title: Analysis of a fungus-specific transcription factor family, the Candida albicans zinc cluster proteins, by artificial activation

status: Public on Jul 29 2013

city: Würzburg

first: Rebecca

last: Schillig

address: Josef-Schneider-Straße 2 /Bau D15

country: Germany

institute: Institute for Molecular Infection Biology

summary: The zinc cluster proteins are a family of transcription factors that are unique to the fungal kingdom. In the pathogenic yeast Candida albicans, zinc cluster transcription factors control the expression of virulence-associated traits and play key roles in the development of antifungal drug resistance. Gain-of-function mutations in several zinc cluster transcription factors, which result in constitutive overexpression of their target genes, are a frequent cause of azole resistance in clinical C. albicans isolates. We found that zinc cluster proteins can also be artificially activated by C-terminal fusion with the heterologous Gal4 activation domain. We used this strategy to create a comprehensive library of C. albicans strains expressing all 82 zinc cluster transcription factors of this fungus in a potentially hyperactive form. Screening of this library identified regulators of invasive filamentous growth and other phenotypes that are important during an infection. In addition, the approach uncovered several novel mediators of fluconazole resistance, including the multidrug resistance regulator Mrr2, which controls the expression of the major C. albicans multidrug efflux pump CDR1. Artificial activation therefore is a highly useful method to study the role of zinc cluster transcription factors in C. albicans and other fungi of medical, agricultural, and biotechnological importance.

overall_design: In total, 15 samples are analysed: 3 replicates of 5 different strains. The 3 replicates of SC5314 are the wild type reference.

first: Joachim

last: Morschhäuser


title: Transcriptional signature of progesterone-induced germinal vesicle breakdown in the fathead minnow ovary (Pimephales promelas)

status: Public on Jul 19 2013

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

country: USA

institute: UF

summary: A growing number of studies have examined transcriptional responses to sex steroids along the hypothalamic-pituitary-gonadal axis in teleost fishes.  However, data is are lacking on the molecular signaling cascades that underlie progesterone signaling.  The objectives of the present study were to characterize the transcriptional response in the ovary of fathead minnow (Pimephales promelas) (FHM) in response to progesterone (P4) using transcriptomics.  Female FHM ovaries were exposed in vitro to 500 ng P4/L.  Germinal vesicle migration and breakdown (GVBD) was observed and microarrays were used to identify gene cascades affected by P4. Microarray analysis identified 1,265 differentially expressed transcripts after P4 treatment (p < 0.05).  Functional enrichment analysis revealed that transcripts involved in the molecular functions of protein serine/threonine kinase activity, ATP binding, and activity of calcium channels were increased in the female ovary after P4 treatment.  There was an overwhelming response of genes involved in structural constituent of ribosome to bethat were down-regulated with P4.  There was also evidence for gene changes in steroid and maturation-related transcripts.  Pathway analyses identified cell cycle regulation, insulin action, hedgehog, and B cell activation as pathways containing an over-representation of highly regulated transcripts.  Significant regulatory sub-networks of P4-mediated transcripts included genes regulated by tumor protein p53 and E2F transcription factor 1, suggesting that downstream expression targets of these two proteins may be preferentially involved in P4-mediated GVBD.  These data provide novel insight into the molecular signaling cascades that may underlie P4-signaling in the ovary and identifies genes and processes that may indicate premature GVBD due to environmental pollutants that mimic progestins.

overall_design: 3 control and 4 treatment; biological replicates

first: Natàlia

last: Garcia-Reyero

middle: J

first: Kevin

last: Kroll

first: Lynn

last: Escalon

first: Daniel

last: Spade

first: Nancy

middle: D

last: Denslow


title: Effects of 17α-ethinylestradiol (EE2) on molecular signaling cascades in mummichog (Fundulus heteroclitus)

status: Public on Jul 18 2013

summary: The objective of this study was to gain mechanistic insight into how mummichog are able to produce eggs during exposures to high levels of EE2. Mummichog were exposed to 0, 50 or 250 ng/L of EE2 for 14 d. A mummichog microarray was used to identify genomic responses associated with high EE2 exposure, and effects of EE2 on target genes involved in lipid mobilization and transport and steroidogenesis, two important (EE2 regulated) pathways involved in egg production, were measured using real-time PCR. In addition, changes at higher level biological endpoints such as plasma steroid production and gonad morphology were measured to examine downstream responses to EE2. There were no differences in gonadosomatic index, liversomatic index, gonad development, or plasma estradiol levels after exposure to EE2, although testosterone decreased with EE2 exposures. Similar to other species, mummichog showed alterations to plasma steroid levels, and similar processes at the molecular level were identified as being altered by EE2, including cell processes associated with lipids. However, unlike other species, mummichog showed no differences in GSI or ovarian development. Fatty acids were affected at both the transcript and translation level, which suggests they are a major target of estrogens. Lipids are important for both growth and reproduction, and provide oocytes with nutrients. Interestingly, mummichog showed no effect on apolipoprotein expression, which is important in lipid transport. Therefore, it is hypothesized that mummichog are normally able to transport lipids for energy and nutrients to the ovary, while this is affected in other species. Novel gene regulatory networks for protein modification targets were also constructed to learn more about the potential roles of estrogens in the teleost liver. Although post-translational modifications (PTMs) are important regulatory mechanisms, the roles of PTMs in protein regulation in fish and the susceptibility of PTMs to aquatic pollutants are largely unexplored and may offer novel insight into mechanisms of endocrine disruption.

overall_design: Mummichog were exposed to 0, 50, and 250 ng/L EE2 for 14 days. Microarray analysis was performed with five biological replicated (5 control, 5 EE2 50 ng/L, 5 EE2 250 ng/L). Female liver tissue was used for the analysis.

first: Meghan

middle: A

last: Doyle

first: Thijs

last: Bosker

first: Chris

first: Deborah

middle: L

last: MacLatchy

first: Kelly

middle: R

last: Munkittrick


title: comparison of the transcriptome of the conditional afpig-a mutant and the wild-type

status: Public on Jul 22 2013

city: beijing

first: jianghong

last: yan

state: beijing

address: NO.1 West Beichen Road

country: China

institute: Institute of Microbiology

summary: In order to gain a better understanding of the mechanism of increased cell death triggered by deficient GPI anchoring, we constructed a whole genome microarray using the Agilent eArray 5.0 program.The chip specification is 8×15K. The genome sequences were downloaded from the following site:http://www.ncbi.nlm.nih.gov/genome?Db=genome&Cmd=Search&Term=txid330879[orgn]. Each gene was represented by one 60-nt oligonucleotide probe, and 358 genes out of the 9630 total were replicated 14 times.Using this microarray,we got 3274 genes which were induced or reduced at least 1.5 fold in the afpig-a mutant comparing to the wild-type.

overall_design: Mycelia of the afpig-a mutant and the wild-type were harvested from strains grown in liquid CM at 37°C for 36h with shaking at 200 rpm and ground by hand.Total RNA was extracted to do the hybridization.cRNAs were labled with Cy3 NHS ester.afpig-a_37 was sample, afpig_37_1a,afpig_37_2a,afpig_37_3a and afpig_37_4a were biological repeats. w_37 was control,w_37_1a,w_37_2a,w_37_3a and w_37_4a were biological repeats.Four independent experiments were performed. Each time we got a set of differentilly expressed genes.Differentially expressed genes were selected with P≤0.05, FC≥1.5 by T-test methods using the independent four sets data.

first: cheng

last: jin


title: Mechanistic information on perfluorooctanoic acid (PFOA) exposure in zebrafish (Danio rerio)

status: Public on Jul 20 2013

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary: Perfluorooctanoic acid (PFOA) is one of the most used perfluorinated compounds in numerous applications and can be detected in environmental samples from around the globe. The aquatic environment is an important site for PFOA deposit. Nevertheless, the exact mode of action and its resulting toxicological effects on aquatic organisms remain largely unknown. To gain a more extensive understanding of the mode of action of teleost PFOA toxicity, transcriptomics, proteomics, biochemical parameters and reproduction were integrated in the present study. Male and female zebrafish were exposed to nominal concentrations of 0.1; 0.5 and 1 mg/l PFOA for 4 and 28 days resulting in an accumulation which was higher in males compared to females. These gender-related differences were likely caused by different elimination rates due to distinct hormone levels and differences in transport activity by solute carriers. The general mode of action of PFOA was believed to be an increase of the mitochondrial membrane permeability which caused effects on the electron transport system at the biochemical level and resulted in alterations of the oxidative phosphorylation, oxidative stress and apoptosis at the gene transcript and protein level. As a consequence, evidence for the replacement of the affected cells and organelles to sustain tissue homeostasis was found at the molecular level. The higher energy demand, due to these adverse effects, was provided by lowering the glycogen stores. Despite this increase in metabolic expenditure, no effects on reproduction were found indicating that the fish seemed to cope with exposure to the tested concentrations of PFOA.

overall_design:
Adult zebrafish (Danio rerio) were exposed to nominal concentrations of 0mg/l; 0.1mg/l; 1mg/l PFOA (perfluorooctanoic acid) for 28 days. Three different 25 litre aquaria per exposure concentration were used resulting in 3 biological replicates with each aquarium containing 8 male and 8 female zebrafish. The livers of 6 male fish and 6 female fish were pooled separately and snap frozen in liquid nitrogen. A reference sample was made by pooling equal amounts of RNA from all samples.

