title: Expression data of vascular smooth muscle cell in patients with suspected giant cell arteritis (GCA)

status: Public on Nov 18 2015

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary:
There is a remodelling process which occurs in affected vessels during GCA and vascular smooth muscle cells are key cells in this process. Thickening of vessel might be responsible for vessel occlusion.
We isolated vascular smooth muscle cells from temporal artery biopsies of patients with suspected GCA and used expression chips in order to identify genes up- and down-regulated in VSMC from patients with proven GCA compared to VSMC from patients with possible GCA and to VSMC from patients with another diagnosis.

overall_design: Vascular smooth muscle cells were isolated at the time of temporal artery biopsy (TAB) and 3 groups of VSMC were compared according to patient's final diagnosis : (1) TAB+GCA=histology proven GCA, (2) TAB-GCA=GCA lacking histological proof and (3) GCA-control=other diagnosis than GCA.

first: A

last: Regent

first: I

last: Mouthon


title: MicroRNA expression data in human fetal lungs

status: Public on Nov 26 2015

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

country: USA

institute: University of Pittsburgh

summary: Microarray data of human fetal lungs between 16-23 weeks of gestation. The results provide a general insight into the microRNA expression profile during the canalicular phase of lung development.

overall_design: Lung tissue samples for microarray analysis were obtained through the University of Pittsburgh Health Sciences Tissue Bank through an approved IRB protocol and de-identified using an honest broker system. Total RNA was labeled with Cy3 and hybridized on Agilent 8X15K microRNA array (Agilent Technologies, Santa Clara, CA). After 20 hours hybridization, arrays were washed and scanned according to the manufacturer’s protocol.

middle: V

first: Naftali

last: Kaminski


title: Integrative gene expression profiling analysis of human quiescent hepatic stellate cells

status: Public on Nov 23 2015

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Unveiling the regulatory pathways maintaining hepatic stellate cells (HSC) in a quiescent (q) phenotype is essential to develop new therapeutic strategies to treat fibrogenic diseases. To uncover the miRNA-mRNAs regulatory interactions in qHSCs, HSCs were FACS-sorted from healthy livers and activated HSCs were generated in vitro. MiRNA Taqman array analysis showed HSCs expressed a low number of miRNA, from which 46 were down-regulated and 212 up-regulated upon activation. Computational integration of miRNA and gene expression profiles revealed that 66% of qHSCs miRNAs correlated with more than 6 altered targeted mRNAs (17,28±10,7 targets/miRNA), whereas aHSC-associated miRNAs had an average of 1,49 targeted genes. Interestingly, interaction networks generated by miRNA-targeted genes in qHSCs were associated with key HSCs activation processes. Next, selected miRNAs were validated in healthy and cirrhotic human livers and miR-192 was chosen for functional analysis. Down-regulation of miR-192 in HSC was found to be an early event during fibrosis progression in mouse models of liver injury. Moreover, mimic assays for miR-192 in HSCs revealed its role in HSC activation, proliferation and migration. Together, these results uncover the importance of miRNAs in the maintenance of qHSC phenotype and form the basis for understanding the regulatory networks in HSCs.

overall_design: Transcriptomic profile derived from four quiescent hepatic stellate (QHSC), four activated hepatic stellate (AHSC), three liver sinusoidal endothelial (LSEC) and two hepatocytes cells (HEP).

first: M

last: Coll

middle: E

last: Taghdouini

first: L

last: Perea

last: Mannaerts

last: Vila-Casadesús

first: D

last: Blaya

first: J

middle: J

middle: A

last: Grunsven

first: P

last: Sancho


title: A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases [MAF siRNA]

status: Public on Nov 12 2015

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS.  We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS.

overall_design: Naïve CD4+ T cells were isolated from buffy coat of four healthy donors using a naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with TGF-β (1 ng/mL), IL-1β (10 ng/mL), IL-6 (25 ng/mL), IL-21 (25 ng/mL) and IL-23 (25 ng/mL) for Th17, and TGF-β (10 ng/mL) and IL-2 (10 ng/mL) for Treg. Cells were cultured for six days in Iscove’s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th17 and Treg cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K v2 microarray kit, according to the manufacture’s instruction (Agilent Technologies).

first: Mika

last: Gustafsson

middle: R

first: Sandra

last: Hellberg

first: Aelita

last: Konstantinell

first: Daniel

last: Eklund

first: Jan

last: Ernerudh

first: Antonio

last: Lentini

first: Robert

last: Liljenström

first: Johan

last: Mellergård

first: Hui

last: Wang

first: Colm

last: Nestor

first: Huan

last: Zhang

first: Mikael

last: Benson


title: caArray_laird-00224: TCGA Ovarian: Analysis of DNA Methylation for Ovarian Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27) (USC)

status: Public on Nov 21 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

type: Methylation profiling by genome tiling array

summary: TCGA Analysis of DNA Methylation Using Illumina Infinium Human DNA Methylation 27 platform

overall_design:
laird-00224
Assay Type: Methylation
Provider: Illumina
Array Designs: jhu-usc.edu_OV.HumanMethylation27.1.adf, jhu-usc.edu_OV.HumanMethylation27.v2
Organism: Homo sapiens (ncbitax)
Tissue Sites: Ovary, Ovary, NOT SPECIFIED, PERITONEUM (OVARY), OMENTUM
Material Types: Control Cell Line, Solid normal_tissue, organism_part, Primary solid_tumor, whole_organism, Recurrent Solid Tumor
Disease States: Serous Cystadenocarcinoma, Serous cystadenocarcinoma, NOT SPECIFIED


title: A crucial role of the zinc finger protein PfZnFP-G in sexual differentiation of the malaria parasites, Plasmodium falciparum

status: Public on Nov 24 2015

city: Singapore

first: Yen-Hoon

last: Luah

address: Nanyang Technological University 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

type: Genome binding/occupancy profiling by array

summary: We described the biological role of a putative zinc finger protein (Plasmodb id: PF3D7_1008600), which plays an important role during the initiation and subsequent progression of gametocytogenesis in P. falciparum. Hence we termed the protein P. falciparum Zinc Finger Protein for Gametocytogenesis (PfZnFP-G). During the asexual intraerythrocyic developmental cycle (IDC), PfZnFP-G levels peak during the schizont stage during which it is localized in the nucleus. During the IDC, PfZnFP-G appears to be stochastically expressed in ~3% parasite population. Deactivation of PfZnFP-G appears to suppress, but not fully inhibit, production of gametocytes and vice versa overproduction of PfZnFP-G stimulates gametocytogenesis. In addition, PfZnFP-G is capable of associating with DNA binding preferentially to intergenic, promoter regions of the genome, and this binding correlates positively with transcription, particularly of other gametocyte specific genes. PfZnFP-G is also expressed in the mid-to-late gametocytes where it is present in the cytoplasm. Overall, these results suggest a dual function of PfZnFP-G in gametocytogenesis including: (i) commitment as a transcription factor and (ii) gametocyte maturation as a putative RNA binding protein.

overall_design: Transgenic 3D7 wild type parasite lines were generated with PfZnFP-G tagged, over-expressed and knocked-out. Transcriptional profiles across the parasite life cycle were generated. Genome occupancy of PfZnFP-G were also investigated and compared to the corresponding transcriptional profiles.

first: Eng-How

last: Lim

first: Lei

last: Zhu

first: Zbynek

last: Bozdech


title: Gene expression response of Medicago truncatula roots treated with Nod-LCOs

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

country: Germany

institute: Leibniz Universität Hannover

summary: Legumes interact with rhizobia, leading to the development of root nodules. Diffusible rhizobial signals were identified as Nod-LCOs. Applying Nod-LCOs on plantlet roots, we used GeneChips to detail the global programme of gene expression in response to the external application of Nod-LCOs.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: To harvest tissues for transcriptome profiling, three biological replicates consisting of 10 plantlets per treatment were selected. After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment (Nod-LCOs) or control solutions and harvested. During harvest, one mm of the root tip of each plantlet was removed and discarded. The remaining 2 to 2.5 cm of the distal root region were cut off and directly frozen in liquid nitrogen.

first: Natalija

last: Hohnjec

first: Lisa

last: Czaja

first: Jörg

middle: D

last: Becker


title: Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation

status: Public on Nov 20 2015

city: Houston

first: Shen

last: Gu

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: We describe an 18-month-old male (BAB7221)with split-hand malformation.  Custom high-density array and digital droplet PCR revealed the copy-number gains were actually quadruplications in the mother (BAB7219), the fetus (BAB7218) and her later born son (BAB7221). This quadruplication-normal-quadruplication pattern was shown to be expanded from the triplication-normal-triplication CNV at the same loci in the maternal grandmother (BAB8247).

overall_design: High density custom aCGH detecting all 6 individuals in the family

first: James

last: Lupski


title: p53-induced miRNAs upon CKIα ablation

status: Public on Nov 27 2015

city: Jerusalem

first: Moshe

last: Biton

address: hadassah ein kerem

department: Lautenberg Center for immunology

country: Israel

institute: Hebrew University

summary: Continuously renewing tissues are often divided into proliferative and post-mitotic differentiated zones, which must retain their function also following stress and damage. Here we show how p53 operates via its two effector arms miR-34a or p21 to control enterocyte proliferation along the crypt villus axis. Whereas cell cycle is commonly regulated via the Rb pathway by CDK inhibitors, we found that in the gut epithelium, crypt cell proliferation upon p53 activation is primarily controlled by miR-34a, regulating pRb phosphorylation via the Cyclin D/CDK4 complex. Surprisingly, p21 has little effect on pRb phosphorylation and crypt cell proliferation, yet functions to secure post-mitotic villus cell quiescence via the Rb-like (RBL) /E2F4 complex, implicating distinct functions of the Rb and RBL machineries in tissue renewal. It thus appears that mammalian2tissue control of the cell cycle is far more specialized than previously appreciated, providing new opportunities to target specific tissue components for therapeutic purposes.

overall_design: To assess a putative role of p53-induced miRNAs in regulating enterocyte proliferation upon CKIα ablation in the mouse gut (CKIαΔgut), we profiled the microRNAs in enterocytes purified from heterozygous CKIα+/Δgut control (CKIα Het), CKIαΔgut (CKIα KO) and doubly-deleted CKIα/p53Δgut (CKIα/p53 DKO) mice (n=3 per pooled group). Fold change of each miRNA expression in CKIαΔgut or CKIα/p53Δgut was relatively quantified (RQ) to CKIα Het specimens.


title: miR-487b, miR-3963 and miR-6412 delayed myogenic differentiation in C2C12 mouse myoblast-derived cells.

