title: Global gene expression in Moraxella catarrhalis ATCC 43617 grown under iron-replete and iron-limiting conditions

summary:
Total RNA samples were isolated from M. catarrhalis grown in BHI (iron-replete condition, designated DF0) and in BHI containing 30 mM Desferal (iron-limiting condition, designated DF30).  Total RNA and M. catarrhalis genome-directed primers (GDPs) were used for synthesis of Cy3- or Cy5-labeled cDNA samples.  Three independent M. catarrhalis growth experiments and total RNA isolations were used for synthesis of cDNA samples, and a total of six DNA microarray hybridizations were performed in this study.
Keywords: Effect of Growth Environment on Global Gene Expression by Moraxella catarrhalis

overall_design: A Moraxella catarrhalis DNA microarray was constructed based on the nucleotide sequence of the genome of M. catarrhalis strain ATCC 43617.  The ORFs in the genome were identified by using GLIMMER 2.02.  The 1,761 annotated ORFs were used to design 70-mer oligonucleotides that would specifically anneal to each ORF.  Because genome-directed primers that annealed within the 3' 30% of each ORF were used to synthesize cDNA, each 70-mer probe was designed to anneal to a region within the 5' 70% of each ORF.


title: Effects of Pkd1 inactivation defined by important developmental switch in post-natal kidney maturation

status: Public on Dec 01 2007

city: Baltimore

first: Gregory

middle: G

last: Germino

state: MD

address: 720 Rutland Ave., room 958

department: Medicine, Division of Nephrology

country: USA

institute: Johns Hopkins School of Medicine

summary:
Autosomal dominant polycystic kidney disease (ADPKD) is an important cause of end stage renal disease for which there is no proven therapy 1. Mutations at PKD1 are the principal cause of disease. The disease begins in utero2 and is slowly progressive but it is not known whether cystogenesis is an ongoing process during adult life. We now show that inactivation of Pkd1 in mice prior to post-natal day 13 results in severely cystic kidneys within three weeks, whereas inactivation at day 14 and later results in cysts only after five months. We found that cellular proliferation was not appreciably higher in cystic specimens than in age-matched controls but that the abrupt change in response to Pkd1 inactivation corresponded with a previously unrecognized brake point during renal growth and significant changes in gene expression. These findings suggest that the effects of Pkd1 inactivation are defined by a developmental switch that signals the end of the terminal renal maturation process. These studies show that Pkd1 regulates tubular morphology in both developing and adult kidney but the pathologic consequences of inactivation are defined by the organ’s developmental status, with important clinical implications for our understanding of disease and our approach to therapy.
Keywords: Developmental status comparison

overall_design:
Goal: Analyze differences in gene expression during late stages of post-natal kidney maturation (i.e. P11, P12, P14 and P15).
Paper: Klaus Piontek, Luis F. Menezes, Miguel Garcia-Gonzalez, David L. Huso, Gregory G. Germino. Effects of Pkd1 inactivation defined by major developmental switch in post-natal kidney maturation.
Design: Kidneys were harvested from wild-type mice at post-natal days 11,12,14 and 15. Four animals (one kidney/animal) and two technical replicates per time point were used.

first: Klaus

last: Piontek

first: Luis

middle: F

last: Menezes

first: Miguel

middle: A

last: Garcia-Gonzalez

first: David

middle: L

last: Huso


title: Identification of Myc-regulated microRNAs in mouse B cell lymphomas

status: Public on Dec 05 2007

first: Tsung-Cheng

last: Chang

address: 733 N. Broadway

institute: Johns Hopkins University School of Medicine

summary:
We previously described the use of a spotted oligonucleotide array to identify the mir-17 cluster as a direct transcriptional target of Myc.  In order to determine whether Myc regulates additional miRNAs, we produced custom microarrays with an expanded set of probes capable of assaying the expression of 313 human miRNAs and 233 mouse miRNAs.  miRNA expression was assayed in a murine model of Myc-induced B cell lymphoma.  In this system, bone marrow from p53-/- mice is infected with a retrovirus that produces a Myc-estrogen receptor fusion protein (MycER).   Infected cells form polyclonal B cell lymphomas in the presence of 4-hydroxytamoxifen (4-OHT), which activates the MycER fusion protein.  RNA from subcutaneous tumors with high Myc activity (animals treated continuously with 4-OHT) and low Myc activity (animals in which 4-OHT was withdrawn after tumor formation) was analyzed.
Keywords: Dose Response

platform_organism:
Caenorhabditis elegans
Mus musculus
Human betaherpesvirus 5
human gammaherpesvirus 4
Murid gammaherpesvirus 4
Human gammaherpesvirus 8

overall_design: RNA from 2 subcutaneous MycER tumors with high Myc activity (animals treated continuously with 4-OHT) and 2 tumors with low Myc activity (animals in which 4-OHT was withdrawn after tumor formation) was analyzed.

first: Duonan

last: Yu

first: Dan

middle: E

last: Arking

first: Kristin

middle: M

last: West

first: Andrei

last: Thomas-Tikhonenko

first: Joshua

middle: T

last: Mendell


title: Identification of Myc-regulated microRNAs in human P493 cells

summary:
We previously described the use of a spotted oligonucleotide array to identify the mir-17 cluster as a direct transcriptional target of Myc.  In order to determine whether Myc regulates additional miRNAs, we produced custom microarrays with an expanded set of probes capable of assaying the expression of 313 human miRNAs and 233 mouse miRNAs.  P493-6 cells which are Epstein-Barr virus-immortalized human B cells that harbor a tetracycline (tet)-repressible allele of Myc were studied.  These cells are tumorigenic in immunocompromised mice and represent a model of human B cell lymphoma.  miRNA expression profiles were examined in the high Myc (-tet) and low Myc (+tet) state.
Keywords: Dose response

platform_organism:
Caenorhabditis elegans
Homo sapiens
Human betaherpesvirus 5
human gammaherpesvirus 4
Murid gammaherpesvirus 4
Human gammaherpesvirus 8

overall_design: P493 cells with high Myc (-tet) and low Myc (+tet) were compared.


title: Wildtype (N2) C. elegans: Control vs. 10mM LiCl treated for 48hr at 25oC

city: Novato

first: Gawain

last: McColl

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Age Research

summary:
Transcriptional profiling of adult C. elegans comparing control untreated  with populations exposed to 10mM LiCl.  Populations treated from larval stage L4  for 48hr at 25oC.  10mM LiCl contained in the Nematode Growth Media (NGM)
Keywords: Drug treatment

overall_design: Two-condition experiment, Control vs. 10mM LiCl treated populations. Biological replicates: 6 control, 6 LiCl treated, independently grown and harvested. All samples compared against common reference total RNA from mixed stage wildtype (N2) worms. One replicate per array.

first: Gordon

middle: J

last: Lithgow


title: Murine myoblasts : Control vs. Reversine treated cells

status: Public on Dec 04 2007

city: suwon

first: Eun Kyung

last: Lee

state: Gyeonggi-do

address: 300 Cheoncheon-dong, Jangan-gu

department: pharmacy

country: South Korea

institute: Sungkyunkwan university

summary:
Transcriptional profiling of mouse myoblasts comparing control untreated C2C12 cells with reversine-treated C2C12 cells.
Keywords: Differentiation state analysis

overall_design: Two-condition experiment, C2C12 cells vs. reversine-treated C2C12 cells. Biological replicates: 2 control, 2 reversine-trated cells, independently grown and harvested. One replicate per array.

first: Eun

middle: K

first: Jeung

middle: W

last: Han


title: Whole genome survey of the obesity model lean congenic mice B6.C-D7Mit353

city: Foster City

first: Yongming

last: Sun

address: 850 Lincoln Center Dr

institute: Applied Biosystems

summary:
We have analyzed the differential expression between the obesity model lean congenic B6.C-D7Mit353 (1) and the background C57BL/6J strains, in four different tissues of male mice: Brain, GWAT (Gonadal White Adipose Tissue), liver and muscle (gastrocnemius). From the 32,381 mouse genes covered by the Applied Biosystems AB1700 microarray system, we identified 330 genes passing FDR at 5% and 188 genes passing FDR at 1%, in any one of the four tissues examined. None of the genes that passed FDR testing were in the congenic donor region. 65 genes from the 8 megabases congenic region were assayed; only six genes (Thrsp, Kctd14, Myo7a, Capn5, Dgat2 and Mtap6) passed statistical significance filtering but not FDR filtering. (1) Diament & Warden 2004: PMID 14569280.
Keywords: Congenic mice whole genome gene expression survey

overall_design: Brain, GWAT, liver and muscle RNA were extracted from biological triplicates of the congenic B6.C-D7Mit353 (Brain samples: Br353C1b, Br353C4a, Br353C5b; Liver samples: L571, L409, L552; Adipose samples: GWAT407, GWAT409, GWAT571; Muscle samples: Gas409, Gas407, Gas552) and the background C57BL/6J strains (Brain samples: BrB1b, BrB3b, BrB5b; Liver samples: Lb570, Lb572, Lb573, GWAT572; Adipose samples: GWAT615, GWAT411; Muscle samples: Gas408, Gas615, Gas570). Digoxigenin-UTP labeled cRNA was generated and linearly amplified from 1 ug of total RNA. Array hybridization, Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following the manufacturer's protocol.

first: Bertrand

last: Perroud

first: Julie

last: Blake

first: Craig

middle: H

last: Walden


title: Differential DNA methylation profiles in estrogen-pre-exposed breast epithelial cells

city: Columbus

first: Alfred

last: Cheng

state: OH

address: OSU Biomedical Research Tower 460 W. 12th Ave.

institute: The Ohio State University

type: Methylation profiling by genome tiling array

summary:
This study tried to determine whether exposure of breast stem/progenitor cells to estrogen disrupts the epigenome of progeny epithelial cells.  DNA methylation profiles were compared between control and pre-exposed epithelial cells using a genome-wide detection method called MeDIP-chip.
Keywords: MeDIP-chip

overall_design: Breast stem/progenitor cells were continuously exposed to 17beta-estradiol (E2, 70 nM) or DMSO (vehicle control) for two weeks and then placed on 2-dimensional collagen substratum for 2-3 weeks for epithelial cell differentiation. DNA from control and pre-exposed cells were extracted and MeDIP ssays were performed using antibodies against 5-methylcytosine. The immunoprecipitated and input DNA were used to probe the Agilent human CpG island microarray. Dye-swap experiments were also performed.

