title: Geminin promoter occupancy and Geminin-dependent histone acetylation during neuroectodermal cell specification

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: The nucleoprotein Geminin (Gmnn) promotes neural cell fate acquisition of embryonic stem cells, while knockdown reduces the efficiency of neural gene activation. This occurs, at least in part, through Geminin’s ability to promote histone hyperacetylation at neural genes, to activate their expression. In mouse models in vivo, Geminin deficiency in the embryonic neural tube between embryonic days 8.5-10.5 also reduces the expression of genes controlling neural specification and/or differentiation, contributing to neural tube defects. To determine where Geminin binding and Gmnn-dependent acetylation occurs throughout the genome, we performed ChIP-chip analysis (these data) and ChIP-seq analysis (GSE77246) to define Geminin-bound chromatin locations in mouse embryonic stem cells (ESCs) and in ESC-derived neuroectoderm.  We also performed ChIP-chip analysis of H3K9 acetylation in ESC-derived neuroectoderm, with or without Doxycycline-dependent Gmnn knockdown, to define the requirements for Geminin activity for histone acetylation of promoters during neural fate specification.

overall_design: For ChIP sample preparation for promoter occupancy assays, three independent biological replicates each were generated for the following sample types: (1) Geminin ChIP in ESCs (2) Geminin ChIP in ESC-derived neuroectoderm after 2.5 days of N2B27 monolayer culture, using the N18 Gmnn antibody (Santa Cruz sc-8449). (3-4) A clonal A2lox embryonic stem cell line engineered for Doxycycline-dependent Gmnn knockdown (KD) was differentiated in N2B27 medium for 2.5 days with or without 500ng Doxcycline and these samples were used for H3K9ac ChIP (antibody Abcam; Ab10812) to assess Geminin-dependent histone acetylation (H3K9ac in GemKD cells on day 2.5, three biological replicates each were generated with Gmnn knockdown (plus Dox) or under control conditions (no Dox).  The A2lox mouse ES cell line (Iacovino et al., Stem Cells 2011, 29(10): 1580-88) and a clonal derivative engineered for Doxycycline-dependent Gmnn shRNA.expression (Yellajoshyula et al., PNAS 2011, 108(8): 3294-99) were routinely propagated on feeder cells (mouse embryonic fibroblast cells, Chemicon) in DMEM (Invitrogen) supplemented with 15% fetal calf serum (Hyclone), 1 mM sodium pyruvate, 1 mM Non-Essential amino acids, 1mM L-Glutamine (Invitrogen), 10−4 M 2-mercaptoethanol (Sigma) and 103 units per ml of leukemia inhibitory factor (ESGRO, Chemicon). Monolayer neural differentiation of ES cells was done as previously described (Ying and Smith, Methods in Enzymology 2003, 365: 327-41). Briefly, ES cells cultured on feeder cells were dissociated and plated at 1x105/cm2 for one day on 0.1% gelatin-coated tissue culture dishes. After 24 hours, cells were plated onto 0.1% gelatin-coated tissue culture dishes at low density (1x104 cells/cm2) in N2B27 medium and cultured for 2.5 days.

first: Dhananjay

last: Yellajoshyula

first: Savita

last: Sankar

first: Bo

last: Zhang


title: A 17-Gene Stemness Score for Rapid Identification of High-Risk AML Patients [NanoString]

status: Public on Dec 02 2016

city: Toronto

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

country: Canada

institute: Univerity of Toronto

summary: In AML, most patients are initiated on standard chemotherapy and afterwards assigned to a post-remission strategy based on genetically-defined risk categories. However, outcomes remain heterogeneous, indicating the need for novel biomarker tests that can rapidly and accurately identify high-risk patients, allowing better stratification of both induction and post-remission therapy. As patient outcomes are linked to leukemia stem cell (LSC) properties that confer therapy resistance and drive relapse, LSC-based biomarkers may be highly informative. We tested 227 CD34/CD38 cell fractions from 78 AML patients for LSC activity in xenotransplantation assays. Comparison of microarray-based gene expression (GE) profiles between 138 LSC+ and 89 LSC? fractions identified 104 differentially-expressed LSC-specific genes. To obtain prognostic signatures, we performed statistical regression analysis of LSC GE against patient outcome using a training cohort of 495 AML patients treated with curative intent. A score calculated as the weighted sum of expression of 17 LSC signature genes (LSC17) was strongly associated with survival in 4 independent datasets (716 AML cases) spanning all risk categories in multi-variate analysis; an optimized 3-gene sub-score (LSC3) was prognostic in favorable risk subsets. These scores were robust across GE technology platforms, including the clinically serviceable NanoString system (LSC17: HR=2.73, P<0.0001; LSC3: HR=6.3, P<0.02). The LSC17 and LSC3 scores provide rapid and accurate identification of high-risk patients for whom conventional chemotherapy is non-curative. These scores will enable evaluation in clinical trials of whether such patients may benefit from novel and/or more intensified therapies during induction or in the post-remission setting.

overall_design: 307 primary AML patient samples were analyzed for mRNA expression of 17 LSC signature and 9 reference genes. One lane of each NanoString cartridge was reserved for synthetic oligonucleotides to control for batch effects.

middle: W

first: Amanda

last: Mitchell

first: James

middle: A

last: Kennedy

first: Claire

last: Chen

first: Jessica

middle: L

last: McLeod

first: Narmin

last: Ibrahimova

first: Andrea

last: Arruda

first: Andreea

last: Popescu

first: Vikas

last: Gupta

first: Aaron

middle: D

last: Schimmer

first: Andre

middle: C

last: Schuh

first: Karen

last: Yee

first: Lars

last: Bullinger

first: Klaus

middle: H

last: Metzeler

first: Tobias

last: Herold

first: Christian

last: Buske

first: Bob

last: Löwenberg

first: Peter

middle: J

last: Valk

last: Zandstra

first: Mark

last: Minden

first: John

middle: E

last: Dick

first: Jean

last: Wang


title: Genomic profiling of 49 gastric cancer cell lines by array-based comparative genomic hybridization

status: Public on Dec 01 2016

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

type: Genome variation profiling by genome tiling array

summary: In this study, we investigated amplifications and deletions of 49 gastric cancer cell lines by 244k oligonucleotide-based array comparative genomic hybridization.

overall_design: 49 gastric cancer cell lines

first: Yuka

last: Hirashita

first: Kazuyoshi

last: Yanagihara

first: Kuniaki

last: Shirao

first: Masatsugu

last: Moriyama


title: Rare germline copy number variations and disease susceptibility in familial melanoma

city: Rockville

first: Rose

last: Yang

state: MD

address: 9609 Medical Center Dr

department: Division of Cancer Epidemiology and Genetics

country: USA

institute: National Cancer Institute

summary:
Mounting evidence suggests that copy number variations (CNVs) can contribute to cancer susceptibility.  The main goal of this study was to evaluate the role of germline CNVs in melanoma predisposition in high-risk melanoma families. We used genome-wide tiling comparative genomic hybridization and SNP arrays to characterize CNVs in 335 individuals (240 melanoma cases) from American melanoma-prone families (22 with germline CDKN2A or CDK4 mutations).
We found that the global burden of overall CNVs (or deletions or duplications separately) was not significantly associated with case-control or CDKN2A/CDK4 mutation status after accounting for the familial dependence. However, we identified several rare CNVs that either involved known melanoma genes (e.g. PARP1, CDKN2A) or co-segregated with melanoma (duplication on 10q23.23, 3p12.2 and deletions on 8q424.3, 2q22.1) in families without mutations in known melanoma high-risk genes. Some of these CNVs were correlated with expression changes in disrupted genes based on RNASeq data from a subset of melanoma cases included in the CNV study. These results suggest that rare co-segregating CNVs may influence melanoma susceptibility in some melanoma-prone families and genes found in our study warrant further evaluation in future genetic analyses of melanoma.

overall_design: We used genome-wide tiling comparative genomic hybridization to characterize CNVs in 255 individuals from American melanoma-prone families (22 with germline CDKN2A or CDK4 mutations).

first: Jianxin

last: Shi

first: Weiyin

last: Zhou

first: Bin

last: Zhu

first: Paula

last: Hyland

first: Hunter

last: Bennett

first: Yanzi

last: Xiao

first: Xijun

last: Zhang

first: Laura

middle: S

last: Burke

first: Lei

last: Song

first: Chih

last: Hsu

first: Chunhua

last: Yan

first: Qingrong

last: Chen

first: Daoud

last: Meerzaman

first: Casey

last: Dagnall

first: Laurie

last: Burdette

first: Belynda

last: Hicks

first: Neal

last: Freedman

first: Stephen

last: Chanock

first: Meredith

last: Yeager

first: Margaret

last: Tucker

first: Alisa

middle: M

last: Goldstein

first: Xiaohong

middle: R


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

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

overall_design: Six week-old male TRAP rats were intravenously injected with 1mg of OBP-801 or saline 2 times a week. After 8 weeks, rats were sacrificed and total RNAs were extracted from ventral and lateral prostate. The RNA was isolated with the RNeasy Micro kit (Qiagen); RNA samples were amplified, And the cDNA was hybridized onto rat microarrays.

first: Shinya

last: Sato


title: Layers infected by Salmonella Enteritidis

city: Shandong Taian

first: gui

middle: xian

last: wu

address: Taishanqu daizongdajie

country: China

institute: Shandong agriculture university

summary: Global gene expression profiling in spleen in chicken inoculated with S. enteritidis and control was conducted to screen differentially expressed genes and identify the key gene, signalling pathways and important biological processes that related to the infection of S. enteritidis

overall_design: The 20-week old white leghorn layers were infected by Salmonella Enteritidis. Control group was mock infected by PBS. The spleen samples were collected at 7 and 14dpi for expression profile screening using Agilent 44K chicken microarray. Four biological replicates were used in each group at each timepoints. The balanced design was used for microarray experiment.

