title: Comparison of 2 aspen genotypes having similar carbon assimilation rates but different allocation patterns under elevated CO2

city: Huntsville

first: Leland

middle: J.

last: Cseke

state: AL

address: 301 Sparkman Dr.

department: Biological Sciences

institute: The University of Alabama Huntsville

summary:
• Reference to published study making use of this data:  • Cseke LJ, Tsai C-J, Rogers A, Nelsen MP, White HL, Karnosky DF, Podila GK. (2009) Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different allocation patterns under elevated CO2. New Phytologist. submitted.
• This study compared the leaf transcription profiles, physiological characteristics, and primary metabolites of two Populus tremuloides genotypes (clones 216 and 271) known to differ in their responses to long-term elevated [CO2] (e[CO2]) at the Aspen FACE site near Rhinelander, WI.  • Physiological responses of these clones are similar in photosynthesis, stomatal conductance, and leaf area index under e[CO2] yet very different in growth enhancement (0-10% in clone 216; 40-50% in clone 271). While few genes responded to long-term exposure to e[CO2], the transcriptional activity of leaf e[CO2]-responsive genes was distinctly different between the clones, differentially impacting multiple pathways during both early and late growing seasons.   • Analysis of transcript abundance and carbon/nitrogen biochemistry suggests that the CO2-responsive clone (271) partitions C into pathways associated with active defense/response to stress, carbohydrate/starch biosynthesis and subsequent growth. The CO2-unresponsive clone (216) partitions C into pathways associated with passive defense (e.g. lignin, phenylpropanoid) and cell wall thickening.   • This study indicates that there is significant variation in expression patterns between different tree genotypes in response to long-term exposure to e[CO2]. Consequently, future efforts to improve productivity or other advantageous traits for carbon sequestration should include an examination of genetic variability in CO2 responsiveness.

Keywords: Tree genotype comparison under elevated [CO2]

platform_organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

overall_design: 24 two-channel arrays, directly comparing RNA from trees grown in the ambient (control) [CO2] to RNA derived from the same genotype grown under e[CO2].  For each of 4 experimental conditions (clone 216 early season; clone 271 early season; clone 216 late season; clone 271 late season), three independent biological replicates derived from trees grown in three independent replicate FACE rings were used.  In addition, each clone and time point included dye swap reciprocal two-color experiments for each biological replicate. Thus, six data points per cDNA are included (three biological replicates with two technical replicates each).

middle: J

first: Chung-Jui

last: Tsai

first: Holly

last: White

middle: F

last: Karnosky

first: Gopi

middle: K

last: Podila


title: Halibut Microdiet Series

status: Public on Mar 31 2009

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

country: Canada

institute: National Research Council

summary:
Halibut switched to a microdiet and compared to control fed diet at 2, 10, 20 and 30 day post switch. 3 individual controls isolated and RNA pooled for a global control for each time point.

Keywords: Diet comparison over a time course, for 1 diet compared to a reference.

overall_design: Two colour design, Microdiet fed vs control fed, 4 time points, 3 biological replicates per time point.

first: Harry

middle: M

last: Murray

first: Santosh

middle: P

last: Lall

first: Rajesh

last: Rajaselvam

first: LeeAnne

last: Boutlier

first: Brian

last: Blanchard

first: Stefanie

last: Colombo

first: Vindhya

last: Mohindra

first: Manuel

last: Yufera

first: Leah

middle: C

last: Knickle

middle: G

first: Robert

last: Flight

first: Michael

middle: E

last: Reith

first: Susan

last: Douglas


title: Halibut Soydiet Series

summary:
Halibut fed two different diets containing either fishmeal(control) or 25-30% soybean meal for 20 days. Diets compared from fish (5) at day 1, day 10 and day 20 to follow the developement of the soybean-induced enteritis. All experimental samples run against universal RNA (cDNA prepared from 1 ug of a pooled universal RNA consisting of equal amounts of RNA from five developmental stages from hatching until post-metamorphosis).

Keywords: Diet comparison over a time course, experimental diet compared to a reference.

overall_design: Two colour design, Soybean meal (SBM) fed vs control fed, 3 time points, 3 biological replicates per time point.

last: Boutilier


title: Gene expression profiles for different tissues obtained from newly hatched (day 0) and 7 day-old broiler chickens

status: Public on Mar 27 2009

city: Beltsville

first: Mark

last: Richards

state: MD

address: 10300 Baltimore Avenue

department: ANRI

country: USA

institute: USDA, ARS

summary:
The embryo to neonate transition is a critical period of development that has significant impact on broiler production. During this time important genetic programs governing metabolism and growth are established. The goal of this work was to study the effects of early post-hatch (PH) development and time of initiation of feeding on activation of the genetic programs regulating tissue growth and metabolism in liver, brain, duodenum and breast muscle in broiler chickens.
We used chicken genome GeneChip microarrays in a replicated experiment to detail the global program of gene expression in liver, whole brain, duodenum and breast muscle during the post-hatch transition in response to the initiation of feeding.

overall_design: Tissue samples were collected at hatch and 7 days post-hatch for RNA extraction and hybridization on Affymetrix chicken genome GeneChip microarrays. We analyzed three replicate samples of total RNA on separate microarrays for each tissue at hatch and at day 7 post-hatch in order to increase the resolution of expression profiles. To that end, for each tissue we pooled samples from 4-5 individual chicks at both time points to increase representation of the replicate total RNA samples analyzed on the microarrays.

first: Monika

last: Proszkowiec-Weglarz

middle: W

last: Rosebrough

first: John

last: McMurtry

first: Roselina

last: Angel


title: Nutrient limitation-induced regulation of Phanaerochaete chrysosporium genes

status: Public on Mar 30 2009

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

summary:
Transcript profiles of Phanerochaete chrysosporium grown on carbon-limited medium, nitrogen-limited medium and replete medium. Array design based on the DoE's Joint Genome Institute's v2.1 annotation. Goal is to define genes involved in lignin degradation.

Keywords: gene expression under three different culture conditions

overall_design: From a data set of 10,004 unique alleles, each Roche NimbleGen (Madison, WI) array featured 12 unique 60mer probes per gene, all in triplicate. (Seven gene models composed mostly of repetitive DNA were represented by only 2 to 11 60mers.) Total RNA was purified from the five abovementioned media. In short, cultures were harvested by filtering through Miracloth (Calbiochem, EMD Biosciences, Gibbstown, NJ), squeeze dried and snap frozen in liquid nitrogen. Pellets were stored at -80 C until use. Extraction buffer was prepared by combining 10 ml 690 mM para-aminosalicylic acid (sodium salt) (Sigma-Aldrich, St. Louis, MO) with 10 ml 56 mM triisopropylnapthalene sulfonic acid (sodium salt) (Sigma-Aldrich), and placed on ice. To this was added 5 ml 5X RNB (1.0 M Tris, 1.25 M NaCl, 0.25 M EGTA). The pH of the 5X RNB was adjusted to 8.5 with NaOH. The mixture was kept on ice and shaken just before use.  Frozen fungal pellets were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. The ground mycelia were transferred to Falcon 2059 tubes (VWR International, West Chester, PA), and extraction buffer was added to make a thick slurry. The samples were vortexed vigorously and placed on ice until all samples were processed.  One half volume TE-saturated phenol (Sigma-Aldrich) and ¼ volume chloroform (Sigma-Aldrich) were added to each sample and vortexed vigorously.  Samples were spun at 2940 x g in a fixed-angle rotor for 5 minutes.  The aqueous layer was removed to a new tube, and phenol:chloroform extractions were repeated until the interface between the aqueous and organic layers was clear. The final aqueous extractions were placed in clean 2059 tubes, to which was added 0.1 volume 3M sodium acetate, pH 5.2, (DEPC-treated) and 2 volumes absolute ethanol. The tubes were shaken vigorously and stored overnight at -20˚C.  The tubes were spun 1 hour at 2940 x g, the supernatants were decanted, and the pellets were resuspended in 4 ml RNase-free H2O. Total RNA was purified using the RNeasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol for RNA cleanup. RNAs were eluted from the RNeasy spin columns using two spins, for a final volume of 2 ml. The eluted RNAs were ethanol precipitated and stored overnight at -20˚C. The RNAs were spun 1 hour at 2940 x g, washed 1x with 70% ethanol, and resuspended in 50-100ul RNase-free H2O. Three biological replicates per medium were used (15 separate arrays).   RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland). In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 400U of SuperScript II (Invitrogen) for 60 min at 42˚C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07U/ul DNA ligase (Invitrogen), 0.27U/ul DNA polymerase I (Invitrogen), 0.013U/ul RNase H (Invitrogen), at 16˚C for 2 hours.  Immediately following, 10U T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16˚C. Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies) for 10 minutes at 37˚C. Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.  One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D. unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37˚C. Array hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42˚C. Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4. DNASTAR ArrayStar v2.1 (Madison,WI) software was used to quantify and visualize data. Analyses were based on three biological replicates per culture medium. Quantile normalization and robust multi-array averaging (RMA; ) were applied to the entire dataset.


title: Intracellular expression pattern of recombinant Mtb strain TB294 overexpressing sigma factor A

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary: We previously showed that increased expression of the principal sigma factor, SigA, mediates the capacity of Mycobacterium tuberculosis 210 strains to grow more rapidly in human monocytes, compared to other strains. To identify SigA-regulated genes that favor intracellular mycobacterial growth, we used microarray analysis to compare gene expression between a recombinant M. tuberculosis 210 strain bearing a sense sigA construct and a vector control during growth in MonoMac6 cells. The most strongly upregulated gene in the sense sigA transformant was Rv2416c, which has previously been shown to enhance intracellular survival of M. smegmatis, and has been designated as eis. Real-time PCR confirmed marked upregulation of eis mRNA by the intracellular sense sigA transformant, and lysates of this transformant contained high concentrations of the Eis protein. Chromatin immunoprecipitation demonstrated that SigA bound the eis promoter region in live bacteria. Deletion of the eis gene reduced growth of M. tuberculosis in macrophages, and complementation of eis reversed this effect. We conclude that SigA regulates eis expression, which in turn contributes to the enhanced capacity of the M. tuberculosis 210 strain to grow in human macrophages.

