title: Natural variation in brain gene expression profiles of aggressive and nonaggressive individual sticklebacks

status: Public on Feb 28 2017

city: Cleveland

first: Yibayiri

middle: Osee

last: Sanogo

state: OH

address: 9500 S Euclid Ave

department: Genomics Core

country: USA

institute: Cleveland Clinic Foundation

summary: We examine whether there are differences in gene expression between aggressive versus nonaggressive behavioral types of individuals within a natural population of male threespined sticklebacks (Gasterosteus aculeatus). We compared gene expression profiles of aggressive male sticklebacks to nonaggressive males in four regions of the brain (brainstem, cerebellum, diencephalon and telencephalon). We identified new candidate genes related to aggressiveness, including SLC38a, a solute carrier which has been linked to GABAergic neuron reuptake of glutamine.

overall_design: 2 conditions: control: non-aggressive fish; and experimental: aggressive fish. Biological replicates 6. Four brain regions.

first: Alison

middle: M

last: Bell

first: Syed

last: Bokhari

middle: O


title: Gene expression analysis in primary blasts of AML patients and CD34+normal progenitors after 6 hours of HDACi treatment.

status: Public on Mar 01 2017

city: Naples

first: Angela

last: Nebbioso

state: Italy

address: Vico Luigi De Crecchio 7

department: Biophysics, Biochemestry and General Patology

country: Italy

institute: Seconda Università degli Studi di Napoli

summary: AML blasts and CD34+ normal progenitors were treated with SAHA, and gene expression profiles were compared to 6-hours treatments. The analysis revealed commonly regulated genes in these systems by HDACi.

overall_design: Total RNA were obtained from AML blasts and normal progenitors after 6 hours of treatment with SAHA and gene expression profiles were compared.


title: Expression data from the complex I mutant gas-1 (fc21)  C. elegans worms in comparison to wildtype N2 Bristol worm and under the inluence of antioxidant drug treatment

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

summary: We studied genome-wide expression profiles of C. elegans young adult worms, complex I mutant gas-1(fc21) compare to the wild type N2 Bristol worm and the effect of different antioxidant drug treatment on the gene expression profile in gas-1(fc21).

overall_design:
4 biological replicates of wildtype (N2 Bristol) synchronized worms grown on OP50 bacteria, 4 biological replicates of the complex I  mutant C. elegans synchronized young adults and 4 biological replicates of synchronized complex I mutant worm treated with the different antioxidant drugs  were used as sources of total RNA, each for hybridization to a single Affymetrix whole-genome microarray.  Comparison of the data was intended to reveal causes of different antioxidant drug treatment on gene expresssion profile  in the complex I mutant gas-1(fc21) worms.  These array data are part of a bigger project of antioxidant drug effects that also includes RNAseq data deposited in SRA as Bioproject PRJNA2751152.
Wild-type vs complex I mutant vs complex I mutant treated with antioxidant drug comparison as a method for studying the possible beneficial effect of these drugs.

first: Falk

last: Marni

first: Zhang

last: Zhe

first: Erzsebet

last: Polyak


title: Affymetrix SNP array data for Chinese Lung Adenocarcinomas (ADCs)

city: Shanghai

first: Hongbin

last: Ji

address: YueYang Rd

country: China

institute: SIBCB

summary: Chinese lung adenocarcinomas genomic copy number data

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from tumor samples.
Copy number analysis of Affymetrix SNP 6.0 arrays was performed for all tumor samples.

first: H

first: Q

last: Wu

first: J

last: Zhang

first: Z

last: Fang


title: Gene expression analysis in AML systems after 6 hours of HDACi treatments

summary: K562, U937 and NB4 AML cell lines were treated with 2 HDACi, MS-275 and SAHA, and gene expression profiles were analysed to 6-hours treatments. The analysis revealed commonly regulated genes in the 3 cell lines and by 2 HDACi.

overall_design: Total RNA were obtained from 3 AML cell lines after 6 hours of treatment with SAHA and MS-275 and gene expression profiles were compared to untreated cells (control).


title: Root and rosette leaves transcriptome of Arabidopsis Col-0 and nrt1.5 mutant

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

summary: Differentially regulated genes in rosette leaves and roots of hydroponically grown Arabidopsis thaliana Col-0 and nrt1.5-5 mutant plants were identified by microarray analyses.

overall_design: Arabidopsis thaliana Col-0 wild type and nrt1.5-5 (GABI_347B03) mutant plants were grown hydroponically under short day conditions (10 h/14 h light/dark) in nitrogen limiting conditions. From nine weeks old plants rosette leaves no. 13 and younger and roots were separately harvested for transcriptome analysis.

first: Navina

last: Drechsler

first: Christine

last: Rausch


title: Comprehensive analysis of differentially expressed  lncRNAs and mRNAs  in aged mice

city: Beijing

first: changwei

last: wei

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

department: Department of Anesthesiology

institute: Beijing Chao-Yang Hospital, Capital Medical University

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

summary:
Long non-coding RNAs (lncRNAs) are RNA molecules with a transcript length of more than 200 nucleotides, which do not encode proteins (non-coding), yet they participate in the regulation of gene expression through multiple mechanisms in the form of RNA. A total of 51 lncRNAs and 21 mRNAs whose expression changed significantly, were identified. Five deregulated lncRNAs and five mRNAs were confirmed by quantitative real-time polymerase chain reaction (PCR) in 10 paired samples. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed to explore the principal functions of the deregulated genes. Furthermore, correlated expression networks of coding-noncoding co-expression (CNC) was constructed by using bioinformatics methods.
We predicted the potential targets of lncRNAs by using bioinformatics methods. In summary, novel lnRNAs were identified as potential biomarkers and therapeutic targets for POCD treatment.

overall_design: In this study, we comprehensively compared the expression profiles of lncRNAs and mRNA in 6 hippocampal tissues from POCD mice and 6 hippocampal tissues from control mice by microarray. Mice from the POCD group were experienced tibia fracture surgery, mice from the control group did not receive any prior treatment or surgery.

first: Changwei

last: Wei

first: Suwei


title: Synergistic effects of microgravity and space radiation (Nimblegen)

city: Dalian

first: Ying

last: Gao

state: Liaoning

address: Linghai Road 1

institute: Dalian Maritime university

summary:
Space radiations and microgravity both could cause DNA damage in cells, but the effects of microgravity on DNA  damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceflight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed.
The analyzation this study are further described in Gao, Y., Xu, D., Zhao, L., Zhang, M. and Sun, Y. (2015) Effects of microgravity on DNA damage response in Caenorhabditis elegans during Shenzhou-8 spaceflight. International journal of radiation biology, 91, 531-539.

overall_design: In our study, wild type, dys-1 mutant and ced-1 mutant strains of C.elegans endured four conditions during shenzhou-8 spaceflight mission, including spaceflight static condition(ss), spaceflight 1-g centrifugal condition(sc), ground control condition(gc) and no-transport control.  Limited to the quantity of worm samples, we performed technical-repeat test but not sample-repeat test.Accordingly, 12 mRNA microarrays were performed.

first: Yeqing

last: Sun


title: Analysis of microRNA expression profiles in clear cell papillary renal cell carcinoma compared to normal adjacent tissue.

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: Clear cell papillary renal cell carcinoma (CCPRCC) is a low-grade renal neoplasm with morphological characteristics mimicking both clear cell renal cell carcinoma (CCRCC) and papillary renal cell carcinoma (PRCC). However, despite some overlapping features, their morphological, immunohistochemical, and molecular profiles are distinct. To better understand the biology of this tumor, we analyze the miRNA expression profiles of a set of CCPRCC by microarrays.

overall_design: We analyze the miRNA expression profiles of clear cell papillary renal cell carcinoma (CCPRCC) compared to matched normal renal parenchyma using microarray. We further compare CCPRCC with other RCC histologic subtypes using publicly available datasets, identifying common and distinctive microRNA signatures along with the associated signaling pathways and biological processes.

first: Enrico

last: Munari

first: Apurva

last: Chitre

first: Masamichi

last: Hayashi

first: Guido

last: Martignoni

first: Matteo

last: Brunelli

first: Stefano

last: Gobbo

first: Pedram

last: Argani

first: Mohamad

last: Allaf

first: Mohammad

last: Hoque

first: George

last: Netto


title: Expression data from Smad3 knockout embryonic stem cells and wild type embryonic stem cells

status: Public on Feb 10 2017

city: Hong Kong

first: Ping

last: Yuan

address: Prince Wales Hospital

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
smad3 is the central component of TGF-beta pathway. We examined the role of Smad3 in ES cell differentiation and teratoma formation.
In this data set, we include expression data from Smad3 knockout ES cell and wild type ES cells.

overall_design: total 2 samples.

first: Peng

last: Li


title: Chip-chip from THP1 and HUVEC cells with ROR-alpha

city: Istanbul

first: Nihan

middle: Erginel

last: Unaltuna

address: Capa Millet Cad. Fatih

department: Genetics

country: Turkey

institute: University of Istanbul

type: Genome binding/occupancy profiling by genome tiling array

summary:
ROR-alpha is a nuclear receptor, activity of which can be modulated by natural or synthetic ligands including cholesterol. Due to its possible involvement in, and potential therapeutic target for atherosclerosis, we aimed to identify ROR-alpha target genes in monocyte and endothelial cell lines, THP1 and HUVEC, respectively.
ChIP-on-chip analysis of ROR-alpha demonstrated that ROR-alpha may target more than 3000 genes in monocytic and endothelial cells.

overall_design: Comparison of DNA immunoprecipated with anti-ROR-alpha antibody vs DNA immunoprecipated with anti-IgG antibody from CGP52608 treated cells.

first: Cagri

last: Gulec

first: Neslihan

last: Coban

first: Bilge

last: Ozsait-Selcuk

first: Sema

last: Sirma-Ekmekci

first: Ozlem

last: Yildirim

last: Erginel-Unaltuna


title: Altered integrin expression patterns revealed by microarray in matched human melanomas (snp)

city: Budapest

first: Laura

last: Vizkeleti

address: Üllői str. 93.

department: 2nd Deptartment of Pathology

country: Hungary

institute: Semmelweis University

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

summary:
Metastatic process is considered the predominant cause of melanoma-specific death, decreasing survival dramatically, and resulting in difficulties in the effective treatment. Large variety of molecular pathways associated with disease development and progression suggests that no individual molecular alteration is crucial in these processes per se.
Our aim was to gain insight into the molecular alterations behind metastasis formation, and to determine to what extent the profiles of primary melanoma and the corresponding metastasis are similar or distinct. High-throughput gene expression profiling was performed in combination with DNA microarrays to define significantly altered genes between matched primary and metastatic melanoma cell lines and tissue samples. Invasive behavior of different cell lines was determined using Matrigel invasion assays, and invasive primary clones were cultured selectively. Real-time qRT-PCR was applied to define integrin expression profiles of cell line pairs and melanoma tissue samples.