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary:
We newly identified skeletal muscle differentiation-associated miRNAs by comparing miRNA expression profile between C2C12 cell and Wnt4-overexpressing C2C12 cell. miR-487b, miR-3963 and miR-6412 are significantly down-regulated in
differentiating C2C12 cells, and transfection of  their mimics resulted in reduced expression of myogenic differentiation markers including Troponin T, myosin heavy chain fast and slow type.

overall_design: Single analysis for each condition (proliferating C2C12 cells, differentiating C2C12 cells, proliferating Wnt4-overexpressing C2C12 subline cells

first: T

last: Nohno

first: N

last: Katase


title: Dystrophic single myofibers vs. control single myofibers

status: Public on Nov 25 2015

city: Bergisch Gladbach

first: Silvia

last: Rueberg

state: NRW

address: Friedrich-Ebert-Str. 68

department: MACSmolecular Business Unit

institute: Miltenyi Biotec GmbH

summary: MicroRNA-expression profile of dystrophic single fibers compared to wild type single fibers isolated from different muscles of mdx and C57BL mice.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Myofibers were isolated from different muscle types (tibialis, diaphragm and quadriceps) of gender- (male) and age- (3 month old and half)  matched wt and dystrophic mice. 9 total samples per animal model (C57BL, mdx), 3 replicates per muscle type.

first: Yvan

last: Torrente


title: Exercise dependent gene regulation in cartilage

status: Public on Nov 10 2015

city: Columbus

first: Jin

last: Nam

state: OH

address: 305 W. 12th Ave., 4010 Postle Hall

institute: The Ohio State University

summary:
Objective. Exercise is crucial for maintaining cartilage integrity and providing prophylaxis against the onset of osteoarthritis (OA). Here we systematically examined the exercise driven transcriptional activation/repression of genes from healthy articular cartilage to dissect the metabolic pathways responsible for its potential benefits.
Methods. Healthy Sprague-Dawley rats were either not exercised (control) or subjected to daily exercise (low intensity treadmill walking) for 2, 5, or 15 days. Subsequently, articular cartilage from distal femoral heads was harvested, RNA extracted and the transcriptome-wide regulation of gene expression analyzed by Affymetrix microarray chips. Kyoto Encyclopedia of Genes and Genome (KEGG) database was used to identify the metabolic pathways regulated by exercise.
Results. Microarray analysis of articular cartilage from exercised rats revealed two fold or greater up or down regulation of 926 transcripts for up to 15 days, as compared to control rat cartilage. The KEGG pathway analysis revealed that exercise transcriptionally activates/suppresses genes that encode proteins involved in regulating 123 metabolic pathways. These pathways control the biosynthesis of molecules associated with extracellular matrix, intermediate metabolites, cell signaling, cell growth and differentiation, cytoskeletal rearrangements, and inflammation including those associated with OA.
Conclusions. Our findings highlight that exercise is a robust transcriptional regulator of a wide array of genes in the healthy cartilage. The actions of exercise collectively regulate metabolic pathways that are critical for strengthening cartilage while attenuating detrimental effects of proteolytic enzymes and inflammatory pathways to provide prophylaxis against inflammatory joint diseases.

overall_design: Sprague Dawley rats (n=5 per group, 12-14 weeks old females, Harlan Labs, IN) were housed at 5 animals/cage in individually ventilated cages with sterile Aspen bedding, and standard environmental enrichment. The cages were maintained at 12-h light/12-h dark cycle at 21°C  in a pathogen free unit. All rats had ad libitum access to water and food and allowed normal cage activity. Animals randomly assigned to each group were either not exercised (Controls/Group I) or exercised (treadmill walking, 12 m/min for 45 min daily) for 2 (Group II), 5 (Group III), or 15 (Group IV) days13. Articular cartilage on the condyles of distal femurs were carefully dissected on ice under a stereomicroscope (10–15 mg/femur), immediately placed on dry ice and pulverized (3x30 seconds at 2500 RPM) in a Mikrodismembrator S (Sartorius, Germany). RNA was extracted using Trizol reagent (Invitrogen, CA), and RNA quality verified by a Bioanalyzer 2100 (Agilent, CA)13. The Whole Transcript (WT) cDNA Synthesis and Amplification Kit and WT Terminal Labeling Kit (Affymetrix, CA) were used for cDNA synthesis and labeling from 300 ng RNA template as recommended by the manufacturers. Labeled samples from 3 different rats from each group were hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Array and scanned with GeneChip Scanner 3000 7G System (Microarray Shared Resource Facility, OSU Comprehensive Cancer Center)13.

first: Sudha

last: Agarwal


title: DBCP Exposed Rat Testis Transcript Content

status: Public on Nov 29 2015

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

summary: Rats were exposed to sub-chronic low doses of the  the germ cell toxicant 1,2-dibromo-3-chloropropane (DBCP) or corn oil (control for DBCP), for 3 months. Some rats in each group underwent 3 months of post-exposure recovery.

overall_design: The apical endpoints and mating studies used in animal models for reproductive toxicity testing are not practical or translatable for human risk assessment, which typically focus on the analysis of semen and serum hormones. Because of these limitations, effort has been devoted to developing sperm molecular biomarkers that stably reflect male reproductive function. The goals of this work were to 1) identify biomarkers of testis damage within rat sperm after sub-chronic low dose exposures to the germ cell toxicant 1,2-dibromo-3-chloropropane [DBCP] for 3 months) using gene array analysis; and 2) compare these biomarkers to traditional endpoints.DBCP-treated rats had decreased body and epididymides weights, which also resolved after recovery, but no altered sperm transcripts.

first: Kim

last: Boekelheide


title: A DNA microarray-based assay to detect dual infection with two dengue virus serotypes

status: Public on Nov 30 2015

city: México

first: Maria

middle: L

last: Muñoz

address: Av. Instituto Politécnico Nacional 2508

department: Genetics and Molecular Biology

country: Mexico

institute: CIVESTAV-IPN

summary:
Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples.
Background
Dengue is a mosquito-borne viral infection causing a major public health problem globally. Dengue virus (DENV) is the causative agent of dengue fever (DF) and dengue hemorrhagic fever (DHF) and includes four distinct serotypes (DENV-1, DENV-2, DENV-3, and DENV-4). DENV-2 and DENV-3 have been associated with severe dengue disease, consequently, laboratory testing for DENV is needed to confirm the diagnosis of DENV
infection, serotype and to differentiate dengue from other febrile tropical illnesses. In addition, surveillance of mosquitoes infected with DENV is needed to monitor the infection rates within vector mosquito populations harboring specific serotype to provide an early warning sign to predict epidemics.

Results
In this work we have applied microarray analysis to simultaneously determine the serotype of multiple RNA samples from human or mosquitoes. The proposed microarray method can be used for i) rapid and reliable dengue diagnosis; ii) serotyping and iii) surveillance of mosquitoes infected with dengue. These microarrays were useful to confirm the presence of DENV-2 in 94 serum samples, DENV-3 in three samples from Juchitan,  Oaxaca and one case from Juchitan, Oaxaca contained DENV-2 and -3. Moreover by using these microarrays we also determined DENV in pools of gravid females mosquitoes collected in several sites of nineteen Mexican states in 2005. Mosquito pools from 31 cities in the states of Yucatan, Campeche, Tabasco, Chiapas, Veracruz, Oaxaca, Guerrero, Tamaulipas and
Colima were infected with DENV-2, six cities in Yucatán, Tabasco, Morelos, Tamaulipas, Colima, and Nayarit with DENV-1, three from Tabasco, Veracruz and Oaxaca with DENV 3 and two with two serotypes simultaneously (Ciudad Mante with DENV-1 and DENV-2, and Tavela with DENV-2 and DENV-3).

Conclusion
Here we show the success of applying microarrays assay to provide a consistently robust qualitative detection of dengue serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) in serum samples from patients or in pools of gravid female mosquitoes collected in the field of nineteen Mexican states. Interestingly, we did not detect any mosquito or serum sample containing DENV-4.

platform_organism:
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4

overall_design: Three replicates (Experiment 1 to 3) were performed, each one hybridized with four specific primers obtained from different serotpyes of dengue virus.

first: Alvaro

last: Díaz-Badillo

first: Gerardo

last: Pérez-Ramírez

first: Victor

last: Altuzar

first: Juan

last: Burgueño

first: Julio

middle: G

last: Mendoza-Alvarez

first: Jorge

middle: P

last: Martínez-Muñoz

first: Alejandro

last: Cisneros

first: Joel

last: Navarrete-Espinosa

first: Feliciano

last: Sanchez-Sinencio


title: Ovarian Cancer prognosis: Different methylation in patients with PFS <3 years vs. >3 years

status: Public on Nov 16 2015

city: Jena

first: Norman

last: Häfner

address: Bachstrasse 18

department: Gynecology

institute: Jena University Hospital

summary: Identification of differently methylated regions of CpG islands in epithelial ovarian cancer (EOC) tissue from patients with progression free survival <3 years (worse outcome) vs. patients with PFS >3 years (good outcome, relapse free until last follow up). Patients were homogenous in regard to clinical (FIGO III/IV, serous histology, optimally resected (macroscopically tumor free), platin-taxan chemotherapy) and molecular properties (immunohistochemistry for p16, BRCA1, Ki67 and p53)).

overall_design: Comparative hybridization of enriched, methylated DNA from 2 pools of good vs. 2 pools of worse prognosis EOC (each pool with DNA from 3 tumors)

first: Daniel

last: Steinbach

first: Matthias

last: Dürst

first: Ingo

middle: B

last: Runnebaum


title: MetSearch: A screening platform for the discovery of genes implicated in metastatic dormancy and reactivation

