title: septante project-Impact of genetically modified plants on bacteria from rhizosphere

status: Public on Mar 21 2012

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

institute: INRA

summary: rs11-02_opine - septante project - We have tools to estimate this modification for the bacterial part. On the other hand, concerning the plant part, we know plants produce opines compounds but we dont know if this expression can modify the transcriptional state of the plant. - Transgenic lines producing respectively octopine and mannopine and the WT line were grown in hydroponic tanks (containing nutritive solution) under short day conditions (8h light, 24°C). Whole plant aged of one month were harvested and frozen in nitrogen liquid. The plants were ground with a mortar and pestle and RNA extraction was performed with the RNeasy extraction kit (QIAGEN). The RNA concentration estimation was performed on a NANODrop spectrophotometer (Nanodrop).

overall_design: 6 dye-swap - normal vs transgenic comparaison

first: Pascal

last: Ratet

first: Samuel

last: Mondy

first: Sandrine

last: Balzergue

first: Yves

last: Dessaux

first: Marie-Laure

last: Martin-Magniette


title: ws vs clca2/35a2/352.7-Root molecular responses of nitrate transporter mutants

status: Public on Mar 01 2012

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

summary: ra10-04_roots - ws vs clca2/35a2/352.7 - What are the transcriptional adaptations induced by genetically modifying vacuolar nitrate transport - Plants were grown for 12 days after germination in vertical Petri dishes onto a 2mM NO3 medium (derived from Armengaud et al 2004) in long days (16h light at 65 µE). Samples consisted of pooled roots from at least 30 to 50 plants per sample. The experiment has been repeated 4 times (exp IFX1-IFX3-CPLA2-CPLA3)and samples were harvested around 11h in the morning (ie 3h after illumation).

overall_design: 10 dye-swap - gene knock out, genotype comparison, normal vs transgenic comparison

first: Ludivine

last: Taconnat

first: Patrick

last: Armengaud


title: Transcriptomic response of skeletal muscle to lipopolysaccharide in the gilthead seabream (Sparus aurata)

status: Public on Mar 16 2012

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

summary: The physiological consequences of an activation of the immune system in fish are not well understood. In particular, skeletal muscle, due to its essential role in locomotion and whole-animal energy homeostasis, is a potentially important target of inflammation. In this study, we have evaluated the in vivo effects of lipopolysaccharide (LPS) on the white and red skeletal muscle transcriptome of the gilthead seabream (Sparus aurata) by microarray analysis at 24 and 72 hours after injection. In white muscle, the transcriptomic response was characterized by an up-regulation of genes involved in carbohydrate catabolism and protein synthesis at 24 hours and a complete reversal of this pattern at 72 hours. In red muscle, an up-regulation of genes involved in carbohydrate catabolism and protein synthesis was observed only at 72 hours after LPS administration. Interestingly, both white and red muscles showed a similar consistent down-regulation of immune genes at 72 hours post-injection. However, genes involved in muscle contraction showed a general up-regulation in response to LPS in both types of muscle. In summary, LPS administration causes muscle type-specific responses regarding the expression of genes involved in carbohydrate and protein metabolism and a common decreased expression of immune genes in skeletal muscle, concomitant with increased expression of genes for contractile elements. Our results evidence a robust and tissue-specific transcriptomic response of the skeletal muscle to an acute inflammatory challenge.

overall_design: Total RNA from pooled control (n = 5) and LPS-treated (n = 5) sea bream white and red muscle tissues was labeled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain). We used a dye swap experimental design and each cDNA from a pooled RNA sample was hybridized to two microarrays. For the first slide, test and control cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. Therefore, samples from individual fish within each group were pooled and expression values shown represent the means of 6 × 2 = 12 technical replicates. A total of eight slides were used in this study.

first: Elisavet

last: Kaitetzidou

first: Diego

last: Crespo

first: Yoryia

last: Vraskou

first: Efthimia

last: Antonopoulou


title: Severe alkaline pH stress induces a glucose starvation-related transcriptional response in S. cerevisiae

status: Public on Mar 02 2012

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

summary: Alkaline pH stress invokes in S. cerevisiae a potent and fast transcriptional response that includes many genes repressed by glucose. Certain mutants in the glucose-sensing and response pathways, such as those lacking the Snf1 kinase, are sensitive to alkalinization. We show that addition of glucose to the medium improves growth of wild type cells at high pH, fully abolish the snf1 alkali-sensitive phenotype and attenuates high pH-induced Snf1 phosphorylation at Thr210. The elm1 mutant, lacking one of the three upstream Snf1 kinases (tos3, elm1 and sak1), is markedly alkali sensitive, whereas the phenotype of the tos3 elm1 sak1 strain is even stronger than that of snf1 cells and it is not fully rescued by glucose supplementation. DNA microarray analysis reveals that about 75% of genes induced at short term by high pH are also induced by glucose scarcity.  Snf1 mediates, in full or in part, the activation of a significant subset (38%) of short-term alkali-induced genes, including those coding high-affinity hexose transporters and phosphorylating enzymes. Induction of genes encoding enzymes involved in glycogen (but not trehalose) metabolism is largely dependent of the presence of Snf1. Therefore, the function of Snf1 in adaptation to glucose scarcity appears crucial for alkaline pH tolerance. Incorporation of micromolar amounts of iron and copper to a glucose-supplemented medium result in an additive effect and allows near normal growth at high pH, thus indicating that these three nutrients are key limiting factors for growth in an alkaline environment.

overall_design:
We identified the changes in the expression profiles caused by alkalinization of the medium (pH8 vs. pH5.5 for 10 min) in several strains:

wild type cells (4 chips),
snf1 mutant cells (4 chips)

We also identified the transcriptomic changes that occur after glucose deprivation (0.05% vs 2% for 15 min) in:

wild type cells (2 chips)
snf1 mutant cells (2 chips)

Total: 12 chips

first: Raquel

last: Serrano

first: Maria

last: Platara

first: Carlos

last: Casado

first: Amparo

last: Ruiz

first: Joaquin

last: Ariño


title: knock out mutant n575260-NAD biosynthesis in Arabidopsis : role of quinolinate phosphoribosyltransferase

status: Public on Feb 03 2012

city: Evry

first: Eddy

last: Blondet

summary: rs11-01_nad - knock out mutant n575260 - Study of the impact of a deregulation in the NAD concentration in arabidopsis - Study of the biosynthesis of NAD in Arabidopsis. Involvment of QPRTgene using the knock out mutant N575260 from Salk.

overall_design: 2 dye-swap - gene knock out

first: Sandrine

last: Balzergue

first: Pierre

last: Pétriacq

first: Bertrand

last: Gakière


title: Undomesticated Bacillus subtilis SlrA regulon:  wild-type vs two copies of slrA

status: Public on Feb 02 2012

city: New York

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

country: USA

institute: New York University

summary: Transcriptional profiling of Bacillus subtilis str 3610 cells comparing wild-type to cells containing two copies of the gene slrA.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: wild-type vs slrAx2.  Biological replicates 3

first: Ashley

last: Bate

first: Richard

last: Bonneau

first: Daniel

last: Kearns


title: The DNA methylation landscape of small cell lung cancer

status: Public on Jan 26 2012

city: Duarte

first: Marc

last: Jung

state: CA

address: 1500 East Duarte Street

department: Biology

institute: City Of Hope

type: Methylation profiling by genome tiling array

summary: Small cell lung cancer (SCLC) is a disease characterized by aggressive clinical behavior and lack of effective therapy. Due to its high tendency of early dissemination, only a third of patients have limited-stage disease at the time of diagnosis. SCLC is thought to derive from neuroendocrine cells of the lung. Although several molecular abnormalities in SCLC have been described, there are relatively few studies on epigenetic alterations in this type of tumor. Here, we have used methylation profiling with the methylated CpG island recovery assay (MIRA) in combination with microarrays and conducted the first genome-scale analysis of methylation changes that occur in primary SCLC and SCLC cell lines. Among hundreds of tumor-specifically methylated genes, we identified 73 gene targets that are methylated in more than 77% of primary SCLC tumors, most of which have never been linked to aberrant methylation in tumors. These targets have excellent potential for development of biomarkers for early detection of SCLC. SCLC cell lines had an ~3-fold greater number of hypermethylated genes than primary tumors. Gene ontology analysis indicated a significant enrichment of methylated genes functioning as transcription factors and in processes of neuronal differentiation. Motif analysis of tumor-specific methylated regions identified enrichment of binding sites for several neural cell fate-specifying transcription factors including NEUROD1, HAND1, ZNF423 and REST. We hypothesize that functional inactivation of their corresponding binding sites by DNA methylation can lead to an escape route for early progenitor cells towards the malignant state and may contribute to the origin of SCLC.

overall_design: Comparison between healthy and SCLC tumor DNA methylation profiles

first: Satish

last: Kalari

first: Kemp

middle: H

last: Kernstine

first: Takashi

last: Takahashi

first: Gerd

last: Pfeifer


title: Trancriptomic analysis in Salmonella typhimurium infection [invA_vs_14028s]

status: Public on Jan 31 2012

first: Soubigou-Taconnat

last: Ludivine

summary:
au10-06_salmonella_eduardob - inva_vs_14028s
Transcriptomic analysis between Salmonella wt and different 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 disease comparison

first: Eduardo

last: Bueso

first: Heribert

last: Hirt

first: Marie-Laure

last: Martin-Magniette


title: cdka mutants-cdka mutants

status: Public on Mar 20 2012

summary: rs10-06_cdka - cdka mutants - difference in global transcript in mutants with an affected cell cycle progression         - compare wild type plants with mutant plants that show a reduced activity of CDKA1, the key cell cycle regulator in Arabidopsis thaliana

overall_design: 6 dye-swap - wt vs mutant comparison

first: Delphine

last: Gey

last: Bouyer

first: Arp

last: Schnittger


title: 2 doses of ionising radiations (x-rays) -Transcriptomic analysis of effects of ionising radiation on Arabidopsis thaliana.

status: Public on Feb 25 2012

summary: au09-03_gamma-irradiation - 2 doses of ionising radiations (x-rays)  - Metabolic pathways involved in the response of plants to ionising radiation treatment. - Arabidopsis thaliana (Col-0) seeds were grown in Petri dishes under sterile conditions until they had 2-rosette-leaves (on average 10 days). Then they received a dose of 10 or 40 gray of X-ray (Faxitron HP). Plant were harvested 2 and 26 hours after irradiation, immediatly frozen and stored at -80°C until RNA extraction (Rneasy plant mini Kit, Qiagen) . Experiment was carried in duplicates and a non irradiated control was done for each time.

