title: Expression Profiling of Tissues versus Primary Cultures from Colorectal Cancer Patients

status: Public on May 29 2011

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

department: Biochemistry

institute: National University of Singapore

summary: The main aim of this study is to evaluate how comparable the established colorectal primary tumor cultures are to the original tumor tissues obtained directly from patients in terms of their genomic profile for which they can be eventually utilized to improve in vitro drug assessment and facilitate personalized treatment. Here, we used colorectal cancer patient samples collected after surgery to perform a gene expression comparison study between original tissues and self-established primary cultures. Subsequently, we also investigated the possibility of using primary cells from patients’ tumors as a model for assessing drug response by characterizing the modifications in gene-drug associations of the primary cells which occurred during the establishment of cell cultures. On an auxiliary note, cytogenetic studies are only possible in cultured cells and not in tissue samples, hence, in this study we also evaluated the potential of genome stability analysis on primary cells as an alternative method to improve our understanding of the genomic changes which occur in cancer initiation and progression.

overall_design: Using cRNA microarrays, gene expression of low-passage colorectal tumor primary cultures were compared against colorectal tumor tissues obtained directly from patients.

first: Gregory

middle: L

last: Bellot

first: Jane

last: Wong

first: Wei

last: Tan

first: Ling

last: Tay

first: Dean

last: Koh

first: Xueying


title: Genome-wide expression in the hippocampus of dab1 homozygous mutants in C57BL/6 and BALB/c mice.

status: Public on Jun 01 2011

city: Syracuse

first: Tohru

last: Matsuki

state: NY

address: 766 Irving Avenue

department: Depertment of Neuroscience and Physiology

country: USA

institute: SUNY Upstate Medical University

summary: Differential gene expression in the hippocampus was analyzed between Dab1 and wild type mice on the C57BL/6 and BALB/c mouse strains.

overall_design: Total RNA obtained from isolated hippocampus at postnatal day 19 was analysed for gene expression between C57BL6 and BALB/c wild type or dab1 mutant mice. Three samples from separate mice were analyzed from each genotype and strain.

first: Marcel

middle: P

last: Van der Brug

first: Brian

middle: W

last: Howell


title: Antagonistic role of MBNL1 and LIN28 promotes specific alteration of pre-miR-1 processing and is associated with heart defects in DM

status: Public on May 26 2011

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary: Myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults, is caused by the expression of expanded CUG repeats, which sequester the MBNL1 RNA binding protein. Cardiac involvement, which is characterized by conduction defects and arrhythmias, is the second cause of death of DM1 patients. Down-expression of miR-1 in mice leads to cardiac conduction disturbances and to arrhythmias. Here, we show that miR-1 expression is decreased in DM1 hearts, due to a mis-regulation of the processing of pre-miR-1. MBNL1 binds to UGC motifs located within the pre-miR-1 loop and competes binding of LIN28, which promotes uridylation and blocks pre-miR-1 processing. Finally and consistent with a down-regulation of miR-1, known, GJA1, and novel, CACNA1C, targets of miR-1 are increased in DM1 hearts. CACNA1C and GJA1 encode the main calcium and gap junction channels in heart, respectively, and their mis-regulation may contribute to the heart arrythmias and conduction defects observed in DM1 patients.

overall_design: Total RNA of 3 control and 3 CDM1 primary culture of muscle cells differentiated 10 days  into myotubes was extracted using Trizol and analyzed by Agilent microarray.

first: Frédérique

last: Rau

first: Nicolas

last: Charlet-Berguerand


title: Effect of Artemisinin on Aspergillus fumigatus gene expression program

status: Public on May 11 2011

city: Delhi

first: Santosh

middle: Kumar

last: Upadhyay

state: Delhi

address: Near Jubilee Hall, Mall Road Delhi

department: Allergy and infectious Disesases

country: India

institute: Institute of Genomics and Integrative Biology

summary: We examined the antifungal activity of artemisinin against Aspergillus fumigatus (A. fumigatus), a pathogenic filamentous fungus responsible for allergic and invasive aspergillosis in humans and analyzed transcript profiles of the fungus on exposure to Artemisinin. A. fumigatus spores were cultured for 48 h and then treated with artemisinin (at MIC50 concentration) or solvent control (DMSO) for 3 h to study its transcriptomic profiles.

overall_design: Total RNA (7 µg) from A. fumigatus treated with solvent control (DMSO) or artemisinin was reverse transcribed separately using fluorescein-labeled dCTP or biotin-labeled dCTP from Micromax TSA labeling kit (Cy3 or Cy5 dyes are differentially deposited to these labeled cDNAs, post-hybridization, using tyramide signal amplification (TSA) protocol). Labeled cDNAs from test and control sample were mixed in equal amount and hybridized to microarray slide(s). After hybridization, the slides were processed as per the protocol of the Micromax TSA labeling kit and scanned in both the Cy3 and the Cy5 channels with a model 4200 Axon Instruments scanner with a 10-µm resolution. Each of the signals was converted into a resolution of 16 bits per pixel. A dye swap experiment with a biological replicate was performed to ensure the reproducibility of each gene expression pattern.TIFF images were analyzed using GenePix Pro 6.0 software. The signal intensity value of each spot was reduced by the local background level for each spot. Diagnosis and normalization of microarray data (DNMAD) program was used for print-tip loess normalization of microarray data and for merging the data from dye-swap experiments . M-values obtained from this program were converted to log ratio (test/reference) and fold modulation. Genes having less than 3 spots in 2 dye swap slides were discarded and only those having their all fold change values (from 3 or 4 replicates in 2 slides; as each target is spotted twice on the slide) within a coefficient of variation ± 0.5 were used for analysis. Gene expression ratios of ≥2 (fold upregulation or downregulation) in both replicates (dye swap) were considered to be differentially expressed genes.

middle: K

first: Poonam

last: Gautam

first: Taruna

last: Madan

first: Seemi

middle: F

last: Basir


title: LPS hypersensitivity of gp130 mutant mice is independent of elevated hematopoietic TLR4 signaling

status: Public on May 17 2011

city: Clayton

first: Jodee

middle: Ann

last: Gould

state: Victoria

address: 27-31 Wright Street

country: Australia

institute: Monash Institute of Medical Research

summary: The inflammatory mediator IL6 induced by LPS, which signals via TLR4, has been shown to feedback and augment TLR4 signaling when over-produced in LPS hypersensitive gp130F/F mice.  The identity of the LPS/TLR4 responsive inflammatory signaling pathways and gene networks which are modulated by IL6 are unknown.  Therefore, to understand the molecular consequences of gp130 hyperactivity in non-haemopoietic tissue on LPS-induced systemic inflammation, global gene expression profiling of livers was performed.

overall_design: The mouse 22K compugen oligo array from the Adelaide Microarray Facility was used to investigate the effect of LPS treatment on the livers of wildtype and gp130F/F mutant mice. Livers of both wildtype mice and gp130F/F mice at 6hr post LPS injection and also control livers wer collected.  Each experimental group had 3 independant mice.  In total 12 arrays were performed with a total of three biological replicates.  A common reference design was used for this experiment.  RNA extracted from eight pooled 17.5dpc C57BL/6 mouse embryos was used as the reference sample.  6 wildytpe mice and 6 gp130F/F mice were used in this study, with 3 mice of each genotype treated with LPS.

first: Brendan

middle: J

last: Jenkins

middle: A

first: Claire

last: Grennhill

first: Matthias

last: Ernst

first: Ashley

last: Mansell

first: Paul

last: Hertzog


title: Toxoplasma gondii lysine acetyltransferase GCN5-A functions in the cellular response to alkaline stress and expression of cyst genes

status: Public on May 25 2011

city: Indiananpolis

first: William

last: Sullivan

state: IN

address: 635 Barnhill Dr.

department: Pharmacology & Toxicology

institute: Indiana University

summary: Parasitic protozoa such as the apicomplexan Toxoplasma gondii progress through their life cycle in response to stimuli in the environment or host organism.  Very little is known about how proliferating tachyzoites reprogram their expressed genome in response to stresses that prompt development into latent bradyzoite cysts.  We have previously linked histone acetylation with the expression of stage-specific genes, but the factors involved remain to be determined.  We sought to determine if GCN5, which operates as a transcriptional co-activator by virtue of its histone acetyltransferase (HAT) activity, contributed to stress-induced changes in gene expression in Toxoplasma.  In contrast to other lower eukaryotes, Toxoplasma has duplicated its GCN5 lysine acetyltransferase (KAT).  Disruption of the gene encoding for TgGCN5-A did not produce a severe phenotype under normal culture conditions, but here we show that the TgGCN5-A null mutant is deficient in recovering from alkaline pH, a common stress used to induce bradyzoite differentiation in vitro.  The TgGCN5-A knockout is incapable of up-regulating key marker genes expressed during development of the latent cyst form.  Complementation of the TgGCN5-A knockout restores the expression of these stress-induced genes and reverses the stress recovery defect.  We also describe a genome-wide analysis of the Toxoplasma transcriptional response to alkaline pH stress, finding that TgGCN5-A knockout parasites fail to up-regulate 68% of the stress response genes that are induced 2-fold or more in wild-type.  Using chromatin immunoprecipitation, we verify an enrichment of TgGCN5-A at the upstream regions of genes activated by alkaline pH exposure, including developmentally regulated genes.

overall_design: Wild-type and GCN5-A- Knockout organisms were subjected to control and stress treatments

first: Arunasalam

last: Naguleswaran

first: Eliana

middle: V

last: Elias

first: Jeanette

middle: N

last: McClintick

first: Howard

last: Edenberg


title: Investigating RDX neurotoxicity in rat brain using gene expression analysis and transcriptional network modeling

status: Public on May 31 2011

city: Vicksburg

first: Mitchell

last: Wilbanks

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

summary: ABSTRACT: The central nervous system is remarkably plastic in its ability to recover from trauma. We examined recovery from hexahydro-1,3,5-trinitrotriazine  (RDX) induced seizures in rat through changes in transcriptional networks. Transcriptional networks from time series experiments provide a good basis for organizing and studying the dynamic behavior of biological processes. The goal of this work was to identify networks affected by chemical exposure and track changes in these networks as animals recover. We examined brain microarray data from rats exposed to 0, 1.2, 12, 24, and 47 mg RDX/kg body weight at different time points after exposure (24hr, 48hr, 7d, 14d, 28d and 90d).  RESULTS  A credible transcriptional network was constructed from the gene expression microarray data, which predicts the role of some key genes such as heat shock proteins, neuropeptide Y, thyrotropin-releasing hormones, growth factors, and ion channels in neurotransmission and neuroprotective mechanisms. Examination of the dynamic changes in expression within this network over time provided insight into CNS protective mechanisms from traumas.