first: XIANYAO

last: LI

first: YUKAI

last: QI

first: GUIXIAN

last: WU


title: Differentiation of K562 with PMA treatment

city: New Delhi

first: Alok

last: Bhattacharya

address: JNU

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

summary: K562 cells were treated with 20nM PMA. Cells were harvested after 48 hours and RNA was extracted with miRvana RNA isolation kit. Expression profiling was done on Agilent platform.

overall_design: K562 cells were treated 20nM PHORBOL 12-MYRISTATE 13-ACETATE (PMA) and harvested after 48 hours for RNA extraction. Control cells were treated equal amount of solvent (DMSO) in which PMA was dissolved.

first: Mohd

last: Ahmad


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

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

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

overall_design: Refer to individual Series


title: Transcriptome analysis of annotated coding genes and sORF in AtPropep3 (AT13) and treated AtPep3 (AT13 peptide)

status: Public on Nov 30 2016

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

institute: Kyushu Institute Technology

summary: There are seedling samples with duplicates.

overall_design: Total RNA was extracted from overexpressing plants, treated plants with peptide and non-treated wild type of plants with two biological replicates

first: Kentaro

last: Nakaminami


title: Genome-wide analysis of DNA methylation in neuroblastoma cell lines identifies MEGF10 as a novel epigenetically repressed tumour suppressor gene.

city: Bristol

first: Keith

middle: William

last: Brown

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

type: Genome binding/occupancy profiling by genome tiling array

summary:
Background: Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis.  Despite recent genome-wide mutation analyses, most neuroblastomas do not contain recognisable driver mutations, suggesting that epigenetic changes could underlie many cases. Methods: To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we compared neuroblastomas to their neural crest precursor cells, using genome-wide DNA methylation analysis; probing CpG island promoter microarrays with methyl CpG-immunoprecipitated DNA. Results: We identified 93 genes that were significantly differently methylated between neuroblastoma cell lines and neural crest cells, of which 26 (28%) were hypermethylated and 67 (72%) were hypomethylated.  Concentrating on hypermethylated genes to identify candidate tumour suppressor loci, we found the cell engulfment and adhesion factor gene MEGF10 to be epigenetically repressed by DNA hypermethylation or by H3K27/K9 methylation in neuroblastoma cell lines.  MEGF10 showed significantly down-regulated expression in neuroblastoma tumour samples; furthermore patients with the lowest-expressing tumours had reduced relapse-free survival.  Knock-down of MEGF10 expression in neuroblastoma cell lines promoted cell growth.
Conclusion: Our results suggest that MEGF10 is a clinically relevant, epigenetically-deregulated neuroblastoma tumour suppressor.

overall_design: Comparison of DNA methylation in human neural crest cells with four human neuroblastoma cell lines.

first: Jessica

last: Charlet


title: Transgenic AhDGR-OE vs Wild type Col 0 Arabidopsis plants

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

summary: Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing AhDGR gene from Amaranthus hypochondriacus.

overall_design: One experiment WT vs AhDGR OE plant leaves.

first: Paola

last: Palmeros-Suárez

first: John

middle: P


status: Public on Nov 29 2016

city: Beijing

first: gaijing

last: Han

address: 17 nanli Panjiayuan

department: State Key Laboratory of Molecular Oncology

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
Purpose: Esophageal squamous cell carcinoma (ESCC) is a serious malignant tumor, it affects human health. We analyzed the correlation between serum Stathmin levels and ESCC, further elucidated the molecular mechanisms how Stathmin promotes ESCC cell invasion and metastasis. Methods: Stathmin levels in ESCC and healthy control serum was detected by enzyme-linked immunosorbent assay (ELISA), and analyzed the clinical parameters. We established ESCC cells with Stathmin overexpression or knockdown, next evaluated the effects of Stathmin on invasion, metastasis and proliferation in ESCC.  The expression levels of the integrin family, focal adhesion kinase (FAK) protein and extracellular signal-regulated kinase (ERK) were detected by immunoblotting. Results: Serum levels of Stathmin were significantly higher in ESCC and associated with lymph node metastasis, tumor stage and size. Furthermore, we found Stathmin promotes migration, invasion and proliferation of ESCC cells in vitro and in vivo. Further study confirmed that the activation of integrinα5β1/FAK/ERK pathway is increased in Stathmin overexpression cells, this pathway contribute to strengthen cell adhesion. Stathmin accelerates the cell motility by enhancing cell adhesion ability. Conclusion: Stathmin may be a potential biomarker for ESCC clinical detection, and it can promotes ESCC cell invasion and metastasis through the integrinα5β1/FAK/ERK pathway.
The differentially expressed genes were analyzed by Human Transcriptome Array, and confirmed by RT-PCR.

overall_design: Stathmin overexpression cell and control cell gene expression analysis each contain two biology repeat. Sample 1 and sample 3 represent stathmin overexpression cell, sample 2 and sample 4 represent control cell.

first: Gaijing

first: Yang

last: Xu


title: Seasonal Variation in the Skin Transcriptome of Bottlenose Dolphins (Tursiops truncatus)

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

summary: As apex predators, cetaceans are recognized as sentinels for the health of marine ecosystems.  The ability to identify the impacts of anthropogenic contamination on the health of a species requires long term monitoring to establish baseline health parameters.  This makes health measurements that can be sampled from free ranging animals highly desirable.  In the current study, we investigate the utility of skin gene expression profiling to monitor the physiological, health, and contaminant exposure status in bottlenose dolphins.   Remote integument biopsies were obtained from bottlenose dolphins at three locations in the northern Gulf of Mexico prior to oil exposure (May 2010) and during summer and winter of the two years (2010-2011) following their exposure to oil from the Deepwater Horizon oil spill.  A bottlenose dolphin-specific oligonucleotide microarray was used to characterize the skin transcriptomes of 94 individuals from three genetically distinguishable populations in Barataria Bay, Louisiana, Chandeleur Sound, Louisiana, and Mississippi Sound, Mississippi.  Location did not significantly affect the transcriptome patterns of the dolphins included in the study.  In contrast, season had a profound effect on gene expression, with nearly one-third of all genes on the array differing significantly in expression between winter and the warmer seasons (p<0.01, fold-change >1.5). Gene ontology enrichment analysis revealed that processes related to cell proliferation, motility and differentiation dominated the seasonal differences in expression, which likely reflects the differences in ambient temperature to which the skin is exposed, and possibly changes in blood flow.  More subtle differences were seen between spring and summer transcriptomes (1.5% differentially expressed), with two presumed oil-exposed animals presenting gene expression profiles more similar to the summer (exposed) animals than the other spring animals.   Xenobiotic pathway components also showed some seasonal trends, which may reflect crosstalk between xenobiotic pathways and those regulating corticoids, hormones, and cytokines.  Seasonal effects have not previously been considered in studies assessing gene expression in cetaceans, but clearly must be taken into account when applying transcriptomic analyses to investigate their exposure or health status.

first: Frances

last: Van Dolah

middle: G

first: Lauren

last: McGeorge

first: Eric

last: Zolman

first: Todd

last: Speakman

first: Patricia

last: Rosel

last: Mullen

first: Lori

last: Schwacke


title: Genomic maps of TUG1 in human glioma stem cell

status: Public on Nov 23 2016

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

institute: Nagoya City University Graduate School of Medical Sciences

summary: Glioblastomas show heterogeneous histological features. These distinct phenotypic states are thought to be originated by the glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells that have different functional characteristics. We found TUG1, a large non-coding RNA (lncRNA) is highly expressed in GSCs. TUG1 was reported to interact with PRC2 via its exon 2 and represses its target gene expression in trans. In order to identify the genetic loci enriched with TUG1 in GSC, we performed modified RNA pull-down assay coupled with promoter-microarray analysis using BrU-labeled TUG1.

overall_design: RNA pull-down assay coupled with promoter-microarray analysis was performed as two-color hybridization on Agilent human whole genome catalog 2x400k array.

first: Atsushi

last: Natsume

first: Fumiharu

last: Ohka

first: Keiko

last: Shinjo

first: Akira

last: Hatanaka

first: Norihisa

last: Ichimura

first: Yutaka

last: Kondo


title: Array CGH of interspecific hybrid yeasts using multi-species array platform

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

summary: Four hybrid yeast strains isolated from a variety of industrial substrates were hybridized to an array-CGH platform containing probes to query the whole genomes of seven different Saccharomyces species.  For most of the strains we found evidence of multiple interspecific hybridization events and multiple introgressed regions.  The strains queried were GSY205 (isolated from a cider fermentation), GSY505 (a contaminant from a lager beer fermentation), GSY2232 (a commercial wine yeast strain), and GSY312 (a commercial lager beer strain).  Additionally, 3 different rare viable spores derived from laboratory-created interspecific S. cerevisiae-S. bayanus (aka S. uvarum) hybrids were queried, before and after evolution in chemostats, via S. cerevisiae-S. bayanus microarrays.

platform_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

overall_design: Four experimental arrayCGH hybridizations (the four strains mentioned in the summary) were performed, plus a variety of control hybridizations:  4 self-self controls, 1 control each with only one of the seven Saccharomyces species, 1 control using pooled DNA from the 6 non-cerevisiae species, 1 control using pooled S. cerevisiae strains.  Additional aCGH microarray hybridization data from evolved lab-created interspecific hybrid spores are also included in this study.