overall_design: A total of 4 human melanoma cell line pairs and 3 matched fresh/frozen primary lesions and lymph node metastatses were analyzed with Affymetrix CytoScan 750K microarrays to determine the main CNVs and LOHs, correlating with metastasis formation.

last: Vízkeleti

first: Tímea

last: Kiss

first: Viktória

last: Koroknai

first: Szilvia

last: Ecsedi

first: Orsolya

last: Papp

first: István

last: Szász

first: Róza

last: Ádány

first: Margit

last: Balázs


title: Gene expression analysis in AML cell lines and in primary blasts of AML patients after 6 hours of HDACi treatment.

first: Angela

last: Nebbioso

summary: AML cell lines (K562, U937 and NB4) were treated with MS27-275 (MS) and SAHA for 6 hours and the gene expression analysis revealed commonly regulated genes by the 2 HDACi. AML blasts were treated with SAHA for 6 hours and gene expression profiles were compared to commonly regulated genes by MS and SAHA in AML cell lines. The analysis revealed commonly regulated genes in these systems by SAHA.

overall_design: Total RNA were obtained from 3 AML cell lines and AML blasts after 6 hours of treatment with SAHA and MS and gene expression profiles were compared.


title: Molecular profiling of the developing lacrimal gland

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

summary: Although normal function of the lacrimal gland (LG) is essential for vision (and thus, for human well-being), the LG remains rather poorly understood at molecular level. The purpose of this study was to identify new genes and signaling cascades involved in LG development.

overall_design: To characterize and compare lacrimal glands isolated from embryonic and adult mice, we studied gene expression in these glands using Mouse Exonic Evidence Based Oligonucleotide (MEEBO) microarrays. To perform this experiment, RNA extracted from lacrimal glands of 3-month-old (adult) mice and embryonic day 16.5 (E16.5) fetuses was used for microarray analysis. A total of three independent biological replicates of E16.5 lacrimal glands and three independent biological replicates of adult lacrimal glands were obtained for comparative profiling.

first: Daniel

last: Pelaez


title: Modulation of extracytoplasmic function sigma factor promoter selectivity by spacer region sequence

city: Ithaca

first: Ahmed

last: Gaballa

state: NY

address: 370 Wing Hall, Cornell Univ

institute: Cornell University

summary: The ability of bacteria to adapt to stress depends on their ability to conditionally express specific sets of genes. Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma (σ) factors that regulate functions important for survival under conditions eliciting cell envelope stress. Of these, four have been studied in detail: σM, σW, σX and σV . The regulons of these four σ factors overlap, although the sequences that determine promoter selectivity are incompletely understood. A major role in promoter selectivity has been ascribed to the core promoter -10 and -35recognition elements. Here, we demonstrate that a homopolymeric T-tract motif, proximal to the-35 recognition element, functions in combination with the core promoter sequences to2determine selectivity for ECF sigma factors. This motif is critical for promoter activation by σV, contributes to activation by σM and σX, but has relatively little effect for σW. We propose that this motif, which is a feature of the deduced promoter consensus for a subset of ECF s factors from many species, affects confirmation or curvature of the DNA to influence promoter activity. The differential effect of this region amongst ECF s factors thereby provides a mechanism to modulate the nature and extent of regulon overlap.

overall_design:
Two-condition experiment (with or without IPTG induction of sigV), in WT or strain lacking all 7 ECF sigma factor
Please note that the complete_normalized_data.txt contains the data for control probes (resulting in 4,128 data rows).

first: Gaballa

last: Ahmed

first: Guariglia-Oropeza

last: Veronica

first: Durr

last: Franziska

first: Butcher

last: Bronwyn

first: Chen

last: Albert

first: John

last: Helmann


title: Expression data from postnatal piglet hippocampus, investigating how lactoferrin benefit early neurodevelopment and cognition

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

institute: Nestle research center- Beijing hub

summary:
Lactoferrin supplementation in pig milk replacer could promote cognitive functions in postnatal piglet behaviour experiment. There are 3 groups of 3-day-old postnatal piglets, feeding basal level, medium dose(0.6g/L) and high dose(1.2g/L) lactoferrin. After 35days  feeding, medium dose group showed better performance in behaviour experiment.
We used microarrays to detail the global programme of gene expression underlying the nervous system development and memory formation.

overall_design: There are 3 treatment groups and 12 replicates for each group. The 3 treatment groups are control group feeding basal level, medium dose(0.6g/L) and high dose(1.2g/L) lactoferrin. Pig hippocampus tissues were collecteded for RNA extraction and hybridization on Affymetrix microarrays.

first: Yujie

last: Shi


title: GENETIC VARIATION IN CHROMOSOME Y REGULATES SUSCEPTIBILITY TO INFLUENZA A VIRUS INFECTION

status: Public on Feb 07 2017

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

summary: Males of many species, ranging from humans to insects, are more susceptible than females to parasitic, fungal, bacterial, and viral infections. One mechanism which has been proposed to account for this difference is the ‘immunocompetence handicap model’ which posits that the higher infectious disease burden in males is due to testosterone (T), which drives the development of secondary male sex characteristics at the expense of suppressing immunity. However, emerging data suggest that cell-intrinsic (chromosome X and Y) sex-specific factors may also contribute to the sex differences in infectious disease burden. Using a murine model of influenza A virus (IAV) infection and a panel of chromosome Y (ChrY) consomic strains on the C57BL/6J background, we present data showing that genetic variation in ChrY influences IAV pathogenesis in males. Specific ChrY variants increase susceptibility to IAV in males and augment pathogenic immune responses in the lung, including activation of pro-inflammatory IL-17-producing γδ T cells, without affecting viral replication. Additionally, susceptibility to IAV segregates independently of copy number variation (CNV) in multicopy ChrY gene families that influence susceptibility to other immunopathologic phenotypes, including survival following infection with Coxsackievirus B3. These results demonstrate a critical role for genetic variation in ChrY in regulating susceptibility to infectious disease.

overall_design: B6 mice vs B6 ChrY-PWD consomic mice, both infected with IAV, whole lung at day 7 post-infection, 5 biological replicates (mice) each

middle: N

first: Cory

last: Teuscher


title: Transcriptome response of the Streptococcus pneumoniae D39 wild-type to Aspirin

status: Public on Feb 26 2017

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Transcriptome Comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 0 mM to 5mM Aspirin

overall_design: Two conditions design comparison of one strain including a dye swap.

first: Muhammad

last: Afzal


title: What is the transcriptomic contrast between a TDNA-mutant and its respective wild-type from young Arabidopsis rosette?

status: Public on Feb 01 2017

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra15-07_burxcol_465 - burxcol-465 - What is the transcriptomic contrast between a TDNA-mutant and its respective wild-type from young rosette grown in precisely-controlled conditions on our phenotyping robot (Phenoscope)? - The candidate gene (AT1G36310) was identified through QTL mapping and cloning for rosette leaf growth trait in a Bur x Col RIL set. It corresponds to a medium effect on growth and a major effect on other traits (leaf colour and pigments). We are now exploiting an independent TDNA-insertion line (SALK_135308) in the Col-0 background) to study its effect in a simple genetic context. This is a simple comparison between homozygous T-DNA (2 lines) and their respective WT (2 lines).

overall_design: 2 dye-swap - gene knock out

first: Olivier

last: Loudet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Identification of genes misregulated in developing seeds of Arabidopsis in response to myb92 mutation and to MYB92 overexpression

summary: ra15-01_myb92 - identification of genes misregulated to myb92 mutant and myb92 oe. - What are the genes over expressed or down regulated in seeds in response to a myb92 mutation or to MYB92 overexpression? - Plants of the different genotypes (wild-type, myb92 mutant, MYB92 overexpressing line) were grown in a green house, their flower were tagged and seeds were harvested 14 days after anthesis. Seeds were extracted from the siliques, stored at -80°C prior to RNA extraction.

overall_design: 4 dye-swap - gene knock in (transgenic),gene knock out,normal vs transgenic comparaison

first: Sébastien

last: Baud


title: Clock-controlled diurnal gene expression changes on a genome-wide scale

summary:
au14-07_clock - llhh clock transcriptome - Correlate clock-controlled diurnal gene expression changes with H2Bub chromatin mark changes on a genome-wide scale. - Wild type seedlings(Col-0)have been grown under Light/Dark conditions(12 h Light:12 h Dark)and thermocycles(23°C day:19°C night).After 10 days of entrainment, the conditions were switched to continuous light and temperature (LLHH) for 2 days. Seedlings have been harvested the 2nd day after the switch at Zeitgeber time 24 and 36 that correspond to dawn and dusk, respectively.

llhh clock transcriptome-LLHH clock transcriptome.

overall_design: 3 dye-swap - time course

first: Frédy

last: Barneche


title: Expression data from LPS/IFNgamma-treated Tet2-/- and Tet2+/+ mouse macrophages.

status: Public on Jan 24 2017

city: Boston

first: Chia-Ling

last: Wu

state: MA

address: 700Albany St

department: Whitaker Cardiovascular Institute

institute: Boston University

summary: We examined the effect of ablation of Tet2, an epigenetic regulator of gene transcription, in the global programme of gene expression underlying pro-inflammatory activation of macrophage.

overall_design: Thioglycllate-elicted macrophages were isolated from the Tet2 -/- mice and their wildtype littermates (N=3/group), treated with LPS and IFNg for 10 hours, and isolated for total RNA. Whole-genome transcript profiling was performed using Affymetrix microarray to identify genes that were dysregulated due to Tet2 ablation under the inflammation stimuli.

first: José

last: Fuster

first: Kenneth

last: Walsh


title: Expression data from Tet2-/- and Tet2+/+ mouse macrophages without any stimuli.

summary: We examined the effect of ablation of Tet2, an epigenetic regulator of gene transcription, in the global programme of gene expression at baseline, without pro-inflammatory activation, in macrophages.

overall_design: Thioglycllate-elicted macrophages were isolated from the Tet2 -/- mice and their wildtype littermates (N=3/group) and isolated for total RNA. Whole-genome transcript profiling was performed using Affymetrix microarray to identify genes that were dysregulated due to Tet2 ablation under the inflammation stimuli.