A carriage wheel design was used in which all samples were connected to the reference sample and the main contrasts of interest were made directly on the same microarrays as frequently as possible. This design resulted in technical triplicates of each sample.

first: Lucia

last: Vergauwen

first: Donald

last: Benoot

first: Kris

last: Laukens

first: Dries

last: Knapen


title: Characterization of the starvation response in the Arabidopsis dcl1-9 mutant

status: Public on Jul 15 2013

city: Oeiras

first: Elena

last: Baena-Gonzalez

address: Rua da Quinta Grande 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

summary: The SnRK1 protein kinase, the plant ortholog of mammalian AMPK and yeast Snf1, is activated by the energy depletion caused by adverse environmental conditions. Upon activation, SnRK1 triggers extensive transcriptional changes to restore homeostasis and promote stress tolerance and survival partly through the inhibition of anabolism and the activation of catabolism. Despite the identification of a few bZIP transcription factors as downstream effectors, the mechanisms underlying gene regulation, and in particular gene repression by SnRK1, remain mostly unknown.   microRNAs (miRNAs) are 20-24nt RNAs that regulate gene expression post-transcriptionally by driving the cleavage and/or translation attenuation of complementary mRNA targets. In addition to the well-established role of miRNAs as regulators of plant development, mounting evidence implicates miRNAs in the response to environmental stress.   Given the involvement of miRNAs in stress responses and the fact that some of the SnRK1-regulated genes are miRNA targets, we postulated that miRNAs drive part of the transcriptional reprogramming triggered by SnRK1 activation. To test this we have performed comparative analyses of the transcriptional response to energy deprivation between WT and dcl1-9, a mutant deficient in miRNA biogenesis.

overall_design: To assess the impact of miRNA deficiency on the starvation response we performed transcriptomics analyses of WT and dcl1-9 plants by subjecting leaves to 6h of light (control) or darkness (starvation)

first: Ana

last: Confraria

first: Cláudia

last: Martinho

first: Alexandre

last: Elias

first: Ignacio

last: Rubio-Somoza

last: Baena-González


title: Inducing pluripotency from mouse somatic cells by small-molecule compounds [Phalanx Mouse OneArray]

first: chun

last: liu

address: beijing

institute: Peking University

summary: Pluripotent stem cells can be induced from somatic cells, providing an unlimited cell resource for regenerative medicine. However, genetic manipulation and difficult-to-manufacture strategies used in reprogramming limit their clinical applications. Here, we show pluripotency can be induced from mouse somatic cells by specific small-molecule compounds. The completely chemically-induced pluripotent stem cells (CiPSCs) can be stably maintained in embryonic stem cell (ESC) culture medium and resemble ESCs in terms of their gene expression profiles, epigenetic status, and potential for differentiation and germline transmission. These findings suggest that exogenous master genes are dispensable for cell fate reprogramming and pave the way for the clinical application of somatic reprogramming techniques. Pluripotent stem cells can be induced from somatic cells, providing an unlimited cell resource for regenerative medicine. However, genetic manipulation and difficult-to-manufacture strategies used in reprogramming limit their clinical applications. Here, we show pluripotency can be induced from mouse somatic cells by specific small-molecule compounds. The completely chemically-induced pluripotent stem cells (CiPSCs) can be stably maintained in embryonic stem cell (ESC) culture medium and resemble ESCs in terms of their gene expression profiles, epigenetic status, and potential for differentiation and germline transmission. These findings suggest that exogenous master genes are dispensable for cell fate reprogramming and pave the way for the clinical application of somatic reprogramming techniques. Chemicals' acronyms: V, VPA; C, CHIR; 6, 616452; T, tranylcypromine; F, FSK; Z, DZNep; P, PGE2; R, RG108; S, SRT1720; M, 2-Me-5HT; D, D4476; B, Sodium butyrate.

overall_design:
To compare the global gene expression pofile of mouse embryonic fibroblasts (MEFs), mouse adult lung fibroblasts (MAFs), mouse neonatal fibroblasts (MNFs), adipose-derived stem cells (ADSCs), chemical induced pluripotent stem cells (CiPS), embryonic stem cells (ESCs) and OSKM-iPSCs. We profiled the mRNA expression of each sample by microarray (Mouse OneArray® v2, Phalanx).
Different sample set was normalized for different purpose. Set1: MEFs1, CiPS34, MNF CIPS7, CiPS50 CiPS21, OSKM-iPS1 and ESCs1 were analyzed, each sample have three replicates; Set2: MNFs, MAFs, ADSCs, MNF CiPS1, MAF CiPS3, CiPS45, ADSC CiPS2, OSKM iPS2 and ESCs2 were analyzed, each sample have three replicates; Set3: WT MEFs, ESCs3, CiPS WT1 and CiPS WT2 were analyzed, each sample have two replicates; Set4: MEFs2, SKM-FSK1, SKM-FSK2 and ESCs4 were analyzed, each sample have three replicates; Set5: MEFs3, ESCs5, CiPSCs, D12, D20 and D32 were analyzed, each sample have two replicates.

first: Pingping

last: Hou

first: Yanqin

last: Li

first: Xu

last: Zhang

first: Chun

last: Liu

first: Jingyang

last: Guan

first: Honggang

first: Yang

last: Zhao

first: Hongkui

last: Deng


title: Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds [Set2]

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best studied sulfur-oxidizing anoxygenic phototrophic bacteria and has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organism’s high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur or sulfite as compared to photoorganoheterotrophic growth on malate. Differential expression (at least twofold) of 1149 genes was observed, corresponding to 30% of the A. vinosum genome. A total of 549 genes were identified for which relative transcription increased at least twofold during growth on one of the different sulfur sources while relative transcription of 599 genes decreased. A significant number of genes that were strongly induced have documented sulfur-metabolism-related functions. Among these are the dsr genes including dsrAB for dissimilatory sulfite reductase and the sgp genes for the proteins of the sulfur globule envelope thus confirming former results. In addition we were able to identify new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Two of these were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for the oxidation of sulfide and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: In this study, the relative genomic expression profiles of A. vinosum DSM 180T growing photolithoautotrophically on different reduced sulfur compounds were determined in comparison to those of cells grown photoorganoheterothrophically on malate (RCV medium) at exactly the same light intensity. The malate-containing medium was supplied with 0.815 mM sulfate in order to satisfy the sulfur-requirement for biosynthesis of sulfur-containing cell constituents. Three independent photolithoautotrophic cultures each, grown on sulfide, thiosulfate or sulfite were harvested 1 h, 2 h or 7 h, respectively, after inoculation. When elemental sulfur was the substrate, four independent cultures were harvested 3 h after inoculation.

first: Thomas

last: Weissgerber

first: Nadine

last: Dobler

first: Jeanette

last: Latus

first: Yvonne

last: Stockdreher

first: Christiane

last: Dahl


title: Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds [Set1]

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


title: Continuous gene expression profile of leaf throughout the entire growth of rice in 2010

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

summary: A continuous gene expression profiling of leaves at regular interval from transplanting until harvesting was performed to understand the changes of transcriptional program and physiological state throughout entire growth of the rice plant in 2010.

overall_design: For continuous gene expression profile of leaf, the uppermost fully-expanded leaf in the main stem was sampled at 12:00 PM at regular intervals of 7 days encompassing 17 different growth stages with three replicates during a normal rice growing season in 2010.

first: Baltazar

last: Antonio

first: Nobukazu

last: Namiki

first: Yoshiaki

last: Nagamura


title: aCGH for bile duct cancer

status: Public on Jul 13 2013

city: Seoul

first: Mee Joo

last: Kang

address: 101 Daehak-ro, Chongno-gu

country: South Korea

institute: Seoul National University College of Medicine

type: Genome variation profiling by genome tiling array

summary: Assays in bile duct cancer patients showed 984 CNVs in 306 CNV regions (CNVR) distributed throughout all 22 chromosomes. Bile duct cancer patients had a mean of 21.8 gains and 19.2 losses of genes, with an average of 35.9 CNVRs per patient. Frequent sites of gains were at chromosomes 22q11.22, 2p11.2-p.11.1, 14q32.33 and 17q12, whereas frequent sites of losses were at 19q12-q13.43.

overall_design: Investigation of CNV in 24 bile duct cancer tissue samples

first: Mee-Joo

first: Jin-Young

last: Jang


title: A New System for Comparative Functional Genomics of Saccharomyces Yeasts

status: Public on Jul 12 2013

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

type:
Expression profiling by array
Genome variation profiling by array

summary: Whole genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting dataset reveals that gene expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.

platform_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

overall_design:
Samples GSM1153177-GSM1153193 represent gene expression and transposon mapping arrays. The other arrays from the paper are also available from GEO accession GSE16544.

The arrays indicated as "alpha factor" are gene expression arrays. The mutant and wt strains, as indicated, were exposed to alpha factor and sampled for gene expression at the time indicated. Each sample was hybridized versus a common mixed reference, as described in the manuscript.

