title: Expression profiling of B.subtils SMY wild-type, (p)ppGpp0, ΔcodY (p)ppGpp0 and guaB- (p)ppGpp0 cells upon amino acid starvation (RHX) or guanosine (Guo) treatment.

status: Public on Nov 01 2013

city: Houston

first: Jue

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The nucleotide (p)ppGpp is crucial for viability during amino acid limitation in bacteria, yet how it accomplishes this remains unknown. We found that the absence of (p)ppGpp in Bacillus subtilis cells leads to multiple amino acid auxotrophy, and that (p)ppGpp allows for prototrophy by reducing GTP levels. We provide evidence that reduction of GTP levels relieves the requirements for branched-chain amino acids primarily by preventing hyperactivity of the GTP-dependent transcriptional regulator CodY, but that GTP levels can also play an important role in regulating transcription of many amino acid biosynthesis genes independently of CodY. Thus, CodY-dependent and independent regulation of transcription by GTP levels plays overlapping yet distinct physiological roles in allowing amino acid prototrophy. Finally, supplementing these required amino acids does not protect against cell death upon nutrient downshift, but allows for sustained growth following this transition. We conclude that regulation of GTP levels by (p)ppGpp allows cells to adapt to conditions of amino acid limitation by first allowing survival during shifting nutrient conditions, and then allowing amino acid prototrophy by transcriptionally regulating amino acid biosynthesis. This strategy may be used to ensure viability during amino acid limitation in evolutionarily divergent bacteria.

sample_organism: Bacillus subtilis subsp. subtilis str. SMY

overall_design: Twelve-condition experiment: wt, wt+RHX, wt+Guo, (p)ppGpp0, (p)ppGpp0+RHX, (p)ppGpp0+Guo, ΔcodY (p)ppGpp0, ΔcodY (p)ppGpp0+RHX, ΔcodY (p)ppGpp0+Guo, guaB- (p)ppGpp0, guaB- (p)ppGpp0+RHX, guaB- (p)ppGpp0+Guo. Biological replicates: 3 for each sample. Reference: a mixture of wt RNA from different growth phases and wt backgrounds.

first: Allison

last: Kriel


title: Over-expression of Akt1 Induces Skin Hypertrophy and Generates an Obesity Model in Zebrafish

status: Public on Dec 31 2010

city: Chung-Li

first: Chung-Der

last: Hsiao

address: 200, Chung-Pei Rd.

department: Bioscience Technology

country: Taiwan

institute: Chung Yuan Christian University

summary: Recent evidences have demonstrated phosphatidylinositol3-kinase (PI3-K)/Akt signaling pathway participates in cell growth, cell survival, and adipocyte differentiation in vitro. However, the in vivo evidence to support Akt function on adipogenesis is limited. To achieve this goal, we generated the stable zebrafish transgenics of Tg(krt4:myrAkt1)cy18 carrying human constitutive active form of Akt1 (myrAkt1) that driven by a skin-specific krt4 promoter. The Tg(krt4:myrAkt1)cy18 display severely skin hypertrophy at embryonic stages, and support Akt1 function as a key gene on cell size control. When transgenics reached sexual maturation, they display obese phenotype due to adipocyte hypertrophy and up-regulation of adipogenesis-related genes. Collectively, our findings provided a direct evidence to support Akt play provital roles on cell size control as well as adipogenesis in vivo. In addition, the obese zebrafish line of Tg(krt4:myrAkt1)cy18 provide a new platform to study obesity and its related chronic diseases mechanism in vivo.

overall_design:
The AB strain of Zebrafish (Danio rerio) were obtained from ZIRC (http://zebrafish.org/zirc/home/guide.php), and kept in the stock of Chung Yuan Christian University. Zebrafish were raised in a local tap water at 28.0±0.5℃ and under a constant photoperiodism of 14 hour light cycle/10 hour dark cycle. Zebrafish embryos were collected in 10 cm diameter Petri dishes containing 20 mL fish water after spawning and raised at 28.0±0.5℃. To prevent the disease of Zebrafish embryo, few drops methylen blue were added into fish water. At 5 to 7 dpf, larvae were transferred to 10 liter tanks containing 8.0 liter of fish water and fed with living Paramecium. After 14 dpf, larvae were feed with living artemia (OSI, USA) until adulthood.
We dissected two tail tissues (as a pooled sample) from six month-old wild-type and Tg(krt4:myrAkt1)cy18 (n=5), and homogenized in Trizol reagent (Ambion) to isolate total RNA according to the manufacture instruction. The RNA was treated with DNase I at 25℃ for 10 minutes to remove DNA contamination and then cleanup by RNase-free spin columns (Qiagen). The total RNA concentration was determined by spectrophotometry (ND-1000 ; NanoDrop Technol, Wilmington, DE), and the RNA quality was checked by running electrophoresis in RNA-denatured gels. All total RNA were stored at -20℃. For real-time quantitative RT-PCR, 1μg of total RNA were reverse-transcribed with reverse transcriptase and the excess RNA were digested E.coli RNase H to enhance the cDNA purity.
The commercial Zebrafish 14K oligo microarray chip was obtained from Institute of Cellular and Organismic Biology at Academia Sinica and contained 14067 oligonucleotides represent 9666 unique genes with a redundancy of 31%. The detail oligonucleotide description can be obtained from Ocimun Biosolution (http://www.ocimumbio.com/web/default.asp). We used SuperScriptTM Indirect cDNA Labeling System kit (Invitrogen) to generate the fluorescently labeled probes. Total RNA isolated from WT and Tg(krt4:myrAkt1)cy18 were reversed transcribed into cDNA and coupling for Alexa Fluor 555 and Alexa Fluor 647 fluorescent dyes (Invitrogen), respectively. Before hybridization, the Zebrafish microarray chips were pretreated with 1% bovine serum albumin, 4X SCC, and 1% sodium dodecylsulfate (SDS) for 45min at 42℃, and then hybridized in SlideHybTM buffer (Ambion) for overnight at 42℃. After hybridization, chips were washed with 2X SSC and 0.5% SDS for 15min at 25℃ and finally with 0.5X SSC and 0.5% SDS for 15min at 25℃. The fluorescence intensities of Alexa Fluor 555 and Alexa Fluor 647 targets were scanned by Genepix scanner (Molecular Devices, Sunnyvale, CA, USA) and the acquired date were analyzed by Genepix and Genespring software (Aglient Technologies, Foster City, CA, USA).

first: Che-Yu

last: Chu


title: Comparative xylose metabolism among the ascomycetes C. albicans, S. stipitis and S. cerevisiae

status: Public on Oct 30 2013

city: Montreal

first: Daniel

last: Dignard

state: QC

address: 6100, Royalmount

department: HHT

country: Canada

institute: NRC

summary: The ascomycetes Saccharomyces cerevisiae, Candida albicans and Scheffersomyces stipitis metabolize the pentose sugar xylose very differently. S. cerevisiae fails to grow on xylose, while C. albicans can grow, and S. stipitis can both grow and ferment xylose to ethanol.  However, all three species contain highly similar genes that encode xylose reductase and xylitol dehydrogenase required to convert xylose to xylulose, on which all three fungi grow. We have created C. albicans strains deleted for either or both the xylose reductase gene GRE3, and the xylitol dehydrogenase gene XYL2.  As expected, all the mutant strains cannot grow on xylose, while the gre3 mutant can grow on xylitol. The gre3 and xyl2 mutants are complemented efficiently by the XYL1 and XYL2 from S. stipitis respectively. Intriguingly, the S. cerevisiae GRE3 and SOR1 genes can complement the gre3 and xyl2 mutants respectively, showing that S. cerevisiae contains the enzymatic capacity for converting xylose to xylulose. In addition, the gre3 xyl2 double mutant is effectively rescued by the xylose isomerase (XI) gene of either Piromyces or Orpinomyces, suggesting that the XI provides an alternative to the missing oxido-reductase functions in the mutant required for the xylose-xylulose conversion. Overall this work establishes that C. albicans strains engineered to lack essential steps for xylose metabolism provide a platform for the analysis of xylose metabolism enzymes from a variety of species, and confirms that S. cerevisiae has the genetic potential to convert xylose to xylulose, although non-engineered strains cannot proliferate on xylose as the sole carbon source.

sample_organism:
Saccharomyces cerevisiae
Candida albicans SC5314

overall_design: Transcription profile of cells in xylose compared to glucose. Two sets: Candida albicans, 1 condition ; Saccharomyces cerevisiae 2 conditions / in xylose (SX) or no sugar (S) (replicates with dye-swap)

first: Doreen

last: Harcus

first: Guylaine

last: Lepine

first: Chris

last: Askew

first: Martine

last: Raymond

first: Malcolm

last: Whiteway

first: Cunle

last: Wu


title: Mammary gland development: cross-species analysis of the mammary gland transcriptome in pregnant or lactating wild type female Sprague Dawley rats.

