title: Development of gene expression signatures for chicken LMH cells infected with infectious laryngotracheitis virus (ILTV)

status: Public on Oct 24 2015

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

country: China

institute: Xi'an Jiaotong University

summary: To explore the molecular events in LMH cells upon infectious laryngotracheitis virus (ILTV) infection, transcriptional profiling of LMH cells infected with ILTV was compared with uninfected control cells.

overall_design: Gene expression in LMH cells with or without virus infection was measured at two day post infection. Four independent experiments were performed.

first: Shengwang

last: Liu


title: Differential effects of and on Wnt-signaling in adult and fetal bone marrow-derived MSC

status: Public on Oct 14 2015

city: Amsterdam

first: Maja

middle: Maria

last: Paciejewska

state: noord holland

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Research

summary: Expression analysis of adult and fetal derived MSCs

overall_design: Three biological replates for both adult and fetal bone -marrow derived mesenchymal stromal cells (MSC)

middle: M

first: Marijke

middle: W

last: Maijenburg

first: Christian

last: Gilissen

first: Marion

last: Kleijer

first: Kim

last: Vermeul

first: Kees

last: Weijer

first: Joris

middle: A

last: Veltman

first: Marieke

last: von Lindern

first: C. Ellen

last: van der Schoot

first: Carlijn

last: Voermans


title: Prostate Cancer Risk SNPs enriched in Androgen Receptor Binding Sites

status: Public on Oct 12 2015

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: Genome-wide association studies (GWAS) have identified dozens of genomic loci, whose single nucleotide polymorphisms (SNPs) predispose to prostate cancer (PCa). However, the biological functions of these common genetic variants and the mechanisms to increase disease risk are largely unknown. We integrated chromatin-IP coupled sequencing (ChIP-seq) and microarray expression profiling in the TMPRSS2-ERG gene rearrangement positive DuCaP cell model with the NHGRI GWAS PCa risk SNPs catalog, in an attempt to identify disease susceptibility SNPs localized within functional androgen receptor binding sites (ARBSs). Among the 48 GWAS index SNPs and 2,702 linked SNPs defined by the 1000G project 104 were found to be localized in the AR ChIP-seq peaks. Of these risk SNPs, rs11891426 T/G in the 7th intron of its host gene melanophilin (MLPH) was found located within a putative auxiliary ARE motif, which we found enriched in the neighborhood of canonical ARE motifs. Exchange of T to G attenuated the transcriptional activity of the MLPH-ARBS in a reporter gene assay. The expression of MLPH protein in tissue samples from prostate cancer patients was significantly lower in those with the G compared to the T allele. Moreover, a significant positive correlation of AR and MLPH protein expression levels was also confirmed in tissue samples. These results unravel a hidden link between AR and a functional PCa risk SNP rs11891426, whose allele alteration affects androgen regulation of its host gene MLPH. This study shows the power of integrative studies to pin down functional risk SNPs and justifies further investigations.

overall_design: Prostate cancer cell lines LNCaP and DUCaP cells were cultured in the absence or presence of R1881, an androgen in three independent experiments. Differential gene expression was determined by comparing R1881 treated samples with the corresponding controls (EtOH treated samples).

first: Huajie

last: Bu

first: Narisu

last: Narisu

first: Thomas

last: Manke

first: Bettina

last: Schlick

first: Georg

last: Schäfer

first: Lorenza

last: Pasqualini

first: Peter

last: Chines

first: Michal

middle: R

last: Schweiger

last: Fuchsberger

first: Helmut

last: Klocker


title: MicroRNA expression profiling of colorectal normal mucosa, adenoma and adenocarcinoma tissues

status: Public on Oct 16 2015

city: Beijing

first: Xiaoyu

last: Shi

address: Chao Yang District Pan Jia Yuan Nan Li No.17

department: Cancer Institute (Hospital)

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

summary: Approximately two decades ago, Vogelstein and Fearon proposed the adenoma-carcinoma sequence of sporadic CRC development and illustrated the accumulation of genetic alterations during the stepwise progression, thereby providing a guideline for clinical practice. Although the detection and excision of precancerous lesions could prevent colorectal cancer and reduce mortality, 6% of adenomas will ultimately develop into colorectal cancer. Thus, this genetic model for colorectal tumorigenesis may not completely reflect the complex essence of the disease and whether the mode of initiation of the events in the multistep progression affects the outcome of CRC is still unknown. In this study, mRNA and miRNA expression profiling was performed with human colorectal tissues, including normal mucosa, adenoma and adenocarcinoma. Then, an integrated approach was adopted to establish the regulatory interaction networks that were correlated with colorectal carcinogenesis. Finally, a 55-gene signature whose expression was down-regulated in precancerous lesions compared to normal tissue was identified as a potential early indicator of CRC survival. The results suggested that genes related to immunity and homeostasis played a critical role in protection against adenoma initiation and that the altered molecular events that influence colorectal cancer prognosis may be set in an early, precancerous stage.

overall_design: Four types of human colorectal tissues were selected by colonoscopic resection or colorectal surgery, including 15 normal mucosae, 39 low-grade adenomas (mild or moderate atypical hyperplasia), 20 high-grade adenomas (severe atypical hyperplasia or carcinoma in situ) and 33 adenocarcinomas. MicroRNA expression profiling analysis of these samples was performed on Agilent 8×16K Human miRNA Microarray V3 (G4470C).

first: Yueming

last: Zhang

first: Bangrong

last: Cao

first: Ning

last: Lu

first: Lin

last: Feng

first: Xuebing

last: Di

first: Naijun

last: Han

first: Chenghua

last: Luo

first: Guiqi

last: Wang

first: Shujun

last: Cheng

first: Kaitai


title: The miRNA expression profiles in three subtypes of lung carcinomas

status: Public on Oct 21 2015

city: Shanghai

first: Lu

last: Shaohua

address: No. 180 Feng Lin Road

department: Department of Pathology

institute: Zhongshan Hospital

summary: To identify unique miRNA profiles in lung carcinomas, we evaluated the expression levels of 723 miRNAs in LCM-selected small cell lung carcinoma(SCLC), adenocarcinoma(AC) and squamous cell carcinoma(SQ) cells derived from 82 snap-frozen surgical specimens using microarrays. Hierarchical clustering analysis showed that 16 of 16 SCLC, 28 of 36 AC, and 29 of 30 SQ were correctly classified using 16 differentially expressed miRNAs.

overall_design: Expression profiles of 723 human miRNAs were investigated in selected LCM cancerous cell populations and normal cells derived from 16 SCLC, 36 AC, 30 SQ and 44 adjacent normal tissues.

first: Y

last: Jin

middle: L

last: Liu

first: S

middle: H


title: KP1019 (trans-[tetrachlorobis(1H-indazole) ruthenate(III)]) Dependent Transcription in WT Saccharomyces cerevisiae

status: Public on Oct 26 2015

city: Memphis

first: Mary

middle: Elizabeth

last: Miller

state: TN

address: 2000 North Parkway

department: Biology

country: USA

institute: Rhodes College

summary: To characterize cellular response to the anti-cancer ruthinium complex KP1019, budding yeast Saccharomyces cerevisiae transcripitonal response to KP1019 was measured using microarray analysis. Although KP1019 molecular mechanism of action remains a matter of debate, the drug has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro.  KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug.  Here we use a transcriptomic approach to characterize KP1019 induced transcriptional changes.

overall_design: Two concentrations of KP1019 (40 micrograms/mL and 80 micrograms/ml were assayed by microarray analysis to obtain comparative expression data for treated and untreated cells of the budding yeast Saccharomyces cerevisiae (strain BY4741).  Two biological replicates of each concentration were done. Each biological replicate was done in duplicate to allow for dye reversal controls.

middle: E


title: Expression mRNA data from human blood samples measured using the NanoString nCounter platform

status: Public on Oct 17 2015

city: New York

first: Maria

middle: D

last: Chikina

state: NY

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Background: The diagnosis of Parkinson’s disease (PD) is usually not established until advanced neurodegeneration leads to clinically detectable symptoms.  Previous blood PD transcriptome studies show low concordance, possibly due to the use of microarray technology, which has high measurement variation. The Leucine-rich repeat kinase 2 (LRRK2) G2019S mutation predisposes to PD. Using preclinical and clinical studies, we sought to develop a novel statistically motivated transcriptomic-based approach to identify a molecular signature in the blood of Ashkenazi Jewish PD patients including LRRK2 mutation carriers.  Methods: Using a digital gene expression platform to quantify 175 mRNA markers with low coefficients of variation (CV), we first compared whole blood transcript levels in mouse models 1) over-expressing wild-type (WT) LRRK2, 2) overexpressing G2019S LRRK2, 3) lacking LRRK2 (knockout), 4) and in WT controls. We then studied an Ashkenazi Jewish cohort of 34 symptomatic PD patients (both WT LRRK2 and G2019S LRRK2) and 32 asymptomatic controls.  Results: The expression profiles distinguished the 4 mouse groups with different genetic background. In patients, we detected significant differences in blood transcript levels both between individuals differing in LRRK2 genotype and between PD patients and controls. Discriminatory PD markers included genes associated with innate and adaptive immunity and inflammatory disease. Notably, gene expression patterns in L-DOPA-treated PD patients were significantly closer to those of healthy controls in a dose-dependent manner.  Conclusions: We identify whole blood low CV mRNA signatures correlating with LRRK2 genotype and with PD disease state. This approach may provide insight into pathogenesis and a route to early disease detection.

overall_design: Human venous blood samples were collected from 34 patients with PD symptoms and 32 healthy controls. Samples were collected in PAXgene® blood RNA tubes (Beckton Dickinson, Franklin Lakes, NJ), and stored at -80°C until RNA isolation. Total RNA was extracted using the PAXgene® blood miRNA kit, following the manufacturer’s instructions (Qiagen). Using 100 ng total RNA, mRNA levels were assayed by direct digital detection.

first: Christophe

middle: P

last: Gerald

first: Xianting

last: Li

first: Yongchao

last: Ge

first: Hanna

last: Pincas

first: Venugopalan

last: Nair

first: Aaron

middle: K

last: Wong

first: Arjun

last: Krishnan

first: Olga

middle: G

last: Troyanskaya

first: Deborah

last: Raymond

first: Rachel

last: Saunders-Pullman

first: Susan

middle: B

last: Bressman

first: Zhenyu

last: Yue

first: Stuart

middle: C

last: Sealfon


title: Expression analysis of WT and COMP KO peritoneal macrophages elicited by thioglycollate

city: Haidian District

first: Yi

last: Fu

state: Beijing

address: 38 Xueyuan Rd

department: Physiology and Pathophysiology

institute: Peking University Health Science Center

summary: Investigation of whole genome gene expression level changes in COMP KO macrophages compared with WT macrophages.