middle: S

first: Tim

last: Huang


title: Chromosomal abberations and transcriptional characteristics linked to the pathogenesis of diffuse large b-cell lymphomas

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary:
We superimposed array comparative genomic hybridization (aCGH) data onto existing expression array profiles (GSE3892) to sift out the pivotal genes underlying the pathogenesis of a well defined series of diffuse large B-cell lymphomas (DLBCL). 280 gained and over-expressed genes were identified, located on chromosomes 1q, 3q, 7, 12p12, 18q and 21q. At the most frequently gained region the oncogene MDMX/MDM4 was concurrently over-expressed, which is a critical regulator of p53 function. In regions of frequent chromosomal loss, 36 genes were concurrently down-regulated, restricted to 6q and 15p. These putative tumor suppressor genes included PERP, MAP3K5, CCNDBP1 and β2M, and loss of 6q was associated with poor clinical outcome. Genes identified and chromosomal regions validated in an independent series of DLBCL patients.
Keywords: comparative genomic hybridization

overall_design:
Overall design fields: Copy number profiles (array CGH) of a series of 42 Diffuse large B-cell lymphoma patient samples were analyzed a) for frequency of aberrations and b) for impact on gene expression. No duplicate samples or dye-swaps were analyzed.
a) Statistical analysis of Array CGH data
Calling: Areas of gains and losses and their frequencies throughout the dataset were determined from the Bluefuse ratios within the statistical package “CGHcall” (van de Wiel et al., 2007). Briefly, after smoothing outliers and median normalization, “DNAcopy” segmentation (Olshen et al., 2004) was applied within CGHcall, after which a call was assigned to each position on the genome. Within CGHcall the probabilities of the calls were determined per chromosomal arm, and a cellularity correction of 0.75 was applied to each sample because tumor cellularity in all DLBCL is estimated to be maximal 75%, taking into account all stromal, endothelial en infiltrating lymphocytes. After calling, we applied “CGHregions” (van de Wiel and van Wieringen 2007) to determine regions of consecutive clones with highly similar calls for all samples. This dimension reduction further increases robustness and statistical power for downstream statistical analyses. Called data were used for all downstream analyses.

b) Integration with expression data
To integrate called array CGH data with expression array data, the array CGH and expression integration tool, ACE-it (van Wieringen et al., 2006), was used. For ACE-it analysis chromosomal amplifications were included in the gains. ACE-it uses the one-sided Wilcoxon rank sum to test which chromosomal aberrations recurrently affect RNA expression and adjust p-values for multiple testing. Only those clones were taken into account which had at least 20% (9) of the  samples in one of the other calling states (gain or loss). Only genes were considered relevant with a false discovery rate of <0.1.
References
- Olshen AB, Venkatraman ES, Lucito R, Wigler M (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-72.
- van de Wiel MA, Kim KI, Vosse SJ, van Wieringen WN, Wilting SM, Ylstra B (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23: 892-4.
- van de Wiel MA, van Wieringen WN. CGHregions: dimension reduction for array CGH data with minimal information loss. Cancer Informatics. In press 2007.
- van Wieringen WN, Belien JA, Vosse SJ, Achame EM, Ylstra B (2006) ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data. Bioinformatics 22: 1919-20.

first: Joost

last: Oudejans

first: Wessel

middle: N

last: van Wieringen

first: Marianne

last: Tijssen

first: Sjoerd

last: Vosse

first: Chris

last: JLM Meijer

first: Gerrit

last: Meijer

first: Bauke

last: Ylstra


title: Transcriptional profiles of T.rubrum treated with PHS11A

status: Public on Nov 30 2007

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

summary:
A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and transcriptional profiles of the responses to PHS11A, a fatty acid synthase inhibitor, were determined.
Keywords: treatment with fatty acid synthase inhibitor

overall_design: The expression profiles of Trichophyton rubrum treated with PHS11A were compared to those of Trichophyton rubrum without drug. Each treatment has three replicates.


title: Interplay between genetic background and genome evolution

city: San Francisco

first: Antoine

last: Snijders

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

summary:
We used genome-wide microarray comparative genomic hybridization to investigate the response of cells of related genetic backgrounds to challenge with methotrexate to gain a better understanding of the underlying defects which foster specific aberrations.
Keywords: array CGH

overall_design: Array CGH experiments of cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

first: Mario

last: Hermsen

first: Joshua

last: Baughman

first: Tineke

last: Buffart

first: Bing

last: Huey

first: Pavla

last: Gajduskova

first: Ritu

last: Roydasgupta

first: Taku

last: Tokuyasu

first: Jane

last: Fridlyand

first: Donna

last: Albertson


title: Role of NF-kB in aging

city: Stanford

first: Howard

last: Chang

address: CCSR 2142

department: Dermatology

institute: Stanford University

summary:
To address the role of NF-kB in aging in vivo, we utilized a well-characterized system that allows inducible and site-specific inhibition of NF-kB activity in murine skin. The hormone binding domain of the mutant estrogen receptor that is responsive to 4-hydroxytamoxifen (4-OHT) was fused to a mutant of p50 (IDNkB, inducible dominant negative NF-kB) that dimerizes with other NF-kB subunits but is unable to bind DNA, thus dominantly inhibiting NF-kB activity. Expression was driven within the basal layer of murine epidermis by the keratin 14 promoter in transgenic mice. To test whether NF-kB activity is required to maintain age-associated gene expression, we applied topical 4-OHT and ethanol vehicle (EtOH) for two weeks to the right (R) and left (L) dorsal flanks, respectively, of chronologically aged transgenic mice (O, 18-23 months). Young transgenic mice (Y, 1 month) were treated in parallel as control. Skin samples were harvested and analyzed for gene expression using mouse cDNA microarrays containing 35,217 elements, representing 18,880 unique genes.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Adam

last: Adler


title: Cell-cycle regulation of cohesin stability along fission yeast chromosomes

city: Bethesda

first: Christine

middle: Katrin

last: Schmidt

address: 41 Library Drive, Bldg. 41, C619

department: LRBGE

institute: NCI (NIH)

type: Genome binding/occupancy profiling by genome tiling array

summary:
Sister chromatid cohesion is mediated by cohesin but the process of cohesion establishment during S phase is still enigmatic. Recent data indicate that in mammalian cells, cohesin binding to chromatin is dynamic in G1 but becomes stabilized during S phase. Whether the regulation of chromosomal cohesin turn-over is integral to the process of cohesion establishment is unknown. Here, we provide evidence that fission yeast cohesin also displays dynamic behaviour. Cohesin association with G1 chromosomes requires continued activity of the cohesin loader Mis4/Ssl3, implying that repeated loading cycles maintain cohesin binding. Cohesin retention on G1 chromosomes was improved by deletion of wpl, the fission yeast ortholog of mammalian WAPL, suggestive of a conserved mechanism that controls cohesin stability on chromosomes. wpl is non-essential, indicating that a change in wpl-dependent cohesin turnover is not integral to the mechanism of cohesion establishment. Instead we find that cohesin instability is down-regulated during S phase in a reaction independent of DNA replication. Hence, cohesin stabilization might be a pre-requisite for cohesion establishment rather than its consequence.
Keywords: ChIP-chip

overall_design:
Experiments in budding and fission yeast have shown that the cohesin loading factors are dispensable for viability in G2, when cohesion has been established (Bernard et al., 2006; Ciosk et al., 2000). In fission yeast, inactivation of the loading machinery at that time no longer affects cohesin binding to chromosomes (Bernard et al., 2006). In mammalian cells, about one-third of nuclear cohesin becomes stably bound to chromatin in G2 (Gerlich et al., 2006). Since the binding of cohesin to chromosomes appears labile in G1, but stabilized in G2, we asked how cohesin becomes stable during the intervening S phase. Spreads showed that Rad21 was only slightly decreased in HU arrested cells after inactivation of the cohesin loading factors Mis4 or Ssl3.
In this series we analyzed whether cohesin association was equally stabilised at all its association sites along chromosome arms. Rad21 binding was therefore analyzed on a chromosome-wide scale by ChIP followed by hybridization to an oligonucleotide tiling array covering chromosomes 2 and 3. We compared the Rad21 binding pattern in HU arrested wild-type versus ssl3-29 cells after the shift to the restrictive temperature. Four 50 kb regions from chromosome 2 are shown in Figure 5, and the complete chromosome 2 in Supplemental Fig.2 (based on samples GSM209708 & GSM209722 compared to the SUP sample GSM209740, provisional accession numbers). This showed that cohesin peaks remained indistinguishable in their relative height and positions whether or not Ssl3 was inactivated. We conclude that, unlike in G1, the loading machinery is dispensable for the stable binding of cohesin to chromosomes in S phase cells.
The experiment was repeated twice with slightly changed parameters (16B12 vs 12CA5 anti-HA antibody, 8.5h vs 9h HU arrest at 20C,  3h at 36C vs 3h at 37C inactivation in HU, see samples for details).

first: Pascal

last: Bernard

first: Sabine

last: Vaur

first: Sonia

last: Dheur

first: Julie

last: Drogat

first: Sylvie

last: Genier

first: Karl

last: Ekwall

first: Frank

last: Uhlmann

first: Jean-Paul

last: Javerzat


title: Yeast mRNA decay analysis after addition of 3 & 10 µ/mL thiolutin

status: Public on Nov 29 2007

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary:
Time course after the addition of the transcriptional inhibitor thiolutin at 3 and 10 µg/mL to an exponential growing culture of S. cerevisiae in YPD.
Keywords: time course, mRNA stability analysis

overall_design: Total RNA from BQS252 yeast strain (Mat a, ura3-52 derived from FY1679) growing in exponential phase in YPD was extracted at 30 minutes after thiolutin 3 and 10 µg/mL addition. All the samples were hybridized on the same nylon array. 2 replicates.