title: Effect of ftr mutation on Arabidopsis transcriptome - Redox regulation in plants

summary: au15-02_trx - effect of ftr mutation on arabidopsis trancriptome - Recherche nouvelles fonctions pour le système TRX plastidial. -  - Comparison Mut1 vs sauv1 at the same developmental stage (8-10 leaves) as Mut1 at the time of sampling - Comparison Mut1 vs sauv1 at the same age (11 weeks) as Mut1 at the time of sampling - Comparison Mut2 vs sauv2 at the same developmental stage (8-10 leaves) as Mut1 at the time of sampling - Comparison Mut2 vs sauv2 at the same age (9 weeks) as Mut1 at the time of sampling Mut1 = ftrb Sauv1 = Col-0 Mut2 = ftra1.a2 Sauv2 = WT segregant from crossing between ftra1 (in WS genetic background) and ftra2 (in Col background)

overall_design: 8 dye-swap - gene knock out

first: Emmanuelle

last: Issakidis-bourguet


title: Effect of light on translatome of Arabidopsis seeds during germination

summary: au14-10_wd40 - effet of light on translatome of arabidopsis seeds during germination - Does light regulates germination via polysome association ? - At harvest seeds are dormant.They stay dormant if stored at -20°C.A.Th dormant seeds dont germinate at 25°C in darkness.Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients)were extracted from imbibed seeds for 20h at 22°C in darkness and light(3 biological replicates). Transcriptome and translatome are compared for light vs dark for 20h of imbibition. In silico comparison will allow to compare transcriptome and translatome for each type of sample.

overall_design: 6 dye-swap - treated vs untreated comparison

first: Christophe

last: Bailly


title: Impact on Arabidopsis thaliana transcriptome of multifunctional silica nanoparticles based on metal atom clusters

summary: au14-09_silice - clustop transcriptomics. - Understand and categorize plant mechanisms implicated in the interaction with nanoparticles, both in the phenomena responsible for toxicity as in accommodation, see detoxication. - Phytotoxicity of Cs2[Mo6Br14]@SiO2 nanoparticles and their components, i.e. Cs2[Mo6Br14] clusters and SiO2 nanoparticles, has been studied usign Arabidopsis thaliana cell suspension culture. Cs2[Mo6Br14]@SiO2 nanoparticles used here are composed of 7,5% clusters and 92,5% SiO2. Thus, to compare to the impact of a 100 mg/L Cs2[Mo6Br14]@SiO2 nanoparticle treatment (CS), we also treated Arabidopsis cells with clusters at 7,5 mg/L (C), SiO2 at 92,5 mg/L (S), and combined 7,5 mgCMB/L plus 92,5 mgSiO2/L (C+S).

overall_design: 8 dye-swap - treated vs untreated comparison

first: Fransisco

last: Cabello-hurtado


title: Observation of the effects of the product Tn on the expression of A. thaliana genes -  Project TN 2014: effect on Arabidopsis thaliana

summary: au14-01_tn - Observation of the effects of the product Tn on the expression of genes of A. thaliana. - Observation of the effects of the product Tn on the expression of genes of Arabidopsis thaliana related to nutrition and development. - Each plant is sprayed with a product. 24h or 48h after treatment, a leaf is removed for RNA extraction and analysis.

overall_design: 6 dye-swaps - dose response.

last: Klarzynski

first: Marie

middle: L


title: Insights into the function of long noncoding RNAs in sepsis revealed by gene co-expression network analysis

status: Public on Jan 31 2017

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

summary: Transcriptional profiling of neutrophyl granulocytes from 24 subjects was used to investigate their differences regarding sepsis and aging using gene network approaches.

overall_design: Two-color hybridization design. Aliquots of total RNA isolated from adult or elder individuals with sepsis or healthy controls were labeled with Cy3 and co-hybridized with a common reference RNA pool (Universal Human Reference RNA, Agilent, cat #740000) labeled with Cy5 to Agilent DNA SurePrint G3 Human Gene Expression 8x60k v2 Oligoarray (design ID # 039494) . Biological replicates: 6. No technical replicates.

first: Diogo

middle: V

last: Pellegrina

first: Fabiano

middle: P

last: da Silva

first: Patrícia

last: Severino


title: CCN3 is a therapeutic target that promotes OPN upregulation and coagulation cascades activation in hepatocellular carcinoma

status: Public on Jan 06 2017

first: Qingan

last: Jia

address: Shanghai City Medical College Road 138

department: Department of General Surgery, Huashan Hospital

institute: Fudan University

summary: Total RNA extracted from Hep3B-CCN3 and Hep3B-vector cells were performed in triplicate using the Human OneArray microarray analyses

overall_design: Total RNA was extracted from Hep3B-CCN3 and Hep3B-vector cells. Isolations and microarray analyses were performed in triplicate using the Human OneArray

first: Qingguang

last: Liu


title: Expression data from regenerating axolotl forelimbs

status: Public on Jan 10 2017

first: James

middle: R

last: Monaghan

address: 360 Huntington Ave

department: Biology

institute: Northeastern University

summary: Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we identified expression patterns that explain PD duplication including upregulation of proximal homeobox gene expression and silencing of distal-associated genes whereas limb truncation was associated with disrupted skeletal differentiation. Overall, mechanisms were identified that regulate RAR’s multifaceted roles in the salamander limb including regulation of skeletal patterning during epimorphic regeneration, skeletal tissue differentiation during regeneration, and homeostatic regeneration of intact limbs.

overall_design: We performed microarray gene expression analysis on forelimbs that will eventually regenerate normally (DMSO-treated), become PD duplicated (RA-treated), or become truncated (LE135-treated). Genes were identified as statistically significant if they passed a false discovery rate (FDR) < 0.05 determined after an ANOVA analysis (533 significant probe sets), and changed from control DMSO samples > 1.5 fold change (FC) in either treatment group (327 significantly changed probe sets). Juvenile axolotls 8.8cm total length (TL) (high = 10.1cm, low = 7.4cm) and 4.58 average snout to vent length (SVL) received forelimb amputations at the distal zeugopod. Between days 7-14 dpa, individually housed animals were dosed with RA, LE135, or DMSO (n = 16/treatment). Drugs were changed every other day. Blastemas containing as little stump tissue as possible were collected from all 48 animals at 14 dpa and single forelimbs from four separate individuals were pooled together to yield four independent biological replicate samples for each treatment group.


title: Analysis of the role for TgAP2IX-4 in regulating gene expression in Toxoplasma development

status: Public on Jan 26 2017

city: St. Louis

first: Joshua

middle: B

last: Radke

state: Missouri

address: 660 Euclid Ave, CB8230

department: Molecular Microbiology

institute: Washington University School of Medicine

summary:
Differential expression analysis of TgAP2IX-4 knockout parasites in the developmentally competent Prugnaid delta ku80 (PruQ, Type II) genetic background.
The role for TgAP2IX-4 was evaluated, in vitro, as tachyzoites (pH 7.0) and induced bradyzoites (48h pH 8.2) in three strains: PruQ-parent; AP2IX-4 knockout; complemented AP2IX-4 knockout

overall_design: 11 total samples.  Each condition presented as 2 biological replicates, with the exception of the complemented AP2IX-4 strain with has 3 biological replicates

first: Dong-Pyo

last: Hong

first: Sherri

last: Huang

first: Michael

middle: W

last: White

first: William

last: Sullivan

last: Holmes

first: Ting-Kai


title: The effect of Bcl6 on the liver sex difference

status: Public on Jan 19 2017

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai University

summary: To confirm the effect of Bcl6 on the liver sex differrence, we performed the gene expression analysis in male and female wile type mice and male and female liver specific Bcl-6 deficient mice.

overall_design: Male and female wild type mice and  male and female liver specific Bcl-6 deficient mice were dissected. RNA extraction was performed from livers for the microarray analysis.

first: Hiromi

last: Chikada


title: Intrinsic subtype and gene expression changes between matched primary and metastatic samples of breast cancer patients

status: Public on Jan 08 2017

city: Barcelona

first: Juan

middle: Miguel

last: Cejalvo

state: Barcelona

address: Carrer Villaroel 170

country: Spain

institute: Hospital Clinic Barcelona

summary: We compared expression of 105 breast cancer-related genes between matched primary and metastatic breast cancer

overall_design: The analysis was performed on 246 (123 pairs) formalin-fixed paraffin-embedded tumor tissue using the nCounter platform

first: Aleix

last: Prat


title: ra15-06_oxmyc4 - atmyc4 overexpression in arabidopsis (ws) - Identification of new transcription factors for lignin biosynthesis

status: Public on Jan 05 2017

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: ra15-06_oxmyc4 - atmyc4 overexpression in arabidopsis (ws) - identification of new transcription factors for lignin biosynthesis - Compare the gene transcription in the mature stem of Arabidopsis wild type (ws) and AtMYC4 overexpressors (inws background)

overall_design: 3 dye-swap - normal vs transgenic comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Richard

last: Sibout

first: Marie-Laure

last: Martin-Magniette


title: mRNA expression in white adipose tissue of adult F2 female offspring from F0-fathers fed a chow or high-fat diet

status: Public on Jan 01 2017

city: Stockholm

first: Thais

last: de Castro Barbosa

state: Stockholm

address: von Eulers väg 4a

department: Physiology and Pharmacology

summary:
The purpose of this study was to investigate whether paternal high-fat diet (HFD) transgenerationally remodels the epigenome of spermatozoa to alter metabolism in the F1 and F2 generation offspring
White adipose tissue mRNA expression profiling of F2-female offspring from F0-founders fed either a chow or a chronic HFD challenged. Adult females were challenged or not a high-fat diet for 12 weeks. White adipose tissue was dissected at an endpoint experiment. Rats were subjected to 4 hours fasting prior to anesthesia with pentobarbital and tissue collection.

overall_design: F2-females Sprague-Dawley rats from F0 founders fed or not a high-fat diet  were also subjeted to high-fat consumption for 12 weeks. At terminal experiment, gonadal white adipose from 6 to 7 animals per group was collected, prepared and subjeted to the array analysis.

first: Romain

last: Barres

first: Juleen

last: Zierath

first: Anna

last: Krook


title: Molecular pathways underlying inhibitory effect of antimicrobial peptide Nal-P-113 on bacteria biofilms formation of Porphyromonas gingivalis W83 by DNA microarray

status: Public on Jan 20 2017

city: Shenyang

first: Hongyan

last: Wang

state: Liaoning Province

address: Nanjing North St. 117

department: Department of Periodontology

institute: School of Stomatology, China Medical University

type: Expression profiling by high throughput sequencing

summary: The aim of this study is to determine the effects of different concentration Nal-P-113 in biofilm formation. Besides, we performed gene expression profiling in Nal-P-113-treated P. gingivalis W83 to delineate the underlying molecular mechanism of Nal-P-113-inhibited biofilm formation.

