title: Comparison of genome wide binding of S. cerevisiae condensin, topo II and cohesin by ChIP

first: claudio

last: d'ambrosio

summary:
The chromosomal condensin complex gives metaphase chromosomes structural stability. In addition, condensin is required for sister chromatid resolution during their segregation in anaphase. How condensin promotes chromosome resolution is poorly understood. Chromosome segregation during anaphase also fails after inactivation of topoisomerase II (topo II), the enzyme that removes catenation between sister chromatids left behind after completion of DNA replication. This has led to the proposal that condensin promotes DNA decatenation, but direct evidence for this is missing and alternative roles for condensin in chromosome resolution have been suggested. Using the budding yeast rDNA as a model, we now show that anaphase bridges in a condensin mutant are resolved by ectopic expression of a foreign (Chlorella virus) but not endogenous topo II. This suggests that catenation prevents sister rDNA segregation, and that yeast topo II is ineffective in decatenating the locus without condensin. Condensin and topo II colocalize along both rDNA and euchromatin, consistent with coordination of their activities. We investigate the physiological consequences of condensin-dependent rDNA decatenation and find that late decatenation determines the late segregation timing of this locus during anaphase. Regulation of decatenation therefore provides a means to finetune segregation timing of chromosomes in mitosis.

Keywords: ChIP-chip, Cell Cycle

overall_design: Comparison of the chromosomal association pattern of the condensin subunit Brn1 with that of topo II along budding yeast chromosomes. As control, the binding pattern of the cohesin subunit Scc1 is also included. (Figure 2 in the corresponding manuscript depicts the Brn1 association pattern as obtained from averaging two independent biological ChIP experiments C15_IP_2200_NOC and C16_IP_2200.)

first: Claudio

last: D'Ambrosio

first: Gavin

last: Kelly

first: Yuki

last: Katou

first: Takehiko

last: Itoh

first: Katsuhige

last: Shirahige

first: Frank

last: Uhlmann


title: Human Embryonic Stem Cell Sublines

status: Public on Jul 18 2008

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

country: USA

institute: WiCell

type: Genome variation profiling by genome tiling array

summary: Human embryonic stem (ES) cell lines acquire recurrent karyotypic abnormalities that may promote growth and survival in long-term culture.  Cells with these abnormalities are often present at low levels in human ES cell cultures, requiring subcloning for isolation and analyses.  We have developed a rapid method to isolate either abnormal or normal clones from karyotypically mosaic human ES cell cultures that we call Genetic Diagnosis at Passage (G-DAP).  We have used this technique to isolate three distinct abnormal sublines from H9 human ES cells in continuous culture.  These sublines were characterized by G-banding, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and array comparative genomic hybridization (aCGH).  One subline (H9.DT) has, as it’s only abnormality, a duplication of 12p capped by a 5q subtelomere.  A related subline (H9.TSF) has an additional copy of the derivative chromosome 12, partial trisomy of 17q, and trisomy 14.  The third subline (H9.DE) has an interstitial deletion of 18q as the sole anomaly.  Despite these karyotypic abnormalities, all three sublines retain markers of the undifferentiated state.  The subline H9.TSF demonstrated the ability to form embryoid bodies consisting of all three germ layers.  Significantly, H9.DT and H9.TSF sublines show a classic karyotype progression that mirrors that seen in both hematopoietic and solid tumors.  This progression was accompanied by an impressive increase in growth potential.  The isolation of human ES cell sublines with clonal cytogenetic abnormalities provides a valuable tool for study of factors that promote in vitro genetic changes and for analysis of mechanisms of aneuploidy related to genetic progression found in human cancers.

overall_design: Four distinct abnormal human embryonic stem cell sublines were studied with comparative genomic hybridization (CGH) and cytogenetic methodology. A rapid method called Genetic Diagnosis at Passage (G-DAP) was developed to to isolate either abnormal or normal clones from karyotypically mosaic human ES cell cultures.

first: Karen

last: Montgomery

first: Chuhu

last: Yang


title: P. aeruginosa virulent factor to barley

status: Public on Jul 25 2008

city: College Station

first: Akihiro

last: Ueda

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

summary:
To identify the difference of gene expression in barley upon P. aeruginosa PAO1 and less pathogenic PA5021 mutant
Keywords: Disease response

overall_design: Barley were infected with PAO1, the PA5021 mutant, or without bacteria (control) for 12 h at 25C.

first: Thomas

middle: K

last: Wood


title: The Genetic Network Controlling the Arabidopsis Transcriptional Response to Pseudomonas syringae pv. maculicola

city: St Paul

first: lin

last: wang

state: MN

address: 350 Cargill building, 1500 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary:
Expression profiling of wild-type plants and mutants with defects in key components of the defense signaling network was used to model the Arabidopsis network 24 hours after infection by Pseudomonas syringae pv. maculicola strain Psm ES4326. Results using the Affymetrix ATH1 array
revealed that expression levels of most pathogen-responsive genes were affected by mutations in coi1, ein2, npr1, pad4, or sid2. These five mutations defined a small number of different expression patterns
displayed by the majority of pathogen-responsive genes. P. syringae pv. tomato strain Pst DC3000 elicited a much weaker salicylic acid response than Psm ES4326. Additional mutants were profiled using a custom array. Profiles of pbs3 and ndr1 revealed major effects of these mutations and allowed PBS3 and NDR1 to be placed between the EDS1/PAD4 node and the SA synthesis node in the defense network. Comparison of coi1, dde2, and jar1 profiles showed that many genes were affected by coi1, but very few were affected by dde2 or jar1. Profiles of coi1 plants infected with Psm ES4326 were very similar to those of wild-type plants infected with bacteria unable to produce the phytotoxin coronatine, indicating
that essentially all COI1-dependent gene expression changes in this system are caused by coronatine.

overall_design: This experiment consists of three biological replicates. For each genotype, two leaves per plant were pooled from three pots to prepare total RNA.

first: Lin

last: Wang

first: Jane

last: Glazebrook


title: Monkeypox and Vaccinia infection of cultured human cells

status: Public on Jul 17 2008

city: Cambridge

first: Kate

last: Rubins

state: MA

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary:
We analyzed effects of monkeypox (MPX) and vaccinia (VAC) infection on cultured human cells.  Our custom-designed arrays contain >18,000 human genes as well as genes for each open reading frame of MPX and VAC.
A reference experiement design type is where all samples are compared to a common reference.
Compound Based Treatment: Chemical used for treating infected cells
Infection: Virus used for infection
Cell Line: Cell line used for infection
Time: Time cells were harvested after infection
Keywords: reference_design

platform_organism:
Homo sapiens
Monkeypox virus
Orthopoxvirus vaccinia
Variola virus

overall_design: Experiments used primary human monocytes with mock infection, VAC-Western Reserve, VAC-NYBOH, MPX-Zaire, gamma irradiated (killed) MPX-Zaire, and Ebola-Zaire (EBOV) (deposited March 2004).  The next set of experiments used primary human monocytes (Mf7.29) and primary human fibroblasts (S100) with mock infection, VAC-Western Reserve, MPX-Zaire, and gamma irradiated MPX-Zaire (g-MPX) (deposited August 2004).  The final set used primary human monocytes (Mph), primary human fibroblasts (NHDF), and HeLa cells with mock infection, VAC-Western Reserve, MPX-Zaire, and gamma irradiated MPX-Zaire (g-MPX).  Some cells were treated with ionomycin + PMA (I+P), cycloheximide (CHX) or hydroxyurea (HU).  (deposited November 2005).  Total RNA from cells was harvested at each timepoint, preserved in Trizol, Trizol-extracted total RNA, 1 round amplified (Ambion MessageAmp I), directly labeled by Cy5 incorporation during reverse transcription of amplified RNA. Each sample was hybridized versus a common reference (Stratagene Universal Human Reference RNA plus a mix of poxvirus transcripts from all timepoints).  The  reference was1 round of amplification (Ambion MessageAmp I), directly labeled by Cy3 incorporation during reverse transcription of amplified reference RNA.  Cy3 and Cy5 samples were hybridized to a custom human-poxvirus array.  Fluorescent images of hybridized microarrays were acquired using the GenePix 4000B and GenePix 4200AL microarray scanners.


title: SitkaSpruce_FB3-425_Bark_PissodesStrobi_Herbivory

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

summary:
Based on the generation of ESTs, we developed a spruce cDNA microarray composed of 21,843 cDNA elements selected from 12 cDNA libraries representing developmental stages of xylem, phloem, bark and roots, as well as elicitor-treated bark.  Clones on the array were selected from a CAP3 assembly of 50,770 hq 3’ ESTs, and were carefully chosen to represent a minimally redundant gene set.  Using this array we examined global changes in the transcriptome of Sitka spruce attacked for two days by stem-boring white pine weevils.  Differentially expressed genes were determined using three criteria: fold-change between weevil-treated and untreated control > 1.5-fold, P value < 0.05 and Q value < 0.05.  After 48 h of weevil feeding, 1,857 (8.5%) microarray elements identified transcripts as up-regulated, compared to 1,374 (6.3%) down-regulated.
Keywords: Stress response

overall_design: Eight hybridizations were performed comparing weevil-treated bark after 48 hours of continuous feeding and untreated control bark harvested at the same time.  RNA isolated from each of the four individual weevil-treated trees was compared directly against the four individual untreated control trees using two hybridizations with a dye flip for each tree pair.

first: Steven

middle: G

last: Ralph


title: Transcription profiling of PhoP-regulon members under low Mg2+ Ca2+ condition of Xanthomonas oryzae pv. oryzae PXO99A

status: Public on Jul 16 2008

city: Davis

first: Malinee

last: Sriariyanun

state: CA

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

summary:
In bacteria, two-component regulatory system (TCSs) is generally characterized by a simple phosphotransfer scheme, composed of a sensor domain (a histidine kinase) and a  response domain (a response regulator), which is responsible for detection of external stimuli. PhoP-PhoQ TCS of Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of bacterial leaf blight disease in rice, was previously shown to be negatively regulated by RaxR-RaxH, another TCS that senses population cell density as well as modulates the activity of AvrXA21,  a bacterial effector, recognized by a bacterial blight resistance gene, Xa21. In this work, whole-genome microarray was performed to analyze transcription profiling and identify member of PhoP regulon under Mg2+ and Ca2+ limited condition. This analysis revealed that PhoP governs broad cellular pathways including stress defense response, cation transportation, general metabolism, broad regulatory system, bacterial motility, and bacterial virulence. Array results provide a set of candidate genes, further biochemical pathway analysis, and signaling pathway crosstalks that need to be characterized to understand PhoP-dependent mechanisms and also suggest a putative regulatory loop between two phoP-phoQ and raxR-raxH TCSs. Implication of this analysis suggested that Xoo adopt PhoP-PhoQ system to perceive extracellular signals from certain environment such as low concentration of metal ions, and to regulate intracellular signals of other regulatory systems.

