title: Differential gene expression in Roseburia inulinivorans grown on inulin and starch

city: Aberdeen

first: Gill

last: Campbell

address: Greenburn Road

department: Rowett Institute of  Nutrition and Health

institute: University of Aberdeen

summary: Roseburia inulinivorans is a recently identified motile representative of the Firmicutes that contributes to butyrate formation from a variety of dietary polysaccharide substrates in the human large intestine. Microarray analysis was used here to investigate substrate-driven gene expression changes in R. inulinivorans A2-194.  A cluster of fructo-oligosaccharide (FOS)/inulin utilisation genes induced during growth on inulin included one encoding a b-fructofuranosidase protein that was prominent in the proteome of inulin-grown cells. This cluster also included a 6-phosphofructokinase and an ABC transport system, while a distinct inulin-induced 1-phosphofructokinase was linked to a fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS II transport enzyme). Real-time PCR analysis demonstrated that the b-fructofuranosidase and adjacent ABC transport protein showed greatest induction during growth on inulin, whereas the 1-phosphofructokinase enzyme and linked PTS II transport system were most strongly up-regulated during growth on fructose, indicating that these two clusters play distinct roles in the utilization of inulin.  The R. inulinivorans B-fructofuranosidase was over-expressed in E. coli and shown to hydrolyse fructans ranging from inulin down to sucrose, with greatest activity on fructo-oligosacharides. Genes induced on starch included the major extra-cellular a-amylase and two distinct a-glucanotransferases together with a gene encoding a flagellin protein. The latter response may be concerned with improving bacterial access to insoluble starch particles.

overall_design: RNA was purified from mid-exponential phase (OD650 = 0.4) cultures of R. inulinivorans grown on basal YCFA supplemented with a single substrate of either starch or inulin using the RNeasy RNA purification kit (Qiagen), and the mRNA component enriched using the MICROBExpress system (Ambion). The purified RNA (1 ug) was labelled by reverse transcription (Amersham), employing random nonamer extension incorporating either dCTP-Cy3 or dCTP-Cy5 dyes. In order to ensure reproducibility, and to obtain statistically significant results, the dye labelling was swapped for a second hybridisation. RNA purified from a separate biological replicate was labelled and hybridised twice in the same way.

first: Karen

last: Scott

first: Jenny

last: Martin

first: Christophe

last: Chassard

first: Marlene

last: Clerget

first: Joanna

last: Potrykus

first: Claus-Dietar

last: Mayer

first: Pauline

last: Young

first: Garry

last: Rucklidge

first: Alan

middle: G

last: Ramsay

first: Harry

last: Flint


title: Saccharomyces cerevisiae grown in nitrogen depletion with oligodT priming

status: Public on Jul 20 2010

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

country: USA

institute: Yale University

summary:
Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development.
Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences.

overall_design: Saccharomyces cerevisiae S288c was grown on two different media and two different primers were used for reverse transcription: oligo(dT) and Multi-Targeted Primer [MTP] protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2). Two biological replicates and dye swapping

first: Jeffrey

middle: P

last: Townsend


title: Cell of origin influences molecular and functional properties of murine induced pluripotent stem cells

status: Public on Jul 19 2010

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

type: Methylation profiling by genome tiling array

summary:
Induced pluripotent stem cells (iPSCs) have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPSCs generated from different cell types are molecularly and functionally similar. Here, we show that iPSCs obtained from fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPSCs into embryoid bodies (EBs) and different hematopoietic cells. Importantly, continuous passaging of iPSCs largely attenuates these differences. Our results suggest that low-passage iPSCs retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and  ltered differentiation capacity. These observations might affect ongoing attempts to use iPSCs for disease modeling and also could be exploited for potential therapeutic applications to enhance differentiation into desired cell lineages.

Keywords: DNA methylation profiling

overall_design: Direct comparison of DNA methylation in iPS cells derived from different tissues

middle: E

first: Jose

middle: M

last: Polo

first: Ari

last: Melnick

first: Konrad

last: Hochedlinger


title: DNA methylation data from mouse iPS cells, ES cells, and ntES cells

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

summary:
Genome-wide DNA methylation was studied to determine whether iPS cells retain epigenetic memory at loci associated with its tissue of origin.
We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in mouse iPS cells.

overall_design: We isolated genomic DNA from mouse stem cells and hybridized to custom-designed Nimblegen microarrays (Me and CHARM arrays).

first: Kitai

last: Kim

first: George

middle: Q

last: Daley

first: Andrew

last: Feinberg


title: Comparative genome hybridization of meningococcal isolates using 1 color microarray

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

summary: Meningococcal strains from different serogroups and different clonal complexes were compared using cGH analyses in a one color experiment.

overall_design: DNA isolated from the various strains were compared using a single color microarray.


title: Concerted action of Helios and Ikaros balances the strength of B cell receptor signaling and controls the expression of inositol 5-phosphatase SHIP

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary:
Inositol 5-phosphatase SHIP is differentially expressed in Ikaros and Helios deficient cells. In the absense of Ikaros SHIP is upregulated where as in the absense of Helios it is downregulated. Ikaros binds to the promoter of the SHIP gene.
Article provides insight into the mechanisms of action Ikaros employs to regulate BCR signaling.

overall_design: Two replicates of Ikaros deficient and wild type DT40 avian B cells.

first: Jukka

last: Alinikula

first: Kalle-Pekka

last: Nera

first: Olli

last: Lassila


title: Gene expression based analysis of CroV infection of Cafeteria roenbergensis

status: Public on Jul 18 2010

city: Plymouth

first: Michael

middle: James

last: Allen

address: Prospect Place

country: United Kingdom

institute: Plymouth Marine Laboratory

summary: In this study, total RNA was extracted from cultures of Cafeteria infected with the Cafeteria roenbergensis virus BV-PW1 (CroV) and hybridised to a CroV microarray in order to determine the temporal expression profile during infection.

sample_organism:
Cafeteria roenbergensis
Cafeteria roenbergensis virus BV-PW1

overall_design: A straightforward measure of whether each spot was on or off was determined as the infection progressed starting at 0 h post infection (control), then 1, 2, 3, 6, 12, 24, 48 and 72 h pi. Oligonucleotides 50-70 bp in length were designed for 452 predicted CroV ORFs and printed onto amino silane treated glass slides.

middle: J

first: Matthias

last: Fischer


title: Expression analysis of Meiotic drive system in Aedes aegypti during spermatogenesis

status: Public on Jul 21 2010

city: Notre Dame

first: Dongyoung

last: Shin

state: IN

address: Galvin Science building

department: Biology

institute: Universoty of Notre Dame

summary:
Investigation of whole genome gene expression level changes of testes in the meiotic drive system in aedes aegypti during spermatogenesis compared to non drive strain.
The meiotic drive system in Aedes aegypti causes the female determining chromosome to fragment during spermatogenesis.

overall_design: A six chip study using total RNA from three separately extracted non driving strain testes of Aedes aegypti and three separately extracted meiotic drive strain testes of Aedes aegypti.

first: David

middle: W

last: Severson


title: Comparative genome hybridization of meningococcal isolates II

summary: Meningococcal strains from different serogroups and different clonal complexes were compared using cGH analyses

overall_design: DNA isolated from the various strains were compared using a common reference design where the common reference comprised of a pool of all individual DNA´s.


title: Adaptation of Geobacter sulfurreducens to Overcome the Loss of a Key Periplasmic c-Type Cytochrome

status: Public on Jul 22 2010

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

summary:
ppcA is a member of a family of small, periplamic c-type cytochromes in Geobact sulfurreducens.  The ppcA mutant displays displays a growth defect on ferric citrate medium, but the mutant has been adapted to grow to near wild-type levels on ferric citrate.  The aim of this study was to elucidate gene expression changes responsible for this adaptive growth.
Keywords: cell type comparison

overall_design: Three biological replicates were hybridized in duplicate on 12K Combimatrix sense-detecting arrays, the experiment (ppcA mutant) was labeled with Cy5, and the control (wildtype) was labeled with Cy3.

first: Laurie

middle: N

last: DiDonato

first: Raymond

last: DiDonato Jr.

first: Kelly

last: Nevin

first: Brad

middle: L

last: Postier

first: Anna

last: Liu

first: Bo

last: Xu

first: Trevor

last: Woodard

middle: R


title: Neurospora crassa early sexual development with oligod(T) priming

status: Public on Jul 17 2010

first: Francesc

last: Lopez

overall_design: Neurospora crassa mat A FGSC#2489 2 developmental stages and oligo(dT) primers.

first: Jeffrey

last: Townsend


title: Patterns of microRNA Expression in Non-Human Primate

status: Public on Jul 16 2010

city: Bethesda

first: Andrew

last: Lewis

address: 29 Lincoln Drive

department: Division of Viral products

institute: Food and Drug Adminstration

summary:
MicroRNAs (miRNAs) are small noncoding RNAs that negatively regulate gene expression post-transcriptionally. They play a critical role in developmental and physiological processes and have been implicated in the pathogenesis of several diseases including cancer. To identify miRNA signatures associated with different stages of neoplastic development, we examined the expression profile of 776 primate miRNAs in the following cells: primary African green monkey kidney (pAGMK) cells; spontaneously immortalized, non-tumorigenic, low-passage VERO cells (10-87 LP); tumorigenic, high-passage VERO cells (10-87 HP); and a cell line (10-87 T) derived from a 10-87 HP cell tumor xenograft in athymic nude mice.  When compared with pAGMK cells, the majority of miRNAs were expressed at lower levels in 10-87 LP, 10-87 HP, and 10-87 T cells. We identified 10 up-regulated miRNAs whose level of expression correlated with VERO cell evolution from a non-tumorigenic phenotype to a tumorigenic phenotype.

