title: lncRNA expression data

status: Public on Aug 05 2010

first: Susan

middle: C

last: Wu

address: 32-026 Lineberger Comprehensive Cancer Center

department: Biochemistry

institute: UNC Chapel Hill

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: Once thought to be transcriptional noise, large non-coding RNAs (lncRNAs) have recently been demonstrated to be functional molecules.  Cell type-specific expression patterns of lncRNAs suggest that their transcription may be regulated epigenetically.  Using a custom-designed microarray, here we examine the expression profile of lncRNAs in embryonic stem (ES) cells, lineage-restricted neuronal progenitor cells (NPC), and terminally differentiated fibroblasts. In addition, we also analyze the relationship between their expression and their promoter H3K4 and H3K27 methylation patterns. We find that numerous lncRNAs in these cell types undergo changes in the levels of expression and promoter H3K4me3 and H3K27me3.  Interestingly, lncRNAs that are expressed at lower levels in ES cells exhibit higher levels of H3K27me3 at their promoters. Consistent with this result, knockdown of the H3K27me3 methyltransferase Ezh2 results in derepression of these lncRNAs in ES cells.  Thus, our results establish a role for Ezh2-mediated H3K27 methylation in lncRNA silencing in ES cells and reveal that lncRNAs are subject to epigenetic regulation in a similar manner to that of protein-coding genes.

overall_design: lncRNA expression analysis was performed in 5 different cell types:  (1) ES cells, (2) neuroprogenitors, (3) tail tip fibroblasts, (4) Ezh2 knockdown #1 ES cells, and (5) Ezh2 knockdown #2 ES cells.  Total RNA was extracted and RNA quality was assessed via Agilent Bioanlayzer.  mRNA was amplified using the Low RNA Linear Amplification Kit (Agilent Technologies) by standard manufacturer's protocol.  Hybridization of experimental RNA labeled with Cy5 and Cy3-labeled Universal Reference RNA (Ambion) was carried out by standard protocol on a custom-designed array manufactured by Agilent Technologies.  Briefly, three unique 60nt probes were designed for each entry in the Fantom3 database and were synthesized along with lineage marker control probes on a 2x105K format array.  Upon array scanning, data was quality filtered, normalized by the Lowess method, and all probes corresponding to a given lncRNA were averaged using the UNC Microarray Database (UNCMD). Intraclass correlation analysis was carried out in the UNCMD.

first: Eric

last: Kallin

first: Yi

last: Zhang


title: Genome-scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin resistant parasites

city: La Jolla

first: Neekesh

middle: V

last: Dharia

state: CA

address: 10550 N Torrey Pines Road

country: USA

institute: The Scripps Research Institute

type: Genome variation profiling by genome tiling array

summary: Here we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos regions using genome-scanning, a microarray-based technique which delineates the majority of single-base changes, indels and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon is highly structured with a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes indicating mutations arising during self-mating or mitotic replication. The data also reveal that 1 or 2 meioses separate different isolates showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pair-wise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase clindamycin EC50 in strains harboring one of these mutations. This evidence of clindamycin resistant parasites in the Amazon suggests a shift should be made in health policy away from quinine+clindamycin therapy for malaria in pregnant women and infants and that the development of new lincosamide antibiotics for malaria should be reconsidered.

overall_design: Genome DNA from Peruvian Isolates vs. Reference 3D7

first: Elizabeth

middle: A

last: Winzeler


title: Environmental functional genes for soil microbes in South East Queensland, Australia

city: St Lucia

first: Regina

last: Sintrajaya

state: Queensland

address: Mansfield Pl, Blg 62 John Hines Lvl 3

department: School of Biological Science

country: Australia

institute: The University of Queensland

summary:
Custom made functional gene micoarray (E-FGA) consisting of 13,056 mRNA-enriched anonymus microbial clones from dirverse microbial communities to profile microbial gene transcript in agricultural soils with low and high flux of N2O. A total of 96 genes displayed expression that differed significantly between low and high N2O emitting soils.
Creation and validation of an cDNA microarray from environmental microbial mRNA, to use as a monitoring tool for microbial gene expression

sample_organism:
synthetic construct
uncultured microorganism

overall_design: Microbial expression profiles comparing two high N2O-emitting sites (3 soil replicates and microarrays each) and two low N2O-emitting sites (3 soil replicates and microarray each) from sugarcane site in Mackay, Australia

first: Ken

last: McGrath

first: Peer

middle: M

last: Schenk


title: Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray

city: Athens

first: Shalabh

last: Sharma

state: GA

address: Department of Marine Science

department: Marine Science

institute: UGA

summary: The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd.

platform_organism:
Sulfitobacter sp. EE-36
Roseovarius nubinhibens ISM
Ruegeria pomeroyi DSS-3
Pseudooceanicola batsensis HTCC2597
Jannaschia sp. CCS1
Ruegeria sp. TM1040
Yoonia vestfoldensis SKA53
Oceanicola granulosus HTCC2516
Roseobacter sp. MED193
Roseovarius sp. 217
Sulfitobacter sp. NAS-14.1
Sagittula stellata E-37
Maritimibacter alkaliphilus

overall_design: DMSP-related gene expression in the Roseobacter group was investigated using an environmental microarray. Coastal seawater from the Gulf of Mexico was collected and dispensed into 20-L microcosms. Two replicate cubitainers were amended with nutrients (N and P) to stimulate phytoplankton bloom, while two untreated cubitainers served as controls. The microcosms were incubated at 27ºC in a temperature-controlled incubator on a 12 h light/dark cycle for total of 7 days. Ten RNA samples (Day 0: 2 conditions with 1 biological replicate each; Days 2 and 4: 2 conditions with 2 biological replicates each) were prepared for microarray hybridization. After total RNA extraction, rRNAs were removed and mRNA transcripts were amplified and labeled with Alexa Fluor 647. Two technical replicates were hybridized from each RNA sample. The microarray was designed based on selected Ruegeria pomeroyi DSS-3 genes and their orthologs in 12 other sequenced Roseobacter genomes. Probes were designed from the orthologs using the Hierarchical Probe Design (HPD) algorithm.

first: J

last: Rinta-Kanto

first: H

last: Bürgmann

first: S

last: Gifford

last: Sun

first: R

middle: P

last: Kiene

first: M

last: Moran


title: Role of MicroRNA-214 in Ginsenoside-Rg1-induced Angiogenesis

city: Hong Kong

first: Patrick

middle: YK

last: Yue

address: Waterloo Road

department: Biology

country: Hong Kong

institute: Hong Kong Baptist University

summary:
MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional gene modulators. Ginsenoside-Rg1, one of the active components of ginseng, has been confirmed by us as an angiogenesis inducer. Using miRNA microarray analysis, a total of 15 (including miR-214) and 3 miRNAs were found to be down- or up-regulated by Rg1 in human umbilical vein endothelial cells (HUVEC), respectively. Since miR-214 is closely related to endothelial nitric oxide synthase (eNOS) and hence angiogenesis; its expression was further validated by qRT-PCR.
We also investigated the role of miR-214 on eNOS expression and in tubulogenesis of HUVEC by transfection of specific miRNA inhibitor or precursor. Our results suggested that Rg1 can down-regulate miR-214 expression in HUVEC, leading to an increase in eNOS expression which can promote angiogenesis. This result signifies a new understanding towards how a simple natural compound can affect physiological changes through modulation of miRNA expression.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The study is used to investigate the role of miRNA-214 in Rg1-induced human endothelial cells.

first: Lai

middle: S

last: Chan

first: Y

middle: K

first: Nai

last: Mak

first: N

last: Wong


title: Microarray analysis of the miRNA levels in plasma from healthy donors

status: Public on Aug 03 2010

city: Shanghai

first: Guokun

last: Wang

address: 168 Changhai Road

country: China

institute: Changhai Hospital

summary: To further understanding of mature microRNA in plasma from healthy people, we have employed microRNA microarray as a discovery platform with the potential to identify the plasma microRNA levels of healthy people. Human peripheral blood was drawn from 4 healthy donors, and plasma was obtained by two-step centrifugation. Equal of total RNA from the plasma was detected by microRNA microarray including 866 human and 89 human viral miRNAs (Sanger miRBase, release 12.0). About 170 miRNAs could be detected by microarray in all 4 samples of plasma. Among them, 6 microRNAs (miR-451, miR-16, miR-133a, miR-1, miR-499 and miR-208a) were detected in the RNA from the same plasma by real-time PCR.

overall_design: Freshly peripheral bloods from 4 healthy donors were drawn into EDTA tubes, and were processed within 1 hour by two-step centrifugation to remove the blood cells and the cellular debris. Small RNA was prepared using the mirVana PARIS kit, and was quantified using a NanoDrop-1000 spectrophotometer. Equal of RNA from the plasma was detected by microRNA microarray to identify the microRNAs levels in plasma of healthy people.

first: Qing

last: Jing

first: Guo-kun


title: Cellodextrin utilization by Bifidobacterium breve UCC2003

status: Public on Aug 11 2010

city: Cork

first: Karina

last: Pokusaeva

address: Western Road

country: Ireland

institute: University College Cork

summary: The transcription of the cldEFGC gene cluster of Bifidobacterium breve UCC2003 was shown to be induced upon growth on cellodextrins, implicating these genes in the metabolism of these sugars. Phenotypic analysis of a B. breve UCC2003::cldE insertion mutant confirmed that the cld gene cluster is exclusively required for cellodextrin utilization by this bacterium. HPAEC-PAD analysis of medium samples obtained during growth of B. breve UCC2003 on a mixture of cellodextrins revealed its ability to utilize cellobiose, cellotriose, cellotetraose and cellopentaose, with cellotriose representing the preferred substrate. The cldC gene of the cld operon of B. breve UCC2003 was shown to be the first described bifidobacterial β-glucosidase exhibiting hydrolytic activity towards various cellodextrins.

