title: PTHRP/Adenylate cyclase promotes parietal whereas Wnt/β-catenin signaling promotes visceral endoderm differentiation of rat XEN cells.

city: Berlin

first: Ilya

last: Chuykin

address: Robert-Rossle str 10

department: Molecular Biology of Peptide Hormones

institute: Max-Delbruck Center for Molecular Medicine

summary: In this study we showed that rat XEN cells grown in the presence of a GSK3 inhibitor exhibited enhanced formation of cell contacts and decreased motility. In contrast, treatment with forskolin induced the PE formation and epithelial-mesenchymal transition (EMT) in rat XEN cells. Using microarray and real-time PCR assays, we found that VE versus PE formation of rat XEN cells was correlated with change in expression levels of VE or PE marker genes.  Similar to forskolin, EMT was prompted upon treatment of rat XEN cells with recombinant parathyroid hormone related peptide (PTHRP), an activator of the cAMP pathway in vivo. Taken together, our data suggest that rat XEN cells are PrE-like cells. The activation of Wnt pathway in rat XEN cells leads to the acquisition of VE characteristics, whereas the activation of the PTHRP/cAMP pathway leads to EMT and the formation of PE.

overall_design: Rat XEN cells were cultured in four different conditions with 3 parallels for each condition: (1-3) without treatments control, (4-6) 2 days treated with CHIR alone, (7-9) 1 day treated with CHIR and 1 day with both CHIR and forskolin, and (10-12) 1 day treated with forskolin alone. In all samples on DAY1 cells were plated, at DAY2 cells were cultured in usual conditions (DMEM F12 medium and 10% Fetal Bovine Serum, both from Sigma) and inhibitor of GSK3 kinase  3 μM CHIR99021 (Axon Medchem) was added in samples 4-9. On DAY3 all cells were cultured in medium with 0.1% serum to exclude the influence of serum and in CONTROL (1-3) cells were cultured without experimental treatments, in CHIR (4-6) cells were further cultured with  3 μM CHIR99021, in CHIR plus FORSKOLIN cells were cultured with  3 μM CHIR99021 and 10μM Forskolin (Sigma), in FORSKOLIN cells were cultured for 1 day with 10 μM Forskolin. On DAY4 RNA was isolated.

first: Herbert

last: Schulz

first: Kaomei

last: Guan

first: Michael

last: Bader


title: Transcriptome analysis of MDS42 and MG1655

status: Public on Feb 01 2013

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

type: Expression profiling by genome tiling array

summary: A genome reduced E. coli strain MDS42 and its parent strain MG1655 were applied for the comparative transcriptome analysis. Genome-wide transcriptional changes due to genome reduction and heat shock were comprehensively evaluated.

overall_design: The target strains exponetially grown in the minimal media were collected for the transcriptome analysis. Every 7 and 3 biological replications for the steady growth and  heat shock conditions were performed, respectively. Cell growth was strictly controlled.

first: Tetsuya

last: Yomo


title: Genes associated with prostate cancer are differentially expressed in African American and European American men (matched normal specimens)

status: Public on Jan 31 2013

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

country: USA

institute: Karmanos Cancer Inst., Wayne State University

summary: A total of 1,507 probes measured the expression of 517 genes on the custom Illumina DASL assay testing if select genes showed cancer-specific differential expression according to race. Genes were chosen for inclusion in the assay based on existing evidence from the literature and our own data for their importance to prostate cancer, prostate cancer aggressiveness, or cancer in general

overall_design: 163 FFPE tumor matched normal (control) samples (80 African American, 83 European American) were assayed

first: Greg

last: Dyson

first: Isaac

middle: J

last: Powell


title: Genes associated with prostate cancer are differentially expressed in African American and European American men (tumor specimens)

summary: A total of 1,507 probes measured the expression of 517 genes on the custom Illumina DASL assay testing if select genes showed cancer-specific differential expression according to race. Genes were chosen for inclusion in the assay based on existing evidence from the literature and our own data for their importance to prostate cancer, prostate cancer aggressiveness, or cancer in general.

overall_design: 639 FFPE tumor samples (270 African American, 369 European American)


title: Genes associated with prostate cancer are differentially expressed in African American and European American men

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

overall_design: Refer to individual Series


title: E12.5 Murine lateral cortical progenitor cells:  Pax6sey/sey vs. Pax6+/+

city: Edinburgh

first: Ian

last: Simpson

address: 10 Crichton Street

department: Institute for Adaptive and Neural Computation

country: United Kingdom

institute: University of Edinburgh

summary: The mechanisms by which the early spatiotemporal expression patterns of transcription factors such as Pax6 regulate the region-specific proliferation rates of neural progenitors are poorly understood. Pax6 is expressed in a gradient across the developing cortex and is essential for normal corticogenesis. We found that constitutive or conditional loss of Pax6 increases cortical progenitor proliferation by amounts that vary regionally with normal Pax6 levels. We compared the gene expression profiles of equivalent Pax6-expressing progenitors isolated from Pax6+/+ and Pax6-/- cortices and identified many negatively-regulated cell cycle genes including those encoding Cyclins and Cdks. Biochemical assays indicated that Pax6 directly represses Cdk6 expression. Cyclin/Cdk repression inhibits retinoblastoma protein (pRb) phosphorylation, thereby limiting the transcription of genes directly promoting mitosis, and we showed that Pax6 inhibits pRb phosphorylation and represses several genes involved in DNA replication. Our results indicate that Pax6’s modulation of the cell cycles of cortical progenitors is regional and direct.

overall_design: Two condition experiment, Pax6sey/sey vs Pax6+/+ cortical progenitor cells from lateral cortex.  3 biological replicates.  Each replicate contains RNA from cells pooled from 4 individual E12.5 embryos

first: David

last: Price

first: T

middle: I


title: Stochastic genome - nuclear lamina contacts are linked to histone H3K9 dimethylation (methylation data)

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

type: Methylation profiling by genome tiling array

summary: The nuclear lamina (NL) interacts with hundreds of large genomic regions termed lamina-associated domains (LADs). The dynamics of these interactions and the relation to epigenetic modifications are poorly understood. We visualized the fate of LADs in single cells using a novel 'molecular contact memory' approach. In each interphase nucleus, only ~30% of LADs are positioned at the periphery; these LADs are in intermittent molecular contact with the NL but remain constrained to the periphery. Upon mitosis, LAD positioning is not detectably inherited but instead is stochastically reshuffled. Contact of individual LADs with the NL correlates with their degree of H3K9 dimethylation in single cells, and inactivation of the H3K9 methyltransferase G9a reduces the NL contact frequencies. These results indicate that nuclear positioning and histone modification of LADs are both stochastic yet linked in single cells. Collectively, these results highlight principles of the dynamic spatial architecture of chromosomes.

overall_design: LaminB1-chromatin interactions were assayed in human HT1080 cells by induction of Dam_LMNB1 expression in a stable cell line with shield1.

first: Jop

last: Kind

first: Ludo

last: Pagie

first: Havva

last: Ortabozkoyun

first: Shelagh

last: Boyle

first: Wendy

last: Bickmore


title: Testosterone differentially affects expression in the hypothalamus and the ventromedial telencephalon (VmT) of Juncos; Potential for sexual conflict assessed via testosterone-mediated transcriptional changes in peripheral tissues of a songbird

status: Public on Jan 30 2013

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary:
Despite sharing much of their genomes, males and females are often highly dimorphic, reflecting at least in part the resolution of sexual conflict in response to sexually antagonistic selection. Sexual dimorphism arises owing to sex differences in gene expression, and steroid hormones are often invoked as a proximate cause of sexual dimorphism. Experimental elevation of androgens can lead to masculinization of behavior, physiology, and gene expression, but knowledge of the role of hormones remains incomplete, including how the sexes differ in their gene expression in response to exposure to hormones. We addressed these questions in a bird species with a long history of behavioral endocrinological and ecological study, the dark-eyed junco (Junco hyemalis), using a species-specific microarray. Focusing on two brain regions involved in sexually dimorphic behavior and regulation of hormone secretion, we identified 1,639 genes that differed in expression by sex in the ventromedial telencephalon and 768 in hypothalamus. In response to experimentally elevated testosterone, females exhibited a more “male-like” expression pattern than control females; unexpectedly, male expression patterns became more “female-like” rather than hyper-masculinized when compared to control males. This sex difference in pattern arose both because testosterone altered regulation of different genes in each sex and because testosterone altered regulation of the same genes differentially, i.e., up in one sex, down in the other. Hormonally regulated gene expression is a key genetic and physiological mechanism underlying sexual dimorphism, and further study should help to explain how it relates to the resolution of sexual conflict.

Males and females can be highly dimorphic in metabolism and physiology despite sharing nearly identical genomes, and males and females both respond phenotypically to elevated testosterone, a steroid hormone that alters gene expression. Only recently has it become possible to learn how a hormone like testosterone affects global gene expression in non-model systems, and whether it affects the same genes in males and females. To investigate the transcriptional mechanisms by which testosterone exerts its metabolic and physiological effects on the periphery, we compared gene expression by sex and in response to experimentally elevated testosterone in a well-studied bird species, the dark-eyed junco (Junco hyemalis). We identified 324 genes in the liver, and 733 in the pectoralis muscle that were differentially expressed between males and females. In addition, we identified 1,872 genes that were differentially expressed between testosterone-treated and control individuals in at least one tissue and sex. Testosterone-treatment altered the expression of only130 genes in both males and females in the same tissue. These substantial differences in transcriptional response to testosterone suggest that males and females may employ different pathways when responding to elevated testosterone, despite the fact that many phenotypic effects of experimentally elevated testosterone are similar in the sexes. In contrast, of the 130 genes that were affected by testosterone-treatment in both sexes, 78% were regulated in the same direction (e.g. either higher or lower in testosterone-treated than control males and females). Thus, it appears that testosterone acts through both unique and shared transcriptional pathways in males and females, suggesting multiple mechanisms by which sexual conflict can be mediated.

overall_design:
Hypothalamus: 24 samples were analyzed; all were biological (not technical) replicates. 6 from males treated with testosterone [MT], 6 from control males [MC], 6 from females treated with testosterone [FT], and 6 from control females [FC]. All hybridizations were paired, and all treatment groups were compared, but no sample was analyzed more than once.

