title: The gene expression of normal pancreatic and PDAC tisssues.

status: Public on Aug 13 2015

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

summary: Expression profiling of 8 normal pancreatic and 14 PDAC tissues. Data was generated from Affymetrix arrays. Results provide a global profile of over 50,000 genes in normal and tumorous tissues, and comparison of the differentially expressed genes between the normal and tumor groups.

overall_design: Gene expression was profiled and compared between normal pancreatic and PDAC RNA samples globally, using Affymetrix GeneChip® Human Genome U133 Plus 2.0array.

first: Daniel

last: Brackett

first: Jinmai

last: Jiang


title: Comparison of gene expression in AhR WT (+/+) and AhR KO (-/-) primary mouse keratinocytes

status: Public on Jul 01 2015

city: University Park

first: Adam

middle: B.

last: Glick

state: PA

address: 101 Life Sciences Bld

department: Veterinary and Biomedical Sciences

country: USA

institute: The Pennsylvania State University

summary: The AhR is a ligand activated transcription factor that may be important in normal skin physiology. We compared gene expression profiles between  AhR Wt and AhR KO primary mouse keratinocyte cultures. We identified 391 genes that were differentially expressed with a 1.5 fold cutoff and p<.05, and identified the AhR as an important regulator of genes involved in normal epidermal differentiation.

overall_design: AhR Wt primary keratinocyte cultures (n=4) were compared with AhR KO primary keratinocyte cultures (n=3)

first: Ellen

last: van den Bogaard

first: Michael

last: Podolsky

first: Jos

last: Smits

first: Xin

last: Liu

first: Joost

last: Schalkwijk

first: Gary

last: Perdew


title: Limited evidence for consistent changes in maize DNA methylation patterns following environmental stress.

status: Public on Jan 07 2016

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

type: Methylation profiling by genome tiling array

summary:
DNA methylation is a chromatin modification that is sometimes associated with epigenetic regulation of gene expression.  As DNA methylation can be reversible at some loci, it is possible that methylation patterns may change within an organism that is subjected to environmental stress. In order to assess the effects of abiotic stress on DNA methylation patterns in maize (Zea mays), we subjected seedlings to heat, cold and UV stress treatments.  Tissue was later collected from individual adult plants that had been subjected to stress or control treatments and used to perform DNA methylation profiling to determine whether there were consistent changes in DNA methylation triggered by specific stress treatments.  The DNA methylation profiling was performed by immunoprecipitation of methylated DNA followed by microarray hybridization to allow for quantitative estimates of DNA methylation abundance throughout the low-copy portion of the maize genome.  By comparing the DNA methylation profiles of each individual plant to the average of the control plants it was possible to identify regions of the genome with variable DNA methylation.  However, we did not find evidence of consistent DNA methylation changes resulting from the stress treatments used in this study.  Instead, the data suggest that there is a low-rate of stochastic variation that is present in both control and stressed plants.
Methylation profiles in flag leaf tissue of maize inbred lines under various stress conditions using a custom 1.4M feature NimbleGen array.

overall_design: Methylation profiles of flag leaf tissue from 18 B73 inbred lines that underwent various stresses as seedlings. This includes 5 cold treatment plants, 4 UV treated plants, 3 heat treated plants, and 6 total control plants (no stress). All methylation profiling was done on a custon 3x1.4M NimbleGen array platform (meDIP-chip).

first: Steven

first: Nathan

last: Springer


title: Single-base resolution DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi, by whole-genome bisulfite sequencing (MethylC-seq).

status: Public on Jun 28 2015

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

country: China

institute: China Agricutural University

type: Methylation profiling by high throughput sequencing

summary: Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. DNA methylation in the gene body region, especially in the internal exons, was higher than in the 5’ and 3’ flanking regions of genes.Differentially methylated region (DMR) analysis indicated widespread differences between the Leghorn and Fayoumi lines. Of particular interest, many identified DMR-associated genes were significantly enriched in immune-related groups, which indicate that DNA methylation may regulate host immune response to pathogen infection in chickens as these two genetic lines have demonstrated differential resistance to a few pathogens. This work establishes a comprehensive and precise DNA methylation pattern in chickens and lays a solid foundation for future studies on epigenetic modifications related to poultry growth, disease, and development.

overall_design: DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi,which were generated by deep sequencing, using Illumina GAII

first: Rujiao


title: Gene expression profiling of the prostate biopsy samples from African American and European American prostate cancer patients

status: Public on Jul 27 2015

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

summary: Prostate cancer (PCa) tends to be more aggressive and lethal in African Americans (AA) compared to European Americans (EA). To further understand the biological factors accounting for the PCa disparities observed in AA and EA patients, we performed gene profiling analysis using Affymetrix human exon 1.0 ST arrays to identify the differentially expressed genes in AA and EA patients.

overall_design: 35 prostate biopsy specimens (tumor and adjacent normal tissues) were collected from 20 African American and 15 European American prostate cancer patients. RNA samples, purified from the collected biopy specimens, were process and applied to Affymetrix human exon ST 1.0 arrays. Array data was normalized, batch corrected and analyzed (1-way ANOVA) using Partek Genomics Suite program.

first: Norman

last: Lee


title: Transcriptomic effects of Capridine on the acute promyelocytic leukemia HL-60 cell line

status: Public on Aug 27 2015

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: We used Agilent human gene expression arrays to test whether Capridine, a chemotherapeutic agent with specificity towards prostate cancer, deregulates the genomic fabric of acute myeloyd leukemia in HL-60 cells. This cell line was derived at the National Cancer Institute from a 36-year-old woman with acute promyelocytic leukemia. We found that Capridine down-regulates the pathways responsible for formation of hematopoietic progenitor cells, for anti-apoptosis and for proliferation of clonal neoplastic cells. Our results indicates the therapeutic potential of Capridine against acute myeloid leukemia.

overall_design: Two-conditions: HO = not treated, HA = Capridine-treated HL-60 cells. Four biological replicates of each condition. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: HO1 & HO3 were compared with HA1 & HA3, HO2 & HO4 were compared  with HA2 & + HA4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

middle: A

first: Robert

last: Suriano

first: Priyanka

last: Mukherjee

first: Tanay

last: Gupta

first: Anvita

first: Sanda

first: John

middle: T

last: Fallon

first: Jan

last: Geliebter

first: Abraham

last: Mittelman

first: Raj

middle: K

last: Tiwari


title: The small molecule compound Y15 and PF04554878 in TT cells

status: Public on Jul 03 2015

city: buffalo

first: Dan

state: NY

address: Elm & Carlton Streets

institute: RPCI

summary: Global gene expression in TT cells treated with FAK inhibitors

overall_design: TT cells were untreated and treated with Y15 small molecule FAK inhibitor at 10 microM or another FAK inhibitor PF04554878 at 10microM, total RNA was isolated and gene expression was analyzed using Illumina chips

first: Vita

last: Golubovskaya

first: Shalana

last: O'Brien

first: Song

first: David

last: Ostrov

first: William

last: Cance


title: Gene expression signature predicting post-relapse survival of myeloma patients identified by co-culture of myeloma cells with osteoclasts and osteoblast progenitors

city: Little Rock

first: Joshua

last: Epstein

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciances

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

overall_design: Refer to individual Series


title: Expression data from murine adipose tissue

status: Public on Jun 03 2015

city: Riyadh

first: Kate

middle: S

last: Collison

address: Department Biological & Medical Research

country: Saudi Arabia

institute: King Faisal Specialist Hospital & Research Centre

summary:
Our previous studies have linked Trans-fat and monosodium glutamate (MSG) to the development of Nonalcoholic Fatty Liver Disease (NAFLD). We have also shown that MSG can interact with another commonly consumed food additive, aspartame, to impair glucose homeostasis, which is also disrupted in NAFLD. This most  recent nutrigenomic study shows how aspartame, MSG and Trans-fat can unfavorably alter hepatic and adipose tissue gene expression.
We used microarray analysis to examine changes in adipose gene transcription in response to TFA MSG and/or ASP feeding in male C57Bl/6J mice.

overall_design: Our study animals were bred from female C57Bl/6J mice fed a standard chow diet until 6 weeks of age whereupon they were placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating. The four dietary regimens used in this study were: [1] TFA diet: consisting of 20% (w/w) Partially Hydrogenated Vegetable Shortening (Test Diet #5C4M containing 8.68% w/w Trans fatty acids; Test Diet Purina, USA), with ad lib drinking water. [2] MSG+TFA diet: TFA diet with ad lib drinking water containing 0.75 g/L of L -Glutamic acid monosodium salt hydrate (MSG catalog G1626 Sigma Aldrich). [3] ASP+TFA diet: (TFA diet with ad lib drinking water containing 0.25 g/L Asp-Phe methyl ester (aspartame, ASP, catalog A5139 Sigma Aldrich). [4] ASP+MSG+TFA diet: TFA diet with ad lib drinking water containing 0.25 g/L aspartame and 0.75 g/L monosodium glutamate. After the 3-week period of adjustment to the respective diets, 15 male offspring were bred, weaned and maintained on these diets for the duration of the study. Offspring were weaned at 4 weeks of age . Adipose tissue (15 per diet group) were used at 20 weeks for RNA extraction and hybridization on Affymetrix microarrays.

first: Nadine

middle: J

last: Makhoul

first: Marya

middle: Z

last: Zaidi


title: Expression data from murine liver and adipose tissue


title: DNA methylation analysis of Rhabdoid tumor of the kidney, Clear cell sarcoma of the kidney and Ewing's sarcoma family of tumors

status: Public on Jun 12 2015

city: Seyagaya-ku

first: Hitomi

last: Ueno

country: Japan

institute: National Center for Child Health and Development

summary: Genome wide DNA methylation profiling of Rhabdoid tumor of the kidney, Clear cell sarcoma of the kidney, Ewing's sarcoma family of tumors and non-neoplastic kidney. The Illumina Infinium HumanMethylation 27 BeadChip was used to obtain DNA methylation profiles across approximately 27000 CpGs  . Samples included 3 Rhabdoid tumor of the kidney, 3 Clear cell sarcoma of the kidney, 3 Ewing's sarcoma family of tumor and 3 non-neoplastic kidney.

overall_design: Bisulfite converted DNA from the 12 samples were hybridized to the Illumina Infinium HumanMethylation27 Beadchip.