overall_design: Single RDX Exposure with Various Time Points, Brain Tissue Investigation:  Sprague-Dawley female rats were exposed to a single oral gavage of one of four concentrations of RDX or vehicle control with sampling periods of 24h, 48h, 7d, 14d, 28d, or 90d.  Brain tissue was investigated for differential expression in response to RDX exposure and provide insight into CNS protective mechanisms associated with RDX exposure.

first: Tanwir

last: Habib

middle: S

first: Venkata

last: Thodima

first: Barbara

last: Escalon

first: Xin

last: Guan

first: Mohamed

last: Elasri

first: Sharon

last: Meyer

first: Edward

last: Perkins


title: The dynamics of E1A in regulating networks and canonical pathways in quiescent cells

status: Public on May 01 2011

city: Cleveland

first: Jean-Eudes

last: Dazard

state: Ohio

address: 10900 Euclid Avenue

department: Proteomics and Bioinformatics

institute: Case Western Reserve University

summary: Adenoviruses force quiescent cells to re-enter the cell cycle to replicate their DNA, and for the most part, this is accomplished after they express the E1A protein immediately after infection. In this context, E1A is believed to inactivate cellular proteins (e.g., p130) that are known to be involved in the silencing of E2F-dependent genes that are required for cell cycle entry. However, the potential perturbation of these types of genes by E1A relative to their functions in regulatory networks and canonical pathways remains poorly understood. We have used DNA microarrays analyzed with Bayesian ANOVA for microarray (BAM) to assess changes in gene expression after E1A alone was introduced into quiescent cells from a regulated promoter. Approximately 2,401 genes were significantly modulated by E1A, and of these, 385 and 1033 met the criteria for generating networks and functional and canonical pathway analysis respectively, as determined by using Ingenuity Pathway Analysis software. After focusing on the highest-ranking cellular processes and regulatory networks that were responsive to E1A in quiescent cells, we observed that many of the up-regulated genes were associated with DNA replication, the cell cycle and cellular compromise. We also identified a cadre of up regulated genes with no previous connection to E1A; including genes that encode components of global DNA repair systems and DNA damage checkpoints. Among the down-regulated genes, we found that many were involved in cell signalling, cell movement, and cellular proliferation. Remarkably, a subset of these was also associated with p53-independent apoptosis, and the putative suppression of this pathway may be necessary in the viral life cycle until sufficient progeny have been produced. These studies have identified for the first time a large number of genes that are relevant to E1A’s activities in promoting quiescent cells to re-enter the cell cycle in order to create an optimum environment for adenoviral replication.

overall_design: Six independent cell cultures (n = 6) were randomly assigned to two treatment groups with three independent biological replicates per group. The control group, denoted ‘Q’, are quiescent cells without Doxycycline, i.e. no E1A expression (untreated for 8 hr, total RNA harvested 1 hour after). The stimulated group, denoted ‘S’, are stimulated cells with Doxycycline, i.e. with E1A expression (treated with Doxycycline for 8 hr, total RNA harvested 1 hour after treatment).

first: Keman

last: Zhang

first: Jingfeng

last: Sha

first: Omar

last: Yasin

first: Linda

last: Cai

first: Chien

last: Nguyen

first: Mrinal

last: Ghosh

first: Jennifer

last: Bongorno

first: Marian

last: Harter


title: Identification of a gene expression signature for survival prediction in type I endometrial carcinoma

city: Göteborg

first: Kristina

last: Levan

address: Blå Stråket 2

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

summary: Endometrial cancer is the most common malignancy of the female reproductive tract. In many cases the prognosis is favourable, but 22% of affected women die from the disease. We aimed to study potential differences in gene expression between endometrioid adenocarcinomas from survivors (5-year survival) and non-survivors. Forty-five patients were included in the investigation, of which 21 were survivors and 24 were non-survivors. The tumours were analysed with genome-wide expression array analysis, represented by 13526 genes. Distinct differences in gene expression were found between the groups. A t-test established that a set of 218 genes were significantly differentially expressed (P < 0.001) between the two survival groups, and in a cross validation test 40 of the 45 (89%) tumours were classified correctly. The 218 differentially expressed genes were subjected to hierachical clustering analysis which yielded two clusters both exhibiting over 80% homogeneity with respect to survival. When the additional constraint of fold change (FC>2) was added the hierachical clustering yielded similar results.

overall_design:
Tumour cDNA from both groups (survivors vs. non-survivors) were hybridised together with the same reference, and we were able to calculate the relative expression level value for the sample
Stage I tumours are expected to have a favourable prognosis. However, in our tumour material there were six non-survivors with stage I tumours. Five out of six stage I non-survivors clustered in the non-survival fraction. Our findings suggest that a subgroup of early stage endometroid adenocarcinomas can be correctly classified as potentially aggressive by using molecular biology in combination with conventional markers, thereby providing a tool for a more accurate classification and risk evaluation of the individual patient.


title: microRNA expression during skeletal muscle differentiation and exercse in skeletal muscle.

status: Public on May 14 2011

city: Otsu,

first: hirotaka

last: yamamoto

state: Shiga,

address: Tsukinowa, Seta,

country: Japan

institute: Shiga University of Medical Science

summary: To investigate microRNAs related to mitochondria biogenesis in skeletal muscle, microRNA expressions during skeletal muscle differentiation and exercise were analyzed in vivo and in vitro.

overall_design: Murine skeletal muscle cell (C2C12) were assigned to undifferentiated, differentiated, and passively stretched (exercise mimicked). C57BL/6S mice were assigned to resting, acute exercise (1day), and chronic exercise (7days). Low molecular weight RNA (< 200 nucleotides) was isolated from C2C12 cell or tibialis anterior muscle of mice and hybridized to Ncode microRNA microarrays. The experiment was performed using a loop design for the data analysis.

first: Katsutaro

last: Morino


title: Effect of endoglin loss on embryoid bodies

status: Public on May 16 2011

city: Minneapolis

first: Rita

last: Perlingeiro

state: MN

address: 312 Church ST SE; NHH 4-124

department: Medicine

institute: University of Minnesota

summary: Analysis of embryonic sten cell-derived embryoid bodies following endoglin knock out. Loss of endoglin leads to profound reduction of key hematopoietic regulators including SCL, LMO2, Gata2, and TGF-β signaling molecule ALK-1. Results provide insight into molecular mechanisms underlying hemangioblast and primitive hematopoietic development.

overall_design: Total RNA obtained from differentiated day 3 EBs of endoglin knock out ES cells were compared to wild type E14 control ES cells.

first: Liying


title: Gene expression on 144 arrays representing 125 workers exposed to a range of benzene exposures

city: Berkeley

first: Alan

last: Hubbard

state: CA

address: School of Public Health, Div. of Biostatistics,101 Haviland Hall, MC 7358

department: Division of Biostatistics

institute: UC Berkeley

summary:
Human toxicogenomic studies to date have been of limited size, have mainly addressed exposures at the upper end of typical ranges of human exposure, and have often lacked precise, individual estimates of exposure. Previously, we identified genes associated with exposure to high (>10 ppm) levels of the leukemogen, benzene, through transcriptomic analyses of blood cells from small numbers of occupationally exposed workers. Here, we have expanded the study to 125 workers exposed to a wide range of benzene levels, including <1 ppm. Study design, and analysis with a mixed effects model, removed sources of biological and experimental variability and revealed highly significant widespread perturbation of gene expression at all exposure levels. Benzene is an established cause of acute myeloid leukemia (AML), and may cause one or more lymphoid malignancies in humans. Interestingly, acute myeloid leukemia was among the most significant pathways impacted by benzene exposure in the present study. Further, at most exposure levels, immune response pathways including T cell receptor signaling, B cell receptor signaling, and Toll like receptor signaling were impacted, providing support for the biological plausibility of an association between lymphoma and benzene exposure. We also identified a 16-gene expression signature modified by all levels of benzene exposure, comprising genes with roles in immune response, inflammatory response, cell adhesion, cell-matrix adhesion, and blood coagulation. Overall, these findings support, and expand upon, our current understanding of the mechanisms by which benzene may induce hematotoxicity, leukemia and lymphoma. Furthermore, this study shows that with good study design and analysis, transcriptome profiling of the blood of chemically-exposed humans can identify relevant biomarkers across a range of exposures and inform about potential associations with disease risks.
Key words: occupational exposure

overall_design: 29 workers exposed to <<1ppm benzene at most dosimetry reading over a 14-month period (Very Low), 30 exposed to average <1ppm (Low), 11 exposed to 5-10 ppm (High), 13 exposed to >10 ppm (Very High), and 42 unexposed controls (Control) who were frequency-matched to these subjects on the basis of age and gender were analyzed (technical replicates on some subjects, see SubjectID/description).


title: Macrophages in Human Colorectal Cancer are Pro-inflammatory and Prime T Cells towards the Anti-Tumor Type-1 Inflammatory Response

status: Public on May 12 2011

city: Singapore

first: Siew-Min

last: Ong

address: 8A Biomedical Grove, Immunos Level 4

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Analysis of interaction between tumor cells and macrophages at the gene expression level.

overall_design: Total RNA obtained from tumor cells cultured as (1) spheroids alone, (2) tumour cells sorted out from co-culture spheroids with macrophages, and (3) co-culture spheroids of tumor cells and macrophages


title: Copy number variants in candidate genes are genetic modifiers of Hirschsprung disease

status: Public on May 06 2011

city: Baltimore

first: Qian

last: Jiang

address: 733 N Broadway Street

institute: JHMI

type: Genome variation profiling by genome tiling array

summary: Hirschsprung disease (HSCR) is a neurocristopathy characterized by absence of intramural ganglion cells along variable lengths of the gastrointestinal tract. The HSCR phenotype is highly variable with respect to gender, segment length of aganglionosis, familiality and the presence of additional anomalies. By molecular genetic analysis, a minimum of 11 neuro-developmental genes (RET, GDNF, NRTN, SOX10, EDNRB, EDN3, ECE1, ZFHX1B, PHOX2B, KIAA1279, TCF4) are known to harbor rare high-penetrance mutations that confer a large risk to the bearer. In addition, two other genes (RET, NRG1) harbor common low-penetrance polymorphisms that contribute only partially to risk and act as genetic modifiers. To broaden this search, we examined whether a set of 67 proven and candidate HSCR genes harbored additional modifier alleles. In this pilot study, we utilized a custom-designed array CGH with ~33,000 test probes at an average resolution of ~185bp to detect gene-sized or smaller copy number variants (CNVs) within these 67 genes in 18 heterogeneous HSCR patients. Using stringent criteria, we identified CNVs at three loci (MAPK10, ZFHX1B, SOX2) that are novel, involve regulatory and coding sequences of these neuro-developmental genes and show association with HSCR in combination with other congenital anomalies.

overall_design:
Two-condition experiment: Patient vs. Control. Sex-matched controls. Technical replicates: 4 were examined twice and 3 were studied in triplicate.

