title: Identification of Circulating Fibrocytes and Dendritic Derivatives in Corneal Endothelium of Patients with Fuchs' Dystrophy [RT-qPCR array CAPH10409]

status: Public on Jan 24 2017

city: Leuven

first: Joost

middle: J

last: van den Oord

address: Minderbroedersstraat 12, block q, box 1032

department: Department of Imaging & Pathology

country: Belgium

institute: KU Leuven

summary:
PURPOSE: Fuchs’ endothelial corneal dystrophy (FECD) is a degenerative eye disorder affecting 4% of Americans older than 40. It is the leading indication for corneal endothelial (CE) transplantation for which there is a global donor shortage. This study aimed to gain further insight into the pathophysiology of FECD and identify targets for nonsurgical therapy.

METHODS: CE from patients with late-onset FECD was compared with that of normal controls using microarray expression analysis (n = 4 FECD, n = 4 normal), reverse transcriptase quantitative PCR (n = 9 FECD, n = 8 normal), and immunohistology (n = 55 FECD, n = 15 normal).

RESULTS: This led to the identification of circulating fibrocytes and their dendritic derivatives in all examined CE samples with FECD (in all clinical stages of symptomatic FECD and independent of prior cataract surgery). These cells were not present in normal CE. In this study we characterize their morphology, protein expression profile, number, and localization within the CE layer of patients with FECD.

CONCLUSIONS: Circulating fibrocytes and their dendritic derivatives are a new aspect of FECD that deserves further investigation. Because they are known to cause fibrosis in a variety of organs, they may play a similar role in FECD and might be a valuable target for nonsurgical therapy.

overall_design: This study was performed on CE monolayers with Descemet membrane from patients with late-onset FECD. Microarray expression analysis was performed on 8 samples (n = 4 FECD, n = 4 normal). RT-qPCR was done for 179 genes of interest and at least three reference genes (n = 9 FECD, n = 8 normal). Molecules of interest were validated with immunohistochemical and immunofluorescent staining on fresh corneal endothelial whole-mounts (n = 55 FECD, n = 15 normal). All stainings were optimized on external control tissues, which were included as batch controls. Dye swaps ensured specificity of double staining.

first: An-Katrien

last: De Roo

first: Jasper

last: Wouters

first: Olivier

last: Govaere

first: Beatrijs

last: Foets


title: Genome-wide analysis of gene expression in pericytes extracted from pulmonary aterial hypertension (PAH) patients

status: Public on Jan 19 2017

city: Stanford

first: Vinicio

last: de Jesus Perez

state: CA

address: Pulmonary and Critical Care Medicine

country: USA

institute: Stanford University School of Medicine

summary: Performed a transcriptome analysis of patient-derived donor control and PAH lung pericytes followed by functional genomics analysis. Diseased pericytes demonstrated significant enrichment of genes involved in various metabolic processes

overall_design: Total RNA isolated from three IPAH pericytes vs. three Control donor pericytes

first: Ke

last: Yuan

first: Ning-Yi

last: Shao


title: Identification of Circulating Fibrocytes and Dendritic Derivatives in Corneal Endothelium of Patients with Fuchs' Dystrophy [RT-qPCR array CAPH10410]


title: Histone posttranslational modification ChIP-chip from Oikopleura dioica gonads

status: Public on Jan 26 2017

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

type: Genome binding/occupancy profiling by genome tiling array

summary: In multicellular organisms, histone posttranslational modifications plays roles in transitions associated with the cell cycle, development, germline specification, gametogenesis and inheritance. Here we defined adaptations of an epigenome in tunicates, sister group to vertebrates, to strong secondary genome compaction in the larvacean, Oikopleura dioica, that has separate sexes and male heterogamy. We profiled 19 histone post-translational modifications in homogeneous ovary and testis samples and used the combinatorics of these marks to define chromatin states. We supplemented these with profiles of RNA polymerase II, CTCF and p300 binding sites and integrated existing annotation and expression data to characterize distinct epigenomic landscapes of the ovary and testis.

overall_design: Comparison of chromatin landscapes of polyploid nurse nuclei and mitotic male germ line in early branching chordate

first: Pavla

last: Navratilova

first: Gemma

last: Danks

first: Abby

last: Long

first: John

last: Manak


title: Gal R regulates gene expression while arranging chromosome structure.

status: Public on Jan 25 2017

city: Bethesda

first: Andrei

middle: Nikolai

last: Trostel

state: Maryland

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

institute: National Institutes of Health

type: Expression profiling by genome tiling array

summary: To understand the altered gene expression in galR minus cells, the cells were grown in the absence of D-galactose and tiling array analysis was performed for transcriptome profiling.

overall_design: Total RNAs were isolated from Escherichia coli galR minus strain grown in the absence of D-galactose. The transcriptome profile of galR minus cells was figured out in relation to wild type.

first: Dale

last: Lewis

first: Zhong

last: Qian

first: Sang

last: Lee

first: Sankar

last: Adhya


title: Phenotypical and gene expression analyses of Rfo-sa1 resistant eggplant interaction with Fusarium oxysporum f. sp. melongenae and Verticillium dahliae

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Eggplant is susceptible to fungal wilts caused by Fusarium oxysporum f. sp. melongenae and Verticillium dahliae. Wild relatives represent a good source of resistance and ILs have been obtained through introgression of the Rfo-sa1 locus conferring resistance to Fusarium oxysporum from the allied species S. aethiopicum into cultivated eggplant. In this work, a deep phenotypical characterization was performed according to the progression of symptoms along the stem and the disease severity in leaves. This analysis showed that the Fom -resistant ILs carrying introgression of the Rfo-sa1 locus displayed significantly improved tolerance to Verticillium attack after a preliminary inoculation with F. oxysporum. This positive effect was particularly evident when Verticillium inoculation was done simultaneously or after the Fusarium one. Transcript profiling carried out using a combination of SSH, microarray and qRT-PCR analyses from inoculated roots with a selected combinations of fungal pathogens enabled the identification of 164? differentially expressed genes at least in one condition. Overall, our results highlighted a number of candidate genes putatively involved in early defence responses or signalling pathways activated upon infection of eggplant either with Fom  and Vd and thus leading to a broad Rfo-sa1 mediated tolerance against both these wilt pathogens.

overall_design: S. melongena roots mock inoculated, Fusarium oxysporum f. sp. Melongenae inoculated, Verticillium dahlie inoculated and inculated by both Fusarium and Verticillium have been collected in biological triplicate at 0, 4 and 8 hours post infection to evaluate expression levels with an array contructed from ESTs and RAD tags

first: Barbierato

last: Valeria

first: Toppino

last: Laura

first: Rinaldi

last: Paola

first: Sala

last: Tea

first: Valè

last: Gianpiero

first: Ferrarini

last: Alberto

first: Delledonne

last: Massimo

first: Bassolino

first: Bagnaresi

last: Paolo

first: Rotino

middle: G

last: Leonardo


title: Profiling of CD14+ monocytes from paired rheumatoid arthritis (RA)-patient peripheral blood and synovial fluid samples

status: Public on Jan 30 2017

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

summary: CD14+ monocytes sorted from the synovial fluid or peripheral blood of rheumatoid arthritis patients were analyzed by full transcriptome microarray analysis. Monocytes from healthy control samples (peripheral blood) were also profiled.

overall_design: A total of 26 samples consisting of 16 paired and 2 un-paired synovial fluid and peripheral blood derived CD14+ monocytes from RA-patients, as well as peripheral blood CD14+ monocytes from 8 healthy control subjects were compared. Sorted monocytes (at least of 95% purity) from each of the donors were obtained individually, and compared by full transcriptome profiling.

first: Klaus

middle: S

first: Leonie

last: Taams


title: Inflammatory signals linking inverse, erythrodermic and chronic plaque psoriasis

status: Public on Jan 27 2017

city: Ann Arbor

first: Andrew

last: Johnston

state: Michigan

address: 1301 East Catherine Street

department: Dermatology

institute: University of Michigan

summary: Inverse and erythrodermic psoriasis are rare subtypes of psoriasis.  Whereas the former is characterized by shiny erythematous non-scaly plaques in the body folds, the latter has widespread redness with fine scale, covering over 80% of the body-surface area, and can be life-threatening.  Both are considered to be clinical subtypes of chronic plaque psoriasis, and often co-exist or evolve from plaque psoriasis (Boyd and Menter, 1989; Omland and Gniadecki, 2015), but the pathogenic mechanisms involved are unknown, and current treatments are frequently unsatisfactory.  To assess shared and unique processes between chronic plaque, inverse, and erythrodermic psoriasis we analyzed archived formalin-fixed paraffin-embedded biopsies of clinically and histologically confirmed chronic plaque  (n=12), inverse (n=40) and erythrodermic psoriasis cases (n=30) and healthy control skin (n=20) using Affymetrix ST 2.1 Arrays.  Compared with healthy skin, psoriatic plaque lesions yielded 2450 differentially expressed genes (DEGs) (FDR, p<0.05), inverse psoriasis lesions yielded 408 DEGs (FDR, p<0.05) and erythrodermic psoriasis lesions yielded 447 DEGs (FDR, p<0.05).  In total 294 genes were found to be shared among the three disease subtypes (FDR, p<0.05).  While the overlap only accounted for 12% of the DEGs in chronic plaque psoriasis, it accounted for 66% and 72% of DEGs in erythrodermic and inverse psoriasis respectively.