first: Hajime

last: Okita

first: Nobutaka

last: Kiyokawa

first: Kazuhiko

last: Nakabayashi

first: Kenichiro

last: Hata


title: Overexpression of mutant EGFR (E746-A750del) enhances the tumourigenic properties of MCF10CA1a cells

status: Public on Apr 06 2015

city: Herston

first: Georgia

last: Trench

state: QLD

address: 300 Herston Rd

department: Cancer Genetics

country: Australia

institute: QIMR Berghofer Medical Research Institute

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

summary: Basal-like and triple negative breast cancer (TNBC) share common molecular features, poor prognosis and a propensity for metastasis to the brain. Amplification of EGFR occurs in ~50% of basal-like breast cancer and mutations in the epidermal growth factor receptor (EGFR) have been reported in up to ~ 10% of Asian TNBC patients.  In non-small cell lung cancer several different mutations in the EGFR tyrosine kinase domain confer sensitivity to receptor tyrosine kinase inhibitors, but the tumourigenic potential of EGFR mutations in breast cells and their potential for targeted therapy is unknown.  Constructs containing wild type, G719S or E746-A750 deletion mutant forms of EGFR were transfected into the ‘near normal’ MCF10A breast cells and their tumorigenic derivative, MCF10CA1a.  These transfected lines were used to investigate the effects of EGFR over-expression and mutation on proliferation, migration, invasion, response to gefitinib, and tumour formation in vivo.  We also carried out copy number analysis and whole exome sequencing of the MCF10A and MCF10CA1a cell lines.  Both activating mutations of EGFR increased the proliferative ability of MCF10A and MCF10CA1a cell lines, and increased the anchorage-independent growth and sensitivity to gefitinib in MCF10A cells.  In addition, the EGFR-E746-A750 deletion increased the migratory and invasive abilities of the MCF10CA1a cell line in vitro, and greatly increased the formation and growth of MCF10CA1a tumours in vivo.  Compared to MCF10A cells, MCF10CA1a cells had large regions of gain on chromosome 9 and the long arm of chromosome 3, deletion in the short arm of chromosome 7, and mutations in many genes implicated in cancer.  The EGFR E746-A750 deletion mutation, and to a lesser extent G719S, greatly enhance the oncogenic properties of MCF10A cell line, and increase sensitivity to gefitinib. Although the addition of EGFR E746-A750 renders the MCF10CA1a cells more tumourigenic in vivo it is not accompanied by increased sensitivity to gefitinib, perhaps because of additional mutations, including the PIK3CA H1047R mutation, that the MCF10CA1a cell line has acquired.  Screening TNBC/basal-like breast cancer for EGFR mutations may prove useful for directing therapy but, as in non-small cell lung cancer cancer, accompanying mutations in PIK3CA may confer gefitinib resistance.

overall_design: DNA extracted from MCF10A and MCF10CA1a cell lines were analyzed for copy number differences using Illumina Human Omni 2.5M SNP arrays.

first: Darrell

middle: C

last: Bessette

first: Erik

last: Tilch

first: Tatjana

last: Seidens

first: Michael

last: Quinn

first: Fares

last: Al-Ejeh

first: Wei

last: Shi

first: Sibylle

last: Cocciardi

first: Amy

last: McCart Reed

first: Jodi

middle: M

last: Saunus

first: Adrian

middle: P

last: Wiegmans

first: Peter

last: Simpson

first: Sunil

last: Lakhani

first: Kum

last: Khanna

first: Sean

last: Grimmond

first: Nic

last: Waddell

last: Chenevix-Trench


title: Association between distinct gene and miRNA expression profiles and utilization of stereotyped subset #4 in the cells of CLL patients [MicroRNA Profiling]

status: Public on Jun 01 2015

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Highly homologous B-cell receptors, stereotyped BCR, are expressed in a recurrent fraction of patients with chronic lymphocytic leukemia (CLL). In this study, we investigated the biological and molecular features of leukemic cells from 16 patients utilizing stereotyped subset #4 BCR (IGHV4-34) in a prospective cohort of 462 Binet stage A CLL patients. All subset #4 patients were characterized by the IGHV mutated gene configuration and by the absence of unfavorable cytogenetic lesions, and NOTCH1 and SF3B1 mutations. Gene expression profiling demonstrated a significant downregulation of WDFY4, MF2A and upregulation of PDGFA, FGFR1 and TFEC genes in leukemic cells from subset #4 compared to those from the remaining IGHV-mutated patients. Similarly, in the cells from subset #4 cases there was a specific miRNA expression pattern involving the upregulation of miR-497 and miR-29c. Furthermore transfection of miR-497 mimic in primary leukemic CLL cells induced a downregulation of BCL2, known to be a validated target of this miRNA. Our data identify a distinct gene and miRNA expression profile of the cells from subset #4 patients, providing further evidence for the putative role of BCR in shaping the features of the leukemic cells.

overall_design: This series of microarray experiments contains the gene expression profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 217 patients (Binet stage A). Peripheral blood mononuclear cells from CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation. For gene and miRNA expression profiling experiments CLL cells were enriched by negative selection with the EasySep-Human B cell enrichment kit without CD43 depletion (Stem Cell Technologies) using the fully automated protocol of immunomagnetic cell separation with RoboSepTM (Stem Cell Technologies).

first: Francesco

last: Maura

first: Giovanna

last: Cutrona

first: Laura

last: Mosca

first: Serena

last: Matis

first: Marta

last: Lionetti

first: Sonia

last: Fabris

first: Monica

last: Colombo

first: Carlotta

last: Massucco

first: Daniele

last: Reverberi

first: Massimo

last: Gentile

first: Anna

last: Recchia

first: Sabrina

last: Bossio

last: Negrini

first: Pierfrancesco

last: Tassone

first: Davide

last: Rossi

first: Gianluca

last: Gaidano

first: Agostino

last: Cortelezzi

last: Di Raimondo

first: Fortunato

last: Morabito

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: Genome-wide association studies for sheep growth and meat production traits using Illumina OvineSNP50 BeadChip

status: Public on May 01 2015

first: Li

last: Zhang

address: Yuanmingyuan Street

institute: CAAS

summary: Mear prodution is the most important trait for sheep. In this study, we performed a Genome-wide association study (GWAS) by using Illumina Ovine SNP50 BeadChip in 329 purebred sheep phenotyped for 11 growth and meat production traits (birth weight, weaning weight, 6-month weight, eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height at withers , chest girth and shin circumference). A total of 319 sheep and 48,198 SNPs were fitted using TASSEL 3.0 software as random effects in a mixed linear model. 36 chromosome-wise significant SNPs were identified for 7 traits and 10 of them reached genome-wide significance level consistently for post-weaning gain. Gene annotation was implemented based on the latest version3.1 ovine genome sequence (released October 2012), and meanwhile we referenced genomic information of human, bovine, mouse and rat. More than one-third SNPs (14 out of 36) were located within ovine genes , some other were located close to ovine genes (878bp-398165bp apart).

overall_design: 329 sheep DNA were scanned using OvineSNP50 Beadchip and  the association is done between the SNP data and 11 different meat prodution traits

first: Lixin

last: Du


title: Epigenetic silencing of HAND2 is a crucial step in endometrial carcinogenesis

status: Public on Aug 15 2015

city: London

first: Shahzia

last: Anjum

address: Gower Street

country: United Kingdom

institute: University College London

summary: Here we demonstrate that epigenetic silencing of HAND2 is a key step in endometrial carcinogenesis. We performed an epigenome-wide methylation analysis of >27,000 CpG sites in endometrial cancers and controls and identified methylation of HAND2 as one of the most common hypermethylated and silenced genes in endometrial cancer.

overall_design: Bisulphite converted DNA from the 87 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

first: Allison

last: Jones

first: Andrew

middle: E

last: Teschendorff

first: Quanxi

last: Li

first: Tim

last: Mould

first: Michal

last: Zikan

first: David

last: Cibula

first: Heidi

last: Fiegl

first: Shih-Han

last: Lee

first: Elisabeth

last: Wik

first: Richard

last: Hadwin

first: Rupali

last: Arora

first: Charlotte

last: Lemech

first: Henna

last: Turunen

first: Päivi

last: Pakarinen

first: Ian

last: Jacobs

first: Helga

last: Salvesen

first: Milan

last: Bagchi

first: Indrani

first: Martin

last: Widschwendter


title: Human Bronchoalveolar Lavage Cells Gene Expression After Exposure to Increasing Doses of Ozone

status: Public on Jun 15 2015

city: San Francisco

first: Mehrdad

last: Arjomandi

state: CA

address: 4150 Clement St, 3A-20

institute: UCSF

summary: Ozone, the major component of air pollution, is an oxidant gas.  Inhalation of high ambient levels of ozone causes oxidative stress and airway inflammation.  To assess the biological responses of airway inflammatory cells to ozone-induced oxidative stress, we examined the gene expression of airway inflammatory cells in response to inhalation of ozone.

overall_design: Nineteen subjects, with and without asthma, were exposed to clean air (0 ppb), low (100ppb), and high (200ppb) ambient levels of ozone for 4 hours on three separate occasions in a climate-controlled chamber followed by bronchoscopy with bronchoalveolar lavage (BAL) 20 hours after the end of exposure in a repeated measure design.  The BAL cells mRNA expression was examined using Affymetrix GeneChip Microarray.

first: Andrea

last: Tham


title: Consistent and Heritable Alterations of DNA Methylation are Induced by Tissue Culture in Maize

status: Public on Mar 24 2015

first: Steve

last: Eichten

summary: Plants regenerated from tissue culture and their progenies are expected to be identical clones, but often display heritable molecular and phenotypic variation. We characterized DNA methylation patterns in callus, primary regenerants, and regenerant-derived progenies using immunoprecipitation of methylated DNA (meDIP) to assess the genome-wide frequency, pattern, and heritability of DNA methylation changes. Although genome-wide DNA methylation levels remained similar following tissue culture, numerous regions exhibited altered DNA methylation levels. Hypomethylation events were observed more frequently than hypermethylation following tissue culture. Many of the hypomethylation events occur at the same genomic site across independent regenerants and cell lines. The DNA methylation changes were often heritable in progenies produced from self-pollination of primary regenerants. Methylation changes were enriched in regions upstream of genes and loss of DNA methylation at promoters was associated with altered expression at a subset of loci. Differentially methylated regions (DMRs) found in tissue culture regenerants overlap with the position of naturally occurring DMRs more often than expected by chance with 8% of tissue culture hypomethylated DMRs overlapping with DMRs identified by profiling natural variation, consistent with the hypotheses that genomic stresses similar to those causing somaclonal variation may also occur in nature, and that certain loci are particularly susceptible to epigenetic change in response to these stresses. The consistency of methylation changes across regenerants from independent cultures suggests a mechanistic response to the culture environment as opposed to an overall loss of fidelity in the maintenance of epigenetic states.