overall_design: 3 samples were picked up from wild strain P.gingivalis W83 and 1 sample was treated with 6.25 ug/mL antimicrobial peptide. The total RNA was extracted and labeled with Klenow, and then hybridism with P.gingivalis W83 chip. The commercial GeneChip P.gingivalis W83 Genome Array used here was provided by CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Roche NimbleGen (Wisconsin, USA). Five replicates of the genome were included per chip. An average of 19 different 60-base oligonucleotides (60-mer probes) represented each gene in the genome. Array hybridization, washing, scanning and data analysis were performed at the CapitalBio Corporation, Beijing, China and carried out according to the NimbleGen’s Expression user’s guide. The arrays were scanned using MS200 scanner (NimbleGen), and NimbleScan software (NimbleGen) was used to extract fluorescent intensity raw data from the scanned images. The expression data of probes were normalized using quantile normalization and expression data of genes were generated using the Robust Multichip Average (RMA) algorithm. In a comparison analysis, two class unpaired method in the Significant Analysis of Microarray software (SAM, version 3.02) was performed to identify significantly differentially expressed genes between TEST and CONTROL groups. Genes were determined to be significantly differentially expressed with a selection threshold of false discovery rate, FDR<5% and fold change＞2.0 in the SAM output result.

first: Li

last: Lin


summary: au14-11_levure - study of a kinetic answer - Effect of a mixture of molecules stemming from industrial process - Cells were submitted to products and harveted at time 0, 1 4 and 4 hrs

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

first: Eric

last: Ruelland


title: au14-05_pi4kbeta1beta2 - Transcriptome changes induced in the pi4kbeta1beta2 sid2 triple mutant

summary: au14-05_pi4kbeta1beta2 - pi4kbeta1beta2 sid2 triple mutant - What are the transcriptome changes induced in the pi4kbeta1beta2 sid2 triple mutant ? - The pi4kbeta1beta2 sid2 triple mutant plants were compared to sid2 plants or to pi4kbeta1beta2 double mutant plant. As a control the pi4kbeta1beta2 double mutant was compared to WT.

overall_design: 6 dye-swap - genotype comparaison


title: Interaction between NIH:OVCAR-3 cells and mesenchymal stroma/stem cells (MSC)

status: Public on Dec 30 2016

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

institute: Hannover Medical School

summary: A co-culture of 60% GFP-labeled human mesenchymal stem cells (MSCGFP) and 40% mcherry-labeled NIH:OVCAR-3 tumor cells were incubated in MSC culture medium for up to 7 days in cell culture plates (diameter 10 cm, Greiner BioOne GmbH, Frickenhausen, Germany) at an initial density of 2,000 cells/cm2.

overall_design: All 4 biological samples were processed in a single color microarray design

first: Yuanyuan

last: Yang


title: Long Noncoding RNA and mRNA Expression Profile in Laryngeal Squamous Cell Carcinoma

status: Public on Dec 29 2016

city: Beijing

first: Lin

last: Feng

state: Beijing

address: No.1, Dong Jiao Min Xiang Street  Dong Cheng District

institute: Beijing Tongren Hospital

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

summary: To investigate the aberrant expressed lncRNA and mRNA and identify the potential lncRNA correlated with core mRNA in LSCC, we screened lnRNA and mRNA expression profile in 9 pairs of primary Stage IV LSCC tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays, conducted in-depth integrated bioinformatics analysis of lncRNA and mRNA, and performed qRT-PCR assays to further validate their expressions in an independent cohort of 30 pairs tissue samples

overall_design: lnRNA and mRNA expression profile in 9 pairs of primary Stage IV laryngeal squamous cell carcinoma (LSCC) cancer tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays

first: Ru


title: Expression analysis of Wild-type and lncKdm2b-deficient ILC3s

status: Public on Dec 26 2016

first: Benyu

last: Liu

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: Investigation of differentially expressed genes in  lncKdm2b-deficient ILC3s

overall_design: Gene expression profiling using Lin-CD45+ROR gt+ ILC3s from lncKdm2b deletion mice or WT littermates. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA).

first: Buqing

last: Ye

first: Zusen

last: Fan


title: Differential miRNA expression profiles of primary and relapse lesions of breast cancer patients receiving tamoxifen

city: Chengdu

first: Xiaorong

last: Zhong

state: Sichuan

address: 5 Gongxing Lane, Wuhou District

institute: West China Hospital, Sichuan University

summary: Long-term tamoxifen treatment significantly improves the survival of hormone receptor-positive (HR+) breast cancer (BC) patients. However, tamoxifen resistance remains a big challenge for endocrine therapy. We aimed to identify prognostic biomarkers for tamoxifen treatment and explore their role in tamoxifen resistance. We used Exiqon miRCURY™ LNA Array (v.18.0) to detect the miRNA expression profiles in the primary tumors and their matched recurrent/metastatic lesions from six HR+ breast cancer patients who relapsed after TAM treatment. Fold changes ≥ 2 and P values < 0.05 were defined as differential expression. We found that 28 miRNAs were significantly downregulated in recurrent/metastatic lesions compared to primary tumors, and 54 miRNAs were significantly upregulated.

overall_design: In this study, 6 primary tumor samples and 6 matched recurrent/metastatic lesion samples from six HR+ breast cancer patients who relapsed after TAM treatment were analyzed by microRNA array.

first: Hong

last: Zheng


title: Gene expressions in rat intracranial aneurysms

status: Public on Jan 14 2017

city: Kyoto

first: Tomohiro

last: Aoki

address: Konoe-cho, Yoshida, Sakyo-ku

institute: Kyoto University

summary: Specimens from aneurysms and control arterial walls were analyzed.

overall_design: Aneurysmal lesion at 3 weeks after the induction was analyzed.

first: Shuh

last: Narumiya


title: CHO cells: Serum free adapted cells (Control) vs. Serum adapted cells

status: Public on Dec 24 2016

city: Vienna

first: Gerald

last: Klanert

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Biotechnology

summary: Transcriptional profiling of CHO-K1 cells comparing to in-house serum-free and suspension adapted CHO-K1 cells in the exponential phase. Goal was to determine the effects of serum on CHO-K1 cells.

overall_design: Two-conditions experiment: Serum free adapted CHO cells vs. Serum adapted CHO cells. Biological replicates: 4, Technical replicates: 2 (Dye Swap).

first: Smriti

last: Shridhar

first: Norbert

last: Auer

first: Nicole

last: Borth

first: David

last: Kreil


title: Microarray screening for microRNAs differentially expressed in whole blood samples of patients with clinically significant rejection after liver transplantation

city: Berlin

first: Nathanael

last: Raschzok

address: Augustenburger Platz 1

department: Department of Surgery; Campus Charite Mitte / Campus Virchow Klinikum

institute: Charité - Universitätsmedizin Berlin

summary:
To investigate whether differentially expressed microRNAs in peripheral blood could be associated with clinically significant, histologically proven acute cellular rejection after liver transplantation, a microRNA microarray screening was performed with RNA isolated from
PaxGene whole blood samples from patients with ACR within the first three postoperative weeks and from patients without clinical signs of rejection within the first 6 months after transplantation.

overall_design: 19 blood samples from 19 patients with biopsy proven acute cellular rejection within the first 21 days after transplantation (taken prior or immediately after the start of the anti-rejection therapy), and 17 blood samples from 16 randomly selected stable controls (taken at the postoperative days [POD] 7 or 14).

first: Anja

last: Reutzel-Selke

first: Rosa

last: Schmuck

first: Laura

last: Tannus

first: Mehmet

middle: H

last: Morgul

first: Corinna

last: Dietel

first: Annekatrin

last: Leder

first: Benjamin

last: Struecker

first: Hannes

last: Sallmon

first: Michael

last: Bartels

first: Johann

last: Pratschke

first: Igor

last: Sauer


title: Neuro-like differentiation of SH-SY5Y human cell line

city: Porto Alegre

first: Marco

middle: Antonio

last: De Bastiani

state: Rio Grande do Sul

address: Ramiro Barcelos 2600

institute: Universidade Federal do Rio Grande do Sul

summary: Microarray technology has become a very useful tool in studying complex diseases, since it enables to evaluate the expression of thousands of transcripts simultaneously and elucidate known as well as new processes and phenomena. In this context, the diseases that affect the central nervous system remain a challenge for scientists and the search for suitable experimental models that allows correlations with clinical events is crucial. Therefore, it has been proposed that the differentiation model of human neuroblastoma cell line SH-SY5Y into cells with neuronal profile with retinoic acid might be an interesting tool to study neurodegenerative diseases. However, we know little about the mecanisms or the pathways involved in this process of differentiation. Here we conducted a microarray analysis to uncover changes in each phenotype (undifferentiated cells and differentiated cells), thus, elucidating the regulatory networks of this model and extracting molecular signatures of this process.

overall_design: This data consists of 16 microarray samples from SH-SY5Y (ATCC) cell line either untreated or submitted to neuronal differentiation protocols with retinoic acid (RA) only or retinoic acid+BDNF. At the beginning of both differentiation protocols, we decrease FBS concentration in medium to 1% and add 10 uM RA. To evaluate RA-only differentiation stimulation, samples RNA were colleted 4 days and 7 days after FBS decrease to 1% and RA addition. In the RA + BDNF differentiation protocol, in addition to FBS decrease and RA 10 uM, there is an addition of BDNF 50 ng/ml at day 4. The neuronal differentiation process was confirmed by the decrease in cell proliferation rates and increase in neurite density.

middle: A

first: Castro

last: Mauro

first: Fábio

last: Klamt

first: Bianca

last: de Aguiar

last: Pfaffenseller


title: MS23, a master basic helix-loop-helix factor in maize, regulates the birth and maturation of tapetum

status: Public on Dec 31 2016

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
A cascade of basic helix-loop-helix transcription factors guide tapetal cell development in maize anthers, using proteins conserved in Arabidopsis and rice but deployed with a distinctive timing.
Anthers were dissected and staged to be 1500 μm in length (+/- 100 μm) and samples were compared between mutants and fertile siblings on an Agilent 4x44 custom microarray.
Analysis included MS32 which is another basic helix-loop-helix factor that acts later during tapetal differentiation.

overall_design: For each mutant versus fertile sib comparison, 2 biological replicates were used with direct comparisons made between fertile and sterile siblings of the same mutant background.

last: Guo-Ling

first: Virginia

last: Walbot

first: Mai

last: Lan


title: Gene expression of bovine embryo derived stem-like cells (eSLCs)

status: Public on Dec 23 2016

city: Seoul

first: Daehwan

last: Kim

address: 1, Gwanak-ro, Gwanak-gu, Seoul

country: South Korea

institute: Seoul national university

summary: Gene expression of bovine eSLCs from three different origins using three inhibitors

overall_design: Gene expression of bovine embryo derived stem-like cells from three different origins, in vitro produced, somatic cell nuclear transfer and parthenogenesis.

first: D

first: S

last: Roh

first: Y

middle: G

last: Jung


title: Mechanisms involved in porcine early embryo survival following ethanol exposure

city: Québec

first: Florence

last: Pagé-Larivière

state: Québec

address: 2440, boulevard Hochelaga

country: Canada

institute: Laval University

summary: We aimed to determine the toxicogenomic impacts and the mechanisms involved in preimplantation embryonic survival following 0.2% ethanol exposure in porcine embryos. Gene expression changes were measured with a porcine embryo specific microarray and confirmed by RT-qPCR. Compared to control, ethanol exposure led to a 43% decrease in blastocyst rate and activated pathways associated with oxidative stress and nervous system damage, such as TP53 and TGF.