overall_design: A two-chip study used mRNA extracted from peritoneal macrophages pooled from 6 WT and COMP KO mice individually. In each array, 44,170 genes were probed. To identify differentially expressed genes, we performed a Fold Change filtering between the two compared arrays. The threshold is Fold Change >= 2.0.

first: FU

last: YI

first: GAO

last: CHENG

first: KONG

last: WEI


title: 3 cases of renal cell carcinomas with TFEB amplification

city: Nice

first: annie

last: peyron

address: 28 av Valombrose

country: France

institute: CHU Nice

type: Genome variation profiling by genome tiling array

summary: We report here 3 cases of a very rare entity of renal cell carcinomas (RCCs) that present an amplification of TFEB gene. This amplification, as well as translocation t(6;11) involving TFEB and MALAT1, leads to un overexpression of TFEB protein and seems to be a pejorative prognosis factor among TFEB RCCs

overall_design: sample was analysed by arrayCGH method using Agilent recommendations. Sample was labeled in Cy5 and co-hybridized with control DNA cy3 labeled.

first: L

last: Mendel

first: D

last: Ambrosetti

first: J

middle: F

last: Michiels

first: F

last: Pedeutour


title: Cellular adhesion promotes prostate cancer cells escape from dormancy

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Dissemination of prostate cancer (PCa) cells to the bone marrow is an early event in the disease process. In some patients, following initial treatment, disseminated tumor cells (DTC) proliferate to form active metastases after a prolonged period of undetectable disease known as tumor dormancy. Identifying mechanisms of PCa dormancy and reactivation remain a challenge due to the lack of in vitro models. Here, we characterized in vitro PCa dormancy-reactivation by inducing three apparently dormant patient-derived xenograft (PDX) lines to proliferate through tumor cell contact with each other and with bone marrow stroma. Proliferating PCa cells demonstrated tumor cell-cell contact and integrin clustering on immunofluorescence. Global gene expression analyses on proliferating cells cultured on bone marrow stroma revealed a downregulation of TGFB2 in all of the three proliferating PCa PDX lines when compared to their non-proliferating counterparts. Furthermore, constitutive activation of myosin light chain kinase (MLCK), a downstream effector of integrin-beta1 and TGF-beta2, in non-proliferating cells resumed cell proliferation. This cell proliferation was associated with an upregulation of CDK6 and a downregulation of E2F4. Taken together, our data provide evidence to support cellular adhesion and downregulation of TGFB2 as a potential mechanism by which PCa cells escape from dormancy. Targeting TGF-beta 2-associated mechanism could provide novel opportunities to prevent lethal PCa metastasis.

overall_design: Custom Agilent-016162 44K whole human genome expression oligonucleotide microarrays were used to profile dormant and proliferating cells isolated from three separate LuCaP xenograft lines grown in co-culture with bone marrow stromal cells isolated from a patient with PCa bone metastases. RNA from 10 cells was amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Nazanin

last: Ruppender

first: Sandy

last: Larson

first: Bryce

last: Lakely

first: Lori

last: Kollath

first: Lisha

last: Brown

first: Roger

first: Holly

last: Nguyen

first: Peter

middle: S

last: Nelson

first: Eva

last: Corey

first: Linda

last: Snyder

first: Robert

last: Vessella

first: Colm

last: Morrissey

first: Hung

last: Lam


title: Transcriptomics of human pleural mesothelial cell line Met-5A infected with Streptococcus pneumoniae

status: Public on Oct 20 2015

city: Nottingham

first: Patrick

middle: Jason

last: Tighe

state: Nottinghamshire

address: University Hospital

department: School of Molecular Medical Sciences

country: United Kingdom

institute: The University of Nottingham

summary: The objectives of the study were to examine the gene expression profile of human pleural mesothelial cells following infection with Streptococcus pneumoniae. The abstract is as follows: Streptococcus pneumoniae (Spn) is a major causative organism of empyema, an inflammatory condition occurring in the pleural sac. In this study, we used human and Spn cDNA microarrays to characterize the transcriptional responses occurring during initial contact between Spn and a human pleural mesothelial cell line (PMC) in vitro. Using stringent filtering criteria, 42 and 23 Spn genes were up-and down-regulated respectively. In particular, genes encoding factors potentially involved in metabolic processes and Spn adherence to eukaryotic cells were up-regulated e.g. glnQ, glnA, aliA, PsaB,  LytB and nox. After Spn initial contact, 870 human genes were differentially regulated and the largest numbers of significant gene expression changes were found in canonical pathways for eukaryotic initiation factor 2 signaling (60 genes out of 171), oxidative phosphorylation (32/103), mitochondrial dysfunction (37/164), eIF4 and p70S6K signaling (28/142), mTOR signaling (27/182), NRF2-mediated oxidative stress response (20/177), epithelial adherens junction remodeling (11/66) and ubiquitination (22/254). The cellular response appeared to be directed towards host cell survival and defense. Spn did not activate NF-kB or phosphorylate p38 MAPK or induce cytokine production. Moreover, Spn infection of TNF-α pre-stimulated PMC inhibited production of IL-6 and IL-8 secretion by >50% (p<0.01). In summary, his descriptive study provides datasets and a platform for examining further the molecular mechanisms underlying the pathogenesis of empyema.

overall_design: Met-5A cells were infected with strain D39 at a MOI of 200 for 2h; RNA was extracted from 5 independent experiments and used for microarray analysis as follows: Analysis of gene expression profile of human Met-5A cells. Protocol designi) Human Microarrays: ii) Synthesis and purification of human cDNA and in-vitro transcription to yield amino-allyl RNA (aRNA). iii) Microarray slide hybridisation and data analysis.

first: Myron

last: Christodoulides

middle: J

first: Claire

last: Heath

first: Maria

last: del Mar Cendra

first: Alastair

last: Watson

first: Jean-Philippe

last: Auger

first: Anish

last: Pandey


title: Expression mRNA data from mouse blood samples measured using the NanoString nCounter platform

last: Chikina

overall_design: Mouse blood samples were collected via heart puncture method. Total RNA was immediately isolated using the QIAamp RNA Blood Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. Total RNA was extracted using the PAXgene® blood miRNA kit, following the manufacturer’s instructions (Qiagen). Using 100 ng total RNA, mRNA levels were assayed by direct digital detection.

first: Christophe

last: Gerald

first: Xianting

last: Li

first: Yongchao

last: Ge

first: Hanna

last: Pincas

first: Venugopalan

last: Nair

first: Aaron

last: Wong

first: Arjun

last: Krishnan

first: Olga

last: Troyanskaya

first: Deborah

last: Raymond

first: Rachel

last: Saunders-Pullman

first: Susan

last: Bressman

first: Zhenyu

last: Yue

first: Stuart

last: Sealfon


title: Global miRNA expression profiling of Junb-deficient murine embryonic fibroblasts

status: Public on Oct 13 2015

city: Heidelberg

first: Marina

last: Schorpp-Kistner

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: The AP-1 transcription factor subunit Junb acts as a context-dependent transcriptional regulator. While positive regulatory functions of Junb are widely studied, the mechanism by which Junb exerts negative regulatory functions remains unclear. miRNAs could translate repressor functions of Junb. Therefore, the aim of this study was to identify Junb-dependent miRNAs in immortalized fibroblasts (MEFs) derived from murine Junb knock-out and wildtype embryos. Cells were published previously in Licht et al. (2010) J Clin Invest. 120(7):2307-18.

overall_design: Junb knock-out clones (n=2) and wildtype clones  (n=2) have been screened for the expression of all currently known murine miRNAs.

first: Kristin

last: Kiesow


title: UV (UVC, 10J/m2) light irradiation effect on human hepatoma Hep3B cells

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

summary:
human hepatoma Hep3B cells were treated with 10 J/m2 UV light versus untreated
Alternative pre-mRNA processing plays a key role in the response to DNA damage as well as in neoplastic transformation. We found that two Ewing Sarcoma (ES) cell lines exhibit different sensitivity to UV light irradiation, with Hep3B_UV_40J-N-MC cells being more sensitive than LAP-35 cells. RNA profiling during the response to low doses of UV light irradiation revealed genes differentially regulated between the two cell lines. In particular, UV light irradiation induced a novel isoform of the RNA helicase DHX9 which is targeted to nonsense-mediated decay (NMD) and therefore causes down-regulation of DHX9 in Hep3B_UV_40J-N-MC cells, but not in LAP-35 cells. DHX9 protein forms a complex with RNA polymerase II (RNAPII) and EWS-FLI1 to enhance transcription, and we found that down-regulation of DHX9 by UV light irradiation in Hep3B_UV_40J-N-MC cells impairs the recruitment of EWS-FLI1 to target genes and increases sensitivity to DNA damage. Notably, sensitivity of Hep3B_UV_40J-N-MC cells to irradiation correlated with enhanced phosphorylation and decreased processivity of RNAPII upon irradiation, which in turn causes inclusion of the novel DHX9 exon in Hep3B_UV_40J-N-MC cells exposed to UV light, an observation that could be recapitulated in LAP35 cells by pharmacological reduction of RNAPII processivity. Our data suggest that EWS-FLI1 oncogene activity could be targeted by modulation of DHX9 gene expression.

overall_design: Three biological replicates were labeled in direct and dye-swap microarray experiments and hybridized onto an Agilent custom splicing-sensitive microarray platform

first: Belén

last: Miñana

first: MariaPaola

last: Paronetto


title: Expression profiling of tissues within the sugarcane maturing stalk

city: St Lucia

first: Rosanne

middle: Elena

last: Casu

state: QLD

address: Queensland Bioscience Precinct, 306 Carmody Rd

country: Australia

institute: CSIRO Agriculture Flagship

summary: Sugarcane accumulates high concentrations of sucrose in the mature stalk, with numerous physiological processes in maturing stalk tissue both directly and indirectly involved. A considerable portion of carbohydrate metabolism is also devoted to cell wall synthesis and fibre production. Previously, we have identified differentially expressed transcripts correlated with sucrose accumulation and fibre production in various internodes of the sugarcane stalk. In this study, we have examined tissue-specific expression patterns to further explore gene pathways responsible for sucrose accumulation and fibre synthesis. We performed large-scale expression profiling of storage parenchyma, vascular bundles and rind dissected from a maturing stalk internode from field-grown commercial sugarcane harvested at 11 months of age. We identified 10 cellulose synthase subunit genes in sugarcane and examined significant differences in the expression of their corresponding transcripts and those of several sugar transporters between the different tissues. These were further correlated with differential expression patterns for transcripts of specific COBRA-like proteins and other proteins with acknowledged roles in cell wall metabolism. We found that the sugar transporters ShPST2a, ShPST2b and ShSUT4 were significantly up-regulated in storage parenchyma while ShSUT1 was up-regulated in vascular bundles. Two co-ordinately expressed groups of cell wall related transcripts were also identified. One group which is associated with primary cell wall synthesis (ShCesA1, ShCesA7, ShCesA9 and Shbk2l3) was up-regulated in parenchyma. The other group which is associated with secondary cell wall synthesis (ShCesA10, ShCesA11, ShCesA12 and Shbk-2) was up-regulated in rind. We also report an unexpected paucity in differential expression of cell wall-related genes in vascular bundles. Our results indicate that there is spatial separation for elevated expression of these important targets in both sucrose accumulation and cell wall synthesis, allowing for increased clarity in our understanding of sucrose transport and fibre synthesis in sugarcane.

