title: Physical mapping of bread wheat chromosome 5A: an integrated approach

status: Public on Aug 13 2015

city: Fiorenzuola d'Arda

first: Delfina

last: Barabaschi

address: Via San Protaso 302

institute: CRA-Genomics Research Centre

summary: The huge size, the redundancy and the great repeated portion of the bread wheat genome [Triticum aestivum (L.)], placed it among the most difficult species to be sequenced and dissected at the genetic, structural and evolutionary levels. To overcome the limitations, a strategy based on the genome compartmentalization in individual chromosomes and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium. A total of 95,812 BAC clones of short (5AS) and long (5AL) arm-specific BAC libraries, were fingerprinted and assembled into contigs by complementary analytical approaches based on FingerPrinted Contigs and Linear Topological Contig. Combined anchoring approaches based on PCR marker screening, microarray and BlastN searches, applied to interlinked genomic tools, that is genetic maps, deletion bin map, high-density neighbor map, BAC end sequences, genome zipper and chromosome survey sequences, allowed the development of a high quality physical map, with an anchored physical coverage of 75% for 5AS and 53% for 5AL, with high portions (64 and 48%, respectively) ordered along the chromosome. The gene distribution along the wheat chromosome 5A compared with the closest related genomes showed a pattern of syntenic blocks belonging to different chromosomes of Brachypodium, rice and sorghum and regions involving translocations and inversions. The physical map presented here is currently the most comprehensive map for 5A chromosome and represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits, and a reference for the 5A sequencing projects.

overall_design: 55 DNA pools of short arm of chromsome 5A and 63 DNA pools of long arm of 5A. The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

first: Federica

last: Magni

first: Andrea

last: Volante

first: Agata

last: Gadaleta

first: Hana

last: Simkova

first: Simone

last: Scalabrin

first: MariaLucia

last: Prazzoli

first: Paolo

last: Bagnaresi

first: Katia

last: Lacrima

first: Vania

last: Michelotti

first: Francesca

last: Desiderio

first: Luigi

last: Orrù

first: Valentina

last: Mazzamurro

first: Agostino

last: Fricano

first: AnnaMaria

last: Mastrangelo

first: Paola

last: Tononi

first: Nicola

last: Vitulo

first: Irena

last: Jurman

first: Zeev

last: Frenkel

last: Cattonaro

first: Michele

last: Morgante

first: Antonio

last: Blanco

first: Jaroslav

last: Dolezel

first: Massimo

last: Delledonne

last: Stanca

last: Cattivelli

first: Giampiero

last: Valè


title: An RNAi screen probing signaling control of human embryonic stem cells establishes the cell cycle-regulated restriction of the exit from pluripotency (CCNB1 overexpression)

status: Public on Jul 28 2015

city: Singapore

first: Kevin Andrew

last: Gonzales

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: Analysis of effect of Cyclin B1 overexpression on differentiating hESCs at the gene expression level. The hypothesis tested in the present study was that Cyclin B1 overexpression prevents the exit from pluripotency in hESCs. Results provide important information on the effect of Cyclin B1 on hESCs, such as changes in expression of TGFb-related genes and pluripotency markers, as well as mesodermic and neuroectodermic genes.

overall_design: Total RNA obtained from CCNB1 overexpressing hESCs incubated in medium without bFGF and TGF-beta for 0, 48 and 96 hours.


title: Acute heat stress induces differential gene expressions in the small yellow follicles of a broiler-type strain of Taiwan country chickens

status: Public on Jul 21 2015

city: Taichung

first: San

middle: Yuan

last: Huang

address: Kuo-Kuang Rd.

department: Animal science

country: Taiwan

institute: National Chung Hsing University

summary: To realize the gene expression in response to acute heat stress in chicken small yellow follicles, we have employed whole genome microarray expression profiling as we have employed whole genome microarray expression profiling as a tool to identify genes response to acute heat stress. Female B strain Taiwan country chickens were subjected to acute heat stress (38℃) for 2 h, and then exposed to 25℃, with small yellow follicles collected 0, 2, and 6 h after the cessation of heat stress, using non heat-stressed hens as a control group (n = 3 hens per group). Based on a chicken 44K oligo microarray, 69, 51, and 76 genes were upregulated and 58, 15, 56 genes were downregulated after heat treatment of H2R0, H2R2, and H2R6, respectively, using a cutoff value of two-fold or higher in the small yellow follicles of the heat-stressed chickens from those of the control chickens. Upregulation of heat shock protein 25, interleukin 6, metallopeptidase 1, and metalloproteinase 13, and downregulation of type II alpha 1 collagen, discoidin domain receptor tyrosine kinase 2, and Kruppel-like factor 2 were confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).

overall_design: Acute heat stress induced small yellow follicles gene experssion in B strain Taiwan country chicken was measured at 0, 2, and 6 h of recovery after 2 h of 38 Celsius degree acute heat stress.

first: San-Yuan

first: Chuen-Yu

last: Cheng

first: Wei-Lin

last: Tu

first: Shih-Han

last: Wang

first: Pin-Chi

last: Tang

first: Chi-Feng

last: Chen

first: Hsin-Hsin

first: Yen-Pai

last: Lee

first: Shuen-Ei


title: Host-virus transcriptome dynamics determined from microarray analyses

status: Public on Aug 30 2015

city: Sydney

first: Miguel

middle: A

last: Hernández-Prieto

state: NSW

address: Macleay Building A12

department: School of life and environmental sciences

country: Australia

institute: University of Sydney

summary: Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host ranges relative to other cyanophages. It is currently unknown whether broad-host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH8102, WH7803 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage.

sample_organism:
Synechococcus sp. WH 7803
Prochlorococcus marinus str. NATL2A
Parasynechococcus marenigrum WH 8102
Synechococcus sp. WH 8109

platform_organism:
Synechococcus sp. WH 7803
Parasynechococcus marenigrum WH 8102
Synechococcus sp. WH 8109
Synechococcus phage syn9
Cyanophage P-TIM40

overall_design: We investigated the transcriptional response of three Synechococcus strains (WH7803, WH8102 and WH8109) to infection by the Syn9 cyanophage as well as the transcriptional program of the Syn9 phage during infection of these three hosts. We further investigated the transcriptional program of the P-TIM40 cyanophage during infection of Prochlorococcus NATL2A and compared these to the results for the Syn9 cyanophage. For Syn9 infection of the three Synechococcus hosts, the dataset consisted of 121 microarray measurements from three biological replicates at different time points after phage addition (2-5 min and 0.5, 1, 1.5, 2, 3, 4 h) of infected and uninfected control cultures. This resulted in a total of 42, 39 and 40 microarrays for WH7803, WH8102, and WH8109, respectively. For P-TIM40 infection of Prochlorococcus NATL2A, four time points (0.5, 1, 2 and 3 h after infection) were analyzed from three biological replicates for a total of 12 microarray measurements. Custom-made Affymetrix microarrays (SYN-PHG) were used for this study.

first: Ayalla

last: Fedida

first: D

last: Stazic

first: C

last: Steglich

first: Matthias

last: Futschik

first: Debbie

last: Lindell


title: Characterization of AceA regulons in Bradyrhizobium japonicum under desiccation stress

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

country: USA

institute: University of Texas at Arlington

summary: Differential gene expression was analyzed between B. japonicum wild type (Bj110) and aceA mutant (BjΔaceA) exposed to desiccation stress to find AceA regulons under the culture condition.

overall_design: B. japonicum USDA110 wild type and aceA mutant were cultured under desiccation stress (27% RH for 24 h), then their tracrpitional profiles were compared.

first: Jeong

middle: M

last: Jeon

first: Hae-In


title: Low Co vs high Co in CDM

status: Public on Jul 13 2015

city: Groningen

first: Irfan

last: Manzoor

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Comparison of the Streptococcus pneumoniae D39 wild-type in CDM Plus 0mM CO and CDM plus 0,5 mM Co

overall_design: Two condition design comparison of Wild-type strain including a dye swap

first: Sulman

last: Shafeeq

first: Oscar

middle: P

last: Kuipers


title: Aspergillus nidulans ∆pkaA strain grown on avicel as sole carbon source

status: Public on Jul 15 2015

city: Ribeirão Preto

first: Leandro

middle: Jose

last: Assis

state: São pAULO

address: Av. do Cafe S/N

department: FCFRP

country: Brazil

institute: USP

summary: Transcriptome of A. nidulans  ∆pkaA strain 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) and minimal media plus avicel for 8 and 24 hours. ∆pkaA strain. Three biological repetitions of each timepoint of ∆pkaA

first: Neil

last: Brown

first: Gustavo

last: Goldman


title: E.coli BL21 vs HLT013

status: Public on Jun 18 2015

city: Seoul

first: Hyeon-Cheol

address: 136, Changgyeonggung-ro,Jongro-gu

department: Research center

country: South Korea

institute: BPgene Co., Ltd.

summary:
Transcriptional profiling of E. coli strain comparing control BL21 with recombineered HLT013.
HLT013 strains was derived from BL21 and capable of producing thymidine.

overall_design: BL21 vs. HLT013. Biological replicates. independently grown and harvested. One replicate per array.

first: Jin-Sook

last: Kim

first: Jin-Ha


title: Altered Gene Expression in the Schistosome- Transmitting Snail Biomphalaria glabrata following Exposure to Niclosamide, the Active Ingredient in the Widely Used Molluscicide Bayluscide

status: Public on Jul 23 2015

city: Albuquerque

first: Si-Ming

last: Zhang

state: NM

address: Castetter Hall

institute: University of New Mexico

summary: In order to understanding the mechanisms of action of niclosamide, the active ingredient in the molluscicides, we used a Biomphalaria glabrata oligonucleotide microarray to investigate the effect of three sublethal exposures to niclosamide on the transcriptional responses of the snail B. glabrata relative to untreated snails. In addition to inducing biotransformation activity and inducing stress responses, niclosamide exposures also resulted in altered function of vesicle trafficking and may affect the snail’s oxygen binding capacity.