overall_design: 4 pools of 10 control porcine blastocysts were compared to 4 pools of 10 ethanol-exposed porcine blastocysts in a microarray experiment.

last: Page-Lariviere

first: Celine

last: Campagna

first: Marc-Andre

last: Sirard


title: Agilent Chip Data of the Post-Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Agilent, miRNA, batch 1)

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

institute: PICB

summary: We report the application of Agilent technology for high-throughput profiling of the post-transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA),  with acupuncture, Methotrexate, Isofluorane anesthetic and placebo treatments, as well as the healthy control.

overall_design: The experiment is designed as 5 arms: epidermal needle manipulation (AP/MEC), Methotrexate injection (MTX), Isofluorane anesthetic (ANE, used as anesthesia control) and placebo (PLA, used as control) on CIA induced rheumatoid arthritis (RA) rats, as well as the normal rats (NORA, healthy control). Whole blood sampling was carried out before any therapy in RA (RA_T0) and NORA (NORA_T0) groups, and in the other groups (AP/MEC, MTX,ANE, PLA and NORA) at 1 hour and 34 days after the start of therapeutic treatments.  Finally, 24 total RNA samples (two replicates for each sampling) extracted from 24 blood samples (Peripheral blood mononuclear cells, PBMC ) were analyzed using Agilent technology (Agilent-031189 unrestricted_Rat_miRNA_v16.0_Microarray).

first: Valentina

last: Devescovi

first: Yuanhua

last: Liu


title: Chromatin immunoprecipitation assay of EVI1 in MCF7 and HCC1937 breast cancer cells untreated and everolimus-adapted

status: Public on Dec 22 2016

first: Miguel Angel

last: Pujana

address: Gran Via 199

institute: Institut Catala d'Oncologia IDIBELL

summary: Inhibitors of the mechanistic target of rapamycin (mTOR) are currently used to treat advanced metastatic breast cancer. However, whether an aggressive phenotype is sustained through adaptation or resistance to mTOR inhibition remains unknown. Here, complementary studies in human tumors, cancer models and cell lines reveal transcriptional reprogramming that supports metastasis in response to mTOR inhibition. This cancer feature is driven by EVI1 and SOX9. EVI1 functionally cooperates with and positively regulates SOX9, and promotes the transcriptional upregulation of key mTOR pathway components (REHB and RAPTOR) and of lung metastasis mediators (FSCN1 and SPARC). The expression of EVI1 and SOX9 is associated with stem cell-like and metastasis signatures, and their depletion impairs the metastatic potential of breast cancer cells. These results establish the mechanistic link between resistance to mTOR inhibition and cancer metastatic potential, thus enhancing our understanding of mTOR targeting failure.

overall_design: Two conditions: everolimus-adapted (>120 days) and untreated (parental) MCF7 and HCC1937 cells.

first: Helena

last: Aguilar

first: Francesca

last: Mateo

first: Miguel


title: Molecular characterization of a series of 7 NF1-associated human MPNSTs

status: Public on Dec 21 2016

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

institute: Paris Descartes University

type: Genome variation profiling by genome tiling array

summary: 7 MPNSTs from 7 neurofibromatosis-type 1 patients were screened with a high resolution array-CGH. Each MPNST DNA (somatic tumor DNA) was individually hybridized on Agilent whole human genome 244K microarrays (Platform GPL4091) using the pooled genomic constitutional DNA (lymphocytes DNA) from the normal control patients as reference, in order to detect tumor-specific aberrations.

overall_design: NF1-associated MPNST DNA vs. pooled normal constitutional DNA

first: Meena

last: Upadhyaya


title: Low oxygen and FGF2 effects on the transcriptome of the adult human dermal fibroblasts

city: Worcester

first: Tanja

last: Dominko

address: 100 Institute Rd

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: Adult human dermal fibroblasts reside in vivo under low oxygen tension. Thus, low oxygen culture conditions represent a physiological state for adult human dermal fibroblasts. We have also previously shown that low oxygen and addition of basic fibroblast growth factor (FGF2) lead to prolonged life-span of adult human dermal fibroblasts.  Therefore, we set to determine effects of low oxygen and FGF2 on the gene expression signature of adult human dermal fibroblasts. This global analysis will allow identification of genes affected and pathways regulated by low oxygen and FGF2.

overall_design: Adult human dermal fibroblasts were grown in four different experimental conditions (2% oxygen, 2% oxygen with addition of 4 ng/ml FGF2, 19% oxygen, and 19% oxygen with addition of 4 ng/ml FGF2) and their transcriptomes were compared. Current study includes one biological replicate and three technical replicates of each sample (total of 12 samples).

first: Olga

last: Kashpur


title: Citrus limon: Control vs. Xanthomonas citri AT inoculation

status: Public on Dec 18 2016

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

summary: Transcriptional Profiling of non-inoculated Citrus limon leaves vs. 48h inoculation with Xanthomonas citri AT

overall_design: Two-condition experiment, non-inoculated vs. Inoculated leaves. Three biological replicates, one replicate per array.

first: Maria

last: Marano

first: Roxana

last: Roeschin


title: Citrus limon: Control vs. Xanthomonas citri T2 inoculation

summary: Transcriptional Profiling of non-inoculated Citrus limon leaves vs. 48h inoculation with Xanthomonas citri T2


title: Citrus limon: Control vs. Xanthomonas citri inoculated

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

overall_design: Refer to individual Series


title: Expression data from CD8+TIM-3+ and CD8+TIM-3- T cells sorted from follicular lymphoma lymph nodes

status: Public on Dec 15 2016

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

summary:
Exhaustion markers are expressed by T lymphocytes in Follicular Lymphoma (FL). Through these, TIM-3 has been recently identified as a poor pronostic factor when expressed by FL CD4+ T cells.
Before this study, there was no molecular characterization of unstimulated CD8+ T cells, expressing - or not - TIM-3. We used microarrays to compare the global gene expression profile between CD8+TIM-3+ T cells and CD8+TIM-3- T cells freshly sorted from follicular lymphoma biopsies.
Abstract from the associated publication:   Up-regulation of T-cell immunoglobulin-3 (TIM-3) has been associated with negative regulation of the immune response in chronic infection and cancer, including lymphoma. Here, we investigated the possible correlation between TIM-3 expression by ex vivo cytotoxic T cells (CTL) from follicular lymphoma (FL) biopsies and their functional unresponsiveness that could limit the favorable impact of CTL on disease progression. We report a high percentage of CD8+TIM-3+ T cells in lymph nodes of FL patients. When compared to their CD8+TIM-3- counterparts, CD8+TIM-3+ T cells exhibited defective cytokine production following TCR engagement. Furthermore CD8+TIM-3+ T cells display ex vivo markers of lytic granule release and remain unresponsive to further TCR-induced activation of the lytic machinery. Although confocal microscopy showed that TIM-3 expression on CD8+ T cells correlated with minor alterations of immunological synapse, a selective reduction of ERK signaling in CD8+TIM-3+ T cells was observed by phospho-flow analysis. Finally, short relapse free survival despite rituximab(R)-chemotherapy was observed in patients with high content of TIM-3+ cells and a poor infiltrate of granzyme B+ T cells in FL lymph nodes. Together, our data indicate that, besides selective TCR early signaling defects, TIM-3 expression correlates with unresponsiveness of ex vivo CD8+ T cells in FL. They show that scores based on the combination of exhaustion and cytolytic markers in FL microenvironment might be instrumental to identify patients at early risk of relapses following R-chemotherapy.

overall_design: CD3+CD8+TIM-3+ and CD3+CD8+TIM-3- T cells from FL lymph nodes (n=3 patients) were sorted by flow cytometry and then the 6 samples were selected for RNA extraction and hybridization on GeneChip® Human Gene 2.0 ST microarrays.

first: Camille

last: Laurent


title: Carbon sources tune antibiotic susceptibility in Pseudomonas aeruginosa via TCA cycle control

status: Public on Dec 20 2016

city: Cambridge

first: Jason

last: Yang

address: 415 Main St, Rm 2017

department: Biological Engineering

institute: MIT / Broad Institute

summary:
This study examines the mechanisms underlying fumarate- and glyoxylate-mediated changes in tobraymcyin sensitivity in PAO1 cells

Grant ID: NIH Grant K99 GM 118907
Grant title: Effects of Host Metabolic Variation on Antibiotic Susceptibility
Funding Source: NIH NIGMS
Name: Jason Yang

overall_design: Stationary phase PAO1 cells were resuspended in M9 supplemented with 15 mM fumarate, 30 mM glyoxylate, or their combination. Cells were incubated for 1 hr at 37C with shaking and then harvested for RNA extraction.

first: Sylvain

last: Meylan

first: James

last: Collins


title: Expression profiling in exosomal miRNAs of CML patients with musculoskeletal pain associated with discontinuation of Imatinib

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary: An approximately 60% of chronic myeloid leukemia (CML) patients who achieved a deep molecular response for more than 2 years maintained a major molecular response after discontinuation of imatinib. These findings indicate the possibility that a portion of CML patients treated with Tyrosine kinase inhibitors (TKIs) could discontinue TKI therapy, although long-term prognosis and/or adverse events after TKIs cessation remain unclear. Recent reports showed that transient musculoskeletal pain occurs in approximately 30% of CML patients after stopping imatinib. To ascertain the factors underlying musculoskeletal events after TKI cessation, we investigated exosomal miRNA in five CML patients who did not experience musculoskeletal events and five patients with musculoskeletal pain after stopping TKIs.

overall_design: Peripheral blood was obtained approximately 3 months after successful TKI cessation in CML patients. Exosomes were extracted by using Total Exosome Isolation Reagent, and the exosomal miRNA profiling was performed with a TaqMan Low-Density Array. The relative expression level of each gene was calculated by using the comparative thresholds cycle (Ct) method. Synthetic spike control (ath-miR-159) was used as an invariant control for the exosomal miRNA.


title: Targeting BET proteins improves the therapeutic efficacy of BCL-2 inhibition in T-cell acute lymphoblastic leukemia