Keywords: Comparative transcription profiling under limited Mg2+ Ca2+ condition

platform_organism: Xanthomonas oryzae pv. oryzae KACC 10331

overall_design: Three biological and dye-swap replicates, total six samples for each dataset. Three datasets contained; (i) phoP knockout mutant vs. wildtype PXO99A in low concentration (10 µM) of MgCl2 and CaCl2, (ii) phoP knockout mutant in low (10 µM) vs. high (10mM) concentration of MgCl2 and CaCl2, and (iii) PXO99A in low (10 µM) vs. high (10mM) concentration of MgCl2 and CaCl2.

first: Young-Su

last: Seo

first: Peijian

last: Cao

first: Pamela

last: Ronald


title: Transcriptional analysis of the sweet orange interaction with the citrus canker pathogens

city: Campinas

first: Celso

middle: Eduardo

last: Benedetti

state: São Paulo

address: R. Giuseppe Maximo Scolfaro, 10000

department: Center for Molecular and Structural Biology

country: Brazil

institute: Brazilian Synchrotron Light Laboratory

summary:
We have used the citrus GeneChip array (GPL5731) to survey the transcription profiles of sweet orange in response to the bacterial pathogens Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas axonopodis pv. aurantifolii (Xaa). Xac is the causal agent of the citrus canker disease on a wide range of citrus species, including sweet oranges (Citrus sinensis). On the other hand, Xaa is pathogenic to Mexican lime (Citrus aurantifolia) only, and in sweet orange it triggers a defense response. In order to identify the genes induced during the defense response (Xaa-responsive genes) or citrus canker development (Xac-responsive genes), we conducted microarrays hybridization experiments at 6 and 48 hours after bacterial infiltration (habi). The analysis revealed that genes commonly modulated by Xac and Xaa are associated with basal defenses normally triggered by pathogen-associated molecular patterns, including those involved in reactive oxygen species production and lignification. Significantly, Xac-infected leaves showed considerable changes in the transcriptional profiles of defense-, cell wall-, vesicle trafficking- and cell growth-related genes between 6 and 48 habi. This is consistent with the notion that Xac suppresses host defenses near the beginning of the infection and simultaneously changes the physiological status of the host to promote cell enlargement and division. Finally, Xaa triggered a MAP kinase signaling pathway involving WRKY and ethylene-responsive transcriptional factors known to activate downstream defense genes.
Keywords: Comprehensive transcriptional analysis of the Citrus-Xanthomonas interaction

overall_design: Adult leaves of sweet orange were infiltrated with the bacterial suspensions or water (mock control). Two stages were selected after bacterial infiltration for RNA extraction and hybridization on Affymetrix microarrays. In total, these experiments consist of two biological replicates of six samples: water-infiltrated leaves, Xaa-infiltrated leaves and Xac-infiltrated leaves, at both 6 and 48 (habi).

first: R

middle: A

last: Cernadas

first: AC

last: Pinto

first: C

middle: E


title: Comparative expression analysis between TTHB212 deletion mutant and wild-type of T. thermophilus HB8

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

country: Japan

institute: RIKEN Harima Institute

summary:
We observed the expression profile of the total mRNA of TTHB212 deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TR) medium at 70°C compared with that of wild type.
Keywords: cell type comparison

overall_design: Three wild-type and mutant T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 5 h for wild-type and 7 h for TTHB212 deletion mutant, respectively, and then crude RNA was extracted. In order to compare mRNA expression in the TTHB212 deletion mutant with that of wild type, the expression of each mRNA was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

first: Keiko

last: Sakamoto

first: Yoshihiro

last: Agari

first: Miwa

last: Ohmori

first: Seiki

last: Kuramitsu


title: Effect of TbDRBD3 depletion on procyclic T. brucei transcriptome

status: Public on Jul 15 2008

city: Armilla

first: Antonio

middle: M

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

country: Spain

institute: CSIC

summary:
In trypanosomes, the apparent lack of regulation of RNA polymerase II-dependent transcription initiation poses a challenge to understand how these eukaryotes adjust gene expression in order to adapt to the contrasting environments they find during their life cycles. Evidence so far indicates that mRNA turnover and translation are the major control points in which regulation is exerted in trypanosomes. However, very little is known about which proteins are involved, and how do they regulate the abundance and translation of different mRNAs in different life stages. In this work, an RNA-binding protein, TbDRBD3, has been identified by affinity chromatography, and its function addressed using RNA interference, microarray analysis and immunoprecipitation of mRNA-protein complexes. The results obtained indicate that TbDRBD3 binds to a subset of developmentally regulated mRNAs encoding membrane proteins and intermediate metabolism enzymes, and that this association promotes the stabilization of the target transcripts. These observations raise the possibility that TbDRBD3-mRNA complexes act as a post-transcriptional operon, and provide a framework to interpret how trypanosomes regulate gene expression in the absence of transcriptional control.
Keywords: Effect of depletion of an RNA-binding protein on the transcriptome

overall_design: In order to analyze whether TbDRBD3 has a role in the regulation of mRNA turnover, the transcriptome of procyclic trypanosomes depleted of TbDRBD3 was compared to that of uninduced cells using hybridizations of genomic microarrays. RNA samples were isolated from cells harvested after 48 hours of induction with tetracycline. At this point, cell growth was barely affected and trypanosomes remained highly motile. 15 µg of RNA were reverse-transcribed in the presence of 100 ng of oligo(dT)12-18, 0.25 mM dATP, 0.25 mM dTTP, 0.25 mM dGTP, 0.05 mM dCTP, 0.05 mM Cy3- or Cy5-dCTP, 50 mM Tris-HCl, pH 8.3, 75 mM KCl, 3 mM MgCl2, 5 mM DTT, 40 U of RNaseOUT (Invitrogen) and 400 U of Superscript III reverse transcriptase (Invitrogen). Reactions were incubated for 3 hours at 50ºC, stopped by heating at 70ºC for 15 min and treated with 5 U of RNase H for 20 min at 37ºC. cDNA was purified using the MinElute kit (Qiagen), ethanol precipitated and resuspended in hybridization buffer. Genomic T. brucei microarray glass slides containing ca. 24,000 independent random genomic clones (Brems et al., 2005) were pre-hybridized and hybridized as described (Diehl et al., 2002). Four hybridizations (two biological replicates with a dye swap each) were analyzed.


title: Examining the immediate early targets of Gata4 and Gata5.

city: Cardiff

first: Kathryn

last: Maddison

address: Museum Avenue

department: Genetics

country: United Kingdom

institute: Cardiff University

summary:
Gata factors are amongst the genes expressed early on in the process of cardiogenesis. We used microarrays to examine the immediate early targets of Gata4 and Gata5 in the Xenopus leavis animal cap cardiogenesis model. We hope to use these data to examine the roles of Gata4 and Gata5 in cardiogenesis and also to begin to dissect out the common and distinct targets of Gata4 and Gata5.
Keywords: genetic modification, gene overexpresison.

overall_design: Xenopus leavis embryos were injected at the one cell stage with dexamethasone-inducible Gata4 or Gata5 mRNA constructs (to examine endodermal and mesodermal targets) or with Gata4 in the presence of Dkk1 (to examine mesodermal targets.) Embryos were cultured to stage 9, whereupon animal caps were excised and cultured for 2.5 hours in media containing dexamethasone to induce the constructs and cycloheximide to block de novo protein synthesis and thus give only immediate early targets.

first: Branko

last: Latinkic


title: Heterogeneous genetic profiles in soft tissue myoepitheliomas

status: Public on Jul 14 2008

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

summary:
Myoepithelioma, mixed tumor and parachordoma are rare soft tissue tumors thought to represent different morphologic variants of the same family of tumors, hereafter referred to as MMP tumors. The genetic basis of these neoplasms is poorly investigated. However, they morphologically resemble mixed tumor of the salivary glands (a.k.a. pleomorphic adenoma). This is the first study characterizing whole genome DNA copy number changes in MMP tumors and the genomic imbalances detected in four MMP tumors and one pleomorphic adenoma were diverse. The only recurrent aberration of known importance for tumor development was homo- and heterozygous deletions of the region in 9p21-22 which harbors the CDKN2A and CDKN2B genes. Defined by the deletion in case 3, the region 1.27-4.82 Mb on chromosome 19 was heterozygously lost in all cases, including the pleomorphic adenoma. A complex pattern of aberrations was seen in the primary tumor of case 2 with amplifications, interrupted by normal copy numbers and losses, of regions on chromosomes 6, 9, and 13.
Keywords: comparative genomic hybridization, soft tissue myoepithelioma, mixed tumor, parachordoma, pleomorphic adenoma

overall_design: Cases 1-3 and 5-6 were analyzed using 32k array CGH and male genomic DNA (Promega) was used as reference.

first: K

last: Hallor

first: M

middle: R

last: Teixeira

middle: D

last: Fletcher

first: S

last: Bizarro

first: J

last: Staaf

first: H

last: Domanski

first: F

last: VultvonSteyern

first: I

last: Panagopoulos

first: N

last: Mandahl

last: Mertens


title: Clostridium acetobutylicum ATCC 824 time course with Agilent Arrays

status: Public on Jul 21 2008

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary:
Using our newly designed C. acetobutylicum arrays we analyzed the mRNA changes during a time course experiment (up to 66 h) paying special attention on the study of the late timepoints.
Keywords: time course

overall_design: Samples were taken from a Bioflow II reactor at 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation. Two slides per timepoint were hybridized on a dye swap configuration. The control mRNA was generated by combining samples taken at 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation. For timepoints 6, 8, 14, 32, 38, 66 our internal quality control check suggested a larger than normal variation of the intensities in the control channel and a third slide was hybridized. The discarded slides are GSM141189, GSM141203, GSM141222, GSM141229 and GSM141242.