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: We have developed a screening platform for the isolation of genetic entities involved in metastatic reactivation. Retroviral libraries encoding cDNAs from highly metastatic breast cancer cells or pooled microRNAs were transduced into breast cancer cells that become dormant upon infiltrating the lung. Upon inoculation in the tail vein of mice, the cells that had acquired the ability to undergo reactivation generated metastatic lesions. Integrated retroviral vectors were recovered from these lesions, sequenced, and subjected to a second round of validation. By using this strategy, we identified canonical genes and microRNAs that mediate metastatic reactivation in the lung. To identify genes that oppose reactivation, we screened an expression library encoding shRNAs and we identified target genes that encode potential enforcers of dormancy. Our screening strategy enables the identification and rapid biological validation of single genetic entities that are necessary to maintain dormancy or to induce reactivation. This technology should facilitate the elucidation of the molecular underpinnings of these processes.

overall_design: We conducte miRNA microarray analysis (Agilent Technologies) as a complementary technique to examine miRNA expression profiles in our tumor progression series model, comparing the non-metastatic cells lines (67NR, 168FARN, 4TO7) with that of the metastatic cell line (4T1). By studying these profiles, we can identify sets of miRNAs that regulate the different steps of metastasis, namely intravasation, survival in the circulatory system and at distant sites, and extravasation and metastases formation, as represented by the different cell lines.

first: Hua

last: Gao

first: Filippo

last: Giancotti


title: Profiling of Brat associated mRNAs from Drosophila embryos by RIP-CHIP

status: Public on Nov 13 2015

city: Regensburg

first: Julia

middle: C

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

institute: University of Regensburg

summary:
The Drosophila TRIM-NHL protein Brain tumor (Brat)  plays important roles during early embryogenesis, in cell fate decisions, during neurogenesis and in mature neurons. Brat is an RNA-binding protein and functions as translational repressor. However, which RNAs Brat regulates and how RNA-binding specificity is achieved, is unknown.   Using RNA-Immunoprecipitation we identify Brat-bound mRNAs in Drosophila embryos and define a consensus binding motif.
Microarrays were used to profile Brat-associated RNAs from fly embryos.

overall_design: Flag-myc-Brat was precipitated from Drosophila embryo lysates and bound RNAs were profiled using microarrays. Precipitation from wild type flies served as negative control.

first: Inga

last: Loedige

first: Michael

last: Krahn

first: Gunter

last: Meister


title: Profiling of circulating microRNAs in patients with Barrett’s esophagus and esophageal adenocarcinoma

status: Public on Nov 19 2015

city: Utrecht

first: Jantine

last: van Baal

state: Utrecht

address: Heidelberglaan 100

department: Department of Gastroenterology and Hepatology

country: Netherlands

institute: University Medical Center Utrecht, The Netherlands

summary: miRNAs were extracted from plasma samples of healthy volunteers, patients with Barrett’s esophagus and patients with esophageal adenocarcinoma. We used the Serum / Plasma Focus miRNA PCR panel (Exiqon, Denmark) to quantitate miRNA presence in the different patient groups.

overall_design: PCR miRNA profiling. miRNA from three different patient groups were extracted from their plasma.

first: Pauline

last: Bus

first: Christine

last: Kestens

first: Fiebo

last: Ten Kate

first: Wilbert

middle: M

last: Peters

first: Joost

middle: H

last: Drenth

first: Jeanine

last: Roodhart

first: Peter

last: Siersema

middle: W


title: Daphnia magna exposed to non-polar narcotics (aliphatic alcohol) and polar narcotics (substituted benzene derivatives)

status: Public on Nov 14 2015

city: Antwerp

first: Melissa

last: Penninck

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

summary: MOA categorization of chemicals with narcotic mechanism by combining gene transcription profiling and physiological effect assessment after EC10 exposure in systems biology approach in Daphnia magna.

overall_design: Universal reference design, reference is a mixture of aliquots from control and exposed samples. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.

first: M

first: L

last: Vergauwen

first: D

last: Knapen

first: R

last: Blust


title: miR-19b mediates lung epithelial-mesenchymal transition via PTEN signaling in response to mechanical stretch

city: Guangzhou

first: pu

last: mao

address: 151 Yanjiang Street West

country: China

institute: Guangzhou Institute of Respiratory Diseases

summary: Alveolar epithelial type II (AEII) cells are the first line host in response to mechanical ventilation. We tested the hypothesis that the modulation of microRNA on AEII cells in response to mechanical stretch may participate in the ventilator-induced lung injury. This experiment is designed to screen miRNAs that are deregulated during mechanical stretch of AEII cells.

overall_design: primary human AEII cells were isolated from distal portions of normal lung tissues of three oncologic patients undergoing lung resection and characterized by the expression pro-SP-C, α-ENac and Green DND-26 staining. AEII cells were seeded into BioFlex Culture 6-well plates (Flexcell International Corporation, Hillsborough, NC) at a density 5×10^5 cells/well in small airway cell growth medium (SAGM, Lonza, Walkersville, MD) containing 1% FBS for 24 h. The cells were then subjected to cyclic stretch for 48 h at a frequency of 20 cycles/min and 20% elongation (FX-5000; Flexcell International Corporation, Hillsborough, NC). Static resting cells served as controls. After mechanical stretch, Stretched and static AEII were subjected to miRNA array (Exiqon miRCURY™ LNA Array v.18.0) analysis.

first: Yimin

last: Li

first: Pu

last: Mao


title: Expression data from the brain of cynomolgus macaques upon intrastriatal administration of baculoviral vectors

first: Timothy

middle: Weixin

last: Kwang

address: 46 Kim Yan Road, The Herencia #01-14/15

institute: Tessa Therapeutics Pte. Ltd.

summary: Recombinant insect baculoviral vectors efficiently transduce several types of cells in the brain and can possibly be used for gene therapy for brain disorders. To verify the suitability of using these viral vectors to develop gene therapy strategies in the brain, we evaluated immune reactions upon acute administration of baculoviral vectors into the brain of the cynomolgus macaque using microarray global gene expression profiling.

overall_design: Adult male cynomolgus macaques (Macaca fascicularis) were administered with baculovirus BV-HSVtk purified by membrane chromatography + high-speed centrifugation (MC+HS) into the brain.

first: Ghayathri

last: Balasundaram


title: Gene expression response in roots of Medicago truncatula mutants treated with Myc-LCOs

first: Helge

last: Küster

summary:
Legumes interact with soil fungi, leading to the development of arbuscular mycorrhizal (AM) roots. Diffusible AM fungal signals were identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs).
Applying Myc-LCOs on roots of symbiotic mutants, we used GeneChips to detail the global programme of gene expression in these mutants in response to the external application of Myc-LCOs.

Keywords: Expression profiling by array

overall_design: To harvest tissues for transcriptome profiling, three biological replicates consisting of 10 plantlets per treatment were selected. After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment (Myc-LCOs) or control solutions and harvested. During harvest, one mm of the root tip of each plantlet was removed and discarded. The remaining 2 to 2.5 cm of the distal root region were cut off and directly frozen in liquid nitrogen.

first: Natalija

last: Hohnjec

first: Lisa

middle: F

last: Czaja

first: Claudia

last: Hogekamp

first: Fabienne

last: Maillet

first: Jörg

last: Becker

first: Jean

last: Dénarié


title: Microarray analysis of bovine oocyte from distinct follicle sizes reveals gradual transcripts accumulation

status: Public on Nov 15 2015

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

country: Canada

institute: Laval University

summary: The objective of the study was to compare the transcriptome of the bovine oocyte coming from distinct follicle sizes.

overall_design: The different follicle sizes (<3mm; 3-5mm; 5-8mm and >8mm) were compared with microarray using a reference design (<3mm as a referece) for a total of three comparisons (<3mm vs 3-5mm; <3mm vs 5-8mm; <3mm vs >8mm). Overall, 18 hybridizations, corresponding to the three biological replicates (different week of oocyte collection) and three comparisons were done using a dye-swap set-up.

first: Rémi

first: Marc-André

last: Sirard


title: Affymetrix Human Exon 1.0 ST Array data for human induced pluripotent stem cells (hiPSCs) and human fibroblasts

status: Public on Nov 28 2015

city: Tampere

first: Reija

last: Autio

address: Korkeakoulunkatu 1

department: SGN

country: Finland

institute: Tampere University of Technology

summary:
Human genomic variations are associated with several phenotypic traits, such as facial features or hereditary diseases. These variations can be, for example, single nucleotide polymorphisms (SNPs) or copy number variations (CNVs). Several genome-wide studies detecting the  correlations between genomic variants and gene expression levels have been performed. In this study, we have studied human embryonic stem cells and human induced pluripotent stem cells and  computationally identified the associations between SNPs and expression levels of exons, transcripts and genes as well as associations between CNVs and gene expression levels. We have identified SNP genotypes and gene copy numbers with genome wide Affymetrix SNP arrays and expression levels are measured with Affymetrix Exon arrays. For identifying SNPs that reliably correlate with expression levels, we filtered out the values that may cause variability to the expression values, such as the values measured with probes locating in SNP-areas. Additionally, we perform downstream analyses such as transcription factor binding site analysis and enrichment analysis. Further, we detected the  genes that could be associated both with CNVs and SNPs and as expected according to earlier studies, we identify a few of this kind of genes. Overall, we could find several CNVs that correlated with gene expression levels while only few cases of SNPs that correlated with expression levels could be found as the sample size was small.  However, as stem cells are hoped to be used in personalized disease treatments, our findings are important and provide  a useful test set for experimental laboratory studies. In addition, our results open an interesting future direction to study how our findings correlate with the diversity of stem cell lines such as the variation in their differentiation potential.
In the study, data from GEO Series GSE15097 and Series GSE26173 was also used.

overall_design: Eight human induced pluripotent stem cell samples and three fibroblasts were hybridized to exon arrays.