overall_design:
In order to investigate differences in gene expression patterns of B. breve UCC2003 when grown on cellobiose or cellodextrins as compared to growth on glucose, DNA microarray experiments were performed. Total RNA was isolated from B. breve UCC2003 cultures grown on cellobiose, cellodextrins, or glucose (see Materials and Methods). The cultures were harvested at the time points that ensured that B. breve UCC2003 was metabolizing cellobiose or cellodextrins as opposed to the residual glucose present in the cellodextrin preparation.
Analysis of the DNA microarray data was obtained from two independent biological replicates.

first: Mary

last: O’Connell-Motherway

first: John

last: MacSherry

first: Gerald

middle: F

last: Fitzgerald

first: Douwe

last: van Sinderen


title: Comparison of the expression profiles of wild type (WT) and Oct-6-deficient (Oct-6-/-) macrophages in response to poly(I:C) treatment

status: Public on Aug 02 2010

city: Vienna

first: Elisabeth

last: Hofmann

address: Veterinaerplatz 1

department: Institute of Animal Breeding and Genetics

country: Austria

institute: University of Veterinary Medicine Vienna

summary: Identification of target genes of the POU-transcription factor Oct-6 in macrophages after poly(I:C) treatment

overall_design: WT and Oct-6-/- fetal-liver macrophages were treated with poly(I:C) for 8 hours or were left untreated (3 independent expreiments = biological replicates). 200 genes differentially regulated in the absence of Oct-6  could be identified.

first: Ursula

last: Reichart

first: Christian

last: Gausterer

last: Guelly

first: Dies

last: Meijer

first: Mathias

last: Müller

first: Birgit

last: Strobl


title: BS-90 strain resistance in M-line Biomphalaria glabrata

status: Public on Aug 01 2010

city: Albuquerque

first: Patrick

last: Hanington

state: NM

address: 1 University of New Mexico

department: Department of Biology, University of New Mexico

institute: Center for Evolutionary and Theoretical Immunology

summary:
Transcriptional profiles ofBS-90 snails sized 8-12mm exposed to E. paraensei (BS-90 are susceptible) and S. mansoni (BS-90 are resistant) and unexposed controls

Keywords: Dose response

overall_design: Five individual snails from the treatment group were pooled to make up 3 repliactes.  After exposure to the indicated parasite snails were collected and RNA was isolated at 12hours, 1, 2, 4, 8, 16, and 32 days. Three unexposed control groups were also analyzed.

first: Michelle

last: Forys

first: Coen

last: Adema

first: Eric

last: Loker


title: TIF1g and cdc73 ChIP-chip data from K562 cells

city: Boston

first: Xiaoying

last: Bai

state: MA

address: 1 Blackfan Circle

institute: Children's Hospital Boston

type: Genome binding/occupancy profiling by genome tiling array

summary: We performed small-scale ChIP-chip (chrom 3,21, 22, X and Y) to reveal target locus of TIF1g and cdc73.

overall_design: DNA fragments pulled down by chromatin immunoprecipitation, amplified and hybridization on Affymetrix tiling arrays.

first: Leonard

middle: I

last: Zon


title: Size resistance in M-line Biomphalaria glabrata

summary:
Transcriptional profiles of snails sized 12-20mm exposed to E. paraensei and unexposed controls

Keywords: Dose response

overall_design: Five individual snails from the treatment group were analyzed at 12hours, 1, 2, 4, 8, and 16 days. Five unexposed control snails were also analyzed.


title: Selective control of metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae

city: Chicago

middle: Michael

last: Zaborske

state: IL

address: 929 E 57th St

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: When eukaryotic cells are deprived of amino acids, uncharged tRNAs accumulate and activate the conserved GCN2 protein kinase. We examine how yeast growth and tRNA charging or aminoacylation is affected during amino acid depletion in the presence and absence of GCN2.  tRNA charging is measured using a microarray technique which allows for simultaneous measurement of all cytosolic tRNAs. A fully prototrophic and its isogenic GCN2 deletion strain were used.

overall_design: We measured relative tRNA charging levels in yeast strains with an intact and deleted GCN2.

first: Xiaochen

last: Wu

first: Ronald

last: Wek

first: Tao

last: Pan


title: Acquired resistance in M-line Biomphalaria glabrata vs. Sensitized (exposed to irradiated only) and Infected (exposed to viable only) E. paraensei

summary:
Transcriptional profile of snails with induced acquired resistance (exposed first to irradiated E. paraensei miricidia) after secondary challenge with viable miricidia. Compared to snails exposed to irradiated miricidia only or to viable miricidia only. Experiments were done over the course of 16 days, with 8 day intervals between sensitization and secondary challenge.

Keywords: Dose response

overall_design: Each replicate is comprised of 5 individual snails from the specified treatment group. Three replicates of each treatment were analyzed on the Snail oligo array.


title: Poplar tissue types 2

city: corvallis

first: palitha

last: dharmawardhana

state: OR

address: 321 richarson hall,OSU

institute: OSU

summary: Global gene expression pattern of phloem and xylem tissue were determined using a Nimblegen microarray based on JGI v1.1 gene models. Xylem tissue from both Populus trichocarpa Nisqually-1 and Populus tremula X Populus alba hybrid were used in the study.

sample_organism:
Populus trichocarpa
Populus tremula x Populus alba

overall_design:
Xylem tissue: Three biological replicates were hybridized to three arrays
Phloem tissue: Two biological replicates were hybridized to two arrays

first: Palitha

last: Dharmawardhana

first: Steve

last: Strauss

first: Amy

last: Brunner


title: B. thailandensis genes induced by subinhibitory concentration of glyphosate

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

summary: Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material and lack of poly(A)-tails. We described, here, a novel method for single bacterium TTA, using a Burkholderia thailandensis model exposed to subinhibitory concentration of the antibacterial agent, glyphosate. Utilizing B. thialandensis microarray to assess the TTA method showed little gene bias (< 2 fold-change) and absence (~5-6%) when compared to the larger scale non-amplified RNA samples. B. thailandensis genes important to possibly recuperate and balance the intracellular amino acid pool were induced (or repressed) by the aromatic amino acid biosynthesis inhibitor, glyphosate. We validated our single-cell microarray data at the multi-cells and single-cell levels with lacZ and gfp reporter-gene fusions, respectively. This novel method will rejuvenate and expand the prokaryotic transcriptomic field.

overall_design: Two identical cultures of B. thailandensis wildtype strain E264 were grown in 1x M9 minimal medium supplemented with 1% Brij-58 and 20 mM glucose (MG) to mid-log phase. One culture was induced by final concentration of 0.01% (w/v) glyphosate for 30 minutes. Total RNA was then purified from B. thailandensis uninduced and induced samples, converted to cDNA and hybridized onto B. thailandensis 70mer triplicate array

first: Yun

last: Kang


title: Poplar tissue types 1

summary: Global gene expression pattern of different poplar tissue types were determined using a Nimblegen microarray based on JGI v1.1 gene models. All tissue except reproductive tissue were obtained from the same clone used for the poplar genome sequencing project (Populus trichocarpa Nisqually-1). Reproductive tissue were from wild Populus trichocarpa trees.

overall_design: Replicates: Two biological replicates per tissue type (except 'phloem and cortex' and 'roots from tissue culture') were hybridized to two arrays.


title: Genomic comparison of M. tuberculosis (Mtb) clinical isolates of the Beijing family and clinical isolate HN878 dosR::hyg derivatives versus Mtb laboratory strain H37Rv ATCC27294

city: Montreal

first: Pilar

last: Domenech

state: Quebec

address: 1001 Décarie Boulevard

department: IDIGH Program

country: Canada

institute: Research Institute of McGill University Health Centre

summary: Genomic comparisons among different lineages Mtb isolates.

overall_design:
Laboratoy strain Mtb H37Rv was compered to nine Mtb clinical isolates of the Beijing lineage. One, two or three  replicates were performed for each comparison.
Laboratory strain Mtb H37Rv was also compared to two laboratory, genetically-modified derivates from Mtb HN878 clinical isolate in which one copy of the dosR gene was inactivated. Two replicates were performed for each comparison.

first: Michael

last: Reed


title: Subtractive cloning of differentially expressed genes in chick heart/hemangioblast precursor cells

status: Public on Aug 04 2010

city: Gambelas

first: Margaret

middle: Carvalho

last: Bento

state: Faro

department: Biomedical and Medicine

country: Portugal

institute: University of Algarve

summary: Genetic evidence has implicated several genes as being critical for heart development. However, the inducers of these genes as well as their other targets and the pathways they constitute, remain largely unknown. In the avian embryo, Cerberus (cCer) transcripts are detected in the anterior mesendoderm including the heart precursor cells and in the left lateral plate mesoderm.   We have identified a promoter element of chick cCer able to drive EGFP expression into the heart and the hemangioblast precursor cells, allowing us to identify a population of cells that consistently exit from the anterior primitive streak region from as early as stage HH3+ and that later will populate the heart.  In order to identify and study novel genes expressed and involved in the correct development and differentiation of the vertebrate H/HPC (Heart/ Hemangioblast Precursor Cells) lineages, a differential screening using Affymetrix GeneChip system technologies was performed. Remarkably, this screening led to the identification of more than 800 transcripts potentially expressed in these precursor lineages.  We have identified unknown genes that are differentially expressed in the H/HPC precursor lineages. By developing a procedure to isolate the heart precursor cells using the cer2.5-EGFP construct, we were able to specifically isolate a population of H/HPC expressing already known cardiac markers, and a long list of still uncharacterized genes. From those, we defined by WISH that at least some of these in silico identified transcripts are in fact expressed in these cell populations and more importantly, functionally required for heart formation.More importantly, our study unveiled several uncharacterized genes that can now be used for further studies.

overall_design:
Portions of chick embryos were selected and excised at early stages of development for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of embryos at early gastrula stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected and excised portions of the embryos according to morphological criteria and EGFP expression.