Technical replicates: 408.3.1, 408.3.2
Technical replicates: 300.3.1, 300.3.2
Technical replicates: 354.3.1, 354.3.2
Technical replicates: 355.3.1, 355.3.2
Technical replicates: 63.3.1, 63.3.2, 63.3.3
Technical replicates: 122.7.1, 122.7.2, 122.7.3
Technical replicates: 413.3.1, 413.3.2, 413.3.3

first: Yen-Yi

last: Ho

first: Li

last: Hao

first: Courtney

last: Nichols

first: Aravinda

last: Chakravarti


title: Comparison of hepatic gene expression in response to fasting or 2 week high fat diet

status: Public on Apr 02 2011

city: Leiden

first: Anja

last: Schiel

address: Einthovenweg 20

department: Human Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
The metabolic syndrome represents a cluster of well-documented risk factors for the development of type 2 diabetes and cardiovascular disease. Next to visceral obesity, dyslipidemia and insulin resistance, excessive triglyceride accumulation in the liver has been implicated to play a role in the development of the metabolic syndrome.
To investigate the underlying molecular changes leading to hepatic steatosis we performed microarray analysis on livers of mice either fasted over night or fed a high fat diet for 2 Weeks. We analysed 7 500 genes and subsequently performed a pathway analysis to identify changes in hepatic genes in both models.
Fasting induced a high number of differentially expressed hepatic genes, resulting in an change towards an energy saving phenotype. In contrast only a small number of genes were differentially expressed after high fat diet.
Fasting promoted gluconeogenesis and b-oxidation, strongly suppressed cholesterol synthesis and activated pathways to preserve hepatic function. High fat diet induced steatosis was accompanied by the activation of the stearoyl-CoA desaturase and the lipogenic transcription factor Srebp-1c, both implicated in the development of hepatic insulin resistance. These changes reflect the activation of different gene expression programs in response to plasma lipid overload.
Keywords: Diet intervention

overall_design: Two conditions, fasting and high fat diet. 5 biological replicates for comparison of high fat diet versus fasting and controls versus high fat diet, 4 biological replicates for the comparison of controls versus fasting. All biological replicates are performed as technical replicates in the form of a dye-swap. Total number of arrays hybridises is therefore 28.

middle: E

first: Ko-Willems

last: van Dijk


title: Modulation of gene expression in heart and liver of hibernating black  bears (Ursus americanus)

status: Public on May 10 2011

city: Shanghai

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

country: China

institute: Shanghai institute for biology science

summary: We analyzed gene expression in the American black bear, Ursus americanus, using a custom 12,800 cDNA probe (BA02) microarray to detect differences in expression that occur in heart and liver during winter hibernation in comparison to summer active animals. We identified 245 genes in heart and 319 genes in liver that were differentially expressed between winter and summer. The expression of 24 genes was significantly elevated during hibernation in both heart and liver. These genes are mostly involved in lipid catabolism and protein biosynthesis and include RNA binding protein motif 3 (Rbm3), which enhances protein synthesis at mildly hypothermic temperatures. Elevated expression of protein biosynthesis genes suggests induction of translation that may be related to adaptive mechanisms reducing cardiac and muscle atrophies over extended periods of low metabolism and immobility during hibernation in bears. Coordinated reduction of transcription of genes involved in amino acid catabolism suggests redirection of amino acids from catabolic pathways to protein biosynthesis. We identify common for black bears and small mammalian hibernators transcriptional changes in the liver that include induction of genes responsible for fatty acid β oxidation and carbohydrate synthesis and depression of genes involved in lipid biosynthesis, carbohydrate catabolism, cellular respiration and detoxification pathways. Our findings show that modulation of gene expression during winter hibernation represents molecular mechanism of adaptation to extreme environments.

overall_design: Black bears sampled during winter hibernation were compared with the animals sampled during summer. Two tissue types, liver and heart, were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and five summer active bears were studied in experiments with liver tissue, six hibernating and five summer active animals were tested with heart tissue.

first: Vadim

middle: B

last: Fedorov

first: Anna

last: Goropashnaya

first: O

last: Tøien

first: Nathan

middle: C

last: Stewart

first: Celia

last: Chang

first: Jun

last: Yan

first: Louise

last: Showe

first: Michael

first: Brain

middle: M

last: Barnes


title: Microarray analysis on livers, spleens and hearts of mice fed a normal diet and supplemented with either oil palm phenolics (OPP) or distilled water

status: Public on Apr 26 2011

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

summary: OPP (1500 ppm gallic acid equivalent (GAE)) was supplemented to BALB/c mice given a normal diet to observe for possible biological activities. Livers, spleens and hearts were harvested six weeks after the feeding regimen for gene expression studies. Results from the separate microarray data analysis carried out on the different organs show that OPP may have pleiotropic biological properties in vivo.

overall_design: Total RNA obtained from livers, spleens and hearts of BALB/c mice given OPP (six weeks after the feeding regimen) were compared to controls given distilled water (liver: three replicates in the treatment group versus four replicates in the control group; spleen and heart: four replicates in the treatment group versus four replicates in the control group for both organs)

first: Shamala

middle: D

last: Sekaran

first: Ravigadevi

last: Sambanthamurthi


title: Transcriptome partitioning in mouse fertilization.

status: Public on Apr 21 2011

city: Regensburg

first: Matthias

last: Maneck

address: Franz-Josef-Strauß-Allee 11

department: Department of Pathology

country: Germany

institute: University of Regensburg

summary: RNA transcripts are distributed non-uniformly in the oocytes of many animals, such that newly-divided embryo cells (blastomeres) inherit distinct transcriptomes following fertilization. In animals such as the frog, Xenopus laevis, programmed transcript regionalization directs early embryonic axis formation and is essential for normal development. However, it is unknown whether such transcriptome asymmetry directs embryogenesis in mammals, or indeed, whether it occurs at all. We here address this by transcript profiling of matching sub-cellular structures and single cells in mouse oocytes and early embryos and analytical strategies exploiting the paired data structure. Spindle samples contained a set of transcripts that was distinguishable from that of the unfertilized metaphase II (mII) oocytes from which each spindle was microsurgically dissected. Immediately following fertilization, cytokinesis produces a 1-cell embryo (zygote) and associated spindle-enriched second polar body (Pb2) whose transcript profiles also differed one from the other, partially reflecting the enrichment of spindle-associated transcripts. Non-uniform transcript distribution within zygotes did not lead to programmed transcriptome asymmetry between the blastomeres of nascent two-cell embryos, or between the second mitotic products of 3-cell embryos. These findings suggest that mammalian oocytes and zygotes exhibit transcript regionalization without subsequent transcriptome asymmetries between respective early mitotic products. This contrasts the situation in Xenopus and places constraints on the ability of maternal transcriptomic prepatterning to prescribe early mammalian development.

overall_design:
16 Zygote vs. Polar body pairs, 10 spindle vs. oocyte pairs, 22 2-cell embryos and 8 3-cell embryos were analysed.
Although the raw data are two channel, only the Cy5 signal of each file was analyzed. The Cy5 channel for each gene is normalized to the average Cy5 intensity of the gene across all samples.

first: Matthew

last: VerMilyea

first: Naoko

last: Yoshida

first: Isabell

last: Blochberger

first: Emi

last: Suzuki

first: Toru

first: Rainer

last: Spang

first: Christoph

last: Klein

first: Anthony

last: Perry


title: Systems genetics approach to low dose radiation sensitivity in BXD recombinant inbred mice

status: Public on Apr 01 2011

city: Knoxville

first: Rachel

last: Lynch

state: TN

address: 2640 Morgan Circle Drive, 51f McCord Hall

department: Life Sciences

institute: University of Tennessee

summary: The immune system illustrates the challenges of assigning risk to low dose radiation (LDR) exposure in a population. While high radiation doses clearly suppress immune function, a number of studies have shown that LDR affects immune cell subpopulations in ways that could be beneficial. In the intact organism, defining the consequences of LDR is further complicated by the impact of genetic background, particularly in systems such as the immune system for which both radiosensitivity and genetic effects are profound.  We employed a systems genetics approach to test for heritable differences in LDR responses. Mice from 39 BXD recombinant inbred (RI) strains were exposed to 10cGy gamma radiation to determine effects on immune function and oxidative stress 48h after irradiation. LDR significantly enhanced neutrophil phagocytosis in a manner that was independent of genetic background. In contrast, genetic background significantly impacted LDR-induced changes in spleen superoxide dismutase activity. Transcriptome data from spleens of the BXD parental strains highlighted the impact of genetic background on LDR responses and also indicate that genetic variation in radiosensitivity is further unmasked at low radiation doses. Taken together, these data highlight the need to consider genetic variation when assessing LDR outcomes.

overall_design: Adult C57BL/6J and DBA/2J mice (10 weeks old) were exposed to low dose (10cGy) or high dose (1Gy) gamma radiation. Mice were sacrificed 24h after radiation or sham exposure & spleens were harvested for transcriptomic analysis.

first: Brynn

middle: H

last: Voy


title: Differential gene expression in mice liver following apigenin administration

status: Public on Apr 27 2011

city: Lucknow

first: Prabhat

last: Singh

state: Uttar Pradesh

address: MG Marg

department: Toxicology

institute: Central Drug Research Institute

summary: Differential gene expression in mice liver after apigenin administration. Gene expression from control mice were compared with apigenin treated mice at different dose level.

overall_design: To study differential expression primarily at high stringency and in dose dependent manner was to increase the statistical confidence in the detection of important genes and cellular processes with a probable role in the initiation and propagation of toxicity as well as those possibly involved in regeneration during the early phase of tissue response.