first: Nathan

last: Cheng

first: Shawn

middle: W

last: Jones

first: Ryan

last: Sillers

first: Carlos

middle: J

last: Paredes

middle: T


title: Transcript profiling in Actinobacillus pleuropneumoniae after adherence to, or planktonic growth over, SJPL cells.

status: Public on Jul 09 2008

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

summary: Host-pathogen interactions are of great importance in understanding the pathogenesis of infectious microorganisms. We developed in vitro models to study porcine respiratory tract pathogens using an immortalized epithelial cell line, the St. Jude Porcine Lung (SJPL) cell line.  In conditions where cytotoxicity was absent or low, the transcriptomic profile of A. pleuropneumoniae after contact with the porcine lung epithelial cells was determined using DNA microarrays. Genes such as tadB, rcpA, members of a putative adhesion locus, and a gene with high homology to the Hsf autotransporter adhesin of Haemophilus influenzae were upregulated as well as genes pgaBC involved in biofilm biosynthesis, while capsular polysaccharide-associated genes were downregulated.

overall_design: Samples from A. pleuropneumoniae grown by either adhesion to SJPL cells or planktonic growth over SJPK cells were combined with samples from A. pleuropneumoniae grown in DMEM medium and co-hybridized on the microarray.  Four hybridizations were conducted for each sample combination type. Microarray analysis was carried out using the TM4 Suite of softwares (TIGR) and the SAM algorithm, using a false discovery rate (FDR) value of 0%.  For the planktonic and adhesion experiments, Cy5 signal (test) was compared to Cy3 signal (control) in order to obtain a list of significant differentially expressed genes.  In order to obtain the list of differentially expressed genes between planktonic growth and adhesion, log2 ratios were compared in TM4 also using the SAM algorithm.  Functional classification was performed using TIGR’s Comprehensive Microbial Resource.

first: Eliane

last: Auger

first: Mahendrasingh

last: Ramjeet

first: Irazù

last: Contreras

first: John

last: Nash

first: Josée

last: Harel

first: Marcelo

last: Gottschalk

first: Martin

last: Olivier

first: Mario

last: Jacques


title: Response in Shewanella oneidensis MR-1 and so2426 deletion mutant to Hexavalent Chromium over a 24 hour period

city: Oak Ridge

first: Karuna

last: Chourey

state: TN

address: 1, Bethel Valley Road

department: Chemical Sciences Divison

institute: Oak Ridge National Lab

summary:
Shewanella oneidensis MR-1 exhibits diverse metal ion-reducing capabilities and thus is of potential utility as a bioremediation agent.  Knowledge of the molecular components and regulatory mechanisms dictating cellular responses to heavy metal stress, however, remains incomplete.  In a previous work, the S. oneidensis so2426 gene, annotated as a DNA-binding response regulator, was demonstrated to be specifically responsive at both the transcript and protein levels to acute chromate [Cr(VI)] challenge.  To delineate the cellular function of SO2426 and its contribution to metal stress response, we integrated genetic and physiological approaches with a genome-wide screen for target gene candidates comprising the SO2426 regulon.

Keywords: Time course

overall_design: At each timepoint (post chromate shock) samples were collected from WT and mutant which were grown in biological triplicates. Final number was 6 samples per time point.

first: Dorothea

last: Thompson


title: Oct3/4 expression and notch signaling in bone marrow stromal cells reprogrammed by Xenopus egg extract

status: Public on Jul 11 2008

first: Vanessa

last: Hall

address: Solvegatan 17

summary:
Bone marrow stromal cells (BMSCs) are multipotent stem cells that preferentially differentiate into mesenchymal cells. If they can be dedifferentiated into embryonic stem cell-like cells, they will be a highly attractive source for cell therapy. Cell and egg extracts have been used in a few studies to evaluate nuclear reprogramming, but these have not examined cell pluripotency in any detail. In this study, we used a cell reversible permeabilization method to treat BMSC with Xenopus laevis mitotic egg extract. We observed an upregulation of the pluripotent protein Oct3/4 in BMSCs treated by this extract. We also further evaluated transcriptional changes with a focused stem cell oligonucleotide array. A number of genes involved in the Notch or Wnt signaling pathways were upregulated in BMSC exposed to Xenopus egg extract. In conclusion, our microarray data from BMSCs exposure to egg extracts may provide interesting clues regarding factors involved in nuclear reprogramming. Our approach is an alternative method towards dedifferentiation of cells without genetic modification, which is preferable in the clinical situation.

Keywords: Cell type comparison

overall_design: Expression profiling was performed on murine bonemarrow stromal cells cultured in-vitro versus stromal cells exposed to Xenopus extract and compared with murine embryonic stem cells


title: MiR-21 Promotes Glioma Invasion by Targeting MMP Regulators.

status: Public on Jul 12 2008

city: boston

first: Galina

last: Gabriely

address: 4 blackfan circle

institute: HMS

summary: Substantial data indicate that microRNA-21 (miR-21) is significantly elevated in glioblastoma (GBM) and in many other tumors of various origins. This miRNA has been implicated in various aspects of carcinogenesis, including cellular proliferation, apoptosis and migration. We demonstrate that miR-21 regulates multiple genes associated with glioma cell apoptosis, migration, and invasiveness, including RECK and TIMP3, suppressors of malignancy and inhibitors of matrix metalloproteinases (MMPs). Specific inhibition of miR-21 with antisense olgonucleotides leads to elevated levels of RECK and TIMP3 and therefore reduces MMP activities in vitro and in a human model of glioma in nude mice. Moreover, down-regulation of miR-21 in glioma cells leads to decrease of their migratory and invasion abilities. Our data suggest that miR-21 contributes to the glioma malignancy by down-regulation of MMP inhibitors that leads to activation of MMPs thus promoting invasiveness of cancer cells. Our results also indicate that inhibition of a single oncomir like miR-21 with specific antisense molecules can provide a novel therapeutic approach for “physiological” modulation of multiple proteins whose expression is de-regulated in cancer.

overall_design: A172 glioma cells treated with anti-miR-21, mismatch control antagomiR, or miR-21 mimetic duplex were compared to mock-treated A172 glioma cells as a reference.  Cells were harvested at 6 and 24 hours post-treatment, comprising six pairs of samples in all.  No replicate samples are included.  Agilent microarrays (anti-miR-21, mismatch control antagomiR,and matching mock treatments) were hybridized as fluor-reversed pairs of arrays.  Affymetrix microarrays were hybridized as single technical replicates.

first: Thomas

last: Wurdinger

first: Santosh

last: Kesari

first: Christine

middle: C

last: Esau

first: Julja

last: Burchard

first: Peter

middle: S

last: Linsley

first: Anna

last: Krichevsky


title: Expression profiling of Atm deficient murine thymic lymphoma

city: Heidelberg

first: Hendrik

last: Reuter

department: Moleculare Genetics B060

country: Germany

institute: DKFZ

summary:
To find genes deregulated in the pathogenisis of T-cells in Atm deficient mice, we performed expression profiling of Atm deficient thymic lymphomas, wildtype thymi and Atm deficient thymi without macroscopic enlargement, representing an intermediate stage in the process of tumorigenisis.
Keywords: genetic modification, disease state analysis

overall_design: To evaluate differential gene expression of Atm deficient thymic lymphoma we performed microarray based expression profiling of 8 Atm deficient thymic lymphomas, 6 wildtype thymi, 1 thymus of an Atm heterozygous mouse and 18 thymi of Atm deficient mice without  macroscopic enlargement.

first: Meinhard

last: Hahn

last: Lichter


title: Pediatric RTIs

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
This series includes 278 microarrays used to detect respiratory viruses in a set of nasopharyngeal lavage specimens from children with respiratory tract infections

Objective: To assess the utility of a pan-viral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections.
Study Design: The Virochip was compared to conventional clinical direct fluorescent antibody (DFA) and PCR-based testing for the detection of
respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children.
Results:  The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA  panels, and was similar to virus-specific PCR (sensitivity 85-90%, specificity 99%, PPV 94-96%, NPV 97-98%) in the detection of respiratory syncytial virus, influenza A, and rhino-/enteroviruses.  The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect.
Conclusions:  Given its favorable sensitivity and specificity profile and greatly expanded spectrum of detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric respiratory tract infections.
Keywords: viral detection

overall_design: The series includes 278 clinical specimens

first: Charles

last: Chiu

first: Anatoly

last: Urisman

first: Tara

middle: L

last: Greenhow

first: Silvi

last: Rouskin

first: Shigeo

last: Yagi

first: David

last: Schnurr

first: Carolyn

last: Wright

first: W

last: Drew

last: Wang

first: Peggy

last: Weintrub

first: Joseph

first: Don

last: Ganem


title: Expression of Escherichia coli treated with cefsulodin and mecillinam, alone and in combination

city: University Park

first: Mary

middle: Elizabeth

last: Laubacher

state: PA

address: 317 S Frear

department: Biochemistry Microbiology and Molecular Biology

institute: Pennsylvania State University

summary:
Gram-negative bacteria possess stress responses to maintain the integrity of the cell envelope.  Stress sensors monitor outer membrane permeability, envelope protein folding, and energization of the inner membrane.  The systems used by Gram-negative bacteria to sense and combat stress resulting from disruption of the peptidoglycan layer are not well characterized.  The peptidoglycan layer is a single molecule that completely surrounds the cell and ensures its structural integrity.  During cell growth new peptidoglcyan subunits are incorporated into the peptidoglycan layer by a series of enzymes called the penicillin-binding proteins (PBPs).  To explore how Gram-negative bacteria respond to peptidoglycan stress, global gene expression analysis was used to identify Escherichia coli stress responses activated following inhibition of specific PBPs by the β-lactam antibiotics mecillinam and cefsulodin.  Inhibition of PBPs with different roles in peptidoglycan synthesis has different consequences for cell morphology and viability, suggesting that not all perturbations to the peptidoglycan layer generate equivalent stresses.  We demonstrate that inhibition of different PBPs resulted in both shared and unique stress responses.  The regulation of capsular synthesis (Rcs) phosphorelay was activated by inhibition of all of the PBPs tested.  Furthermore, we show that activation of the Rcs phosphorelay increased survival in the presence of these antibiotics, independently of capsule synthesis.  Both activation of the phosphorelay and survival required signal transduction via the outer membrane lipoprotein RcsF and the response regulator RcsB.  We propose that the Rcs pathway responds to peptidoglycan damage and contributes to the intrinsic resistance of E. coli to β-lactam antibiotics.
We used microarrays to identify changes in gene expression resulting from treatment of Escherichia coli with the β-lactam antibiotics cefsulodin, mecillinam, or the combination.
Keywords: dose response, stress response

overall_design: E. coli was treated with two b-lactam antibiotics, cefsulodin and mecillinam, alone and in combination to identify the expression changes in response to antibiotic-induced peptidoglycan stress.  E. coli was grown to an OD of 0.2 at which time low concentrations of cefsulodin and mecillinam were added individually or in combination.  Samples of the bacteria were collected 5 minutes before treatment as well as 5, 20 and 40 minutes after treatment.  Untreated cells were also collected at the same time points to serve as controls.  At least three biological replicates were collected for all time points and samples, however, only the replicates for the 40 minute time points and the combination time points were hybridized to the arrays as no changes observed for the individual treatments, even at the 40 minute time point.