title: Alcohol-induced anxiolysis is mediated through inhibition of microRNA-494 expression in the amygdala

city: Chicago

first: Subhash

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

summary: MicroRNA profiling of adult rat amygdala following acute ethanol (1g/kg IP) exposure

overall_design: Two experimental groups, Control vs. Acute Ethanol. Biological replicates: 3 control, 3 acute ethanol (Each RNA sample was pooled from two rats)

first: Tara

last: Teppen

first: Harish

last: Krishnan

first: Huaibo

last: Zhang

first: Amul

last: Sakharkar


title: TIFA links Aurora A to NF-κB survival pathway to support chemoresistance in acute myeloid leukemia

status: Public on Nov 21 2016

city: Taipei City

first: Pei-Yu

last: Wu

address: 128 Academia Road, Section 2, Nankang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Aberrant secretion of cytokines contributes to pathogenesis of leukemia and is considered a prognostic signature for recurrence of AML. We asked whether molecular targeting of TIFA can perturb NF-κB-dependent secretion of leukemic cytokines and attain better therapeutic efficacy. We performed cytokine antibody array to profile cytokines secreted by U937 cells in response to TIFA dominant-negative fragments and cytarabine treatment.

overall_design: 4 samples. There are 4 groups: U937 vector cells, U937 vector cells treated with cytarabine, U937 F1F2 cells treated with cytarabine, and U937 F1F2 cells treated with cytarabine.

first: Tong-You

last: Wei

first: Ting-Jung

first: Ming-Daw

last: Tsai


title: Hsf1-ChIP-on-chip: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

status: Public on Nov 11 2016

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

type: Genome binding/occupancy profiling by array

summary: An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA-box promoters are more dynamic because TBP recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA-box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.

overall_design: Hsf1 was depleted from the nucleus using a low dose of rapamycin (0.15 µM) and cells were crosslinked and harvested at different times after the rapamycin addition (0, 15, 30, 60 and 90 minutes). As a control, WT cells were taken along that were subjected to 90 minutes of the same rapamycin concentration. Subsequently, the cells were harvested and ChIP was performed using an anti-GFP antibody. All immunoprecipitations (IPs) were done in biological quadruplicate. After cleanup, the DNA was hybridized to high-density tilling arrays, with the IP sample in one channel and the corresponding input in the other channel. Two out of the four replicates were used for the dye-swap.

first: Wim

last: de Jonge

first: Eoghan

last: O'Duibhir

first: Philip

last: Lijnzaad

first: Dik

last: van Leenen

first: Patrick

last: Kemmeren

first: Frank

last: Holstege


title: A Novel Regulatory Region for Amylose Synthesis in Rice Grains Identified by Systems Genetics Approach.

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

summary: A deeper understanding of the genetics of rice grain starch structure is crucial in tailoring grain digestibility and ensuring cooking quality to meet consumer preferences. Significant association peaks on chromosomes 6 and 7 were identified through genome-wide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known and novel genes with high correlation to the proportion of amylose and amylopectin. A novel SNP in the promoter region of Granule Bound Starch Synthase I (GBSS I) was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A novel GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a non-synonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose novel target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related non-communicable diseases.

overall_design: A microarray experiment was conducted strictly following the One-Color Microarray-Based Gene Expression Analysis protocol using a custom 8 x 60K microarray slide for rice (Agilent,Germany). The cDNA synthesis and cRNA labelling were done using a single-color Low Input Quick Amp Labeling Kit. Microarray hybridization was conducted in a SureHyb chamber assembly using the large-volume Hi-RPM Gene Expression Hybridization Kit.Raw data were generated from the TIFF file using Agilent Feature Extraction software. The quality of the data was judged per batch using the PDF QC report and as a group using QC Validation software. Differentially expressed genes (DEGs) between haplotype 8 (highamylose) and haplotype 4 (waxy) were analyzed.The microarray data sample for haplotype8 highamylose are GQ00086,GQ00125,GQ00170 and haplotype4 waxy are GQ00205,GQ00212.

first: Vito

last: Butardo Jr

first: Roslen

last: Anacleto

first: Sabiha

last: Parween

first: Irene

last: Samson

first: Krishna

last: de Guzman

first: Crisline

last: Alhambra

first: Gopal

last: Misra

first: Nese


title: Rat Astrocyte-Neuron Co-cultures versus purified co-cultured Astrocytes versus Astrocyte alone

status: Public on Nov 09 2016

city: Amsterdam

first: Mark

last: Verheijen

address: De Boelelaan 1085

institute: CNCR, Vrije University Amsterdam

summary:
Profiling of transcriptional changes in rat astrocytes when co-cultured with neurons: comparison of astrocytes cultured alone with astrocytes co-cultured with mouse hippocampal neurons. Co-cultured astrocytes are isolated using cold jet, a novel tool for these neuron-glia cultures.
Over the last decade, the importance of astrocyte-neuron communication in neuronal development and synaptic plasticity has become increasingly clear. Since neuron-astrocyte interactions represent highly dynamic and reciprocal processes, we hypothesized that at least part of the involved astrocyte genes may be regulated as a consequence of their interactions with maturing neurons. In order to identify such neuron-induced astrocyte genes in vitro, we tested the effectiveness of the ‘cold jet’, a new method for separation of neurons from co-cultured astrocytes. The cold jet method is performed under ice-cold conditions and avoids protease-mediated isolation of astrocytes or time-consuming centrifugation, yielding intact astrocyte mRNA with approximately 90% of neuronal RNA removed. Using this method, we executed genome-wide profiling in which RNA derived from astrocyte-only cultures was compared with astrocyte RNA derived from differentiating neuron-astrocyte co-cultures. Data analysis revealed changes in expression of a large number of mRNAs and biological processes, including novel findings. Thus, cold jet is an efficient method to separate astrocytes from neurons in co-culture, and in this study reveals that neurons induce robust gene-expression changes in co-cultured astrocytes.

overall_design: Three-condition experiment, 1) Co-cultures neurons and astrocytes, vs. 2) Astrocytes from co-cultures purified by cold jet treatment, vs 3) Astrocyte alone with cold jet treatment. Two  biological replicates per condition, each replicate derived from >3 independent samples.

first: Andrea

last: Goudriaan


title: MOT1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

first: Marian

last: Groot Koerkamp

overall_design:
The genotype of yeast strains was modified for nuclear depletion experiments as follows: By4742-aa : tor1-1; fpr1del; RPL13A-FKBP12-NAT;MET15;his3-1;leu2; lys2; ura3; matalpha. Mot1-aa: Mot1-FRB-yEGFP-3V5.
Mot1 was depleted from the nucleus by adding 7.5 uM (standard) rapamycin to the cells. Newly synthesized mRNA were extracted using 4tU labeling at different time points: before (0 min) and 10, 20 and 30 minutes after Mot1 depletion. mRNA synthesis rates were measured using two-channel microarrays. Two independent cultures were hybridized on two separate microarrays. For the first hybridization, the Cy5 (red) labeled cRNA from the WT-aa or Mot1-aa strain is hybridized together with the Cy3 (green) labeled cRNA from a 4tU-refpool. This 4tU-refpool was created by pooling 4tU labeled mRNA from three independently grown WT-aa strains without addition of rapamycin. For the replicate hybridization, the labels are swapped.

last: O’Duibhir


title: HSF1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

overall_design:
The genotype of yeast strains was modified for nuclear depletion experiments as follows: By4742-aa : tor1-1; fpr1del; RPL13A-FKBP12-NAT;MET15;his3-1;leu2; lys2; ura3; matalpha. Hsf1-aa: Hsf1-FRB-yEGFP.
Hsf1 was depleted from the nucleus by adding either 7.5 uM (standard) or 0.15 uM (slow) rapamycin to the cells. Newly synthesized mRNA were extracted using 4tU labeling at different time points: before (0 min) and 15, 30, 60 and 90 minutes after Hsf1 depletion. mRNA synthesis rates were measured using two-channel microarrays. Two independent cultures were hybridized on two separate microarrays. For the first hybridization, the Cy5 (red) labeled cRNA from the WT-aa or Hsf1-aa strain is hybridized together with the Cy3 (green) labeled cRNA from a (4tU-)refpool. This 4tU-refpool was created by pooling 4tU labeled mRNA from two independently grown WT-aa strains without addition of rapamycin. For the replicate hybridization of the slow depletion timecourse, the labels are swapped.

first: Wim

last: de Jonge


title: Alteration of gene expression profile of cerebelllar neuron-enriched cultures from neonatal rats by nicotine, acetamiprid, or imidacloprid treatment [imidacloprid]

status: Public on Oct 04 2016

city: Setagaya-ku

first: Junko

last: Kimura-Kuroda

state: Tokyo

address: 2-1-6, Kamikitazawa

department: Department of Brain Development and Neural Regeneration

institute: Tokyo Metropolitan Institute of Medical Science

summary: Neonicotinoids are considered safe because of their low affinities to mammalian nicotinic acetylcholine receptors (nAChRs) relative to insect nAChRs. However, because of importance of nAChRs in mammalian brain development, there remains a need to establish the safety of chronic neonicotinoid exposures with regards to children’s health. Here we examined the effects of long-term (14 days) and low dose (1 μM) exposure of neuron-enriched cultures from neonatal rat cerebellum to nicotine and two neonicotinoids: acetamiprid and imidacloprid. Immunocytochemistry revealed no differences in the number or morphology of immature neurons or glial cells in any group versus untreated control cultures. However, a slight disturbance in Purkinje cell dendritic arborization was observed in the exposed cultures. Next we performed transcriptome analysis on total RNAs using microarrays, and identified significant differential expression (p < 0.05, q < 0.05, ≥1.5 fold) between control cultures versus nicotine-, acetamiprid-, or imidacloprid-exposed cultures in 34, 48, and 67 genes, respectively. Common to all exposed groups were nine genes essential for neurodevelopment, suggesting that chronic neonicotinoid exposure alters the transcriptome of the developing mammalian brain in a similar way to nicotine exposure. Our results highlight the need for further careful investigations into the effects of neonicotinoids in the developing mammalian brain.