overall_design:
Methylation profiles in callus, R0, and R1 tissue culture samples of maize using a custon 1.4M feature NimbleGen array.
25 Samples (15 R0 samples, 6 R1 samples, 1 callus tissue, and 3 A188 control samples).

first: Scott

last: Stelpflug

first: Steven

first: Peter

last: Hermanson

first: Nathan

last: Springer

first: Shawn

last: Kaeppler


title: Molecular Insight into Thiopurine Resistance: Transcriptomic Signature in Lymphoblastoid Cell Lines

status: Public on Mar 09 2015

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: Despite significant improvements in acute lymphoblastic leukemia (ALL) treatment, long-term survival is still challenging. 6-mercaptopurine (6-MP), a thiopurine agent part of maintenance therapy, is of particular importance for determining clinical outcome and preventing relapse. Genetic inheritance in thiopurine metabolism plays a major role in interindividual clinical response variability to thiopurine. However, thiopurine resistance remains mostly unexplained. Using lymphoblastoid cell lines (LCLs) selected for their extreme resistant phenotype to thiopurine drugs, we performed a genome-wide expression profiling in order to highlight underlying mechanisms of thiopurine resistance. We established a transcriptomic signature of 32 genes predicting thiopurine resistance, including GTPBP4, a GTP-binding protein which is a p53 interactor. Besides, among the differentially expressed genes between resistant and sensitive cell lines, gene ontology analysis highlights the involvement of RNA processes and cell cycle in thiopurine resistance. A comprehensive pathway analysis revealed the overexpression of the ATM/p53/p21 pathway, which is activated in response to DNA damage and resulting in a cell cycle arrest. Furthermore, an increased expression of TNFRSF10D, a p53 target gene, or CCNG2, a negative regulator of cell cycle, could result in a cell cycle arrest and have associated with resistance. Finally, ARHGDIA under-expression in resistant cell lines could constitute a novel molecular mechanism contributing to thiopurine resistance in relation thiopurine pharmacodynamics, based on Rac1 inhibition and apoptosis. Our study represents a step toward the knowledge of underlying molecular mechanisms contributing to thiopurine resistance and potential therapeutic targets in the field of personalized medicine.

overall_design: Transcriptomic analysis of thiopurine-resistant LCLs (n=5) compared to thiopurine-sensitive LCLs (n=6); t test for each gene after RMA process.

first: Laurent

last: Chouchana

first: Ana

last: Fernández-Ramos

first: Catherine

last: Marchetti

first: Irène

last: Ceballos-Picot

first: Philippe

middle: H

last: Beaune

first: David

last: Gurwitz

first: Marie

last: Loriot


title: Reduced a-MSH underlies hypothalamic endoplasmic reticulum stress-induced hepatic gluconeogenesis

status: Public on Jun 18 2015

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: Alterations in endoplasmic reticulum (ER) homeostasis have been implicated in the pathophysiology of obesity and type-2 diabetes (T2D). Acute ER stress induction in the hypothalamus produces glucose metabolism perturbations. However, the neurobiological basis linking hypothalamic ER stress with abnormal glucose metabolism remains unknown. Here we report that genetic and induced models of hypothalamic ER stress are associated with alterations in systemic glucose homeostasis due to increased gluconeogenesis (GNG) independent of body weight changes. Defective alpha melanocyte-stimulating hormone (a-MSH) production underlies this metabolic phenotype, as pharmacological strategies aimed at rescuing hypothalamic a-MSH content reversed this phenotype at metabolic and molecular level. Collectively, our results posit defective a-MSH processing as a fundamental mediator of enhanced GNG in the context of hypothalamic ER stress, and establish a-MSH deficiency in proopiomelanocortin (POMC) neurons as a potential contributor to the pathophysiology of T2D.

overall_design: Total RNA was extracted from whole-liver of 6-week old control (3 biological replicates) and POMCMfn2KO mice (5 biological replicates)

first: Marc

last: Schneeberger

first: Alicia

middle: G

last: Gomez-Valadés

last: Sebastián

first: Sara

last: Ramirez

first: Ainhoa

last: Garcia

first: Yaiza

last: Esteban

first: Anne

last: Drougard

first: Albert

last: Ferrés-Coy

first: Analía

last: Bortolozzi

first: Pablo

last: Garcia-Roves

first: John

last: Jones

first: Bruno

last: Manadas

first: Antonio

last: Zorzano

first: Ramon

last: Gomis

last: Claret


title: RNA sequencing analysis of abdominal adipose tissue in 7 week old juvenile broiler chickens divergently selected for high or low body weight

status: Public on Mar 14 2015

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

type: Expression profiling by high throughput sequencing

summary:
Chickens divergently selected for either high growth (HG genotype) or low growth (LG genotype) at SRA-INRA, France were used to profile abdominal adipose gene expression at 7 wk of age. The HG and LG chickens are different in various phenotypic and metabolic measurements, including growth rate, abdominal fat, plasma glycemia, insulinemia, T4, T3, triglyceride and NEFA. The HG and LG chickens are valuable as a model for biomedical and agricultural traits. Massively parallel RNA sequencing (RNA-Seq) was completed on an Illumina HiSeq 2000 System for transcription analysis of HG and LG abdominal fat. Need information on data processing, statistical analysis, and differential expression.
Keywords: abdominal fat, divergently selected chickens, growth, transcriptional profiling, differentially expressed genes

overall_design: Abdominal fat mRNA profiles of high growth (HG genotype) or low growth (LG genotype) chickens at 7 weeks of age were generated by deep sequencing (on an Illumina HiSeq 2000 system).

first: C

middle: W

last: Resnyk

first: E

last: Le Bihan-Duval

first: M

last: Duclos

first: J

last: Simon

first: L

first: T

last: Porter

first: S

last: Aggrey

first: B

last: Abasht


title: Gene expression profiling in the liver of 3-month old mice with a mutant Wrn protein treated with vitamin C compared to  3-month old WT mice

status: Public on Mar 07 2015

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

country: Canada

institute: Centre de Recherche du CHU de Québec

summary: Werner syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS is believed to be involved in different aspects of transcription, replication, and/or DNA repair. We generated a mouse model with a deletion in the helicase domain of the murine WRN homologue that recapitulates most of the WS phenotypes including an abnormal hyaluronic acid excretion, higher reactive oxygen species (ROS) levels, increased genomic instability and cancer incidence resulting in a 10-15% decreased life span expectancy. In addition, WS patients and Wrn mutant mice show hallmarks of a metabolic syndrome including premature visceral obesity, hypertriglyceridemia, insulin-resistant diabetes type 2 and associated cardiovascular diseases. In this study, we compared the expression profile of liver tissues from 3 months old Wrn mutant mice treated with 0.4% vitamin C to wild type animals.

overall_design: Microarray analyses were performed on the liver tissues of 3 months old mice. Four independent biological replicates of this experiment (wild type vs vitamin C treated Wrn mutant mice) were carried out on four replicates of each genotype.

first: Eric

last: Paquet


title: Gene expression profiling in the liver of 3-month old mice with a mutant Wrn protein compared to 3-month old WT mice

status: Public on Mar 05 2015

summary: Werner syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS is believed to be involved in different aspects of transcription, replication, and/or DNA repair. We generated a mouse model with a deletion in the helicase domain of the murine WRN homologue that recapitulates most of the WS phenotypes including an abnormal hyaluronic acid excretion, higher reactive oxygen species (ROS) levels, increased genomic instability and cancer incidence resulting in a 10-15% decreased life span expectancy. In addition, WS patients and Wrn mutant mice show hallmarks of a metabolic syndrome including premature visceral obesity, hypertriglyceridemia, insulin-resistant diabetes type 2 and associated cardiovascular diseases. In this study, we compared the expression profile of liver tissues from 3-month old Wrn mutant mice 3-month old to wild type animals before the mutant animals exhibited any microscopic phenotype.

overall_design: Microarray analyses were performed on the liver tissues of 3 months old mice. Four independent biological replicates of this experiment (wild type vs Wrn mutant mice) were carried out with a dye swap on two replicates of each genotype.


title: MicroRNA expression data from APPswe/PS1deltaE9 transgenic mice cortex

city: Shenzhen

first: Jun

last: Wan

state: Guangdong Province

address: No. 1120, Lianhua Road

institute: Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To characterize the differentially expressed microRNAs between APPswe/PS1deltaE9 transgenic mice cortex and normal wild type mice cortex

overall_design: We isolated APPswe/PS1delataE9 and wild type mice brain cortexes for microRNA sequencing.

first: Hongxue

last: Luo


title: Transcriptome analysis of normal and cancerous bladder tissues.

status: Public on Feb 05 2015

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: The aim of this research was to explore activation/deactivation of signaling pathways during cancerogenesis.

overall_design: Tissue samples from malignant tumors were obtained from patients who had undergone surgery. Tissue samples from non-cancer controls were collected from autopsies of healthy donors killed in road  accidents. Both the tumors and normal tissues were evaluated by a pathologist to confirm the diagnosis and estimate the tumor cell numbers. All tumor samples used in this study contained at least 80% tumor cells. Tissue samples were immediately stabilized in RNAlater (Qiagen) and then stored at −80°C.

middle: V

first: Alexander

last: Aliper

first: Andrey

last: Golubov

first: Olga

last: Kovalchuk

first: Anton

last: Abuzdin


title: Role of IRAKM in IL-33-induced dendritic cell activation

status: Public on Mar 03 2015

city: Boston

first: M. Simo

last: Arredouani

state: MA

address: 330 Brookline Ave.

department: Surgery

institute: Beth Israel Deaconess Medical Center

summary:
To gain additional insight into the role of IRAKM in dendritic cell activation in response to IL-33 challenge, we profiled transcriptomes of mouse DC2.4 dendritic cell lines
with or without IRAKM following IL-33 treatment in vitro.

overall_design: IRAKM-sufficient and deficient DC2.4 cells were cultured overnight in the absence or presence of IL-33. Gene expression profiling was performed using Affymetrix platform.

first: Arredouani

last: Simo

first: Nechama

last: Morris


title: Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (ATAC-Seq)

city: Worcester

first: Barbara

last: Tabak

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gene regulatory elements such as enhancers have profound effects on cellular function, health and disease. Our understanding of mammalian enhancer function is limited by the lack of technology that would allow for a rapid and thorough test of their cell type-specific function. Here we describe a novel Cas9-effector system that enables rapid testing and functional annotation of native enhancers in embryonic stem cells.