overall_design: The M. tuberculosis DNA microarray consisted of 4,295 70-mer oligonucleotides representing the 3,924 predicted open reading frames of the H37Rv strain (http://www.sanger.ac.uk) and 371 probes designed to detect sequences in the CDC1551 strain (http://www.tigr.org). The arrays were prepared by spotting oligonucleotides (Tuberculosis Genome set version 1.0, Operon Biotechnologies) onto poly-L-lysine coated glass microscope slides, as described (Pang et al., 2007). Total RNA from two independent experiments was prepared from M. tuberculosis harvested from infected MonoMac6 cells, as described above. cDNA synthesis, labeling, hybridization, scanning, image acquisition and normalization were performed, as described (Pang et al., 2007), and for each experiment, a dye flip was performed. Data were filtered by removing all spots that were below the background noise or flagged as ‘bad’. Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest mean background of the chip.  The ratio of the average median intensity of Cy5 over the average median intensity of Cy3 was determined for each spot and the fold change values were calculated.  Expression changes were considered significant if there was at least a 2-fold or higher change in expression between TB294-pSigA and TB294-pCV in three of the four array experiments.

first: Shiping

last: Wu

first: Peter

last: Barnes

first: Buka

last: Samten

first: Xiuhua

last: Pang

first: Sebastien

last: Rodrigue

first: Patricia

last: Soteropoulos

first: Luc

last: Gaudreau

middle: T

last: Howard


title: Cells following mtDNA loss, or NAR1 repression

status: Public on Mar 24 2009

city: Seattle

first: Daniel

last: Gottschling

state: WA

address: 1100 Fairview Avenue N., Mailstop A3-025

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Expression analysis of cells the given amount of time after mtDNA was lost (or Nar1 expression was repressed) compared to pretreatment (or NAR1 being fully expressed).

overall_design: One time course experiment (Cells a given amount of time following mtDNA loss compared to cells with intact mtDNA), with 2 two condition experiments (Cells with the ATP1-111 genotype 27 hours following mtDNA loss compared to the same cells with intact mtDNA, and cells 27 hours following repression of NAR1 comared to cells expressing NAR1). Each data point had 3 biological replicates, and was dye-swapped. One replicate per array.

first: Joshua

last: Veatch


title: Endothelial transcriptomic responses in a mouse model of type II diabetes

status: Public on Mar 28 2009

city: Honolulu

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

summary:
Aortic endothelia from mice exposed to dietary model of type II diabetes at 4, 6 and 8 weeks of exposure to Bio-Serv #S3282 diet.  Objective: Type II diabetes is associated with endothelial dysfunction, which can contribute to accelerated atherosclerosis and subsequent cardiovascular events. We seek to identify transcripts dysregulated in vivo in response to chronic exposure to high dietary fat that leads to diabetes.
Methods: Beginning at 8 weeks of age, male Tie2-GFP mice (transgenically expressing green fluorescent protein exclusively within the endothelia) were fed a 60% fat calorie diet (Bio-Serv #S3282); age-matched mice were fed normal chow. After 4, 6, and 8 weeks on the diet, aortae and skeletal muscles (gastrocnemius, biceps femoris, and plantaris) were excised, minced, and collagenolytically digested. Each tissue digest was then subjected to FACS in order to obtain 10,000 endothelial cells. Transcriptomic analyses were performed with microarrays containing the Operon Murine V4 oligo set, and highly dysregulated genes were confirmed by real-time PCR. Results: By 4 weeks, Tie2-GFP mice receiving a high fat diet exhibited a fasting glucose of 215+17 mg/dL vs. 134+23 mg/dL in controls; by 6 weeks, a high fat diet resulted in lower glucose tolerance vs. control diet. Following 4, 6, and 8 weeks of high-fat regimen, aortic endothelial transcripts up-regulated by greater than 2-fold in biologically replicate experiments included macrophage inflammatory protein 2 (Mip2), chemokine (C-C motif) ligand 9 (CCL9), galectin-3 (Gal-3), and 5-lipoxygenase-activating protein (FLAP). Endothelial transcripts up-regulated in skeletal muscle included Mip2, CCL8 and 9, FLAP, gal-1 and 3, and ferritin light chain 1 (FTL1); transcripts down-regulated in muscle included endothelin-1 (ET-1) and insulin-like growth factor II (IGF II). Discussion: Gal-3 and FTL-1 are known to increase in response to advanced glycation end-products and oxidized LDL, respectively. However, the down-regulation of ET-1 and IGFII was surprising, as the transcription of these genes has previously been thought to exacerbate atherosclerosis. In conclusion, a comprehensive analysis of the endothelial transcript-level response to a dietary model of Type II diabetes has revealed novel regulation of transcripts with roles in inflammation, insulin sensitivity, oxidative stress, and atherosclerosis. Understanding the mechanism of diabetes-associated endothelial dysfunction may lead to improved therapies that lower the risk of cardiovascular complications in diabetic patients.

overall_design: Each experiment is performed with a technical  replicate i.e. dye reversal.  there is a biological replicate of the 4 week time point

first: April

last: Darrow

first: Ralph

middle: V

last: Shohet


title: Evaluation of a Low Density DNA Microarray for Small B-Cell non-Hodgkin’s Lymphoma Differential Diagnosis

status: Public on Mar 25 2009

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

summary:
Lymphomas are classified according to the World Health Organization (WHO) classification which defines subtypes on the basis of clinical, morphological, immunophenotypic, molecular and cytogenetic criteria.
Using this model, 8 of 9 of the validation samples were classified successfully. This pilot study demonstrates that such a microarray tool may be a promising diagnostic approach for small B-cell non-Hodgkin’s lymphoma.

Keywords: Small B-Cell non-Hodgkin’s Lymphoma, Low Density DNA Microarray, Diagnosis

overall_design: Fresh-frozen tumor biopsies performed before treatment and clinical data were obtained retrospectively from 68 patients in five different institutions after lab investigations involving cytology, immunohistochemistry, cytogenetics (conventional cytogenetics and fluorescent in situ hybridization [FISH]), and/or molecular analysis. The samples were then classified unanimously by a panel of five pathologists as one of the 4 subtypes: 17 B-CLL, 14 MZL, 23 FL and 14 MCL. The immunohistochemical criteria used for identifying the 4 subtypes of SBCL were: CD20+/-, CD5+, CD23+ for B-CLL; CD20+, CD5+, CD23-, Cyclin D1+ for MCL; CD20+, CD10+, Bcl2+ for FL; CD20+, CD5-, CD10- for S-MZL. 28 samples were rejected for technical issues with RNA. The remaining 40 samples include the 4 different subtypes with this following distribution: Follicular Lymphoma/FL (n=15), Mantle Cell Lymphoma/MCL (n=7), B-Chronic Lymphocytic Leukemia/B-CLL (n=6) and Splenic Marginal Zone Lymphoma/S-MZL (n=12). The expression profile of 107 genes was evaluated in these 40 samples defined as a training set. Replicates were performed for samples of sufficient quantity, and a total of 79 gene expression profiles, comprised of 12 samples in triplicate, 15 samples in duplicate and 13 samples evaluated singly, were then analyzed.   A second group of 13 patients was defined as test set and used to validate the gene signatures highlighted from the training set analysis. These patients were selected by a pathologist independent from the first analysis and include 4 FL, 3 B-CLL, 5 MCL and 1 S-MZL. Four samples were rejected for technical issues with RNA. The remaining 9 samples include the 4 different subtypes: 2 FL, 3 B-CLL, 3 MCL and 1 S-MZL. A total of 13 gene expression profiles were analyzed (4 samples evaluated in duplicate and 5 samples investigated singly).

first: Jean-Pierre

last: Gillet

first: Thierry

last: Molina

first: Jacques

last: Jamart

first: Philippe

last: Gaulard

first: Karen

last: Leroy

first: Josette

last: Brière

first: Ivan

last: Théate

first: Catherine

last: Thieblemont

first: André

last: Bosly

first: Michel

last: Hérin

last: Hamels

first: José

last: Remacle


title: Gene expression profile of embryonic retinas expressing c-hairy1, Delta-1, or Wnt2b

city: Wako

first: Shinichi

last: Nakagawa

state: Saitama

address: Hirosawa 2-1

country: Japan

institute: RIKEN ASI

summary:
Expression profile of embryonic retinas expressing exogenous c-hairy1, Delta-1, or Wnt2b. These genes inhibits neuronal differentiation, and the results provide insight into the mechanism that keeps retinal progenitor cells undifferentiated.

In the vertebrate retina, stem cell-like progenitor cells are maintained in a distinct region, called the ciliary marginal zone (CMZ). Canonical Wnt signaling regulates the maintenance of the progenitor cells in the CMZ. However, its downstream molecular mechanisms have remained largely unclear. Here, we show that c-hairy1, an established Notch signaling effector, mediates the Wnt-dependent maintenance of CMZ progenitor cells in chickens. Interestingly, unlike other developmental contexts where Hes gene expression is regulated by Notch signaling, the c-hairy1 expression in the CMZ is regulated by Wnt signaling. c-hairy1 is necessary and sufficient for the expression of a set of molecular markers characteristic of the CMZ, and Wnt2b fails to induce CMZ markers when c-hairy1 activity is inhibited. Furthermore, microarray analysis identifies multiple Wnt-responsive transcription factors that activate c-hairy1 expression. We thus propose that c-hairy1 functions as a node downstre am of Wnt signaling to maintain progenitor cells in the CMZ.

overall_design: Total RNA was purified from E6.5 retinas transfected either with c-hairy1, Wnt2b, Delta, or mock-expressing RCAS plasmid using Trizol reagent (Invitrogen). Microarray analysis using Gene Chip Chicken Genome Array (Affymetrix) was performed according to the manufacturer’s protocols. Data were analyzed using GCOS (Affymetrix) and dChip (Li and Wong, 2001). GCOS and dChip produced similar results.  The data submitted is from GCOS. To explore candidates for new Wnt target genes, genes with higher expression in Wnt2b-expressing retina than control or Delta1-expressing retinas were selected for further analysis.

first: Fumi

last: Kubo


title: Focused microarrays as a method to evaluate subtle changes in chicken embryonic heart gene expression

city: Raleigh

first: Jean

middle: Eduardo

last: de Oliveira

state: NC

address: 2711 Founders Dr

department: Poultry Science

institute: North Carolina State University

summary:
Microrrays plataforms with thousands of gene sequences have limited capacity to pick up subtle small changes in gene expression. A focused two-color microarray platform was designed for high replication and to use statistical power to detect small changes
Keywords: time course, embryo development

overall_design: Individual samples from 8 embryos  were arraged on a complete interwoven loop design where each treatment (embryonic ages 7, 15, 19 and 20) was replicated 8 times (4 dye-swaps).

first: Shelly

last: Druyan

first: Chistopher

last: Ashwell


title: The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

first: Carrie

middle: A.

last: Smith

address: 2510 Gardner Hall

department: Department of Plant Pathology

institute: NC State University

summary:
Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs.  These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi.  Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus.   An Affymetrix GeneChip® microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus.  RNA expression analysis showed that 32 NATs and 2709 genes were differentially expressed between 37°C, the optimum temperature for growth, and 28°C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism.  This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus and shows that although less than 10% of putative NATs are differentially expressed in response to temperature, some of the NAT-cis gene interactions are likely to be important.

