title: A circadian gene expression atlas in mammals assayed by microarray

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

summary: To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional “rush hours” preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy.

overall_design: 288 samples total covering 12 different tissues, with no replicates. Each tissue sampled every 2 hours for 2 days (24 samples per tissue).

first: Ray

last: Zhang

middle: F

first: Heather

middle: I

last: Ballance

first: Michael

middle: E

last: Hughes

first: John

last: Hogenesch


title: The side population of human pancreatic cancer expresses cancer stem cell-associated genes

status: Public on Sep 26 2014

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Purpose: To explore the side population (SP) in pancreatic ductal adenocarcinoma (PDAC) for its gene expression profile and its association to cancer stem cells (CSC) and to evaluate the value of genes from its gene signature on patient survival.

Experimental design: Side and main population (MP) cells were isolated from 11 human PDAC resection specimens using fluorescence-activated cell sorting (FACS) after Hoechst incubation. Total RNA was extracted for whole-genome analysis. A gene signature for the purified SP (pSP; depleted from immune/endothelial CD45+/CD31+ cells) was developed and validated with the nCounter system on expression data of 78 primary PDAC using Cox regression analyses for disease-free and overall survival.

Results: An SP was identified in all PDAC samples. Whole-genome expression profiling of pSP revealed upregulation of genes related to therapy-resistance and of CSC-associated genes and pathways. A pSP signature of 32 up- or downregulated genes was capable of discriminating SP from MP in an independent set of 10 PDAC samples, and some contributing genes had a prognostic value in a separate series of 78 patients who underwent surgery for PDAC.

Conclusion: Pancreatic cancer contains an SP with chemo-resistant and CSC-associated molecular characteristics. Genes from a newly defined pSP gene signature are related to survival of patients who undergo surgical resection for pancreatic cancer, and might therefore represent potential therapeutic targets.

overall_design: Microarray analysis was performed on SP and MP samples from 11 different human PDAC samples.

first: Anke

last: Van den broeck

first: Hugo

last: Vankelecom

first: Wouter

last: Van Delm

first: Lies

last: Gremeaux

first: Jasper

last: Wouters

first: Joke

last: Allemeersch

first: Olivier

last: Govaere

first: Tania

last: Roskams

first: Baki

last: Topal


title: Strength training with suppressed testosterone level

status: Public on Sep 30 2014

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

country: Denmark

institute: Bispebjerg Hospital

summary: Human subjects were randomized for treatment with a GnRH-analogue, Goserelin, which suppresses endogenous testosterone or placebo for 12 weeks. Strength training was performed during the last 8 weeks. The suppression of testosterone resulted in an attenuation of the normal muscle adaptation to strength training (increased muscle mass and strength). To identify molecular signals involved in the response to testosterone levels, biopsies were obtained 4 hours after the last training session and gene expression compared with Affymetrix 3' microarrays. This timepoint should capture goserelin effect on both constitutive expression, training induced changes as well as acute exercise induced (4 hours) differences in mRNA levels.

overall_design: Four subject from the placebo group and five subjects from the Goserelin group were compared. Total RNA from vastus lateralis mmuscle biopsies were purified and analyzed on Affymetrix HG-U133 Plus 2.0 arrays.

first: Thue

last: Kvorning


title: Standard of hygiene and immune adaptation in newborn infants [15 rehybridized/batch correction samples]

status: Public on Sep 25 2014

city: Turku

first: Essi

last: Laajala

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology

summary: The prevalence of immune-mediated diseases such as allergies and autoimmune diseases is on the rise in the developed world. Microbial exposure is known to modulate the risk for these diseases. In order to explore differences in the gene expression patterns induced in utero in infants born in contrasting standards of living and hygiene, we collected umbilical cord blood RNA samples from full-term newborn infants born with normal vaginal delivery in Finland (modern society), Estonia (rapidly developing society) and the Republic of Karelia, Russia (poor economical conditions). Transcriptomic profiles were analyzed using whole genome microarrays including gender, gestational age, birth month and HLA allele genotype as confounding variables in the analysis. The data revealed that the whole blood transcriptome of Finnish and Estonian neonates differ from their Karelian counterparts. Samples from Karelian infants had an increase in transcripts associated with LPS induction and bacterial sepsis observed in 1-year-old infants in earlier studies. The results suggest exposure to toll like receptor (TLR) ligands and a more matured immune response in infants born in Petrozavodsk compared to the Finnish and Estonian infants. These results further support the concept of a conspicuous plasticity in the developing immune system: the environmental factors that play a role in the susceptibility/protection towards immune-mediated diseases begin to shape the neonatal immunity already in utero and direct the maturation of both the adaptive and the innate immune responses in accordance with the surrounding microbial milieu.