first: Kirsti

last: Laurila

first: Lingjia

last: Kong

first: Elisa

last: Närvä

first: Samer

last: Hussein

first: Timo

last: Otonkoski

first: Riitta

last: Lahesmaa

first: Harri

last: Lähdesmäki


title: Whole genome expression signature of SWCNT and MWCNT vs. asbestos subchronic exposures to human pleural mesothelial cells

city: Morgantown

first: Todd

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

institute: National Institute for Occupational Safety and Health

summary: Malignant mesothelioma is one of the most aggressive forms of cancer known. Recent studies have shown that carbon nanotubes (CNTs) are biopersistent and induce mesothelioma in animals, but the underlying mechanisms are not known. Here, we investigate the effect of long-term exposure to CNTs on the aggressive behaviors of human pleural mesothelial cells, the primary cellular target of human lung mesothelioma. We show that sub-chronic exposure (4 month) to single- and multi-walled CNTs induced proliferation, migration and invasion of the cells similar to that observed in asbestos-exposed cells. An up-regulation of several key genes known to be important in cell invasion, notably matrix metalloproteinase-2 (MMP-2), was observed in the exposed mesothelial cells as determined by real-time PCR. Western blot and enzyme activity assays confirmed the increased expression and activity of MMP-2. Whole genome expression microarray analysis further indicated the importance of MMP-2 in the invasion gene signaling network of the exposed cells. Knockdown of MMP-2 in CNT and asbestos-exposed cells by shRNA-mediated gene silencing effectively inhibited the aggressive phenotypes. This study provides new evidence for CNT-induced cell invasion and indicates the role of MMP-2 in the process.

overall_design: Whole genome expression profiling was conducted on human immortalized pleural mesothelial cells (MeT5A) following 4 month in vitro sub-chronic exposure to six separate treatments to assess differences in carbon nanotube (CNT) vs. asbestos potential tumorigenesis signaling.  Dispersed single wall CNT (D-SWCNT), multi-wall CNT (D-MWCNT), crocidolite asbestos (ASB) and saline (SAL) exposed cells were compared to Survanta® dispersant (DISP) passage control cells.  DISP and SAL cells served as control treatments for CNT- and ASB-exposed cells, respectively.  Each treatment possessed 3 biological cDNA replicates.  One technical replicate was performed per biological sample.

first: Liying

last: Rojanasakul


title: Grapevine cell cultures transcriptomic response to methyl jasmonate and cyclodextrin elicitors

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: The specificity and synergisms of methyl jasmonate and cyclodextrin elicitor effects in grapevine were analysed at the transcrptomic level. To this end, 12-14 day old cell cultures established from Vitis vinifera L. cv Monastrell calli were elicited with 50 mM cyclodextrin (CD), 100 µM methyl jasmonate (MJ) or the combination of both elicitros (MJ+CD). The experiment was carried out in triplicate and untreated cell cultures were followed in parallel as a control. Cells of each culture were isolated just prior and 24h after the treatment to obtain RNA. GrapeGen GeneChip microarray hybridization was performed from each sample.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Pablo Carbonell-Bejerano.  The equivalent experiment is VV44 at PLEXdb.]

overall_design: treatment: Control - time: 0 hrs(3-replications);  treatment: Control - time: 24 hrs(3-replications);  treatment: MJ - time: 0 hrs(3-replications);  treatment: MJ - time: 24 hrs(3-replications);  treatment: CD - time: 0 hrs(3-replications);  treatment: CD - time: 24 hrs(3-replications);  treatment: MJ+CD - time: 0 hrs(3-replications);  treatment: MJ+CD - time: 24 hrs(3-replications)

first: Pablo

last: Carbonell-Bejerano

first: Diego

last: Lijavetzky


title: Adaptive mechanism of Campylobacter jejuni to treatment with a novel CmeABC efflux pump inhibitor (-)-α-Pinene

city: Ljubljana

first: Jasna

last: Kovac

address: Jamnikarjeva 101

department: Department of Food Science and Technology

country: Slovenia

institute: University of Ljubljana, Biotechnical Faculty

summary:
Objectives: The aim of the study was to characterize (-)-α-Pinene, which is one of the chemical constituents of Alpinia katsumadai seed essential oil responsible for its resistance modulatory activity in Campylobacter jejuni.
Methods: Broth microdilution method was used to evaluate the antimicrobial and resistance modulatory potential of (-)-α-Pinene and ethidium bromide accumulation assay to determine its efflux-inhibitory activity in subinhibitory concentration. The target efflux system was identified using knock-out mutants in several efflux related genes. Furthermore, the influence of subinhibitory concentration of (-)-α-Pinene on C. jejuni NCTC 11168 was investigated using microarray technology in order to elucidate the adaptive mechanism of bacteria to treatment with this phytochemical. Knock-out mutants of key adaptation genes were constructed and their role in adaptation to several stress factors, including (-)-α-Pinene, different osmolites and pH, was investigated using Biolog phenotypical microarrays and CFU counts.
Results: (-)-α-Pinene was confirmed as highly efficient Campylobacter jejuni resistance modulator, due to its efflux inhibitory activity, which was significantly higher compared to reference inhibitors CCCP and reserpine. The CmeABC along with newly characterized CmeI (Cj1687) was confirmed as its main target efflux system. The transcriptional analysis indicated that the heat shock regulators HspR and HrcA are the main transcription regulators involved in adaptation to (-)-α-Pinene treatment.
Conclusions: (-)-α-Pinene is a novel CmeABC and CmeI efflux inhibitor, which evokes the heat shock response in Campylobacter jejuni.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design:
Influence of (-)-α-Pinene on gene expression in C. jejuni NCTC 11168 was determined by expressional analysis and qRT-PCR. Exponential phase culture was adjusted to OD600=0.2 in MHB using spectrophotometer (Smart Spec, Bio-Rad, Hercules, CA, USA). Five ml of culture was treated with 62.5 mg/L of (-)-alpha-pinene dissolved in DMSO. Only DMSO (0.048 %) was added to untreated samples. Cultures were treated for 2 h, incubated microaerobically shaking (160 rpm) at 42°C. Experiments were carried out in 4 biological replicates. RNA Protect Bacteria reagent (Qiagen, Maryland, USA) was added to the culture and total RNA was isolated using RNeasy mini kit (Qiagen) and treated with Ambion® Turbo DNA-freeTM kit (Invitrogen, USA).
Microarrays with 4751 probes targeting 1756 genes specific for Campylobacter jejuni subsp. jejuni NCTC 11168 (Mycroarray, Biodiscovery-LLC, MI, USA) were used for gene expression analysis. The cDNA was synthesized with random hexamers, SuperScriptTM III Reverse Transcriptase and amynoallyl dUTP (all supplied by Invitrogen, USA) and labeled with monofunctional NHS-ester dye Amersham C3 or Cy5 (GE Healthcare, Buckinghamshire, UK). Concentration of cDNA and labeling efficiency was determined spectrophotometrically with NanoDrop 1000. Four biological replicates were hybridized to four microarrays according to manufacturer’s protocol, incubated for 24 hours at 42⁰C and scanned at 532-nm (Cy3) and 635-nm (Cy5) wavelengths using GenePix 4100A (Molecular Devices, Sunnyvale, CA) following the manufacturer's protocol. Fluorescence intensities of each spot were extracted using GenePix Pro 7.0 (Molecular Devices).

last: Kovač

first: Katarina

last: Šimunović

first: Zuowei

last: Wu

first: Anja

last: Klančnik

first: Franz

last: Bucar

first: Zhang

last: Qijing

first: Sonja

last: Smole Možina


title: Expression profiling of mendelian and non-mendelian F1 in gpr-1 overexpressing worms.

status: Public on Nov 11 2015

city: Göttingen

first: Judith

last: Besseling

address: Am Faßberg 11

department: Sleep and Waking

institute: Max Planck Institute for Biophysical Chemistry

summary:
According to Mendel's laws, each parent makes an equal genetic contribution to an offspring in sexually reproducing organisms. The bipolar mitotic spindle controls the equal segregation of paternal and maternal chromosomes during the first cell division. By overexpression of a single protein, GPR-1, in the maternal strain we changed the structure of the mitotic spindle from bipolar to two monopolar spindles to segregate maternal and paternal chromosomes into different cell lineages, resulting in non-mendelian segregation for entire genomes. To follow maternal and paternal segregation of the chromosomes we used red and green histone markers respectively. By mating gpr-1-overexpressing hermaphrodites with wild-type males, mendelian F1 worms that express both markers simultaneously in all tissues and non-mendelian F1 worms that express red and green markers in different tissues will be produced representing embryos with bipolar and embryos with two monopolar spindles.  Thus, we show that the rules of genetic inheritance can be changed, which may inspire the formation of a new field of synthetic zoology.
Transcriptional profiling was done to investigate the differences in gene expression between mendelian and non-mendelian offspring.

overall_design: Approximately 60 adult worms were used per sample. Four conditions were collected: hermaphrodites of the paternal strain, hermaphrodites of the maternal strain, co-segregating (mendelian) F1 after crossing of parental strains, and (non-mendelian) F1 that segregates the paternal genotype to body wall muscle, intestine + germline and the maternal genotype to the nervous system after crossing of parental strains.

first: Henrik

last: Bringmann


title: caArray_laird-00098: TCGA Analysis of DNA Methylation for GBM Using Illumina Golden Gate BeadArray platform (IlluminaDNAMethylation_OMA003_CPI)

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

overall_design:
laird-00098
Assay Type:  Methylation
Provider: Illumina
Array Designs: jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA003_CPI.1.adf, jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA003_CPI.2.adf, jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA003_CPI.3.adf, jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA003_CPI.4.adf, jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA003_CPI.5.adf
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain
Material Types: organism_part, solid_tumor, cell, synthetic_DNA, organism_part, genomic_DNA
Disease States: GLIOBLASTOMA MULTIFORME


title: caArray_laird-00051: TCGA Analysis of DNA Methylation for GBM Using Illumina Golden Gate BeadArray platform

overall_design:
laird-00051
Assay Type: Methylation
Provider: Illumina
Array Designs: jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA002_CPI.1.adf, jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA002_CPI.2.adf, jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA002_CPI.4.adf, jhu-usc.edu_GBM.IlluminaDNAMethylation_OMA002_CPI.5.adf
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain, cell
Material Types: genomic_DNA, synthetic_DNA, organism_part, solid_tumor, cell
Disease States: GLIOBLASTOMA MULTIFORME


title: miRNA profiling in camptothecin-treated or untreated hepatoma-derived exosomes

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

summary: Totally 1,308 miRNAs were examined. Three miRNAs (hsa-miR-1976, 4728-3p, and 877-3p) were upregulated with fold change excess 0.8 and six miRNAs (hsa-miR-4497, -204-3p, -6126, -5787, -1273e, and -1908-3p) were downregulated in the exosome released from camptothecin-treated hepatoma.