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

summary: Cross-species hybridization analysis of mammary glands during pregnancy and lactation. Results provide insight into putative conserved molecular mechanisms regulating mammary gland development. This study was performed to identify orthologous transcripts that are differentially co-expressed in the mammary gland at 2 stages of development (pregnancy and lactation) in wild type Sprague-Dawley rats.

overall_design: Key points are examined in a time series of Sprague Dawley rat mammary gland development, secretory activation and lactation. Triplicate rat (three biological replicates) at each time point were used for statistical power totalling 12 individual arrays in this study. Rats were as staged pregnant day 1 the day that post coital plug was observed, and similarly, lactation day 1 was the first day after birth. Whole mammary glands No. 4 (inguinal) were obtained from female rats at stages of development: virgin (adulthood, 14 wks of age), Pregnant (5 and 14 days of pregnancy) and Lactating (day 1 and 12 postpartum). The two-color (Cy5/Cy3) microarray experiment was designed to hybridize samples from each group against a common reference, a pool of RNA from mammary gland of three parous or virgin female rats.

first: Gabriel

last: Hernandez-Stengele

first: Raul

last: Sanchez

first: Emmanuel

last: Salazar

first: Fausto

last: Sanchez-Muñoz

last: Encarnacion

first: Jorge

last: Ramirez-Salcedo

first: Ramon

middle: M

last: Coral-Vazquez

first: Maricela

last: Rodriguez-Cruz


title: How does orotic acid affect the growth of R.etli CE3?

status: Public on Oct 12 2013

summary: Growth inhibition of Rhizobium etli and other organisms by exogenous OA has not been previously reported. We conducted genome-wide transcriptomic analysis to determine the possible mechanism by which OA exerts its growth-inhibitory effect on R. etli CE3. The observed changes fall into several broad categories. First, the decreased expression of genes involved in protein synthesis (including ribosomal genes), replication and energy production indicates that the cells arrest or at least slow their growth, which agrees with the observed growth arrest induced by OA. The upregulation of a key enzyme (PrsAch) for 5'-phosphoribosyl-1'-pyrophosphate (PRPP) synthesis suggests that cells exposed to OA suffer PRPP deprivation. We hypothesized that the PRPP pools were depleted as a result of an increase in the synthesis of OMP stimulated by exogenous OA. PRPP depletion would result in a marked decrease in purine synthesis, which would lead to an imbalance between purine and pyrimidine nucleotides, causing arrest of DNA synthesis and a lack of energetic nucleotides (ADP, ATP).

overall_design: Three independent biological materials with one dyeswap were performed.

first: Andres

last: Andrade


title: One Year RDX Exposure, Liver Tissue Investigation

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC

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

overall_design: Adult fathead minnows were exposed to 0.83 mg/L (0.15 mg/L standard deviation) in experimental units including 2 male and 4 fish.  Five replicate males were randomly sampled with replacement from each of 8 control and 8 RDX-exposed experimental units at 1d, 1mo, 3mo, 6mo, 9mo and 12mo sampling periods.  Liver tissue was investigated for differential expression in response to RDX exposure.

first: Sandra

last: Brasfield

first: Jacob

middle: K

last: Stanley

first: Mitchell

middle: S

last: Wilbanks

first: Pornsawan

last: Chappell

first: Edward

middle: J

last: Perkins

first: Guilherme

middle: R

last: Lotufo

first: Richard

middle: F

last: Lance


title: Expression profiling of the genes responding to zearalenone and its analogues using estrogen-responsive genes.

status: Public on Mar 11 2010

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

country: Japan

institute: scinet company

summary:
Comparing the expression profiles of the genes in response to estrogen or 17b-estradiol (E2) and a mycotoxin, zearalenone (ZEA), and its analogues.

Keywords: Gene expression profiling

overall_design: Two-condition experiment, E2- or ZEA-treated vs. control cells. 2 to 3 biological replicates, independently grown and harvested. Two to three replicates per array.

first: Meher

last: Parveen

first: Yun

last: Zhu

first: Ryoiti

last: Kiyama


title: Transcriptional analysis of sweet orange in response to TAL effector-dependent infection

status: Public on Sep 11 2013

city: Gainesville

first: Jeffrey

middle: B.

last: Jones

state: FL

address: 1453 Fifield Hall

department: Plant Pathology

institute: University of Florida

summary: We used this microarray data to survey the differentially expressed genes in sweet orange by comparing leaves challenged with X. citri ssp. citri (Xcc) strain 306 with the pthA4 gene and leaves challenged with mutant Xcc306ΔpthA4 without the pthA4 gene 120 hours after inoculation. The deletion of the pthA4 gene reduced the virulence of Xcc306, and eliminated pustule formation. The gene expression changes after inoculation of these two strains represent PthA4-mediated molecular events in a susceptible reaction.

overall_design: Xcc306 wild-type strain and pthA4 gene deletion mutant Xcc306ΔpthA4 were used to inoculate fully expanded young leaves in sweet orange (Citrus sinensis) at the concentration of 5 X 10^8 cfu/ml using syringe with needle in a quarantine greenhouse facility at the Citrus Research and Education Center, Lake Alfred, FL. The leaves were harvested 120 hours after inoculation for RNA isolation. To allow stringent statistical data analysis, three biological replicates were conducted and three technical replicates were pooled for each strain. RNA extraction was performed by using RNeasy Plant Mini Kit (Qiagen, Valencia, CA). The quantity and quality of RNA were determined on a ND-8000 Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington,DE). Microarray labeling, hybridization, washing, scanning, and data analysis were performed at ICBR facility at University of Florida in Gainesville. Statistical tests were performed using BioConductor statistical software, open source software based on the R programming language. Robust Multichip Analysis (RMA) approach was used for normalizing the raw data. Differential expression analysis was carried out using a linear modeling approach and the empirical Bayes statistics as implemented in the Limma package. Differentially expressed genes with fold change higher than 3 and an adjusted P-value (FDR) less than 0.05 were considered as differentially expressed genes at a statistically significant level.

first: Yang

last: Hu

middle: B

first: Nian

last: Wang


title: Neonatal antibotic prophylaxis modulates intestinal immunity and prevents necrotizing enterocolitis in preterm neonates

status: Public on Aug 21 2013

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

summary:
Caesarean-delivered preterm pigs were fed 3 d of parenteral nutrition followed by 2 d of enteral formula feeding. Antibiotics (n=11) or control saline (n=13) were given twice daily from birth to tissue collection at d 5. NEC-lesions and intestinal structure, function, microbiology and immunity markers were recorded.
We used Affymetrix microarrays to investigate gene expression in intestinal tissues of preterm piglets treated with antibiotics or control saline.

overall_design: Twenty-four preterm piglets were delivered by caesarean section on day 105 of gestation from two healthy sows. All piglets were initially provided with parenteral nutrition via a vascular catheter, combined with small amounts of minimal enteral nutrition. On day three, all parenteral nutrition was stopped and total enteral nutrition was given through an oro-gastric feeding tube. Piglets were allocated into controls ( n=13) and an intervention group receiving oral and systemic broad-spectrum antibiotics ( n=11). To assure high systemic and intra luminal MIC values antibiotics were given both orally and intramuscularly. All antibiotics were given directly after feeding with an oral bolus and control pigs were given corresponding amounts of saline. On day five, all piglets were euthanized, and small intestinal tissue collected.

first: Imke

last: Mulder


title: Copy number analysis of OVCAR-3 and CDK2 resistant sublines

status: Public on Sep 01 2013

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Cyclin E1 (CCNE1) is amplified in various tumor types including high-grade serous ovarian cancer where it is associated with poor clinical outcome. We have demonstrate that suppression of the Cyclin E1 partner kinase, CDK2, induces apoptosis in a CCNE1 amplicon-dependent manner. Little is known of mechanisms of resistance to CDK inhibitors. We therefore generated OVCAR-3 sublines with reduced sensitivity to CDK2 inhibitors and profiled by SNP copy number microarrays.