overall_design: 8 dye-swap - dose response,time course

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Fransisco

last: Cabello-hurtado

first: Sandrine

last: Balzergue


title: Modeling the Transcriptional Consequences of Epidermal Growth Factor Receptor Ablation in Ras-Initia

status: Public on Jan 11 2012

city: Bethesda

first: Stuart

last: Yuspa

state: MD

address: 37 Convent Dr.

institute: NCI

summary: EGFR targeted therapy is in clinical use to treat squamous cell carcinoma of the head and neck and other cancers of lining epithelium. Activating Ras mutations are a negative prognostic factor for response to EGFR ablation therapy in multiple cancer types. Furthermore, the major adverse consequence of this therapy is an acneiform papulopustular eruption on normal skin. To better understand Ras signaling in an EGFR depleted environment, we performed gene expression profiling on oncogenic Ras transformed and wildtype mouse keratinocytes with EGFR ablated chronically by genetic deletion or acutely by drug treatment. We were able to identify a 25 gene signature specific to the Ras-EGFR ablation interaction and a distinct 19 gene EGFR ablation signature on normal keratinocytes. EGFR ablation in the context of wildtype Ras reduces ontologies favoring cell cycle control and transcription while ablation in the context of oncogenic Ras enriches ontologies for ion channels and membrane transporters, particularly focused on calcium homeostasis. The study showed substantial differences in ontologies between chronic EGFR ablation and acute pharmacological ablation, both with and without Ras activation. Pathway and biochemical analysis indicates that activation of p38α is a response to both acute and chronic abrogation of EGFR signaling under conditions of Ras activation. This was confirmed in oncogenic RAS transformed human keratinocytes and in tumors developing in orthografts of EGFR ablated mouse keratinocytes transformed by oncogenic Ras. EGFR ablation in the absence of oncogenic Ras revealed Erk and IL-1β related pathways. These findings reveal previously unrecognized interactions between Ras and EGFR signaling in squamous tumor cells that could influence the therapeutic response to EGFR ablation therapy.

overall_design: Keratinocyte samples were collected from CD-1 EGFR total wild type and knock-out mice. Each of these were treated with 3 different EGFR tyrosine kinase inhibitors (AG1478, Erlotinib, PD153035) in combination with and without ras transduction. Control samples included untreated keratinocyte samples. Universal mouse reference RNA was used as the reference sample. Most groups contained 5 biological replicates, one being a reverse fluoro for a total of 63 samples.


title: Fertile offspring derived from mouse spermatogonial stem cells cryopreserved for more than 14 years

status: Public on Jan 13 2012

city: Philadelphia

first: xin

last: wu

state: PA

address: 3850 baltimore Ave,

department: Animal Biology

institute: School of Veterinary Medicine, University of Pennsylvania

type: Genome variation profiling by genome tiling array

summary: To evaluate the possible deleterious affects prolonged cryopreservation and assisted reproductive technologies may have on the DNA of F0 progeny, we used array-based comparative genomic hybridization (CGH) for analysis of genomic DNA.

overall_design: ICSI-derived progeny were generated from ♂ (ZFLacZ sperm) x ♀ (DBA x C57BL/6 oocyte), where the ZFLazZ transgenic mice were originally generated from an SJL x C57BL/6 background.

first: Xin

last: Wu

first: Shaun

middle: M

last: Goodyear

first: Lara

middle: K

last: Abramowitz

first: Marisa

middle: S

last: Bartolomei

first: John

middle: W

last: Tobias

first: Mary

middle: R

last: Avarbock

first: Ralph

middle: L

last: Brinster


title: Effect of milk and soy formula feeding on hepatic gene expression in the neonatal pig

status: Public on Jan 05 2012

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

summary: The majority of babies in the US are formula-fed instead of breast fed. There are major differences in the composition of formulas and  breast milk and yet little is known about metabolic differences in babies as the result of feeding these very different diets and how that might affect development or disease risk in later life. One concern is that soy-based formulas might have adverse health effects in babies as a result of the presence of low levels of estrogenic phytochemicals – genistein and daidzein which are normally present in soy beans. In the current study, we used a piglet model to look at this question. Piglets were either fed breast milk from the sow or were fed two different infant formulas (cow’s milk-based or soy-based) from age 2 days to 21 days when pigs are normally weaned onto solid food.  Blood glucose and lipids were measured. Formula-fed pigs were found to have lower cholesterol than breast fed piglets and in addition had larger stores of iron in their liver.Microarray analysis was carried out to see if changes in liver gene expression could explain these effects of formula feeding. It was found that overall gene expression profiles were influenced by formula feeding compared to breast fed neonates. Gender-independent and unique effects of formula influenced cholesterol and iron metabolism. Further, soy formula feeding in comparison to milk-based formula failed to reveal any estrogenic actions on hepatic gene expression in either male or female pigs.

overall_design: Piglets (female, male) were either fed breast milk from the sow or were fed two different infant formulas (cow’s milk-based or soy-based) from age 2 days to 21 days when pigs are normally weaned onto solid food.

first: Martin

middle: J

last: Ronis

first: Ying

last: Chen

first: Horatio

last: Gomez-Acevedo

first: Jamie

last: Badeaux

first: Michael

last: Blackburn

first: Thomas

last: Badger


title: gene profiling of turnip crinkle virus (tcv) sirna-Gene profiling of Turnip Crinkle Virus (TCV) siRNA in A.thaliana

status: Public on Apr 01 2012

first: Soubigou-Taconnat

last: Ludivine

summary: rs10-05_tcv - gene profiling of turnip crinkle virus (tcv) sirna - 1. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in A.thaliana? 2. There are also differentially regulated during an evolution and a fitness process? - This is a plant evolution project on TCV in which, the biological questions are: 1. What are the genes (including miRNA precursors) that are differentially regulated in Col0 and dcl234 mutant in wt conditions? 2. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in Col0 and dcl234 mutant? 3. There are also differentially regulated between the plant generations 1 (G1) and 11 (G11)? 4. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA after fitness experiment?

overall_design: 24 dye-swap - gene knock out,treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Virginia

last: Ruiz-Ferrer

first: Ludivine

last: Taconnat

first: Marie-Laure

last: Martin-Magniette


title: DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1

status: Public on Feb 15 2012

city: La Jolla

first: Dwight

last: Kuo

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: MBF and SBF transcription factors regulate a large family of coordinately expressed G1/S genes required for early cell-cycle functions including DNA replication and repair. SBF is inactivated upon S-phase entry by Clb/CDK whereas MBF targets are repressed by the co-repressor, Nrm1. Using genome-wide expression analysis of cells treated with methyl methane sulfonate (MMS), hydroxyurea (HU) or camptothecin (CPT), we show that genotoxic stress during S phase specifically induces MBF-regulated genes. This occurs via direct phosphorylation of Nrm1 by Rad53, the effector checkpoint kinase, which prevents its binding to MBF target promoters. We conclude that MBF-regulated genes are distinguished from SBF-regulated genes by their sensitivity to activation by the S-phase checkpoint, thereby, providing an effective mechanism for enhancing DNA replication and repair and promoting genome stability.

overall_design: Modified Loop Time-series design, time points at 0, 30, 45, 60 and 75 minutes. Conditions are untreated (UT), methyl methane sulfonate (MMS-0.033%), camptothecin (CPT-50uM), and hydroxyurea (HU-0.2M)


title: cell wall mutants -Differentially expressed genes in stems of Arabidopsis deficient in monolignol export and in stems of Arabidopsis plants expressing a hydroxycinnamoyl-CoA hydratase/lyase

status: Public on Jan 01 2012

summary: au10-13_cellwall - cell wall mutants  - What is the impact of the loss of function of monolignol exporters? How does the plant cope with these transporters? Is there any compensation mechanism induced? What is the impact on lignin and cell wall biosynthesis? Does expression of a hydroxycinnamoyl-CoA hydratase/lyase in Arabidopsis stems generate a stress and affect genes involoved in cell wall biosynthesis? - Determine differentially expressed genes in stems of Arabidopsis plants lacking 2 monolignol exporter proteins. mRNA from stems of wild-type and transgenic 7-week-old plants grown in the same conditions were extracted and used for transcriptomic analysis. Three independant cultures were conducted for biological replicates. Determine differentially expressed genes in stems of Arabidopsis plants that express a hydroxycinnamoyl-CoA hydratase/lyase. mRNA from stems of wild-type and transgenic seven-week-old plants grown in the same conditions were extracted and used for transcriptomic analysis. Three independant cultures were conducted for biological replicates.

overall_design: 6 dye-swap - gene knock in (transgenic),normal vs transgenic comparaison

first: Dominique

last: Loque


title: salmonella_prgh - Trancriptomic analysis in Salmonella typhimurium infection

first: edu

last: bueso

address: gaston cremieux

summary:
au10-06_salmonella_eduardob - salmonella_prgh - 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.

Keywords: normal vs disease comparison

overall_design: 2 dye-swap - CATMA arrays

first: Eduardo

last: Bueso

first: Heribert

last: Hirt


title: mpk6 - Flagellin response in mpk mutants

summary:
au-09-01_mpk_flagellin_edu - mpk6 - Investigate flagellin mpk dependent genes - Comparision between mpk6 and Col-0 seedlings.

Keywords: gene knock out


title: mpk4 flg22 - Flagellin response in mpk mutants

summary:
au-09-01_mpk_flagellin_edu - mpk4 flg22 - Investigate flagellin mpk dependent genes - 2 weeks mpk4 plants treated or untreated with 1h with 1 microM flg22

Keywords: treated vs untreated comparison


title: salmonella_14028s - Trancriptomic analysis in Salmonella typhimurium infection

summary:
au10-06_salmonella_eduardob - salmonella_14028s - 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.

Keywords: normal vs disease comparison


title: mpk3 flg22 - Flagellin response in mpk mutants

summary:
au-09-01_mpk_flagellin_edu - mpk3 flg22 - Investigate flagellin mpk dependent genes - 2 weeks mpk3 plants treated 1 h with 1 microM flg22.

