title: Transcriptional analysis of Rest/Nrsf silencing in N18 neuroblastoma cell line

status: Public on Jun 06 2010

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

institute: INSERM U675

summary:
The vertebrate-specific transcription factor RE-1 silencing transcription factor or neuron-restrictive silencer factor (REST/NRSF) was first described as a negative regulator restricting expression of neuronal genes to neurons in a variety of genetic contexts. However, REST/NRSF has a more general role in the regulation of gene expression that involves chromatin remodelling via a SWI/SNF complex. We identified a 677 gene repertoire of potential REST/NRSF-dependent genes taking advantage of Rest/Nrsf gene silencing in a mouse cell line. Using Ka/Ks analysis, we found that REST/NRSF protein, REST/NRSF interactors and the products of REST/NRSF-dependent genes display significantly higher rates of protein evolution in primates than in rodents. The McDonald-Kreitman test indicated positive selection for human REST/NRSF and nuclear RNA-binding proteins encoded by REST/NRSFdependent genes. In these proteins, we demonstrated sites under positive selection within the primate’s clade. Importantly, the REST/NRSF-dependent gene repertoire is statistically enriched in genes disrupted in neuropsychiatric diseases such as schizophrenia. In addition, we found that Smarca2 (Brm), Smarcd3 (Baf60c), Smarce1 (Baf57), Hdac1, RcoR1, and Mecp2, which are part of the REST/NRSFSWI/SNF chromatin remodelling complex, are transcriptionally regulated by REST/NRSF. Changing their gene dosage in vitro induced abnormal dendritic and dendritic spine phenotypes that were previously observed in rodent models of neuropsychiatric diseases. Altogether, these results suggest that genes encoding proteins of the REST/NRSF-SWI/SNF pathway display primate-specific accelerated
evolution. It may be hypothesized that the subset of genes involved in this pathway, which display a primate evolutionary signature in specific sites, may represent a novel gene candidate repertoire for neuropsychiatric diseases.

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL2872, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Of 44,290 spots, 2756 are controls. The remaining 41,534 spots represent 33,661 unique transcripts which correspond to 20,202 unique human genes. Six independent (NRSF silencing overexpression, six individual samples) measurements were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dyeswapping experiments).

first: Yann

last: Loe-Mie

first: Aude-Marie

last: Lepagnol-Bestel

first: Adi

last: Doron-Faigenboim

first: Nicolas

last: Ramoz

first: Sandrine

last: Imbeaud

first: Hervé

last: Delacroix

first: Lawrence

last: Aggerbeck

first: Tal

last: Pupko

first: Philip

last: Gorwood

first: Michel

last: Simonneau

first: Jean-Marie

last: Moalic


title: Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis

status: Public on May 07 2010

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

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

overall_design: Refer to individual Series

first: Ignasi

last: Forné

first: Barbara

last: Castellana

first: Rubén

last: Marín-Juez

first: Joan

last: Cerdà

first: Joaquin

last: Abián


title: The transcriptome of swarming Proteus mirabilis

status: Public on Jun 07 2010

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

country: USA

institute: University of Michigan Medical School


title: A Sinorhizobium meliloti IAA-overproducing strain improves phosphate solubilization and Medicago plant yield

status: Public on May 20 2010

city: Napoli

first: Carmen

last: Bianco

address: Via p. Castellino 111

country: Italy

institute: IGB-CNR


title: The contribution of QS components vjbR and N-dodecanoyl homoserine lactone on gene regulation in Brucella melitensis

status: Public on Apr 23 2010

city: College Station

first: Jenni

last: Weeks

state: TX

address: 4467 TAMU

institute: Texas A&M University


title: Effect of Dietary Supplementation of Selenium (Organic vs. Inorganic) on Liver Gene Expression Profile in Beef Heifers

status: Public on Apr 19 2010

city: Lexington

first: Shengfa

middle: F

last: Liao

state: KY

address: 214 WP Garrigus Bldg

department: Dept of Animal & Food Sciences

institute: University of Kentucky

summary:
Selenium (Se) is an essential nutrient for beef cattle health and commercial production. The molecular mechanisms responsible for the physiological responses of the animal to dietary Se supplementation, however, have not been evaluated. Furthermore, the potential effect of two chemical forms (organic vs. inorganic) of Se on gene expression by Se-sufficient cattle has not been evaluated.
Microarray analysis using the GeneChip Bovine Genome Array (Affymetrix, Inc., Santa Clara, CA) was conducted to determine if dietary Se supplementation in organic vs. inorganic form (OSe vs. ISe) differentially affects the liver gene expression profile in growing beef heifers.

overall_design: Sodium selenite (Prince Se Concentrate; Prince Agri Products, Inc., Quincy, IL) was used as the source of ISe form. Se-enriched yeast (Sel-Plex; Alltech, Inc., Nicholasville, KY) was used as the source of OSe form. Thirty Angus heifers (BW 393 ± 9 kg) were randomly assigned to 3 dietary treatments (n = 10): Control (Ctrl) group received no dietary Se supplementation; ISe treatment group daily received dietary supplementation of Se at 3 mg/animal from ISe source; OSe treatment group daily received dietary supplementation of Se at 3 mg/animal from OSe source.  Six animals were randomly selected from each of 3 treatment groups for RNA extraction and microarray analysis.

first: Walter

middle: R

last: Burris

first: James

middle: A

last: Boling

middle: C

last: Matthews


title: OsMKK4 regulated genes

status: Public on Jul 30 2010

city: Tsukuba

first: Hirohiko

last: Hirochika

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Genome and Biodiversity Research

country: Japan

institute: National Institute of Agrobiological Sciences

summary: OsMKK4 is a rice MAPKK and immediately activated by treatment with chitin elicitor, a fungal MAMP. OsMKK4DD is a constitutively active mutants of OsMKK4. We identified OsMKK4 regulated genes using a conditional gain-of-function transgenic system and rice 44K oligoarray.

overall_design: We used transgenic rice expressing OsMKK4 in wild-type and constitutive active forms under the dexamethazone (DEX)-inducible promoter. Callus of the DEX inducible OsMKK4DD or OsMKK4WT line was compared with vector control line using two-color method with 3 biological replicates.

first: Mitsuko

last: Kishi-Kaboshi

first: Akira

last: Takahashi


title: Transcription profiling of horned and polled and scurs cattle

status: Public on May 01 2010

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: Transciprional profiling of horn forming region of Bos taurus comparing horned, polled and scurred cattle.

overall_design: 3 condition experiment, Polled vs Horned, Polled vs Scurred, Scurred vs Horned, male and female samples, including dye swaps. 5 chips. No confounding between sex and chip. No confounding between indivdual and chip.

first: M

last: Mariasegaram

first: K

last: Prayaga


title: Expression data from early Bovine embryo

status: Public on Apr 15 2010

city: Urbana

first: Dan

last: Xie

state: IL

address: 3215 Digital Computer Lab, MC-278, 1304 W. Springfield Ave

department: Bioengineering

institute: University of Illinois at Urbana and Champaign

summary:
The process of early development of mammals is subtly and accurately controlled by the regulation networks of embryo cells. Time course expression data measured at different stages during early embryo development process can give us valuable information by revealing the dynamic expression patterns of genes in genome wide scale. In this study, bovine embryo expression data were generated  at oocyte, one cell stage, two cell stage, four cell stage, eight cell stage, sixteen cell stage, morula, and blastocyst. By comparing this data set with data generated with similar process on other species, we can study the trascriptom under a revolutionary scheme.

Keywords: time course

overall_design: Bovine embryos were harvested at successive stage from oocyte to blastocyste. Total RNAs were extracted, amplified and hybridized onto Affymetrix microarrays.


title: Arabidopsis thaliana tetraploid transcriptome

city: Freising

first: Ramon

middle: Angel

last: Torres-Ruiz

address: Emil-Ramann-Str. 8

department: Genetik

country: Germany

institute: Technische Universität München, WZW

summary:
The aim of this study was to analyze the impact of autotetraploidy on gene expression in Arabidopsis thaliana by comparing diploid versus tetraploid transcriptomes. In particular, this included the comparison of the transcriptome of different tetraploid A. thaliana ecotypes (Col-0 vs. Ler-0). The study was extended to address further aspects. One was the comparison of the transcriptomes in subsequent generations. This intended to obtain information on the genome wide stability of autotetraploid gene expression. Another line of work compared the transcriptomes of different diploid vs. tetraploid tissues. This aimed to investigate whether particular gene groups are specifically affected during the development of A. thaliana autotetraploids.
Samples 1-8: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines.
Samples 9-12: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines.
Samples 13-24: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines.
Samples 25-32: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines.
Samples 33-36: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Ler-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines.
Samples 37-40: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Col-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines.
Samples 41-44: Arabidopsis thaliana Col-0/Ler-0 diploid transcriptome. Transcriptional profiling and comparison of diploid Col-0 vs. diploid Ler-0 seedlings. The experiment was carried out with pedigree of esrablished lines.
Samples 45-48: Arabidopsis thaliana Col-0/Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid Col-0 vs tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 and Ler-0 lines.

overall_design:
Samples 1-8: Comparison of diploid vs tetraploid seedling material (ca. 100 each) of four different tetraploid lines (no. 1326-28, -26, -19 and , -12) each with repetition with different seedling batches; eight biological replicates. 4 replicates with Cy3-label of tetraploid and Cy5-label of diploid material and 4 replicates with reversed label.
Samples 9-12: Comparison of diploid vs tetraploid seedling material (ca. 100 each) of four different tetraploid lines (no. 1026-41, -40, -10 and , 3116-6); four biological replicates.
Samples 13-24: Comparison of diploid vs tetraploid (6-8th) leaves material of four different tetraploid lines (no. 1326-28, -26, -19 and , -12). This was repeated with leaves of four different individual plants from line 1326-28 and 1326-26 each; twelve biological replicates.
Samples 25-32: Comparison of diploid vs tetraploid (6th-8th) leaves material of four different tetraploid lines (no. 1026-41, -40, -10 and , 3116-6). This was repeated with other plants of the same lines; eight biological replicates.
Samples 33-36: Comparison of tetraploid-F2 vs tetraploid-F3 seedling material (ca. 100 each) of four different tetraploid lines (no. 1026-41, -40, -10 and , 3116-6); four biological replicates.
Samples 37-40: Comparison of tetraploid-F2 vs tetraploid-F3 seedling material (ca. 100 each) of four different tetraploid lines (no. 1326-28, -26, -19 and , -12); four biological replicates.
Samples 41-44: Comparison of diploid Col-0 vs Ler-0 seedling material (ca. 100 each) of established lines; 2 X 2 biological replicates with reversed label.
Samples: 45-48: Comparison of seedling material (ca. 100 each) of tetraploid Col-0 lines (no. 1326-28, -26, -19 and , -12) vs seedling material (ca. 100 each) of tetraploid Ler-0 lines (no. 1026-41, -40, -10 and , 3116-6); four biological replicates.