overall_design: Arrayed samples included parental OVCAR-3 cells and five independently derived sublines resistant to PHA-533533 (OVCAR3-533533-R1, -R3, -R5, -R6, -R7). The resistant cell lines were arrayed after drug selection (P5).

first: David

last: Bowtell


title: Global profiling of B. subtilis comparing wild-type to mutants with altered cytoplasmic membrane composition

status: Public on Oct 09 2008

city: Ithaca

first: John

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

summary: The Bacillus subtilis membrane contains diacylglycerol-based lipids with at least five distinct headgroups that impart distinct physical and chemical properties to the lipid bilayer. Here, we describe the phenotypic characterization of mutant strains lacking one or more of the following lipids: glycolipids (ugtP mutants), phosphatidylethanolamine (pssA and psd mutants), lysylphosphatidylglycerol (mprF), and cardiolipin (ywnE and ywjE). Alterations of membrane lipid headgroup composition are generally well tolerated by the cell and even severe alterations lead to only modest effects on growth proficiency. Mutants with decreased levels of positively charged lipids display an increased sensitivity to a cationic antimicrobial compounds and cells lacking glycolipids are sensitive to the lantibiotic sublancin and are defective in swarming motility. A quadruple mutant strain (ugtP pssA mprF ywnE), with a membrane comprised predominantly of phosphatidylglycerol, is viable and grows at near wild-type rates, although it forms long, coiled filaments. Transcriptome comparisons identify numerous regulons with altered expression in ugtP mutant cells, the pssA mprF ywnE triple mutant, and the uptP pssA mprF ywnE quadruple mutant. These effects include a general decrease in expression of the SigD and FapR regulons, and increased expression of cell envelope stress responses mediated by ?M and the YvrGHb two-component system.

overall_design: WT vs.ugtP single mutant (U), WT vs. mprFpssAywnE triple mutant (T) or WT vs. ugtPmprFpssAywnE quadruple mutant (Q). Each experiment (WT vs. mutant) was conducted four times using three independent total RNA preparations (3 independent experiement + dye swap). For the 3 datasets used for final analysis wild-type was labeled with Alexa Fluor 555 and mutants with Alexa Fluor 647. For dye swap experiments wild-type was labeled with Alexa Fluor 647 and mutants with Alexa Fluor 555.

first: Letal

middle: I

last: Salzberg

middle: D


title: Measuring cell-type specific differential methylation in human brain tissue

status: Public on Aug 08 2013

first: Carolina

last: Montano

state: United States

address: 855 N Wolfe Street

department: Molecular Medicine

institute: Johns Hopkins School of Medicine

type: Methylation profiling by genome tiling array

summary: We investigated genome-wide DNA methylation of NeuN+ and NeuN- fractions in three brain regions using comprehensive high throughput arrays for relative methylation (CHARM).

overall_design: We isolated genomic DNA from cell-sorted post-mortem brains using NeuN antibody and hybridized to Nimblegen microarrays (091020_HG19_CHARM_HX1 arrays).

first: Andrew

middle: P

last: Feinberg

first: Rafael

last: Irizarry

first: Margaret

last: Taub

first: Walter

middle: E

last: Kaufmann

first: Konrad

last: Talbot

first: Raquel

last: Gur


title: MicroRNA response to Snail overexpression in lung cancer cell lines

status: Public on Jul 17 2013

city: Los Angeles

first: Steven

last: Dubinett

state: CA

address: 10833 Le Conte Avenue

department: Medicine-Pulmonary

institute: University of California, Los Angeles

summary: Analysis of four lung cancer cell lines transfected with a vector expressing the transcriptional repressor Snail versus a vector control. Aberrant Snail expression is known to induce an EMT program in lung cancers.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Four lung cancer cell lines (H292, H358, H441, H1437) with stable overexpression of the human SNAI1 gene and vector expressing controls were collected at equal confluency with the miRNeasy Mini kit (Qiagen). One microgram of total RNA was labeled using miRCURY LNA™ microRNA Array Power Labeling kit by the UCLA Clinical Microarray Core. The labeled miRNAs were hybridized to Exiqon miRCURY LNA microRNA Array-6th Generation according to the manufacturer’s instructions. This array includes 927/648/351 human/mouse/rat miRNAs as well as 438 miRPlus miRNAs. The miRNA array slides were scanned using Axon GenePix 4000B scanner (Axon Instruments, Foster City, CA) and processed by using the GenePix Pro 6.0 software (Axon Instruments). The raw data were normalized by using a combination of housekeeping miRNA, spike-in miRNA and invariant endogenous miRNAs.

first: J

middle: L

last: Grant


title: Using natural variation Drosophila to discover previously unknown ER stress genes

status: Public on Apr 30 2013

first: Clement

middle: Y

last: Chow

address: 227 Biotech Bldg

summary: To measure natural variation in ER stress transcriptional response in a subset of lines from the Drosophila Genetic Reference Panel

overall_design: Transcriptional response to Tunicamycin and control conditions was measured at 8 hours of exposure (20 lines) and 20 hours of exposure (8 lines).

first: C


title: Short-term growth hormone treatment on the liver and muscle transcriptome in rainbow trout (Oncorhynchus mykiss)

status: Public on Jun 24 2008

city: Kearneysville

first: Scott

last: Gahr

state: WV

address: 11861 Leetown Rd.

institute: NCCCWA/ARS/USDA

summary:
Although studies have established that exogenous growth hormone (GH) treatment stimulates growth in fish, its effects on target tissue gene expression are not well characterized.  We assessed the effects Posilac® (Monsanto Co., St. Louis, MO), a recombinant bovine somatotropin, on tissue transcript levels.  Transcript abundance was measure in liver and muscle using the GRASP 16 K cDNA microarray.  A selection of the genes identified as altered with the microarray, and also transcripts for insulin-like growth factors, growth hormone receptors (GHR) and myostatins were measured by realtime PCR in the liver, muscle, brain, kidney, intestine, stomach, gill and heart.  In general, transcripts identified as differentially regulated in the muscle on the microarray showed similar direction of expression in the other non-hepatic tissues.  Rainbow trout were selected from two high growth rate and two low growth rate families.  A total of 113 and 67 transcripts were identified by microarray as differentially expressed with GH treatment across growth rate for muscle and liver respectively.  The largest proportion of the transcripts represented novel transcripts, followed by immune and metabolism related genes.  The immune related genes were primarily modulated in the liver and indicate activation of a non-specific immune response.  The metabolic genes include lipid metabolism, oxidative phosphorylation and one carbon metabolism pathway transcripts.  Most notable among the growth axis genes measured by realtime PCR were increases in GHR1 and-2 transcript in liver and muscle.  Our results indicate that short-term GH treatment activates the immune system, shifts the metabolic sectors and modulates growth regulating genes.
Keywords: Growth Hormone Injection Muscle and Liver Gene Expression

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Rainbow trout (hatched March 2005) selected for extreme growth rate were obtained from NCCCWA brood stock.  Families were selected based on body weight at 7 months of age and thermal growth coefficient for the final month of growth.  The two high growth families used in the study were in the top 2% in terms of growth rate, and the low growth families were in the lowest 10% for growth rate.  Fish acclimated to the new tanks for two weeks prior to initiation of the treatments.  Fish from each family were randomly selected to receive one of three treatments:  1) Posilac® injection (120 mg/kg BW, n = 4 per family); 2) vehicle injection (n = 4 per family); or 3) untouched controls (n = 2 per family). We had determined there was no effect to growth or the GH/IGF-I axis in the vehicle treated fish, and therefore, all of the microarray hybridizations were made between the GH and vehicle injected groups.  This study included a total of 16 two-channel arrays designed for the direct comparison of GH treatment levels.  That is, for each of the four groups, 1) High Growth Rate Liver; 2) Low Growth Rate Liver; 3) High Growth Rate Muscle; and 4) Low Growth Rate Muscle, four slide were hybridizes using individual RNA samples from individual fish.  RNA isolation from each tissue/organ sample was handled separately (without pooling) with the purpose of using biological replications.  We hybridized two slides with the GH cDNA labeled with Alexa 555 and vehicle cDNA labeled with Alexa 647; and two slides, using unique RNA samples, for the with GH cDNA labeled with Alexa 647 and tissue from the vehicle injected group labeled with Alexa 647 within each tissue and growth rate.  Sixteen slides were used in the current study representing 32 individual tissue samples, meaning a total of four biological replicates for each treatment group.