Keywords: treated vs untreated comparison


title: mpk6 flg22 - Flagellin response in mpk mutants

summary:
au-09-01_mpk_flagellin_edu - mpk6 flg22 - Investigate flagellin mpk dependent genes - 2 weeks mpk6 flg22 treated 1h with 1 microM flg22.

Keywords: treated vs untreated comparison


title: mpk3 - Flagellin response in mpk mutants

summary:
au-09-01_mpk_flagellin_edu - mpk3 - Investigate flagellin mpk dependent genes - Comparisions between mpk3 and Col-0. 2 weeks seedlings.

Keywords: wt vs mutant comparison


title: bzip9-Energetic Homeostasis and Sugar Signaling

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

summary: bra-inra09-01_bioen - bzip9 - Diversification of the Molecular Mechanisms Involved in the Control of the Energetic Balance in Angiosperms - To elucidate the role of selected bZIP transcription factors (AtbZIP3, AtbZIP9, AtbZIP63; the expression of these genes is repressed by glucose and are poorly characterized) involved in glucose-triggered transcriptional cascade, the target genes of these bZIP TF will be identified. The glucose-mediated regulations of these bZIP genes will be investigated by identifying the cis-regulatory sequences and the upstream regulatory factors. The functional conservation of the corresponding bZIP orthologues in sugar cane and rice will be evaluated.

overall_design: 12 dye-swap - genotype comparison

first: Jean-Pierre

last: Renou

first: Michel

last: Vincentz


title: abi4-Energetic Homeostasis and Sugar Signaling

summary: bra-inra09-01_bioen - abi4 - Diversification of the Molecular Mechanisms Involved in the Control of the Energetic Balance in Angiosperms - Abi4 is regulator pleotropic that interview in the metabolism glucose

overall_design: 12 dye-swap - wt vs mutant comparison

first: Sandra

last: Pelletier


title: Transdifferentiation from root to shoot apical meristem

status: Public on Feb 01 2012

summary: au10-15_cineroots - transdifferentiation - Study of the molecular mechanism during transdifferenciation from root apical meristem to shoot apical meristem  - culture in middle with different hormons, permits transdifferenciation from root to shoot tissues.

overall_design: 6 dye-swap - time course

first: Marco

last: Da Costa


title: Microarray analysis reveals genes and functional networks relevant to the predisposition for inverted teats in pigs

status: Public on Dec 31 2011

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
The inverted teat defect is an inherited disorder characterised by the failure of teats to protrude from the udder surface. The number and identity of relevant genes are unknown.
Simultaneously, 24,123 probe-sets were screened, of which some 15,000 had present calls and were analysed for differential expression between mesenchymal and epithelial tissue of three categories of teats, i.e. normal teats of non-affected (NN) and affected animals (AN) and inverted teats (AI) of the later.

overall_design:
RNAs of mesenchymal and epithelial teat tissues of 5 non-affected and 5 affected animals were hybridized to Affymetrix Porcine Genome Arrays.
ANOVA

first: Siriluck

last: Ponsuksili

first: Kunsuda

last: Chomwisarutkun

first: Eduard

last: Murani


title: cordycepin-Energetic Homeostasis and Sugar Signaling

summary: bra-inra09-01_bioen - cordycepin - Diversification of the Molecular Mechanisms Involved in the Control of the Energetic Balance in Angiosperms - To evaluate the importance of mRNA stability control in glucose signaling, genome wide RNA transcript levels changes will be evaluated in response to short term treatments with glucose or glucose plus abscisic acid (ABA) under conditions of transcriptional inhibition in Arabidopsis. The underlying mechanisms will be investigated for a selected number of co-regulated genes (transcription factors, kinases).

overall_design: 12 dye-swap - treatment variations

first: Sandrine

last: Balzergue


title: bak1 bkk1 flg22 - Flagellin response in mpk mutants

summary: au-09-01_mpk_flagellin_edu - bak1 bkk1 flg22 - Investigate flagellin mpk dependent genes. - 2 weeks Bak1bkk1 plants treated with flg22 1h 1 microM


title: Reconstruction of an integrative gene regulatory meta-network reveals cell cycle and antiviral response as major drivers of cervical cancer

status: Public on Dec 29 2011

first: Natalia

last: Shulzhenko

address: 9000 Rockville Pike

department: Laboratory of Cellular and Molecular Immunology

institute: NIAID, USA

summary:
Cervical cancer is the one of the most common cancer type among women worldwide, with Human Papillomavirus (HPV) playing a causal role in this disease.  We applied a novel integrative approach to understand the disease process and find its major drivers. We performed a meta-analysis of gene expression and chromosomal aberration studies comprising data on over 500 patients for the reconstruction of a regulatory meta-network. We found that two sub-networks representing cell cycle and antiviral response (largely involving interferon pathways) were driven by chromosomal amplifications of key regulator genes. In the majority of patients, the two types of drivers were located in the same regions of chromosomal aberrations on 3q, 1q and 1p suggesting that a synergistic effect of both processes is necessary for cervical oncogenesis. In addition, our results revealed a cause of antiviral response in the tumor supporting a model of cervical carcinogenesis in which the loss of episomal HPV mediated by immune response promotes the expression of integrated viral oncogenes and tumor progression.
This series is a part of meta-analysis on gene expression in cervical cancer

overall_design: Forty cervical cancer biopsies and twenty normal adjacent tissue samples were obtained from patients with cervical squamous cell carcinomas. Twelve tumor samples were hybridized as pools of two samples, due to RNA quantity limitations. So, in total, there are 34 cervical cancer and 20 normal sample arrays. We used an internal reference design, where the reference RNA sample consisted of a pool of amplified RNAs from cervical cancer biopsies.

first: Karina

last: Mine

first: Gerdine

last: Sanson

first: Andrey

last: Morgun


title: Col-0 flg22 - Flagellin response in mpk mutants

first: edu

last: bueso

summary:
au-09-01_mpk_flagellin_edu - col-0 flg22 - Investigate flagellin mpk dependent genes - 2 weeks Col-0 plants treated 1h with flg22 1uM

Keywords: treated vs untreated comparison

first: Marie-Laure

last: Martin-Magniette


title: bak1bkk1 - Flagellin response in mpk mutants

summary:
au-09-01_mpk_flagellin_edu - bak1bkk1 - Investigate flagellin mpk dependent genes by comparision between bak1bkk1 and col-0.

Keywords: gene knock out

first: Eduardo

last: Bueso

first: Heribert

last: Hirt


title: Gene expression differences between the brachial and femoral artery of the Rapacz HC swine

city: West Lafayette

first: Martin

last: Bahls

address: 800 W Stadium Ave

institute: Purdue University

summary: The age groups were used to investigate how gene expression differences between the brachial and the femoral artery effect the heterogeneous atherosclerotic disease initiation and progression.

overall_design: Total RNA was isolated from brachial and femoral arteries of four one week, six one year, and five two year old Rapacz HC swine.


title: transcriptome analyses of n8514 and wox14-Floral stem gene expression affected by the AtWOX14 gene mutation

status: Public on Dec 24 2011

first: Eddy

last: Blondet

summary: au11-01_wox14bis - transcriptome analyses of n8514 and wox14 - Our scope is to establish a functional link to organ initiation and development in Arabidopsis by identifying genes that are deregulated in the wox14 mutant background. - The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. In Arabidopsis thaliana, an intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was transient during lateral root formation, anthers and stem development . A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Transcriptome analyses of the N8514 transposon donor line and the issued wox14 floral stem basis grown on soil for 8 weeks (growth stage 6) in LD condition is done to identify genes that are deregulated in the wox14 mutant background.

overall_design: 2 dye-swap - gene knock out,normal vs transgenic comparaison

first: Yves

last: Deveaux


title: Expression data from Porcine alveolar macrophages of piglets experimentally infected with Haemophilus parasuis serotype 4 (HPS4) for 28 days

status: Public on Dec 20 2011

city: Wuhan

first: Liu

last: Shuqing

state: Hubei province

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huazhong agricultural university

summary:
Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Haemophilus parasuis is the etiological agent of Glasser’s disease in pigs. Haemophilus parasuis is the etiological agent of Glasser’s disease in pigs.
We used microarrays to study the transcriptome of PAMs infection with HPS4.

overall_design: Healthy Pigs were inoculated intranasally with 2 ml of  4.5×108CFU/ml colony forming units of HPS4 strain MD0322. And the PAMs were isolated at 28 dpi. RNA extraction were extracted from PAMs that obtained from infection pigs and control pigs and hybridization on Affymetrix microarrays.

first: Li

last: Wentao

first: He

last: Qigai


title: Expression data of multiple sclerosis patients receiving subcutaneous Interferon-beta-1a therapy [U133 Plus 2.0]

status: Public on Dec 06 2011

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary: The purpose of this study was to characterize the transcriptional effects induced by subcutaneous IFN-beta-1a treatment (Rebif, 22 µg or 44 µg three times a week) in patients with relapsing-remitting form of multiple sclerosis (MS). By using Affymetrix DNA microarrays, we obtained genome-wide expression profiles of peripheral blood mononuclear cells from 12 MS patients within the first two years of IFN-beta administration.

overall_design: EDTA blood samples were taken from all patients immediately before first and second IFN-beta injection as well as after 1 month, 1 year and 2 years. Total RNA of Ficoll-isolated peripheral blood mononuclear cells from each sample was extracted, labeled and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays to quantify the mRNA levels. This GEO entry provides the U133 Plus 2.0 microarray data.

first: Dirk

last: Koczan

first: Robert

last: Goertsches

first: Uwe

last: Zettl


title: Expression data of Sham and post-MI myocardium from swine

status: Public on Dec 21 2011

city: Amsterdam

first: Diederik

last: Kuster

address: van der Boechorststraat 7

country: Netherlands

institute: VU University Medical Center

summary:
The molecular mechanism underlying cardiac remodeling following myocardial infarction have been incompletely understood. Until now, most studies have been performed in rodents. We studied cardiac remodeling in the physiologically more relevant animal model, the swine.
Microarray analysis was performed on animals that underwent either sham surgery or permanent ligation of the left coronary artery (MI). RNA was isolated from the remote, non-ischemic, regions of the left ventricle.

overall_design: RNA was isolated from 8 sham and 8 MI animals three weeks after surgery. Each group contained 4 males and 4 females. Animals used for the study were 2-3 months old Yorkshire x Landrace swine. Only neutered males entered the study.