The Tn7 array uses Transposon Specific Extraction to map the location of an insertion element.  The extracted sample is hybridized versus genomic DNA.

first: Amy

last: Caudy

first: Olga

last: Troyanskaya


title: Comparison of foliage of diploid potato clones 07506-01 and 12120-03

city: Fredericton

first: Helen

middle: H.

last: Tai

state: New Brunswick

address: P. O. Box 20280, 850 Lincoln Rd.

department: Potato Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Verticillium dahliae Kleb., a soil-borne fungus that colonizes vascular tissues, induces wilting, chlorosis and early senescence in potato. Difference in senescence timing found in two diploid potato clones, 07506-01 and 12120-03, was studied and genetic variation in response to V. dahliae infection was identified as a causal factor. The clone, 07506-01, was infected with V. dahliae but did not develop symptoms, indicating tolerance to the pathogen. The other diploid clone, 12120-03 had low levels of pathogen with infection and moderate symptoms indicating partial resistance. 07506-01 was found to carry two susceptible alleles of the Ve2 gene and 12120-03 carried one Ve2 resistant and one susceptible allele. Infected leaves of the two clones were compared using gene expression profiling with the Potato Oligonucleotide Chip Initiative (POCI) microrarray. The results provide further evidence for differences in response of the two clones to infection with V. dahliae. Chlorophyll biosynthesis was higher in the tolerant 07506-01 compared to partially resistant 12120-03. On the other hand, expression of fungal defense genes, Ve resistance genes and defense phytohormone biosynthetic enzyme genes was decreased in 07506-01 compared to 12120-03 suggesting defense responses were suppressed in tolerance compared to resistance. Transcription factor gene expression differences pointed to the WRKY family as potential regulators of V. dahliae responses in potato.

overall_design: Two-color microarray comparison of two clones, three biological replicates of each clone, one dye swap technical replicate

middle: H

first: Claudia

last: Goyer

first: H

middle: W

last: Platt

first: David

last: De Koeyer

first: Agnes

last: Murphy

first: Pedro

last: Uribe

first: Dennis

last: Halterman

first: Charlotte

last: Davidson


title: The Antarctic Krill Euphausia superba Shows Diurnal Cycles of Transcription under Natural Conditions.

status: Public on Jul 23 2013

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

country: Italy

institute: University of Padova

summary:
BACKGROUND: Polar environments are characterized by extreme seasonal changes in day length, light intensity and spectrum, the extent of sea ice during the winter, and food availability. A key species of the Southern Ocean ecosystem, the Antarctic krill (Euphausia superba) has evolved rhythmic physiological and behavioral mechanisms to adapt to daily and seasonal changes. The molecular organization of the clockwork underlying these biological rhythms is, nevertheless, still only partially understood.
METHODOLOGY/PRINCIPAL FINDINGS:The genome sequence of the Antarctic krill is not yet available. A normalized cDNA library was produced and pyrosequenced in the attempt to identify large numbers of transcripts. All available E. superba sequences were then assembled to create the most complete existing oligonucleotide microarray platform with a total of 32,217 probes. Gene expression signatures of specimens collected in the Ross Sea at five different time points over a 24-hour cycle were defined, and 1,308 genes differentially expressed were identified. Of the corresponding transcripts, 609 showed a significant sinusoidal expression pattern; about 40% of these exibithed a 24-hour periodicity while the other 60% was characterized by a shorter (about 12-hour) rhythm. We assigned the differentially expressed genes to functional categories and noticed that those concerning translation, proteolysis, energy and metabolic process, redox regulation, visual transduction and stress response, which are most likely related to daily environmental changes, were significantly enriched. Two transcripts of peroxiredoxin, thought to represent the ancestral timekeeping system that evolved about 2.5 billion years ago, were also identified as were two isoforms of the EsRh1 opsin and two novel arrestin1 sequences involved in the visual transduction cascade.
CONCLUSIONS: Our work represents the first characterization of the krill diurnal transcriptome under natural conditions and provides a first insight into the genetic regulation of physiological changes, which occur around the clock during an Antarctic summer day

overall_design: Gene expression profiling was carried out in krill fished at different times throughout the 24 hours cycle (local times: 01:00, 06:00, 10:00, 15:00, and 18:00) with the ‘‘Krill 1.1’’ custom platform (Agilent). We analyzed four different biological replicates for each time point for a total of 20 microarray experiments.

first: Alberto

last: Biscontin

first: Alessandro

last: Albiero

first: Gabriele

last: Sales

first: Caterina

last: Millino

first: Gabriella

middle: M

last: Mazzotta

last: Bertolucci

first: Rodolfo

last: Costa


title: Cerebellar Gene Expression Profile Analysis in a Rat Model of Acute Alcohol Intoxication

city: Beijing

first: Ji-lai

last: Liu

state: Beijing

address: Taiping road 27

department: Biochemistry and Molecular Biology

institute: Beijing Institute of Radiation Medicine

summary:
To identify possible target molecules for acute alcohol intoxication therapy, we used microarray analysis to compare cerebella gene expression profiles of control and acute alcohol-intoxicated rats.
We first established a model of acute alcohol intoxication in SD rats, and then used rat cDNA microarray to profile mRNA expression in the cerebella of alcohol-intoxicated rats (experimental group) and saline-treated rats (control group).

overall_design: A six chip study using total RNA recovered from three separate experimental groups and three separate control groups. We first established a model of acute alcohol intoxication in SD rats, and then used rat cDNA microarray to profile mRNA expression in the cerebella of alcohol-intoxicated rats (experimental group) and saline-treated rats (control group). Cerebellar tissues from three rats were ground to a mixed sample,so we use 3 rats in one group.


title: Gene expression in human fungal pathogen Coccidioides immitis changes as mycelia differentiate into spherules and mature

status: Public on Jul 11 2013

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary:
Coccidioides immitis (C. immitis) is a dimorphic fungus that causes disease in mammals including human beings. It grows as a mycelium in the soil but differentiates into a pathogenic structure called a spherule in the host.
We compared the transcriptome of C. immitis mycelia and day 2 and day 8 spherules grown in vitro using a custom custom oligonucleotide microarray from Nimblegen.

overall_design: C. immitis RS strain isolated from infected mice was grown on agar. Arthroconidia was harvested and inoculated into mycelial spores. RNA was extracted from spores at different days post-inoculation and hybridized to a custom Nimblegen array, in order to identify differentially expressed genes between mycelia and spherules.

first: Theo

middle: N

last: Kirkland

first: Christopher

last: Woelk


title: Lethal dissemination of H5N1 influenza virus is associated with dysregulation of inflammation and lipoxin signaling in a mouse model of infection

status: Public on Jul 16 2013

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

summary: Periodic outbreaks of highly pathogenic avian H5N1 influenza viruses and the current H1N1 pandemic highlight the need for a more detailed understanding of influenza virus pathogenesis. To investigate the host transcriptional response induced by pathogenic influenza viruses, we used a functional-genomics approach to compare gene expression profiles in lungs from wild-type 129S6/SvEv and interferon receptor (IFNR) knockout mice infected with either the fully reconstructed H1N1 1918 pandemic virus (1918) or the highly pathogenic avian H5N1 virus Vietnam/1203/04 (VN/1203).

overall_design: Eight- to 10-week-old female wild-type and IFNR1-/- mice (on a 129S6/SvEv background) were anesthetized by intraperitoneal injection of 0.2 ml of 2,2,2-tribromoethanol in tert-amylalcohol (Avertin; Sigma-Aldrich, Milwaukee, WI). Ten times the 50% lethal dose (LD50), 3.2 × 10^4 PFU (1918) or 7 × 10^3 PFU (VN/1203), in 50 μl of infectious virus diluted in phosphate-buffered saline (PBS) was inoculated intranasally (i.n.). Lung tissue was harvested for microarray analysis from infected animals at 1, 3, and 4 days post-innoculation. For RNA isolation, lungs were frozen in individual tubes and stored in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol). Separate microarrays were run for each infected mouse. This included 2 animals/time point for 1918 virus-infected mice (24 animals total) or 3 animals/time point for VN/1203-infected mice (36 animals total). Lung tissue from three uninfected wild type 129S6/SvEv mice was collected as a mock control. Equal masses of total RNA from the lung tissue of the three mice were pooled prior to being run on microarray. Two-channel microarrays were used to determine gene expression in the lungs. For each individual infected lung, gene expression from an infected lung was compared to gene expression from the pooled RNA from the mock control.

first: Christian

last: Cilloniz

first: Mary

last: Pantin-Jackwood

first: Chester

last: Ni

first: Alan

middle: G

last: Goodman

first: Xinxia

last: Peng

first: Sean

middle: C

last: Proll

first: Victoria

middle: S

last: Carter

first: Elizabeth

last: Rosenzweig

first: Kristy

last: Szretter

first: Jacqueline

last: Katz

first: Marcus

last: Korth

middle: E

last: Swayne

first: Terrence

last: Tumpey


title: Comparison of two clones (4106a and FRC) of Myzus Persicae (Sulzer) (Hemiptera: Aphididae)

city: Harpenden

first: Chris

last: Bass

state: Hertfordshire

address: West Common

department: Biological Chemistry

institute: Rothamsted Research

summary:
The aim of this experiment was to compare the transciptome of the peach-potato aphid (Myzus persicae) clone 4106a (a laboratory insecticide-susceptible standard collected from potato in Scotland in 2000) with clone FRC (an insecticide resistant aphid clone collected from peach in France in 2009) to identify which genes are over or underexpressed in the resistant phenotype.
The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies) by the Georg Jander Lab and is based on a previously described array containing probes for >10, 000 M. persicae unigenes produced by Sanger sequencing (Ramsey, Wilson et al. 2007) augmented with an additional 30, 517 probe set designed on EST unigene sequences identified in a 454 sequencing project (Ramsey, Rider et al. 2010). The final slide layout consists of four arrays of 45, 220 60-mer probes and these are produced by Agilent by in situ oligonucleotide synthesis. References: Ramsey, J. S., D. S. Rider, et al. (2010). "Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae." Insect Molecular Biology 19: 155-164.  Ramsey, J. S., A. C. C. Wilson, et al. (2007). "Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design." BMC Genomics 8.

overall_design: Two-condition experiment, 4106a vs. FRC Myzus persicae clones. Biological replicates: 4 pools of RNA extracted from ten 15 day old aphids of each clone. Technical Replicates: Two technical reps incorporating a dye swap. Total replication: eight replicates for each clone.