Several miRNAs that were components of the tumorigenic phenotype-specific signatures in our AGMK model are also found in a variety of human tumors. This may prove to be of general relevance to the biology of neoplastic development as it occurs both in vivo as well as in vitro. In addition, one or more of these miRNAs could be potential biomarkers for the expression of the tumorigenic phenotype of VERO cells.

platform_organism:
Lemur catta
Ateles geoffroyi
Lagothrix lagotricha
Macaca mulatta
Macaca nemestrina
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Saguinus labiatus

overall_design:
The spontaneousely transformed VERO cells, non-tumorigenic, were pasasged at low density in culture up to 250. The high passage (p250) was found to be tumorigenic. The cell line from xenograft of high passage was also established. We then evaluated patterns of miRNA expression in pAGMK cells and in derivatives of the 10-87 VERO cell line (10-87 LP cells, 10-87 HP cells, and 10-87 T cells) in an attempt to identify the miRNAs whose altered expression might correlate with, and perhaps be involved in, the evolution of the neoplastic phenotypes that occurred during passage of these AGMK cells in tissue culture.

performed high-throughput miRNA profiling to audit the expression level of miRNAs in pAGMK cells and in VERO cells at non-tumorigenic and tumorigenic stages of neoplastic development. The analysis involved pAGMK cells, non-tumorigenic 10-87 low-passage VERO cells (10-87 LP) tumorigenic, high-passage VERO cells (10-87 HP) and a cell line (10-87 T) derived from a 10-87 HP cell tumor xenograft in athymic nude mice.

first: Belete

last: Teferedegne

first: Haruhiko

last: Murata

first: Mariam

last: Quiñones

first: Keith

last: Peden

last: Lewis Jr


title: The response of Desulfotomaculum reducens MI-1 to U(VI) exposure: a transcriptomic study

status: Public on Jul 15 2010

city: Neuchâtel

first: Pilar

last: Junier

address: Rue Emile-Argand 11

department: Institute of Biology

country: Switzerland

institute: University of Neuchâtel

summary: Desulfotomaculum reducens is the first Gram-positive sulfate- and metal- reducing bacterium for which the transcriptomic response to uranium exposure has been evaluated. The genes upregulated during fermentative growth in the presence of U(VI) as compared to its absence included those encoding for proteins involved in respiration such as NADH quinone oxidoreductase and heterodisulfide reductase. This finding suggested that electrons were shuttled to the electron transport chain during fermentation which points to the reduction of U(VI) as a metabolic process. While U(IV) is typically insoluble and readily removable by filtration, U(IV) produced during active growth was not retained by a 0.2 µm pore size filter and filtration was not sufficient to differentiate between U(VI) and U(IV).  In addition, genes involved in iron homeostasis were upregulated in the presence of uranium, which was consistent with the upregulation of genes involved in c-type cytochrome biogenesis. Despite the upregulation of cytochrome biosynthesis genes, the sole c-type cytochrome encoded in the genome was not differentially expressed. Finally, genes encoding metal efflux pumps were also upregulated indicating the toxic nature of uranium. Analysis of the time-dependent gene expression showed that sporulation was the dominant process at the early stationary phase and that the presence of U at that stage did not impact expression.

overall_design: This data set is a time course comparing sulfate and uranium reduction with fermentative growth.

first: Rizlan

last: Bernier-Latmani


title: Nitrosomonas europaea expression analysis of biofilm growth and biofilms exposed to phenol and toluene

city: Corvallis

first: Ellen

last: Lauchnor

state: OR

address: 102 Gleeson Hall

department: School of Chemical, Biological and Environmental Engineering

institute: Oregon State University

summary: The physiological and transcriptional response of Nitrosomonas europaea biofilms to phenol and toluene was examined and compared to suspended cells.  Biofilms were grown in Drip Flow Biofilm Reactors under continuous flow conditions of growth medium containing ammonia as growth substrate.  The responses of N. europaea biofilms to the aromatic hydrocarbons phenol and toluene were determined during short-term (3 h) additions of each compound to the biofilms.  Ammonia oxidation in the biofilms was inhibited 50% by 60 uM phenol and 100 uM toluene.  These concentrations were chosen for microarray analysis of phenol- and toluene-exposed N. europaea biofilms.  Liquid batch cultures of exponentially growing N. europaea cells were harvested alongside the biofilms to determine differential gene expression between attached and suspended growth of N. europaea.

overall_design:
Four sample groups of N. europaea cells were used in this study, with biological triplicates of each group.  Groups were:  Control (untreated) biofilms, phenol-exposed biofilms, toluene-exposed biofilms, and exponentially growing suspended cells.

Biofilms were grown in Drip Flow Biofilm Reactors containing 4 independent growth channels and subject to 2 hour inhibition tests.  During each experiment, 2 biofilm channels served as control with no inhibitor present and the other 2 biofilm channels were exposed to either 60 uM phenol or 100 uM toluene.  Nitrite production was monitored throughout the experiment, and the given concentrations of phenol and toluene resulted in 50% inhibition of ammonia oxidation by the biofilms.  Suspended cells were grown in batch reactors.

Three 4-plex NimbleGen microarray chips were used, and each chip contained one sample from each experimental group.

QC of samples was determined by spectrophotometric methods and using Agilent bioanalyzer traces to determine purity and integrity of RNA and cDNA.  A sample tracking report was used to verify the correct hybridization of each sample to the intended array.

first: Tyler

middle: S

last: Radniecki

first: Lewis

last: Semprini


title: Wnt/Ca2+/NFAT signaling maintains survival of Ph+ leukemia cells upon inhibition of Bcr-Abl

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

institute: University of Colorado, Denver

summary: Although Bcr-Abl kinase inhibitors have proven effective in the treatment of chronic myeloid leukemia (CML), they generally fail to completely eradicate Bcr-Abl+ leukemia cells. To identify genes whose inhibition sensitizes Bcr-Abl+ leukemias to killing by Bcr-Abl inhibitors, we performed an RNAi-based synthetic lethal screen with imatinib in CML cells. This screen identified numerous components of a Wnt/Ca2+/NFAT signaling pathway. Antagonism of this pathway led to impaired NFAT activity, decreased cytokine production and enhanced sensitivity to Bcr-Abl inhibition. Furthermore, NFAT inhibition with cyclosporin A facilitated leukemia cell elimination by the Bcr-Abl inhibitor dasatinib and markedly improved survival in a mouse model of Bcr-Abl+ acute lymphoblastic leukemia (ALL). Targeting this pathway in combination with Bcr-Abl inhibition could improve treatment of Bcr-Abl+ leukemias.

overall_design: We utilized a genome-wide shRNA library in combination with microarray analysis to screen for gene targets in chronic myeloid leukemia cells that cooperate with imatinib.

first: Mark

middle: A

last: Gregory

first: Tzu

first: Paolo

last: Neviani

first: Francesca

last: Alvarez-Calderon

first: Christopher

last: Eide

first: Thomas

last: O'Hare

first: Vadyn

last: Zaberezhnyy

first: Richard

middle: T

last: Williams

first: Brian

last: Druker

first: Danilo

last: Perrotti

first: James

last: DeGregori


title: Roles for the Transcription Elongation Factor NusA in Both DNA Repair and Damage Tolerance Pathways in Escherichia coli

status: Public on Jul 14 2010

city: Boston

first: Diogo

middle: M.

last: Camacho

address: 44 Cummington Street

department: Biomedical Engineering

institute: Howard Hughes Medical Institute

summary: Here we report our observations that have led us to propose that the transcription elongation factor NusA promotes a novel class of transcription-coupled repair (TCR) in addition to its previously proposed role in recruiting translesion synthesis (TLS) DNA polymerases to gaps encountered during transcription. Earlier we have reported that NusA physically and genetically interacts with the TLS DNA polymerase DinB (DNA pol IV). We find that Escherichia coli nusA11(ts) mutant strains, at the permissive temperature, are highly sensitive to nitrofurazone (NFZ) and 4-nitroquinolone-1-oxide but not to ultraviolet radiation. Gene expression profiling suggests this sensitivity is unlikely to be due to an indirect effect on gene expression affecting a known DNA repair or damage tolerance pathway. We demonstrate that an N2-furfuryl-dG (N2-f-dG) lesion, a structural analog of the principal lesion generated by NFZ, blocks transcription by E. coli RNA polymerase (RNAP) when present in the transcribed strand, but not when present in the non-transcribed strand. Our genetic analysis suggests that NusA participates in a nucleotide excision repair (NER)-dependent process to promote NFZ resistance. We provide evidence that transcription plays a role in the repair of NFZ-induced lesions through the isolation of RNAP mutants that display altered ability to survive NFZ exposure. We propose that NusA participates in a novel class of TCR involved in the identification and removal of a class of lesion, such as the N2-f-dG lesion, which are accurately and efficiently bypassed by DinB in addition to recruiting DinB for TLS at gaps encountered by RNAP.

overall_design: Wild-type and nusA11 samples were analyzed, with 3 replicates per sample.