overall_design:
Comparing between results of these two samples revealed novel miRNA regulation upon anti-cancer drug treatments
exosomal miRNAs from CPT-treated hepatoma and unrteated

first: ShaoChen


title: Trasncript abundance alters by RhlB P238L mutation

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

institute: Academia Sinica

summary: PNPase, one of the major enzymes with 3ʹ-to-5ʹ single-stranded RNA (ssRNA) degradation and processing activities, can interact with the RNA helicase RhlB independent of RNA degradosome formation in E. coli. Here we report that loss of interaction between RhlB and PNPase impacts cysteine homeostasis in E. coli. By random mutagenesis, we identified a mutant RhlBP238L that loses 75% of its ability to interact with PNPase, but retains normal interaction with RNase E and RNA in addition to exhibiting normal helicase activity. Applying microarray analyses to an E. coli strain with impaired RNA degradosome formation, we investigated the biological consequences of a weakened interaction between RhlB and PNPase.

overall_design: BL21(DE3) rne131 DrhlB expressing with pFlag-only, pFlagRhlB or pFlagRhlBP238L grown at 30°C in LB medium to an OD600 of 0.55-0.6. Biological replicates:6 for flag-only, 3 for FlagRhlB and 3 for FlagRhlBP238L independently grown and harvested.

first: Rajinikanth

last: Gogiraju

first: Ni-Ting

last: Chiou


title: Radiotolerance of Rhodospirillum rubrum S1H

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

summary:
In the present study, the susceptibility of the purple pigmented photosynthetic alphaproteobacterium Rhodospirillum rubrum S1H to gamma irradiation was investigated and its molecular response was characterised by means of gene expression analysis.   R. rubrum S1H appears to be about 4 times more sensitive than the model strain Escherichia coli MG1655 to cobalt-60 gamma irradiation. Whole genome response of R. rubrum to 25 Gy revealed the common expression of SOS response related genes in both rich and minimal media. Quantitative expression of the lexA gene was followed after various recovery time following gamma irradiation and showed differential gene expression pattern between minimal and rich medium. This work paves the way for forthcoming molecular studies on the effect of ionizing radiation on R. rubrum S1H and the other MELiSSA strains.
Keywords: Rhodospirillum rubrum; ionizing radiation tolerance; microarray; quantitative PCR.

overall_design: Two-condition experiments. Comparing samples after exposure to gamma (Co-60) irradiation with a non-irradiated sample. At least biological duplicates. Each array contains 3 technical replicates.

first: Felice

last: Mastroleo

first: Muhammad

middle: S

last: Islam


title: Transcriptomics comparison and transcriptional architecture improvement of Clostridium thermocellum ATCC27405 using systems biology data and bioinformatics approaches

status: Public on Nov 08 2015

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

type: Expression profiling by genome tiling array

summary:
Background: Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium with a great potential to be a consolidated bioprocessing biocatalyst that can ferment cellulose to ethanol. To understand its physiology and genetic targets for future strain development, we have carried out several studies including ethanol-tolerant mutant resequencing and ethanol shock experiments.
Methods: In this study, several approaches were applied to enrich mRNA for next-generation sequencing based RNA-Seq and the transcriptomic profiling of C. thermocellum ethanol shock responses was investigated using high-density tiling array and RNA-Seq. Correlations among different transcriptomic platforms of expression array, tiling array, and RNA-Seq were then compared, and data generated from systems biology studies were used for transcriptional architecture improvement.
Results: Our results indicate that cloning-based Sanger sequencing can be used for mRNA enrichment ratio determination, and low-copy number plasmid performed better than high-copy one for cDNA library construction. In addition, high correlations were observed among same array platform using different analyses as well as those between two different array platforms of tiling and expression array when probe intensity was compared. Correlations between RNA-Seq and array results especially the one between RNA-Seq and tiling array are also high. Moreover, combining both RNA-Seq and microarray data the transcriptional architecture of C. thermocellum including the prediction and verification of novel transcript (gene), transcriptional start site (TSS), CAZyme genes, ncRNA, and operon were systematically updated and improved.
Conclusions: RNA-seq has high correlation with array-based transcriptomic platforms and can provide additional information for transcriptional architecture and genome annotation improvement, which will facilitate future omics-based studies.

overall_design: A twelve array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different time points of  30, 60, and 120 min post-inoculation with 3.95 g/L [0.5% (v/v)] treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.

last: Yang

first: Richard

last: Giannone

first: Timothy

last: Tschaplinski

first: Zamin

first: Nancy

last: Engle

first: Dice

last: Lezlee

first: Miguel

last: Rodriguez Jr

first: Robert

last: Hettich

first: Martin

last: Keller

first: Steven

last: Brown


title: Combined transcriptomics classifier analysis reveals a set of adverse effect genes for use as potential endpoint in effect based screening

status: Public on Nov 09 2015

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

summary: Environmental risk assessment relies heavily on the use of bioassays to assess the environmental impact of chemicals. Gene expression is gaining acceptance as a valuable mechanistic endpoint in bioassays and effect-based screening. Data analysis and its results however, are often complex and not directly applicable in risk assessment. Classifier analysis is a promising method to turn complex gene expression analysis results into answers suitable for risk assessment. We have assembled a large gene expression dataset assembled from multiple studies and experiments in the springtail Folsomia candida, with the aim of selecting a set of genes that can be trained to classify general toxic stress. By performing differential expression analysis prior to classification we were able to select a set of 135 genes which was enriched in stress related processes. This set was then used to classify two test sets comprised of chemical spiked soils, polluted soils and clean soils and compared to another, more traditional feature selection for classification. The gene set presented here outperformed the more traditionally selected gene set. This gene set has the potential to be used as a biomarker to test for adverse effects caused by chemicals in springtails to provide endpoints in environmental risk assessment.

overall_design: The data presented in our manuscript is part of a larger experiment which was performed in single, large loop design. Only the samples used in the study presented here are named while the other samples will remain unnamed. All the data can still be used for normalization after which the analysis presented in the manuscript can be replicated. A single channel, interwoven loop design was used to test animals exposed to a control and to 5 concentrations of cadmium and phenanthrene (cadmium concentrations are: cad_1 till cad_5: 5.8, 14.5, 28.9, 57.9 and 115.8 mg/Kg respectively and phenanthrene concentrations are: phe_1 till Phe_5: 0, 4.6, 11.4, 22.9, 45.8 and 91.6 mg/Kg soil respectively). Exposures lasted for 2 days and used 4 biological replicates per condition each containing 30 grams soil and 30 individuals.

middle: E

first: Thierry

middle: K

last: Janssens

first: Juliette

last: Legler

first: Nico

last: van Straalen

first: Dick

last: Roelofs


title: Expression analysis of zebrafish liver after exposure in naphthalene

status: Public on Nov 07 2015

city: changchun

first: Hongshan

last: Chen

address: jingyue  street 2555

department: environment

institute: Northeast normal university

summary: Investigation of whole genome gene expression level changes in zebrafish liver under naphthalene treated（high-concentration group and low-concentration group）, compared to the solvent control group revealed that 76 genes and 88 genes were differentially expressed respectively in the fish caged at the low-concentration and high-concentration. KEGG pathway and GO analysis of the differentially expressed genes, showed significant enrichment in several meaningful categories.

overall_design: Healthy 5-month-old adult zebrafish (AB strain) maintenance and chemical exposure to 84μg/L and 840μg/L naphthalene and 0.005% Dimethyl sulfoxide as the solvent control were performed according to published research protocols. Prior to exposure, the fish were acclimatized in 50L aerated fresh water in glass tanks for 2 weeks, under controlled environmental conditions with the water temperature maintained at 26±0.5℃ for 16-h light and 8-h dark photoperiod. After 21 d of treatment, adult zebrafish livers were removed by dissection, and immediately transferred to RNA-later Stabilization Reagent(Qiagen,76106) , prior to storage at 4℃ for histopathological and microarray analysis. NimbleGen Gene Expression 12X135K zebrafish microarrays and One-Color DNA labeling Kit (NimbleGen, WI) were used for genome-wide expression analysis of naphthalene-treated zebrafish.

first: chen

last: hongshan

first: sheng

last: lianxi

first: bian

last: hongfeng


title: The involvement of body appearance in influencing the biofilm formation by Escherichia coli K-12 through RodZ

status: Public on Nov 05 2015

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

country: South Korea

institute: Chonbuk National University

summary:
Fifty five genes were induced or reduced (2.5-fold) by the absence of rodZ genes
Among them, curli production-, cell division-, and biofilm-associated genes as well as phage-related genes were regulated by the RodZ, significantly

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Three-condition experiment, BW25113 WT/pCA24N vs. rodZ/pCA24N vs. rodZ/pCA24N-RodZ. For preparing the total RNA, each cells were grown at 37°C upto OD600=0.5 and then keep growing with 1 mM IPTG for additional 6 h

first: Sangnam

last: Oh


title: Bortezomib resistance in CCRF-CEM cell line [miRNA]

status: Public on Nov 04 2015

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Bortezomib is a proteasome inhibitor used in severel different hematological malignancies. Resistance to this drug is still poorly understood. In order get more insight in the resistance mechanism, we developed several bortezomib resistant subclones of the CCRF-CEM T-ALL cell line. On these subclones comparative Genome hybridization (arrayCGH) for DNA copy number analysis gene expression and micro-RNA expression arrays were performed.

overall_design: We performed micro-RNA on two different bortezomib resistant subclones of the CCRF-CEM cell line. The resistant subclones were compared to the parental CCRF-CEM wildtype cell line.

first: Niels

last: Franke

first: Gertjan

last: Kaspers

first: Yehuda

last: Assaraf

first: Johan

last: van Meerloo

first: Denise

last: Niewerth

first: Floortje

last: Kessler

first: Pino

middle: J

last: Poddighe

first: Serge

last: Smeets

first: Bauke

last: Ylstra

first: Chonglei

last: Bi

first: Wee

last: Chng

first: Terzah

last: Horton

first: Rene

middle: X

last: Menezes

first: Renée

last: Musters

first: Sonja

last: Zweegman

first: Gerrit

last: Jansen

first: Jacqueline

last: Cloos


title: Bortezomib resistance in CCRF-CEM cell line [CGH]

first: Daoud

last: Sie

overall_design: We performed comparative Genome hybridization (arrayCGH) for DNA copy number analysis on four different bortezomib resistant subclones of the CCRF-CEM cell line. The resistant subclones were compared to the parental CCRF-CEM wildtype cell line and reference DNA.