last: Duncker


title: LIF-Dependent, Pluripotent Stem Cells Established from Inner Cell Mass of Porcine Embryos

status: Public on Dec 02 2011

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary:
The pig is important for agriculture and as an animal model in human and veterinary medicine, yet, despite over 20 years of effort, it has proved a difficult species from which to generate pluripotent stem cells analogous to those derived from mouse embryos. Here we report the production of LIF-dependent, so called naïve type, pluripotent stem cells from the inner cell mass of porcine blastocysts by up-regulating expression of KLF4 and POU5F1. These cells resemble mouse ES cells and are distinct from the FGF2-dependent, induced pluripotent cell type derived from porcine somatic cells.
Transcript profiling utilized Affymetrix porcine microarrays were conducted to compare the gene expressions associated with pluripotency in the two LIF-dependent pESK lines (pESK I & II, passage 14 & 5, respectively) with a naïve phenotype and two porcine iPSC lines (ID4 & ID6, both passage 7, GSE15472) with a primed phenotype that re-programming of porcine fetal fibroblasts (EGFP-PFF, GSE15472). The pESK lines clustered separately from the porcine iPSC lines, EGFP-PFF and primary cultures established from explants of porine umbilical cord (PUC).

overall_design: Porcine pluripotent stem cells were derived from the inner cell mass with transduction with human KLF4 by lentiviral transduction.

first: Bhanu

middle: P

last: Telugu

first: R

last: Roberts


title: Plant Viral Movement Protein-expressing Yeast Transcriptome compared with Non-Functional Plant Viral Movement Protein-expressing Yeast Transcriptome

status: Public on Dec 01 2011

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

summary: Virus life cycle heavily depends on their ability to command the host machinery in order to translate their genomes. By using a yeast-based approach we have found that over expression of the PNRSV MP caused a severe growth defect in yeast cells. cDNA microarrays analysis carried out to characterise at the molecular level the growth interference phenotype reported the induction of genes related to amino acid deprivation suggesting that expression of MP activates the GCN pathway in yeast cells.

overall_design: Yeast cell cultures were grown 24h in minimal medium with doxycycline (100 mg/ml). These cultures were then diluted to an OD600 nm of 0.1 into fresh minimal medium without doxycycline. At 6 h total RNA was extracted from yeast cells transformed with the pCM:MPpnrsv and MPpnrsvΔHR, a non-functional MPpnrsv mutant lacking its hydrophobic region.

last: Murguia


title: Plant Viral Movement Protein-expressing Yeast Transcriptome compared with wild-type Yeast Transcriptome

overall_design: Yeast cell cultures were grown 24h in minimal medium with doxycycline (100 mg/ml). These cultures were then diluted to an OD600 nm of 0.1 into fresh minimal medium without doxycycline. At 6 h total RNA was extracted from yeast cells transformed with the empty pCM262 vector (pCM construct) and pCM:MPpnrsv.


title: ChIP-chip of E. coli K-12 MG1655 with antibody against ArgR-8myc, Lrp-8myc, and TrpR-8myc under various conditions.

first: Bernhard

last: Palsson

type: Genome binding/occupancy profiling by genome tiling array

summary: We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the ArgR, Lrp, and TrpR regulon experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of  E. coli K-12 MG1655 harboring ArgR-8myc, Lrp-8myc, or TrpR-8myc under various conditions.

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

overall_design: A twelve ChIP-chip study under six separate culture conditions.  The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome.

first: Byung-Kwan

last: Cho

first: Stephen

last: Federowicz

first: Young-Seoub

last: Park

first: Karsten

last: Zengler

middle: O


title: Impact of exercise training on endothelial transcriptional profiles in healthy swine: A genome-wide microarray analysis

city: North Chicago

first: J

middle: Wade

last: Davis

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

summary: While the salutary effects of exercise training on conduit artery endothelial cells have been reported in animals and humans with cardiovascular risk factors or disease, whether a healthy endothelium is alterable with exercise training is less certain.  The purpose of this study was to evaluate the impact of exercise training on transcriptional profiles in normal endothelial cells using a genome-wide microarray analysis.  Brachial and internal mammary endothelial gene expression was compared between a group of healthy pigs that exercise-trained for 16-20 weeks (n=8) and a group that remained sedentary (n=8).  We found that a total of 130 genes were up regulated and 84 genes down regulated in brachial artery endothelial cells with exercise training.  In contrast, a total of 113 genes were up regulated and 31 genes down regulated in internal mammary artery endothelial cells (>1.5-fold and false discovery rate<15%).  Although there was an overlap of 66 genes (59 up regulated and 7 down regulated with exercise training) between the brachial and internal mammary arteries, the identified endothelial gene networks and biological processes influenced by exercise training were distinctly different between the brachial and internal mammary arteries. These data indicate that a healthy endothelium is indeed responsive to exercise training and support the concept that the influence of physical activity on endothelial gene expression is not homogenously distributed throughout the vasculature.

overall_design: Brachial and internal mammary endothelial gene expression was compared between a group of healthy pigs that exercise-trained for 16-20 weeks (n=8) and a group that remained sedentary (n=8). The arteries were taken from the same animals, and after quality assessment, so there were 29 total arrays (15 unique pigs), 14 with an array for both the brachial artery and the internal mammary artery (IMA), and the remaining 1 having only brachial. One pig had bad RNA quality and is missing from both IMA and brachical. Therefore, there were 15 IMA (7 SED, 8 EX) and 14 brachial arrays (7 SED, 7 EX) that were used in this study.

first: Jaume

last: Padilla

first: M

last: Laughlin


title: Primary cultures of glomerular parietal epithelial cells or podocytes with proven origin

status: Public on Nov 16 2011

first: Gregor

last: Warsow

address: Ernst-Heydemann-Str. 8

department: Medical Department

summary: Parietal epithelial cells (PECs) are crucially involved in the pathogenesis of rapidly progressive glomerulonephritis (RPGN) as well as in focal and segmental glomerulosclerosis (FSGS). In this study, transgenic mouse lines were used to isolate pure, genetically tagged primary cultures of PECs or podocytes using FACsorting. By this approach, the morphology of primary glomerular epithelial cells in culture could be resolved: Primary podocytes formed either large cells with intracytoplasmatic extensions or smaller spindle shaped cells, depending on specific culture conditions. Primary PECs were small and exhibited a spindle-shaped or polygonal morphology. In the very early phases of primary culture, rapid changes in gene expression (e.g. of WT-1 and Pax-2) were observed. However, after prolonged culture primary PECs and podocytes still segregated clearly in a transcriptome analysis - demonstrating that the origin of primary cell cultures is important. Of the classical markers, synaptopodin and podoplanin expression were differentially regulated the most in primary PEC and podocyte cultures. However, no expression of any endogenous gene allowed to differentiate between the two cell types in culture.  Finally, we show that the transcription factor WT1 is also expressed by PECs. In summary, genetic tagging of PECs and podocytes is a novel and necessary tool to derive pure primary cultures with proven origin. These cultures will be a powerful tool for the emerging field of parietal epithelial cell biology.

overall_design: Total RNA for genechip analysis was derived from:  1) Primary parietal cells isolated by FACS sorting of glomeruli cultivated in  1a) RPMI media  1b) EGM-MV media     2) Primary podocyte cells isolated by FACS sorting of glomeruli cultivated in   2a) RPMI media  2b) EGM-MV media

first: Nazanin

last: Kabgani

first: Tamara

last: Grigoleit

first: Kevin

last: Schulte

first: Antonio

last: Sechi

first: Sibille

last: Sauer-Lehnen

first: Carmen

last: Tag

first: Peter

last: Boor

first: Christoph

last: Kuppe

first: Sandra

last: Schordan

first: Jörg

last: Mostertz

first: Ravikumar

last: Chilukoti

first: Georg

last: Homuth

first: Nicole

last: Endlich

first: Frank

last: Tacke

first: Ralf

last: Weiskirchen

last: Fuellen

first: Karlhans

first: Juergen

last: Floege

first: Bart

last: Smeets

first: Marcus

last: Moeller


title: Regulation of global gene expression in human Loa loa infection is a function of chronicity

status: Public on Nov 24 2011

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

summary: Differential gene expression to parasite and nonparasite antigen was seen in infected patients with lifelong exposure to the human filarial parasite Loa loa (endemics) compared with patients who became infected due to temporary residence or travel in an endemic country (expatriates).

overall_design: CD4+ and CD8+ cells were isolated; comparison was done between unstimulated cells from 2 patient groups and between parasite microfilarial (MfAg) and nonparasite streptolysin O (SLO) antigen-stimulated cells with unstimulated cells; Technical replicates (2 unstimulated; 2 each antigen)

first: Cathy

last: Steel

first: Thomas

middle: B

last: Nutman


title: The role of sepsis in the development of limb muscle weakness in a porcine ICU model

status: Public on Oct 19 2011

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

country: Sweden

institute: uppsala university

summary:
Background : The aim of this study is to improve our understanding of the mechanisms underlying the role of sepsis 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  endotoxin-induced sepsis.
Results : An increased expression of genes involved in chemokine activity 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 sepsis has an additive deleterious role in acute quadriplegic myopathy. Sepsis-induced molecular mechanisms involving chemokine/innate immunity and heat shock proteins are forwarded as probable mechanisms underlying the decreased force generating capacity.
Conclusions : This sepsis had significant effect on biceps femoris muscle force-generation capacity but not on fiber size. However, significant differences were observed between the MV and  MV+SEP in the transcriptional regulation of an increased expression of genes involved in chemokine activity genes like MCP-1 and transcriptional regulation genes like JUNB, STAT3 and BHLHB2. A decreased expression in genes regulating heat shock proteins like HSP 90, HSP 70 and αB-crystallin, cytoskeletal & sarcomeric like MAP1A, MyBP-C1 and MYH7 and oxidative stress response like SRXN1 and SOD2 were also apparent. Therefore, it appears that sepsis has an additive negative role in acute quadriplegic myopathy.

overall_design:
Four female domestic piglets (Sus scrofa, average body weight 25.5 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 betamethasone 0.1 mg/kg (Betapred; GSK, Slona, Sweden) twice daily for 5days. Endotoxemia was induced by a continuous infusion of Escherichia coli endotoxin, serotype O26:B6 (Sigma Labkemi, Stockholm, Sweden) at 36 µg/kg/h for 1h.
Key words : Treatment, immobilization, muscle function.