overall_design: In order to reveal how sublethal exposures of niclosamide to the snail B. glabrata affects the snail’s gene expression. The three sublethal doses of niclosamide tested are 0.15 mg/L (dose 1), 0.10 mg/L (dose 2), and 0.05 mg/L (dose 3). The control snails did not exposed to the niclosamid (0%). The snails were exposed to a given dose for 24 hours. Twenty live snails from each dose or control group were collected and randomly divided into four replicate groups, each with five snails, for subsequent RNA extraction and transcriptome analysis


title: Age associated differences in miRNA signatures are restricted to CD45RO negative T cells and are associated with changes in the cellular composition, activation and cellular ageing

status: Public on May 23 2015

first: Anke

last: van den Berg

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

institute: University Medical Center Groningen

summary: MicroRNAs (miRNAs) have emerged as important players in the regulation of T-cell functionality. However, comprehensive insight into the extent of age-related miRNA changes in T cells is lacking. We established miRNA expression patterns of CD45RO- naïve and CD45RO+ memory T-cell subsets isolated from peripheral blood cells from young and elderly individuals. Unsupervised clustering of the miRNA expression data revealed an age-related clustering in the CD45RO- T cells, while CD45RO+ T cells clustered based on expression of CD4 and CD8. Seventeen miRNAs showed an at least 2-fold up- or downregulation in CD45RO- T cells obtained from young as compared to old donors. Validation on the same and independent samples revealed a statistically significant age-related upregulation of miR-21, miR-223 and miR-15a. In a T-cell subset analysis focusing on known age-related phenotypic changes, we showed significantly higher miR-21 and miR-223 levels in CD8+CD45RO-CCR7- TEMRA compared to CD45RO-CCR7+ TNAIVE-cells. Moreover, miR-21 but not miR-223 levels were significantly increased in CD45RO-CD31- post-thymic TNAIVE cells as compared to thymic CD45RO-CD31+ TNAIVE cells. Upon activation of CD45RO- TNAIVE cells we observed a significant induction of miR-21 especially in CD4+ T cells, while miR-223 levels significantly decreased only in CD4+ T cells. Besides composition and activation, we showed a borderline significant increase in miR-21 levels upon an increasing number of population doublings in CD4+ T-cell clones. Together, our results show that ageing related changes in miRNA expression are dominant in the CD45RO- T-cell compartment. The differential expression patterns can be explained by age related changes in T-cell composition, i.e. accumulation of CD8+ TEMRA and CD4+ post thymic expanded CD31- T cells and by cellular ageing, as demonstrated in a longitudinal clonal culture model.

overall_design: MicroRNA profiling was performed in eight T cell subsets: CD4 naive (CD3+CD4+CD45RO-), CD8 naive (CD3+CD4-CD45RO-), CD4 memory (CD3+CD4+CD45RO+) and CD8 memory (CD3+CD4-CD45RO+) T cells derived from 5 healthy young and 5 healthy old participants.

first: Nato

last: Teteloshvili

first: Joost

last: Kluiver

first: Kornelis

middle: S

last: van der Geest

first: Roelof

middle: J

last: van der Lei

first: Pytrick

last: Jellema

first: Graham

last: Pawelec

first: Elisabeth

last: Brouwer

first: Bart

last: Kroesen

first: Anne

last: Boots


title: MicroRNAs and Metabolites in Serum Change after Chemotherapy and Impact on Haematopoietic Progenitor Cells

status: Public on Jun 01 2015

city: Bergisch-Gladbach

first: Yvonne

last: Diener

address: Friedrich-Ebert-Str. 68

country: Germany

institute: Miltenyi Biotec GmbH

summary: Hematopoietic reconstitution after chemotherapy and hematopoietic stem cell transplantation (HSCT) requires massive activation of the stem cell pool. In a previous study, we have shown that there are systemically released factors in patient serum after HSCT that may play an important role in hematopoietic recovery, and that these serum samples significantly stimulate hematopoietic stem and progenitor cell (HPC) in vitro expansion. Aberrant microRNA (miRNA) expression is a feature of leukemia and miRNAs also play a significant role in normal hematopoiesis and differentiation. In this study, we have addressed the question if miRNAs and metabolic pathways are involved in HPC activation after HSCT. Serum from patients before chemotherapy and after chemotherapy during aplasia was used as supplement for in vitro cultivation of CD34+ HPCs. Serum taken after chemotherapy significantly enhanced HSC proliferation and maintained a primitive CD34+ immunophenotype. Microarray analysis revealed that 23 miRNAs are differentially expressed in serum before and after chemotherapy - particularly miRNA-320 and miRNA-1275 were down-regulated and miRNA-3663-3p was up-regulated. This suggest that hematopoietic regeneration after chemotherapy might be tightly regulated by miRNAs and this opens new perspectives for in vivo stimulation of the stem cell pool.

overall_design: Serum taken from 9 patients before and after chemotherapy as well as 7 healhy donors was analyzed for miRNA expression.

first: Ute

last: Bissels

first: Andreas

last: Bosio

first: Thomas

last: Walenda

first: Wolfgang

last: Wagner


title: Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production

status: Public on May 15 2015

city: Nanjing

first: Dong

last: Liu

state: Jiangsu

address: No. 30, Puzhu South Road

department: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering

country: China

institute: Nanjing Tech University

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

platform_organism:
Clostridium acetobutylicum
Arthrobacter sp.
Clostridium acetobutylicum DSM 1731

overall_design: Refer to individual Series


title: Expression data from seedligs of wild type tomato  seedlings (control) and InsP 5-ptase tansgenic line  (L7) exposed to light stress

status: Public on Jun 15 2015

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

institute: University of Arkansas at Little Rock

summary: Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in tomato InsP 5-ptase transgenic lines exposed to continous light for 7 days (light stress).

overall_design: The RNA was isolated from seedlings of wild-type (WT) and Ins P 5-ptase transgenic line 7 that were germinated on MS medium in a growth chamber with 50 umol m-2 s-1 light intencity at 12 h day-light and 12 h dark for 10 days and then exposed to continous light for 7 days. Affymetrix platform was used for expression analysis.


title: Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [II]

summary: Immobilization of Clostridium acetobutylicum B3 onto fibrous matrix  by surface-adsorption was developed and applied to biobutanol production. The immobilized C. acetobutylicum B3 cells formed biofilm and showed dramatically improved butanol tolerance and production rate. DNA array-based transcriptional analysis of C.acetobutylicum B3 biofilm cells was conducted to elucidate the gene expression profile of the biofilm cells. Results showed that about 16% of the whole genome was differentially expressed. The most apparently differentially expressed genes were involved in amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, and coenzyme transport and metabolism.

platform_organism:
Arthrobacter sp.
Clostridium acetobutylicum DSM 1731

overall_design: Samples for biofilm cells and planktonic cells were withdrawn at four diffierent fermentation phases. The gene expression pattern of biofilm cells were investigated relative to that of planktonic cells from the same phase. The experiment was carried out twice independently. Cotton fibrous matrix (60 g/L) was used  as biofilm carrier.

first: Jiahui

last: Xu

first: Yanyan

last: Wang

first: Yong

last: Chen

first: Hanjie

last: Ying


title: Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [I]

platform_organism:
Clostridium acetobutylicum
Arthrobacter sp.


title: Genomic and transcriptomic analyses of sebacinoid fungi

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

summary: The recent release of a large number of genomes from ectomycorrhizal, orchid mycorrhizal and root endophytic fungi have provided deep insight into fungal lifestyle-associated genomic adaptation. Comparative analyses of symbiotic fungal taxa showed that similar outcomes of interactions in distant related root symbioses are examples of convergent evolution. The order Sebacinales represents a sister group to the Agaricomycetes (Basidiomycota) that is comprised of ectomycorrhizal, ericoid-, orchid- mycorrhizal, root endophytic fungi and saprotrophs (Oberwinkler et al., 2013). Sebacinoid taxa are widely distributed from arctic to temperate to tropical ecosystems and are among the most common and species-rich groups of ECM, OM and endophytic fungi (Tedersoo et al., 2012, Tedersoo et al., 2010, Oberwinkler et al., 2013).  The root endophyte Piriformospora indica and the orchid mycorrhizal fungus S. vermifera (MAFF 305830) are non-obligate root symbionts which were shown to be able to interact with many different experimental hosts, including the non-mycorrhizal plant Arabidopsis thaliana. These two fungi display similar colonization strategies in barley and in Arabidopsis and the ability to establish beneficial interactions with different hosts (Deshmukh et al., 2006). Colonization of the roots by P. indica and S. vermifera results in enhanced seed germination and biomass production as well as increased resistance against biotic and abiotic stresses in its experimental hosts, including various members of the Brassicaceae family, barley, Nicotiana attenuata and switchgrass (Ghimire, 2011, Ghimire et al., 2009, Ghimire et al., 2011, Waller et al., 2008, Barazani et al., 2007, Deshmukh et al., 2006). Microarray experiments were performed to identify and characterize conserved sebacinoid genes as key determinants in the Sebacinales symbioses.

sample_organism:
Arabidopsis thaliana
Serendipita indica
Serendipita vermifera

overall_design: Arabidopsis roots were inoculated with either Sebacina vermifera or Piriformospora indica and grown for up to 14 days. Additionally S. vermifera and A. thaliana were grown on 1/10 PNM medium alone. Samples were taken 3, 7 and 14 dpi (Arabidopsis), 3dpi (1/10 PNM, S. vermifera) and 7dpi (1/10 PNM, A. thaliana). Each experiment was performed in three independent biological repetitions. The experiments are follow-ups of previous experiments deposited under GSE47775.

first: Alga

last: Zuccaro


title: The alteration of DNA methylation driven by HIV infection based on a pair of monozygotic twins (MeDIP-chip)

status: Public on Apr 20 2015

city: Hong Kong

first: Yinfeng

last: Zhang

address: 1 shatin road

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Methylation profiling by genome tiling array

summary:
In this study, we have investigated the relationship between genome-wide DNA methylation pattern and HIV infection using the methylated DNA immunoprecipitation - microarray method. A pair of monozygotic twins was recruited: one of the twins was infected with HIV while the other was not.
The immunoprecipitated CpG-methylated DNA from HIV positive subject (test) and from HIV negative subject (input control) were labelled with Cy5 and Cy3 respectively

overall_design: The methylated genomic DNA fragments from HIV+ and HIV- twins were hybridized on the same chip since the identical genetic background

first: Stephen

last: Tsui


title: Zebrafish liver transcriptome in response to chronic treatment with environmentally relevant 5-FU

status: Public on Apr 23 2015

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: The fluoropyrimidine 5-fluorouracil (5-FU) is an antimetabolite that exerts its anticancer effects through inhibition of DNA synthesis and replication by inhibiting thymidylate synthase, and by incorporation of its metabolites into RNA and DNA. 5-FU is used in most of the currently applied regimens for the treatment of patients with cancers of the gastrointestinal tract, breast, head, neck, and belongs to the most consumed cytostatic drugs. After application, 5-FU is via hospital and municipal waste water effluents released into the aquatic environment, where it can harm non-target organisms. The aim of this study was to evaluate changes in gene transcription in liver of adult F1 zebrafish (Danio rerio) continuously exposed to 5-FU at environmentaly relevant concentrations of  0.01 µg/L and 1 µg/L.