Ventromedial telencephalon: 24 samples were analyzed; all were biological (not technical) replicates. 6 from males treated with testosterone [MT], 6 from control males [MC], 6 from females treated with testosterone [FT], and 6 from control females [FC]. All hybridizations were paired, and all treatment groups were compared, but no sample was analyzed more than once.

Liver: 24 samples were analyzed; all were biological (not technical) replicates. 6 from males treated with testosterone, 6 from control males, 6 from females treated with testosterone, and 6 from control females. All hybridizations were paired, and all treatment groups were compared, but no sample was analyzed more than once.

Pectoralis: 24 samples were analyzed; all were biological (not technical) replicates. 6 from males treated with testosterone, 6 from control males, 6 from females treated with testosterone, and 6 from control females. All hybridizations were paired, and all treatment groups were compared, but no sample was analyzed more than once.

first: Mark

middle: P

last: Peterson

first: Kimberly

middle: A

last: Rosvall

first: Jeong-Hyeon

last: Choi

first: Charles

last: Ziegenfus

first: Haixu

last: Tang

first: John

middle: K

last: Colbourne

first: Ellen

middle: D

last: Ketterson


title: time course expression profile of ap1-cal after induction of an ap1-transgene-Time course of meiotic gene expression in Arabidopsis

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: rs11-09_meotic - time course expression profile of ap1-cal after induction of an ap1-transgene - CDKs are major regulators of the mitotic as well as the meiotic cell cycle. In comparison with the mitotic cell cycle much less is known about the regulation of meiosis, especially in plants. One of the reasons for this is the very low abundance and the difficult accessibility of cell undergoing meiosis. We have developed a system to enrich for meiocytes. This will be the material with which we will search for CDK substrates in a biochemical approach. To first get an overview about the meiotic genes expressed in this system, we want to perform here a time series at four time points after the induction that leads to the synchronized development of meiocytes. The in the microarray identified genes, will then set the frame for the upcoming biochemical experiments. - An ap1-cal double mutants carrying an Glucocorticoid-receptor fusion to AP1 was indcued and samples were collected 2 days after induction (dai), 8dapi, 9dai, 10dai and 11dai. Then, the expression profile of 2dai were compared with 8dai, 8 with 9, 9 with 10, and 10 with 11.

overall_design: 12 dye-swap - time course

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Arp

last: Schnittger

first: Marie-Laure

last: Martin-Magniette


title: Identification of inflammation-related microRNAs deregulated in the plasma from intracerebral hemorrhage patients

status: Public on Jan 19 2013

city: Jinan

first: Fan

last: Jiang

state: Shandong

address: 107 Wen Hua Xi Road

country: China

institute: Shandong University

summary: We tested the hypothesis that circulating microRNAs (miRNAs) present in plasma might display a specific signature in patients with intracerebral hemorrhage (ICH). Global miRNA profiles were determined with the Agilent Human miRNA Microarray platform, 027233. ICH patients display a characteristic inflammation-related miRNA profile as compared to healthy controls.

overall_design: Plasma samples were collected from the following 6 subject groups: male ICH patients (n=8), female ICH patients (n=7), male healthy control (n=4), female healthy control (n=4), male ischemic stroke patients (n=8) and female ischemic stroke patients (n=8). Total RNAs isolated from 1 ml plasma were pooled for each group. A fixed volume of RNA sample was withdrawn from each pool and used for microarray detection.

first: Dong

last: Guo

first: Junni

last: Liu

first: Weihua

last: Wang

first: Fang

last: Hao

first: Xuedong

last: Sun

first: Xiao

last: Wu

first: Peili

last: Bu

first: Yun

last: Zhang

first: Yu

first: Fengqing

first: Qunye


title: miRNA expression during in vitro mouse T cell activation (D011.10+ CD4 T cells)

status: Public on Jan 27 2013

city: San Francisco

first: Andrea

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: Array of global miRNA expression during an in vivo effector and anergic T cell response

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 250 ng RNA isolated from mouse D011.10+ CD4 T cells, activated in vivo for 5 days

first: Yelena

last: Bronevetsky

first: Alejandro

last: Villarino

first: K

middle: M

last: Ansel


title: Gene Expression between two cell layers in maize shoot apical meristem

status: Public on Jan 28 2013

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

type: Expression profiling by high throughput sequencing

summary: All above ground organs of higher plants are ultimately derived from shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, and monocot SAMs such as maize are comprised of two cell layers, a single cell layered tunica (L1) and a corpus (L2).  Although recent research has revealed roles of these cell layers in the SAM, intra- and inter-cell-layer signaling networks involved in organ development remain largely unknown except for a few differentially expressed genes. Here, we used Illumnia technology to conduct RNA-seq of L1 and L2 cell layers in maize B73 maize shoot apical meristem.

overall_design:
Single sequencing library was constructed for L1 and L2 cell layer. Each library was sequenced using 2 lanes on a Solexa flow cell.
Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.

first: Yi

last: Jia

first: Kazuhiro

last: Ohtsu

middle: S


title: Comparative Transcriptional Profiling of the Axolotl Limb Identifies a Tripartite Regeneration-Specific Gene Program

status: Public on Jan 01 2013

city: Dresden

first: Dunja

last: Knapp

address: Fetscherstraße 105

country: Germany

institute: DFG-Center for Regenerative Therapies Dresden

summary: Identifying the genetic program that induces limb regeneration in salamanders is an important resource for regenerative medicine, which currently lacks tools to promote regeneration of functional body structures.  The genetic network underlying limb regeneration has been elusive due to the complexity of the injury response that occurs concomitant to blastema formation.  Here we performed parallel expression profile time courses of non-regenerative lateral wounds versus amputated limbs in axolotl.  We show that limb regeneration occurs in three distinguishable phases--early wound healing followed by a transition phase leading to establishment of the limb development program.  By focusing on the transition phase, we identified 93 strictly regeneration-associated genes involved in oxidative stress response, chromatin modification, epithelial development and limb development.  The specific expression of the genes was confirmed by in situ hybridization.  Regeneration-specific expression databases are critical resources for understanding how regeneration-relevant phenotypes can be induced from adult cells

overall_design: Regeneration of the axolotl forelimb lower arm was compared with the healing of a deep lateral injury in a high density timecourse (uncut, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h and 528h after injury).  Three independent biological replicates were performed using separate clutches of animals. Amputated and lateral wound samples were made as matched contralateral samples of four pooled animals per timepoint.

first: Herbert

last: Schulz

first: Cynthia

last: Rascon

first: Michael

last: Volkmer

first: Juliane

last: Scholz

first: Eugen

last: Nacu

first: Mu

last: Le

first: Sergey

last: Novozhilov

first: Akira

last: Tazaki

first: Stephanie

last: Protze

first: Tina

last: Jacob

first: Norbert

last: Huebner

first: Bianca

last: Habermann

first: Elly

last: Tanaka


title: Transcriptome profiling of Botrytis cinerea  conidial germination reveals upregulation of infection-related genes during the pre-penetration stage

status: Public on Jan 18 2013

city: Kaiserslautern

first: Michaela

last: Leroch

department: Phytopathology

institute: University of Kaiserslautern

summary: Investigation of whole genome gene expression level changes in Botrytis cinerea wild type conidia during germination in comparison to the bmp1 MAP kinase deletion mutant.

platform_organism:
Botrytis cinerea B05.10
Botrytis cinerea T4

overall_design: A 18 chip study using total RNA recovered from four different time points for the wild-type and one time point for the bmp1 deletion mutant. Each time point was analyzed with three biological replicates. Expression level of 20,885 genes from Botrytis cinerea strain B05.10 and T4 with three 60mer probes per gene was analysed.

first: Astrid

last: Kleber

first: Evelyn

last: Silva

last: Coenen

first: Dieter

last: Koppenhöfer

first: Amir

last: Shmaryahu

first: Pablo

last: Valenzuela

first: Matthias

last: Hahn


title: Gene expression profiling of Fast vs. Slow Chinese Hamster Ovary cell lines using Wye3aHamster array

city: Dublin

first: Padraig

last: Doolan

address: Glasnevin

country: Ireland

institute: Dublin City University

summary: A 3rd generation Wye3aHamster microarray chip was used to carry out a differential expression microarray study of a panel of 30 slow- and fast-growing production cell lines, identifying a priority list of 240 transcripts  (110 Up; 130 Down) that passed a statisical filter (ANOVA p-value <0.05, 1.3 fold-change) when the samples were grouped into fast versus slow and pairwise compared and a minimum Pearson Correlation Coefficent (PCC) of >0.7 when growth rate was used as a continuous variable (i.e. included genes have to satisfy BOTH criteria, not just one). This yielded a list of 240 genes. The 240-member genelist yielded 223 Annotated IDs, 203 of which are Unique and all of which are associated with contributing to a high rate of growth in production CHO cell lines.

overall_design: Prospective samples were isolated from 2 distinct groups of clones (slow growers and fast growers), all chosen from the same project (transfection of product transgene into parent line) generated at Pfizer Inc., Bioprocess R&D, Andover, MA, USA. Each group comprised 5 distinct clones, all of which had comparable Qp characteristics. The clones were passaged for 3 or 4 passages over 3-4 days to stabilise the phenotype and freeze stocks. Samples for array hybridization were generated in batch shake flask culture (60ml working volume) with AS1 medium and without feeds or temperature shift. Samples were collected at a single time point (72hrs - mid/late log) and each clone was grown in triplicate flasks, yielding a total of 30 samples for collection and processing. Two bioprocess-relevant variables, viable cell density (VCD) and viability were measured. From the VCD, the growth rate (h-1) was calculated.