first: Vicent

last: Pelechano

first: José

last: Pérez-Ortín


title: Listeria monocytogenes and Listeria innocua SigB Regulons as defined by salt-stressed and early stationary-phase cells

city: Ithaca

first: Sarita

last: Raengpradub

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

summary:
In several gram-positive bacterial genera including Bacillus, Staphylococcus, and Listeria, sigma B (σB) has been identified as a stress-responsive alternative sigma factor responsible for initiating transcription of genes (the σB regulon) involved in response to stress-inducing environmental conditions. In L. monocytogenes, a foodborne pathogen of considerable threat to public health and the food industry, σB is involved in regulation of stress response and virulence gene expression. We have defined the σB regulon in L. monocytogenes during early stationary phase and under salt stress (0.3M NaCl) conditions using whole-genome microarrays, identifying 168 genes that generated ≥2.0-fold higher signals in the parental strain 10403S than in an isogenic sigB null mutant (ΔsigB), categorized into nine functional groups including stress-response genes (12), virulence genes (5), and genes related to transport (26) and metabolism (45). To gain a broader biological perspective of the σB stress response system, we applied these microarrays to Listeria innocua under the same environmental conditions.  Our studies revealed 64 candidates in the L. innocua σB regulon with ≥2.0-fold higher signals in the parent than in a ΔsigB mutant; 49 of the 64 genes overlap with the L. monocytogenes σB regulon, indicating extensive overlap in σB-controlled genes between the two species. Further transcriptional analysis using TaqMan quantitative real time RT-PCR was performed for selected genes that displayed contrasting fold changes among the four microarray data sets (two stress conditions per species). We report novel members of the L. monocytogenes σB regulon, as well as the initial definition of the L. innocua σB regulon. Our comparative studies of the σB stress response systems in L. monocytogenes and L. innocua revealed features of the σB regulon that are conserved and unique to the two species.
Keywords: Listeria monocytogenes, Listeria innocua, SigB regulon, salt stress, stationary phase

sample_organism:
Listeria monocytogenes
Listeria innocua

platform_organism:
Listeria monocytogenes
Listeria innocua

overall_design: Independent RNA isolations were performed for each growth experiment (log phase cells exposed to BHI+0.3M NaCl and early stationary phase cells). Three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations (salt-stressed and early stationary phase), RNA from the parent strain L. monocytogenes 10403S were hybridized to RNA from the isogenic sigB null mutant.

first: Martin

last: Wiedmann

first: Kathryn

last: Boor


status: Public on Nov 22 2007

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

summary:
Human fibroblast-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express both cell surface markers and genes that characterize human embryonic stem (ES) cells.
Keywords: Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells

overall_design: After prolonged undifferentiated proliferation, these fibroblast-derived cells maintain the developmental potential to differentiate into derivatives of all three primary germ layers in both embryoid bodies and teratomas. These pluripotent cell lines were derived by the transduction of Oct4, Sox2, Nanog, and Lin28 into genetically unmodified, diploid human fibroblasts.  Such human induced pluripotent cell lines should have broad applications in both the development of in vitro models of human disease and transplantation medicine.

first: Junying

last: Yu

first: Kim

last: Smuga-Otto

first: Karen

last: Heidarsdottir

first: Ron

last: Stewart

first: James

last: Thomson


title: Transcriptomic profiling of the livers of blue catfish (Ictalurus furcatus) after infection with Edwardsiella ictaluri

city: Auburn

first: Eric

last: Peatman

state: AL

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

institute: Auburn University

summary:
We have utilized a high-density oligonucleotide microarray for catfish in order to study the transcriptomic responses of blue catfish following infection with E. ictaluri and to identify and develop important immune-related markers for future characterization and genetic mapping.   Microarray analysis of the transcriptome profile of the blue catfish liver following infection with the Gram negative bacterium led to the identification of 103 differentially expressed transcripts. Results indicated the strong upregulation of several pathways likely involved in the inflammatory immune response.  A multifaceted response to infection was observed, encompassing the complement cascade, iron regulation, inflammatory cell signaling, and antigen processing and presentation.  The induction of several components of the MHC class I-related pathway following infection with an intracellular bacterium is reported here for the first time in fish.  Taken together, the microarray results add to our understanding of the teleost immune responses and will provide a solid foundation for future functional characterization, genetic mapping, and QTL analysis of immunity-related genes from catfish.
Keywords: Disease state analysis

platform_organism:
Ictalurus punctatus
Ictalurus furcatus

overall_design: Global gene expression in the blue catfish liver 3 days after infection with virulent Edwardsiella ictaluri was measured utilizing a new 28K catfish microarray. Three replicate pools of RNA (n=25) for control fish and three replicate pools (n=25) for infected fish were analysed on 6 separate arrays. Gene calls from at least 6 probe pairs/transcript were generated in RMA, and normalized values from treatment and control replicates were compared in SAM to identify differentially expressed genes. Criteria of two-fold expression change and a 10% FDR rate were used to determine a set of significantly up- and down-regulated genes. Representative results were confirmed by real-time RT-PCR.

first: Puttharat

last: Baoprasertkul

first: Jeffery

last: Terhune

first: Rex

last: Dunham

first: Zhanjiang

last: Liu


title: Expression profiling of T.rubrum treated with PH11B

status: Public on Nov 21 2007

first: Qi

last: Jin

summary:
T. rubrum was treated with PH11B,a potent  eucaryotic fatty acid synthase inhibtor. A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and transcriptional profiles of the responses to PH11B were determined. Some class-specific and mechanism-independent changes in gene expression were found.
Keywords: fatty acid synthase inhibition

overall_design: The expression profiles of Trichophyton rubrum treated with PH11B were compared to those of Trichophyton rubrum without drug. Each treatment has three replicates.


title: NSCB_human_gene_expression_Serial1

status: Public on Nov 20 2007

first: Melodee

last: Patterson

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

summary:
This series of experiments will serve as quality control for NIH registered
human embryonic stem (hES) cell lines. For example, hES cell marker genes, such as POU5F1, SOX2 and NANOG, should have high expression levels, while differentiation markers, such as NEUROD1 and PAX6, should have low expression levels. The difference between different stem cell lines should be revealed by the difference between expression levels of different markers.
Keywords: Expression Chip

overall_design: In this series of experiments, mRNAs from different human embryonic stem cells (hESCs) are used as sample, while genomic DNA of hESC H1 cell line is used as reference. mRNAs are labeled with Cy5 and hESC H1 gDNA is labeled by Cy3. Normalized ratios of Cy5 VS Cy3 can reveal expression level of different genes in different hESC lines. hESC markers should have high levels of expression, while differetiation markers should have low levels of expression.

last: Mongomery

first: Chuhu

last: Yang


title: CodY of Streptococcus pneumoniae: link between nutritional gene regulation and virulence

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary:
CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillis subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY-mutant and examined the effect on gene and protein expression by microarray and 2D DIGE analysis. The pneumococcal CodY-regulon was found to consist predominantly of genes involved in amino acid metabolism, but also several other cellular processes, such as carbon metabolism and iron uptake. By means of electrophoretic mobility shift assays and DNA footprinting, we showed that most targets identified are under direct control of CodY. By mutating DNA predicted to represent the CodY-box based on the L. lactis consensus, we demonstrated that this sequence is indeed required for in vitro DNA-binding to target promoters. Similar to L. lactis, DNA-binding of CodY was enhanced in the presence of the branched chain amino acids isoleucine, leucine, and valine, and not by GTP. We observed in experimental mouse models that CodY is transcribed in the murine nasopharynx and lungs, and is specifically required for colonization. This finding was underscored by the diminished ability of the codY-mutant to adhere to nasopharyngeal cells in vitro. In conclusion, pneumococcal CodY predominantly regulates genes involved in amino acid metabolism and contributes to the early stages of infection, i.e. colonization of the nasopharynx.
Keywords: codY

sample_organism:
Streptococcus pneumoniae
Streptococcus pneumoniae TIGR4

first: Wouter

last: Hendriksen


title: Expression data from MDCK cells exposed to HGF +/- MAPK inhibitors

city: philadelphia

first: Xiaofeng

last: Zuo

state: PA

address: 380 S. University Ave.

institute: University of Pennsylvania

summary:
Gene expression in Madin Darby canine kidney cells grown for 7 days to confluence on Transwell filters and exposed to HGF +/- inhibitors of the MAPK pathway (MAPK is one of the pathways activated when HGF binds to the CMET receptor tyrosine kinase).
We used microarrays to detail the program of gene expression in MDCK cells and identified genes specifically regulated by HGF via the MAPK pathway.
Keywords: signaling pathway analysis

overall_design: MDCK cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression of genes regulated by the MAPK pathway following HGF induction.

first: Josh

last: Lipschutz


title: Validation of gene expression from rice locus (dye-swap experiment)

status: Public on Nov 28 2007

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

summary:
Transcription from 23K TIGR-loci were confirmed by full-length cDNA mapping, but other 33K TIGR-loci were not confirmed. However, it was not natural to think that full-length cDNA libraries was included almost rice genes, because the transcription of 3K CDS-ANE were confirmed by other transcriptome resources in TIGR OSA1. So, for detection of gene expression from FL-locus and TIGR-locus, we designed about 82K 60mer oligo probes based on TIGR Pseudomolecules release 2. However, TIGR-locus was revised according to revised Pseudomolecules and other additional transcriptome resources. Therefore designed 82K probes were re-mapped on TIGR4 ,and 63455 probes were mapped on 43090 locus
Keywords: tissue type comparison

overall_design:
organisms: Oryza sativa ssp. japonica (Nipponbare)
organisms: Oryza sativa ssp. indica (IR64)
tissue: shoot, root, panicle, callus of Nipponbare
tissue: shoot of IR64
hybridization : two dye method
hybridization : dye-swap experiment
control: Nipponbare shoot
replication: 2 times
array: 2 arrays per 1 experiment (total 16 arrays)

first: Setsuko

last: Kimura

first: Shigemi

last: Iizumi

first: Il-Ryong

last: Choi

first: Shoshi

last: Kikuchi


title: TestChip Expression data of skeletal muscle from of HRT users and non-users

status: Public on Nov 19 2007

city: Jyväskylä

first: Eija

last: Pöllänen

address: PO Box 35/Viveca

department: Department of Health Sciences

country: Finland

institute: University of Jyväskylä

summary:
Modification of Gene Expression of Skeletal Muscle in Response to postmenopause with or without Hormone Replacement Therapy. Test samples randomly selected from a larger study in order to verify the validity of microarray experiment.
Keywords: time course analysis from HRT users and non-users

overall_design: comparison of gene expression in skeletal muscle of healthy postmenopausel women

first: Paula

last: Ronkainen

first: Harri

last: Suominen

first: Timo

last: Takala

first: Satu

last: Koskinen

first: Jukka

last: Puolakka

first: Sarianna

last: Sipilä

first: Vuokko

last: Kovanen


title: Gene expression profiles in testis of pigs with extreme high and low levels of androstenone.