overall_design: One color design, control and treatment in two concentrations; 6 pools of 3 individuals per treatment

first: Špela

first: Ana

last: Rotter


title: Gene expression-based, individualized outcome prediction for autism

status: Public on Apr 17 2015

city: Changsha

first: Fengzhen

last: Huang

address: 87# Xiangya Road Changsha, Hunan 410008P.R.China

institute: Xiangya Hospital, Central South University

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of 91 up-regulated and 67 down-regulated miRNAs in 5 autism spectrum disorder (ASD) cases and 5 controls.

overall_design: In the study presented here, a well-defined cohort of 5 autism spectrum disorder cases and 5 controls was used to acquire expression profiles of 91 up-regulated and 67 down-regulated miRNAs, leading to the first global miRNA expression profile of ASD in China.

first: Hong

last: Jiang


title: Lactococcus lactis subsp. cremoris GE2-14 (GE2-14) vs Lactococcus lactis subsp. cremoris GE2-14 ΔaguR (GE2-14 ΔaguR)

status: Public on Jul 08 2015

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

summary: Trancriptional profiling of  GE2-14 ΔaguR mutant strain in which the aguR gene of the agmatine deiminase cluster has been deleted. We compared the expression profiling of GE2-14 cells with the expression profiling of GE2-14 ΔaguR mutant cells. The goal was to determine the effect of the aguR deletion on the transcriptional profiling of GE2-14

sample_organism: Lactococcus cremoris subsp. cremoris GE214

overall_design: Two strains GE2-14 (reference) vs. GE2-14 ΔaguR (test) cells in same conditions. Three biological replicates, two technical replicates and one dye swap.

first: Daniel

last: Linares

first: Beatriz

last: del Rio

first: Begoña

last: Redruello

first: Anne

last: de Jong

first: Oscar

last: Kuipers

first: Maria

last: Fernandez

middle: C

last: Martin

first: Miguel

last: Alvarez


title: Primary bovine extra-embryonic cultured cells: a new resource for the study of in vivo peri-implanting phenotypes and mesoderm formation

status: Public on Apr 18 2015

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

country: France

institute: INSERM UMRS-1139

summary: In addition to nourishing the embryo, extra-embryonic tissues (EETs) contribute to early embryonic patterning, primitive hematopoiesis, and fetal health. These tissues are of major importance for human medicine, as well as for efforts to improve livestock efficiency, but they remain incompletely understood. In bovines, EETs are accessible easily, in large amounts, and prior to implantation. We took advantage of this system to describe, in vitro and in vivo, the cell types present in bovine EETs at Day 18 of development. Specifically, we characterized the gene expression patterns and phenotypes of bovine extra-embryonic ectoderm (or trophoblast; bTC), endoderm (bXEC), and mesoderm (bXMC) cells in culture and compared them to their respective in vivo micro-dissected cells. After a week of culture, certain characteristics (e.g., gene expression) of the in vitro cells were altered with respect to the in vivo cells, but we were able to identify “cores” of cell-type-specific (and substrate-independent) genes that were shared between in vitro and in vivo samples. In addition, many cellular phenotypes were cell-type-specific with regard to extracellular adhesion. We evaluated the ability of individual bXMCs to migrate and spread on micro-patterns, and observed that they easily adapted to diverse environments, similar to in vivo EE mesoderm cells, which encounter different EE epithelia to form chorion, yolk sac, and allantois. With these tissue interactions, different functions arose that were detected in silico and corroborated in vivo at D21-D25. Moreover, analysis of bXMCs allowed us to identify the EE cell ring surrounding the embryonic disc (ED) at D14-15 as mesoderm cells, which had been hypothesized but not shown prior to this study. We envision these data will serve as a major resource for the future in the analysis of peri-implanting phenotypes in response to the maternal metabolism and contribute to subsequent studies of placental/fetal development in eutherians.

overall_design: Amplified material was indirectly labelled using "random" hexamers. One independent target was generated and hybridised onto one array. 1-3 measurements per cell type were generated.

first: I

last: Hue

first: D

last: Evain-Brion

first: T

last: Fournier

first: S


title: Transcriptional profile of the tail of zebrafish deiodinase knockdown

status: Public on Apr 10 2015

city: Wilrijk

first: Lucia

last: Vergauwen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

summary: The role of deiodinase-mediated TH effects in early vertebrate development is only partially understood. Therefore, we investigated the role of deiodinases during early development of zebrafish until 96 hours post fertilization at the level of the transcriptome, biochemistry, morphology and physiology using morpholino (MO) knockdown. Knockdown of D1+D2 (D1D2MO) and knockdown of D3 (D3MO) both resulted in transcriptional regulation of metabolism and (muscle) development in abdomen and tail, together with reduced growth, impaired swim bladder inflation, reduced protein content and reduced motility. The reduced growth and impaired swim bladder inflation in D1D2MO could be due to lower levels of T3 which is known to drive growth and development. The pronounced upregulation of a large number of transcripts coding for key proteins in ATP-producing pathways in D1D2MO could reflect a compensatory response to a decreased metabolic rate, also typically linked to hypothyroidy. Compared to D1D2MO, the effects were more pronounced or more frequent in D3MO, in which hyperthyroidy is expected. More specifically, increased heart rate, delayed hatching and increased carbohydrate content were observed only in D3MO. An increase of the metabolic rate, a decrease of the metabolic efficiency and a stimulation of gluconeogenesis using amino acids as substrates may have been involved in the observed reduced protein content, growth and motility in D3MO larvae. Furthermore, expression of transcripts involved in eye development and phototransduction was decreased in both knockdown conditions, suggesting that both may impair eye development and function. This study provides new insights, not only into the role of deiodinases, but also into the importance of a correct TH balance during vertebrate embryonic development.

overall_design: A-optimal design. Experimental design, D1D2MO vs SCMO and D3MO vs SCMO. Biological replicates: 4 SCMO, 4 D1D2MO, 4 D3MO

first: Enise

last: Bagci

first: Majolein

last: Heijlen

first: An

last: Hagenaars

last: Houbrechts

first: Camilla

middle: V

last: Esguerra

first: Ronny

last: Blust

first: Veerle

last: Darras

first: Dries

last: Knapen


title: Transcriptional profile of the abdomen of zebrafish deiodinase knockdown

first: Anne


title: Transcriptional profile of the head of zebrafish deiodinase knockdown


title: Transcriptional profile of deiodinase knockdown in zebrafish head, abdomen and tail


title: Expression data from tomato roots and leaves treated with or without Cd.

status: Public on Mar 25 2015

city: Tianjin

first: Guo

last: Jun kang

address: Fu kang Road No.31

institute: Agro-Environmental Protection Institute, Ministry of Agriculture

summary: We used microarrays to detail the global gene expression in tissues from tomato roots and leaves treated with or without Cd.

overall_design: Tissues from tomato roots and leaves treated with or without Cd were for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun

middle: K

last: Guo


title: RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (Promoter)

status: Public on Mar 31 2015

city: Sheffield

first: Neil

middle: Robert

last: Chapman

state: South Yorkshire

address: Tree Root Walk

department: Oncology and Metabolism

country: United Kingdom

institute: University of Sheffield

type: Genome binding/occupancy profiling by genome tiling array

summary: A study to define the binding loci of RelA-containing NF-kappaB dimers in a human myometrial smooth muscle cell line after exposure to TNF.

overall_design: Monolayers of PHM1-31 cells were exposed to TNF (10ng/ml) for 1 hour or left unstimulated. The Chromatin immunoprecipitation (ChIP) assay was performed to recover RelA-bound chromatin or non-specifically bound chromatin with IgG. That chromatin was prepared and used to probe Affymetrix GeneChIP 1.0R  Human Promoter arrays. Three biological replicates of each experiment were conducted. Datasets were subsequently analysed in Partek Genomics Suite V6.6 where baseline was normalised by subtraction of IgG values from conrresponding RelA-immunoprecipitated samples. Control samples immunoprecipitated with RelA were then compared with TNF-stimulated samples immunoprecipitated with RelA.

first: Victoria

last: Cookson

first: Sarah

middle: L

last: Waite

first: Paul

middle: R

last: Heath

last: Hurd

first: Saurabh

last: Gandhi


title: Expression data from roots and first two leaves of tomato seedlings growing on regular MS medium or MS medium supplemented with multi-wall carbon nanohorns (25 ug/ml)

status: Public on Jan 01 2015

first: Mariya

last: Khodakovskaya

summary:
To investigate effects of single-walled carbon nanohorns (SWCNHs) om total expression profile of tomato seeds and plants we introduced SWCNHs in MS agar medium in concentration of 25 ug/ml
Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in tomato seeds and seedlings in response to SWCNHs

overall_design:
Seeds (1 day on medium) and 11-days old seedlings of  wild type tomato seedlings (cv. Micro-Tom) growing on regular MS agar medium or MS medium supplemented with carbon nanohorns (25 ug/ml) were selected for RNA extraction and hybridization on Affymetrix microarrays.
Keywords: stress responses


title: Arabidopsis thaliana seedlings: Wild type vs. sdg26, atx1, sdg25, clf, ldl1 ldl2 and combined mutants

status: Public on Dec 22 2014

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

institute: IBMP-CNRS

summary: Transcriptional profiling of 16-day-old seedlings of Arabidopsis wild type control and mutants is performed using Aligent’s Whole Arabidopsis Gene Expression Microarray (4x44K).

overall_design: Two-condition experiment, seedlings of wild type control vs. Mutant sdg25, sdg26, sdg25 sdg26, atx1, sdg26 atx1, clf, sdg26 clf, ldl1 ldl2, sdg25 ldl1 ldl2 or sdg26 ldl1 ldl2. Three biological replicates: 3 control, 3 each of the ten mutants, independently grown under 12h light/ 12h dark photoperiods and harvested.

first: Sarfraz

last: Shafiq

first: Aiwu

last: Dong


title: Expression data from Wild type (WT) and AtCBF1 OX potato plants exposed to different abiotic stresses

status: Public on Mar 01 2015

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

summary:
Potato plants are sensitive to multiple abiotic stresses such as drought, low temperature and high light.
We analyzed the transcriptome of WT potato plants as well as that of transgenic potato plants expressing the Arabidopsis stress related transcription factor CBF1 that confers tolerance to multiple stresses.