title: Steady State Thermal Acclimation in the Eurythermal Goby fish, Gillichthys mirabilis

city: Pacific Grove

first: Cheryl

last: Logan

state: CA

address: 120 Ocean View Blvd

institute: Stanford University

summary: The goal of this study was to identify transcriptional resonses to thermal acclimation in a highly eurythermal fish. Specifically, what are the  genes necessary to maintain homostasis at different temperatures and do these genes underlie any known acclimatory responses? Gillichthys mirabilis (goby fish) were acclimated to 3 temperatures (9C, 19C and 28C) for one month.  Gill tissue from 7-9 individuals were dissected and immediately flash frozen in liquid nitrogen.  Total RNA was extracted, reverse transcribed into cDNA, labeled with cy5 and hybridized against a common reference (cy3) on 2-color cDNA microarray developed for this species. Significant genes were determined by expression differences between groups (one-way ANOVA, FDR<0.05) .

overall_design: Common reference design

first: George

last: Somero


title: Expression analysis of zebrafish TIF1g-deficient, cdc73 deficient and double-deficient embryos

status: Public on Jul 13 2010

first: Xiaoying

last: Bai

address: 1 Blackfan Circle

institute: Children's Hospital Boston

summary: Investigation of whole genome gene expression level changes in zebrafish TIF1g-deficient, cdc73 deficient and double-deficient embryos, compared to the wild-type ebryos.

overall_design: A twelve-chip study using total RNA isolated from gata1-GFP positive cells (sorted by FACS) from 12 somite-stage wild type embryos, TIF1g morholino injected, Cdc73 morpholino injected and double morpholino injected embryos.

first: Leonard

middle: I

last: Zon


title: Chip-chip from E. coli MG1655 cells with different methods to detect SeqA and σ32 binding and causes of high background

status: Public on Jul 12 2010

city: Marburg

first: Torsten

last: Waldminghaus

address: Hans-Meerwein-Straße

department: Philipps-Universität Marburg

institute: Synmikro

type: Genome binding/occupancy profiling by genome tiling array

summary:
Reinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: non-unique sequences, incomplete reversion of crosslinks, washing with spin-columns and insufficient RNase treatment.
We used a publishd method giving a high background signal and a modified chromatin immunoprecipitation method which could greatly reduce the false positive rate and apply it to analyze genome wide binding of SeqA and σ32 binding in E. coli.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA polymerase binding in wt E. coli MG1655 with old method (two biological relpicates); comparison of SeqA-binding to wt with old and modified method (two biological replicates each); comparison of SeqA-binding with old and modified method to E. coli ΔseqA (one array each); comparison of crosslinked/reversed to non crosslinked E. coli chrom. DNA; σ32 binding at 30°C and 43°C (two biological replicates each); σ32 binding at 30°C and 43°C with shortened RNase digestion during ChIP (one array each).

first: Kirsten

last: Skarstad


title: Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice, aCGH 1

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

type: Genome variation profiling by genome tiling array

summary:
Genomic radiation signature illuminates low-dose effects with sharply reflected transcriptome in Ptch1-deficient medulloblastomas.
Cancer risks of low-dose radiation are of great concern especially in relation to rapidly increasing medical exposures; however, their accurate assessments cope with many challenges and difficulties, partly due to the inability to distinguish radiation-induced tumors from spontaneous ones.  Here, we analyzed the dose-dependent effect of radiation on medulloblastoma development in Ptch1 heterozygous mice on C3B6F1 background.  The incidence and latency of medulloblastoma increased and shortened with increasing radiation dose, respectively.  Amazingly, radiation contributed to tumorigenesis even at 50 mGy and 100% of mice got medulloblastoma with 1.5 Gy.  Loss of heterozygosity (LOH) analysis on a total of 164 tumors indicated that spontaneous tumors showed LOH in broad regions on chromosome 13, including Ptch1 and distally-extending telomeric portion (S-type).  In contrast, tumors developed after 3 Gy irradiation exhibited interstitial losses around Ptch1 (R-type).  A clear dose-dependent increase in the proportion of R-type tumor at intermediate doses suggested R-type to be a reliable radiation signature.  Array-CGH analysis indicated the R-type-specific copy-number reduction around Ptch1 and LOH-type-independent frequent gains of whole chromosome 6. Integrated expression microarray analysis indicated that expression levels of many genes within the altered genomic regions faithfully reflected the genomic copy-number changes.  Furthermore, it was also suggested that these expression changes in turn influenced on many other genes, such as Tgfb2 and Tgfb3, on widespread genomic regions.  This is the first demonstration that radiation-induced tumors developed after low-dose irradiation can be characterized quite precisely by interstitial deletion of Ptch1 and by associated gene expression profile.

overall_design: Twelve medulloblastomas were analyzed by array-CGH method.

first: Yuka

last: Ishida

first: Shizuko

last: Kakinuma

first: Kazutaka

last: Doi

first: Kazumi

last: Yamauchi

first: Mutsumi

last: Kaminishi

first: Seiji

last: Kito

first: Yuki

last: Ohta

first: Yoshiko

last: Amasaki

first: Hiroyuki

last: Moritake

first: Toshiaki

last: Kokubo

first: Mayumi

last: Nishimura

first: Tetsu

last: Nishikawa

first: Okio

last: Hino

first: Yoshiya

last: Shimada


title: mRNA Expression Profiling of pooled medulloblastoma samples

status: Public on Jul 09 2010

city: Heidelberg

first: Stefan

last: Pfister

address: INF 580

department: Molecular Genetics

institute: German Cancer Research Center

summary:
mRNA expression analysis of 4 different pools of medulloblastoma samples with characteristic cytogenetic aberrations

Keywords: Genetic modification

overall_design: Comparison of tumor RNA 1 (equally represented, pooled mRNA of tumors with cytogenetic aberration 1)  versus tumor RNA (equally represented, pooled mRNA of tumors without cytogenetic aberration 1). Whole-genome screening for differential gene expression.

first: Marc

last: Remke

first: Till

last: Milde


title: Identification of follicular marker genes as pregnancy predictors for human IVF

status: Public on Jul 10 2010

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: Multiple pregnancy represents an important health risk to both mother and child in fertility treatment. To reduce a high twin rate, restriction to one embryo transfer is needed. Morphological evaluation methods for predicting embryo viability has significant limitations. Tight communication exists between the follicular cells (FCs) and the oocyte; therefore, developmental competence may be determined by markers expressed in the surrounding FCs. In this study, cells were recovered on a per-follicle basis by individual follicle puncture. Hybridization analysis using a custom-made complementary DNA microarray containing FC transcripts was performed. Genes expressed in FCs associated with good morphological transferred embryos were identified from follicles associated with a pregnancy outcome (pregnancy group) or no pregnancy (non-pregnancy group). Ten candidates from the Pregnancy group and three from the Non-pregnancy group were validated by qRT-PCR. The best predictors associated with pregnancy were UDP-glucose pyrophosphorylase-2 (UGP2) and pleckstrin homology-like domain, family A, member 1 (PHLDA1). Genes assessment showed no significant candidate genes associated with non-pregnancy outcome, but GA-binding protein transcription factor β1 (GABPB1) showed a tendency to be potentially more expressed in the non-pregnancy group. These markers could be related to granulosa luteinisation process and could be used to improve embryo selection for successful single embryo transfer.

platform_organism:
Homo sapiens
Bos taurus

overall_design: Two pools were made for the hybridizations. 7 patients who produced follicular cells from oocytes that resulted in a 100% pregnancy success rate (positive samples; n=9 follicles) were chosen for the competant pool and 7 patients who produced follicular cells from oocytes that resulted in a transferred embryo with unsuccessful pregnancy (negative samples; n=9 follicles) were chosen for the incompetant pool. The hybridization were done in dye-swap.

first: Mélanie

last: Hamel

first: Isabelle

last: Dufort

first: Claude

last: Robert

first: Marie-Claude

last: Léveillé

first: Arthur

last: Leader


title: Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice, aCGH 2

first: Takashi

last: Takabatake

overall_design: Three medulloblastomas were analyzed by array-CGH method.

first: Yuka

last: Ishida

first: Shizuko

last: Kakinuma

first: Kazutaka

last: Doi

first: Kazumi

last: Yamauchi

first: Mutsumi

last: Kaminishi

first: Seiji

last: Kito

first: Yuki

last: Ohta


title: Intracellular transcriptional adaptation of Mycobacterium tuberculosis complex (MTC) clinical isolates inside activated murine macrophages

city: Ithaca

first: David

last: Russell

state: NY

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

institute: Cornell University

summary:
This study uses microarray analyses to examine transcriptional responses of Mycobacterium tuberculosis complex clinical isolates to phagosomal cues encountered inside activated (IFN-gamma+LPS) murine bone marrow-derived macrophages 24hr post-infection. Transcript levels of intracellular mycobacteria were compared to extracellular bacteria of the same strain (An aliquot of the inoculum used to infect macrophages was incubated in the absence of macrophages for 24hr in an identical flask).
Set of arrays that are part of repeated experiments

Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed


title: R. microplus expression profiles of larvae pre-attachment and feeding adult female stages in B. indicus and B. taurus

city: Brisbane

first: Manuel

middle: Rodriguez

last: Valle

state: QLD

address: 665 Fairfield road, Yeerongpilly

department: Emerging Technologies

country: Australia

institute: DEEDI

summary:
Comparative microarray analysis of Rhipicephalus (Boophilus) microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and B. taurus cattle
Global analysis of gene expression changes in R. microplus during larval, pre-attachment and early adult stages of its life cycle feeding on Bos indicus and Bos taurus cattle were compared using gene expression microarray analysis. Among the 13 601 R. microplus transcripts from BmiGI Version 2 we identified 297 up and 17 down regulated transcripts were differentially expressed   between R. microplus feeding on tick resistant cattle [Bos indicus (Brahman)] compared to R. microplus feeding on tick susceptible cattle [Bos taurus (Holstein-Friesian)]. These include genes encoding enzymes involved in primary metabolism, and genes related to stress, defence, cell wall modification, cellular signaling, receptor and cuticle. Microarrays were validated by qRT-PCR analysis of selected transcripts including the validation of three housekeeping genes. The analysis of all tick stages under survey suggested a coordinated regulation of defence proteins, proteases, and protease inhibitors to achieve successful attachment and survival of R. microplus on different host breeds particularly Bos indicus cattle.