overall_design: V6.5 mouse ES cells according to the protocol as described

first: Rene

last: Maehr

first: Manuel

last: Garber


title: Identification of a DNA methylation signature in blood from subjects affected by Down syndrome

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

summary: Down syndrome is characterized by a wide spectrum of clinical signs, which include cognitive and endocrine disorders and haematological abnormalities. Although it is well established that the causative defect of Down syndrome is the trisomy of chromosome 21, the molecular bases of Down syndrome phenotype are still largely unknown. We used the Infinium HumanMethylation450 BeadChip to investigate DNA methylation patterns in whole blood from 29 subjects affected by Down syndrome (DS), using their healthy relatives as controls (mothers  and unaffected siblings). This family-based model allowed us to monitor possible confounding effects on DNA methylation patterns deriving from genetic and environmental (lifestyle) factors. The identified epigenetic signature of Down syndrome includes differentially methylated regions that, although enriched on chromosome 21, interest most of the other chromosomes and can be functionally linked to the developmental and haematological defects characteristic of the disease.

overall_design: DNA was extracted from whole peripheral blood using the QIAamp 96 DNA Blood Kit (QIAGEN) and quantified by Quant-iT™ PicoGreen (Invitrogen). Sodium bisulphite conversion of 500 ng of each sample was performed using the EZDNA Methylation-Gold Kit according to the manufacturer's recommendation for Illumina Infinium Assay. 4 ul of bisulfite converted DNA were hybridized on Infinium HumanMethylation 450 BeadChip, following manufacturer’s instructions. Arrays were scanned by HiScan SQ scanner (Illumina) and the intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation levels of each CpG is reported as beta value.

first: Davide

last: Gentilini

first: Alessio

last: Boattini

first: Enrico

last: Giampieri

first: Chiara

last: Pirazzini

first: Cristina

last: Giuliani

first: Elisa

last: Fontanesi

last: Scurti

first: Daniel

last: Remondini

first: Miriam

last: Capri

first: Guido

last: Cocchi

first: Alessandro

last: Ghezzo

first: Alberto

last: Del Rio

first: Donata

last: Luiselli

first: Giovanni

last: Vitale

first: Daniela

last: Mari

first: Gastone

last: Castellani

first: Mario

last: Fraga

first: Anna

last: Di Blasio

first: Stefano

last: Salvioli

first: Claudio

last: Franceschi

first: Paolo

last: Garagnani


title: Expression data from murine liver tissue

first: Kate

last: Collison

summary:
Our previous studies have linked Trans-fat and monosodium glutamate (MSG) to the development of Nonalcoholic Fatty Liver Disease (NAFLD). We have also shown that MSG can interact with another commonly consumed food additive, aspartame, to impair glucose homeostasis, which is also disrupted in NAFLD. This most  recent nutrigenomic study shows how aspartame, MSG and Trans-fat can unfavorably alter hepatic and adipose tissue gene expression.
We used microarray analysis to examine changes in liver gene transcription in response to TFA MSG and/or ASP feeding in male C57Bl/6J mice.

overall_design: Our study animals were bred from female C57Bl/6J mice fed a standard chow diet until 6 weeks of age whereupon they were placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating. The four dietary regimens used in this study were: [1] TFA diet: consisting of 20% (w/w) Partially Hydrogenated Vegetable Shortening (Test Diet #5C4M containing 8.68% w/w Trans fatty acids; Test Diet Purina, USA), with ad lib drinking water. [2] MSG+TFA diet: TFA diet with ad lib drinking water containing 0.75 g/L of L -Glutamic acid monosodium salt hydrate (MSG catalog G1626 Sigma Aldrich). [3] ASP+TFA diet: (TFA diet with ad lib drinking water containing 0.25 g/L Asp-Phe methyl ester (aspartame, ASP, catalog A5139 Sigma Aldrich). [4] ASP+MSG+TFA diet: TFA diet with ad lib drinking water containing 0.25 g/L aspartame and 0.75 g/L monosodium glutamate. After the 3-week period of adjustment to the respective diets, 15 male offspring were bred, weaned and maintained on these diets for the duration of the study. Offspring were weaned at 4 weeks of age . Liver tissue (15 per diet group) were used at 20 weeks for RNA extraction and hybridization on Affymetrix microarrays.

first: Nadine

last: Makhoul

first: Marya

last: Zaidi


title: Association between distinct gene and miRNA expression profiles and utilization of stereotyped subset #4 in the cells of CLL patients [Gene Expression]

first: Luca

last: Agnelli

first: Francesco

last: Maura

first: Giovanna

last: Cutrona

first: Laura

last: Mosca

first: Serena

last: Matis

first: Marta

last: Lionetti

first: Sonia

last: Fabris

first: Monica

last: Colombo

first: Carlotta

last: Massucco

first: Daniele

last: Reverberi

first: Massimo

last: Gentile

last: Recchia

first: Sabrina

last: Bossio

last: Negrini

first: Pierfrancesco

last: Tassone

first: Davide

last: Rossi

first: Gianluca

last: Gaidano

first: Agostino

last: Cortelezzi

last: Di Raimondo

first: Fortunato

last: Morabito

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (BeadChip)

first: Barbara

last: Tabak

summary: Gene regulatory elements such as enhancers have profound effects on cellular function, health, and disease. Our understanding of mammalian enhancer function is limited by the lack of a technology that would allow for a rapid and thorough test of their cell type-specific function. Here, we describe a novel Cas9-effector system that enables rapid testing and functional annotation of native enhancers in embryonic stem cells.

overall_design: Total RNA obtained from R26 dCas9-effector mESC lines after viral delivery of sgRNAs directed against proximal promoter or enhancer regions

first: Rene

last: Maehr


title: Association between distinct gene and miRNA expression profiles and utilization of stereotyped subset #4 in the cells of CLL patients

first: Luca

last: Agnelli

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

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

overall_design: Refer to individual Series


title: Analysis of the transcriptome of adult cardiac myocytes stimulated with CTGF

status: Public on Feb 01 2015

city: OSLO

first: Ingvild

last: Moe

address: Sognsvannsvn 20

country: Norway

institute: Oslo University hospital

summary: Transgenic mice with cardiac-restricted overexpression of connective tissue growth factor (CTGF) have substantially increased tolerance towards ischemia/reperfusion injury. In the transgenic mouse model, we found that CTGF induces expression of severeal genes putatively involved in cardioprotection. The purpose of this study was to determine gene expression in cardiac myocytes stimulated with purified, recombinant CTGF, comparing unstimulated and stimulated samples. The cytoprotective actions of CTGF was recflected in the transcriptome of CTGF-stimulated cardiac myocytes. Gene ontology analysis revealed that genes included under the terms anti-apoptosis, response to wounding, and response to stress were significantly overrepresented in cardiac myocytes exposed to CTGF. Serveral of the most higly up-regulated genes have previously been reported to exert cardioprotective actions and increase tolerance towards ischemia/reperfusion injury.

overall_design: Primary, adult cardiac myocytes were cultured in the absence (n=6) or presence (n=6) of 200 nmol/L recombinant CTGF for 48 hours.

first: Håvard

last: Attramadal


title: RNA-Seq of female, male, and sex-transformed Drosophila melanogaster heads from flies heterozygous for deletions on chromosome X and 3L

status: Public on Mar 26 2015

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: To measure the response to gene dose, we performed mRNA-Seq of fly heads with molecularly defined deletions constructed from DrosDel deficiency lines (Ryder et al. Genetics 2007, 177(1):615-29) on the Illumina HiSeq 2000 platform.

overall_design: We performed single-end next-generation sequencing (RNA-Seq) on poly-A+ RNA extracted from adult female and male heads in biological triplicate. Besides wildtype females (XX) and males (XY) that were heterozygous for deletions, we also sequenced females that were transformed into males (XX males) by using mutations in the sex determination gene transformer-2 (tra2). The original lines with deletions, including 22 deletions on the chromosome X and 12 deletions on the chromosome 3L, were from the DrosDel project. The diploid controls without DrosDel deletions were derived from w1118 (the parental line of DrosDel stocks) or Oregon-R Strain. We sequenced a total of 249 samples.

first: Zhen-Xia

last: Chen


title: MiR-133b regulates the expression of the actin protein TAGLN2 during oocyte growth and maturation: a potential target for infertility therapy

status: Public on Dec 31 2014

city: Foshan

first: Chenglai

last: Xia

address: Renming Xi  11#

institute: Affiliated Foshan Maternity & Chlid Healthcare Hospital, Southern Medical University

summary: In this study, the expression of miRNAs in metaphase I (MI) oocytes treated with or without insulin-like growth factor 1 (IGF-1) was observed by microRNA microarray analysis. Results show that 145 miRNAs were up-regulated and 200 miRNAs were down-regulated in MI oocytes after IGF-1 treatment. MiR-133b, which was up-regulated more than 30-fold, was chosen for further research.

overall_design: The isolated MI oocytes were cultured at 37°C and 5% CO2 in G-2TM PLUS (Vitrolife, Sweden) treated with (45 oocytes) or without (62 oocytes) 200 ng/ml IGF-1 for 24 h (Peprotech, USA), then covered with ovoil (Vitrolife, Sweden). After 24 h, all oocytes were stored at 80°C until RNA was extracted. The average age of patients without IGF-1 treatment was 31.66 ± 3.90. The average age of patients with IGF-1 treatment was 31.25 ± 3.31. No apparent bias was detected between these two groups.

first: Xiao

last: Guo

first: Xia

middle: L

last: Cheng


title: Effect of ferulic acid on Clostridium beijerinckii NCIMB 8052 transcriptome

status: Public on Mar 25 2015

city: Ulsan

first: Siseon

last: Lee

address: UNIST-gil 50

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production and transcriptional responses of C. beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30 and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. Several gene ontology terms and KEGG pathways were identified showing significant change at each status, including ABC transporters, two component system and oxidoreductase activity. Moreover, genes related with efflux systems and heat shock proteins were also strongly up- regulated. Among these, expression of the groESL operon was induced by more than 4-fold and was consequently selected for overexpression to improve C. beijerinckii tolerance to ferulic acid.