overall_design: Wild type and AtCBF1OX transgenic potato plants were exposed to low temperature, high light, drought or kept under control conditions as described below in detail, and transcriptional changes induced by the different stresses were analyzed.

first: Leonardo

last: Storani


title: miRNA expression profiling of primary melanoma tumors (cohort II)

status: Public on Feb 01 2015

city: New York

first: Eva

last: Hernando-Monge

state: NY

address: 550 1st Ave. Smilow 305

institute: NYU Langone Medical Center

summary: We performed global microRNA expression profiling of a cohort of primary melanoma patient samples linked to a well-annotated clinical database. The goal of this study was to identify microRNA that are associated to or correlated with various clinical parameters and patient outcomes. Candidate microRNA were identified for building prognostic models and functional testing.

overall_design: 119 primary melanoma samples were analyzed in two color arrays.  The reference sample used was an equal combination of all samples analyzed.  By this design, ratio data of test sample/reference is mean-centered data.

last: Hernando

first: Doug

last: Hanniford

first: Judy

last: Zhong


title: Transgenic NUP98-HOXA9 Zebrafish Embryos: Unactivated ('lGl') vs. Cre-activated ('NHA9')

status: Public on Oct 30 2014

city: Moncton

first: Daniel

last: Leger

state: New Brunswick

address: 35 Providence Street

department: IARC

country: Canada

institute: Atlantic Cancer Research Institute

summary: Transcriptional profiling of zebrafish embryos at 28 hours post fertilization, comparing control 'unactivated' Tg(spi1::lox-eGFP-lox::NHA9) embryos with experimental 'Cre-activated' Tg(spi1::NHA9) embryos. Goal was to determine the effects of expressing NUP98-HOXA9 oncogene on global and blood cell-specific gene expression in early zebrafish development.

overall_design: Two-condition experiment, unactivated 'lGl' embryos vs. Cre-activated 'NHA9' embryos. Biological replicates: 2 control replicates, 2 experimental replicates.

first: A

last: Forrester

first: Ian

last: Chute

first: Stephen

last: Lewis

first: Jason

middle: N

last: Berman


title: Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss

status: Public on Dec 19 2014

city: Palo Alto

first: Rajini

last: Haraksingh

state: CA

address: 3165 Porter Drive, Room 2270

institute: Stanford University

type: Genome variation profiling by genome tiling array

summary: Background The genetic diversity of loci and mutations underlying hereditary hearing loss is an active area of investigation. To identify loci associated with predominantly non-syndromic sensorineural hearing loss, we performed exome sequencing of families and of single probands, as well as copy number variation (CNV) mapping in a case-control cohort.  Results Analysis of three distinct families revealed several candidate loci in two families and a single strong candidate gene, MYH7B, for hearing loss in one family. MYH7B encodes a Type II myosin, consistent with a role for cytoskeletal proteins in hearing. High-resolution genome-wide CNV analysis of 150 cases and 157 controls revealed deletions in genes known to be involved in hearing (e.g. GJB6, OTOA, and STRC, encoding connexin 30, otoancorin, and stereocilin, respectively), supporting CNV contributions to hearing loss phenotypes. Additionally, a novel region on chromosome 16 containing part of the PDXDC1 gene was found to be frequently deleted in hearing loss patients (OR = 3.91, 95% CI: 1.62-9.40, p = 1.45 x 10-7). Conclusions We conclude that many known as well as novel loci and distinct types of mutations not typically tested in clinical settings can contribute to the etiology of hearing loss. Our study also demonstrates the challenges of exome sequencing and genome-wide CNV mapping for direct clinical application, and illustrates the need for functional and clinical follow-up as well as curated open-access databases.

overall_design: Single replicates of 151 non-syndromic hereditary hearing loss cases and 157 controls with normal hearing were analyzed.

first: Fereshteh

last: Jahanbani

first: Juan

last: Rodriguez-Paris

first: Joel

last: Gelernter

first: Kari

last: Nadeau

first: John

last: Oghalai

first: Iris

last: Schrijver

first: Michael

last: Snyder


title: miRNA expression profiling of primary melanoma tumors (cohort I)

last: Hernando-Monge

overall_design: 92 primary melanoma (well-annotated with long clinical follow-up) and 9 congenital nevi samples were analyzed to Exiqon miRCURY two color arrays.  The reference sample used was an equal combination of all samples analyzed.  By this design, ratio data of test sample/reference is mean-centered data.

first: Iman

last: Osman


title: Effect of obesity on liver immune response to inflammatory stimuli in a diet-obesity model of zebrafish (Danio rerio)

status: Public on Mar 23 2015

city: Leiden

first: Gabriel

last: Forn-Cuní

state: Zuid-Holland

address: Einsteinweg 55

department: IBL-ASH-CO

institute: Universiteit Leiden

summary: We used a Diet-Induced-Obesity approach using the zebrafish (Danio rerio) based on overfeeding to analyze the liver transcriptomic modulation in the disease and to determine how the obesity affects the immune response against an acute inflammatory stimulus as the lipopolysacharide (LPS). Overfed zebrafish were obese and showed signs of steatosis in their liver. Furthermore, the gene modulation profile resembled to that observed in humans. After the inflammatory stimulus, there was a clear differential immune response in normal and overfed fish. In normal fish, the response to LPS reported a typical host defensive reaction comparable to the one occurring in stimulated mammals whereas there was not any significantly modulated gene when comparing the expression of liver from LPS-stimulated with non-stimulated obese zebrafish.

overall_design: Healthy fish were fed two times a day, one with Artemia and the other with standard fish chow while obese fish were fed fish chow two more times a day during 8 months. 10 μg of pure LPS (Sigma) or PBS was intraperitoneally injected and livers were sampled and pooled at 3 hours post injection.

first: Monica

last: Varela

first: C

last: Fernández-Rodríguez

first: Antonio

last: Figueras

first: Beatriz

last: Novoa


title: Detection of chromothripsis-like patterns from custom array platform for chronic lymphocytic leukemia diagnosis (qchip Hemo custom array v1)

status: Public on Dec 04 2014

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

summary: Chronic lymphocytic leukemia (CLL) is the most frequent leukemia in Western countries. The main genetic alterations associated to this disease are loss of 13q14, loss of 11q23, trisomy 12 and, less frequently, 17p13 losses, and are routinely studied using fluorescence in situ hybridization. These genomic aberrations have been demonstrated to be important independent predictors of disease progression in CLL and their detection currently has a direct implication in the treatment strategy of the patients.  It has been widely demonstrated that array-based karyotyping clearly detects DNA gains and losses and allows the identification of CLL abnormalities not included in the standard FISH panel.   We have here established and tested an oligonucleotide-based array platform for the diagnosis of CLL that interrogates the most relevant chromosomal regions related with the disease and may help in the differential diagnosis between CLL and other small B-cell leukemias and may be used as a powerful prognosis tool to stratify the CLL patients.

overall_design: Copy number analysis using Custom Agilent 60K was performed on 133 chronic lymphocytic Leukemia patients (134 samples) with sex-matched control DNAs

first: Lluís

last: Armengol

first: Elias

last: Campo

first: Silvia

last: Beà


title: Detection of chromothripsis-like patterns from custom array platform for chronic lymphocytic leukemia diagnosis

status: Public on Mar 16 2015

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

overall_design: Refer to individual Series


title: Differences in gene expression between fast and slow muscle or between normal and denervated slow muscles

status: Public on Oct 04 2014

city: Matsumoto City

first: Fuminori

last: Kawano

state: Nagano

address: Niimura 2095-1

department: Graduate School of Health Sciences

country: Japan

institute: Matsumoto University

summary:
Fast and slow skeletal muscles show different characteristics and phenotypes. This data obtained from microarray includes the comparison of normal fast plantaris and slow soleus muscles of adult rats.
Characters of slow muscle are strongly dependent on the level of muscular activity. Denervation silences the muscular activity. Therefore, we determined the effects of denervation on gene expression in slow soleus muscle of adult rats.

overall_design: Denervation was performed by transection (~5 mm) of left sciatic nerve at the gluteal level. No treatments were made in the normal control rats. Sampling of soleus and/or plantaris was performed in both normal and experimental groups 28 days after the surgery.

first: Kawano

last: Fuminori


title: miRNA expression profiling of primary melanoma tumors

first: Eva


title: Exposure of Feathead Minnows to Municipal Wastewater Effluent Inhibits the Canonical Wnt Signaling Pathway in the Liver

status: Public on Aug 31 2014

city: Laval

first: Jennifer

last: Arstikaitis

state: Quebec

address: 531, boulevard des Prairies

department: Toxicology/Cellular and Molecular Biology

institute: INRS-Institut Armand Frappier Universite du Quebec

summary: Municipal wastewater effluent can impact its receiving environment. In the St. Lawrence River, male fish living downstream from Montreal exhibit increased hepatic vitellogenin, intersex, delayed spermatogenesis and altered immune function. Few studies have examined genome-wide effects associated with municipal effluent exposure in fish to decipher the mechanisms of toxicity. The present objective was to identify hepatic cellular signaling pathways in fathead minnows following exposure to municipal wastewater effluent. Immature minnows were exposed for 21 days to either 0% (Control) or 20% municipal effluent, the highest concentration in the St. Lawrence River. Hepatic RNA was extracted and used to hybridize a fathead minnow oligonucleotide microarray containing approximately 15K gene sequences.

overall_design: Sixteen samples were examined, 8 control samples and 8 exposed samples.

first: Francois

last: Gagne

first: Daniel

middle: G

last: Cyr


title: Effect of swim-training on caudal fin development in zebrafish larvae

status: Public on Jul 17 2014

city: Wageningen

first: ansa

last: fiaz

address: De Elst 1

institute: Wageningen University

summary: Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10  dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae.

overall_design: Two-condition experiment: control vs trained fish. RNA was isolated from pooled caudal fins of 15 control fish (in duplo: pooled control samples (C2 and C3)) and of 15 trained fish (in duplo: pooled trained samples( T2 and T3)). Subsequently, each pooled RNA sample of control and trained caudal fins was labeled with Cy3 and Cy5 in order to correct for dye bias. We included a technical replicate of the labeled C2 and T2 samples.

first: Ansa

middle: W

last: Fiaz


title: Leishmania major Friedlin V1 lpg1- and lpg2- mutants differentially modulate the Interleukin-12 immune response in human dendritic cells.

status: Public on Jul 26 2014

city: Notre Dame

first: Mary

middle: Ann

last: McDowell

state: Indiana

address: 210 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

summary: Monocyte derived dendritic cells (MDDC) were infected with Leishmania major parasites which were knockout mutants of either lpg1 or lpg2 genes that responsible for expression of surface molecular structures on the parasites in order to assess the effects those molecules have on human host cell gene expression.

overall_design:
Monocyte derived dendritic cells (MDDC) were generated from blood buffy coats collected from four anonymous healthy human donors and infected 10:1 (parasite to host cell) with Leishmania major Friedlin V1 strain wildtype parasites and lipophosphogylcan mutants, where after total RNA was harvested, cDNA generated, and hybridized to human gene transcipt expression arrays to assess differential host cell gene transcriptional expression differences relative to uninfected cells.