overall_design: These 15 rehybridized samples were only utilized in the batch correction and excluded from any further analysis steps. Umbilical cord blood was drawn into Tempus Blood RNA tubes (Applied Biosystems) from children born at the maternity unit of Jorvi hospital (Espoo, Finland; n=4), maternity units of Tartu and Põlva (Estonia; n=4), or two maternity departments in Petrozavodsk (capital of the Republic of Karelia, Russian Federation; n=7) according to the manufacturer´s protocol and then stored in -70 °C until analyzed.

first: Henna

last: Kallionpää

first: Viveka

last: Öling

first: Taina

last: Härkönen

first: Vallo

last: Tillmann

first: Natalya

last: Dorshakova

first: Jorma

last: Ilonen

first: Harri

last: Lähdesmäki

first: Mikael

last: Knip

first: Riitta

last: Lahesmaa


title: Expression data from in vitro decidualized human uterine fibroblast cells (HuF cells) with or without NOTCH1 silencing

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

country: China

institute: South China Agricultural University

summary:
Decidualization is a critical process for embryo implatation during which uterine stromal fibroblasts are transformed into large, epithelioid-like decidual cell. NOTCH1 is recepotor of Notch signaling that plays important roles for cell-cell communication, which involves gene regulatory mechanisms that control multiple cellular differentiation processes during embryonic and adult life.
Here we silenced NOTCH1 by shRNA in HuF cells and studied how it affects decidualization

overall_design: HuF cells were cultured, transfected with NOTCH1 shRNA via a lentivirus system, following by a in vitro induced decidualization by EPC cocktail (36 nM estradiol-17β and 1 μM medroxyprogesterone acetate, and 0.1 mM dbcAMP) for 6 days. RNAs were extracted then hybridized on Affymetrix microarrays. There are four experimental conditions: 1) transfected with empty plasmid; 2) transfected with hNOTCH1 lentiviral-shRNA plasmid; 3) transfected with empty plasmid and treated with EPC cocktail; and 4) hNOTCH1 lentiviral-shRNA plasmid with subsequent treatment of EPC cocktail. HuF cells from two different patients were used in each group (HuF86P4 & HuF88P4).

first: Renwei

first: Asgerally

middle: T

last: Fazleabas


title: Standard of hygiene and immune adaptation in newborn infants [113 cord blood RNA samples]

overall_design: Umbilical cord blood was drawn into Tempus Blood RNA tubes (Applied Biosystems) from children born between January and May 2010 at the maternity unit of Jorvi hospital (Espoo, Finland; n=48), maternity units of Tartu and Põlva (Estonia; n=25), or two maternity departments in Petrozavodsk (capital of the Republic of Karelia, Russian Federation; n=40) according to the manufacturer´s protocol and then stored in −70 °C until analyzed. All newborn infants were full-term (>36 gestational weeks) and born vaginally. 113 cord blood RNA samples were analyzed with Affymetrix U219 gene array. Gender, pregnancy week, month of birth and HLA risk class were included as confounding factors in the analysis model.


title: High-throughput  expression profiling of OCI-Ly3 cell line upon treatment with a panel of 14 known drugs.

city: New York

first: Mukesh

last: Bansal

state: NY

address: 1130 St. Nicholas Ave. Room 908

country: USA

institute: Columbia University

summary:
Analysis of Diffuse Large B-Cell Lymphoma (DLBCL) OCI-LY3 cell line treated with 14 different known drugs at 2 different concentrations and profiled at 6, 12 and 24 hrs after treatment.
We used this gene expression data to design a challenge where participants were required to develop methods to predict activity of compound pairs using gene expression profile following single compound treatment, drug response curve of each compound and baseline genetic profile of OCI-LY3 cell line.