first: Sudhakar

last: Aare

last: Radell

first: Lars

middle: I

last: Eriksson

first: Yi-Wen

last: Chen

first: Eric

last: Hoffman

last: Larsson


title: Invitro Porcine Model Cutaneous Fibrosis

status: Public on Sep 30 2011

city: Seattle

first: Surawej

last: Numhom

state: WA

department: Surgery

institute: University of Washington

summary: The goal was to obtain the differential transcriptome in the deep cones fibroblasts between shallow and deep wounds in Duroc breeds at 20 wks.

overall_design: We made shallow and deep wounds on the backs 2 Duroc pigs, biopsied the wounds at 20 weeks, cultured fibroblasts, extracted and  the RNA from the cultured fibroblasts, and hybridized the Affymetrix GeneChip. We compared wound depth, the system included 1 factors (depth). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.

first: Loren

last: Engrav


title: Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle

status: Public on Sep 20 2011

city: lleida

first: angela

last: canovas

state: lleida

address: 191, rovira roure

institute: irta

summary: A mRNA expression study has been performed 20-25 minutes postmortem obtained samples from Longissimus dorsi  muscle of 59 Duroc x LD/LW pigs to search for gene sequences related to meat quality (pH24, pH45, “Lab” colour coordinates, curing yield and exudation at three different times) or to meat composition (intramuscular fat, content of several fatty acid (C16:0, C18:0, C18:1 and C18:2), ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) traits in order to find targets for selection. Gene ontology analysis, biological pathways and gene networks studies all show, that many more differentially expressed genes (506 vs 279) are related to meat quality (Group P, or perimortem characters) than to meat composition traits (Group L, or  whole life traits). The difference between the number of GO terms annotated, biological pathways and gene networks in groups P and L is notable due to the differences in the complexity of the “generation process” of P-traits and the involvement of other tissues or organs in the generation of variability of L-traits. Also, interactions between a list of differentially expressed genes were found in ECM-receptor interaction, TGF-beta signaling pathway, fatty acid elongation in mitochondria and adipocytokine signalling pathway indicating that a substantial fraction of the gene networks could be associated with interactions between differential expressed genes related to traits under study. A high number of the most overexpressed genes are related to muscle development and functionality and repair mechanisms; they could be good candidates for breeding programs whose main goal is to enhance meat quality.

overall_design: 59 Longissimus Dorsi samples from 59 LD/LW x Duroc cross. A total of 33 traits on composition, conformation and meat quality and compositional traits were recorded in the left Longissimus dorsi muscle.

first: Angela

last: Cánovas

first: Luis

last: Varona

first: Carmen

last: Burgos

first: Almudena

last: Galve

first: José

middle: A

last: Carrodeguas

first: Noelia

last: Ibáñez-Escriche

first: Inmaculada

last: Martín-Burriel

first: Pascual

last: López-Buesa


title: A time series study on BMP6 induced osteoblast differentiation of human mesenchymal stem cells (hMSC)

city: Cold Spring Harbor

first: Weijun

last: Luo

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Lab

summary:
BMP6 mediated osteoblast differentiation plays a key role in skeletal development and bone disease. Unfortunately, the signaling pathways regulated by BMP6 are largely uncharacterized due to both a lack of data and the complexity of the response.
To better characterize the signaling pathways responsive to BMP6, we conducted a time series microarray study to track BMP6 induced osteoblast differentiation and mineralization.

overall_design: Human MSC cells underwent osteogenic induction with BMP6 treatment for 0 hours, 8 hours, 24 hours, and 96 hours, which correspond to four phenotypic groups, i.e. control, preosteoblast (no mineralization), (sub-maximal) mineralization, and maximal mineralization at 14 days after the initiation of BMP treatment (18 days in total). Cells were harvested at 8 hours, 24 hours, 96 hours and 10 days for microarray profiling. Assays were run in duplicate for a total of 26 arrays. We only used 20 arrays in the reference paper.

first: Michael

last: Friedman

first: Peter

last: Woolf

first: Kurt

middle: D

last: Hankenson


title: Nocturnal expression data of Synechococcus in WT and kaiABC-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 of genes are downregulated in the dark, while 10% of genes are upregulated. Here, we employed high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild type and kaiABC-null strains under continuous dark (DD) conditions.
We found that expression profile of a subset of genes on the genome in DD was dramatically affected by kaiABC-nullification, and the magnitude of dark-induction was dependent on time when cells were transferred from light to DD

Keywords: timecourse data (0-12 h) under continuous darkness after dark:light cycles from Synechococcus elongatus PCC 7942 wild type and kaiABC-null strains

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Wild type (WT) and kaiABC-null (DkaiABC) S. elongatus PCC 7942 strains were analyzed under continuous dark (DD) conditions after two 12h:12h light:dark (LD) cycles using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: Two independent experiments in WT and Dkai strains under DD (hours 0, 0.5, 1, 2, 4, 8 and 12).

first: Norimune

last: Hosokawa


title: In Vitro Transcriptome Analysis of Porcine Plexus Epithelial Cells in Response to Streptococcus suis: Functions of the Choroid Plexus in Antimicrobial Defense

status: Public on Aug 15 2011

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: We used microarrays to detail the global gene expression changes following apical infection of porcine choroid plexus epithelial cells (PCPEC) with Streptococcus suis (S. suis)

overall_design: We compared PCPEC either un-treated or infected with wild-type S. suis strain 10 or the acapsular strain 10cpsDEF, respectively, to determine global gene expression changes by microarray analysis

first: L

first: C

last: Schwerk


title: transcripomics on the arabidopsis root tip during phosphate starvation-Transcripomics on the Arabidopsis Root tip during phosphate starvation

status: Public on Sep 09 2011

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

institute: INRA

summary: The objective of this project is to identify genes that are expressed in the Arabidopsis thaliana root tip and that are early induced (or repressed) by phoshate deficiency. Seedlings were germinated and grown (for 6 days) on phosphate rich medium and transfered to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800um) of the primary root was cut under a dissecting microscope. About 100 root tips per condition were harvested and there mRNA was analysed with the use of microarrays.

overall_design: 6 dye-swap - time course,treated vs untreated comparison

first: Tinne

last: De Cnodder

first: Thierry

last: Desnos

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression data from liver sample of pig commercial herd Pix(DLxDE).

status: Public on Oct 31 2011

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
In this study, we used correlation analysis of the expression profiles and carcass traits to produce a list of functional candidate genes under the assumption that genes with strong correlation between their expression values and drip belong to pathways or networks relevant for the control of the trait.
Expression QTL analyses for transcripts showing trait dependent expression were done in order to identify genes which show trait associated expression.

Keywords: Corrrelation and association

overall_design: 150 crosbred pig were hybridized to Affymetrix Porcine Genome Arrays.

first: Siriluck

last: Ponsuksili


title: Expression data from articular and growth plate cartilage

status: Public on Jul 29 2011

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary:
The aim of the current study was to identify molecular markers for articular cartilage that can be used for the quality control of tissue engineered cartilage. Therefore a genom-wide expression analysis was performed using RNA isolated from articular and growth plate cartilage, both extracted from the knee joints of minipigs.

Keywords: Native material or primary cells isolated from articular cartilage and growth plate cartilage

overall_design: Articular and growth plate cartilage were taken for RNA extraction and hybridization on Affymetrix microarrays. Furthermore chondrocytes from each type of cartilage were isolated and cell culture was started and terminated at day 10 or day 20. Total RNA from cultivated cells was extracted, and hybridization on Affymetrix microarrays was performed.

first: Thorsten

last: Schinke


title: comparison of transcriptomes in mad mutants-Transcriptome analysis of miRNA action deficient mutants

status: Public on Sep 15 2011

department: URGV

summary: rs10-04_mad - comparison of transcriptomes in mad mutants - What gene sets are differentially expressed in mad mutants? - Seeds of GFP171.1 (parental line), mad1, mad2, mad3, mad6 and dcl1-12 were sterilized and germinated on Murashige/Skoog medium with 0.9% agar. Plates were stratified at 4C in the dark for 4 days. The plates were then transferred to a growth cabinet at 21C under a 16h light/8h darkness light regime, and the seedlings were harvested 18 days after transfer to the growth cabinet.

overall_design: 10 dye-swap - genotype comparaison

first: Olivier

last: Voinnet

last: Brodersen


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

status: Public on Nov 30 2011

city: Dummerstorf

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

overall_design: Refer to individual Series


title: Fetal programming of hepatic transcriptome in response to gestational dietary protein levels in the pig (HP data set)

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

Keywords: ANOVA

overall_design: per stage offspring of 8 gilts were collected for expression profiling

first: Michael

last: Oster


title: Comparative transcriptomic profiling of peripheral blood mononuclear cells (PBMNCs) isolated from pigs exposed to an atherogenic diet (AD) or to an AD supplemented with Grape Extract (GE) and/or Resveratrol (RES).

status: Public on Jul 23 2011

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

institute: CEBAS-CSIC

summary: We used Affymetrix microarrays to investigate gene expression changes in PBMNCs isolated from female and male pigs to determine significant modulatory effects that may have been induced by the intake of GE and (or) RES during 4 months in animals fed an atherogenic diet (AD) .

overall_design:
The aim of this work was to determine whether the intake of low doses of a Grape Extract (GE; 1 g/70 Kg animal body weight) and (or) Resveratrol (RES; 18 mg/70 Kg animal body weight) exerted any modulatory effects, at the level of gene expression, in PBMNCs isolated from female and male pigs exposed to an atherogenic diet (AD) for 4 months. We isolated PBMNCs, and the corresponding total RNA, from 2 female and 2 male pigs for each group. Pure RNA was extracted from the PBMNCs for microarrays analyses (Affymetrix) and gene differential expression determined between the AD fed animals and control (CT) animals (to determine the effects of a high-fat consumption) and between the AD fed animals supplemented with GE and (or) RES and the animals fed the AD diet alone (to determine the effects of GE and (or) RES on the fat consumption). In addition, the effects of the consumption of GE and RES against a standard control diet (CT) were also determined.
Differential gene expression:
1) AD vs CT (response to exposure to a high-fat diet);
2) AD-GE vs AD (modulatory effects of the intake of a grape extract on high-fat fed animals);
3) AD-GE-RES vs AD (modulatory effects of the intake of a resveratrol-enriched grape extract on high-fat fed animals);
4) AD-RES vs AD (modulatory effects of the intake of resveratrol on high-fat fed animals);
5) CT-GE-RES vs CT (modulatory effects of the intake of a resveratrol-enriched grape extract on animals fes a standard pig chow).

first: Jesus

middle: G

last: Cantalejo

first: Pedro

last: Botías


title: wip overexpressing plants-Transcriptome analysis of WIP overexpressing plants

status: Public on Sep 01 2011

city: EVRY CEDEX

first: Elftieh

last: Samira

address: 2 rue Gaston Crémieux, CP 5708

department: Unité de Recherche en Génomique Végétale

summary:
adt10-01_wip2 - wip overexpressing plants - Identification of genes induced or repressed by WIP genes - The objective is to identify genes responsible for the phenotypes observed in WIP overexpressing lines. WIP transcription factors are involved in reproductive and vegetative development by acting on the remodeling of various tissues. The WIP related processes have a major impact, in particular on reproduction (sex determination, fertilization, development of the seed). The way of action of these transcription factors is probably conserved, their effect depending only on their specificity of expression. Two WIP genes, NTT and TT1, was overexpressed in Arabidopsis thaliana. The objective is to compare the common deregulated genes (and in particular repressed) in the transcriptome of these two overexpressor lines, to highlight their mode of action and the way they act on the tissue in which they are expressed.