Keywords: temperature response

sample_organism:
Zea mays
Aspergillus flavus

overall_design: 3 samples (reps) for each temperature treatment were analyzed with a total of 6 samples.

middle: A

first: Dominique

last: Robertson

first: Bethan

last: Yates

first: Dahlia

last: Nielsen

first: Doug

last: Brown

first: Ralph

last: Dean

first: Gary

last: Payne


title: Asporin is Expressed at Higher Levels in the More Degenerate Human Intervertebral Disc Tissue

city: Charlotte

first: Helen

last: Gruber

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

summary:
Asporin, also known as periodontal ligament-associated protein 1 (PLAP1), is a member of the family of small leucine-rich proteoglycan (SLRP) family. It is present within the cartilage extracellular matrix (ECM), and is reported have a genetic association with osteoarthritis.  Its D14 allele has recently been found to be associated with lumbar disc degeneration in Asian subjects.  There have been no studies, however, of this gene’s normal immunohistochemical localization within the human intervertebral disc, nor of expression levels in Caucasian individuals with disc degeneration. Studies were approved by our human subjects Institutional Review Board.  Methods included immunohistochemical localization of asporin in the disc of humans and the sand rat (a small rodent with spontaneous age-related disc degeneration), and Affymetrix microarray analysis of asporin gene expression in vivo and in vitro.
mmunohistochemical studies of human discs revealed that some, but not all, cells of the outer annulus expressed asporin.  Fewer cells in the inner annulus contained asporin, and it was rarely present in cells in the nucleus pulposus.  Similar patterns were found for the presence of asporin in lumbar discs of sand rats. Substantial relative gene expression levels were seen for asporin in both disc tissue and in annulus cells grown in three-dimensional culture. More degenerate human discs (Thompson grade 4) showed higher expression levels of asporin than did less degenerate (grade 1, 2 and 3) discs, p = 0.004. In the discs of Caucasian subjects studied here, and in the sand rat, greater immunolocalization levels were found in the outer compared to inner annulus.  Localization was rare in the nucleus.  Gene expression studies showed greatest expression of asporin in the more degenerate human discs in vivo.

overall_design: Disc Tissue samples were obtained via the National Cancer Institute Cooperative Tissue Network (CHTN) as well as surgical disc procedures performed on patients with herniated discs and degenerative disc disease. Tissue was fixed and paraffin embedded. Standard laser capture microdissection (LCM) techniques were used to collect the cells from which total RNA was isolated and analyzed via microarray. Based on the Thompson scouring system, unhealthy discs (grade 4) were compared to healthy discs (grades 2,3).

first: Jane

last: Ingram

first: Gretchen

middle: L

last: Hoelscher

first: Natalia

last: Zinchenko

first: Edward

middle: N

last: Hanley Jr

first: Yubo

last: Sun


title: Comparative gene expression study of Lactobacillus acidophilus NCFM and upp mutant (NCK1909)

first: Todd

middle: Robert

last: Klaenhammer

department: Department of Food, Bioprocessing, and Nutrition Sciences

summary: A L. acidophilus NCFM mutant (NCK1909) carrying an in-frame deletion within the upp gene (LBA0770) was constructed as a background host for a newly developed upp-based counterselectable gene replacement system for L. acidophilus.  Since the NCK1909 mutant serves both as the host for genetic exchange and the reference strain for subsequent phenotypic studies of deletion mutants that will be generated from the counterselective gene replacement system, comparative gene expression study was performed to ensure the genotype of NCK1909 is representative of the NCFM parent strain.

overall_design:
Oligoarray hybridization experiments were performed to compare the transcriptional profiles of the NCK1909 mutant with relative to NCFM at early-log (OD600nm 0.3) and mid-log (OD600nm 0.8) phases when cultured in MRS medium at 37 C under ambient atmospheric condition.  These cell density levels represent the growth stages when cells were collected for stress challenge assays (OD600 0.25 to 0.3) and in vitro cell adherence assays (OD600 0.6 to 0.8) during phenotypic analyses.

NCFM and NCK1909 were grown in fresh MRS medium with a 2% inoculum from overnight culture.  Aliquots of cells were collected at OD600nm of 0.3 (early log-phase) and 0.8 (mid-log phase) for total RNA extraction and cDNA synthesis.  Samples were collected from two independent experimental replicates (representing two biological replicates, designated as Rep A and Rep B).  Labeled cDNA samples from NCFM and NCK1909 were coupled with mono-reactive Cy3 and Cy5 dyes (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), respectively.  Comparative hybridizations were performed on samples representing both NCFM and NCK1909 at same growth phases.

first: Yong-Jun

last: Goh

last: Azcarate-Peril

middle: R


title: Amino acid/Nucleotide perturbation in Escherichia coli

status: Public on Mar 26 2009

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Wild-type E. coli are prototrophic for all amino acid and nucleotides. These are synthesized by a network of interconnected metabolic pathways from a handful precursors molecules, which are regulated at the level of gene expression. It was hypothesized in this study, that since metabolic pathways are interconnected, transcriptional regulation should be shared across multiple pathways. To uncover these regulatory interactions, cells growing at steady state were perturbed by the addition of an end-metabolite (aa or nt), and were allowed to recover. The adjustments in biochemical pathways to the perturbation were sampled by profiling mRNA abundance 10 minutes after the perturbation. By limiting the scope and magnitude of the perturbation, mRNA changes are expected to be limited to specific responses to the perturbation and not genome-wide changes associated with larger perturbations such as nutritional shifts and stresses.

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

overall_design: Exponentially growing E. coli cells in M9 minimal medium + 0.4 % glucose were perturbed by the addition of 1 mM amino acid or nucleotide individually, and the transcriptional responses were tracked after 10 minutes. In total, 22 metabolites were tested, including 2-4 biological replicates for each including dye-swaps. In each experiment, the reference channel for the dual channel hybridization were cells at 0 minutes before perturbation.

first: Arkady

middle: B

last: Khodursky


title: Auxin-induced gene expression in mesocotyl elongation of maize inbred line 3681-4 tolerant to deep-sowing

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

country: China

institute: Chinese Academy of Agricultural Sciences

summary: In order to elucidate the molecular mechanism of auxin-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying IAA promotion of maize mesocotyl elongation. Under deep-sowing condition, IAA is transported by auxin transporter-like protein 1 and binds to auxin binding protein ABP20, which results in degradation of Aux/IAA and de-repressing of auxin-inducible genes. Then, transcriptional factor such as MYB, kinase such as LRR, fructose and mannose metabolism and so on are activated. Finally, genes involved in cell wall synthesis and modification are expressed so that mesocotyl elongation of 3681-4 is promoted. Furthermore, gene expression of a key enzyme ACO in ethylene biosynthesis and ethylene receptor ETR2 were up-regulated after the treatment with 10-4 M IAA, which suggested that mesocotyl elongation of 3681-4 inclined to be inhibited when the concentration of applied IAA was increased from 10-4 M to 10-3 M.

overall_design: In two independent experiments, we generate 10-day-old maize mesocotyl-specific gene expression profiles through comparing genome-wide expression patterns of IAA treatment and TIBA (an auxin transportation inhibitor) treatment under 20 cm deep-sowing condition in darkness by using 17,555 Affymetrix maize whole genome array.

first: Zhao

last: Guangwu

first: Fu

last: Junjie

first: Wang

last: Guoying

first: Ma

last: Pan

first: Wu

last: Liwen

last: Jianhua


title: Shared prognostic markers in undifferentiated pleomorphic sarcoma and leiomyosarcoma of the extremities

city: Lund

first: Mef

last: Nilbert

state: Skåne

address: Barngatan 2B

department: Oncology

country: Sweden

institute: Lund University

type: Genome variation profiling by genome tiling array

summary: Soft tissue sarcoma diagnostics and prognostics are challenging, particularly in highly malignant and pleomorphic subtypes such as undifferentiated pleomorphic sarcoma (UPS) and leiomyosarcoma (LMS). We applied 32K BAC-arrays and gene expression profiling to 18 extremity soft tissue LMS and 31 extremity soft tissue UPS with the aim to identify molecular subtype signatures and genomic prognostic markers. Both the gains/losses and gene expression signatures revealed striking similarities between UPS and LMS, which were indistinguishable using unsupervised hierarchical cluster analysis and significance analysis for microarrays. Gene expression analysis revealed just 9 genes, among them Tropomyosin beta, that were differentially expressed. Loss of 4q31 (encompassing the SMAD1 locus), loss of 18q22 and tumor necrosis were identified as independent predictors of metastasis in multivariate stepwise Cox regression analysis. Combined analysis applying loss of 4q31 and 18q22 and presence of necrosis improved the area under receiver operating characteristic curve for metastasis prediction from 0.64 to 0.86. The extensive genetic similarities between extremity soft tissue UPS and LMS suggest a shared lineage of these STS subtypes and the new and independent genetic prognosticators identified hold promise for refined prognostic determination in high-grade, genetically complex STS.

overall_design: Genomic DNA was extracted from a total of 49 samples, 31 Undifferentiated pleomorphic Sarcomas and 18 Leiomyosarcomas. The DNA was labeled using Bioprime array CGH labeling kit (Invitrogen). Promega pooled male DNA was used as reference. Labeled DNA was hybridized onto BAC arrays containing ~32 000 BAC clones printed in singlets. BAC arrays were produced at the SWEGENE DNA Microarray Facility at Lund University.