first: Sanjeev

last: Noel

first: Srikanta

middle: k

last: Rath


title: Transformation of elongation factor 1Bdelta into heat shock response transcription factor by alternative splicing

status: Public on Apr 12 2011

city: Kumamoto

first: Taku

last: Kaitsuka

state: Kumamoto

address: 1-1-1 honjo

department: Department of Molecular Physiology

institute: Graduate School of Life Sciences, Kumamoto University

summary:
Protein translation factors play crucial roles in a variety of stress responses. Here, we show that the eukaryotic elongation factor 1Bdelta (eEF1Bdelta) changes its structure and function from a translation factor into a heat shock response transcription factor by alternative splicing. While eEF1Bdelta is specifically localized in the cytoplasm, the long isoform of eEF1Bdelta (eEF1BdeltaL) is localized in the nucleus and induces heat shock element (HSE)-containing genes in cooperation with heat-shock transcription factor 1 (HSF1). Moreover, the N-terminal domain of eEF1BdeltaL binds with NF-E2-related factor 2 (Nrf2) and induces stress response heme oxygenase 1 (HO-1). Specific inhibition of eEF1BdeltaL with siRNA completely inhibits Nrf2-dependent HO-1 induction. In addition, eEF1BdeltaL directly binds to HSE oligo DNA in vitro and associates with HSE containing the HO-1-enhancer region in vivo. Thus, the transcriptional role of eEF1BdeltaL could provide new insights into the molecular mechanism of stress responses.
We performed microarray analysis to compare the gene expression induced by eEF1Bdelta1 or eEF1BdeltaL overexpression.

overall_design: HEK293 cells transfected with expression plasmids encoding flag-tagged-eEF1Bdelta1 or eEF1BdeltaL protein

first: Masayuki

last: Matsushita


title: Human Lung Adenocarcinomas (Stage 1 and Stage 2 )

status: Public on May 04 2011

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: Comparing Stage 1 and stage 2 lung adenocarcinomas against a standard human reference RNA sample.

overall_design: Two colour design, stage 1 or stage 2 adenocarcinoma vs human reference RNA (Clontech), 5 stage 1 comparisons and 5 stage 2 comparisons

first: Susan

last: Douglas

first: Evelyn

last: Teh

first: Devanand

last: Pinto

first: Zhaolin

last: Xu

first: Drew

last: Bethune


title: Expression data from the Finnish Nodular Lymphocyte Predominant Hodgkin Lymphoma (NLPHL) family and ten controls

status: Public on Apr 14 2011

city: Helsinki

first: Eevi

last: Kaasinen

address: Haartmaninkatu 8

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

summary: Gene expression was studied from the blood derived RNAs of the Finnish family members as well as from 10 controls using GeneChip Human Genome U133 Plus2 (Affymetrix). Eight out of 10 family members in the expression analysis are heterozygous for the NPAT c.2437-2438delAG, three of which are NLPHL cases.

overall_design:
NPAT expression was studied in the NLPHL patients and the carriers of the deletion c.2437-2438delAG (8) compared to the controls and the non-mutation carriers (12).
Note: Case 2 not submitted.  Publication pending.

first: Lauri

last: Aaltonen

first: Pia

last: Vahteristo

first: Silva

last: Saarinen

first: Mervi

last: Aavikko

last: Lehtonen


title: Effects of cholic acid on Rhodococcus sp. RHA1

status: Public on Mar 29 2011

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

institute: University of British Columbia

summary: Two cultures, one grown on cholic acid and the other on pyruvate.

overall_design: 3x dual-channel slides.

first: Maarten

last: Wilbrink

first: Lindsay

last: Eltis

first: Robert

last: van der Geize

first: William

middle: W

last: Mohn


title: Alcohol Consumption Effects During the Inflammatory Stage of Fracture Healing in Rat Bones

city: Temple

first: H

middle: Wayne

last: Sampson

state: TX

address: 702 SW HK Dodgen Loop

department: Systems Biology & Translational Medicine

institute: TAMHSC-College of Medicine

summary: Sprague-Dawley rats were placed on an ethanol-containing or pair-fed Lieber and DeCarli diets for 4 wks prior to surgical fracture.  Following insertion of a medullary pin, a closed mid-diaphyseal fracture was induced using a Bonnarens and Einhorn fracture device. At 3 days post-fracture, the region of the fracture calluses were harvested from the right hind-limb. RNA was extracted and microarray analysis was conducted against the entire rat genome to study the effects of alcohol-consumption on the fracture healing.

overall_design: The experiments were on four rat subjects, i.e., pair-fed rats with subsequent surgical fracture or no surgical fracture, and alcohol-fed rats with subsequent surgical fracture or no surgical fracture. Each rat subject described above has three replicates so 6 kinds of pairing can be made and each pairing has a dye-swap replicate (thus, a total 12 array experiments). The focus of this study is on the pair-fed fracture subject vs. alcohol-fed fracture subject.

first: Hung-Chung

last: Huang

first: Vincent

last: VanBuren


status: Public on Apr 19 2011

city: Seoul

first: Young-Yun

last: Kong

address: San56-1, Silim-dong, Gwanak-gu

department: Department of Biological Sciences, College of Natural Sciences

country: South Korea

institute: Seoul National University

summary: The Notch signaling pathway regulates fate decision, proliferation and differentiation of intestinal epithelial cells. However, the role of Notch signaling in colorectal cancer progression is largely unknown. Here we show that Notch signaling suppresses the progression of colorectal tumorigenesis, even though it augments tumor initiation. In contrast to adenomas of Apcmin mice, Notch-inactivated Apcmin adenomas showed more malignant characteristics, such as submucosal invasion and loss of glandular pattern. Conversely, Notch-activated Apcmin adenomas showed a reversion from high-grade to low-grade features, such as the restoration of adherent junctions. Expression profiling revealed that Notch signaling promotes the differentiation of tumor cells with down regulation of Wnt/beta-catenin target genes and inhibition of epithelial-mesenchymal transition. Comparison of mouse and human expression profiles also suggests the common role of Notch in inhibition of tumor progression. Interestingly, Notch signaling suppressed the expression of beta-catenin responsive genes through chromatin modification of Tcf4/beta-catenin binding sides. Our results suggest that Notch signaling has dual roles in colorectal tumorigenesis: promoting adenoma initiation, while inhibiting tumor progression to colorectal cancer.

overall_design: mRNAs from normal (WT, Notch-activated and Notch-inactivated) and tumor (WT, Notch-activated and Notch-inactivated) tissues were profiled.

first: Bon-Kyoung

last: Koo

first: Hyun-A

last: Kim

first: Ji-Hoon

last: Cho

first: Hee-Jin

last: Chang

first: Young-Min

last: Oh

first: Yoon-Young

first: Hyoung-Soo

last: Lim

first: Jae-Gahb

last: Park

first: Daehee

last: Hwang


title: Loss of cytoplasmic CDK1 predicts poor survival in human lung cancer and confers chemotherapeutic resistance

status: Public on Mar 31 2011

city: Bethesda

first: Phillip

last: Dennis

state: MD

address: 37 Convent Dr.

department: MOB, CCR

institute: NCI

summary:
The dismal lethality of lung cancer is due to late stage at diagnosis and inherent therapeutic resistance. The incorporation of targeted therapies has modestly improved clinical outcomes, but the identification of new targets could further improve clinical outcomes by guiding stratification of poor-risk early-stage patients and individualizing therapeutic choices. We hypothesized that a sequential, combined microarray approach would be valuable to identify and validate new targets in lung cancer. We profiled gene expression signatures during lung epithelial cell immortalization and transformation, and showed that genes involved in mitosis were progressively enhanced in carcinogenesis. 28 genes were validated by immunoblotting and 4 genes were further evaluated in non-small cell lung cancer tissue microarrays. Although CDK1 was highly expressed in tumor tissues, its loss from the cytoplasm unexpectedly predicted poor survival and conferred resistance to chemotherapy in multiple cell lines, especially microtubule-directed agents. An analysis of expression of CDK1 and CDK1-associated genes in the NCI60 cell line database confirmed the broad association of these genes with chemotherapeutic responsiveness. These results have implications for personalizing lung cancer therapy and highlight the potential of combined approaches for biomarker discovery.

In these studies, we systematically profiled gene expression in normal (NHBE), immortalized (BEAS-2B) and fully transformed (NNK-BEAS-2B) human bronchial epithelial cells, as well as a non-small cell lung cancer (NSCLC) cell line (H157) from a smoker. Expression profiles that accompany the immortalization and/or transformation of bronchial epithelial cells were generated, and expression of 28 genes was validated by immunoblotting. 4 of them were further evaluated in immunohistochemical analyses of tissue microarrays that contain NSCLC specimens, surrounding non-diseased tissues and non-pulmonary normal tissues.  Although all 4 genes were predominantly expressed in tumor tissues, loss of expression of cytoplasmic CDK1 was clinically important because it was associated with a poor prognosis for NSCLC patients.  This poor prognostic value may be associated with therapeutic resistance because decreasing levels of cytoplasmic CDK1 in vitro increased resistance to standard chemotherapies used in the treatment of NSCLC, especially microtubule agents where resistance was almost complete. These studies illustrate how a combined microarray approach can facilitate the identification of new, relevant targets in cancer.

overall_design: Fluorescently labeled cDNA were synthesized from 100 microgram RNA by oligo(dT)-primed reverse transcription in the presence of Cy3- or Cy5-dUTP (Amersham Bisciences, Piscataway, NJ). Purified Cy3/Cy5-labelled probes were combined and hybridized in the presence of 2x Denhart's solution, 3.2x saline sodium citrate (SSC), and 0.5% sodium dodecyl sulfate (SDS) in a humidified chamber at 65°C overnight. Prior to scanning (Agilent Technologies, Foster City, CA), slides were successively washed at 22°C in 0.5x SSC/0.1% SDS for 2 min, 0.5x SSC/0.01% SDS for 2 min, and 0.06x SSC for 2 min. Image analyses were performed with the IPLab software (Fairfax, VA). The reference cell (NHBE) was included in every individual hybridization to allow for normalization of each clone’s expression relative to the reference for each cell line (BEAS-2B, NNK-BEAS-2B or H157). A self-to-self hybridization with dye reversal was performed to exclude preferential differences in probe labeling (not included here). Every sample was labeled with Cy5 and Cy3 and hybridized twice. The two fluorescent images (red and green channels) obtained from the scanner constituted the intensity raw data from which differential gene expression ratios and quality control values were calculated. All data were entered into a relational database, using the FileMaker Pro 5 software (Santa Clara, CA). Genes were identified as differentially regulated only if corrected red/green hybridization signals differed by at least two-fold. The genes in each group were alphabetically listed and the ratios of BEAS-2B/NHBE, NNK-BEAS-2B/NHBE or H157/NHBE were graphically visualized by Cluster and TreeView programs (http://rana.lbl.gov/EisenSoftware.htm). These methods fulfilled the MIAME criteria (http://www.mged.org/miame).

