Bente

last: Ruyter


title: Transcriptome inheritance of a citrus somatic hybrid

city: Moncada

first: Gema

last: Ancillo

state: Valencia

address: Ctr. Moncada-Naquera Km 4.5

department: Protección Vegetal y Biotecnología

institute: Instituto Valenciano de Investigaciones Agrarias (IVIA)

summary:
The main objective of the present study was to analyze whether the novel phenotype of this complex three-way tetraploid interspecific hybrid, displaying mixed dominant, codominant and transgressive traits is associated with non additive expression of the two diploid parental genomes.

Keywords: Comparative transcriptomic hybridization

sample_organism:
Citrus x limon
Citrus reticulata
Citrus limon x Citrus reticulata

overall_design: Three replicates for each sample category (C. reticulata Blanco, C. limon (L.) Burm.) and a allotetraploid somatic hybrid between both) were generated and compared by a reference design.

first: Jean

last: Bassene

first: Yann

last: Froelicher

first: Cécile

last: Dubois

first: Rosa

last: Ferrer

last: Navarro

first: Patrick

last: Ollitrault


title: T (Brachyury) gene duplication confers major susceptibility to familial chordoma

status: Public on Oct 04 2009

city: Durham

first: Michael

middle: J

last: Kelley

state: NC

address: 508 Fulton St. (111G)

institute: Duke University

summary: Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex (≥ with ≥ 3 cases) families of chordoma, a cancer of presumed notochordal origin.

overall_design: comparison of test samples from chordoma families to a reference DNA sample


title: Transcriptome Analysis of Ciona intestinalis to Identify Genes Preferentially Expressed in the Larval Brain

status: Public on Oct 02 2009

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

country: Japan

institute: Okayama University

summary: The larval brain of Ciona intestinalis has similar architecture to that of vertebrates, but is only composed of approximately 330 cells.  Transgenic embryos that carried Ci-beta-tubulin(promoter)::Kaede exhibited robust Kaede expression in the larval brain.  Kaede-expressing cells were isolated, and their transcriptome was compared with that of cells that did not express Kaede using an oligonucleotide-based microarray.  Our analysis identified 565 candidate genes that were preferentially expressed in the larval brain, 77 of which have previously been reported to be brain-related.  The 565 genes included transcription factors, such as Otx, en, Pax3/7, Prop-A, Lhx1, Six3/6, Unc4-A, FoxC, and DMRT1; and signal transduction molecules, such as FGF4/5/6, Hedgehog1, Hedgehog2, patched, Fringe1, and Dkk3.  Nearly 30 of the identified genes coded for receptors for neurotransmitters, neuropeptides or hormone pepetides.  In addition, 15 genes encoded neuropeptides and hormone peptides, five of which were novel.  Our catalog of genes that are expressed in the Ciona larval brain provides a foundation for future studies exploring the complex gene regulatory networks that mediate chordate brain development and function.

overall_design: Two samples (Brain vs Cells without Brain),Two biological replicates,Dye Swap design

first: Nori

last: Satoh


title: Oogenesis in Solea senegalensis: Previtellogenic versus vitellogenic ovaries

city: Talence

first: angela

last: tingaud-sequeira

address: avenue des Facultés

country: France

institute: Université Bordeaux 1

summary:
Transcriptionnal profile changes in ovary during the reproductive cycle of Solea senegalensis: from previtellogenic stage to vitellogenic stage obtained at different times during the annual reproductive cycle.
An oligo microarray based on ESTs sequenced from S. senegalensis previously designed (Cerdà et al., 2008, BMC genomics) was used.

overall_design: The two stages of ovary development were directly compared using three individuals for each stage (IR-Pv-1, IR-Pv-2, IR-Pv-3 for previtellogenic individuals and IR-Vt-1, IR-Vt-2, IR-Vt-3 for vitellogenic individuals). For the experiment, the vitellogenic stage was used as the control.

first: Angèle

last: Tingaud-Sequeira

first: François

last: Chauvigné

first: María

last: Agulleiro

first: Esther

last: Asensio

first: Juanjo

last: Lozano

first: Joan

last: Cerdà


title: Oogenesis in Solea senegalensis: Vitellogenic versus mature ovaries

summary:
Transcriptionnal profile changes in ovary during the reproductive cycle of Solea senegalensis: from vitellogenic stage to mature stage obtained at different times during the annual reproductive cycle.
An oligo microarray based on ESTs sequenced from S. senegalensis previously designed (Cerdà et al., 2008, BMC genomics) was used.