overall_design: 20 normal healthy skin biopsies, 12 chronic plaque psoriasis, 40 inverse psoriasis, 30 erythrodermic psorasis

first: Johann

middle: E

last: Gudjonsson


title: Salmonella Typhimurium fimZ mutant

status: Public on Jan 20 2017

city: Taipei

first: Chang

last: Chieh-Hsiang

address: No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: National Taiwan University

summary: Salmonella enterica serovar Typhimurium produces type 1 fimbriae on the outer membrane and such hair-like appendages is proposed to play a significant role in the attachment of the bacteria to host cells and tissues. S. Typhimurium cultured in static broth favors expression of type 1 fimbriae. Conversely, solid agar medium represses type 1 fimbrial expression. Production of type 1 fimbriae is cooperatively regulated by fimZ, fimY, stm0551, fimW, and fimU within the fim gene cluster. FimZ belongs to the response regulator of the two-component regulatory system in bacteria and functions as a DNA binding protein. FimZ can bind to the promoter of the fimbrial major subunit gene fimA to activate its expression and produce type 1 fimbriae. A fimZ mutant in LB5010 strain constructed by allelic exchange was found to be non-fimbriate. Total RNA was extracted from the parental LB5010 and the fimZ mutant strain cultured in static broth and analyzed by hybridization to a S. Typhimurium LT2 DNA microarray. Transcriptomic analysis indicated that the stress response related gene cpxP, soxS and type 1 fimbriae related genes were down-regulated, whereas plasmid-encoded fimbriae, flagella associated genes and virulence genes like virK and mgtC were up-regulated in the fimZ mutant strain. It is possible that FimZ protein may play a role to interact with other genes besides fim genes. Mechanisms of this crosstalk warrant further elucidation.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: RNA transcript of Salmonella Typhimurium LB5010 strain comparing wild-type with fimZ mutant. Two-condition experiment, wild-type vs. fimZ mutant strain.

first: K

last: Yeh

first: C

last: Chang


title: Transcriptomic response in gilthead sea bream (Sparus aurata) liver exposed to gold nanoparticles

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Explore the underlying mechanisms-of-action after short-term (24 h) waterborne exposure to low (0.5 μg/L) and high (50 μg/L) gold nanoparticles (AuNP) concentrations in gilthead sea bream.

overall_design: Transcriptomic analysis was conducted in S. aurata livers exposed to 0, 0.5 or 50 μg/L AuNP for 24 h (n=9 per condition: N total=27 fish) in order to determine the differences on gene expression level between these two concentrations at systemic level. The experimental design included three conditions: (1) non-exposed fish (control); (2) fish exposed to 0.5 μg/L AuNP; (3) fish exposed to 50 μg/L AuNP. Total RNA were extracted invidually and then total RNA samples were grouped into 3 pools of 3 fish for each condition (non-treated fish, 0.5 μg/L, 50 μg/L). The transcriptomic analysis was done following a reference design using the control as reference group.

first: Mariana

last: Teles

first: Lluis

last: Tort


title: Expression analysis of bleomycin induced pulmonary fibrosis mouse model lung tissues

city: Beijing

first: xiaoxi

last: lv

address: No Jia2, Nanwei road, Xi Cheng district

country: China

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Investigation of whole genome gene expression level changes in Bleomycin induced pulmonary fibrosis mouse model lung tissue, compared to the Sham group.

overall_design: Male C57 BL/6 mice (18 g, 6-8 wk) were earmarked before grouping and then were randomly separated into groups by an independent person. To generate mouse models of pulmonary fibrosis, mice were anesthetized with 50 mg/kg pentobarbital i.p. (Merk). Using an insulin syringe, 0.050 ml LPS-free saline clinical grade Bleomycin (Nippon Kayaku) (3.0 U/kg) was directly injected into the trachea. Sham group mice received H2O by the same surgery procedure. Lung tissues were obtained at 21 day after bleomycin injured. RNA samples were obtained from 6 Sham group mice lung tissues and 6 Bleomycin instilled mice lung tissues. Each sample was measured the expression level of 44,170 genes.

first: Xiao-xi

last: Lv

first: Shan-shan

last: Liu


title: Disomes and Disomes lcb3∆ vs. wild-type

city: worcester

first: Eduardo

middle: M

last: Torres

state: MA

address: 364 Plantation Street, LRB-523

department: Department of Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: Transcriptional profiling of aneuploid yeast strains grown in rich medium YEPD

overall_design: Cells were grown in YEPD at 30 degrees


title: Comparative transcriptomic analysis of the roots of intercropped maize by microarray

city: Bejing

first: Jing

last: Dai

address: No.2 Yuanmingyuan West Road, Haidian District

institute: College of Resources & Environmental Sciences, China Agricultural University

summary:
Intercropping is a vital technology in resource-limited agricultural systems with low inputs. Peanut/maize intercropping enhances iron (Fe) nutrition in calcareous soil. Proteomic studies of the differences in peanut leaves, maize leaves and maize roots between intercropping and monocropping systems indicated that peanut/maize intercropping not only improves Fe availability in the rhizosphere but also influences the levels of proteins related to carbon and nitrogen metabolism. Moreover, intercropping may enhance stress resistance in the peanut plant (Xiong et al. 2013b). Although the mechanism and molecular ecological significance of peanut/maize intercropping have been investigated, little is known about the genes and/or gene products in peanut and maize roots that mediate the benefits of intercropping. In the present study, we investigated the transcriptomes of maize roots grown in intercropping and monocropping systems by microarray analysis. The results enabled exploration differentially expressed genes in intercropped maize.
Peanut (Arachis hypogaea L. cv. Luhua14) and maize (Zea mays L. cv. Nongda108) seeds were grown in calcareous sandy soil in a greenhouse. The soil was enhanced with basal fertilizers [composition (mg·kg−1 soil): N, 100 (Ca (NO3)2·4H2O); P, 150 (KH2PO4); K, 100 (KCl); Mg, 50 (MgSO4·7H2O); Cu, 5 (CuSO4·5H2O); and Zn, 5 (ZnSO4·7H2O)]. The experiment consisted of three cropping treatments: peanut monocropping, maize monocropping and intercropping of peanut and maize. After germination of peanut for 10 days, maize was sown. Maize samples were harvested after 63 days of growth of peanut plants based on the degree of Fe chlorosis in the leaves of monocropped peanut. The leaves of monocropped peanut plants exhibited symptoms of Fe-deficiency chlorosis at 63 days, while the leaves of peanut plants intercropped with maize maintained a green color.

overall_design: This Series represents monocropped maize and intercropped maize

first: Wei

last: Qiu

first: Nanqi

last: Wang

first: Penggen

last: Duan

first: Tianjiao

last: Zhang

first: Yuanmei

last: Zuo


title: Mouse male and female astrocytoma cells stably transfected with shRNA targeting Cdca7l

city: Frederick

first: Karlyne

last: Reilly

state: MD

address: West 7th St at Fort Detrick, PO Box B

department: Mouse Cancer Genetics Program

institute: National Cancer Institute, Center for Cancer Research

summary: Cdca7l is expressed higher in male astrocytoma/GBM than female tumors or normal cells, and knockdown of Cdca7l blocks growth of male tumor cells, but not female tumor cells. We stably depleted Cdca7l in mouse astrocytoma cells and compared gene expression to control astrocytoma cells expressing non-targeting scrambled shRNA in male and female cells and to wild type primary astrocytes to identify gene expression differences between male and female cells and between Cdca7l-depleted, scrambled shRNA control cells and wild type primary astrocytes.

overall_design: Independent established cell lines taken from mouse male and female C57BL/6J (B6) mice with astrocytoma were stably transfected with either shRNA targeting Cdca7l or non-targeting scrambled shRNA control. For astrocytoma cells, two independent mouse male astrocytoma cell lines and two independent mouse female astrocytoma cell lines were used: male K4820 astrocytoma cells, male K1861 astrocytoma cells, female K2797 astrocytoma cells, and female K5001 astrocytoma cells (2 technical replicates per each cell line except for K5001). For astrocytes, 3 biological replicates were used for each of 2 groups: C57BL/6J (B6) male astrocytes, C57BL/6J (B6) female astrocytes.

first: Min-Hyung

last: Lee


title: Localization of TAP-proteins in wild-type and tagging yeast

status: Public on Jan 16 2017

city: concepcion

first: matias

middle: ignacio

last: hepp

state: biobio

address: barrio universitario s/n, casilla 160-C

department: bioquimica y biologia molecular

institute: universidad de concepcion

summary: ChIP-chip assays to determine the localization of TAP-protein in wild-type and tagging yeast.

overall_design: Two color experiment. ChIP/Input. Biological replicates=3.

first: Matias

middle: I

last: Hepp

first: Jerry

middle: L

last: Workman

first: Jose

last: Gutierrez


title: Transcriptomic evaluation of bovine granulosa obtained from peri-pubertal oocyte donors

status: Public on Jan 18 2017

city: Quebec

first: David

middle: André

last: Landry

state: Quebec

address: 2440 boul. Hochelaga

department: Animal Science

country: Canada

institute: University Laval

summary: The objective of this study is to investigate the transcriptomic signature of granulosa cells within the same animal at different age after ET program. To explore whether follicle differences are associated with age, we individually compared the effect of ovarian stimulation within the same animal at 8 and 11 months of age (peripubertal stage) and at 14 months of age (post-puberty). Overall, peripubertal donors are showing less differentiation, inflammation and apoptosis signaling which could be associated with lower basal concentration of LH.

overall_design: 10 young Holstein cows were used 3 times each at different ages for ovarian stimulation protocols and oocyte collections (at 8, 11 and 14 months). These oocytes were then fertilized in vitro with adult bull semen, generating 3 lots of embryos per animal. Semen from the same bull was used for all females, at all times. Each animal was used as its own control for age-effect evaluation. EmbryoGENE plateform allowed whole genome assessment of gene expression patterns at the blastocyst stage. Embryos from animals at 8 vs 14 months and at 11 vs 14 months were used for microarray hybridization. Validation was done performing RT-qPCR tests on 7 candidate genes.

middle: A

first: Anne-Marie

last: Bellefleur

first: Rémi

last: Labrecque

first: François-Xavier

last: Grand

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Marc-André

last: Sirard


title: Expression and methylation array analysis of CD19+ B-cells from Chronic lymhocytic leukemia (CLL) patients and age matched healthy donor samples [Methylation]

status: Public on Jan 23 2017

city: Heidelberg

first: Katharina

last: Filarsky

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center

type: Methylation profiling by genome tiling array

summary: Whole genome sequencing revealed CLL as a disease of the genome and epigenome defined by somatic mutations and aberrant DNA-methylation. To uncover the impact of aberrant methylation on transcription, gene expression and methylation array profiling was performed in CLL and B-cells.  DNA from 13 CLL patients and 6 healthy donor samples was analyzed using MCIp-array. Custom made agilent promoter-arrays were used for analysis.

overall_design:
Methyl-CpG-Immunoprecipitation (MCIp) was performed with genomic DNA from CD19+ sorted CLL cells and B-cells from chronic lymphocytic leukemia patients and healthy donors, respecitvely. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by density centrifugation using Biocoll. CD19+ PBMCs were purified using CD19 Micro Beads for magnetic positive selection.
Genomic DNA was isolated using DNA/RNA allprep Kit (Qiagen) and applied to MCIp. High salt fractions were used for array hybridization.