first: Niels

last: Franke


title: Human cystatin D (CST5) locates in the nucleus at sites of active transcription and regulates gene expression

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

institute: Cancer Research Center (CiC-IBMCC)

summary: Cystatin D (CST5) is an inhibitor of several proteases of the cathepsin family that inhibits cell proliferation, migration and invasion of colon carcinoma cells. Some of these effects are unrelated to its antiprotease activity. Here, we use genome-wide expression microarrays to show that cystatin D regulates gene expression (including that of genes encoding transcription factors such as RUNX1, RUNX2, or MEF2C) in HCT116 cells.

overall_design: HCT116 colon adenocarcinoma cell lines stably expressing cystatin D (HCT116-CST5 clone 9 and clone 20), mock-transfected (HCT116-Mock) and un-transfected (HCT116-Untransfected) were generated as described (Álvarez-Díaz et al., 2009, PUBMED:19662683) and genome-wide expression microarrays were obtained to achieve the gene expression profile induced by CST5.

first: Silvia

last: Alvarez-Díaz

first: Gemma

last: Ferrer-Mayorga

first: Noelia

last: Valle

first: Marta

last: Mendes

first: Rodrigo

last: Barderas

first: J

middle: I

last: Casal

first: Carlos

last: López-Otín

first: Olga

last: Tapia

first: Miguel

last: Lafarga

first: Alberto

last: Muñoz


title: Genotyping of 22 Great Danes with Ichthyosis

status: Public on Nov 03 2015

city: Hannover

first: Julia

last: Metzger

address: Buenteweg 17 p

department: Institute for Animal Breeding and Genetics

institute: University of Veterinary Medicine

type: Genome binding/occupancy profiling by SNP array

summary: Genotyping of 22 Great Danes on the Illumina high density BeadChip

overall_design: To perform whole-genome association analysis (GWAS) for Ichthyosis in Great Danes

first: Ottmar

last: Distl


title: Gene expression patterns in house dust mite stimulated CD4 T cells and IgG:IgE ratios

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
PBMC from house dust mite (HDM) sensitized atopics were cultured in the presence or absence of HDM extract for 24 hours.
At the termination of the cultures, CD4 T cells were isolated using immunomagnetic separation. Gene expression was profiled on microarrays.

overall_design: The study design consisted of 45 subjects and two conditions (medium control, HDM stimulation).


title: mRNA and miRNA expression profiles for fresh frozen periampullary adenocarcinomas (pancreatobiliary and intestinal type) and adjacent normal tissues. [miRNA]

status: Public on Nov 06 2015

city: Oslo

first: Vandana

last: Sandhu

state: oslo

address: Ullernchausseen 70

department: Department of Genetics

country: Norway

institute: Radiumhospitalet, Oslo

summary: To study the molecular signatures of mRNAs and miRNAs which can potentially act as a prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas

overall_design: Total RNA was isolated from 10 x 20 µm sections of  83 fresh frozen tumor samples for  miRNA expression profiling. A total of 51 PDAC, 8 bile duct adenocarcinoma, 8 ampulla of pancreatobiliary tye, 7 ampulla of intestinal type, 9 duodenum sample and 6 adjacent normal samples were used. These samples were analysed by microarray analysis using the 60K agilent platform. The expression profiles was RMA normalized for miRNA expression data. Filtering of controls, unannotated genes and low expressed probes was done.

first: Elin

last: Kure


title: Buccal epithelial gene expression in smoky and smokeless coal users

status: Public on Nov 02 2015

city: Boston

first: Teresa

last: Wang

state: MA

address: 72 East Concord St., E-632

department: Computational Biomedicine

country: USA

institute: Boston University

summary: Exposure to indoor air pollution generated from the combustion of solid fuels is a major risk factor for a spectrum of cardiovascular and respiratory diseases, including lung cancer. In China’s rural counties of Xuanwei and Fuyuan, lung cancer rates are among the highest in the country. While the elevated disease risk in this population has been linked to the widespread usage of bituminous (smoky) coal as compared to anthracite (smokeless) coal, the underlying physiologic mechanism that smoky coal induces in comparison to other fuel types is unclear. As we have previously used airway gene-expression profiling to gain molecular insights into the physiologic effects of cigarette smoke, here we profiled the buccal epithelium of residents exposed to the burning of smoky and smokeless coal in order to understand the physiologic effects of solid fuels.

overall_design: Buccal mucosa scrapings were collected from healthy, non-smoking female residents of Xuanwei and Fuyuan counties who burn coal indoors. RNA was isolated and hybridized onto Affymetrix Human gene 1.0 ST GeneChips, capturing the gene-expression response of (n=26) smoky coal users and (n=9) smokeless coal users. 24-hour indoor personal exposure levels (PM2.5, Polycyclic Aromatic Hydrocarbons) were also captured during this sampling period.


title: Dichlorvos exposure results in large scale disruption of energy metabolism in the liver of the zebrafish, Danio rerio

city: Ft. Detrick

first: Christine

last: Baer

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

summary: Background: Exposure to dichlorvos (DDVP), an organophosphorus pesticide, is known to result in neurotoxicity as well as other metabolic perturbations. However, the molecular causes of DDVP toxicity are poorly understood, especially in cells other than neurons and muscle cells. To obtain a better understanding of the process of non-neuronal DDVP toxicity, we exposed zebrafish to different concentrations of DDVP, and investigated the resulting changes in liver histology and gene transcription.     Results: Functional enrichment analysis of genes affected by DDVP exposure identified a number of processes involved in energy utilization and stress response in the liver. The abundance of transcripts for proteins involved in glucose metabolism was profoundly affected, suggesting that carbon flux might be diverted toward the pentose phosphate pathway to compensate for elevated demand for energy and reducing equivalents for detoxification. Strikingly, many transcripts for molecules involved in β-oxidation and fatty acid synthesis were down-regulated. We found increases in message levels for molecules involved in reactive oxygen species responses as well as ubiquitination, proteasomal degradation, and autophagy. To ensure that the effects of DDVP on energy metabolism were not simply a consequence of poor feeding because of neuromuscular impairment, we fasted fish for 29 or 50 h and analyzed liver gene expression in them. The patterns of gene expression for energy metabolism in fasted and DDVP-exposed fish were markedly different.     Conclusion: We observed coordinated changes in the expression of a large number of genes involved in energy metabolism and responses to oxidative stress. These results argue that an appreciable part of the effect of DDVP is on energy metabolism and is regulated at the message level. Although we observed some evidence of neuromuscular impairment in exposed fish that may have resulted in reduced feeding, the alterations in gene expression in exposed fish cannot readily be explained by nutrient deprivation.

overall_design: Dichlorvos induced changes in gene expression in zebrafish were measured after 24 h exposures. A total of 20 arrays were processed with 4 replicates for each exposure condition (low, mid, and high) and 4 replicates for each of 2 control sets. Also, fasting induced changes in gene expression in zebrafish were measured after 24 hours fasting and 50 hours fasting. A total of 12 arrays were processed with 4 replicates for each exposure condition (no fasting, 24h fasting, 50h fasting).

first: Tri

last: Bui-Nguyen

first: John

middle: A

last: Lewis

first: Dongren

last: Yang

first: Pamela

last: Lein

first: David

last: Jackson


title: Expression data from H2A.Z-1 and H2A.Z-2 double KO cells

city: Sendai

first: Yukako

last: Oma

address: Tsutsumidori-Amamiyamachi 1-1, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

summary:
The histone variant H2A.Z is evolutionarily conserved from yeast to vertebrates. H2A.Z regulates gene expression when localized to promoter region. Recently, we identified two genes encoding H2A.Z, H2A.Z-1 and H2A.Z-2 in vertebrate genome. However, it is not clear that both H2A.Z-1 and H2A.Z-2 were required for the function of H2A.Z in gene regulation. To address this issue, we generated the H2A.Z-1 and H2A.Z-2 double knock out (KO) cells in chicken DT40 cells. The expression pattern of H2A.Z-1 and H2A.Z-2 double KO cells was compared with WT cells to characterize the genes regulated by H2A.Z-1 and H2A.Z-2.
We used microarrays to analysis the alternation of gene expression between WT and H2A.Z double KO cells and identify classes of up or down regulated gene by H2A.Z-1 and H2A.Z-2.

overall_design: In H2A.Z-1 and H2A.Z-2 double KO cells, H2A.Z-2 is knocked out constitutively, but H2A.Z-1 conditionally by tetracycline. The expression of H2A.Z-1 transgene is suppressed completely when H2A.Z-1 and H2A.Z-2 double KO cells culture with tetracycline for three days. For this reason, we prepared the total RNA of WT cells and H2A.Z-1and H2A.Z-2 double KO cells treated with tetracycline for three days and hybridization on Affymetrix microarrays.

first: Ryo

last: Matsuda

first: Masahiko

last: Harata


title: The nuclear actin-related protein Arp6 contributes to the radial positioning of chromosome territories.

summary: The chromatin of individual chromosomes is organized into chromosome territories (CTs) in the interphase nucleus. The spatial arrangement of CTs is non-random and evolutionarily conserved. The gene-dense and gene-poor CTs are positioned in the nuclear center and periphery, respectively. As candidates for key molecules involved in nuclear organization, we have investigated the nuclear actin-related proteins (Arps), which include the evolutionarily conserved actin-family together with conventional actin. We used a conditional knockout system with chicken DT40 cells to analyze the functions of the actin-related protein Arp6. Consistent with a previous identification of Arp6 in the SRCAP chromatin remodeling complex, the histone variant H2AZ was significantly decreased in the chromatin of Arp6-deficient cells. Most importantly, Arp6-deficient cells had impaired radial positioning of both gene-poor macrochromosome and gene-rich microchromosome CTs. A transcription microarray analysis of the cells suggests that the radial positioning of CTs impacts only a limited number of genes and plays an active role in repression, rather than in induction. As far as we know, this report is the first observation that an inner nuclear protein is required for the radial distribution of CTs, and will provide new insight into the mechanisms and physical significance of the positioning of CTs in the nucleus.