first: A

last: Carneiro

first: P

last: Francis

middle: O

last: Bendahl

first: J

last: Fernebro

first: M

last: Akerman

first: C

last: Fletcher

last: Rydholm

last: Borg


title: The cytokinin type-B response regulator PtRR13 is a negative regulator of adventitious root development in Populus

city: Gainesville

first: Christopher

last: Dervinis

state: FL

address: 2033 Mowry Road, rm 320

department: SFRC

institute: University of Florida

summary: Adventitious root formation at the base of plant cuttings is an innate de novo organogenesis process that allows massive vegetative propagation of many economically and ecologically important species. The early molecular events following shoot excision are not well understood. Using whole-genome microarrays, we detected significant transcriptome remodeling during 48 hours following shoot removal in Populus softwood cuttings in the absence of exogenous auxin, with 27% and 36% of the gene models showing differential abundance between 0 and 6 hours, and 6 and 24 hours, respectively. During these two time intervals, gene networks involved in protein turnover, protein phosphorylation, molecular transport and translation were among the most significantly regulated. Transgenic lines expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ΔDDKPtRR13) have a delayed rooting phenotype and cause misregulation of COV1, a negative regulator of vascularization; PDR9, an auxin efflux transporter; two AP2/ERF genes with sequence similarity to TINY1. Cytokinin action appeared to disrupt root development 24 hours after shoot excision, when root founder cells are hypothesized to be sensitive to the negative effects of cytokinin. Our results suggest that PtRR13 acts downstream of cytokinin to repress adventitious root formation in intact plants, and that reduced cytokinin signaling after shoot excision enables coordinated expression of ethylene, auxin and vascularization pathways leading to adventitious root development.

overall_design: Populus tremula x Populus alba INRA-clone No. 717-1-B4 plants expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ΔDDKPtRR13) were generated via an Agrobacterium-mediated protocol developed by Han et al. (2000). Non-transgenic and ΔDDKPtRR13 line were grown to a height of 60 cm. A 14 cm tall apical cuttings were collected from the mother plants. Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation. Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting).  Total RNA was extracted with the RNeasy mini kit (Qiagen USA) and DNase treated in-column with the RNase-Free DNase set (Qiagen USA). Double-stranded cDNA was synthesized using SuperScript Double Strand cDNA Synthesis Kit (Invitrogen USA, Carlsbad, CA) with oligo-dT primers following the manufacturer’s protocol except that the synthesis step was extended to 16 hours. Cy-3 labeling and hybridization steps were performed by NimbleGen using their standard procedures. A custom-designed microarray platform was used comprising single 60-mer probes designed against 55,793 annotated gene models from the sequenced genome of P. trichocarpa. Each 60-mer probe was chosen form a group of 6-7 non-overlapping probes designed against different parts of the gene model. The probe whose value was the most similar to the average of 6-7 experimental probes was assumed to be the most reliable for transcript level estimation. A total of 39 microarray chips were used in these experiments: 39 chips = 2 genotypes (NT and ΔDDK) x 4 time points (0, 6, 24 and 48 hours) x 5 biological replications, except for the 0 hour ΔDDK where 4 biological replications were used. Signal intensities were log2 transformed and quantile normalized (Sugiharto et al., 1992). Normalized signals were analyzed in SAS 9.1 (SAS Institute, Cary, NC) using a mixed model analysis of variance (ANOVA) with genotype and genotype by time interactions as fixed effects, and biological replication as a random effect.

first: Gustavo

last: Ramírez-Carvajal

first: Alison

middle: M

last: Morse

first: John

last: Davis


title: Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk

first: Todd

last: Klaenhammer

summary: Lactic acid bacteria have been used as starter strains in the production of fermented dairy products for centuries. Lactobacillus acidophilus is a widely recognized probiotic bacteria commonly added to yogurt and used in dietary supplements. In this study, a whole genome microarray was employed to monitor gene expression of L. acidophilus cells propagated in 11% skim milk (SM) during early, mid and late logarithmic phase, and stationary phase. Approximately 21% of 1,864 ORFs were differentially expressed at least in one time point. Genes differentially expressed in SM included several members of the proteolytic enzyme system. Expression of  prtP (proteinase precursor) and prtM (maturase) increased over time as well as several peptidases and transport systems. Expression of Opp1 (oligopeptide transport system 1) was highest at 4h, while gene expression of Opp2 increased over time reaching its highest level at 12h, suggesting that the two systems have different specificities.  Expression of a two-component regulatory system (2CRS), previously shown to regulate acid tolerance and proteolytic activity,  also increased during the early log and early stationary phases of growth.  Expression of the genes involved in lactose utilization increased immediately (5 min) upon exposure to milk.  The acidification activity, survival under storage conditions, and adhesion to mucin and Caco-2 tissue culture cells of selected mutants containing insertionally inactivated genes differentially expressed in the wild-type strain during growth in milk were examined for any potential links between probiotic properties and bacterial growth and survival in milk.  Some of the most interesting genes found to be expressed in milk were correlated with signaling (AI-2) and adherence to mucin and intestinal epithelial cells, in vitro.

overall_design: A loop experimental design (Vinciotti et al., 2005) was employed in a time course experiment to monitor the transcriptional response of L. acidophilus NCFM during growth in 11% reconstituted skim milk (SM). The culture was initiated in MRS broth and transferred 3-5 times in SM before a 10% inoculation in prewarmed SM.   Cells and RNA samples were obtained from two biological replicates at times of 5  min (pH= 6.4; ≈ 2.1 X 107 cfu/ml), 4h (pH= 5.8; ≈ 3.8 X 107 cfu/ml), 8h (pH= 5.4; ≈ 7.1 X 107 cfu/ml), and 12h (pH= 4.9; ≈ 1.5 X 108 cfu/ml) and compared in an unbalanced loop-design. Samples were compared as follows (Cy3 vs. Cy5): T1 (5 min) vs. T2 (4h), T2 vs. T3 (8h), T3 vs. T4 (12h), T4 vs. T2, T4 vs. T1 and T3 vs. T1.

first: Maria

last: Azcarate-Peril

first: Richard

last: Tallon


title: RNA hybridization from 16 cell lines on Chr21_22v2.0 arrays

city: Santa Clara

first: Thomas

last: Gingeras

state: CA

address: 3380 Central Expressway

institute: Affymetrix, Inc.

type: Expression profiling by genome tiling array

summary:
RNA mapping on Human chromosomes 21/22. This hybridization was done using RNA samples from 16 different human cell lines. The data obtained is from analysis done on Human Genome hs.NCBIv36 or hg18 (UCSC)
Keywords: RNA mapping experiments

overall_design: Two technical replicates were hybridized for all experiments. A total of 16 different samples were used, majority of which were total RNA extracted from whole cells. However for 3 samples (GM06990, HepG2, Human fibroblasts) the RNA extracted was from Cytoplasm.


title: Cancer Genome Anatomy Project (CGAP) Mouse LongSAGE

status: Public on Mar 20 2009

city: Bethesda

first: Cancer Genome Anatomy Project

last: CGAP

department: Cancer Genome Anatomy Project

institute: National Cancer Institute

summary:
This series represents the Cancer Genome Anatomy Project SAGE library collection.  Libraries contained herein were either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.

SAGE libraries are named according to the following convention:
* SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2
* Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.

overall_design: 34 libraries

first: R

last: Strausberg

first: D

last: Gerhard

first: Gregory

middle: J

last: Riggins


title: Scleroderma and Gleevec treatment

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech

summary:
Total RNA was extracted from skin biopsies before and after imatinib (Gleevec) treatment using Qiagen RNeasy fibrous tissue kit. RNA was amplified using the Ambion Amino Allyl MessageAmp II aRNA kit. Amplified skin RNA (labeled with Cy5) and amplified Stratagene Human Universal Reference RNA (labeled with Cy3) were competitively hybridized to HEEBO microarrays in duplicate as described (http://www.microarray.org/sfgf/heebo.do).

161a/b: Patient 1, pre-Gleevec treatment
170a/b: Patient 1, post-Gleevec treatment
215a/b: Patient 2, pre-Gleevec treatment
232a/b: Patient 2, post-Gleevec treatment

A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.

Compound Based Treatment: Treated with 100 mg Gleevec twice daily for 3 months or 200 mg Gleevec daily for 6 months
Keywords: compound_treatment_design

overall_design: Computed


title: Cancer Genome Anatomy Project (CGAP) Mouse SAGE

overall_design: 280 libraries


title: Allogeneic antibodies specifically target AML antigen NuSAP1 after bone marrow transplantation

status: Public on Mar 19 2009

city: Stanford

first: Persis

middle: P

last: Wadia

address: 269 W Campus Drive, CCSR 2210

institute: Stanford University

summary: Identifying the targets of immune response after allogeneic hematopoietic cell transplantation (HCT) promises to provide relevant immune therapy candidate proteins. We used protein microarrays to serologically identify Nucleolar and Spindle Associated Protein 1 (NuSAP1) and Chromatin Assembly Factor 1, subunit B (p60) [CHAF1b] as targets of new antibody responses that developed after allogeneic HCT. Western blots and ELISA validated their post-HCT recognition and enabled ELISA testing of 120 other allo-HCT patients. CHAF1b specific antibodies were predominantly detected in AML patients whereas NuSAP1 specific antibodies were exclusively detected in AML patients one year post-transplant (p<0.0001). Complete genomic exon sequencing failed to identify a nonsynonymous SNP for NuSAP1 and CHAF1b between the donor and recipient cells. Expression profiles and RT-PCR showed NuSAP1 was predominately expressed in the bone marrow CD34+CD90+ hematopoietic stem cells (HSC), leukemic cell lines and B lymphoblasts as compared to other tissues or cells. Thus, NuSAP1 is recognized as an immunogenic antigen in 65% AML patients and suggests a tumor antigen role.  In conclusion, clinically important tumor antigens can be identified as new antibody targets after allogeneic HCT using high density protein microarrays

overall_design:
Plasma Profiling using ProtoArrays: Protein microarrays were obtained (ProtoArrays™ V3, Invitrogen Corporation, Carlsbad, CA) displaying 5,056 full-length human proteins, derived from the Ultimate ORF collection (Invitrogen Corp., Carlsbad, CA) printed in duplicate with N-terminal GST epitopes expressed in Baculovirus and affinity purified under native conditions maintaining their cellular enzymatic activities/native conformations. The arrays also contained control spots consisting of buffer, empty spots, and human IgG printed in four different concentrations (IgG[1] to IgG[4]). The arrays were incubated with blocking buffer for one hr followed by application of the plasma sample diluted 1:150 for 90 min. After washing the array four times for 10 min each with PBST buffer, secondary antibody was added (goat anti-human Alexa 647, Molecular Probes, Eugene, OR) for 90 min. After washing the slides with PBST buffer, the arrays were dried and fluorescent intensity was detected using a microarray scanner (GenePix 4000B, Molecular Devices, CA). All incubations were carried out on a rotating platform at 4 ºC.
ProtoArray data acquisition and measurement: The slides were scanned at a PMT gain of 60% with a laser power of 90% and a focus point of 0 μm. Fluorescence intensity data were acquired using GenePix Pro 6.0 software (Molecular devices, Sunnyvale, CA) with the appropriate “.gal” file downloaded from the ProtoArray central portal on the Invitrogen website (http://www.invitrogen.com/protoarray) by submitting the barcode of each ProtoArray slide

first: Marc

last: Coram

first: Randall

last: Armstrong

first: Michael

last: Mindrinos

first: Atul

last: Butte

first: David

last: Miklos


title: Comparative genome hybridization for Lactobacillus casei

status: Public on Mar 17 2009

first: Hui

last: Cai

address: 1605 Linden Dr

institute: University of Wisconsin

summary: Lactobacillus casei is remarkably adaptive to diverse habitats. To understand the evolution and adaptation of Lb. casei strains isolated from different environments, the gene content of 22 Lb. casei strains isolated from various habitats (cheeses, n=8; plant materials, n=8; and human sources, n=6) were examined by comparative genome hybridization with an Lb. casei ATCC 334-based microarray.