first: Angela

last: Garding

first: Manuela

last: Zucknick

first: Natalia

last: Becker


title: Time-course differential lncRNA and mRNA expressions in radioresistant hypopharyngeal cancer cells

status: Public on Jan 21 2017

city: Jinan

first: shengda

last: cao

state: Shandong Province

address: wenhua west road

department: ENT

institute: Qilu hospital

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

summary: Through measuring expression levels of lncRNAs/mRNAs in RS-FaDu vs. FaDu cells at 0, 24 and 48 h after 4 Gy radiation, we identified a number of lncRNAs/mRNAs with dysregulation. And the microarray data were verified by qRT-PCR assays. By informatics analyses, we predicted pathways, which were potentially associated with radioresistance of hypopharyngeal carcinoma.

overall_design: The radioresistant hypopharyngeal carcinoma cell line (RS-FaDu) was estabished from its parental human hypopharyngeal carcinoma cell line (FaDu) by multi-fractioned radiation. Time-course differential lncRNA and mRNA expression profiles in RS-FaDu vs. FaDu cells were detected by microarray approach, at 0, 2, 48 h after 4 Gy radiation.

first: Dapeng

last: Lei


title: Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues

first: Meghali

last: Goswami

address: 10 Center Drive

department: Hematology

institute: NHLBI

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

overall_design: Refer to individual Series


title: Expression of putative leukemia-associated antigens in healthy human tissues

summary: We analyzed using quantitative real-time PCR (qRT-PCR), gene expression of 65 potential leukemia associated antigens in 12 healthy human tissue types

overall_design: qPCR gene expression profiling

first: Christopher

last: Hourigan


title: miR expression differences in Chronic lymphocytic leukemia patients after ibrutinib therapy

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

summary:
miRs were discovered to be significantly differentially regulated after ibrutinib therapy
Peripheral blood CLL cell samples at pre-treatment, after 2hrs, 24hrs, 8 days, 29 days after threapy were collected and RNA was collected and used for miR nanostring analysis.

overall_design: Samples from 8 patients at each time point were pooled into 2 groups (4 patients per group) to discover miR expression differences.

first: Amy

last: Johnson


title: miRNA profiles of 50 HB tumors

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

summary: Hepatoblastoma (HB) is the most common liver cancer in children, but few pre-treatment tumors have been molecularly profiled. Consequently, there are no validated prognostic or therapeutic biomarkers for HB patients. We report on molecular analysis of 88 clinically-annotated HB tumors. This analysis pointed to three risk-stratifying molecular subtypes—low, intermediate and high risk—that are characterized by differential activation of hepatic progenitor cell markers and metabolic pathways. High-risk tumors are characterized by high NFE2L2 activity and LIN28B, HMGA2, SALL4 and AFP expression, low let-7 expression and HNF1A activity, and high coordinated expression of oncofetal proteins and stem cell markers. Tests on a 35 HB validation set supported these genes as prognostic biomarkers.

overall_design: 88 clinically-annotated frozen pre-clinical HB specimens with corresponding surgical pathology reports were included in the study (Table S1) following histological review. Specimens and clinical annotation were obtained from the COG Tumor Biospecimen Bank in Columbus, Ohio, the Pediatric Oncology Group Hepatoblastoma Biology Study P9346, and Texas-based institutions, under IRB-approved protocols. Whole exome sequencing (WES) was performed on 35 tumors for which matching normal DNA – either a blood sample or tumor-adjacent normal liver – was available (Table S2). Targeted sequencing of the CTNNB1 and NFE2L2 genes and the TERT promoter was completed on all 88 tumors. DNA from 47 HBs, including all 35 samples subjected to WES, was also analyzed by SNP array. RNA and miRNA expression profiling were performed on 50 and 57 tumors, respectively.

first: Pavel

last: Sumazin

first: Yidong

last: Chen

first: Lisa

middle: R

last: Treviño

first: Stephen

middle: F

last: Sarabia

first: Oliver

last: Hampton

first: Kayuri

last: Patel

first: Barry

last: Zorman

last: Thompson

first: Andras

last: Heczey

first: Sarah

last: Comerford

first: David

last: Wheeler

first: Murali

last: Chintagumpala

first: Rebecka

last: Meyers

first: Dinesh

last: Rakheja

first: Milton

last: Finegold

first: Gail

last: Tomlinson

first: D

middle: W

last: Parsons

first: Dolores

last: López-Terrada


title: Localization of Snf5 in wild-type and knockout yeast

first: matias

last: hepp

summary: ChIP-chip assays to determine the localization of Snf5 in wild-type and knockout yeast.

first: Matias

last: Hepp

first: Jerry

last: Workman

first: Jose

last: Gutierrez


title: Expression profiling of grass-clump dwarf in syntheitic hexaploids from triploid hybrids crossed between tetraploid wheat and Aegilops umbellulata.

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

country: Japan

institute: Kobe University

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in a grass-clump dwarf line, which is a synthetic hexaploid line from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon) and a diploid wheat relative Aegilops umbellulata (KU-4052). Up-regulation of metabolic and catabolic processes-related genes for cell wall-associated molecules was observed, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf line.
Unusual expression of the branching-related SPLs and flowering time regulation-related MADS-box genes could explain the grass-clump dwarf phenotype.

overall_design: Expression patterns were compared between the two synthetic hexaploid lines showing the wild-type phenotype (as a reference) and grass-clump dwarf. Total RNA samples were isolated from crown tissues of the plants grown at 24°C under long day (18-h light and 6-h dark) condition for 50 days. Two independent experiments were conducted in each exprement.

first: Moeko

last: Okada


title: Fathead minnow liver samples: control, EE2 and EE2/zm

status: Public on Jan 17 2017

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Transcriptional profiling of fathead minnow liver exposed either to the estrogen EE2 or a mixture of EE2 and the anti-estrogen ZM.

overall_design: Three condition experiment: Control, EE2 or the mixture EE2/ZM; liver tissue; four biological replicates.

first: Natàlia

last: Garcia-Reyero

first: Sumith

last: Jayasinghe

first: Kevin

last: Kroll

first: Tara

last: Sabo-Attwood

first: Nancy

middle: D

last: Denslow


title: Cell fate and adhesion dynamics rely on Ror2-mediated alternative Wnt signaling during tumor progression

first: Jeffrey

last: Rosen

address: One Baylor Plaza M638

department: Department of Molecular and Cellular Biology

summary: Cellular heterogeneity in breast cancer encompasses many features, yet an understanding of the coexistence and regulation of various tumor cell subpopulations remains a significant challenge in cancer biology.  In the current study, we approached tumor cell heterogeneity from the perspective of Wnt pathway biology to address how different modes of Wnt signaling shape the behaviors of diverse cell populations within a heterogeneous tumor landscape.  Using a syngeneic TP53 null mouse model of breast cancer, we identified distinctions in the topology of canonical Wnt b-catenin dependent signaling activity and noncanonical b-catenin independent Ror2-mediated Wnt signaling across subtypes and within tumor cell subpopulations in vivo.  We further discovered an antagonistic role for Ror2 in regulating canonical Wnt/b-catenin activity in vivo, where lentiviral shRNA depletion of Ror2 expression augmented canonical Wnt/b-catenin signaling activity across multiple basal-like models.  Depletion of Ror2 expression yielded distinct phenotypic outcomes and divergent alterations in gene expression programs among different tumors, despite all sharing basal-like features.  Notably, we uncovered cell state plasticity and adhesion dynamics regulated by Ror2, where Ras Homology Family Member A (RhoA) and Rho-Associated Coiled-Coil Kinase 1 (ROCK1) activity downstream of Dishevelled-2 (Dvl2) were implicated.  Collectively, these studies illustrate the integration and collaboration of Wnt pathways in basal-like breast cancer, where Ror2 provides a spatiotemporal function to regulate the balance of Wnt signaling and cellular heterogeneity during tumor progression.

overall_design: Total RNA from murine p53null mammary tumors was hybridized to agilent microarrays for gene expression analysis

last: Roarty

first: Adam

last: Pfefferle

first: Chad

last: Creighton

first: Charles

last: Perou


title: Identification of microRNA profile specific to Cancer Stem-Like Cells directly isolated from Human Larynx Cancer Specimens (Agilent-053955)

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

summary: Our results showed that certain miRNAs in CD133high cells could be used as cancer stem cell markers. Based on these results, we propose that this panel of miRNAs might carry crucial roles in LCa initiation, progression, metastasis, chemoresistance and recurrence through regulating stem cell properties of tumor cells.

overall_design: In this study, we investigated genome-wide miRNA expression profile of laryngeal CSLCs enriched for CD133 surface marker to identify a CSLCs specific miRNA signature. Two group comparison.

first: Michael

last: Ittmann

first: Mustafa

last: Ozen

first: Yiqun

last: Zhang


title: Expression profiling of soleus muscle under the effect of simulated spaceflight

city: Gwangju

first: Kim Ngan

last: Tran

address: 77, Yongbong-ro, Buk-gu

department: Bioenergy and Biomaterials

country: South Korea

institute: Chonnam National University, College of Engineering

summary:
Spaceflight imposes the risk of skeletal muscle atrophy for astronauts. The understanding of muscle atrophy because of spaceflight is limited, but continued efforts are essential for developing countermeasures of this effect.
A distinct difference between spaceflight-induced muscle atrophy and other forms of atrophy is the additional effect of cosmic rays in outer space. To study spaceflight-induced muscle atrophy, we performed two ground-based models of microgravity in a low dose radiation environment and studied transcriptional changes in rat soleus muscle using microarray technology.

overall_design: Rats (Rattus norvegicus) were divided into the following groups consisting of six rats each and were treated accordingly: 1) Group Ct (continuous irradiation for 2 weeks with a total absorbed dose of 50 mSv); 2) Group TS (tail suspension, and irradiation as in group Ct ); and 3) Group DN (denervation, and irradiation as in group Ct). Rats were anesthetized and their soleus muscles were isolated. Total RNA was isolated from individual frozen tissue and RNA pools were prepared for each group. Gene expression profiling were done using two GeneChip@ Rat Gene 1.0 ST arrays.

first: Jong-il

last: Choi


title: Role of Hmo1 and Nhp6 in SWI/SNF occupancy and nucleosome landscape at gene regulatory regions

first: matias

last: hepp


title: Hypoxia-inducible factor 3 is an oxygen-dependent transcription activator and regulates a distinct transcriptional response to hypoxia

status: Public on Jan 13 2017

first: Peng

state: MI

address: 830 N. University Ave.