first: Alfons

last: Gierl

first: Zheng

last: Yu


title: GW7647 and Rosiglitazone treated human differentiated adipocytes

status: Public on Apr 11 2010

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

summary: Objective : This work aimed at characterizing PPARα involvement in metabolism regulation and at comparing PPARα and PPARγ roles in human white adipocytes. Research Design and Methods : Profiling of gene expression alterations was assessed with microarrays and RT-qPCR. Primary cultures of human adipocytes were treated with PPARα agonist GW7647 or PPARγ agonist Rosiglitazone. Western blot were used to determine protein level modifications. Metabolic changes were evaluated with palmitate and glucose oxidation studies and with metabolite measurements. Results : GW7647 induces an upregulation of β-oxidation gene expression and increases palmitate oxidation. Unexpectedly glycolysis was strongly reduced at transcriptional and functional levels by GW7647 while the overall glucose oxidation remains unaltered, leading to a decrease in pyruvate and lactate production. Moreover lipogenesis was downregulated by GW7647 inhibiting triglyceride esterification and de novo lipogenesis. GW7647 induced alterations were abolished by a PPARα antagonist treatment and were clearly different from Rosiglitazone effects. Rosiglitazone had no major impact on glycolysis and β-oxidation but increased glucose incorporation into glycerol backbone of triglycerides. Conclusions : Altogether these results show that PPARα can upregulate β-oxidation in human white adipocytes. Its pharmacological activation may be used to oxidize fatty acids in situ when lipolysis is activated thus preventing their release into systemic circulation.

overall_design: We treated four adipocyte cultures, each one coming from different subjects, with GW7647, Rosiglitazone (ROSI) or DMSO. DMSO treated cells are control samples. Thus we have four paired sample groups for each treatment (GW7647 and ROSI).

first: Carole

last: Ribet

first: Emilie

last: Montastier

first: Carine

last: Valle

first: Veronic

last: Bezaire

first: Anne

last: Mazzucotelli

first: Aline

last: Mairal

first: Dominique

last: Langin


title: Rat hindlimb arteries: Shunt versus Control

status: Public on May 26 2010

city: Bad Nauheim

first: Kerstin

last: Troidl

address: Ludwigstr. 43

institute: Max-Planck-Institute for Heart and Lung Research

summary: Arteriogenesis is defined as the development of a collateral circulation, bypassing an arterial occlusion. We have previously demonstrated that chronically elevated fluid shear stress completely normalized blood flow in femoral artery ligated rabbits. This was realized by a surgical intervention:  the creation of an arterio- venous anastomosis (shunt) between the femoral artery and the accompanying vein. The aim of this study was a gene profiling approach in order to identify differentially expressed genes during collateral growth in the shunt model when compared to pre-existent collaterals (sham).

overall_design: Collateral arteries after shunt versus Control arteries derived from one individual rat were compared on each chip in order to identify blood shear stress responsive genes.  Two condition experiment with three biological replicates (N=3 rats), and two technical replicates (N=2 microarray chips per biological comparison). N= 6 samples, consisting of N=3 Shunt collateral samples and N=3 control artery samples, from N=3 rats were hybridized on duplicate microarray chips, thereby using N=6 chips.

first: O

middle: L

last: Volger


title: Ventral striatal and hypothalamic responses to reduced food intake in healthy animals and rats bearing small tumors

status: Public on Apr 10 2010

city: Bordeaux

first: Jan Pieter

last: Konsman

address: 146, rue Léo Saignat

institute: CNRS


title: Array CGH-based Characterization of Genetic Alterations in Pulmonary Neuroendocrine Tumors

status: Public on Apr 22 2010

city: Bethesda

first: Jih-Hsiang

last: Lee

state: MD

address: 9000 Rockville Pike, building 10 8N254

department: Medical oncology branch

institute: National Cancer Institute

type: Genome variation profiling by genome tiling array

summary: The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on Array Comparative Genomic Hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal (GI) carcinoids. In contrast to the relatively stable karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in SCLC tumors and cell lines in cytogenetic bands encoding JAK2, FGFR1, and MYC family members. In some of those samples, the CN of these genes exceeded 100, suggesting that they could represent driver alterations and potential drug targets in subgroups of SCLC patients. Recurrent CN alterations of a total of 203 genes, including the RB1 gene, and 59 microRNAs, most of which locate in the DLK1-DIO3 domain, were observed  in SCLC tumors, bronchial carcinoids and carcinoids of GI origin; in contrast, CN alterations of the TP53 gene and the MYC family members were observed more frequently in SCLC. These findings suggest the existence of partially shared tumor-specific CN alterations in these tumors. Furthermore, we demonstrated that the aCGH profile of SCLC cell lines highly resemble that of clinical SCLC specimens. Finally, by analyzing potential drug targets, we provide a genomics based rationale for targeting the AKT-mTOR and apoptosis pathways in SCLC.

overall_design: Carcinoids, including 19 bronchial carcinoids and 9 carcinoid of gastrointestinal origin, and small cell lung cancer, including 33 patients' tumor samples and 13 cell line samples, were compared.

first: Johannes

last: Voortman

first: Jonathan

middle: K

last: Killian

first: Miia

last: Suuriniemi

first: Yonghong

last: Wang

first: Marco

last: Lucchi

first: William

middle: I

last: Smith Jr

first: Paul

last: Meltzer

first: Yisong

first: Giuseppe

last: Giaccone


title: PBC tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice.

status: Public on May 21 2010

city: Stanford

first: Keiichi

last: Kodama

state: CA

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

summary: 41K whole genome oligo-microarrays (Agilent Technologies) were used to characterize age-dependent changes in gene expression in peripheral blood cells (PBC) obtained from up to 8 individual NOD mice at 6 different time points (10 days (n=8), and 4 weeks (n=3), 8 weeks (n=7), 12 weeks (n=8), 16 weeks (n=7), and 20 weeks of age (n=4)), compared to NOD.B10 tissue controls. "Milestone Genes" are genes whose expression was significantly changed (approximately 3 fold) as the result of splicing or changes in transcript level. Milestone Genes were identified among genes within type one diabetes (T1D) susceptibility regions (Idd). Milestone Genes showing uniform patterns of changes in expression at various time points were identified. Potential T1D candidate genes were identified among Milestone Genes within Idd regions and/or hierarchical clusters. These studies identified tissue- and age-specific changes in gene expression that may play an important role in the inductive or destructive events of T1D.

overall_design:
NOD/LtJ (NOD), NOD.B10Sn-H2b/J (NOD.B10) female mice of multiple ages were used for this study.
Six Groups of NOD mice were sacrificed at 10 days, and 4, 8, 12, 16, and 20 weeks of age and peripheral blood cells (PBC) were removed and prepared for mRNA analysis. Two Groups of 10 NOD.B10 mice [10 days (n=10) + 20 weeks of age (n=10)] were used as a tissue specific control. Gene (mRNA) expression was analyzed using the 41K Whole Mouse Genome Oligo Microarray Kit (Agilent Technologies), and gene expression data are processed (cy3: NOD, cy5: NOD.B10) and reported as normalized expression ratios: Log 10 (NOD processed signal / NOD.B10 processed signal) (Log ratio).
10days of age; PBC_10d (n=8), 4 weeks of age; PBC_4w (n=3), 8 weeks of age; PBC_8w (n=7), 12 weeks of age; PBC_12w (n=8), 16 weeks of age; PBC_16w (n=7), 20 weeks of age; PBC_20w (n=4)

first: Atul

middle: J

last: Butte

first: Remi

last: Creusot

first: Leon

last: Su

first: Deqiao

last: Sheng

first: Mark

last: Hartnett

first: Hideyuki

last: Iwai

first: Luis

last: Soares

first: Garrison

last: Fathman


title: Geobacter sulfurreducens grown in various conditions: gene expression and RpoN ChIP-chip

status: Public on Jun 28 2010

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

institute: UCSD

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array


title: SuperSeries for the analysis of transcriptional regulation by Thermus themophilus CsoR (TTHA1719)

status: Public on Apr 13 2010

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

summary:
We observed the copper response of Thermus thermophilus HB8 wild-type and csoR deficient strain at 0 and 30 min after the addition of 1.25 mM CuSO4, and zinc response of T. thermophilus HB8 wild-type strain at 0 and 30 min after the addition of 1.0 mM ZnSO4.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Three wild-type and three csoR deficient strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours. Then the 1.25 mM of CuSO4 or 1.0 mM ZnSO4 was added into the medium cultivating wild type, and 1.25 mm CuSO4 was added into the medium cultivating csoR deficient strain, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of copper or zinc ion, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.

first: Yoshihiro

last: Agari

first: Keiko

last: Sakamoto

first: Kazuko

first: Miwa

last: Ohmori

first: Seiki

last: Kuramitsu


title: Peripheral blood stem cell gene and microRNA profiling

status: Public on Apr 01 2010

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

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

summary:
Mobilized-peripheral blood hematopoietic stem cells (HSCs) have been used for transplantation, immunotherapy, and cardiovascular regenerative medicine. Agents used for HPC mobilization include G-CSF and the CXCR4 inhibitor AMD3100. The HSCs cells mobilized by each agent may contain different subtypes and have different functions. To characterize mobilized HSCs used for clinical applications, microRNA (miRNA) profiling and gene expression profiling were used to compare AMD3100-mobilized CD133+ cells from 4 subjects, AMD3100 plus G-CSF-mobilized CD133+ cells from 4 subjects and G-CSF-mobilized CD34+ cells from 5 subjects. The HSCs were compared to peripheral blood leukocytes (PBLs) from 7 subjects.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
human gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus macacae


title: SPL tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice.