first: Doolan

last: Padraig

first: Clarke

last: Colin

first: Aherne

last: Sinead

first: Barron

last: Niall

first: Breen

last: Laura

first: Kinsella

last: Paula

first: Leonard

last: Mark

first: Clynes

last: Martin


title: Baseline NSCLC cell lines compared to a reference mix consisting of 45 NSCLC cell lines

city: Santa Monica

first: Habib

last: Hamidi

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

summary: 34 NSCLC cell lines were transcriptionally profiled against a reference mix of 45 NSCLC cell lines to look subtype specific differential gene expression

overall_design: 34 individual cell lines were compared to a reference mix consiting of 45 NSCLC cell lines

first: Edward

last: Garon

first: Judy

last: Dering

first: Sharon

last: Pitts

first: Naeimeh

last: Kamranpour

first: Richard

last: Finn

first: Amrita

last: Desai

first: Wylie

last: Hosmer

first: Susan

last: Ide

first: Emin

last: Avsar

first: Michael

last: Jensen

first: Cornelia

last: Quadt

first: Manway

last: Liu

first: Steven

last: Dubinett

first: Dennis

last: Slamon


title: Role of enterotoxins in the induction of early immune responses and small-intestinal secretion in ETEC-infected piglets

status: Public on Jan 02 2013

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Enterotoxigenic Escherichia coli (ETEC) strains that produce both heat-stable (ST) and heat-labile (LT) enterotoxins cause severe post-weaning diarrhea in piglets. However, the relative importance of the individual enterotoxins to the pathogenesis of ETEC infection is poorly understood. In this study, we investigated the effect on virulence of an F4+ ETEC strain when removing some or all of its enterotoxins. Several isogenic mutant strains were constructed that lack the expression of LT in combination with one or both types of ST enterotoxins (STa and/or STb). Host early immune responses induced by these mutant strains 4h after infection were compared to the wild type strain GIS26  (O149:F4ac+,  LT+  STa+  STb+). At the same time, the immune response of this wild type ETEC strain was compared to the mock-infected control, demonstrating the expression of porcine inflammatory response genes. For these purposes, the small intestinal segment perfusion (SISP) technique and microarray analysis were used and results were validated by qRT-PCR. We also measured net fluid absorption of pig small intestinal mucosa 4h after infection with wild type ETEC, the mutant strains and PBS (mock-infected). These data indicate an important role for STb in inducing small intestinal secretion early after infection. The microarray analysis of the different mutant strains also revealed an important role for STb in ETEC-induced immune response by the significant differential regulation of immune mediators like matrix metalloproteinase 3, interleukin 1 and interleukin 17. We conclude that STb can play a prominent role in ETEC-induced secretion and early immune response.

overall_design: In three pigs, 6 different treatments were performed. These treatments consisted of 4 mutant enterotoxigenic Escherichia coli GIS26 strains, GIS26 wild type strain, or PBS control. Per pig, the small intestine was divided into 6 loops with an interloop in between to avoid cross-contamination. In conclusion, every pig received each of the 6 treatments ad random.

first: Michaela

last: Loos

first: Marisa

last: Geens

first: Stijn

last: Schauvliege

first: Frank

last: Gasthuys

first: Bruno

last: Goddeeris

first: Theo

last: Niewold

first: Eric

last: Cox


title: Gene expression from healthy male and female porcine aortic valve leaflets

city: Madison

first: Kristyn

last: Masters

email: kmasters@wisc.edu, cmccoy2@wisc.edu

state: WI

address: 1550 Engineering Drive, 2152 ECB

department: Biomedical Engineering

institute: UW-Madison

summary: Calcific aortic valvular disease (CAVD) is characterized by sclerosis of the aortic valve leaflets and recent clinical studies have linked several other risk factors to this disease, including male sex.  In this study we examined potential sex-related differences in gene expression profiles between porcine male and female valvular interstitial cells (VICs) to explore possible differences in CAVD propensity on the cellular level.

overall_design: RNA samples from three male and three female healthy porcine aortic valve leaflets (denuded of endothelial cells) were isolated, processed, and hybridized to Affymetrix® GeneChip Porcine Genome microarrays according to manufacturer’s instructions.  Mean expression values of each probe set in the male samples were compared with those in the female samples.

first: Chloe

last: McCoy

first: Dylan

middle: Q

last: Nicholas


title: Transcriptome of DTAC-resistant Salmonella Enteritidis

status: Public on Dec 31 2012

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Screen for differences in gene expression between a parental Salmonella enterica serovar Enteritidis strain (ATCC4931) and an adapted strain with increased resistance to the widely used antimicrobial sanitizer dodecyltrimethylammonium chloride (DTAC)

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Time course of comparative gene expression changes between log phase parental and adapted Enteritidis strains after 0, 10, 30 and 150 min of exposure to 50% of the respective MIC of DTAC.

first: Steffen

last: Porwollik

first: Jonathan

middle: G

last: Frye

first: Megan

last: Kautz

first: Diane

last: Herson


title: Transgenic mice overexpressing Neuregulin-1 model neurofibroma-malignant peripheral nerve sheath tumor progression and implicate specific chromosomal copy number variations in tumorigenesis.

city: Birmingham

first: Steven

middle: L

last: Carroll

state: AL

address: SC930Ge, 1720 7th Ave South

department: Pathology

institute: University of Alabama at Birmingham

summary: Patients with neurofibromatosis type 1 (NF1) develop benign plexiform neurofibromas that frequently progress to become malignant peripheral nerve sheath tumors (MPNSTs).  A genetically engineered mouse model that accurately models plexiform neurofibroma-MPNST progression would facilitate the identification of somatic mutations driving this process.  We have previously reported that transgenic mice overexpressing the growth factor neuregulin-1 in Schwann cells (P0-GGFβ3 mice) develop MPNSTs.   To determine whether P0-GGFβ3 mice accurately model neurofibroma-MPNST progression, cohorts of these animals were followed to death and necropsied.  94% of the mice developed multiple neurofibromas, with 70% carrying smaller numbers of MPNSTs; nascent MPNSTs were identified within neurofibromas, suggesting that these sarcomas arise from neurofibromas.  Although neurofibromin expression was maintained, P0-GGFβ3 MPNSTs, like human NF1-associated MPNSTs, demonstrated Ras hyperactivation.  P0-GGFβ3 MPNSTs also showed abnormalities in the p16INK4A-cyclin D/CDK4-Rb and p19ARF-Mdm-p53 pathways analogous to their human counterparts.  Array comparative genomic hybridization (CGH) demonstrated reproducible chromosomal alterations in P0-GGFβ3 MPNST cells (including universal chromosome 11 gains) and focal gains and losses affecting 39 genes previously implicated in neoplasia (e.g., Pten, Tpd52, Myc , Gli1, Xiap, Bbc3/PUMA).  Array CGH also identified recurrent focal copy number variations affecting genes not previously linked to neurofibroma or MPNST pathogenesis.  We conclude that P0-GGFβ3 mice represent a robust model of neurofibroma-MPNST progression that can be used to identify novel genes driving neurofibroma and MPNST pathogenesis.

overall_design: Array CGH comparison of malignant peripheral nerve sheath tumor (MPNST) cells vs non-neoplastic Schwann cells

first: Syed

last: Kazmi

first: Stephanie

last: Byer

first: Jenell

last: Eckert

first: Amy

middle: N

last: Turk

first: Richard

last: Huijbregts

first: Nicole

last: Brossier

first: William

middle: E

last: Grizzle

first: Fady

last: Mikhail

first: Kevin

last: Roth


title: The rpoS transcriptome of Pseudomonas protegens Pf-5 grown in rich medium

city: Corvallis

first: Joyce

last: Loper

state: OR

address: 3420 NW Orchard Ave

department: Horticultural Crops Research Laboratory

institute: USDA-ARS

summary: Transcriptomic profiling of an rpoS mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown in nutrient broth supplemented with 1% glycerol to OD600=2.0-2.4 (early stationary phase).

overall_design: Two-condition experiment, the rpoS mutant compared to wild-type Pf-5 grown in nutrient broth supplemented with 1% glycerol to early stationary phase.  There are three biological replicates and two flip-dye replicates for a total of six slides analyzed.  Each slide contains three replicate spots per gene.

first: Teresa

last: Kidarsa

first: Brenda

middle: T

last: Shaffer

first: Aaron

last: Johnson

first: Ian

last: Paulsen


title: Gene Regulation of Intestinal Porcine Epithelial Cells IPEC‑J2 is Dependent on the Site of Deoxynivalenol Toxicological Action

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
Here we analysed different mechanisms of apical and basolateral deoxynivalenol (DON) toxicity reflected in the gene expression.
We used the jejunum derived, polarized intestinal porcine epithelial cell line IPEC‑J2 as an in vitro cell culture model. Luminal and blood stream DON intoxication was mimicked by a DON application from the apical or basolateral compartment of ThinCert® membrane inserts for 72 h.

overall_design: We compared the genome wide gene expression of untreated and DON-treated IPEC-J2 cells by the GeneChip® Porcine Genome Array of Affymetrix.

first: Anne-Kathrin

last: Diesing

first: Constanze

last: Nossol

first: Siriluck

last: Ponsuksili

first: Jeannette

last: Kluess

last: Walk

first: Andreas

last: Post

first: Hermann-Josef

last: Rothkötter

first: Stefan

last: Kahlert


title: Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS

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

overall_design: Refer to individual Series


title: Transcriptional response to tetanus vaccination in porcine PBMCs

summary: Three groups of German Landrace piglets were vaccinated with tetanus toxoid. Transcriptome profiles of PBMC were analysed from blood samples taken 0, 2, 4, 8, 24 and 75 hours after a first vaccination and 0, 2, 4, 8, 24 and 75 hours as well as 14 d after a second vaccination on day 14.

overall_design: pair wise comparison of 0 hours to the respective time points after each vaccination

first: Marcel

last: Adler

first: Eduard

last: Murani


title: Global transcriptome analysis of mammary tissue during fetal bud formation and growth in two pig breeds

summary:
The mammary gland development in swine begins at embryogenesis. The number and identity of relevant genes are unknown.
Simultaneously, 24,123 probe-sets were screened, of which some 12,000 had present calls and were analysed for differential expression between different breeds (german landrace and pietrain) at different stages of development ( 63 and 91 dpc)

overall_design: RNAs of teat from german landrace and pietrain at 63 and 91 dpc were hybridized to Affymetrix Porcine Genome Arrays.

first: Kunsuda

last: Chomwisarutkun


title: Endogenous hairpins-ir71 targets : Gene profiling of Turnip Crinkle Virus (TCV) siRNA in mutants.

first: Soubigou-Taconnat

last: Ludivine

summary:
gnp06-03_microtrac
Endogenous hairpins-ir71 targets
What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in diferent mutants?
Lines IR71 KO n°3 and Col-0 were grown on soil until bolting, Flower buds were then harvested and RNA extracted with Qiagen RNeasy Plant mini kit. RNA was stored at -20°C.