first: Roger

last: Vallejo

first: Gregory

last: Weber

first: Brian

last: Shepherd

first: Jeffrey

middle: T

last: Silverstein

first: Caird

last: Rexroad


title: The impact of breed genotype and tissue compartment on the response of pig macrophages to lipopolysaccharide

status: Public on Apr 13 2013

city: St Lucia

first: ronan

last: kapetanovic

state: QLD

address: The University of Queensland

institute: Institute for Molecular Bioscience

summary:
The domestic pig (Sus scrofa) provides a large animal model for human innate immune responses and inflammation that is also economically important in its own right.
Results: We demonstrate that macrophages can be harvested from 3 different compartments of the pig (lungs, blood and bone-marrow), cryopreserved and subsequently recovered and differentiated in CSF-1.  We have performed surface marker analysis and gene expression profiling on macrophages from these compartments, comparing 25 animals from 5 different breeds and their response to lipopolysaccharide.  The results provide a clear distinction between alveolar macrophages (AM) and monocyte-derived (MDM) and bone-marrow-derived macrophages (BMDM).  In particular, the lung macrophages express the growth factor, Flt1 and its ligand, VEGFA at high levels, suggesting a distinct pathway of growth regulation.  We confirm that pig macrophages more closely resemble human, than mouse, in their set of LPS-inducible genes. Relatively few genes showed breed-specific differential expression, notably CXCR2 and CD302 in alveolar macrophages. In contrast, there was substantial inter-individual variation between pigs within breeds, mostly affecting genes annotated as being involved in immune responses.
Conclusions: Future research will address whether such variation is heritable, and might form the basis for selective breeding for disease resistance or functional genomics.  The domestic pig (Sus scrofa) provides a large animal model for human innate immune responses and inflammation that is also economically important in its own right.  We demonstrate that macrophages can be harvested from 3 different compartments of the pig (lungs, blood and bone-marrow), cryopreserved and subsequently recovered and differentiated in CSF-1.  We have performed surface marker analysis and gene expression profiling on macrophages from these compartments, comparing 25 animals from 5 different breeds and their response to lipopolysaccharide.  The results provide a clear distinction between alveolar macrophages (AM) and monocyte-derived (MDM) and bone-marrow-derived macrophages (BMDM).  In particular, the lung macrophages express the growth factor, Flt1 and its ligand, VEGFA at high levels, suggesting a distinct pathway of growth regulation.  We confirm that pig macrophages more closely resemble human, than mouse, in their set of LPS-inducible genes. Relatively few genes showed breed-specific differential expression, notably CXCR2 and CD302 in alveolar macrophages. In contrast, there was substantial inter-individual variation between pigs within breeds, mostly affecting genes annotated as being involved in immune responses. Future research will address whether such variation is heritable, and might form the basis for selective breeding for disease resistance or functional genomics.

overall_design: 140 Affymetrix Snowball microarray were analysed from 5 different breed (DR, LR, LW, PIE and HAM). 5 pig per breed were used and cells were harvested from Lungs, blood and bone-marrow (AM, MDM and BMDM). Cells were left untreated (0h) or stimulated with LPS Salmonella enterica serotype minnesota Re 595 - 100ng/ml (7h)

first: R

last: Kapetanovic

first: L

last: Fairbairn

first: A

last: Downing

first: D

last: Beraldi

last: Sester

first: T

middle: C

last: Freeman

last: Tuggle

last: Archibald

last: Hume


title: Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer: aCGH Arrays

status: Public on Mar 01 2008

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
Summary: Lung cancer is a leading cause of cancer death, where the amplification of oncogenes contributes to tumorigenesis.  Genomic profiling of 128 lung cancer cell lines and tumors revealed frequent focal DNA amplification at cytoband 14q13.3, a locus not amplified in other tumor types.  The smallest region of recurrent amplification spanned the homeobox transcription factor TITF1 (also known as NKX2-1), previously linked to normal lung development and function.  When amplified, TITF1 exhibited increased expression at both the RNA and protein level.  siRNA-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis.  Our findings indicate that TITF1 amplification and overexpression contribute to lung cancer cell proliferation rates and survival, and implicate TITF1 as a lineage-specific oncogene in lung cancer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Cell Line
Keywords: Logical Set

overall_design:
cDNA microarrays from the Stanford Functional Genomics Facility were used to perform array based Comparative Genomic Hybridization (aCGH) analysis on 52 non-small cell lung cancer (NSCLC) cell lines and 76 NSCLC tumors (36 adenocarcinomas including 2 metastases, and 40 squamous cell carcinomas including 1 metastasis).  In addition, this dataset includes 6 immortalized and 3 non-immortalized lung epithelial cell lines and 1 male vs. female genomic DNA for hybridization control.  Map positions for arrayed cDNA clones were assigned using the NCBI genome assembly, accessed through the UCSC genome browser database (NCBI Build 36).  The most frequent focal DNA amplification not associated with a previously known oncogene occurred at cytoband 14q13.3 where TITF1 resides. The sample labeled normal is a "Normal male vs.female DNA" comparison; the samples: SAEC, HBEC3-UI, HBEC5-UI, HBEC2-KT, HBEC3-KT, HBEC4-KT, HBEC5-KT, HBEC2-E, BEAS-2B are Normal lung epithelial cell lines; samples starting with L are all Lung tumor samples and all the rest are Lung cancer cell lines.
Computed

first: Young

last: Kim

first: Adam

last: Adler

first: Elinor

last: Velasquez

first: Mitchell

last: Garber


title: Allele special primer extension microarray for test 12 SNPs contributed to NSCL/P in northeast China.

status: Public on Apr 09 2013

city: shenyang

first: lu

last: yongping

address: huanggu strict puhe street

country: China

institute: key lab of liaoning province family planning research institution

summary: Nonsyndromic cleft lip with or without palate (NSCL/P) are common birth defects of complex etiology. Multiple interacting loci with possible additional environment factors influence the risk for NSCL/P. 12 single nucleotide polymorphisms (SNPs) in 7 candidate genes were tested using an allele-specific primer extension for both case-control and case-parents analyses in northeast China (236 unrelated patients, 185 mothers and 154 fathers, including 128 complete trios, 400 control individuals). TGFA and IRF6 genes showed a significant associations with NSCL/P. For IRF6, statistical evidence of association between rs2235371 (P=0.003), rs2013162 (P=0.000) and NSCL/P was found in case-control analyses. The Family Based Association Tests (FBAT) showed an over-transmission for C allele of rs2235371 polymorphic (p=0.007). For TGFA, associations between rs3771494, rs3771523 (G3822A), rs11466285 (T3851C) and NSCL/P could be observed both in case-control and FBAT analyses. However, we found no associations between other genes (BCL3, TGFB3, MTHFR1, PVRL1 and SUMO1) and NSCL/P.

overall_design: In the study present, 236 unrelated patient with NSCL/P addition with 185 mothers and 154 fathers and 400 control individuals were tested with the allele special primer extension microarray.

first: Yongping

last: Lu

first: Qiang

last: Liu

first: Wei

last: Xu

first: Zengjian

last: Li

first: Weitian

last: Han

first: Jianxin


status: Public on Apr 01 2013

first: John

last: Helmann

summary: Transcriptional profile of the uppS-RBS (A to C) mutant during log growth phase in LB medium.

overall_design: Bacillus subtilis W168, WT vs. uppS-RBS (A to C). The experiment was conducted two times using three independent total RNA preparations (biological triplicates). Each comparison was performed in dye-swap with the same RNA preparation. For each paried comparison, one sample was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647.