status: Public on May 19 2010

first: Keiichi

summary: 41K whole genome oligo-microarrays (Agilent Technologies) were used to characterize age-dependent changes in gene expression in spleen (SPL) obtained from up to 5 individual NOD mice at 6 different time points (10 days (n=5), and 4 weeks (n=5), 8 weeks (n=3), 12 weeks (n=5), 16 weeks (n=4), and 20 weeks of age (n=5)), compared to NOD.B10 tissue controls.  "Milestone Genes" are genes whose expression was significantly changed (approximately 3 fold) as the result of splicing or changes in transcript level. Milestone Genes were identified among genes within type one diabetes (T1D) susceptibility regions (Idd). Milestone Genes showing uniform patterns of changes in expression at various time points were identified. Potential T1D candidate genes were identified among Milestone Genes within Idd regions and/or hierarchical clusters. These studies identified tissue- and age-specific changes in gene expression that may play an important role in the inductive or destructive events of T1D.

overall_design:
NOD/LtJ (NOD), NOD.B10Sn-H2b/J (NOD.B10) female mice of multiple ages were used for this study.
Six Groups of NOD mice were sacrificed at 10 days, and 4, 8, 12, 16, and 20 weeks of age and spleen (SPL) were removed and prepared for mRNA analysis. Two Groups of 10 NOD.B10 mice [10 days (n=10) + 20 weeks of age (n=10)] were used as a tissue specific control. Gene (mRNA) expression was analyzed using the 41K Whole Mouse Genome Oligo Microarray Kit (Agilent Technologies), and gene expression data are processed (cy3: NOD, cy5: NOD.B10) and reported as normalized expression ratios: Log 10 (NOD processed signal / NOD.B10 processed signal) (Log ratio).
10days of age; SPL_10d (n=5), 4 weeks of age; SPL_4w (n=5), 8 weeks of age; SPL_8w (n=3), 12 weeks of age; SPL_12w (n=5), 16 weeks of age; SPL_16w (n=4), 20 weeks of age; SPL_20w (n=5)


title: A tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip

status: Public on May 05 2010

city: Sendai

first: Hitoshi

last: Hiura

address: 2-1 Seiryo-cho, Aoba-ku

department: Obstetrics and Gynecology

institute: Tohoku University Graduate School of Medicine

type: Methylation profiling by genome tiling array

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The Rpd3L HDAC complex is essential for the heat stress response in yeast

city: Barcelona

first: Eulalia

last: de Nadal

address: Aiguader 88

department: CEXS

institute: UPF

summary: To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. Global gene expression analysis showed that Rpd3 partially regulated gene expression upon heat shock. The Hsf1 and Msn2/4 transcription factors are the main regulators of gene activation in response to heat stress. RPD3-deficient cells had impaired activation of Msn2/4-dependent genes, while activation of genes controlled by Hsf1 was deacetylase independent. Rpd3 bound to heat stress-dependent promoters through the Msn2/4 transcription factors, allowing entry of RNA Pol II and activation of transcription upon stress. Finally, we found that the large, but not the small Rpd3 complex regulated cell adaptation in response to heat stress.

overall_design: Three independent 200 ml cultures of wild-type and rpd3Δ mutant strains were grown to mid-log phase in YPD rich medium at 25ºC (control) or at 39 ºC for 20 min (heat stressed). Results were analyzed comparing thermo-responsive gene expression respect to the control in each individual strain.

first: Clàudia

last: Ruiz-Roig

first: Cristina

last: Vieitez

first: Francesc

last: Posas

first: Eulàlia


title: Gene knock down studies revealed CCDC50 as candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia

status: Public on Jun 03 2010

city: Heidelberg

first: Alexandra

last: Farfsing

address: Im Neuenheimer Feld 280

institute: DKFZ

summary:
The two B-cell non-Hodgkin lymphoma (NHL) entities chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) show recurrent chromosomal gains of 3q25 q29, 12q13 q14 and 18q21-q22. The pathomechanisms affected by these aberrations are not understood. The aim of this study was to identify genes, located within these gained regions, which control cell death and cell survival of MCL and CLL cancer cells. Blood samples from 24 CLL and 6 MCL patients as well as 6 cell lines representing both malignancies were analyzed by gene expression profiling. By comparison of genomic DNA and gene expression, 72 candidate genes were identified. We performed a limited RNAi screen with these candidates in order to identify genes affecting cell survival. CCDC50, SERPINI2 and SMARCC2 mediated a reduction of cell viability in primary CLL cells as well as in cell lines. Gene knock down and a NFkB reporter gene assay revealed that CCDC50 is required for survival in MCL and CLL cells and controls NFkB signaling.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: The gene profile of zebrafish guanine binding protein-like 2 (Gnl2) mutant embryos versus wild-type embryos at 22 hours post-fertilization

status: Public on Mar 31 2010

city: Utrecht

first: Judith

last: Paridaen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Nucleostemin (NS), a member of a family of nucleolar GTP-binding proteins, is highly expressed in proliferating cells and implicated in the control of cell cycle progression, the maintenance of stem cells, and the regulation of cancer cells. The depletion of NS in cell lines and invertebrate animals has been demonstrated to result in defective ribosome biogenesis, while both depletion and overexpression of NS are able to stabilize the tumor suppressor p53 protein. While the existence of p53-independent functions of NS has been previously suggested, these roles to date remain unclear. Here, we report two zebrafish mutants recovered from forward and reverse genetic screens that encode two members of this nucleolar protein family, Guanine nucleotide binding-protein-like 2 (Gnl2) and Gnl3/Nucleostemin (Ns). We show that Gnl2 and Ns are required for pre-rRNA processing and the production of the 60S ribosomal subunit in the developing zebrafish embryo. In addition, we demonstrate that these proteins are required for correct timing of neural differentiation in the brain and retina. In both mutants, cell cycle regulators such as cyclinD1 and the cell cycle inhibitor cdkn1c/p57kip2 are aberrantly expressed. Concomitantly, retinal progenitors fail to exit the cell cycle in a timely fashion and differentiation of retinal cell types is delayed. We show that loss of either Gnl2 or Ns induces the stabilization of p53 and apoptosis in the brain, however the retinal cell differentiation defect in gnl2 mutants is independent of p53 status. This work demonstrates that the loss of either Gnl2 or Ns results in ribosome biogenesis and neural differentiation defects in vertebrates. In addition, the data suggests that the latter phenotype of gnl2 mutants is due to an increase in expression of cell cycle markers cyclinD1 and p57/kip2 and not to the stabilization of p53.

overall_design: Gene expression of gnl2 mutant versus wild-type embryos at 22 hpf. Two biological replicates with dye swap.


title: Expression data from primary ovine fetal turbinate cells infected with Orf Virus IA82 and deletion mutant OV-IA82Δ024

first: Diego

middle: G.

last: Diel

address: 2001, S Lincoln Ave

department: Pathobiology

institute: University of Illinois

summary:
Reverse genetics has been widely used to investigate function of viral genes. In the present study we investigated the gene expression profile of a primary ovine cell (OFTu) in response to infection with the wild type (OV-IA82) and deletion mutant virus (OV-IA82Δ024) aiming to determine possible functions for ORFV024 during ORFV infection.
We used microarray analysis to investigate gene expression profile of OFTu with ORFV OV-IA82 and OV-IA82Δ024.

overall_design: OFTu cells were infected with each virus (m.o.i = 10) and RNA was extratect at 2 and 4 hours post-infection. cDNA was synthesized and hybridized with GeneChip Bovine Genome Array from Affymetrix. Gene expression profile were determined by comparing expression of cells infected with the deletion mutant virus with those infected with the wild type virus in each time point.

first: D

middle: G

first: G

last: Delhon

first: S

last: Luo

first: E

last: Flores

first: J

last: Drnevich

last: Rock


title: Gene expression profile of HNSCC

status: Public on Jun 10 2010

city: Sao Paulo

first: Anna

last: Coló

address: Rua Professor Antonio Prudente, 211

country: Brazil

institute: Hospital A.C. Camargo

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


title: Expression profiling of a lesion mimic genotype, splNF4050-8, that confers blast resistance in rice

city: Lubbock

first: Kameswara Rao

last: Kottapalli

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

summary: Lesion mimic mutants in rice are widely known as spotted leaf (spl) mutants, of which several genotypes exhibit enhanced resistance to different races of Magnaporthe grisea. Besides naturally occurring spotted leaf mutants, tissue culture-induced reverse genetic repositories also act as sources of lesion mimic mutants in rice. We systematically evaluated a large collection of Tos17 mutant panel lines, developed and maintained at the National Institute of Agrobiological Sciences, Tsukuba, Japan, for their reaction to three different races of M. grisea and identified a lesion mimic mutant, NF4050-8, that showed lesions similar to naturally occurring spl5 mutant and enhanced resistance to all three blast races tested. Microarray analysis of ~44,000 rice genes in NF4050-8 with Nipponbare as control during the progressive lesion appearance stage revealed significant up-regulation of numerous defense/pathogenesis-related genes as well as several WRKY domain-containing genes and down-regulation of haem peroxidase gene. Subsequent real-time PCR analysis of WRKY45 and PR1b genes in NF4050-8 and spl5 suggested possible constitutive activation of a defense signaling pathway downstream of Salicylic Acid (SA) but independent of NH1 in these mutant lines of rice.

overall_design: We used Agilent rice oligo microarrays to identify putative defense/pathogenesis-related genes. Leaf tissues of the rice genotypes Nipponbare and NF4050-8 were used in the study. Two replications of microarray experiments were carried out by hybridizing the cRNA from control and progressive lesion appearance stage on 4 x 44k microarray.

first: Raman

last: Babu

first: KameswaraRao


title: Ventral striatal responses to reduced food intake in healthy animals and rats bearing small tumors

first: Jan Pieter

last: Konsman

summary: Anorexia is frequently observed during cancer and associated with increased morbidity and mortality. Our previous work has shown the presence of transcription factors in the ventral striatum of anorectic tumor-bearing rats. The aim of the present study was, therefore, to assess expression of neuropeptides, neurotransmitter-synthesizing enzymes and receptors in this structure. Morris hepatoma 7777 cells injected subcutaneously in Buffalo rats provoked a 15% reduction in food intake and 10% lower body weight when the tumor represented 1-2% of body mass. Mircorarrays and real-time PCR revealed increased ventral striatal prostaglandin D synthase expression in food-restricted animals compared to anorectic tumor-bearing rats. These findings indicate that reduced ventral striatal prostaglandin D synthesis underlies cancer-associated anorexia.