overall_design: 3 dye-swap - gene knock out

first: Virginia

last: Ruiz-Ferrer

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Identification of Yeast Genes that Confer Resistance to Chitosan Oligosaccharide (COS) Using Chemogenomics

status: Public on Dec 22 2012

city: Bethesda

first: Maria

middle: de los Angeles

last: Jaime

state: Maryland

address: 50 South Drive, National Institutes of Health

department: NIDDK - LCDB

institute: NIH

summary:
Abstract: Chemogenomic fitness assays were combined with a transcriptome analysis to understand both the mode of action and the mechanisms of resistance to Chitosan oligosaccharides (COS).  COS are deacetylated chitin compounds, with antimicrobial properties, that are presumed to act by disrupting the cell membrane. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity.  The genes identified encode membrane proteins and members of the protein degradation/ proteosome pathway. The transcriptomes of wild-type and five suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and furthermore, treatment with environmental stressors does not provide resistance to COS.  Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the RAS signal transduction pathway.  Down-regulated transcripts included those encoding protein folding components, and respiratory chain proteins. Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to amphotericin B, fluconazole and terbinafine as the wild-type (vector control).  The gene targets of COS identified in this study suggest that COS’s mechanism of action is different from other commonly studied fungicides, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens.
We selected the 5 overexpressing strains based on the characteristics of the genes. ARL1, encoding a GTPase and is involved in membrane trafficking, was selected since it was observed in the HIP-HOP assay as a sensitive homozygous deletion strain and in the MSP assay as multicopy suppressor. The rest of selected overexpressing strains were BCK2 and MSG5, involved in cell integrity pathways, ERG24 in ergosterol synthesis, and RBA50 in transcription. BCK2 is a Ser-Thr rich protein with protein kinase C activity that acts in signal transduction. Overexpression of BCK2 can rescue defects in yeast cwh43Δ, which displays several cell wall defects [29]. BCK2 overexpression also can suppress a cell lysis defect of mpk1Δ and pck1Δ [30]. MSG5 is also involved in signal transduction. This gene encodes a protein phosphatase involved in cell cycle control through the dephosphorylation of MAPK and is indispensable for restricting the signaling by the cell integrity pathway in yeast [31]. The inhibition of MAPK signaling leads to inhibition of cell differentiation and cell division [32].  The functions of ARL1 and ERG24 and their potential roles in chitosan resistance will be described in more detail in the Discussion. To gain a further understanding on the mode of action and mechanisms of resistance to COS, we performed a transcriptome analysis of the above mentioned five overexpressing strains known to increase resistance to COS-5.44. Each overexpressing strain and the wild type (vector control) were treated with COS-5.44 and RNAs isolated from both treated and untreated cells. The RNAs were converted to labeled cDNA and hybridized to NimbleGen expression microarrays (see Methods).

overall_design: Three cDNA biological replicates either with or without a 60 minutes exposure to COS-5.44 for each of the five overexpressing strains as well as an untransformed wild type BY4743 cells (vector control; for a total of 36 samples) were hybridized to NimbleGen 4X72k microarrays (Roche NimbleGen, Inc. Design ID A6186-00-01, TI4932 60mer expr X4).

first: Luis

middle: V

last: Lopez-Llorca

first: Ana

last: Conesa

first: Anna

last: Lee

first: Guri

last: Giaever

first: J

last: Westwood

first: Corey

last: Nislow


title: The rpoS transcriptome of Pseudomonas protegens Pf-5 growing on pea seed surfaces

first: Joyce

last: Loper

summary: Transcriptomic profiling of an rpoS mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown on pea seed surfaces for 24h.

overall_design: Two-condition experiment, the rpoS mutant compared to wild-type Pf-5 grown on pea seed surfaces for 24 h.  There are three biological replicates and two flip-dye replicates for a total of six slides analyzed.  Each slide contains four replicate spots per gene.

first: Teresa

last: Kidarsa

first: Ian

last: Paulsen


title: The GacA transcriptome of Pseudomonas protegens Pf-5 growing on pea seed surfaces

summary: Transcriptomic profiling of a gacA mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown on pea seed surfaces for 24h.

overall_design: Two-condition experiment, the gacA mutant compared to wild-type Pf-5 grown on pea seed surfaces for 24 h.  There are three biological replicates and two flip-dye replicates for a total of six slides analyzed.  Each slide contains four replicate spots per gene.


title: MicroRNA-138: A Pro-survival OncomiR for Glioma Stem Cells is Associated with Tumor Recurrence [miRNA]

status: Public on Dec 20 2012

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

summary: We report the identification of microRNA-138 (miR-138), as a molecular signature of GSCs and demonstrate a vital role for miR-138 to promote growth and survival of bona fide tumor-initiating cells with self-renewal potential.

overall_design: Total RNA from Glioma Stem Cells and Neural Stem Cells were subjected to microRNA microarray analysis, 3 replicates each.

first: Srikanth

last: Nama


title: Deletion of chromosome 13q and 14q is a common feature of tumors with BRCA2 mutations

status: Public on Nov 23 2012

city: Bordeaux

first: Michel

last: Longy

address: 229 Cours de l'Argonne

department: Genetics

institute: Bergonie Cancer Institute

type: Genome variation profiling by genome tiling array

summary: Genomic profiling to identify common features of breast tumors with BRCA2 mutations.

overall_design: Gene expression data and genomic profiling data were used to identify common features of breast tumors with BRCA2 mutations. The associated expression data and genomic data are either present in Array-express under accession number E-TABM-854 or undergoing submission.

first: Audrey

last: Rouault

first: Richard

last: Iggo

first: Nicolas

last: Sevenet


title: Abrogation of stromal TGF-β signaling induces genetic alterations and SCC development in the neighboring epithelia

status: Public on Dec 06 2012

first: Darawalee

last: Wangsa

state: MD

address: 50 South Drive, Bldg 50, Rm 1408

institute: National Cancer Institute

summary: Specific deletion of Tgfbr2 in FSP1+ fibroblasts (Tgfbr2fspKO) induced development of SCC in forestomach with 100% penetrance. Tgfbr2fspKO mice die by 7 weeks with a median survival of 38 days (Log rank p<0.001). Examination of Tgfbr2fspKO forestomach between embryonic day 16 (E16) and 5 weeks of age suggested that hyperplasia began during week 3 and was followed by dysplasia, carcinoma in situ, and invasive squamous cell carcinoma (SCC). The aim of this study was to elucidate genetic aberrations in the tumor associated stroma and SCC tumor using array comparative genomic hybridization (CGH) analysis. Laser capture micro-dissection was performed using formalin-fixed, paraffin-embedded, 5 week old Tgfbr2fspKO forestomach tissues. Genetic loss of cyclin-dependent kinase inhibitor, Cdkn2a/ p16Ink4A was found in laser captured epithelia of all three Tgfbr2fspKO forestomachs. Surprisingly, no genetic change was seen in the tumor associated stroma. Examination of human esophageal SCC showed a down-regulation of TGFβ receptor 2 (TβRII) in the stromal fibroblasts as well as increased inflammation and DNA damage. Published literature showed that loss of Cdkn2a/p16Ink4A tumor suppressor is the common event in human ESCCs. Our study suggests anti-inflammation may be a new therapeutic option in treating human SCCs with down-regulation of TβRII in the stroma.

overall_design: Laser capture microdissection of Tgfbr2flox/flox (n=3) and Tgfbr2fspKO (n=3) forestomach tissues was performed using an Arcturus XT (Life Technologies, CA, USA). Mouse background strain is C57Bl6.  Frozen tissue sections on PEN membrane frame slides (Applied Biosystems) were H&E stained followed by dehydration using the standard protocol to improve visualization of the cells at the microscope. The epithelia and stroma were identified by morphology, captured using a low-power infrared laser pulse, and transferred onto a cap (Capsure™ Macro LCM Caps, Life Technologies). The DNA was extracted using a QIAamp DNA micro kit (Qiagen, CA, USA). Array-CGH was performed using test DNA from laser captured epithelia and stroma from Tgfbr2fspKO mice. Reference DNA was laser captured from the epithelia of normal forestomach of Tgfbr2flox/flox mice. DNA was labeled with Cy3 (test) or Cy5 (control) fluorescent dyes (Perkin Elmer, MA, USA) according to the BioPrime array CGH genomic labeling protocol (Invitrogen, Carlsbad, CA) and cleaned using Microcon YM-30 filters (Millipore, Billerica, MA). Hybridization was carried out using Mouse Genome CGH Microarray 4x180 K format from Agilent Technologies (Santa Clara, CA) according to CGH Procedures for Genomic DNA Analysis (Agilent Technologies). Slides were hybridized for 20 hours, washed, and scanned with an Agilent microarray scanner. Data was analyzed using Feature Extraction® and CGH Analytics® software packages (Agilent Technologies).

first: B

middle: R

last: Achyut

first: David

last: Bader

last: Robles

last: Wanga

first: Curtis

middle: C

last: Harris

first: Thomas

last: Ried

first: Li

last: Yang


title: In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [NanoString]

status: Public on Nov 02 2012

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: Numerous studies have described the altered expression and the causal role of miRNAs in human cancer. However, to date efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here, we find that Nucleolin (NCL), a major nucleolar protein, post-transcriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, causally involved in breast cancer initiation, progression and drug-resistance. We also show that NCL is commonly overexpressed in human breast tumors, and its expression correlates with that of NCL-dependent miRNAs. Finally, this study indicates that NCL-binding guanosine-rich aptamers affect the levels of NCL-dependent miRNAs and their target genes, reducing breast cancer cell aggressiveness, both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer.

overall_design: HeLa cells were transfected with the control or anti-nucleolin siRNA. After 72hours total RNA was collected and analyzed by NanoString.

first: Flavia

last: Pichiorri

first: Dario

last: Palmieri

first: Luciana

last: De Luca

first: Jessica

last: Consiglio

first: Jia

last: You

first: Alberto

last: Rocci

first: Tiffany

last: Talabere

first: Claudia

last: Pivan

first: Alessandro

last: Lagana

first: Jingwen

last: Guan

first: Pierluigi

last: Gasparini

first: Veronica

last: Balatti

first: Vincenzo

last: Coppola

first: Craig

last: Hofmeister

first: Guido

last: Marcucci

first: John

last: Byrd

first: Stefano

last: Volinia

first: Charles

last: Shapiro

first: Michael

last: Freitas

first: Carlo

last: Croce


title: Role of the Glc7 phosphatase regulatory subunit Ypi1 in progression through mitosis

status: Public on Dec 15 2012

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

summary: Ypi1 is an essential regulator of the Saccharomyces cerevisiae Glc7 protein phosphatase. Although lack of Ypi1 results in a dramatic blockage in the G2/M cell cycle transition, with abnormally shaped large buds and short spindles, the molecular bases for this phenotype are still obscure. We report here that depletion of Ypi1 results in stabilization of the Pds1 securin, suggesting the activation of a G2/M checkpoint. Depletion of Ypi1 in cells deleted for MAD1/MAD2 or RAD9 still resulted in G2/M blockage, in spite that these cells lack key components of the spindle assembly and DNA damage checkpoints signaling, respectively. In contrast, deletion of SWE1, which encodes a protein kinase required for the morphogenesis checkpoint signaling, allowed passage through G2/M and recovery of normal cell morphology, although eventually the cells did not survive. Depletion of Ypi1 caused stabilization of the Swe1 kinase, which resulted in persistent phosphorylation of protein kinase Cdc28 at Y19, a landmark for morphogenesis checkpoint activation. In addition, we observed that lack of Ypi1 lead to depletion of the Cdc11 septin, which explain the failure to form properly assembled septin rings at the bud necks. This defect on septin assembly is likely the origin of the activation of the morphogenesis checkpoint.

overall_design:
Six samples were analyzed: tetO7-ypi1 conditional mutant cells both, in the presence and in the absence of doxycyline for 2, 4 and 6 h.