title: Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein

status: Public on Jul 17 2013

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array

summary: Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome does not carry histones when encapsidated but has been proposed to form  nucleosomes after release into the host cell nucleus. Here, we present  hCMV genome-wide nucleosome occupancy and nascent transcript maps  during infection of permissive human primary cells. We show that  nucleosomes occupy nuclear viral DNA in a nonrandom and highly  predictable fashion. At early times of infection, nucleosomes  associate with the hCMV genome largely  according to their intrinsic DNA sequence preferences, indicating that  initial nucleosome formation is genetically encoded in the virus.  However, as infection proceeds to the late phase, nucleosomes  redistribute extensively to establish patterns mostly determined by  nongenetic factors. We propose that these factors include key  regulators of viral gene expression encoded at the hCMV major  immediate-early (IE) locus. Indeed, mutant virus genomes defcient for IE1 expression exhibit globally increased nucleosome loads and reduced nucleosome dynamics compared with WT genomes. The temporal nucleosome occupancy differences between IE1-defcient and WT viruses correlate inversely with changes in the pattern of viral nascent and total transcript accumulation. These results provide a framework of spatial and temporal nucleosome organization across the genome of a major human pathogen and suggest that an hCMV major IE protein governs overall viral chromatin structure and function.

overall_design:
[i] H3 ChIP-chip measurements of WT human cytomegalovirus (strain TB40E) following infection of MRC-5 cells.  WT 8 hours postinfection, with corresponding mock IgG input control: 3 replicates; WT virus, 48 hours postinfection with corresponding mock IgG input contro:  3 replicates.
[ii] MNase-chip measurements of WT and dlIE1 human cytomegalovirus nucleosomes following infection of MRC-5 cells.  WT 8 hours postinfection, with corresponding sonicated DNA input control: 6 replicates; WT virus 48 hours postinfection,  with corresponding sonicated DNA input control:  6 replicates; WT 96 hours postinfection, with corresponding sonicated DNA input control: 2 replicates;  dlIE1 virus 8 hours postinfection,  with corresponding sonicated DNA input control:  2 replicates; dlIE1 virus 96 hours postinfection,  with corresponding sonicated DNA input control:  2 replicates.
[iii] Total and nascent RNA measurements of WT and dlIE1 human cytomegalovirus transcripts following infection of MRC-5 cells.  WT 8 hours postinfection: 2 replicates; WT virus 96 hours postinfection: 2 replicates; dlIE1 8 hours postinfection: 2 replicates;  dlIE1 virus 96 hours postinfection:  2 replicates; sonicated DNA input control:  10 replicates.

first: Einat

last: Zalckvar

first: Christina

last: Paulus

first: Alexandra

last: Asbach-Nitzsche

first: Yaniv

last: Lubing

first: Carla

last: Winterling

first: Nicholas

last: Strieder

first: Katrin

last: Mücke

first: Felicia

last: Goodrum

first: Eran

last: Segal

last: Nevels


title: Transcription factor transcriptome during somatic embryogenesis (SE) in Arabidopsis thaliana

status: Public on Jul 31 2013

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary: To identify transcription factor (TF) genes exhibiting preferential expression during SE, expression profiles of 1,880 TFs were compared in two genotypes with largely different capacities for SE induction in IZE culture on auxin medium, namely the highly embryonic Col-0 accession and the tanmei mutant unable to form somatic embryos. Our study revealed 729 TFs whose expression changes during the 10-day incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. This study provides comprehensive data focused on the expression of TF genes during SE and provides guidelines for further research on functional genomics of SE.

overall_design: The experiment was designed to monitor the expression of 1,880 TF genes at three distinctive stages of IZE-derived embryogenic culture, which refer to: (i) freshly isolated explants competent to undergo embryogenic transition (0 d), (ii) explant tissue subjected to SE induction (5 d), and (iii) the advanced phase of embryogenesis related to somatic embryo formation (10 d).

first: Marta

last: Gliwicka

first: Katarzyna

last: Nowak

first: Bernd

last: Mueller-Roeber

first: Malgorzata

last: Gaj


title: Evidence for a key role of cytochrome bo3 oxidase in respiratory energy metabolism of Gluconobacter oxydans

status: Public on Jul 26 2013

first: Tino

last: Polen

summary: The obligatory aerobic acetic acid bacterium Gluconobacter oxydans oxidizes a variety of substrates in the periplasm by membrane-bound dehydrogenases, which transfer the reducing equivalents to ubiquinone. Two quinol oxidases, cytochrome bo3 and cytochrome bd, then catalyze transfer of the electrons from ubiquinol to molecular oxygen. In this study, mutants lacking either of these terminal oxidases were characterized. Deletion of the cydAB genes for cytochrome bd had no obvious influence on growth, whereas the lack of the cyoBACD genes for cytochrome bo3 severely reduced the growth rate and the cell yield. Using a respiration activity monitoring system and adjusting different levels of oxygen availability, hints for a low oxygen affinity of cytochrome bd oxidase were obtained, which were supported by measurements of oxygen consumption in a respirometer. The H+/O ratio of the ΔcyoBACD mutant with mannitol as substrate was 0.56 ± 0.11 and more than 50% lower than that of the reference strain (1.26 ± 0.06) and the delta-cydAB mutant (1.31 ± 0.16), indicating that cytochrome bo3 oxidase is the main component for proton extrusion via the respiratory chain. Plasmid-based overexpression of cyoBACD led to increased growth rates and growth yields, both in the wild type and the delta-cyoBACD mutant, suggesting that cytochrome bo3 might be the rate-limiting factor of the respiratory chain.

overall_design: The three transcriptome comparisons of G. oxydans ΔuppΔcyoBACD vs. G.oxydans Δupp were repeated independently three times in biological replicates resulting in 3 hybridizations as termed by sample 1 to 3.

first: Janine

last: Richhardt

first: Bettina

last: Luchterhand

first: Stephanie

last: Bringer

first: Jochen

last: Büchs

first: Michael

last: Bott


title: Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

city: Sheffield

first: Martin-Timothy

last: O'Donoghue

address: Western Bank

department: Department of Animal and Plant Sciences

institute: University of Sheffield

summary: Bryophytes are the most basal of the extant land plants. A major feature of these plants is the biphasic alteration of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. To analyse the differences in the transcriptome of the early gametophyte (protonema) and early and mid-sporophyte phases of the moss Physcomitrella patens, microarray gene expression profiles were performed using dissected sporophyte tissue. Through further analysis the early and mid-sporophyte phases were compared.

overall_design: RNA isolated from the Gametophytic protonemal tissue was hybridised to six microarrays. Each microarray was hybridised with RNA from a separate biological replicate. Three of these microarrays were co-hybridised with RNA isolated from early sporophytes. With the third gametophyte biological replicate and early sporophyte replicate a dye swap was carried out. The remaining three microarrays hybridised with RNA from the gametophytes were co-hybridised with RNA from mid-sporophytic tissue. A dye swap was carried out on the sixth gametophyte replicate and third mid-sporophyte replicate.To meet the quality requirements for the microarray experiment, at least 400 sporophytes were used per extraction. Three or four RNA extracts were then pooled for further precipitation to maximise purity and concentration. Up to 1600 sporophytes were harvested to prepare sufficient RNA for each microarray replicate. In bioinformatic analysis the channels were split into individual channels and the early and mid-sporophyte were compared.

first: Caspar

last: Chater

first: Simon

last: Wallace

first: Julie

last: Gray

first: David

last: Beerling

first: Andrew

last: Fleming


title: Noncoding RNA expression profile of dasatinib-treated chronic myeloid leukemia patients with resistance to imatinib

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

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

summary: Dasatinib has demonstrated efficacy in patients with chronic-phase chronic myeloid leukemia (CML) who had resistance or intolerance to imatinib. However, some patients also develop resistance or intolerance to dasatinib. To identify potential molecular pathways involved in primary resistance to dasatinib in CML, we analyzed gene expression profiles of mononuclear cells of 7 imatinib-resistant patients, collected before and after 1-year dasatinib treatment. Large-scale gene expression was measured with Agilent microarrays covering protein-coding genes and long (>200 nt) noncoding RNAs (lncRNAs). Sets of genes and lncRNAs significantly differentially expressed (>1.5 fold-change; q value ≤10%) were identified. Ingenuity Pathway Analysis pointed to a number of functions, canonical pathways and gene networks that were significantly enriched with differentially expressed genes. In addition to protein-coding genes, lncRNAs have been recently implicated in pathways leading to tumorigenesis. Our data point to new possible regulatory elements involved in dasatinib resistance in CML.

overall_design: Dasatinib pre-treatment and 1-yr post-treatment samples from 3 responders (R) or 4 non-responders (NR) chronic myeloid leukemia (CML) patients were investigated. We analyzed expression of Pre-treatment R vs. Pre-treatment NR; Pre-treatment R vs. Post-treatment NR; Pre-treatment NR vs. Post-treatment NR.

first: Rosana

last: Silveira

first: Yuri

middle: B

last: Moreira

first: Carmino

last: De Souza

first: Fernando

middle: F

last: Costa

first: Sergio

last: Verjovski-Almeida

first: Katia

last: Pagnano


title: Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds

first: Tino

last: Polen

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

overall_design: Refer to individual Series


title: Aspergillus nidulans strains TNO2a3, ∆snfA and ∆schA grown on avicel as sole carbon source

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

summary: Transcriptome of A. nidulans TNO2a3, ∆snfA and ∆schA strains when grown on complete media (CM) and transferred to minimal media plus avicel as a sole carbon source for 8 and 24 hours.

overall_design: Three conditions: complete media (reference) for 24h, and minimal media plus avicel for 8 and 24 hours. Three strains: TNO2a3, ∆snfA and ∆schA. Three biological repetitions of each timepoint of TNO2a3 and ∆schA, and two for each timepoint of ∆snfA.

first: Gustavo

last: Goldman


title: The role of Dichaete in transcriptional regulation the of Drosophila midline [simgal4]

city: Cambridge

first: Steve

last: Russell

address: Tennis Court Road

department: Genetics

institute: University of Cambridge

summary: Dichaete is a developmentally important transcription factor, known to be involved in basic biological processes including segmentation and nervous system development among others. The aim of this experiment was to gain further insight into the role of Dichaete during early embryogenesis, specifically looking at targets in the midline using dominant negative constructs expressed via the UAS/Gal4 system, using simGal4 to drive expression in the midline.