Four GeneChip chicken arrays used for another study were added to the two arrays in this study to ensure a robust model for expression value computation (Note: The 4 samples chick_T2-1, chick_T2-2, chick_T2-3, chick_T2-4, were performed by another group and for a different array, and nothing has to do with our data.  They were only run at the same time and used for normalization. Raw data unavailable.). The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the six arrays were used to obtain model-based gene expression indices (MBEI) based on a PM (Perfect Match)-only model.
Processed data for all 6 samples can be found in supplementary file linked below.

first: José

last: Belo


title: BMP-mediated inhibition of FGF signaling promotes cardiomyocyte differentiation of anterior heart field progenitors

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

summary: The transition from progenitor to differentiated cells is critical for successful organogenesis; subtle alterations in this process can lead to developmental disorders. The anterior heart field (AHF) encompasses a niche in which cardiac progenitors maintain their multipotent and undifferentiated nature by signals from the surrounding tissues, which thus far have been poorly defined. Using systems biology approaches and perturbations of signaling molecules in chick embryos, we revealed a tight crosstalk between the bone morphogenic protein (BMP) and fibroblast growth factor (FGF) signaling pathways within the AHF: BMP4 promotes myofibrillar gene expression and cardiomyocyte contractions, by blocking FGF signaling. Furthermore, inhibition of the FGF-ERK pathway is both sufficient and necessary for these processes, suggesting that FGF signaling blocks premature differentiation of cardiac progenitors in the AHF. Investigating the molecular mechanisms downstream to BMP signaling revealed that BMP4 induced a set of neural crest-related genes; including MSX1, which was sufficient to induce cardiomyocyte differentiation. We suggest that BMP and FGF signaling pathways act via inter- and intra-regulatory loops in multiple tissues, to coordinate the balance between proliferation and differentiation of cardiac progenitors.

overall_design: Splanchnic mesoderm (AHF) explants were dissected and cultured for 0, 3, 12 or 24 hrs on a collagen drop covered with 0.5 ml of dissection medium (10% Fetal Calf Serum, chick embryo extract 2.5% and pen/strep 0.5% in MEM medium). 12 hour time point was used as a duplicate. In all samples, there was control plus BMP4: human recombinant BMP4 (Sigma, 200 ng/mL), which was added to the explant dissection medium.

first: Libbat

last: Tirosh-Finkel

first: Miriam

last: Brodt-Ivenshitz

first: Ayelet

last: Shamai

first: Zhong

last: Yao

first: Rony

last: Seger

first: Eytan

last: Domany

first: Eldad

last: Tzahor


title: Effects of diet and age on canine colon tissue gene expression

city: Urbana

first: Kelly

middle: Scott

last: Swanson

address: 1207 W. Gregory Dr.

institute: University of Illinois

summary: Aging alters gastrointestinal morphology, microbiota, and functionality, and is associated with increased incidence of intestinal disease.  The mechanisms that contribute to these changes are poorly described.  Gene expression in dogs has been evaluated for a few select genes under pathogenic or varying dietary conditions, but global gene expression profiles of aged versus young adult dogs have not been compared previously.  Thus, we used canine microarrays to compare gene expression profiles of colonic epithelial tissue from geriatric and young adult dogs fed 2 different diets.  Colon tissue samples were collected from 6 geriatric (12 yr-old) and 6 young adult (1 yr-old) female beagles after being fed one of two diets (animal protein-based versus plant-protein based) for 12 months.  RNA samples were hybridized to Affymetrix GeneChip Canine Genome Arrays.  Statistical analyses indicated that age had the greatest impact on gene expression, with 212 genes differentially expressed in geriatric dogs.  Although not as robust as age, diet affected mRNA abundance of 66 genes.  The effect of age was most notable, with increased expression in genes related to inflammation, stress response, cellular metabolism and cell proliferation and decreased expression in genes associated with apoptosis and defense mechanism in senior dogs.  The effect of diet on gene expression was not consistent, but appeared to have a greater response in senior dogs.

overall_design: Six geriatric (11.1 yr old) and 6 weanling (8 wk old) female beagles were used.  Three dogs of each age were assigned to one of two dietary treatments and fed for 12 months.  Diets tested in this experiment were previously shown to manipulate energy metabolism.  One diet was an animal-protein based diet (APB) and was composed primarily of highly digestible ingredients and animal-derived protein and fat sources (brewer’s rice, poultry by-product meal, poultry fat) and was formulated to contain 28% protein, 23% fat, and 5% dietary fiber.  The other diet was a plant-protein based diet (PPB) and was composed primarily of moderately digestible plant-derived ingredients (corn, soybean meal, wheat middlings, and meat and bone meal) and was formulated to contain 26% protein, 11% fat, and 15% dietary fiber.  Although the two diets were very different in terms of ingredient and chemical composition, both were formulated to meet or exceed all nutrient requirements for canine growth according to the Association of American Feed Control Officials.  Young dogs were fed ad libitum to allow for adequate growth, while geriatric dogs were fed to maintain baseline BW throughout the experiment.  To produce the desired metabolic effects, the PPB diet was formulated to contain a lower caloric density (APB = 5.38 kcal/g; PPB = 4.75 kcal/g) and have a lower nutrient digestibility than the APB diet.  Thus, dogs fed the PPB diet needed to consume a greater (P<0.05) quantity of food (237 g/d; 1123 kcal/d) than dogs fed the APB diet (166 g/d; 893 kcal/d) to grow (young) or maintain BW (geriatrics).  Even though metabolic indices were altered, mean BW among dietary treatments was not different at any time over the course of the study for young or geriatric dogs.  After 12 months on experiment, animals were fasted for 12 hr and then given a lethal dose (130 mg/kg BW) of sodium pentobarbital (Euthasol, Virbac Corp., Fort Worth, TX) intravenously into the left forearm.  Death was confirmed by lack of respiration and a corneal reflex, and absence of a heartbeat detected with a stethoscope placed under the left elbow.  Colon samples were collected immediately after death was confirmed, flash frozen using liquid nitrogen, and stored at -80oC.  Frozen samples were placed in RNAlater-ICE until epithelial layer could be scraped off and used for microarray analysis.

first: Lawrence

middle: B

last: Schook


title: Global gene expression profile of chicken cecal tonsil in response to campylobacter jejuni challenge in broiler lines

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

summary:
It is essential to understand host response to Campylobacter jejuni infection in order to genetically improve resistance to its colonization in chickens. A custom Agilent chicken 44K array was used to examine gene expression profiles after Campylobacter jejuni infection of two broiler lines (A and B). Day-old chicks were orally inoculated with C. jejuni. After day 7 post-infection, the cecal tonsil was collected for total RNA isolation and cecal content for bacteria burden quantification. Twenty highest and lowest bacterial burden birds and non-infected birds within each line were used to pool four biological replicates for each group. The pair comparisons among high, low bacterial burden, and non-infected group were used. The signal intensity of each gene was normalized by LOWESS method. A mixed model including the fixed effects of dye, line, treatment and line × treatment interaction, and random effects of slide and array was used to identify differentially expressed genes at P < 0.001 by SAS program. Within line A, there were 61, 163, and 90 genes significantly differentially expressed between high and low bacterial burden, high bacterial burden and non-infected group, and low bacterial burden and non-infected group, respectively; 2637, 1684, 561 genes within line B, respectively. The results suggested that genetics, treatment and genetics × treatment interaction played important role in gene regulation of C. jejuni infection. The findings in the current study will lead the identification of potential candidate genes for genetic resistance to C. jejuni infection in chickens.
Keywords: diease state analysis

overall_design: Chickens in two broiler lines were inoculated with 10^5 cfu C. jejuni on one day after hatch. The cecal content and cecal tonsil was collected and bacterial number in cecal content was counted on day 7 after inoculation. Twenty samples were seperated into 3 groups (high burden, low burden, and control) based on bacterial burden of cecal content in each line, 5 samples were mixed randomly into one pool. A dual color, balanced design was carried on for all samples. There comparisons were used in each line, C/H, H/L, L/C, totally, four biological replicates in each line. A Dye swap was used in each pair of comparisons including AC/AH, AH/AL, AL/AC; BC/BH, BH/BL, and BL/BC. Background subtracted signal intensity were collected from 24 arrays and normalized for data analysis.

first: Xianyao

last: Li

first: Christina

middle: L

last: Swaggerty

middle: H

last: Kogut

first: Hsini

last: Chiang

first: Ying

last: Wang

first: Kenneth

last: Genovese

first: Haiqi

last: He

first: Norman

middle: J

last: Stern

first: Scot

middle: E

last: Dowd

first: Haijun


title: Expression data for various strains of Toxoplasma gondii chosen from canonical types (i.e., I,II, and III)

status: Public on Jul 31 2010

city: Philadelphia

first: Paul

last: Davis

state: PA

address: 433 S. University Ave.

institute: University of Pennsylvania

summary: This study establishes a baseline pattern for RNA expression among canonical strains of Toxoplasma gondii grown in tissue culture without perturbation.

overall_design: Parasites cultured within human foreskin fibroblast (HFF) cells grown with D10 media were scraped and harvested ~8-12 hours prior to host cell lysis.  RNA was isolated and applied to a T. gondii Affymetrix array.

first: Amit

last: Bahl

first: David

last: Roos


title: Identification of mRNAs modulated by overexpression of N-terminal G3BP

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu, Oko

country: Japan

institute: Kochi University Medical School

summary: Transcripts upregulated or downregulated by overexpression of N-terminal G3BP were identified through expression profiling of a total of 12,135 genes in comparison with S2-013 clones in which N-terminal G3BP is overexpressed and control clones.

overall_design: We endeavored to identify factors and pathways regulated by CD24 and to obtain leads regarding the mechanism underpinning the observed phenotypic changes by performing cDNA microarray analysis on two S2-013 CD24 RNAi clones and two control clones. Total RNAs from two clones of S2-013 CD24 RNAi or control cells were mixed and used for cDNA microarray analysis.

last: Kelly


title: Traf6 function in the innate immune response of zebrafish embryos

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

country: Netherlands

institute: University of Amsterdam

summary: Transcriptional profiling of the zebrafish embryonic host response to a systemic bacterial infection with Salmonella typhimurium (strain SL1027); comparison between traf6 knock-down and control morpholino treated embryos.