We compared the expression profile of:
1) tetO7-ypi1 + Dox after 2h vs tetO7-ypi1 – Dox after 2h
2) tetO7-ypi1 + Dox after 4h vs tetO7-ypi1 – Dox after 4h
3) tetO7-ypi1 + Dox after 6h vs tetO7-ypi1 – Dox after 6h

A Dye-swap was carried out for each comparison of samples.

Total number of chips analyzed: 6.

first: Maribel

last: Marquina

first: Ethel

last: Queralt

first: Joaquín

last: Ariño


title: Genomic profiling of lymphomas in Canis lupus familiaris

city: Grand Rapids

first: Marie

last: Mooney

address: 333 Bostwick

institute: VanAndel Institute

summary: Comparative oncology is a developing research discipline that is being used to assist our understanding of human neoplastic diseases.  Companion canines are a preferred animal oncology model due to spontaneous tumor development and similarity to human disease at the pathophysiological level. We use a paired RNA sequencing (RNA-Seq)/microarray analysis of a set of four normal canine lymph nodes and ten canine lymphoma fine needle aspirates to identify technical biases and variation between the technologies and convergence on biological disease pathways.   Surrogate Variable Analysis (SVA) provides a formal multivariate analysis of the combined RNA-Seq/microarray data set. Applying SVA to the data allows us to decompose variation into contributions associated with transcript abundance, differences between the technology, and latent variation within each technology. A substantial and highly statistically significant component of the variation reflects transcript abundance, and RNA-Seq proved more sensitive for detection of transcripts expressed at low levels. Latent random variation among RNA-Seq samples is also distinct in character from that impacting microarray samples. In particular, we observed variation between RNA-Seq samples that reflects transcript GC content. Platform-independent variable decomposition without a priori knowledge of the sources of variation using SVA represents a generalizable method for accomplishing cross-platform data analysis.    We identified genes differentially expressed between normal lymph nodes of disease free dogs and a subset of the diseased dogs diagnosed with B-cell lymphoma using each technology. There is statistically significant overlap between the RNA-Seq and microarray sets of differentially expressed genes. Analysis of overlapping genes in the context of biological systems suggests elevated expression and activity of PI3K signaling in B-cell lymphoma biopsies compared with normal biopsies, consistent with literature describing successful use of drugs targeting this pathway in lymphomas.

overall_design:
RNA was extracted from 10 lymphoma fine needle aspirates attained from companion canines. 4 normal lymph node samples were obtained from a Beagle breeding colony at Pfizer, including two samples that were taken from the same dog but different lymph nodes.
This Series represents the Affymetrix gene expression only, not RNA-Seq referenced above.  RNA-Seq data have been submitted to SRA as SRA059558.

first: Jeffrey

last: Bond

first: Noel

last: Monks

first: Emily

last: Eugster

first: David

last: Cherba

first: Pamela

last: Berlinski

first: Steve

last: Kamerling

first: Keith

last: Marotti

first: Heather

last: Simpson

first: Tony

last: Rusk

first: Waibhav

last: Tembe

first: Christophe

last: Legendre

first: Hollie

last: Benson

first: Winnie

last: Liang

last: Webb


title: Differential Expression in UpSET mutant ovaries

status: Public on Dec 07 2012

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

summary: Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domaincontaining protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin.

overall_design: Total mRNA from wildtype and epic mutant ovaries was extracted, labeled and hyb on a custom tiling arrays. Two biological replicates were performed.

first: Ryan

last: Basom


title: Chip-chip from undifferentiated and neuron-differentiated hMSCs cells with EZH2

status: Public on Dec 05 2012

city: Taichung

first: chanshiou

last: Wu

address: No6,Hsueh-shih road

country: Taiwan

institute: china medical university

type: Genome binding/occupancy profiling by genome tiling array

summary:
EZH2 plays an important role in stem cell renewal and maintenance by inducing gene silencing via its histone methyltransferase activity. Previously, we showed EZH2 downregulation markedly enhances neuron differentiation of human mesenchymal stem cells (hMSCs).
To understand how EZH2 regulates neuron differentiation of hMSCs, we wanted to identify the target genes of EZH2. For this reasons we performed ChIP-on-chip experiments using specific EZH2 antibodies followed by a human promoter array for the whole human genome.

overall_design: The 3A6-hMSCs were differentiated into neuron for 5 days, and then 109 cells were harvested for the ChIP-on-chip assay. The procedure was based on the manufacturer's instructions (NimbleGen).

first: Yung-Luen

last: Yu

first: Chen-Shiou


title: Fetal programming of muscle transcriptome in response to gestational dietary protein levels in the pig [LP]

status: Public on Sep 05 2012

first: Klaus

last: Wimmers

summary: German landrace gilts were fed a low protein diet (LP, 6% CP) throughout their whole pregnancy. Subsequently muscle transcriptome profiles of the offspring were analysed at prenatal (94 dpc) and postnatal stages (1, 28, 188 dpn)

overall_design: per stage offspring of 3 gilts were collected for expression profiling

first: Siriluck

last: Ponsuksili

first: Michael

last: Oster


title: Fetal programming of muscle transcriptome in response to gestational dietary protein levels in the pig [HP]

summary: German landrace gilts were fed a high protein diet (HP, 30% CP) throughout their whole pregnancy. Subsequently muscle transcriptome profiles of the offspring were analysed at prenatal (94 dpc) and postnatal stages (1, 28, 188 dpn)


title: dark hypocotyls tor rnai-Dark hypocotyls TOR RNAi

status: Public on Oct 10 2012

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

institute: INRA

summary: fapesp-bra-inra-10-01_bioen_hypocotyl - dark hypocotyls tor rnai - Transcriptional comparison between 2 TOR RNAi mutants versus GUS control. - Sowing after 24h imbibition at 4°C in the dark, on MS1/5, no sucrose, 10 mM ethanol, 8 g/l agar, vertical growth with 3h light, 6 days growth in the dark (20°C), hypocotyls were harvested under green light ; cotyledons and root were removed.

overall_design: 4 dye-swap - normal vs rnai mutant comparaison

first: Christian

last: Meyer

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Marie-Laure

last: Martin-Magniette


title: Fetal programming of muscle transcriptome in response to gestational dietary protein levels in the pig [AP]

summary: German landrace gilts were fed an adequate protein diet (AP, 12% CP) throughout their whole pregnancy. Subsequently muscle transcriptome profiles of the offspring were analysed at prenatal (94 dpc) and postnatal stages (1, 28, 188 dpn)


title: SNP data from 78 pheochromocytomas and paragangliomas

status: Public on Sep 11 2012

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

summary: SNP profiles from 78 pheochromocytomas and paragangliomas were analyzed to detect copy number changes and LOH.

overall_design: 78 pheochromocytomas and paragangliomas were analyzed with Illumina Human610-Quad v1.0 BeadChips.

first: Nelly

last: Burnichon

first: Anne-Paule

last: Gimenez-Roqueplo


title: Fetal programming of muscle transcriptome in response to gestational dietary protein levels in the pig

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

overall_design: Refer to individual Series


title: Time course analysis of dedifferentiation in porcine follicular granulosa cells

status: Public on Nov 21 2012

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

institute: Research Organization of Information and Systems

summary:
Cellular dedifferentiation signifies the withdrawal of cells from a specific differentiated state into a ‘stem cell’-like undifferentiated state. However, the mechanism of dedifferentiation remains obscure. We showed that  follicular granulosa cells (GC), which have distinct functions in vivo, can dedifferentiate during culture in vitro and acquire multipotency.
We investigated the dedifferentiation of GC using global gene expression analyses.

overall_design: Total RNA was isolated from GCs to DFOG cells at 5 time points during dedifferentiation (cultured in 0day, 1day, 2day, 4day and 7day). Each timepoint was performed in triplicate (ie, biological replicates). Using Affymetrix porcine genome array, we performed microarray time course experiments to analyze gene expression profiles during GC dedifferentiation.

first: Yoshinao

last: Oki

first: Takeharu

last: Motohashi

first: Nobuki

last: Sugiura

first: Koichiro

last: Kano


title: Stress-related gene expression in HK-2 cells exposed to pH 7.4, 7.0 or 6.7

city: Liverpool

first: Rana

last: Rustom

address: Duncan Street

department: Metabolic and Cellular Medicine

institute: University of Liverpool

summary: Chronic metabolic acidosis occurs commonly in patients with diseased kidneys and is linked with progression to renal failure. As renal function declines there is loss of nephron mass and adaptive proximal tubular hypertrophy and hypermetabolism. We have previously demonstrated in an in vitro model of chronic acidosis in porcine LLC-PK1 cells increased ammonia generation (oxidative hypermetabolism) linked with tubular cellular dysfunction and increased markers of oxidative stress. The aim of this study was to determine the effect of chronic acidosis in HK-2 cells on changes in gene and protein expression stimulated by oxidative stress.