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

summary: This study aimed to identify Hif-1 and -3 regulated genes in zebrafish embryos. RNA samples were prepared from embryos injected with GFP, Hif-1α, and Hif-3α mRNA. The RNA samples were subjected to DNA microarray analysis using the Agilent 4×44 K (V3) Zebrafish Microarray Chip.

overall_design: Three biological replicates were collected from three independent microinjection experiments. Each RNA sample was extracted from a pool of 60 embryos and labeled with Cy3-CTP. Slides were scanned by the Agilent DNA Microarray Scanner, read by Feature Extraction software 10.7 and normalized by Gene Spring Software 11.0.

first: Cunming

last: Duan


title: Host-Microbial interactions in Idiopathic Pulmonary Fibrosis

status: Public on Jan 14 2017

city: London

first: Philip

last: Molyneaux

address: Dovehouse Street

country: United Kingdom

institute: Imperial College London

summary:
Changes in the respiratory microbiome are associated with disease progression in Idiopathic pulmonary fibrosis (IPF). The role of the host response to the respiratory microbiome however remains unknown. The role of this study is to explore the host-microbial interaction in IPF. Network analysis of gene expression data identified two gene modules that strongly associate with a diagnosis of IPF, BAL bacterial burden (determined by 16S quantitative PCR) and specific microbial OTUs, as well as lavage and peripheral blood neutrophilia. Genes within these modules that are involved in the host defence response include NLRC4, PGLYRP1, MMP9, DEFA4. The modules also contain two genes encoding specific antimicrobial peptides (SLPI and CAMP). Many of these particular transcripts were associated with survival and showed longitudinal over expression in subjects experiencing disease progression, further strengthening their relationship with disease. Integrated analysis of the host transcriptome and microbial signatures demonstrates an apparent host response to the presence of an altered or more abundant microbiome. These responses remain elevated on longitudinal follow up, suggesting that the bacterial communities of the lower airways may be acting as persistent stimuli for repetitive alveolar injury in IPF.
Sixty patients diagnosed with IPF were prospectively enrolled, together with 20 matched controls. Subjects underwent bronchoalveolar lavage (BAL) and peripheral whole blood was collected into PAXgene tubes for all subjects at baseline. For IPF subjects additional samples were taken at 1, 3, and 6 months and (if alive) a year. Gene expression profiles were generated using Affymetrix Human Gene1.1ST Arrays.

overall_design: Survival=Months from Recruitment to composite end point or censoring; Age=Age in years at recruitment; FVC= Percent predicted Forced Vital Capacity; DLCO=Percent predicted Diffusing capacity of the lungs for carbon monoxide; Composite_End_Point=Death or decline in FVC >10% over a six month period, 1=Event, 2=No event.

first: P

first: W

middle: O

last: Cookson

first: M

last: Moffatt

first: T

last: Maher


title: CircRNA expression profiles for 6 human plasma samples derived from patients with gastric cancer

city: Ningbo

first: Junming

last: Guo

address: Jiangbei District Fenghua Road No. 818

institute: Ningbo University School of Medicine

summary: Investigation of circRNA expression profile of gastric cancer

overall_design: A six chip study using total RNA extracted from three plasma samples of gastric cancer patients and three healthy controls


title: mRNA expression during fracture healing in diabetic rats

status: Public on Jan 15 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The association between DM and impaired fracture healing including delayed union and nonunion has been documented in clinical and experimental settings. We examine mRNA expression specific for impaired fracture healing in diabetic rat.

overall_design: 12w, male, Sprague–Dawley rats were divided into two groups. As a model for impaired fracture-repairing ability, diabetic rats were created by a single intravenous injection of 40 mg/kg streptozotocin. Control rats were injected with sodium chloride as a sham treatment. Closed transverse femoral shaft fractures were created in both groups. Briefly, a 1.25-mm diameter K-wire was inserted retrograde into the right femoral intramedullary canal and a closed transverse femoral shaft fracture was produced using a three-point bending apparatus with a drop weight. Five animals from each group were euthanized at post-fracture days 5 and 11 respectively for microarray analysis. At the each time points, the newly generated specific tissues, that is, the fracture callus, were harvested.

first: Shunsuke

last: Takahara

first: Sang

middle: Y

last: Lee

first: Takahiro

last: Niikura

first: Takashi

last: Iwakura

last: Waki

first: Michio

last: Arakura

first: Ryosuke

last: Kuroda

first: Masahiro

last: Kurosaka


title: EZH2 inhibition in multiple myeloma downregulates myeloma associated oncogenes and upregulates microRNAs with potential tumor suppressor functions [mRNA expression]

status: Public on Jan 10 2017

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

summary: Multiple Myeloma (MM) is a plasma cell tumor localized to the bone marrow (BM). Despite current progress in improving patient outcome, MM remains largely incurable. Disease clonal and interpatient heterogeneity has hampered identification of a common underlying mechanism for disease establishment and have slowed the development of novel targeted therapies. Epigenetic aberrations are now emerging as increasingly important in tumorigenesis, thus selective targeting of crucial epigenetic enzymes may provide new therapeutic potential in cancer including MM. Recently, we and others suggested the histone methyltransferase enhancer of zeste homolog 2 (EZH2), to be a potential therapeutic target in MM. Now we show that pharmacological inhibition of EZH2 suppresses the MM cell growth through downregulation of MM-associated oncogenes; IRF-4, XBP-1, PRDM1/BLIMP-1and c-MYC. We also show that downregulation of these genes is mediated via reactivated expression of microRNAs with tumor suppressor functions; primarily miR125a-3p and miR320c. Using chromatin immunoprecipitation (ChIP) we demonstrate that miR125a-3p and miR320c are targets of EZH2 and H3K27me3 in MM cell lines and primary MM cells. Our results further highlight the importance of polycomb-mediated silencing in MM to include microRNAs with tumor suppressor activity. This novel role further strengthens the oncogenic features of EZH2 and its potential as a therapeutic target in MM.

overall_design: 6 samples (3 biological replicates) were used in this analysis. The pairwise comparision of Inactive drug (UNC2400) wth the active drug (UNC1999) was made for each biological replicate.The anti-myeloma effects exerted by EZH2 inhibition was investigated using UNC1999, small specific inhibitor of EZH2, at 120 hours post-treament by analyzing global changes in mRNA and miRNA expression

first: Mohammad

last: Alzrigat


title: Human induced pluripotent stem cell-derived macrophages share ontogeny with MYB-independent tissue-resident macrophages

status: Public on Jan 07 2017

city: Oxford

first: Julian

last: Buchrieser

address: South Parks Road

department: Dunn School of Pathology

institute: Oxford University

summary: Tissue-resident macrophages such as microglia, Kupffer and Langerhans cells derive from Myb-independent yolk sac (YS) progenitors generated before the emergence of hematopoietic stem cells (HSCs). Myb-independent YS-derived resident macrophages self-renew locally, independently of circulating monocytes and HSCs. In contrast, adult blood monocytes as well as infiltrating, gut and dermal macrophages derive from Myb-dependent HSCs. These findings are derived from the mouse, using gene knock-outs and lineage tracing, but their applicability to human development has not been formally demonstrated. Here we use human induced pluripotent stem cells (iPSCs) as a tool to model human hematopoietic development. By using a CRISPR-Cas9 knock-out strategy we show that human iPSC-derived monocytes/macrophages develop in a MYB-independent, RUNX1 and SPI1 (PU.1)-dependent fashion. This result makes human iPSC-derived macrophages developmentally related to and a good model for MYB-independent tissue-resident macrophages such as alveolar and kidney macrophages, microglia, Kupffer and Langerhans cells.

overall_design: The human hiPSC-AH016-3 has been used for all CRISPR-Cas9 mediated gene targeting in this study. iPSC-AH016-3 has been targeted using a double nicking CRISPR-Cas9 strategy for the knock-out of MYB, SPI1 and RUNX1. Seven lines were generated: a WT control line which underwent CRISPR-Cas9 transfection and single cell cloning but is unmodified, 3 MYB double allele knock-outs, a MYB single allele knock-out, a SPI1 double allele knock-out and a RUNX1 double allele knock-out. SNP datasets were generated from knock-out and control lines. Note that the parental line AH016 clone 3 used as the target line in this current study, has been published previously therefore datasets are not given here [GSM2055806. Sandor C RP, Lang C, Heger A, Booth H, Vowles J, Witty L, Bowden R, Hu M, Cowley SA, Wade-Martins R, Webber C (2017) Transcriptomic profiling of purified patient-derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson’s disease. Human Molecular Genetics.]

first: William

last: James

first: Michael

last: Moore


title: Design and validation of microarray for chickpea (Cicer arietinum) based on the analysis of transcriptome data [gene expression]

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Microarrays have increasingly become a powerful tool for high throughput gene-expression studies and discovery of novel biomarker genes. Developed for a large number of organisms, including plants, microarrays are commonly performed for species that have sequenced data, for performing gene expression analysis, miRNA profiling, comparative genomic hybridization (CGH), ChIP-on-chip and SNP analysis. Genomic resources are still very limited for chickpea, a very important food legume crop. Here, we report the design and comprehensive validation of Next Generation Sequencing transcriptome data for chickpea through microarray technology to develop a high-throughput resource for studying the expression of all the transcripts in different biological samples to help functional genomics and breeding programs. This microarray design was developed and validated jointly by Genotypic Technology Private Limited and National Institute of Plant Genome Research. First, we designed 400k probes using reads covering 35k assembled contigs and 100k singletons chickpea transcripts. The 400k chip was hybridized with DNA and RNA samples of chickpea and microarray analysis was carried out. A total of 73,922 probes were found to be specific to chickpea transcripts. Best probes were filtered from the analyzed data and a total of 61,659 probes were selected to develop the final microarray design in 60k gene-expression microarray format. The probes represented 51,444 unique transcripts. The probes were annotated based on their corresponding chickpea transcript and similarity with other plants species. Microarray results were concordant with previous results from the NGS studies. The design of custom oligonucleotide probes for microarrays have varied functional genomic applications and this approach represents a valuable resource for chickpea.