status: Public on Nov 26 2007

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

summary:
Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels. Testicular tissue was collected from 60 boars, 30 with extreme high and 30 with extreme low levels of androstenone, from each of the two breeds Duroc and Norwegian Landrace. The samples were hybridised to porcine arrays containing 26.877 cDNA clones, detecting 563 and 160 genes that were differentially expressed (p < 0.01) in Duroc and Norwegian Landrace, respectively. Of these significantly up- and down-regulated clones, 72 were found to be common for the two breeds, suggesting both general and breed specific mechanisms in regulation of, or response to androstenone levels in boars. Ten of the most significant genes were chosen for verification of expression patterns by quantitative real competitive PCR and real-time PCR. As expected, our results point towards steroid hormone metabolism and biosynthesis as important biological processes for the androstenone levels, but other potential pathways were identified as well. Among these were oxidoreductase activity, ferric iron binding, iron ion binding and electron transport activities. Genes belonging to the cytochrome P450 and hydroxysteroid dehydrogenase families were highly up-regulated, in addition to several genes encoding different families of conjugation enzymes. Furthermore, a number of genes encoding transcription factors were found both up- and down-regulated. The high number of clones belonging to ferric iron and iron ion binding suggests an importance of these genes, and the association between these pathways and androstenone levels is not previously described. This study contributes to the understanding of the complex genetic system controlling and responding to androstenone levels in pig testis. The identification of new pathways and genes involved in the biosynthesis and metabolism of androstenone is an important first step towards finding molecular markers to reduce boar taint.
Keywords: high vs low

overall_design: Testicle samples from animals with extreme androstenone values, 30 high and 30 low from each of the two breeds Norwegian Landrace and Duroc, were used for the experiment. Each microarray was hybridised with one high and one low androstenone sample from the same breed, giving a total of 30 arrays for each breed.

first: Maren

last: Moe

first: Theo

last: Meuwissen

first: Sigbjørn

last: Lien

first: Christian

last: Bendixen

first: Xuefei

last: Wang

first: Lene

last: Conley

first: Ingunn

last: Berget

first: Håvard

last: Tajet

first: Eli

last: Grindflek


title: Heat stress response in Trematomus bernacchii

status: Public on Dec 14 2007

city: Portland

first: Brad

last: Buckley

state: OR

address: 1719 SW 10th Ave

department: Biology

institute: Portland State University

summary:
The goal of this study was to measure the effect of heat stress on the transcriptome of a cold-adapted fish species - Trematomus bernacchii - an Antarctic fish species.
Keywords: Stress response

overall_design: Three control fish are compared to 3 heat-shocked fish, 3 short-term recovery fish and 3 longer term recovery fish.

first: Bradley

first: George

last: Somero


title: Effects of iron overload on gene expression in the cardiac and skeletal muscle of mice

city: Tampere

first: Alejandra

last: Rodriguez-Martinez

address: Biokatu 6

department: Institute of Biomedical Technology

institute: University of Tampere

summary:
Hereditary Hemochromatosis (HH) is an autosomal recessive disorder characterized by an abnormally low expression or functional derangement of the iron regulatory hormone hepcidin. The absorption of dietary iron is disproportionate in these patients, leading to iron deposition in several tissues and consequent damage of organs including liver, heart, and pancreas. Late complications in absence of diagnosis and treatment include cirrhosis, hepatocellular carcinoma, cardiomyopathy and diabetes. Unfortunately, iron overload appears also as an acquired complication. This is the case of a variety of anemias (thalassemias, myelodysplastic syndromes, hemoglobinopathies, etc.) in which compensating mechanisms increase iron absorption. Another cause of iron overload in these patients are the repeated transfusional treatments they receive. It follows that iron overload is a common clinical problem. Therefore, we investigated the effects of iron overload on gene expression in skeletal muscle and heart using microarray technology. Genes with up-regulated expression after iron overload in both skeletal and heart muscle included angiopoietin-like 4, pyruvate dehydrogenase kinase 4 and calgranulin A and B. The expression of transferrin receptor, heat shock protein 1B and DnaJ homolog B1 were down-regulated by iron in both muscle types. Two potential hepcidin regulatory genes, hemojuvelin and neogenin, showed no clear change in expression after iron overload. Concluding, microarray analysis revealed iron-induced changes in the expression of several genes involved in the regulation of glucose and lipid metabolism, transcription and cellular stress responses. These may represent novel connections between iron overload and pathological manifestations of HH such as cardiomyopathy and diabetes.
Keywords: iron induced stress response

overall_design:
C57 male mice were used following the next scheme:
2 diets (iron and control)
2 tissues (cardiac muscle and skeletal muscle)
3 biological replicates in each group

That means the next groups of samples:
1. cardiac muscle from the iron loaded mice, 3 samples, one from each biological replicate
2. cardiac muscle from the control mice, 3 samples, one from each biological replicate
3. skeletal muscle from the iron loaded mice, 3 samples, one from each biological replicate
4. skeletal muscle from the control mice, 3 samples, one from each biological replicate

There were 6 samples from each tissue type and a total of 12 samples in the study.

The iron and control groups were compared for each tissue separately.

last: Rodriguez

first: Mika

last: Hilvo

first: Leena

last: Kytömäki

first: Robert

last: Fleming

last: Britton

first: Bruce

middle: R

last: Bacon

first: Seppo

last: Parkkila


title: Yeast replication in the presence of MMS: WT and isw2 nhp10 strains

city: Seattle

first: Jack

middle: A.

last: Vincent

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson CRC

summary:
The eukaryotic DNA replication machinery must traverse every nucleosome present in the eukaryotic genome during S phase. Since nucleosomes are generally inhibitory to DNA-dependent processes, it is thought that chromatin structure must undergo extensive reorganization to facilitate DNA synthesis. However, the identity of chromatin-remodeling factors involved in replication and how they affect DNA synthesis is largely unknown. Here we show that two ATP-dependent chromatin-remodeling complexes in Saccharomyces cerevisiae, Isw2 and Ino80, function in parallel to promote DNA replication, especially during periods of replication stress. The rate of replication-fork progression is slowed when both chromatin-remodeling pathways are compromised. Both Isw2 and Ino80 complexes are recruited to actively replicating chromatin suggesting that these chromatin-remodeling complexes act directly to promote replication-fork progression. These findings support an important role for ATP-dependent chromatin-remodeling complexes in promoting DNA replication, and define specific stages of replication that require remodeling activity for normal function.

A critical part of this study was the use of microarrays to measure DNA replication progression throughout the genome during MMS treatment. These samples are from experiments where we competed newly replicated DNA against unreplicated DNA on the same microarrays.
Keywords: Time course

overall_design:
Genomic DNA isolated from S.cerevisiae samples taken at 30, 45, 60, 90, and 120 minutes (wild type) or 45, 60, 90, 120, and 150 minutes (isw2 nhp10) after release from G1 arrest (in media containing 0.015% MMS) was digested by restriction enzyme and fractionated into 2 pools: DNA that was replicated in the latest S-phase, and DNA that had not yet been replicated. DNA from each pool was oppositely labeled and co-hybridized to a microarray.

19 total samples:
10 for WT collection
9 for isw2 nhp10 collection

All samples were from the same 2 experiments (1 WT collection, 1 isw2 nhp10 collection)

Each sample has one dye swap pair (with the exception of the 45 min sample from the isw2 nhp10 collection). Dye swapped samples are named identically until the final character (either a or b)

Percent replication values were determined for each corresponding spot on the array as described within.

first: Tracey

last: Kwong

first: Toshio

last: Tsukiyama


title: Yeast mRNA decay analysis after addition of 3 µ/mL thiolutin

status: Public on Nov 17 2007

first: Jose

last: Perez-Ortin

summary:
Time course after the addition of the transcriptional inhibitor thiolutin at 3µg/mL to an exponential growing culture of S. cerevisiae in YPD.
Keywords: time course, mRNA stability analysis

overall_design: Total RNA from BQS252 yeast strain (Mat a, ura 3-52 derived from FY1679) growing in exponential phase in YPD was extracted at different times after thiolutin 3µg/mL addition. All the samples were hybridized on the same nylon array. In order to estimate mRNA stability the intensities where normalized using global poly(A) data from a RNA dot-blot and assuming a first order decaying. There is only 1 replicate.

first: Vicent

last: Pelechano

last: Pérez-Ortín


title: Mouse Fkbp8 activity is required to inhibit cell death and establish DV patterning in the posterior neural tube

status: Public on Nov 16 2007

city: Houston

first: Rebecca

middle: Lee Yean

last: Wong

state: TX

address: 2121 W Holcombe Blvd

department: Center for Environmental and Genetic Medicine

institute: IBT Texas A&M University System HSC

summary:
Mouse Fkbp8 mutants specifically present with spinal cord abnormalities and spina bifida. The aim is to identify gene expression changes in the posterior embryonic tissue lacking the Fkbp8 gene, so as to understand genes or gene pathways important for normal spinal cord development.
Keywords: Genetic modification

overall_design: Heterozygous Fkbp8 mutant mice were intercrossed to obtain embryos of all three genotypes. Posterior tissue (immediately after forelimb bud) was dissected from E9.5 embryos and RNA extracted. Three wildtype tissues and three mutant tissues were used for hybridization on commercially available CodeLink Mouse Whole Genome array.