overall_design: Using cerebellar neuron-enriched cultures from neonatal rats (1 day), chronic exposure of nicotine (1 μM), imidacloprid (1 μM), or acetamiprid (1 μM) was examined from 2 days to 16 days in vitro. After 16 days in vitro, samples (n=6 /each group) of cerebellar neuron-enriched cultures including control and each treatment were taken for gene expression analysis.

first: Masaharu

last: Hayashi


title: Alteration of gene expression profile of cerebelllar neuron-enriched cultures from neonatal rats by nicotine, acetamiprid, or imidacloprid treatment


title: Candida glabrata WT and mutants under iron starvation

status: Public on Oct 05 2016

city: Jena

first: Sascha

last: Brunke

address: Beutenbergstr. 11a

department: MPM

country: Germany

institute: Hans-Knöll-Institut

summary: Transcriptional time series of Candida glabrata under iron starvation (SD medium without Fe). Wild type and deletion mutants of the iron-related transcription factors Aft1 and Sef1, as well as of the iron uptake transporter Ftr1 as a positive control.

overall_design: Common reference design, reference is log-phase wild type in YPD complex medium

first: Franziska

last: Gerwien


title: Different pathogenic stimuli induce specific metabolic rewiring in human monocytes

status: Public on Oct 19 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Recent studies have demonstrated that upon encountering a pathogenic stimulus, robust metabolic rewiring of immune cells occurs. A switch away from oxidative phosphorylation to glycolysis, even in the presence of sufficient amounts of oxygen (akin the Warburg effect), is typically observed in activated innate and adaptive immune cells and is thought to accommodate adequate inflammatory responses. However, whether the Warburg effect is a general phenomenon applicable in human monocytes exposed to different pathogenic stimuli is unknown. Our results using human monocytes from healthy donors demonstrate that the Warburg effect only holds true for TLR4 activated cells. Although activation of other TLRs leads to an increase in glycolysis, no reduction or even an enhancement in oxidative phosphorylation is observed. Moreover, specific metabolic rewiring occurs in TLR4 vs. TLR2 stimulated cells characterized by altered gene expression profiles of pathways related to metabolism, changes in spare respiratory capacity of the cells and differential regulation of mitochondrial enzyme activity. Similarly, results from ex vivo and in vivo studies demonstrate metabolic rewiring of immune cells that is highly dependent on the type of pathogenic stimulus. Although the Warburg effect is observed in human monocytes after TLR4 activation, we propose that this typical metabolic response is not applicable to other inflammatory signalling routes including TLR2 in human monocytes. Instead, each pathogenic stimulus and subsequently activated inflammatory signalling cascade induces specific metabolic rewiring of the immune cell to accommodate an appropriate response.

overall_design: Human CD14+ monocytes, purified from freshly isolated peripheral blood mononuclear cells from 5 healthy donors, were stimulated with either 10 μg/mL Pam3Cys, 10 ng/mL LPS, or cell culture medium alone (RPMI) for 24h, whereafter gene expression profiling was performed.

first: Ekta

last: Lachmandas

first: Lily

last: Boutens

first: Jacqueline

last: Ratter

first: Anneke

last: Hijmans

first: Reinout

last: van Crevel

first: Mihai

last: Netea

first: Rinke

last: Stienstra


title: Alteration of gene expression profile of cerebelllar neuron-enriched cultures from neonatal rats by nicotine, acetamiprid, or imidacloprid treatment [acetamiprid]


title: Alteration of gene expression profile of cerebelllar neuron-enriched cultures from neonatal rats by nicotine, acetamiprid, or imidacloprid treatment [nicotine]


title: Transcript profiling in the liver of early-lactating dairy cows fed conjugated linoleic acid

status: Public on Sep 28 2016

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary: In the present study, transcript profiling was carried out in the liver samples from wk 5 of lactation in order to identify genes and pathways regulated by rumen-protected CLA during early lactation. The first wks after parturition represent a critical phase in the productive cycle of high-yielding dairy cows because the liver experiences pronounced metabolic and inflammatory stress which increases the risk to develop liver-associated diseases, such as fatty liver and ketosis.

overall_design: For microarray analysis, RNA pools (n = 5) each for the CLA group and the control group were prepared. Each RNA pool comprised RNA from 4 different cows. The RNA pools were used for hybridization to the GeneChip® Bovine Genome Array (Affymetrix, High Wycombe, UK).

first: Klaus

last: Eder


title: Fast revascularization of the injured area is essential to support zebrafish heart regeneration

status: Public on Sep 25 2016

city: Bad Nauheim

first: Rubén

last: Marín-Juez

address: Ludwigstrasse 43

institute: Max Planck Institute

summary: To better understand the possible mechanisms that vegfaa mutants display to compensate for the lack of vegfaa, we performed transcriptomic profiling of vegfaa+/+ and vegfaa-/- ventricles. Total RNA was isolated from hearts extracted from vegfaa+/+ and vegfaa-/- fish (8 months old) pooling 4 hearts per sample.

overall_design: Total RNA was isolated from vegfaa+/+ and vegfaa-/- fish was isoleted. Each sample was generated by pooling 4 vegfaa+/+ hearts (Control) and 4 vegfaa-/- hearts (Mutants).

first: Michele

last: Marass

first: Sebastien

last: Gauvrit

first: Andrea

last: Rossi

first: Shih-Lei

last: Lai

first: Stefan

last: Materna

first: Brian

last: Black

first: Didier

middle: Y

last: Stainier


title: Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming

status: Public on Sep 27 2016

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

summary: Clipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties, plant and microbial communities, in particular microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C4 peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. With less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38-137% in response to either clipping or the combined treatment, which could weaken the long-term soil carbon stability and trigger a positive feedback to warming. Clipping alone also increased the abundance of genes for nitrogen fixation, mineralization and denitrification by 32-39%. The potentially stimulated nitrogen fixation could help compensate for the 20% decline in soil ammonium caused by clipping alone, and contribute to unchanged plant biomass. Moreover, clipping tended to interact antagonistically with warming, especially on nitrogen cycling genes, demonstrating that single factor studies cannot predict multifactorial changes. These results revealed that clipping alone or in combination with warming altered soil and plant properties, as well as the abundance and structure of soil microbial functional genes. The aboveground biomass removal for biofuel production needs to be re-considered as the long-term soil carbon stability may be weakened.

sample_organism: Bacteria Archaea Fungi Viruses

platform_organism: Bacteria Archaea Fungi Viruses

overall_design: 24 subsuface (0-15cm) soil samples from an Oklahoma tall grassland experimental warming site were analyzed. These samples consist of four different treatment levels (UU: no clipping-no warming; UW: no clipping-warming; CU: clipping-no warming; CW: clipping-warming) from six biological replicated blocks.

first: Kai

last: Xue

first: Mengting

last: Yuan

first: Jianping

last: Xie

first: Dejun

last: Li

first: Yujia

last: Qin

first: Lauren

last: Hale

first: Liyou

last: Wu

first: Ye

last: Deng

first: Zhili

last: He

first: Joy

last: Van Nostrand

first: Yiqi

last: Luo

first: James

last: Tiedje


title: MeDIP-Chip from deliveries of control fetuses or fetuses with NTDs

status: Public on Sep 24 2016

first: Feifei

last: Ma

address: Road 2 Yabao

institute: Capital Institue of Pediatrics

type: Methylation profiling by genome tiling array

summary: Neural-tube defects (NTDs) are common birth defects of complex etiology. Although many studies have confirmed a genetic component, the exact mechanism between DNA methylation and NTDs remains unclear.In this study,the alteration of methylation from placental tissues of normal infants or with NTDs.Results demonstrated that DNA methylation changed in specific gene location.

overall_design: Comparison the DNA methylation site of placenta tissues between control fetuses with NTD's fetuses

first: Jianxin


title: Gene Expression Profiling in the Hippocampus of Orchidectomized Rats

status: Public on Sep 22 2016

city: Covilhã

first: Telma

last: Quintela

address: Av. Infante D. Henrique

department: Health Sciences Research Centre

country: Portugal

institute: University of Beira Interior

summary: The present study was conducted to identify relevant genes that could be involved in the action of androgens in rat hippocampus. We compared hippocampal gene expression between controls and orchidectomized male rats.

overall_design: For microarray analysis hippocampus were collected from sham (control) and orchidectomized male rats, in a total of 3 biological replicates.

first: Helena

last: Marcelino

first: Isabel

last: Gonçalves

first: Filipa

last: Patriarca

first: Cecilia

last: Santos


title: Profiling of lncRNAs and mRNAs in liver, adipose and muscle tissue in mice under representative metabolic conditions

city: Bethesda

first: Haiming

last: Cao

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: To systemically identify long non-coding RNAs (lncRNAs) regulating energy metabolism, we performed transcriptome analyses to simultaneously profile mRNAs and lncRNAs in key metabolic organs in mice under pathophysiologically representative metabolic conditions. Of 4759 regulated lncRNAs, function-orientated filters yield 359 tissue-specifically regulated and metabolically sensitive lncRNAs which are predicted by lncRNA-mRNA correlation analyses to function in diverse aspects of energy metabolism. An liver metabolically sensitive lncRNA was experimentally confirmed in mice to suppress lipogenesis by forming a negative feedback loop in the SREBP1c pathway. Taken together, this study supports that a class of lncRNAs function as important metabolic regulators, and establishes a framework for systemically investigating the role of lncRNAs in physiological homeostasis.

overall_design: lncRNA and mRNA expressions were measured in liver, adipose, and muscle tissues from male mice under the following five pathophysiologically representative metabolic conditions: 24h fasting, 4h refeeding following 24h fasting, short term (48 hours) high fat diet feeding, long-term (12 weeks) high-fat diet feeding, and ob/ob mouse. Four to five biological replicates were used in each condition.