Please note that the final RMA normalized background value for each array was provided in the characteristics field and any data that was below the background value was filtered out.

first: Michelle

last: Favila

first: Nicholas

last: Geraci

first: Suzanne

last: Hickerson

first: Asha

last: Jayakumar

first: Vinita

last: Tripathi

first: Salvatore

last: Turco

first: Stephen

last: Beverley


title: Differential expression of Rice genes upon Rhodotorula treatment

status: Public on Dec 18 2014

city: Kolkata

first: Anindita

last: Seal

state: West Bengal

address: 35, Ballygunge Circular Road

department: Biotechnology

country: India

institute: University of Calcutta

summary: The experiments were performed to understand the molecular basis of plant growth promotion in rice by Rhodotorula mucilaginosa JGTA-S1, an endophytic yeast from Typha angustifolia

overall_design: Three week old rice plant grown in untreated condition were supplemented with Rhodototorula cell suspension. Shoots were harvested 0hr, 6hrs or 24hrs post treatment. Total RNA isolated from those shoot tissue & used for Microarray. 0 hr treated sample considered here as Control

first: Chinmay

last: Saha


title: Functional characterization of a Drosophila melanogaster mitochondrial deoxynucleotide transporter dRIM2.

status: Public on May 02 2014

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

summary: We have studied the deoxynucleotide transport in Drosophila melanogaster. On the basis of homology with the S. cerevisiae RIM2 gene, encoding a pyrimidine deoxynucleotide carrier (Marrobbio et al. 2006), the CG18317 gene (dRIM2) in the fruit fly may code for a deoxynucleotide carrier. We demonstrated that Drosophila S2R+ cells, silenced for the dRIM2 expression, had a marked defect in the amounts of all mitochondrial dNTPs, both purines and pyrimidines. In vivo dRIM2 homozygous knockout produced a larval lethal phenotype. dRIM2-/- larvae showed (i) impairments in the locomotor behavior, (ii) a decrease in the rates of oxygen consumption and (iii) a depletion of the mtDNA. Following a detailed morphological characterization carried out in dRIM2-/- larvae evidenced an ongoing mitochondrial biogenesis accompanied by an alteration of mitochondria shaping. Additionally, the role of dRIM2 in the purine and pyrimidine metabolism was supported by a microarray analysis. We conclude that dRIM2 is a Drosophila deoxynucleotide carrier, essential for maintaining the mitochondrial functionality.

overall_design: Gene expression profiling was carried out on dRIM-/- and dRIM+/- Drosophila larvae using the Drosophila 1.0 custom platform (Agilent). Total RNA was obtained from the whole body of 3rd instar larvae for each genotype. Four and three biological replicates were analyzed for dRIM-/- and dRIM+/- samples respectively for a total of 7 microarray experiments.

first: Caterina

last: Da Re

first: Elisa

last: Franzolin

first: Alberto

last: Biscontin

first: Cristina

last: Gagliani

first: Antonia

last: Piazzesi

first: Beniamina

last: Pacchioni

first: Carlo

last: Tacchetti

first: Mauro

middle: A

last: Zordan

first: Massimo

last: Zeviani

first: Paolo

last: Bernardi

first: Vera

last: Bianchi

first: Rodolfo

last: Costa


title: Predicting Response and Survival in Chemotherapy-Treated Triple-Negative Breast Cancer

status: Public on Aug 11 2014

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

institute: VHIO

summary:
Gene expression data of pre-treatment samples of GEICAM2006-03 TNBC trial
Patients were randomized to carboplatin or no carboplatin in the neoadjuvant setting

overall_design: In the study presented here, a well-defined cohort of 69 breast samples were used to acquire expression profiles of a total of 543 unique genes (+5 HK genes)

first: Charles

last: Perou


title: Transcriptome analysis of Eggplant (Solanum melongena L.) cv. PPL during fruit development and ripening.

status: Public on Feb 14 2014

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

institute: NRCPB

summary:
Transcriptome analysis of Eggplant cv. PPL during fruit development at 0, 5, 10, 20 and 50 dpa.
Eggplant is third most important solanaceae crop species after potato and tomato. It is a versatile crop adapted to different agro-climatic regions and can be grown throughout the year. Unripe eggplant fruit is consumed as cooked vegetable in various ways. It is low in calories and fats, contains mostly water, some protein, fibre and carbohydrates. To decipher molecular mechanisms involved in fruit development eggplant fruit were collected at 0, 5, 10, 20 and 50 dpa and gene expression profiles were analyzed using Affymetrix tomato GeneChip Genome array.

overall_design: Eggplant plants were was grown under controlled conditions in glasshouse. Flowers were hand-pollinated at anthesis and samples were collected at 0, 5, 10, 20 and 50 days post anthesis (dpa). Total RNA was isolated using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturer’s protocol. Affymetrix tomato GeneChip Genome array (Affymetrix, USA) having 10,000 probe sets was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

first: I

last: Ahmad

first: M

last: Kanakachari

first: K

last: Padmalatha

first: G

last: Dhandapani

first: Neha

last: Jain

first: A

middle: U

last: Solanki

first: P

last: Ananda


title: Microarray analyses of transgenic zebrafish expressing human KIT-D816V gene versus wild-type zebrafish

status: Public on Feb 03 2014

city: Ottawa

first: Sergey

last: Prykhozhij

state: Ontario

address: Room 318/319 | CAREG, 20 Marie-Curie Private

institute: CHEO Research Institute/University of Ottawa


title: microRNA expression data from AG 1522 human fibroblasts post X-ray radiation

status: Public on Jul 30 2014

city: Hefei

first: Wei

last: Han

state: Anhui

address: #155 Shushanghu Road

institute: Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences

summary:
Radioadaptive response (RAR) in mammalian cells refers to the phenomenon where a low-dose ionizing irradiation alters the gene expression profiles, and protects the cells from the detrimental effects of a subsequent high dose exposure.
We focused on microRNA microarray studies, and aimed to characterize the transcriptome for RAR in AG 1522 human skin fibroblasts and to examine the functional regulatory networks at the genetic level. AG 1522 cells were exposed at a specific time point to a challenging dose of 2 Gy in the RAR group, or a priming dose of 5 cGy in the low-dose group.

overall_design: We aimed to have a comprehensive investigation on the RAR induced in the AG 1522 human fibroblasts first exposed to 5 cGy (priming dose) and then followed by 2 Gy (challenge dose) of X-ray through comparisons to those cells which had only received a single 2 Gy dose.

first: Jue

last: Hou


title: Analysis of differentially-expressed genes in Tg(actb2:KIT-D816V) transgenic zebrafish versus wild-type adult kidneys

summary:
Transcriptional profiling of pooled adult  kidneys from transgenic zebrafish expressing human KIT-D816V mutant gene versus wild-type zebrafish was performed. The aim of this experiment was to determine the expression and cellular changes caused by expression of KIT-D816V oncogene in the hematopoietic organ in zebrafish.
This transgenic zebrafish represents a model of systemic mastocytosis with many features of this disease present in adults

overall_design: Two-condition experiment, Tg(actb2:KIT-D816V) versus wild-type(AB), one replicate of each prepared from 3 adult kidneys of each genotype and  a dye-swap hybridization of these RNA samples.

first: Tugce

middle: B

last: Balci

first: Jason

last: Berman


title: A systematic approach to the metastatically relevant microRNA landscape

status: Public on Jan 16 2014

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

institute: German Cancer Research Center (DKFZ)

summary:
Identification of differentially expressed microRNAs in Colorectal Cancer
Distant metastasis is the major determinant of patient outcome in colorectal cancer and microRNAs have emerged as an increasingly important class of molecules which can regulate several steps of the metastatic cascade. By systematically analysing the miR expression profiles of resected metastasis-, corresponding primary tumor- and normal tissues of colorectal cancer patients, we were able to delineate a miR-signature indicative of the metastatically critical microRNA landscape.

overall_design: 9 colorectal cancer patients were profiled comprising 5 patients with tissues from the primary tumor, normal mucosa, secondary metastasis and the background tissue in which the metastasis ocurred. In the remaining 4 patients, one of these four tissue entitities is missing. One patient had two synchronous primary tumors, one in the colon and the other in the rectum.

first: Axel

last: Benner


title: Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) Is Essential for the Zebrafish Development and Bioavailability of Transforming Growth Factor β1a (TGFβ1a)

status: Public on Jan 02 2014

city: Tampere

first: Virpi

last: Kivinen

address: Korkeakoulunkatu 10

country: Finland

institute: Tampere University of Technology

summary: Proprotein convertase subtilisin/kexin (PCSK) enzymes convert proproteins into bioactive end products. Although other PCSK enzymes are known to be essential for biological processes ranging from cholesterol metabolism to host defense, the in vivo importance of the evolutionarily ancient PCSK7 has remained enigmatic. Here, we quantified the expressions of all pcsk genes during the 1st week of fish development and in several tissues. pcsk7 expression was ubiquitous and evident already during the early development. To compare mammalian and zebrafish PCSK7, we prepared homology models, which demonstrated remarkable structural conservation. When the PCSK7 function in developing larvae was inhibited, we found that PCSK7-deficient fish have defects in various organs, including the brain, eye, and otic vesicle, and these result in mortality within 7 days postfertilization. A genome-wide analysis of PCSK7-dependent gene expression showed that, in addition to developmental processes, several immune system-related pathways are also regulated by PCSK7. Specifically, the PCSK7 contributed to the mRNA expression and proteolytic cleavage of the cytokine TGFβ1a. Consequently, tgfβ1a morphant fish displayed phenotypical similarities with pcsk7 morphants, underscoring the importance of this cytokine in the zebrafish development. Targeting PCSK activity has emerged as a strategy for treating human diseases. Our results suggest that inhibiting PCSK7 might interfere with normal vertebrate development.