overall_design: Organism: Chickpea (Cicer arietinum) Custom Agilent 2x 400k Microarray (AMADID: 35301) designed by Genotypic Technology Pvt.Ltd.

first: Rohini

last: Garg

first: Vikash

middle: K

last: Singh

first: Mukesh

last: Jain

first: Raja

last: Mugasimangalam

first: Sudha

middle: N

last: Rao

first: Aiyaz

last: Mohamed

first: Deepti

last: Saini


title: Design and validation of microarray for chickpea (Cicer arietinum) based on the analysis of transcriptome data [CGH]


title: Design and validation of microarray for chickpea (Cicer arietinum) based on the analysis of transcriptome data

type:
Genome variation profiling by array
Expression profiling by array

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


title: Removable insulator facilitates higher-order chromatin remodeling and selective gene expression in the HOXA locus via the retinoic acid signaling [ChIP-chip]

city: Kumamoto

first: Ko

last: Ishihara

address: 2-2-1 Honjyo

department: Priority Organization for Innovation and Excellence

institute: Kumamoto University

summary: Chromatin insulators partition the genome into the functional units to control gene expression especially in complex chromosomal regions. The CCCTC-binding factor (CTCF) is an insulator-binding protein which functions for transcriptional regulation and higher-order chromatin formation. Here we report that a removable CTCF insulator is responsible for the retinoic acid (RA)-mediated higher-order chromatin remodeling and selective gene expression in the human HOXA gene locus. Our detailed chromatin analyses characterized multiple CTCF-enriched sites and RA-responsive enhancers in this locus. These regulatory elements and transcriptionally silent HOXA genes were closely positioned under the basal condition. Notably, upon the RA signaling, the transcription factor RAR/RXR induced the loss of an adjacent CTCF binding and changed the higher-order chromatin conformation of the overall locus, establishing transcriptionally active, poised and repressive domains that were separated by stably localizing CTCF insulators. This study uncovers that removable insulator spatiotemporally switches higher-order chromatin and multiple gene activities at the chromosomal domain levels, via the cooperation of CTCF and key transcription factors.

overall_design: In total 4 samples; 2 input samples with the corresponding ChIP-chip samples.

first: Mitsuyoshi

last: Nakao


title: Genomic DNA of Plasmodium falciparum from field isolates

status: Public on Jan 06 2017

summary:
Comaprision of P.falciparum clinical isolates showing Uncomplicated disease with that shwoing complicated disease(Cerebral malaria)
The experiment was designed to try and identify differences if any, at the genome level between P.falciparum isolates from patients with uncomplicated malaria vs. patients with complicated malaria (Cerebral malaria). The emphasis was to highlight possible amplifications/deletions in different regions of the parasite genome.

overall_design: Agilent two-color  experiment, Custom Plasmodium falciparum 3D7 2x400K CGH microarray (AMADID: G4124A_025327) designed on Agilent platform by Genotypic Technology, Bengaluru

first: Ashis

last: Das

first: Dhanpat

last: Kochar

first: Sanjay

middle: C


title: Disclosing the Molecular Basis of the Postharvest Life of Berry in Different Grapevine Genotypes

status: Public on Jan 09 2017

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

institute: University of Verona

summary: The molecular events that characterize postripening grapevine berries have rarely been investigated and are poorly defined. In particular, a detailed definition of changes occurring during the postharvest dehydration, a process undertaken to make some particularly special wine styles, would be of great interest for both winemakers and plant biologists. We report an exhaustive survey of transcriptomic and metabolomic responses in berries representing six grapevine genotypes subjected to postharvest dehydration under identical controlled conditions. The modulation of phenylpropanoid metabolism clearly distinguished the behavior of genotypes, with stilbene accumulation as the major metabolic event, although the transient accumulation/depletion of anthocyanins and flavonols was the prevalent variation in genotypes that do not accumulate stilbenes. The modulation of genes related to phenylpropanoid/stilbene metabolism highlighted the distinct metabolomic plasticity of genotypes, allowing for the identification of candidate structural and regulatory genes. In addition to genotype-specific responses, a core set of genes was consistently modulated in all genotypes, representing the common features of berries undergoing dehydration and/or commencing senescence. This included genes controlling ethylene and auxin metabolism as well as genes involved in oxidative and osmotic stress, defense responses, anaerobic respiration, and cell wall and carbohydrate metabolism. Several transcription factors were identified that may control these shared processes in the postharvest berry. Changes representing both common and genotype-specific responses to postharvest conditions shed light on the cellular processes taking place in harvested berries stored under dehydrating conditions for several months.

overall_design: Corvina, Sangiovese, Merlot, Oseleta, Syrah and Cabernet Sauvignon berries were collected at full maturity, that was considered the first time point of our experiment (T0, namely time zero of the post-harvest withering process). Syrah and Merlot reached this stage two weeks before the other cultivars. Detached berries were stored under identical controlled environmental conditions until they all reached ~30% weight loss. However, the six cultivars dehydration kinetics greatly differed among each other; the drying process was indeed stopped after ~50 days for Oseleta, Shiraz and Cabernet Sauvignon, after ~70 days for Merlot and after 100 days for Sangiovese and Corvina. In order to monitor the complete dehydration process, berry samples were collected at four time points during the shortest postharvest drying of Oseleta, Shiraz and Cabernet Sauvignon (4 time ponts x 3 biological replicates, namely 12 samples each), at five time points for Merlot (5 time points x 3 biological replicates = 15 samples), and at six time points for the longest drying of Sangiovese and Corvina (6 time points x 3 biological replicates, namely 18 samples each). In total, this work entailed the metabolomic and transcriptomic analysis of 87 samples.

first: Sara

last: Zenoni

first: Flavia

last: Guzzo

first: Silvia

last: Dal Santo

first: Alessandra

last: Amato

first: Andrea

last: Anesi

first: Mauro

last: Commisso

first: Herderich

last: Markus

first: Stefania

last: Ceoldo

first: Linda

last: Avesani

first: Mario

last: Pezzotti

first: Giovanni Battista

last: Tornielli


title: Effect of UV radiation on psoriatic keratinocytes in vitro

status: Public on Jan 12 2017

city: Linköping

first: Charlotta

last: Enerbäck

address: Faculty of Medicine and Health Sciences

department: Ingrid Asp Psoriasis Research Center

institute: Linköping University

summary: The aim of the study was to investigate the apoptotic process in psoriatic keratinocytes. UV radiation was used as apoptosis stimuli. Restults provide insights into the role of UV radiation and apoptosis induction on cultured psoriatic keratinocytes compared to healthy controls.

overall_design: We used microarray to analyze differences in gene expression between UV/Non-UV exposed psoriatic (involved and uninvolved) and control keratinocytes. Keratinocytes were established from skin from two patients and two healthy control individuals for the microarray analysis.

first: Cecilia

middle: B

last: Eding


title: The microbial functional gene diversity in anaerobic digesters under different organic loadings

city: BEIJING

first: LINWEI

last: WU

address: NO.1 TSGINAHU UNIVERSITY

institute: TSINGHUA UNIVERSITY

summary: Anaerobic digestion is a popular and effective microbial process for waste treatment. The performance of anaerobic digestion processes is contingent on the balance of the microbial food web in utilizing various substrates. Recently, co-digestion, i.e., supplementing the primary substrate with an organic-rich co-substrate has been exploited to improve waste treatment efficiency. Yet the potential effects of elevated organic loading on microbial functional gene community remains elusive. In this study, functional gene array (GeoChip 5.0) was used to assess the response of microbial community to the addition of poultry waste in anaerobic digesters treating dairy manure. Consistent with 16S rRNA gene sequences data, GeoChip data showed that microbial community compositions were significantly shifted in favor of copiotrophic populations by co-digestion, as taxa with higher rRNA gene copy number such as Bacilli were enriched. The acetoclastic methanogen Methanosarcina was also enriched, while Methanosaeta was unaltered but more abundant than Methanosarcina throughout the study period. The microbial functional diversity involved in anaerobic digestion were also increased under co-digestion.

overall_design: There were two sets of anaerobic digesters. Three control digesters were fed with dairy manure and the organic loading rate kept constant. The  three treatment digesters were  fed with poultry waste in addition to dairy manure, resulting in step-wise increase in the organic loading rate. Sludge samples were taken at different time points from the six digesters.

first: Yunfeng

last: Yang

first: Linwei

last: Wu


title: Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue

city: Philadelphia

first: Anna

last: King

state: PA

address: 3400 Civic Center Boulevard Building 421

institute: University of Pennsylvania

summary: Circadian profiling of total RNA collected from wildtype and NPY KO murine liver. Liver RNA collected every 4 hours in a 12hr light:12hr dark cycle.

overall_design: 2 genotypes and 6 timepoints, with 2 biological replicates. Total 24 samples.

first: Renske

last: Erion

first: Gang

first: John

last: Hogenesch

first: Amita

last: Sehgal


title: Transcriptome analysis of rice roots in response to plant growth promoting bacterium Bacillus subtilis RR4

status: Public on Jan 05 2017

first: Genotypic

last: technology

summary: The aim of our study is to elucidate the gene expression changes in rice in response to colonization by a plant growth promoting rhizobacteria such as the Bacillus subtilis through microarray high throughput technology. In particular, the effect of B.subtilis on root exudation (secretion of phytochemicals through roots) will be analysed. For this rice plantlets were grown in hydroponics and treated with B.subtilis RR4 for 48 hrs. The root samples of the control and treated plants were then used for the microarray experiment. The data obtained through microarray revealed genes related to cell wall modification, phytohormone synthesis, defense response, root exudation, etc. to be differentially regulated in response to B.subtilis RR4. Real time PCR analysis of few chosen genes (OsMS, OsALMT, OsABC, OsSDH, etc) also confirmed the validity of the microarray data. The initial responses of a plant in response to colonization by the microbe will be changes in cell wall of the plant tissues and the secretion of phytochemicals to attract/repel the colonizing beneficial/pathogenic organism. From analysis of microarray data we found the cell wall related genes which aid in root colonization and the root exudate related genes (biosynthesis and transport) which play a role in providing nutrition for the bacterial growth to be differentially regulated significantly. Analysis of specific genes and their biosynthesis pathways indicated that rice plants responded positively to root colonization by B.subtilis RR4. Notable among the exudation related genes such as Malate synthase and ALMT were found to be upregulated which indicates the significant role played by organic acids particularly malate in recruiting the PGPR towards the plant roots. This recruitment will thereby facilitate plant growth. Subsequently, these genes can be engineered in crop plants to recruit beneficial bacteria which might further open new avenues for improved crop production.