overall_design: In order to identify transcripts that were differentially expressed in storage parenchyma (P), vascular bundles (V) and rind (R) dissected from maturing stalk, we performed hybridisation experiments using the GeneChip Sugarcane Genome Array with RNA amplified from total RNA derived from three biological replicates of field-grown sugarcane variety Q117. Each of the nine samples was hybridised separately to one array.

first: Anne

last: Rae

first: Janine

middle: M

last: Nielsen

first: Jai

last: Perroux

first: Graham

last: Bonnett

first: John

last: Manners


title: microRNA expression of TRAIL-sensitive and TRAIL-resistant Bel-7402 cells

first: Sisi

last: Ma

address: 5 Dong Dan San Tiao

department: National Laboratory of Medical Molecular Biology

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

summary:
To further analyze the change of microRNA (miRNA) between TRAIL-sensitive and TRAIL-resistant Bel-7402 cells
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA from TRAIL-sensitive and TRAIL-resistant Bel-7402 cells were extracted and analyzed using Exiqon miRCURY LNA microRNA array (7th generation) platform, and changes of miRNA were screened out.The 7th generation of miRNA array contains 3100 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 18.0, as well as all viral microRNAs related to these species. In addition, this array contains capture probes for 25 miRPlus™ human microRNAs. These are proprietary microRNAs not found in miRBase.

first: Juan

last: Shi

first: Dexian

last: Zheng


title: Gene Expression Profiling Identifies Interferon Signalling Molecules and IGFBP3 in Human Degenerative Annulus Fibrosus

status: Public on Oct 23 2015

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

summary: Low back pain is a major cause of disability especially for people between 20 and 50 years of age. As a costly healthcare problem, it imposes a serious socio-economic burden. Current surgical therapies have considerable drawbacks and fail to replace the normal disc in facilitating spinal movements and absorbing load. Therefore, the focus of regenerative medicine is on identifying biomarkers and signalling pathways to improve our understanding about the cascades of disc degeneration and allow for the design of specific therapies. We hypothesized that comparing microarray profiles from degenerative and non-degenerative discs will lead to the identification of dysregulated signalling and pathophysiological targets. Microarray data sets were generated from human annulus fibrosus cells and analysed using IPA ingenuity pathway analysis system. Gene expression values were validated by qRT-PCR, and respective proteins were identified by immunohistochemistry. Microarray analysis revealed 17 dysregulated molecular markers and various dysregulated cellular functions, including cell proliferation and inflammatory response, in the human degenerative annulus fibrosus. The most significant canonical pathway induced in degenerative annulus fibrosus was found to be the interferon signalling pathway. In conclusion, this study indicates interferon-alpha signalling pathway activation with IFIT3 and IGFBP3 up-regulation which may affect cellular function in human degenerative disc.

overall_design: 48 samples of intervertebral disc tissue - annulus fibrosus and nucleus pulposus - displaying varying degrees (grades) of degeneration

first: Sibylle

last: Grad

last: Ó'Gaora


title: The effects of UVB and the organic osmolyte betaine on rat epidermal keratinocytes in an organotypic culture system

city: Kuopio

first: Leena

last: Rauhala

address: Yliopistonranta 1 E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary:
Betaine (trimethylglycine) is a non-toxic, highly water-soluble organic osmolyte widely used in skin care due to its assumed moisturizing and protective properties, but only few studies have addressed its specific effects in skin. Here, the cellular and molecular targets of betaine were analyzed by genome-wide expression analysis in organotypic cultures of rat epidermal keratinocytes (REK). In this model, we also examined whether betaine modifies the impacts of acute UVB exposure.
The expression of several genes relevant to epidermal biology, proliferation/differentiation or malignancy as well as solute transport were verified by independent methods (qRT-PCR, western blotting). The data concerning changes in calcium metabolism after UVB exposure has been published separately (Bart et al., Br. J. Dermatol. 171:376-387, 2014).

overall_design: Organotypic cultures of rat epidermal keratinocytes (REK) were prepared by plating cells on a collagen-coated insert (submerged in medium), lifting the confluent cell layer to the air-liquid interface 3 days after plating. These 3D cultures were divided in four treatment groups with three replicates in each: control, betaine (10 mM), UVB (30 mJ/cm2) and betaine + UVB. Betaine was added to the cultures for 11 days, starting from day 4 until sample collection. UVB exposure was performed 24 h prior to sample collection for 2-week-old 3D cultures with a well-formed epidermal layer. For further details on the experimental set-up and characteristics of the UV source, please refer to Bart et al. (Br. J. Dermatol. 171:376-387, 2014) and Rauhala et al. (J. Biol. Chem. 288:17999-18012, 2013).

first: Lasse

last: Hämäläinen

first: Geneviève

last: Bart

first: Thomas

middle: W

last: Dunlop

first: Petri

last: Pehkonen

first: Maarit

last: Kokkonen

first: Pauliina

last: Salonen

first: Timo

last: Kumlin

first: Sanna

last: Pasonen-Seppänen

first: Markku

last: Tammi

first: Raija


title: Differential expression of microRNAs in bovine papillomavirus type 1 (BPV-1) transformed equine cells

city: Glasgow

first: Nuria

last: Terron Canedo

address: Bearsden Road

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow, College of Medical, Veterinary and Life Sciences

summary:
The experiment investigates the effect of BPV-1 on microRNA profile in control cell line and BPV-1 in vitro transformed cell line
A subset of microRNAs have been found differentially expressed in cells containing the BPV-1 genomes compared to control cells

platform_organism:
Homo sapiens
Equus caballus

overall_design: Two experimental conditions (control -EqPalF- and control with BPV-1 genomes -S6-2 cells-) with three replicates per condition.

last: Terron-Canedo

first: William

last: Weir

first: Lesley

last: Nicolson

first: Collette

last: Britton

first: Lubna

last: Nasir


title: UV (UVC, 10J/m2) light irradiation effect on Ewing Sarcoma cells

first: BELEN

last: MINANA

summary:
LAP-35 and SK-N_MC cells were treated with 10 J/m2 UV light versus untreated
Alternative pre-mRNA processing plays a key role in the response to DNA damage as well as in neoplastic transformation. We found that two Ewing Sarcoma (ES) cell lines exhibit different sensitivity to UV light irradiation, with SK-N-MC cells being more sensitive than LAP-35 cells. RNA profiling during the response to low doses of UV light irradiation revealed genes differentially regulated between the two cell lines. In particular, UV light irradiation induced a novel isoform of the RNA helicase DHX9 which is targeted to nonsense-mediated decay (NMD) and therefore causes down-regulation of DHX9 in SK-N-MC cells, but not in LAP-35 cells. DHX9 protein forms a complex with RNA polymerase II (RNAPII) and EWS-FLI1 to enhance transcription, and we found that down-regulation of DHX9 by UV light irradiation in SK-N-MC cells impairs the recruitment of EWS-FLI1 to target genes and increases sensitivity to DNA damage. Notably, sensitivity of SK-N-MC cells to irradiation correlated with enhanced phosphorylation and decreased processivity of RNAPII upon irradiation, which in turn causes inclusion of the novel DHX9 exon in SK-N-MC cells exposed to UV light, an observation that could be recapitulated in LAP35 cells by pharmacological reduction of RNAPII processivity. Our data suggest that EWS-FLI1 oncogene activity could be targeted by modulation of DHX9 gene expression.

first: Belén

last: Miñana

first: MariaPaola

last: Paronetto


title: Identification of miRNA signature associated with HCV infection.

status: Public on Oct 19 2015

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

summary: As part of SMART strategy, we aimed to characterize changes in miRNA expression associated with HCV infection.

overall_design: Huh7.5 hepatoma cells were infected with a cell culture adapted JFH1 strain (JFH-1T; MOI = 0.1).  Mock infection was performed as control.  72 hours-post transfection, RNA isolations were performed.

first: Ragunath

last: Singaravelu


title: H3K27me3 analysis in mouse colonic epithelial cells

status: Public on Oct 15 2015

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

type: Genome binding/occupancy profiling by genome tiling array

summary: H3K27me3 statuses were analyzed in normal mouse colonic epithelial cells and in those exposed to DSS-induced colitis, and aberrant changes of H3K27me3 by DSS-induced colitis were identified.

overall_design: H3K27me3 in colonic epithelial cells isolated from male BALB/c mice without or with DSS treatment were analyzed using Agilent-015279 Mouse CpG Island ChIP-on-Chip Microarray 2x105K.

first: Daigo

last: Ikegami

first: Toshikazu

last: Ushijima


title: Novel Comparative Pattern Count Analysis Reveals a Chronic Ethanol Induced Dynamic Shift In NF-κB Genome-wide Promoter Binding During Liver Regeneration

city: Philadelphia

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1020 Locust St

department: Pathology

institute: Thomas Jefferson University

summary: We analyzed the effect of chronic alcohol intake on the genome-wide binding activity of NF-κB  during  the initial response phase following partial hepatectomy. We analyzed the data in the adapted state as well as in response to partial hepatectomy, using chromatin immunoprecipitation followed by promoter microarray analysis. We found several ethanol-specific NF-κB binding target promoters in the chronic adapted state.. Partial hepatectomy induced a diet-independent shift in NF-κB binding loci relative to the transcription start sites. We employed a novel pattern count analysis to exhaustively enumerate and compare the number of promoters corresponding to the temporal binding patterns between ethanol and isocaloric pair-fed control groups. We found that NF-κB bound genes govern negative regulation of cell growth and inflammatory response immediately following hepatectomy. We, integrated the ChIP-chip results with a time series gene expression data set to identify the NF-κB promoter binding targets that showed differential gene expression changes at the baseline-adapted condition as well as after PHx. We identified a set of differential patterns of NF-κB binding that were specific to the ethanol and pair-fed control groups. We found the regulatory pathways and co-incident transcription factor binding motifs corresponding some of the key comparative-binding patterns.