overall_design: Clostridium beijerinckii NCIMB 8052 was anaerobically pre-cultured in P2 media at 37°C for 9 hours to reach an optical density (OD) at 600nm of 2.0. Then, the culture was transferred to fresh media with or without 0.5 g/L of ferulic acid and cultured for 84 hours. During culturing, the samples were taken from the culture at OD 0.3, 1.4 and 5, which were used to prepare total RNA. For microarray experiment, 100 ng of RNA were finally converted to fluorescent cRNA, which was followed by hybridization, feature scanning and data analysis. Three replicates were tested for OD 0.3 and 1.4 whereas two replicates were used for OD 5.

first: Jin

first: Robert

last: Mitchell


title: De Novo assembly and transcriptome analysis of Atlantic salmon macrophage/dendritic-like TO cells following type I IFN treatment and Salmonid alphavirus subtype-3 infection

city: Oslo

first: Hetron

last: Munang’andu

state: Oslo

address: Ullevålsveien 72

department: Basic Sciences and Aquatic Medicine

institute: Norwegian University of Life Sciences

summary: We used RNA-seq to characterize the transcriptomic changes induced by type I IFN treatment and salmon alphavirus subtype 3 (SAV-3) infection in TO-cells, a macrophage/dendritic like cell-line derived from Atlantic salmon (Salmo salar L) head kidney leukocytes.

overall_design: analysis of a transcriptome of DEGs induced by type I IFN and SAV-3 in TO cells generated by RNA-seq

first: Cheng

last: Xu

first: Øystein

last: Evensen

first: Jiang

last: Li


title: DNA Methylation and RNA Expression Profiles in Lung Adenocarcinomas

status: Public on Feb 03 2015

city: Rochester

first: Zhifu

last: Sun

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

type:
Expression profiling by array
Methylation profiling by array


title: Expression data from the study of the oestrognic activity of glabridin in Ishikawa cells in comparison to 17β-oestradiol (17β-E2)

status: Public on Apr 29 2015

city: Subang Jaya

first: Melissa

middle: Su Wei

last: Poh

state: Malaysia

address: No.1, Jln Taylor’s

country: Malaysia

institute: Taylor's University

summary: The general objective of this study was to investigate the effects of glabridin in Ishikawa cells in comparison to 17β-oestradiol by studying its mechanism of action via Affymetrix GeneChip® PrimeViewTM array

overall_design: The treatments were the unctreated control, 10µM glabridin, 100nM glabridin, 1nM 17β-E2 and the combination treatment of 1nM 17β-E2 with 100nM glabridin. The cells were treated for 72 hours and the RNA were extracted for microarray and RT-qPCR study.


title: Feeder-free directed differentiation of neural crest cells from human embryonic stem cells

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Here we compare the transcriptional profile of neural crest cells differentiated on MS5 feeder cells (Lee et al., 2007 Nature Biotechnology) with neural crest cells differentiated in a feeder-free protocol. As controls, neuroepithelial cells (LSB) and wnt-induced neural crest cells were included.

overall_design: Total RNA was isolated at day 18 or 35 of differentiation from FACS-sorted HNK1+/p75+ cells from MS5-induced (MS5-NC), or feeder-free-induced neural crest cells (NPC-NC). Control samples were wnt-induced neural crest cells at day 11 of differentiation (transgenic sox10-expressing human ES cells were used for this sample) and neuroepithelial cells at day 11 (LSB) (Trizol, Sigma). Samples for each group in triplicate were processed for Illumina Bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

first: Nadja

last: Zeltner

first: Lorenz

last: Studer


title: Generation and Characterization of an immortalized human mesenchymal stromal cell line model

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

institute: Oslo University Hospital


title: Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system

first: Barbara

last: Tabak


title: Generation and Characterization of an immortalized human mesenchymal stromal cell line model [Affymetrix]

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

summary: Human mesenchymal stromal cells (hMSCs) show great potential for clinical and experimental use. Self-renewal and multipotent differentiation capacity are key elements in the increasing interest of this cell type. However, a disadvantage of primary hMSCs is the limited in vitro lifespan, but this can be overcome by introduction of the catalytic subunit of human telomerase reverse transcriptase (TERT). In this paper, the generation and characterization of a TERT-immortalized, non-tumorigenic human bone marrow-derived stromal mesenchymal model cell line is described. The resulting cell line, iMSC#3, maintained capacity to differentiate into osteoblasts and adipocytes, and growth characteristics comparable to primary hMSCs into after long-term culturing (155 population doublings). A detailed characterization of the mRNA- and microRNA transcriptomes during adipocyte differentiation also showed that the iMSC#3 recapitulates this process at the molecular level. Furthermore, iMSC#3 showed no major differences from hMSCs regarding surface marker expression. The cell line had a normal karyotype, and high-resolution array comparative genomic hybridization confirmed that the cells in general had normal copy number. The gene expression profiles of immortalized and primary hMSCs were also similar, whereas the corresponding methylation profiles were more diverse. In conclusion, a human bone marrow-derived stromal cell line was developed, which can be used for basic studies of mesenchymal cells and to functionally study transgenes that might play a role in oncogenic transformation.

overall_design: DNA copy number analysis of iMSC#3

first: Magne

last: Skårn

first: Paul

last: Noordhuis

first: Marjan

last: Veuger

first: Meng

middle: Y

last: Wang

first: Stine

last: Kresse

first: Eivind

last: Egeland

first: Francesca

last: Micci

first: Heidi

last: Namløs

first: Anne-Mari

last: Håkelien

first: Solveig

last: Olafsrud

first: Susanne

last: Lorenz

first: Guttorm

last: Haraldsen

first: Gunnar

last: Kvalheim

middle: A

first: Ola

last: Myklebost


title: Generation and Characterization of an immortalized human mesenchymal stromal cell line model [Illumina adipocyte differentiation]

overall_design: Comparison of gene expression upon adipocyte differentiation of iMSC#3

middle: J


title: The sweet side of ‘OMICS’ approach: Identification of floral nectar proteins in Nicotiana attenuata

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of nectary expressed genes

overall_design: Early and late developmental nectaries were collected between 8 to 10 p.m. from the UT accession grown in the glasshouse for three days

first: Sang-Gyu

last: Kim

first: Pil-Joon

last: Seo

first: Danny

last: Kessler

first: Ian

middle: T

last: Baldwin


title: Generation and Characterization of an immortalized human mesenchymal stromal cell line model [Illumina iMSC#3 and hMSC primary cultures]

first: Leonardo

last: Meza-Zepeda

overall_design: Comparison of gene expression patterns of iMSC#3 and hMSC primary cultures

first: Magne

last: Skårn

first: Paul

last: Noordhuis

first: Marjan

last: Veuger


title: Gene expression regulation in canine mammary neoplastic cells by MDSC

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: The changes in gene expression of canine mammary neoplastic cells due to co-culture with myeloid-derived suppressor cells were assesed.

overall_design: Dye-swap experiment, gene expression in canine mammary neoplastic cells co-cultured with MDSC was compared to neoplastic cells monoculture.

first: Joanna

last: Mucha

first: Agata

last: Homa

first: Małgorzata

last: Bulkowska


title: DNA Methylation and RNA Expression Profiles in Lung Adenocarcinomas [DNA methylation]

first: Zhifu

last: Sun

summary: Lung cancer occurs in never-smokers. Epigenetic changes in lung cancer potentially represent important diagnostic, prognostic, and therapeutic targets. We compared DNA methylation profiles of 28 adenocarcinomas of the lungs of never-smokers with paired adjacent nonmalignant lung tissue. We correlated differential methylation changes with gene expression changes from the same 28 samples. We observed a distinct separation in methylation profiles between tumor and adjacent nonmalignant lung tissue using principal component analysis. Tumors were generally hypomethylated compared with adjacent nonmalignant tissue. Of 1,906 differentially methylated CpG sites between tumor and nonmalignant tissue, 1,198 were within classically defined CpG islands where tumors were hypermethylated compared with nonmalignant tissue. A total of 708 sites were outside CpG islands where tumors were hypomethylated compared with nonmalignant tissue. There were significant differences in expression of 351 genes (23%) of the 1,522 genes matched to the differentially methylated CpG sites. Genes that were not significantly differentially expressed and were hypermethylated within CpG sites were enriched for homeobox genes. These results suggest that the methylation profiles of lung adenocarcinomas of never-smokers and adjacent nonmalignant lung tissue are significantly different. Despite the differential methylation of homeobox genes, no significant changes in expression of these genes were detected.

overall_design: Twenty eight pairs of tumor and adjacent normal lungs were profiled for lung adenocarcinoma patients by gene expression and DNA methylation microarray

first: Aaron

middle: S

last: Mansfield

first: Liang

last: Wang

first: Julie

last: Cunningham

first: Jin

last: Jen

first: Chris

last: Kolbert

first: Ping

last: Yang


title: Glucocorticoid-induced reversal of IL1b stumulated gene expression in OE-E6/7 cells

status: Public on Jan 27 2015

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Studies indicate that high-grade serous ovarian carcinoma (HGSOC), the most common epithelial ovarian carcinoma histotype, originates from the fallopian tube epithelium (FTE).  Risk factors for this cancer include reproductive parameters associated with lifetime ovulatory events.  Ovulation is an acute inflammatory process during which the FTE is exposed to follicular fluid containing both pro- and anti-inflammatory molecules, such as interleukin-1 (IL1), tumor necrosis factor (TNF), and cortisol.  Repeated exposure to inflammatory cytokines may contribute to transforming events in the FTE, with glucocorticoids exerting a protective effect.  The global response of FTE cells to inflammatory cytokines or glucocorticoids has not been investigated.  To examine the response of FTE cells and the ability of glucocorticoids to   oppose this response, an immortalized human FTE cell line, OE-E6/E7, were treated with IL1β, dexamethasone (DEX), IL1β and DEX, or vehicle and genome-wide gene expression profiling was performed.  IL1β altered the expression of 47 genes of which 17 were reversed by DEX.  DEX treatment alone altered the expression of 590 genes, whereas combined DEX and IL1β treatment altered the expression of 784 genes.  Quantitative real time RT-PCR studies validated the gene array data for IL8, IL23A, TACC2 and PI3. Consistent with the array data, Western blot analysis showed increased levels of PTGS2 protein induced by IL1β that was blocked by DEX. These findings support the hypothesis that pro-inflammatory signaling is induced in FTE cells by inflammatory mediators and raises the possibility that dysregulation of glucocorticoid signaling could contribute to increased risk for HGSOC.

overall_design: An immortalized human oviductal cell line, OE-E6/E7 was treated with 10 nM dexamethasone and/or 50 ng/ml IL1b.  Cells were harvested 18 hours after treatment and rna was extracted and used for genome-wide gene expression.