first: Sarah

last: Ades


title: DNA profiling of serous ovarian and Fallopian tube carcinomas with array CGH and MLPA

status: Public on Jul 08 2008

city: Amsterdam

first: Marlies

last: Nowee

state: Noord-Holland

address: Van der Boechorststraat 7

department: Department of Obstetrics and Gynaecology

country: Netherlands

institute: VU University Medical Center

summary:
Primary serous ovarian carcinoma (OVCA) and serous Fallopian tube carcinoma (FTC), both belonging to the BRCA-linked tumour spectrum, share many properties and are treated similarly. However, a detailed molecular comparison has been lacking. We hypothesized that comparative genomic studies of serous OVCAs and FTCs should point to gene regions critically involved in their tumorigenesis. Array comparative genomic hybridization (array CGH) analysis indicated that serous OVCAs and serous FTCs displayed common but also more distinctive patterns of recurrent changes. Targeted gene identification using a dedicated multiplex ligation-dependent probe amplification (MLPA) probe set directly identified EIF2C2 on 8q as a potentially important driver gene. Other previously unappreciated gained/amplified genes included PSMB4 on 1q, MTSS1 on 8q, TEAD4 and TSPAN9 on 12p, and BCAS4 on 20q. SPINT2 and ACTN4 on 19q were predominantly found in FTCs. Gains/amplifications of CCNE1 and MYC, often in conjunction with changes in genes of the AKT pathway, EVI1 and PTK2, seemed to be involved at earlier stages, whereas changes of ERBB2 were associated with advanced stages. The only BRCA1-mutated FTC shared common denominators with the sporadic tumours. In conclusion, the data suggest that serous OVCAs and FTCs, although related, exhibit differences in genomic profiles. In addition to known pathways, new genes/pathways are likely to be involved, with changes in an miRNA-associated gene, EIF2C2, as one important new feature. Dedicated MLPA sets constitute potentially important tools for differential diagnosis and may provide footholds for tailored therapy.

This study also includes 13 of the 14 Fallopian tube carcinoma samples T10112, T10119, T10116, T10118, T10121, T10129, T10109, T10125, T10117, T10126, T10102c, T10107, T10131a (i.e., GSM172360..GSM172530) in Series GSE7180.

overall_design: Genome-wide array CGH experiments of serous ovarian and Fallopian tube carcinomas to determine DNA-change profiles for both tumour types.

first: M

first: A

last: M Snijders

first: D

last: Rockx

first: R

last: de Wit

first: V

last: Kosma

first: k

last: Hämäläinen

first: J

middle: P

last: Schouten

last: Verheijen

first: P

last: van Diest

last: Albertson

last: Dorsman


title: Transcriptional profiles of yeast on acetate exposed to pure nitrogen or carbon monoxide

city: Seattle

first: Kin

last: Chan

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Oxygen lack of various severity can force many organisms to enter into recoverable hypometabolic states. To better understand how organisms cope with oxygen deprivation, our lab had previously shown that when challenged with anoxia, both the nematode Caenorhabditis elegans and embryos of the zebrafish Danio rerio enter into suspended animation, where all life processes that can be observed by light microscopy reversibly halt, pending restoration of oxygen. Here, we show that both sporulating and vegetative cells of the budding yeast Saccharomyces cerevisiae also enter into a similar state of suspended animation when made anoxic on a non-fermentable carbon source. Transcriptional profiling using cDNA microarrays shows upregulation of aerobic metabolism genes in carbon monoxide (CO)-induced anoxia, but not nitrogen (N2) gas-induced anoxia, consistent with the known oxygen-mimetic effects of CO.  Our results lead us to propose a model for oxygen-regulated gene expression in yeast where two oxygen-sensitive mechanisms operate simultaneously, such that treatment with N2 results in both mechanisms signaling a lack of oxygen, while treatment with CO results in one sensing mechanism signaling a lack of oxygen, while the other signals an abundance of oxygen.

overall_design: Cells were pregrown on glucose media.  Cells were then plated onto nylon membranes on acetate solid media and made anoxic using either pure nitrogen or carbon monoxide.  Cells were collected at 15, 30, 45, 60, 120 minutes and 24 hours after initiation of gas exposure.  Reference samples were derived from cells on acetate in room air for corresponding time point.  Six CO-treated samples were compared to room air references and six nitrogen-treated samples were similarly compared to room air references.

first: Mark

middle: B

last: Roth


title: A role for Multidrug Resistance Protein 4 (MRP4; ABCC4) in human Dendritic Cell migration.

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

summary:
The capacity of dendritic cells (DC) to migrate from peripheral organs to lymph nodes (LN) is an important event in the initiation of a T cell-mediated immune response. Previously it was shown that the ATP-binding cassette (ABC) transporters P-glycoprotein (P-gp; ABCB1) and the 2 multidrug resistance protein 1 (MRP1; ABCC1) play a role in both human and murine DC migration. Here we show that a more recently discovered family-member, MRP4 (ABCC4) is expressed on both epidermal and dermal human skin DC and contributes to the migratory capacity of DC. Pharmacological inhibition of MRP4 activity or down-regulation through RNAi in DC resulted in reduced migration of DC from human skin explants and of in vitro generated Langerhans cells. The responsible MRP4 substrate remains to be identified as exogenous addition of MRP4’s known substrates PGE2, leukotriene B4 and D4 or cyclic nucleotides (all previously implicated in DC migration) could not restore migration. This notwithstanding, our data show that MRP4 is an important molecule, significantly contributing to human DC migration towards the draining lymph nodes, and thereby relevant for the initiation of an immune response and a possible target for immunotherapy.

Keywords: cell type comparison, RNAi knockdown for MRP4

overall_design: 2 samples were analyzed to compare. Immature DC cultured from MUTZ3 (reference control) or from MUTZ3-shMRP4 cells

first: Rieneke

last: van de Ven

first: George

last: Scheffer

first: Anneke

last: Reurs

first: Jelle

last: Lindenberg

first: Ruud

last: Oerlemans

first: Gerrit

last: Jansen

first: Jean-Pierre

last: Gillet

first: Joel

middle: N

last: Glasgow

first: Alexander

last: Pereboev

first: David

last: Curiel

first: Rik

last: Scheper

first: Tanja

last: de Gruijl


title: Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae

status: Public on Jul 04 2008

city: Madison

first: CHANG-YI

last: WU

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: UW-Madison

summary:
The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status.  Zap1 acts as both a positive and negative regulator of its target genes.  We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome.  In this study, we have used complementary methods to identify additional Zap1 target genes.  With alternative growth conditions for the microarray experiments and a more sensitive motif identification algorithm, we have identified 31 new potential targets of Zap1 activation.

Keywords: Yeast Saccharomyces cerevisiae whole genome array

overall_design: We compared cells overexpressing a constitutive allele of Zap1v.s. vector alone (E3) and wild type strain in severe zinc deficiency v.s.  zinc-replete condition (E4)

first: Chang-Yi

last: Wu

first: Amanda

last: Bird

first: Lisa

last: Chung

first: Michael

middle: A

last: Newton

first: Dennis

last: Winge

last: Eide


title: IRF4 and Myeloma

status: Public on Jul 07 2008

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary:
Using RNA interference to identify IRF4 target genes.
Keywords: time series design

overall_design: Gene expression was analyzed using Lymphochip cDNA spotted arrays. Myeloma cell lines were infected with control (shluc, Cy3) or shIRF4 (Cy5) constructs, and changes in gene expression were monitored over time after induction of the shRNA with doxycyclin.


title: Differential expression of inflammatory and immune response genes in rams experimentally infected with Brucella ovis

status: Public on Jul 02 2008

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

institute: Instituto de Investigacion en Recursos Cinegéticos

summary: Infection of sheep with Brucella ovis results in ovine brucellosis, a disease characterized by infertility in rams, abortion in ewes and increased perinatal mortality in lambs. During the course of the infection both the ovine immune response and host cell gene expression are modified. The objective of this research was to conduct a preliminary characterization of differential gene expression in rams experimentally infected with B. ovis by microarray hybridization and real-time RT-PCR.

overall_design: Six hybridizations were conducted using total RNA from three individual infected sheep at 15 and 60 days post infection. In each comparison, the control channels contained total RNA from each of the same three sheep at 0 days post infection. Ratios were calculated as B. ovis-infected sheep at 15 and 60 dpc versus uninfected animals at 0 dpc.

first: Pilar

middle: M

last: Muñoz

first: María

last: de Miguel

first: Clara

last: Marin

first: José

last: Blasco

first: Christian

last: Gortazar

first: Katherine

last: Kocan

first: Jose

last: de la Fuente


title: Gene expression profile of M.tuberculosis espR (Rv3849) mutant

first: Paolo

last: Manzanillo

department: Microbiology and Immunology

institute: University of California at San Francisco

summary:
Mycobacterium tuberculosis, a pathogen of global importance, utilizes the ESX-1 protein secretion system to export virulence factors that disarm host macrophages. Although this secretory pathway is critical for virulence, how ESX-1 is regulated is completely unknown. Here we show that EspR (Rv3849) is a key regulator of ESX-1. EspR activates transcription of an operon that includes three ESX-1 components, Rv3616c-Rv3614c, whose expression in turn promotes secretion of ESX-1 substrates.