first: Ling

last: Yang

first: Ping

first: Wenjing

first: Xiangbo

last: Ruan

first: Kurtis

last: Kiesewetter

first: Jun

last: Zhu


title: Gene expression within the prefrontal cortex and amygdala in a developing model of high and low anixety and depression-like behavior in rats

status: Public on Sep 20 2016

city: Blacksburg

first: Sarah

middle: Megan

last: Clinton

state: Virginia

address: 1981 Kraft Dr., Integrated Life Sciences Building 0913

department: School of Neuroscience

institute: Virginia Polytechnic Institute and State University

summary:
Individual differences in human temperament can increase the risk of psychiatric disorders like depression and anxiety. Our laboratory utilized a rat model of temperamental differences to assess neurodevelopmental factors underlying emotional behavior differences. Rats selectively bred for low novelty exploration (Low Responders, LR) display high levels of anxiety- and depression-like behavior compared to High Novelty Responder (HR) rats. Using transcriptome profiling, the present study uncovered vast gene expression differences in the early postnatal HR versus LR limbic brain, including changes in genes involved in cellular metabolism. These data led us to hypothesize that rats prone to high (versus low) anxiety/depression-like behavior exhibit distinct patterns of brain metabolism during the first weeks of life, which may reflect disparate patterns of synaptogenesis and brain circuit development.
All samples were generated from Sprague-Dawley male rats selectively bred for high novelty response (HRs) or low novelty response (LRs).

overall_design: Within each age and brain regions, the sample size of either HR or LR is 5 samples.

first: Chelsea

last: McCoy


title: Transcriptomic data to assess hexavalent chromium mode of action in mice and rats [rat]

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

summary: In order to evaluate the mechanisms underlying hexavalent chromium (Cr(VI)) responses, mice and rats were treated with varying concentrations of Cr(VI) in drinking water, as sodium dichromate dihydrate (SDD). Potential transcriptomic responses were evaluated through microarray analysis.

overall_design:
Mice and rats were exposed to varying concentration of Cr(VI) through drinking water for either 7 or 90 days. Animals were sacrificed on days 8 and 91, respectively, and tissue samples were collected from the small intestine (i.e. duodenum and jejunum) and oral mucosa (palate). Tissue samples were processed and total RNA analyzed using Agilent 4x44K Whole Genome Microarrays.
Please note that two-dye Agilent arrays were used but only Cy3 signal was processed.

first: Chad

last: Thompson

first: Mark

last: Harris


title: Gene expression changes between wildtype (WT) Nicotiana benthamiana plants with and without infection with Potato Spindle Tuber Viroid (PSTVd)

status: Public on Sep 19 2016

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: WT plants (at the five-leaf stage) were infected with PSTVd strain NB by agroinfiltration. Three weeks post infection (3 wpi) young leaves were collected from infected and uninfected (control) WT plants and used in a custom genome-wide gene expression microarray (4x 180K Sureprint G3 microarray, Agilent)

overall_design: One comparison with three biological replicates : leaves of WT N. benthamiana plants infected with PSTVd compared to leaves of uninfected WT N. benthamiana plants

first: Konstantina

last: Katsarou

first: Thomas

last: Van Leeuwen

first: Kriton

last: Kalantidis


title: Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE NanoString)

city: Spartanburg

first: Bernard

last: Omolo

address: 800 University Way

department: Mathematics and Computer Science

institute: University of South Carolina - Upstate

summary:
Background: The KRAS gene is mutated in about 40% of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistatnce to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60% of patients with a wild type KRAS fail to respond to EGFRi treatment, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues.
Methods: In this study, we evaluated the translation of an 18-gene RAS pathway signature score from FF to FFPE in 54 CRC cases, using a head-to-head comparison of five technology platforms. FFPE-based technologies included the Affymetrix GeneChip (Affy), NanoString nCounter(NanoS), Illumina whole genome RNASeq (RNA-Acc), Illumina targeted RNASeq(t-RNA), and Illumina stranded Total RNA-rRNA-depletion (rRNA).
Results: Using Affy_FF as the gold standard, initial analysis of the 18-gene RAS scores on all 54 samples shows varying pairwise Spearman correlations, with (1) Affy_FFPE(r=0.233, p=0.090); (2) NanoS_FFPE(r=0.608, p<0.0001); (3) RNA-Acc_FFPE(r=0.175, p=0.21); (4) t-RNA_FFPE (r=-0.237, p=0.085); and (5) t-RNA (r=-0.012, p=0.93). These results suggest that only NanoString has successful FF to FFPE translation. The subsequent removal of identified problematic samples (n=15) and gene (n=2) further improves the correlations of Affy_FF with three of the five technologies: Affy_FFPE (r=0.672, p<0.0001); NanoS_FFPE (r=0.738, p<0.0001); and RNA-Acc_FFPE (r=0.483, p=0.002).
Conclusions: Of the five technology platforms tested, NanoString technology provides a more faithful translation of the RAS pathway gene expression signature from FF to FFPE than the Affymetrix GeneChip and multiple RNASeq technologies. Moreover, NanoString was the most forgiving technology in the analysis of samples with presumably poor RNA quality. Using this approach, the RAS signature score may now be reasonably applied to FFPE clinical samples.

overall_design: Fifty-four (54) FFPE evaluable tumor specimens were selected from a larger multi-center cohort of 468 well-characterized colorectal adenocarcinoma patients whose tissues were obtained between October 2006 and September 2010 at the University of South Florida. The sample cohort was composed of tumor samples that were available as matched fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pairs.

first: Mingli

first: Fang

last: Lo

first: Michael

last: Schell

first: Sharon

last: Austin

first: Kellie

last: Howard

first: Anup

last: Madan

first: Timothy

last: Yeatman


title: Gene profiling of naive, virus-induced and inflammatory-induced memory CD8 T lymphocytes in homeostatic condition and after stimulation.

city: LYON

first: Jacqueline

last: MARVEL

address: 21 AV TONY GARNIER

country: France

institute: INSERM

summary: Transcriptome analysis comparing naive, protective and non-protective spleen memory CD8 T lymphocytes were conducted to identify key functions associated with memory CD8-mediated immune protection.  Memory CD8 T cells generated in response to influenza or vaccinia infection (Flu-memory and VV-memory) were compared to inflammatory memory cells (TIM) that were generated by peptide in inflammatory context. Gene expression analysis was performed on quiescent and re-stimulated CD8 T cells.

overall_design: Influenza or Vaccinia virus induced memory cells (Flu-TM or VV-TM) were generated in C57BL/6J mice that received naive NP68-specific F5xLy5.1 CD8+ T cells one day before intranasal infection with Flu-NP68 or VV-NP68. Specific memory F5 CD8 T cells from spleens were FACS-sorted at least 6 weeks after immunization. T Inflammatory memory (TIM) cells were generated by i.p. injection of NP68 peptide in naive thymectomized F5 mice. Purified CD8 T cells were stimulated with NP68 peptide (restimulated condition, R) or not (homeostatic condition, H) for 2 hours

last: Marvel

first: Yann

last: Leverrier

first: Sophia

last: Djebali


title: Mycobacterium tuberculosis Persister Stimulon

status: Public on Sep 23 2016

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis mc2 7000 surviving 4 days of isoniazid treatment relative to untreated to investigate genes relevant to survival in genotypically isoniazid-sensitive cells

overall_design: Two condition experiment, 4-day isoniazid treated vs. before treatment. Biological replicates: 3 of each condition, independently grown and harvested. One replicate per array, third array is a dye-flip.


title: Sex hormone responsive genes in rat choroid plexus

status: Public on Sep 18 2016

first: Telma

last: Quintela

summary: In order to gain additional insight into the functional role of sex steroid hormones in the choroid plexus, the present study compared gene expression patterns between sham and gonadectomized female/male rats choroid plexus.

overall_design: For microarray analysis choroid plexus were collected from sham (control) and gonadectomized female and male rats. Equal amounts of RNA extract from the 3 pools of sham (control) or 3 pools of gonadectomized animals were used.

first: Isabel

last: Gonçalves

first: Laura

last: Carreto

first: Manuel

last: Santos

first: Helena

last: Marcelino

first: Filipa

last: Patriarca

first: Cecilia


title: NIPI-3 regulates the expression of C. elegans immune genes

city: Boston

first: Deborah

last: McEwan

state: MA

address: 185 Cambridge St CPZN 7250

institute: MGH

summary:
Many pathogens secrete toxins that target key host processes resulting in the activation of immune pathways. The secreted Pseudomonas aeruginosa toxin Exotoxin A (ToxA) disrupts intestinal protein synthesis which triggers the induction of a subset of P. aeruginosa-response genes in the nematode Caenorhabditis elegans. We found that losing one ToxA-induced C. elegans gene, the Tribbles pseudokinase ortholog nipi-3, results in hypersusceptibility to both P. aeruginosa and ToxA. We determined that NIPI-3 mediates the post-developmental expression of intestinal immune genes and proteins and primarily functions in parallel to known immune pathways, including p38 PMK-1 MAPK signaling.  Here we present the microarray data that was used to determine that (1) nipi-3 regulates immune gene expression and that  (2) nipi-3 and pmk-1 regulate non-overlapping gene sets consistent with them functioning in parallel.
We used microarray analysis to identify the genes regulated by nipi-3 and pmk-1 at the L4 stage.

overall_design: There are nine samples total that comprise three biological replicates of L4 C. elegans animals grown at 20C on OP50. The following genotypes were compared: wild type (N2), nipi-3(fr4), pmk-1(km25).