first: Theodore

last: Brown

first: Alexandra

last: Kollara

first: Carl

last: Virtanen

first: Stephanie

last: Bachman

first: Robin

last: Haw

first: Lincoln

last: Stein


title: Expression data from intestinal epithelium

status: Public on Dec 01 2014

city: Taipei

first: Chiang

middle: Ting

last: Chien

address: No. 88, Tingzhou Road

department: Life Science

country: Taiwan

institute: National Taiwan Normal University

summary:
Oxidative stress and celllular apoptosis of intestinal epithelial tissues relies on the environments from drinking different waters. In the rat intestinal epithelium, the toxic materials or antioxidant materials may affect the genes expression of oxidative stress and apoptosis through the oral intake ofa waters or agents. The up- or down-regulation in the antioxidant genes and apoptosis-related genes may represent the internal microenvironments in the intestine. Therefore, we used intestinal epithelium from rats drinking different waters to test the several genes expression.
We used microarrays to detail the global programme of gene expression underlying damage or protection effect and identified distinct classes of up-regulated or down-regulated genes during drinking different waters test in this process.

overall_design: Rat intestinal epithelium treated with water restriction for 12 hr, tap water, DSW1200 water or selenium water drinking for three days respectiveily

first: C

middle: C


title: Genome-wide analysis of gene expression between a mouse genetic model of glioma (Mut6) and an origin cell type (neural stem cells)

status: Public on Dec 08 2014

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

country: USA

institute: OSU

summary: Comparison of gene expression (mRNA) between neurosphere cultures from Mut6 gliomas and wt SVZ neural stem cells (NSCs)

overall_design: Total RNA obtained from neurosphere cultures from Mut6 gliomas was compared to those from wt SVZ

first: Sheila

last: Alcantara

first: Chang-Hyuk

last: Kwon

first: Brett

last: Whittemore

first: Luis

last: Parada


title: Expression data from 15 month old rat brain subjected to fructose fetal programming

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

country: Denmark

institute: University of Copenhagen

summary:
Fructose has recently been observed to affect brain metabolism and cognitive function in adults. However, possible fetal programming of brain metabolism induced by gestational fructose has not been examined. We evaluated mitochondrial function in the brain of aging (15 month) male offspring of Fischer F344 rat dams fed either a high-fructose diet (50% energy from fructose) or a matched control diet during early life (gestation and lactation).
We used microarrays to detail changes in global programme of gene expression in offspring brains from rats subjected to either a control diet or a high fructose diet during gestation and lactation

overall_design: Pregnant Fischer F344 rats were put on a control diet or a high fructose diet during gestation and lactation starting day 1 of gestation. Offspring was weaned at day 20 after birth and put on a standard chow diet until 15 months of age when they were sacrificed and brain samples obtained followed by RNA extraction and hybridization on Affymetrix microarrays

first: Lea

last: Larsen

first: Laura

middle: K

last: Orstrup

first: Lillian

last: Hansen

first: Niels

last: Grunnet

first: Bjørn

last: Quistorff


title: Gene co-expression network analysis of myostatin regulation at three different mouse developmental timepoints

status: Public on Nov 11 2014

city: Ames

first: James

middle: M

last: Reecy

state: IA

address: 2255 Kildee Hall, Iowa State University

department: Animal Science

institute: Iowa State University

summary:
Myostatin (Mstn) knockout mice exhibit large increases in skeletal muscle mass. However, relatively few of the genes that mediate or modify MSTN effects are known. In this study, we performed co-expression network analysis using whole transcriptome microarray data from Mstn-null and wild-type mice to identify genes involved in important biological processes and pathways related to skeletal muscle and adipose development.Genes differentially expressed between wild-type and Mstn-null mice were identified at 13.5 d.p.c. and 35 days after birth (d35) and further analyzed for shared DNA motifs using DREME.
Known and novel transcription factor binding sites involved in MSTN signal transduction were enriched in differentially expressed genes. The use of regulatory impact factor (RIF), phenotypic impact factor (PIF), and differential hubbing analyses with the partical correlation and information theory (PCIT) co-expression analysis methods identified both known and potentially novel regulators of muscle development. These results provide new details of how MSTN may mediate transcriptional regulation as well as insight into novel regulators of MSTN signal transduction that merit further study regarding their physiological roles in muscle and adipose development.

overall_design: Mstn-null and wild-type mice were reared, sacrificed by CO2 asphyxiation (embryonic timepoints) or cervical dislocation (d35), and tissues were collected from whole embryos (13.5 d.p.c.), hindquarters (17.5 d.p.c.), or pectoralis muscle (d35). After collection, muscles were flash-frozen in liquid nitrogen as previously described  in Steelman et al., 2006. FASEB J. Mar;20(3):580-2. For microarray analysis, 10 μg of RNA from each of three individual animals was pooled to give five pools (N=15, total number of arrays=5) for each genotype/timepoint combination.

first: Xuerong

last: Yang

middle: E

last: Koltes

first: Carissa

last: Park

first: Daiwen

last: Chen


title: Botulinum neurotoxin A induced expression profiles in Raw264.7 cells

status: Public on Dec 20 2014

city: Osong

first: Na-Ri

last: Shin

state: Chungbuk

address: 187 Osongsangmyung2-ro

department: High-risk Pathogen Research

institute: Korea Centers for Disease Control and Prevention, Korea National Institute of Health

summary:
Botulinum neurotoxin type A (BoNT/A) is one of the most potent protein toxins, which makes it a possible biological weapon and therapeutic.
Using microarray analysis we performed global transcriptional profiling of RAW264.7 cells, a murine alveolar macrophage cell line.

overall_design: Time dependent expression profiles after treatment of 1nM or 5nM Botulinum neurotoxin A

first: Yun

last: Kim

first: Nari


title: DNA Methylation and RNA Expression Profiles in Lung Adenocarcinomas [RNA Expression]

first: Zhifu

last: Sun

state: MN

first: Aaron

last: Mansfield

first: Liang

last: Wang

first: Julie

last: Cunningham

first: Jin

last: Jen

first: Chris

middle: P

last: Kolbert

first: Ping


title: EWS-Fli and LNC regulated genes in comparison to GFP samples

status: Public on Nov 01 2014

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

summary: RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries),  EWS-FLI1 (4 libraries), or lnc277 (7 libraries) was isolated with TRIzol (Invitrogen).  Each sample was DNase treated and further purified on an RNeasy  Mini column (Qiagen) before quality analysis on an Agilent 2100 Bioanalyzer.  For each sample, 100-150ng of RNA was synthesized into cDNA, sheared on  a Covaris ultrasonicator, and amplified using the NuGen Encore Complete kit  (NuGen) to produce strand-specific and rRNA-depleted libraries. Samples were  multiplexed (4/lane) for 2x100bp paired-end sequencing on an Illumina HiSeq  2000

first: Alejandro

last: Sweet-Cordero


title: Discovery and Comparative Transcriptome Profiling of Dairy Goat MicroRNAs from Dry Period and Peak Lactation Mammary Gland Tissues

city: Yangling

first: zhuanjian

last: li

address: xinong road

country: China

institute: Northwest A&F University

summary: In this study, two small RNA libraries were constructed using dry period and peak lactation dairy goat mammary gland tissues and sequenced by the Illumina Solexa high-throughput sequencing system. A total of 346 conserved and 95 novel miRNAs were identified in the dairy goat. The expression of miRNAs was confirmed by qRT-PCR in nine tissues and the mammary gland during development cycles. In addition, several candidate miRNAs that may be involved in mammary gland development and lactation were found by the comparison of miRNA expression profiles among different tissue and developmental stages of the mammary gland. This study provides the identification and profile of miRNAs related to the biology of the mammary gland in the dairy goat. The identification of these miRNAs could contribute to understanding the molecular mechanisms of lactation physiology and the development of the mammary gland in the dairy goat.

overall_design: Examination of 2 different developmental stages of the mammary gland

first: Zhuanjian

last: Li

first: Hong


title: Methylation analysis of choroid plexus tumors

first: Diana

last: Merino

address: 686 Bay St.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: The methylation status of a cohort of choroid plexus tumors was examined and unsupervised hierarchical clustering was used to identify molecular distinct clusters of samples.

overall_design: Tumor DNA was extracted from 36 frozen choroid plexus tumors (15 CPCs, 16 choroid plexus papillomas, 5 achoroid plexus papillomas). Samples were bisulfite converted and analyzed on Illumina 450K Infinium methylation bead arrays. No replicates were used

first: Adam

last: Shlien

first: Anita

last: Villani

first: Malgorzata

last: Pienkowska

first: Stephen

last: Mack

first: Vijay

last: Ramaswamy

first: David

last: Shih

first: Ruth

last: Tatevossian

first: Ana

last: Novokmet

first: Sanaa

last: Choufani

first: Rina

last: Dvir

first: Myran

last: Ben-Arush

first: Brent

last: Harris

first: Eugene

middle: I

last: Hwang

first: Rishi

middle: R

last: Lulla

first: Stefan

last: Pfister

first: Maria

middle: l

last: Achatz

first: Nada

last: Jabado

first: Jonathan

last: Finlay

first: Rosanna

last: Weksberg

first: Cynthia

last: Hawkins

first: Michael

middle: D

last: Taylor

first: Uri

last: Tabori

middle: W

last: Ellison

first: Richard

last: Gilbertson

last: Malkin


title: hnRNPK knock down in Ewing cell line

first: Dedeepya

last: Vaka

summary: Ewing sarcoma is a highly aggressive tumor characterized by a translocation between members of the FET family of RNA binding proteins and one of several ETS transcription factors, with the most common translocation being EWS-FLI1. EWS-FLI1 leads to changes in gene expression through mechanisms that are not completely understood. We performed RNA sequencing analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify novel target genes. This analysis identified lnc277 as a previously uncharacterized long non-coding RNA upregulated by EWS-FLI1 in pMPCs. Inhibiting the expression of lnc277 diminished the ability of Ewing sarcoma cell lines to proliferate and form colonies in soft agar whereas inhibiting lnc277 had no effect on other cell types tested. By analyzing gene expression after shRNA knockdown, we found that both EWS-FLI1 and lnc277 repressed many more genes that they induced and that a significant fraction of EWS-FLI1 repressed targets were also repressed by lnc277. Analysis of primary human Ewing sarcoma RNA sequencing data further supports a role for lnc277 in mediating gene repression. We identified hnRNPK as an RNA binding protein that interacts directly with lnc277. We found a significant overlap in the genes repressed by hnRNPK and those repressed by both EWS-FLI1 and lnc277, suggesting that hnRNPK participates in lnc277 mediated gene repression. Thus, lnc277 is a previously uncharacterized long non-coding RNA downstream of EWS-FLI1 that facilitates the development of Ewing sarcoma via the repression of target genes. Our studies identify a novel mechanism of oncogenesis downstream of a chromosomal translocation and underscore the importance of lncRNA-mediated gene repression as a mechanism of EWS-FLI1 transcriptional regulation.