Keywords: Strain comparison

overall_design: Comparison of the global gene expression of three M.tb strains grown in log phase: Erdman strain of M.tb, espR transposon mutant, and the espR transposon mutant complemented with the espR gene

first: Sridharan

last: Raghavan

first: Jeffery

last: Cox


title: A network of transcriptional repression specifies muscle fibre type in the zebrafish embryo

status: Public on Jul 03 2008

city: Cambridge

first: Fiona

last: Wardle

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

type: Genome binding/occupancy profiling by genome tiling array

summary:
The zebrafish u-boot (ubo) gene encodes the transcription factor Prdm1, which is essential for the specification of the primary slow twitch muscle fibres that derive from adaxial cells. Here we show that Prdm1 executes this function by acting as a transcriptional repressor. Expression of the slow twitch isoform of the myosin heavy chain in adaxial cells is achieved by Prdm1 mediated repression of the transcriptional repressor Sox6. Using Chromatin immuno precipitation (ChIP) we found that genes encoding fast specific isoforms of sarcomeric proteins are direct targets of Prdm1. These genes are ectopically expressed in the adaxial cells of ubotp39 mutant embryos, suggesting that Prdm1 promotes slow twitch fibre differentiation by acting both as a global repressor of fast fibre specific genes as well as of a repressor of slow specific genes.
Keywords: ChIP-chip

overall_design: Genomic array design. Microarrays were designed as described below and manufactured by Agilent Technologies (www.agilent.com). We have previously described the ChIP-chip technique in zebrafish and the design of promoter microarrays which cover a 2kb region around the transcription start sites (TSSs) of 11,512 zebrafish genes based on Zv4 (Wardle et al, 2006. Genome Biology 7:R71). In order to capture additional regulatory information further from the basal promoter region we also designed an expanded set of 60mer probes that cover 9kb upstream and 3kb downstream of the TSS of these genes using the same parameters as for the 2kb microarrays.  These probe sequences were re-mapped to Zv6 over the course of the project and the coordinates given are for Zv6. We also incorporated several sets of control probes, both positive and negative. On each array there are 769 negative probes designed against zebrafish gene desert regions and Arabidopsis thaliana genes. In addition we included duplicates of promoter probes for several genes that we anticipated may be bound by factors of interest for this and other studies (tnnt3a, mylz2, myhz2, wnt11, flh, vent, msgn1, myod, fgf8, pcdh8) and these probes are arrayed on both slides slide. Finally on each array there are 1804 controls added by Agilent. The final design contained 352,490 probes divided between two microarray slides. Further information on design and manufacture of the microarrays can be found at the Agilent Technologies website.

first: Jonas

last: von Hofsten

first: Stone

last: Elworthy

last: Gilchrist

first: James

last: Smith

first: Philip

last: Ingham


title: Analysis of gene expression in Df(2R)ED3921 (hmgd/z deficiency) and Df(2R)ED50000 (hmgd deficiency) strains

first: Edwige

last: Hiriart

address: Hills Road

department: Laboratory of Molecular Biology

institute: MRC

summary: We analysed the effect of the deficiency Df(2R)ED3921 and Df(2R)ED50000 on gene expression in embryos (stage 0-11), and wing imaginal discs and brains from 3rd instar larvae. Df(2R)ED3921 and Df(2R)ED50000 were described in Ragab et al. (2005) Genetics 172:1069-1078 2005.

overall_design: RNA from Df(2R)ED3921 and Df(2R)ED50000 embryos was compared to a pool of RNA extracted from wild-type embryos at the same stage. For each genotype, 4 independent biological replicates were performed (2 of these dyes swapped with respect to the other two). The same experimental protocol and genotypes were used for the analysis in dissected wing imaginal discs and brains from 3rd instar larvae.

first: Boris

last: Adryan

first: Andrew

last: Travers


title: Differential expression of genes in the leaves of sugarcane in response to sugar accumulation

status: Public on Jul 01 2008

city: Oxford

first: Alistair

middle: James

last: McCormick

address: South Parks Rd

department: Department of Plant Science

institute: University of Oxford

summary: In C4 sugarcane (Saccharum spp. hybrids), photosynthetic activity has been shown to be regulated by the demand for carbon from sink tissues.  There is evidence, from other plant species, that sink-limitation of photosynthesis is facilitated by sugar-signaling mechanisms in the leaf that affect photosynthesis through regulation of gene expression. In this work, we manipulated leaf sugar levels by cold-girdling leaves (5oC) for 80 h to examine the mechanisms whereby leaf sugar accumulation affects photosynthetic activity and assess whether signaling mechanisms reported for other species operate in sugarcane.  During this time, sucrose and hexose concentrations above the girdle increased by 77% and 81%, respectively.  Conversely, leaf photosynthetic activity (A) and electron transport rates (ETR) decreased by 66% and 54%, respectively.  Quantitative expression profiling by means of an Affymetrix GeneChip Sugarcane Genome Array was used to identify genes responsive to cold-girdling (56 h).  A number of genes (74) involved in primary and secondary metabolic pathways were identified as being differentially expressed.  Decreased expression of genes related to photosynthesis and increased expression of genes involved in assimilate partitioning, cell wall synthesis, phosphate metabolism and stress were observed.  Furthermore four probe sets homologous to trehalose 6-phosphate phosphatase (TPP; EC 5.3.1.1) and trehalose 6-phosphate synthase (TPS; EC 2.4.1.15) were up- and down-regulated, respectively, indicating a possible role for trehalose 6-phosphate (T6P) as a putative sugar-sensor in sugarcane leaves.

overall_design: Twelve month-old field grown Saccharum spp. (L.) hybrid cv. N19 (N19) cultivated at Mount Edgecombe, KwaZulu-Natal (SASRI) were used in the study, which was conducted in November, 2006. Plants were grown on a 5 x 15 m plot located on a north-east facing slope with a gradient of ca. 10o. Cold-girdles were attached to sugarcane leaves (n=4) for a period of 56 h prior to harvest. The girdle consisted of 0.75 cm (diameter) soft plastic tubing, firmly clamped around each leaf, approximately 30 cm from the leaf base. Cooled water maintained at 5oC was then pumped through the tubing using a Grant LTD6G cooling bath (Grant Instruments, Barrington, Cambridge, UK). At harvest, leaf samples were immediately frozen in liquid nitrogen (–196oC) and subsequently milled in an A11 Basic Analysis Mill (IKA, Staufen, Germany). Ground leaf tissue was stored at –80oC in 50 ml centrifuge tubes prior to analysis.

first: Michael

last: Cramer

first: Derek

last: Watt


title: Genomic markers for malignant progression in pulmonary adenocarcinoma.

city: Vancouver

first: Bradley

last: Coe

address: 675 West 10th Ave

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

summary:
Bronchioloalveolar carcinoma (BAC), a subtype of lung adenocarcinoma (ADC) without stromal, vascular, or pleural invasion, is considered an in situ tumor with a 100% survival rate. However, the histological criteria for invasion remain controversial. BAC-like areas may accompany otherwise invasive adenocarcinoma, referred to as mixed type adenocarcinoma with BAC features (AWBF). AWBF are considered to evolve from BAC, representing a paradigm for malignant progression in ADC. However, the supporting molecular evidence remains forthcoming. Here, we have studied the genomic changes of BAC and AWBF by array comparative genomic hybridization (CGH). We used submegabase-resolution tiling set array CGH to compare the genomic profiles of 14 BAC or BAC with focal area suspicious for invasion with those of 15 AWBF. Threshold-filtering and frequency-scoring analysis found that genomic profiles of noninvasive and focally invasive BAC are indistinguishable and show fewer aberrations than tumor cells in BAC-like areas of AWBF. These aberrations occurred mainly at the subtelomeric chromosomal regions. Increased genomic alterations were noted between BAC-like and invasive areas of AWBF. We identified 113 genes that best differentiated BAC from AWBF and were considered candidate marker genes for tumor invasion and progression. Correlative gene expression analyses demonstrated a high percentage of them to be poor prognosis markers in early stage ADC. Quantitative PCR also validated the amplification and overexpression of PDCD6 and TERT on chromosome 5p and the prognostic significance of PDCD6 in early stage ADC patients. We identified candidate genes that may be responsible for and are potential markers for malignant progression in AWBF.

Keywords: array comparitive genomic hybridization, bronchioloalveolar carcinoma, non-small-cell lung carcinoma, prognostic markers

overall_design: Array comparitive genomic hybridization analysis of 29 Lung Adenocarcinomas with Bronchioalveolar Features.

first: Sarit

last: Aviel-Ronen

first: Suzanne

middle: K

last: Lau

first: Gilda

last: da Cunha Santos

first: Chang-Qi

last: Zhu

first: Dan

last: Strumpf

first: Igor

last: Jurisica

first: Wan

last: Lam

first: Ming-Sound

last: Tsao


title: Gene Expression profiling of Salmonella typhimurium Wild Type and HRG Mutant under H2O2 Stress

city: Bangalore

first: Dipshikha

last: Chakravortty

state: Karnataka

address: C.V.Raman AVENUE

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary:
Objective of the study is to find out the differentially regulated genes in Salmonella typhimurium subjected to H2O2 stress. Gene expression profiling was carried out using Agilent microarray platform.
Keywords: H2O2 Stress

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
Bacterial culture (WT & HRG) were grown till early stainary phase for 7 hrs in LB.
600 microgram of H2O2 was added to the cultures for 4hrs.
Total RNA from Treated & Untreated Bacterial cultures were isolated using Trizol.