overall_design:
A pool of cDNA for each experimental group containing an equal amount of cDNA of each individual (n5-8) was used for in vitro transcription to yield multiple copies of amino-allyl-modified antisense RNA (aRNA) using amino-allyl-labeled UTP (Ambion, Austin, TX, USA). Subsequently, aimine groups of the fluorescent Cy3 or Cy5 dyes (Amersham Biosciences, GE Healthcare, Munich, Germany ) were coupled to the a RNA amino allyl groups following manufacturer’s instructions.
Gene expression profiles were examined using Agilent whole rat genome aRNA microarrays (G4131a, Agilent Technologies, Santa Clara, CA, USA) using 0.75 μg of Cy3-labelled RNA and 0.75 μg of Cy5-labelled RNA. A dye-swap chip was included for each comparison to control for differences in dye incorporation.

first: Line

last: Pourtau

first: Susan

last: Leemburg

first: Pascale

last: Roux

first: Thierry

last: Leste-Lassere

first: Patricia

last: Costaglioli

first: Bertrand

last: Garbay

first: Guillaume

last: Drutel

first: Jan-Pieter


title: Il13-stimulation of human paSMCs

status: Public on Apr 17 2010

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

institute: Uniklinikum Giessen

summary: Idiopathic pulmonary arterial hypertension (IPAH) is characterized by medial hypertrophy due to pulmonary arterial smooth muscle cell (paSMC) hyperplasia. Interleukin (IL)-13 is a potent regulator of tissue fibrosis and remodelling, and its effects are dependent on the cell-type specific expression of the IL-13 receptor isotypes IL-4Rα, IL-13Rα1, and IL-13Rα2. In order to identify the possible mechanism how IL-13 can exert its antiproliferative effect on paSMC microarray analysis was performed. For this purpose paSMC were stimulated with IL-13(10ng/ml) for 2h and 6h, respectively and subjected to microarray analysis.

overall_design: Comparison of stimulated versus unstimulated cells. 3 biological replicates, 2 time points

first: Matthias

last: Hecker

first: Zbigniew

last: Zasłona

last: Zakrzewicz

first: Grażyna

last: Kwapiszewska

first: Leigh

last: Marsh

first: Daniel

last: Sedding

first: Walter

last: Klepetko

first: Jürgen

last: Lohmeyer

first: Werner

last: Seeger

first: Norbert

last: Weissmann

first: Ralph

middle: T

last: Schermuly

first: Oliver

last: Eickelberg

first: Rory

middle: E

last: Morty


title: Expression profiling of HeLa cells at S and G2/M phases of mitotic cell cycle.

first: Isabel

last: Novoa

address: Dr. Aiguader, 88

department: Gene Regulation

institute: Center for Genomic Regulation

summary:
We compared the mRNAs expression profile of HeLa cells between two phases of the mitotic cell cycle: S and G2/M phases. Results provide insight into the regulation of transcript levels during mitotic cell cycle progression.  HeLa cells were synchronized with double thymidine blockade (12 hours with 2 mM thymidine, 12 hours release, and 12 hours with 2 mM thymidine),  and cells were taken after 2 hours release (S phase) and 8 hours release (G2/M phase).

Keywords: time course

overall_design: Comparison of mRNAs measured at S phase (2 hours release after double thymidine blockade) and at G2/M phase (8 hours release after double thymidine blockade); 3 biological replicates at each of the two time points; two technical replicates with dye swapping per comparison; additional comparison between G2/M (8h) and S (2h).

first: Javier

last: Gallego

first: Raul

last: Mendez


title: Bovine pre-transfer endometrium and embryo transcriptome fingerprints as predictors of pregnancy success after embryo transfer

status: Public on Mar 25 2010

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

overall_design: Refer to individual Series


title: Bovine pre-transfer endometrium and embryo transcriptome fingerprints as predictors of pregnancy success after embryo transfer (endometrial study)

summary: The aberrant gene expression in the uterine endometrium and embryo has been the major causes of pregnancy failure in cattle. Therefore, selecting cows having adequate endometrial receptivity and embryos of better developmental competence based on the gene expression could increase the number of calves produced by in each cow during its productive life time.

overall_design: We used endometrial and embryo biopsy technology in conjunction with the pregnancy outcome information to establish a direct link between the pre-transfer endometrial or in vivo derived embryo gene expression and pregnancy outcome after embryo transfer. Endometrial samples were collected  from Simmental heifers at day 7 and 14 of the estrous cycle, one cycle prior to embryo transfer.  In the next cycle, embryo biopsies consisting of 60-70% of inner cell mass and trophectoderm were transferred to the recipients at day 7 of the estrous cycle. The remaining 30-40% parts of the embryos were retained for analysis.Pregnancy diagnosis was performed at days 28 and 42 by ultrasonography and at day 56 by rectal palpation. Those heifers returned to heat at day 21 were considered as non pregnant or non receptive endometrium (NP) while those heifers ended up with successful pregnancy and calf delivery was considered as the calf delivery group or receptive endometrium (CD). Following this, the endometrial samples collected during the pre-transfer period and the embryo biopsies retained during embryo transfer were categorized based on the pregnancy outcome. Those endometrial biopsies collected at days 7 and 14 of the estrous cycle from heifers resulted in successful calf delivery were designated as CDd7 and CDd14, respectively and endometrial biopsies taken at days 7 and 14 of the estrous cycle from those subsequently resulted in no pregnancy were designated as NPd7 and NPd14, respectively. Similarly, the embryo biopsies were classified as those embryo biopsies resulted in successful calf delivery and those resulted in no pregnancy

first: Michael

last: Hölker

first: Franca

last: Rings

first: Mehmet

last: Ulas-Cinar

first: Jaana

last: Peippo

first: Ernst

last: Tholen

first: Christian

last: Looft

first: Karl

last: Schellander

first: Dawit

last: Tesfaye


title: Expression data from early preimplantation Bovine embryos

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: The oviduct is a specialized organ playing crucial roles in the success of early reproductive events and it provides an optimal microenvironment for early embryonic development. However, changes in oviductal environment due to estrus synchronization and superovulation hormonal treatments and subsequent influence on embryos transcriptome profile are not yet investigated. For that, the objective of this study was to investigate differences in developmental rate and transcriptome profile of bovine blastocysts cultured under superovulation or synchronization oviductal environment.

overall_design: Influence of oviductal environment on transcriptome abundance of produced blastocysts was examined using the Affymetrix GeneChip Bovine Genome Array. Eighteen Simmental heifers were synchronized, superovulated and artificially inseminated, then nine of them were flushed at day 2 by transvaginal endoscopic means and 2-cell stage embryos were recovered and endoscopicaly transferred to only synchronized recipients. The remaining half of superovulated heifers and the synchronized recipients were flushed at day 7 to collect blastocysts which developed either in superovulated or synchronized oviduct


title: Expression data from different stages and types of oocytes and cumulus cells (CCs)

status: Public on Mar 23 2010

first: Alemu

last: Regassa

address: Endenicher allee 15

department: Animal breeding and husbandry

summary: The bidirectional communication between bovine oocytes and CCs is vital for functioning and development of both cell types. We used microarray to identify genes which are differentially expressed between germinal vesicle (GV)- and metaphase II (MII)-stage oocytes and CCs and those differentially expressed when oocytes mature with or without the other. We also identified genes differentially expressed between CCs at GV and MII stages.

overall_design: Slaughterhouse ovaries were collected and GV-stage cumulus oocyte complexes (COCs) were aspirated. Different stages and types of oocytes and CCs were used for total RNA isolation and hybridisation on Affymetrix microarray.

first: A

first: K

first: D


title: Global analysis of differential polyadenylation of mRNAs during mitotic cell cycle: S phase versus G2/M phase.

first: Isabel

summary:
We compared the poly(A) tail length status of mRNAs of HeLa cells between two phases of the mitotic cell cycle: S and G2/M phases. Hundreds of mRNAs were found to be regulated by changes in their poly(A) tail length during mitotic cell cycle in a phase specific manner. Many of these differentially polyadenylated mRNAs encode proteins related to cell death, cell cycle and cellular growth and proliferation.   HeLa cells were synchronized with double thymidine blockade (12 hours with 2 mM thymidine, 12 hours release, and 12 hours with 2 mM thymidine),  and samples were taken after 2 hours release (S phase) and 8 hours release (G2/M phase). For each condition total RNA was purified by two different procedures: poly(U) chromatography and oligo(dT)-chromatography. Poly(U)-chromatography (Jacobson, 1987): 100 μg of total RNA were bound to poly(U)-sepharose (Sigma) and eluted at 35ºC to isolate mRNAs with short poly(A) tail (<30As, SHORT fraction). Oligo(dT) chromatography: mRNAs were purified independently of their poly(A) tail length with Ambion Poly(A)Purist kit from 20 μg total RNA (ALL fraction).  Jacobson, A. Purification and fractionation of poly(A)+ RNA. Methods in Enzymology (1987) 152: 254-261.