first: Leeyean

first: Melissa

last: Scott

first: Wei

last: Yu

first: Michelle

middle: Y

last: Merriweather

first: Richard

last: Finnell


title: luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling (II)

status: Public on Nov 14 2007

city: College Park

first: liang

last: wang

address: 5115F Plant Science Building

institute: CBR, UMBI

summary:
The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions.
Keywords: Genetic modification

overall_design: Total RNA was extracted from E. coi W3110 wild type and luxS mutant grown in LB plus 0.8% glucose at OD 1.0. The genomic expression was compared between the two strains using Affymetrix E. Coli antisense genome array.

first: Liang

last: Wang

first: Jun

last: Li

first: John

middle: C

last: March

first: James

last: Valdes

first: William

last: Bentley


title: luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling

overall_design: Total RNA was extracted from E. coi W3110 wild type and luxS mutant grown in LB at OD 2.4. The genomic expression was compared between the two strains using Affymetrix E. Coli antisense genome array.

middle: E


title: Drosophila Myb-MuvB/dREAM (ChIP-chip data)

city: Berkeley

first: Soyeon

last: Ahn

address: University of California, Berkeley

department: Statistics

institute: UC Berkeley

summary:
Myb-MuvB (MMB)/dREAM is a nine subunit complex first described in Drosophila as a repressor of transcription, dependent upon E2F2 and the RBFs. Myb, an integral member of MMB, curiously plays no role in the silencing of the test genes previously analyzed. Moreover, Myb plays an activating role in DNA replication in Drosophila egg chamber follicle cells. The essential functions for Myb are executed as part of MMB. This duality of function lead to the hypothesis that MMB, which contains both known activator and repressor proteins, might function as part of a switching mechanism that is dependent upon DNA sites and developmental context.
Keywords: Drosophila Myb-MuvB/dREAM, ChIP-chip

overall_design:
We used proliferating Drosophila Kc tissue culture cells to explore the genomic locations of MMB following chromatin immunoprecipitation  (ChIP) and tiling array analysis. Purified DNAs were then fragmented, TdT labeled and hybridized to the Affymetrix Drosophila genome Tiling Array 1.0 (reverse part number 520054), as previously described (Manak et al. 2006)

Three CEL files were used as input control DNA for all experiments:
Dro_AS_DroS2_Input_C01_B1_T1.CEL
Dro_AS_DroS2_Input_C01_B1_T2.CEL
Dro_AS_DroS2_Input_C01_B1_T3.CEL
Replicate copies of these three files exist on all 5 samples (GSM231023-GSM231027), and therefore, the TAR file for this series will have 5 copies of each of these files (one for each GSM).

first: Daphne

last: Georlette


title: Validation of gene expression from rice locus (self-hybridization)

first: Kouji

last: Satoh

summary:
Transcription from 23K TIGR–loci were confirmed by full–length cDNA mapping, but other 33K TIGR–loci were not confirmed. However, it was not natural to think that full–length cDNA libraries was included almost rice genes, because the transcription of 3K CDS–ANE were confirmed by other transcriptome resources in TIGR OSA1. So, for detection of gene expression from FL–locus and TIGR–locus, we designed about 82K 60mer oligo probes based on TIGR Pseudomolecules release 2. However, TIGR–locus was revised according to revised Pseudomolecules and other additional transcriptome resources. Therefore designed 82K probes were re-mapped on TIGR4 ,and 63455 probes were mapped on 43090 locus
Keywords: tissue type comparison

overall_design:
organisms = Oryza sativa ssp. japonica (Nipponbare), and indica (IR64)
tissues = shoot, root, panicle, callus
hybridization = two dye method
hybridization = self hybridization
replication = two times

first: Setsuko

last: Kimura

first: Shigemi

last: Iizumi

first: Il-Ryong

last: Choi

first: Shoshi

last: Kikuchi


title: M. tuberculosis response to macrophage intracellular cues - Role of contact, phagosome pH, time, strain

first: Kyle

middle: Herman

last: Rohde

address: Vet. Med. Center, C5 101

department: Microbiology and Immunology

summary:
A central feature of Mycobacterium tuberculosis (Mtb) pathogenesis is the ability of Mtb to survive within macrophages (MØ). Despite its critical importance our appreciation of the interplay between these two cells remains superficial. In this study we employed microarrays to conduct a stepwise dissection of Mtb-MØ interaction during the invasion of resting bone-marrow MØ. Contrary to many bacterial pathogens, engagement by MØ receptors without internalization did not alter Mtb gene expression. Subsequently, a high-resolution profile of Mtb invasion-linked gene expression was generated by assaying the Mtb transcriptome at 20 min intervals up to 2 hours post-infection. Transcriptional responses were detected within minutes of phagocytosis, including gene subsets with distinct temporal profiles. Pharmacological manipulation of phagosomal pH and in vitro acid stress studies revealed that vacuole acidification is an important trigger for differential gene expression. Finally, there are marked species-specific differences in the response of Mtb and M. bovis BCG to intraphagosomal cues.
Keywords: time-course, species-specific expression, in vitro and in vivo acid stress

overall_design: M. tuberculosis CDC1551 or BCG RNA was isolated from macrophage associated bacteria using a guanidine thiocyanate based lysis/RNA stablization buffer that rapidly lyses macrophages while permeating mycobacteria to "freeze" and stabilize the transcriptome.  Due to limited RNA yields from intracellular bacteria, total bacterial RNA was linearly amplified, incorporating amino-allyl UTP during in vitro transcription.  aRNA were post-labeled with amine reactive Alexa dyes and samples were hybridized to spotted oligo arrays in treated vs control dual channel format.   A minimum of two biological replicates was conducted for each assay.  Contact-induced gene expression using cytochalasin D-treated macrophages and pH induced gene expression using concanamycin A treated macrophages (2 biological replicates), CDC1551 and BCG 2hr and 24hr intraphagosomal profiles (5 biological replicates), in vitro acid stress at pH 5.5 and 6.5 (3 biological and 2 technical replicates - 6 total arrays) for each condition.

first: Robert

middle: B

last: Abramovitch

first: David

middle: G

last: Russell


city: Basel

first: Martin

last: Buess

state: CH

address: Petersgraben 4

department: Medizinische Onkologie

country: Switzerland

institute: University Hospital Basel

summary:
These 12 arrays are the basis for Figure 1 of the "An interferon-response induced by tumor-stroma interaction in a subset of human breast cancers" manuscript.  Figure 1: Effect of heterotypic interaction between breast cancer cell line MDA-MB231 and CCL-171 fibroblast. Biologically independent replicates of the mono-cultured fibroblast CCL-171, the breast cancer cell line MDA-MB231 and the mixed co-culture of CCL-171 and MDA-MB231 were grown for 48h at low serum conditions and characterized by DNA microarray hybridization. Hierarchical clustering of a total of 4333 elements that display a greater than 3-fold variance in expression in more than 3 different experimental samples. Data from individual elements or genes are represented as single rows, and different experiments are shown as columns. Red and green denote expression levels of the samples. The intensity of the color reflects the magnitude of the deviation from baseline. Unsupervised hierarchical clustering of the experiments grouped the biological replicates together. Gene expression varied considerably between fibroblast and MDA-MB231 as expected for cells of mesenchymal or epithelial origin respectively. The co-culture profile showed mainly intermediate expression levels. However, the vertical black bar marks a cluster of genes induced in all co-cultures compared to both mono-cultures indicating that they are induced by heterotypic interaction
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed


title: Sim3, a NASP (N1/N2) related protein, escorts CENP-A for deposition at fission yeast centromeres

status: Public on Nov 10 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary:
 A defining feature of centromeres is the presence of the histone H3 variant CENP-ACnp1. It is not known how CENP-ACnp1 is specifically delivered to, and assembled into centromeric chromatin. Through a screen for factors involved in kinetochore integrity in fission yeast we identified Sim3. Sim3 is homologous to
known histone binding proteins NASPHuman and N1/N2Xenopus and aligns with Hif1S.cerevisiae to define the SHNi-TPR family. Sim3 associates with CENP-ACnp1 but is distributed throughout the nucleoplasm rather than being concentrated at centromeres. Cells defective in Sim3 function have reduced levels of CENP-ACnp1 at centromeres and display chromosome segregation defects. Newly synthesized CENPACnp1 can be deposited at centromeres by a replication-independent mechanism during G2. Sim3 is required to allow this new CENP-ACnp1 to accumulate at centromeres in S and G2-phase arrested cells.
We propose that Sim3 acts as an escort which hands off CENP-ACnp1 to chromatin assembly factors, allowing its incorporation into centromeric chromatin.
Keywords: Expression of sim3-143 versus wt and sim3-205 versus wt

overall_design: cDNA expression profiling was carried out according to (Xue et al., 2004). We used the S. pombe ORF spotted microarrays (Eurogentec, Belgium custom DNA microarray services). GeneSpring software was used for all data analysis.


title: Global gene expression analysis in the shoot apical meristem of maize

status: Public on Nov 13 2007

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

summary:
All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both SAMs (SAMs per se plus P0 and P1) and above-ground portions of seedlings collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have 14,400 informative spots from maize. Statistical analyses showed that approximately 6.3% and 6.5% of the tested genes were significantly (p <0.0001) up- and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were also up-regulated (p <0.01). The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kinds of enzymes, suggesting these genes play important roles in meristem maintenance and the early stage of leaf development in maize. Interestingly, several retrotransposon-related genes were greatly up-regulated in the SAM. This finding raised the possibility that retrotransposons are involved in regulatory mechanisms of maize SAM.
Keywords: cell type comparison design

overall_design: An experimental aim is to identify genes preferentially expressed in maize SAM by comparing the transcript abundant between SAMs and seedlings using cDNA microarrays that have 14,400 informative spots from maize.