Keywords: gene knock in (transgenic),normal vs transgenic comparaison

overall_design: 6 dye-swap - CATMA arrays

first: Abdelhafid

last: Bendahmane

first: Samira

last: Elftieh


title: Biodiversity and functional genomics of endogenous small RNAs induced upon biotic and abiotic stresses in plants (gemsupv2ts-7)

status: Public on Aug 01 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

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

summary: au10-09_gemsupv2ts-7 - gemsupv2ts-7 - Determine the level of expression in transgenic plants expressing geminiviral gene silencing suppressors. - One transgenic line of Arabidopsis overexpressing the geminiviral silencing suppressor V2TS was grown in adition to a control and their total RNA was extracted in order to study its genetic expression profile.

overall_design: 3 dye-swap - gene knock in (transgenic)

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

last: Bejarano


title: oligosaccharide treatment - 24 hpt-Effect of oligosaccharide treatments on gene expression.

status: Public on Nov 01 2011

first: Eddy

last: Blondet

summary: ra10-03_eliciteur - oligosaccharide treatment - 24 hpt - Do the treatments modify gene expression in a way that can give us a hint as to their use in crop protection? What is the effect of the adjuvant on gene expression? - 6,5-week-old arabidopsis plants grown in short-day photoperiod were spray-treated with water, an adjuvant or oligosaccharides in the adjuvant (10 plants per condition, 4 replicates per condition). 6 hrs, 24 hrs and 48 hrs after the treatment, samples were taken (2 7mm diameter leaf disks per plant, from medium-aged leaves), frozen in liquid nitrogen, and later on total RNA was extracted.

overall_design: 16 dye-swap - treated vs untreated comparison

first: Tinne

last: De Cnodder

first: Xavier

last: Daire

first: Annie

last: Buchwalter

first: Sandrine

last: Balzergue

last: Martin-Magniette


title: Microarray analysis of transcripts in the liver of gilthead sea bream with high plasma cortisol levels induced by slow-release cortisol implants

status: Public on Jul 20 2011

city: Bellaterra-Barcelona

first: Mariana

middle: Pereira Mónica

last: Teles

address: Campus Universitari

institute: Universitat Autònoma de Barcelona

summary: The present work was designed to assess the effects of high plasma cortisol levels induced by slow-release cortisol implants in the mRNA transcription of the GR in the different organs of the Sparus aurata, including liver. For that purpose fish were intraperitoneally injected with the implants containing two different concentrations of cortisol (50 or 200 µg/g body weight) and blood and organs were sampled after 7 and 14 days of implantation. Only fish with 200 µg/g implants exhibited a significant rise in the plasma cortisol.

overall_design: For microarray analysis we used livers of gilthead sea bream (N=36 fish). Fish were injected with 200 µg/g body weight of cortisol and sampled after 7 and 14 days (n=6 for each condition). RNA samples were grouped into pools of 2 animals for each time point. The analysis were carried out considering the transcripts differentially expressed in the group of fish implanted during 7 days with cortisol comparing to control group. Additionally, the transcripts differentially expressed at day 14 were compared with day 7.

first: Sebastian

last: Boltana

first: Simon

last: Mackenzie


title: Expression data of porcine mammary glands from late pregnancy to peak lactation.

status: Public on Jul 16 2011

city: Guangzhou

first: D P

last: Shu

address: 483 Wushan Avenue, Tianhe District

institute: South China Agricultural University

summary:
Sow milk yield and quality is crucial for the survival and growth of piglets. Mammary epithelial cell proliferation, differentiation, milk component production and galactopoietic hormone and cytokine synthesis result from the quantities of differentially expressed genes.
This study used the Affymetrix Porcine GeneChip to acquire a comprehensive picture of transcriptional adaptations in the mammary glands of lactating sows.

overall_design: Mammary tissue samples were collected from six sows at -17, 1 and 17 d relative to parturition. Mammary tissues from two sows were used to extract RNA and were subsequently pooled in equal volumes. Nine pooled samples were hybridized to porcine Affymetrix GeneChips.

first: Danping

first: Baoliang

last: Chen

first: Wutai

last: Guan


title: Athsq1 is linked to Cdkn2a

status: Public on Oct 01 2011

city: Rahway

first: Oscar

last: Puig

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

summary: Common genetic variants in a 58-kilobase (kb) region of chromosome 9p21, near the CDKN2A/B cell proliferation inhibitor genes, are strongly associated with coronary artery disease (CAD). We previously reported a congenic mouse model harboring an atherosclerosis susceptibility locus in a region of homology with the human 9p21 locus. We now report markedly decreased Cdkn2a (cyclin-dependent kinase inhibitor 2a) mRNA expression in macrophages and increased circulating levels of Ly6Chigh inflammatory monocytes in congenic mice compared to controls. A bone marrow (BM) transplantation study revealed that BM-derived cells from Cdkn2a+/- mice are capable of conferring accelerated atherosclerosis, increased inflammatory monocyte subsets and monocyte proliferation in the Ldlr-/- mouse model. These findings provide a mechanistic link between decreased expression of Cdkn2a transcripts, increased monocyte proliferation, and accelerated atherosclerosis.

overall_design: Aorta and macrophages from ten C57BL/6.MOLFc4(51Mb)-Ldlr-/- mice and their control C57BL/6-Ldlr-/- were obtained, RNA purified and hybridized to GPL9734 Affimetrix microarrays.

first: Carrie

last: Welch

first: Alan

last: Tall


title: Photooxidative stress and light acclimation in the PSII antenna-deficient ch1 mutant

status: Public on Dec 09 2011

first: Soubigou-Taconnat

last: Ludivine

summary: cea10-02_light - photooxidative stress  - To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant  - The extracts are carried out starting from sheets of Arabidopis thaliana having pushed on compost in controlled conditions (light: 250 µmol.m-2.s-1, temperature: 22°C day 18°C night, moisture: 55%, photoperiod: 8:00 jour/16h night) during 4 and 8 weeks for respectively the Col0 genotype and the mutant ch1. The acclimatization of the plants is done during 48 H under an average luminous intensity (450 µmol.m-2.s-1, photoperiod 8:00), whereas the stress requires a strong luminous intensity (900 µmol.m-2.s-1, photoperiod 8:00) and low temperature (10°C day, 14°C night) also during 48 hours.

overall_design: 24 dye-swap - genotype comparison, treated vs untreated comparison

first: Ludivine

last: Taconnat

first: Fanny

last: Ramel

first: Marie-Laure


title: Right ventricular failure due to coronary artery ligation

status: Public on Aug 24 2011

city: Uppsala

first: Per

last: Vikholm

address: Akademiska sjukhuset

department: Cardiothoracic Surgery

institute: Uppsala University

summary:
A porcine microarray study of acute right ventricular failure due to coronary artery ligation of the right ventricular free wall.

1. Baseline sample from the free right ventricular wall.

2. Ligation of the coronary arteries on the right ventricular free wall induced right ventricular heart failure. When the pressure in the right atrium rose to >20 mmHg, heart failure samples were taken from the free right ventricular wall.

overall_design: A series of nine pigs, two samples from each animal: baseline and heart failure

first: Laila

last: Hellgren

first: Petter

last: Schiller


title: mpk4/mpk4 gof vs mpk4/mpk4 vs col0   -Transcriptome study of mpk4 complemented line with a hyperactive form of MPK4 (MPK4 GOF).

status: Public on Aug 20 2011

first: Eddy

last: Blondet

summary:
au10-07_mpk4gof - mpk4/mpk4 gof vs mpk4/mpk4 vs col0    - Genes regulated by MPK4 pathway.        - In order to study of the genes controlled by MPK4 pathway we generate mpk4 complemented lines expressing active MPK4 (MPK4 GOF). For the transcriptome analysis we compare the MPK4 GOF to mpk4/MPK4 (complemented mpk4 mutant with a wt MPK4) and to Col0.