first: Chunyu

last: Zhang

first: Abdel

middle: G

last: Elkahloun


title: Expression signatures of the lipid-based Akt inhibitors phosphatidylinositol ether lipid analogues in NSCLC cells

status: Public on Mar 23 2011

summary: Activation of the serine/threonine kinase Akt contributes to the formation, maintenance, and therapeutic resistance of cancer, which is driving development of compounds that inhibit Akt.  Phosphatidylinositol ether lipid analogues (PIAs) are analogues of the products of PI3K that inhibit Akt activation, translocation, and the proliferation of a broad spectrum of cancer cell types.  To gain insight into the mechanism of PIAs, time-dependent transcriptional profiling of 5 active PIAs and the PI3K inhibitor LY294002 (LY) was performed in non-small cell lung cancer (NSCLC) cells using high-density oligonucleotide arrays.  Gene ontology analysis revealed genes involved in apoptosis, wounding response, and angiogenesis were upregulated by PIAs, while genes involved in DNA replication, repair and mitosis were suppressed. Genes that exhibited early differential expression were partitioned into 3 groups; those induced by PIAs only (DUSP1, KLF6, CENTD2, BHLHB2, PREX1), those commonly induced by PIAs and LY (TRIB1, KLF2, RHOB and CDKN1A), and those commonly suppressed by PIAs and LY (IGFBP3, PCNA, PRIM1, MCM3 and HSPA1B). Increased expression of the tumor suppressors RHOB (RhoB), KLF6 (COPEB) and CDKN1A (p21Cip1/Waf1) was validated as an Akt-independent effect that contributed to PIA-induced cytotoxicity. Despite some overlap with LY, active PIAs have a distinct expression signature that contributes to their enhanced cytotoxicity.

overall_design: H157 cells were plated at 2x10^6 in T-75 flasks in RPMI medium 1640 containing 10% FBS and incubated for 24h.  The media was then changed to RPMI medium 1640 with 0.1% FBS and the cells were incubated overnight.  The following morning, cells were treated with 10 microM PIA6 dissolved in DMSO for 0h, 2h, 6h or 12h, and an equal volume of DMSO was added to control samples.  For the PIA comparison, 10 microM PIAs (5, 6, 7, 23, 24, 25) or 10 microM LY294002 (LY) were incubated with the cells for 6h.  In the PIA comparison experiment, the same concentration of PIA7 (an inert analog consisting of only the lipid side chain) was used as a control.  Following incubation, the alterations in cellular morphology were photographed, and cells from 6-well plates were harvested for immunoblot analysis.  Total RNA was extracted from cells treated in T-75 flasks using TRIzol reagent (Invitrogen) and chloroform, and purified according to the RNeasy midiprep spin kit protocol (Qiagen).   Oligonucleotide microarray was performed with dye-swap.  Microarray chips were generated from the 34,580 longmer probe set Human Genome Oligo Set Version 3.0 (Qiagen).  Protocols for cDNA labeling, hybridization, and scanning are available through the National Human Genome Research Institute microarray core.


title: Response of human lymphoblastoid cells to activated medium

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

summary: Transcriptional profiling of human lymphoblastoid TK6 cells comparing mock irradiaed cells resuspended in fresh untreated RPMI 1640 medium with cells resuspended in medium activated by exposure to 2.5 Gy HZE (1 GeV/amu iron ions accelerated at the NASA Space Research Laboratory (NSRL) of Brookhaven National Laboratory).

overall_design: Two-condition experiment, mock irradiated vs. cells exposed to activated medium.  3 biological replicates were independently grown and harvested during three different runs at the NSRL. One replicate per array.


title: Response of human lymphoblastoid cells to HZE (iron ions) or gamma-rays

summary: Transcriptional profiling of human lymphoblastoid TK6 cells comparing mock irradiated cells with cells exposed 24 hours previously to 1.67 Gy HZE (1 GeV/amu iron ions accelerated at the NASA Space Research Laboratory (NSRL) of Brookhaven National Laboratory) or 2.5 Gy 137Cs gamma rays.

overall_design: TK6 cells were mock irradiated or exposed to HZE or gamma-rays, and RNA was harvested 24 hours later.  3 biological replicates were independently grown and harvested during three different runs at the NSRL. One replicate per array.


title: Brain transcriptomic response of the threespine stickleback  Gasteroteus aculeatus to predator cues

status: Public on Apr 24 2011

city: Urbana

first: Yibayiri

middle: Osee

last: Sanogo

state: IL

address: 505 S. Goodwin

department: Integrative Biology

institute: University of Illinois at Urbana-Champaign

summary: In this study, we used whole genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to predator cues using the threespine stickleback, Gasteroteus aculeatus. We showed that exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorhynchus mykiss) for six days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology (GO) enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to predator cues and the control group are primarily related to antigen processing and presentation (involving primarily the major histocompatibility complex (MHC)), transmission of synaptic signals, brain metabolic processes, gene regulation, or visual perception. Pathway analysis identified synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction as the top four pathways that were over-represented.

overall_design: Adult fish were placed in six different 26L tanks with three fish per tank in a partially recirculating flow-through system. Half of the tanks were assigned to the control group and the other half to the experimental group.10 samples were selected for microarray analysis. The ten samples comprised five biological replicates in the experimental group (fish exposed to predator cues) and five biological replicates in the control group (fish not exposed to predator cues), and were evenly distributed across tanks. The cDNA labeling (single color), hybridization, washing and scanning steps were performed in the NimbleGen microarray gene expression service department.

middle: O

first: Shala

last: Hankinson

first: Dan

last: Xie

first: Mark

last: Band

first: Alexandra

last: Obregon

first: Alison

last: Bell


title: Genome-wide Expression Differences in Colonocytes Isolated From Conventionally Raised or Germfree Mice

status: Public on Mar 15 2011

city: Chapel Hill

first: Wei

last: Sun

state: NC

address: UNC

institute: UNIVERSITY OF NORTH CAROLINA CHAPEL HILL

summary: Microarray transcriptome analysis of colonocytes from conventionally raised and germfree mice.

overall_design: 12 samples were analyzed, with 6 germfree (GF) samples vs. 6 conventionally raised (CONV) samples.

first: Scott

middle: J

last: Bultman

first: Dallas

middle: R

last: Donohoe


title: Response of human lymphoblastoid cells to HZE (iron ions), gamma-rays, and activated medium

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

overall_design: Refer to individual Series


title: Transcriptome analysis in Mycobacterium leprae (M. leprae)-infected granuloma of BALB/c nu/nu mice

status: Public on Mar 17 2011

first: Tae Hoon

last: Kim

state: Socho-gu

address: 505 Bonpo-dong

department: Pathology

institute: Medical College of the Catholic University

summary: Our object is to characterize the distinguish gene enrichment group in skin of Mycobacterium leprae (M. leprae)-infected footpads compared to that of Mycobacterium leprae (M. leprae) non-infected footpads.

overall_design: One-condition experiment, Skin of M. leprae non-infected footpads (control) vs. Skin of M. leprae infected footpads (sample). Biological replicates: 3 control and 3 sample, independently grown and harvested from isolator. One replicate per array.

first: Tae-Hoon

first: Tae-Jin

last: Kang

first: Jeong-Sook

first: Eun-Kyung

last: Ahn

first: Sun-Hee

last: Leem

first: Gue-Tae

last: Chae


title: Transcriptional profiles of pediatric SLE neutrophils and Healthy neutrophils cultured with SLE sera or Interferon

status: Public on Mar 10 2011

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: Mature neutrophis were freshly isolated from blood  of pediatric systemic lupus erythematosus (SLE) patients and healthy donors. Illumina microarray was used to assess transcriptional changes between SLE group and Control group. To uderstand further the gene expression difference between SLE and healthy neutrofils, neutrophils from healthy donors were cultured with autologous sera, SLE sera or Interferon and microarray data was used to compare with fresh SLE neutrophils.

overall_design:
(Expt 1) Neutrophils from 21 SLE samples (19 patients) and 12 healthy donors were isolated, and extracted RNAs were used generate microarray data.
(Expt 2) Neutrophils isolated from 2 healthy children (not used in the first experiment) were cultured with autologous sera (control), Interferon alpha (100U and 1000U), and 4 SLE sera and 6 SLE sera for 6 hours and RNAs were extract for microarray experiment.


title: Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (Affymetrix)

status: Public on Mar 03 2011

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

type: Genome binding/occupancy profiling by array

summary: Cross-linking and immunoprecipitation coupled with high-throughput sequencing was used to identify binding sites within 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein which when mutated causes Amyotrophic Lateral Sclerosis (ALS). Use of massively parallel sequencing and splicing-sensitive junction arrays revealed that levels of 601 mRNAs are changed (including Fus/Tls, progranulin, and other transcripts encoding neurodegenerative disease-associated proteins) and 965 altered splicing events are detected (including in sortilin, the receptor for progranulin), following depletion of TDP-43 from adult brain with antisense oligonucleotides. RNAs whose levels are most depleted by reduction in TDP-43 are derived from genes with very long introns and which encode proteins involved in synaptic activity. Lastly, TDP-43 was found to auto-regulate its synthesis, in part by directly binding and enhancing splicing of an intron within the 3’ untranslated region of its own transcript, thereby triggering nonsense mediated RNA degradation.

overall_design:
6 samples of polyA-selected RNA were extracted from control-oligo and Tdp43-targeted oligo mouse striatum, and hybridized to custom splice-junction array.