overall_design: Organism : Oryza sativa , Agilent Custom Rice Gene Expression  44x44k Array (AMADID: 064815) designed  by Genotypic Technology Private Limited.

first: B

last: Usha

first: K

last: Rekha


title: Metagenomic analysis revealed the microbial-mediated soil organic carbon loss under the degeneration succession in alpine meadow

city: Beijing

first: Yuguang

last: Zhang

address: Haidian

institute: Chinese Academy of Forestry

summary: Land cover change has long been recognized that marked effect the amount of soil organic carbon. However, little is known about microbial-mediated effect processes and mechanism on soil organic carbon. In this study, the soil samples in a degenerated succession from alpine meadow to alpine steppe meadow in Qinghai-Tibetan Plateau degenerated, were analyzed by using GeoChip functional gene arrays.

overall_design: soil microbial functional gene diversity; 20 samples were collected from alpine meadow and alpine-steppe meadow in Qinghai-Tibetan, China, with 10 replicates in every site

first: Yu

middle: G

first: Hui

last: Lu


title: Analysis of alternatively spliced transcripts in leaf, root, panicle and seed of rice with a long oligomer microarray

status: Public on Jan 01 2017

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

summary: RNA splicing is a molecular mechanism to increase protein diversities acquired through the evolution while the underlieing driving forces for the phenomenon are unknown especially in terms of gene expression. Rice alternatively spliced transcript detecting microarray (ASDM) was designed and applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi including leaves, roots, panicles at 1 cm stage and young seeds at 20 days after pollination. The comparison of the data between the microarray and RNA-seq shows a ‘bell shape distribution’ and a strong co-lineation for highly expressed genes. The transcripts are classified according to the degree of organ enrichment using coefficient value (CV, the ratio of standard deviation to the mean values); highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. The genes of highly variable group show the characteristics of the organs. The index of the portion of loci with alternatively spliced transcripts in a group (IAS) is designated for these CV groups and showed the higher value in the constitutive group. In addition, within a locus, a transcript with longer cds tends to be higher expressed and the spliced_intron is the most commonly found type of alternative splicing for the extended cds. Thus, constitutively expressed genes might be under evolutionary pressure toward alternative splicing that might have a longer cds. These data show that less resource consuming and better designed microarray might be a niche technology to test the transcriptome analysis including alternatively spliced transcripts in plants.

overall_design: We applied rice ASDM to detect organ specific genes among leaf, root, young flower at panicle 1 cm (P1cm) and seed at 20-30 days after pollination (S21DAP).

first: Songhwa

last: Chae

first: Baek-Hie

last: Nahm


title: Biological characterization of gene response to insulin-induced hypoglycemia in mouse retina

status: Public on Jan 03 2017

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Glucose is the most important metabolic substrate of the retina and maintenance of nor-moglycemia is an essential challenge for diabetic patients. Glycemic excursions could lead to cardiovascular disease, nephropathy, neuropathy and retinopathy. We recently showed that hy-poglycemia induced retinal cell death in mouse via caspase 3 activation and glutathione (GSH) decrease. Ex vivo experiments in 661W photoreceptor cells confirmed the low-glucose induction of death via superoxide production and activation of caspase 3, which was concomitant with a decrease of GSH content. We evaluate herein retinal gene expression 4 h and 48 h after insulin-induced hypoglycemia. Microarray analysis demonstrated clusters of genes whose expression is modified by hypoglycemia and we discuss the potential implication of those genes in retinal cell death. In addition, we highlight, by gene set enrichment analysis, three important pathways, including KEGG lysosomes, KEGG GSH metabolism and REACTOME apoptosis pathways. We tested the effect of recurrent hypoglycemia (three successive 5h periods of hypoglycemia separated by 48 h recovery) on retinal cell death. Interestingly, exposure to multiple hypoglycemic events prevents retinal cell death and GSH decrease, or adapts the retina to external stress by restoring GSH level comparable to control situation. We hypothesize that scavenger GSH is a key compound in this apoptotic process, and maintaining “normal” GSH level, as well as a strict glycemic control, may represent a therapeutic challenge in order to avoid side effects of diabetes, especially diabetic retinopathy.

overall_design: 4 experimental groups, 3 samples per group

first: M

last: Emery

first: N

last: Nanchen

first: F

last: Preitner

last: Thorens

first: D

last: Schorderet

first: R

last: Roduit


title: microRNA-mRNA integral analysis  in CD4+ T cell in primay biliary cholangitis (PBC)

city: Chiba

first: Ryo

last: Nakagawa

address: 1-8-1, Inohana, Chuo-ku

department: Department of Gastroenterology

institute: Chiba University

overall_design: Refer to individual Series


city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: rs11-07_opine2 - septante soil - Transcriptomic changes induced by opine production in Arabidopsis thaliana grown in natural soil - Arabidopsis thalian Col- line was transformed in order to obtain transgenic lines that produce opine compound (octopine and mannopine). Transgenic lines producing respectively octopine and mannopine and the WT line were grown in greenhouse under long-day condition in pots containing half commercial compost and half soil of la Mérantaise and watered with water. Whole plant aged of one month were harvested and frozen in liquid nitrogen. The plants were ground with a mortar an pestls and RNA extraction was performed with the RNeasy extraction kit (QIAGEN) with cristal of PVP. The RNA concentration was measured on a NANODrop spectrophotometer.

overall_design: 6 dye-swap - normal vs transgenic comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Yves

last: Dessaux

first: Marie-Laure

last: Martin-Magniette


title: Sex-biased transcriptome divergence along a latitudinal gradient

status: Public on Jan 04 2017

city: St Lucia

first: Stephen

last: Chenoweth

state: QLD

address: The School of Biological Sciences, The University of Queensland

department: Biological Sciences

country: Australia

institute: The University of Queensland, Australia

summary: Although not all sex-dependent gene expression is adaptive, it is likely an important genomic mechanism that allows each sex to independently adapt to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex-differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11,631 genes across eight populations revealed strong sex differences in the frequency, mode, and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population-specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in D. simulans and D. melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.

overall_design: The goal of our study was to estimate “common garden” mean expression level for genes in each sex, rather than to estimate within population genetic variation. Flies were sampled from eight populations along the east-coast of Australia, covering a straight-line distance of approximately 2,300 km, which spans much of the species natural range (Figure 1). To preserve the natural genetic differences among populations and minimize adaptation to the lab, flies for each population were maintained as isofemale lines (David et al. 2005) (n=12 for all populations with the exceptions of Airlie Beach, n=10 and Cooktown, n=6) until the gene expression assay. At this point, to ensure gene expression was measured on outbred flies, we crossed the isofemale lines within populations following a double round robin mating design that included reciprocal crosses by sex (Stich 2009; Verhoeven et al. 2006). For example, isofemale line 1 × isofemale line 2, isofemale line 1 × isofemale line 3, isofemale line 2 × isofemale line 3, isofemale line 2 × isofemale line 4, and so on. Owing to a smaller number of available lines, a triple round-robin mating design was used for Airlie and all possible pair-wise crosses were performed for Cooktown. A total of 18 F1 crosses were randomly selected for RNA processing from each population with 6 crosses assigned to each of three biological replicates. Five flies were randomly selected from each cross in order to produce pools of 30 adult virgin flies (3 days old) per biological replicate. The samples were snap frozen in liquid nitrogen without the use of CO2 anesthesia. Freezing began at 10:22 am and was completed by 1:40 pm. All flies were frozen in a random order with respect to sex and population. All flies were reared in 50ml vials containing standard yeast medium at 25°C with a 12 hour day/night cycle and adult flies were held in vials for three days in same sex groups of 5 before being frozen.

first: Scott

last: Allen

first: Russell

last: Bonduriansky

first: Carla

last: Sgro


title: Toxin mediates sepsis caused by methicillin-resistant Staphylococcus epidermidis

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

summary:
Bacterial sepsis is a major killer in hospitalized patients. Coagulase-negative staphylococci (CNS) with the leading species Staphylococcus epidermidis are the most frequent causes of nosocomial sepsis, with most infectious isolates being methicillin resistant.  However, which bacterial factors underlie the pathogenesis of CNS sepsis is unknown. While it has been commonly believed that invariant structures on the surface of CNS trigger sepsis by causing an over-reaction of the immune system, we show here that sepsis caused my methicillin-resistant S. epidermidis is to a large extent mediated by the methicillin resistance island-encoded peptide toxin, PSM-mec. PSM-mec contributed to bacterial survival in whole human blood and resistance to neutrophil-mediated killing, and caused significantly increased mortality and cytokine expression in a mouse sepsis model. Furthermore, we show that the PSM-mec peptide itself, rather than the regulatory RNA in which its gene is embedded, is responsible for the observed virulence phenotype. While toxins have never been clearly indicated in CNS infections, our study shows that an important type of infection caused by the predominant CNS species, S. epidermidis, is mediated to a large extent by a toxin. Of note, these findings suggest that CNS infections may be amenable to virulence-targeted drug development approaches.
We used microarrays to detail the global gene expression between S. epidermidis strain Rp62A and S. epidermidis strain Rp62A isogenic Δpsm-mec deletion mutants

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: We used microarrays to detail the global gene expression between five strains of Se.