overall_design: 4 independent biological replicates. 3.5-4.5h old embryos were collected, and the RNA was extracted using Trizol. The UAS-dominant negative construct expressing embryos were compared to UAS-GFP expressing controls. Construct expression was driven using simgal4.

first: Jelena

last: Aleksic

first: Bettina

last: Fischer


title: Full genome expression profiling of primary colorectal cancer (CRC)

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

summary: Fresh-frozen primary tumor samples from CRC patients were analyzed from their gene expression. Full genome unsupervised clustering identified three intrinsic subtypes that are associated with tumor and clinical characteristics.

overall_design: Primary CRC samples (188) were hybridzed against a common colon cancer reference pool (CRP).


title: miRNA profiles of Wilms tumor patients and controls

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

summary: Blood-borne miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior to and after preoperative chemotherapy according to the SIOP protocol 2001. We did not find a significant difference between the miRNA signatures of both groups. However, both Wilms tumor patients prior to and after chemotherapy showed a miRNA signature different from that of healthy controls. The signature of Wilms tumor patients prior to chemotherapy showed an accuracy of 97.5% and of patients after chemotherapy an accuracy of 97.0%, each as compared to healthy controls. Our results provide evidence for a blood-borne Wilms tumor miRNA signature largely independent of four weeks preoperative chemotherapy treatment.

overall_design: This project analyzes peripheral blood profiles of Wilms tumor patients and controls in order to detect specific profiles. n=19 normal controls and n=23 Wilms tumor patients were screened for the complete miRNA repertoire. Please note that each miRNA has been measured in seven replicates and the median of the replica has been computed.

first: Christina

last: Backes


title: Expression analysis of Aspergillus oryzae grown on different carbon sources

city: Gothenburg

first: D.B.R.K. Gupta

last: Udatha

state: Sweden

address: Medicinaregatan 9C

department: Department of Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

summary:
In this study, we focused on chemically defined inducers or substrates to drive expression of cellulases, hemicellulases and accessory enzymes in the model filamentous fungus Aspergillus oryzae.
Cellohexaose (O-CHE), mannohexaose (O-MHE), xylopentaose (O-XPE), arabinoheptaose (O-AHP), 1,3:1,4-β-glucohexaose (O-BGHEXA), 63-α-D-glucosyl-maltotriosyl-maltotriose (O-GMH), 61-α-D-galactosyl-mannotriose (O-GM3), xyloglucan (X3Glc4-borohydride reduced; O-X3G4R), turanose (TYR) and sophorose (SOP) were used to induce the plant polysaccharide degradation machinery of A. oryzae.

overall_design: The strain used in this study was the A. oryzae sequenced strain RIB40, obtained from IBT culture collection at Technical University of Denmark. To obtain a global view of the A. oryzae transcriptome activated for plant biomass conversion, mRNA from growth after 2 h on 10 different carbohydrate active enzyme inducers (di- and –oligo saccharides) was subjected to custom-designed Agilent microarray analysis.

first: Evangelos

last: Topakas

first: D

first: Melanie

middle: Z

last: Khodaie

first: Margarita

last: Salazar

first: Lisbeth

last: Olsson

first: Mikael

last: Andersen

first: John

last: Smith


title: The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation

city: Philadelphia

first: Russ

middle: P.

last: Carstens

state: PA

address: 575 Clinical Research Building, 415 Curie Boulevard

department: Renal Division, Department of Medicine

institute: University of Pennsylvania

summary: Alternative pre-mRNA splicing is a prevalent mechanism in mammals that promotes proteomic diversity, including expression of cell-type specific protein isoforms.  We characterized a role for RBM38 (RNPC1) in regulation of alternative splicing during late erythroid differentiation.  We used an affymetrix human exon junction (HJAY) splicing microarray to identify a panel of RBM38-regulated alternatively spliced transcripts.   Using microarray databases, we noted high RBM38 expression levels in CD71+ erythroid cells and thus chose to examine RBM38 expression during erythroid differentiation of human hematopoietic stem cells, detecting enhanced RBM38 expression during late erythroid differentiation.  In differentiated erythroid cells, we validated a subset of RBM38-regulated splicing events and determined that RBM38 regulates activation of Protein 4.1R (EPB41) exon 16 during late erythroid differentiation.  Using Epb41 minigenes, Rbm38 was found to be a robust activator of exon 16 splicing.  To further address the mechanism of RBM38-regulated alternative splicing, a novel mammalian protein expression system, followed by SELEX-Seq, was used to identify a GU-rich RBM38 binding motif.  Lastly, using a tethering assay, we determined that RBM38 can directly activate splicing when recruited to a downstream intron.  Together, our data support the role of RBM38 in regulating alternative splicing during erythroid differentiation.

overall_design:
siRNA knockdown of RBM38 was perfomed in human MCF-7 breast cancer cells. The efficiency of RBM38 knockdown was monitored by western blot using an RBM38 antibody (Santa Cruz Biotechnology, SC-85873). We conducted HJAY exon and exon junction array profiling on RNAs from four siRBM38 treated MCF-7 samples vs. four sicontrol treated MCF-7 samples
Control / knockdown comparison.

first: Laurie

middle: A

last: Heinicke

first: Behnam

last: Nabet

first: Shihao

last: Shen

first: Yi

last: Xing

middle: P


title: Global Rsh-dependent transcription profile of Brucella suis during stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses.

status: Public on Jul 08 2013

city: Montpellier

first: Stephan

last: Kohler

address: 1919 Route de Mende

country: France

institute: CNRS

summary: In the intracellular pathogen Brucella spp., the activation of the stringent response, a global regulatory network providing rapid adaptation to a variety of growth-affecting stress conditions such as nutrient deficiency, is essential for replication in the host. A single, bi-functional enzyme Rsh catalyzes synthesis and hydrolysis of the alarmone (p)ppGpp, responsible for differential gene expression under stringent conditions. cDNA microarray analysis allowed characterization of the transcriptional profiles of the B. suis 1330 wild-type and rsh mutant in a synthetic minimal medium, partially mimicking the nutrient-poor environment of the intramacrophagic vacuole. A total of 379 genes (11.6% of the genome) were differentially expressed in a rsh-dependent manner, of which 52% were up-regulated and 48% were down-regulated. The pleiotropic character of the response was confirmed, as the genes encoded factors belonging to various functional groups, comprising an important number of transcriptional regulators, cell envelope proteins, stress factors, transport systems, and energy metabolism proteins. Several virulence genes were under the positive control of (p)ppGpp. Methionine was the only amino acid whose biosynthesis was absolutely dependent on stringent response in B. suis. The study illustrated the complexity of the processes involved in adaptation to nutrient starvation, and contributed to a better understanding of the correlation between stringent response and Brucella virulence. Most interestingly, it clearly indicated (p)ppGpp-dependent cross-talk between at least three stress responses playing a central role in Brucella adaptation to the host: nutrient, oxidative, and low-oxygen stress.

overall_design:
Two-condition experiment, wild-type against rsh mutant. Biological replicates: 4 wild-type, 4 rsh mutant, independently grown in minimal medium (under nutrient starvation condition) and harvested. One replicate per array.
Please note that Channel 1 (Cy3) on each hybridization was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with wild-type versus rsh mutant.

first: Nabil

last: Hanna

first: Safia

last: Ouahrani-Bettache

first: Kenneth

middle: L

last: Drake

first: L

last: Adams

last: Köhler

first: Alessandra

last: Occhialini


title: Intense THz pulses down-regulate genes associated with skin cancer and psoriasis: a new therapeutic avenue?

status: Public on Jul 09 2013

city: Lethbridge

first: Olga

last: Kovalchuk

state: Alberta

address: 4401 University Drive West

institute: University of Lethbridge

summary: We show that exposure of artificial human skin tissue to intense, picosecond-duration THz pulses affects expression levels of numerous genes associated with non-melanoma skin cancers, psoriasis and atopic dermatitis. Genes affected by intense THz pulses include nearly half of the epidermal differentiation complex (EDC) members. EDC genes, which are mapped to the chromosomal human region 1q21, encode for proteins that partake in epidermal differentiation and are often overexpressed in conditions such as psoriasis and skin cancer.  In nearly all the genes differentially expressed by exposure to intense THz pulses, the induced changes in transcription levels are opposite to disease-related changes.

overall_design: Total RNA from exposed artificial human skin tissues to picosecond-duration broadband (0.2–2.5 THz) THz pulses with 1 kHz repetition rate, 1/e2 spot-size diameter of 1.5 mm and pulse energies of either 1.0 μJ or 0.1 μJ.  For comparison, we have exposed skin tissues to UVA pulses (400 nm, 0.1 ps, 0.024 μJ).

first: Lyubov

middle: V

last: Titova

first: Ayesheshim

middle: K

last: Ayesheshim

first: Andrey

last: Golubov

first: Rocio

last: Rodriguez-Juarez

first: Rafal

last: Woycicki

first: Frank

last: Hegmann


title: Aging Experiment

status: Public on Jul 10 2013

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary: Lifelong murine gene expression profiles in relation to chronological and biological aging in multiple organs

overall_design: Five tissues: Kidney, Liver, Lung, Spleen, Brain. Six timepoints: 13wks, 26 wks, 52wks, 78wks, 104wks, 130wks. One Genotype: C57Bl/6, 3 replicates

middle: J

first: Joost

last: Melis

first: Raoul

last: Kuiper

first: Tessa

last: van der Hoeven

first: Joke

last: Robinson

first: Gijsbertus

middle: T

last: van der Horst

first: Timo

last: Breit

first: Jan

last: Vijg

first: Martijn

last: Dollé

middle: H

last: Hoeijmakers

first: Harry

last: van Steeg


title: Allele-specific chromosome conformations induced by a transgene- and locus-dependent imprinting

status: Public on Jul 03 2013

city: Lausanne

first: Nicolas

last: Lonfat

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL - Ecole Polytechnique Fédérale de Lausanne

summary: A reporter transgene displayed parental imprinting in mouse embryos when positioned into the Itga6 gene.  The strong lacZ pattern of expression scored in embryos inheriting the transgene from a male was not present when transmitted from a female. The transgene exhibited maternal allele-specific DNA hyper-methylation acquired in the germ-line and histone modifications corresponded to profiles described at known imprinted loci. Chromosome conformation analyzes revealed distinct, parent-of-origin interaction domains, with a more compact structure characterizing the maternally inherited repressed allele. The analysis of such transgene insertions with a selective potential to induce imprinting may help understanding the mechanisms identifying particular loci as targets for allele-specific repression.