overall_design: A673 Ewing cells expressing an shRNA targeting hnRNPK or control were subjected to paired end RNA sequencing and compared to shGFP control.

first: Michelle

last: Marques Howarth

first: Alejandro

last: Sweet-Cordero


title: Generation and Characterization of an immortalized human mesenchymal stromal cell line model  [Illumina DNA methylation]

first: Leonardo

middle: A.

last: Meza-Zepeda

overall_design: Comparison of DNA methylation patterns of iMSC#3 and hMSC primary cultures

first: Magne

last: Skårn

first: Paul

last: Noordhuis

first: Marjan

last: Veuger

first: Meng

middle: Y

last: Wang

first: Stine

middle: H

last: Kresse

first: Eivind

middle: V

last: Egeland

first: Francesca

last: Micci

first: Heidi

last: Namløs

first: Anne-Mari

last: Håkelien

first: Solveig

last: Olafsrud

first: Susanne

last: Lorenz

first: Guttorm

last: Haraldsen

first: Gunnar

last: Kvalheim

first: Ola

last: Myklebost


title: MicroRNA Expression Profiles identify genes of apoptosis, anabolism and catabolism in patients with Intervertebral Disc Degeneration different from Spinal Trauma

status: Public on Dec 29 2014

city: Xi'an

last: Zhao

address: Xiwu Road

department: Orthopaedic Surgery

institute: Xi'an Jiaotong University

summary: The pathogenesis of IDD is still unclear, and microRNA has been reported playing an important role in occurrence and development of many diseases. But to date, the research about the role of microRNA in IDD is rare.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: To compare the differences of microRNA expression profiles between intervertebral disc degeneration (IDD) and spinal trauma, and to screen the changed microRNA for further pathogenesis research of IDD.The microRNAs expression of 3 degenerative intervertebral disc (IVD) specimens and 3 traumatic intervertebral disc specimens were individually analyzed using microarray technique

first: Bo

first: Qiang

last: Yu


title: Chromatin-dependent regulation of the RNA polymerases II and III activity throughout the transcription cycle

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

summary: We have developed a new genome-wide protocol for nascent transcription analysis at high resolution in the yeast Saccharomyces cerevisiae. This protocol is based in run-on labeling of nascent RNA with a biotinylated precursor. We call it BioGRO for biotin-based genomic run-on.

overall_design: 7 samples total; 5 BioGRO samples (4 mutants and 1 WT); and 2 ChIP-chip samples (Rpb3 IP and its input).

first: Antonio

last: Jordán-Pla

last: Perez-Ortán

first: Lola

last: de-Miguel

first: Sebastián

last: Chávez

first: Vicent

last: Pelechano


title: Global host transcriptional profiles following Mycobacterium avium subsp. paratuberculosis infection in mice

status: Public on Oct 31 2014

city: Seoul

first: Min-Kyoung

last: Shin

address: 1, Gwanak ro, Gwanak gu

institute: Seoul National University

summary: We focused on how Mycobacterium avium subsp. paratuberculosis influences the subsequent host response to investigate the host immunopathology accompanying the host anti-mycobacterial immune response during Mycobacterium avium subsp. paratuberculosis infection in spleen of mice.

overall_design: We analyzed altered transcription in the spleen of mice at 3, 6, and 12 weeks following Mycobacterium avium subsp. paratuberculosis infection.

first: Shin

last: Min-Kyoung

first: Yoo

last: Han Sang


title: Effect of 6 weeks of high fat diet on gene expression in human subcutaneous adipose tissue of twins

status: Public on Oct 10 2014

city: Nuthetal

first: Martin

middle: A

last: Osterhoff

address: Arthur-Scheunert-Allee 155

department: Clinical Nutrition

institute: German Institute of Human Nutrition

summary: Food composition of diets strongly determines the risk of experiencing inflammation related metabolic or cardiovascular disease. We aimed to determine the extent of inheritance of inflammatory responses to isocaloric changes in food composition as a prerequisite of personalized dietary recommendations in human twins.

overall_design: 34 monozygotic and 12 dizygotic healthy pairs of twins recruited from a twin register (HealthTwiSt, Berlin, Germany) or by public advertisements completed the study. All participants received a low fat diet (55% carbohydrate, 30% fat, 15% protein) for 6 weeks (CID1=LF thereafter) followed by 6 weeks of a high fat diet (40% carbohydrate, 45% fat, 15% protein) (CID2=HF1 after 1 week, and CID3=HF6 after 6 weeks of high fat diet). Both diets were isocloric. A physical examination, anthropometry (DEXA scan), and medical history were obtained and 12h fasted blood was collected at 8:00 a.m. on study days. Resting energy expenditure (indirect calorimetry) and physical activity level (PAL) was assessed by questionnaire and dietary food records for five days were completed before and during the study. Fasting blood levels of cytokines, chemokines and adipokines were determined by ELISA. The participants were instructed, trained and accompanied by an experienced nutritionist. Individual energy requirements were calculated based on participants REE and PAL. Participants received a list of 94 foods items and individual daily meal plans on how to exchange and combine these foods and energy intake was adjusted according to body weight if needed. Seven days before the LF, HF1 and HF6 examination days 70 percent of the food was provided to ensure standardized dietary patterns for all participants. A biopsy of periumbilical abdominal subcutaneous adipose tissue was performed on each CID for gene expression analysis.

first: Andreas

middle: F

last: Pfeiffer

first: Michael

last: Kruse

first: Alexander

middle: S

last: Mosig


title: Gene profiling of P. falciparum and A. gambiae: an assessment of parasite maturation and of host response to infection

status: Public on Oct 01 2014

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary:
Simultaneous analysis of Plasmodium falciparum and Anopheles gambiae gene expression: an assessment of parasite maturation and of the mosquito response to infection.
Malaria is probably the most lethal and most prevalent parasitic disease in the world, causing more than one million deaths per year. In spite of intensive research, no vaccine exists and good vaccine candidates are still a necessity. Plasmodium sporozoites from mosquito midguts are not as infective as those from salivary glands, presenting a different type of motility which is presumably associated with their invasive capacity. It is assumed that these differences are due to maturation of sporozoites, which happens either in the salivary glands or somewhere along the way from the midgut to the glands. Indeed, the invasion of the salivary gland is considered to be an essential step for malaria transmission to the host and it is known to causes expression of multiple genes in the parasite and activation of some immune-response genes in the insect. Here we compared the gene expression profile of P. falciparum parasites from midgut and salivary glands in order to search for genes involved in parasite maturation; on the assumption that any differentially expressed genes found under this condition could be potentially related to the higher infectivity of the salivary gland derived sporozoites and therefore would be potentially good vaccine candidates. Also, because very little is known about mosquito genes involved in the response to Plasmodium, we compared the gene expression profile of infected and uninfected midguts and salivary glands.  Our results demonstrate that, upon infection, at least 13 genes are differentially expressed in the mosquito midgut and 43 in the salivary gland. Gene ontology enrichment analysis showed that among other things, in mosquito salivary glands, infection causes multiple genes related to chitin metabolism to be differentially expressed. Also and more importantly, at least 54 genes were differentially expressed in P. falciparum from salivary glands in comparison to midgut (19 down-regulated and 35 up-regulated). Last, we show for the first time that P. falciparum causes multiple genes in the salivary gland to be regulated and that some of those genes could be potentially beneficial to the parasite.

sample_organism:
Plasmodium falciparum
Anopheles gambiae

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Gene expression profile of P. falciparum parasites from midgut and salivary glands; gene expression profile of mosquitos' infected vs. uninfected midguts and salivary glands.

last: Waisberg

first: Alvaro

last: Molina-Cruz

first: Steven

last: Porcella

first: Louis

last: Miller

first: Susan

middle: K

last: Pierce

first: Carolina

last: Barillas-Mury


title: MicroRNA Profiles and Differential Expression in Normal Skin Samples from the Uyghur and Han Populations in Xinjiang

status: Public on Oct 16 2014

city: Urumqi

first: Xiu-Juan

last: Wu

state: Xinjiang

address: 91 Tianchi Road

department: Department of Dermatology

institute: People’s Hospital of Xinjiang, Uygur Autonomous Region

summary: This study investigated the microRNA (miRNA) expression profiles in normal skin samples from the Uyghur and Han populations in Xinjiang and analyzed the miRNA expression differences between the two populations. The 7th generation miRCURYTM LNA Array kit (containing 3100 probes) was used to detect the miRNA expression in 10 Uyghur and 10 Han normal skin samples and to compare the miRNA expression differences between the two populations. A total of 2041 miRNAs were present in normal Uyghur and Han skin samples. In particular, 2039 miRNAs were present in normal Uyghur skin, of which 295 miRNAs were expressed more than 2.0-fold and 1461 miRNAs were expressed less than 0.5-fold of the average value. Moreover, 2041 miRNAs were expressed in normal Han skin, of which 279 miRNAs were expressed more than 2.0-fold and 1414 miRNAs were expressed less than 0.5-fold of the average value. Considering both populations together, 228 miRNAs were expressed more than 2.0-fold and 1353 miRNAs were expressed less than 0.5-fold of the average value. In the Han population, 76 miRNAs were upregulated and 171 miRNAs were downregulated compared with the Uyghur population (p < 0.05). A total of 13 miRNAs had fold changes that were greater than 10, and 9 miRNAs had fold changes that were between 3 and 10. The upregulated miRNAs were miR-1, miR-106b-5p, miR-1915-5p, miR-200c-3p, miR-221-3p, miR-222-3p, miR-3139, miR-4802-3p, miR-507, miR-541-3p, miR-876-3p, and kshv-miR-K12-2-5p. The downregulated miRNAs were miR-1207-3p, miR-206, miR-2116-5p, miR-3667-5p, miR-374b-3p, miR-4423-5p, miR-4450, miR-4468, miR-542-3p, miR-548ao-3p, and miR-553. Specific miRNA expression patterns were observed in normal Uyghur and Han skin samples, and the miRNA expression patterns differed significantly between the two populations.