overall_design: GeneChip HT HG-U219 array plates were used to analyze gene expression changes induced by treatment with 14 drug compounds in OCI-Ly3 cells at 6, 12 and 24h. 3 replicates were analyxed for each drug/time combination. Vehicle (DMSO)-treated control samples were used for comparison with each replicate. Altogether 282 samples were analyzed in this study.

first: Michela

last: Mattioli

first: Charles

last: Karan

first: Andrea

last: Califano

first: Gustavo

last: Stolovitzky


title: Global quadriceps skeletal muscle transcript data from fasted male BXD strains on chow or high fat diet

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

summary:
Transcript data from quadriceps skeletal muscle from fasted-state male BXD strains on Quadriceps, Chow or Quadriceps, High fat diet
We used microarrays to compare the skeletal muscle expression differences across males in the BXD strain family and across two diverse diets

overall_design: 29-week-old male mice were fasted overnight (6pm-9am), anesthetized under isoflurane, and perfused, then quadriceps were snap-frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Evan

middle: G

last: Williams


title: Tissue- and Aging-specific DNA-Methylation Patterns are erased in Mesenchymal Stromal Cells derived from Induced Pluripotent Stem Cells. [Methylation profiling]

status: Public on Sep 24 2014

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Standardization of mesenchymal stromal cells (MSCs) remains a major obstacle in regenerative medicine. Starting material and culture expansion affect cell preparations and render comparison between studies difficult. In contrast, induced pluripotent stem cells (iPSCs) assimilate towards a ground-state and may therefore give rise to more standardized cell preparations. We reprogrammed bone marrow MSCs into iPSCs which were subsequently re-differentiated towards MSCs. These iPS-MSCs revealed similar morphology, immunophenotype, in vitro differentiation potential, and gene expression profiles as primary MSCs. DNA methylation (DNAm) profiles of iPSCs maintained some donor-specific characteristics, whereas tissue-specific, senescence-associated, and age-related DNAm patterns were erased during reprogramming. iPS-MSCs reacquired senescence-associated DNAm during culture expansion but they remained rejuvenated with regard to age-related DNAm. Overall, iPS-MSCs and MSCs are similar in function but differ in their epigenetic makeup.

overall_design: 12 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Joana

last: Frobel

first: Hatim

last: Hemeda

first: Michael

last: Lenz

first: Bernd

last: Denecke

first: Tomo

last: Šarić

first: Martin

last: Zenke


title: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells [twins]

city: Oviedo

first: Agustin

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

summary: In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone posttranslational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal stem cells obtained from individuals aged 2 to 92 identified 18735 hypermethylated and 45407 hypomethylated CpG sites associated with aging. As in differentiated cells, hypermethylated sequences were enriched in chromatin repressive marks. Most importantly, hypomethylated CpG sites were strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type-independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs and differentiated cells, providing a new avenue for the identification of DNA methylation changes over time. DNA methylation profiling of genetically identical individuals showed that both the tendency of DNA methylation changes and scedasticity depended on non-genetic as well as genetic factors. Our results indicate that the dynamics of DNA methylation during aging depend on a complex mixture of factors that include the DNA sequence, cell type and chromatin context involved, and that, depending on the locus, the changes can be modulated by genetic and/or external factors.

overall_design: Total DNA isolated by standard procedures from peripheral blood of 24 samples obtained from 12 pairs of MZ twins aged 21 to 66.