*Addendum
Depending on the analysis software used, these CEL files may not load correctly using default parameters. This is due to the custom chip type of MJAY not being used during the array scanning step. There are three workarounds known for this problem so far.
1) If using APT, use multiple --chip-type parameters. Specifically, --chip-type mjay --chip-type MJAY --chip-type MoEx-1_0-st-v1.1sq
2) Edit the CEL file by converting to text using the APT command apt-cel-convert, then replacing the MoEx-1_0-st-v1.1sq in the DatHeader line with MJAY (all caps).
3) Edit the .pgf, .clf, and antigenomics.bmp files to use the MoEx-1_0-st-v1.1sq array instead of MJAY for the chip_type and lib_set_name options. (works on AltAnalyze software)

first: Don

last: Cleveland


title: Profiling of Gene expression in Mycobacterium leprae (M. leprae)-infected footpad of BALB/c nu/nu mice

summary: Our goal is to understand the mechanism of granuloma formation in molecular level using Mycobacterium leprae (M. leprae)-infected footpads.

overall_design: One-condition experiment, M. leprae non-infected footpads (control) vs. M. leprae infected footpads (sample). Biological replicates: 6 control, 6 (sample), independently grown and harvested from isolator. One replicate per array.

first: Tae

first: Hye

last: Park

first: Seung

first: Gue

middle: T


title: Gene Expression Profiling Reveals a Massive, Aneuploidy-Dependent Transcriptional Deregulation and Distinct Differences between Lymph Node–Negative and Lymph Node–Positive Colon Carcinomas

city: Goettingen

first: Marian

last: Grade

address: Robert-Koch-Str. 40

department: Surgery

institute: University Medical Center Goettingen, Georg-August-University

summary: To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P < 1e-7). A significant proportion of these genes mapped to chromosome 20 (P = 0.01). Seventeen genes had a >5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node-negative and lymph node-positive tumors (P < 0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. The microarray-derived gene expression levels of 20 deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concor- dance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a signif- icant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/B-catenin signaling cascade, suggesting similar pathogenic pathways. [Cancer Res 2007;67(1):41-56]

overall_design: Samples of tumor and/or mucosa from a total of 65 colon cancer patients, i.e. 103 arrays

first: Michael

last: Ghadimi

first: Thomas

last: Ried


title: The effect of Δ122p53, a Δ133p53α-like isoform, on global gene expression in response to DNA damage in mouse splenocytes

status: Public on Mar 02 2011

city: Dunedin

first: Aaron

last: Jeffs

address: PO Box 56

country: New Zealand

institute: University of Otago

summary: The p53 protein is a pivotal tumor suppressor that is frequently mutated in many human cancers, although precisely how p53 prevents tumors is still unclear.  To add to its complexity several isoforms of human p53 have now been reported.  The Δ133p53α isoform is generated from an alternative transcription initiation site in intron 4 of the p53 gene (TP53) and lacks the N-terminus.  Elevated expression of Δ133p53α has been observed in a variety of tumors.  To explore the functions of Δ133p53α, we created a mouse expressing an N-terminal deletion mutant of p53 (Δ122p53) that corresponds to Δ133p53α.  Δ122p53 mice show decreased survival and a different and more aggressive tumor spectrum compared to p53 null mice, implying that Δ122p53 is a dominant oncogene.  Consistent with this, Δ122p53 also confers a marked proliferative advantage on cells and reduced apoptosis.  In addition to tumor development Δ122p53 mice show a profound pro-inflammatory phenotype having increased serum concentrations of interleukin (IL)-6 and other pro-inflammatory cytokines and lymphocyte aggregates in the lung and liver as well as other pathologies.  Based on these observations, we propose that human Δ133p53α also functions to promote cell proliferation and inflammation, one or both of which contribute to tumor development.

overall_design: Total RNA was isolated from pooled splenocytes from four 5-6 week old mice with different p53 status (wild type, p53-/-, or Δ122p53) subjected to DNA damaging or control treatments.

first: Hamish

last: Campbell

first: Antony

last: Braithwaite


title: Microarray analysis of Wolbachia infected Anopheles gambiae Sua5B cells

city: Baltimore

first: Grant

last: Hughes

address: 615 N Wolfe St

department: Bloomberg School of Public Health

institute: Johns Hopkins

summary:
Wolbachia, an endosymbiotic bacterium, is being investigated as a vector control agent in several insect species. Along with the well known classical reproductive parasitism Wolbachia employs against its host to spread within the population, it is emerging that the bacteria can protect the host against pathogens and reduced pathogen transmission. Anopheles mosquitoes, which transmit malaria, have never been found to harbour Wolbachia in nature, and despite numerous transinfection attempts, no stable line has been developed.
However recently, two strains of Wolbachia, wAlbB from Aedes albopictus, and wRi from Drosophila simulans were cultured in Anopheles gambiae Sua5B cells. These cell lines provides an amenable system to study Wolbachia-Anopheles interaction in the absence of a stable transinfected line. It has been proposed that the compromised vector competence of Wolbachia infected insects is due to an up regulation of the basal immune state. We therefore completed a genome wide expression profile of Wolbachia infected Anopheles, assessing both wAlbB and wRi infected cells in parallel against uninfected Sua5B cells.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Two strains of Wolbachia, wRi from Drosophila simulans and wAlbB from Aedes albopictus were transfered into Anopheles gambiae Sua5B cells via the shell vial technique. After over 30 passages, these Wolbachia infected cells lines were then compared, in parallel, to the original uninfected Sua5B cells using Affymetrix microarrays.

middle: L

first: Xiaoxia

last: Ren

first: Jose

last: Ramirez

first: Jason

middle: A

last: Bailey

first: Anne

last: Jedlicka

last: Rasgon


title: Detection of unbalanced insertions by aCGH and FISH

status: Public on Feb 28 2011

city: Spokane

first: Blake

middle: C.

last: Ballif

state: WA

address: 2820 North Astor Street

department: Research & Development

institute: Signature Genomic Laboratories

summary: Insertions occur when a segment of one chromosome is translocated and inserted into a new region of the same chromosome or a non-homologous chromosome. We report 69 cases with unbalanced insertions identified using array CGH and FISH, representing 1.25% of 5,683 cases referred to our laboratory for array CGH and found to have copy-number abnormalities. Although the majority of insertions were non-recurrent, several recurrent unbalanced insertions were detected, including three der(Y)ins(Y;18)(q?11.2;p11.32p11.32)pat inherited from parents carrying an unbalanced insertion. The clinical significance of these recurrent rearrangements is unclear, although the small size, limited gene content, and inheritance pattern of each suggests the phenotypic consequences may be benign. Moreover, cryptic, submicroscopic duplications were observed at or near the insertion sites in two patients, further confounding the clinical interpretation of these insertions. Using FISH, linear amplification and array CGH we identified a 126-kb duplicated region from 19p13.3 inserted into MECP2 at Xq28 in a patient with symptoms of Rett syndrome. Our results demonstrate that although the interpretation of most non-recurrent insertions is unclear without high-resolution insertion site characterization, the potential for an otherwise benign duplication to result in a clinically relevant outcome through the disruption of a gene necessitates the use of FISH to determine whether copy-number gains detected by array CGH represent tandem duplications or unbalanced insertions. Further follow-up testing using techniques such as linear amplification coupled with array CGH or sequencing should be used to determine gene involvement at the insertion site after FISH has identified the presence of an insertion.

overall_design: 88 total samples analyzed. No replicates included. Each sample run against a standard sex-matched control.

first: Nicholas

last: Neill

first: Allen

middle: N

last: Lamb

first: Sumit

last: Parikh

first: J

last: Ravnan

first: Roger

last: Schultz

first: Beth

last: Torchia

first: Jill

last: Rosenfeld

first: Lisa

last: Shaffer


title: Genes Differentially Expressed as a Result of Enforced Pokemon Expression  in MCF-7 cell

status: Public on Feb 25 2011

city: Shenzhen

first: Xuyu

last: Zu

address: Lishui Road

institute: Graduate School at Shenzhen,Tsinghua University

summary:
Pokmeon is an oncogenic transcription factor involved in cell growth, differentiation, and oncogenesis,but its regulatory network in breast cancer cells remians elusive .
We used microarray to determine the down stream target genes of pokemon by using  the MCF-7 cell line with stable ectopic expression of pokemon.

overall_design: The MCF-7 cell clones with high ectopic expression of pokemon were screened by the Hygromycin B,and the control cell line was also obtained by introducing empty vector .Both the RNA were extracted  and hybridized  with 22k cDNA spots from CapitalBio, Chin

first: Yuyang

last: Jiang


title: Transcriptional Profiling of Diabetic Neuropathy in BKS-db/db Mouse, a Model for Type 2 Diabetes

status: Public on Feb 18 2011

city: Ann Arobr

first: Manjusha

last: Pande

address: 2800 Plymouth Rd.

department: BRCF

institute: University of Michigan

summary: A better understanding of the molecular mechanisms underlying the development and progression of diabetic neuropathy (DN) is essential for the design of mechanism-based therapies. We examined changes in global gene expression to define pathways regulated by diabetes in peripheral nerve. Microarray data for 24 week-old BKS db/db and db/+ mouse sciatic nerve were analyzed to define significantly differentially expressed genes (DEGs); DEGs were further used for functional enrichment analysis and network analysis to identify biological processes and pathways differentially regulated in the db/db nerve.  Expression profile clustering was performed to identify co-expressed DEGs. A set of co-expressed lipid metabolism genes was used for promoter sequence analysis.We identified 4,017  DEGs; 2,122 genes were up-regulated and 1,895 genes were down-regulated in the db/db relative to the db+ samples. Over-represented biological processes identified by the functional enrichment analysis include cell cycle, lipid metabolic process, lipid transport, carbohydrate metabolic process, response to stress, apoptosis, axonogenesis and cell adhesion. Pathways regulated in the db/db nerve include lipid metabolism, carbohydrate metabolism, energy metabolism, PPAR signaling, apoptosis, and axon guidance. The majority of DEGs in the glycolysis, TCA cycle, oxidative phosphorylation, fatty acid metabolism, glycerolipid metabolism, mitochondrial fatty acid elongation, lipid transport, adipocytokine signaling, PPAR signaling, and apoptosis pathways are up-regulated, whereas most of the axonogenesis-related genes are down-regulated in db/db nerve. A network of DEGs based on their co-citation in literature identified regulatory relationship between Tnf-α and key genes from the regulated pathways. Promoter sequence analysis identified over-represented transcription factor binding site (TFBS) motifs in the promoter regions of twenty two co-expressed lipid metabolism-related genes suggesting coordinated regulation of these genes by multiple transcription factors (TF). Furthermore, TF binding to these TFBS and differentially regulated in our data are annotated with nervous system development and immune response suggesting possible co-regulation of lipid metabolism, nervous system development and stress response genes. Gene expression changes in our data are consistent with pathological characteristics observed in DN including axon degeneration and demyelination, and support existing hypotheses regarding hyperglycemia mediated nerve damage in DN.  Our findings support the role of hyperglycemia-induced oxidative stress and ischemia in nerve injury. Our results also support the hypothesis of oxidized lipid-mediated nerve injury and increased mitochondrial oxidative stress in dyslipidemia. Moreover, our analyses revealed a possible co-regulation mechanism connecting hyperlipidemia, stress response and axonal degeneration.