platform_organism:
Lacticaseibacillus casei
Lactobacillus helveticus

overall_design: Comparative genome hybridization was performed against an Affymetrix custom microarray designed to include 2,661 (97%) chromosomal and 17 (85%) plasmid CDSs predicted to occur in Lb. casei ATCC 334, as well as all predicted CDSs in the draft Lb. helveticus CNRZ 32 genome.  CDSs that were not included in the microarray design were all transposase-encoding genes.

first: Jeff

last: Broadbent

first: Rebecca

last: Thompson

first: James

last: Steele


title: Drug-inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

type: Genome binding/occupancy profiling by genome tiling array

summary: Plasmodium and Toxoplasma are parasites of major medical importance that belong to the Apicomplexa phylum of protozoa. These parasites transform into various stages during their life cycle and express a specific set of proteins at each stage. Although still little is known of how gene expression is controlled in Apicomplexa, histone modifications, particularly acetylation, are emerging as key regulators of parasite differentiation and stage conversion. Here, we investigated the anti-Apicomplexa effect of FR235222, a histone deacetylase (HDAC) inhibitor. We show that FR235222 is active against a variety of Apicomplexa genera, including Plasmodium and Toxoplasma, and is more potent than other HDACi such as TSA and the clinically relevant compound, pyrimethamine. We identify TgHDAC3 as the target of FR235222 in Toxoplasma tachyzoites and demonstrate the crucial role of the conserved and Apicomplexa HDAC-specific residue TgHDAC3 T99 in the inhibitory activity of the drug. We also show that FR235222 induces differentiation of the tachyzoite (replicative) into the bradyzoite (non replicative) stage. Additionally, via its anti-TgHDAC3 activity, FR235222 influences the expression of ~370 genes, a third of which are stage-specifically expressed. These results identify FR235222 as a potent HDAC inhibitor of Apicomplexa, and establish HDAC3 as a central regulator of gene expression and stage conversion in Toxoplasma and likely other Apicomplexa.

overall_design: Freshly released tachyzoites were needle-passed, and filtered using a 3-µm nucleopore membrane. Parasites were resuspended into fresh DMEM supplemented with 10% (v/v) FBS and 25 mM HEPES buffer pH7.2. Parasites were incubated in the presence of FR235222 (40 nM) or DMSO (0.1%) for 4 h at 37°C with 5% CO2. For ChIP-chip experiments freshly released tachyzoites (~5 x 109 at ~12 x 107 parasites/mL) were fixed for 15 min in 1% formaldehyde. Increase in AcH4 signals was verified by immunoblot to verify that FR235222 treatment was effective. To prepare chromatin samples, fixed parasites were lysed in MNase buffer (0.32 M Sucrose, 50 mM Tris-HCl pH7.8, 4 mM MgCl2, 3 mM CaCl2, 100 mM NaCl, 0.25% (v/v) NP40, 5%  (v/v) glycerol, protease inhibitor EDTA-free cocktail (Roche)) and DNA was digested for 4 min at 37°C by MNase (2 units/mL). Digestion was stopped with 20 mM EDTA and chromatin was recovered in the soluble fraction after centrifugation at 10,000 g at 4°C; this constituted the S1 fractions. Pelleted materials were resuspended in dialysis buffer (1mM Tris-HCl pH7.8, 0.2 mM EDTA) containing 1 mM PMSF and protease inhibitor cocktail (Roche®) and dialyzed overnight at 4°C against the same solution. Then dialyzed materials were centrifuged and supernatant were harvested; this constitutes the S2 fractions. For chromatin immunoprecipitations, fractions S1 and S2 were pooled and DNA quality was verified by electrophoresis on 2% agarose gels; oligonucleosome ladder of 100-1000 bp were obtained. The histone-DNA complexes were immunoprecipitated with anti-acetyl histone H4 (Upstate®, catalog # 06-866) antibodies according to NimbleGen’s protocol (http://www.genomecenter.ucdavis.edu/expression_analysis/documents).

first: Alexandre

last: Bougdour

first: Daniele

last: Maubon

first: Patricia

last: Baldacci

first: Philippe

last: Ortet

first: Olivier

last: Bastien

first: Anthony

last: Bouillon

first: Jean

middle: C

last: Barale

first: Herve

last: Pelloux

first: Robert

last: Menard

first: Mohamed

last: Hakimi


title: Transcriptome analysis of in vitro endotoxin tolerant human monocytes

status: Public on Mar 14 2009

city: Madrid

first: Eduardo

last: Lopez-Collazo

address: Paseo de la Castellana, 261

country: Spain

institute: Research Unit, Hospital La Paz

summary: Monocyte exposure to lipopolysaccharide (LPS) induces a transient state in which these cells are refractory to further endotoxin stimulation. Here we demonstrate the transcriptome analysis of in vitro generated LPS refractory monocytes upon subsequent re-exposure to LPS for different time points.

overall_design: Total RNA obtained from human monocyte exposure treated with LPS for 3h, 6h, or 24h, subsequent to endotoxin tolerization or not.

first: Carlos

last: del Fresno Sanchez


title: IFN-alpha induced gene expression profile in NOD/BDC2.5 and NOD mice.

status: Public on Mar 13 2009

first: Hugh

last: McDevitt

department: Departments of Microbiology and Immunology and Medicine

institute: Stanford University School of Medicine

summary: With the goal of identifying changes in gene expression in CD4(+) T cells during the development of diabetes in the nonobese diabetic (NOD) mouse, we used DNA microarrays to analyze gene expression in CD4(+) T cells from the pancreatic draining lymph nodes of NOD/BDC 2.5 T cell receptor transgenic and WT NOD mice at different ages. At 4 and 6 weeks of age, we found up-regulation of a number of genes that are known to be induced by IFN-alpha. IFN-alpha levels and IFN-alpha-producing plasmacytoid dendritic cells were increased in the PLNs of 3- to 4-week-old NOD mice. Moreover, blockade of IFN-alpha receptor 1 in NOD mice by a neutralizing antibody at 2-3 weeks of age significantly delayed the onset and decreased the incidence of type 1 diabetes, increased the relative number of immature dendritic cells in the PLNs, and enhanced the ability of spleen CD4(+) T cells to produce IL-4 and IL-10. These findings demonstrate that IFN-alpha in the PLNs is an essential initiator in the pathogenesis of type 1 diabetes in NOD mice.

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

first: Qing

last: Li


title: Characterization of microRNA expression in colorectal cancer

city: San Diego

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

summary:
MiRNAs have differential expression between normal colon and cancer tissues, and could be targets for CRC therapies and be further developed as potential diagnostic and prognostic analytes.
Keywords: classification

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 66 samples from 49 patients


title: Copy number abnormality, MYC activity and the genetic fingerprint of normal B-cells and the microRNA profile of DLBCL-21

city: Boston

first: Cheng

state: MA

address: 44 Binney St

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

summary: A better understanding of the pathogenesis of diffuse large B-cell lymphoma (DLBCL) has clarified its relationship to normal B-cells, pointed to distinct mechanisms of cell transformation, and facilitated the design of novel treatments. However, these data derive from mRNA genes studies, whereas genome-wide integrative investigations of the role of microRNAs (miRNAs) in DLBCL are still unavailable. We used array-CGH and microarray-based expression analyses to map the abnormalities targeting miRNAs in DLBCLs (n=86). Using training and validation DLBCL cohorts, we defined a collection of miRNAs that robustly segregates these tumors in three unique subsets. This miRNA-driven substructure appears to influence disease outcome, is independent of other mRNA-based DLBCL classifications, and stems from copy number changes targeting the miRNA genome, MYC activity, and the miRNA fingerprints of mature normal B-cells. Our data have uncovered clinically relevant additional molecular complexity in DLBCL and have established a blueprint for the detailed characterizations of miRNAs that are pertinent to B-cell lymphoma biology.

overall_design: Total RNA was isolated from 21 frozen DLBCL samples using Trizol and hybridized (100ng, single channel, Cy3-labeled) to microarray slides (8 complete microarrays/slide) and washed following manufacturer’s guidelines. The arrays were subsequently scanned and the intensity of the hybridization signals obtained using the Feature Extraction software (Agilent Technologies).

first: Ricardo

last: Aguiar


title: Identification of a subgroup of head and neck cancers lacking numerical chromosomal aberrations

status: Public on Mar 12 2009

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary:
ABSTRACT
Two major subgroups of head and neck squamous cell carcinomas (HNSCC) are currently distinguished based on etiology and pattern of genetic alterations; tumors with biologically active human papillomavirus (HPV) and tumors without. It is at present unclear whether additional genetically distinct subgroups exist within HPV-negative HNSCC. Aim of this study is to genetically classify HNSCC without HPV involvement and to correlate the genetically defined classes to tumor and patient characteristics. By means of array comparative genomic hybridization (aCGH) we determined DNA copy number variation in thirty-nine HPV-negative, but further unselected HNSCC. Unsupervised analysis of aCGH data distinguished two genetic groups in HPV-negative HNSCC, one characterized by a low level of chromosomal alterations (N=9), and another by a high level of chromosomal alterations (N=30). Absence of chromosomal aberrations was significantly associated with wild-type TP53, a low level of alcohol consumption, a female gender and a better prognosis. The tumors were negative for microsatellite instability. The discovery of this new class of HNSCC with unique genetic and clinical characteristics has important consequences for future basic and clinical studies.

overall_design: All DNAs are isolated from fresh frozen HNSCC specimen. All tissue specimens were microdissected to obtain at least 90% tumor DNA. All sampels are hybridized against a pool of reference DNA of normal individuals of the opposite gender.