overall_design: The microarray was conducted by NimbleGen Systems Inc following the method reported by Saldivar [Saldivar L et al., Insect Mol Biol 2008, 17(6):597-606]. 10 samples: 2 larva, 2 pre-attachment larva in B. indicus and 2 in B. taurus, and 2 adult ticks in B. indicus and 2 in B. taurus

last: Rodriguez Valle

first: Cedric

last: Gondor


title: Saccharomyces cerevisiae grown in nitrogen depletion with MTP priming

city: West Haven

first: Francesc

last: Lopez

institute: Yale University

summary:
Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development.
Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences.

overall_design: Saccharomyces cerevisiae S288c was grown on two different media.

first: Jeffrey

middle: P

last: Townsend


title: Effects of clorgyline, a monoamine oxidase A inhibitor, on high grade prostate cancer cells

city: Stanford

first: Donna

last: Peehl

department: Department of Urology

institute: Stanford University School of Medicine

summary: Monoamine oxidase A (MAO-A), a mitochondrial enzyme that degrades monoamines including neurotransmitters, is highly expressed in basal cells of the normal human prostatic epithelium and in poorly differentiated (Gleason grades 4 and 5), aggressive prostate cancer (PCa). Clorgyline, an MAO-A inhibitor, induces secretory differentiation of normal prostate cells. We systematically assessed gene expression changes induced by clorgyline in E-CA cells using high-density oligonucleotide microarrays. Genes differentially expressed in treated and control cells were identified by Significance Analysis of Microarrays. Expression of genes of interest was validated by quantitative real-time polymerase chain reaction.

overall_design: time series design

first: Hongjuan

last: Zhao


title: Profiling antibody responses to M. tuberculosis proteins in TB suspects’ sera using full-proteome microarrays.

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: Understanding the immune response to tuberculosis requires greater knowledge of humoral responses.  To characterize antibody targets and the effect of disease parameters on target recognition, we developed a systems immunology approach that integrated detection of antibodies against the entire Mycobacterium tuberculosis proteome, bacterial metabolic and regulatory pathway information, and patient data.  Probing ~4,000 M. tuberculosis proteins with sera from >500 suspected tuberculosis patients worldwide revealed that antibody responses recognized ~10% of the bacterial proteome.  This result defines the immunoproteome of M. tuberculosis, which is rich in membrane-associated and extracellular proteins.  Most serum reactivity during active tuberculosis focused onto ~0.5% of the proteome.  Within this pool, which is selectively enriched for extracellular proteins (but not for membrane-associated proteins), relative target preference varied among patients.  The shift in relative M. tuberculosis protein reactivity observed with active tuberculosis defines the evolution of the humoral immune response during M. tuberculosis infection and disease.

overall_design: Peripheral blood was collected from prospectively enrolled TB suspects among subjects seeking care for pulmonary symptoms at clinics associated with national TB control programs in 11 countries.  M. tuberculosis proteome microarrays representing 4099 bacterial protein spots were probed with sera from 561 TB suspects.  Based on the final diagnosis, they belonged to two classes: TB (n=254) and Non-TB Disease (n=307).  In addition, healthy individuals negative to Latent TB Infection (LTBI neg, n=64) were also tested (negative control sera).  Each serum was tested with a single array and no replicate experiments were performed. The reactivity of a serum to an M. tuberculosis protein (reactivity call) was defined based on the distribution of negative control sera intensity for that protein using Z-statistics. Based on the distribution of reactivity calls, 27 outlier samples reacting with more than 20 proteins were excluded from further analysis. The association of reactivity calls of each protein with TB/NTBD status of TB suspects was determined by estimating odds ratio and 95% confidence interval.

first: Maria

last: Gennaro


title: ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-LSD1 or anti-SUZ12 antibodies on human HG18 Nimblegen promoter arrays

status: Public on Jul 08 2010

first: Miao-Chih

last: Tsai

address: 269 Campus Drive, CCSR 2140

summary:
Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes.  A 5’ domain of HOTAIR binds Polycomb Repressive Complex 2 (PRC2) while a 3’ domain of HOTAIR binds the LSD1/CoREST/REST complex.  The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1, and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, and thereby specify the pattern of histone modifications on target genes.
LSD1 and SUZ12 co-occupied on 721 genes in human foreskin fibroblasts. Coordinate loss of SUZ12 and LSD1 occupancy was caused by HOTAIR knockdown.

overall_design: Comparison occupancy of LSD1 and SUZ12 of siGFP and siHOTAIR foreskin fibroblasts on human HG18 promoter arrays. Human foreskin fibroblasts were transfected with siGFP or siHOTAIR. The cells were harvested and ChIP analysis with anti-LSD1 and anti-SUZ12 antibodies was performed.


title: Intracellular transcriptional adaptation of Mycobacterium tuberculosis complex (MTC) clinical isolates inside resting murine macrophages

summary:
This study uses microarray analyses to examine transcriptional responses of Mycobacterium tuberculosis complex clinical isolates to phagosomal cues encountered inside resting murine bone marrow-derived macrophages 24hr post-infection. Transcript levels of intracellular mycobacteria were compared to extracellular bacteria of the same strain (An aliquot of the inoculum used to infect macrophages was incubated in the absence of macrophages for 24hr in an identical flask).
Set of arrays that are part of repeated experiments

Keywords: Biological Replicate


title: Evaluation of the physiology of medaka for standardized toxicity tests of chemicals

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

summary: The “Fish Acute Toxicity Test” in the “OECD Guideline for Testing of Chemicals” is an essential test for environmental toxicity.  Here we have tried to evaluate the physiology of medaka during this test procedure by using genomics.  Genomics technology can provide genome-wide expression profiles of mRNA, and these profiles correspond to the physiology of organisms.  Thus, a comparison of mRNA expression profiles gives information on the reproducibility of experimental conditions.  Expression profiles of mRNA were measured for medakas maintained within the allowable range of the test conditions and also under extreme conditions beyond the guidelines limits. We confirmed the high physiological reproducibility of medaka kept in the recommended conditions of the “Fish Acute Toxicity Test” in the “OECD Guideline for Testing of Chemicals" from the expression profiles obtained under all experimental conditions except for the type of feeding.

overall_design:
This series contains gene expression profiles in medaka fish under 15 kinds of physiological conditions. Each physiological series included with 3 independent males and 3 independent felames, except Strain JPRI (GSM385865-GSM385868).

*** No processed data for Samples GSM385886, GSM385887. ***

first: Hitoshi

last: Iwahashi

first: Katsuyuki

last: Kishi

first: Katsunori

last: Suzuki

first: Yasuyuki

last: Hayashi


title: Mock or KSHV cells (BJABJ, BCBL, TIME and HUVEC) vs common reference (mixture of RNA from both infected and uninfected cells)

status: Public on Jul 07 2010

city: San Francisco

first: Sanjay

last: Chandriani

address: 513 Parnassus Avenue

institute: UCSF

type: Expression profiling by genome tiling array

summary:
Expression profiling of latently infected cells using a custom tiling microarray
HUVEC and TIME cells were infected BCBL-1-derived KSHV. Mock infected HUVEC and TIME cells served as controls for each of these two stably infected cells, respectively. BJAB cells served as uninfected controls for the BCBL-1 cells. KSHV-infected cells are induced to enter lytic cycle with valproate or Adenovirus-RTA. Cells were harvested at indicated time points and analyzed.

platform_organism:
Homo sapiens
Human herpesvirus 8 type M

overall_design: Three condition experiment: mock infected, latently infected cells and lytically infected. Three cell types (BJAB cells served as uninfected controls for the BCBL-1 cells).

first: Don

last: Ganem

first: Yiyang

last: Xu


title: Heritability of the expression of defense-related genes in the outer stem of Interior spruce (Picea glauca x engelmannii)

city: Vancouver

first: Dr. Kermit

last: Ritland

state: BC

address: 2424 Main Mall

department: Forest Sciences

institute: University of British Columbia

summary:
Inferring the heritability of gene expression is one of the main areas of the field of genetical genomics. With the possibility to treat the abundances of gene transcripts as a suite of quantitative traits, genetical genomics can make an extensive use of the microarray technology.
Here we extended a major method for estimating the heritability of a quantitative trait, single parent-offspring regression, to assess the heritability of the expression of genes with two-channel microarrays. In a series of maternal parent-offspring pairs of Interior spruce (Picea glauca x engelmannii, our focus in the outer stem tissues is the expression of defense-related genes, the heritability of which can affect fitness and necessary for evolution by natural selection.