Keywords: time course

overall_design: Comparison of ALL fraction mRNAs and SHORT fraction mRNAs measured after 2 hours (S phase) and 8 hours release (G2/M) from double thymidine blockade; 3 biological replicates at each of the two time points; two technical replicates with dye swapping per comparison.


title: Hypothalamic responses to reduced food intake in healthy animals and rats bearing small tumors

first: Jan Pieter

last: Konsman

address: 146, rue Léo Saignat

institute: CNRS

summary: Anorexia is frequently observed during cancer and associated with increased morbidity and mortality. Our previous work has shown the presence of transcription factors in the hypothalamus of anorectic tumor-bearing rats. The aim of the present study was, therefore, to assess expression of neuropeptides, neurotransmitter-synthesizing enzymes and receptors in this structure. Morris hepatoma 7777 cells injected subcutaneously in Buffalo rats provoked a 15% reduction in food intake and 10% lower body weight when the tumor represented 1-2% of body mass. Real-time PCR showed that tumor-bearing rats did not display the increase in hypothalamic agouti-related peptide mRNA observed in food-restricted weight-matched animals. These findings indicate that blunted hypothalamic AgRp mRNA expression underlies cancer-associated anorexia.

first: Line

last: Pourtau

first: Susan

last: Leemburg

first: Pascale

last: Roux

first: Thierry

last: Leste-Lassere

first: Patricia

last: Costaglioli

first: Bertrand

last: Garbay

first: Guillaume

last: Drutel

first: Jan-Pieter


title: Gilthead seabream pathogen exposure to Enteromyxum leei

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

sample_organism:
Sparus aurata
Enteromyxum leei


title: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

country: United Kingdom

institute: Cardiff University


title: Tricellular pollen and pollen mother cells (11447)

status: Public on Jul 31 2010

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

country: China

institute: Shanghai Inst. Plant Phys. & Eco.

summary: We isolated tricellular pollen (TCP) and pollen mother cells (PMC) of rice using laser microdissection, and did microarray analysis with Agilent 44k rice array.

overall_design: 2 biological rep of TCP and 2 biological rep of PMC were label by Cy3, comparing to 4 rep of seedling sample labled by Cy5

first: Xiang


title: A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

status: Public on Dec 14 2010

city: Zagreb

first: Tomislav

last: Domazet-Loso

address: Bijenicka cesta 54

department: Division of Molecluar Biology

country: Croatia

institute: Ruder Boskovic Institute

summary: Parallels between phylogeny and ontogeny have been discussed since almost two centuries and a number of theories have been proposed to explain such patterns. Especially elusive is the so-called phylotypic stage, a phase during development where species within a phylum are particularly similar to each other. While this has formerly been interpreted as a recapitulation of phylogeny, it is nowadays thought to reflect an ontogenetic progression phase, where strong constraints on developmental regulation and gene interactions exist. Several studies have shown that genes expressed during this stage evolve slower, but it has so far not been possible to derive an unequivocal molecular signature associated with this stage. We use here a combination of phylostratigraphy and stage specific gene expression data to generate a cumulative index that reflects the evolutionary age of the transcriptome at given ontogenetic stages. Using zebrafish ontogeny and adult development as a model, we find that the phylotypic stage does indeed express the oldest transcriptome set and that younger sets are expressed during early and late development, thus faithfully mirroring the hourglass model of morphological divergence. Reproductively active animals show the youngest transcriptome, with major differences between males and females. Intriguingly, aging animals express also increasingly older genes. Comparisons with similar datasets from flies and nematodes show that this pattern occurs across phyla. Our results suggest that an old transcriptome marks the phylotypic phase and that phylogenetic differences at other ontogenetic stages correlate with the expression of newly evolved genes.

overall_design: Zebrafish (Danio rerio) were kept in 12L flow-through tanks at 26.5 °C (around 60 animals per tank). For accurate staging, fertilized eggs were collected within 15 min intervalls and incubated in Petri dishes at 28.5°C with water changes every 2-6 hours. After hatching, larvae were transferred to 1 liter tanks and kept at 28.5 °C. We took 72 samples in at least two biological replicates (147 experiments in total) that correspond to 61 stages across zebrafish ontogeny (50 stages before the sex could be clearly recognized plus 11 adult stages of males and females each). Staging was done according to post-fertilization time. Embryos were additionally staged under the dissecting microscope to check for the consistency of post-fertilization timing and morphological development at standard temperature (28.5 °C). Only healthy animals that showed the expected morphological features for a given post-fertilization time were sampled. Each sample contained around 50 individuals until the 1 day and 3 hour embryo stage, 15 individuals until the 10 day larval stage, 10 individuals until the 18 day larval stage, 5 individuals until the 45 days juvenile stage, while in later juvenile and adult stages we sampled males and females separately and each sample contained 2 individuals. All samples were snap frozen in liquid nitrogen and stored at -80 °C until RNA extraction. To avoid severe biases due to the excess of unfertilized eggs we squeezed eggs from adult females before freezing them in liquid nitrogen.

first: Diethard

last: Tautz


title: Microarray analysis of Japanese encephalitis virus infected Neuro2a cells

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Microarray profiling of alterations in cellular gene expression induced by Japanese encephalitis virus of Neuro2a cells

overall_design: Agilent two-color experiment,Organism: Mouse ,Slides, Agilent’s Mouse Microarray G4121B with 22000 features, Labeling kit: Agilents Low input RNA linear amplification Kit Cat # 5184-3523, Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA

first: Soma

last: Das

first: Vasanthapuram

last: Ravi

first: Anita

last: Desai


title: CD99 inhibits neural differentiation of human Ewing sarcoma cells

status: Public on Mar 08 2010

city: Bologna

first: Katia

last: Scotlandi

address: Via di Barbiano 1/10

institute: Istituto Ortopedico Rizzoli

summary: Ewing sarcoma (EWS) is an aggressive bone tumor of uncertain cellular origin. CD99 is a membrane protein that is expressed in most cases of EWS, although its function in the disease is unknown. Here we have shown that endogenous CD99 expression modulates EWS tumor differentiation and malignancy. We determined that knocking down CD99 expression in human EWS cell lines reduced their ability to form tumors and bone metastases when xenografted into immunodeficient mice and diminished their tumorigenic characteristics in vitro. Further, reduction of CD99 expression resulted in neurite outgrowth and increased expression of β-III tubulin and markers of neural differentiation. Analysis of a panel of human EWS cells revealed an inverse correlation between CD99 and H-neurofilament expression, as well as an inverse correlation between neural differentiation and oncogenic transformation. As knockdown of CD99 also led to an increase in phosphorylation of ERK1/2, we suggest that the CD99-mediated prevention of neural differentiation of EWS occurs through MAPK pathway modulation. Together, these data indicate a new role for CD99 in preventing neural differentiation of EWS cells and suggest that blockade of CD99 or its downstream molecular pathway may be a new therapeutic approach for EWS.

overall_design: Ewing Sarcoma cell lines and CD99 inhibited cell lines were profiled on Agilent Human 1A Microarray (V2) G4110B (GPL887) arrays.

first: A

last: Rocchi

first: M

last: Manara

last: Sciandra

first: D

last: Zambelli

first: F

last: Nardi

first: G

last: Nicoletti

first: C

last: Garofalo

first: S

last: Meschini

last: Astolfi

middle: P

last: Colombo

last: Lessnick

first: P

last: Picci

first: K


title: mRNA expression in human hepatitis c virus (HCV) liver biopsy samples

city: Seattle

first: Xinxia

last: Peng

state: WA

address: Rosen Building, 960 Republican St.

department: Microbiology

institute: University of Washington

summary: In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all mRNA profiles.

overall_design: This series includes mRNA profiles of 30 samples, 24 HCV positives and 6 HCV negatives. Each sample was repeated 4 times (3 for 3 samples) with dye swaps.

first: Yu

last: Li

first: Kathie-Anne

last: Walters

first: Elizabeth

last: Rosenzweig

first: Sharon

last: Lederer

first: Lauri

middle: D

last: Aicher

first: Sean

last: Proll

first: Michael

last: Katze


title: microRNA and mRNA expression in human hepatitis C Virus


title: Effects of Plasmodium berghei infection on Anopheles gambiae during oocysts development

status: Public on Dec 31 2011

city: Acton

first: Sebastian

last: Kurscheid

state: ACT

address: 57 Garran Road

department: JCSMR

institute: Australian National University

summary: Plasmodium ssp. are pathogens in their vertebrate hosts and also cause deleterious effects to their insect vectors. We show here, however, that Plasmodium-infected mosquitoes more efficiently accumulate energy resources (glycogen) during oocyst development, and survive better when they are starved. Microarray analysis revealed that mosquito metabolism is altered by the presence of rapidly growing oocysts in the midgut. Plasmodium infection is associated with enhanced expression of several insulin-like peptides in mosquitoes and blocking insulin-like signaling results in diminished Plasmodium development. We conclude that Plasmodium infection dramatically changes mosquito metabolism pathways, epitomized by enhanced insulin-signaling, and thereby confer a survival advantage to the insects during periods of starvation. Manipulation of this pathway may provide new strategies to influence the ability of mosquitoes to transmit the protozoa that cause malaria.

overall_design: One-condition experiment: P. berghei infected vs uninfected mosquitoes; 10 mosquitoes per sample; 4 biological replicates for each group; two different time points, 10 and 17 days post infection; control mosquitoes were from same batch as infected mosquitoes that were fed on clean mice.

first: Yang

middle: O

last: Zhao


title: Gene expression of cytosolic glutamine synthetase 1;1 knock-out mutant rice

status: Public on Mar 01 2010

city: Sendai

first: Tomoyuki

last: Yamaya

address: 1-1Tsutsumidori-Amamiyamachi, Aoba-ku

department: Gladuate School of Agricultural Science

institute: Tohoku University

summary: Rice grown in paddy fields prefers to use ammonium ions as a major source of inorganic nitrogen. Glutamine synthetase (GS) catalyzes the conversion of ammonium ions to glutamine. In three cytosolic GS in rice, OsGS1;1 has the critical role for normal growth and grain filling. To understand a role of GS1;1, we performed transcriptional profiling of wild type Nipponbare and GS1;1 mutant plants in seedling using the Agilent Rice Oligo Microarray.

overall_design:
organisms: Oryza sativa L. cv. Nipponbare
mutant: GS1;1 mutant rice (Tos17 insertion NC2373)
growth substrates: The germinated seedlings were grown hydroponically in one-fourth concentration of the hydroponic culture solution with 1.0 mM NH4Cl as nitrogen source. The culture solution was replaced as new one every morning at 10:00 am.
age: 18 days after sowing
tissue: 4th leaf blade derived from 4 plants
tissue: 4th leaf sheath derived from 4 plants
tissue: roots derived from a plant
WT vs. GS1;1 mutant rice
hybridization : two dye method
hybridization: Dye-swap experiment

first: Mayumi

last: Tabuchi


title: Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome

status: Public on Mar 24 2010

city: Urbana

first: min

last: li

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

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


title: Functional analysis of HSFB transcription factors [22°C]

city: Tsukuba

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Biological and molecular function of Arabidopsis HSFB transcription factors was studied.

overall_design:
Three biological replicates were taken to compare the transcriptome between 35S:HSFB1 plant and wild-type plant. Plants were grown on normal condition in MS agar medium and RNA was extracted from root of 22d-old seedlings.
Same experiment was done for 35S:mutHSFB1 plant.
Four biological replicates were taken to compare the transcriptome between hsfb1 hsfb2b double knockout plant and wild-type plant. Plants were grown on normal condition in MS agar medium and RNA was extracted from 7d-old whole seedlings.