first: Li

last: Qin

first: Fei

last: Da

first: Daniel

last: Tan

first: Thuan

middle: H

last: Nguyen

first: Chih-Lung

last: Fu

first: Vee

last: YTan

first: Joshua

last: McCausland

middle: E

first: Hwang-Soo

last: Joo

first: Shu

last: Queck

first: Gordon

last: Cheung

first: Michael

last: Otto


title: The peripheral blood transcriptome identifies dysregulation of inflammatory response genes in polycystic ovary syndrome

city: Guangzhou

first: Liang

last: Zhang

state: Guangdong

address: Xingnan Road 521

department: Translational Medicine Research Center

institute: Guangdong Women and Children Hospital

summary: Polycystic ovary syndrome (PCOS) is a common endocrine disorder in women resulting in ovulation failure and other metabolic problems. However, the underlying mechanisms of it remain largely uncertain due to its complexity of clinical manifestations. Since PCOS is believed as a systemic disorder involved endocrine, metabolism, immune system and many organs, we therefore want to know what happen in the peripheral blood of patients with PCOS. To this purpose, gene expression patterns of peripheral blood from 10 PCOS patients and 10 healthy women were profiled by microarray. The significance analysis of microarray (SAM) software was employed to screen the differentially expressed genes (DEGs) and gene ontology (GO) was used for functional enrichment analysis. Also, quantitative reverse-transcription PCR (qRT-PCR) was performed to confirm the results from microarray. 181 DEGs with a fold change >2.0 and q-value <0.05 were identified between the groups. Of these genes, 149 were up-regulated and 32 down-regulated in PCOS. Importantly, 14 genes associated with inflammatory response pathway were highly enriched in PCOS. Furthermore, qPCR assays validated the dysregulated inflammatory response genes. Our observation reinforces the hypothesis that PCOS is characterized by the presence of systemic inflammatory changes and inflammation is implicated in the pathogenesis of this entity. Further elucidation of the aberrant expression of inflammation-related genes how to affect the pathogenesis of PCOS may lead to the development of novel preventative and therapeutic strategies.

overall_design: The dual-color approach was adopted in our study, 8 PCOS samples and 8 healthy controls labeled with Cy3, pooled control labeled with Cy5 , respectively.

first: Nian-jun

last: Su

first: Jian

last: Ma

first: De-feng

last: Feng

first: Shuai

last: Zhou

first: Zi-tao

last: Li

first: Wei-ping

first: Hua

last: Deng

first: Jia-ying

last: Liang

first: Xu-hui

last: Yang

first: Yue-mei

first: Feng-hua

last: Liu


title: Survivin deficient liver of mice after partial hepatectomy

city: Shanghai

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

summary: The liver possesses remarkable regenerative capacity in response to injury. Upon partial hepatectomy (PHx), terminally differentiated hepatocytes in the remaining liver enter the cell cycle and restore the liver mass and function within weeks. However, liver regeneration is often impaired in livers with chronic diseases. Survivin, an inhibitor of apoptosis protein (IAP) and member of chromosome passenger complex (CPC), plays versatile roles in cell mitosis and apoptosis. We and others found that the expression of Survivin was highly increased in liver during PHx-induced liver regeneration, which indicated that Survivin played important roles in this process. However, the function of Survivin in liver regeneration remains largely undefined. Here, using mice with genetic deletion of Survivin, we found that during PHx-induced liver regeneration Survivin regulated both hepatocyte G1/S phase transition by inhibiting the expression of p21 and G2/M phase transition by regulating the localization of CPC. Moreover, restoration of Survivin expression in Survivin-deficient hepatocytes inhibited p21 expression and promote both hepatocyte G1/S and G2/M transition during PHx-induced liver regeneration.

overall_design: Four samples are Survivin deleted liver, 0, 24, 36, 48 hours after PHx separately; four samples are Survivin wild type liver, 0, 24, 36, 48 hours after PHx separately.

first: Dan


title: Shewanella piezotolerans WP3 wild-type strain  under salt shock

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University


title: Design and validation of 8X60k gene-expression microarray for chickpea (Cicer arietinum) based on the transcriptome data

first: Genotypic

last: technology

summary: Microarrays have increasingly become a powerful tool for high throughput gene-expression studies and discovery of novel biomarker genes. Developed for a large number of organisms, including plants, microarrays are commonly performed for species that have sequenced data, for performing gene expression analysis, miRNA profiling, comparative genomic hybridization (CGH), ChIP-on-chip and SNP analysis. Genomic resources are still very limited for chickpea, a very important food legume crop. Here, we report the design and comprehensive validation of Next Generation Sequencing transcriptome data for chickpea through microarray technology to develop a high-throughput resource for studying the expression of all the transcripts in different biological samples to help functional genomics and breeding programs. This microarray design was developed and validated jointly by Genotypic Technology Private Limited and National Institute of Plant Genome Research. First, we designed 400k probes using reads covering 35k assembled contigs and 100k singletons chickpea transcripts. The 400k chip was hybridized with DNA and RNA samples of chickpea and microarray analysis was carried out. A total of 73,922 probes were found to be specific to chickpea transcripts. Best probes were filtered from the analyzed data and a total of 61,659 probes were selected to develop the final microarray design in 60k gene-expression microarray format. The probes represented 51,444 unique transcripts. The probes were annotated based on their corresponding chickpea transcript and similarity with other plants species. Microarray results were concordant with previous results from the NGS studies. The design of custom oligonucleotide probes for microarrays have varied functional genomic applications and this approach represents a valuable resource for chickpea.

overall_design: Agilent one-color experiment,Organism: Chickpea (Cicer arietinum)  ,Custom Agilent  8x60k Microarray Gene expression  (AMADID: 37094 )

first: Rohini

last: Garg

first: Vikash

last: Singh

first: Mukesh

last: Jain

first: Raja

last: Mugasimangalam

first: Sudha

last: Rao

first: Aiyaz

last: Mohamed

first: Deepti

last: Saini


title: Shewanella piezotolerans WP3 wild-type strain salt shock for 90 min

summary: The WP3 strains was cultured at 20°C and salt shocked with 12% (w/v) NaCl for 90 min. The transcriptional profiles after and before salt shock were compared.

overall_design: Three biological replicates sample and 6 technical replicates for each experiment

first: Shengkang

first: Fengping

last: Wang


title: Identification of a novel long-range enhancer driving Sonic Hedgehog expression in neural progenitor cells

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

type: Genome variation profiling by genome tiling array

summary:
A novel long-range enhancer for Shh - Shh-Brain-Enhancer-6 (SBE6) – that is located 100kb upstream of Shh and that is required for the proper induction of Shh expression during neural differentiation
ChIP-on-chip for H3K4me1 and H3K27ac in ESCs and NPCs showed a gain of these two enhancer marks in NPCs at SBE6 which identified this sequence as having potential enhancer activity.

overall_design: Comparison of H3K4me1 and H3K27ac profiles between ESCs and NPCs at the Shh locus

first: Nezha

last: Benabdallah

first: Philippe

last: Gautier

first: Betul

last: Hekimoglu-Balkan

first: Shipra

last: Bhatia

first: Wendy

last: Bickmore


title: Expression profiling of severe growth abortion (SGA) in triploid hybrids crossed between tetraploid wheat and Aegilops umbellulata.

status: Public on Jan 24 2017

city: Kobe

first: Shigeo

last: Takumi

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in SGA plants, which are triploid hybrids crossed between tetraploid wheat and a diploid wheat relative Aegilops umbellulata. Of the up-regulated genes, cell death and carboxy-lyase activity-related genes were the most frequently found in crown tissues of SGA plants. On the other hand, photosynthesis-related genes were highly down-regulated in crown tissues of SGA plants. In addition, transcript accumulation levels of shoot apical meristem (SGA)-related genes such as knotted-1 like homeobox (Knox) genes  were also repressed in SGA plants.
The microarray analysis strongly suggests that an autoimmune response-like reaction might be triggered by intergenomic incompatibility between the AB and U genomes in SGA. In addition, SAM-related  and cell cycle-related genes were dramatically down-regulated in crown tissues of SGA, indicating that abnormalities of SAM are associated with the abnormal growth phenotypes in SGA.

overall_design: Expression patterns were compared between the two triploid hybrids showing the wild-type phenotype (as a reference) and severe growth abortion. Total RNA samples were isolated from the 7-day-old crown tissues. Two independent experiments were conducted in each exprement.

first: Moeko

last: Okada


title: Shewanella piezotolerans WP3 wild-type strain salt shock for 30 min

first: Huahua

last: Jian

summary: The WP3 strains was cultured at 20°C and salt shocked with 12% (w/v) NaCl for 30 min. The transcriptional profiles after and before salt shock were compared.

last: Li


title: Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary:
Background & Aims: Most inflammatory bowel diseases (IBDs) are classic polygenic disorders represented by common alleles. However, multiple determinants of very early-onset IBD characterized by a more extensive disease course remain largely unknown. The present study aimed to define the genetic architecture of pediatric and adult-onset IBDs in the Polish population.

Results: Of 82 SNPs validated/replicated for association with IBD, a novel BRD2 (rs1049526) association was found in both pediatric (OR= 2.35) and adult (OR= 2.66) patients. Thirty SNPs were shared between pediatric and adult patients; 22 and 30 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare/infrequent, potentially deleterious variants in IBD-associated or innate immunity-associated genes. Both groups of variants were over-represented in affected children. Two highly deleterious homozygous variants, HLA-DRB1 c.565_566insC and NCF4 p.Arg8Trp, were found in two affected children, and WAS p.Glu131Lys was found in one child and one adult patient.

Conclusions: Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare/low frequency deleterious variants in affected children suggests a contribution by yet unexplained genetic components.

overall_design:
A total of 1495 patients were recruited at Gastroenterology Departments at different Polish hospitals, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA sample-based genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls.

Please note that no data processing was applied and thus only theta values from unprocessed file were provided in the 'Matrix_signal_intensities.txt' file.