last: Bayón

first: Rocío

last: Urdinguio

first: Estela

last: Toraño

first: Maria

last: Garcia

first: Antonella

last: Carella

first: Sandra

last: Petrus-Reurer

first: Cecilia

last: Ferrero

first: Pablo

last: Martinez-Camblor

first: Isabel

last: Cubillo

first: Javier

last: García-Castro

first: Jesús

last: Delgado-Calle

first: Flor

middle: M

last: Perez-Campo

first: José

middle: A

last: Riancho

first: Clara

last: Bueno

last: Menendez

first: Anouk

last: Mentink

first: Katia

last: Mareschi

first: Fabian

last: Claire

first: Corrado

last: Fagnani

first: Emanuela

last: Medda

first: Virgilia

last: Toccaceli

first: Sonia

last: Brescianini

first: Sebastián

last: Moran

first: Manel

last: Esteller

first: Alexandra

last: Stolzing

first: Jan

last: de Boer

first: Lorenza

last: Nisticò

last: Stazi

first: Mario

last: Fraga


title: Standard of hygiene and immune adaptation in newborn infants

first: Essi

last: Laajala

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

overall_design: The series of 113 samples (GSE53471) was used in all data analysis steps and the series of 15 (GSE53472) rehybridized samples was only utilized for batch correction. Refer to individual Series for details.


title: Expression analysis of Reh cells after transfection with constitutively active variants of IRF5 (IRF5-4D) and/or constitutively active IKKβ(EE)

city: Berlin

first: Karl

last: Koechert

address: Robert-Roessle-Str. 10

institute: Max-Delbrueck-Centre for Molecular Medicine

summary: Genome-wide gene expression analysis of Reh cells following transfection with constitutively active IRF5-4D, constitutively active IKKβ(EE), or both in combination.

overall_design: Affymetrix U133 Plus 2.0 oligonucleotide arrays were hybridized to determine the gene expression profile of acute lymphoblastic leukemia-derived Reh cells following transfection with i) control constructs, ii), a constitutively active variant of IRF5 (IRF5-4D), iii) a constitutively active variant of the IkB kinase β (IKKβ(EE)), or iv) IRF5-4D in combination with IKKβ(EE). All hybridizations were done in biological duplicates.

first: S

last: Kreher

first: M

last: Janz

first: K

last: Köchert

last: Hummel

last: Mathas


title: Tissue- and Aging-specific DNA-Methylation Patterns are erased in Mesenchymal Stromal Cells derived from Induced Pluripotent Stem Cells.

first: Wolfgang

last: Wagner

type:
Expression profiling by array
Methylation profiling by array

overall_design: Refer to individual Series


title: The effect of XUESAITONG on gene expression profile after focal cerebral ischemia in rats

status: Public on Sep 23 2014

city: Hangzhou

first: Xiaohui

last: Fan

state: Zhejiang

address: Yuhangtang 866

institute: Zhejiang Univ.

summary:
Xuesaitong injection (XST), a standardized patent Chinese medicine of Panax notoginseng roots (Sanqi in Chinese), has long been used for effective prevention and treatment of stroke in China. However, the mechanisms underlying its effects against ischemic stroke are still poorly understood. In this study, we focused on the polypharmacology of XST against ischemic stroke with a XST-regulated stroke network analysis.
Male Sprague Dawley rat model of MCAO and reperfusion were administered XST for 7 days while the control group was not treated.

overall_design:
Three conditions were compared with three replicates each. These are:
(1) sham; (2) model (3) XST treatment. Whole genome microarray analysis was performed using Affymetrix rat Genome 230 2.0 chips.

first: Linli

last: WANG

first: Zheng

last: Li

first: Xiaoping

last: Zhao

first: Jihong

last: Yang


title: DNA Methylation in Hodgkin's and non-Hodgkin's lymphoma

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. Overall, our study provides a framework for model studies of HL and NHL pathologies.

overall_design: Examination of DNA Methylation in L1236, L428, Reh and Namalwa cell lines.

first: Amine

last: Bouhlel

first: Stephan

last: Köcher

first: Björn

last: Lamprecht

first: Peter

middle: N

last: Cockerill

first: Constanze

last: Bonifer


title: ALDH-positive MCF-7 cells

city: Setagaya-ku

first: Yasunari

last: Kanda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of Pharmacology

country: Japan

institute: National Institute of Health Sciences

summary:
We used an Aldefluor assay system to study the signaling pathways that regulate the frequency and maintenance of ALDH-positive cell population in MCF-7 cells as a CSC model.
Through microarray analysis, we investigated a possible receptor that increases the proportion of the ALDH-positive cell population in MCF-7 cells.