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University


title: Affymetrix SNP array data for Trp53-null mammary tumors developed in a mouse model with a K8+ luminal cell origin

city: Boston

first: Zhe

last: Li

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: Mammary epithelium is hierarchically organized, with multipotent basal mammary stem cells (MaSCs) producing both luminal and basal cells during development or upon transplantation. Recent studies suggested that most breast cancers, including Basal-Like breast cancer (BLBC), might originate from luminal cells, and oncogenic events, such as ectopic expression of PIK3CA(H1047R), could induce multipotency in committed luminal cells. p53 is the most commonly mutated gene in human breast cancer; in particular, its inactivating mutations are found in most BLBCs, raising a question as to whether p53-loss plays a key role in acquisition of multipotent MaSC-like properties by luminal cells. By in situ lineage-tracing, we found that induced loss of p53 in Keratin 8 (K8)+ luminal cells led to their clonal expansion, due to increased cell cycle activity and attenuated apoptosis control, but did not directly affect their luminal identity. All induced mice eventually developed either Claudin-Low mammary tumors with 9qA1 (Yap1) amplification or Basal-Like tumors with 6qA1-A2 (Met) amplification. These data suggest that although p53 does not directly control the luminal fate, its loss facilitates acquisition of MaSC-like properties by luminal cells and predisposes them to development of mammary tumors with loss of luminal identity.

overall_design: Genomic DNAs from mammary tumors developed in Trp53L/L females 6-7 months after intraductal injection of Ad-K8-Cre adenovirus or from mammary glands of a strain background-matched wild-type female were prepared and subjected to mouse diversity SNP array analysis.

first: Ying

last: Xie

first: Luwei

last: Tao


title: Plasma Cell Niche

status: Public on Dec 16 2016

city: Bethesda

first: Marjorie

last: Robert-Guroff

state: MD

address: 41 Medlars Drive

department: Vaccine Branch

institute: National Cancer Institute

summary:
Sorted cells from bone marrow and rectal mucosa of SIV-infected rhesus macaques were analyzed for expression of factors associated with plasma cell recruitment, adhesion, or maintenance
mRNA expression anaylsis was performed on 16 CD2-CD19-CD20-HLA-DR+ and 16 CD2-CD19-CD20-HLA-DR- bone marrow cells, and 7  CD2-CD19-CD20-HLA-DR+ and 3 CD2-CD19-CD20-HLA-DR- rectal cells using a custom CodeSet produced by NanoString Technologies containing 44 niche factor genes of interst, 12 cell-type specific genes, and  9 reference genes identified in Genevestigator.

overall_design: Rhesus macaque CD2-CD19-CD20- cells from 20 bone marrow and 20 rectal tissue samples were sorted into HLA-DR+ and HLA-DR- populations representing antigen-presenting cells, and polymorphonuclear cells, respectively. Isolated mRNA was subject to expression analysis using a 65-gene custom CodeSet manufactured by NanoString Technologies and analyzed on their nCounter Analysis System.

first: Julia

middle: M

last: Shaw


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig3a-a]

status: Public on Dec 13 2016

city: Bunkyo-ku

first: Kazuyoshi

last: Takeda

address: 2-1-1 Hongo

department: Biomedical Research Center

institute: Juntendo Univ.

summary: Copy number alteration in out-growing mouse tumor cells comparing that in the original tumor cells that was primarily inoculated into the indicated mice.  Goal is to determine the effects of IFN-gamma producing tumor-specific CTL on targeted tumor cell gene expression.

overall_design: genomic DNA of out-growing tumor cells was compared with that of primary inoculated tumor cells by a-CGH assay


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig8b]


title: Gene expression profile of small intestine tissue from C57BL/6 mice with or without faecal microbiota transplantation

city: Tianjin

first: Ming

last: Cui

address: 238 Baidi Road

department: Institute of Radiation Medicine,

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: To further decipher the alteration of gene expression profile of irradiated mice with or without faecal microbiota transplantation (FMT), we performed FMT for 10 days following total body irradiaton (6.5 Gy gamma ray). Twenty-one days after irradiation, the mice were euthanized and the small intestine tissues excised.

overall_design: The male (and female) mice were separated into four groups randomly, The mice in Group A were treated with saline as negative control; the mice in Group B were treated with sex-matched FMT; the mice in Group C were treated with sex-mismatched FMT and the mice in Group D were sex-mixed (the weight of male and female stool was 1:1) FMT. FMTs were performed for 10 days following total body irradiaton (6.5 Gy gamma ray ). Twenty-one days after irradiation, the mice were euthanized and the small intestine tissues excised.


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig3a-b]


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig7b]


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig5a]


title: miRNAs are required for post-induction stage sweat gland development [mRNA]

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: miRNAs modulate processes in development, aging and cancer formation. However, miRNA function in sweat gland development has not been previously studied. By generating skin specific Dicer knockout mice, we show that miRNAs are required for post-induction stage sweat gland development.

overall_design: Wide Type vs Dicer cKO embryonic mouse footpads

first: Changyi

first: Piao

last: Yulan


title: miRNAs are required for post-induction stage sweat gland development [miRNA]


title: cDNA microarray analysis comparing transcription levels in the heads of control and hangAE10 mutants of D. melanogaster

status: Public on Dec 09 2016

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

department: Biology

institute: Humboldt University Berlin

summary:
To identify putative transcripts that might interact with Hang, we performed a cDNA microarray experiment in which we compared transcription levels in the heads of control and hangAE10 mutants.
Experimental and control probes were simultaneously hybridized to custom-made glass cDNA microarrays (DGC Drosophila v1 6k array, GEO accession no. GPL22680) that contained 6024 PCR-amplified cDNAs (the DGC 1.0 collection of 5849 non-redundant cDNAs was kindly provided by the Berkeley Drosophila Genome Project) and analysed using a GenePix 4000A Microarray Scanner (Axon Instruments, Union City, CA). Values were further processed as log2-transformed ratios and analysed with Microsoft Excel, Cluster analysis (Eisen et al., 1998), and the Significance Analysis of Microarrays (SAM) software package (Tusher et al., 2001). The ratios were filtered to eliminate all values that did not produce signals above background in at least four out of the five replicate experiments. cDNA spots for which the expression between two hybridized samples of RNA with a log2 value > 0.8 differed in at least two experiments were retained for further analysis.

overall_design: For each of the five replicate experiments, separate hybridization probes were produced from approximately 1000 fly heads. Experimental samples were generated from male hangAE10 flies, while control samples were generated from PZ[+] flies.Following Trizol (Invitrogen Inc.)-based RNA isolation, samples were labelled with Cy3 and Cy5 fluorophores (Amersham Inc.) in a reverse transcription reaction, as described previously (Klebes et al., 2002).

first: Henrike

last: Scholz


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig3b]


title: miRNA profiles associated with adynamic bone disease

status: Public on Dec 08 2016

first: In-Wha

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmacy and Research Institute of Pharmaceutical Sciences

institute: Seoul National University

summary: Mineral and bone disorder (MBD) is observed universally in patients with chronic kidney disease (CKD). Detrimental MBD-related skeletal changes include increased prevalence of fracture, cardiovascular disease, and mortality. MicroRNAs (miRNAs) have been identified as useful biomarkers in various diseases, and the aim of this study was to identify miRNAs associated with parathyroid hormone level in peritoneal dialysis (PD) patients. The PD patients were enrolled and grouped by their intact parathyroid hormone (iPTH) levels. Of the patients, total RNA was extracted from whole blood samples (n=15) and underwent miRNA microarray analysis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The patients with peritoneal dialysis were enrolled and grouped by their intact parathyroid hormone (iPTH) levels. Total RNA was extracted from whole blood samples. Total RNA from 15 patients underwent miRNA microarray analysis. 8 patients with iPTH ≥ 150 pg/mL (HP) and 7 patients with iPTH < 150 pg/mL (LP) had their miRNA profiles compared.

first: Sohyun

last: Jeong

first: Jung

last: Oh

first: Kook-Hwan


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig5b]


title: Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells


title: Uncovering obsessive-compulsive disorder risk genes in a pediatric cohort by high-resolution analysis of copy number variation.

status: Public on Dec 11 2016

city: Toronto

first: Stephen

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: The Affymetrix CytoScan HD 2.5M and Illumina HumanOmni2.5  arrays are high resolution SNP platform for studying copy number variations in the human genome.  Both platforms have widely being used in both clinical and research settings for identifying causative variants as well as interrogating the genome for benign variants. We employed both platforms to investigate the risk factor CNVs in trios diagnosed with OCD. We genotyped 307 unrelated probands (including 174 complete parent-child trios; mean age of probands 7.9±3.5 years) and compared their genotypes to those of 3,861 population controls, in order to identify rare CNVs (<0.5% frequency) of at least 15 kb in size that might contribute to OCD. We uncovered de novo CNVs and Decipher Syndromes in probands. We have identified additional potentially risk factor CNVs impacting the coding sequencing of genes involved in brain functions.

overall_design: We employed Affymetrix Chromsome Analysis Suite (ChAS), iPattern, Nexus, and Partek algorithms to call CNVs from the CytoScan HD array data. Similarly, we detected CNVs from OMNI2.5M microarray data using iPattern, PennCNV, CNVPartition, and QuantiSNP. We defined a stringent set of variants when each variant was called by at least by two algorithms. We defined the ancestry and relatedness of the samples using PLINK

first: Paul

middle: D

last: Arnold

first: Matthew

middle: J

last: Gazzellone

first: Mehdi

last: Zarrei


title: Pyrimidine-diones structure containing small molecule inhibits Streptococcus pneumoniae in-vitro biofilms growth

status: Public on Dec 12 2016

city: Seoul

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

institute: Korea University

summary:
Streptococcus pneumoniae is a Gram positive bacterium that causes severe invasive infection such as pneumonia, septicemia, meningitis and otitis media especially in children, the elderly and immune-compromised patients. Pneumococcal colonization and disease is often associated with biofilm formation. Bacteria in biofilms exhibit elevated resistance both to antibiotics and to host defense systems, which often results in persistent and difficult-to-treat infections. Therefore, the ongoing treat to human health posed by pneumococcal biofilms has prompted extensive research aimed to identify alternative targets and new antimicrobial agents that are effective against bacteria biofilms. The effective anti-biofilm strategies should include inhibition of microbial adhesion to the surface and of colonization, interference with the signal molecules modulating biofilm development and the disaggregation of the biofilm matrix.
In this study, we examine the effect of DAM inhibitor small molecule pyrimidine-diones on streptococcus pneumoniae D-39 strain growth (planktonic and biofilm) and evaluate the changes in global gene expression using c-DNA microarray. The microarray analysis was performed on total RNA extracted from biofilms grown in 24-well microtiter plate with 7µm/ml pyrimidine-diones small molecule and control biofilms (biofilms grown without pyrimidine-diones small molecule). To validate the results of microarray, real-time RT-PCR was performed on 12 differentially expressed genes from six different functional groups. cDNA-microarray analysis detected a total of 259 genes that were significantly differentially expressed in biofilm growth with pyrimidine-diones small molecule. 204 genes were significantly down expressed and 55 genes were significantly up expressed in biofilms grown with 7µm/ml pyrimidine-diones small molecule. Among the 204 down expressed genes, 45 were hypothetical protein encoding gene and 159 were functional protein encoding genes. Of 55 up-regulated genes 21 were hypothetical genes and 34 were functional protein encoding genes. The functional annotation showed that gene involve in fatty acid metabolism, cell division, cell cycles, DNA metabolism, cell assembly were significantly down regulated and galactose metabolism related gene were up-expressed in biofilm grown with pyrimidine-diones small molecule.