overall_design: Data were quantile normalized within 4C/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix), generating signal.bar files. For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp. For Inv(rel5-Itga6) tissues, two independent 4C experiments were performed and merged in the .bar file.

first: N

first: D

last: Duboule


title: Campylobacter jejuni Cj1000 regulon

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

institute: University of Ottawa

summary: Transcriptional regulation mediates adaptation of pathogens to environmental stimuli and is important for host colonisation. The Campylobacter jejuni genome sequence reveals a surprisingly small set of regulators, mostly of unknown function, suggesting an intricate regulatory network. Interestingly, C. jejuni lacks the homologues of ubiquitous regulators involved in stress response found in many other Gram-negative bacteria. Nonetheless, cj1000 is predicted to code for the sole LysR-type regulator in the C. jejuni genome, and thus may be involved in major adaptation pathways. A cj1000 mutant strain was constructed and found to be attenuated in its ability to colonise 1-day old chicks. Complementation of cj1000 mutation restored the colonisation ability to that of wild type levels. The mutant strain was also outcompeted in a competitive colonisation assay of the piglet intestine. High resolution oxygraphy was carried out for the first time on C. jejuni and revealed a role for Cj1000 in controlling O2 consumption. Furthermore, microarray analysis of the cj1000 mutant revealed both direct and indirect regulatory targets, including genes involved in energy metabolism and oxidative stress defences. These results highlight the importance of Cj1000 regulation in host colonisation and in major physiological pathways.

overall_design: Microarray data was collected from three independent biological replicates and 3-9 technical replicates for each biological replicate.

first: Annika

last: Flint

first: Jennifer

last: Li

first: Virginie

last: Dufour

first: Christine

last: Baysse


title: BRAF siRNA NHGRI_Liang_BRAF

status: Public on Jul 07 2013

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

summary:
BRAF, one of three RAF serine/threonine kinases (ARAF, BRAF and CRAF), plays a major role in the RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) signaling pathway, which mediates cellular responses to growth signals. Recently a high frequency (~60%-70%) of activating BRAF mutations (predominantly V600E) has been reported in malignant melanoma. In order to identify the downstream effects of BRAF signaling on melanoma cell growth and gene expression, cDNA microarray analysis was carried out following BRAF siRNA or MEK1/2 inhibitor (U0126) treatment.
Keywords: time series, siRNA

overall_design: time series, siRNA, drug treatment

first: Paul

last: Meltzer

first: Yizheng

last: Liang


title: A gene regulatory network involving the class II ERF transcriptional repressors in leaf senescence of Arabidopsis thaliana

status: Public on Jul 02 2013

city: Tsukuba

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Leaf senescence is the final developmental process that includes the mobilization of nutrients from old leaves to newly growing tissues. The progression of leaf senescence requires dynamic but coordinated changes of gene expression. Although several transcription factors (TFs) are known to be involved in both negative and positive modes of regulation of leaf senescence, detailed mechanisms that underlie the progression of leaf senescence are largely unknown. We report here that the class II ERF transcriptional repressors are controlled by proteasome and regulate the progression of leaf senescence in Arabidopsis. Since we had previously demonstrated that NtERF3, a model of tobacco class II ERFs, specifically interacts with a ubiquitin-conjugating enzyme, we examined the stability of NtERF3 and found that bacterially produced NtERF3 was rapidly degraded by plant protein extracts in vitro. Whereas NtERF3 accumulation was low in plants, it was increased by treatment with a proteasome inhibitor. Arabidopsis class II ERFs, namely, AtERF4 and AtERF8, were also controlled by proteasome and stabilized by aging of plants. The transgenic plants in which NtERF3, AtERF4, and AtERF8 were individually expressed under the control of the 35S promoter exhibited the precocious leaf senescence. Our microarray and RT-PCR analyses revealed that AtERF4 regulated expression of genes involving in various stress responses and leaf senescence. In contrast, aterf4 aterf8 mutant exhibited delayed leaf senescence. Taken together, we present the important role of class II ERFs in the regulation of leaf senescence.

overall_design: Transcriptomes of 35S:AtERF4-HA and 35S:NLS-GFP-HA (control) Arabidopsis two-weeks seedling were compared.

first: Koyama

last: Tomotsugu

first: Nii

last: Haruka

first: Mitsuda

last: Nobutaka

first: Kitajima

last: Sakihito

first: Ohme-Takagi

last: Masaru

first: Sato

last: Fumihiko


title: Mitochondrial two-component signaling systems in Candida albicans

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary: Two-component signal transduction pathways are one of the primary means by which microorganisms respond to environmental signals. These signaling cascades originated in prokaryotes and were inherited by eukaryotes via endosymbiotic lateral gene transfer from ancestral cyanobacteria. We report here that the nuclear genome of pathogenic fungus Candida albicans contains elements of a two-component signaling pathway that seem to be targeted to the mitochondria. In C. albicans two-component response regulator protein Srr1(Stress Response Regulator) contains a mitochondrial targeting sequence at the N-terminus, and fluorescence microscopy reveals mitochondrial localization of GFP-tagged Srr1p. Moreover, phylogenetic analysis indicates that C. albicans Srr1p is more closely related to histidine kinases and response regulators found in marine bacteria compared to other two-component proteins present in the fungi. These data suggest conservation of this protein during the evolutionary transition from endosymbiont to a subcellular organelle. We used microarray analysis to determine if the phenotypes observed with srr1Δ/Δ mutant could be correlated with gene transcriptional changes. Expression of mitochondrial genes was altered in the srr1Δ/Δ null mutant in comparison to the wild type. Furthermore, apoptosis significantly increased in the srr1Δ/Δ mutant strain compared to wild type, suggesting activation of mitochondria dependent apoptotic cell death pathway in the srr1Δ/Δ mutant. This study shows for the first time that a lower eukaryote like C. albicans possesses a two-component response regulator protein that has survived in mitochondria and regulates a subset of genes whose functions are associated with oxidative stress response and programmed cell death (apoptosis).

overall_design: Candida albicans wildtype or srr1 null cells were left untreated or were treated with either 8mM H2O2 for one hour prior to RNA isolation.

first: John

last: Mavrianos

first: Elizabeth

last: Berkow

first: Chirayu

last: Desai

first: Mona

last: Batish

first: Marissa

last: Rabadi

first: P

middle: D

last: Rogers

first: Eliseo

last: Eugenin

first: Neeraj

last: Chauhan


title: Expression analysis of sporulating Bacillus subtilis strain 168 deleted for prpE gene

city: Gdansk

first: Adam

last: Iwanicki

address: Debinki 1

department: Department of Medical Biotechnlogy

country: Poland

institute: Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk

summary: Investigation of whole genome gene expression level changes in sporulating Bacillus subtilis 168 delta-prpE mutant, compared to the wild-type strain.  The mutation engineered into this strain results in impaired germination of spores.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: A six chip study using total RNA extracted from three separate wild-type cultures of sporulating Bacillus subtilis 168 and three separate cultures of sporulating mutant strain, Bacillus subtilis 168 delta-prpE, in which prpE (yjbP BSU11630) gene coding for a protein phosphatase is deleted entirely.  Each chip consists of four fields able to measure the expression level of 4,104 genes from Bacillus subtilis subsp. subtilis strain 168 NC_000964 with eight 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.

first: Krzysztof

last: Hinc

first: Anna

last: Ronowicz

first: Arkadiusz

last: Piotrowski

first: Michał

last: Obuchowski


title: Molecular basis for chromatin binding and regulation of MLL5

status: Public on Jul 01 2013

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

summary: The human mixed lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle and survival, however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its PHD finger with the histone mark H3K4me3. The 1.48 Å resolution crystal structure of the MLL5 PHD finger in complex with the H3K4me3 peptide reveals a non-canonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a His-Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, MLL5, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide insight into the molecular basis for the recruitment, exclusion and regulation of MLL5 at chromatin.

overall_design: For determaning MLL5 chromatin profile, DamID-MLL5 chromatin profiling was determined in C2C12 cells . Three biological replicates were performed. Normalized data was averaged and HMM approach was applied to establish the bound regions (Straub, T., Grimaud, C., Gilfillan, G. D., Mitterweger, A., and Becker, P. B. (2008). PLoS Genet 4, e1000302)

first: Muzaffar

last: Ali

first: Wei

last: Zhao

first: Scott

last: Rothbart

first: Qiong

last: Tong

first: Susan

middle: M

last: Parkhurst

first: Brian

last: Strahl

first: Lih-Wen

last: Deng

first: Mark

last: Groudine

first: Tatiana

middle: G

last: Kutateladze


title: A bovine lymphosarcoma cell line infected with Theileria annulata exhibits an irreversible reconfiguration of host cell gene expression

status: Public on Jul 04 2013

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

summary:
The experiment investigates bovine gene expression in response to BW720c treatment in uninfected and Theileria annulata-infected cell cultures
Theileria annulata, an intracellular parasite of bovine lymphoid cells, induces substantial phenotypic alterations to its host cell including continuous proliferation, cytoskeletal changes and resistance to apoptosis. While parasite induced modulation of host cell signal transduction pathways and NFκB activation are established, there remains considerable speculation on the complexities of the parasite directed control mechanisms that govern these radical changes to the host cell. Our objectives in this study were to provide a comprehensive analysis of the global changes to host cell gene expression with emphasis on those that result from direct intervention by the parasite. By using comparative microarray analysis of an uninfected bovine cell line and its Theileria infected counterpart, in conjunction with use of the specific parasitacidal agent, buparvaquone, we have identified a large number of host cell gene expression changes that result from parasite infection. Our results indicate that the viable parasite can irreversibly modify the transformed phenotype of a bovine cell line. 50% of genes with altered expression failed to show a reversible response to parasite death, a possible contributing factor to initiation of host cell apoptosis. The genes that did show an early predicted response to loss of parasite viability highlighted a sub-group of genes that are likely to be under direct control by parasite infection.  Network and pathway analysis demonstrated that this sub-group is significantly enriched for genes involved in regulation of expression and chromatin modification. The results provide evidence that the Theileria parasite has the regulatory capacity to generate widespread change to host cell gene expression in a complex and reversible manner.