first: Yong

middle: H

last: Lee


title: Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer: Expression Arrays

summary:
Lung cancer is a leading cause of cancer death, where the amplification of oncogenes contributes to tumorigenesis.  Genomic profiling of 128 lung cancer cell lines and tumors revealed frequent focal DNA amplification at cytoband 14q13.3, a locus not amplified in other tumor types.  The smallest region of recurrent amplification spanned the homeobox transcription factor TITF1 (also known as NKX2-1), previously linked to normal lung development and function.  When amplified, TITF1 exhibited increased expression at both the RNA and protein level.  siRNA-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis.  Our findings indicate that TITF1 amplification and overexpression contribute to lung cancer cell proliferation rates and survival, and implicate TITF1 as a lineage-specific oncogene in lung cancer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Cell Line
Keywords: Logical Set

overall_design:
cDNA microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling on 33 non-small cell lung cancer (NSCLC) cell lines, 1 immortalized and 2 non-immortalized lung epithelial cell lines. Mann-Whitney U-Test (p=0.046) was performed to demonstrate that TITF1 increased expression was correlated with TITF1 gene amplification (as shown by aCGH analysis).  NHBEC, SAEC and BEAS-2B are Normal lung epithelial cell lines, the others are Lung cancer cell lines
Using regression correlation


title: Expression profile in response to salt-treatment in wheat using 11k wheat array

status: Public on Oct 02 2007

city: Yokohama

first: Kanako

last: Kawaura

address: Maioka-cho 641-12

institute: Kihara Institute for Biological Research, Yokohama City University

summary:
Global expression analysis of transcripts in response to salt treatment was carried out for common wheat using oligo-DNA microarrays. Microarrays have been designed from unique wheat genes classified from a large number of expressed sequence tags (ESTs). Two-week-old seedlings of common wheat were treated with 150 mM NaCl for 1, 6 and 24 hours and their roots and shoots were separately subjected to microarray analyses. Consequently, 5996 genes showed changes in expression of more than two-fold, and were classified into 12 groups according to correlations in gene expression patterns. These salt-responsive genes were assigned functions using Gene Ontology (GO) terms. Genes assigned to transcription factor, transcription-regulator activity and DNA binding functions were preferentially classified into early response groups. On the other hand, those assigned transferase and transporter activity were classified into late response groups. These data on gene expression suggest that multiple signal transduction pathways in response to salt treatment exist in wheat. Salt-responsive transcription factors (TFs), namely AP2/EREBP, MYB, NAC and WRKY, were selected and their expression patterns compared with those of rice. Most showed different expression patterns in wheat and rice in response to salt treatment. Furthermore, comparing the microarray data for wheat and rice, only a small number of genes were up- or down-regulated in common in response to salt treatment. These findings suggest that salt-responsive mechanisms distinct from rice might be present in wheat, and wheat genes can contribute to providing novel gene resources for breeding of salt-tolerant crops.
Keywords: time cource, stress response

overall_design: Microarray hybridization was performed by a competitive two-color method including color-swap experiments. Chinese Spring wheat was grown for two weeks and treated with 150mM NaCl for 0, 1, 6 and 24 hours. RNA samples were extracted from roots and shoots.

first: Keiichi

last: Mochida

first: Yasunari

last: Ogihara


title: Paternally induced transgenerational inheritance of susceptibility to diabetes in mammals (NimbleGen expression)

status: Public on Dec 29 2012

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

institute: Institute of Zoology, Chinese Academy of Sciences

summary: The global prevalence of type 2 diabetes (T2D) is increasing, and it is contributing to the susceptibility to diabetes and its related epidemic in offspring. Although the impacts of paternal T2D on metabolism of offspring have been well established, the exact molecular and mechanistic basis that mediates these impacts remains largely unclear. Here we show that paternal T2D increases the susceptibility to diabetes in offspring through the gametic epigenetic alterations. Paternal T2D led to glucose intolerance and insulin resistance in offspring. Relative to controls, offspring of T2D fathers exhibited altered gene expression patterns in the pancreatic islets, with downregulation of several genes involved in glucose metabolism and insulin signaling pathway. Epigenomic profiling of offspring pancreatic islets revealed numerous changes in cytosine methylation depending on paternal T2D, including reproducible changes in methylation over several insulin signaling genes. Paternal T2D altered overall methylome patterns in sperm, with a large portion of differentially methylated genes overlapped with that of pancreatic islets in offspring. Our study revealed, for the first time, that T2D can be inherited transgenerationally through the mammalian germline by an epigenetic manner.

overall_design: For all comparisons shown, male F0 founders were weaned from mothers at 3 weeks of age, and sibling males were put into cages with high-fat diet (33% energy as fat) or control diet until 12 weeks of age, at which point mice fed with HFD were injected intraperitoneally with a low dose of STZ and kept on the same diet for 4 weeks. Fasting blood glucose was examined each week post-STZ for 4 weeks, and only glucose level at 7~11 mM was considered as type 2 diabetes. Females were always raised on standard diet. At 16 weeks, male F0 founders were mated with females. After 1 or 2 days, males were removed, and pregnant females were left alone until their litters were 3 weeks of age. Note that we always used virgin females to avoid confounding effects brought about by the females. At 3 weeks of age a portion of the offspring were sacrificed and islets were generated, each from an independent father.Samples from six control and six paternal type 2 diabetes offspring were chosen for microarray analysis.

first: Yanchang

last: Wei

first: Qing-Yuan

last: Sun


title: SNP array analysis of neuroblastoma tumors

status: Public on Jun 30 2007

city: Boston

first: Rani

middle: E.

last: George

state: MA

address: Dana 322, 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Chromosome 1p LOH was seen in one-third of cases. LOH events on chromosomes 11q and 1p were generally accompanied by copy number loss. The one exception was on chromosome 11p, where LOH in all 4 cases was accompanied by normal copy number or diploidy, implying uniparental disomy. Amplification of MYCN was also noted, and also, amplification of a second gene, ALK, in a single case.
Keywords: SNP array analysis

overall_design: We analyzed paired blood and primary tumor samples from 22 children with high-risk neuroblastoma for loss of heterozygosity (LOH) and DNA copy number change.

first: Edward

last: Attiyeh


title: Aspergillus nidulans: Control (0 h starvation) vs. induction of starvation (12 h and 24 h) for WT, delta xprG and delta atmA

status: Public on Dec 07 2012

city: Ribeirão Preto

first: Nadia

middle: Graciele

last: Krohn

state: São Paulo

address: Av do Cafe

department: Pharmacy

country: Brazil

institute: University of São Paulo

summary: Transcriptional profiling of A. nidulans comparing starvation for 0 (reference), 12 and 24 h. The main objective was to identify genes specifically regulated during starvation by atmA and xprG. The results of the experiment were further validated by real-time PCR.

overall_design:
Experimental procedure: Three A. nidulans strains were used in this study: WT, delta atmA and delta xprG. Strains were grown on minimal medium for 24 h (0 h starvation reference), then exposed to 12 and 24 h starvation.

atmA: ATM, Ataxia-Telangiectasia mutated; Malavazi, I., Savoldi, M., Da Silva Ferreira, M. E., Soriani, F. M., Bonato, P. S., De Souza Goldman, M. H. and Goldman, G. H. (2007), Transcriptome analysis of the Aspergillus nidulans AtmA (ATM, Ataxia-Telangiectasia mutated) null mutant. Molecular Microbiology, 66: 74-99 (PMID 17880424).

xprG: extracellular protease; Margaret E. Katz, Karen-Ann Gray, Brian F. Cheetham, (2006) The Aspergillus nidulans xprG (phoG) gene encodes a putative transcriptional activator involved in the response to nutrient limitation, Fungal Genetics and Biology, 43, 190-199 (PMID 16464624).


title: Oncorhynchus mykiss liver cells: Small vs. Large fish

status: Public on Nov 29 2012

city: Guelph

first: Andrea

middle: Lynne

last: Kocmarek

state: Ontario

address: Science Complex, University of Guelph

department: Intergrative Biology

institute: University of Guelph

summary: Transcriptional profiling of rainbow trout liver cells comparing liver cells from small fish with liver cells from large fish at two time periods.

overall_design: Two-condition experiment, small vs. large-fish liver cells. Sept. and Dec. spawning fish.  Biological replicates: 4 small replicates, 4 large replicates for each time period.