first: Frederick

last: Ausubel


title: The effect of onion exposure on gene expression profiles in intestinal Caco-2 cells

status: Public on Sep 16 2016

first: Nicole

last: de Wit

address: Bornse Weilanden 9

department: Food & Biobased Research

institute: Wageningen UR

summary: Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of food compounds on (intestinal) health. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were incubated with in vitro digested onion extracts for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify onion-induced gene expression profiles in Caco-2 cells, digested yellow onion and white onion samples were compared to a digest control samples. Results: We found that yellow onion (n=5586, p<0.05) had a more pronounced effect on gene expression than white onion (n=3688, p<0.05). However, a substantial number of genes (n=3281, p<0.05) were affected by both onion variants in the same direction. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Conclusion: our data indicate that the in vitro Caco-2 intestinal model can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.

overall_design: Microarray analysis was performed on 21-days differentiated Caco-2 cells incubated with digested white onion (WOd), digested yellow onion (YOd) and saline digest (Sd = control) for 6 hours. This experiment was performed three times, so three independent biological replicates per treatment were included in the microarray analysis.

first: Coen

last: Govers

first: Mark

middle: V

last: Boekschoten

first: Jurriaan

last: Mes


title: Gene expression data from Mycobacterium tuberculosis-infected WT and miR-155-/- bone-marrow derived macrophages [validation]

status: Public on Sep 14 2016

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary:
How the complex interaction between Mycobacterium tuberculosis (Mtb) and the host is regulated during infection is still not well understood. Using a systems biology approach, we demonstrate here that miR-155 is one of several microRNAs that regulate host gene expression over the first 48 hours of Mtb infection in macrophages. miR-155 regulates the cell survival of Mtb-infected macrophages through SHIP1/AKT signaling.
Using timecourse gene expression data, we constructed a miRNA regulatory network for the innate immune response to Mtb infection by WT macrophages. The network suggested a role for seven miRNAs in regulating the host response to Mtb, with miR-155 being one of them. We then validated a role for miR-155 by comparing the response between WT and miR-155-/- macrophages.

overall_design:
Three replicates of WT C57BL/6 BMMs were collected at 0, 4, 8, 24, and 48 hours post-infection with Mycobacterium tuberculosis, H37Rv strain (MOI 5). The regulatory network was then validated with WT and miR-155-/- BMM samples collected at 0 and 8 hours post-infection (three replicates each).
This dataset represents WT and miR-155-/- BMM samples collected at 0 and 8 hours post-infection (three replicates each).

first: James

last: Sissons

first: Alissa

last: Rothchild

first: Alan

last: Aderem


title: Gene expression data from Mycobacterium tuberculosis-infected WT and miR-155-/- bone-marrow derived macrophages

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

overall_design: Refer to individual Series


title: Assessing the mutagenic and estrogenic effect potential of pharmaceuticals and of their transformation products. Implications in the gene expression profiling

status: Public on Sep 13 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Mixtures of diclofenac, sulfamethoxazole and ofloxacin and their photolysed mixtures were evaluated for their mutagenicity and estrogenicity. Implications in the gene expression profiling were evaluated as well
Microarrays were used to understand the effects of exposure to mixtures of pharmaceuticals as contaminants of emerging concern

overall_design: For a better understanding of photolabile pharmaceuticals, human breast cancer cells T47D-KBluc were exposed to a mixture of diclofenac (50uM), sulfamethoxazole (50uM) and ofloxacin (50uM). A part of the setup was irradiated with UV-Light for 15 minutes to test the reaction of possible created products.

first: Marlen

middle: I

last: Vasquez

first: Despo

last: Fatta-Kassinos


title: Gene expression data from Mycobacterium tuberculosis-infected WT and miR-155-/- bone-marrow derived macrophages [timecourse]

overall_design:
Three replicates of WT C57BL/6 BMMs were collected at 0, 4, 8, 24, and 48 hours post-infection with Mycobacterium tuberculosis, H37Rv strain (MOI 5). The regulatory network was then validated with WT and miR-155-/- BMM samples collected at 0 and 8 hours post-infection (three replicates each).
This dataset represents three replicates of WT C57BL/6 BMMs were collected at 0, 4, 8, 24, and 48 hours post-infection with Mycobacterium tuberculosis, H37Rv strain (MOI 5).


title: Analyses of transcriptomic responses to heavy metal exposure  in Manila clam collected in Venice lagoon areas characterized by different anthropogenic impact

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: A Ruditapes philippinarum microarray platform was developed to assess variations on transcritpomic response to copper exposures in Manila clam colelctted in Venice lagoon areas subjected to different anthropogenic impact

overall_design: A comparative analysis of gene expression was conducted in Manila clam R.philippinarum collected in different areas of Venice lagoon and exposed to copper.  After sampling, clams were transferred to the laboratory in refrigerated boxes. Thirty clams per site were immediately used (WILD) for tissue collection. In particular, to perform gene expression analyses digestive gland has been dissected and transferred in RNAlater® solution. To increase homogeneity across samples the average size of all collected animals was similar.  A total of 100 clams have been considered for chemical analyses to reveal concentration of dioxins and furans (PCDDs/PCDFs), polychlorinated biphenyls (PCBs), dioxin-like PCBs (PCBs-DL), hexachlorobenzene (HCB), Cu, Cd, Pb, Hg), in clam whole-body. The remaining clams were kept in the laboratory for 7 days in two different tanks with a sandy bottom and aerated seawater (31 ± 1 psu salinity, 8 ± 0.5 °C, 8.1 pH) and were fed microalgae (Isochrysis galbana). The seawater was renewed every other day. After the 7-day acclimation period (ACCL), 30 clams per tank (=site) were used for digestive gland collection, whereas the remaining clams were exposed to 50 µg Cu l-1 (as CuSO4) for 7 more days, which is an environmentally realistic concentration. In this case, the clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal). The seawater was changed daily, and copper and microalgae (I. galbana at an initial concentration of approximately 150,000 cells l-1) were added. Digestive gland were collected after 1 (T1), 3 (T2) and 7 (T3) days of exposure. Gene expression profiling was performed using an Manila clam-specific oligo-DNA microarray of 15,037 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Milan

last: Massimo

first: Pauletto

last: marianna

first: Matozzo

last: Valerio


title: Antifungal effect of Perillyl alcohol (PA) on C. albicans SC5314

status: Public on Sep 15 2016

city: Gurgaon

first: Saif

last: Hameed

state: Haryana

address: Amity Education Valley

institute: Amity University Haryana

summary: Transcriptional profiling of Candida cells comparing the control vs PA treated cells

overall_design: Agilent custom one-color experiment,Organism: Candida albicans, Whole Genome Candida albicans 8x15K (AMADID: 026377) designed  by Genotypic Technology Private Limited. One-condition experiment, control vs. PA treated cells.

first: Moiz

middle: A

last: Ansari

first: Zeeshan

last: Fatima


title: Global gene expression analysis of donor cells, low passage episomal stromal and non-stromal primed myeloid iPSC, and hESC

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

summary: Global gene expression analysis of (a) human embryonic stem cells, (b) low passage episomal stromal-primed iPSC derived from growth-factor activated CD34+ myeloid progenitors from cord blood or GCSF mobilized peripheral blood, and (d) samples of donor fibroblasts or myeloid progenitors

overall_design: Total RNA was harvested from indicated donor cells, hESC, or iPSC. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series. A single sample of each cell line was used for this analysis.

first: Tea

last: Park

first: Jeffrey

last: Huo

first: C

last: Talbot

first: Wayne

last: Yu

first: Karan

last: Verma

first: Ludovic

last: Zimmerlin

first: Ann

last: Peters

first: Ian

last: Kaplan

first: Kejin

last: Hu

first: Igor

last: Slukvin

middle: T


title: Global CpG Methylation profiling of donor cells, induced pluripotent stem cells, and human embryonic stem cells

summary: Global CpG methylation profiling using Illumina 27k Infinium platform of (a) human embryonic stem cells, (b) low passage episomal stromal-primed myeloid iPSC, (c) intermediate passage fibroblast iPSC, and (d) samples of corresponding donor cells.

overall_design: Genomic DNA was harvested from indicated donor cells, hESC, or iPSC. A single sample of each cell line was used for this analysis.

first: Kurinji

last: Pandiyan

middle: C

first: Renee

last: Reijo-Pera

first: Stephen

middle: B

last: Baylin


title: Global gene expression analysis of donor cells, low passage episomal stromal-primed myeloid iPSC, and intermediate passage fibroblast iPSC.

summary: Global gene expression analysis of (a) human embryonic stem cells, (b) low passage episomal stromal-primed myeloid iPSC, (c) intermediate passage fibroblast iPSC, and (d) samples of corresponding donor cells.

overall_design: Total RNA was harvested from indicated donor cells, hESC, or iPSC, and analyzed on Illumina HumanHT-12 V3.0 expression beadchips. A single sample of each cell line was used for this analysis.


title: Gene profiling of naive and Listeria monocytogenes-induced memory CD8 T lymphocytes in homeostatic condition and after stimulation.

status: Public on Sep 09 2016

first: Jacqueline

last: MARVEL

summary: Transcriptome analysis comparing naive and Listeria monocytogenes-induced spleen memory CD8 T lymphocytes were conducted to identify key functions associated with memory CD8-mediated immune protection.  Gene expression analysis was performed on quiescent and re-stimulated CD8 T cells.

overall_design: Listeria monocytogenes-induced memory cells (LM-memory) were generated in C57BL/6J mice that received naive NP68-specific F5xLy5.1 CD8+ T cells one day before i.v. infection with 3000 Listeria monocytogenes bacteria expressing NP68 epitope. Specific memory F5 CD8 T cells from spleens were FACS-sorted at least 6 weeks after immunization. Naive F5 CD8 T cells were purified from naive F5 mice. Purified CD8 T cells were stimulated with NP68 peptide (restimulated condition, R) or not (homeostatic condition, H) for 2 hours.