first: Miho

last: Ikeda

first: Masaru

last: Ohme-Takagi


title: Sex-related transcriptional differences in Day 7 bovine in vitro produced blastocysts

status: Public on Feb 24 2010

city: Madrid

first: Pablo

last: Bermejo-Álvarez

state: Madrid

address: Ctra La Coruña Km 5,9

department: Reproducción Animal

institute: INIA

summary:
Sexual dimorphism in mammals is mostly attributable to sex-related hormonal differences in fetal and adult tissues; however, this may not be the sole determinant. Though genetically-identical for autosomal chromosomes, male and female preimplantation embryos could display sex-specific transcriptional regulation which can only be attributted to the differences in sexual chromosome dosage.
We used microarrays to analyze sex-related transcriptional differences at the blastocyst stage.

overall_design: Day 7 bovine in vitro produced bovine blastocysts produced with sorted semen from 3 different bulls. Pooled RNA from 60 blastocysts of one sex and produced with one bull was used per chip. Three replicates of each sex per bull. In total, 18 Bovine GeneChip (Affymetrix) were used (3 replicates X 3 bulls X 2 sexes).

first: Dimitrios

last: Rizos

first: Detlef

last: Rath

first: Pat

last: Lonergan

first: Alfonso

last: Gutiérrez-Adán


title: Gene expression profiling soybean stem tissue early response to Sclerotinia sclerotiorum


title: Effects of scanning sensitivity and multiple scan algorithms on microarray data quality

status: Public on Mar 22 2010

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

summary:
A number of methods have been proposed to incorporate multiple scans at different intensities to reduce the quantification error and to minimize effects of saturation, but no direct comparison of their efficacy has been made.  Here we used 40 technical replicates to compare individual scans at low, medium and high sensitivity with three methods for combining data from multiple scans (either 2 scan or 3 scan cases) using a variety of metrics

Keywords: Multiple Scans

overall_design: Agilent 22K oligonucleotide microarrays were used to examine the reproducibility of data from 3 scans at different PMT settings and from data obtained from 3 methods that incorporate data from multiple scans.  In this study the Stratagene Universal Mouse RNA reference was used.

first: Errol

middle: M

last: Thomson


title: Gene expression profile in rice developing caryopsis exposed to high temperature

status: Public on Mar 15 2010

city: Joetsu

first: Hiromoto

last: Yamakawa

state: Niigata

address: Inada 1-2-1

department: Hokuriku Research Center

institute: National Agricultural Research Center

summary: To summarize the impact of high temperature on rice grain filling, we performed the rice 44k oligo microarray analysis.

overall_design: Total RNA was extracted from developing caryopses ripened under 33˚C/28˚C (high temperature) and 25˚C/20˚C (Control), and subjected to 44k oligo-DNA microarray with 3 biological replicates.

first: Makoto

last: Hakata


title: Response to nicotine in heads of the tobacco aphid Myzus persicae

status: Public on Feb 23 2010

city: Ithaca

first: John

middle: Sawyer

last: Ramsey

state: NY

address: Comstock Hall

institute: Cornell University


title: Transcription factor Rbf1 is the master regulator for b-mating type controlled pathogenic development in Ustilago maydis

status: Public on Jun 01 2010

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology


title: p53 binding in mouse embryonic stem cells untreated or treated with adriamycin

status: Public on Jan 19 2010

city: Bethesda

first: Jing

last: Huang

institute: National Cancer Institute

type: Genome binding/occupancy profiling by array

summary: Both p53 and the Wnt signaling pathways play important roles in tumorigenesis and development. However, few studies, particularly on a genome-wide scale, have linked these two pathways. Here we show that p53 directly regulates the Wnt signaling pathway in murine embryonic stem cells (mESCs) using an integrated genome-wide approach. A chromatin-immunoprecipitation-based microarray assay (ChIP-chip) reveals that the Wnt signaling pathway is significantly over-represented in p53 bound genes.  Using gene expression microarray and real-time PCR, we demonstrate that the expressions of many Wnts are robustly induced by various stresses, including DNA damage and hypoxia that activate p53. Importantly, the activation of p53 is a prerequisite for the induction of Wnts. Moreover, conditional medium (CM) collected from ultraviolet (UV)-treated mESCs contains an anti-differentiation activity, which can be lowered by either the addition of Wnt signaling inhibitors into the CM or the reduction of p53 levels in UV-treated mESCs. These results suggest that stressed mESCs utilize the p53-Wnt signaling axis to signal neighboring mESCs to delay the differentiation. Together, our results uncover a novel connection between p53 and the Wnt signaling pathways in mediating cell-to-cell communication in mESCs, and provide insights into the functions of these two pathways in tumorigenesis and development

overall_design: ChIP-chip assay was done per Agilent’s ChIP-chip protocol (Version 10.0). The goal of this experiment is to identify the p53 binding sites in cells untreated or treated with adriamycin (DNA damage).

first: Li

last: Mangmang

first: Lee

last: Kyoung-Hwa

first: Michalowski

last: Aleksandra

first: Zhang

last: Xinyue

first: Liao

last: Hongling

first: Chen

last: Lingyi

first: Wu

last: Xiaolin

first: Huang

last: Jing


title: Effects of IGF 1 on primary breast fibroblasts, MCF-7 breast cancer cells and CCL-171 fibroblasts

status: Public on Jan 21 2010

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

overall_design: Refer to individual Series


title: Effects of biocides on gene expression in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

status: Public on Mar 06 2010

city: Calgary

first: Phoebe

middle: Meng-Hsin

last: Lee

address: 2500 University Dr NW

department: Biological sciences

institute: University of Calgary

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough


title: Somatic Mutation Screen of Clear Cell RCC

status: Public on Jan 05 2010

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

overall_design:
Systematic somatic mutation screening of 4000 genes in human clear cell renal cell carcinoma. Information on corresponding somatic mutations in each sample can be found at http://www.sanger.ac.uk/genetics/CGP/Studies/.
To access mutation information in these samples please query the COSMIC database with the IDs listed in GSE17895_Cancer_Genome_Project_ID.txt.gz. (http://www.sanger.ac.uk/genetics/CGP/cosmic/)

first: Kyle

middle: A

last: Furge

first: Bin

last: Teh


title: Gene expression programs in PBMCs elicited by 6 major mediators of the immune response.

city: London

first: Simon

last: Waddell

department: Division of Cellular and Molecular Medicine St. George's

institute: University of London Tooting

summary:
Abstract:  Background Interferons are key modulators of the immune system, and are central to the control of many diseases. The response of immune cells to stimuli in complex populations is the product of direct and indirect effects, homotypic and heterotypic cell interactions. Dissecting the global transcriptional profiles of immune cell populations may provide insights into this regulatory interplay. The host transcriptional response may also be useful in discriminating between disease states, and in understanding pathophysiology. The transcriptional programs of cell populations in health therefore provide a paradigm for deconvoluting disease-associated gene expression profiles.
Results: We used human cDNA microarrays to (1) compare the gene expression programs in human peripheral blood mononuclear cells (PBMCs) elicited by 6 major mediators of the immune response: interferons a, b, w and g, IL12 and TNFa; and (2) characterise the transcriptional responses of purified immune cell populations (CD4+ and CD8+ T cells, B cells, NK cells and monocytes) to IFNg stimulation. We defined a highly stereotyped response to type I interferons, while responses to IFNg and IL12 were largely restricted to a subset of type I interferon-inducible genes. TNFa stimulation resulted in a distinct pattern of gene expression. Cell type-specific transcriptional programs were identified, highlighting the pronounced response of monocytes to IFNg, and emergent properties associated with IFN-mediated activation of mixed cell populations.
Conclusions: This information provides a detailed view of cellular activation by immune mediators, and contributes an interpretive framework for the detection and definition of host immune responses in a variety of disease settings.

This SuperSeries is composed of the SubSeries listed below.


title: Identification of genes that are regulated by the A and B isoforms of the human progesterone receptor

status: Public on Mar 04 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: T47D breast cancer cells were used for this microarray gene expression study.

overall_design: case vs control


title: Analysis of the turkey skeletal muscle transcriptome through development and between genetic lines

status: Public on Feb 01 2010

city: East Lansing

first: Kelly

middle: R

last: Sporer

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University


title: AB* zebrafish embryos exposed to 1 ng/mL TCDD from 1d to 5d post-fertilization.

city: Morrisville

first: Patrick

last: Hurban

address: 100 Perimeter Park Dr Ste C

department: Scientific Affairs

institute: Cogenics, Inc.

summary: Transcriptomic profiling of the response to dioxin in developing zebrafish embryos, at 24, 48, 72, 96, and 120 h post-fertilization. The goal was to elucidate mechanisms by which dioxin causes toxicity in zebrafish; this dose was previously shown to induce teratogenesis.

overall_design: Two conditions (dioxin or DMSO exposure), 5 timepoints, 4 replicates per timepoint derived from 4 entirely separate experiments; multiple pooled embryos per replicate. Embryo RNA was compared on each chip to a universal reference RNA obtained from zebrafish Zf4 cells (embryonic fibroblast cells).