overall_design: Gene expressions of zebrafish were measured at 6 and 24 hours post fertilization of the fish samples with PCSK7 blocked with morpholino technology. For each time point, triplicate samples pooled from 18-35 zebrafish embryos were used. Also gene expressions from triplicate control samples were measured.

first: Hannu

last: Turpeinen

first: Anna

last: Oksanen

first: Sampo

last: Kukkurainen

first: Annemari

last: Uusimäki

first: Mika

last: Rämet

first: Mataleena

last: Parikka

first: Vesa

last: Hytönen

first: Matti

last: Nykter

first: Marko

last: Pesu


title: Tg(actb2:KIT-D816V) transgenic zebrafish versus wild-type at 28 hpf

first: Sergey

last: Prykhozhij

summary:
Transcriptional profiling of 28 hpf zebrafish transgenic expressing human KIT-D816V mutant gene versus wild-type embryos was performed. The aim of this experiment was to determine the expression changes caused by expression of KIT-D816V oncogene.
This transgenic zebrafish represents a model of systemic mastocytosis with many features of this disease present in adults, but no very clear phenotypes in embryos. Thus, we attempted to determine if there are certain expression changes, which can be used as molecular features of active KIT expressed in these embryos.

overall_design: Two-condition experiment, Tg(actb2:KIT-D816V) versus wild-type(AB), 4 replicate experiments with a dye-swap each time


title: Drug screening for Dravet syndrome using Scn1a zebrafish mutants

status: Public on Jan 04 2014

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

country: USA

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: Severe myoclonic epilepsy of infancy (SMEI), or Dravet syndrome (DS), is a catastrophic pediatric epilepsy with severe intellectual disability, impaired social development, and persistent drug-resistant seizures.  One of its primary monogenic causes is a mutation in SCN1A (Nav1.1), a type I voltage-gated sodium channel.  In mice, Nav1.1 mutation is associated with reduced sodium current, altered interneuron firing, cognitive deficits, autistic-like traits and seizures.  Here we describe a larval zebrafish Nav1.1 mutant that recapitulates salient features of the human SCN1A mutation phenotype.  Between three and seven days post-fertilization, Nav1.1 mutants exhibit spontaneous abnormal electrographic activity, hyperactivity and convulsive behaviors.  Transcriptomic analysis of Nav1.1 mutants was remarkable for the relatively small fraction of genes that were differentially expressed (~2%) and the lack of compensatory changes in expression for other SCN subunits.  Pharmacological studies confirmed an antiepileptic action for the ketogenic diet, benzodiazepine, valproate, potassium bromide and stiripentol in Nav1.1 mutants; acetazolamide, phenytoin, ethosuximide had no effect, carbamazepine and vigabatrin made seizures worse.  Using this mutant, we screened a chemical library of 320 compounds and identified four compounds that reduced spontaneous seizure-like behavior and one compound (clemizole) that inhibited convulsive behavior and electrographic seizures.  Drug-resistant scn1a zebrafish mutants described here represent a new direction in modeling pediatric epilepsy and could be used to identify novel lead compounds for DS patients

overall_design: 4 Control sibling samples (sample= 10 pooled larvae) and 4 Nav1.1 mutants (sample= 10 pooled larvae)   were collected at 6 dpf (days post fertilization). The  Nav1.1 mutants were selected based on phenotype (dark color).

first: Scott

last: Baraban

first: Gabriela

last: Hortopan


title: Upregulated Hedgehog Signaling Promotes Zebrafish CNS Tumorigenesis

status: Public on Sep 07 2013

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Using a cytokeratin 5 gene promoter, we ectopically expressed a constitutively active zebrafish smoothened (smoa1) in presumably glial progenitor cells of zebrafish CNS. Stable transgenic zebrafish developed retinal tumors and low grade glioma of the optic nerve. Microarray analysis showed upregulation of Hh downstream targets of ptc1, gli1 and gli2a in tumors. Immunofluorescence studies confirmed overexpression of Pax2, GFAP, S100 and Sox2, specifically in gliomas. We also detected upregulated expression of phosphorylated pRb and Mdm2 associated with gliomagenesis. Our results suggest that dysregulated Hh signaling initiates tumorigenesis in zebrafish CNS. Zebrafish optic nerve maintains phosphorylated pRb expression, therefore provides a unique niche for pathogenesis of glioma.

overall_design: RNAs from 4 gross eye tumors (from fish of 4 months of age) and 4 normal eyes from wil-type control fish were extracted and used for array analysis

first: Bensheng

last: Ju

first: Michael

last: Taylor


title: Nitrogen source-dependent capsule induction in human pathogenic Cryptococcus species.

status: Public on Sep 25 2013

city: Durham

first: Aubrey

last: Frazzitta

state: North Carolina

address: 0557 Duke Hospital South Research Drive

department: Medicine

institute: Duke University Medical Center

summary: Cryptococcus neoformans causes meningoencephalitis and is an increasing human health threat.  C. neoformans is neurotropic, and persists in the cerebrospinal fluid (CSF) of the mammalian host during infection.  In order to survive in the host, pathogenic fungi must procure nutrients such as carbon and nitrogen.  To enhance our understanding of nutrient acquisition during infection by Cryptococcus species, we examined utilization of nitrogen sources available in CSF.  We screened for growth and capsule production of 817 global environmental and clinical isolates on various sources of nitrogen.  Capsule production was assessed using ammonium and urea in the presence or absence of benomyl to determine the relationship of urea exposure to capsule production.  Since urea is metabolized to ammonia and CO2 (a known signal for capsule induction), we examined urea metabolism mutants for their response to urea regarding capsule production.  Non-preferred nitrogen sources were found to greatly affect capsule production in pathogenic species of Cryptococcus.  Urea induced the greatest magnitude of capsule production.  Capsule induction by urea was greater in Cryptococcus gattii strains than in C. neoformans strains.  In addition, both environmental and clinical strains grew robustly on uric acid, casamino acids, creatinine, and asparagine as sole nitrogen sources.  While substantial growth on nitrate was not apparent at day 3, growth was apparent by day 6 for all serotypes.

overall_design: In this study, transcription profiles of urea pathway mutants (ure1 and amt1/2) and WT Cryptococcus neoformans strains were compared in a dye-swap experiment following 1hr exposure to proline or proline + urea (.25g/L).

middle: E

last: Price

first: Jennifer

last: Tenor

first: Marisol

last: Betancourt-Quiroz

first: Dena

last: Toffaletti

last: Cheng

first: John

last: Perfect


title: Comparative transcriptome analysis of responses to water deficit in Solanum lycopersicum and S. pimpinellifolium roots

status: Public on Dec 01 2013

first: Takuya

last: Nakazato

state: Tennessee

address: 3774 Walker Avenue

institute: The University of Memphis

summary: Understanding the genetic basis of plants’ response to environmental stresses such as drought and salinity is vital for improving the future crop productivity and for deciphering the evolutionary mechanisms of adaptation and speciation. Here, we screened for genes and functional groups that are potentially involved in drought tolerance in tomato by comparing genome-wide transcriptome profiles of drought-sensitive S. lycopersicum and drought-tolerant S. pimpinellifolium populations under control and water deficit conditions. We also compared the transcriptome profiles from this study and a previous salt treatment study to investigate expression similarities and differences in gene expression patterns between water and salt stress responses, which are physiologically and biochemically similar. Stress-induced genes such as dehydration responsive element binding (DREB) protein, ABA-response element binding factor (AREB)-like protein, heat shock proteins, and chaperones were commonly up-regulated in S. lycopersicum and S. pimpinellifolium. Genes such as WRKY transcription factors and 1-aminocyclopropane-1-carboxylate (ACC) synthase exhibited striking differences in both the baseline expression under the control condition as well as expression changes in response to water deficit, suggesting that the two species have accumulated heritable differences in gene expression patterns. At the genome scale, there was a tendency that down-regulated genes in S. lycopersicum are more neutral or even up-regulated in S. pimpinellifolium, suggesting that S. pimpinellifolium may be able to maintain cellular activities during prolonged droughts. In comparison of water and salt stress responses, known stress-induced genes such as DREB protein, AREB-like protein, and nine-cis-epoxycarotenoid dioxygenase (NCED) were commonly up-regulated in response to these stresses. However, we also found fundamental differences between these stress responses in terms of genome-wide expression patterns, partly attributable to the difference in how these stresses were applied during the experiments.

sample_organism:
Solanum lycopersicum
Solanum pimpinellifolium

overall_design: We compared Affymetrix microarray transcriptome profiles of root tissues from three natural populations each of S. lycopersicum and S. pimpinellifolium (3-4 individuals in each population as biological replicates under control (well-watered) and water deficit treatments.

first: Shirlean

last: Goodwin

first: Thomas

last: Sutter


title: Gene expression at four stages of the developing zebrafish embryo

status: Public on Dec 09 2013

city: Worcester

first: Steven

last: Weicksel

state: Massachusetts

address: 55 Lake Ave

department: BMP

institute: UMass Medical School

summary: Nucleosome arrangement in promoter regions has been shown to play an important role in gene regulation.  Genome wide studies in yeast, flies, worms, mammalian ES and transformed cell lines have found well positioned nucleosomes with an area of nucleosome depletion flanking transcription start sites.  This Nucleosome arrangement has been shown to be dependent on sequence (cis-regulatory factors), DNA binding factors (trans-regulatory factors) and ATP-dependant chromatin modifiers.  However, little is understood about how the nascent embryonic genome positions nucleosomes during development.  This is particularly intriguing since the embryonic genome undergoes a whole scale rechromatinization event upon fusion of sperm and oocyte.  Using four stages of early embryonic zebrafish development we map nucleosome positions at the promoter region of 34 zebrafish hox genes.  We find that nucleosome arrangement at the hox promoters is a dynamic process which happens over several stages.  We also find evidence that trans-regulatory factors play a greater role in nucleosome positioning over cis-regulatory elements.  Finally we provide evidence that transcriptional activation is the driving force behind the arrangement of nucleosomes at the promoters of hox gene during early development.

overall_design: Four tissue types: 2, 4, 6, and 9 hours post fertilzation embryos. Two treatments: Untreated (WT), and Retinoic Acid treated embryos(RA).

first: Charles

last: Sagerstrom


title: B. subtilis response to rotten meat volatiles.