overall_design: MCF-7 were stained with Aldefluor and ALDH-positive cells were sorted using flow cytometry. Gene expression profiles of ALDH+ cells were compared with ALDH- cells.

first: Naoya

last: Hirata

first: Shigeru

last: Yamada

first: Yuko

last: Sekino


title: Expression data of macrophage phenotypes treated with interleukin-1alpha

status: Public on Sep 21 2014

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

institute: Kumamoto University

summary: Identification of the difference in responsiveness to interleukin-1alpha between M1 and M2 macrophage phenotypes.

overall_design: To identify the difference in responsiveness to interleukin-1alpha between M1 and M2 macrophage phenotypes, we performed micorarray analysis of gene expression in two phenotypes with or without the treatment of interleukin-1alpha.


title: Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia.

status: Public on Sep 18 2014

city: London

first: Leonard

middle: C

last: Schalkwyk

address: De Crespigny Park

department: IOP-SGDP

country: United Kingdom

institute: King's College London

summary:
Background: Schizophrenia is a severe neuropsychiatric disorder that is hypothesized to result from disturbances in early brain development, and there is mounting evidence to support a role for developmentally-regulated epigenetic variation in the molecular etiology of the disorder. Here, we describe a systematic study of schizophrenia-associated methylomic variation in the adult brain and its relationship to changes in DNA methylation across human fetal brain development.
Results: We profile methylomic variation in matched prefrontal cortex and cerebellum brain tissue from schizophrenia patients and controls, identifying disease-associated differential DNA methylation at multiple loci, particularly in the prefrontal cortex, and confirming these differences in an independent set of adult brain samples. Our data reveal discrete modules of co-methylated loci associated with schizophrenia that are enriched for genes involved in neurodevelopmental processes and include loci implicated by genetic studies of the disorder. Methylomic data from human fetal cortex samples, spanning 23 to 184 days post-conception, indicates that disease-associated differentially methylated positions are significantly enriched for loci at which DNA methylation is dynamically altered during human fetal brain development.
Conclusions: Our data support the hypothesis that schizophrenia has an important early neurodevelopmental component, and suggest that epigenetic mechanisms may mediate these effects.

overall_design: Prefrontal cortex (PFC) and cerebellum samples were obtained from 46 brains archived in the London Brain Bank for Neurodegenerative Disorders (LBBND). Of these 22 were schizophrenia cases, ands of the cases 12 were male.

first: Ruth

last: Pidsley

first: Joana

last: Viana

first: Eilis

last: Hannon

first: Helen

last: Spiers

first: Claire

last: Troakes

first: Safa

last: Al-Saraj

first: Naguib

last: Mechawar

first: Gustavo

last: Turecki

first: Nicholas

last: Bray

first: Jonathan

last: Mill


title: Gene expression profile of CD4+ T-cells restimulated by anti-CD3 and anti-ICOS compared to anti-CD3 alone

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

summary: Engagement of the ICOS receptor represents a key event in a process that culminates in Bcl6 expression and acquisition of the TFH and TFR phenotype. To better understand the essentials of ICOS-mediated signaling pathway, we profiled the changes in gene expression elicited after co-ligation of ICOS and CD3 compared with CD3 ligation alone.

overall_design: Naïve CD4+ T-cells were purified from single cell suspensions of B6 spleen and stimulated with anti-CD3 and anti-CD28 for 2d followed by resting overnight before 20 min of incubation with anti-CD3 and/or anti-ICOS and cross-linking with goat anti-hamster Ab for 8h. RNA was prepared, amplified, labeled and hybridized to Mouse Gene 1.0 ST Array (Affymetrix), in quadruplicates for anti-CD3 ligation and duplicates for anti-CD3/ anti-ICOS co-ligation.