overall_design:
S. pneumoniae D-39 strain (NCTC 7466) is an encapsulated, serotype 2 pathogenic strain. It was obtained from the Health Protection Agency Culture Collections (HPA, Salisbury, UK). Bacteria were routinely grown in tryptic soy broth (TSB; BD Difco, Detroit, MI, USA) or on blood agar (BA; Hye In, Seoul, Korea) supplemented with 5 % v/v sheep blood at 37 °C in an atmosphere of 5% CO2. Small molecule pyrimidine-diones with chemical name 1-(4 bromophenyl)-5-(2-furylmethylene)-3-phenyl-2-thioxodihydro-4, 6 (1H,5H)-pyrimidinedione was purchased from Chembridge, USA. Stock solution of small molecule pyrimidine-diones was prepared in DMSO.
In vitro biofilm formation was carried out in 24-well, flat-bottom, polystyrene microtiter plate (BD falcon, MD, USA) in static model. S. pneumoniae grown up to mid-logarithmic phase in TSB medium was diluted 1:100 with fresh sterile TSB medium, inoculated 1.5 mL in 24-well microtiter plate and, incubated for 15 hours at 37°C in 5% CO2. Pyrimidine-diones small molecule was supplied at the concentration of 7µm/ml. Control biofilm were supplied with equal concentration of DMSO. After incubation medium was discarded, and the plates were gently washed three times with 1.5 mL sterile, cold phosphate buffer saline (PBS). Adherent cell were scraped and immediately processed for RNA extraction. All experiments were performed in triplicate (3 independent biological replicates).

middle: K

first: Jae-Jun

last: Song


title: miRNAs are required for post-induction stage sweat gland development


title: Cell density, Her2 and progesterone signaling regulate dissemination of breast cancer cells [Gene expression]

city: Regensburg

first: Christoph

middle: Andreas

last: Klein

state: Bavaria

address: Franz-Josef-Strauß-Allee 11

department: Experimental Medicine and Therapy Research

institute: University of Regensburg

summary: Disseminated breast cancer cells display genotypes disparate from the predominant clone of the primary tumor before manifestation of metastasis, suggesting that cancer cell dissemination occurs preferentially early; however, the underlying molecular mechanisms are unknown. Investigating metastasis in a Her2-driven mouse model, we found that the progesterone-induced paracrine cytokines Wnt4 and Rankl induced migration and early dissemination shortly after Her2 activation. Once tumorigenic growth was established, progesterone receptor (PgR) expression was lost and Wnt4/Rankl induced proliferation. The altered response from migration to proliferation was determined by cell density involving miRNA-regulated PgR expression and was reversible. Cells from early, low-density lesions displayed more functional stemness traits than cells from dense, advanced tumors, migrated more and founded significantly more metastases. The data suggest that many metastases are derived from early-disseminated cancer cells, implying that our concepts for systemic therapy need to be revised.

overall_design: Gene expression analysis was performed for 10 normal, 7 ADH, 19 primary tumor and 7 lung metastatic tissue samples.

first: Hedayatollah

last: Hosseini

first: Martin

last: Hoffmann

first: Gunter

last: Meister


title: Identification of microRNA expression profiles in the gill, intestine and hepatic caecum of amphioxus

city: Beihai

first: Xin

last: Liao

state: Guangxi

address: 2# JinHaian Road

department: School of Life Sciences

institute: Nanjing University

summary: The amphioxus, as a simple basal chordate model, plays an important and unique role on providing insights into the evolution of tissues and organs of the vertebrates. To understand the unique features of the amphioxus during evolution, it’s important to identify the gene and microRNA (miRNA) expression profiles of amphioxus tissues or organs. However, the systematic examination of these expression profiles is not conducted. Here, we focused on characterizing the miRNA expression patterns of three amphioxus digestive organs (the gill, intestine and hepatic caecum) that are believed to be the first line of immune defense.

overall_design: three samples from three organs of B. belcheri

first: Junyuan

last: Chen


title: Aerobic and Anaerobic Growth of Streptococcus pneumoniae D39

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

institute: Indiana University

summary: The catalase-negative, facultative anaerobe Streptococcus pneumoniae D39 is naturally resistant to hydrogen peroxide (H2O2) produced endogenously by pyruvate oxidase (SpxB).  Here, we investigate the adaptive response to endogenously produced H2O2. We show that lactate oxidase, which converts lactate to pyruvate, positively impacts pyruvate flux through SpxB and that ∆lctO mutants produce significantly lower H2O2. In addition, both the SpxB and pyruvate dehydrogenase complex (PDHC) pathways contribute to acetyl-CoA production during aerobic growth, and the pyruvate format lyase (PFL) pathway is the major acetyl-CoA pathway during anaerobic growth. Microarray analysis of the D39 strain cultured under aerobic vs. strict anaerobic conditions show up-regulation of spxB, a rhodanese-like protein (spd0091), tpxD, sodA, piuB, piuD and an Fe-S protein biogenesis operon under H2O2-producing conditions. Proteome profiling of H2O2-induced sulfenylation reveals that sulfenylation levels correlate with cellular H2O2 production, with endogenous sulfenylation of ≈50 proteins.  Deletion of tpxD increases cellular sulfenylation 5-fold and has an inhibitory effect on ATP generation.  Two major targets of protein sulfenylation are glyceraldehyde-3-phosphate dehydrogenase (GapA) and SpxB itself, but also include pyruvate kinase, LctO, AdhE and acetate kinase (AckA).  Sulfenylation of GapA is inhibitory, while the effect on SpxB activity is negligible, consistent with this cell-abundant protein functioning as a “sink” for endogenous H2O2.  Strikingly, four enzymes of capsular polysaccharide biosynthesis are sulfenylated, as are enzymes associated nucleotide biosynthesis via ribulose-5-phosphate.  We propose that LctO/SpxB-generated H2O2 functions as a signaling molecule to down-regulate capsule production and drive altered flux through sugar utilization pathways.

overall_design: Three independent hybridizations using independent RNA preparations from the strain IU1690 (replicate 1 and 2) and strain IU1781 (replicate 3) were performed. Strain IU1781 is isogenic with IU1690 except for the rpsL1 mutation. Reference samples were grown aerobically while experimental samples were grown anaerobically. Dye swap was performed with the reference strain labeled with Cy3 in two hybridizations and Cy5 in one hybridizations.

first: Kyle

last: Wayne

middle: T

first: Malcolm

middle: E

last: Winkler


title: Integrative "-omics" analysis in primary human hepatocytes unravels persistent mechanisms of cyclosporine A-induced cholestasis (MeDIP)

status: Public on Dec 06 2016

city: Maastricht

first: Jarno

last: Wolters

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

type: Methylation profiling by genome tiling array

summary: Cyclosporine A (CsA), is an endecapeptide with strong immunosuppressant activities and has contributed significantly towards clinical progress in organ transplantation. Furthermore, it has various toxic effects in the kidney and especially in the liver where it may induce cholestasis. The CsA drug-induced cholestasis (DIC) pathway includes important genes involved in the uptake, synthesis, conjugation and secretion of bile acids, which can be verified also in hepatic models in vitro. However, whether changes in CsA-induced cholestasis pathway induced in vitro are persistent thus presenting important biomarkers for repeated dose toxicity, has not yet been investigated. We therefore performed multiple -omics analyses, including whole genome analysis of DNA methylation, gene expression and microRNA expression in primary human hepatocytes (PHH) cultured in sandwich configuration, during and after terminating CsA treatment.   For this, cells were exposed to a non-cytotoxic dose of 30 µM CsA daily for 3 and 5 days. To investigate the persistence of induced changes upon terminating the CsA exposure of 5 days, a subset of PHH was subjected to a washout period (WO-period) of three days. DNA methylation (using NimbleGen 2.1 deluxe promoter arrays), transcriptomic (using Affymetrix Human Genome U133 Plus 2.0 arrays) and microRNA (using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays) analyses were performed on days 3, 5 and 8. Identification of differentially methylated genes (DMGs), differentially expressed genes (DEGs), and differentially expressed microRNAs (DE-miRs) was performed using several R packages.   DMGs, DEGs and DE-miRs were found after CsA treatment of PHH for 3 and 5 days as well after the WO-period. Interestingly, 828 persistent DEGs and 6 persistent DE-miRs, but no persistent DMGs, were found after the WO-period. These persistent DEGs and DE-miRs showed concordance for 22 genes (13 genes upregulated in gene expression and downregulated in microRNA expression; 9 genes downregulated in gene expression and upregulated in microRNA expression). Some of the persistent transcriptomic changes as well as DE-miRs could be successfully mapped onto the DIC pathway, while epigenetic changes not. Furthermore, 29 persistent DEGs in vitro showed changes in the same direction as observed in livers from cholestasis patients. None of those 29 DEGs were present in the DIC pathway or cholestasis adverse outcome pathway.  We have for the first time demonstrated a persistent impact of gene expression and microRNA expression related to DIC after repeated dose administration of CsA in vitro.

overall_design: 18 samples (3 time-points (3 days, 5 days and 8 days) with triplicates of control-samples (0.5% DMSO) and treatment-samples (30µM CsA))


title: Integrative "-omics" analysis in primary human hepatocytes unravels persistent mechanisms of cyclosporine A-induced cholestasis

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

overall_design: Refer to individual Series


title: Integrative "-omics" analysis in primary human hepatocytes unravels persistent mechanisms of cyclosporine A-induced cholestasis (miRNA)


title: Integrative "-omics" analysis in primary human hepatocytes unravels persistent mechanisms of cyclosporine A-induced cholestasis (RNA)


title: Induction of PLT1, PLT3, PLT4, PLT5 and PLT7 in whole seedlings

city: Wageningen

first: Luca

last: Santuari

address: Droevendaalsesteeg 1

department: Plant Sciences Group

institute: Wageningen University

summary: Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated. PLETHORA (PLT) transcription factor gradients were shown to guide the progression of cell differentiation at different positions in the Arabidopsis root. While well-described transcription factor gradients in animals specify distinct cell fates within an essentially static context, the PLT gradient is unique in its ability to control cell differentiation in a growing organ during continuous production and expansion of cells. To understand the output of these gradients we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient regulates cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, reinforcing their role as master regulators of organ development.

overall_design: Biological replicates: 4 for the mock treatment, 3 for 6 hours DEX induction of 35S-PLT[1,4,5,7]-GR, 2 for 35S-PLT3-GR.