Keywords: genotype comparaison

overall_design:
6 dye-swap - CATMA arrays
Comparisons of MPK4 GOF to mpk4/MPK4 (complemented mpk4 mutant with a wt MPK4) and to Col0.

first: Catherine-

last: Colas des Francs-Small

first: Jean

last: COLCOMBET

first: Souha

last: Berriri

first: Sandrine

last: Balzergue


title: Differential expression in laccase mutants of Arabidopsis thaliana

status: Public on Jul 02 2011

summary: ra10-01_laccases; laccase mutations. We demonstrated that laccases are involved in lignin polymerisation. Mutants have already been tested on microarrays and there is few differences compared to wild-type. The laccase mutation seems surgical. We possess a new double mutant, called snips, with a semi-dwarf phenotype, and we want to determine its profile.

overall_design:
Each mutant was compared to wild type. All plants were harvested at the same developmental stage in the same growth chamber between 10h30 and 11h.
10 dye-swaps. CATMA arrays.

first: Jean-Pierre

last: Renou

last: Martin-Magniette


title: Expression data from Porcine alveolar macrophages of piglets experimentally infected with Streptococcus suis serotype 2 (SS2) for 7 days

status: Public on Jul 15 2011

city: Wuhan

first: Tao

middle: Wen

last: Li

state: Hubei

address: No.1, Shizi_shan street, Hongshan district

department: Division of Animal Infectious Disease

institute: Huazhong agricultural university, State Key Laboratory of Agricultural Microbiology

summary: Porcine alveolar macrophages (PAMs) play an important role in innate immunity. Streptococcus suis serotype 2 is a pathogen responsible for several diseases in both pigs and humans. We used microarrays to study the transcriptome of PAMs infected with SS2.

overall_design: Healthy pigs were inoculated intranasally with 2 ml of 4.84×10^6 colony-forming units of SS2 strain SC19. The PAMs were isolated at 7 dpi. RNA was extracted from PAMs obtained from infected pigs and control pigs, and hybridized on Affymetrix microarrays.

first: Li

last: Wentao

first: Liu

last: Shuqing


title: Expression data from Porcine alveolar macrophages infection with Haemophilus parasuis (HPS)

status: Public on Jun 28 2011

first: Wang

last: Yang

address: Shizishan street No.1

institute: Huazhong agricultural university

summary:
Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Haemophilus parasuis is the etiological agent of Glasser’s disease in pigs.
We used microarrays to study the transcriptome of PAMs infection with Haemophilus parasuis.

overall_design: Healthy Pigs were intratracheally challenged with H.parasuis strain 0165. And the PAMs were isolated at 6 dpi. RNA extraction were extracted from PAMs that obtained from infection pigs and control pigs and hybridization on Affymetrix microarrays. We sought to obtain the differently expressed genes that related to H.parasuis infection to understand the mechanism of PAMs against H.parasuis.

last: Chong


title: primary floral stem 40cm-Modifications of transcriptome in primary floral stem of Arabidopsis thaliana deregulated for a peroxydase involved in the lignification.

status: Public on May 25 2011

summary:
ra07-01_prx34 - primary floral stem 40cm - The At3g49120 gene codes for the peroxidase 34 (PRX 34), an enzyme potentially involved in the polymérisation of monolignols, the lignin precursors. This enzyme is expressed in primary floral stem and its absence has an impact on the lignin quantity and biomass (at the young stage). Here, its question to characterize several mutants. - Each mutant compare to wild type, samples only primary floral stem of 40cm

Keywords: normal vs transgenic comparaison

overall_design: 2 dye-swap - CATMA arrays


title: Analysis of glycosyltransferase gene expression in human monocytes, macrophages and DC

status: Public on Jun 14 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: So far, although differentiation and activation of Ag presenting cells, including monocytes, dendritic cells (DCs) and macrophages are accompanied by programmed remodelling of cell surface glycosylated molecules with potentially biologically important consequences, no global analysis of the expression of genes involved in glycan biosynthesis (essentially glycosyltransferases (GTs) and modification (mainly sulfotransferases) has been reported in these cells. Our project aims to obtain global information relating to the expression of genes encoding GTs and sulfotransferases in human monocytes, DCs and macrophages isolated or differentiated from the same donor. We also aimed to compare the expression profile of these genes in immature versus mature (immunostimulatory phenotype) DCs and macrophages (LPS stimulation, 4 and 18 hrs). To this end we have performed three independent experiments (n = 7 x 3 samples) using the dedicated gene microarray (glycogene-chip v3). Although, globally the data are interesting(please see the summary below), they lack significance and are not yet exploitable. The relatively high variability between samples probably results from the human donor sources given their heterogeneous genetic makeup and natural history. Thus, to reach significance, we believe that additional donors need to be analyzed. Of note, the time point “4hrs” can be omitted since it does not appear to be indicative. Three x 5 samples would be thus necessary.

overall_design:
Utilizing a focused gene microarray, we intended to compare the glycosyltransferase (GT) and sulfotransferase gene expression profile of human monocytes relative to immature dendritic cells (DCs) and to macrophages and to characterize variations in DCs and macrophages undergoing maturation. Micro-array analysis indicated that monocytes express transcripts for a full set of enzymes involved in the biosynthesis of N- and O-glycans potentially elongated by poly-LacNAc chains with type II terminal sequences. Monocytes also express, at a very good level, genes encoding enzymes involved in glycosaminoglycan biosynthesis, but seem to have a limited capacity for glycolipid biosynthesis. Immature DCs and macrophages exhibit similar pattern of GT and sulfotransferase expression with only a limited number of cell type specific gene expression. Approximately 15 % of GT and sulfotransferase transcripts varied in both DCs and macrophages, the majority of them being up-regulated compared to monocytes. Strikingly, stimulation of DCs and Ms with lipopolysaccharide caused a general alteration in gene expression, in particular in DCs, mainly affecting genes found to be positively modulated during the differentiation steps. LPS treatment also caused a relatively minor increase in gene expression in macrophages whereas in DCs, the expression levels of a significant number of genes were enhanced. Validation of this analysis was partially provided by quantitative RT-PCR and flow cytometry of cell surface glycan epitopes. Collectively, this preliminary study implies an important modification of the pattern of glycosylation in differentiated and activated APCs with potential biological consequences.
Our project aims to obtain global information relating to the expression of genes encoding GTs and sulfotransferases in human monocytes, DCs and macrophages isolated or differentiated from the same donor. We also aimed to compare the expression profile of these genes in immature versus mature (immunostimulatory phenotype) DCs and macrophages (LPS stimulation, 4 and 18 hrs).

first: François

last: Romagne


title: Expression data from longissimus dorsi muscle of Meishan pigs

status: Public on Jul 01 2011

first: Xiaoting

last: Feng

address: 1 Shizishan Street

institute: Huazhong Agricultural University

summary:
The skeletal muscle growth and development is a very complicated but precisely regulated process with interwoven molecular mechanisms. Skeletal muscle is a very heterogeneous tissue that is made up of a large variety of functionally diverse fiber types. Muscle mass is therefore largely determined by the number and size of those fibres. These fibre characteristics are determined by hyperplasia before birth and by hypertrophy after. Around 65 dpc and three postnatal stages (newborn, 3 days; young, 60 days; and mature, 120 days) are key time points in swine skeletal muscle growth and development.
We used microarrays to detail the global programme of gene expression underlying porcine skeletal muscle growth and development.

overall_design: Porcine longissimus dorsi muscles were selected at four stages of development for RNA extraction and hybridization on Affymetrix microarrays. We sought to investigate the global gene expression patterns accompanying the skeletal muscle development. To that end, we selected longissimus dorsi muscles at four time-points: 65 days post coitus, 3 days, 60 days and 120 days afterbirth.

first: Hui

last: Qian


title: della-regulation in darkness versus light-DELLAs contribute to skotomorphogenesis

status: Public on Jun 13 2011

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

summary:
rs09-09_della-dark - della-regulation in darkness versus light - Identification of DELLA-dependent downstream targets in darkness - Aim was to determine downstream target of DELLA proteins involved in skotomorphogenesis. Wt, ga1-3, ga1-3_rga_gai_rgl1_rgl2_rgl3 global seeds were sterilized, sown on MS agar plates then put for stratification for 3 days at 4°C. Plates were placed in growth cabinet at 22°C for 5 days in darkness or in continous light.

Keywords: gene knock out

overall_design: 9 dye-swap - CATMA arrays

first: Pascal

last: Genschik

first: Patrick

last: Achard

first: Marie-Laure


title: genes regulated by ros and dme-Genetic dissection of endosperm development

status: Public on Jun 02 2011

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

summary: rs10-02_ros_dme - genes regulated by ros and dme - Genes regulated by ros/dme? - Seeds of Col x ROS-/-/DME+/- 3 and 6 days after pollination (DAP) were harvested. Seeds of the cross Col x Col (3 and 6 DAP) were used as a control.

overall_design: 4 dye-swap - gene knock out

first: Arp

last: Schnittger


title: Expression data from porcine adrenal gland

status: Public on May 31 2011

first: Eduard

last: Murani

department: Molecular Biology

summary: To gain insight into the adrenal stress response, we analyzed differential mRNA expression of genes associated with stress induced by aggressive behaviour in the pig

overall_design: In an animal experiment various levels of aggressive behaviour and stress were induced by mixing groups of unfamiliar pigs with different aggressiveness. To analyze adrenal stress response we selected two experimental groups for comparison, each comprising eight animals (n=16) which differed significantly in aggressive behaviour and plasma cortisol levels. To identify differentially expressed genes, we compared the adrenal transcriptome of these two groups of pigs, using the Affymetrix GeneChip porcine Genome Array.

first: Klaus

last: Wimmers


title: Effect of DJ-1 on early development in porcine nuclear transfer embryos

status: Public on Apr 07 2011

city: Kyoto

first: Kei

last: Miyamoto

address: Oiwakecho, Kitasirakawa, Sakyo-ku

department: Agriculture

institute: Kyoto university

summary: We aimed to identify a reprogramming factor in mammalian oocytes. DJ-1 is one candidate gene of the factor. Inhibition of DJ-1 function in nuclear transfer embryos affected developmental abilities. The downstream effect of this DJ-1 inhibition was examined using microarrays.

overall_design: Nuclear transfer (NT) embryos (23-26 embryos per each sample) were collected at 28 h after nuclear transfer when many of the embryos had just reached the 2-cell stage. Total RNA was extracted and hybridized on the Affymetrix GeneChip Porcine Genome Array. Global transcripts were compared among NT embryos injected with anti-DJ1 antibody (αDJ1-NT_1), NT embryos injected with IgG (IgG-NT_1), non-injected NT embryos (NT_1) and donor cells (DonorCell_1). Biologically different samples of αDJ1-NT (αDJ1-NT_2) and IgG-NT (IgG-NT_2) were prepared and the microarray analysis was repeated. In both trials, NT embryos injected with IgG (IgG-NT_1 or IgG-NT_2) were used as controls.


title: Oligonucleotide microarray for Sparus aurata

status: Public on Apr 23 2011

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

summary:
This study describes the development and validation of the Aquagenomic Sparus aurata oligonucleotide-microarray (SAQ) based on the Agilent Technology system (eArray) to provide a platform for studies on the gene expression of gilthead seabream.  The platform developed used all available public ESTs stored and annotated in the Aquagenomic Consortium seabream library (10K).