S.typhimurium microarray was custom designed using multiple 60mer oligonucleotides covering all known transcripts of S.typhimurium genome. Array was designed at Genotypic Technology using Agilent Technologies e-Array platform.
1 microgram of RNA is polyadenylated using poly-A polymerase (pAp) enzyme and labeled using Agilents Lirak kit as per manufacturer recommended protocol (www.agilent.com).
1650ng of labeled Sample, mixed with appropriate amount of blocking buffer and hybridization buffer (Agilent Technologies) (Web link). The hybridization mix was applied on to the backings and hybridized to custom designed 60mer s.TYPHIMURIUM microarray using sure hyb chambers at 65degC for 16 hours. Slides were washed with gene expression wash buffer 1 and 2 (Agilent Technologies) followed by Acetonitrile.Laser detection of Cyanine 3 fluorescence is performed using a confocal scanning instrument containing tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.
Slides were scanned at 5 micron resolution using Agilent scanner.Automated feature extraction was done using Agilent’s Feature Extraction Software.

Analysis of feature extracted data was done using Agilent’s GeneSpring GX V 7.3.1 software. Pre-processing of the replicate experiment data was done to flag the outliers. The normalization was done using GeneSpring GX using the recommended Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples (Treated Vs Control).
Genes with log2 ratio of 1.8 and above in replicate experiments were considered as up regulated and 0.55 and below was considered down regulated. p-value was calculated by GeneSpring GX for each gene on the basis of replicate probes to indicate statistical significance

first: Amit

last: Lahiri

first: Priyanka

last: Das


title: Chromatin Immunoprecipitation of UV treated AdHBx cells with anti-HBx antibodies

city: Singapore

first: Wah Heng

last: Lee

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary:
Direct gene targets of HepG2 cells transduced with Adenoviral vector carrying HBx vs Adenoviral vector under UV treatment
Keywords: ChIP-chip profiling

overall_design: One-condition experiment, AdHBx (experimental) UV vs AdEasy (vector control) UV.  HepG2 cells were infected with either recombinant HBx adenoviruses (AdHBx) or control adenoviruses (AdEasy). Seventy-two hours later, infected cells were exposed for 30 seconds to UVC (254 nm) irradiation with a germicidal lamp calibrated to deliver 8 or 16 J/m2.  Cells were then harvested for either ChIP-chip profiling or expression microarray profiling.

first: Caroline


title: Bacillus subtilis 168 cells: wild-type vs. (ccpN-yqfL) double mutant

city: Thiverval-Grignon

first: Thierry

last: Doan

address: INRA

department: Microbiologie

country: France

institute: INRA

summary:
Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a (ccpN-yqfL) double mutant.

Abstract of the associated publication (article accepted):
The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Two-condition experiment: wt vs. (ccpN-yqfL) double mutant.
2 totally independent comparisons were performed different days with 2 independent RNA preparations and 2 sets of macroarrays.

first: Simon

last: Tannler

first: Eliane

last: Fischer

first: Dominique

last: Le Coq

first: Emmanuel

last: Jamet

first: Uwe

last: Sauer

first: Stephane

last: Aymerich


title: Identification of Phox2b-regulated genes by expression profiling of cranial motoneuron precursors on NeuroDev microarray

status: Public on Jun 30 2008

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

summary:
Branchiomotor neurons are an important class of cranial motor neurons that innervate the branchial-arch-derived muscles of the face, jaw and neck. They arise in the ventralmost progenitor domain of the rhombencephalon characterized by expression of the homeodomain transcription factors Nkx2.2 and Phox2b. Phox2b in particular plays a key role in the specification of branchiomotor neurons. In its absence, generic neuronal differentiation is defective in the progenitor domain, and no branchiomotor neurons are produced. Conversely, ectopic expression of Phox2b in spinal regions of the neural tube promotes cell cycle exit and neuronal differentiation and at the same time induces genes and an axonal phenotype characteristic for branchiomotor neurons. How Phox2b exerts its pleiotropic functions, both as a proneural gene and a neuronal subtype determinant, has remained unknown.
To gain further insight into the genetic programme downstream of Phox2b we searched for novel Phox2b-regulated genes by cDNA microarray (here NeuroDev slides) analysis of facial branchiomotor neuron precursors from heterozygous and homozygous Phox2b mutant embryos.
Keywords: Phox2b-regulated genes identification

overall_design: Four biological replicates each in dye swap

first: Patrick

last: Pla

last: Le Crom

first: Christo

last: Goridis


title: Genotypic and gene expression studies in Congenital Melanocytic Nevi: insight into initial step of tumoral melanogenesis

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

summary:
Large Congenital Melanocytic Naevi have a higher propensity to malignant transformation compared to acquired naevi. They thus represent a good model for studying initial steps of melanocarcinogenesis.  We have performed genotypic (karyotype, FISH and mutational analyses) and differential expression studies on a large cohort of medium (n=3) and large (n=24) congenital melanocytic naevi. Unlike malignant melanoma, chromosomal abnormalities were rare and single, a feature probably reflecting the benignity of these lesions. Mutational screening showed a high frequency of NRAS mutations in our series, while BRAF mutations were less common. Differential expression study between tumoral and normal melanocytes did not show significant alterations of cellular processes such as cell proliferation, cell migration/invasion, angiogenesis, apoptosis, and immune/inflammatory responses.  However, significant down-regulation of genes involved in pigmentation and up-regulation of genes playing a role in DNA protection were observed. Lastly, our micro-arrays displayed up-regulation of genes mediating chemoresistance in cancer. As alteration of pigmentation mechanisms can trigger oxidative damage, increased expression of genes involved in maintenance of DNA integrity might reflect the ability of naevocytic cells to self protection against cellular stress. Furthermore, the observed alterations linked to chemoresistance might partially account for the well known inefficacy of chemotherapy in malignant melanoma.
Keywords: cell type comparison

overall_design: 6 Large Congenital Melanocytic Naevi (CMN), (4 BRAFV600E mutated samples and 2 cases with chromosomal translocations involving BRAF) were co-hybridized with normal control (pool of 13 foreskins) on Human Exonic Evidence Based Oligonucleotide (HEEBO) arrays (Stanford Functional Genomics Facility, California, USA) containing 44544 70mer probes. Hybridizations were replicated with dye swap.

first: Barbara

last: Dessars

first: Linda

last: De Raeve

first: Hakim

last: El Housni

first: Anne

last: Lefort

first: Renato

last: Morandini

first: Ghanem

last: Ghanem

first: Benoît

last: Van den Eynde

first: Wenbin

last: Ma

first: Diane

last: Roseeuw

first: Gilbert

last: Vassart

first: Frédérick

first: Pierre

last: Heimann


title: mutants-Transcriptomic analysis of mkk2 upon Cold stress

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

summary:
adt06-03-mkk2 - mutants - early response targets of MKK2 upon cold stress treatment and its role in adaptation. - Several mutants in MKK pathway were tested against the wild type.
Keywords: gene knock out

overall_design: 12 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Heribert

last: Hirt

first: Marie-Laure

last: Martin-Magniette


title: Juvenile idiopathic arthritis: peripheral blood cells

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

institute: Wakayama Medical University

summary:
Systemic-onset juvenile idiopathic arthritis (soJIA) is a rheumatic disease in childhood characterized by systemic symptoms and a relatively poor prognosis. The peripheral leukocytes are thought to play the pathological role of soJIA although the exact cause is still obscure. In this study, we aimed to clarify the cellular functional abnormality in those cells. Here, we analyzed the gene expression profile in peripheral leukocytes from 51 patients with soJIA, 6 patients with poly-articular type JIA (polyJIA) and 8 healthy children utilizing DNA microarrays. A total of 3,491 genes, including genes related to immune reponse and metabolism, were differentially expressed in patients with soJIA compared to healthy individuals. The result provides insight into the pathogenesis of soJIA.
Keywords: disease state analysis

overall_design: Total RNA was extracted from peripheral leukocytes from 51 soJIA patients, 6 poly-articular type JIA patients, and 8 healthy children. The gene expression profile was analyzed with DNA microarrays.

first: Satoru

last: Ishikawa

first: Toru

last: Mima

first: Chieko

last: Aoki

first: Naoko

last: Yoshiwo-Hoshino

first: Yasuo

last: Adachi

first: Tomoyuki

last: Imagawa

first: Masaaki

last: Mori

first: Minako

last: Tomiita

first: Naomi

last: Iwata

first: Takuji

last: Murata

first: Mari

last: Miyoshi

first: Syuji

last: Takei

first: Yukoh

last: Aihara

first: Shumpei

last: Yokota

first: Kenichi

last: Matsubara


title: Microarray expression of B-cell Non-Hodgkins Lymphoma cases

city: Madrid

first: Mohit

last: Aggarwal

address: Melchor F. Almagro 3

institute: CNIO

summary:
Transcriptional profiling of major types of B-cell NHL clinical samples. While comparing all the types together, their expression was compared against reactive lymph nodes, except SMZL whose expression was compared against normal splenic cells.
Keywords: disease state analysis

overall_design: Clinical samples; 8 reactive lymph nodes, 5 splenic controls Vs 187 cases (38 MCL, 38 CLL, 9 BL, 27 SMZL, 36 DLBCL, 33 FL , 6 nMZL)

first: Miguel

last: Piris


title: miRNA expression profiling during C2C12 myogenesis

city: St Lucia

first: Chung Fai

last: Wong

state: Q

address: 306 Carmody Rd

department: Livestock Industries

country: Australia

institute: CSIRO

summary:
This study profiled the expression of miRNA during myogenesis of the C2C12 mouse myoblast cell line. Cells were harvest at different stages during myogenesis including proliferating, confluence, 1 day post-differentiation induction, 2 day post-differentiation induction and 4 days post-differentiation induction.
Keywords: time course

platform_organism:
Arabidopsis thaliana
Caenorhabditis elegans
Drosophila melanogaster
Gallus gallus
Macaca mulatta
Homo sapiens
Bos taurus
Mus musculus
Rattus norvegicus

overall_design: This experiment was a reference design miRNA microarray where all time points were compared to a pooled proliferating C2C12 sample, made up of 4 proliferating biological replicates. Each time point had four bioloigcal replicates of which two were labelled with Cy3 and two were labelled with Cy5.