first: Harvey

last: Cantor


title: Transcriptome and Epigenome analysis of fetal and adult liver samples

city: Tartu

first: Lili

last: Milani

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

type: Methylation profiling by genome tiling array


title: Epigenome analysis of fetal and adult liver samples

summary: Genome wide DNA methylation analysis of 96 adult and 14 fetal liver samples

overall_design: The study includes 110 individuals, 14 fetal and 96 adult samples, no replicates. Liver samples from 14 fetuses were obtained at gestational week 8-12. Adult liver samples were collected from 52 organ donors who had met accidental death and 44 liver samples from patients undergoing liver resection due to malignant tumors, most commonly from patients with metastatic colon cancers. Liver biopsies from these patients were collected from 'healthy' tissue that showed no visible pathological changes compared to the adjacent tumor.

first: Magnus

last: Ingelman-Sundberg


title: Inflammatory profile of NOD.Batf3-/- islets

status: Public on Sep 29 2014

city: St. Louis

first: Javier

last: Carrero

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: NOD mice deficient in the transcription factor Batf3 never develop diabetes. The goal of this study was to determine if NOD.Batf3-/- mice islets had any inflammatory signature associated with type 1 diabetes. Islets of Langerhans were isolated from NOD, NOD.Batf3-/-, and NOD.Rag1-/- and then compared to determine inflammatory gene profiles. At 6 and 8 weeks of age, NOD.Batf3-/- islets had an absence of inflammatory gene expression and were almost identical to uninflamed NOD.Rag1-/- islets.  This work shows that absence of the Batf3 transcription factor is sufficient to prevent all the inflammatory sequelae of autoimmune diabetes.

overall_design: RNA was isolated from the pancreatic islets of Langerhans of 27 experimental mice. Mice were aged either 6 or 8 weeks. Three genotypes were tested: NOD, NOD.Rag1-/-, and NOD.Batf3-/-. There were 3-6 biological replicates per condition. All mice were female. All data was normalized using RMA in Arraystar.

first: Stephen

last: Ferris


title: Epigenome analysis of the human visceral adipose tissue

status: Public on Sep 17 2014

city: Groningen

first: Lude

last: Franke

state: Please Select

address: Hanzeplein 1

department: Genetics

country: Netherlands

institute: UMCG

summary: Visceral adipose tissue samples were obtained from severely obese individuals that underwent bariatric surgery. The goal of this study was to identify tissue specific methylation QTLs. Whole-transcriptome subcutaneous adipose tissue methylation levels were determined in 71  individuals with a BMI >35 kg/m2.

overall_design: Bisulphite converted DNA from the 71 visceral adipose tissue samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.


title: Intratumor heterogeneity of gene expression profiles in early stage non-small cell lung cancer (NSCLC)

city: Heidelberg

first: Michael

last: Meister

state: Select One

address: Roentgenstr. 1

department: STF

institute: Thoraxklinik-Heidelberg

summary:
Gene expression profiling of NSCLC tissues let to the establishment of several prognostic, predictive gene signatures with little overlap.
To study factors introducing variability into gene expression microarray studies we compared interpatient (patient-to-patient) and intrapatient (tumor sub-sample) variations in gene expression profiles in stage I and II NSCLC tissues. We identified 128 probe sets which showed variable intratumoral expression

overall_design: Four different sites (A,B,C,D) of individual primary tumors and matched distant normal lung tissue (N) from 20 patients were used to establish gene expression patterns captured by Affymetrix HG-U133 Plus 2.0 arrays (n = 100).

first: Anton

last: Belousov

first: Elizabeth

last: Xu

first: Phillip

last: Schnabel

first: Arne

last: Warth

first: Hans

last: Hoffmann

first: Hendrik

last: Dienemann

first: Julia

last: Riedlinger

first: Heinz

last: Bodenmueller

first: Werner

last: Zolg

first: Felix

middle: J

last: Herth

first: Thomas

last: Muley


title: Epigenome analysis of the human muscle

summary: Muscle tissue samples were obtained from severely obese individuals that underwent bariatric surgery. The goal of this study was to identify tissue specific methylation QTLs. Whole-transcriptome subcutaneous adipose tissue methylation levels were determined in 60 individuals with a BMI >35 kg/m2.

overall_design: Bisulphite converted DNA from the 60 muscle samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.