overall_design:
Parent-offspring pairs of Interior spruce planted as a part of Tree Breeding and Improvement Program of the Forest Genetics Section, British Columbia Ministry of Forests and Range, Prince George, BC, Canada (http://www.for.gov.bc.ca/hre/forgen/interior/spruce.htm#1) were used. A total of 30 trees, comprising 15 parent-offpsring pairs were sampled. These include15 offsprings and 15 maternal parents (grafts), which were planted within ~ 1Km range west (122º 42’ 43’’W, 53º 45’41’’N) of the offsprings, hence grown in a relatively similar environment. The bark and the attached phloem were separated from inner layers in the mid-morning hours of June 25, 2008, flash-frozen in liquid nitrogen, and transferred into separate containers.
A chain design was decided for gene expression profiling (a total of 45 slides) using the Treenomix third generation cDNA microarray platform (GEO accession #: GPL5423). Array350 kit (Genisphere, Hatfield, USA) was chosen for the microarray hybridizations. The slides were scanned with a ProScanArray scanner (PerkinElmer, Downers Grove, IL, USA), and the scanned TIF images were processed by ImaGene software (BioDiscovery, Inc., El Segundo, CA, USA) to quantify spot signals. Normalization was done between arrays using variance stabilizing (VSN) method for ratio based analysis of the expression data.

first: Rokneddin

last: Albouyeh

first: Richard

last: White

first: Mack

last: Yuen

first: Carol

first: Kermit


title: Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high resolution tiling arrays

city: Montreal

first: Adnane

last: Sellam

address: 6100 Royalmount

department: Anatomy and Cell Biology

institute: Adnane Sellam

summary: Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. Here we have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to C. albicans pathogenicity, including biofilm, lab-grown yeast and serum-induced hyphae as well as cells isolated from the mouse caecum. This work provides a genome-wide experimental validation for a large number of predicted ORFs for which transcription had not been detected by other approaches. Additionally, we identified more than 2000 novel transcriptional segments, including new ORFs and exons, non-coding RNAs (ncRNA) as well as convincing cases of antisense gene transcription. We also characterized the 5’- and 3’-untranslated regions (UTR) of expressed ORFs, and established that genes with long 5’UTRs are significantly enriched in regulatory functions controlling filamentous growth. Furthermore, we found that genomic regions adjacent to telomeres harbor a cluster of expressed ncRNAs. To validate and confirm new ncRNA candidates, we adapted an iterative strategy combining both genome-wide occupancy of the different subunits of RNA polymerases I, II and III, and expression data. This comprehensive approach allowed the identification of different families of ncRNA. In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to a discovery of new ORF and non-coding genetic elements.

overall_design:
We have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to Candida albicans pathogenicity, including biofilm, lab-grown yeast and serum-induced hyphae as well as cells isolated from the mouse caecum. We also adapted a strategy in which genome-wide occupancy of different subunits of RNA polymerases (RNAP) I, II and III, is combined with expression data to annotate ncRNAs resulting from real transcriptional events. For this purpose we have performed ChIP-chip of subunits that represent the three RNAP machines in C. albicans cells growing in rich media (YPD) at 30°C.

In this study, we performed peak detection only for RNA Polymerase III (Rpc82p). All detected peaks and their genomic features are included as a supplementary file on the Sample record (GSM561024).

first: Hervé

last: Hogues

first: Christopher

last: Askew

first: Faiza

last: Tebbji

first: Marco

last: vanhetHoog

first: Hugo

last: Lavoie

last: Kumamoto

first: Malcolm

last: Whiteway

first: André

last: Nantel


title: Resting versus activated T cells

first: john

last: Iacomini

address: 221 Longwood Ave. LMRC 303

department: renal division

institute: brigham and womens hospital

summary: miRNA profiling of resting and activated T cells

overall_design: Two condition experiment, resting versus activated T cells, measured pooled samples from three independent stimulations

first: John

first: Jessamyn

last: Bagley


title: Comparison of genes regulated by TviA in S. Typhi and Typhimurium

city: Davis

first: Sebastian

last: Winter

address: One Shields Ave

department: MMI

institute: UC Davis

summary: Bacterial pathogens causing systemic disease commonly evolve from organisms associated with localized infections but differ from their close relatives in their ability to overcome mucosal barriers by mechanisms that remain incompletely understood. Here we investigated whether acquisition of a regulatory gene, tviA, contributed to the ability of Salmonella enterica serotype Typhi to disseminate from the intestine to systemic sites of infection during typhoid fever. To study the consequences of acquiring a new regulator by horizontal gene transfer, tviA was introduced into the chromosome of S. enterica serotype Typhimurium, a closely related pathogen causing a localized gastrointestinal infection in immunocompetent individuals. Modulation of gene expression by TviA in serotype Typhi and Typhimurium was determined by profiling and found to be very comparable. Expression of flagellin, a pathogen associated molecular pattern (PAMP), was repressed by TviA when bacteria were grown at osmotic conditions encountered in tissue, but not at higher osmolarity present in the intestinal lumen. TviA-mediated flagellin repression enabled bacteria to evade sentinel functions of human model epithelia and resulted in increased bacterial dissemination to the spleen in a chicken model.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The effect of tviA on gene expression profiles in S. Typhimurium was determined by comparing a tviA expressing strain (IR715(pTVIA1) with a control strain harboring the empty cloning plasmid (IR715 (WSK29). S. Typhimurium strains were cultured in SOB broth (low salt), a condition known to induce expression of TviA. Total RNA was extracted from one cultures of each strain. cDNA was differentially labeled with Alexa Fluor 555 and 648 (including a technical replicate in which the labeling of the samples was inversed [flip dye]), respectively and competitively hybridized on S.Typhimurium arrays (PFGRC, version 4). GSM509223 has 4 GPR files which are technical replicates of a competitive hybridization of cDNA from IR715(pWSK29) and IR715(pTVIA1). The profiles obtained from S. Typhimurium was compared with the corresponding data set for S. Typhi (comparing a (delta)tviB-vexE (tviBCDEvexABCDE) mutant and a (delta)viaB (tviABCDEvexABCDE) mutant) from GEO accession number GSE15752.

middle: E

first: Andreas

last: Baumler


title: Azole Resistance Mechanism in Candida glabrata

city: Bethesda

first: Huei-Fung

last: Tsai

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

summary: Microarray was used to analyze azole resistance of Candida glabrata oropharyngeal isolates from 7 hematopoietic stem cell transplant recipients receiving fluconazole prophylaxis. Transcriptional profiling of the sequential-paired clinical isolates by microarray revealed 19 genes upregulated in the majority of resistant isolates compared to their paired-susceptible isolates. All seven resistant isolates had greater than two fold upregulation of CgPDR1, a master transcriptional regulator of PDR network, and all 7 resistant isolates showed upregulation of known CgPDR1-target genes. The altered transcriptome can be explained in part by the observation that all 7 resistant isolates had acquired a single nonsynonymous mutation in their CgPDR1 ORF. Four mutations occurred in the regulatory domain (L280P, L344S, G348A, S391L) and one in the activation domain (G943S) while two mutations (N764I, R772I) occurred in an undefined region. Association of azole resistance and the CgPDR1 mutations was investigated in the same genetic background by introducing the CgPDR1 sequences from one sensitive and five resistant isolates into a laboratory azole-sensitive strain (cgpdr1) via integrative transformation. The cgpdr1 strain was restored to wild-type fluconazole susceptibility when transformed with CgPDR1 from the susceptible isolate but became resistant when transformed with CgPDR1 from the resistant isolates. However, despite the identical genetic background, upregulation of CgPDR1 and CgPDR1-target genes varied between the 5 transformants, independent of the domain locations in which the mutations occurred. In sum, gain-of-function mutations in CgPDR1 not only contributed to the clinical azole resistance but different mutations had varying degrees of impact on the CgPDR1-target genes.

overall_design: Two groups (C1S/84 and C16R/84) consisted of 4 biological replicates in which a complemented strain sample was paired with the laboratory wild type strain 84 sample. Each group included 1 reciprocally labeled sample.


title: miRNAs expression in the splenic CD4+ T cells and B cells isolated from MRL/lpr mice at 5 and 16 weeks of age

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

country: China

institute: Renji Hospital, JiaoTong University School of Medicine

summary:
To identify any differentially expressed miRNAs in the CD4+ T cells of lupus.
MicroRNAs (miRNAs) have been implicated as fine-tuning  regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including human lupus.  By using high-throughput microRNA profiling analysis, we identified that two miRNAs (miR-21 and miR-148a) overexpressed in CD4+ T cells from both lupus patients and lupus-prone MRL/lpr mice,which promote cell hypomethylation by repressing DNA methyltransferase 1 (DNMT1) expression.

overall_design:
We isolated the splenic CD4+ T cells and B cells  from MRL/lpr mice at 5 and 16 weeks of age.Cells were collected and total RNA was extracted for the TaqMan® Low Density Assay v2.0
Normalization was performed with snoRNA202, reference snRNAs for mouse.Comparative real-time PCR was performed in triplicate, including no-template.controls. Relative expression was calculated with the comparative cycle threshold method.


title: KIM5 intracellular expression profiling

city: Stony Brook

first: Hana

middle: S.

last: Fukuto

address: CMM rm350, Stony Brook University

department: Microbiology and Molecular Genetics/Center for Infectious Diseases

institute: Stony Brook University

summary: Microarrays were used to determine the transcriptional profile of Y. pestis that is  growing inside macrophages.  J774A.1 macrophage-like cells were infected with Y. pestis KIM5 and incubated in the presence of gentamicin in tissue culture media.  RNA was isolated from intracellular bacteria at various time points post infection.  Control bacteria were grown for 4 hours in tissue culture medium under the same conditions without macrophages or gentamicin.  The transcriptional profiles of intracellular Y. pestis at different time points were compared to those of control Y. pestis using the 70-mer oligonucleotide microarrays obtained from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute (Y. pestis microarray version 2).