status: Public on Sep 04 2013

city: Groningen

first: Arjan

middle: Oedse Geert

last: Oldebesten

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: To find a promoter upregulated in the presence of rotten meat, we exposed B. subtilis 168 to the volatiles of rotten meat (mixed beef/pork) and performed a microarray comparing it to B. subtilis  which was not exposed to the meat. The results where used to build iGEM Groningen 2012s Food Warden, a spoiled meat detector. Find more information at: 2012.igem.org/Team:Groningen

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: One condition design; including dye swap, two technical replicates and two experimental replicates

first: Alicja

last: Daszczuk

first: Yonathan

last: Dessalegne

first: Ismaȇl

last: Drenth

first: Elbrich

last: Hendriks

first: Emeraldo

last: Jo

first: Tom

last: van Lente

middle: O

first: Jonathon

last: Parrish

first: Wlada

last: Poljakova

first: Annisa

last: Purwanto

first: Renske

last: van Raaphorst

first: Mirjam

last: Boonstra

first: Auke

last: van Heel

first: Martijn

last: Herber

first: Sjoerd

last: van der Meulen

first: Jeroen

last: Siebring

first: Robin

last: Sorg

first: Matthias

last: Heinemann

first: Oscar

middle: P

last: Kuipers

first: Jan-Willem

last: Veening


title: Liver transcriptome changes and adaptation of zebrafish to transport-associated stress

status: Public on Mar 04 2013

city: Bodø

first: Anusha

last: Dhanasiri

state: Nordland

address: Universitetsalleen 11

department: Faculty of biosciences and Aquaculture

country: Norway

institute: University of Nordland

summary: Liver plays a key role during the stress adaptation process.  Therefore to understand the molecular adjustments that occur in fish to counter the stress during transport, transcriptional changes in zebrafish liver were analyzed with a 4x44K oligo array using total RNA extracted from fish prior to transport (basal), immediately after packing (0 h) and during the mock transport (48 and 72 h).

overall_design: Each sampling point [prior to transport (basal), immediately after packing (0 h) and during the mock transport (48 and 72 h)] had 4 biological replicates and each replicate consisting of a pool of total RNA extracted from liver of 5 individual fish. Those 4 biological replicates or pools were prepared of fish either from 4 different tanks in the rearing system (basal) or from 4 different transporting bags (0, 48 and 72 h).  Sixteen microarrays (4 replicates x 4 time points) were performed using Agilent Zebrafish Oligo Microarray (V3) (4x44K)

first: Viswanath

last: Kiron

first: Jorge

middle: M

last: Fernandes


title: Multi-tissue gene expression profiles of human brain (CR)

status: Public on Apr 25 2013

city: New York

first: Jun

last: Zhu

address: One Gustave L Levy, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn Medical School at Mount Sinai

summary: The genetics of complex disease produce alterations in molecular interactions of cellular pathways which collective effect may become clear through the organized structure of molecular networks. To characterize molecular systems associated with late-onset Alzheimer´s disease (LOAD), we constructed gene regulatory networks in hundreds of autopsied brain tissues from LOAD patients and non-demented subjects. We demonstrate that LOAD reconfigures specific portions of the molecular interaction structure, and via an integrative network-based approach we rank ordered these sub-networks (modules) for relevance to LOAD pathology, highlighting the immune/microglia module as the top ranking. Through a Bayesian inference approach we identified multiple key causal regulators for LOAD brains.

overall_design: Autopsied tissues from dorsolateral prefrontal cortex (PFC), visual cortex (VC) and cerebellum (CR) in brains of LOAD patients, and non-demented healthy controls, collected through the Harvard Brain Tissue Resource Center (HBTRC), were profiled on a custom-made Agilent 44K array (GPL4372_1). All subjects were diagnosed at intake and each brain underwent extensive LOAD-related pathology examination.  Gene expression analyses were adjusted for age and sex, postmortem interval (PMI) in hours, sample pH and RNA integrity number (RIN).  In the overall cohort of LOAD and non-demented brains the mean ± SD for sample PMI, pH and RIN were 17.8±8.3, 6.4±0.3 and 6.8±0.8, respectively.  230 samples with all PFC, VC, and CR tissue profiled were included for further multi-tissue analysis.

first: Bin

last: Zhang

first: Chris

last: Gaiteri

first: Liviu-Gabriel

last: Bodea

first: Zhi

last: Wang

first: Joshua

last: McElwee

first: Chunsheng

first: Tao

last: Xie

first: Linh

last: Tran

first: Radu

last: Dobrin

first: Eugene

last: Fluder

first: Brunce

last: Clurman

first: Manikandan

last: Narayanan

first: Christine

last: Suver

first: Hardik

last: Shah

first: Milind

last: Hahajan

first: John

last: Lamb

first: Cliona

last: Molony

first: David

middle: J

last: Stone

first: Vilmundur

last: Gudnason

first: Amanda

last: Myers

first: Eric

last: Schadt

first: Harald

last: Neumann

first: Valur

last: Emilsson


title: Lipocalin 2 is present in the EAE brain and is modulated by natalizumab

status: Public on Jun 30 2012

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Multiple sclerosis (MS) is a demyelinating disease causing major neurological disability in young adults. We characterized the transcriptome of the choroid plexus (CP), which is part of the blood-brain barriers and the major site of cerebrospinal fluid (CSF) production, in the experimental autoimmune encephalomyelitis mouse model of MS. Genes encoding for adhesion molecules, chemokines and cytokines displayed the most altered expression, supporting the CP as a site of immune-brain interaction in MS. The gene encoding for lipocalin 2 (LCN2) was the most up-regulated, and CSF LCN2 levels coincided with the phases of active disease.

overall_design: Total RNA was isolated with Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer?s instructions. After quality assessment using the Agilent Bioanalyzer (Agilent Technologies, CA, USA), 100ng of total RNA from 3 pooled controls and 3 or 2 pooled samples of each experimental autoimmune encephalomyelitis (EAE) phase were amplified and labelled with the Illumina TotalPrep RNA Amplification Kit (Illumina Inc., San Diego, CA, USA). The labeled cRNA was then hybridized using the recommended protocol in a total of two Illumina Whole-Genome MouseRef-8 expression Beadchips (Illumina Inc., San Diego, CA, USA).

first: Fernanda

last: Marques

first: Sandro

middle: D

last: Mesquita

first: João

middle: C

last: Sousa

first: Fuying

last: Gao

first: Daniel

middle: H

last: Geschwind

first: Sandra

last: Columba-Cabezas

first: Francesca

last: Aloisi

first: Matilda

last: Degn

last: Cerqueira

first: Nuno

first: Margarida

last: Correia-Neves

first: Joana

last: Palha


title: Transient knockdown of LIS1 results in seizures, differential gene expression and a neuronal migration disorder in developing zebrafish

status: Public on Jun 15 2013

first: Scott

last: Baraban

address: 513 Parnassus Ave

department: Neurosurgery

institute: UCSF

summary: Mutation or deletion of LIS1 (Lissencephaly-1) underlies classical lissencephaly, a migration disorder resulting in brain malformation, epilepsy and mental retardation.  Orthologues for LIS1 genes (lis1a and lis1b) are ubiquitously expressed in developing zebrafish larvae, but the functional consequences of Lis1 knockdown are unknown.  Here we used lis1-specific morpholino oligonucleotides (MOs, targeting protein translation or mRNA splicing, respectively) to transiently knockdown Lis1 expression in zebrafish.  Injection of lis1 MOs resulted in morphological changes including microcephaly.  At four days post-fertilization, lis1 morphants exhibited spontaneous convulsive behavior and abnormal large-amplitude electrographic discharge resembling that seen in acute and genetic zebrafish models of epilepsy.  Abnormal brain development and neuronal migration defects were observed when lis1 MO injections were made into fluorescent reporter lines demarcating interneuron distribution (Dlx5a/6a:GFP) and brain structure (GBT0133:mRFP). Microarray analysis for ~44,000 Danio rerio transcripts identified 215 up-regulated and 160 down-regulated genes.  Quantitative PCR and whole-mount in situ hybridization were used to validate these results for twenty and seven genes, respectively.  These findings in a simple vertebrate model reproducing neuroanatomical and epileptic hallmarks of the human condition represent a novel approach to the study of childhood seizure disorders associated with a single gene mutation

overall_design: 4 WT samples (sample= 10 pooled larvae) and 4 Lis1Morphants slight phenotype (sample= 10 pooled larvae)   were collected at 4dpf (days post fertilization). The morphants were selected based on phenotype and seizure behavior. Both groups of fish derived from same pools of eggs

first: Gabriela

last: Hortopan


title: Microarray analysis of gene expression from different developmental stages of the tomato fruit

status: Public on Aug 29 2012

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

summary: The goal of this research was to measure the gene expression levels thoughout 10 stages of tomato fruit development. Whole buds, flowers or fruits were collected at various developmental timepoints.

overall_design: Total RNA was extracted from 10 stages of flower and fruit development. A single technical and biological repeat was performed. cDNA was amplified and labelled using standard Affymetrix protocols.

first: Runchun

last: Jing

first: Karim

last: Sorefan

first: Frank

last: Schwach

first: Vincent

last: Moulton

first: Tamas

last: Dalmay


title: Identification of miRNAs regulated by vitamin D within primary human osteoblasts

status: Public on Aug 01 2012

city: Coral Gables

first: Thomas

last: Lisse

state: Florida

address: 1801 Memorial Drive

institute: University of Miami

summary: Identified a series of miRNAs transcriptionally regulated by vitamin D treatment within osteoblasts. Several miRNAs were validated in dose escalation experiments. Furthermore, downstream miRNA targets were appraised and found to regulate target message and protein levels. These findings were assessed in early and late passaged osteoblasts and found an age-dependent regulation of some miRNAs, while others were considered constituitiously expressed. Inhibitor studies of one key bone-related miRNA demonstrated the importance of this miRNA to regulate vitamin D-mediate osteoblastic differentiation during mineralizaition.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Three independent sets of passage 8 primary human osteoblasts were either treated with vehicle (ethanol) or 1,25D3 (10nM) for 6 hours. Total RNA was collected using the miRNA Vana kit (ABI) and then quality assessed, and sent for miRNA array processesing.