overall_design: Adult (8-10 week old) Sprague-Dawley rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks, with the pair-fed calorie-matched littermate controls receiving liquid diets in which ethanol calories were replaced by carbohydrate .  When their weight reached 275-350 g, they were anesthetized and subjected to 70% partial hepatecomy by surgical removal of medial and left lateral lobes as per standard procedure. The medial and left lateral lobes were flash frozen using liquid nitrogen-cooled aluminum clamps to serve as within-animal, 0 hour controls. At 1 hou and 6 hours post-PHx, rats (three biological replicates per time) were again anesthetized and the remnant liver tissue was excised and flash-frozen as before. Following excision of the remaining liver mass, rats were sacrificed by cervical dislocation. Liver tissue from 0h, 1h and 6h post-PHx was subjected to chromatin immunoprecipitation. Immunoprecipitated samples (ChIP) from 0h, 1h, and 6h post-PHx were used to identifiy genome-wide NF-κB binding sites using microarrays (ChIP-chip).

first: Lakshmi

last: Kuttippurathu

first: Biswanath

last: Patra

first: Jan

last: Hoek


title: Expression data from the process of chilling stress causing Alternaria alternata infection and leading to cotton leaf senescence

status: Public on Oct 28 2015

city: Beijing

first: Wei

last: Liu

address: State Key Laboratory for Biology of Plant Diseases and Insect Pests,  Institute of Plant Protection, Chinese Academy of Agricultural Sciences,  100193, Beijing, People’s Republic of China

summary:
Cotton premature leaf senescence often occurred with an increasing frequency in many cotton growing areas and caused serious reduction in yield and quality of cotton has been one of the impontant factors that restrict severely the production of cotton.Our laboratory studies showed chilling stress is the key factor that induced A. alternatia infection, caused Alternaria disease and then lead to cotton leaf senescence, but the molecular mechanism of cotton premature leaf senscence is still unclear.
We used microarrays to study molecular mechanism of chilling stress causing Alternaria alternata infection and leading to cotton leaf senescence and find the key genes during this process.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Plants were grown in growth chamber with a 14/10 hours photoperiod, 28℃/22℃. Three-to-four leaves stage cotton plants were pre-treated by chilling stress with the low temperatures of 16/12℃ day/night for a fixed time length of 3 days. While, the normal growth plants were sustained growing at optimal temperature of 28/20℃ day/night. And then, both chilling stress pre-treated and normal growth cotton plants were inoculated with Alternaria. alternata isolate A1. The mock inoculations were performed with sterilized water. Cotton leaf Samples were respectively collected at 3, 6 days after inoculation (DAI) for RNA extraction and hybridization on Affymetrix microarrays. To that end, we collected 8 samples, i.e. chilling stress pre-treated cotton leaves: 3 DAI (C) and its mock control (D), 6 DAI (E) and its mock control (F); normal growth cotton leaves: 3 DAI (H) and its mock control (I), 6 DAI (J) and its mock control (K). All samples were arranged in completely randomized designed with three replications for each treatment.

first: Shanshan

last: Zhang

first: Fangjun

last: Qi

first: Weibo

last: Zhai

first: Wenwei

first: Guiliang

last: Jian


title: Plasmodium parasites mount an arrest response against dihydroartemisinin [Microarray]

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

summary: Control of malaria is threatened by emerging parasite resistance to artemisinin drug (ART) therapies. The molecular details of how Plasmodium malaria parasites response to ART and how this relates to resistance is not clear. To determine how parasites respond to ART by altering gene expression, we performed a transcriptomic study of dihydroartemisinin (DHA) response in P. falciparum K1 strain and in P. berghei ANKA strain.  Microarray data from DHA-treated P. falciparum trophozoite stage parasites were compared with data from other ART treatments. Genes with consistent changes in expression were identified, which includes notably down-regulation of cytosolic ribosomal protein genes. RNA-seq data revealed a similar pattern of transcriptomic change, although the pattern was much clearer in that more than one-third of P. falciparum trophozoite genes are differentially expressed with greater statistical support for down-regulation of ribosomal protein genes. The poor overlap of differentially-expressed genes between microarray and RNA-seq and less-well defined patterns for the former suggests that the accuracy of microarray is limited by technological bias. The trophozoite response to DHA is overall “ring-like” and less “trophozoite-like”, which is consistent with previous findings that Plasmodium can enter a quiescent ring-like state to resist ART. RNA-seq data from DHA-treated P. falciparum rings reveal a more muted response, although there is considerable overlap of differentially expressed genes with DHA-treated trophozoites. In contrast, P. falciparum schizonts are unresponsive to DHA, suggesting that the protective response acts mainly to arrest parasite development through the G2/M checkpoint. The transcriptional response of P. berghei to DHA treatment in vivo in infected mice is strikingly similar to the P. falciparum in vitro ring and trophozoite responses, in which ribosomal protein genes are notably down-regulated. These results suggest Plasmodium species respond to DHA in the same way. This knowledge could be applied to outwit the parasite to deliver more effective artemisinin therapies, and maybe hinder the development of drug resistance.

overall_design: Two condition drug-treatment experiment, Dihydroartemisinin vs. Vehicle control treatment with matched reference untreated controls.  Biological replicates: 5 independently grown and harvested experimental culture replicates. One replicate of treatment/reference time-point per array.

first: Sastra

last: Chaothieng

first: Pavita

last: Tipsombatboon

first: Jittima

last: Piriyapongsa

first: Chayaphat

last: Wongsombat

first: Nattida

last: Suwannakitti

first: Pongpisid

last: Koonyosying

first: Chairat

last: Uthaipibull

first: Sumalee

last: Kamchonwongpaisan

first: Yongyuth

last: Yuthavong


title: Real-time quantitative PCR analysis of undifferentiated and differentiated murine embryonic stem cells

city: San Francisco

first: Andrei

last: Goga

state: CA

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

summary: Wildtype murine embryonic stem cells were kept undifferentiated or treated with retinoic acid for 4 days. We used SABioscience p53 Signaling Pathway Array to quantitate gene expression of genes involved in survival and cell death from the immature and the differently activated cells.

overall_design: qPCR gene expression profiling.  Undifferentiated and differentiated murine embryonic stem cells (biological triplicates) were treated separately as indicated in the summary. Equal amount total RNA from each sample was used for gene expression analysis.

first: Eric

last: Wang

first: Nichole

middle: A

last: Reyes

first: Collin

last: Melton

first: Noelle

last: Huskey

first: Olga

last: Momcilovic

first: Robert

last: Blelloch

first: Scott

last: Oakes


title: Fxr-deficiency in mouse liver slices aggravates cyclosporin A toxicity by upregulation of pro-inflammatory genes and downregulation of genes involved in mitochondrial functions

status: Public on Oct 22 2015

city: Wageningen

first: Ewa

last: Szalowska

address: Akkermaalsbos 2

institute: RIKILT-Wageningen UR

summary:
The transcription factor farnesoid X receptor (FXR) governs bile acid and energy homeostasis, is involved in inflammation, and has protective functions in the liver. In the present study we investigated the effect of Fxr deficiency in mouse precision cut liver slices (PCLS) exposed to a model hepatotoxicant cyclosporin A (CsA). It was anticipated that Fxr deficiency could aggravate toxicity of CsA in PCLS and pinpoint to novel genes/processes regulated by FXR.
To test this hypothesis, PCLS obtained from livers of wild type mice (WT-PCLS) and Fxr-knockout mice (FXRKO-PCLS) were treated with 40µM CsA for 24h and 48h. ATP and histological assays were applied to assess the viability of PCLS. DNA microarrays combined with bioinformatics analysis were used to identify genes and processes that were affected by CsA in WT-PCLS and/or FXRKO-PCLS. In addition, WT-PCLS and FXRKO-PCLS were exposed to the endogenous FXR ligand chenodeoxycholic acid (CDCA) and subjected to q-PCR to determine whether subsets of known FXR-targets and the identified genes were regulated upon FXR activation in an FXR-dependent manner.
No difference in viability was observed between WT-PCLS and FXRKO-PCLS upon CsA treatment. Transcriptomics data analysis revealed that CsA significantly upregulated stress-response and inflammation and significantly downregulated processes involved in lipid and glucose metabolism in both WT-PCLS and FXRKO-PCLS. However, only in FXRKO-PCLS, CsA upregulated additional pro-inflammatory genes and downregulated genes related to mitochondrial functions. Furthermore, only in WT-PCLS, CDCA upregulated a subset of known FXR-target genes as well as the regulator of inflammation and mitochondrial functions peroxisome proliferator- activated receptor delta (Ppar delta).
Although FXR governs energy metabolism, no major differences in response to CsA could be observed between WT-PCLS and FXRKO-PCLS in regulation of processes involved in lipid and glucose metabolism. This finding indicates that CsA does not directly affect FXR functions in relation to the above mentioned processes. However, the more pronounced induction of pro-inflammatory genes and the downregulation of genes involved in mitochondrial functions only in FXRKO-PCLS suggest that FXR deficiency aggravates CsA-induced inflammation and impairs mitochondrial functions. Therefore, FXR can exert its hepatoprotective functions by controlling inflammation and mitochondrial functions, possibly involving an FXR-PPAR delta cross-talk.
Precision cut liver slices (PCLS) obtained from livers of wild type (WT) and farnesoid X receptor knockout (FXRKO) mice were exposed for 24 hours to 40uM of CyclosporinA (CsA).

overall_design:
For all exposure experiments, PCLS were obtained from 5 WT and 5 FXRKO mice. Slices obtained from each biological replicate were cultured apart and each culture consisted of 3 co-incubated slices. The exposure experiments were performed at 2 days; at day1, PCLS obtained from livers of 3 WT mice and 2 FXRKO mice were used and at day 2, PCLS obtained from livers of 2 WT mice and 3 FXRKO mice were used.
WT-PCLS and FXRKO-PCLS were exposed to 40 µM CsA for 24 h. CsA was added to the culture medium as a stock solution in DMSO (final concentration of DMSO in the medium was 0.1% v/v). Slices incubated with 0.1% v/v DMSO served as control.