The main reason for not normalizing the data was that it was derived from pooled samples. Sample pools were of different sizes, some were mixed sex.
Data normalization algorithms were in general optimized for genotype calling (which is impossible for these samples), and thus may introduce possible artifact introduction. Thus "the less the better" approach was made with the data analysis. PCA hasn't revealed any alarming stratification. Raw theta values were used as an input for Student's t-test. Clusters of significant probes were selected for validation in individual patients.

first: Agnieszka

last: Paziewska

first: Michalina

last: Dabrowska

first: Katarzyna

last: Paczkowska

first: Michal

last: Mikula

first: Filip

last: Ambrozkiewicz

first: Ewa

last: Hennig

first: Jerzy

last: Ostrowski


title: Expression Patterns of Non-Alcoholic Fatty Liver Disease genes and Efficacy of Green Tea on Hyperlipidemic Animal Model

city: Kualalumpour

first: sanaz

last: koosha

address: Department of pharmacology, faculty of medicine, UM

department: pharmacology

country: Malaysia

institute: university of Malaya

summary: Currently, there are no established treatments for NAFLD/NASH. Treatment recommendations include weight reduction through both diet and physical exercise, and weight-loss surgery for extreme obesity. Most medical regimens target components of the metabolic syndrome or oxidative stress associated with the pathogenesis of NASH. These include anti-obesity regimens, insulin sensitizers, anti-hyperlipidemics, and antioxidants. Thus, a need exists to validate approaches that might help the development and progression of hepatic steatosis, oxidative stress, and inflammation in association with NAFLD.

overall_design: Total RNA was extracted from liver tissues of treated and untreated (NAFLD) groups and submitted for whole genome expression analysis.

first: Mohammed

last: Alshawsh

first: Zahurin

last: Mohamed

first: Shamsul

last: Mohd Zain

first: Sanaz

last: Koosha

first: Atefeh

last: Seyyedan

first: Adaikalavan

last: Ramasamy

first: Nik

last: Nik Mustapha

first: Rosmawati


title: MicroRNA-expression in tonsillar and base of tongue cancer related to HPV and clinical outcome

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

summary: Background: Human papillomavirus-16 (HPV) causes the majority of oropharyngeal squamous cell carcinomas (OPSCC), especially tonsillar and base of tongue cancer. HPV-positive cancer patients have better clinical outcomes than HPV-negative patients and several groups have suggested de-intensification of treatment schedules in order to avoid unnecessary side effects in the former group. Current TNM classification falls short in predicting OPSCC patients’ prognosis highlighting the unmet need for novel biomarkers. Here we tested the expression and the prognostic role of microRNAs (miRs) in relation to HPV status and clinical outcome in 220 patients with OPSCC distributed in three independent cohorts. Methods: MiR expression was assessed in three cohorts of OPSCC patients by NanoString nCounter Technology (training; n=78), Real-Time PCR (validation; n=93) and miR-Sequencing (TCGA; n=51).  In-Situ Hybridization was used to define miR localization.  Differences in progression free (PFS) and overall survival (OS) according to miR expression were assessed using the Kaplan-Meier method and compared using the log rank test.  Univariate and multivariate analyses using Cox proportional hazards method established the relationship between miR expression, HPV-status, clinical-pathological variables and survival. Results: miR-155 and miR-193b-3p were dysregulated in HPV-negative compared to HPV-positive OPSCC. MiR-193b-3p up-regulation was associated with worse PFS and OS in the training and validation cohorts and the TCGA cohort respectively. MiR-193b-3p prognostic effect was independent of HPV-status. Among HPV-positive patients, over-expression of miR-301b and down-modulation of miR-185b correlated with improved survival. Conclusion: Expression analysis for specific miRs in combination with tumor HPV-status and clinical-pathological variables may be useful in the prediction of clinical outcome for OPSCC patients.

overall_design: microRNA-expression was tested in OPSCC (TR) cancer and 18 controls (HT).

first: Nicola

last: Valeri

first: Torbjörn

first: Carlo

middle: M

last: Croce


title: Affect of Interferon Gamma on Chordoma Cells

city: Bethesda

first: Jacob

last: Richards

state: MD

address: 10 Center Drive, Room 8B09, MSC 1750

department: Center for Cancer Research

institute: National Cancer Institute

summary:
IFN-g-induced gene expression profiles of UM-Chor1 cells were assessed by microarray analysis
Chordoma is a rare bone tumor derived from notochord, which has shown to be resistant to conventional therapy, including chemotherapy and radiotherapy. Immunotherapy has the potential to be effective in cancers with resistance to conventional therapy. Checkpoint inhibition, including Programmed cell Death 1 (PD-1)/Programmed cell Death protein 1 (PD-L1) blockade has shown great promise in treating diverse cancers. The purpose of this study was to investigate the potential of anti-PD-L1 antibody therapy for chordoma. To this end, using 4 chordoma cell lines, we examined the expression of PD-L1 and performed in vitro NK cells killing assay for antibody-dependent cell-mediated cytotoxicity (ADCC) activity mediated by the anti-PD-L1 antibody, avelumab. Here, the expression of PD-L1 was markedly upregulated by IFN-g in all 4 chordoma cell lines, which resulted in increasing the sensitivity to ADCC. Next, to model a patient that received a tumor-antigen specific vaccine, chordoma cells were co-incubated with brachyury specific CD8+ T cells, culminating in significant upregulation of PD-L1 on the tumor cells mediated by CD8+ T cells IFN-g production. The functional consequence was the sensitivity of chordoma cells to ADCC mediated by avelumab. Finally, residential cancer stem cell subpopulations of chordoma cells were killed by avelumab-mediated ADCC to the same degree as non-cancer stem cell populations. Our findings show the potential of avelumab therapy in chordoma; a) alone, to enable endogenous NK cells to kill chordoma cells via ADCC, or b) in conjunction with T cells immunotherapy such a vaccine, to exploit enhanced NK cell killing of chordoma cells via ADCC.

overall_design: UM-Chor1 cells were treated or untreated with 50 ng/mL of IFN-gamma for 24 hours. Three replicates of control (C1) or treated (G1) were analyzed.

first: James

last: Hodge


title: Shewanella piezotolerans WP3 wild-type strain salt shock for 60 min

first: Huahua

last: Jian

summary: The WP3 strains was cultured at 20°C and salt shocked with 12% (w/v) NaCl for 60 min. The transcriptional profiles after and before salt shock were compared.

first: Shengkang

last: Li

first: Fengping

last: Wang


title: Nonkeratinizing Carcinoma Tissues: Tumor vs. Adjacent non-tumor tissues

city: Beijng

first: bobby

last: zhang

address: DaTun road 15th

institute: IBP

summary: Nasopharyngeal carcinoma (NPC) is one of the common malignant tumors, accounting for first place in head and neck malignant tumors. Nonkeratinizing carcinoma (NKC) is the major histologic type of NPC. We performed Transcriptional profiling of NKC comparing tumor with adjacent non-tumor tissues using. Goal was to identify and investigate dryregulated lncRNAs and mRNA in NKC at genome-wide scale.

overall_design: Two-paired experiment, Tumor vs. Adjacent Non-tumor Tissues. Biological replicates: 7 paired samples.

first: Bao

last: Zhang

first: Dongpeng

first: Jun

last: Tang

first: Jing

last: Wu

first: Xiaomin

last: Chen

first: Dongdong

first: Mingzhou

last: Guo

first: Yuejian

first: Jianjun

last: Luo

first: Runsheng


title: Gene expression change in placental labyrinth zone from Pregnancy-Associated Hypertension (PAH) mice with different Nrf2 expression.

city: Sendai

first: Masahiro

last: Nezu

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University School of Medicine

summary: We analyzed differences in placental gene expressions.  We examined the mRNA expression profile in placental labyrinth zone from normal pregnant mice, and PAH mice with different Nrf2 expressions (WT, Nrf2 Knockout [KO], Keap1 Knockdown [KD])

overall_design: Human Angiotensinogen (hAGT) transgenic female mice showes perinatal hypertension (PAH mice) by mating male human Renin (hREN) transgenic mice. But hAGT female mice did not showes gestational hypertension (Normal pregnancy; NP mice) by mating male hAGT mice.  We performed microarray analyses using placental labyrinth zone from NP mice and three types of PAH mice with different Nrf2 expression(PAH mice, PAH-Nrf2KO mice PAH-Keap1KD mice), n = 2 each.

first: Tomokazu

last: Souma

first: Norio

last: Suzuki

first: Masayuki

last: Yamamoto


title: DNA Methylation analysis of polybrominated diphenyl ethers (PBDEs) treated hepatocellular carcinoma

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

summary: DE-71, a commercial mixture of the polybrominated diphenyl ethers (PBDEs), is used as flame retardant and the potential exposure to PBDEs is an emerging public health concern. It has been clarified that long term exposure to PBDEs induces hepatocellular carcinoma  in mouse. In this study, we analyzed how DE-71 impacts on DNA methylation in hepatocellular carcinoma.

overall_design: DE-71 (technical pentabromodiphenyl oxide; CAS. No. 32534-81-9) was obtained from Great Lakes Chemical Corporation (West Lafayette, IN - Lot 2550OA30A). The chemical was administered to male B6C3F1/N mice (Taconic Farms, Inc. (Germantown, NY) by oral gavage in corn oil 5 days per week at doses of 100 mg/kg/day for up to 18 months.    Frozen liver tissue/tumors were collected for DNA extraction at necropsy of control and high dose mice at 18 months. Methylated CpG Island Recovery Assay (MIRA) was used.

first: Takashi

last: Shimbo

first: Paul

last: Wade

first: Ruchir

last: Shah


title: Whole genome expression profiling of Brassica juncea BnCRY2aOE transgenics vis-à-vis wild-type

status: Public on Dec 31 2016

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

institute: University of Delhi South Campus

summary: The BnCRY2aOE transgenics over-expressing a blue light photoreceptor (BnCRY2a) flowered earlier than wild-type plants by more than two weeks. To identify the downstream candidate genes involved in regulating the early flowering phenotype in the transgenics, a genome-wide microarray analysis of the transgenic plant vs. wild type was performed. The microarray data analysis revealed the differential up-regulation of many genes involved in flower development, cell growth and differentiation and hormone biosynthesis/signalling in comparison to wild-type.

overall_design: The wild-type and BnCRY2aOEtransgenic plants were grown in transgenic containment facility. Fully expanded leaves were harvested from 45-d-old wild-type and transgenic plants (two biological replicates for each) for performing whole genome expression profiling using Gene Expression B. napus (Brassica) Oligo Microarray 4x44K (AMADID: 22520, Cat# G2519F_022520) Agilent platform.Overall, there were 4 samples: two for wild-type (control samples), other two for transgenics (test samples).

first: Sushma

last: Mishra

first: Pooja

last: Sharma

middle: P


title: Expression data of cultured bovine granulosa cells plated at different initial cell densities

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

summary: In previous studies it has been shown that bovine granulosa cells (GC) cultured at a high plating density dramatically change their physiological and molecular characteristics, thus resembling an early stage of luteinization. During the present study, these specific effects on the GC transcriptome were comprehensively analysed of the same cell culture model comparing GC cultured at normal and high density.

overall_design: Granulosa cells cultured at different plating densities (normal and high; 3 replicates each) were used and processed for microarray analysis

first: Anja

last: Baufeld