middle: S

last: Rieger

first: Rene

middle: F

last: Chun

first: Martin

last: Hewison

first: John

last: Adams


title: Circadian clock drives novel functions through transcriptional cascade

status: Public on Apr 26 2012

city: Shanghai

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

institute: Shanghai institute for biology science

summary: Using larval zebrafish as a model system, we applied a genome-wide transcriptome approach that allowed us to investigate circadian gene expression that can be associated with various tissues and cell types. Our analysis of circadian gene regulatory network revealed a general principle: circadian clock controls diverse aspects of circadian physiology through transcriptional cascade of transcription factors (TFs). As a proof of this principle, we focused on microphthalmia-associated transcription factor a (mitfa), a dark-induced TF controlling melanogenesis in melanocytes. We demonstrated experimentally that there is a circadian rhythm of melanin synthesis mediated by mitfa. The circadian rhythm of mitfa is in turn driven by both endogenous clock and external light/dark cycle. The circadian rhythm of melanin synthesis may play an important role in zebrafish’s adaptation to daily cycle of lighting condition in the environment.

overall_design:
Total RNA of larval sample was extracted using Trizol (Invitrogen) according to the manufacturer’s instruction. The quantity and quality of the RNA samples were assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies) and an Agilent 2100 bioanalyzer (Agilent). 12 LD RNA samples and 12 DD RNA samples were used for Agilent whole zebrafish 4x44K microarray, which contains 43,603 probes for a whole-genome transcriptional profile.
Morpholinos  oligonucleotides (MOs) were purchased from Gene Tools. All MOs except standard control were designed to target the start codon region of the genes. MOs were used at the following final doses: clock MO, 2.5 ng; mitfa MO, 9 ng or 13ng (microarray analysis). MOs were pressure-injected into 1- to 2-cell stage embryos at a volume of 1nl using Picospritzer II injectors as previously described (Janik et al. 2000). Each MO sample contained 40 individually treated larvae. Then the sample are collected and microarray are conducted just as before.

first: Ying

last: Li

first: Guang

first: Jiulin

last: Du

first: Jun

last: Yan


title: Microarray analysis of gene expression under different light conditions

status: Public on May 02 2012

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

institute: RIKEN CSRS

summary: The size of tomato fruits are largely dependent on growth conditions. To obtain insights on how light intensity contributes to translocation from a leaf and a fruit, we developed a plant irradiation system based on light-emitting diodes (LEDs) to a leaf. By using this system, we investigated the changes of transcript profiles of tomato leaves and fruits grown under different light conditions.

overall_design: 20 samples were analyzed (14 leaf samples and 6 pericarp samples); 2-3 biological replicates were used.

first: Atsushi

last: Fukushima

first: Tomoko

last: Nishizawa

first: Mariko

last: Hayakumo

first: Shoko

last: Hikosaka

first: Kazuki

last: Saito

first: Eiji

last: Goto


title: Expression data from Ralstonia solanacearum-inoculated tomato stem

status: Public on Oct 06 2012

city: Tsukuba

first: Takeaki

last: Ishihara

state: Ibaraki

address: 3-1-1 Kannondai

department: National Agricultural Research Center

institute: National Agriculture and Food Research Organization

summary:
Bacterial wilt caused by Ralstonia solanacearum is a lethal, soil-borne disease of tomato. Control of the disease with chemicals and crop rotation is insufficient, because the pathogen is particularly well adapted for surviving in the soil and rhizosphere. Therefore, cultivar resistance is the most effective means for controlling bacterial wilt, but the molecular mechanisms of resistance responses remain unclear.
We used microarrays to obtain the characteristics of the gene expression changes that are induced by R. solanacearum infection in resistant cultivar LS-89 and susceptible cultivar Ponderosa.

overall_design: Stems of LS-89 and Ponderosa seedlings at the five to six leaf-stage were inoculated just above the cotyledon by cutting the stem to one-third of its diameter with a razor, adding 5 µl of bacterial suspension (1e+6 CFU/ml of R. solanacearum strain 8107S) or distilled water for mock inoculation to the opening, then clipping the wound site to avoid bending. Inoculated plants were grown in a growth chamber at 30ºC under 30,000 lux light intensity for 12 h/day. At 1 dpi, stems were sampled by dissecting 5 mm long sections at 5 mm below the inoculation site. For each hybridization, RNA from 15 plants was used. Three biological replicates of microarray analysis were performed.

first: Kazuhiro

last: Nakaho


title: Expression data from bovine corpus luteum treated with equine chorionic gonadotropin (eCG)

status: Public on May 09 2012

city: Sao Paulo

first: Luciana

middle: Alves

last: Fatima

state: Sao paulo

address: Orlando marques de Paica, 87

department: Surgery - Animal Anatomy

country: Brazil

institute: University of Sao Paulo

summary: In order to indentify genes regulated by eCG, and involved in CL development and progesterone increases, the transcriptome was evaluated using the microarray technology

overall_design: Cows (Bos indicus) were divided into control, stimulated  and superovulated groups.  The stimulated group received 400 IU of eCG on day 8 and the superovulated group received 2000 IU of eCG on day 4 after the beginning of synchronization. Corpus luteum were collected at day 6 after ovulation e the trasncripitome was available by microarray.

first: Mario

last: Binelli

first: P

last: Baruselli

first: Bruce

last: Murphy

first: Paula

last: Papa


title: Nrf2b: a novel zebrafish paralog of the oxidant-responsive transcription factor Nrf2.

status: Public on Dec 20 2011

city: Hamilton

first: Andrew

middle: G.

last: McArthur

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

summary: We identified a novel paralog of the antioxidant response element transcription factor, Nrf2 in zebrafish.  To determine whether the paralogs Nrf2a and Nrf2b regulate different sets of genes, we performed loss-of-function experiments followed by microarray-based gene expression profiling, performed on embryos in which expression of Nrf2a, Nrf2b, or both paralogs was knocked down.

overall_design: Embryos at the 1-4 cell stage were injected with 3-5 nl of a control morpholino (MO) or gene-specific MO to knockdown Nrf2a, Nrf2b, or a Nrf2a+b combination. At 48 hpf, triplicate groups of 5 embryos were exposed to 2 µM of tert butyl hydroquinone or 2% DSMO for 4 hours. At 52 hpf, embryos were fixed in RNA Later and stored at -80°C. RNA was extracted, bioanalyzed, labeled with Cy3 and hybridized to the Agilent V3 4x44K zebrafish microarray (cat. #G2519F-026437) at the Genome Technology Core of the Whitehead Institute (Cambridge, MA). Raw array data obtained from the Whitehead Institute were extracted using Agilent's feature extraction software using background detrending (spatial and multiplicative).Prior to normalization, Cy3 values below 5 were set to 5. The data were then normalized using the non-linear scaling method based on rank invariant probes. After normalization but before statistical analyses, probes not significantly above background in all microarrays were removed (3147 probes in all; based on Agilent’s 2.6 standard deviation method). None of the probes were saturated for Cy3 signal on any microarray, so no further filtering was applied. There were a total of 40,456 probes for statistical analyses. Statistical tests were performed using MeV v4. Data were log transformed and median centered for each probe. An ANOVA was run for morpholino injection, with p-value based on 1000 permutations of the data and alpha of 0.01. The probes found significant in the ANOVA were subsequently examined using Rank Product (RP) analysis to identify probes up- and down-regulated by the MO injection For each RP test, a two-class unpaired RP analysis was performed using 100 permutations of the data with a false discovery rate (FDR) ≤10%.

first: Alicia

middle: R

last: Timme-Laragy

first: SibelI

last: Karchner

first: Diana

middle: G

last: Franks

first: Matthew

last: Jenny

first: Rachel

last: Harbeitner

first: Jared

middle: V

last: Goldstone

first: Mark

last: Hahn


title: Glyco-gene expression in naive and activated murine regulatory T-cells vs. conventional T-cells

status: Public on Sep 06 2011

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: In collaboration with Professor Anne Dell at the South Kensington Campus of Imperial College London, we have conducted preliminary glycomic surveys of C57BL/6 CD25+ and CD25- CD4+ T cells. Cells selected in serum-containing culture medium demonstrated unusual N-glycan profiles compared to those prepared in phosphate buffered saline (PBS). These profiles were subsequently shown to result from cellular sequestration of glycoproteins present in fetal calf serum (FCS) used to supplement the medium (1).   Analysis of the N-glycan profile of murine CD4+CD25+ Tregs prepared in PBS revealed distinct differences from CD4+CD25- T cells – namely, a reduction in sialic acid capping and loss of core fucose.

overall_design:
Preliminary studies are underway to ascertain the minimum medium required to sustain general T cell survival, whilst maintaining ‘clean’ glycomic profiles. The effect of glycoprotein withdrawal on CD25+ and CD25- CD4+ T cells in culture was investigated by selecting the cells in FCS-free medium and incubating them for six hours with either FCS-containing medium, or PBS supplemented with FCS, fetuin or fetuin-derived glycans. Early apoptosis was measured using Annexin-V (BD Biosciences, Heidelberg, Germany) and late apoptosis using 7-aminoactinomycin D (7-AAD) (BD Biosciences), in parallel with a complementary apoptosis detection method – measurement of the mitochondrial membrane potential using the BD™ Mitoscreen Kit (BD Biosciences).
This apoptosis staining study demonstrated that there was a remarkably higher percentage of death in both CD25+ and CD25- CD4+ T cells cultured in PBS versus cells cultured in RPMI-1640 or medium containing FCS. Both CD25+ and CD25- CD4+ T cells were highly susceptible to apoptosis in glycoprotein-free medium, demonstrating their exquisite sensitivity to the lack of glycoprotein survival factors. Continuing studies are addressing the minimum medium required to sustain cells undergoing polyclonal activation in vitro and the impact of activation on the N-glycan profiles of Tregs versus conventional T cells.

To complement this work, we used Core E resources to investigate glycosyltransferase gene expression in freshly isolated versus activated C57BL/6 CD25+ and CD25- CD4+ T cells. Three populations of murine CD4+ T cells were isolated from the spleens of C57BL/6 mice by flow-assisted cell sorting: CD25+CD45RBlow, CD25-CD45RBhigh and CD25-CD45RBlow. An RNeasy mini kit (QIAGEN, Manchester, UK) was used for total RNA extraction, following the manufacturer’s protocol. A microarray assay was performed using the Glyco-gene Chip v4, containing 1,127 probe sets targeting glycosylation-related transcripts including genes encoding proteins that are either heavily glycosylated or involved in glycosylation, as well as 119 probe sets targeting reference (‘housekeeping’) transcripts. Robust Multichip Average (RMA) software was used to convert intensity to expression values.

first: Oliver

last: Garden

first: Alex

middle: T

last: Moffit