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: All 20 normal skin tissues were obtained from surgical specimens immediately after resection from Jan 2012 to Sep 2013 in the Department of Dermatology, People’s Hospital of the Xinjiang Uyghur Autonomous Region, China. The samples were flash frozen in liquid nitrogen and stored at -180℃ until RNA extraction.  RNA labeling and hybridization were completed by KangChen Bio-tech Inc. (Shanghai, China) according to the manufacturer's instructions. Briefly, Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0) which contains probes for 3100 mature miRNA. Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner. Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

first: Xiong-Ming

last: Pu


title: Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups

first: Diana

middle: M

last: Merino

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

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

overall_design: Refer to individual Series

first: Adam

last: Shlien

first: Anita

last: Villani

first: Margaret

last: Pienkowska

first: Stephen

middle: C

last: Mack

first: Vijay

last: Ramaswamy

first: David

middle: J

last: Shih

first: Ruth

last: Tatevossian

first: Ana

last: Novokmet

first: Sanaa

last: Choufani

first: Rina

last: Dvir

first: Myran

last: Ben-Arush

first: Brent

middle: T

last: Harris

first: Eugene

last: Hwang

first: Rishi

last: Lulla

first: Stefan

last: Pfister

first: Maria

last: Achatz

first: Nada

last: Jabado

first: Jonathan

middle: L

last: Finlay

first: Rosanna

last: Weksberg

first: Cynthia

last: Hawkins

last: Taylor

first: Uri

last: Tabori

last: Ellison

first: Richard

last: Gilbertson

last: Malkin


title: Root transcriptome comparison between grapevines Cabernet Sauvignon, 140 Ruggeri and K51-40 (+/- salt stress)

status: Public on Sep 30 2014

city: Urrbrae

first: Sam

last: Henderson

state: South Australia

address: Hartley Grove

country: Australia

institute: University of Adeladie

summary: Salt tolerance in grapevine is associated with the exclusion of chloride ions (Cl–) from the shoot. The rate-limiting step for this process has been identified as the passage of Cl– between the root symplast and the xylem apoplast through membrane integral proteins. To identify candidate genes for these proteins we used a custom microarray to compare the root transcriptomes of three grapevine varieties (Vitis spp.) that differ in their capacity to exclude Cl– from shoots. When challenged with 50 mM Cl– there were transcriptional responses that differed across the rootstocks 140 Ruggeri (a good Cl– excluder) and K51-40 (a poor Cl– excluder), and Cabernet Sauvignon (an intermediate Cl– excluder and Vitis vinifera control). The magnitude of these salt-induced changes correlated with the amount of Cl– accumulated in shoots. Abiotic-stress responsive transcripts (e.g. heat shock proteins) were induced in 140 Ruggeri. Respiratory transcripts were repressed in Cabernet Sauvignon. Expression of hypersensitive response and ROS scavenging transcripts were altered in the sensitive K51-40. Despite these differences, no obvious candidate Cl– transporters were identified from the salt treatment. In contrast, under control conditions where differences in shoot Cl– exclusion between rootstocks were still significant, we identified a number of genes encoding putative ion channels including VvSLAH3, VvALMT1, and possible regulators of these proteins such as VvSnRK2.6 and calcium dependent protein kinases (CDPK) as being differentially expressed between rootstocks. Members of the low affinity nitrate transporter (NRT1), and chloride channel (CLC) families were also identified. We propose these as useful candidates for further study within breeding programs aimed at improving plant salt tolerance in grapevine and other crops.

sample_organism: Vitis cinerea var. helleri x Vitis rupestris

overall_design: Comparative: genotype versus genotype (control); and control (0 mM Cl) versus salt (50 mM Cl). Rooted leaves were grown as described by Gong et. al. (2010) (Journal of Experimental Botany). After 2 weeks of hydroponic growth, plants were exposed to 0 mM or 50 mM chloride stress for 4 days. Three biological replicates were used for 140 Ruggeri. Four biological replicates were used for Cabernet Sauvignon. Four biological replicates were used for K51-40. Each biological replicate consisted of total roots from four individual plants pooled together.

first: Ute

last: Baumann

first: Matthew

last: Gilliham


title: Ectoderm and mesenchyme gene expression in the developing mouse face

city: Aurora

first: Joan

last: Hooper

state: CO

department: Cell and Developmental Biology

institute: University of Colorado School of Medicine

summary:
This investigation provides a robust multi-dimensional compendium of gene expression data relevant to mouse facial development. It profiles the transcriptome ofectoderm and mesenchyme from the three facial prominences in a time series encompassing their growth and fusion. Analysis of the dataset identified more than 8000 differentially expressed genes comprising dramatically different ectoderm and mesenchyme programs. The mesenchyme programs included many genes identified in earlier analyses as well hundreds of genes not previously implicated in craniofacial development. The ectoderm programs included over a thousand genes that highlight epithelial structure, cell-cell interactions and signaling.
The dataset includes 45 .cel files, DABG probability and RMA log2 expression values for each probeset, and statistics for 9457 probesets representing 8575 genes.

overall_design: 45 total samples, with 15 conditions sampling three ages (E10.5, E11.5, E12.5), three facial prominences (mandibular, maxillary and fronto-nasal) and two tissue layers (ectoderm or mesenchyme), with 3 biological replicates per condition. Differential expression was determined after median filter for variance with three-way ANOVA, Benjamini-Hochberg multiple testing correction

middle: E

first: Weiguo

last: Feng

first: Trevor

last: Williams


title: Expression data from E10.5 mouse embryo heads

status: Public on Dec 30 2014

city: New York,

first: Shugaku

last: Takeda

state: NY

department: Human Oncology & Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Taspase1 (threonine aspartase) is a 50kD endopeptidase of the family of proteases possessing an Asparaginase_2 homology domain. Loss of Taspase1 function in Taspase1 null (Tasp1-/-) mice led to craniofacial malformations. We used microarrays to determine which genes are affected by loss of Taspase1 during craniofacial development.

overall_design: E10.5 mouse embryo head (prosencephalon and mesencephalon) were dissected for RNA extraction and hybridization on Affymetrix microarrays. To identify which genes are regulated by Taspase1 during development, we used RNA from three wild type and three Taspase1 KO embryos.


title: Expression data from citrus embryogenic calli with engineered carotenoid accumulation

status: Public on Sep 23 2014

city: Wuhan

first: hongbo

last: Cao

address: No.1,Shizishan Street · Hongshan District

department: Key Laboratory of Horticultural Plant Biology

institute: Huazhong Agricultural University

summary:
Carotenoids have been demonstrated to be indispensable plant secondary metabolites that are involved in photosynthesis, antioxidation, and phytohormone biosynthesis. Carotenoids are likely involved in other biological functions that have yet to be discovered.
In this study, we utilized genomic expression investigation to gain a deep insight into the carotenoid-related biological processes in the citrus calli overexpressing CrtB.

sample_organism:
Citrus x paradisi
Citrus x tangelo

overall_design: Abortive ovule embryogenic calli from four citrus genotypes were used in this study. They were derived from Star Ruby grapefruit (C. paradise Macf.), Marsh grapefruit (C. paradise Macf.), and Sunburst mandarin [Citrus reticulata Blanco × (C. paradisi Macf. × C. reticulata)], designated as RB, M, and SBT, respectively. Engineered cell models (ECMs) were established by over-expressing 35S::CrtB (tp–rbcS–CrtB) [CrtB protein, phytoene synthase from Erwinia herbicola (now known as Pantoea agglomerans), containing a Pea rbcS transit peptide] in citrus embryogenic calli. Twenty-day-old calli were harvested and used for RNA extraction and hybridization on Affymetrix microarrays.

first: Hongbo

first: Xiuxin

last: Deng


title: Modulated electro-hyperthermia related mRNA expression profile development in HT-29 xenograft mouse model.

status: Public on Sep 01 2014

city: Budapest

first: Andras

last: Furedi

state: HU

address: Magyar tudosok krt 2

department: Molecular Life Sciences

country: Hungary

institute: HUN-REN RCNS

summary:
HT-29 human colorectal adenocarcinoma cells were xenografted into both femoral regions of 6 to 8-week old Balb/c (nu/nu) mice. After 18 days electromagnetic heat treatment was performed.
We used microarray technology to identify the heat treatment releted gene expression alterations using human tumor xenograft mouse model.

overall_design: Fresh frozen tissue sections were performed from the xenograft and tumorous regions were microdissected for total RNA isolation and gene expression analysis purposes.

first: Tibor

last: Krenács

first: Nóra

last: Meggyesházi

first: Sándor

last: Spisák


title: Feasibility and Interpretation of the Genome-wide Infinium Methylation Data Derived from Ligated Formalin Fixed Paraffin Embedded Paired Tumor and Normal Tissue.

status: Public on Oct 23 2014

city: Chicago

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

summary: Formalin-fixed paraffin-embedded (FFPE) samples are a highly desirable resource for epigenetic studies, but there is no suitable platform to assay genome-wide methylation in these widely available resources. Recently, Thirwell et al. (2010) have reported a modified ligation-based DNA repair protocol to prepare FFPE DNA for the Infinium methylation assay. In this study, we have tested the accuracy of methylation data obtained with this modification by comparing paired fresh-frozen (FF) and FFPE colon tissue from colorectal cancer patients. We report locus-specific correlation and concordance of tumor-specific differentially-methylated loci (DML), both of which were not previously assessed.

overall_design: We used Illumina’s Infinium Methylation 27 K chip for 12 pairs of FF and 12 pairs of FFPE tissue from tumor and surrounding healthy tissue from the resected colon of the same individual after repairing the FFPE DNA using Thirwell’s modified protocol.

first: Farzana

last: Jasmine

first: Ronald

last: Rahaman

first: Shantanu

last: Roy

first: Maruf

last: Raza

first: Rupash

last: Paul

last: Rakibuz-Zaman

first: Rachelle

last: Paul-Brutus

first: Charlotte

last: Dodsworth

first: Mohammed

last: Kamal

first: Habibul

last: Ahsan

middle: G


title: pMPC EF vs control 3seq

first: Dedeepya

last: Vaka

overall_design: RNA from primary human bone marrow derived mesenchymal cells either control or with inducible expression of  EWS-FLI1 for 13 days was used to prepare PolyA selected cDNA libraries.

first: Michelle

last: Marques Howarth

first: Alejandro

last: Sweet-Cordero