overall_design:
HK-2 cells were were seeded onto 6 well plates at a density of 4x104 cells/well and cultured for 72 h in growth medium (DMEM/Ham s F12 medium supplemented with 5.5 mM glucose, 2 mM L-glutamine, 5 ug/ml insulin, 5 ug/ml transferrin, 5 ng/ml sodium selenite, 0.4 ug/ml hydrocortisone, 5 ng/ml epidermal growth factor, 100 U/ml penicillin, 100 ug/ml streptomycin, and 10% FCS). The medium was then replaced by growth media buffered to pH 7.4, 7.0 or 6.7 with 12.5 mM bis-Tris and cells were cultured for further 48 h. Media were changed to serum free media (SFM) buffered by 12.5 mM bis-Tris to pH 7.4, 7.0 or 6.7 and cells were harvested and RNA isolated after 24 h.
Total RNA was isolated from HK-2 cells on 3 different occasions using Tri-reagent (Sigma, UK) as recommended by the manufacturer's protocol. The RNA from the respective replicate samples were pooled together and the RNA content was measured using RiboGreen RNA Quantitation Reagent (Molecular Probes, Invitrogen, UK). The integrity of the total RNA was verified on a denaturing agarose-formaldehyde gel.

first: Stephanie

last: Dillon

first: John

last: Alexander

first: Liliana

last: Shalamanova

first: Frank

last: McArdle

first: Malcolm

middle: J

last: Jackson


title: Aneuploidy as a mechanism for stress-induced liver adaptation

status: Public on Jul 17 2012

city: Pittsburgh

first: Andrew

middle: W.

last: Duncan

state: PA

address: 450 Technology Drive, Suite 300

institute: University of Pittsburgh

summary: Over half of the mature hepatocytes in mice and humans are aneuploid and yet retain full ability to undergo mitosis. This observation has raised the question of whether this unusual somatic genetic variation evolved as an adaptive mechanism in response to hepatic injury. According to this model, hepatotoxic insults select for hepatocytes with specific numerical chromosome abnormalities, rendering them differentially resistant to injury. To test this hypothesis, we utilized a strain of mice heterozygous for a mutation in the homogentisic acid dioxygenase (Hgd) gene located on chromosome 16. Loss of the remaining Hgd allele protects from fumarylacetoacetate hydrolase (Fah) deficiency, a genetic liver disease model. When adult mice heterozygous for Hgd and lacking Fah were exposed to chronic liver damage, injury-resistant nodules consisting of Hgd-null hepatocytes rapidly emerged. To determine whether aneuploidy played a role in this phenomenon, array comparative genomic hybridization (aCGH) and metaphase karyotyping were performed. Strikingly, loss of chromosome 16 was dramatically enriched in all mice that became completely resistant to tyrosinemia-induced hepatic injury. The frequency of chromosome 16-specific aneuploidy was approximately 50%. This result indicates that selection of a specific aneuploid karyotype can result in the adaptation of hepatocytes to chronic liver injury. The extent to which aneuploidy promotes hepatic adaptation in humans remains under investigation.

overall_design: 8 mouse hepatocyte samples were analyzed. Genomic DNA samples were derived from wild type mice (2), Hgd-/- Fah-/- mice off NTBC (2) and Hgd+/- Fah-/- off NTBC (4). Samples were compared to sex-mismatched reference genomic DNA isolated from wild type mouse splenocytes.

middle: W

first: Weimin

last: Bi


title: viromouv-Analysis of the genic expression modifications of Arabidopsis Companion cells infected by plants viruses

status: Public on Nov 09 2012

first: Soubigou-Taconnat

last: Ludivine

summary: ra10-02_viromouv - viromouv - transcriptome analysis of Arabidopsis Companion cells after infection by plants viruses - Transgenic plants expressing GFP under the control of a companion cell specific promoter were infected by two different viruses: LMV and TuYV. Companion cell protoplasts from these plants were sorted by FACS and extracted RNA were compared to healthy companion cell protoplasts.

overall_design: 10 dye-swap - normal vs disease comparison

first: Frederic

last: Revers

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Marie-Laure

last: Martin-Magniette


title: study of the transcriptional consequences of a growth qtl candidate (sg1)-Functional characterization of Shoot Growth 1 (Sg1)

status: Public on Jul 23 2012

summary: ra11-04_qtl - study of the transcriptional consequences of a growth qtl candidate (sg1) - We want to compare the transcriptome of Sg1 insertion mutant to a WT background to understand if this candidate has a role in gene expression regulation at the genome-wide level. - We are analysing a QTL named Sg1 quantitatively affecting the shoot growth in Arabidopsis thaliana. Sg1 mutation exhibits a large set of phenotypic consequences (growth, fitness,…), and the penetrance of these defects increase over generations. The CATMA collaboration aims to perform a T-DNA mutant vs WT analysis, with the WT control being derived from the heterozygous T-DNA parent. A first homozygous generation hypotheticaly derived from the heterozygous T-DNA parent and a 4th homozygous generation showing more severe phenotypes are being compared to the WT (dye swap, biological repetitions). Whole plants were harvested 10 DAG at 11am for each genotype.

overall_design: 4 dye-swap - gene knock out

first: Olivier

last: Loudet


title: Exploration of genes expression with a DNA microarray Cancerochip.

status: Public on Jul 01 2012

city: angers

first: frederique

last: savagner

address: 4 rue larrey

institute: Inserm

summary:
Our goal was to search for new molecular markers of the mitochondrial implication in the thyroid tumorigenesis.
Using a DNA microarray (Cancerochip), we explored a collection of thyroid samples representing 4 classes of thyroid tumors.

overall_design: 45 thyroid tumoral and paired control tissues representing 4 classes (benign follicular tumors [FTA], oncocytic variants of follicular tumors [OT], papillary thyroid carcinomas [PTC] and tumors of uncertain malignancy potential [TUMP]) of thyroid tumors were explored for the expression of 6866 genes.

first: Caroline

last: Jacques

first: Frédérique

last: Savagner

first: Catherine

last: Chevalier

first: Raluca

last: Teusan


title: Pulmonary alveolar macrophages (PAMs) of Tongcheng piglets response to HP-PRRSV infection in vivo

city: Wuhan

first: Bang

last: Liu

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

institute: Huazhong Agricultural University

summary:
Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is the most economically important disease in pig populations. Lung damage is one major pathological condition following PRRSV infection, often leading to animal death. In vivo, PRRSV productive infection occurs predominately in alveolar macrophages of the lung.
Here, transcriptome profiling of pulmonary alveolar macrophages (PAMs) from Tongcheng piglets pre- and post- infection of highly pathogenic PRRSV has been performed using porcine Affymetrix GeneChip.

overall_design: All animal procedures were performed according to protocols approved by the Biological Studies Animal Care and Use Committee of Hubei Province, China. Piglets used in this study were free from PRRSV, pseudorabies virus (PRV) and porcine circovirus type 2 (PCV2) determined by ELISA test for serum antibodies. Twelve of 5-week-old boars were obtained from three litters (four piglets per litter), and raised in pathogen-free facilities. In order to perform a paired experiment, every four full-sib individuals were divided equally into two groups: one infected group and one control group with 6 piglets in each group. The infected groups were challenged with PRRSV-Wuh2 (3 ml/15 kg, 10-5 TCID50/ml) by intramuscular inoculation. Slaughters were carried out at 0 days post-infection (dpi) for uninfected (control) groups, and at 5 or 7 dpi for infected groups. The PAMs for microarray analysis were collected by bronchoalveolar lavage from three uninfected pigs and three infected pigs at 5 dpi. Total of 6 microarrays have been hybridized in this experiment.

first: Ping

last: Zhou

first: Shanli

last: Zhai

first: Xiang

last: Lin

first: Tengfei

last: Jiang

first: Xueying

last: Hu

first: Yunbo

first: Bin

last: Wu

first: Xuewen

last: Xu

first: Jin-Ping

last: Li


title: action of microgravity on root development-Action of microgravity on root development

status: Public on Aug 01 2012

first: Soubigou-Taconnat

last: Ludivine

summary: au11-03_gravite - action of microgravity on root development - Action of microgravity on root development - Arabidopsis were grown on horizontal or vertical clinostat for 4, 8 or 12 days. Seedlings on horizontal clinostat were in simulated microgravity and seedlings on vertical clinostat are considered as a control. Comparison was made between plants grown on simulated microgravitry and vertical position.

overall_design: 6 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Eugénie

last: Carnero diaz

first: Marie-Laure


title: Microdissection vs. no microdissection: Transcriptome bias induced by protocols used in microdissection

status: Public on Jun 01 2012

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

summary: gnp07_regeneome_microdissectionbias - microdissection vs no microdissection - Transcriptome bias induce by protocols used in microdissection - To compare RNA from flowers and RNA from microdissected flowers to know bias induce by microdissection (dissection from all tissues were collected to have a representation of entire flower)

overall_design: 2 dye-swap - treated vs untreated comparison

first: jean-denis

last: Faure

last: Martin-Magniette


title: Strome MES-4, H3K36me3  and H3K27me3 in mes-4 RNAi EEMB

status: Public on May 30 2012

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: ChIP-chip of MES-4, H3K36me3 and H3K27me3 in mes-4 RNAi C. elegans early embryo

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: mes-4 RNAi; Developmental Stage: Early Embryo; Genotype: N2; Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS:  temperature 24

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner


title: CUC2 mutant tissues vs. wild type cuc2-Gnp07_Regeneome_cuc2

summary: gnp07_regeneome_cuc2 - cuc2 - CUC2 is expressed in meristem. It permits to create organs boundaries. It is also expressed in leave margins. Is there a mecanism meristem like in leave margins? - To compare wt and cuc2 leaf margins. And compare teeth and hollow inside the arabidopsis leaf margin.

overall_design: 8 dye-swap - tissue comparison,wt vs mutant comparison

first: Jean-Pierre

last: Renou


title: mes-2, mes-4 or mes-2; mes-4 mutants vs. wild type

summary: Trascriptional profiling of C. elegans adult germ lines comparing mes-2(bn11)unc-4(e120) mutants and unc-4(e120) (wild type), mes-4(bn85) mutants and N2 (wild type), mes-2(bn11)unc-4(e120); mes-4(bn85) and unc-4(e120) (wild type) at 20 degrees.

overall_design: One-condition experiment, mutant vs. WT.  Biological replicates 4 mutant, 4 wildtype harvested indepedently.  One mutant replicate and one WT replicate per array.