first: Moira

middle: M

last: Ferguson

first: Roy

middle: G

last: Danzmann


title: Early Epigenetic Downregulation of Tumor Suppressor WNK2 during Pancreatic Ductal Adenocarcinoma Development

status: Public on Nov 01 2012

city: Heidelberg

first: Celine

last: Dutruel

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary: BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) is usually incurable. Contrary to genetic mechanisms involved in PDAC pathogenesis, epigenetic alterations are ill defined. Here we determine the contribution of epigenetically silenced genes to the development of PDAC.    METHODS: We investigated methylated DNAs from PDACs, chronic pancreatitis and normal pancreatic tissues using Methyl-CpG immunoprecipitation followed by microarray hybridization. Promoter methylation of selected genes was confirmed with the Epityper assay. Expression levels were evaluated by quantitative RT-PCR. WNK2 was further investigated in tissue microarrays, methylation analysis of early pancreatic intraepithelial neoplasia (PanINs), mouse models for PDAC and pancreatitis, re-expression studies after demethylation, and cell growth assays using WNK2 overexpression.    RESULTS: A total of 3.8% of 27.800 interrogated CpG islands were hypermethylated in PDAC versus normal and chronic pancreatitis tissues. Hypermethylation was confirmed in 12 out of 13 selected islands and was associated with gene silencing in 4 of them. The most prominently hypermethylated gene, WNK2, was further investigated. Demethylation assays confirmed the link between methylation and expression. WNK2 hypermethylation was higher in pancreatic tumor cells than in surrounding inflamed tissues and was observed in PanIN lesions as well as in a PDAC mouse model. WNK2 mRNA and protein expression were lower in PDAC and chronic pancreatitis compared to normal tissues both in patients and mouse models. Overexpression of WNK2 led to a reduced cell growth and WNK2 expression in tissues correlated negatively with the expression of pERK1/2, a downstream target of WNK2 responsible for cell proliferation.    CONCLUSIONS: WNK2 is downregulated by promoter hypermethylation early in PDAC pathogenesis and may support tumor cell growth via the ERK-MAPK pathway.

overall_design: 3 types of pancreatic tissue samples: 5 normals, 2 chronic pancreatitis, 7 tumors (PDAC)

first: Frank

last: Bergmann

first: Manuela

last: Zucknick

first: Dieter

last: Weichenhan

first: Nathalia

last: Giese

first: Peter

last: Schirmacher

first: Jens

last: Werner

first: Christoph

last: Plass

first: Odilia

last: Popanda

last: Schmezer


title: Gene expression comparison between the murine T-cell hybridoma 6-13-64 ICOS(-) population and ICOS(+) population

status: Public on Apr 01 2012

city: Noda

first: Ryo

last: Abe

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biological Sciences

institute: Tokyo University of Science

summary: ICOS (Inducible Costimulator) is a T cell costimulatory molecule. We found that the cloned T-cell hybridoma 6-13-64 consists of two populations, ICOS expressing and non-expressing. The aim of this study is to screen for candidate genes that regulate ICOS gene expression by transcriptional profiling and comparison of the ICOS-positive and ICOS-negative subpopulations isolated from the 6-13-64 T-cell hybridoma.

overall_design: One-condition experiment, ICOS(-) vs. ICOS(+) cells. Independently grown and harvested. One replicate per array.

first: Masashi

last: Watanabe


title: SNP data from 125 hepatocellular carcinomas and 112 paired normal samples

status: Public on Feb 27 2012

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

summary: SNP array data from 125 hepatocellular carcinomas were used to detect recurrent copy number alterations.

overall_design: 99 hepatocellular carcinomas and 86 matched normal samples were analyzed with Illumina HumanCNV370-Duo v1.0 chips. 26 hepatocellular carcinomas and 26 matched normal samples were analyzed with Illumina HumanOmniExpress BeadChip.

last: Letouze

first: Sandrine

last: Imbeaud

first: Jessica

last: Zucman-Rossi


title: Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations [CNV]

status: Public on Nov 01 2011

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

institute: SA Pathology

summary:
Nonsense-mediated mRNA decay (NMD) surveillance pathways are best known to be involved in the degradation of mRNA with premature termination codons (PTCs). More recent studies demonstrate that the role of NMD pathways goes well beyond the degradation of PTC containing mRNA, into the regulation of cell function and thus normal development.
We have taken advantage of the availability of naturally occurring loss of function mutations in the UPF3B gene, a major component of the exon junction complex (EJC), to inquire about genome-wide consequences of compromised NMD. We identify that about 5% of the lymphoblastoid cell transcriptome is directly or indirectly impacted upon in patients with UPF3B mutations with minimal effect on alternative splicing. We identify UPF3A-NMD as a likely, major modifier of the UPF3B patient phenotype through variable UPF3A protein stabilisation. Among the most consistently deregulated direct targets of UPF3B-NMD we identify the ARHGAP24 as the most likely gene implicated in the neuronal phenotype of UPF3B patients.

overall_design: To assess the impact of UPF3B-NMD deficiency on human transcriptome, we sequenced polyA RNA extracted from lymphoblastoid cell lines of patients (n=4) and controls (n=2). We complemented the analysis using Affymetrix Human Exon 1.0 St array using total RNA of the same cell line from patients (n=5, 3 of whom were also sequenced) and controls (n=5). Moreover, we overlapped identified differently expressed genes with copy number variation data of the patients, obtained using Illumina Human Omniexpress chip, to exclude possible false positive.

first: Lam

middle: S

last: Nguyen

first: Lachlan

last: Jolly

first: Cheryl

last: Shoubridge

first: Wai-kin

last: Chan

first: Lulu

last: Huang

first: Frederic

last: Laumonnier

first: Martine

last: Raynaud

first: Jayson

last: Rodriguez

first: Anand

last: Srivastava

first: A

last: Addington

first: Miles

middle: F

last: Wilkinson

first: Mark

last: Corbett


title: Identification of expression quantitative trait loci (eQTL) in human liver

status: Public on Oct 10 2011

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

summary: We performed genome-wide mRNA profiling of 149 human surgical liver samples from Caucasian donors with detailed medical documentation. The overall purpose of the study was to identify expression quantitative trait loci (eQTL) in human liver.

overall_design: 149 liver samples of Caucasian origin were included in the study on the analysis of RNA expression (Illumina Human_WG6_V2) and genotype (HumanHap_300_V1)

first: Adrian

last: Schröder

first: Kathrin

last: Klein

first: Stefan

last: Winter

first: Matthias

last: Schwab

first: Andreas

last: Zell

first: Ulrich

last: Zanger


title: Bacillus subtilis Δ7ECF Pxyl-sigV + xylose vs Δ7ECF Pxyl-sigV - xylose , 168 + lysozyme vs 168 - lysozyme

status: Public on Aug 23 2011

first: John

middle: D.

last: Helmann

address: 372 Wing Hall

institute: Cornell University

summary:
To define the ECF sigma sigV - regulated genes during log growth phase in LB media under induction conditions for sigV

The seven extracytoplasmic function (ECF) sigma (σ) factors of Bacillus subtilis are broadly implicated in resistance to antibiotics and other cell envelope stressors mediated, in part, by regulation of cell envelope synthesis and modification enzymes. We here define the regulon of σV as including at least 20 operons many of which are also regulated by σM, σX, or σW. The σV regulon is strongly and specifically induced by lysozyme and this induction is key to the intrinsic resistance of B. subtilis to lysozyme. Strains with null mutations in either sigV or in all seven ECF σ factor genes (Δ7ECF) have essentially equal increases in sensitivity to lysozyme. Induction of σV in the Δ7ECF background restores lysozyme resistance, whereas induction of σM, σX or σW does not. Lysozyme resistance results from the ability of σV to activate the transcription of two operons: the autoregulated sigV-rsiV-oatA-yrhK operon and dltABCDE. Genetic analyses reveal that oatA and dlt are largely redundant with respect to lysozyme sensitivity: single mutants are not affected in lysozyme sensitivity whereas a double oatA dltA mutant is as sensitive as a sigV null strain. Moreover, the triple sigV oatA dltA mutant is no more sensitive than the oatA dltA double mutant, indicating that there are no other σV-dependent genes necessary for lysozyme resistance. Thus, σV confers lysozyme resistance by activation of two cell wall modification pathways: O-acetylation of peptidoglycan catalyzed by OatA and D-alanylation of teichoic acids by DltABCDE.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Strains Δ7Pxyl-sigV + xylose vs. Δ7Pxyl-sigV - xylose, 168 + lysozyme vs. 168 - lysozyme. Each experiment was conducted 6 times using three independent total RNA preparations (biologlical triplicates). For each paired comparison, one sample was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647. For each comparison, three replicates were performed with dyeswap with the same RNA preparation.