overall_design: The two stages of ovary development were directly compared using three individuals for each stage (IR-Mt-1, IR-Mt-2, IR-Mt-3 for mature individuals and IR-Vt-1, IR-Vt-2, IR-Vt-3 for vitellogenic individuals). For the experiment, the mature stage was used as the control.


title: Oogenesis in Solea senegalensis: mature versus atretic ovaries

summary:
Transcriptionnal profile changes in ovary during the reproductive cycle of Solea senegalensis: from mature stage to atresia stage obtained at different times during the annual reproductive cycle.
An oligo microarray based on ESTs sequenced from S. senegalensis previously designed (Cerdà et al., 2008, BMC genomics) was used.

overall_design: The two stages of ovary development were directly compared using three individuals for each stage (IR-Mt-1, IR-Mt-2, IR-Mt-3 for mature individuals and IR-At-1, IR-At-2, IR-At-3 for atretic individuals). For the experiment, the atretic stage was used as the control.


title: Oogenesis in Solea senegalensis: vitellogenic versus atretic ovaries

summary:
Transcriptional profile changes in ovary during the reproductive cycle of Solea senegalensis: from vitellogenic stage to atresia stage obtained at different times during the annual reproductive cycle.
An oligo microarray based on ESTs sequenced from S. senegalensis previously designed (Cerdà et al., 2008, BMC genomics) was used.

overall_design: The two stages of ovary development were directly compared using three individuals for each stage (IR-Vt-1, IR-Vt-2, IR-Vt-3 for vitellogenic individuals and IR-At-1, IR-At-2, IR-At-3 for atretic individuals). For the experiment, the atretic stage was used as the control.


title: Differential expression of rituximab responders vs. non responders on 3 different blood cell types

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

institute: Vall d'Hebron Hospital Research Institute

summary:
New and effective therapeutical options are available for the treatment of Rheumatoid Arthritis. One of such treatments is rituximab, and chimeric anti-CD20 antibody that selectively depletes the CD20+ B cell subpopulation.
Similar to established anti-TNF alpha therapies, there is a subgroup of RA patients that do not  experience significant clinical response. Therefore, one of the major necessities in actual RA therapeutical management is to identify reliable predictors of the response to this therapies. In the present study we have evaluated 3 blood cell types (i.e. whole blood, isolated B cells and isolated CD4 T cells) using microarray gene expression profiling to identify their potential use as biomarkers for rituximab response.
In all three tissues evaluated, we have identified statistically significant differentially expressed genes. The most relevant candidates have been reevaluated using RealTime PCR. These genes were: TRAF1 and arginase 1 in whole blood, Toll-Like Receptor 4 (TLR4) in CD4+ T cells and AT-rich interactive domain 3A (ARID3A) in B cells.
In the present study we have demonstrated the potential of different blood cell types for the prediction of the response to rituximab. In particular, we have found a set of relevant candidate genes that could be the basis for future treatment response prediction.

overall_design: We have recruited 9 RA patients starting immunotherapy with rituximab. The same day of the first infusion we obtained the three different cell type samples: whole blood (preserved in PaxGene tubes), B cells (using negative selection) and CD4+ T cells (using negative selection). At week 24 of treatment we determined the clinical response using the RelDas score. All tissue samples were processed in parallel (i.e. RNA extraction and microarray profiling with Illumina WG6 Beadchip) in order to minimize the technical variability. The three datasets were normalized separately using quantile normalization. After performing differential expression analysis between Responders and Non-Responders we identified significantly expressed genes in all three cell types. The most significant gene candidates were validated using the Taqman Real-Time PCR assays.

first: Sara

last: Marsal


title: Budding yeast cohesin (Mcd1) distribution in mitotically arrested cells

status: Public on Oct 01 2009

city: Aurora

first: Paul

last: Megee

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver School of Medicine

summary: genomic localization of the budding yeast cohesin complex was mapped in mitotically arrested cells by Mcd1 ChIP followed by hybridization to high-density tiled microarrays

overall_design: Cells were synchronized first in G1 and then released into media containing the microtubule poison nocodazole. Cells were fixed and processed for ChIP once arrested as large-budded cells. Immunoprecipitated DNA and total genomic DNA not subjected to immunoprecipitation were competitively hybridized to Nimblegen whole genome arrays.