first: Laura

last: Gaydos

last: Rechsteiner


title: Time course of the transcriptional response of three porcine intestinal sections to Salmonella typhimurium infection

status: Public on Jun 20 2012

city: Campanillas

first: Rocio

last: Bautista

state: Malaga

address: C/ Severo Ochoa, 34. Parque Tecnologico

department: Edificio de Bioinnovacion

institute: Universidad de Malaga

summary:
The GeneChip Porcine Genome Array was used to identify the transcriptional response upon Salmonella typhimurium infection in three porcine intestinal sections (jejumun, ileum and colon) along a time course of 1,2 and 6 days post infection.
The objetives in this study were i) characterize transcriptional changes upon S. typhimurium infection in the intestinal mucosa; ii) identify differences among porcine intestinal sections in inmune resposes against S. typhimurium; iii) identify change that could be associated to salmonellosis pathogenesis and symtomatology; and finally, iv) identify transcriptional changes that could be induced by S. typhimurium in order to get bacterial survival and successful colonization.

overall_design:
Sixteen male and female crossbreeds weaned piglets, approximately 4 weeks of age, were used in this study. Before infection, faecal samples from each animal were analyzed to confirm that piglets were free of Salmonella. Pigs were housed in an environmentally controlled isolation facility at 25ºC and under constant light with ad libitum access to feed and water. After an acclimation period of 5 days, pigs were challenged orally with 108 cfu of Salmonella enterica serovar Typhimurium phagetype DT104 (n=12), whereas the control group (n=4) received sterile medium orally. The four non-infected control pigs were necropsied two hours prior to experimental infection. Four randomly chosen infected pigs were necropsied at 1 day post infection (dpi), 2 dpi and 6 dpi, respectively. Faecal swabs, blood and tissues samples were aseptically collected. Ileum was collected, sectioned in pieces of around 10 cm and immediately frozen in liquid nitrogen for mucosa isolation and RNA purification. To ensure the inoculated pigs were infected, faecal samples were cultured and checked for positive Salmonellae organism

Four reps per treatment and tissue group except 'Ileum 1dpi' has only 3 replicates.

first: Melania

last: Collado-Romero

first: Cristina

last: Arce

first: Rocío

first: M

last: Claros

first: Ana

last: Carvajal

first: Juan

last: Garrido


title: Strome Mes-4, H3K36me3  and H3K27me3 in N2 EEMB

summary: ChIP-chip of Mes-4, H3K36me3 and H3K27me3 in N2 C. elegans early embryo

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: N2; Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 2 or 3; EXPERIMENTAL FACTORS:  temperature 20


title: Microdissection: Transdifferentiation of Root Apical Meristem to Shoot Apical Meristem

summary: gnp07_regeneome_transdifferenciation - microdissection - Study of the moleculars mecanism during transdifferenciation of Root ApicalMeristem to Shoot Apical Meristem - middle of growth permits to induce transdifferenciation of root apical meristem to shoot apical meristem

overall_design: 6 dye-swap - time course

first: Sandrine

last: Balzergue

first: Phillipe

last: Rech

first: Marco

last: Da Costa


title: Transcript and chromatin analysis in mes-2, mes-4, and mes-2; mes-4 double mutants


title: Competitive Action of Butenolides from Plant-Derived Smoke on the Germination Process of Lettuce

status: Public on May 01 2012

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

summary: Sensing environmental cues is essential for plants in order to respond properly to, adapt to and survive changes in the environment and disturbances. Smoke-derived germination active compounds are important cues which provide a strong chemical signal to seeds in the soil seed bank about the available germination niche created by the passage of fire. The germination stimulatory activity can largely be attributed to the presence of the butenolide, 3-methyl-2H-furo[2,3-c]pyran-2-one (karrikinolide; KAR1). More recently, a related fire-borne butenolide, 3,4,5-trimethylfuran-2(5H)-one (inhibenolide A; InhA), was shown to have an inhibitory effect on germination. The aim of this study was to extensively characterize the interaction of these potent smoke-derived compounds in the highly KAR1-sensitive Lactuca sativa cv. ‘Grand Rapids’ achenes.

overall_design: A time course microarray analysis of KAR1- and InhA-treated achenes was performed using custom-made Agilent microarrays. Early time points for sampling the transcriptome were chosen by taking into account the fact that treatment with KAR1 is irreversible (by leaching with water) after 2 h, and that the KAR1-treated achenes enter an InhA-insensitive stage after 9 h. Therefore, samples were harvested after 2 and 10 h of initial exposure to 0.1 µM KAR1 or 10 µM InhA, and after 24 h, when germinated and non-germinating achenes could be distinguished visually. To assess the divergence between the expression patterns induced by the two compounds, a sample of achenes treated with 0.1 µM KAR1 and 10 µM InhA simultaneously, was harvested after 2 h. At 24 h, samples were collected from germinating and non-germinating achenes separately, and equal amounts of mRNA were pooled. Although this design implies that there is a small chance of losing data, our primary aim at 24 h was to screen for differences between the KAR1- and InhA-induced transcriptome. Achenes germinated in distilled water served as controls and were compared to the experimental samples treated as described above.

first: Vilmos

last: Soós


title: Expression data from pig uterus in response to embryos at blastocyst satge and oocytes

status: Public on Apr 19 2012

city: Sheffield

first: Carmen

last: Alminana

address: Tree Root Walk

department: Academic Unit of Reproductive and Developmental Medicine, Human Metabolism Department

institute: University of Sheffield

summary: The maternal tract plays a critical role in the success of early embryonic development providing an optimal environment for establishment and maintenance of pregnancy. Preparation of this environment requires an intimate dialogue between the embryo and her mother. To advance our understanding of the process by which a foreign blastocyst is accepted by the maternal endometrium and better address the clinical challenges of infertility and pregnancy failure, it is imperative to decipher this complex molecular dialogue. The objective of the present work is to define the local response(s) of the maternal tract towards the embryo during the earliest stages of pregnancy.

overall_design: In order to identify the uterine gene expression modified in the presence of the embryo when compared to the oocyte we used a novel model that eliminated genetic variability. Using laparoscopic insemination one oviduct was inseminated with spermatozoa and the contralateral oviduct was injected with diluent. This model allowed us to obtain samples from the oviduct and the uterine horn containing either embryos or oocytes from the same sow. Uterine horn pig samples containing embryos at blastocyst stage and and their contralateral uterine horn containing oocytes from individual sows were collected for RNA isolation and hybridization on Affymetrix microarrays. Three biological replicates were performed (n= 3 sows) and a total of 6 arrays were used for microarrays study (3 arrays for uterine horn samples containing embryos (inseminated-side) and 3 arrays for samples containing oocytes (non-inseminated side).

first: Paul

last: Heath

first: Stephen

last: Wilkinson

first: Jonatan

last: Sanchez-Osorio

last: Cuello

first: Inmaculada

last: Parrilla

first: Maria

middle: A

last: Gil

first: Jose

last: Vazquez

first: Jordi

last: Roca

first: Emilio

last: Martinez

first: Alireza

last: Fazeli


title: Effects of dietary fat types on growth performance, pork quality, and gene expression in growing-finishing pigs

status: Public on May 23 2012

city: Suwon

first: Bong-Hwan

last: Choi

address: 77 chuksan-gil

department: Animal Genomics & Bioinformatics Division

country: South Korea

institute: National Institute of Animal Science

summary:
This study was performed to determine the effects of dietary fat sources, i.e., beef tallow, soybean oil, olive oil and coconut oil (each 3% in feed), on the growth performance, meat quality and gene expression in growing-finishing pigs.
The results of this study indicate that the type of dietary fat affects fatty acid composition and insulin signaling-related gene expression in the longissimus dorsi muscle of pigs.

overall_design: Effects of dietary fat types on meat quantity, meat quality and gene expression in pig.

first: Jun-Cheol

last: Park

first: Seung-Chang

last: Kim

first: Sung-Dae

last: Lee

first: Hong-Chul

last: Jang

first: Nam-Kuk

first: Seung-Hwan

first: Hyun-Jung

last: Jung

first: In-Cheul

first: Hwan-Hoo

last: Seong


title: SNP data from 12 childhood adrenocortical tumors from outside Brazil

status: Public on Apr 02 2012

first: Eric

last: Letouzé

summary: SNP array data from 12 childhood adrenocortical tumors (ACT) were used to identify recurrent chromosome rearrangements and candidate driver genes.

overall_design: 12 childhood ACT were analyzed with Illumina Human610-Quad v1.0 BeadChips.

first: Roberto

last: Rosati

first: Mabrouka

last: Doghman

first: Jean-Christophe

last: Mas

first: Gerard

middle: P

last: Zambetti

first: Bonald

last: Figueiredo

first: Enzo

last: Lalli


title: Yeast response to acid stress

city: Valencia

first: Guillem

last: Hueso

address: Avenido de los Naranjos

institute: IBMCP

summary: Intracellular pH affects many cellular systems but its mechanisms of regulation and perception are mostly unknown. Weak organic acids such as acetate are potent fungistatic agents used in food preservation, but their intracellular targets are poorly understood. We thus searched for transcriptional response in Saccharomyces cerevisiae to intracellular acidification caused by two hours 30mM acetic acid treatment.

overall_design: Two independent experiments were performed for both acid-treated/non-treated cells. The experimental design for both cases was a Balanced Block Design with four biological replicates, two of them dye swaps.

first: Jorge

last: Perez-Valle


title: The Caucasus as an asymmetric semipermeable barrier to ancient human migrations

status: Public on Apr 18 2012

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

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

summary: The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.

overall_design: 204 samples were analysed with the Illumina platform Human610-Quad v 1.0 and are described herein.

first: Richard

last: Villems

first: Bayazit

last: Yunusbayev

first: Mari

last: Jarve


title: Expression data of muscle and draining lymph node after intramuscular ISCOM-Matrix vaccine adjuvant treatment

status: Public on Apr 01 2012

city: Uppsala

first: Viktor

last: Ahlberg

address: PO Box 588

department: Dept of Biomedical Sciences and Veterinary Public Health

country: Sweden

institute: Swedish University of Agricultural Sciences

summary:
ISCOM vaccines induce a balanced Th1/Th2 response and cytotoxic T lymphocytes. The adjuvant component, ISCOM-Matrix, consists of purified saponin fractions, cholesterol and phospholipids. The mode of action for the ISCOM-Matrix is known to some extent but still we lack knowledge of important segments in initiation of the immune response. The study was performed to analyze the early transcriptional responses to the ISCOM-Matrix alone, without the use of co-administered antigen. Matrix M (AbISCO® 100) was given as intramuscular injection and after 24 hours the pigs was sacrificed for gene expression analysis, performed for the injection site and the draining lymph node.
Results revealed 594 and 362 genes to be differentially expressed (FC > 2; q < 0.05) at the injection site and in the lymph node, respectively. This show that the ISCOM-Matrix, without any antigen added, has a clear immunomodulatory effect at the site of administration as well as in the draining lymph node.