title: Global gene expression in the maize shoot apical meristem

summary:
All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both whole SAMs (SAMs, P0 and P1) and whole seedlings (above ground part of seedlings) collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have about 30,000 maize cDNA clones. Statistical analyses showed that approximately 7% and 8% of the tested genes were significantly up-regulated and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were significantly up-regulated. Many histone genes and cell cycle related genes were also significantly up-regulated. Those observations validated our microarray results. The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kind of enzymes, suggesting those genes play important roles in meristem maintenance and the early stage of leaf development in maize. Surprisingly, several retrotransposon-related genes were greatly up-regulated with the statistical significance. This finding raised the possibility that retrotransposons are involved in regulatory mechanism of maize SAM.
Keywords: cell type comparison design

overall_design: An experimental aim is to identify genes preferentially expressed in maize SAM by comparing the transcript abundant between whole SAMs and whole seedlings using cDNA microarrays that have about 30,000 maize cDNA clones.


title: epithelial-mesenchymal interaction of the breast

summary:
These 95 arrays are the basis for Figure 2 of our manuscript "An interferon-response induced by tumor-stroma interaction in a subset of human breast cancers". Abstract:Background Communication between different cell types is a cardinal feature of multi-cellular organisms and perturbations in these cell-cell interactions are a key feature of cancer.  However, little is known about the systematic effects of cell-cell interaction on global gene expression in cancer.  Methods and Findings We used an ex vivo culture model to simulate tumor-stroma interaction by systematically co-cultivating breast cancer cells with stromal fibroblasts and determined associated gene expression changes with cDNA microarrays. The picture of heterotypic interaction effects that emerged from this analysis is complex, reflecting the variation in signaling capacities and responsiveness of the involved cells. A frequent and prominent response to epithelial-mesenchymal interaction was an induction of interferon-response genes, observed in 4 of the 7 breast cancer cell lines in response to co-culture with fibroblasts, but not in normal mammary epithelial cells.  In response to close contact with these breast cancer cells, the fibroblasts secreted type I interferons, which, in turn, induced expression of the IRGs in the tumor cells.  Immunohistochemical analysis of human breast cancer tissues showed that STAT1, the key transcriptional activator of the interferon-response genes, and itself an IRG, was expressed in a subset of the cancers, with a striking pattern of elevated expression in the cancer cells in contact with, or close proximity to, the tumor stroma ? paralleling the response seen in our ex vivo model. In vivo, expression of the interferon-response genes was remarkably coherent, providing a basis for segregation of the 295 early-stage breast cancers into two groups. Tumors with high expression levels (n=161) of IRG were associated with significantly shorter overall survival; 59 % at 10 years versus 80% for tumors with low interferon-response gene expression levels (n=134) (log-rank p=0.001).  Conclusion Our results suggest that an interaction between some breast cancer cells and stromal fibroblasts can induce an interferon response, and that this response may be associated with a greater propensity for tumor progression.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: A. fumigatus wild type and delta phoB(PHO80) strains transcriptome analysis for growth upon minimal medium 0.1 mM Pi

status: Public on Nov 09 2007

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

summary:
Phosphate is an essential ion for fungal growth, required for proper DNA and phospholipids biosyntesis, energetic metabolism and signal transduction. The systems for inorganic phosphate (Pi) acquisition in eukaryotic cells (PHO) have been characterized as a low-affinity (that assures a supply of Pi at normal or high external Pi concentrations) and a high-affinity (activated in response to Pi starvation). Here, as an initial step to understand the PHO pathway in A. fumigatus, we characterized the PHO80 homologue, phoB(PHO80). We showed that the delta phoB(PHO80) mutant has a severe polar growth defect and there is an interaction between PhoB(PHO80), calcineurin and calcium metabolism. Microarray hybridizations carried out with RNA obtained from wild type and delta phoB(PHO80) mutant cells showed that Afu4g03610 [phoD(PHO84)], Afu7g06350 [phoE9(PHO89)], Afu4g06020 [phoCPHO81)], and Afu2g09040 (vacuolar transporter Vtc4) were more expressed either in the delta phoB(PHO80) mutant background or in 0.1 mM Pi.
Keywords: gene expression array-based (log2 ratio)

overall_design:
For the microarray experiments, 1.0 x 10(10) conidia of A. fumigatus wild type [delta akuB(ku80)] and delta phoB(PHO80) strain were used to inoculate 300 ml of liquid cultures (Minimal Medium with 0.1 mmol/L or 11 mmol/L of phosphate) in 500-ml erlenmeyer flasks and allow to grow for 6 and 10 hours in a reciprocal shaker (250 rpm) at 37°C. After this time, the cultures were centrifuged and their RNA were extracted. Hybridization experiments were competitive using probes derived from wild type and deltaphoB(PHO80) strain grown for 6 and 10 hours in MM with 0.1 mmol/L or 11 mmol/L of phosphate, using the wild type strain as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

Following normalization, the values for each gene's in-slide replicates were condensed (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects (see Supplementary files linked below).

first: Paula

middle: F

last: Gouvea

first: Frederico

middle: M

last: Soriani

first: Iran

last: Malavazi


title: Genomic profile of maize response to A. flavus infection identifies genes associated with biotic and abiotic resistance

city: Mississippi State

first: Rowena

middle: Yvette

last: Kelley

state: MS

address: 810 Highway 12 East

department: Corn Host Plant Resistance Research Unit (CHPRRU)

institute: USDA-ARS

summary:
The experiment consisted of a field design containing two maize inbred lines Va35 and Mp313E. Va35 has yellow kernels and is susceptible to kernel infection by Aspergillus flavus (A. flavus). Mp313E is a white dent maize inbred line and was released primarily as a source of resistance to kernel infection by A. flavus. The test ears were inoculated with Aspergillus flavus and collected two days after inoculation. Non-inoculated ears collected 16 days after pollination were also used as a control. The microarray experimental design was a randomized complete block design with three replications. One microarray slide was used for each field plot.  Each slide contained the inoculated and non-inoculated sub-treatments. A second slide for one replication of each genotype contained a dye swap for the inoculation treatment and three subsamples (dots) within the slide represented each contig.
Keywords: Direct comparison

overall_design: Two-condition experiment, inoculated vs. uninoculated maize ears for Va35 and Mp313E. Biological replicates: 3 control, 3 inoculated, 2 dye-swap, independently grown and harvested. One replicate per array.


title: Expression data of skeletal muscle from HRT users and non-users

status: Public on Nov 12 2007

first: Eija

last: Pöllänen

summary:
Modification of Gene Expression of Skeletal Muscle in Response to postmenopause with or without Hormone Replacement Therapy.
Even though menopause is often accompanied with first signs of age-associated changes in muscle structure and function, the effects of hormone replacement therapy (HRT) or menopause-related decline in estrogen production in the muscles of postmenopausal women is not well understood. We have used a randomized double-blinded study design together with an explorative microarray experiment to characterize possible effects of continuous, combined HRT and estrogen deprivation on the skeletal muscle of fifteen early postmenopausal women from which 10 used HRT and 5 used placebo for 12-months in a douple-blinded design.
Keywords: time course analysis from HRT users and non-users

overall_design: comparison of gene expression in skeletal muscle of healthy postmenopausel women using HRT (n=10) vs not-using HRT (n=5)

last: Ronkainen

first: Harri

last: Suominen

first: Timo

last: Takala

first: Satu

last: Koskinen

first: Jukka

last: Puolakka

first: Sarianna

last: Sipilä

first: Vuokko

last: Kovanen


title: A. fumigatus wild type strain transcriptome analysis upon 200 mM CaCl2 treatment.

summary:
CRZ is a C2H2 zinc finger transcription factor activated by calcineurin, a protein phosphatase activated by calcium-calmodulin, in different stress conditions related with calcium cell accumulation. CRZ binds to a specific element on the promoter region of genes called CDRE (calcineurin-dependent response element) shown to be sufficient for calcium- and calcineurin-dependent gene expression. In order to investigate which pathways are involved under calcium stress conditions, we determined the transcriptional profile of A. fumigatus wild type strain. Conidia were incubated at 37°C in complete medium for 16 hours and were challenged with 200 mM calcium chloride for 10 minutes. At each time point, the mycelia were harvested by centrifugation and used for competitive microarray hybridizations. We were able to observe a decreased mRNA expression of genes encoding transcription factors and genes that encode GPI anchored proteins, an arrestin domain protein, and a fatty acid synthase beta subunit. In contrast, increased mRNA expression was observed for several genes involved in transcription, development, calcium metabolism, transport, cell cycle and signal transduction mechanisms, and lipid transport and metabolism.
Keywords: gene expression array-based (log2 ratio)

overall_design:
For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus wild type [CEA17 delta akuB(KU80)] strain were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37°C. After this time, the control culture was centrifuged for mycelia recovery and RNA extraction. The other cultures were added by calcium chloride (200 mM) and incubated for 10 more minutes before centrifugation and RNA extraction. Hybridization experiments were competitive using probes derived from 10 minutes calcium chloride shock cultures using timepoint zero (control) as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

Following normalization, the values for each gene's in-slide replicates were condensed (median variance <0.01), and the flip-dye replicates were averaged to compensate for dye-specific effects (see Supplementary file linked below).

middle: H


title: A. fumigatus wild type and delta phoB(PHO80) strains transcriptome analysis for growth upon minimal medium 11 mM Pi

summary:
Phosphate is an essential ion for fungal growth, required for proper DNA and phospholipids biosyntesis, energetic metabolism and signal transduction. The systems for inorganic phosphate (Pi) acquisition in eukaryotic cells (PHO) have been characterized as a low-affinity (that assures a supply of Pi at normal or high external Pi concentrations) and a high-affinity (activated in response to Pi starvation). Here, as an initial step to understand the PHO pathway in A. fumigatus, we characterized the PHO80 homologue, phoB(PHO80). We showed that the delta phoB(PHO80) mutant has a severe polar growth defect and there is an interaction between PhoB(PHO80), calcineurin and calcium metabolism. Microarray hybridizations carried out with RNA obtained from wild type and delta phoB(PHO80) mutant cells showed that Afu4g03610 [phoD(PHO84)], Afu7g06350 [phoE9(PHO89)], Afu4g06020 [phoCPHO81)], and Afu2g09040 (vacuolar transporter Vtc4) were more expressed either in the delta phoB(PHO80) mutant background or in 11 mM Pi.
Keywords: gene expression array-based (log2 ratio)

overall_design:
For the microarray experiments, 1.0 x 10(10) conidia of A. fumigatus wild type [delta akuB(ku80)] and delta phoB(PHO80) strain were used to inoculate 300 ml of liquid cultures (Minimal Medium with 11 mmol/L of phosphate) in 500-ml erlenmeyer flasks and allow to grow for 6 and 10 hours in a reciprocal shaker (250 rpm) at 37°C. After this time, the cultures were centrifuged and their RNA were extracted. Hybridization experiments were competitive using probes derived from wild type and deltaphoB(PHO80) strain grown for 6 and 10 hours in MM with 11 mmol/L of phosphate, using the wild type strain as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