first: Tessa

last: Pronk

first: Ad

last: Peijnenburg


title: Expression mRNA data from human and mouse blood samples measured using the NanoString nCounter platform

city: New York

first: Maria

last: Chikina

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

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

sample_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Karyotype assessment of whole human blastocysts by aCGH

city: Oxford

first: Dagan

last: Wells

address: 8000 Alec Issigonis Way

institute: University of Oxford

summary:
The use of in vitro fertilization (IVF) has revolutionized the treatment of infertility and is now responsible for 1-5% of all births in industrialized countries. During IVF, it is typical for patients to generate multiple embryos. However, only a small proportion of them possess the genetic and metabolic requirements needed in order to produce a healthy pregnancy. The identification of the embryo with the greatest developmental capacity represents a major challenge for fertility clinics. Current methods for the assessment of embryo competence are proven inefficient and the inadvertent transfer of non-viable embryos is the principal reason why most IVF treatments (approximately two-thirds) end in failure. In this study, we investigate how the application of proteomic measurements could improve success rates in clinical embryology. We describe a procedure that allows the identification and quantification of proteins of embryonic origin, present in attomole concentrations in the blastocoel, the enclosed fluid filled cavity that forms within five-day old human embryos. By using targeted proteomics, we demonstrate the feasibility of quantifying multiple proteins in samples derived from single blastocoels, and that such measurements correlate with aspects of embryo viability, such as chromosomal (ploidy) status. This study illustrates the potential of high-sensitivity proteomics to measure clinically relevant biomarkers in minute samples and, more specifically, suggests that key aspects of embryo competence could be measured using a proteomic-based strategy, with negligible risk of harm to the living embryo. Our work paves the way for the development of “next-generation” embryo competence assessment strategies, based on functional proteomics.
This subset of experiments were used to determine embryonic karyotype. Differences in proteomic profiles of euploid and aneuploid embryos were then investigated.

overall_design: Karyotype was used as a marker for embryo viability to associate with blastocoel proteomic profiles generated using targeted mass spectrometry.

first: Maurizio

last: Poli

first: Alessandro

last: Ori

first: Souraya

last: Jaroudi

first: Katharina

last: Spath

first: Martin

last: Beck


title: miRNA gene expression signatures for IhhN protein induced cells

city: Shanghai

first: Lu

last: Shen

address: RM 218 Little White House 1954 Huashan RD

department: Bio-X Institutes

institute: Shanghai Jiao Tong University

summary: Previous studies demonstrated that hererozygous missense mutations in IHH could lead to a decreasing IHH signaling efficacy and cause brachydactyly type A1 (BDA1). For revealing difference of Gli1-mediated downstream regulatory effects between wild type IHH signaling and E95K mutant IHH signaling, we have employed whole genome microarray miRNA expression profiling as a discovery platform to identify miRNAs with the potential to take part in Gli1-mediated cis-regulatory network.

overall_design: miRNA expressions of Wild type IhhN protein-induced or E95K mutant IhhN protein-induced  were measured after 48-hour incubation in the presence of 750nM protein. Non-protein induced cells were as control.

first: Shengying

last: Qin


title: To study gene expression of PHO13 deleted Xylose isomerase (XI) harboring strain in xylose fermentation

status: Public on Oct 08 2015

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

institute: Kobe University

summary: The main objective is to improve xylose fermentation by deletion of PHO13 gene in Xylose isomerase (XI) harboring yeast strains. Microarray analysis was performed to investigate effects of PHO13 deletion on the gene expression prolife of xylose-fermenting strains.

overall_design: Samples for 2 strains (control, PHO13 deleted strain) were taken after 9h of xylose fermentation.  Each samples were triplicated resulting in total of 6 samples.

first: Takahiro

last: Bamba

first: Tomohisa

last: Hasunuma


title: Small artery remodeling depends on the genetic background in spontaneously hypertensive rats (mRNA)

status: Public on Oct 02 2015

city: Amsterdam

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

summary: Spontaneously hypertensive rats (SHR) have been used frequently as a model for human  essential hypertension. However, both the SHR and its normotensive control, the Wistar Kyoto rat  (WKY), consist of genetically different sublines.   We tested the hypothesis that discrepant data in literature regarding the pathophysiology of  vascular remodeling in hypertension result from the use of different rat sublines.    Using micro-arrays, we studied miRNA and mRNA expression in resistance  arteries of WKY and SHR from three different sources, at 6 weeks and 5 months of age. Both WKY  and SHR showed an age-related expression pattern that involved many genes related to the  extracellular matrix. In SHR, this pattern was more extensive and included a specific increase in miR132-3p,  and type III deiodinase. Direct comparison of WKY to SHR also yielded differences in  expression, including thrombospondin 4. Heterogeneity in gene expression among sublines was  associated with differences in blood pressure, body weight, vascular remodeling, endothelial function,  and vessel ultrastructure. Common features in vessels from SHR were an increase in wall thickness,  wall-to-lumen ratio, and internal elastic lamina thickness.   These results indicate that endothelial dysfunction, vascular stiffening, and inward  remodeling of small arteries are not common features of hypertension, but are subline-dependent.  Relatively minor differences in genetic background associate with different types of vascular  remodeling in hypertensive rats. The clinical implication of this study is that more research into   personalized treatment in hypertension is warranted.

overall_design: 2x2 factorial design with 2 ages (6 weeks and 5 months) and 2 strains (WKY and SHR). For each strain 3 genetically different sublines were used. Per combination of conditions (age, strain, subline) one biological replicate was used (12) and for 4 a technical replicate was included (16 arrays in total). Each test sample consists of the mRNA pooled from the vessels of five animals. As common-reference an equimolar pool of all test samples used. SHR/NCrl, WKY/NCrl, and stroke-prone SHR (SHR/SP) rats were obtained from Charles River, the Netherlands. The SHR/NHsd and WKY/NHsd rats were derived from Harlan UK, (Bicester, U.K.) and bred at the local animal facility of the Universidad Autónoma de Madrid, Spain. WKY/NTac rats were obtained from Taconic Farms (Germantown, NY, USA).

first: Erik

last: Bakker


title: Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 10987

status: Public on Oct 10 2015

first: Janneke

last: Wijman

address: Bomenweg 2

institute: Wageningen UR

summary: Planktonic and biofilm cells of Bacillus cereus ATCC 14579 and ATCC 10987 were studied using microscopy and transcriptome analysis. By microscopy, clear differences could be observed between biofilm and planktonic cells as well as between the two strains. By using hierarchical clustering of the transcriptome data, little difference was observed between the biofilm cells of B. cereus ATCC 14579 and ATCC 10987. Different responses between biofilm and planktonic cells could be identified using transcriptome analysis. Biofilm formation seemed to cause a shift in metabolism with up- or down-regulation of genes involved in different metabolic pathways. Genes involved in motility were down-regulated. No clear up-regulation related to capsular or extracellular polysaccharides was observed. Sporulation was observed in biofilm cells using microscopy, which was corroborated with up-regulation of genes involved in sporulation in biofilm cells. The results obtained in this study provide insight in general and strain specific behavior of B. cereus cells in multicellular communities.

overall_design: Planktonic cell samples were isolated at mid-logarithmic growth and stationary growth phase. Biofilm cell samples were isolated after 12 and 24 hours of growth. Each conditions was compared to the three other conditions.The experiments were performed in duplicate and the duplicate samples were hybridized with a dye-swap.

first: Maarten

last: Mols

first: Marcel

last: Tempelaars

first: Tjakko

last: Abee


title: Small artery remodeling depends on the genetic background in spontaneously hypertensive rats (microRNA)

summary: Spontaneously hypertensive rats (SHR) have been used frequently as a model for human essential hypertension. However, both the SHR and its normotensive control, the Wistar Kyoto rat (WKY), consist of genetically different sublines. We tested the hypothesis that discrepant data in literature regarding the pathophysiology of vascular remodeling in hypertension result from the use of different rat sublines.  Using micro-arrays, we studied miRNA and mRNA expression in resistance  arteries of WKY and SHR from three different sources, at 6 weeks and 5 months of age. Both WKY and SHR showed an age-related expression pattern that involved many genes related to the  extracellular matrix. In SHR, this pattern was more extensive and included a specific increase in miR132-3p, and type III deiodinase. Direct comparison of WKY to SHR also yielded differences in  expression, including thrombospondin 4. Heterogeneity in gene expression among sublines was associated with differences in blood pressure, body weight, vascular remodeling, endothelial function,  and vessel ultrastructure. Common features in vessels from SHR were an increase in wall thickness, wall-to-lumen ratio, and internal elastic lamina thickness.   These results indicate that endothelial dysfunction, vascular stiffening, and inward remodeling of small arteries are not common features of hypertension, but are subline-dependent.  Relatively minor differences in genetic background associate with different types of vascular remodeling in hypertensive rats. The clinical implication of this study is that more research into   personalized treatment in hypertension is warranted.

overall_design: 2x2 factorial design with 2 ages (6 weeks and 5 months) and 2 strains (WKY and SHR). For each strain 3 genetically different sublines were used. Per combination of conditions (age, strain, subline) one biological replicate was used (12 arrays in total). SHR/NCrl, WKY/NCrl, and stroke-prone SHR (SHR/SP) rats were obtained from Charles River, the Netherlands. The SHR/NHsd and WKY/NHsd rats were derived from Harlan UK, (Bicester, U.K.) and bred at the local animal facility of the Universidad Autónoma de Madrid, Spain. WKY/NTac rats were obtained from Taconic Farms (Germantown, NY, USA).


title: rat T Cells: Sham vs. SNI

status: Public on Oct 01 2015

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: DNA methylation profiles of T cells comparing 9 months post Spared Nerve Injury (SNI) rats with Sham rats.

overall_design: Two-condition experiment, Sham vs. SNI rat T cells. Biological replicates: 8 Sham replicates, 8 SNI replicates.

first: Renaud

last: Massart

first: Matthew

last: Suderman


title: rat PFC: Sham vs. SNI

summary: DNA methylation profiles of prefrontal cortec (PFC) comparing 9 months post Spared Nerve Injury (SNI) rats with Sham rats.

overall_design: Two-condition experiment, Sham vs. SNI rat PFC. Biological replicates: 8 Sham replicates, 7 SNI replicates.


title: Spatio-temporal evolution of the primary glioblastoma genome (aCGH)

status: Public on Oct 06 2015

city: Seoul

first: Jinkuk

last: Kim

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

summary: Tumor recurrence following a standard treatment is the major cause of mortality for glioblastoma (GBM) patients. However, insights on the evolutionary process of the tumor have been limited due to the lack of longitudinally sampled cases. Here, we describe our genomic analyses of 38 GBM patients with pre- and post-treatment samples for each individual (78 tumor samples in total; aCGH data were obtained for 36 among the 78).  A substantial shift in the landscape of driver alterations was associated with distant appearances of the recurrent tumors from the initial tumor, suggesting that the genomic profile of an initial tumor can mislead targeted therapies for the distant recurrent tumor. In addition, in contrast to the previous work on IDH1-R132H low-grade gliomas, our GBM patients rarely developed hypermutation following the standard treatment, supporting the safety of temozolomide for IDH1-wild type, primary GBMs under the current standard regimen.