overall_design: Six pigs, castrated males, 11 weeks old was used for the experiment. They were sorted two weeks prior the treatment and kept separate throughout the experiment. 3 pigs were intramuscularly (biceps femoris) injected with ISCOM-Matrix (AbISCO® 100) suspended in 1 ml sterile saline. 3 control animals were similarly injected with saline only. The pigs were sacrificed after 24 hours and muscle tissue from injection site and draining (internal iliac) lymph nodes were collected and transferred to RNAlater for RNA isolation.

first: Karin

last: Bengtsson

first: Per

last: Wallgren

first: Caroline

last: Fossum


title: salmonell inva-Trancriptomic analysis in Salmonella typhimurium infection

status: Public on Apr 07 2012

first: Soubigou-Taconnat

last: Ludivine

department: URGV

summary: au10-06_salmonella - salmonell inva - Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system. - Plants were grown during 14 days in solid medium and were transfered to liquid medium during 16 h. at 9 am samonella was added to a final concentration of OD600=0.2

overall_design: 2 dye-swap - normal vs antisense mutant comparison

first: Eduardo

last: Bueso

first: Heribert

last: Hirt

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: SNP data from 30 pheochromocytomas and paragangliomas.

status: Public on Mar 23 2012

first: Eric

last: Letouzé

summary: SNP profiles from 30 pheochromocytomas and paragangliomas were analyzed to detect identical-by-descent haplotypes, highlighting a founder mutation of SDHD in two samples.

overall_design: 30 pheochromocytomas and paragangliomas were analyzed with Illumina Human610-Quad v1.0 BeadChips.

last: Letouze

first: Nelly

last: Burnichon

first: Anne-Paule

last: Gimenez-Roqueplo


title: The function of corticosteriods in the development of limb muscle weakness in a porcine ICU model

status: Public on Apr 12 2012

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

institute: uppsala university

summary:
Background: The aim of this study is to improve our understanding of the mechanisms underlying the function of corticosteriods in the limb muscles of ICU patients with acute quadriplegic myopathy (AQM) by using a unique porcine ICU model, i.e., 5-day longitudinal experiments where animals are sedated, mechanically ventilated and exposed to factor triggering AQM that is  hydrocortisone.

Results: An increased expression of genes involved in kinase activity, cell cycle regulation and transcriptional regulation. A decreased expression in genes regulating heat shock proteins, cytoskeletal & sarcomeric and oxidative stress response were also apparent. Therefore, it appears that CS has an additive deleterious role in acute quadriplegic myopathywere also apparent.

Conclusions: CS induced molecular mechanisms involving kinase activity and heat shock protein genes were forwarded as probable mechanisms underlying the decreased force generating capacity.

overall_design:
Eight female domestic piglets (Sus scrofa, average body weight 26.4 kg) were used in this study. Piglets were immobilized by anesthesia and mechanically ventilated via a tracheotomy for a period of five days. During this study period, the animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 - 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed.  Core body temperature (blood) was maintained in the range of 38.5 - 40°C by a servo controlled heating pad.  The animals received intravenous crystalloid fluid (Ringeracetat) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 - 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and bensylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period. A neuromuscular blocking agent (NMBA) was administered as a continuous infusion of pancuronium bromide 0.1mg/kg/h (Pavolun; Organon, Boxtel, The Netherlands) for 5days while a corticosteroid (CS) was given as bolus doses of hydrocortisone.
Keywords: Treatment, immobilization, muscle function.

first: Sudhakar

last: Aare

first: Peter

last: Radell

first: Lars

middle: I

last: Eriksson

first: Yi-Wen

last: Chen

last: Hoffman

last: Larsson


title: sg1-sg3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

status: Public on Mar 28 2012

city: evry

address: 2 rue gaston crémieux

summary: ra09-01_qtlleafgrowth - sg1-sg3 - What are the transcriptional consequences of the allelic contrast at SG3, SG1 and EGO3 loci mapped for its effect on shoot growth and identified at the gene level - Plants were grown in the in vitro conditions where we have mapped and cloned the concerned QTL and which allows us to see the phenotype linked to the segregation of the natural alleles. We are comparing 2 genotypes descending from a RIL from the Bur x Col RIL set, homozygous and identical everywhere in the genome except for the 23.4 kb at SG1 loci where one genotype is Bur (97.4 and 175.4) and the other is Col (97.1 and 175.1).

overall_design: 4 dye-swap - genotype comparison

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Olivier

last: Loudet


title: ego3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

last: Ludivine

summary: ra09-01_qtlleafgrowth - ego3 - What are the transcriptional consequences of the allelic contrast at SG3, SG1 and EGO3 loci mapped for its effect on shoot growth and identified at the gene level - Plants were grown in the in vitro conditions with 60 mM mannitol, where we have mapped and cloned the concerned QTL which allows us to see the phenotype linked to the segregation of the natural alleles. We are comparing 2 genotypes descending from a RIL from the Cvi x Col (H1 is Col allele containing HIF, and A2 is Cvi allele containing HIF).

overall_design: 2 dye-swap - genotype comparison


title: Profiling of Candida glabrata during Phagocytosis by Neutrophils

status: Public on Mar 01 2012

city: Bethesda

first: John

last: Bennett

address: Building 10 - Magnuson Clinical Center, 12C103B

department: NIAID

institute: National Institutes of Health

summary: Our purpose is to clarify the global transcriptional profile in Candida glabrata phagocytized in human neutrophil.

overall_design: Three biological replicates with dye-swap for each, total of 6 arrays, were performed for PMN experiments and two biological replicates with one dye-swap, total 3 arrays, were performed for carbohydrate and nitrogen depletion experiments at 30 and 60 min incubation, respectively.


title: Circadian expression data of Synechococcus in WT, rpoD6-null, sasA-null and rpaA-null strains

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

country: Japan

institute: Waseda University

summary: In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, most genes show rhythmic expression controlled by the Kai-based clock under continuous light conditions (LL). We found that rpoD6-null mutants impaired expression of clock-controlled genes peaking at hours 8-10 in LL, while sasA-null or rpaA-null mutants each arrested the expression profiles at subjective dawn.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Time-course data (0-24 h) of wild type (WT), rpoD6-null, sasA-null and rpaA-null S. elongatus PCC 7942 strains analyzed under continuous light (LL) conditions after two 12h:12h light:dark (LD) cycles using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing 2,515 predicted protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also for the almost homologous strain, S. elongatus PCC 7942.

first: Norimune

last: Hosokawa

first: Takai

last: Naoki


title: Reduced Airway Surface pH Impairs Bacterial Killing in the Porcine Cystic Fibrosis Lung

status: Public on Mar 30 2012

city: Iowa City

first: Shyam

last: Ramachandran

address: 240G EMRB

department: Pediatrics

country: USA

institute: Univ of Iowa

summary: Cystic fibrosis (CF) is a life-shortening disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene.  Although bacterial lung infection and the resulting inflammation cause most of the morbidity and mortality, how loss of CFTR first disrupts airway host defense has remained uncertain.  We asked what abnormality impairs elimination when a bacterium lands on the pristine surface of a newborn CF airway?  To investigate this defect, we interrogated the viability of individual bacteria immobilized on solid grids and placed on the airway surface.  As a model we studied CF pigs, which spontaneously develop hallmark features of CF lung disease.  At birth, their lungs lack infection and inflammation, but have a reduced ability to eradicate bacteria.  Here we show that in newborn wild-type pigs, the thin layer of airway surface liquid (ASL) rapidly killed bacteria in vivo, when removed from the lung, and in primary epithelial cultures.  Lack of CFTR reduced bacterial killing.  We found that ASL pH was more acidic in CF, and reducing pH inhibited the antimicrobial activity of ASL.  Reducing ASL pH diminished bacterial killing in wild-type pigs, and increasing ASL pH rescued killing in CF pigs.  These results directly link the initial host defense defect to loss of CFTR, an anion channel that facilitates HCO3- transport.  Without CFTR, airway epithelial HCO3- secretion is defective, ASL pH falls and inhibits antimicrobial function, and thereby impairs killing of bacteria that enter the newborn lung.  These findings suggest that increasing ASL pH might prevent the initial infection in patients with CF and that assaying ASL pH or bacterial killing could report on the benefit of therapeutic interventions.

overall_design: 11 samples of trachea primary airway epithelial cultures representing CFTR+/+ and CFTR-/- pigs. Pig samples representing 14 bronchus and 12 trachea tissue samples submitted in GSE21071.


title: Maternal tract distinguish between spermatozoa and other pathogenic and non-pathogenic entities

status: Public on Feb 15 2012

first: Ahmed

last: Aldarmahi

department: Reproducitve Medicine

country: United Kingdom

institute: The University of Sheffield

summary: The mammalian oviduct is a dynamic organ and the venue of important events leading to the establishment of pregnancy. Oviductal epithelial cells are involved in direct contact and specific interactions with different self and non-self entities (oocyte, sperm, etc.).The aim of this study was to determine if the oviduct is able to distinguish between different types of non-self-entities. We used an in vitro model to determine genes altered in oviductal epithelial cell (OPEC) in response to the presence of spermatozoa, mammalian somatic cells (red blood cell) or bacteria. We hypothesised that alteration of OPEC expression profile in response to boar spermatozoa (friendly non-self entity), red blood cells (non-pathogenic, non-self entity) and bacteria (pathogenic non-self entity) is indicative of recognition of self and non-self entities by these cells as well as recognition of pathogenic from non-pathogenic non-self entities.

overall_design: Oviductal epithelial cells (OPEC) were co-incubated in the presence of (i) bacteria (1 x 10˄8 bacteria), (ii) sperm (1 X 10 ˄ 6 spermatozoa/ml) or (iii) red blood cell (5 x 10 ˄ 6 red blood cell/ml) for 24 hours in HAM-12 media. Three biological replicates were performed for each group and a total of 12 Affymetrix Porcine arrays were used to identify the expression profiles of OPEC alone (3 arrays) or in the presence of (i) bacteria (3 arrays), (ii) sperm (3 arrays) or (iii) red blood cells (3 arrays).

first: Sarah

last: Elliott

first: Robert

last: Poole

first: Paul

last: Heath

first: Alireza

last: Fazeli