overall_design: RNA from samples of Yersinia pestis KIM5 at 3 time points in were compared to 12 Yersinia pestis in DMEM for 4 hours.

last: Fukoto

first: Anton

last: Svetlanov

first: Lance

last: Palmer

first: Wali

last: Karzai

first: James

middle: B

last: Bliska


title: Effect of Rom1 silencing on gene expression in Entamoeba histolytica

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

institute: Stanford Uninversity

summary: Entamoeba histolytica trophozoites epigenetically silenced for ameobapore A (G3 parasites) were additionally silenced for the Rhomboid gene Rom1 (EHI_197460) using the mechanism outlined in Mirelman et al. Parasite. 2008 Sep;15(3):266-74 (PMID 18814693). Rom1 silencing was confirmed by RT-PCR. Gene expression in these parasites was compared to that of the parent G3 strain.

overall_design: RNA was isolated from axenically grown G3 and Rom1 silenced parasites, and hybridized to a custom Affymetrix array for E. histolytica. Two biological replicates were performed for each condition.

first: Leigh

last: Baxt

first: Rivka

last: Bracha

first: Elena

last: Rastew

first: David

last: Mirelman

first: Upinder

last: Singh


title: Basal in vitro transcriptomes of Mycobacterium tuberculosis complex (MTC) clinical isolates

last: Russell

summary: This study uses microarray analyses to examine baseline gene expression profiles for Mycobacterium tuberculosis complex clinical isolates relative to reference strain CDC1551 during log phase growth in vitro in 7H9 broth. For this in vitro analyses, log-phase mycobacteria in starter cultures grown to mid-log from frozen stocks were inoculated into 7H9-OADC medium in 25-cm2 vented flasks at an OD of ~0.05 and grown without shaking for ~1 week to an OD of ~0.5-0.6.

overall_design: Computed


title: ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-H3K4me2, anti-LSD1  or anti-SUZ12 antibodies on HOX tiling array

first: Miao-Chih

institute: Stanford University

summary:
Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes.  A 5’ domain of HOTAIR binds Polycomb Repressive Complex 2 (PRC2) while a 3’ domain of HOTAIR binds the LSD1/CoREST/REST complex.  The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1, and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, and thereby specify the pattern of histone modifications on target genes.
Coordinate loss of SUZ12 and LSD1 occupancy caused by HOTAIR knockdown were concentrated in proximal promoters of HOXD genes. These regions correspondingly lost H3K27me3 and gained H3K4me2, the respective histone methylation products of PRC2 and LSD1 complexes.

overall_design: Comparison occupancy of LSD1 and SUZ12 of siGFP and siHOTAIR foreskin fibroblasts on HOX tiling array. Human foreskin fibroblasts were transfected with siGFP or siHOTAIR. The cells were harvested and ChIP analysis with anti-H3K4me2, anti-LSD1 and anti-SUZ12 antibodies was performed.


title: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous, laboratory fermentation

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail.  In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory, namely two wheat and two spelt fermentations with daily back-slopping. Hereto, the in-house developed functional gene LAB microarray was used, representing 406 genes that play a key role in sugar and nitrogen metabolism, functional metabolite production, stress responses and health and safety characteristics. The results reveal the activation of different key metabolic pathways, the ability to use different energy sources, and successful acid and oxidative stress responses. Also, a new algorithm was developed to compute a net expression profile for each of the represented genes, thereby exceeding the species level.

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

overall_design: The labeled aRNA of the sourdough fermentation samples was hybridized using a loop design, i.e. subsequent samples (e.g. 27 h and 51 h, 51 h and 75 h etc.) were hybridized together on the microarray and the loop was closed by hybridizing the last sample with the first.

first: Joke

last: Allemeersch

first: Stefan

last: Weckx

first: Roel

last: Van der Meulen

first: Gino

last: Vrancken

first: Luc

last: De Vuyst

first: Paul

last: Van Hummelen


title: Gene expression analysis of HEK293T cells after CHMP5 gene modulation

first: maria

last: shahmoradgoli

state: BW

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Microarray-based gene expression analysis identified genes differentially expressed in HEK293T cells after CHMP5 gene modulation.

overall_design: In this study,  HEK293T cells, silenced  for CHMP5 using sh-CHMP5  was compared to genome wide expression changes when compared to cellular transfections with a  sh-luciferase control by Significance Analysis of Microarray data. Further, overexpression of CHMP5 using the vector pCMV_CHMP5 was compared to cellular transfections with an empty vector pCMV in the cell line HEK293T

first: Maria

last: Shahmoradgoli

first: Felix

last: Engel


title: Expression Profile of Primary Colorectal Cancers and associated Liver Metastases

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

summary:
Comparison of expression profiles of primary colorectal cancers with liver metastases of the same patient. Additionally, expression data of normal colon and liver tissue.
Abstract of publication will be included upon publication

Keywords: expression profiling, colorectal cancer, colon cancer, liver metastasis, normal colonic tissue, normal liver tissue

overall_design: RNA of 18 primary colorectal cancers, 18 matched liver metastases, 7 normal colon epithelium samples and 5 normal liver tissue samples hybridized on Human Sentrix-6 V2 (Illumina)

first: Bernhard

middle: F

last: Radlwimmer

first: Peter

last: Lichter


title: Paired non-cancerous and cancerous miRNA expression of esophageal adenocarcinoma and squamous cell carcinoma patients

first: Ewy

last: Mathe

address: 37 Convent Dr.

institute: National Cancer Institute/National Institutes of Health

summary: Identifying biomarkers predictive for early esophageal cancer detection is critical considering the dismal survival rates.  We investigated the involvement of microRNAs (miRNAs), their utility as biomarkers, and their association with survival in esophageal cancer, including Barrett’s associated and sporadic adenocarcinoma (ADC), and squamous cell carcinoma (SCC).  MiRNA expression was measured in cancerous and adjacent non-cancerous tissue pairs collected from 76 US and Japanese patients enrolled in 3 distinct cohorts.  In ADC patients, miR-21, miR-194, miR-293, and miR-223 expression was elevated, while miR-375 and miR-203 expression was reduced in cancerous tissue compared to non-cancerous tissue.   Increased levels of miR-192 and miR-194 were observed in Barrett’s associated compared to sporadic ADC cancerous tissue. In SCC patients, miR-21, miR-181b, miR-155, and miR-146b expression was elevated while miR-375 and miR-203 levels were reduced in cancerous tissue compared to non-cancerous tissue.  Significantly, elevated mir-21 expression in non-cancerous tissue was strongly associated with worse prognosis, independent of nodal status and age.  Sample classification using miRNA expression yielded accuracies as high as 86% for diagnosis and 78% for Barrett’s esophagus status.  Our results highlight that miRNAs are deregulated in esophageal carcinogenesis and Barrett’s esophagus, and that their expression is associated with survival in cancer patients.  Sample classification using miRNA expression demonstrates their potential utility as biomarkers for esophageal carcinoma diagnosis.

platform_organism:
Homo sapiens
Mus musculus

overall_design: MiRNA microarray expression was measured using miRNA microarray chips version 3 (Ohio State University) in 44 SCC cases and 32 ADC cases, of which 18 were also diagnosed with Barrett’s esophagus.

last: Mathé

first: Giang

middle: H

last: Nguyen

first: Elise

middle: D

last: Bowman

first: Anuradha

last: Budhu

first: Aaron

middle: J

last: Schetter

first: Rosemary

last: Braun

first: Chang-Gong

last: Liu

first: Xin

middle: W

last: Wang

first: Carlo

middle: M

last: Croce

first: Curtis

middle: C

last: Harris


title: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation

first: Rekin's

last: Janky

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

first: Joke

last: Allemeersch

first: Stefan

last: Weckx

first: Roel

last: Van der Meulen

first: Gino

last: Vrancken

first: Luc

last: De Vuyst

first: Paul

last: Van Hummelen


title: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation.

summary: Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory, namely two wheat and two spelt fermentations with daily back-slopping. Hereto, the in-house developed functional gene LAB microarray was used, representing 406 genes that play a key role in sugar and nitrogen metabolism, functional metabolite production, stress responses and health and safety characteristics. The results reveal the activation of different key metabolic pathways, the ability to use different energy sources, and successful acid and oxidative stress responses. Also, a new algorithm was developed to compute a net expression profile for each of the represented genes, thereby exceeding the species level.


title: Absolute expression level of Saccharomyces bayanus genes

status: Public on Jul 06 2010

city: Boston

first: Alex

last: Tsankov

address: 155 Bay State

institute: MIT

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces bayanus genes

overall_design: Total RNA was collected in mid-log phase from Saccharomyces bayanus cells grown in rich medium (abbreviated CM, in house recipe).   RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Saccharomyces bayanus.

first: Alexander

first: Oliver

last: Rando

first: Aviv

last: Regev


title: Absolute expression level of Saccharomyces kluyveryii genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces kluyveryii genes

overall_design: Total RNA was collected in mid-log phase from Saccharomyces kluyveryii cells grown in rich medium (abbreviated CM, in house recipe).   RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Saccharomyces kluyveryii.


title: Absolute expression level of Saccharomyces mikatae genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces mikatae genes

overall_design: Total RNA was collected in mid-log phase from Saccharomyces mikatae cells grown in rich medium (abbreviated CM, in house recipe).   RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Saccharomyces mikatae.


title: Absolute expression level of Saccharomyces castellii genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces castellii genes

overall_design: Total RNA was collected in mid-log phase from Saccharomyces castellii cells grown in rich medium (abbreviated CM, in house recipe).   RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Saccharomyces castellii.