overall_design: aCGH experiments were performed for 36 pre- or post-treatment human glioblastoma tissues using the Agilent Human Whole Genome 180K CGH microarray according to manufacturer's protocol. Random human male normal tissue gDNA (Cy5 labeled) was used as a reference for each experiment.

first: Hee

last: Cho

first: Chul-Kee

last: Park

first: In-Hee

last: Lee

first: Peter

first: Do-Hyun

last: Nam


title: Constitutive activation of Stat3 in mouse epidermis

city: College Station

first: Penny

last: Riggs

state: TX

address: 2471 TAMU

department: Animal Science

institute: Texas A&M University

summary: Potential Stat3 target genes involved in hair follicle formation were examined using mouse whole-genome microarray analysis. Global gene expression patterns in the epidermis of transgenic mice with keratinocytes expressing a constitutively active Stat3BK5.Stat3C mice (Sano et al., 2005) were compared with the pattern in the epidermis of wild-type mice. Of approximately 130 differentially expressed genes detected by microarray, approximately 70 genes were significantly up-regulated in epidermis by constitutive activation of Stat3. Thirty three of these genes were hair follicle related genes. These genes included trichohyalin, hair keratins, and keratin-associated proteins that are expressed in the hair shaft and inner root sheath as essential structural components for hair growth (Winter et al., 1997). To confirm the microarray results, five genes whose expression was up-regulated in the epidermis of BK5.Stat3C mice were chosen for quantitative RT-PCR analysis. Consistent with the microarray data, the expression of Tchh, Krtap16-8, Krtap6-1, Krt33a, and Krt25d was significantly increased in the epidermis of BK5.Stat3C mice compared to wild-type mice. In addition, Krtap16-1, which was not identified by microarray analysis but is localized on mouse chromosome 16, was highly expressed in the epidermis of BK5.Stat3C mice in comparison to wild-type (Figure 1f).

overall_design: RNA samples were prepared from dorsal epidermis of female FVB mice (control) and BK5.Stat3C mice. Epidermal RNA from two mice from each group was pooled.  One microarray hybridization of control vs transgenic was performed for this particular study.  All remaining expression analysis was conducted by RT-PCR.

first: Dae


title: Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores

status: Public on Oct 05 2015

city: Vancouver

first: Juergen

last: Ehlting

state: BC

address: 321 - 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

summary:
Arabidopsis thaliana plants were infested i) with sucking insect herbivores (the generalist aphid Myzus persicae and the specialist aphid Brevicoryne brassicae), ii) with chewing insect herbivores (generalist caterpillars of Spodoptera exigua and specialist caterpillars of Pieris rapae) or iii) were treated by wounding. For each treatment, rosette leaves were harvested at two time points (6h and 24h) after removal of insects. For chewing herbivores and wounding both local, i.e. immediately damaged leaves, and systemic, i.e. undamaged leaves from the same plant, were collected. Control plants were uninfested, but otherwise equally treated and harvested in parallel.
We tested the hypothesis that Arabidopsis can recognize and respond differentially to insect species at the transcriptional level using a genome wide microarray. Transcriptional reprogramming was characterized using co-expression analysis in damaged and undamaged leaves at two times in response to mechanical wounding and four insect species. In all, 2778 (10.6%) of annotated genes on the array were differentially expressed in at least one treatment. Responses differed mainly between aphid and caterpillar and sampling times. Responses to aphids and caterpillars shared only 10% of up-regulated and 8% of down-regulated genes. Responses to two caterpillars shared 21% and 12% of up- and down-regulated genes, whereas responses to the two aphids shared only 7% and 4% of up-regulated and down-regulated genes. Overlap in genes expressed between 6h and 24h was 3-15%, and depended on the insect species. Responses in attacked and unattacked leaves differed at 6h but converged by 24h. Genes responding to the insects are also responsive to many stressors and included primary metabolism. Aphids down-regulated amino acid catabolism; caterpillars stimulated production of amino acids involved in glucosinolate synthesis. Co-expression analysis revealed 17 response networks. Transcription factors were a major portion of differentially expressed genes throughout and responsive genes shared most of the known or postulated binding sites.

overall_design: For each treatment, four (or three) replicate arrays were hybridized for a total of 59 arrays. Total RNA from replicate control plants harvested at each time point and treatment was pooled in order to minimize variability between individuals. Labeled cDNA derived from the pooled control RNA was co-hybridized with labeled cDNA derived from RNA isolated from individual plants treated with the described herbivores. This results in four biological replicates for each treatment. In order to account for possible dye biases, within each treatment group two treatment samples were labeled using Cy3 (with controls labeled with Cy5) and the remaining two were labeled using Cy5 (with control samples labeled with Cy3). Hybridization orders were randomized in order to avoid biases due to the hybridization time. analyzed.

first: Heidi

last: Appel

first: Howard

last: Fescemyer

first: Jürgen

first: Dave

last: Weston

first: Erin

last: Rehrig

first: Trupti

last: Joshi

first: Dong

last: Xu

first: Jörg

last: Bohlmann

first: Jack

last: Schultz


title: Gene expression in Rhagoletis pomonella and R. zephyria transplanted into snowberry and apple fruits

city: Manhattan

first: Gregory

last: Ragland

state: KS

address: 123 West Waters Hall

department: Entomology

institute: Kansas State University

summary: Gene expression in feeding larvae reciprocally transplanted into snowberry and apple fruits

sample_organism:
Rhagoletis pomonella
Rhagoletis zephyria

overall_design:
R. pomonella feeding in snowberry did not survive. The design includes R. pomonella feeding in apple and R. zephyria feeding in apple and snowberry
2 color Agilent custom microarrays, 6 biological replicates, 2-3 technical replicates, total 24 total 2-color arrays (however, R. pomonella feeding in snowberry arrays not included).
Sample types:
PA = R. pomonella larva transplanted into apple
ZA = R. zephyria larva transplanted into apple
ZS = R. zephyria larva transplanted into snowberry

first: Dietmar

last: Schwarz


title: Transcriptome profiling reveals that feeding live zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis.

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

institute: Memorial University of Newfoundland

summary: In this study, microarrays were used to investigate the larval cod transcriptome response to zooplankton supplementation in the diet.

overall_design: The experiment consisted of three different feeding regimes/diets as follows: Treatment 1 (6 replicate tanks): rotifers/Artemia with Ori-Green (Skretting, USA) enrichment (RA) 3 feedings per day (9 am, 3 pm and 9 pm), with rotifers fed until the fish reached  ~ 9 mm [~ 30 days post-hatch (dph)].  Treatment 2 (4 replicate tanks): rotifers with Ori-Green enrichment, supplemented with 5-10% wild caught zooplankton (RA-Zoo: zooplankton were > 90% copepods) from 2 dph until 30 dph. Treatment 3 (6 replicate tanks): Rotifers/Artemia with Ori-Green enrichment 4 days per week and Rotifers/Artemia with protein hydrolysate (RA-PH) enrichment 3 days per week (Monday, Wednesday and Friday),with rotifers fed until the fish reached ~ 9 mm. Whole larvae from each feeding regimes/diets were sampled when fish in particular treatment reached an average length of   ~ 9 mm. Individual DNAse-treated, column-purified total RNA samples from 8 fish per group (9 mm RA, 9 mm RA-PH and 9 mm RA-Zoo larvae) were used for microarray analysis using the Atlantic cod 20K oligonucleotide microarray platform (Booman et al. 2011) and a common reference experimental design.  On each array, RNA from an individual fish was hybridized together with a common reference RNA. All test samples were labeled with Cy5. The common reference was labeled with Cy3.

first: Matthew

middle: L

last: Rise

first: Jennifer

middle: R

last: Hall

first: Gordon

last: Nash

first: Marije

last: Booman

first: Tomer

last: Katan

first: A

last: Gamperl


title: Small artery remodeling depends on the genetic background in spontaneously hypertensive rats

first: Perry

middle: D

last: Moerland

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


title: The Long Noncoding RNA SNHG1 Regulates Both the Local and Distal Genes in Cancer

first: Guifeng

last: Wei

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Many long noncoding transcripts are involved in cancer progression. Here, we utilized high-throughput microarray to compare the transcriptome alterations between the SNHG1 knockdown or control in HCT116 cell lines. Two independent siRNAs were designed against the SNHG1 cDNA sequence. Thus, we identified 302 genes which were expressionally changed. Moreover, Gene Ontology and pathway enrichment analysis revealed that several gene signature were significantly  enriched, such as MAPK signaling pathway, growth factor activity and transcriptional corepresssor activity. Further, GSEA analysis suggested NF-kB signaling pathway, PI3K/Akt pathway were markedly associated with SNHG1-reuglated genes. The present study indicated that SNGH1 regulated both the local and distal genes in cancer progression.

overall_design:
HCT116 cells with SNHG1 knockdown and control. Three biological replicates of each condition were analyzed on Agilent microarray.
Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated). Thus, the raw data files (one file per two sample records) were linked as Series supplementary file and are indicated in the corresponding sample 'description' field.

first: Y

last: Sun

first: G

first: H

last: Luo

first: J

first: R

last: Chen


title: Enhanced diversity and aflatoxigenicity in interspecific hybrids of Aspergillus flavus and Aspergillus parasiticus

city: Raleigh

first: Ignazio

last: Carbone

state: NC

address: 851 Main Campus Drive, Suite 233

department: Plant Pathology

institute: North Carolina State University - Center for Integrated Fungal Research

summary: Aspergillus flavus and A. parasiticus are two of the most important aflatoxin-producing species that contaminate agricultural commodities worldwide.  Both species are heterothallic and undergo sexual reproduction in laboratory crosses.  Here, we examine the possibility of interspecific matings between A. flavus and A. parasiticus.  These species can be distinguished morphologically and genetically, as well as by their mycotoxin profiles.  Aspergillus flavus produces both B aflatoxins and cyclopiazonic acid (CPA), B aflatoxins or CPA alone, or neither mycotoxin; Aspergillus parasiticus produces B and G aflatoxins or the aflatoxin precursor O-methylsterigmatocystin, but not CPA.  Only four out of forty-five attempted interspecific crosses between compatible mating types of A. flavus and A. parasiticus were fertile and produced viable ascospores.  Single ascospore strains from each cross were isolated and were shown to be recombinant hybrids using multilocus genotyping and array comparative genome hybridization.  Conidia of parents and their hybrid progeny were haploid and predominantly monokaryons and dikaryons based on flow cytometry.  Multilocus phylogenetic inference showed that experimental hybrid progeny were grouped with naturally occurring A. flavus L strain and A. parasiticus.  Higher total aflatoxin concentrations in some F1 progeny strains compared to midpoint parent aflatoxin levels indicate synergism in aflatoxin production; moreover, three progeny strains synthesized G aflatoxins that were not produced by the parents, and there was evidence of putative allopolyploidization in one strain.  These results suggest that hybridization is an important diversifying force resulting in the genesis of novel toxin profiles in these agriculturally important species.