title: Expression profiling of prospero mutant VNC cells in Drosophila embryos

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary: Paper abstract: Stem cells have the remarkable ability to give rise to both self-renewing and differentiating daughter cells. Drosophila neural stem cells segregate cell-fate determinants from the self-renewing cell to the differentiating daughter at each division. Here, we show that one such determinant, the homeodomain transcription factor Prospero, regulates the choice between stem cell self-renewal and differentiation. We have identified the in vivo targets of Prospero throughout the entire genome. We show that Prospero represses genes required for self-renewal, such as stem cell fate genes and cell-cycle genes. Surprisingly, Prospero is also required to activate genes for terminal differentiation. We further show that in the absence of Prospero, differentiating daughters revert to a stem cell-like fate: they express markers of self-renewal, exhibit increased proliferation, and fail to differentiate. These results define a blueprint for the transition from stem cell self-renewal to terminal differentiation.

overall_design: 6 wildtype samples and 6 prospero mutant samples were hybridised to arrays against a commom reference sample (generated from whole embryo cDNA). The prospero samples were indirectly compared to the wildtype samples via the common reference. Half the wildtype and half of the prospero arrays were dye-swapped.

first: Andrea

middle: H

last: Brand


title: Genomic Profiles Associated with Early Micrometastasis in Lung Cancer: Relevance of 4q Deletion

status: Public on Oct 05 2009

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary:
PURPOSE: Bone marrow (BM) is a common homing organ for early disseminated tumor cells (DTC) and their presence can predict the subsequent occurrence of overt metastasis and survival in lung cancer. It is still unclear whether the shedding of DTC from the primary tumor is a random process or a selective release driven by a specific genomic pattern.
EXPERIMENTAL DESIGN: DTCs were identified in BM from lung cancer patients by an immunocytochemical cytokeratin assay. Genomic aberrations and expression profiles of the respective primary tumors were assessed by microarrays and FISH analyses. The most significant results were validated on an independent set of primary lung tumors and brain metastases.
RESULTS: Combination of DNA copy number profiles (array CGH) with gene expression profiles identified five chromosomal regions differentiating BM-negative from BM-positive patients (4q12-q32, 10p12-p11, 10q21-q22, 17q21 and 20q11-q13). Copy number changes of 4q12-q32 were the most prominent finding, containing the highest number of differentially expressed genes irrespective of chromosomal size (p=0.018). FISH analyses on further primary lung tumor samples confirmed the association between loss of 4q and the BM-positive status. In BM-positive patients 4q was frequently lost (37% vs. 7%), whereas gains could be commonly found among BM-negative patients (7% vs. 17%). The same loss was also found to be common in brain metastases from both small and non-small-cell lung cancer patients (39%).
CONCLUSIONS: Thus, our data indicates for the first time that early hematogeneous dissemination of tumor cells might be driven by a specific pattern of genomic changes.

overall_design: In the present study, we investigated whether the early dissemination of tumor cells into BM is associated with a specific molecular pattern in primary lung cancer. For the detection of DTCs, we used an immunocytochemical cytokeratin (CK) assay that allows the identification of one tumor cell in the background of one million normal BM cells . The specificity of this assay was previously demonstrated by the analysis of almost 200 non-carcinoma control patients . By using high-resolution comparative genomic hybridization (CGH) and expression arrays we compared the genomic aberration and expression profiles of lung carcinomas from patients with and without DTCs in the BM. A three step analysis with independent measurement technologies revealed tumor-specific genetic signatures associated with early hematogeneous dissemination of NSCLC cells into BM. Interestingly, the most prominent aberration identified was also frequently observed in brain metastases, suggesting a potential involvement in both tumor cell dissemination and metastatic progression.

first: Michaela

last: Wrage

first: Salla

last: Ruosaari

last: Eijk

first: Jussuf

middle: T

last: Kaifi

first: Jaakko

last: Hollmén

first: Emre

middle: F

last: Yekebas

first: Jakob

last: Izbicki

first: Ruud

last: Brakenhoff

first: Thomas

last: Streichert

first: Sabine

last: Riethdorf

first: Bauke

last: Ylstra

first: Klaus

last: Pantel

first: Harriet

last: Wikman


title: microRNA (miRNA) expression from human 293 cells

city: Dallas

first: Zain

last: Paroo

state: TX

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern Medical Center

summary:
Expression phospho-mimic TRBP enhanced in vitro miRNA production and cellular expression of ectopic miRNA.
We used miRNA microarray experiments to determine the effect of expression of phopsho-mimic TRBP on global endogenous miRNA expression.