platform_organism:
Theileria annulata
Bos taurus

overall_design: Six experimental conditions with three replicates per condition. Total RNA prepared from cell cultures. BL20 (uninfected bovine lymphosarcoma cell line), BL20 24 hours post-BW720c treatment, BL20 48 hours post-BW720c, TBL (T. annulata infected bovine cell line), TBL 24 hours post-BW720c, TBL 48 hours post-BW720c. Each hydridisation represents bovine and parasite gene expression on a single channel and 2 technical replicates of each probeset are represented on the chip.

first: Jane

last: Kinnaird

first: Zeeshan

last: Durrani

first: Sreerekha

last: Pillai

first: Margaret

last: Baird

last: Shiels


title: Lack of hepatic response of microRNA in mice following DB[a,h]A exposure (Agilent miRNA)

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary: Dibenzo[a,h]anthracene  DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5,  and  25  mg/kg/day  DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each  DB[a,h]A  dose  tested,  and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis  revealed  minor  changes  in  the  mRNA  expression  for the two lowest doses. Differential expression of 19 up-regulated  and  22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25  mg/kg/day  DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32  down-regulated  (FDR-adjusted  P  <  0.05  and  fold-change  > 1.5). Major effect on mRNA expression resulted from exposure  to  the  highest  dose  (25  mg/kg/day)  of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change  >  1.5  (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism,  glucose  metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated  miRNA  response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold.

overall_design: RNA samples from 5 control and 4-5 mice per treatment group (6.25mg/kg, 12.50mg/kg, and 25mg/kg) containing 100 ng were labelled using Agilent’s miRNA complete labelling and Hyb Kit (Agilent Tech, Mississauga, ON, Canada).

first: Amal

middle: I

last: Malik

first: Andrea

last: Rowan-Carroll

first: Christine

last: Lemieux

first: Paul

last: White

first: Carole

last: Yauk


title: An Easy Operating Pathogen Microarray (EOPM) Platform for Rapid Screening of Vertebrate Pathogens

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

summary: An Easy Operating Pathogen Microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed and further implemented in a user-friendly interface.

overall_design: A microarray was designed with probes for vertebrate-infecting virus sequences in EMBL, 18S rRNA fungi and parasite sequences from EMBL, and 16S rRNA sequences of bacteria from RDP, synthesized on the Agilent platform. The array was tested using 2 color dyes on cultured microbes and on clinical samples from sick and healthy people, looking for differences in clinically ill people compared to a number of healthy "controls".

first: Weiwei

last: Huang

first: Yinhui

last: Yang

first: Xinlei

last: Zhang

first: Changan

last: Zhao

first: Aihua

last: Yin

first: Xiaozhuang

first: Zhengxin

last: He

first: Yongqiang

last: Jiang

first: Liang


title: Benzene effects on leaves: Study of benzene metabolism in higher plants.

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary:
au12-01_detox; Improving the knowledge of the metabolic pathways of benzene in higher plants
Cabbages (Brassica oleracea Var. Prover)are directly submitted to a one dose of benzene (3ppm) during 1 hour or 3 hours. The comparison is realized between samples treated and untreated to the benzene for both exhibitions.

overall_design: 4 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Sylvain

last: Dumez

first: Marie-Laure

last: Martin-Magniette


title: Permanganate ChIP-seq analysis of Pol II in nonheat shocked and heat shocked Drosophila S2R+ cells and nonheat shocked BG3 cells

city: University Park

first: David

middle: Scott

last: Gilmour

state: Pennsylvania

address: 465 North Frear

department: Biochemistry and Molecular Biology

institute: Penn State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The genomic distribution of transcriptionally engaged Pol II in control and heat shocked cells was determined by combining formaldehyde crosslinking and permanganate oxidation of transcription bubbles

overall_design: Cells treated in succession with formaldehyde and then permanganate, were subjected to chromatin precipitation with Rpb3 antibody, and then the pattern of permanganate modifications were mapped genome-wide

first: Jian

last: Li

middle: S


title: affy_cotton_2011_12-Comparative transcriptional profiling of cotton fibers in Gossypium hirsutum and Gossypium barbadense using EST pyrosequencing and microarray hybridization

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturer’s recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip® Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). -

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: 4 arrays - Cotton; x comparison between two genotypes in cell type

first: Thierry

last: Lagrange

first: Stephanie

last: Huguet

first: Danny

last: Llewellyn

first: Jean-Marc

last: Lacape


title: Response to salt stress of Raptor mutants

summary:
ra12-03_raptor-nacl -
Characterization to raptor mutants (partner of the kinase TOR) and of their answer to the salt stress. - Sowing on metal grids on MS/2 medium with continuous light. Transfer after 12 days of culture for 3h to liquid MS/2 medium containing or not 200 mM NaCl.

overall_design: 7 dye-swap - gene knock out, treated vs untreated comparison

first: Christian

last: Meyer


title: An RNA-binding protein Spo5 promotes meiosis II through the regulation of cyclin Cdc13

city: Tokyo

first: Akira

last: Yamashita

address: Hong

department: Department of Biophysics and Biochemistry

institute: University of Tokyo

summary: To determine the range of genes whose expression is regulated by Spo5 under nitrogen starbation, comparison of gene expression profiles between a wild-type strain and a deletion mutant of spo5, which encodes the meiosis specific RNA-binding protein Spo5.

overall_design: Cells of the wild-type (JY882) and spo5∆ (MA482) fission yeast strains were grown to the mid-log phase in liquid MM and shifted to nitrogen-free MM–N at 25ºC. The cells were harvested 6 h after this shift, the tempereture was raised to 34ºC. RNA was prepared from each sample after the temperature shift and analyzed on a DNA microarray covering 5,073 genes.

first: Mayumi

last: Arata


title: Expression data from in vivo experiment comparing untreated controls with animals treated with bevacizumab (Avastin)

city: Houston

first: John

last: de Groot

state: TX

address: 1515 Holcombe Blvd

institute: UT - MD Anderson Cancer Center

summary:
Bevacizumab induces glioblastoma resistance in two in vivo xenograft models. Two cell lines were developed with acquired resistance to bevacizumab. Gene expression difference were analyzed between treated and untreated tumors.

Purpose: Antiangiogenic therapy reduces vascular permeability and delays progression but may ultimately promote an aggressive treatment-resistant phenotype. The aim of the present study was to identify mechanisms responsible for glioblastoma resistance to antiangiogenic therapy.

Experimental Design: Glioma stem cell (GSC) NSC11 and U87 cell lines with acquired resistance to bevacizumab were developed from orthotopic xenografts in nude mice treated with bevacizumab. Genome-wide analyses were used to identify changes in tumor subtype and specific factors associated with resistance.

Results: Mice with established parental NSC11 and U87 cells responded to bevacizumab, whereas glioma cell lines derived at the time of acquired resistance to anti-VEGF therapy were resistant to bevacizumab and did not have prolongation of survival compared to untreated controls. Gene expression profiling comparing anti-VEGF therapy-resistant cell lines to untreated controls demonstrated an increase in genes associated with a mesenchymal origin, cellular migration/invasion, and inflammation. Gene Set Enrichment Analysis (GSEA) demonstrated that bevacizumab-treated tumors showed a highly significant correlation to published mesenchymal gene signatures. Mice bearing resistant tumors showed significantly greater infiltration of myeloid cells in NSC11 and U87 resistant tumors. Invasion-related genes were also upregulated in both NSC11 and U87 resistant cells, which had higher invasion rates in vitro compared with their respective parental cell lines.