first: Serge

last: Smeets

first: Ruud

middle: H

last: Brakenhoff

first: Bauke

last: Ylstra

first: Wessel

last: van Wieringen

first: Mark

last: van de Wiel

first: René

last: Leemans

first: Boudewijn

last: Braakhuis


title: ChIP-on-chip of BCL6

city: new york

first: weimin

last: ci

state: NY

address: 1300 York ave

department: medicine

institute: weill cornell college of medicine

summary: Identification BCL6 target genes in primary germinal center cells and DLBCL cell lines by ChIP-on-chip

overall_design: Three replicates in each type of cells


title: Gene expression during mouse OS25 ES cell differentiation

status: Public on Mar 11 2009

city: Bron

first: Clémence

last: Kress

address: 18 avenue du Doyen Lépine

institute: INRAE, Inserm

summary: Position within chromosome territories, and localisation at transcription factories, are two facets of nuclear organisation that have been associated with active gene expression. However, there is still debate about whether this organisation is a cause or consequence of transcription. We induced looping out from chromosome territories (CTs), by the activation of Hox loci during differentiation, to investigate consequences on neighbouring loci. This microarray study aims at analyzing the expression of genes close to Hoxb and Hoxd clusters in parallel with their nuclear position.

overall_design: OS25 mouse ES cells were differentiated using retinoic acid in two independent experiments, and control undifferentiated cells were also cultured. For each experiment, labelled cDNAs were prepared from undifferentiated and differentiated cells and hybridized together on VUMC MACF Mouse 38K oligo v64 microarrays. Labelling dyes (Cy3 / Cy5) were swapped for cDNAs from the second differentiation experiment.

first: Wendy

last: Bickmore

first: Céline

last: Morey


title: microRNA expression in bone marrow cells from Gfi1 deficient mice

city: Columbus

first: Terry

last: Camerlengo

state: OH

address: Biological Research Tower 12 ave

department: Biomedical Informatics

institute: Ohio State University

summary: Growth factor independent-1 (Gfi1) is a zinc finger transcription factor with a SNAG amino-terminal repressor domain and is critically required for normal myelopoesis. Gfi1 is normally expressed in HSCs and induced during differentiation from CMPs to GMPs. Gfi1 loss-of-function mutation in mice and humans induces an arrest during myeloid differentiation and an absolute block to the formation mature neutrophils. This comparative microarray study was initiated to identify microRNAs which are potentially regulated by Gfi1 during granulopoiesis.

overall_design: The Gfi1 null allele from Orkin (deletion of exons 2 and 3) was backcrossed to B6 or Balb/c mice for at least 7 generations.  RNA was isolated from low density bone marrow samples from Gfi1+/+ and Gfi1-/- B6 littermates, as well as Gfi1+/+ and Gfi1-/- Balb/c littermates.

first: H

last: Grimes

first: A

last: Baktula

first: C

last: Velu


title: Differential expression of stem cell-specific genes in P7 and P28 dentate gyrus neural progenitors

city: Dallas

first: Steve

last: Kernie

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary:
In order to identify cell-autonomous factors that might be regulating the neurogenic niche, type 1 and 2 progenitors were FACS sorted from P7 and P28 animals and their cDNA was hybridized to a stem cell-specific microarray.

Keywords: differential gene expression analysis

overall_design: Two samples per microarray (P7 and P28).  Each microarray experiment was done in triplicate. P7 is the control sample.

first: Jennifer

last: Gilley

first: Steven

middle: G


title: Repertoire of miRNAs in epithelial ovarian cancer determined by next generation sequencing of small RNA cDNA libraries

city: Seattle

first: Muneesh

last: Tewari

address: 1100 Fairview Ave, N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: MicroRNAs (miRNAs) are small regulatory RNAs that are implicated in cancer pathogenesis and have recently shown promise as blood-based biomarkers for cancer detection. Epithelial ovarian cancer is a deadly disease for which improved outcomes could be achieved by successful early detection and enhanced understanding of molecular pathogenesis that leads to improved therapies. A critical step toward these goals is to establish a comprehensive view of miRNAs expressed in epithelial ovarian cancer tissues as well as in normal ovarian surface epithelial cells.

overall_design: Methodology: We used massively parallel pyrosequencing (i.e., “454 sequencing”) to discover and characterize novel and known miRNAs expressed in primary cultures of normal human ovarian surface epithelium (HOSE) and in tissue from three of the most common histotypes of ovarian cancer.  Deep sequencing of small RNA cDNA libraries derived from normal HOSE and ovarian cancer samples yielded a total of 738,710 high-quality sequence reads, generating comprehensive digital profiles of miRNA expression. Expression profiles for 498 previously annotated miRNAs were delineated and we discovered six novel miRNAs and 39 candidate miRNAs. A set of 124 miRNAs was differentially expressed in normal versus cancer samples and 38 miRNAs were differentially expressed across histologic subtypes of ovarian cancer. Taqman qRT-PCR performed on a subset of miRNAs confirmed results of the sequencing-based study.

first: Stacia

middle: K

last: Wyman

first: Rachael

last: Parkin

first: Patrick

last: Mitchell

first: Brian

last: Fritz

first: Kathy

last: O'Briant

first: Andrew

last: Godwin

first: Nicole

last: Urban

first: Charles

middle: W

last: Drescher

first: Beatrice

last: Knudsen


title: Gene expression in three independent resynthesized Brassica napus allopolyploid lines and their diploid progenitors

city: Columbia

first: Robert

middle: Thomas

last: Gaeta

state: MO

address: 117 Tucker Hall, Department of Biological Sciences, University of Missouri

department: Biological Sciences

institute: University of Missouri

summary:
We anlalyzed gene expession using an Arabidopsis 26K 70mer spotted microarray
Differential expression was tested using two ANOVA models: 1) a per-gene variance ANOVA, and 2) a common variance ANOVA

sample_organism:
Brassica napus
Brassica rapa
Brassica oleracea
Brassica sp.

overall_design: We compared gene expession between the diploid progenitors (Brassica rapa and Brassica oleracea), and tested mid-parent expression in the allopolyploids by comparison to a reference sample (composed of a 1:1 mix of parental RNA).  Two biological replicates (composed of pooled leaf tissue) were each analzed with two dye swaps in a randomized complete block design(RCBD).

middle: T

first: Suk

last: Young-Yoo

first: J

last: Pires

first: R

last: Doerge

first: Z

last: Chen

first: Thomas

last: Osborn


title: microRNA-101 represses EZH2 in cancer

city: Los Angeles

first: Jeffrey

last: Friedman

address: 1441 Eastlake Ave.

institute: USC/Norris Comprehensive Cancer Center

summary: To determine the phenotypic overlap between restoring miR-101 expression in bladder cancer cells and knocking down EZH2.

overall_design: Either control precursors, pre-miR-101, control siRNA, or EZH2 siRNA were transfected in triplicate into UM-UC-3 cells for 72 hours at a final concentration of 50 nM.


title: Gene expression in lung fibroblasts

city: Pittsburgh

first: Louis

middle: Justine

last: Vuga

state: PA

address: 3459 Fifth Ave, 628NW

department: Pulmonary Allergy, and Critical Care Medicine

institute: University of Pittsburgh

summary:
Pulmonary fibrosis is a chronic, progressive, and lethal interstitial lung disease. It is characterized by extracellular matrix deposition, fibroblast proliferation, and accumulation. Fibroblasts from normal or UIP histology were cultured and analyzed.
Keywords: Fibroblasts from normal histology lung tissue or UIP histology lung tissue

overall_design: Five samples of primary human lung fibroblasts were obtained from explanted lungs of patients with Usual Interstitial Pneumonia (UIP) at the University of Pittsburgh Medical Center (Pittsburgh, PA, USA) and three samples of primary normal human lung fibroblasts were acquired from normal histololgy lung tissues of organ donors. The experimental protocol was approved by the University of Pittsburgh Institutional Reviews Board (IRB). Total RNA was extracted and used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays. Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647. The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite, and visually inspected for defects and quality control parameters as recommended by the manufacturer.

first: Naftali

last: Kaminski


title: Time course of response of ML-DmD4-c1 cells to ecdysone

city: Bloomington

first: Lucy

last: Cherbas

state: IN

department: CGB

institute: Indiana University

summary:
The changes in transcript titers are described for Drosophila ML-DmD4-c1 cells following 5-48 hr treatment with 20-hydroxyecdysone.
Keywords: hormone response

overall_design: RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 3-4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.

first: Yi

last: Zou

first: Peter


title: Bovine endometrium at day 18 of pregnancy after transfer of in vitro produced or somatic cell nuclear transfer embryos

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary:
Although somatic cell nuclear transfer (SCNT) cloning is more efficient in bovine than in all other species tested so far, there is a high rate of pregnancy failure that has been linked to structural and functional abnormalities of the placenta. We tested the hypothesis that these changes may originate from disturbed embryo-maternal interactions in the pre-implantation period. Therefore, we evaluated the transcriptome response of the endometrium to SCNT embryos (produced from five different donor cell cultures) as compared to embryos derived from in vitro fertilization (IVF). SCNT embryos and IVF embryos were cultured under identical conditions to the blastocyst stage (Day 8) and transferred to recipients. The recipients were slaughtered at day 18 of pregnancy and the uterus was recovered. Pregnancy was verified by the presence of at least one normally developed embryo. Transcriptome profiling of endometrium samples using a custom cDNA microarray covering transcripts expressed in the endometrium and/or oviduct epithelium revealed 58 transcripts that were differently abundant between endometrium samples from SCNT vs. IVF pregnancies. Prominent examples are NR2F2 (encoding the orphan nuclear receptor COUP-TFII) and GJA1 (encoding connexin 43). Both transcripts are known to play important roles in placentation and were significantly less abundant in endometrium from SCNT vs. IVF pregnancies. These findings suggest that placental failure in bovine clone pregnancies may originate from abnormal embryo-maternal communication already in the pre- or peri-implantation period. Endometrium transcriptome profiles may serve as a novel readout to evaluate SCNT embryos for their ability to induce pregnancy with a functional placenta.