title: Epigenome analysis of the human subqutaneous adipose tissue

summary: Subcutaneous adipose tissue samples were obtained from severely obese individuals that underwent bariatric surgery. The goal of this study was to identify tissue specific methylation QTLs. Whole-transcriptome subcutaneous adipose tissue methylation levels were determined in 71 individuals with a BMI >35 kg/m2.

overall_design: Bisulphite converted DNA from the 71 subcutaneous adipose tissue samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.


title: Expression data from advanced stage of murine pancreatic ductal adenocarcinoma (PDAC) and control pancreas

status: Public on Sep 16 2014

city: Marseille

first: Ghislain

last: BIDAUT

address: 27 Bd Leï Roure

department: Bioinformatics

country: France

institute: Centre de Recherche en Cancérologie de Marseille

summary: We used microarrays to detail the global gene expression signature of PDAC and to identify distinct up- and down-regulated transcripts in these tumors compared to control pancreas. We also established from this dataset the metabolic signature of PDAC in order to define new metabolic therapeutic target for pancreatic cancer.

overall_design: PDAC were removed at an advanced stage of tumorigenesis in 7 to 10-weeks old mice with Mixed genetic background : B6CBAF1 x C57BL/6 x 129/Sv x FVB/n. Apparent signs used to determined the time of sacrifice : weight loss, lower activity and dull coat.

first: Sophie

last: Vasseur

first: Fabienne

last: Guillaumond

first: Ezequiel

last: Calvo

last: Bidaut


title: Epigenome analysis of the human liver

first: Lude

last: Franke

summary: Liver tissue samples were obtained from severely obese individuals that underwent bariatric surgery. The goal of this study was to identify tissue specific methylation QTLs. Whole-transcriptome subcutaneous adipose tissue methylation levels were determined in 67 individuals with a BMI >35 kg/m2.

overall_design: Bisulphite converted DNA from the 67 Liver samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Irradiated feeder cells and Y-27632

status: Public on Sep 15 2014

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary: Expression data from this experiment is part of a larger project aimed at defining the individual effects and synergistic effects of ROCK inhibitor Y-27632 and conditioned media from irradiated J2 cells when applied to epithelial cells. This data set consists of four individual samples, each of which are total RNA collected from human foreskin keratinocyte cells, either grown in F medium (control), treated with Y-27632, grown in conditioned medium (as described in associated publication), or both treatments.

overall_design: Four total RNA samples from HFK cells grown in F media (control) or treated with either Y-27632, conditioned media from irradiated J2 cells, or both.

first: Geeta

last: Upadhyay


title: Expression analysis in hipsc-derived neurons exposed to botulinum neurotoxin A subtype 1 and a type A atoxic derivative

city: Madison

first: Jacob

last: Scherf

state: WI

address: 1550 Linden Dr

department: Bacteriology

institute: University of Wisconsin-Madison

summary:
Transcriptome analysis of RNA extracted from human induced pluripotent stem cell (hipsc)-derived neurons exposed to botulinum neurotoxin type A1 (BoNT/A1) and an atoxic derivative, BoNT/A ad.
Botulinum neurotoxin type A1 (BoNT/A1) is a potent protein toxin responsible for the potentially fatal human illness botulism.  Despite this, the long-lasting flaccid muscle paralysis caused by BoNT/A has led to its rise as a powerful and versatile bio-pharmaceutical.  The flaccid paralysis is due to specific cleavage of SNAREs by BoNTs inside neurons.  However, potential effects of BoNTs on intoxicated neurons besides the cleavage of SNAREs have not been studied in detail. In this study we investigated by microarray analysis the effects of BoNT/A and a catalytically inactive derivative (BoNT/A ad) on the transcriptome of human induced pluripotent stem cell (hiPSC)-derived neurons at 2 days and 2 weeks after exposure.  While there were only minor changes in expression levels at 2 days post exposure, at 2 weeks post exposure 492 genes were differentially expressed more than 2-fold in BoNT/A1-exposed cells when compared to non-exposed populations, and 682 genes were differentially expressed in BoNT/A ad-exposed cells.  The vast majority of genes were similarly regulated in BoNT/A1 and BoNT/A ad-exposed neurons, and the few genes differentially regulated between BoNT/A1 and BoNT/A ad-exposed neurons were regulated less than 3.5 fold.  These data indicate a similar response of neurons to BoNT/A1 and BoNT/A ad exposure.  The most highly regulated genes in cells exposed to either BoNT/A1 or BoNT/A ad are involved in neurite outgrowth and calcium channel sensitization.