title: Absolute expression level of Kluyveromyces lactis genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Kluyveromyces lactis genes

overall_design: Total RNA was collected in mid-log phase from Kluyveromyces lactis cells grown in rich medium (abbreviated CM, in house recipe).   RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Kluyveromyces lactis.


title: Absolute expression level of Kluyveromyces waltii genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Kluyveromyces waltii genes

overall_design: Total RNA was collected in mid-log phase from Kluyveromyces waltii cells grown in rich medium (abbreviated CM, in house recipe).   RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Kluyveromyces waltii.


title: Absolute expression level of Candida glabrata genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Candida glabrata genes

overall_design: Total RNA was collected in mid-log phase from Candida glabrata cells grown in rich medium (abbreviated CM, in house recipe). RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Candida glabrata


title: Absolute expression level of Saccharomyces paradoxus genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces paradoxus genes

overall_design: Total RNA was collected in mid-log phase from Saccharomyces paradoxus cells grown in rich medium (abbreviated CM, in house recipe). RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Saccharomyces paradoxus.


title: Absolute expression level of Debaryomyces hansenii genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Debaryomyces hansenii genes

overall_design: Total RNA was collected in mid-log phase from Debaryomyces hansenii cells grown in rich medium (abbreviated CM, in house recipe). RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Debaryomyces hansenii.


title: ChIP-chip from different B cell stages with Abs to H3K4me3, H3K4me1, H3K9,K14-diacetyl, H3K27me3 and RNA polymerase II

city: Omaha

first: Himabindu

last: Ramachandrareddy

state: NE

address: 600 South 42nd st

department: Pathology and microbiology

institute: University of Nebraska Medical Center

summary:
B cell differentiation stage specific histone modifications detected within and upstream of genes that play critical roles in B cell differentation.
Germinal center B cell stage specific activating histone marks in regions far upstream of the BCL6 promoter regulate BCL6 expression.

overall_design: comparison of histone modifications of genes having a role in B cell differentiation in human primary tonsillar naïve B-cells and germinal center B-cells and in CL01, SUDHL16 and U266 cell lines.

first: Wing

last: Chan

first: Timothy

last: McKeithan


title: Meta-transcriptomic analysis of the response of river biofilms to pharmaceutical products using anonymous DNA microarray

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

institute: NRC-BRI

summary: Low concentrations of pharmaceutical compounds were shown to induce transcriptional responses in isolated microorganisms, which could have consequences on ecosystem dynamics. In order to test if these transcriptional responses could also be observed in complex river microbial communities, biofilm reactors were inoculated with water from two distinct rivers and supplemented with environmentally relevant doses of four pharmaceutical products (erythromycin-ER, gemfibrozil-GM, sulfamethazine-SN and sulfamethoxazole-SL). To follow the expression of functional genes, we constructed a 9,600 features anonymous DNA microarray platform onto which cDNA from the various biofilms was hybridized.

sample_organism:
environmental samples
environmental samples

overall_design: The reactor design for biofilm development has been previously described (Lawrence et al., 2004; Lawrence et al., 2000). Two duplicate experiments were carried out, with reactors being inoculated with either water from the WC (nutrient rich) or the SSR (nutrient poor). Treatments consisted in the addition of various pharmaceutical compounds: 1 µg l-1 erythromycin (ER), 1 µg l-1 gemfibrozil (GM), 0.5 µg l-1 sulfamethazine (SN), 0.5 µg l-1 sulfamethoxazole (SL). Nothing was added to control reactors (CO). All treatments were replicated independently three times. A reference sample (composite sample from Wascana Creek reactors used to construct the microarray) was hybridized (Cy5) on each slide.

first: John

middle: R

last: Lawrence

first: Charles

last: Greer


title: Effects of pulp and paper mill effluents on gene expression in the fathead minnow hypothalamus

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

institute: University of Ottawa

summary:
We evaluated the possible mechanisms by which exposures to pulp and paper mill effluents gene expression in the fathead minnow hypothalamus

Keywords: Toxicology

overall_design:
Sexually mature fathead minnows were exposed to 100% pulp and paper mill effluents for 5 days.  Tanks contained 4 females and 2 males.  A total 4 tanks per effluents were used in this experiment.
TM5, TM6, and KM4 represent different pulp and paper mill effluents from different mills coded for by FPInnovations-Paprican.

middle: T

first: Carole

middle: L

last: Yauk

first: Andrew

last: Williams

first: Andrea

last: Rowan-Carroll

first: Vance

last: Trudeau


title: Absolute expression level of Yarrowia lipolytica genes

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Yarrowia lipolytica genes

overall_design: Total RNA was collected in mid-log phase from Yarrowia lipolytica cells grown in rich medium (abbreviated CM, in house recipe). RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Yarrowia lipolytica.


title: CGH profiles of primary breast carcinomas from HBOC (Hereditary Breast and Ovarian Cancer) families

status: Public on Jul 05 2010

city: Hamburg

first: Simon

middle: A

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

summary: 89 tumors from women that were eligible for, and subjected to, routine diagnostic testing according to the HBOC criteria but were negative for pathogenic BRCA1/2-mutations or carried an UV in either BRCA1/2

overall_design: A BRCA2-classifier was built using array-CGH profiles of 28 BRCA2-mutated and 28 sporadic breast tumors. The classifier was validated on an independent group of 19 BRCA2-mutated and 19 sporadic breast tumors. Subsequently, we tested 89 breast tumors from suspected hereditary breast (and ovarian) cancer (HBOC) families, in which either no BRCA1/2 mutation or an UV had been found by routine diagnostics.


title: CGH profiles of BRCA2-mutated breast tumors

summary: Prediction of BRCA2-association in hereditary breast carcinomas with array-CGH

overall_design: Chromosomal aberrations in BRCA2 samples

first: Petra

last: Nederlof


title: Transcriptional analysis of signal transduction-related genes in experimental models of HER-2/neu-derived epithelial and mesenchymal tumors

status: Public on Jul 03 2010

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

country: Italy

institute: University of Verona

summary: Transcriptional expression of a restricted set of cancer signal transduction-related gesen were comparatively quantified in HER2/neu transgenic mammary tumors, mesenchymal and epithelial tumor cell lineages, both estabilished from HER-2/neu transgenic tumors, and syngeneic mesenchymal stem cells.

overall_design: In the study presented here, HER-2/neu transgenic mouse mammary tumors, previously described (Galie et al Carcinogenesis 2005 26(11):1868) mesenchymal (A17) and epithelial (BB1) cell lineages estabilished from murine HER-2/neu transgenic mammary tumors, and syngeneic mesenchymal stem cells, underwent transcriptional analysis using microarrays containing probes for 112 signal transduction-related genes and controls (GEArray Q Series Mouse Signal Transduction in Cancer Gene Array, MM-044, Superarray, Friederick, MD, USA).

first: Augusto

last: Amici


title: Absolute expression level of Candida albicans genes

first: Alex

last: Tsankov

summary: Total RNA versus genomic DNA hybridization on custom arrays designed for all Candida albicans genes

overall_design: Total RNA was collected in mid-log phase from Candida albicans cells grown in rich medium (abbreviated CM, in house recipe).   RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Candida albicans

first: Alexander

first: Oliver

last: Rando


title: Neurospora crassa early sexual development with MTP priming

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary:
Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development.
Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences.

overall_design: Neurospora crassa mat A FGSC#2489 Three developmental stages and two different primers used for reverse transcription: mycelium oligo(dT) M1 protoperithecia oligo(dT) PP1 perithecia oligo(dT) PT1 mycelium oligo(dT)+ Multi-Targeted Primer [MTP] (M2) protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2)

first: Jeffrey

middle: P

last: Townsend


title: RpoE regulon in Rhodobacter sphaeroides

status: Public on Jul 01 2010

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

summary: In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that contain RpoE-dependent promoters within R. sphaeroides. Transcript pattern clustering and a RpoE-binding sequence model were used to predict candidate promoters that respond to singlet oxygen stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides RpoE-dependent promoters that control the transcription of 15 genes activated by singlet oxygen.

overall_design: DNA immunoprecipitated with polyclonal antibodies against RpoE or the Beta' subunit of RNA polymerase was labelled with Cy5 and hybridized on two-color tilling arrays (triplicates for each) with genomic DNA as an input control labelled with Cy3.

first: Timothy

last: Donohue

first: Robert

last: Landick


title: ChIP-chip of Geobacter sulfurreducens PCA with antibody against RNAP and RpoD under various conditions

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: We applied a ChIP-chip approach to elucidate the binding profiles of RNAP and RpoD experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays.

overall_design: A 21 ChIP-chip study using immunoprecipitated DNA (IP-DNA)  from three culture conditions for RNAP and four culture conditions for RpoD.  The high-density oligonucleotide tiling arrays used consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G. sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures).

first: Yu

last: Qiu

first: Byung-Kwan

last: Cho

first: Young-Seoub

last: Park

first: Derek

last: Lovley

middle: O

first: Karsten

last: Zengler


title: Transcriptome analysis of Geobacter sulfurreducens under multiple growth conditions

summary: Investigation of comprehensive information about the transcripts (boundary, level, etc.)  across the entire G. sulfurreducens genome in mulitple growth conditions, including in biofilm and on electrode.