first: Veronica

last: Guariglia-Oropeza


title: Benign Breast Cores from Healthy Women Treated with Tamoxifen or Placebo

status: Public on Jul 22 2011

city: Dallas

first: David

last: Euhus

address: 5323 Harrry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

summary: Five years of tamoxifen reduces breast cancer risk by nearly 50% but is associated with significant side-effects and toxicities.  A better understanding of the direct and indirect effects of tamoxifen in benign breast tissue could elucidate new mechanisms of breast carcinogenesis, suggest novel chemoprevention targets, and provide relevant early response biomarkers for Phase II prevention trials.  Seventy-three women at increased risk for breast cancer were randomized to tamoxifen (20 mg daily) or placebo for three months. Blood and breast tissue samples were collected at baseline and post-treatment.  Sixty-nine women completed all study activities (37 tamoxifen and 32 placebo).  The selected biomarkers focused on estradiol and IGFs in the blood, DNA methylation and cytology in random periareolar fine needle aspirates, and tissue morphometry, proliferation, apoptosis, and gene expression (microarray and RT-PCR) in the tissue core samples. Tamoxifen downregulated ets-oncogene family members ETV4 and ETV5 and reduced breast epithelial cell proliferation independent of CYP2D6 genotypes or effects on estradiol, ESR1 or IGFs.  Reduction in proliferation was correlated with downregulation of ETV4 and DNAJC12. Tamoxifen also modulated expression of RAB GTPases, and several genes involved in epithelial-stromal interaction, and reduced tumor suppressor gene methylation. Three months of tamoxifen did not affect breast tissue composition, cytological atypia, preneoplasia or apoptosis. Tamoxifen may durably reduce breast cancer risk through downregulation of ETV4 and ETV5 which could deplete mammary progenitor populations.    This pathway has the potential to provide novel targets and early response biomarkers for phase II prevention trials.

overall_design: Randomized prospective double blinded placebo-controlled trial of tamoxifen (20 mg daily) versus placeo in women at increased risk for breast cancer. Gene expression was assessed in whole breast tissue cores obtained at baseline and after three months of treatment for 35 women. Core biopsies were obtained in the late luteal phase (day 28 +/- 2) for premenopausal women (N = 19). Breast lobules from the baseline and post-treatment cores were microdissected for 5 tamoxifen subjects.


title: The GntR family repressor YtrA responds to cell wall antibiotics

status: Public on Jun 17 2011

city: Ithaca

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Reduction in membrane phosphatidylglycerol content leads to daptomycin resistance in Bacillus subtilis

status: Public on Jun 16 2011

summary: Transcriptional response of Bacillus subtilis to daptomycin in wild-type and in a daptomycin resistant mutant.

overall_design: Bacillus subtilis 168, WT (-DAP) vs. DapR1 (-DAP), WT (+DAP) vs. DapR1 (+DAP), DapR1 (+DAP) vs. DapR1 (-DAP). Each experiment was conducted at least twice using two independent total RNA preparations. For daptomycin untreated comparison between 168 WT and DapR1 mutant, DapR1 was labeled with Alexa Fluor 647 and WT was labeled with Alexa Fluor 555. For daptomycin treated experiments between WT and DapR1, DapR1 was labeled with Alexa Fluor 647 and WT  with Alexa Fluor 555. For treated vs. untreated DapR1, the DAP treated samples were labeled with Alexa Fluor 647 and the untreated with Alexa Fluor 555. For dye swap, untreated DapR1 was labeled with Alexa Fluor 647 and DAP treated with Alexa Fluor 555.

first: Anna-Barbara

last: Hachmann


title: Transcriptional profiling of yeast transcription factor deletion strains (rox1, xbp1 or phd1) and wild-type strains in response to hydrogen peroxide or butanol

status: Public on May 17 2011

city: Seattle

first: Jennifer

middle: Joy

last: Smith

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

summary:
The goal of this study was to determine the effect of transcription factor deletions on the expression of subtelomeric genes in the presence of environmental stimuli.
This study is a component of a larger study, which identified that environment-responsive transcription factors bind proto-silencer elements and regulate subtelomeric silencing.  Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of different stress response pathways, and control of lifespan.  Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing activities or to protect chromosomal regions from spreading epigenetic control.  Here, using condition-specific genome wide chromatin immunoprecipitation and expression data, we show that multiple environment-responsive yeast transcription factors act as silencing factors when conditionally associated with subtelomeric proto-silencing regions called X elements.  In this context, some factors control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others influence boundaries of silencing, regulating telomere-proximal genes in Y’ elements.  These data suggest a fundamental mechanism to coordinate telomere biology related to aging and adaptation with cellular environment and the activities of other cellular processes.

overall_design: Each experiment was performed with two biological and two technical replicates of each condition resulting in a total of four replicates.  Each experiment includes two replicates in each labeling orientation (two replicates of Cy3/Cy5 and two replicates of Cy5/Cy3 (test sample/reference sample)).  There are two replicates per array.

middle: J

first: Leslie

last: Miller

first: Laura

last: Vazquez

first: Yakun

last: Wan

last: Aitchison


title: Response of Shewanella oneidensis wild type and arcA mutant strains to H2O2

status: Public on Aug 01 2012

city: Hangzhou

first: haichun

last: gao

address: 388 Yuhangtang Rd.

institute: Zhejiang University

summary: We undertook a transcriptional profiling to identify genes coping with H2O2-induced oxidative stress in S. oneidensis. The data revealed that the well conserved scavenging genes such as as ahpCF, katB, and katG formed the first line of defense while iron-sulfur protecting proteins may not play a significant role.

overall_design: Experimental cells collected 5 min after H2O2 treatment; Control cells collected just before H2O2 treatment. In total, 8 samples were studied (4 for wild type and 4 for arcA mutant, 4 replicates).

first: Haichun

last: Gao


title: Bacillus subtilis CU1065: WT vs fur, fur vs fur fsrA, fur vs fur fbpAB, fur vs fur fbpC, and fur vs fur fbpABC

status: Public on Feb 19 2011

summary:
Global tranascriptional profiling of Bacillus subtilis cells comparing fur mutant to mutants of the iron-sparing response: fur fsrA double mutant, fur fbpAB triple mutant, fur fbpC double mutant, and  fur fbpABC quadruple mutant
Abstract of associated manuscript: The Bacillus subtilis ferric uptake regulator (Fur) protein is the major sensor of cellular iron status. When iron is limiting for growth, derepression of the Fur regulon increases the cellular capacity for iron uptake and mobilizes an iron-sparing response mediated, in large part, by a small non-coding RNA named FsrA. FsrA functions together with three small, basic proteins (FbpABC) to repress many "low-priority" iron-containing enzymes. We have used transcriptome analyses to define the scope of the iron-sparing response and to define subsets of genes dependent on either FbpAB or FbpC for their repression. Enzymes of the tricarboxylic acid cycle, including both aconitase and succinate dehydrogenase, are major targets of FsrA-mediated repression and, as a consequence, flux through this pathway is significantly decreased under iron limitation. FsrA also mediates a physiologically significant repression of iron-sulfur containing enzymes required for ammonium assimilation (the GltAB glutamate synthase) and catabolism of lactic acid (LutABC). Repression of the lutABC operon requires both FsrA and FbpB which supports a model in which the Fbp proteins function to enable repression of subsets of the FsrA regulon.

overall_design: WT vs fur (fur), fur vs fur fsrA (fsrA), fur vs fur fbpAB (AB), fur vs fur fbpC (C), and fur vs fur fbpABC (ABC). Each experiemnt (fur vs mutant) was conducted three times using three independent total RNA preparations (2 independent experiement + 1 independent dye swap).

first: Gregory

last: Smaldone

middle: D


title: Genomic investigation of year long and multi-generational exposures of fathead minnow to the munitions compound RDX

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

address: 3909 Halls Ferry Rd.

institute: US Army ERDC


title: CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer (aCGH)

status: Public on Sep 08 2009

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

institute: Stanford University

summary:
Title: CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer

Summary: Breast cancer exhibits clinical and molecular heterogeneity, where expression-profiling studies have identified five major molecular subtypes.  The basal-like subtype, expressing basal epithelial markers and negative for estrogen receptor (ER), progesterone receptor (PR) and HER2, is associated with higher overall levels of DNA copy number alteration (CNA), specific CNAs (like gain on chromosome 10p), and poor prognosis.  Discovering the molecular genetic basis of tumor subtypes may provide new opportunities for therapy.  To identify the driver oncogene on 10p associated with basal-like tumors, we analyzed genomic profiles of 172 breast carcinomas.  The smallest shared region of gain spanned just seven genes at 10p13, including calcium/calmodulin-dependent protein kinase ID (CAMK1D), functioning in intracellular signaling but not previously linked to cancer.  By microarray, CAMK1D was overexpressed when amplified, and by immunohistochemistry exhibited elevated expression in invasive carcinomas compared to carcinoma in situ.  Engineered overexpression of CAMK1D in non-tumorigenic breast epithelial cells led to increased cell proliferation, and molecular and phenotypic alterations indicative of epithelial-mesenchymal transition (EMT), including loss of cell-cell adhesions and increased cell migration and invasion.  Our findings identify CAMK1D as a novel amplified oncogene linked to EMT in breast cancer, and as a potential therapeutic target with particular relevance to clinically unfavorable basal-like tumors.

overall_design:
Overall design: cDNA microarrays from the Stanford Functional Genomics Facility were used to carry out array-based Comparative Genomic Hybridization (array CGH) analysis of 172 human breast tumor specimens, in comparison to normal female DNA.  Map positions for arrayed cDNA clones were assigned using the NCBI genome assembly, accessed through the UCSC genome browser database (NCBI Build 36).  The CLuster Along Chromosomes (CLAC) method was used to call DNA gains and losses.