sample_organism: Aspergillus parasiticus x Aspergillus flavus

platform_organism:
Zea mays
Aspergillus flavus
Aspergillus oryzae

overall_design: aCGH comparison between 3 strains of Aspergillus:  2 parental of either A. flavus (PF) and A. parasiticus (PP) and 1 progeny (F1) analyzed at the probe level.  A total of six trio comparisons were made from a total of 56 isolates analyzed by aCGH.  Trio comparisons are as follows:  IC278 (PF), IC327 (PP) and IC1603 (F1); IC278 (PF), IC65 (PP) and IC1612 (F1); IC278 (PF), IC65 (PP) and IC1616 (F1); IC278 (PF), IC324 (PP) and IC1622 (F1); IC278 (PF), IC324 (PP) and IC1630 (F1); and finally IC278 (PF), IC33 (PP) and IC1637 (F1).

first: Rodrigo

last: Olarte

first: Carolyn

last: Worthington

first: Bruce

last: Horn

first: Geromy

last: Moore

first: Rakhi

last: Singh

first: James

middle: T

last: Monacell

first: Joe

last: Dorner

first: Eric

last: Stone

first: De-Yu

last: Xie


title: Genetic characterization of the MCF-10A cell line

city: Hamilton

first: Caitlin

last: Mills

address: 1280 Main St West

institute: McMaster University

summary: The MCF-10A cells in our laboratory were karyotyped using array CGH. The results were compared against previously published karyotypes for the cell line.

overall_design: Biological replicates of unperturbed, parental MCF-10A cells in our lab were analyzed using a dye swap method. Pooled male genomic DNA was used for the reference.

first: Douglas

last: Boreham

first: David

last: Andrews


title: Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus

first: Janneke

last: Wijman

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

sample_organism:
Bacillus cereus ATCC 10987
Bacillus cereus ATCC 14579

overall_design: Refer to individual Series


city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

summary: Runt-related transcription factor 3 (RUNX3) has been described as a tumor suppressor for gastric cancer and other solid malignancies. Despite its key role in physiological T-cell differentiation, there is rare information on its relevance for the development of human T-cell lymphoma or leukemia. Here we show that alterations of RUNX3 by either heterozygous deletion or methylation of its distal promoter can be observed in the tumor cells of 15/21 (71%) patients suffering from Sézary Syndrome (SS), an aggressive variant of cutaneous T-cell lymphoma. In consequence, mRNA levels of RUNX3/p46, the long isoform of RUNX3 – controlled by the proximal promoter – are significantly lower in SS tumor cells. Re-expression of RUNX3/p46 promotes apoptosis and slows down proliferation in a RUNX3/p46low cell line of cutaneous T-cell lymphoma. By this we present the first evidence that RUNX3 can act as a tumor suppressor in a human T-cell malignancy and suggest that this effect is predominantly mediated through the long isoform of this transcription factor, which has not been in the focus of previous studies.

overall_design: For the study The long isoform of RUNX3 acts as a tumor supressor in human T-cell lymphoma genomic aberrations of tumor material of 23 patients suffering from Sézary syndrome were analyzed using aCGH. 20 tumor samples are already included into the study GSE19000 and were re-evaluated with focus on chromosomal region 1p36. This data set is comprised of the 20 previous samples plus aCGH data of patients 21, 22 and 23.


title: rat: Sham vs. SNI

first: Moshe

last: Szyf


title: Cigarette smoking alters plasma microRNA expression profile in healthy young male smokers

city: beijing

first: zhang

last: suwei

address: changping

institute: capitalbio

summary: The stability of circulating miRNAs, their non-invasive sampling techniques and deregulation in diseases make them potential candidate biomarkers of biological effect. Here,  we used microarray technique to detect the plasma miRNA expression profiles of 28 healthy young male smokers (present smokers) and 12 non-smokers. As a result, we found that the expression levels of 35 miRNAs were significantly changed in the plasma of present smoker. Furthermore, some of the deregulated miRNAs were confirmed by qRT-PCR. Finally, the enrichment functions and associated diseases of the deregulated miRNA were analyzed as well.

overall_design: Cigarette smoking induced gene expression in human blood was measured. Forty independent experiments were performed using plasma from 28 present-smokers and 12 never-smokers.

first: Bing

last: Shi


title: Metformin suppressed maturation of human visceral preadipocytes in vitro with upregulation of miR-1246 and miR-3687

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

overall_design: Micro RNA expression of HPrAD-vis cells, a cell line of human visceral preadipovytes, with or without administration of metformin for 1 week and 2 weeks were assessed in vitro.

first: Koji

last: Fujita

first: Tsutomu

last: Masaki


title: Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 14579

city: Wageningen

first: Maarten

last: Mols

first: Marcel

last: Tempelaars

first: Tjakko

last: Abee


title: Allergic contact dermatitis to nickel is characterized by a specific microRNA signature [skin]

city: Hellerup

first: Marianne

middle: Bengtson

last: Løvendorf

address: Niels Andersens Vej 65

department: Dermato-Allergology

country: Denmark

institute: Gentofte Hospital

summary: Our findings demonstrate that nickel-challenged skin in subjects with allergy to nickel is characterized by a specific miRNA signature compared to vehicle-challenged skin. In addition, we found that miRNA expression changes are different in allergic contact dermatitis (ACD to nickel) compared to irritant contact dermatitis (ICD).

overall_design:
Two-condition experiment, day 0 vs. day 11 after challenge of the skin from DPCP-sensitized subjects with DPCP. Biological replicates: 6 healthy subjects. One replicate per array. Sample 1-12 (A29-A40)
Two-condition experiment, nickel vs. vehicle challenged skin. Biological replicates: 3 subjects with allergy to nickel, 3 subjects with no history of dermatitis. One replicate per array.  Sample 13-24 (A41-A52)

first: Beatrice

last: Dyring-Andersen

first: Marie

last: Vennegaard

first: Anders

last: Clemmensen

first: Charlotte

last: Bonefeld

first: Mads

last: Røpke

first: Lone

last: Skov


title: Allergic contact dermatitis to nickel is characterized by a specific microRNA signature


title: Global Transcriptional Repression: Initial and Essential Step for Plasmodium Sexual Development [expression array]

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: Gametocytes are nonreplicative sexual forms that mediate malaria transmission to a mosquito vector. They are generated from asexual blood stage parasites, which proliferate in the circulation. However, it remains largely unknown as to how this transition is genetically regulated. Here, we report that an Apetala2 (AP2) family transcription factor, AP2-G2, regulates the transition as a transcriptional repressor. Disruption of AP2-G2 in the rodent malaria parasites, Plasmodium berghei, did not prevent commitment to the sexual stage but halted their development before manifesting sex-specific morphologies. ChIP-seq analysis revealed that AP2-G2 targets approximately 1,500 genes and recognizes a five-base motif on their promoters. Most of these target genes are required for asexual proliferation in the blood by the parasites, thereby suggesting that AP2-G2 blocks the program for asexual replication of parasites in the blood. DNA microarray analysis showed that the identified targets constituted approximately 70% of the upregulated genes in AP2-G2-depleted parasites, and a promoter assay using a centromere plasmid demonstrated that the binding motif functions as a cis-acting negative regulatory element. These results suggest that global transcriptional repression, which occurs during the initial phase of gametocytogenesis, is an essential step to promote conversion to the sexual stage.

overall_design: To identify target genes of AP2-G2, microarray analysis was performed between  AP2-G2(−) and wild-type parasites. To establish synchronous infection in Wistar rats, whole blood was harvested from rats infected with AP2-G2(-) or wild-type parasites and cultured for 16 h. Mature schizonts were purified from the culture with Nicodenz  and inoculated into rats. Whole blood was harvested from these rats at 19 h after the innoculation. Four  biologically independent experiments were performed in both AP2-G2(-) and wild-type parasites. To kill asexual stage parasites, eight-week-old female Balb/c mice infected with AP2-G2(-) or wild-type parasites were treated with sulfadiazine in drinking water (10 mg/l) for two days. Five  biologically independent experiments were performed in both  AP2-G2(−) and wild-type parasite samples.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Tomomi

last: Kato


title: Allergic contact dermatitis to nickel is characterized by a specific microRNA signature [PBMCs]

summary: We found that peripheral blood mononuclear cells (PBMCs) (from subjects with allergy to nickel) stimulated with nickel were characterized by a specific miRNA signature that were different from vehicle-stimulated PBMCs.

overall_design: Two-condition experiment, nickel vs. vehicle challenged peripheral blood mononuclear cells (PBMCs). Biological replicates: 3 subjects with allergy to nickel, 3 subjects with no history of dermatitis. One replicate per array.  Sample 1-12 (A28-A39)

middle: B


title: The miR-200 Family and their Targets in Regulation of Type II Cell Differentiation in Human Fetal Lung

city: Dallas

first: Carole

last: Mendelson

address: 5323 Harry Hines Blvs

department: Biochemistry

institute: University of Texas Southwestern Medical Center

summary: Type II cell differentiation and expression of the major surfactant protein, SP-A, in midgestation human fetal lung (HFL) are markedly induced by cAMP and inhibited by TGF-β. cAMP induction of SP-A promoter activity is mediated by increased phosphorylation and in vivo binding of TTF-1/Nkx2.1, a critical transcription factor in lung development. To further define mechanisms for developmental induction of surfactant synthesis in HFL, herein, we investigated the potential role of microRNAs (miRNAs, miRs). To identify and characterize differentially regulated miRNAs in mid-gestation HFL explants during type II pneumocyte differentiation in culture, we performed miRNA microarray analysis of RNA isolated from epithelial cells from midgestation HFL explants before and after culture ± Bt2cAMP. Interestingly, the miR-200 family was significantly upregulated during type II cell differentiation; miR-200 family induction was inversely correlated with expression of its known targets, transcription factors ZEB1 and ZEB2, and TGF-b2. miR-200 antagonists inhibited TTF-1 and SP-A expression and upregulated TGF-β2 and ZEB1 expression in type II cells. Overexpression of ZEB1 in cultured type II cells decreased DNA binding of endogenous TTF-1, blocked cAMP stimulation of SP-A and inhibited miR-200 expression,whereas, cAMP markedly inhibited ZEB1/2 and TGF-β. Importantly, overexpression of ZEB1 or miR-200 antagonists in HFL type II cells markedly suppressed accumulation of lamellar bodies, organelles that store surfactant. Our findings suggest that the miR-200 family and ZEB1, which exist in a double-negative feedback loop regulated by TGF-β, serve important regulatory roles in the developmental regulation of type II cell differentiation and SP-A expression in HFL.