first: Renze

last: Heidstra


title: Induction of pPLT2-PLT2-GR in Quiescent Center (QC) cells

overall_design: Three biological replicates. Mock, 1 hour and 4 hours induction.


title: Induction of 35S-PLT2-GR in whole seedlings

overall_design: Three biological replicates. Mock and 6 hours induction.


title: Candida albicans: Control vs. sulfite-treated cells

status: Public on Dec 03 2016

city: Houston

first: Michael

last: Gustin

state: TX

address: George R. Brown Hall, W200G, 6100 Main Street

department: Biosciences

country: USA

institute: Rice University

summary: Transcriptional profiling of Candida albicans cells comparing control untreated C. albicans cells with sulfite-treated C. albicans cells. Sulfite is a toxic molecule that C. albicans encounters in its human host. Both wild type and ∆zcf2 mutant cells were used. The goal was to determine the effects of sulfite on C. albicans gene expression, and to determine which of the genes areZcf2-depedent.

overall_design: Two-condition experiment, C. albicans cells vs. sulfite-treated C. albicans cells. 2 strains used: wild type and ∆zcf2 mutant cells. Biological replicates: 2 control replicates for each strain, 2 sulfite-treated replicates for each strain. Two technical replicates for each biological replicate in which the flourescent dyes were swapped.

first: Yasmin

last: Chebaro


title: Cochlear transcriptome after noise trauma and dexamethasone therapy in mice

city: Okayama

first: Yukihide

last: Maeda

address: 2-5-1 Shikata, Kita-Ku

department: Department of Otolaryngology-, Head and Neck Surgery

institute: Okayama University Hospital

summary: In order to elucidate molecular mechanisms of noise-induced hearing loss and dexamethasone therapy in the cochlea (inner ear), transcriptome of cochlear samples was analyzed after induction of hearing loss by exposure to intense noise in mice. Dexamethasone was intraperitoneally injected immediately following the noise trauma. Cochlear transcriptome was analyzed at 12h and 24h following the noise trauma and dexamethasone administration.

overall_design: The samples included cochlear RNA from 1) Baseline, neither noise exposure nor dexamethasone, 2) Noise only, 3) 12h after noise and dexamethasone administration (Dex12h), 4) 12h after noise and control saline (Control12h), 5) 24h after noise and dexamethasone administration (Dex24h), and 6) 24h after noise and control saline (Control24h) groups (6 mice for each group).

first: Yuikihide

first: Ryotaro

last: Omichi

first: Akiko

last: Sugaya

first: Shin

last: kariya

first: Kazunori

last: Nishizaki


title: Root avoidance of toxic metals requires the GeBP-LIKE 4 transcription factor in Arabidopsis thaliana.

status: Public on Dec 01 2016

city: Pohang

first: Youngsook

last: Lee

state: Gyeongsangbuk-do

address: 77 Cheongam-ro, Nam-gu

department: Life Sciences

institute: Pohang University of Science and Technology

summary: Plants reorganize their root architecture to avoid growth into unfavorable regions of the rhizosphere. In a screen based on chimeric repressor gene-silencing technology, we identified the Arabidopsis thaliana GeBP-LIKE 4 (GPL4) transcription factor as an inhibitor of root growth that is induced rapidly in root tips in response to cadmium (Cd). We tested the hypothesis that GPL4 functions in the root avoidance of Cd by analyzing root proliferation in split medium, in which only half of the medium contained toxic concentrations of Cd. The wild-type (WT) plants exhibited root avoidance by inhibiting root growth in the Cd side but increasing root biomass in the control side. By contrast, GPL4-suppression lines exhibited nearly comparable root growth in the Cd and control sides and accumulated more Cd in the shoots than did the WT. GPL4 suppression also altered the root avoidance of toxic concentrations of other essential metals, modulated the expression of many genes related to oxidative  stress, and consistently decreased reactive oxygen species concentrations. We suggest that GPL4 inhibits the growth of roots exposed to toxic metals by modulating reactive oxygen species concentrations, thereby allowing roots to colonize noncontaminated regions of the rhizosphere.thereby re-allocating root biomass toward non-contaminated rhizosphere areas and minimizing root exposure to toxic metals.

overall_design: Cadmium induced genes expression was analyzed in Columbia-0 (Col-0) and GPL4 suppressed plants by CRES-T . 2-week-old whole seedlings of Col-0  and GPL4 CRES-T treated with liquid 1/2 MS without and with 70 µM CdCl2 for 2 hours.Two replicates were used for each treatment and each line.

first: D

last: Khare

first: N

last: Mitsuda

first: S

first: W

middle: Y

last: Song

last: Hwang

first: M

middle: O

last: Takagi

first: E

last: Martinoia

first: J

middle: U

first: Y


title: Decreases in 15-lipoxigenase metabolites in Olmsted syndrome model rats

city: Toyonaka-shi

first: Masato

last: Wakabayashi

state: Osaka

address: 3-1-1, Futaba-cho

institute: Shionogi & Co., Ltd.

summary:
Olmsted syndrome (OS) is a congenital dermatosis characterized by palmoplantar keratoderma and periorificial keratotic plaque. TRPV3 (transient receptor potential vanilloid subtype 3) is the causative gene of OS and encodes a thermosensitive Ca2+-channel. However, the molecular mechanism causing the pathological development of OS is unclear. We aimed to reveal the molecular mechanism underlying the OS pathology from the perspective of lipid metabolism. Comprehensive lipidomics as well as microarray analyses were conducted on samples from non-lesional skin area of an OS rat model (Ht rats).
Infiltration of mast cells, eosinophils, and neutrophils and an increase in fibrotic region were detected in unaffected skin area of Ht rats. Among ~600 lipid species examined, levels of 15-lipoxygenase (LOX) metabolites, the precursors of anti-inflammatory and pro-resolving lipid mediators, and dihydroceramides were decreased by ≥16-fold in Ht rats compared to wild type rats. Consistent with the decreases in the 15-LOX metabolites, expression levels of the 15-LOXs, Alox15 and Alox15b, were largely reduced. On the other hand, expression levels of the cytokines/chemokines Il36b, Ccl20, Cxcl1, and Cxcl2 and those of the Ca2+-binding proteins S100a8 and S100a9, which are implicated in epidermal proliferation, were increased. The pro-inflammatory state of Ht rats caused by decreases in 15-LOX metabolites and increases in cytokines/chemokines may contribute to the pathogenesis of OS.

overall_design: Effect of TRPV3 gain of function mutation on non-lesioned dorsal skin tissue from pool samples of n = 3 wild-type and of n=3 Ht rats. Biological replicates: a replicate for 25-wk wild-type and 25-wk Ht.

first: Takeshi

last: Yoshioka


title: Adrenal cortex expression data of a German Holstein X Charolaise cross

city: Dummerstorf

first: Bodo

last: Brand

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute of Farm Animal Biology

summary: The importance of the adrenal gland in regard to lactation and reproduction in cattle has been recognized early. Due to consumers interest in animal welfare and the impact of stress on economically important traits in farm animals the adrenal gland and its function within the stress response is still of increasing interest. Especially the molecular mechanisms and pathways that are involved in the stress related effects on economically important traits in farm animals are not studied in full detail. Gene expression is an important mechanism underlying complex traits. Genetic variants affecting the transcript abundance are thought to affect the manifestation of an expressed phenotype. Therefore we investigated the genetic background of adrenocortical gene expression by applying an adaptive linear rank test to identify genome-wide expression quantitative trait loci (eQTL) for adrenal cortex transcripts in cattle.

overall_design: Adrenocortical expression-profiling of 147 cows slaughtered at day 30 after parturition in their second lactation

first: Juliane

last: Friedrich

first: Siriluck

last: Ponsuksili

first: Manfred

last: Schwerin


title: Expression data from control and gentamicin-treated chick basilar papilla

city: Boston

first: Zheng-Yi

last: Chen

state: MA

address: 243 Charles Street

department: Otolaryngology

institute: MEEI

summary: In chick basilar papilla, hair cells can be regenerated after gentamicin treatment. To identify genes and pathways involved in this process, we performed microarray analysis on the basilar papilla 0, 48 and 72 hours after gentamicin.

overall_design: 12-16-day-old chicks were treated with gentamicin to induce death of hair cells. Basilar papilla samples at different time points after gentamicin treatment were dissected and the basal halves were collected for RNA extraction. Total RNA was extracted from the pooled samples. Biological duplicates of the pooled RNA were used for microarray.

first: Mingqian

last: Huang

first: Douglas

last: Cotache


title: HAL2 overexpression induces iron acquisition and enhanced salt resistance in bdf1Δ

city: Jinan

first: Xiaoming

last: Bao

state: Shandong

address: Shanda Nan Road 27

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: The strain bdf1Δ+HAL2 improved salt resistance of bdf1∆. To gain further insight into the mechanism of bdf1∆ salt sensitivity, DNA microarray analysis was performed to determine the reason for the salt sensitivity of bdf1∆ cells and the process of how HAL2 overexpression and HDA1 deletion improves salt resistance. Transcriptomic analysis under salt treatment (0.5 mol.L-1 NaCl for 45 min) was performed using four different strains: bdf1∆,  W303, bdf1Δ+HAL2 and bdf1∆hda1∆. The transcription of 1,393 genes were significantly changed( > 2-fold) in bdf1∆ compared with W303 upon NaCl stress (0.5 mol.L-1 NaCl for 45 min). Only 108 genes were significantly changed ( > 2-fold) in bdf1Δ+HAL2 compared with bdf1∆ upon NaCl stress (0.5 mol.L-1 NaCl for 45 min).  Only 88 genes were significantly changed ( > 2-fold) in bdf1Δ+HAL2 compared with bdf1∆ upon NaCl stress (0.5 mol.L-1 NaCl for 45 min).

overall_design: bdf1∆ vs W303 upon NaCl stress (0.5 mol.L-1 NaCl for 45 min);bdf1Δ+HAL2 vs bdf1Δ under salt treatment (0.5 mol.L-1 NaCl for 45 min); bdf1Δhda1Δ vs bdf1Δ under salt treatment (0.5 mol.L-1 NaCl for 45 min).

first: Lei

first: Mingpeng

last: Wang

first: Jin

last: Hou

first: Jiafang

last: Fu

first: Yu

last: Shen

first: Liu

last: Fanghua

first: Zhaojie

last: Zhang


title: miRNA expression data of rat prostate cancer tissue treated with OBP-801, novel HDAC inhibitor

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: miRNA expression was obtained from non-treated or OBP-801 treated TRAP rats which develop prostate cancer. The primary aim was to identify miRNAs which regulate prostate carcinogenesis induced by OBP-801.

overall_design: Six week-old male TRAP rats were intravenously injected with 1mg of OBP-801 or saline 2 times a week. After 8 weeks, rats were sacrificed and miRNAs were extracted from ventral and lateral prostate and were run on miRNA arrray.

first: Shinya

last: Sato