Keywords: response to different embryos

overall_design: Nineteen German Fleckvieh (Simmental) heifers were slaughtered at day 18 of pregnancy. Cycle-synchronized recipient heifers received either IVP or SCNT embryos at day 7 of the estrous cycle. Animals were slaughtered at day 18. Endometrial (intercaruncular) tissue samples were obtained from 10 pregnant animals after transfer of IVP embryos and from 9 pregnant animals after transfer of SCNT embryos.

first: Karin

last: Gross

first: Susanne

middle: E

last: Ulbrich

first: Horst-Dieter

last: Reichenbach

first: Helmut

last: Blum

first: Eckhard

last: Wolf


title: Time course of response of Kc cells to ecdysone

summary:
The changes in transcript titers are described for Drosophila Kc167 cells following 5-48 hr treatment with 20-hydroxyecdysone.
Keywords: hormone response

overall_design: RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone.  A total of 3-13 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.


title: Gene expression data from mouse postnatal brain development

status: Public on Mar 10 2009

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

summary:
In development, timing is of the utmost importance, and the timing of various developmental processes are often changed during evolution.
We measured the timing of gene expression changes in the brains of two species of mice throughout postnatal development.

sample_organism:
Mus musculus
Mus spretus

overall_design: Mus musculus and Mus spretus mice were bred at the MPI-EVA mouse facility. Whole brain samples were collected from mice of 3 different age classes: newborns, pups and young adults. RNA extracted from the dissected tissue was hybridized to Affymetrix MG-430 2.0 GeneChip arrays.

first: Anna

last: Lorenc

first: Michael

last: Dannemann

last: Lachmann

first: Svante

last: Pääbo

first: Philipp

last: Khaitovich


title: Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC

city: Cincinnati

first: Lee

last: Denson

address: 3333 Burnet Avenue

institute: CCHMC

summary:
Colon gene expression in human IBD. The three major clinical subsets of Inflammatory Bowel Disease (IBD) include colon-only Crohn's Disease (CD), ileo-colonic CD, and Ulcerative Colitis (UC).  These experiments tested differential colon gene expression in these three types of IBD, relative to healthy control samples, and the local degree of mucosal inflammation as measured by the CD Histological Index of Severity (CDHIS). Colon biopsy samples were obtained from IBD patients at diagnosis and during therapy, and healthy controls. The global pattern of gene expression was determined using GeneSpring software, with a focus upon candidate genes identified in a recent genome wide association study in pediatric onset IBD. Data suggested that two of these candidate genes are up regulated in pediatric IBD, partially influenced by local mucosal inflammation.
These experiments tested differential colon gene expression in healthy, CD, and UC samples for candidate genes identified in a recent pediatric onset IBD genome wide association study.
Keywords: Single time point in CD and UC and healthy controls.

overall_design: Colon RNA was isolated from biopsies obtained from CD and UC at diagnosis and during therapy and healthy controls. Samples were obtained from the most proximal affected segment of colon. Microarray experiments were performed as described in the CCHMC microarray core, and data was analyzed as described above in the summary. The '107' internal control CEL files (for batches 1,2,3,4,5) used for normalization of the Sample VALUEs are also contained within this data set.


title: Gene expression changes during primate postnatal brain development

summary:
In development, timing is of the utmost importance, and the timing of various developmental processes are often changed during evolution. During human evolution sexual maturation has been delayed relative to other primates and this may have played a critical role for both the increase of human brain size and the rise of human-specific cognitive traits .
We measured the timing of gene expression changes in the brains of humans, chimpanzees, and rhesus macaques throughout postnatal development.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Human, chimpanzee and rhesus macaque post-mortem brain samples from the dorsolateral prefrontal cortex region were collected. The caudate nucleus region was additionally sampled for humans. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to young adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® U133-plus2.0 GeneChip® arrays.

first: Henriette

last: Franz

first: Thomas

last: Giger

first: Birgit

last: Nickel

first: Sabine

last: Bahn

first: Maree

last: Webster

first: Cynthia

last: Weickert


title: Time course of response of CME W1 Cl.8+ cells to ecdysone

first: Lucy

last: Cherbas

summary:
The changes in transcript titers are described for Drosophila CME W1 Cl.8+ cells following 5-48 hr treatment with 20-hydroxyecdysone.
Keywords: hormone response

overall_design: RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.

first: Yi

last: Zou

first: Peter


title: Gene expression profiling of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE)

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

summary:
Biomphalaria glabrata infection by the Schistosoma mansoni free-swimming miracidium and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and triggers a variety of physiological, biochemical and molecular changes.  Here, we describe a genome-wide analysis of the S. mansoni miracidium and developing sporocyst.
Keywords: life-cycle, development, host-interaction

overall_design: We generated transcriptomic profiles of the developing larval stages of Schistosoma mansoni using long serial analysis of gene expression (LongSAGE).  Five cDNA libraries were constructed from miracidia and in vitro cultured 6- and 20-day old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of the B. glabrata embryonic (Bge) cell line.  From five libraries, 314,799 SAGE tags were sequenced and resulted in a total of 21,440 unique sequence tags.  A total of 254 tags were differentially expressed during “conditioned” development and 236 tags were differentially expressed during “un-conditioned” development.  In addition, 53 tags were found to be differentially expressed between 6-day conditioned and unconditioned sporocysts and 42 tags between 20-day conditioned and unconditioned sporocysts.

last: Taft

first: Jon

last: Vermeire

first: Jeremiah

last: Bernier

first: Shanda

middle: R

last: Birkeland

last: Cipriano

first: Alexandria

last: Papa

first: Timothy

last: Yoshino


title: Time course of response of ML-DmBG3-c2 cells to ecdysone

summary:
The changes in transcript titers are described for Drosophila ML-DmBG3-c2 cells following 5-48 hr treatment with 20-hydroxyecdysone.
Keywords: hormone response


title: Gene Expression Data of Hibernating and Summer Active Black Bears

city: FAIRBANKS

first: Anna

last: Goropashnaya

state: AK

address: 311 Irving I Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

summary:
We conducted a large-scale gene expression screen using the 3,200 cDNA probe microarray developed specifically for Ursus americanus to detect expression differences in liver and skeletal muscle that occur during winter hibernation in comparison to animals sampled during summer. The expression of 12 genes, including RNA binding protein motif 3 (Rbm3), that are mostly involved in protein biosynthesis, was induced during hibernation in both liver and muscle. The Gene Ontology and Gene Set Enrichment analysis consistently showed a highly significant enrichment of the protein biosynthesis category by over-expressed genes in both liver and skeletal muscle during hibernation.
Coordinated induction in transcriptional level of genes involved in protein biosynthesis is a distinctive feature of the transcriptome in hibernating black bears. This finding implies induction of translation and suggests an adaptive mechanism that contributes to a unique ability to reduce muscle atrophy over prolonged periods of immobility during hibernation. Comparing expression profiles in bears to small mammalian hibernators shows a general trend during hibernation of transcriptional changes that include induction of genes involved in lipid metabolism and carbohydrate synthesis as well as depression of genes involved in the urea cycle and detoxification function in liver.

overall_design: Black bears sampled during winter hibernation were compared with the animals sampled during summer. Two tissue types, liver and muscle, were hybridized on a custom 3,200-gene nylon membrane microarray platform with three replicates for each gene (9.600 spots in total). Six hibernating and five summer active bears were studied in experiments with liver tissue, five hibernating and five summer active animals were tested with muscle tissue.

first: V

middle: B

last: Fedorov

first: A

first: O

last: Toien

first: N

last: Stewart

middle: Y

last: Gracey

first: C

last: Chang

first: S

last: Qin

first: G

last: Pertea

first: J

last: Quackenbush

first: L

last: Showe

first: M

first: B

last: Boyer

last: Barnes


title: Genome-wide characterization of light-inducible responses reveals a hierarchical light-sensing cascade in N. crassa

status: Public on Mar 09 2009

city: Hanover

first: Chen-Hui

last: Chen

state: NH

address: 702 Remsen

department: Genetics

institute: Dartmouth College

summary:
To better understand the roles of WC-1, WC-2 and other putative photoreceptors in mediation of light signals and to identify new components in light sensing cascades, we used microarrays with genome-wide coverage to characterize light-inducible transcriptional changes in Neurospora crassa. After unsupervised hierarchical clustering of 90 microarrays, 316 genes, representing about 3.21% of the total genome, showed robust and consistent light responses. As expected, WC-1 and WC-2 knockout strains both exhibited severe impairments in response to a continuous white light stimulus, confirming their dominant roles in light sensing cascades. Knockout strains of 5 newly-identified light-inducible transcription factors were further characterized for their potential function in mediating light signals. Interestingly, one early light-inducible transcription factor, Submerged Protoperithecia-1 (SUB-1), appeared to be essential in mediating a large number of late light response, providing a direct molecular connection between early and late light responses. Furthermore, a novel motif, which is overrepresented among late light responsive genes, was demonstrated to be necessary for full induction of late light responses in vivo. Taken together, these results reveal a simple hierarchical light-sensing cascade in Neurospora, which is initially invoked by light-activated White Collar Complex (WCC) binding to Light Response Elements (LREs) of the primary target genes, including SUB-1. Subsequently, the induction of SUB-1 and other activators activate downstream targets. Thus, light responses of well-defined timing and amplitude can be orchestrated to meet the differential needs of underlying biological processes.
Keywords: time course, light response

overall_design: Two-color microarray, totally 135 arrays were used to characterize light response in different photoreceptor knockout strains. Alexa Fluor 555 was consistently used to label cDNA synthesized from reference RNA, which is a mixture containing equal amounts of RNA samples harvested from different circadian time points and light treatment durations. The same batch of pooled RNA was used as a reference for each array experiment. Alexa Fluor 647 was used exclusively to label cDNA representing sample RNA.

first: Carol

last: Ringelberg

first: Robert

last: Gross

first: Jennifer

last: Loros

first: Jay

last: Dunlap


title: Liver gene expression profiling of transforming growth factor beta receptor 2 heterozygous knockout (Tgfbr2+/-) mice

status: Public on Mar 08 2009

first: Xia

last: Yang

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

summary: Transforming growth factor beta receptor 2 (Tgfbr2) was predicted as a causal gene for abdominal using a novel statistical method named LCMS (Schadt et al., 2005, Nature Genetics). In order to validate this prediction, we profiled the liver tissues of Tgfbr2 heterozygous knockout mice (Tgfbr2+/-)  and their littermate wild-type (wt) controls to examine the gene expression signature as well as pathways/networks resulting from the single gene perturbation.

overall_design: 6 Tgfbr2+/- mice and 4 wt controls were profiled. Reference pool included RNA extracted from the liver of 6 wt control mice. Dye-swap was involved in the profiling.


title: Liver gene expression profiling of complement component 3a receptor 1 knockout (C3ar1-/-) mice

summary: Complement component 3a receptor 1 (C3ar1) was predicted as a causal gene for abdominal using a novel statistical method named LCMS (Schadt et al., 2005, Nature Genetics). In order to validate this prediction, we profiled the liver tissues of complement component 3a receptor 1 knockout (C3ar1-/-) mice and their littermate wild-type (wt) controls to examine the gene expression signature as well as pathways/networks resulting from the single gene perturbation.