first: Andrey

last: Alexeyenko

first: Deena

last: Wassenberg

first: Edward

middle: K

last: Lobenhofer

first: Jerry

last: Yen

first: Erik

middle: L

last: Sonnhammer

first: Elwood

last: Linney

first: Joel

middle: N

last: Meyer


title: Glucose Shortens the Lifespan of Caenorhabditis elegans by Down-Regulating Aquaporin Gene Expression

status: Public on Jan 01 2010

city: POHANG

first: SEUNG-JAE

last: LEE

state: GYEONGBUK

address: SAN 31 HYOJA-DONG, NAM-GU

department: LIFE SCEICNE

country: South Korea

institute: POHANG UNIVERSITY OF SCIENCE AND TECHNOLOGY

summary:
Many studies have addressed the effect of dietary glycemic index on obesity and diabetes, but little is known about its effect on lifespan itself.   We found that adding a small amount of glucose to the medium (0.1-2%) shortened the lifespan of C. elegans.  Glucose shortened lifespan by inhibiting the activities of lifespan-extending transcription factors that are also inhibited by insulin signaling: the FOXO family member DAF-16 and the heat shock factor HSF-1.  This effect involved the down-regulation of an aquaporin glycerol channel, aqp-1.  We show that changes in glycerol metabolism are likely to underlie the lifespan-shortening effect of glucose, and that aqp-1 may act cell non-autonomously as a feedback regulator in the insulin/IGF-1 signaling pathway.  Insulin down-regulates similar glycerol channels in mammals, suggesting that this glucose-responsive pathway might be conserved evolutionarily.  Together these findings raise the possibility that a low-sugar diet might have beneficial effects on lifespan in higher organisms.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Comparative gene expression analysis of the rat gastrointestinal tract epithelia

status: Public on Jan 03 2010

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

country: USA

institute: UCLA

summary: Background: The molecular basis of segment specific epithelial functions of the stomach and bowel has not been established. Regionally unique molecular properties of epithelial cells can be identified using cell-specific gene expression in each epithelial region by comparative mRNA analysis. Aim: To describe segment-specific epithelial mRNA content by comparative mRNA analysis of purified epithelial cell suspensions of stomach, small and large bowel. Results: 12% of all annotated genes show segment specific enrichment. The gastric (>3000 genes) and ileal (519 genes) mucosa show the most diverse expression profile. (a) Stomach: The gastric mucosa expresses the machinery for acid secretion, digestive enzyme release, and hormone release by gastric enteroendocrine cells. Associated with acid secretion is a specific set of K+, Cl-, and bicarbonate channels. Novel is a pathway for glucose and fatty acid sensing, iodine and glutamate uptake, and taurine synthesis. Specific sets of transcription factors control epithelial (Barx1, Runx) and enteroendocrine (FoxA2/N4) cell differentiation. (b) Small Bowel: This epithelium expresses genes coding for a unique fructose/glucose uptake and utilization mechanism. Enteroendocrine signalling to the gastric function is present. The upper portion expresses genes for iron uptake, bicarbonate secretion, and detoxification of food contents. Epithelial differentiation is transcriptionally controlled by Meis2/Pdx1 and Onecut 2. Expression of digestive enzymes, lipid/bile acid uptake and utilization increases distally. The ileal epithelium is also involved in innate and acquired immune defence, regulation of motility, and electrolyte and water re-absorption. Transcriptional regulation of enterocyte and goblet cell differentiation is mainly controlled by increasing expression of Cdx1 and 2. (c) Colon: This epithelium is mainly involved in Ca++-, K+, and water re-absorption, fatty acid uptake and sensing, and innate and acquired immune defence. Epithelial differentiation is controlled by Hox transcription factors in addition to Cdx1/2. Conclusion: This regional survey of gene expression by the GI tract epithelium reveals unique epithelial properties, raising several important questions as to the role of the proteins encoded in gut physiology.

overall_design: Rat stomach, small, and large bowel segments were inverted and subjected to a short pronase digestion and elutriation to obtain purified mucosal cells. RNA was isolated, labelled for microarray hybridization, and comparative whole rat genome expression analysis (Agilent) performed. 3 independent isolations of mucosal cell total RNA, labeled with either cy3 or cy5 were performed. All microarrays are scanned and the intensities normalized over background using a microarray scanner from Agilent Technologies including proprietary software. All microarray data sets (single channel) are imported into the microarray data analysis software Genespring 7.3 (Agilent, USA) and normalized intensities compared. Each individual normalized intensity was divided by the median of intensity of all 15 data points and the statistical significance of difference of the mean calculated using Genespring 7.3 microarray analysis software (Agilent). A p-value of less than  < 0.05 was considered as a significant difference.

middle: W

first: Miriam

last: Goebel

first: Andreas

last: Stengel

first: George

last: Sachs


title: DNA copy number data from the CTCR-OV01 study

status: Public on Feb 28 2010

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary: All patients with suspected ovarian cancer (Raised CA 125 and a complex pelvic mass in a perimenopausal woman) were radiologically staged using CT scan and a chest x-ray. Patients with evidence of intra-abdominal metastasis and/or malignant pleural effusion were approached for entry to the study. Tissue biopsy was obtained either under radiological control (core needle biopsy) or via laparoscopic surgery (punch biopsy). Patients with histologicaly confirmed epithelial ovarian cancer were randomized to receive either three cycles of carboplatin (AUC 7) or paclitaxel (175 mg/m2).

overall_design: Patients with suspected ovarian cancer had a biopsy obtained before and after 3 cycles of either Carboplatin or Paclitaxel.

first: Ahmed

last: Ahmed

first: Thomas

last: Hardcastle

first: Maria

last: Garcia

first: James

last: Brenton


title: Cadmium and temperature probe selection and validation experiment for custom array production

status: Public on Dec 31 2009

city: Antwerpen

first: Dries

last: Knapen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp


title: Legionella pneumophila small RNAs and deletion of 6S RNA

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

sample_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1


title: Timecourse of gene expression after oprhaning of virgin Solenopsis invicta fire ant queens

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

institute: University of Lausanne

summary: In species with social hierarchies, the death of dominant individuals typically upheaves the social hierarchy and provides an opportunity for subordinate individuals to become reproductives. Such a phenomenon occurs in the monogyne form of the fire ant, Solenopsis invicta, where colonies typically contain a single wingless reproductive queen, thousands of workers and hundreds of winged non-reproductive virgin queens. Upon the death of the mother queen, many virgin queens shed their wings and initiate reproductive development instead of departing on a mating flight. Workers progressively execute almost all of them over the following weeks.   To identify the molecular changes that occur in virgin queens as they perceive the loss of their mother queen and begin to compete for reproductive dominance, we collected virgin queens before the loss of their mother queen, six hours after orphaning and 24 hours after orphaning. Their RNA was extracted and hybridized against microarrays to examine the expression levels of approximately 10,000 genes. We identified 297 genes that were consistently differentially expressed after orphaning. These include genes that are putatively involved in the signaling and onset of reproductive development, as well as genes underlying major physiological changes in the young queens.

overall_design: 3 samples: 0h, 6h, 24; five queens pooled per samples; each replicate loop of 3 samples was taken from an independent colony; 8 biological replicates (colonies) used. Hybridization according to a Dye-balanced loop design (no technical replication)

first: John

last: Wang

first: Laurent

last: Keller


title: Comparison of precocious and non-precocious salmon

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

institute: NUI Galway

platform_organism:
Oncorhynchus mykiss
Salmo salar


title: Arabidopsis thaliana root tip: ago1-101, scr-3 and Col-0

city: Ikoma

first: Keiji

last: Nakajima

state: Nara

address: 8916-5 Takayama

department: Graduate School of Biological Sciences

country: Japan

institute: Nara Institute of Science and Technology

summary: Transcription profiling of Arabidopsis thaliana root tip region comparing argonaute1-101 (SALK_035319), scr-3 and wild-type Col-0.

overall_design: Dye-swapped two replicates for each pair of ago1-101/Col-0 and scr-3/Col-0.

first: Shunsuke

last: Miyashima


title: Forward genetics in Candida albicans reveals the Arp2/3 complex is required for hyphal formation, but not endocytosis

status: Public on Jan 23 2010

city: Montréal

first: Elias

last: Epp

address: 1205 Docteur Penfield

first: Andrea

last: Walther

first: Guylaine

last: Lépine

first: Zully

last: Leon

first: Alaka

last: Mullick

first: Martine

last: Raymond

first: Jürgen

last: Wendland

first: Malcolm

last: Whiteway


title: Identification of flap structure specific endonuclease 1 as a factor involved in LTM formation of aversive learning

status: Public on Dec 30 2009

city: San Juan

first: Sandra

last: Pena de Ortiz

state: PR

address: Gandara Ave., JGD Bldg. Rooms 108, 204

department: Department of Biology

country: Puerto Rico

institute: University of Puerto Rico

summary: We proposed that DNA recombination/repair processes play a role in memory formation.   Here, we used microarray analysis of rat amygdala genes to identify possible DNA recombination/repair factors involved in memory consolidation of conditioned taste aversion (CTA).  Among the genes that showed statistically significant differential expression, we identified fen-1, encoding a flap-structure specific DNA endonuclease.  Amygdalar fen-1 mRNA induction was associated to the illness component of CTA, since it could be observed by the pairing of a flavor and gastrointestinal illness, by the illness itself, but not by the presentation of the flavor alone.  No CTA related induction of fen-1 expression was observed in the insular cortex.  Importantly, functional validation studies demonstrated that amygdalar suppression of  fen-1 expression impaired memory consolidation of CTA.  Overall, our studies helped identify a new DNA recombination/repair candidate factor involved in memory formation of aversive experiences.

overall_design: Two comparisons were established between the cRNA samples: CTA versus Flavor-only and CTA versus Toxin-only. For each comparison, the microarray experiment was repeated four times using new biological samples, each consisting of a sample pool from 3 animals. Two of the four biological replicates were performed as dye-swaps in order to correct for dye bias effects.

first: Lorena

last: Saavedra- Rodríguez

first: Humberto

middle: G

last: Ortiz-Zuazaga

first: Lissette

last: Andrés

first: Fernando

last: Ramírez

first: Karen

last: Rodríguez

first: Adrinel

last: Vázquez

last: Peña de Ortiz


title: Oligotrophic growth of the extremely thermophilic bacterium C. saccharolyticus on simple and complex sugars

status: Public on Dec 29 2009

city: Raleigh

first: Amy

last: VanFossen

address: 840 Main Campus Dr.  Rm3305

department: Chemical and Biomolecular Engineering

institute: NC State Unversity


title: Expression data from the longuissimus dorsi muscle of Qinchuan cattle, Qinghai yak and Guangxi buffalo at 36 months

status: Public on Dec 23 2009

city: Yangling

first: Yingying

last: Zhang

address: No.22 Xinong Road, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China.

institute: National Beef Cattle Improvement Center

summary:
Sex condition has been demonstrated to alter meat quality and sex is a major factor that affects the fatty acid composition of lipids of carcass dissectible or intramuscular depot fats. But the possible genetic molecular mechanism of gender causing meat quality differences is not well defined. Qinchuan cattle, Qinghai yak and Guangxi buffalo are three typical indigenous species of cattle in China. Obivious differences of meat quality exist among the three species of cattle. Few studies have been conducted to elucidate the muscle tissue expression of genes involved in pathways and mechanisms leading to meat quality differences beyond the phenotype properties of beef.
Bovine Genome Arrays were used to construct muscle expression profiles of the longuissimus dorsi from Qinchuan cattle at 36 months and screen differentially expressed genes in the longuissimus dorsi muscle tissues among different genders of Qinchuan cattle, between Qinchuan cattle and Qinghai yak, and between Qinchuan cattle and Guangxi buffalo.