last: Marvel

first: Sophia

last: Djebali

first: Yann

last: Leverrier


title: Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants

status: Public on Sep 10 2016

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary:
Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix–loop–helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the posttranslational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation.
We used microarray data to investigate the contribution of different pathways to cold tolerance of Arabidopsis thaliana .

overall_design: The lines wt (wild type; Col-0), bri1-301, ces-D and qM (quadruple mutant of bee1, bee2, bee3 and ces-2) were treated with 4°C for 3 d and analysed in quadruplicate. As control plants of the same lines were kept at 21°C and also analysed in quadruplicate.

first: Marina

last: Eremina

first: Simon

middle: J

last: Unterholzner

first: Ajith

last: Rathnayake

first: Marcos

last: Castellanos

first: Mamoona

last: Khan

first: Karl

last: Kugler

first: Sean

last: May

first: Klaus

middle: F

last: Mayer

first: Wilfried

last: Rozhon

first: Brigitte

last: Poppenberger


title: investigation of the pathogenesis of H1N1 influenza virus and swine streptococcus suis serotype 2 co-infection in pigs by microarray analysis

city: wuhan

first: Lin

last: xian

state: Hubei

address: shizishan street,number 1

department: College of Veterinary Medicine

institute: Huazhong Agricutural University

summary: Swine H1N1 influenza virus and streptococcus suis serotype 2 (SS2) are two important contributors to the porcine respiratory disease complex, which have significant economic impacts. Clinically, swine influenza virus and swine streptococcus suis co-infection is common, which will increase the mortality. However, the pathogenesis of the co-infection remains largely unkown. To explore it, gene expression profiling was to performed to detect comprehensive analysis of the global host response induced by H1N1 virus infection alone, SS2 infection alone, H1N1-SS2 co-infection and PBS control.

overall_design: A total of 12 healthy pigs were randomly allocated to 4 groups with 3 pigs each: H1N1 group, SS2 group, H1N1-SS2 group and control group. At the age of 35 days, pigs in H1N1 and H1N1-SS2 groups were intranasaly challenged with A/swine/Hubei/101/2009(H1N1) strain and others were treated similarly with PBS. 3 days after H1N1 virus challenge, pigs in SS2 and H1N1-SS2 groups were inoculated intranasally with PBS containing SS2 strain ZY05, others were treated similarly with PBS.

last: Xian

first: Huang

last: Canhui

first: Shi

last: Jian

first: Wang

last: Ruifang

first: Sun

last: Xin

first: Jin

last: Meilin


title: Global gene expression analysis of human embryonic stem cells, adult fibroblasts, and CD34+ cord blood (CB) cells before, during, and after generation of stromal primed and non-stromal primed episomal induction of pluripotency

first: Elias

last: Zambidis

summary: Global gene expression analysis of (a) human embryonic stem cells, (b) adult fibroblasts with and without nucleofection of SOKM, (c) CD34+ cord blood cells at various time points during induction of pluripotency with SOKM, with or without co-culture with bone marrow stromal cells (BMSC), and (d) resulting stromal primed and non-stromal primed cord blood CD34+ myeloid iPSC

overall_design: Total RNA was harvested from adult fibroblasts, adult fibroblasts three days after nucleofection with 4F (SOKM),  human myeloid progenitors: Non-nucloefected CD34+ Day -3 unstimulated cord blood (CB) cells, Day 0 growth factor stimulated CB cells, Day +3 CB cells with or without nucleofection at Day zero and with or without Day zero to Day +3 co-culture with bone marrow stromal cells (BMSC), followed by FACS-purification of CD45+ myeloid progenitors, Day 23 CB cells nucleofected on day zero and co-cultured on BMSC from Day Zero to Day +3, undifferentiated H9 human embryonic stem cells, and low passage episomal stromal-primed iPSC derived from growth-factor activated CD34+ myeloid progenitors from cord blood or GCSF mobilized peripheral blood. Illumina HumanHT-12 V4.0 expression beadchips were used for all samples in this series. Three independent samples of each condition were each run on individual microarrays.

first: Tea

middle: S

last: Park

first: Jeffrey

last: Huo

first: C

last: Talbot

first: Wayne

last: Yu

first: Karan

last: Verma

first: Ludovic

last: Zimmerlin

first: Ann

last: Peters

first: Ian

last: Kaplan

first: Kejin

last: Hu

first: Igor

last: Slukvin


title: DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods

status: Public on Sep 06 2016

city: Ribeirao Preto

first: Victor

middle: Hugo

last: Aquino

state: Sao Paulo

address: Avenida do Cafe, s/n

department: Fculty of Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

summary: Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods.

sample_organism:
Aedes albopictus
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4
Chikungunya virus
Zika virus

overall_design: The SMAvirusChip v2 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4943  viral probes for the detection of 416 viruses (112 viruses transmitted by small mammals and 304 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.

first: Mohd

last: Khan

first: Amanda

last: Trabuco

first: Helda

middle: L

last: Alfonso

first: Mario

last: Figueiredo

first: Weber

last: Batista

first: Soraya

last: Badra

first: Luiz

first: Marco

last: Lavrador

middle: H


status: Public on Sep 05 2016

sample_organism:
Aedes aegypti
Aedes albopictus
Homo sapiens
Togaviridae
Flaviviridae
Flavivirus
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4
St. Louis encephalitis virus
West Nile virus
Yellow fever virus
Rhabdoviridae
Piry virus
Dengue virus
Chikungunya virus
Rio Mamore hantavirus
Mayaro virus
Ilheus virus
Chlorocebus sabaeus
Mucambo virus
Bussuquara virus
Cacipacore virus
Iguape virus
Rocio virus
Guaroa virus
Oropouche virus

overall_design: The SMAvirusChip v1 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4209 viral probes for the detection of 409 viruses (109 viruses transmitted by small mammals and 300 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.


title: Gene expression signatures in activated CD4 T cells to predict_vaccine responses

status: Public on Sep 12 2016

city: Palo Alto

first: Jorg

last: Goronzy

address: Rm E4201, Bldg100, 3801 Miranda Ave

department: Medicine

institute: Stanford University

summary: To decipher the molecular mechanisms underlying_variable_vaccine responses, T- and B-cell responses to_vaccination with a life zoster_vaccine were examined in individuals of different ages. Diminished generation of long-lived memory T cells in older individuals was mainly caused by increased T cell loss after the peak response while the expansion of antigen-specific T cells was not affected by age. Gene expression in activated CD4 T cells co-expressing HLA-DR and CD38 at the time of the peak response identified gene modules related to cell cycle regulation and DNA repair that correlated with the contraction phase of the T cell response and consequently the generation of long-lived memory cells.

overall_design: We immunized 17 individuals aged 50 to 75 years with the life zoster vaccine Zostava. We measured VZV-specific T cell frequencies by IFN-γ–specific ELISpot, and VZV-specific antibody titers by ELISA. Gene expression in purified CD4 T cells co-expressing CD38 and HLA-DR were measured on day 0, day8 and day 14 after varicella zoster vaccination (VZV) in 17 individuals. Gene expression was correlated with vaccination-induced changes in the frequencies of VZV-specific T cells

first: Qian

last: Qi

first: Sabine

last: Le Saux

first: Mary

middle: M

last: Cavanagh


sample_organism:
Aedes aegypti
Aedes albopictus
Homo sapiens
Togaviridae
Flaviviridae
Flavivirus
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4
St. Louis encephalitis virus
West Nile virus
Yellow fever virus
Rhabdoviridae
Piry virus
Dengue virus
Chikungunya virus
Rio Mamore hantavirus
Mayaro virus
Ilheus virus
Chlorocebus sabaeus
Mucambo virus
Bussuquara virus
Cacipacore virus
Iguape virus
Rocio virus
Zika virus
Guaroa virus
Oropouche virus


title: Lipid biosynthesis coordinates a Mitochondrial to Cytosolic Stress Response

status: Public on Sep 08 2016

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary:
Defects in mitochondrial metabolism have been increasingly linked with age-onset protein misfolding diseases such as Alzheimer’s, Parkinson’s, and Huntington’s. In response to protein folding stress, compartment-specific unfolded protein responses (UPRs) within the endoplasmic reticulum, mitochondria, and cytosol work in parallel to ensure cellular protein homeostasis. While perturbation of individual compartments can make other compartments more susceptible to protein stress, the cellular conditions that trigger cross-communication between the individual UPRs remain poorly understood.
We have uncovered a conserved, robust mechanism linking mitochondrial protein homeostasis and the cytosolic folding environment through changes in lipid homeostasis. Metabolic restructuring caused by mitochondrial stress or small molecule activators trigger changes in gene expression coordinated uniquely by both the mitochondrial and cytosolic UPRs, protecting the cell from disease-associated proteins. Our data suggest an intricate and unique system of communication between UPRs in response to metabolic changes that could unveil new targets for diseases of protein misfolding.

overall_design: Because the induction of the MCSR due to hsp-6 RNAi required both hsf-1 and dve-1, key transcription factors required for the HSR and UPRmt, respectively, we asked which gene sets are coordinately regulated by both factors.  We performed microarray analyses to determine which genes have their expression altered by hsp-6 RNAi and whether these genes are regulated either by hsf-1, dve-1 or both

first: Hyun-Eu

last: Kim

middle: R

first: Milos

last: Simic

first: Rebecca

last: Kohnz

first: Daniel

middle: K

last: Nomura

first: Jenni

last: Durieux

first: Celine

middle: E

last: Riera

first: Melissa

last: Sanchez

first: Erik

last: Kapernick

first: Suzanne

last: Wolff

first: Andrew

last: Dillin


title: Effect of high CO2 levels and low temperature storage on table grapes quality harvested at two maturity stages.