first: ChungFai

first: Ross

last: Tellam


title: mkk2_mkk2_and_wrky19_cold_time_course-Transcriptomic analysis of mkk2 upon Cold stress

first: Frederique

last: Bitton

summary:
adt06-03-mkk2 - mkk2_mkk2_and_wrky19_cold_time_course - early response targets of MKK2 upon cold stress treatment and its role in adaptation. - seedlings were put to 4 ° comparing wild type ColO versus mkk2 knockouts, MKK2 overexpressors and wrky19 knockouts.
Keywords: time course,wt vs mutant comparison

overall_design: 18 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Heribert

last: Hirt

first: Marie-Laure

last: Martin-Magniette


title: Comparison of regenerating and non regenerating transgenic stage 52 Xenopus hind limbs

city: Dunedin

first: Caroline

last: Beck

address: 340 Great King Street

department: Zoology

country: New Zealand

institute: University of Otago

summary:
Epimorphic regeneration is the process by which complete regeneration of a complex structure such as a limb occurs through production of a proliferating blastema. This type of regeneration is rare among vertebrates but does occur in the African clawed frog Xenopus laevis, traditionally a model organism for the study of early development. Xenopus tadpoles can regenerate tails, limb buds and the lens of the eye, although the ability of the latter two organs to regenerate diminishes with advancing developmental stage. Using a heat shock inducible transgene that remains silent unless activated, we have established a stable line of transgenic Xenopus in which the BMP inhibitor Noggin can be over-expressed at any time during development.  We have previously shown that activation of this transgene blocks regeneration of the tail and limb of Xenopus tadpoles. In the current study, we have taken advantage of this transgenic line to directly compare gene expression in same stage regenerating vs. non-regenerating hind limb buds.  Using Affymetrix gene chip analysis, we have identified genes whose expression levels are linked to regenerative success. These include the BMP inhibitor Gremlin and the stress protein Hsp60 (no blastema in zebrafish). Analysis of overrepresented Gene Ontology functional groupings suggests that successful regeneration in the Xenopus hind limb depends on induction of stress response pathways. Furthermore, as expected, genes involved in embryonic development and growth are also significantly over-represented in regenerating early hind limb buds.
Keywords: Differential expression, regeneration

overall_design: This series was used to identify differentially expressed genes between regenerating wild type stage 52 hind limb buds and those of their transgenic siblings which are blocked in BMP signalling and fail to regenerate. Two biological replicates of each type were examined. Each replicate is made up of dissected distal stump tissue from 20 hindlimbs 3 days after amputation.  The single timepoint of 3 days was chosen to fall after wound healing had occurred but before re-differentiation and corresponds to the cone shaped blastema stage of successfull regenerates. BMP signalling is blocked using a single insertion transgene (N1) expressing noggin under the control of an inducible heat shock promoter, and all tadpoles are siblings derived from a single backcross to a wild type animal to minimise genetic variation.

first: Esther

last: Pearl

first: Donna

last: Barker

first: Robert

last: Day


title: Global Transcriptome Profiles in the Nodes of Rice During Spatial and Temporal Development

status: Public on Jun 26 2008

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

summary:
The following study was conducted to better understand the genetics of the spatial and temporal development of rice, especially as this relates to the development of lignocellulosic tissues. To do so, an oligonucleotide array was designed and created by the Plant Sciences Institute at Iowa State University. A total of 43,776 spots were printed on two separate platforms, the first contained 23,040 spots while the second contained 20,736. RNA was collected from nodes of rice seedlings at several different time points, as nodes are highly lignified tissues. Comparisons were performed to identify those genes exhibiting differential regulation across time at an anatomical position as well as across anatomical distance. For example, node 1 was compared across days 46, 53, 60, and 67 and at day 67 node 1 was compared to nodes 2, 3, and 4. Similar comparisons were performed for nodes 2, 3, and 4 where applicable.

Keywords: Time course and anatomical development in rice

overall_design:
For each comparison, 6 replicates and multiple power settings were considered. Dye-swaps were performed between replicates.

A diagram of the comparisons made in this experiment may be found in ISU_RiceArray_LoopDesign.pdf (linked below as a Supplementary file).


title: CSMA mouse transcriptome analysis project

status: Public on Jun 27 2008

city: Hayward

first: Daixing

last: Zhou

address: 25861 Industrial Blvd

department: Bioinformatics

institute: Solexa

summary:
The mouse Reference Transcriptome Database (MRTD) is the result of a multi-institute initiative funded with Federal Funds from the National Cancer Institute (NCI) and National Institutes of Health (NIH).
When completed, this database will contain quantitative and comprehensive gene expression data obtained from more than one hundred different mouse samples. These data was initially acquired using the Massively Parallel Signature Sequencing (MPSS™) technology invented by Sidney Brenner and reduced to practice by Lynx Therapeutics, Inc. With recent advent of Illumina's Genome Analyzer technology, it was decided that Illumina?s current Genetic Analyzer is better suited for the project by its Clonal Single Molecule Array (CSMA™) technology. It is therefore adapted for the first 14 samples as displayed here.  All samples are and will be sequenced at the Illumina facility in Hayward, CA. The data will be maintained and hosted by both the National Center for Biotechnology Information (NCBI->GEO).
The high homology between human and mouse, the wealth of biological information available, the clinical relevance of the disease models, the completion of the genome sequencing, and the ease of manipulation of the genome make mouse the prime animal model for biomedical research. All these factors influenced the decision to choose this small mammalian as the first transcriptome to be sampled to this unprecedented depth. Eventually this database will contain a large collection of normal tissues or cell types that will serve as the basis for further disease state studies.
CSMA™ is the ideal technology for establishing such a reference database. It provides superior sensitivity and dynamic range and it is the only technology that can routinely provide the sampling depth (2 to 5 million tags per sample) needed for accurately and quantitatively determining the expression level of every gene in a particular sample. In this database each individual sample has been sequenced to a depth of at least 2 million 20 nucleotide long expressed sequence tags.
Unlike most other gene expression technologies that provide analog expression data, CSMA™ provides digital expression information, which is crucial for data exchange, comparison and expansion.
Our goal is to enable researchers to directly access accurate expression information without conducting additional bench work. The database should also be useful for investigators interested in comparing their own set of CSMA™ data to the healthy tissues made available here. Because of the additive nature of this database, researchers will be able to gain insights on the expression levels of their gene(s) of interest across nearly a hundred samples while they will only need to conduct a few additional experiments targeted to their own area of interest.
Keywords: Illumina Genetic Analyzer Sequencing, Clonal Single Molecule Array

overall_design: 14 libraries; 7 tissues from male and female


title: Transcriptional and translational gene regulation in the maize pulvinus

city: Raleigh

first: Henrietta

last: Myburg

state: NC

address: 42218 Gardner Hall

department: Botany

institute: NC State University

summary:
Not much is known about the molecular processes involved during gravitropism in monocot plants such as maize.  A microarray based study on the expression of genes after a gravity stimulating the maize pulvinus will provide us with valuable information and a better understanding of the underlying molecular processes involved in monocot gravitropism.
Objectives for this study included the identification of genes that were regulated at the transcriptional and translation level during gravitropism in the maize pulvinus.  This was achieved by microarray analysis of total RNA versus polyribosome associated RNA during a time-course of gravity stimulation of the maize pulvinus.
Keywords: time course

overall_design: Six week old maize plants were gravity stimulated by 90º reorientation.  Upper (slow elongation) and lower (fast elongation) halves of the most gravity competent pulvini were harvested over a time course ranging from 2 minutes up to one hour (2min, 5 min, 15min, 30min, 60min).  Pulvini samples from control (vertical, no gravity stimulation) plants were harvested and labeled as left and right.  For each time point, total mRNA and polyribosome-associated mRNA were purified and the transcript profiles analyzed using Affymetrix GeneChip® Maize Genome Arrays.  The experiment was repeated twice (two growing seasons) and represent two biological repetitions.

first: Raul

last: Salinas-Mondragon

first: Rebecca

last: Hammond

first: Eric

last: Davis

first: Heike

middle: W

last: Sederoff


title: Cardiac and pulmonary responses to diesel engine particulate in Apo E(-/-) mice

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

summary:
Mice deficient in Apolipoprotein E (Apoe E(-/-)) vs wild type mice were exposed to diesel engine particulate by single dose intratracheal instillation.  The transcript-level response of the hearts after 24h  and of the  lungs after 24 h and 5 days were subsequently analyzed by the 2-color microarray method.
Keywords: stress response, disease state analysis

overall_design: Four mice of the Apo E (-/-) strain were exposed to diesel engine particulate from the National Institute of Standards and Technology via intratracheal instillation.  Controls consisted of 4 littermates exposed to saline vehicle.  Four wild type mice were similarly exposed to diesel particulate and four to vehicle control.  24 hours after exposure, mice were humanely sacrificed by carbon dioxide asphyxiation and the hearts and lungs were collected and frozen for analysis of total RNA.  2 color microarrays were utilized to compare pooled RNA representing all four animals of each strain, and  in each condition and in each tissue.

middle: G

first: Ria

last: Nag

first: Ralph

middle: V

last: Shohet


title: Expression patterns of cDNAs in gamma-irradiation induced T-cell lymphomas

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

summary:
This set of data contains the expression levels of cDNAs in T-cell lymphoblastci lymphomas induced by gamma-irradiation. These tumor samples were compared to normal thymuses
Keywords: Tumor profiles, comparison of tumoral versus wilf-type tissues, lymphomas and leukemias

overall_design: C57BL/6J animals were maintained in our animal facilities following the appropriate ethical recommendations from our institutions. For tumor induction, 4-week-old mice of both sexes were exposed to four weekly doses of 1.75 Gy/dose of ionizing gamma radiation. Treated mice were observed daily until moribund, then sacrificed and autopsied. DNA, RNA and proteins were isolated from these samples using routine procedures.

first: María

middle: J

last: Bueno

first: Ignacio

last: Pérez de Castro

first: José

last: Fernández-Piqueras


title: Comparative Genomic hybridization of gamma-irradiated T-cell lymphomas

summary:
This analysis compares the signal of DNA from T-cell lymphoblastic lymphomas induced by gamma-irradiation versus normal thymuses
Keywords: Tumor profiles, comparison of tumoral versus wilf-type tissues, lymphomas and leukemias


title: Gamma-irradiation induced T-cell lymphomas (miRNA study)

summary:
This set of data contains the expression levels of cDNAs in T-cell lymphoblastic lymphomas induced by gamma-irradiation. These tumor samples were compared to normal thymuses
Keywords: Tumor profiles, comparison of tumoral versus wild-type tissues, lymphomas and leukemias

first: George

last: Calin

first: Carlo

last: Croce


title: Bacillus subtilis 168 cells: wild-type vs. ccpN (non polar)

first: Thierry

last: Doan

summary:
Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a ccpN (yqzB) non polar mutant.