overall_design: Two-way factorial dual colour design with factor 1 'infection with Salmonella enterica serovar Typhimurium (S. typhimurium)' and factor 2 'morpholino knock-down of traf6' using a common reference made from the sample pool. All infection experiments were performed using mixed egg clutches of ABxTL strain zebrafish. Embryos injected with traf6 morpholino or a 5bp mismatch control morpholino were staged at 27 hours post fertilization (hpf) by morphological criteria and approximately 250 cfu of DsRed expressing Salmonella bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Pools of 20-40 infected and control embryos were collected 8 hours post infection (hpi). For the microarray analysis, the whole procedure was preformed in triplicate on separate days. The triplicates are marked 1,2 and 3.

first: O

middle: W

last: Stockhammer

first: H

first: F

last: Wittink

first: T

last: Breit

first: A

last: Meijer

last: Spaink


title: Absence of di-auxie during simultaneous utilization of glucose and xylose by Sulfolobus acidocaldarius

city: Emeryville

first: Robert

last: Dahl

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

summary: Sulfolobus acidocaldarius has been previously reported to grow on a broad range of sugars, but there is limited information on the ability of the organism to metabolize multiple sugars simultaneously. We report here the ability of S. acidocaldarius to utilize glucose and xylose simultaneously without di-auxie effect. The organism utilized a mixture of 1 g/L glucose and 1 g/L xylose with a growth rate of 0.079 h-1 compared to 0.074 h-1 and 0.22 h-1 when the organism was grown on xylose 2 g/L and 2 g/L glucose respectively as sole carbon sources. An increase in xylose concentration to 2 and 4 g/L in a medium containing 1 g/L glucose resulted in a growth rate of 0.082 and 0.085 h-1. However, increasing glucose concentration by 2 and 4 g/L when xylose concentration was maintained at 1 g/L decreased the growth rate to 0.062 and 0.052 h-1 respectively. S. acidocaldarius appeared to be utilizing the sugars at a rate roughly proportional to their concentration in the medium, resulting in complete utilization of these sugars at same time. The organism did not show preference for either glucose or xylose when it was grown on both sugars. Similar results were obtained with a combination of glucose, arabinose and galactose. These observations strongly suggest that S. acidocaldarius does not regulate utilization of the sugars tested herein using carbon catabolite repression (CCR) commonly found in most bacteria. The mechanism by which the organism utilized a mixture of sugar is yet to be elucidated. However, we were able to identify genes encoding for the putative glucose ABC transporters; but the putative xylose transporter was not identified.

overall_design:
A study of S. acidocaldarius grown in glucose, xylose, or the two carbon sources combined in mid-log. Analyzed on Nimblegen 4-plex S. acidocaldarius DSM 639 array
weblink: http://microbesonline.org/cgi-bin/microarray/viewExp.cgi?expId=1723

first: Chijioke

last: Joshua

first: Peter

last: Benke

first: Jay

middle: D

last: Keasling


title: Determination of ncRNAs repressed by Isw2

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N

department: Basic Science

institute: Fred Hutchinson Cancer Research Center

type: Non-coding RNA profiling by genome tiling array

summary: It has previously been shown that Isw2 represses cryptic antisense transcripts from the 3’-end of three genes.  However, whether Isw2 generally functions to repress cryptic RNA transcription is currently unknown.  We thus sought to determine the loci at which Isw2 is required to repress cryptic non-coding RNA (ncRNA) expression and to map their transcription start sites relative to nucleosome positions on a global scale.

overall_design: We hybridized total RNA from Isw2 deletion strains to high-resolution, strand-specific microarrays tiling chromosomes III, VI, and XII, covering ~14% of the genome.  Because the exosome complex efficiently degrades cryptic transcripts and are not expected to alter the frequency of ncRNA transcription, deletion of components in the exosome pathway, either TRF4 or RRP6, in combination with ISW2 (Δisw2 trf4 and Δisw2 rrp6, respectively) is required to stabilize some cryptic transcripts.  Furthermore, because it is unclear how cryptic RNA transcripts are processed in vivo, especially in the absence of Trf4 or Rrp6, we avoided any selection or amplification of RNA.  At least three replicates (including at least one biological and one technical replicate) each of WT, Δisw2, Δtrf4, Δrrp6, Δisw2 trf4 and Δisw2 rrp6 were analyzed.

first: Adam

middle: N

last: Yadon

first: Daniel

last: Van De Mark

first: Ryan

last: Basom

first: Jeffrey

last: Delrow

first: Iestyn

last: Whitehouse


title: DNMT3B7 disrupts embryonic development and accelerates lymphomagenesis

status: Public on Jul 30 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: Cancer cells have an altered distribution of DNA methylation and express aberrant DNA methyltransferase 3B transcripts, which encode truncated proteins. To test if a truncated DNMT3B isoform disrupts DNA methylation in vivo, we constructed transgenic mice expressing DNMT3B7, a common truncated DNMT3B isoform in cancer cells. DNMT3B7 transgenic mice exhibit altered embryonic development, including lymphopenia, craniofacial abnormalities, and cardiac defects, similar to Dnmt3b-deficient animals, but rarely develop cancer.  However, DNMT3B7 expression increases the frequency of mediastinal lymphomas in Eμ−myc animals. Eμ-myc/DNMT3B7 lymphomas have more chromosomal rearrangements, increased global methylation levels, and more locus-specific perturbations in DNA methylation patterns compared to Eμ-myc lymphomas. Our results demonstrate that a truncated DNMT3B protein can alter tumorigenesis, suggesting a similar role in human tumors.

overall_design: Direct comparison of DNA methylation in lymphoma samples from Eu-Myc vs Eu-Myc/Dnmt3b7 mice.

first: Lucy

last: Godley

first: Ari

last: Melnick


title: Transcriptome comparison of B. anthracis Ames and isogenic sinR-null mutant, UTA21

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: To establish the SinR regulon in B. anthracis, gene expression of the fully  virulent Ames strain and the isogenic sinR-null strains were compared using expression microarray analysis.

overall_design: Cultures of  the two B. anthracis strains tested were grown in triplicate in LB broth to mid-exponential phase (O.D.600 = 0.5-0.6) or early stationary phase of growth (O.D.600 = 3.5-3.9).  Cells were pelleted through centrifugation and frozen at -80ºC.  Total RNA was isolated using a hot phenol method, converted to cDNA, fragmented, labeled, and hybridized to our Affymetrix microarray.  Estimates of gene expression were calculated using GCOS software v1.4.


title: One Year RDX Exposure, Brain Tissue Investigation

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: We investigated ecotoxicological effects and toxicogenomic responses in fathead minnows (Pimephales promelas) exposed to an environmentally-relevant concentration (0.83 mg/L) of the munitions compound cyclotrimethylenetrinitramine (RDX) in one year and multi-generational assays.  In the one year assay, RDX effects were discerned by comparing breeding groups reared in control or RDX-exposure conditions for one year.  RDX had no detectable effect on gonad-somatic index, or condition factor in females assayed at 1 day and at 1, 3, 6, 9, and 12 months, however the liver-somatic index was significantly increased versus controls only at the 12 month time point.  RDX had no effect on live-prey capture rates at all time points assayed and no significant impacts on egg production, fertilization or hatch success in the 1-year exposure trial.  Genomic analyses indicated that RDX exposure caused limited differential expression of transcripts within time points and no functional conservation of effects indicative of RDX exposure among time points for either brain or liver tissues in the one year exposure.  In the multi-generational assay, the effects of acute (96h) exposure to RDX were compared in fish reared to the F2 generation in either control or RDX-exposure conditions.  The RDX-reared fish were not observed to have appreciably enhanced RDX tolerance versus the control-reared fish.  However, significant differences in gene expression were observed among the control and RDX-reared fish related to neuro-excitatory glutamate metabolism, sensory signaling and processes in neurological development.  In total, our results indicate that exposure to an RDX concentration approximating maximum levels observed in the field (0.83 mg/L) caused limited impacts in fathead minnows in a one year exposure, however caused altered expression in genes involved in neural function in a multi-generational exposure.

overall_design: Adult fathead minnows were exposed to 0.83 mg/L (0.15 mg/L standard deviation) in experimental units including 2 male and 4 fish.  Five replicate males were randomly sampled with replacement from each of 8 control and 8 RDX-exposed experimental units at 1d, 1mo, 3mo, 6mo, 9mo and 12mo sampling periods.  Brain tissue was investigated for differential expression in response to RDX exposure.  Data were analyzed in 3 separate investigations.  First, the Reference vs Reference data were analysed to determine an empirical false positive detection rate.  Next, in order to meet milestones set up by our upper management, we were forced to generate results prior to the end of the bioassay.  Therefore, we investigated gene expression among Control and RDX-exposed fish in the 1 day - 6 month sampling periods.  Investigation of gene expression among the control and RDX-exposed fish for the 9 month and 12 month time periods were investigated separately.

first: Sandra

middle: M

last: Brasfield

first: Jacob

last: Stanley

first: Mitchell

last: Wilbanks

first: Pornsawan

last: Chappell

first: Edward

last: Perkins

first: Guilherme

middle: R

last: Lotufo

first: Richard

last: Lance


title: miRNA profiling in cervical carcinomas, low and high-grade intraepithelial cervical lesions and normal cervical tissues

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

institute: University of Aveiro

summary: Background. MicroRNAs (miRNAs) are short (~22 nt) non-coding regulatory RNAs that control gene expression at the translational level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. This prompted the development of miRNA-chips for cancer diagnosis or prognosis, opening a new door to understand carcinogenesis. Cervical cancer is one of the most common cancers in women worldwide. Therefore, there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform developed in house containing probes for mature miRNAs. Results. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL) and 9 low-grade squamous intraepithelial lesion (LSIL) samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, miRNAs deregulation in malignant and pre-malignant cervical tissues was detected after tackling the high variability observed. We were also able to identify putative targets of relevant candidate miRNAs.  Conclusions. Our results show that miRNA deregulation may play an important role in the malignant transformation of cervical squamous cells. In addition, deregulated miRNAs highlight new candidate targets allowing a better understanding of the molecular mechanism of this tumour type.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study we used a common reference design experiment where the common reference used was a commercial RNA from normal cervix (Ambion) and the test samples were 4 pre-treatment squamous cell cervical carcinoma, 7 high-grade Squamous Intraepithelial Lesion (CINII, n=2 and CIN III, n=5) sample, 9 low-grade Squamous Intraepithelial Lesion (CIN I) samples, 19 normal cervix samples and 4 pools of normal cervix samples.