overall_design: The total RNA was extracted with RNeasy Maxi Kit (QIAGEN) according to the manufacturer protocol. The poly-A mRNA was isolated from total RNA using Oligotex-dT30 Super (JSR corporation) and biotinylated cRNA was synthesized according to Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix). Shortly, 2 ug of poly-A mRNA was reverse transcribed to cDNA using 100 pmol of a T7-Oligo (dT) Primer (Invitrogen), and biotinylated cRNA was prepared by in vitro transcription amplification. For hybridization, 15 ug of biotinylated cRNA was fragmented and added into a hybridization cocktail containing four biotinylated hybridization controls (bioB, bioC, bioD, and cre) as recommended by the manufacturer. GeneChip Chicken genome Arrays (Affymetrix) were hybridized with the cocktail at 45˚C for 16 hours. After washing with Non-Stringent wash buffer (6xSSPE, 0.01% Tween20) and staining with SAPE in the Affymetrix GeneChip Fluidics Station 400, the GeneChips were read using the Affymetrix GeneChip scanner 3000 7G. These systems and data analyses were operated with the GeneChip Operating Software 1.3.

first: Eri

last: Ohfuchi Maruyama

first: Hideyuki

last: Tanabe

first: Hiroshi

last: Kitamura

first: Shigenobu

last: Tone

first: Felix

last: Habermann

first: Johann

last: von Hase

first: Christoph

last: Cremer

first: Tetsuya

last: Hori

first: Tatsuo

last: Fukagawa


title: Identification and Comparative Analyses of Myocardial miRNAs Involved in Fetal Response to Maternal Undernutrition

city: Portland

first: Alina

last: Maloyan

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Medicine

institute: Oregon Health and Science University

summary: Poor maternal nutrition during pregnancy causes intrauterine growth retardation, which, in turn,  is associated with increased risk of cardiovascular and metabolic diseases in later life

overall_design: Fetal hearts were collected from baboon fetuses born to regularly fed and undernurished mothers.  Total RNA was isolated, and fetal cardiac miRNA were  profiled

first: Peter

last: Nathanielsz


title: Ethynylestradiol (EE2) effect on global gene expression in primary rainbow trout (Oncorhynchus mykiss) hepatocytes

status: Public on Oct 31 2015

first: Maria

middle: Therese

last: Hultman

address: Gaustadalléen 21

department: Ecotoxicology

institute: NIVA

summary: To study short term (48h) hepatic transcriptional changes and identify potential modes of action in primary rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to 0.03, 0.3, 3 and 30nM EE2. The transcriptional gene expression analysis involved a high density (60k) custom designed oligonucleotide salmonid microarray in combination with quantitative real-time polymerase chain reaction (qPCR). Differently expressed genes (DEGs) were obtained after application of a one-way analysis of variance (ANOVA) and Tukey posthoc test. Enrichment analysis was performed based on Gene Ontology (GO) to determine the biological roles of the DEGs. The obtained DEGs were further mapped against mammalian orthologs. The successfully mapped DEGs were further subjected to a gene network analysis based on well-curated mammalian protein -protein interactions, followed by a canonical and toxicity pathway analysis. The pathways and network analysis were performed in order to link DEGs to specific and toxicological/biological functions.

overall_design: Isolated primary rainbow trout hepatocytes were exposed to 0.03-30nM ethynylestradiol for 48h. The cells were sampled and used for gene expression analysis. A total of 4 biological replicates were analyzed for each concentration, including solvent (DMSO) control.

middle: T

first: You

last: Song

first: Knut

last: Tollefsen


title: Influence of NaCl on gene expression in Dickeya dadantii

status: Public on Nov 01 2015

city: Rennes

first: carlos

last: blanco

address: 263 avenue Général Leclerc

department: SVE

country: France

institute: université rennes 1

summary: Growth in 0.3 M NaCl M63 minimal medium affects the transcriptome of Dickeya dadantii 3937.in comparison to that of cells grown in M63 medium.

overall_design: NimbleGen design name 2005-05-31_Ogg_Erwinia_24mer, NimbleGen design ID 2181 A 1:2 expression design for 4597 genes from Dickeya dadantii 3937 with 20 24-mer probe pairs (PM/MM) per gene. Each probe is replicated 2 times. The design includes random GC and other control probes. Protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.

last: Blanco


title: Transcriptomic analysis of colonic epithelial cells in adult rats born with intra-uterine growth retardation.

city: NANTES

first: Gwenola

last: LE DREAN

address: CHU Hôtel Dieu

institute: INRA

summary:
The impact of intra-uterine growth retardation (IUGR) was analyzed on gene expression of the colonic epithelial cells from adults rats fed a standard or a high-fat diet.
The hypothesis tested in this study was that IUGR induces sustainable effects on colonocyte transcriptome that may alter further nutritional adaptations at adulthood, especially to high-fat diet.

overall_design: Total RNA extracted from control (C) and IUGR (R) rats fed chow (Normal Diet, ND) or  high-fat diet (HFD).

first: Jean-Pierre

last: Segain

last: Le Dréan

first: Philippe

last: Guardiola

first: Vianney

last: Haure-Mirande

first: Pierre

last: de Coppet


title: Characterization of genomic alterations in radiation-related breast cancer among childhood cancer survivors, using comparative genomic hybridization (CGH) arrays

city: Bethesda

first: Rose

last: Yang

address: 9100 Rockville pike

institute: NIH

type: Genome variation profiling by genome tiling array

summary: Evaluation of aCGH profile of 32 breast tumors from the childhood cancer survivor study

overall_design: Breast cancer cases, most of them received high-dose chest radiation during childhood for the treatment of their first cancers


title: Gene expression-based analysis of Streptococcus uberis 0140J and the MtuR (sub0472) mutant

city: Sutton Bonington

first: Sharon

last: Egan

state: Leicestershire

address: Sutton Bonington Campus

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

summary: Comparison of bacterial strain S. uberis 0140J with an isogenic mutant (same strain) with a lesion 338 basepairs downstream of the ATG start codon of the MtuR or sub0472 gene. Bacteria were grown in stationary culture in THB media at 37°C in the presence of 1mM manganese with triplicate samples of RNA extracted at early exponential (OD550 =0.43) and late exponential (OD550 =0.78) phases of growth. Microarray analysis was performed on custom-made S. uberis 0140J arrays containing 3780 features of 60mer oligonucleotides in triplicate with two probes for each individual gene.

overall_design: We investigated the role of MtuR in vivo and the effect of its absence on the transcriptional control of gene expression using a custom-designed genome-wide S. uberis 0140J microarray containing 3780 features in triplicate with two probes for each individual gene. Triplicate samples were analysed in a loop design with Cy5 and Cy3 dye-swaps performed, and gene expression was compared at two different phases of bacterial growth (early and late logarithmic).

first: James

last: Leigh


title: A cross species and multi-omics (including metabolomics) analysis in pancreatic neuroendocrine tumours (miRNA)

status: Public on Oct 30 2015

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

institute: Institute of Cancer Research (ICR), London

summary: Pancreatic neuroendocrine tumor (PanNET) is relatively infrequent but is nevertheless metastatic. Seeking to extend a new paradigm of personalized medicine, we performed an integrative analysis of transcriptomic (mRNA and microRNA) and mutational profiles and defined three clinically relevant human PanNET subtypes. Importantly, cross-species analysis revealed two of these three subtypes in a well-characterized, genetically engineered mouse model (RIP1-Tag2) of PanNET and its cell lines. Each subtype share similarities to distinct cell types in pancreatic neuroendocrine development, features are reflected in their metabolic profiles. Subtype-specific molecular signatures metabolites are proposed to identify these subtypes.

overall_design: Total RNA was extracted from fresh frozen archival patient PanNET samples and hybridized on Agilent microRNA arrays. All normalization methods were performed on the Total Gene Signal from Agilent "GeneView" data files in R, an open source statistical scripting language (http://www.r-project.org). Except for VSN, data were log2 transformed after adding a small constant such that the smallest value of the data set was 1 before taking the log. Scaling normalization was performed by dividing each array by its mean signal intensity and then by rescaling to the global mean intensity of all arrays. Quantile normalization was performed using the "normalize.quantiles" function from R package "affy" from the Bioconductor project (http://www.bioconductor.org).

first: A

first: C

last: Grotzinger

first: B

last: Wiedenmann

first: D

last: Hanahan


title: Role of miRNA in inflammatory bowel disease

city: New Delhi

first: Raju

last: Ranjha

state: Delhi

address: Lab. No.441, School of Life Sciences,

department: School of Life Sciences

country: India

institute: Jawaharlala Nehru University

summary: This is a miRNA expression analysis by microarray. Comparison was made beween Ulcerative Colitis (UC) vs control, Active UC vs Remission, Ascending Colon vs Rectosigmoid area of Colon. The samples were labeled using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ and hybridized on the miRCURY LNA™ microRNA Array (7th gen) following the scheme you outlined in the sample submission form.  The technical data quality assessment showed that the labeling was successful as all capture probes for the control spike-in oligo nucleotides produced signals in the expected range. Following normalization of the quantified signals (background corrected) using the global Lowess regression algorithm, we have performed an unsupervised as well as supervised data analysis.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
RNA from 4 samples pooled in each category. NA- Sample from ascending colon Active Ulcerative colitis; RA- Sample from rectosigmoid colon Active Ulcerative colitis; NC- Sample from ascending colon Control individuals; RC-Sample from rectosigmoid colon Control individuals; NR- Sample from ascending colon remission Ulcerative colitis; RR- Sample from rectosigmoid colon remission Ulcerative colitis; Comparision was done in UC vs Control, Ascending Colon vs Rectosigmoid area in UC and Ascending Colon vs Rectosigmoid area in Controls
The supplementary file samplesinfo_2146-1.csv includes additional information about the raw data files