Set of arrays that are part of repeated experiments

Keywords: Biological Replicate
Biological Replicate
Computed

first: Young

last: Kim

first: Anne-Lise

last: Borresen-Dale


title: Daptomycin stimulon in Bacillus subtilis W168

status: Public on Dec 11 2008

summary: Abstract of associated manuscript: Daptomycin is the first of a new class of cyclic lipopeptide antibiotics used against multidrug-resistant Gram-positive pathogens. The proposed mechanism of action involves disruption of the functional integrity of the bacterial membrane in a Ca2+-dependent manner. We have used transcriptional profiling to demonstrate that treatment of Bacillus subtilis with daptomycin strongly induces the lia operon including the autoregulatory LiaRS two-component system (homologous to Staphylococcus aureus VraSR). The lia operon protects against daptomycin and deletion of liaH, encoding a phage shock protein A (PspA)-like protein, leads to 3-fold increased susceptibility. Since daptomycin interacts with the membrane, we tested mutants with altered membrane composition for effects on susceptibility. Deletion mutations of mprF (lacking lysyl-phosphatidylglycerol) or des (lipid desaturase) increased daptomycin susceptibility, whereas overexpression of MprF decreased susceptibility. Conversely, depletion of the cell for the anionic lipid phosphatidylglycerol led to increased resistance. Fluorescently-labeled daptomycin localized to the septa and in a helical pattern around the cell envelope and was delocalized upon depletion of phosphatidylglycerol. Together, these results indicate that the daptomycin-Ca2+ complex interacts preferentially with regions enriched in anionic phospholipids and leads to membrane stresses that can be ameliorated by PspA family proteins.

overall_design: Bacillus subtilis W168, WT (+DAP) vs. WT (-DAP). The experiment was conducted in triplicate using three independent total RNA preparations. For WT-rep1 and WT-rep2, daptomycin treated samples were labeled with Alexa Fluor 647 and untreated samples with Alexa Fluor 555. For WT-rep3, the daptomycin treated sample was labeled with Alexa Fluor 555 and the untreated sample with Alexa Fluor 647.

first: Esther

middle: R

last: Angert


title: Sigma(M) regulated genes under antibiotic stress (vancomycin)

status: Public on Dec 05 2008

last: Helmann

summary: Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. Genes regulated by sigma(M) have a characteristic pattern of induction in response to cell envelope-acting antibiotics as evidenced by hierarchical clustering analysis. sigma(M) also contributes to the expression of the Spx transcription factor and thereby indirectly regulates genes of the Spx regulon. Cell envelope stress responses also include regulons controlled by sigma(W), sigma(B) and several two-component regulatory systems (e.g. LiaRS, YycFG, BceRS). Activation of the sigma(M) regulon increases expression of proteins functioning in transcriptional control, cell wall synthesis and shape determination, cell division, DNA damage monitoring, recombinational repair and detoxification.

overall_design:
WT (-van) vs. WT (+van), sigM (-van) vs. sigM (+van), WT (-van) vs. sigM (-van), WT (+van) vs. sigM (+van), WT (-van) vs. spx (-van), WT (+van) vs. spx (+van). Each experiment was conducted at least twice using two independent total RNA preparations. For vancomycin untreated and treated experiments, untreated samples were labeled with Alexa Fluor 555 and treated samples with Alexa Fluor 647. For WT vs. mutant experiments, wild type was labeled with Alexa Fluor 555 and mutants with Alexa Fluor 647. For dye swap experiment, wild-type was labeled with Alexa Fluor 647 and mutant with Alexa Fluor 555.
Bacillus subtilis CU1065, WT (-van) vs. WT (+van), sigM (-van) vs. sigM (+van), WT (-van) vs. sigM (-van), WT (+van) vs. sigM (+van), WT (-van) vs. spx (-van), WT (+van) vs. spx (+van)

first: Warawan

last: Eiamphungporn


title: Small RNA SBS signatures identified from maize using Illumina's SBS technology

status: Public on Oct 01 2008

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wildtype maize and in the isogenic mop1-1 loss-of-function mutant using Illumina’s sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth.  Similar to rdr2 in Arabidopsis, in mop1-1, the 24 nt (nucleotide) endogenous heterochromatic short-interfering siRNAs were dramatically reduced resulting in an enrichment of miRNAs and trans-acting siRNAs (ta-siRNAs). In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic ~22 nt class of small RNAs. These data suggest that maize, unlike Arabidopsis, has a second mechanism for heterochromatic siRNA production.  The enrichment of miRNAs and loss of 24 nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced.

overall_design:
This library was derived from maize variety K55 wild-type and mop1 mutant.  Immature ears were harvested from plants grown outdoors in Tuscon, AZ.  The material was harvested from plants 68 days after germination, with the floral tissue including young tassels 2-3 cm long.  Total RNA was isolated using a standard TRIZOL-based method and the small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by sequencing with Illumina's SBS method. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.

Raw data are unavailable from Illumina


title: Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer

status: Public on Mar 01 2008

summary:
Lung cancer is a leading cause of cancer death, where the amplification of oncogenes contributes to tumorigenesis.  Genomic profiling of 128 lung cancer cell lines and tumors revealed frequent focal DNA amplification at cytoband 14q13.3, a locus not amplified in other tumor types.  The smallest region of recurrent amplification spanned the homeobox transcription factor TITF1 (also known as NKX2-1), previously linked to normal lung development and function.  When amplified, TITF1 exhibited increased expression at both the RNA and protein level.  siRNA-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis.  Our findings indicate that TITF1 amplification and overexpression contribute to lung cancer cell proliferation rates and survival, and implicate TITF1 as a lineage-specific oncogene in lung cancer.

This SuperSeries is composed of the SubSeries listed below.


title: Expression profile in response to salt-treatment in wheat

status: Public on Oct 02 2007

city: Yokohama

first: Kanako

last: Kawaura

address: Maioka-cho 641-12

institute: Kihara Institute for Biological Research, Yokohama City University

first: Keiichi

last: Mochida

first: Yasunari

last: Ogihara


title: Expression profile in response to salt-treatment in wheat using 22k microarray

summary:
Analysis of transcripts in response to salt treatment. In order to design the 22k wheat oligo-DNA microarray, a total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan.  These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray.  Following a multi-step selection of the sense strand, 21,939 60-mer oligo DNA probes were selected for attachment on the microarray slide.  This 22k oligo DNA microarray was used to examine the transcriptional response of wheat to salt stress.  More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots.  With the microarray, we identified 1,811 genes whose expressions changed more than two-fold in response to salt.  These included genes known to mediate the response to salt as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering.  These gene expression patterns were also confirmed by real-time reverse transcription (RT)-PCR.  Many of the genes with unknown function were clustered together with genes known to be involved in the response to salt stress.  Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes.  Also, functional analysis of these wheat genes should provide new insight into the response to salt stress.  Finally, these results indicate that the 22k oligo DNA microarray is a reliable method for monitoring global gene expression patterns in wheat.
Keywords: time cource, stress response

overall_design: Microarray hybridization was performed by a competitive two-color method including color-swap experiments. Chinese Spring wheat was grown for two weeks and treated with 150mM NaCl for 0, 1, 6 and 24 hours. RNA samples were extracted from roots and shoots.Each experiment was design for comparison in control and treated sample.