first: Patricia

first: João

middle: P

last: Marques

first: Ana

last: Soares

first: Laura

last: Carreto

first: Manuel

last: Santos


title: M. smegmatis response to energy- and oxygen-limitation in continuous culture

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: Transcriptional profiling of M. smegmatis grown at 69h doubling time compared to 4.6h doubling time both at 50% air saturation. Transcriptional profiling of M. smegmatis grown at 69h doubling time with 50%, 2.5% and 0.6% air saturation.

overall_design: Two-condition experiment. Biological replicates: 5 independently grown and harvested. One replicate per array.

first: Gregory

last: Cook


title: Single feature polymorphism array 16K Unigenes: marker discovery in melon

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

institute: Agricultire Research Organization

summary: One of the methods used to search for molecular markers is DNA hybridization to microarrays. Microarray hybridization of DNA from different individuals can reveal differences between them (single-feature polymorphisms (SFPs)). These SFPs can be used as markers for breeding purposes, or they can be converted to conventional markers by sequencing. This method has been utilized in a few different plants to discover genetic variation using Affymetrix arrays that exist for only a few organisms. We applied this approach, with some modifications, for marker discovery in melon.

overall_design: For marker discovery, we used DNA from the parents of our mapping population, developed by Katzir's group from a cross between representatives of two subspecies of Cucumis melo L.: PI414723 (subspecies agrestis) and 'Dulce' (subspecies melo). Two biological replicates from PI414723 and two from 'Dulce' were used. Each biological replicate contained gDNAs pooled from 10 different plants. gDNA samples were labeled and hybridized using standard Agilent procedures for comparative genomic hybridization (CGH). The inter-population genetic variation was detected using two arrays, with one of the biological replicates of 'Dulce' against one of the PI414723 replicates on each array. The intra-population variation was detected by hybridizing the PI414723 replicates against each other and the 'Dulce' replicates against each other. Intra-population variation was estimated to ensure that the genetic variation between these populations is based on alleles that are fixed in the population and not due to intra-population variation.

first: Amir

last: Sherman


title: Streptococcus mutans UA159 control vs. Streptococcus mutans UA159 supplemented with 20 uM 4,5-dihydroxy-2,3-pentadione (DPD) at 3 different pH values

status: Public on Jul 29 2010

city: Jerusalem

first: reuven

last: aharoni

address: 28 mara

department: oral biology

institute: hebrew university

summary: Transcriptional profiling of  early logarithmic phase culture (O.D=0.2-0.3) of  Streptococcus mutans UA159 comparing control of untreated Streptococcus mutans UA159 bacteria  with Streptococcus mutans UA159 bacteria spplemented with 20µM synthetic DPD (pre-AI-2) which regulates gene expression via AI-2 quorum sensing system.Three compairisons  were performed at pHs of  7,6 and 5.

overall_design: Six-condition experiment, control bacteria vs. bacteria supplemented with DPD at different ph. Biological replicates: pH 7: 4 control, 4 DPD-supplemented independently grown and harvested. One replicate per array.pH 6:  4 control, 4 DPD-supplemented independently grown and harvested. One replicate per array. pH 5: 2 control, 2 DPD-supplemented independently grown and harvested. One replicate per array.

first: Reuven

last: Aharoni

first: Asaf

last: Sol

first: Doron

last: Steinberg


title: MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers

city: San Diego

first: Andrew

last: Hinton

state: CA

address: 3525 John Hopkins Ct.

department: Pediatrics

institute: UC, San Diego

summary:
Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues.  Definitive endoderm (DE) is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung).
We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm.

overall_design: hESCs (H9) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation.  Samples were collected at day 0 (hESCs),  and day 4 (DE).


title: MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm in feeder-free conditions

summary:
Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues.  Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung).
We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm.

overall_design: hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation.  Samples were collected at day 0 (2 samples), day 2 (3 samples) and day 4 (3 samples).


title: MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm on MEF feeder layers

summary:
Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues.  Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung)
We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm

overall_design: hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE. formation.  Samples were collected at day 0 (hESCs),  and day 4 (DE).


title: Breast tumor DNA methylation

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

summary:
Using primary breast tumors from 162 women from the Kaiser Division of Research Pathways Study and the Illumina GoldenGate methylation bead-array platform, we measured CpG loci associated with cancer-related genes
162 tumor specimens from the initial diagnostic biopsy were obtained from the KPNC tumor biorepository for methylation analysis. All tumor specimens were from patients who did not receive neoadjuvant chemotherapy.

overall_design: The Pathways Study is a prospective cohort study of breast cancer survival actively recruiting women diagnosed with invasive breast cancer from the Kaiser Permanente Northern California (KPNC) patient population since January 2006. Further study details are provided in Kwan ML et al. Cancer Causes Control 2008. Written informed consent is obtained from all participants before they are enrolled in the study. The study was approved by the IRB of KPNC and all collaborating sites.

middle: C

first: Johh

middle: K

last: Wiencke

first: Karl

middle: T

last: Kelsey


title: IGH analysis in pro-B cells with H3K4me3, H3K4me2 and H3K9ac

status: Public on Jul 28 2010

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

institute: Instutute of Molecular Pathology

summary: STAT5 and IL-7 signaling are thought to control B-lymphopoiesis by regulating key transcription factor genes and activating VH gene segments at the Igh locus. Using conditional mutagenesis, we demonstrate that transgenic Bcl2 expression rescued the development of Stat5-deleted pro-B cells by compensating for the loss of Mcl-1. Ebf1 and Pax5 expression as well as VH recombination were normal in Bcl2-rescued pro-B cells lacking STAT5 or IL-7Ra. In agreement with this finding, STAT5-expressing pro-B cells contained little or no active chromatin at most VH genes. In contrast, Igk rearrangements were increased in STAT5- or IL-7Ra-deficient pro-B cells, consistent with direct binding of STAT5 to the intronic iEk enhancer in wild-type pro-B cells. Hence, STAT5 and IL-7 signaling control cell survival and suppress premature Igk recombination in early B-lymphopoiesis.

overall_design: comparison of wt vs Rag2-/- pro-B cells

first: Shane

last: McManus


title: ChIP-chip from DmD8 cells with Twist antibodies after 30 minutes Notch activation

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

summary:
The transcription factor Twist is a critical cooperating factor that confers transcriptional specificity to the Notch pathway in muscle progenitor cells (DmD8)
ChIP analysis of Twi show that Twist binding is significantly enriched in Notch responsive region in DmD8 cells

overall_design: 3 replicates of Twist ChIP after30 min. Notch activation.

first: Alena

last: Krejci

first: Fred

last: Bernard


title: Analysis of the human endothelial cell response to pathogenic Leptospira interrogans vs. non-pathogenic Leptospira biflexa (Eahy1 data)

status: Public on Jul 27 2010

city: Milwaukee

first: Jenifer

last: Coburn

state: WI

address: 8701 Watertown Plank Rd.

department: ID/CBID

institute: Medical College of Wisconsin

summary: The overall goal of these experiments was to determine how human endothelial cells respond to pathogenic Leptospira interrogans. Leptospira interrogans causes leptospirosis, the most widespread zoonotic infection in the world. A hallmark of leptospirosis is widespread endothelial damage, which in severe cases leads to hemorrhage. In these experiments, we infected two endothelial cell lines with pathogenic Leptospira interrogans serovar Canicola strain Ca12-005, and as controls, with the non-pathogenic Leptospira biflexa serovar Patoc strain Pfra. As additional controls, uninfected cells were also included in the analyses.

overall_design: The cell line used was Ea.hy926, a macrovascular line (Edgell, C. J.,et al. 1990.  In vitro Cell. & Dev. Biol. 26:1167-1172, and Edgell, C. J., et al. 1983. Proc. Natl. Acad. Sci. 80:3734-3737). Infection times were performed at a multiplicity of infection (# bacteria/endothelial cell) of 10 for either 1 hour or 3 hours, after which RNA was harvested and reverse transcribed. Labeled cDNAs were used to probe HEEBO arrays purchased from Microarrays Inc. (Nashville, TN). In each of three biological replicate experiments, for each time point, three comparisons were made. First, the L. interrogans-infected cells were compared to the L. biflexa-infected cells. Second, the L. Interrogans-infected cells were compared to the uninfected cells. Third, the L. biflexa-infected cells were compared to the uninfected cells. A second endothelial cell line, HMEC (Ades et al, 1992. HMEC-1: establishment of an immortalized human microvascular endothelial cell line. J Invest Dermatol. 99:683-690), which is of microvascular origin, was also used; raw data files are provided separately.