Following normalization, the values for each gene's in-slide replicates were condensed (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects (see Supplementary files linked below).


title: Utility of the Del-Mar 14K Chicken Microarray for Transcriptional Profiling in Different Orders of the Class Aves

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

summary:
The purpose of this microarray experiment was to validate the Del-Mar 14K Chicken Integrated Systems Microarray for different chicken tissues and to determine the utility of this chicken cDNA microarray for other closely related and more distant avian species. The Del-Mar 14 K array was constructed from cDNAs amplified from EST clones sequenced from five normalized chicken cDNA libraries derived from neuroendocrine (5,929), abdominal fat (4,800), liver (2,635), skeletal muscle (2,398), reproductive tract (2,008), 387 long (70mer) oligonucleotides and 72 quality control spots. The array contains 17,770 cDNA clones, where protein matches were found by BlastX analysis for 68% of chicken contigs and 46% of singleton sequences represented on the array. A reference RNA design was used for the hybridization of total RNA from four chicken tissues (liver, abdominal fat, breast muscle and hypothalamus) and the cross-species hybridization (CSH) of total RNA from tissue from birds representing four orders of the Class Aves [Galliformes (chicken, Coturnix quail and domestic turkey), Anseriformes (Peking duck), Falconiformes (American kestrel) and Passeriformes (American tree sparrow)]. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from chicken liver, abdominal fat, breast muscle and hypothalamus. Each of the 43 microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the avian tissue samples and Cy5-labled cDNA targets from the reference chicken RNA pool. Loess-normalized data were used to determine the number of cDNAs expressed in chicken tissues and the number of genes (cDNAs) detectable by cross-hybridization with various avian tissue samples. The Cy5-labeled reference samples were used to determine the coefficient of variation across the 43 microarrays. This study shows a remarkably high level of cross hybridization of Cy3-labeled cDNA targets from a wide range of avian species to the Del-Mar 14K microarray, where 38 to 62% of the cDNA probes on the chicken array (genes) were detectable.
Keywords: Transcriptional profiling, Del-Mar 14K Chicken Integrated Systems Microarray validation, multi-tissues, cross-species hybridization, class Aves

sample_organism:
Anas platyrhynchos
Gallus gallus
Meleagris gallopavo
Passer montanus
Falco sparverius
Coturnix japonica

overall_design: A reference design was used for microarray hybridizations, where a reference RNA pool was made from an equal amount of high-quality total RNA extracted from chicken liver, abdominal fat, breast muscle and hypothalamus. Each of the 43 microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the avian tissue samples and Cy5-labled cDNA targets from the reference chicken RNA pool.

first: Nares

last: Trakooljul

first: Tom

last: Porter

middle: A


title: Expression data from hybrid male Xenopus sex reversal experiment

status: Public on Nov 07 2007

city: Bethesda

first: John

last: Malone

state: MD

department: LCDB/NIDDK

institute: NIH

summary:
Gene expression was examined in genetic females that were sex-reversed to be phenotypically male compared to normal hybrid males
We used microarrays to test expression in the gonad of sex-reversed males (ZW) compared to normal males (ZZ)
Keywords: treatment

overall_design: RNA from testis of sexually mature individuals was extracted and hybridized onto Affymetrix microarrays.

first: Pawel

last: Michalak


title: Microarray gene expression profiling of 27k cDNAs in 23 healthy porcine tissues

city: Aarhus

first: Henrik

last: Hornshøj

address: Brendstrupgårdsvej 100

department: Department of Molecular Medicine

institute: Aarhus University

summary:
Background. Gene expression microarrays have been intensively applied to screen for genes involved in specific biological processes of interest such as diseases or responses to environmental stimuli. For mammalian species, cataloging of the global gene expression profiles in large tissue collections under normal conditions have been focusing on human and mouse genomes but is lacking for the pig genome. Methodology/Principal Findings. Here we present the results from a large-scale porcine study establishing microarray cDNA expression profiles of approximately 20.000 genes across 23 healthy tissues. As expected, a large portion of the genes show tissue specific expression in agreement with mappings to gene descriptions, Gene Ontology terms and KEGG pathways. Two-way hierarchical clustering identified expected tissue clusters in accordance with tissue type and a number of cDNA clusters having similar gene expression patterns across tissues. For one of these cDNA clusters, we demonstrate that possible tissue associated gene function can be inferred for previously uncharacterized genes based on their shared expression patterns with functionally annotated genes. We show that gene expression in common porcine tissues is similar to the expression in homologous tissues of human. Conclusions/Significance. The results from this study constitute a valuable and publicly available resource of basic gene expression profiles in normal porcine tissues and will contribute to the identification and functional annotation of porcine genes.
Keywords: Microarray, Gene expression survey, Large-scale, Normal Healthy tissues, cDNA, Whole genome, Transcriptome

overall_design: The microarray experiment was carried out using a two-channel common reference design with two independent RNA extractions from each tissue sample. For each total-RNA extraction, 20 μg was labeled with Alexa 594 and 20 μg with Alexa 488 using SuperScript Indirect cDNA labeling System from Invitrogen. The RNA extracts labeled with Alexa 488 was collected from all tissue samples, mixed and used as reference sample referred to here as a the common reference. The RNA extracts labeled with Alexa 594 were used individually as labeled tissue samples. The labeled RNA extracts were used in two batches of 23 hybridizations corresponding to the two independent RNA extraction batches. One labeled tissue sample RNA (Alexa 594) and one labeled common reference sample RNA (Alexa 488) was thus hybridized to each of 46 microarrays. The same common reference sample was thus used in all the 46 (2x23) hybridizations. Two rounds of hybridizations on a Discovery XT hybridization station from Ventana were carried out corresponding to the two RNA batches. The hybridized microarrays were scanned and converted into TIFF images using Scanner and ScanArray Express software from Perkin Elmer.

first: Lene

middle: N

last: Conley

first: Jakob

last: Hedegaard

first: Christian

last: Bendixen

first: Peter

last: Sørensen

first: Frank

last: Panitz


title: Expression data from hybrid female Xenopus sex reversal experiment

summary:
Gene expression was examined in genetic males that were sex-reversed to be phenotypically female compared to normal hybrid females
We used microarrays to test expression in the gonad of sex-reversed females (ZZ) compared to normal females (ZW)
Keywords: treatment

overall_design: RNA from the ovary of sexually mature individuals was extracted and hybridized onto Affymetrix microarrays.


title: Drosophila Sex Hierarchy Regulated Gene Expression in Adult Head and Central Nervous System Tissues

status: Public on Nov 06 2007

city: Los Angeles

first: Thomas

middle: Daniel

last: Goldman

state: CA

address: 1050 Childs Way Room 201B

department: Molecular and Computational Biology

institute: University of Southern California

summary:
The Drosophila sex determination hierarchy controls all aspects of somatic sexual differentiation, including sex-specific differences in adult morphology and behavior. To gain insight into the molecular-genetic specification of reproductive behaviors and physiology, we identified genes expressed in the adult head and central nervous system that are regulated downstream of sex-specific transcription factors encoded by doublesex (dsx) and fruitless (fru). We used a microarray approach and identified 54 genes regulated downstream of dsx. Furthermore, based on these expression studies we identified new modes of DSX-regulated gene expression.  We also identified 90 and 26 genes regulated in the adult head and central nervous system tissues, respectively, downstream of the sex-specific transcription factors encoded by fru. In addition, we present molecular-genetic analyses of two genes identified in our studies, calphotin (cpn) and defective probocisis response (dpr), and begin to describe their functional roles in male behaviors.  We show that dpr and dpr-expressing cells are required for the proper timing of male courtship behaviors.
Keywords: genetic modification

overall_design: Two-condition experiment, control versus genetic mutant. RNA harvested from adult head or dissected central nervous system tissue. Biological replicates: 4 control, 4 mutant. Independently grown and harvested. One replicate per array.

middle: D

first: Michelle

last: Arbeitman


title: Chromosome 1 tile path array (version 1) analysis of astrocytomas

city: Cambridge

first: Koichi

last: Ichimura

address: Addenbrooke's Hospital Box 231

department: Pathology

country: United Kingdom

institute: University of Cambridge

summary:
Copy number assessment of chromosome 1 in astrocytic tumors using a chromosome 1 tile path array. Goal was to determine the patterns of chromosome 1 copy number alterations in astrocytic tumors.
Keywords: Comparative Genomic Hybridization

overall_design: Single hybridization per case. 1 diffuse astrocytomas WHO grade II, 6 anaplastic astrocytomas WHO grade III, 5 glioblastomas WHO grade IV were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

first: Artemis

middle: P

last: Vogazianou

first: Danita

last: Pearson

first: Cordelia

last: Langford

first: Simon

last: Gregory

first: V

last: Collins

first: Rachel

last: Cooper


title: Whole genome comparison between Erhlichia chaffeensis strains

city: Columbus

first: Koshiro

last: Miura

state: OH

address: 1900 Coffey Rd

department: Veterinary Biosciences

institute: The Ohio State University

summary:
Ehrlichia chaffeensis is an obligatory intracellular organism, and causes human monocytic ehrlichiosis (HME), a tick-borne illness.  Clinical signs of HME vary from　asymptomatic infection to severe mobility that requires hospitalization or death.  After whole genome sequencing of this bacterium, 425 open reading frames (38%) of 1115 in the genome were found as hypothetical gene with unknown function.  A little is known about pathogenicity gene(s) and strain variation of this bacterium to date.  Previously several E. chaffeensis strains were shown to be different based on comparison of limited gene sequences (p120, OMP-1[p28]s, and VLPT).
To elucidate strain genetic variations and associated virulency, we carried out comparative genome hybridization (CGH) of E. chaffeensis Arkansas, Wakulla and Liberty strains, since these strains are most distinct in the previous studies.  The tiling array containing approximately 300,000 probes of 29 nt spaced as dense as 8 bp on both strands of the genome of E. chaffeensis Arkansas was used.
Keywords: Comparative genome hybridization

sample_organism:
Ehrlichia chaffeensis
Ehrlichia chaffeensis str. Arkansas

overall_design: Two samples were examined.