Conclusions: Our studies identify multiple pro-inflammatory factors associated with resistance and identify a proneural-to-mesenchymal transition (PMT) in tumors resistant to antiangiogenic therapy.

overall_design: Glioma cell lines were injected into the caudate of nude mice and were allowed to grow untreated (samples labeled control) or were treated with 10 mg/kg IP twice weekly with bevacizumab (samples labeled Avastin). At the time of animal death, tumor tissue from the mouse was removed, and RNA was isolated and analyzed using gene expression. U87R and NSC11R represent cells resistant to bevacizumab (Avastin).


title: Microarray Expression Analysis of ASPP2 Knockdown in HCC-LM3 cell lines

city: Shanghai

first: fang

middle: fang

last: bu

address: Yin Road, New Building 10-11th Floor

department: 1International Joint Cancer Institute

institute: Second Military Medical University

summary: ASPP2, also known as 53BP2L, belongs to ASPP family of proteins. ASPP2 is proved to be a haploinsufficient tumor suppressor in ASPP2-deficient mouse models with ASPP2+/- mice having a high incidence of spontaneous tumors and γ-irradiation-induced tumors. Clinical data reveals that ASPP2 is frequently decreased in a variety of cancers.  We have previously showed that ASPP2 was frequently down-regulated by methylation and decreased expression of ASPP2 was positively correlated with recurrence and poor prognosis in HCC patients. We also investigated that ASPP2 may induce apoptosis, inhibit cell migration and invasion in vitro, but the underlying molecular mechanism remains unknown.This chip experiment was carried out to investigation of whole genome gene expression level changes induced by ASPP2 knockdown.

overall_design: HCC-LM3 cells were infected with LV-shASPP2 or LV-shNon control virus, one week later total RNA was extracted using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). Three biological replicates were included .Six samples were amplified and labeled using a NimbleGen One-Color DNA Labeling Kit.

last: Zhao

first: Fangfang

last: Bu


title: Distinct signal transduction pathways downstream of the (P)RR revealed by microarray and ChIP-chip analyses [Expt: ChIP-chip]

status: Public on Jul 05 2013

city: Berlin

first: Daniela

last: Zaade

address: Hessische Straße 3-4

department: Center for Cardiovascular Research

institute: Charité

summary: We performed a set of microarray and chromatin-immunoprecipitation (ChIP)-chip experiments using siRNA against the (pro)renin receptor ((P)RR), stable overexpression of PLZF, the PLZF translocation inhibitor genistein and the specific V-ATPase inhibitor bafilomycin to dissect transcriptional pathways downstream of the (P)RR.

overall_design: In this dataset, we include the ChIP-chip data obtained from PLZF overexpressing KELLY cells, from PLZF overexpressing HEK293T cells and from KELLY as well as HEK293T cells both stably transfected with an insertless control vector.

first: Heiko

last: Funke-Kaiser


title: Genome-wide analysis of gene expression in response to bortezomib treatment [human cell lines].

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary:
Genome-wide analysis of gene expression in response to bortezomib treatment (33 nM) in cell lines before and after selection for resistance.
Multiple myeloma (MM) is a hematologic malignancy characterized by the proliferation of neoplastic plasma cells in the bone marrow. While the first-to-market proteasome inhibitor bortezomib/VELCADE has been successfully used to treat myeloma patients, drug resistance remains an emerging problem. In this part of the study, we identify signatures of bortezomib sensitivity by gene expression profiling (GEP) using The human myeloma cell lines MM1.S and U266 (obtained from ATCC). Finally, these data reveal complex heterogeneity within MM and suggest resistance to one drug class reprograms resistant clones to make them more sensitive to a distinct class of drugs. This study represents an important next step in translating pharmacogenomic profiling and may be useful for understanding personalized pharmacotherapy of MM patients.

overall_design: Transcript profiling timecourses after treatment with Bortezomib treatment (33nm) in two myeloma cell lines.


title: Visual automated fluorescence electrophoresis provides simultaneous quality, quantity, and molecular weight spectra for genomic DNA from archived neonatal blood spots

first: Tara

middle: Leah

last: Klassen

address: One Baylor Plaza

department: Neurology

institute: Baylor College of Medicine

summary:
The Guthrie 903 card archived dried blood spots (DBS) are a unique but terminal resource amenable for individual and population wide genomic profiling.
The limited amounts of DBS-derived genomic DNA (gDNA) can be whole-genome amplified (WGA) producing sufficient gDNA for genomic applications, albeit with variable success, and optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential.
Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology affording precise quality, quantity and molecular weight of double-stranded DNA from a single microliter of sample.
The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array.

overall_design: The Swedish Repository of DBS samples collected on Guthrie 903 cards for neonatal screening of inborn diseases provided deidentified 3mm blood spot punches. There were total of eight (8) samples representing two (2) decades; 1970s: 1975, 1976, 1977, 1978; 1980s: 1980, 1982, 1984, 1986. gDNA was extracted and whole genome amplified prior to aCGH experiments using control female reference genomic DNA. The objective was to show that large rearrangements (e.g. loss of chrX in male samples) can be detected in WGA gDNA from blood spots >30 years old.

first: Alica

last: Goldman


title: Huh7 cells exist as a mixed population of cells with distinct patterns of gene methylation

city: Dallas

first: Qiuyue

last: Chen

address: 5323 Harry Hines Blvd.

department: Molecular Genetics

institute: UT Southwestern Medical Center

type: Methylation profiling by genome tiling array

summary: A powerful approach to study innate antiviral response is to compare the difference between wild type Huh7 cells, which do not support robust replication of hepatitis C virus (HCV)2, versus certain subclones of Huh7 cells that are permissive for HCV replication. We generated two permissive cell lines and two independent non-permissive subclone from Huh7 cells. We compared the global methylation pattern of these different cells and find that Huh7 cells exist as a heterogeneous population of cells with distinct patterns of gene methylation.

overall_design: Comparison of Huh7, HRP1, HRP4, Huh7-pNeo1 and Huh7-pNeo2 cells.


title: tiling hen2 and mtr4-HEN2 is a cofactor of the nuclear exosome in Arabidopsis

status: Public on Jun 30 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

summary: til-ath-2011_3 - tiling hen2 and mtr4 - Identification and comparison of the RNA substrates that accumulate in hen2 and mtr4 mutants. Total RNA extracted from WT, hen2 and mtr4 mutants was used for oligo-dT primed cDNA preparation. Samples were hybridised to NimbleGen whole genome tiling arrays.

overall_design: 8 dye-swapped samples. Gene knockout, genotype comparison, normal vs. transgenic comparison.

first: Heike

last: Lange

first: Dominique

last: Gagliardi

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Susceptibility of neoplastic transformation of human dental pulp stem cells DPSC in hypoxia

city: Valencia

first: Rut

last: Lucas

address: Autopista Saler 16,

country: Spain

institute: Centro Investigación Príncipe Felipe

summary: Neoplastic transformation of DPSC cultured under Hypoxia  versus normoxia. Molecular characterization of cell markers associated with tumorigenicity.

overall_design: DPSC array CGH profiles of experimental (HX48h and HX72h) and reference (NX48 and NX72h) genomic DNA samples

first: R

first: J

last: Sanchez-Puelles


title: Functional genomic analyses of Bifidobacterium bifidum PRL2010 highlight how this microorganism interact with the human host

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma

summary: Bifidobacteria represents one of the dominant group of microorganisms colonizing the intestine of infants. However, the genetic determinants supporting the establishment and the interaction with the human hosts are still largely unknown. Most commensal bacteria interacting with eukaryotic hosts express adhesive molecules on their surfaces that modulate interaction with host cell receptors or with soluble macromolecules. Whole genome transcription profiling of B. bifidum PRL2010, a strain isolated from infant stool, under in vitro as well as in vivo conditions revealed the expression of few common extracellular proteins among which type 1 pili encoding genes.

overall_design: To investigate the molecular mechanisms sustaining the interaction of PRL2010 strain with the human gut, we first explored the global genome transcription profiling of this strain in a in vitro human model such as in the presence of HT29 cell lines. The transcriptome was analyzed using a custom B. bifidum PRL2010 array representing the 90% of this organism’s protein coding genes. To better evaluate the conserved responses by B. bifidum, the in vivo transcriptomes were quantified against a diverse set of transcriptome patterns identified for in vitro laboratory cultures of the strain, i.e., B. bifidum responses after growth on an cell’s monolayers growth medium (DMEM); B.bifidum responses after growth on synthetic medium (MRS). Briefly, we analized  five conditions, two of which are also used as references. Every experiment was performed in duplicate and in vivo condition was performed in quadruplicate.


title: Derivation of monkey parthenogenetic haploid embryonic stem cells

status: Public on Jun 26 2013

first: Linyu

last: Shi

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences

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

overall_design: Refer to individual Series

first: Jinsong

last: Li


title: Intestinal Salmonella Typhimurium infection leads to miR-29a induced Caveolin 2 regulation

status: Public on Jun 25 2013

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

country: Germany

institute: Freie Universitaet Berlin

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


title: Effects of 20 months Dietary Methionine Restriction on Gene Expression in inguinal white adipose tissue of Fischer 344 Rats

city: Baton Rouge

first: Kirsten

last: Stone

address: 6400 Perkins Rd

country: USA

institute: Pennington Biomedical Research Center

summary: Dietary methionine restriction (MR)  has been shown to increase lifespan and decrease adiposity in rodents. This study was designed to examine the transcriptional effects of MR in metabolically relevant tissues. This experiment contains data from the inguinal white adipose tissue (IWAT).

overall_design: We analyzed MR-induced changes in gene expression using pooled RNA from IWAT of rats fed either a control purified amino acid diet (DL-methionine content of 0.86%) (CON) or a methionine-restricted diet (DL-methionine content of 0.172%)(MR). Rats were fed Purina rodent diet 5001 until 32 days of age and were then randomly assigned to be fed CON diet or MR diet  for 20 months.

first: A

last: Boudreau

first: E

last: Plaisance

first: B

middle: E

last: Hasek

first: N

middle: R

last: Lenard

first: L

last: Stewart

first: T

last: Henagan

middle: W

last: Gettys


title: mRNA expression data from monkey PG-haESCs, ICSI-derived ESCs and somatic fibroblasts

country: China

summary:
Haploid cells are amenable for genetic analysis because they contain only one set of chromosomes. Here,we report the derivation of haESCs from monkey parthenogenic blastocysts. These cells, which we designated PG-haESCs (parthenogenic haploid embryonic stem cells), express classical ESC markers, are pluripotent, and can differentiate to different cell lines from all three embryonic germ layers in vivo and in vitro.
We used microarrays to compare the gene expression levels among PG-haESC, ICSI-derived ESCs and female monkey somatic fibroblasts.

overall_design: We used ICSI-derived ESCs and somatic fibroblasts isloated from female individuals as control. Gene expression profiles of all the cell lines were analysed on an Affymetrix Rhesus Macaque array.