title: Analysis of the human endothelial cell response to pathogenic Leptospira interrogans vs. non-pathogenic Leptospira biflexa (HMEC data)

overall_design: The cell line used fhere was a microvascular endothelial line, HMEC (Ades et al, 1992. HMEC-1: establishment of an immortalized human microvascular endothelial cell line. J Invest Dermatol. 99:683-690); due to loss of the original analysis files, only raw data files are provided. Infection times were performed at a multiplicity of infection (# bacteria/endothelial cell) of 10 for either 1 hour or 3 hours, after which RNA was harvested and reverse transcribed. Labeled cDNAs were used to probe HEEBO arrays purchased from Microarrays Inc. (Nashville, TN). In each of three biological replicate experiments, for each time point, three comparisons were made. First, the L. interrogans-infected cells were compared to the L. biflexa-infected cells. Second, the L. Interrogans-infected cells were compared to the uninfected cells. Third, the L. biflexa-infected cells were compared to the uninfected cells. A second endothelial cell line,


title: Investigations of gene expression in fathead minnow (Pimephales promelas) brain tissue reveal toxicological impacts of RDX exposure

first: Kurt

last: Gust

summary: Production, usage and disposal of the munitions constituent (MC) cyclotrimethylenetrinitramine (RDX) has led to environmental releases on military facilities.  The chemical attributes of RDX are conducive for leaching to surface water which may put aquatic organisms at risk of exposure.  Because RDX has been observed to cause aberrant neuromuscular effects across a wide range of animal phyla, we assessed the effects of RDX on central nervous system (CNS) function in the representative aquatic ecotoxicological model species, fathead minnow (Pimephales promelas).  A brain-tissue based cDNA library enriched for transcripts differentially expressed in response to RDX exposure was developed for fathead minnow and was transitioned to custom cDNA-based microarrays.  All 4,128 cDNAs were sequenced, quality filtered and assembled yielding 3,018 unique sequences and 945 significant blastx matches (E ≤ 10-5).  Bioassays were conducted exposing fathead minnows to RDX at 0.625, 1.25, 2.5, 5, 10 mg/L or an acetone-spike control for 10d.  Overt toxicity of RDX in fathead minnow occurred only at the highest exposure concentration resulting in 50% mortality. Conversely, Bayesian analysis of microarray data indicated significant changes in transcript expression in fathead minnow brain tissue at RDX concentrations as low as 0.625 mg/L.  In total, 154 microarray targets representing 44 unique transcript identities were differentially expressed in RDX exposures, the majority of which were validated by RT-qPCR.  Investigation of molecular pathways, gene ontology and individual gene functions indicated that RDX exposures affected metabolic processes involved in:  oxygen transport, neurological function, calcium binding / signaling, energy metabolism, cell cycle / cell proliferation, oxidative stress and ubiquitination.  In total, our study indicated that RDX exposure affected molecular processes critical to CNS function in fathead minnow.

overall_design: 10 Day RDX Exposure, Brain Tissue Investigation: Sub-adult fathead minnows were exposed to RDX in a 10d dose-series experiment (0.625, 1.25, 2.5, 5.0, or 10 mg/L RDX) which included an acetone-spike control (1% acetone).  Each experimental treatment included 8 replicate fish (48 total fish) and endpoints included mortality, total weight and neurotoxicogenomics. The 1.25mg/L dose was not included in the microarray experiment. Please see attached PDF file for detailed 'Balanced, Interwoven Loop Design'.

first: Mitchell

middle: S

last: Wilbanks

first: Xin

last: Guan

first: Mehdi

last: Pirooznia

first: Tanwir

last: Habib

first: Leslie

last: Yoo

first: Henri

last: Wintz

first: Ed

last: Perkins


title: Trivalent arsenic inhibits the functions of chaperonin complex

status: Public on Jul 26 2010

city: Baltimore

first: Daniel

last: Yuan

state: MD

address: 733 N. Broadway, Suite 351

department: Molecular Biology and Genetics

institute: Johns Hopkins Univ School of Medicine

summary:
The goal of this study was to identify yeast mutants with arsenite hypersensitivity.
Keywords: dose response

overall_design: Matched pools of yeast knockout (YKO) mutants were grown in paired growth media lacking or containing arsenite at various concentrations. The relative abundances of the YKO mutants were profiled using microarrays. Three types of pools were used in this study: (1) heterozygous diploid mutants; (2) haploid mutants obtained as progeny from the heterozygous diploid pool; and (3) haploid mutants also containing a null mutation of the prefoldin gene PFD1.

first: Xuewen

last: Pan

first: Stefanie

last: Reissman

first: Nick

last: Douglas

first: Zhiwei

last: Huang

first: Xiaoling

last: Wang

first: J

last: McCaffery

first: Judith

last: Frydman

first: Jef

last: Boeke


title: Phosphorus starvation induced genes in Brassica carinata

city: Hannover

first: Frank

last: Stahl

state: Niedersachsen

address: Callinstr. 5

department: Technische Chemie

country: Germany

institute: Leibniz Universität Hannover

summary: The purpose of the present study is to determine the effect of Phosphorus deficiency on gene expression level using microarray analysis to identify genes responsible for root hair development. Phosphorus deficiency induced the formation of root hairs to explore a greater soil volume but molecular mechanisms were unknown. Therefore, microarray experiments were performed using root tips of Brassica carinata cultivars Bale and Bacho, respectively differing in root hair length during Phosphorus deficiency. Experimental design was carried out in nutrient solution in a climate chamber with controlled environmental conditions (20°C, 16h day/8h night cycle, 70% relative humidity) in a randomized design. 25 root tips from 10 day old seedlings grown without Phosphorus of 1cm length were harvested and immediately frozen in liquid nitrogen. Gene expression analyses were performed

overall_design: Results from xy microarrays are summarized in this study. The samples originate from roots of cultivars Bale and Bacho grown in Phosphorus deficient conditions. Microarrays were hybridized with Cy3 and Cy5 labeled cDNA from Bale and Bacho both during Phosphorus deficiency using a dye swap approach

first: Melanie

last: Bremer

first: Manfred

last: Schenk

first: Philipp

last: Rüdinger


status: Public on Jul 24 2010

city: Debrecen

first: Beata

last: Scholtz

address: Nagyerdei krt 98.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen Medical and Health Science Center

summary:
Aim: To determine the miRNA expression profile of SCLC cell lines vs. normal lung tissue.
Keywords: disease state analysis

overall_design: Total RNA isolated from SCLC cell lines H69, HTB-172, HTB-173 and HTB-184 were compared to a mixed RNA sample derived from 6 normal lung tissue samples (fresh surgical material), from 6 tumor-free patients.  The same reference sample (normal lung) was used on all 4 microarrays.


title: Julidochromis species male vs. female 20100721

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

summary: Whole brain gene expression profiling for Julidochromis transcriptus male vs. female and Julidochromis marlieri male vs female to identify sex-role biased and sex biased gene expression in these species that exhibit conventional and reversed sex-biased behavior respectively.

sample_organism:
Julidochromis marlieri
Julidochromis transcriptus

overall_design: 5 J. transcriptus male vs. female and 5 J. transcriptus female vs. male hybridizations compare 4 males and 4 females in a balanced loop design with dye-swaps that is independent of the 5 J. marlieri male vs. female and 5 J. marlieri female vs. male hybridizations compare 4 males and 4 females also in a balanced loop design with dye swaps.

first: Renn

last: C.P. Suzy


title: Karyotyping of maltose-fermenting Saccharomyces yeasts with differing maltotriose utilization profiles

status: Public on Jul 22 2010

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Aims: We performed an analysis of maltotriose utilization by 52 Saccharomyces yeast strains able to ferment maltose efficiently and correlated the observed phenotypes with differences in the copy number of genes possibly involved in maltotriose utilization by yeast cells.
Methods and Results: The analysis of maltose and maltotriose utilization by laboratory and industrial strains of the species Saccharomyces cerevisiae and Saccharomyces pastorianus (a natural S. cerevisiae/Saccharomyces bayanus hybrid) was carried out using microscale liquid cultivation, as well as in aerobic batch cultures. All strains utilize maltose efficiently as a carbon source, but three different phenotypes were observed for maltotriose utilization: efficient growth, slow/delayed growth and no growth. Through microarray karyotyping and pulsed-field gel electrophoresis blots, we analysed the copy number and localization of several maltose-related genes in selected S. cerevisiae strains. While most strains lacked the MPH2 and MPH3 transporter genes, almost all strains analysed had the AGT1 gene and increased copy number of MALx1 permeases.
Conclusions: Our results showed that S. pastorianus yeast strains utilized maltotriose more efficiently than S. cerevisiae strains and highlighted the importance of the AGT1 gene for efficient maltotriose utilization by S. cerevisiae yeasts.
Significance and Impact of the Study: Our results revealed new maltotriose utilization phenotypes, contributing to a better understanding of the metabolism of this carbon source for improved fermentation by Saccharomyces yeasts.

overall_design: Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

first: Barbara

last: Dunn

first: Boris

last: Stambuk


title: Transcriptomes of genetically distinct E. coli O157:H7 strains

city: East Lansing

first: galeb

last: abu-ali

state: MI

address: NFSTC

department: NFSTC

institute: michigan state university

summary: Transcriptomes of 24 clinical strains of E. coli O157:H7 that differ phylogenetically and by Shiga toxin profiles were compared after 30 min co-incubation with epithelial cells.

overall_design: Total RNA was harvested from the 24 O157:H7 strains exposed to, but not attached to, MAC-T epithelial cell monolayers for 30 min, using a previously described in vitro model of O157:H7 exposure to MAC-T cells. The microarray platform (Operon E. coli oligo set version 1.0.2) probes for 5978 ORFs from E. coli O157:H7 Sakai, O157:H7 EDL 933, and K12 MG1655, and for 110 ORFs from the pO157 plasmid.  Thirty-six dye-swap hybridizations were performed between four groups with six strains per group, according to a balanced double loop design.  Strains were grouped based on cladestx profiles and each strain was considered an independent biological replicate of its group (n=6).  The six strains from each group were randomly hybridized with six strains from every other group; each hybridization compared a pair of strains that differed in either clade or stx profile, or both.

first: Galeb

last: Abu-Ali

first: Lindsey

last: Ouellette

first: Scott

last: Henderson

first: David

last: Lacher

first: James

last: Riordan

first: Thomas

last: Whittam

first: Shannon

last: Manning


title: Gene transcription profiles and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna

status: Public on Jul 23 2010

city: Gent

first: Michiel

last: Vandegehuchte

address: Jozef Plateaustraat 22

department: Applied ecology and environmental biology

country: Belgium

institute: Ghent University (UGent)

summary: A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the exposed and non-exposed hypomethylated daphnids, a large proportion of common genes were similarly up- or downregulated, indicating a possible effect of the DNA hypomethylation. Two of these genes can be mechanistically involved in DNA methylation reduction. The similar transcriptional regulation of two and three genes in the F0 and F1 exposed daphnids on one hand and their non-exposed offspring on the other hand, could be the result of a one-generation temporary transgenerational epigenetic effect, which was not accumulative.