overall_design: We established isogenic cell lines stably expressing phospho-mutant and phospho-mimic TRBP using Flp-In 293 cells and a Flp Recombinase Target system.  After monoclonal cell colonies were selected, cells were cultured for two weeks.  Total RNA was harvested when cells were ~75% confluent.  Initial analysis was performed using one sample from each experimental group.  Subsequent analysis included an additional two samples for each group.  miRNA with values less than 500 were not included in analysis.


title: Array comparative genomic hybridization in sporadic and coeliac disease-related small bowel adenocarcinomas

summary:
Background: The molecular pathogenesis of small intestinal adenocarcinomas (SBA) is not well understood. Defining its molecular pathogenesis may lead us to better clinical interventions.
Aim: to identify the molecular changes characteristic of SBA.
Methods:  Forty-eight SBA (thirty-three non coeliac disease (CD)-related and 15 CD-related) were characterized for chromosomal aberrations, by high resolution array comparative hybridization (aCGH), microsatellite status (MSI) and APC promoter methylation and mutation status. Furthermore, molecular alterations found in CD-related SBA were compared to non-CD related SBA.
Results: Chromosomal changes were observed in 77% of the SBA. The most frequently (>10%) DNA copy number changes found were gains on 5p15.33-5p12, 7p22.3-7q11.21, 7q21.2-7q21.3, 7q22.1-7q34, 7q36.1, 7q36.3, 8q11.21-8q24.3, 9q34.11-9q34.3, 13q11-13q34, 16p13.3, 16p11.2, 19q13.2 and 20p13-20q13.33 and losses of 4p13-4q35.2, 5q15-5q21.1 and 21p11.2-21q22.11. Seven highly amplified regions on 6p21.1, 7q21.1, 8p23.1, 11p13, 16p11.2, 17q12-q21.1 and 19q13.2 were also identified. CD-related and non CD-related SBA displayed similar chromosomal aberrations. Promoter hypermethylation of the APC gene was found in 48% non CD-related and 73% CD-related SBA. No nonsense mutations were found. Last, 10% of the non CD-related SBA were MSI, whereas 43% of the CD-related SBA were MSI.
Conclusions: Our study characterized specific chromosomal aberrations and amplifications involved in SBA pathogenesis. At the chromosomal level, CD-related and non CD-related SBA do not differ. The involvement of the MMR system in the pathogenesis of the CD-related SBA was larger than what has been observed in no CD-related SBA. No nonsense mutations were found in SBA, but frequent promoter methylation in CD-related SBA.

overall_design: Forty-eight SBA (thirty-three non coeliac disease (CD)-related and 15 CD-related) were characterized for chromosomal aberrations against a Human pool, by high resolution array comparative hybridization (aCGH),

first: Begona

last: Diosdado

first: Tineke

middle: E

last: Buffart

first: Russel

last: Watkins

first: Beatriz

last: Carvalho

first: Marianne

last: Tijssen

first: Anne

last: Bolijn

first: Fraser

last: Lewis

first: Karen

last: Maude

first: Caroline

last: Verbeke

first: Iris

last: Nagtegaal

first: Heike

last: Grabsch

first: Chris

last: Mulder

first: Phil

last: Quirke

first: Peter

last: Howdle

first: Gerrit

middle: A

last: Meijer


title: Human Genome-Wide SpliceArrray - MAQC samples A, B, C, D

city: Gaithersburg

first: Michael

middle: Ian

last: Brenner

state: MD

address: 217 Perry Parkway bld 5

institute: ExonHit Therapeutics

summary: The human Genome-Wide SpliceArray (GWSA), a novel microarray platform, utilizes an existing probe design concept to monitor such transcript diversity on a genome scale.  The human GWSA allows the detection of alternatively spliced events within the human genome through the use of exon body and junction probes to provide a direct measure of each transcript, through simple calculations derived from expression data. This report focuses on the performance and validation of the array when measured against standards recently published by the Microarray Quality Control (MAQC) Project.

overall_design:
Four samples types (A, B, C, D) were hybridized in triplicate to the human Genome-wide SpliceArray platform resulting in a total of 12 data files.  The sample types are those that were previously described and used in the Microarray Quality Control (MAQC) Project and include the following:
Sample A = Universal Human Reference RNA;
Sample B = Human Total Brain RNA;
Sample C =a mixture of sample A and B RNAs - 75% sample A+25% sample B;
Sample D =a mixture of sample A and B RNAs - 25% sample A+75% sample B.
cDNA was amplified from the RNA samples, and subsequently fragmented and biotin-labeled.  Prepared target from each of the 12 samples (4 sample types, 3 replicates each) was separately hybridized to 12 human Genome-wide SpliceArray (GWSA) products.