title: Toxicogenomic analysis of rural and urban air particles

status: Public on Oct 26 2015

city: Barcelona

first: Sofia Raquel

middle: Soares

last: Mesquita

state: Cataluña

address: C/ Jordi Girona 18-26

department: Quimica Ambiental

country: Spain

institute: IDAEA-CSIC

summary:
Atmospheric particulate matter (PM) is a recognized risk factor for the global burden of disease in human populations. We are presenting here the application of toxicogenomics in the evaluation of the toxic effects of organic content of atmospheric particle matter (PM), from urban and rural environments (city of Barcelona and village of La Pobla, NE Spain), using the developing zebrafish embryo. The main goal is to identify the metabolic pathways involved in the adverse effects observed in zebrafish embryos exposed to PM organic content from urban and rural environments, also allowing the selection of genes of interest that are differentially expressed. The relevance of particle size to the PM toxicity is also addressed. Indeed, the zebrafish embryos were exposed to PM of aerodynamic diameter larger than 7.2 μm and smaller than 0.5 μm (PM10 and PM0.5, respectively). PM0.5 concentrated biological and toxic activities linked to organic substances. Transcriptomic analyses showed strong induction of the AhR signalling pathway (a.k.a. dioxin-like activity) for embryos exposed to both rural and urban extracts, correlating with the concentrations of PAHs. Urban extracts, with strong contribution of traffic emissions, specifically de-regulated oxidative stress-related genes, as well as pancreatic and eye-lens specific genes, two organs known to be affected by air pollution in humans. Exposure to rural extracts, with high contribution of wood burning emissions, affected genes implicated in basic cellular functions, in agreement with their strong embryotoxicity.  Extracts from rural and urban samples elicited both common and specific transcriptome responses, suggesting different potentially adverse outcomes depending on PM source and composition.
The authors thank the financial support of the Spanish Ministry (project TEA-PARTICLE, grant number CGL2011-29621) and the Portuguese Foundation for Science and Technology for the doctoral grant of Sofia R. Mesquita (SFRH/BD/80710/2011) funded by the Program POPH-QREN through the Portuguese Ministry of Education and Science and the European Social Fund, and support through project PEst-C/MAR/LA0015/2013.

overall_design:
The PM filter samples used in the present study were PM10 and PM0.5 from the urban site - total of 4 samples from 2 sampling months; and PM0.5 from the rural site - total of 2 samples from 2 sampling months (PM10 samples from the rural site were not tested due to their very low concentration in organic compounds, and insignificant biological activity, previously measured). Sampling occurred during the cold periods of the year 2012/2013. The organic fraction of PM samples was extracted by sonication using a mixture of dichloromethane:methanol. Then, the extracts were filtered, evaporated and re-dissolved in Dimethyl sulfoxide (DMSO). Zebrafish fertilized eggs were exposed to PM organic extracts (0.2% DMSO) from the urban and rural sites from 24 to 120h post-fertilization. Total RNA was isolated from whole embryos (pools of 20 individuals), using Trizol reagent protocol (Invitrogen Life Technologies, Carlsberg, CA). The microarray study was performed using the Agilent Two-colour D. rerio Oligo Microarray v3 platform, following the Agilent Microarray – Based Gene Expression Analysis protocol. Three biological replicates were performed for each PM sample and controls. Biological replicates, a technical replicate and a self-to-self, were simultaneously amplified and labelled using Cyanine 3 (Cy3) and Cyanine 5 (Cy5) dye. After cRNA purification (RNeasy Kit, Quiagen GmbH, Hilden, Germany), the cRNA concentration and labelling were quantified in the NanoDrop spectrophotometer, obtaining incorporation rates in the range of 15-20pmol of cyanide dye/µl cRNA and yield values > 0.825ug, as recommended. cRNA was fragmented and hybridized in 4x44K arrays,  for 17h at 65oC. After the hybridization the array slides were washed, and immediately scanned using Microarray Scanner Agilent G2505C system. Data was extracted using Agilent Feature Extraction Software v10.5.1.1, and the quality of microarray data was evaluated using the Quality Control report provided by Agilent Software.
Based on the microarray data analysis, 22 primers were selected and designed using Primer Express 2.0 software (Applied Biosystems, Foster City, CA). Genes were quantified by real-time PCR to validate the microarray data, and a subset of 13 genes were further selected by their robust behaviour in the validation assays, allowing to differentiate the toxic potential of PM from urban and rural sources.

first: Sofia

middle: R

first: Barend

middle: L

last: van Drooge

first: Eva

last: Oliveira

first: Joan

middle: O

last: Grimalt

first: Carlos

last: Barata

first: Natividade

last: Vieira

first: Laura

last: Guimarães

first: Benjamín

last: Piña


title: Gene expression analysis of abscisic acid responsive genes in AR7 mutant

status: Public on Oct 22 2015

city: Setagaya-ku

first: Kenji

last: KOMATSU

state: Tokyo

address: 1-1-1 Sakuragaoka

department: Department of Bioproduction Technology

country: Japan

institute: Tokyo University of Agriculture

summary: To obtain the gene expression profiles of the moss Physcomitrella patens ABA insensitive mutant AR7, we performed microarray analysis of wildtype plant and AR7 using a custom Physcomitrella oligonucleotide microarray, which carries probes for 33,942 gene models of Physcomitrella genome version 1.1. on a 4 x 44 K Agilent platform.

overall_design:
Because this microarray slide has 4 arrays, one GPR file has 8 entities (4    arrays x 2 channels).    We scanned the same slide thrice on different gain level of the scanner, so    we have the three GPR files.
1) The three GPR files were processed by GenePix Pro 6.1 and we got three    set of 4 array(block) data. (total: 12 arrays data)            Block 1: Cy3 WT ABA(+), Cy5 AR7 ABA(+)            Block 2: Cy3 AR7 ABA(+), Cy5 WT ABA(+)            Block 3: Cy3 AR7 ABA(-), Cy5 AR7 ABA(+)            Block 4: Cy3 AR7 ABA(+), Cy5 AR7 ABA(-)    Some spots on the array were dropped off by GenePix Pro.        2) The ratios were calculated from log2( (Cy5 foreground intensity - Cy5    background intensity) /    (Cy3 foreground intensity - Cy3 background intensity) ).        3) We applied the global normalization to each array data. (total: 12    arrays data)        4) We unified the three set of data. If the ratio for a spot in    AS01_high.gpr was available, we used the ratio in AS01_high.gpr for the    spot.    However, if the ratio was unavailable, we checked the ratio for the spot in    AS01_middle.gpr.    If the ratio in AS01_middle.gpr was available, we used the ratio in    AS01_middle.gpr for the spot.    If the ratio in AS01_middle.gpr was unavailable, we used the ratio in    AS01_low.gpr for the spot.  (total: 4 arrays data)        5) We applied LOWESS method to the unified data. (total: 4 arrays data)

last: Komatsu

first: Yoichi

last: Sakata

first: Daisuke

last: Takezawa

first: Masashi

last: Saruhashi

first: Totan

last: Ghosh

first: Kenta

last: Arai

first: Yumiko

last: Ishizaki

first: Kazuya

last: Hagiwara

first: Yuh

last: Shiwa

first: Keiichi

last: Izumikawa

first: Taishi

last: Umezawa


title: Transcription factor activating protein 2 beta (TFAP2B) mediates noradrenergic neuronal differentiation in neuroblastoma

status: Public on Oct 27 2015

city: Cologne

first: Fakhera

last: Ikram

state: NRW

address: Kerpener str. 62

department: Pediatric Oncology and Hematology

country: Germany

institute: University Children´s Hospital

summary: Single-color gene expression profiles from IMR-32 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. To gain insights into the molecular processes occurring upon TFAP2B re-expression, we performed gene expression measurements in TFAP2B and GFP expressing transgenic IMR-32 neuroblastoma cell lines at d2 and d7 of transgene induction.

overall_design: Single-color gene expression profiles from IMR-32 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. Total RNA of TFAP2B- and GFP-expressing IMR-32 cells was isolated at day 2 and day 7 using Trizol.

first: Matthias

last: Fischer

first: Falk

last: Hertwig


title: Transcriptome analysis of thermal adaptive E. coli (part 1)

status: Public on Oct 14 2015

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

summary: Transcriptome analyses of the Escherichia coli cells acquired in the thermal adaptive evolution (Kishimoto et al, 2010, PLoS Genet) were performed. The ancestor strain (Anc) and the evolved strains (41B, 43B, 45L and 37L) were analyzed. The cells exponetially growing at the regular (37ºC) and/or evolutionary (41~45ºC) temperatures and in response to heat shock at 45ºC were collected for microarray analyses. Multiple transcriptome analyses identified the specific evolutionary direction and bias for thermal adaptation.

overall_design: Five different strains (both the evolved cells and the ancestor) exponentially growing at regular and evolutionary temperatures and responding to heat shock were collected for the transcriptome analysis. Every 2-3 biological replications were performed.

first: Kazuki

last: Kitahara

first: Yuki

last: Matsumoto

first: Tetsuya

last: Yomo


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 5]

status: Public on Oct 01 2015

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

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

summary: Sporadic breast cancer (SBC) is a common and heterogeneous disease. There is no reliable way of early prediction of risk for SBC in the general population. We studied 282 females with SBC concentrating on copy number aberrations in tumor-free breast tissue (uninvolved margin, UM) outside the area of primary tumor (PT). Totally 1162 UMs (1-14 per breast) were studied. PT and blood/skin as control was also analyzed. Comparative analysis between genetic profiles for UM(s), PT(s) and blood/skin from the same patient is the core of study design. We identified 108 patients with at least one aberrant UM specimen, representing 38.3% of all cases. Gains were the dominating mutations in microscopically normal breast cells and gain of ERBB2, with overexpression of HER2 protein, was the most common aberration in normal cells. Five additional receptor genes (EGFR, FGFR1, IGF1R, LIFR and NGFR) also showed gains, and these were occasionally present in combination with the gain of ERBB2. Up to 67.6% of patients showed gain of one or more of these genes in normal cells. The aberrations found in normal cells from UMs were previously described in cancer literature, which suggest their causative, driving role in this disease. We demonstrate that analysis of normal cells from cancer-bearing patients leads to identification of genetic signatures that may predispose to SBC. Early detection of signals suggesting a predisposition towards development of SBC, long before detectable tumors are formed, is a key to the anticipated shift into a preventive paradigm of personalized medicine of breast cancer.

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The 301-400 samples out of 811 experiments runned on platform GPL18224 (Infinium HumanOmniExpressExome)


title: Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 3]

overall_design:
We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available.
The 101-200 samples out of 811 experiments runned on platform GPL18224 (Infinium HumanOmniExpressExome)