overall_design: The experimental design used in the current study is as follows. A set of neonates (0-24h) taken from the laboratory culture was divided into two batches. One batch was transferred to modified standard M4 medium (Elendt and Bias, 1990) and cultured for three generations (CtrlF0–CtrlF2). A second batch of neonates was transferred into the same medium, with the Zn concentration adjusted to 388 µg/L. A group of F1 neonates born from this ZnF0 generation was then cultured in this Zn-contaminated medium [Zn(+)F1]. Another group of these F1 neonates was transferred back to the control medium [Zn(-)F1]. In this way, Zn(-)F1 daphnids were only briefly exposed to Zn during the first hours of their life-cycle. Offspring of the F1Zn(-) organisms were also cultured in the control medium [Zn(-/-)F2, which were named F2Zn(-) in Vandegehuchte et al. (2009))]. Offspring of the Zn(+)F1 daphnids were in turn divided in a similar manner into two batches, one of which was cultured further in Zn-contaminated medium [Zn(+)F2] while the other one was transferred to the control medium [Zn(+/-)F2]. Each combination of generation and exposure history is termed a ‘treatment’. Three replicates of ten adult daphnids each per treatment were sampled for RNA extraction on the day the next generation was started. In general, a universal reference design was used in which the reference sample was a pool composed of differently aged daphnids cultured in aerated carbon-filtered tap water, enriched with selenium (1 µg/L) and vitamins (7.5 mg/L thiamine, 100 µg/L cyanocobalamin and 75 µg/L biotin). Dye-bias effects were accounted for by regularly swapping Cy3 and Cy5 for labelling treatments/reference pool samples.

middle: B

first: Dieter

last: De Coninck

first: Tine

last: Vandenbrouck

first: Wim

last: De Coen

first: Colin

last: Janssen


title: Differential Gene Expression in G. uraniireducens during Growth on Iron or Manganese Oxide as Electron Acceptor

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: G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate.

overall_design: 3 biological replicates hybridized in duplicate

first: Dawn

last: Holmes


title: Gene transcription in carbamazepine- and minocycline-induced DRESS

status: Public on Jul 21 2010

city: ROUEN

first: Baptiste

last: JANELA

address: 22 boulevard gambetta

country: France

institute: INSERM

summary: Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS) is a severe, drug-induced reaction that involves both the skin and viscera. To understand the immunological components of DRESS, we prospectively assessed 40 DRESS patients. The patients were evaluated for phenotype, cytokine secretion, repertoire of CD4+ and CD8+ peripheral blood T lymphocytes and viral reactivation. A subgroup of patients was analyzed using microarrays.

overall_design: Patients with carbamazepine- or minocycline- induced DRESS were pooled separately for analysis. RNA from total PBMCs and CD4+ and CD8+-sorted blood T cells was amplified. Expression of 894 genes of immunological interest was analyzed with a PIQOR TM arrays (Miltenyi). Gene expression was individually compared between day 0 and 90 in the minocycline-induced DRESS patients.  Control groups included patients taking minocycline carbamazepine, and healthy patients without medication.

last: Janela

first: Damien

last: Picard

first: Philippe

last: Musette


title: Ciona intestinalis (ascidian): control vs. TBT exposed

status: Public on Jul 20 2010

city: Sapporo

first: Sorin

middle: Vasile

last: Sabau

address: 5-1-1-1 Minamisawa, Minamiku

institute: Tokai University

summary: Transcriptional profiling of Ciona intestinalis comparing ethanol exposed asidian (control)  with  TBT exposed ascidian.

overall_design: Two conditions experiment comparing ethanol exposed asidian (control)  with  TBT exposed ascidian.

first: N

last: Satoh


title: Comparison of Gene Expression in Lung of Pigs Exhibiting Different Susceptibilities to Glasser's Disease

city: Edmonton

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

institute: University of Alberta

summary: Haemophilus parasuis is the causative agent of Glasser’s disease in pigs, but this bacterium is also routinely isolated from healthy animals. Whether colonization of the respiratory tract ultimately results in the onset of disease is determined by a combination of environmental, bacterial and host factors that are incompletely understood. This study used DNA microarrays to identify genes that were differentially expressed in the lung of colostrum deprived animals previously characterized as being either ‘Resistant’ or ‘Susceptible’ to infection by H. parasuis in a bacterial challenge experiment at either 24 or 72 hours post-inoculation. Gene expression profiles were obtained by comparing gene expression between each group and a pool of ‘Uninfected control’ animals. The aims of the experiment were: 1) To identify genes associated with resistance and susceptibility to H. parasuis. 2) To identify genes associated with the molecular pathology of Glasser's disease. 3) To identify genes involved in the host response to infection in the lung.

overall_design: Lung tissue RNA from 6 'Fully Resistant' (2 at 24 hours and 4 at 72 hours post-inoculation) and 6 'Susceptible' pigs (2 at 24 hours and 4 at 72 hours post-inoculation), together with pools of RNA from 9 mock inoculated control animals were used in this experiment. This two-colour microarray experiment utilized a reference design. Labelled target DNA from the pool of mock infected control animals (the reference) was co-hybridized with labelled target prepared from individual 'Fully Resistant' or 'Susceptible' animals to a porcine oligonucleotide microarray. Four technical replicates were carried out for each animal (2 sets of dye-swaps);a total of 48 hybridizations. The design allowed for four comparisons to be made: 1. Fully Resistant vs Control at 24 hours. 2) Fully Resistant vs Susceptible at 24 hours. 3) Fully Resistant vs Control at 72 hours. 4) Fully Resistant vs Susceptible at 72 hours.

first: Jamie

first: Carole

last: Sargent

first: Lucina

last: Galina

first: Dan

last: Tucker


title: Bacillus subtilis 168, WT  vs. ΔMWX, WT vs. Δ7ECF, Δ7ECF vs. ΔMWX.

city: Ithaca

first: John

middle: D.

last: Helmann

address: 372 Wing Hall

institute: Cornell University

summary: Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma factors. Three (sigma M, sigma W and simga X) mediate responses to cell envelope active antibiotics. The functions of sigma Y, sigma Z, sigma V, and YlaC remain largely unknown, and strong inducers of these sigma factors and their regulons have yet to be defined. Here, we define transcriptomic and phenotypic differences under non-stress conditions between strains carrying deletions in all seven ECF sigma factor genes (Δ7ECF), a  sigMWX triple mutant (∆MWX), and the parental 168 strain. Our results identify >80 genes as at least partially dependent on ECF sigma factors and, as expected, most of these are dependent on sigma M, sigma W or sigma X which are active at a significant basal level during growth. Several genes, including the eps operon encoding enzymes for exopolysaccharide (EPS) production, were decreased in expression in Δ7ECF but affected little if at all in ΔMWX. Consistent with this observation, Δ7ECF (but not ∆MWX) showed reduced biofilm formation. Extending previous observations, we also note that ∆MWX is sensitive to a variety of antibiotics and Δ7ECF is either as sensitive as, or slightly more sensitive than, the ΔMWX strain to these stressors. These findings emphasize the overlapping nature of the seven ECF s factor regulons in B. subtilis, confirm that three of these (sigma M, W or X) play the dominant role in conferring intrinsic resistance to antibiotics, and provide initial insights into the roles of the remaining ECF sigma factors.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Strains WT  vs. ΔMWX, WT vs. Δ7ECF, Δ7ECF vs. ΔMWX. Each experiment was conducted three times using three independent total RNA preparations (biological triplicates). For each paried comparison,  one sample was  was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647. For each comparison, one replicate was performed with dyewap with the same RNA preparation.

first: Yun

last: Luo


title: Characterization of transcription patterns of bacteriophage fRSL1 genes during infection cycle.

city: Higashi-Hiroshima

first: Takashi

last: Yamada

state: Hiroshima

address: 1-3-1 Kagamiyama

institute: Hiroshima University

summary: fRSL1 is a jumbo myovirus stably and lytically infecting the phytopathogenic bacterium Ralstonia solanacearum. In this study, we investigate the infection cycle of fRSL1 and provide a genomic, proteomic and transcriptomic view of this phage. Its 231-kbp genome sequence showed many genes lacking detectable homologs in the current databases and was vastly different from previously studied phage genomes. In addition to these orphan proteins, fRSL1 was found to encode several enzymes that are unique among known viruses. These include enzymes for the salvage pathway of NAD+ and for the biosynthetic pathways of lipid, carbohydrate and homospermidine. A chitinase-like protein was found to be a potential lysis enzyme. Our proteomics analysis suggests that fRSL1 virions contain at least 25 distinct proteins. We identified six of them including a tail sheath protein and a topoisomerase IB by N-terminal sequencing. Based on a DNA microarray analysis, we identified two transcription patterns.

sample_organism:
Ralstonia solanacearum
Ralstonia phage phiRSL1

overall_design: Total RNA was isolated from 3 ml of fRSL1-infected MAFF730138 cells (containing 1 x 108 CFU infected at moi 0.5 ~ 4) at 0, 10, 30, 90 min, and 30 h post infection (p.i.) using an RNAprotect Bacteria Reagent kit (Qiagen K.K., Tokyo, Japan) according to the manufacturer’s protocol. The integrity and concentration of total RNA were measured using a bioanalysis unit (Agilent 2100 Bioanalyser, Aligent Tech. Palo Alto, CA). Fluorescence-labeled antisense RNA was synthesized by direct incorporation of Cy5-UTP (GE Healthcare Bio-Science Corp., Piscataway, NJ), using each RNA sample and an RNA Transcript SureLABEL Core kit (Takara Bio Inc.). The labeled antisense RNAs were hybridized simultaneously to the microarray chip. DNA microarray preparation, hybridization, processing, scanning, and analyses were performed by Filgen Inc. (Nagoya Japan). For each fRSL1 ORF, 1 to 5 coding sequences of 35 to 40 nucleotide-long were synthesized. A total of 1,100 sequences were put in duplicate on a 40 x 55 array chip. The fluorescence images of hybridized microarrays were obtained with a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA). The Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD) was used to determine the signal intensity of each spot and its local background. Scan data images were alalyzed using Microarray Data Analysis Tool Ver3.0 software (Filgen Inc.)

first: Souichi

first: Hiroki

last: Ishikawa

first: Akiko

last: Fujiwara

first: Takeru

last: Kawasaki

first: Makoto

last: Fujie

first: Hiroyuki

last: Ogata


title: NaphS2 Gene Expression During Anaerobic Degradation of Naphthalene

first: Derek

last: Lovley

summary:
Degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene by anaerobic microorganisms is poorly understood.  Strain NaphS2, an anaerobic sulfate reducing marine delta-proteobacterium is capable of using naphthalene and the aromatic compound benzoate, as well as pyruvate, as an electron donors in the presence of sulfate.