title: Potato Gene Expression Associated with the RB-mediated Broad-Spectrum late blight resistance

city: Madison

first: Lara

middle: Colton

last: Kramer

state: WI

address: 1575 Linden Drive

department: Horticulture

institute: University of Wisconsin - Madison

summary:
Late blight, caused by the oomycete Phytophthora infestans, is one of the most damaging potato diseases. Genetic resistance is one of the most effective means to control the destruction caused by this pathogen. Transgenic potato lines harboring a resistance gene, RB, confer broad-spectrum, rate-reducing late blight resistance. A microarray approach was used to understand what genes are manipulated in the potato background after the addition of the RB gene that contribute to the late blight resistant phenotype.

Keywords: Time course, disease state analysis

overall_design:
CRD (3x2x2) Split-Split Plot: 3 sampling time points after inoculation (2, 5, 10 hours), Two genotypes (Katahdin with and without the RB gene), Inoculation with P. infestans or mock inoculation with water.
48 arrays were hybridized in total; 12 in each biological replicate. Each genotype with the mock and late blight inoculated samples was hybridized on two arrays using a dye-swap procedure. Each genotype had a total of 6 arrays across the three sampling time points.

last: Colton Kramer

first: Jiming

last: Jiang


title: Synthetic Fire Ant Venom Transcriptosome Analysis

city: Jackson

first: Donna

middle: C.

last: Sullivan

state: MS

address: 2500 North State Street

department: Medicine

institute: University of Mississippi Medical Center

summary:
Human U937 cells were maintained in RPMI 1640 media. Solenopsin B added at a concentration equivalent to the IC50, 13 micro Molar.  Triplicate cultures were prepared at two separate time points, 1 and 6 hours.

Keywords: Transcriptosome analysis employing DNA/cDNA glass microarray.

overall_design: Two-condition experiment, U937 cell and Sol B treated U937 cells at two time points: 1 and 6 hours post exposure.  Biological replicates: 3, independently grown and harvested. One replicate per array.

middle: C

first: Robin

last: Rockhold


title: Brugia pahangi mature vs immature microfilariae

city: Oshkosh

first: Kathryn

last: Griffiths

address: 800 Algoma Blvd

department: Biology and Microbiology

institute: University of Wisconsin Oshkosh

summary:
Filarial nematodes are arthropod-borne nematodes that cause a variety of economically important diseases such as onchocerciasis (river blindness), lymphatic filariasis, and heartworm disease.  The most widespread filarial disease of humans is lymphatic filariasis, caused by worms in the genera Wuchereria and Brugia. Lymphatic filariasis is an economic and social burden in endemic countries and affects approximately 119 million people worldwide (Michael, 1997). In humans, the worms live in and block the lymph vessels, causing improper flow of lymph, and inflammation of the lymphatic system. The symptoms are fever, swollen limbs and genitals, generalized malaise, and can progress to a debilitating condition known as elephantiasis

This research focuses on the transmission of these worms to the disseminating mosquito host, and it is based on the interesting observation that mf must be at least 7 days old to successfully infect the mosquito (de Hollanda, 1982). Newborn mf that have not ‘matured’ cannot successfully penetrate the midgut of the mosquito, and subsequently cannot develop to the L3 stage (Fuhrman, 1987). Previous work done by another group 20 years ago suggests that the molecular makeup of the worm surface changes during this maturation process (Furman, 1983 a and b).  We used microarray analysis to characterize changes in gene expression that take place during the mf maturation process. Understanding the gene expression changes that occur as the mf mature will allow us to understand the nature of the philological transition that allows mf to move from the human to the mosquito host. With this information in hand, we can eventually identify parasite molecules that could be targeted to either stop parasite reproduction or prevent transmission of the mf to the mosquito. This would stop parasite transmission in endemic areas.

overall_design: Brugia pahangi mature mf (30 days and older) RNA was compared to immature mf (3 days and younger).  Three biological replicates were performed each with two technical replicates

first: George

last: Mayhew

first: Rebecca

last: Zink

first: Sara

last: Erickson

first: Jeremy

last: Fuchs

first: Bruce

last: Christensen

first: Colleen

last: McDermott

first: Michelle

last: Michalski


title: Brugia malayi mature vs immature microfilariae

overall_design: Two biological replicates were performed each with two technical replicates.