overall_design: Epithelial cells were isolated from midgestation Human Fetal Lung explants before and after 48 and 96 h of culture in the absence or presence of Bt2cAMP. RNA was extracted from the isolated epithelial cells using a miRNeasy kit (Qiagen). After passing a quality control test, the RNA was sent to LC Sciences (http://www.LCsciences.com), for miRNA microarray analysis of the 894 mature human miRNAs known at that time, using quadruple replicates of the ‘before culture’ and the 48 h and 96 h incubation time points.

first: Houda

last: Benlhabib

first: Wei

last: Guo

first: Brianne

last: Pierce


title: Analysis of global gene expression signatures in sweet potato as affected by temperature stress

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Global gene expression signatures was analysed through microarray expression profiling as a discovery platform to identify up and down regulated ESTs that represent genes involved in metabolic pathways in the leaf, fibrous root and storage root (tuber forming root) of sweetpotato (Ipomoea batatas) as affcted by high temperature stress (40oC) compared to ambient temperature (30oC). Also Global gene expression signatures was analysed by the same procedure to explore up and down regulated ESTs in tuberous root of sweet potato in comparison with fibrous root of Ipomoea cornea and identify unique ESTs that represent genes involved in tuber formation in sweet potato.

sample_organism:
Ipomoea batatas
Ipomoea carnea

overall_design: Organism : Ipomoea batatas  Custom Ipomoea batatas  8x60k Gene Expression Microarray (AMADID:044020) designed  by Genotypic Technology Private Limited.

first: Velumani

last: Ravi

first: Swarup

last: Chakrabarti

first: Thangaraj

last: Makeshkumar

first: Raju

last: Saravanan

first: Janardanan

last: Sreekumar


title: Intraspecific diversity among partners drives functional variation in coral symbioses

city: University Park

first: John

middle: Everett

last: Parkinson

address: 208 Mueller Lab

department: Biology

institute: Penn State University

summary: Coral reefs are declining globally.  Temperature anomalies disrupt coral-algal symbioses at the molecular level, causing bleaching and mortality events.  In terrestrial mutualisms, diversity in pairings of host and symbiont individuals (genotypes) results in ecologically and evolutionarily relevant stress response differences.  The extent to which such intraspecific diversity provides functional variation in coral-algal systems is unknown.  Here we assessed functional diversity among unique pairings of coral and algal individuals (holobionts).  We targeted six genetically distinct Acropora palmata coral colonies that all associated with a single, clonal Symbiodinium ‘fitti’ strain in a natural common garden.  No other species of algae or other strains of S. ‘fitti’ could be detected in host tissues.  When colony branches were experimentally exposed to cold stress, host genotype influenced the photochemical efficiency of the symbiont strain, buffering the stress response to varying degrees.  Gene expression differences among host individuals with buffered vs. non-buffered symbiont responses included biochemical pathways that mediate iron availability and oxygen stress signaling—critical components of molecular interactions with photosynthetic symbionts.  Spawning patterns among hosts reflected symbiont performance differences under stress.  These data are some of the first to indicate that genetic interactions below the species level affect coral holobiont performance.  Intraspecific diversity serves as an important but overlooked source of physiological variation in this system, contributing raw material available to natural selection.  Note: in the final publication, only ambient and cold treatments are discussed, but there was an additional hot treatment for each genotype at 34C.  Most colonies expired after 6 hours, so PAM data could not be collected.  The microarray data from 3.5 hours are included here.

overall_design: Hybridization followed a dual channel loop design using two biological replicates from each treatment that maximized power to detect differential expression in contrasts between regulationphenotype and temperature as well as the amount of data obtained from each slide (Simon and Dobbin 2003). A total of 12 arrays on one 12 plex slide were used. Each array measures the expression level of 135,185 genes from the elkhorn coral (Acropora palmata) transcriptome (Polato et al. 2011). Two 60-mer probes were designed for each contig (n = 85,260), and a single probe was designed for each singleton sequence (n = 45,390). Two additional probes each were developed for sequences associated with annotation information relating to calcium metabolism and stress response (n = 4,798). Replicate probes for individual sequences from the assembled transcriptome were not identical; rather they represented multiple different 60-mer sequences from the original template.

middle: E

first: Anastazia

last: Banaszak

first: Naomi

last: Altman

first: Todd

middle: C

last: LaJeunesse

first: Iliana

last: Baums


title: New functional signatures for understanding melanoma biology from tumor cell lineage-specific analysis [single channel experiments]

status: Public on Sep 30 2015

city: VILLEJUIF

first: Bastien

last: Job

address: 39 rue Camille Desmoulins

institute: Institut Gustave Roussy

summary: The identification of molecular signatures specific to distinct tumor types is urgently required for the design of therapies overcoming treatment resistance. It remains unclear whether such signatures are shared among tumors and corresponding cell lines, a key issue given the use of cell lines for drug development. We developed SCA (similarity core analysis) an unsupervised computational framework for extracting the core molecular features common to tumors and corresponding cell lines. We  applied this algorithm to mRNA and miRNA expression data from various sources, comparing melanoma cell lines with melanoma metastases as an example. The signature obtained was associated with phenotypic characteristics  in vitro and the core genes  CAPN3 and  TRIM63 were identified as new actors in melanoma cell migration and invasion. About 90% of the genes in the melanoma signature are potentially regulated by an intrinsic network of transcription factors known to regulate neural development (TFAP2A, DLX2, ALX1, MITF, PAX3, SOX10, LEF1 and GAS7) and three miRNAs (211-5p, 221-3p, 10a-5p). The SCA signature effectively discriminated between two subpopulations of melanoma patients with significant difference in overall survival. Furthermore, it classified MEKi and BRAFi resistant and sensitive melanoma cell lines. The SCA algorithm is potentially applicable to any tumor cell type.

overall_design: 21 melanoma cell lines are analyzed in single color

first: Forian

last: Rambow

first: Valérie

last: Petit

first: Franck

last: Gesbert

first: Véronique

last: Delmas

first: Hannah

last: Seberg

first: Guillaume

last: Meurice

first: Eric

last: Van Otterloo

first: Philippe

last: Dessen

first: Caroline

last: Robert

first: Daniel

last: Gautheret

first: Robert

last: Cornell

first: Alain

last: Sarasin

first: Lionel

last: Larue


title: Transcriptional profile of Bacillus subtilis sigF-mutant during vegetative growth and under sporulating conditions

city: Groningen

first: Wout

last: Overkamp

address: Nijenborgh 7

institute: Rijksuniversiteit Groningen, Department of Molecular Genetics

summary: Bacillus subtilis’ sigma factor F is the first forespore specific transcription factor and controls genes required for the early stages of prespore development. The role of sigF is well studied under conditions that induce sporulation. Here, the impact of a sigF disruption on the transcriptome of exponentially growing cultures is studied by micro-array analysis. This is relevant because in various experiments, such as industrial fermentation, prolonged experimental evolution or zero-growth studies, sporulation is an undesirable trait that should be avoided, e.g by a sigF mutation. Under conditions that typically don’t induce sporulation, the transcriptome showed minor signs of sporulation initiation. The number of genes differentially expressed and the magnitude of expression were, as expected, quite small in comparison with sporulation conditions. The genes mildly down-regulated were mostly involved in anabolism and the genes mildly up-regulated were mostly involved in catabolism, in particular fatty acid degradation genes. Probably this is related to the arrest at sporulation stage II occurring in the sigF mutant where additional energy is required for further growth of the polar compartments formed.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Wildtype strain was compared to sigF-mutant under both sporulating conditions and vegetative conditions (3 slides for each condition, consisting of 2 biological replicates)

first: Oscar

middle: P

last: Kuipers


title: Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays

city: Mexicali

first: RICARDO

last: SALOMON

state: Baja California

address: De la Normal street S/N and Blvd. Benito Juárez Col. Insurgentes Este

department: Engineering Institute

country: Mexico

institute: Autonomous University of Baja California

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

summary:
Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. Microarray technologies have recently been used to study the bovine genome. The objective of the present study was to develop CNVs in Holstein cows from the Northwest of Mexico using the Affymetrix Axiom Genome-Wide BOS 1 Array, which assays 648,315 SNPs and provides a wide coverage for
genome-wide studies. We applied the two most widely used algorithms for the discovery of CNVs (PennCNV and QuantiSNP) and found 56 CNV regions (CNVRs) representing 0.33% of the bovine genome (8.46 Mb). These CNVRs ranged from 1.5 to 970.8 kb with an average length of 151 kb. They involved 103 genes and showed a 28% overlap with CNVRs already reported. Of the 56 CNVRs found, 20 were novel. In this study we present the first genomic analysis of CNVs in Mexican cattle using highdensity SNP data. Our results provide a new reference basis for future genomic variation and association studies between CNVs and phenotypes,
especially in Mexican cattle.

overall_design: 12 Mexican cows of Holstein breed, were genotyped by Affymetrics Axiom Genome-Wide Bos 1 Array for the copy number variations identification.

first: Ricardo

last: Salomon Torres

first: Rafael

last: Villa Angulo

first: Carlos

first: Victor Manuel

last: Gonzalez Vizcarra


title: Comparison of the expression profiles of the 630E (JIR8094) strain and a prdR mutant (LB-CD8) after 4h growth in TY supplemented with L-proline

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary:
Clostridium difficile, a proteolytic Gram-positive anaerobe, has emerged as a significant nosocomial pathogen. Stickland fermentation reactions are thought to be important for growth of C. difficile. In Stickland reactions, pairs of amino acids donate and accept electrons, generating ATP and reducing power in the process. Reduction of the electron acceptors proline and glycine requires the D-proline reductase (PR) and the glycine reductase (GR) enzyme complexes, respectively. PrdR, a sigma54-dependent regulator, activates transcription of the PR-encoding genes in the presence of proline and negatively regulates the GR-encoding genes, suggesting that PrdR is a central metabolism regulator that controls preferential utilization of proline and glycine to produce energy via the Stickland reactions.

Here, transcriptional profiling of the C. difficile 630E strain vs. a prdR mutant (LB-CD8) after 4h of growth in the presence of proline is performed.

overall_design: Two-condition experiment: 630E (JIR8094) strain vs. prdR mutant (LB-CD8) grown in TY supplemented with 30 mM L-proline. 2 biological replicates for each condition, including a dye-swap.

first: Laurent

last: Bouillaut

first: Thomas

last: Dubois

first: Marc

last: Monot