In order to identify genes involved in the naphthalene degradation pathway, we compared gene expression in NaphS2 during growth on benzoate vs. pyruvate, naphthalene vs. pyruvate, and naphthalene vs benzoate.

overall_design:
For each experimental set, aRNA from NaphS2 was labelled Cy5 (experiment) or Cy3(control) with three biological replicates hybridized in duplicate.

In addition, because of the size of the predicted genome of NaphS2, ORFs were divided into two separate array designs, designated set1 and set2, such that set1 and set2 represent two separate array designs (probe sets) to be treated separately in statistical analysis.

first: Raymond

middle: J

last: DiDonato

first: Kuk-Jeong

last: Chin


title: MicroRNA expression from ARPE-19 cells:  control and PDTC treated.

city: Bethesda

first: Cynthia

last: Jawoski

address: bldg 6, room 136

department: NEI

institute: NIH

summary: The cultured cell line ARPE-19 is frequently employed in studies of rpe function.  Here we have identified the microRNAs expressed in RPE cells in the presence and absence of PDTC (pyrrolidine dithiocarbamate), an antioxidant.

overall_design: Analysis used microrNA extracted from untreated cells as a control for cells treated with PDTC

last: Jaworski

first: R

last: Kutty


title: Investigation of barley brittle stem mutants

city: Glen Osmond

first: Ute

last: Baumann

state: SA

address: Hartley Grove

department: Australian Centre for Plant Functional Genomics

institute: University of Adelaide

summary: The barley brittle stem mutants, fs2, designated X054 and M245, have reduced levels of cellulose compared with their isogenic parents Ohichi and Shiroseto.  A custom-designed microarray, based on Agilent technology and including genes involved in cell wall metabolism, was used to compare transcript levels in the mutant and parental lines. For both mutants, the microarray revealed a marked decrease in mRNA for the HvCesA4 cellulose synthase gene in specific zones of stem internodes, and this was confirmed by quantitative PCR.

overall_design: Genes expression was measured for the upper and lower zones from the 4th internodes of stems. Plant were at Zadocks developmental stage 49. Gene expression was compared between mutants and their wildtype parents.

first: Antony

last: Bacic

first: Mary

last: Beatty

first: Rachel

last: Burton

first: Kanwarpal

last: Dhugga

first: Geoffrey

last: Fincher

first: Andrew

last: Harvey

first: Gang

last: Ma

first: Filomena

last: Pettolino

first: J

last: Rafalski

first: Carl

last: Simmons

first: Neil

last: Shirley

first: Jillian

last: Taylor

first: Scott

middle: V

last: Tingey


title: DNA methylation profiles of human active and inactive X chromosomes

city: New York

last: Sharp

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: X chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell. In order to characterize epigenetic changes that accompany this process, we measured DNA methylation levels in both 45,X Turner syndrome patients, who carry a single active X chromosome (Xa) and normal 46,XX females, who carry one Xa and one inactive X (Xi). Methylated DNA was immunoprecipitated and hybridized to tiling oligonucleotide arrays, generating epigenetic profiles of active and inactive X chromosomes. We observed that XCI is accompanied by changes in DNA methylation specifically at CpG islands. While the majority of CpG islands show increased methylation levels on the Xi, XCI results in reduced methylation at ~20% of CpG islands. Both intra- and inter-genic CpG islands are epigenetically modified, with the biggest increase in methylation occuring at the promoters of genes silenced by XCI. In contrast, genes escaping XCI have low levels of promoter methylation, while genes that undergo polymorphic silencing show intermediate increases in methylation proportionate to their frequency of inactivation. Thus promoter methylation and susceptibility to XCI are correlated. We observed a global correlation between CpG island methylation and the evolutionary age of different X chromosome strata, and that genes escaping XCI show increased methylation within gene bodies. We utilized our epigenetic map to predict both novel genes escaping XCI, and to identify sequence features that may contribute to the XCI process. Finally, as our study included Turner syndrome patients with single X chromosomes of both maternal and paternal origin we searched for parent-of-origin specific methylation differences, but found no evidence to support imprinting on the human X chromosome. Our study provides the first epigenetic profile of active and inactive X chromosomes, giving novel insights into the phenomenon of dosage compensation.

overall_design: Methylated DNA was enriched by immunoprecipitation using antibodies against 5-methylcytosine. meDIP and input DNA was labeled with cy5 and cy3 respectively and hybridized to Nimblegen arrays comprising 2.1 million 50-85mers covering human chromosomes 20, 21, 22, X and Y at a mean density of ~1 probe per 100bp. Resulting log2 fluorescence ratios correspond to methylation levels. Seven patients with Turner syndrome (45,X karyotype), and three normal females (46,XX karyotype) were analyzed. Of the Turner syndrome cases, four had a maternally-derived X, and three had a paternally-derived X chromosome.

first: Elisavet

last: Stathaki

first: Eugenia

last: Migliavacca

first: Yann

last: Dupre

first: Patricia

last: Jacobs

first: Stylianos

middle: E

last: Antonarakis


title: MicroRNAs and mRNAs differentially expressed in 5 glioblastoma spheroid cultures upon ATRA treatment

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: Microarray-based gene expression analysis identified microRNAs and mRNAs differentially expressed in 5 glioblastoma spheroid cultures upon ATRA treatment.

overall_design: In this study, a set of 5 glioblastoma spheroid cultures was used to acquire microRNA expression profiles, leading to the identification of differentially expressed microRNAs between untreated and ATRA-treated cultures. In this study, a set of 5 glioblastoma spheroid cultures was used to acquire expression profiles of a total of 16,651 transcripts, leading to the identification of differentially expressed genes between untreated and ATRA-treated cultures by Significance Analysis of Microarray data.

first: Aurélie

first: Felix

last: Engel


title: Mapping of NIPP1-WT and NIPP-RATA binding sites to ENCODE regions

status: Public on Jul 19 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: To gain unbiased insight into the association of NIPP1 with regulatory, coding and intergenic regions of the human genome, DamID experiments and subsequent analysis by ENCODE arrays were performed. The DamID method uses fusions of the bacterial Dam DNA methylase and the protein of interest, to direct the enzymatic activity to the protein’s genomic binding sites, where the DNA is methylated. Methylated DNA is then extracted, enriched and further analysed by microarray. The PP1 (Protein Phosphatase 1) interacting protein NIPP1 has been implicated to play a role in regulation of gene expression through PRC2 function, but also has a function in splicing. The array analysis was performed to obtain a general picture of the sites of chromatin association of NIPP1 and specifically their spatial relation to coding regions as well as to identify target regions to be analysed in more detail. In addition, a PP1 binding deficient mutant (NIPP1-RATA) was analysed, thus allowing to distinguish PP1 dependent and independent sites of association with the genome by microarray analysis. NIPP1-WT is referred to as FDN and the mutant referred to as RATA in the following descriptions.

overall_design: DamID for FDN (NIPP1-WT) (2 replicates) and DamID for RATA (NIPP1 mutant) (2 replicates) vs. control (DamID without fused protein) (2 replicates)

first: Janina

last: Görnemann

first: Aleyde

last: Van Eynde

first: Mathieu

last: Bollen


title: Luminal-like and basal-like in vivo breast cancer xenograft models

last: Stanford Microarray Database

summary: The number of relevant and well-characterized cell lines and xenograft models for studying human breast cancer are few, and may represent a limitation for this field of research. With the aim of developing new breast cancer model systems for in vivo studies of hormone dependent and independent tumor growth, progression and invasion, and for in vivo experimental therapy studies, we collected primary mammary tumor specimens from patients, and implanted them in immunodeficient mice. Primary tumor tissue from 29 patients with breast cancer was implanted subcutaneously with matrigel in SCID mice, in the presence of continuous release of estradiol. The tumors were transferred into new animals when reaching a diameter of 15mm and engrafted tumors were harvested for morphological and molecular characterization from passage six. Further, gene expression profiling was performed using Agilent Human Whole Genome Oligo Microarrays, as well as DNA copy number analysis using Agilent Human Genome CGH 244K Microarrays. Of the 30 primary tumors implanted into mice (including two implants from the same patient), two gave rise to viable tumors beyond passage ten. One showed high expression levels of estrogen receptor-alpha protein (ER) while the other was negative. Histopathological evaluation of xenograft tumors was carried out at passage 10-12; both xenografts maintained the morphological characteristics of the original tumors (classified as invasive grade III ductal carcinomas). The genomic profile of the ER-positive xenograft tumor resembled the profile of the primary tumor, while the profile obtained from the ER-negative parental tumor was different from the xenograft. However, the ER-negative parental tumor and xenograft clustered on the same branch using unsupervised hierarchical clustering analysis on RNA microarray expression data of "intrinsic genes". A significant variation was observed in the expression of extracellular matrix (ECM)-related genes, which were found downregulated in the engrafted tumors compared to the primary tumor. By IHC and qRT-PCR we found that the downregulation of stroma-related genes was compensated by the overexpression of such molecules by the mouse host tissue. The two established breast cancer xenograft models showed different histopathological characteristics and profound diversity in gene expression patterns that in part can be associated to their ER status and here described as basal-like and luminal-like phenotype, respectively. These two new breast cancer xenografts represent useful preclinical tools for developing and testing of new therapies and improving our knowledge on breast cancer biology.

first: Anne-Lise

last: Borresen-Dale