title: Bone microarray profiles from the Hybrid Mouse Diversity Panel

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Significant advances have been made in the discovery of genes affecting bone mineral density (BMD); however, our understanding of its genetic basis remains incomplete.  In the current study, genome-wide association (GWA) and co-expression network analysis was used in the recently described Hybrid Mouse Diversity Panel (HMDP) to identify and functionally characterize novel BMD genes.  In the HMDP, a GWA of total body, spinal and femoral BMD revealed four significant associations (-log10P > 5.39) affecting at least one BMD trait on chromosomes (Chrs.) 7, 11, 12 and 17.  The associations implicated a total of 163 genes with each association harboring between 14 and 112 genes.  This list was reduced to 26 functional candidates by identifying those genes that were regulated by local eQTL in bone or harbored potentially functional non-synonymous (NS) SNPs.  This analysis revealed that the most significant BMD SNP on Chr. 12 was a NS SNP in the additional sex combs like-2 (Asxl2) gene that was predicted to be functional.   The involvement of Asxl2 in the regulation of bone mass was confirmed by the observation that Asxl2 knockout mice had reduced BMD.  To begin to unravel the mechanism though which Asxl2 influenced BMD, a gene co-expression network was created using cortical bone gene expression microarray data from the HMDP strains.  Asxl2 was identified as a member of a co-expression gene module enriched for genes involved in the differentiation of myeloid cells.  In bone, osteoclasts are bone-resorbing cell of myeloid origin, suggesting that Asxl2 may play a role in osteoclast differentiation.  In agreement, the knockdown of Asxl2 in bone marrow macrophages impaired their ability to form osteoclasts.  This study identifies a new regulator of BMD and osteoclastogenesis and highlights the power of GWA and systems genetics in the mouse for dissecting complex genetic traits.

overall_design: RNA from cortical bone (femoral diaphysis free of marrow) were profiled from 99 Hybrid Mouse Diversity Panel strains were profiled.  Sixteen-week old male mice were used in this study.  A total of 1-3 mice per strain were arrayed.

first: Charles

last: Farber


title: Cardiac gene expression profiling of Salvador mutant mice

status: Public on Feb 12 2011

city: Houston

first: Todd

middle: Ryan

last: Heallen

state: Texas

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

summary: In this study, we identified a number of genes whose expression are regulated by the Hippo tumor suppressor pathway. To disrupt Hippo signaling in the mouse heart, we inactivated the single mammalian Salv ortholog using a Salv conditional null allele and the Nkx2.5 cre allele that directs cardiac cre activity. Total RNA from embryonic hearts were used for expression profiling of 17,455 unique genes.

overall_design: Genes transcriptionally regulated by the Hippo pathway during cardiogenesis were identifed through expression profiling of 17,455 unique genes in Salvador mutant (Salv CKO) embryonic hearts. Total RNA from E9.5-stage hearts were pooled into biological replicate samples (2 control and 2 Salv CKO) and were used to generate expression profiles.


title: Different isoforms of Maxwell´s Demon, a conserved cell membrane protein, mediate lose/win decisions during cell competition

status: Public on Feb 09 2011

city: Madrid

first: Eduardo

last: Moreno

address: Melchor Fernandez-Almagro

department: Molecular Oncology

country: Spain

institute: CNIO

summary:
Cell competition promotes the elimination of weaker cells from a growing population. Here we investigate how cells of Drosophila wing imaginal discs distinguish “winners” from “losers” during cell competition. Using genomic and functional assays we have identified Maxwell`s Demon (Mwd), a cell membrane protein conserved in multicellular animals.
Our results suggest that the membrane protein Mwd is a dedicated component of the cell competition response that is required and sufficient to label cells as “winners” or “losers”. In Drosophila, the mwd locus produces three isoforms, mwdubi, mwdLose-A and mwdLose-B. Basal levels of mwdubi are constantly produced. During competition the mwdLose isoforms are upregulated in prospective loser cells. Cell-cell comparison of relative mwdLose and mwdubi levels ultimately determine which cell undergoes apoptosis. This “extracellular code” may constitute an ancient mechanism to terminate competitive conflicts among cells.

overall_design: Two samples have been analysed: tub>dmyc>Gal4 transgene cells (competitor) and tub>cd2>Gal4 control cells (non competitor) at different time points (0, 12, 24 and 48 hours). Each experiment was replicated 6 times, three of them by dye swap.

first: Christa

last: Rhiner

first: Jesús

middle: M

last: López-Gay

first: Davide

last: Soldini

first: Sergio

last: Casas-Tinto

first: Francisco

last: Martín

first: Luis

last: Lombardia


title: Gene expression profiles of mouse Blimp1 +/gfp and Blimp1 gfp/gfp regulatory T cells

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

summary: Regulatory T (Treg) cells are required for peripheral tolerance. Recent evidence indicates that Treg cells can adopt specialized differentiation programs in the periphery that are controlled by transcription factors usually associated with T helper differentiation. We demonstrate that expression of the transcription factor Blimp1 defines a population of Treg cells that localize predominantly to mucosal sites and produces IL-10. Blimp1 is required for IL-10 production by these cells and for their tissue homeostasis. A list of differentially expressed genes were identified from this whole-genome expression profiling experiment.

overall_design: Mouse Blimp1 +/gfp and Blimp1 gfp/gfp regulatory T cells were analyzed. Three replicates each.

first: Gordon

middle: K

last: Smyth

first: Stephen

last: Nutt

first: Axel

last: Kallies


title: Gene expression profiling of primary tumors, lymph node and liver metastases in midgut carcinoid tumors.

status: Public on Feb 10 2011

city: Uppsala

first: Katarina

last: Edfeldt

address: Akademiska Sjukhuset

department: Surgical Sciences

institute: Uppsala University

summary: In order to clarify the gene expression and identify genes involved in tumor progression, gene expression profiling was performed on tumor specimens. Samples comprised 18 primary tumors, 17 lymph node (LN) metastases and 7 liver metastases. Patients were grouped according to clinical data and histopathology into indolent or progressive course. RNA was subjected to a spotted oligo microarray and B-statistics were performed. Differentially expressed genes were verified using quantitative RT-PCR. Self-organising maps demonstrated three clusters. Eleven primary tumors separated in one cluster, 5 LN metastases in another whereas all liver metastases, 7 primary and 12 LN metastases, formed a third cluster. There was no correlation between indolent and progressive behaviour. The primary tumors with Ki67 > 5%, with low frequency of the carcinoid syndrome and a tendency towards shorter survival grouped together. Primary tumors differed in expression profile from their associated LN metastases. ACTG2, GREM2, REG3A, TUSC2, RUNX1, TPH1, TGFBR2 and CDH6 were differentially expressed between clusters and subgroups of tumors. The expression profile that assembles tumors as being genetically similar on the RNA expression level may not be concordant with the clinical disease course. This study reveals different gene expression profiles and novel genes not previously known to be involved in neuroendocrine tumorigenesis, and which may be of importance for tumor progression.

overall_design: Gene expression comparisons between 18 primary tumors, 17 lymph node metastases and 7 liver metastases.

first: Peyman

last: Bjorklund

first: Goran

last: Akerstrom

first: Gunnar

last: Westin

first: Per

last: Hellman

first: Peter

last: Stalberg


title: Differential methylation profiling of colon tumors

status: Public on Feb 07 2011

city: Leiden

first: Eddy

last: van Roon

address: Albinusdreef 2

institute: LUMC

summary: Differential methylation profiling of 18 colon tumor samples vs normal colon mucosa using the LogRatios of samples/reference panel

overall_design: 18 colon tumors and 8 normal mucosa

middle: H

first: Judith

last: Boer


title: New targets of TEAD1 revealed by ChIP-on-chip

status: Public on Feb 01 2011

city: wuhan

first: haifang

last: qiu

address: lion street 1

institute: Huazhong Agricultural University

summary: TEAD1 acts as a key molecule of muscle development, and trans-activates multiple target genes involved in cell proliferation and differentiation pathways. However, its target genes in skeletal muscles, regulatory mechanisms and networks are unknown. Here, we use ChIP-on-chip to identify direct target genes of TEAD1.

overall_design: All animal procedures were performed according to protocols approved by Hubei Province, P. R. China for Biological Studies Animal Care and Use Committee. Skeletal muscle tissues were collected from three adult Kunming mice.

first: Haifang

last: Qiu

first: Fengli

last: Wang

first: Chuxin

last: Liu

first: Xuewen

last: Xu

first: Bang


title: Genomic profiling of ten prostate cancer cell lines

city: Ann Arbor

first: xiaosong

last: wang

state: MI

address: 1500 E. Medical Center Drive

summary: Prostate cancer cell lines grow in full serum under standard conditions were profiled on Agilent-014698 Human Genome CGH Microarray 105A. Digestion, labeling, hybridization and data analysis of genomic DNA were performed according to the Agilent Technologies (Santa Clara, CA) protocol version 6.0 for 105 K arrays.

overall_design: Ten prostate cancer cell lines were included in the profiling, 22RV1, C4-2B, CA-hpv-10, DU145, LAPC4, MDAPCa-2b, NCI660, PC3, VCaP, and WPE1-NB26. All cell lines were grown in accordance with the distributor's instructions. All samples except DU145 were hybridized once on 105k Agilent Human Genome CGH microarrays according to manufacturers instructions. Two replicate hybridizations were done for DU145 cell line. Human Adult Male Normal Genomic DNA (6 normal individuals, Promega, #G1471) was used as a reference in all hybridizations. DNA from cell line samples were labeled with Cy5 and DNA from reference were labeled with Cy3.

first: Xiaojun

last: Jing

first: Xiaosong

first: Xuhong

last: Cao

first: Scott

last: Tomlins


title: HUVECs cultured under normal or high laminar shear stress

city: Bristol

first: Stephen

middle: John

last: White

address: Level 7 Queens Building, Bristol Royal Infirmary

department: Bristol Heart Institute

country: United Kingdom

institute: University of Bristol

summary: Many studies have characterised the effect of normal laminar shear stress (LSS) on endothelial responses, however elevated shear stress, as would be experienced overlying a stenotic plaque, has not been studied in depth. Therefore we used transcriptomics and related functional analyses to compare cells exposed to laminar shear stress at 15 or 75 dynes/cm2 for 24 hours (LSS15-normal or LSS75-high shear stress).

overall_design: Human umbilical vein endothelial cells (HUVEC n=4 per flow condition from different batches of pooled donor HUVEC p2) were cultured for 24 hours on gelatin coated slides under laminar shear stress of either 15 dynes/cm2 or 75 dynes/cm2 (LSS15 or LSS75) to assess the effect of high shear stress on endothelial cells. Total RNA was obtained using Qiagen kit and array analysis performed by Service XS (Leiden, Netherlands).