overall_design: 3 C3ar1-/- mice and 4 wt controls were profiled. Reference pool included RNA extracted from the liver of 6 wt control mice. Dye-swap was involved in the profiling.


title: Liver gene expression profiling of zinc finger binding protein 90 (Zfp90) transgenic mice

summary: Zinc finger binding protein 90 (Zfp90) was predicted as a causal gene for abdominal using a novel statistical method named LCMS (Schadt et al., 2005, Nature Genetics). In order to validate this prediction, we profiled the liver tissues of Zfp90 transgenic mice (Zfp90 tg) and their littermate wild-type (wt) controls to examine the gene expression signature as well as pathways/networks resulting from the single gene perturbation.

overall_design: 3 Zfp90 tg mice and 4 wt controls were profiled. Reference pool included RNA extracted from the liver of 4 wt control mice. Dye-swap was involved in the profiling.


title: Liver gene expression profiling of lipoprotein lipase heterozygous knockout mice

summary: Lipoprotein lipase (Lpl) was predicted as a causal gene for abdominal using a novel statistical method named LCMS (Schadt et al., 2005, Nature Genetics). In order to validate this prediction, we profiled the  liver tissues of lipoprotein lipase heterozygous knockout mice (Lpl+/-) and their littermate wild-type (wt) controls to examine the gene expression signature as well as pathways/networks resulting from the single gene perturbation.

overall_design: 8 Lpl+/- mice and 8 wt controls were profiled. Reference pool included RNA extracted from the liver of 9 wt control mice. Dye-swap was involved in the profiling.


title: Schistosoma japonicum differentially expressed gene at different development stage

city: shanghai

first: yuan

last: chunxiu

institute: shanghai research institute of domestic animal parasitolgy

summary:
Analysis of differentially expressed gene of different parasite stage helps to determine which genes are likely to be the key players in transition through a developmental stage, thus help to further understand schistosome biology and host-parasite relationship, facilitate the discovery of novel gene products than could represent targets for the development of new drugs and vaccines to control schitosomiasis.Samples were analyzed at cercariae, egg and adult worm stage.
Keywords = Schistosoma japonicum
Keywords = different development stage
Keywords = differentially expressed gene
Keywords: time-course

first: Chunxiu

last: Yuan

first: Xingang

last: Feng

first: Jiaojiao

last: Lin


title: Liver gene expression profiling of cytosolic malic enzyme knockout mice

summary: Cytosolic malic enzyme (Me1) was predicted as a causal gene for abdominal using a novel statistical method named LCMS (Schadt et al., 2005, Nature Genetics). In order to validate this prediction, we profiled the liver tissues of Me1 knockout mice (Me1-/-) and their littermate wild-type (wt) controls to examine the gene expression signature as well as pathways/networks resulting from the single gene perturbation.

overall_design: 3 Me1-/- mice and 5 wt controls were profiled. Reference pool included RNA extracted from the liver of 5 wt control mice. Dye-swap was involved in the profiling.


title: Gene Expression Profiles of Sporadic Canine Hemangiosarcoma are Uniquely Associated with Breed

status: Public on Mar 07 2009

city: Denver

first: Beth

last: Tamburini

state: CO

address: 1400 Jackson Street, K503

department: Immunology

institute: University of Colorado Denver

summary:
Abnormal function of genes is at the root of most cancers, but heritable cancer syndromes account for a very small minority of all tumors in humans and domestic animals. The majority of cancers are “sporadic,” that is, they are not heritable in the strictest sense. Instead, sporadic cancers occur due to interactions of unknown intrinsic (heritable) and environmental factors that lead to malignant transformation and uncontrolled growth. Identification of heritable risk factors in sporadic human cancers is difficult because individual genetic backgrounds are very heterogeneous. To this end, individual genetic backgrounds of purebred dogs are more homogeneous, and dog breeds show different predilection to develop specific cancers. Here, we used genomic screens based on gene expression profiling to identify sets of genes that may contribute to the development of canine hemangiosarcoma, a relatively common endothelial sarcoma. Specific genes in a single breed (Golden Retrievers) are modulated by (or with) heritable risk traits, showing functional features that appear to modulate tumor behavior. Our results suggest these methods are suitable to identify genes that will enhance our understanding of how these cancers happen, as well as possible treatment targets that will improve outcomes of both human and canine cancer patients.

Keywords: Hemangiosarcoma, microarray, heritability, GSEA, canine

overall_design: 10 samples were analysed.  6 Golden Retrievers with hemangiosarcoma, 3 non-Golden Retrievers with hemangiosarcoma, and 1 mixed breed Golden Retriever with hemangiosarcoma. The experiment was designed to find genes associated with breed and hemangiosarcoma to asses genetic make-up on disease susceptibility and/or progression

middle: A

first: Susan

last: Trapp

first: Tzu

middle: L

last: Phang

first: Jill

last: Schappa

first: Lawrence

last: Hunter

first: Jaime

middle: F

last: Modiano


title: Effect of AdpA deficiency on S. griseus cells grown in SMM medium

city: Bunkyo-ku

first: Yasuo

last: Ohnishi

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

institute: University of Tokyo

summary: Comparative hybridization of wild type versus AdpA deficient mutant  grown on SMM medium

sample_organism: Streptomyces griseus subsp. griseus NBRC 13350

overall_design: 3 x dual channel slides, dye swap

first: Genki

last: Akanuma

first: Hirofumi

last: Hara

first: Sueharu

last: Horinouchi


title: Requirement for Sun1 in the expression of meiotic reproductive genes and piRNA

city: Bethesda

first: Ya-Hui

last: Chi

state: MD

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Disease

institute: National Institutes of Health

summary: The inner nuclear envelope (NE) proteins interact with the nuclear lamina and participate in the architectural compartmentalization of chromosomes. The association of NE proteins with DNA contributes to the spatial rearrangement of chromosomes and their gene expression. Sun1 is an inner nuclear membrane (INM) protein that locates to telomeres and anchors chromosome movement in the prophase of meiosis. Here, we have created Sun1-/- mice and found that these mice are born and grow normally but are reproductively infertile. Detailed molecular analyses showed that Sun1-/- P14 testes are repressed for the expression of reproductive genes and have no detectable piRNA. These findings raise a heretofore unrecognized role of Sun1 in the selective gene expression of coding and non-coding RNAs needed for gemetogenesis.

overall_design: Total RNA was isolated from E14.5 mouse embryonic fibroblasts (MEFs) and and day 9 and 14 mouse whole testes.  cDNA samples from paired (same parents) wt (Cy3-labled) and Sun1-/- (Cy5-labled) mice were mixed and hybridized.

first: Lily

middle: I

last: Cheng

first: Timothy

last: Myers

first: Jerrold

middle: M

last: Ward

first: Elizabeth

last: Williams

first: Qin

last: Su

first: Larry

last: Faucette

first: Kuan-Teh

last: Jeang


title: Transcriptional comparison of Drosophila cell lines using Kc167 as standard

first: Lucy

last: Cherbas

summary:
A series of Drosophila melanogaster cell lines were each compared directly to the cell line Kc167.
Keywords: Cell line comparison

overall_design: Each slide is a comparison of RNA from a Drosophila cell line to RNA from the cell line Kc167.  3-4 biological replicates were done; dye swaps were included

first: Yi

last: Zou

first: Peter


title: A functional and regulatory network associated with PIP expression in human breast cancer

status: Public on Mar 06 2009

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

summary:
Background
The PIP (prolactin-inducible protein) gene has been shown to be expressed in breast cancers, with contradictory results concerning its implication. As both the physiological role and the molecular pathways in which PIP is involved are poorly understood, we conducted a combined gene expression profiling and network analysis studies on selected breast cancer cell lines presenting distinct PIP expression levels and hormonal receptor status, to explore the functional and regulatory network of PIP co-modulated genes.

Results
Microarray analysis allowed identification of genes co-modulated with PIP independently of modulations resulting from hormonal treatment or cell line heterogeneity. Relevant clusters of genes that can discriminate between [PIP+] and [PIP-] cells were identified.
Functional and regulatory network analyses based on knowledge database revealed a master network of PIP co-modulated genes, including many interconnecting oncogenes and tumor suppressor genes, half of which were detected as differentially expressed through high-precision measurements. The networks identified appear associated with an inhibition of proliferation coupled with an increase of apoptosis and an enhancement of cell adhesion in breast cancer cell lines. Finally, the STAT5 motif was identified in promoters of an important part of genes belonging to the PIP networks.

Conclusion
Our global exploratory approach was found to be an effective strategy to identify the biological pathways modulated along with the PIP expression, thus supporting good prognostic value of disease-free survival time in breast cancer based on previous reports focusing on PIP’s favorable signature. Moreover, our data allowed us to provide the first insight in its regulatory subnetwork in which STAT5 appears as a potential key regulator.

overall_design:
Microarray analyses were applied to breast cancer cell lines (T47D, MCF7, MDA-MB231, VHB1) with or without DHT treatment following a randomized and blinded unbalanced design. To assess data reproducibility and minimize dye bias effects, four independent RNA preparations were collected for each DHT-treated and -untreated cell lines  and each of the samples was measured at least twice times, once with Cy3 and once with Cy5. For some samples additional technical replicates were achieved. To ensure robustness and flexibility in data analysis, a reference design was used with a universal reference sample (Stratagene, USA) serving as a baseline for the comparisons of tumor samples.
Hybridizations were performed onto an 11K human array (GPL3282), which provides a genome-wide coverage of functional pathways. Raw data were obtained using the ArrayVision™ 7.0 software (Imaging Research Inc., USA); the resulting hybridization data points collected from 86 arrays were stored in a a MIAME-compliant database and pre-processed for normalization and filtering as described in [Graudens et al., Genome Biol 2006, 7: R19; PMID: 16542501]. Statistical comparison was done considering that samples can be divided into subgroups according to PIP expression level: two-classes (weak expression of PIP gene considered as negative, [PIP-], and positive expression of PIP gene, [PIP+]1) or three classes comparisons (low [PIP-], moderate [PIP+]2 and high [PIP++] expression level) were conducted.

first: Marie-anne

last: Debily

last: El Marhomy

first: Virginie

last: Boulanger

first: Eric

last: Eveno

first: Régine

last: Mariage-Samson

first: Alessandra

last: Camarca

first: Charles

last: Auffray

first: Dominique

last: Piatier-Tonneau