Abstract of associated publication (article accepted):
The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes.

overall_design:
Two-condition experiment, wt vs. ccpN mutant.
4 experiments were performed different days with 3 independent RNA preparations (from separate cultures) and 3 independent sets of macroarrays:
Experiment 1 (samples wt1 and ccpN1): total RNA extract1  /  membranes set A
Expereince 2 (samples wt2 and ccpN2): total RNA extract 2  /  membranes set A
Experiment 3 (samples wt2 and ccpN2): total RNA extract 3   / membranes set B
Experiment 4 (samples wt2 and ccpN2): total RNA extract 3   / membranes set C

first: Simon

last: Tannler

first: Eliane

last: Fischer

first: Dominique

last: Le Coq

first: Emmanuelle

last: Jamet

first: Uwe

last: Sauer

first: Stephane

last: Aymerich


title: Gene expression profiling as a tool for sediment risk assessment: a pilot study using Caenorhabditis elegans whole genome microarrays

status: Public on Jun 25 2008

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

summary: Toxicity of river sediments are assessed using whole sediment toxicity tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. Moreover, natural sediment properties, such as grain size distribution and organic carbon content, can influence the test parameters by masking pollutant toxicity. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bioavailable fraction of pollutants. The nematode Caenorhabditis elegans is ideally suited for these purposes, as (i) it can be exposed to whole sediments, and (ii) its genome is fully sequenced and widely annotated. In this pilot study we exposed C. elegans for 48 h to three sediments varying in degree of contamination with e.g. heavy metals and organic pollutants. Following the exposure period, gene expression was profiled using a whole genome DNA-microarray approach.

overall_design: Whole genome DNA microarray experiments were performed using a common reference design to identify differentially expressed genes in nematodes exposed to one of three river sediments of differing pollution level. Each sample consists of the 5 “biological replicates”.

first: Suresh

middle: C

last: Swain

last: Menzel

first: Stefanie

last: Rienau

middle: R


title: Salmonella typhimurium igaA(T191P) and related

city: Austin

first: Rasika

last: Harshey

state: TX

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

summary:
We have exploited a spontaneously isolated mutant IgaA(T191P) that is near-maximally activated for the Rcs system, to identify a vast set of genes that respond, and report new regulatory properties of this signaling system in Salmonella enterica serovar Typhimurium. Microarray data show that the Rcs system normally functions as a positive regulator of SPI-2 and other genes important for growth of Salmonella in macrophages, although when highly activated, the system completely represses the SPI-1/SPI-2 virulence, flagellar, and fimbrial biogenesis pathways. The auxilliary protein RcsA, which works with RcsB to positively regulate colanic acid and other target genes, not only stimulates but also antagonizes the positive regulation of many genes in the igaA mutant. We show that RcsB represses motility through the 'RcsB box' in the promoter region of the master operon flhDC, and that RcsA is not required for this regulation. Curiously, RcsB selectively stimulates expression of the flagellar Type 3 secretion genes fliPQR; an RcsAB box located downstream of fliR influences this regulation. We show that excess colanic acid impairs swimming and inhibits swarming motility, consistent with the inverse regulation of the two pathways by the Rcs system.

The work was published in Journal of Bacteriology:

Wang Q, Zhao Y, McClelland M, Harshey RM.
The RcsCDB signaling system and swarming motility in Salmonella enterica serovar Typhimurium: dual regulation of flagellar and SPI-2 virulence genes.
J Bacteriol. 2007 Sep 28; [Epub ahead of print]
PMID: 17905992 [PubMed - as supplied by publisher]
Keywords: Comparative genomic hybridization

platform_organism:
Salmonella
Salmonella enterica

overall_design: Microarray was used to reveal the gene expression profiles in igaA(T191P) and related strains at two growth stages (log and stationary phases). Quantitative RT-PCR was used for detail studies.


title: Identification of markers associated with deregulated hTERT during HPV-medaited transformation

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary:
Although high-risk human papillomavirus (HPV) infection plays a major role in the development of cervical cancer, additive oncogenic events are involved as well. One key event involves increased activity of telomerase resulting from a deregulated expression of its catalytic subunit hTERT. Our previous microcell-mediated chromosome transfer studies revealed that introduction of human chromosome 6 in the HPV16 immortalized keratinocyte cell line FK16A and in the HPV16 containing cervical cancer cell line SiHa induced growth arrest, resulting from a repression of hTERT mRNA expression and telomerase activity. Here, this model was used to analyze expression profiles associated with hTERT deregulation in HPV transformed cells. Microarray expression analysis of 12 FK16A/chromosome 6 hybrids, four of which were negative for endogenous hTERT and 8 of which were positive for endogenous hTERT, resulted in the identification of 164 differentially expressed genes. Differential expression of a selection of 5 genes was verified by real-time RT-PCR. Of these 164 genes, 32 were also differentially expressed in other HPV transformed cells with deregulated hTERT. For 2 of these genes, encoding AQP3 and MGP, altered expression in hTERT positive cervical carcinomas was confirmed by real-time RT-PCR and immunohistochemistry, respectively. In summary we identified 32 candidate biomarkers for deregulated hTERT mRNA expression which may enable the identification of cervical premalignant lesions that are at highest risk to progress to invasive cancer.
Keywords: microarray expression analysis, hTERT, cervical cancer

overall_design: 12 previously established cell hybrids, all carrying the same genetic background were subjected to microarray expression analysis. These hybrids were generated by the introduction of chromosome 6 in the HPV16 immortalized cell line FK16A, which resulted in a suppression of hTERT expression and telomerase activity. 8 hybrids were endogenous hTERT positive and 8 hybrids were hTERT negative. Additionally primary keratinocytes (hTERT negative), parental cell line FK16A and cervical cancer cell line SiHa (both hTERT positive) were hybridized.

first: Jillian

last: de Wilde

first: Saskia

last: Wilting

first: Chris

last: Meijer

first: Mark

last: van de Wiel

first: Bauke

last: Ylstra

first: Peter

last: Snijders

first: Renske

last: Steenbergen


title: MYC threshold required to maintain tumor phenotype

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

summary:
We demonstrate that there is a  level of MYC expression that is required for maintaining a tumor phenotype and at this threshold there is a switch from a state of cellular proliferation to a state of proliferative arrest and apoptosis. We analyzed changes in gene expression by oligonucleotide microarray analysis and quantitative PCR and found significant changes (FDR=5%) in 2348 down regulated genes and 1573 upregulated genes. Critical changes in gene expression that occurred at or near the threshold level of MYC expression includes genes that have been implicated in G1/S, G2/M cell cycle checkpoint pathways and death receptor/apoptosis signaling.
Keywords: Dose response - MYC inactivation by doxycycline treatment

overall_design: 11 samples, replicates not included

first: Catherine

last: Shachaf


title: Gene expression during hyper and hypoosmotic stress adaptation in Gillichthys mirabilis

status: Public on Jun 24 2008

city: Pacific Grove

first: Tyler

last: Evans

address: 120 Oceanview Blvd

summary: This study investigates changes in gene expression associated with adaptation to acute hyper- and hypoosmotic stress in Gillichthys mirabilis gill tissue. Gene expression data was captured as a time course (1, 2, 4, 12 hours past exposure) during the first 12 hours following abrupt transfer to osmotic stress media.

overall_design: We employed a custom made Gillichthys mirabilis cDNA microarray. A total of 39 arrays were used in this study: 12 hyperosmotic stress samples, 12 hypoosmotic stress samples, 12 control samples, and 3 time=0 samples. Three individuals were hybridized at each of the four time points (1, 2, 4, 12 hours past exposure) for experimental and control fish (giving a total of 12). All samples were hybridized against a common reference sample containing pooled cDNAs from several individuals.


title: Global transcriptional profiling of Saccharomyces cerevisiae treated with allicin

status: Public on Jun 23 2008

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

summary: We employed CapitalBio Corporation to investigate the global transcriptional profiling of Saccharomyces cerevisiae  treated with allicin.

overall_design: S. cerevisiae strain L1190 was incubated in a rotary shaker. Subsequently, allicin was added to the culture and DMSO to the control. Then, the yeast cells were further incubated for a certain time and total RNA was extracted by a hot acidic phenol method. The experimental sample and control sample were incorporated and dissolved in  hybridization solution after labelled. Arrays hybridization was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight and washed with two consecutive solutions. Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software. A space- and intensity-dependent normalization based on a LOWESS program was employed.


title: Analysis of AML/MDS patients with 11q/MLL amplification

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

summary:
AML/MDS patients carrying 11q amplifications involving the mixed lineage leukemia gene (MLL) locus are characterized by a complex aberrant karyotype (CAK) frequently including deletions within 5q, 17p and 7q, a later onset and fast progression of the disease with extremely poor prognosis. We and others have shown that the MLL gene is overexpressed in amplified cases; however, in most of the cases the amplified region is not restricted to the MLL locus. In the present study we investigated 19 patients with AML/MDS and MLL gain/amplification. By means of array CGH performed in 12 patients we were able to delineate the minimal deleted regions within 5q, 17p and 7q and identified three independent regions 11q/I-III that were amplified in all cases. Gene expression profiles established in 15 cases (GSE10258) were used to define candidate genes within these regions. Interestingly, analysis of our data suggests an interdependency of loss of 5q and 17p and expression of genes present in 11q23-25. Furthermore, we demonstrate that the gene expression signature can be used to discriminate AML/MDS with MLL amplification from several other types of AML, thus, indicating specific pathogenesis present in this entity.
Keywords: comparative genomic hybridization; array CGH

overall_design:
In this study, aCGH analysis performed on 12 DNA samples derived from patients with AML, preselected for the presence of MLL amplifications, were analysed on a submegabase resolution BAC array. No replicates, no dye swap was done.
Gene expression profiling performed for 15 AML patients (GSE10258).