first: Yasuko

last: Rikihisa


title: Chromosome 1 tile path array (version 2) analysis of astrocytomas

overall_design: Single hybridization per case. 8 diffuse astrocytomas WHO grade II, 16 anaplastic astrocytomas WHO grade III, 72 glioblastomas WHO grade IV were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.


title: Expression data from 12 human thyroid tissue classes and 2 cell lines

city: angers

first: Jean-Fred

last: Fontaine

address: 4 rue Larrey

country: France

institute: INSERM

summary:
It is often difficult to distinguish histologically between the different types of follicular thyroid carcinoma, particularly when they are less invasive. Thus, the identification of specific gene or protein markers would help to apply the thyroid tumor sub-classification recently proposed by the WHO. However, the selection of the best set of markers for each class of follicular thyroid tumor needs a large-scale comparison of the gene and protein expression patterns of the various types of tumor.
Keywords: disease comparison

overall_design: classification of pathologies and gene markers for the thyroid pathologies

first: Frédérique

last: Savagner

first: Délphine

last: Mirebeau-Prunier

first: Patrice

last: Rodien

first: Brigitte

last: Franc

first: Rémi

last: Houlgatte

first: Yves

last: Malthièry


title: HrcA Regulon in Listeria monocytogenes

status: Public on Nov 03 2007

city: Ithaca

first: Sarita

last: Raengpradub

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

summary:
The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes.
We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression between ΔhrcA and wt.  Combined with microarray analysis, Hidden Markov Model searches show HrcA directly repress at least 8 genes.
Keywords: Listeria monocytogenes, HrcA regulon, stationary phase

overall_design: Independent RNA isolations were performed for each growth experiment (log phase cells). For wt vs. hrcA null mutant comparisons, three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from the parent strain (10403S) was hybridized to RNA from the hrcA null mutant.

first: Yuewei

last: Hu

first: Martin

last: Wiedmann

first: Kathryn

middle: J

last: Boor


title: Large scale gene expression of Vero cell correlated to infection of infectious bursal disease virus

status: Public on Nov 05 2007

city: Hangzhou

first: Jiyong

last: Zhou

state: Zhejiang Province

address: 268 Kaixuan road

department: Colege of Animal Science

institute: Zhejiang University

summary:
Infectious bursal disease virus (IBDV) is the pathogenic agent of infectious bursal disease (IBD). Scine it was observed in 1957, IBD spread worldwidely in the chicken flocks, is a important immunosuppressive disease and an threat to poultry industry. Although many studies have be done about IBDV, interaction of IBDV infection and IBDV-encoding genes to host cell gene expression are little known. In this study, the LongSAGE library of Vero-cell, IBDV- infected vero cell, Vero-cell transfected with IBDV-VP5 gene, Vero-cell transfected with IBDV A frament and Vero-cell transfected with IBDV VP243 frament were obtained. We got 96,213 gene tags (17 nucleotides), which represented 24,475 transcripts.
Keywords: Transcripts of different state vero-cell

overall_design:
1.Cloning of the full-length genomic A-segment, VP5 ORF cDNA, VP243 ORF cDNA of IBDV
2.Establishing cloned Vero cell lines expressing VP5, VP243 and A fragment of IBDV
3.Construction of Long-SAGE libraries
4. Sequencing

first: Juxiu

last: Ye

first: Yongzhi

last: Wang

first: Junqing

last: Guo

first: Qingxin

last: Chen

first: Lingyan

last: Li

first: Xiaojuan

last: Zheng

first: Lianlian

last: Hong

first: Yongping

last: Wu


title: The orphan response regulator DigR is required for synthesis of extracellular matrix fibrils in Myxococcus xanthus

status: Public on Nov 02 2007

city: Marburg

first: Lotte

last: Sogaard-Andersen

address: Karl-von-Frisch-Str.

department: Ecophysiology

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

summary:
In Myxococcus xanthus, two component systems have crucial roles in regulating motility behavior and development. Here, we describe an orphan response regulator consisting of an N-terminal receiver domain and a C-terminal DNA binding domain, which is required for A- and type IV pili dependent gliding motility. Genetic evidence suggests that phosphorylation of the conserved, phosphorylatable aspartate residue in the receiver domain is required for DigR activity. Consistent with the defect in type IV pili dependent motility, a digR mutant is slightly reduced in type IV pili biosynthesis and the composition of the extracellular matrix fibrils is abnormal with an increased content of polysaccharides and decreased accumulation of the FibA metalloprotease. Using genome-wide transcriptional profiling, 118 genes were identified that are directly or indirectly regulated by DigR. These genes only include two genes, agmQ and cheY4, previously implicated in A- and type IV pili dependent motility, respectively. In silico analyses showed that 36% of the differentially expressed genes are likely to encode exported proteins. Moreover, four genes encoding homologs of ECF sigma factors, which typically control aspects of cell envelope homeostasis, are differentially expressed in a digR mutant. We suggest that the DigR response regulator has an important function in cell envelope homeostasis and that the motility defects in a digR mutant are instigated by the abnormal cell envelope and abnormal expression of agmQ and cheY4.
Keywords: vegetative analysis (delta)DigR / DK1622 (wt)

overall_design: 5 biological replicates each; normalized ratios to vegetative cells of  DK1622 (wt)

last: Overgaard

first: Sigrun

last: Wegener-Feldbrügge


title: Expression profile for early stationary phase E. coli W3110 expression profile

first: Jun

address: Rm 173, Building 14 A

summary:
Quorum signal uptake is an indispensable part of quorum sensing regulations.  The coperative regulation of uptake repressor and kinase  precisely signale the cells for quorum sensing uptake and terminate the quorum sensing signal production.
We use the DNA microarray to detail the E. coli quorum sensing uptake reuglations and related gene regulations.
Keywords: specific growth

overall_design: W3110 wild type and its isogenic mutants lsrR, lsrK's RNA samples were extracted and hybridized for Affymetrix array.

middle: L

last: Bentley


title: Temporal and Spatial Transcriptional Profiles of Aging in Drosophila

city: Baltimore

first: Haruyoshi

last: Yamaza

address: 6200 Seaforth Street

department: Laboratory of Experimental Gerontology

institute: National Institute on Aging

summary:
Genetic analyses suggest that alterations in gene expression at the molecular and tissue levels can have profound effects on aging for multi-cellular organisms. However, much remains unknown about the normal pattern of genetic changes in different tissues and how these tissues interact during aging. To investigate tissue-specific aging systematically, we measured expression profiles of aging in Drosophila melanogaster in seven tissues representing nervous, muscular, digestive, renal, reproductive, and storage systems. In each tissue, we  identified hundreds of age-related genes mostly showing gradual changes of transcript levels with age. Age-relatedgenes showed clear tissue-specific transcriptional patterns; less than 10% of age-related genes in each tissue shared expression patterns with any other tissue; less than 20% of age-related biological processes were shared between tissues. A significant portion of tissue-specific age-related genes are those involved in physiological functions regulated by the corresponding tissue. However, limited overlaps of age-related function groups among tissues particularly those involved in proteasome function suggest some common mechanisms of transcription regulation in aging across tissues. This study defined global, temporal and spatial changes associated withaging at the molecular and tissue levels. Analyses indicated that different tissues might age in different patterns or at different rates. This study addressed comprehensively the relationship of age-related changes among different tissues in one organism, providing a foundation to address tissue-specific regulation in aging. RNA was then amplified by a one-step linear amplification protocol to generate amplified RNA (aRNA). Experiment aRNA refers to amplified RNA from flies of 15, 20, 30, 45 and 60 days old, and reference aRNA refers to amplified RNA from flies of 3 days old, and experiment and reference aRNAs were labeled with fluorescent dye Cy3 and Cy5, respectively. For each tissue, RNA from the corresponding tissue of 3-day old flies was used as the reference RNA and expression profiles at each of the five age-points was measured twice by using independently prepared duplicated samples.
Keywords: Drosophila melanogaster; Tissue-specific; Brain; Muscle; Gut; Malpighian tubule; Accessory gland; Testis; Adipose tissue; Genome-wide, aging

overall_design: Seven types of tissues or organs of the male fly strain w1118 , accessory gland, testis, brain, gut, malpighian tubule, dorsal thoracic muscle and abdominal fat body were hand dissected out of flies at age of 3, 15, 20, 30, 45 and 60 days old. Tissues or organs from four males of the same age were pooled together and used for each RNA sample preparation.

first: Ming

last: Zhan

first: Yu

last: Sun

first: Jason

last: Sinclair

first: Huai

first: Sige

last: Zou


title: Differential gene expression analysis of iodide treated rat thyroid follicular cell line PCCl3

city: Sao Paulo

first: Edna

middle: Teruko

last: Kimura

state: SP

address: Av Prof Lineu Prestes 1524 sala 414

department: ICB - Cell and Developmental Biology

institute: USP - University of Sao Paulo

summary:
The inhibitory effect of supra physiological iodide concentrations on thyroid hormone synthesis (Wolff-Chaikoff effect) and thyrocyte proliferation is largely know as iodine autoregulation. However, the molecular mechanisms by which iodide excess modulate thyroid functions remains unclear. In this work, we analyzed the rat follicular cell PCCl3 transcriptome profile under untreated and treated conditions with 10-3M sodium iodide (Na/I). Serial Analysis of Gene Expression revealed several transcripts differentially expressed in response to the iodide showing that excess iodide affects almost all aspects of thyroid cell function and differentiation acting on the iodine autoregulatory mechanism through a complex process.
Keywords: comparative genomic analysis

overall_design: PCCl3 cells were cultured under untreated and treated conditions with 10-3M NaI during 24 hours

first: Suzana

last: Leoni

first: Pedro

last: Galante

first: Julio

last: Ricarte

middle: T