status: Public on Sep 04 2016

city: Spain

first: M. Teresa

last: Sanchez-Ballesta

address: Jose Antonio Novais 10

country: Spain

institute: ICTAN-CSIC

summary: Table grapes cv. Cardinal are highly perishable and their quality deteriorates during postharvest storage at low temperature mainly because of sensitivity to fungal decay and senescence of rachis. The application of a 3-day CO2 treatment with 20 kPa CO2 at 0C reduced total decay and retained fruit quality in early and late-harvested table grapes during postharvest storage. In order to study the transcriptional responsiveness of table grapes to low temperature and high CO2 levels in the first stage of storage and how the maturity stage affect these changes, we have performed a comparative large-scale transcriptional analysis. In the first stage of storage, low temperature led to a significantly intense change in grape skin transcriptome irrespective of fruit maturity, although there were different changes within each stage. In the case of CO2 treated samples, in comparison to fruit at time zero, only slight differences were observed. Functional enrichment analysis revealed that major modifications in the transcriptome profile of early- and late-harvested grapes stored at 0C are linked to biotic and abiotic stress-responsive terms. However, in both cases there is a specific reprogramming of the transcriptome during the first stage of storage at 0C in order to withstand the cold stress. Thus, genes involved in gluconeogenesis, photosynthesis, mRNA translation and lipid transport were up-regulated in the case of early-harvested grapes, and genes related to protein folding stability and intracellular membrane trafficking in late-harvested grapes. The beneficial effect of high CO2 treatment maintaining table grape quality seems to be an active process requiring the induction of several transcription factors and kinases in early-harvested grapes, and the activation of processes associated to the maintenance of energy in late-harvested grapes.

overall_design: Table grapes harvested at two maturity stages (early and late). 3 biological replicates. Early-harvested (MI:12.45) : Time zero, 3 days air 0C, 3 days high CO2 levels 0C. Late-harvested (MI: 41.08):  Time zero, 3 days air 0C, 3 days high CO2 levels 0C.

first: M


title: Alteration of Gene Expression Profile in Spontaneously Hypertensive Rats Treated with Protein Hydrolysate of Blue Mussel (Mytilus edulis) by DNA Microarray Analysis

status: Public on Sep 01 2016

city: Hangzhou

first: Junli

last: Feng

address: Hangzhou, Jiaogong Road 149#

institute: Zhejiang Gongshang University

summary: The aim of this study was to investigate the antihypertensive effect of enzymatic hydrolysis of blue mussel protein (HBMP) in rats. Spontaneously hypertensive rats (SHRs) were orally administration with high- or low-dose of HBMP for 28 days. Major components of the renin-angiotensin (RAS) system in serum of SHRs from different groups were analyzed, and gene expression profiling were performed in the kidney of SHRs, using the Whole Rat Genome Oligonucleotide Microarray. Results indicated although genes involved in RAS system were not significantly altered, those related to blood coagulation system, cytokine and growth factor, and fatty acids metabolism were remarkablely changed. Several genes which were seldom reported to be implicated in pathogenesis of hypertension also showed significant expression alterations after oral administration of HBMP.

overall_design: SHRs were randomly divided into three groups (n=10): control group (rats were orally administered with water, 3mL), low-dose group (rats were orally administered with HBMP, 10 mg/kg/day, 3mL), and high-dose group (rats were orally administered with HBMP, 20 mg/kg/day, 3mL). After orally administered with HBMP for 4 weeks, all rats were killed and the kidneys were dissected. For each group, equivalent amounts of RNA from four individual rats were mixed, and transcribed to Cy3-labeled cRNA using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA). Then, Cy3-labeled cRNA from each group was hybridized to the Whole Rat Genome Oligonucleotide Microarray ver. 3.0 (4X44k, G2519F-028282) (Agilent Technologies), following the manufacturer's hybridization protocol.


title: Gene expression variation in mediastinal (pulmonary-draining) lymph nodes of heaves-affected horses versus controls

city: Ithaca

first: Donald

last: Miller

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health

institute: Cornell University

summary: We undertook gene expression microarray experiments to identify genes that are differentially expressed in heaves-affected horses versus matched controls. Mediastinal (pulmonary-draining) lymph nodes were sterilely obtained from affected and control horses, dissected, and frozen at -80oC. RNA was extracted from these tissues for downstream applications. These experiments utilized a commercially available Agilent horse array that featured >43,000 probes on a 4x44k array format.

overall_design: Mediastinal lymph node RNA from seven heaves-affected horses was compared to matching RNA from healthy, normal control horses.

first: Dorothy

last: Ainsworth


title: Study of microRNA associated with galectin-9 and anti-tumor effect in cholangiocarcinoma

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The miRNAs expression was markedly altered with the treatment of galectin-9 in vivo and various miRNAs induced by galectin-9 also may contribute to tumor growth of cholangiocarcinoma in vivo.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 2019 human miRNA probes in the tumorous tissues in vivo that was treated with and without galectin-9.

first: K

last: Kobayashi

first: T

last: Masaki


title: Identifying protective host signatures to West Nile Virus infection in the collaborative cross [spleen]

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

type:
Expression profiling by array
Other

summary: To accurately identify the unique transcriptional signatures in collaborative cross mice after exposure to West Nile Virus (or mock/no virus) , RNA isolated from spleen tissue and was analyzed using the nanostring immunology panel.

overall_design: We screened RNA from 95 spleen samples over 8 different CC backgrounds. Across the 8 CC lines. Samples were captured at 4, 7, and 12 days post infection of West Nile Virus (WNV).

first: Richard

last: Green

first: Courtney

last: Wilkins

first: Sunil

last: Thomas

last: Gale jr


title: Determining Neurovirulance host expression patterns in diverse genetic backgrounds [brain]

summary: To accurately identify the unique transcriptional signatures in collaborative cross mice after exposure to West Nile Virus (or mock/no virus) , RNA isolated from Brain tissue and was analyzed using the nanostring immunology panel.


title: DNA methylation profiling of rhabdomyosarcoma tumor samples

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

summary: In order to identify the specific DNA methylation pattern of different rhabdomyosarcoma (RMS) samples we performed a genome-wide study using Human DNA methylation platform (Agilent).

overall_design: DNA methylation profiling was carried out in 15 RMS tumor samples using the Human DNA methylation microarray (Agilent) consisting of about 244,000 (60-mer) probes design to interrogate about 27,000 known CpG islands. Enriched-methylated dsDNA for each sample was labeled with Cy5 dye and the control genomic DNA for each sample was labeled with Cy3 dye using Agilent Genomic DNA labeling kit PLUS (Agilent).

first: Lucia

last: Tombolan

first: Barbara

last: Celegato

first: Caterina

last: Millino

first: Beniamina

last: Pacchioni

first: Paolo

last: Martini

first: Chiara

last: Romualdi

first: Angelica

last: Zin

first: Elena

last: Poli

first: Angelo

last: Rosolen


title: Study of microRNA associated with metformin’s anti-tumor effect in cholangiocarcinoma

first: Satoshi

last: Kondo

summary: The miRNAs expression was markedly altered with the treatment of metformin in vivo and various miRNAs induced by metformin also may contribute to tumor growth of cholangiocarcinoma in vivo.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 985 human miRNA probes in the tumorous tissues in vivo that was treated with and without metformin.

last: Fujimori


title: Plasma MicroRNA-16 Is a Biomarker for Diagnosis, Stratification, and Prognosis of Hyperacute Cerebral Infarction

city: shanghai

first: tian

last: chunou

address: 168 changhai road

department: Neurosurgery Department

institute: Changhai Hospital, Second Military Medical University, China

summary: Indices for diagnosis of hyperacute cerebral infarction (HACI) and prediction of prognosis are essential for timely and appropriate management. MicroRNAs(miRNAs) regulating gene expression following stroke have potential use as prognostic markers of HACI. Here, we explored whether concentrations of circulating miRNAs could be correlated with clinical outcomes and thus form the basis of a system of stroke stratification. Plasma samples from patients with HACI (n = 7) and age-matched healthy volunteers (HVT, n = 4) were screened by microarray to find differentially expressed miRNAs, which were further verified by quantitative reverse transcription polymerase chain reaction(qRT-PCR) (HACI:HVT = 33:23). The target genes of the miRNAs with verified differential expression were investigated by GO and KEEG analysis. Using the TOAST (OCSP) criteria and the 3-month modified Rankin Score(mRS), relationships between the expression patterns of specific miRNAs, stroke stratification，and clinical prognosis were determined. The microarray analysis revealed 12 differentially expressed miRNAs. Among seven selected miRNAs verified with qRT-PCR, miR-16 expression in the HACI group was the most significantly different from the HVT group (P < 0.01). Bioinformatics analysis showed that the potential target genes of miR-16 were mainly involved in programmed cell death and the p53 signaling pathways. Receiver operating characteristic(ROC) analysis showed that the area under curve(AUC) of miR-16 was 0.775 (sensitivity 69.7% and specificity 87%) and 0.952 (sensitivity 100% and specificity 91.3%) in overall patients and patients with large artery atherosclerosis (LAAS), respectively. Elevated miR-16 expression was associated with the stroke subtype of LAAS, total anterior circulation infarction, partial anterior circulation infarction, and poor prognosis (P < 0.05). A diagnostic method based on rapid measurement of plasma miR-16 has potential to identify hyperacute cerebral infarction with LAAS with high sensitivity and specificity, which would inform and improve early treatment decisions and disease management.

overall_design: Plasma samples from patients with hyperacute cerebral infarction(HACI)(n=7) and age-matched healthy controls(HVT)(n=4) were screened by microarray to find differentially expressed miRNAs.Time duration from stroke onset to admission was less than 6 hours.

first: Chunou

last: Tian

first: Bo

last: Hong