title: Gene expression profiling of placenta from women with early- and late-onset preeclampsia reveals differences in angiogenesis

first: Katja

last: Junus

address: University Hospital

department: Department of Women's and Children's Health

summary: Preeclampsia (PE) is a serious pregnancy associated disorder. Recently, it has been proposed that the role of the placenta differ between the two sub-groups early- and late-onset PE. To further elucidate differences between the two sub-groups, we conducted transcriptional profiling of human placenta comparing early- with late-onset PE. The analysis showed differences in angiogenesis associated genes.

overall_design: Two-condition experiment, early-onset PE (n=8) vs. late-onset PE (n=7).

first: Matts

last: Olovsson


title: Genome-wide transcriptional analysis of the primitive erythroid (EryP) lineage differentiation

status: Public on Jan 25 2011

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

country: USA

institute: Yale University

summary: During mammalian postimplantation development, primitive erythroblasts (EryP) or red blood cells are the first cell type to be specified from nascent mesoderm, late in gastrulation.   EryP arise in the yolk sac from a transient wave of progenitors, enter the circulation soon thereafter, and continue to mature in a stepwise and synchronous fashion.  We have taken advantage of a transgenic mouse line in which a green fluorescent reporter is expressed specifically in the EryP lineage to identify and purify EryP at different stages of maturation from  E7.5 through E12.5.  A transcriptional profile that encompasses key developmental landmarks of this lineage was determined using a genome-wide microarray analysis (Illumina platform).

overall_design: Dataset is a lineage-specific transcription profiling of EryP development on consecutive days from E7.5 through E12.5.  At least 3 independent biological replicates were used for each developmental time point.

first: Joan

last: Isern

first: Zhiyong

last: He

first: Stuart

last: Fraser

first: Margaret

last: Baron


title: Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
This study looked for signals produced in UV-B irradiated leaves, and possibly induced in shielded leaves, that modulate physiological responses in maize.  Transcriptome and proteomics profiling tracked changes in
exposed and shielded organs.  Metabolic profiling was examined for signaling molecules.  Exposure of just the top leaf substantially alters the transcriptome of both irradiated and shielded organs, with greater changes
as an additional 1-2 leaves are irradiated.  Transcriptome, proteome and metabolome changes are UV-B regulated in shielded organs.  Early steps in signal transduction and possible signal molecules are identified
utilizing a time course experiment.

Keywords: UVB, maize, leaves, ears

overall_design: Compared irradiated leaves in a time course, irradiated leaves versus shielded leaves, and shielded ears on plants with irradiated leaves.  Also compared different number of leaves being irradiated. Spike-in controls were included.

first: Paula

last: Casati

first: Mabel

last: Campi

first: Virginia

last: Walbot

first: Darren

last: Morrow


title: A human transcriptome array for high-throughput clinical studies (with a comparison to RNA-seq technology) [expression array]

status: Public on Jan 27 2011

city: Palo Alto

first: Weihong

last: Xu

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

summary: A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies.  This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts.  The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis.  The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing.  This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data.  When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies.

overall_design: Examination exon/gene expression of liver and muscle in quadraplicate using both the array technology and RNA-Seq

first: Junhee

last: Seok

first: Michael

last: Mindrinos

first: Wenzhong

last: Xiao

first: Ronald

last: Davis

last: Tompkins


title: Gene expression profiling on FePro labeled bone marrow stromal cells

status: Public on Jan 24 2011

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Superparamagnetic iron oxide nanoparticles (SPION) are increasingly used to label human bone marrow stromal cells (BMSCs, also called mesenchymal stem cells) to monitor their fate by in vivo MRI and histology after Prussian blue (PB) staining. SPION-labeling appears to be safe as assessed by in vitro differentiation of BMSCs, however, we chose to determine the effect of labeling on maintaining the “stemness” of cells within the BMSC population. Colony forming efficiency, CD146 expression, gene expression profiling, bone and myelosupportive stroma formation in vivo were evaluated. SPION-labeling did not alter these assays. Equivalent bone with host hematopoiesis was formed by SPION-labeled and unlabeled BMSCs. PB+ adipocytes were noted, definitively demonstrating their donor origin, as well as PB+ pericytes, indicative of self-renewal of the stem cell in the BMSC population. This study confirms that SPION labeling does not alter the differentiation potential of the subset of stem cells within BMSCs.

overall_design: We performed gene expression profiling on BMSCs labeled with FePro. For comparison, gene express profiling on human embryonic stem cells (hES) WA09 (H9) and adult cells: fibroblasts (FB), endothelial cells (EC) and smooth muscle cells (SMC) was conducted. Total RNA from PBMCs pooled from six normal donors was amplified into aRNA to serve as the reference.


title: Population genetic properties of differentiated human copy number polymorphisms

city: Seattle

first: Catarina

middle: D

last: Campbell

address: 3720 15th Avenue NE

department: Genome Sciences

institute: Univerisity of Washington

summary: Copy number variants (CNVs) can reach appreciable frequencies in the human population, and several of these copy number polymorphisms (CNPs) have been recently associated with human diseases including lupus, psoriasis, Crohn disease, and obesity. Despite new advances, significant biases remain in terms of CNP discovery and genotyping. Developing a novel method based on single channel intensity data and benchmarking against copy numbers determined from sequencing read-depth, we successfully obtained CNP genotypes for 1489 CNPs from 487 human DNA samples from diverse ethnic backgrounds. This customized microarray was enriched for segmental duplication-rich regions and novel insertions of sequences not represented in the reference genome assembly or on standard single nucleotide polymorphism (SNP) microarray platforms. We observe that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions (p = 0.015) and that bi-allelic CNPs show greater stratification when compared to frequency-matched SNPs (p = 0.0026). Although bi-allelic CNPs show a strong correlation of copy number with flanking SNP genotypes, the majority of multi-copy CNPs do not (40% with r >0.8). We selected a subset of CNPs for further characterization in 1873 additional samples from 62 populations (947 samples analyzed by microarray; 926 samples analyzed with PCR based assays); this revealed striking population-differentiated structural variants in genes of clinical significance such as the OCLN gene, a tight junction protein involved in hepatitis C viral entry. Our new microarray design allows these variants to be rapidly tested for disease association and our results suggest that CNPs (especially those that are not in linkage disequilibrium with SNPs) may have contributed disproportionately to human diversity and selection.

overall_design:
487 test samples and 1 reference (NA12878), CNP 180K array v2.1.
947 test samples and 1 reference (NA12878), CNP 180K array v3.0.

first: Nick

last: Sampas

first: Anya

last: Tsalenko

first: Peter

last: Sudmant

first: Jeffrey

last: Kidd

first: Maika

last: Malig

first: Tiffany

last: Vu

first: Laura

last: Vives

last: Tsang

first: Laurakay

last: Bruhn

first: Evan

middle: E

last: Eichler


title: Zebrafish embryos: hdac1 Morphants vs Standard control morphants

status: Public on Jan 21 2011

city: Sheffield

last: Harrison

address: Firth Court, Western Bank

department: MRC Centre for Developmental and Biomedical Genetics

institute: University of Sheffield

summary: Transcriptional profiling of hdac1 morphant zebrafish embryos in comparison to standard control injected embryos.  Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG), splice blocking morpholino (Hdac1 Splice) or Hdac1 mismatch control morpholino (Hdac1 control).  RNA was extracted and compared in a two-colour hybridisation to the comman reference Standard control morpholino injected embryos.

overall_design: Common reference experiment, hdac1 morphants vs. standard control morphants. Biological replicates: 2 (except Splice which was technical rather than biological)

first: Aristophanes

middle: S

last: Georgiou

first: Herman

middle: P

last: Spaink

first: Vincent

last: Cunliffe


title: Zebrafish 27hpf embryos: hdac1 mutant (hi1618) vs sibling

first: Michael

summary: Transcriptional profiling of hdac1 mutant zebrafish in comparison to their sibling embryos.  Embryos resulting from a cross between heterozygous hdac1 mutant zebrafish (hi1618/+) where cultured together then mutants separated from the siblings one the basis of phenotype and RNA extracted from the two groups at 27hpf was compared in a two-colour hybridisation.

overall_design: Two-condition experiment, hdac1 mutants vs. sibling. Biological replicates: 2 (separate mating) Technical replicates: 4 (2 of which are dye-swap)

middle: R


title: Zebrafish embryos: hdac1 Morphants vs Standard control morphants at 12, 18 and 27 hpf

summary: Transcriptional profiling of hdac1 ATG morphant zebrafish embryos in comparison to standard control injected embryos.  Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG) or Standard control morpholino (StCo).  RNA was extracted at 12, 18 and 27hpf from both sets of embryos and compared with a two-colour hybridisation.

overall_design: Timecourse experiment, hdac1 ATG morphants vs. standard control morphants. Biological replicates: 3

middle: T


title: Zebrafish hdac1 mutant and morphant embryos

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

overall_design: Refer to individual Series


title: CNVs of chromosome 17p13.1 might be linked to high risk of lung cancer in heavy smokers

status: Public on Jan 10 2011

city: Seu-gu

first: Jaeku

last: Kang

state: Daejeon

address: 685, Gasuwon-dong

department: Department of Pharmacology

institute: College of Medicine, Konyang University

summary: There are inherited genetic factors that cause different responses to cigarette smoking exposure among individuals. We tried to identify these differences in heavy smokers by examining copy number variations (CNVs) between lung cancer patients and healthy controls. To rule out the CNVs infulenced by age, smoking history and sex, those were matched in both groups.

overall_design: Array CGH was performed  by MACArrayTM KARYO 4.5K BAC-chip, peripheral blood lymphocyte DNA from 10 lung cancer patients and 10 healthy controls. Commercial DNA (46 XY, GM 10851, Coriell, USA) was used as the reference.

first: Minhyeok

last: Lee

first: Yeiwon

first: Hyun-Jung

last: Cho

first: Jeeyoung

last: Hong

first: Sun-Jung

last: Kwon

first: Chang-Gyo

last: Park

first: Hoi-Young

first: Ji-Woong

last: Son


title: expression of human and mouse breast cancer cell lines

status: Public on Jan 15 2011

first: Bin

last: Zhang

address: 1100 Fairview Ave North

department: Network Biology

institute: Sage Bionetworks

summary:
Multiple breast cancer cell lines with different metastatic capabilities
The goal of this study is to identify metastasis related genes in breast cancer
We obtained RNA from each cell line using regular Trizol and RNA purification kit.

Keywords: Expression profiling by array

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Wu

last: Guojun

first: Zhang

last: haijun

first: Meng

last: Fanyan