sample_organism:
Bos taurus
Bos grunniens
Bubalus bubalis

overall_design: Qinchuan cattle intact males, castrated males and females born within a 30-day period and of similar genetic background and reared under the same experimental conditions were used in the current study. Differentially expressed genes among the different genders were screened out, mainly involved in collagen metabolism, protein anabolism and catabolism signal transduction, regulation of cell growth and development and immunity. In addtion, this study has conducted the comparison of the muscle tissues gene expression profile of Qinchuan cattle with those of Qinghai yak and Guangxi buffalo.

first: Linsen

last: Zan

first: Hongbao

last: Wang


title: CD38 modulates CXCR4 signals in chronic lymphocytic leukemia cells: potential therapeutic implications

status: Public on Dec 22 2009

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary:
Recent data indicate that CD38, a cell surface enzyme and receptor, is part of the complex network of signals underlying the development, maintenance and progression of chronic lymphocytic leukemia (CLL). Here we show that CD38 signals directly facilitate short- (ERK1/2 phosphorylation) and long-term (chemotaxis) effects induced by CXCL12 exposure. Use of i) a specific enzyme inhibitor, ii) an agonistic anti-CD38 monoclonal antibody (mAb) and iii) microarray studies led to the conclusion that the receptor-like functions of CD38 are responsible for the observed effects. Interactions between CD38 and its non substrate ligand CD31 define a genetic signature characterized by modulation of a significant number of genetic pathways, involved in proliferation and migration. Blocking CD38 with domain-specific mAbs significantly lowers CXCL12 effects, in terms of ERK1/2 phosphorylation and chemotaxis. The molecular explanation behind the blocking activity of these mAbs lies in physical proximity between CD38 and the CXCL12 receptor CXCR4, as demonstrated by i) co-immunoprecipitation, ii) confocal microscopy and iii) direct measurement of CXCL12 binding to its receptor. Lastly, blocking anti-CD38 mAbs were successfully used in vivo to interfere with CLL cell recirculation from blood to the lymphoid organs, an event critically controlled by CXCL12. These results represent a first step towards the validation of anti-CD38 mAbs as potential therapeutics for certain CLL patients.

Keywords: gene expression profiling by microarray, CLL, CD31, CD38

overall_design: CLL cells from 10 patients were immediately collected (“basal” profile) or cultured for 5 days in the presence of L-CD31+ transfectants (“L-CD31+” profile) or mock-transfectants, used as controls (“L-mock” profile). Extracted RNA was co-hybridized to arrays representing 41,000 human unique genes and transcripts to define a genome-wide signature of the events taking place after CD31/CD38 interactions.

first: Silvia

last: Deaglio

first: Semra

last: Aydin

first: Tiziana

last: Vaisitti

first: Luciana

last: Bergui

first: Davide

last: Rossi

first: Giovanni

last: D’Arena

first: Lisa

last: Bonello

first: Maurizia

last: Grand

first: Giovanna

last: Chiorino

first: Alberto

last: Horenstein

first: Gianluca

last: Gaidano

first: Fabio

last: Malavasi


title: Effects of haloperidol on zebrafish and fathead minnow gene expression

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

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

sample_organism:
Danio rerio
Pimephales promelas

platform_organism:
Danio rerio
Pimephales promelas


title: Global gene expression profile for pearl oyster

status: Public on Feb 05 2010

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University


title: Profiling of caf1a and caf1b mutants

city: La Jolla

first: Justin

last: Walley

state: CA

address: 9500 Gilman Ave

department: Biological Sciences

institute: UCSD

summary: Identify the genes which are misexpressed in Atcaf1a and Atcaf1b mutants before and in response to mechanical wounding.

overall_design: 3 biological replicates were utilized for every genotype x treatment combination.  All samples were pooled and labeled with cy5 to serve as the reference.

first: Katayoon

last: Dehesh


title: Molecular analysis of glioblastoma stem cell-like spheroid cultures identifies novel tumor-relevant genes

status: Public on Feb 13 2010

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ


title: Sfh and H-NS binding sites in the Salmonella Typhimurium genome

status: Public on Dec 07 2009

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

institute: Moyne Institute of Preventive Medicine

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: A gene-specific requirement of RNA polymerase II CTD phosphorylation on serine 2 for sexual differentiation in fission yeast

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: The switch from cellular proliferation to differentiation occurs to a large extent through specific programs of gene expression. In fission yeast, the master regulator of sexual differentiation, ste11, is induced by environmental conditions leading to mating and meiosis. We show that phosphorylation of serine 2 (S2P) in the C-terminal domain (CTD) of the largest subunit of the RNA polymerase II (PolII) enzyme by the Lsk1 cyclin dependent kinase has only a minor impact on global gene expression during vegetative growth but is critical for the induction of ste11 transcription during sexual differentiation. The recruitment of the Lsk1 kinase initiates in the vicinity of the transcription start site of ste11, resulting in a marked increase of S2P on the ste11 unit including an extended 5’-untranslated region (5’-UTR). This pattern contrasts with the classical gradient of S2P towards the 3’ region. In the absence of S2P, both PolII occupancy at the ste11 locus and ste11 expression are impaired. This results in sterility which is rescued by expression of the ste11 coding sequence from the adh1 promoter. Thus, the S2P polymerase plays a specific, regulatory role in cell differentiation through the induction of ste11.

overall_design: For the ChIP-chip experiments, 3-4 biological replicates were performed for each tagged protein of interest. For the expression experiments, two biological samples were hybridized for each mutant strain (replicates 1 and 2), with two dye-swap technical replicates per sample (replicates 3 and 4).

first: Damien

last: Coudreuse

last: van Bakel

first: Monique

last: Dewez

first: Julie

last: Soutourina

first: Tim

last: Parnell

first: Jean

last: Vandenhaute

first: Brad

last: Cairns

first: Michel

last: Werner

last: Hermand


title: Small fish comp tox ZF haloperidol 96 h ovary

summary: This experiment was conducted as part of an overall study aimed at examining effects of a dopamine receptor antagonist on reproduction, behavior, and gene expression in cyprinid fish.  Relative to gene expression, we hypothesized that if haloperidol disrupted normal regulation of the HPG axis, there may be robust transcriptional alterations in the ovary of exposed females that might serve as useful markers of exposure and/or effects. For the purposes of this study, robust transcriptional alterations were defined as those detected in two separate fish species (fathead minnow and zebrafish), exposed to the same concentration of haloperidol for the same duration.  There is a companion fathead minnow microarray experiment (GSE15115) that these data are compared to.  Transcriptional responses in the ovary of the two species are compared in terms of differentially expressed genes, enriched gene ontology categories they represent, and associated pathways.

overall_design:
Fathead minnow and zebrafish microarray experiment
Samples for microarray analysis were generated in a separate, 96 h, continuous flow-through experiment. Nominal treatment concentrations for the microarray experiment were 0 and 50 μg haloperidol/L. Chemical (or control water) delivery was initiated 24 h prior to adding fish to the tanks. To start the experiment, fathead minnows (4 males, 4 females per tank) were added to each of three tanks per treatment group, while zebrafish (6 males, 6 females per tank) were added to each of two tanks per group. The time of fish addition was staggered by replicate within each treatment such that all samples from a given exposure tank could be collected within 60 min of the intended 96 h exposure duration. After 96 h, male and female zebrafish and female fathead minnows were anesthetized in buffered MS-222 and weighed. Whole gonads were removed, weighed, and preserved in RNAlater.

Aliquots of six ovary RNA samples per treatment group, generally those with greater RIN and three from each replicate tank, were submitted to an Agilent certified facility, MOgene, LC (St. Louis, MO, USA) for microarray analysis, along with a reference pool of RNA prepared from adult male and female zebrafish liver, brain, and gonad tissues (Martinovic et al. 2009).

first: Natalia

last: Garcia-Reyero

first: Dalma

last: Martinovic

first: Nathaniel

middle: D

last: Mueller

first: Jenna

middle: E

last: Cavallin

first: Elizabeth

middle: J

last: Durhan

first: Kathleen

last: Jensen

first: Michael

last: Kahl

first: Lindsey

middle: S

last: Blake

first: Edward

last: Perkins

first: Gerald

middle: T

last: Ankley


title: Gene expression signature predictive of rapid response to imatinib mesylate in Gastrointestinal Stromal Tumor (GIST)

status: Public on Nov 24 2009

city: Baltimore

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

summary: Gene expression profiling using oligonucleotide microarrays performed on tumor samples obtained before and after imatinib mesylate (IM) therapy.  Rapid responding (to IM) samples were compared to non-responding/stable disease samples as measured by CT scan measurements to identify a gene signature that can predict rapid response to IM.

overall_design: 54 samples, 29 pre-treatment biopsy samples, 25 post-treatment/post-surgery tumor samples from Gastrointestinal Stromal Tumors

first: Andrew

last: Godwin

first: Lori

last: Rink

first: Yuliya

last: Skorobogatko

last: Kossenkov


title: Murine lung tumors- HER2(V659E) and KRAS(G12V) vs normal lung

status: Public on Dec 01 2009

city: Cambridge

first: James

last: Abraham

state: MA

address: 75 Sidney Street

department: Bioinformatics

institute: AVEO Pharmaceuticals

summary: Transcriptiional profling of 13 normal lung samples, 18 lung KRAS(G12V) tumor samples, and 18 lung HER2(V659E) tumor samples

overall_design: 13 normal lung samples, 18 lung KRAS(G12V) tumor samples, and 18 lung HER2(V659E) tumor samples hybridized against Stratagene universal mouse reference RNA with dye swap

first: Yinghui

last: Zhou

first: William

middle: M

last: Rideout III

first: Angela

last: Bressel

first: Shailaja

last: Reddypalli

first: Joerg

last: Heyer


title: Genome-wide transcriptional profiling of Nf1-haploinsufficiency

status: Public on Nov 30 2009

city: Bethesda

first: Alexander

last: Pemov

address: 49 Convent Drive

institute: National Institutes of Health

overall_design: Refer to individual Series


title: Comparative transcriptome and phenotype analysis of acid-stressed Bacillus cereus strains

status: Public on Nov 25 2009

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

department: ATV

institute: Wageningen University

platform_organism:
Bacillus cereus ATCC 10987
Bacillus cereus ATCC 14579