In fish, lipopolysaccharide (LPS) gives a robust cytokine response that is stimulated by crude LPS preparations, some component of the LPS complex are responsible for this stimulation. Peptidoglycan (PGN) is a component of G-negative bacteria (found as a contaminant of crude LPS preparations) able to be recognized by macrophages inducing depth transcriptional modulations and a strong inflammatory response. For microarray analysis, head kidney macrophage cultures were used (N = 36 fish). Each cell culture was stimulated with equal concentrations of PGN and LPS from E. coli O111:B4 strain (10 ug/mL): non-stimulated cell cultures (control n = 9 fish), stimulated during 6 h with LPS (n = 9), and stimulated during 1 h (n = 9), and 6 h (n = 9) with PGN. A loop microarray design approach was used for the study. All experimental RNA samples were labelled with a single colour dye (Cy3) and each stimulated sample was compared to the control sample (pool without stimulation) labelled with the same dye (Cy3). Our microarray analyses identified differential transcriptional modulations in macrophages stimulated with both LPS and PGN at the level of differentially activated RNA transcripts related with the regulation of transcriptional program, prostaglandin synthesis or highlighting the expression of responsive gene-cassettes tightly related to LPS-PGN host recognition.

overall_design: A total of 43,398 oligonucleotide probes were used to construct a high-density seabream microarray based on the Agilent 4 × 44 K design format. Microarray hybridization validation was made by analyzing the gene expression profiles in primary cultures of seabream macrophages (MC). 7,285 transcripts with annotated sequences were spotted in triplicate onto the slide (total probes 21,855), as well as 8,377 ESTs without annotation, 183 enriched sequences (gene bank) with 15 replicated probes (total probes 2,745), and finally 1,417 internal control probes of Agilent (N = 43,398).

last: Boltaña

first: Simon

last: MacKenzie


title: ChIP-chip of E. coli K-12 MG1655 with antibody against PurR-8myc under various conditions.

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the PurR regulon experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of  E. coli K-12 MG1655 harboring PurR-8myc under various conditions.

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

overall_design: A four ChIP-chip study under two separate culture conditions.  The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome.

first: Byung-Kwan

last: Cho

first: Stephen

last: Federowicz

first: Young-Seoub

last: Park

first: Karsten

last: Zengler

middle: Ø


title: Loss of p53 in enterocytes generates an inflammatory microenvironment enabling invasion and metastasis of carcinogen-induced colorectal tumors

status: Public on Mar 24 2011

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

summary: Loss of p53 is considered to allow progression of colorectal tumors from the adenoma to the carcinoma stage. Using mice with an intestinal epithelial cell (IEC) specific deletion of p53, we demonstrate that single loss of p53 is not sufficient to initiate intestinal tumorigenesis, but markedly enhances carcinogen-induced tumor incidence and leads to invasive cancer and lymph node metastasis. While during the initiation stage p53 controls DNA damage and IEC survival, during tumor progression, loss of p53 is associated with the formation of an inflammatory microenvironment and activation of NF-kB and Stat3. Thus, we propose a novel p53 controlled tumor suppressive function that is independent of its well-established role in cell cycle regulation, apoptosis and senescence.

overall_design: 4 AOM induced cancers derived from Tp53DEIC mice were isolated and DNA was extracted. These were compared to genomic DNA isolated from healthy  littermate control animals. Agilent Mouse 4x180K arrays were used (Design ID 27411).

first: Florian

last: Greten


title: Comparison of IND induced vs. mock treated seedlings: Transcriptome profiling upon induction of the transcription factor IND

status: Public on May 12 2011

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

summary: rs10-03_ind - comparison of ind induced vs mock treated seedlings - Identification of miRNAs regulated by IND - Transgenic seeds containing an IND transgene under the control of a dexamethasone inducible promoter were germinated and grown in liquid Murashige/Skoog medium under a 16h light/8h darkness light regime. After seven days of growth, seedlings were either mock-treated or treated with 10 micromolar dexamethasone for 24 hours.

overall_design: 3 dye-swap - induced vs non-induced comparison

first: Olivier

last: Voinnet

first: Peter

last: Brodersen

first: Sandrine

last: Balzergue

last: Martin-Magniette


title: Peripheral blood transcriptome responses to Salmonella Typhimurium in pigs differing in Salmonella shedding phenotypes

status: Public on May 28 2011

city: Ames

first: Chris

last: Tuggle

address: Kildee Hall 2255

institute: Iowa State University

summary: Salmonella species infect many vertebrate species, and pigs colonized with Salmonella enterica serovar Typhimurium (ST) are usually asymptomatic, making detection of these Salmonella-carrier pigs difficult. The variable fecal shedding of this gram-negative bacteria in such pigs is an important cause of foodborne illness and zoonotic disease. To investigate gene pathways and biomarkers associated with the variance in Salmonella shedding following experimental inoculation, we have initiated the first analysis of the whole blood transcriptional response induced by Salmonella. A population of pigs (n=40) was inoculated with ST and the peripheral blood and feces were collected between 2 and 20 days post-inoculation. Two groups of pigs with either low shedding (LS) or persistent shedding (PS) phenotypes were identified. The global transcriptional changes in response to ST inoculation were identified by Affymetrix Genechip?analysis of peripheral blood RNA at day 0 and day 2 post-inoculation.

overall_design: Forty pigs (n=40) was inoculated with ST. Four low shedding (LS) pigs and six persistent shedding (PS) pigs were identified. Transcriptom of peripheral blood collected at 0 and 2 dpi were identified by Affymetrix Genechip analysis.


title: primary floral stem 20cm-Modifications of transcriptome in primary floral stem of Arabidopsis thaliana deregulated for a peroxydase involved in the lignification.

city: Evry

institute: INRA

summary:
ra07-01_prx34 - primary floral stem 20cm - The At3g49120 gene codes for the peroxidase 34 (PRX 34), an enzyme potentially involved in the polymérisation of monolignols, the lignin precursors. This enzyme is expressed in primary floral stem and its absence has an impact on the lignin quantity and biomass (at the young stage). Here, its question to characterize several mutants. - Each mutant compare to wild type, samples only primary floral stem of 20cm

Keywords: normal vs transgenic comparaison

overall_design: 4 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Marie-Laure


status: Public on May 20 2011

summary:
au10-03_hub1 - kinetics of gene expression after light exposure in hub1-3 mutant compared to wild-type - Role of histone UbH2B in the regulation of gene expression in response to light - RNA from 5-day-old wild-type and hub1-3plants in 3 conditions were used for hybridization: 5 days of darkness, 5 days of darkness + 1 hour of light and 5 days of darkness + 6 hours of light.

Keywords: genotype comparaison,time course

overall_design: 10 dye-swap - CATMA arrays


title: rnai-Transcriptomic analyses approach to identify genes associated with organ growth downstream TCTP in Arabidopsis

status: Public on Mar 17 2011

first: Delphine

last: Gey

summary:
ra09-02_tctp - rnai - Identification of effector genes that act downstream of AtTCTP, using knockout ( tctp-2), RNAi expressing line (35S::RNAi-AtTCTP) and over expressing line (35S::AtTCTP) - transcriptome analysis in leaf of 35S::RNAi-AtTCTP versus wild type

Keywords: normal vs rnai mutant comparison

first: Mohammed-

last: Bendahmane

last: Brioudes


title: over expression-Transcriptomic analyses approach to identify genes associated with organ growth downstream TCT...

summary:
ra09-02_tctp - over expression - Identification of effector genes that act downstream of AtTCTP, using knockout ( tctp-2), RNAi expressing line (35S::RNAi-AtTCTP) and over expressing line (35S::AtTCTP) - transcriptome analysis in leaf of 35S::AtTCTP versus wild type

Keywords: gene knock in (transgenic)


title: Expression data from post mortem porcine skeletal muscle

status: Public on Jan 19 2011

city: Bologna

first: Giuliano

last: Galimberti

address: Via delle Belle Arti, 41

country: Italy

institute: Università di Bologna

summary: We set up a pilot study using Affymetrix Gene Chip® Porcine Genome Arrays to evaluate the impact of time lags from death on gene expression profiling of porcine skeletal muscle at four post mortem time points (up to 24 hrs) during the routine processing of fresh tights

overall_design: Post mortem skeletal muscle samples were obtained from three commercial hybrid pigs of female sex (of about 160 kg each) raised in the same commercial farm and slaughtered under normal conditions at the same abattoir within 1 minute of each other after stunning by CO2 (concentration 87%) using a dip lift system (Butina, Denmark). A portion of semimembranosus muscle (3-5 g) was sampled from the left legs at 20 minutes (T0) after death following the normal operation of the abattoir. Other samples were collected from the same muscle at the same position after 2 (T1), 6 (T2) and 24 (T3) hrs post mortem in the same abattoir following the cold chain at the abattoir until 4 °C. After sampling, tissues were snap frozen in liquid nitrogen and stored at -80 °C till RNA extraction.

first: Luca

last: Fontanesi

first: Daniela

last: Calò


title: Inflammation and Extracellular Matrix Genes Differentially Expressed Following Overlapping Zotarolimus- and Sirolimus-Eluting Stent Implantation

status: Public on Apr 22 2011

city: Atlanta

first: Andrew

last: Huang

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

summary: An unanticipated complication of the use of bare metal stents in percutaneous transluminal coronary angioplasty is in-stent restenosis resulting in  >50% late lumen diameter loss in treated patients. In an effort to reduce in-stent restenosis, drug eluting stents containing the immunosuppressant sirolimus or zotarolimus have recently been developed. We report here the molecular response of arterial tissue to the implanting of these drug-eluting stents.

overall_design: Gene expression profiling was performed on 4 artery segments surrounding bare metal stents (BMS), 4 artery segments surrounding sirolimus-eluting stents (SES), and 4 artery segments surrounding zotarolimus-eluting stents (ZES) implanted into porcine animal models for 28 days.

first: Jing

last: Chen

first: Lilya

last: Matyunina

first: Dongming

last: Hou

first: Jaipal

last: Singh

first: Nicolas

last: Chronos

first: John

middle: F

last: McDonald


title: knockout-Transcriptomic analyses approach to identify genes associated with organ growth downstream TCTP in Arabidopsis

summary:
ra09-02_tctp - knockout - Identification of effector genes that act downstream of AtTCTP, using knockout ( tctp-2), RNAi expressing line (35S::RNAi-AtTCTP) and over expressing line (35S::AtTCTP) - transcriptome analysis in leaf of tctp-2 knock out versus wild type

Keywords: gene knock out

first: Florian