overall_design: A five array study using total RNA recovered from two separate culture conditions of G. sulfurreducens.  G. sulfurreducens were harvested one week after growth on electrode or to form biofilm. The high-density oligonucleotide tiling arrays used consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G. sulfurreducens genome (NimbleGen). Experiments were conducted as two (electrode) or three (biofilm) biological replicates (different cultures).


title: Genomic Profile of Primary Colorectal Cancers and associated Liver Metastases

first: Daniel

last: Stange

summary:
Comparison of genomic alterations of primary colorectal cancers with liver metastases of the same patient
Keywords: array CGH, colorectal cancer, colon cancer, liver metastasis

overall_design: 21 primary colorectal cancers and 21 matched liver metastases hybridized against sex-matched control pools

middle: E

last: Radlwimmer

first: Peter

last: Lichter


title: Expression data from stage 54 Xenopus laevis larvae treated with 20 nM triiodothyronine (T3)

city: Flagstaff

first: Brian

middle: Thomas

last: Searcy

state: AZ

address: P.O. Box 5640, Northern Arizona University

department: Dept of Biological Sciences

institute: Northern Arizona University

summary:
Induction of Xenopus laevis larvae metamorphosis is dependent on exposure to TH.  Metamorphosis involves the regression, growth or remodeling of almost all the tissues in the animals body.
Metamorphosis in frogs is induced by thyroid hormone. Each organ system has a unique morphological and genetic program that it follows while undergoing metamorphosis involving both the upregulation and downregulation of genes.  In this array we examined the change in gene expression in the tail of larvae undergoing precocious metamorphosis following induction with thyroid hormone.

overall_design: Whole stage 54 xenopus larvae were exposed to either vehicle for 48 hours or 20 nM T3 for 6 or 48 hours.  Total RNA was then purified from tail tissue and the samples were examined by hybridization to the Affymetrix Xenopus array.  Developmental stage 51-54 Xenopus larvae were selected because these stages do not express high levels of endogenous T3 but are still capable of morphologically responding to exposure.

first: Catherine

last: Propper

first: Philip

last: Stafford

first: Stephen

last: Beckstrom-Sternberg

first: James

first: Angela

last: Schwendiman

first: Jenifer

last: Soto-Pena


title: Scylla paramamosain mature gonads: Ovary vs. Testis

city: Xiamen

first: zou

last: zhihua

state: Fujian

address: NO.43 Yindou road

department: Fishry college

institute: Jimei University

summary: In order to identify unexpected, or indeed previously uncharacterized genes may be important in sex- or gonad development, we developed a custom cDNA microarray represent 3837 unique transcripts of Scylla paramamosain derived from our EST project. Thirty-nine putative transcripts were observed to differentially expressed in testis and ovaries (P<0.05).

overall_design: Two-condition experiment, Ovary vs. Testis. Biological replicates: 3 Ovaries, 3 Testis, 2 dye-swaps.

first: Yilei

last: Wang

first: Ziping

last: Zhang

first: Zhihua

last: Zou


title: The In Vitro Interaction of Aspergillus fumigatus and Human immature Dendritic Cells

city: Atlanta

first: John

last: Varga

state: GA

address: 1510 Clifton Road

department: Pediatrics

institute: Emory University

summary: Dendritic cells (DC) play an important role in host immunity by acting as a bridge between the innate and adaptive immune systems.  They are antigen presenting cells that obtain microbial antigens by direct phagocytosis of the microbe or by cross presentation of antigens taken up from the surrounding environment.  Monocyte derived DC were co-cultured with resting conidia of Aspergillus fumigatus at an MOI of 5 for 12 hours, cells were sampled every three hours.  RNA was extracted from both organisms at each time point and hybridised to micro-arrays, whole genome Aspergillus fumigatus array (JCVI) and a custom immune array for DC.      The genes up-regulated by DC in the presence of A. fumigatus indicated that the cells were producing a pro-inflammatory response.  There was an increase in IL8 expression over time confirming its association with germ tube emergence.  Over the course of the experiment there was increased expression of 210 genes by A. fumigatus, GO analysis indicated significant up-regulation of the following biological processes: fermentation, drug transport, pathogenesis, transport, tyrosine catabolism and response to oxidative stress.  There were two clusters of temporally regulated genes showing up regulation before 6hr and after 6 hrs.  This may be related to the increased mortality exhibited in DC at 6h.  The initial analysis of A. fumigatus gene expression in response to DC shows similarity to its response to neutrophils with an up-regulation in catabolism and response to oxidative stress.

overall_design: A. fumigatus AF293 cells were grown in the presence and absence of human dendritic cells for 0h - 12h.  Hybridizations were performed with biological replicates and flip-dye pairs.

first: C

last: Morton

first: J

first: A

last: Hornbach

first: M

last: Mezger

first: H

last: Sennefelder

first: S

last: Kneitz

first: O

last: Kurzai

last: Einsele

first: N

last: Fedorova

first: W

last: Nierman

first: T

last: Rogers

last: Loeffler


title: Aspergillus fumigatus  HapX-mediated iron starvation adaption is required for virulence.

summary: Iron is an essential cofactor for a wide range of cellular processes. Previous studies have shown that siderophore-mediated uptake and intracellular handling of iron are crucial for virulence of Aspergillus fumigatus. Here we show that the bzip-type transcription factor HapX plays a crucial role in the transcriptional remodeling required for adaption to iron starvation in this opportunistic fungal pathogen. HapX was found to be interconnected in a negative feed-back loop with the previously identified iron regulator SreA: SreA repressed expression of hapX during iron sufficiency and HapX repressed sreA during iron starvation. Genome-wide transcriptional profiling and analysis of selected metabolites (protophorphyrine IX, siderophores and amino acids) indicated extensive metabolic remodeling in response to iron starvation. HapX was found to participate in both, repression and activation of genes during iron starvation. HapX was in particular required for repression of iron-dependent and mitochondrial-localized activities including respiration, TCA cycle, amino acid metabolism, iron-sulfur-cluster biosynthesis and heme biosynthesis. Pathways positively affected by HapX included production of siderophores and the ribotoxin and major allergen AspF1. Analysis of the free amino acid pool revealed HapX-dependent coordination of the production of siderophores with the supply of its precursor ornithine. Consistent with the hapX expression pattern, HapX-deficiency was deleterious with respect to growth rate and conidiation during iron depleted but not iron-replete conditions. HapX-deficiency caused significant attenuation of virulence in a murine model aspergillosis underlining that A. fumigatus faces iron starvation in the host and that the HapX-dependent metabolic reprogramming is therefore crucial for virulence.

overall_design: A. fumigatus 293 and hapX mutants were grown in the presence and absence of iron and in cultures shifted from no iron to iron-containing conditions after 1 h incubation.  Hybridizations were performed with biological replicates for wt vs hapX +/- iron.   For the iron-shift experiments, there were biological replicates for wt in both conditions and for hapX in -iron but there was only a single biological sample for hapX iron-shift sample.  All hybs were performed with flip-dye pairs.

first: Nicola

last: Beckmann

first: Fabio

last: Gsalla

first: Markus

last: Schrettl

first: Thorsten

last: Heinekamp

first: Ilse

last: Jacobsen

first: Tarek

last: Moussa

first: Shaohua

first: Ernst

last: Werner

first: William

first: Axel

last: Brakhage

first: Hubertus

last: Haas


title: Mesothelioma integrative genomics: DNA methylation

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

summary: Integrated profiling of somatic molecular alterations present in tumors is necessary to further our understanding of the tumorigenic process. We investigated the potential relationships between gene copy number alterations and DNA methylation profiles in a case series of pleural mesotheliomas (n=23). Gene copy number (CN) alterations profiled with 500K SNP arrays and DNA methylation measured at over 750 cancer-related genes with methylation bead-arrays were examined concomitantly. Considering each probed locus, there were no instances of significantly correlated CN alteration and methylation (no loci with Q < 0.05) and averaging loci over their associated genes revealed only two genes with significantly correlated CN and methylation alterations (Q < 0.04). In contrast to the lack of discrete correlations, the overall extent of tumor CN alteration was significantly associated with DNA methylation profile when comparing CN alteration extent among methylation profile classes (P < 0.02), and there was evidence that this association was partially attributable to prevalent allele loss observed at the maintenance DNA methyltransferase DNMT1. Taken together, this work indicates a strong association between global genetic and global epigenetic dysregulation in mesothelioma rather than a discrete, local coordination of gene inactivation, and further highlights the utility and necessity of integrative genomics approaches in cancer biology.

overall_design:
Mesotheliomas were obtained following surgical resection at Brigham and Women’s Hospital through the International Mesothelioma Program from a pilot study conducted in 2002 and an incident case series beginning in 2005 as previously described (PMIDs: 19118007 and 19638575). All patients provided informed consent under the approval of the appropriate Institutional Review Boards. Clinical information, including histologic diagnosis was obtained from pathology reports. The study pathologist confirmed the histologic diagnoses and further assessed the percent tumor from resected specimens (mean >60%).

DNA extraction and methylation analysis:
DNA from fresh frozen tissue and matched whole blood was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA) following the manufacturer’s protocol. Tumor DNA was modified with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research, Orange, CA). Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility using methods described in (28).  The GoldenGate methylation data used in the analysis has been previously described (PMIDs: 19118007 and 19638575).

first: Karl

last: Kelsey


title: miRNA expression in human heart

first: Qing

last: Li

address: 600 YiShan Road

institute: Institute of Microsurgery on Extremities

summary: Microarray analysis of the miRNA expression profile of the human heart

overall_design: The total RNA from human heart is size fractionated, and the small RNAs (< 300 nt) isolated are used for miRNA microarray

last: Jing