overall_design: 18 samples were used for this project: 6 populations were exposed to BoNT/A1, 6 to BoNT/A ad, and 6 were non-exposed.  All exposures lasted for 48h, at which point 3 samples of each exposure group were harvested (2d condition), and the remaining 3 samples were grown for an additional 12d (2wk condition). Analysis was performed using the Affymetrix HG U133 Plus 2.0 array, and data was extracted using the Affymetrix Expression Console v 1.2.0.20 software

first: Xiaoyang

middle: S

last: Hu

first: William

middle: H

last: Tepp

first: Konstantin

last: Ichtchenko

first: Eric

last: Johnson

first: Sabine

last: Pellett


title: Expression profile for overproduction of DosP

city: State College

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary:
Persister cells are a sub-population of all bacterial cultures which exhibit a non-inheritable, multi-drug tolerance when subjected to lethal antibiotic challenge.  These persisters arise as a result of metabolic dormancy, and can resume growth subsequent to antibiotic challenge, leading to recalcitrance of bacterial infections.
Overproduction of DosP, an oxygen sensing protein with phosphodiesterase activity, increases bacterial persistence.  Here we performed a microarray to determine the expression profile induced by DosP as a means to elucidate mechanisms of persister cell formation.

overall_design: dosP was overexpressed in Escherichia coli K-12 BW25113 and compared to the empty vector.

first: Kwan

middle: W

last: Brian

first: Osbourne

middle: O

last: Devon

first: Wood

middle: K

last: Thomas


title: Leukocytes methylome of melanoma patients with and without CDKN2A mutations

city: Sao Paulo

first: Érica Sara

middle: Souza de

last: Araújo

state: Sao Paulo

address: Taguá st, 440

department: CIPE - Internacional Center for Research and Training

country: Brazil

institute: A. C. Camargo Cancer Center

summary: We investigated if the presence of germline CDKN2A mutations or the occurrence of cutaneous melanoma could induce constitutive genome-wide DNA methylation changes. We analyzed the leukocytes’ methylomes of eight patients carrying CDKN2A mutations, eight sporadic melanoma patients  and compared them with healthy controls (n=8). The genome-wide DNA methylation profiling was obtained using the Infinium HumanMethylation450 BeadChip platform (Illumina).

overall_design: Illumina 450k methylation array profiling performed on melanoma patients carrying germline CDKN2A mutations (n=8), sporadic melanoma patients (n=8) and health individuals (n=8)

first: Fabio

last: Marchi

first: Tatiane

last: Rodrigues

first: Henrique

last: Vieira

first: Hellen

last: Kuasne

first: Maria Isabel

last: Achatz

first: Luciana

middle: F

last: Moredo

first: Bianca

last: Sá

first: João

middle: P

last: Duprat

first: Helena Paula

last: Brentani

first: Carla

last: Rosenberg

first: Dirce

last: Carraro

first: Ana Cristina

middle: V

last: Krepischi


title: Cell population kinetics of collagen scaffolds in ex vivo oral wound repair

status: Public on Sep 11 2014

city: Ann Arbor

first: William

last: Giannobile

state: Michigan

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

summary:
This study sought to provide a novel ex vivo model for analyzing healing kinetics and gene expression of primary human gingival fibroblasts (hGF) within collagen scaffolds.
Sponge type and gel type scaffolds with and without platelet-derived growth factor-BB (PDGF) were assessed in an hGF containing matrix.

overall_design: Four samples were analyzed; gel w/ and w/o PDGF and scaffold w/ and w/o PDGF

first: Christoph

last: Gorlach

first: Hermann

last: Agis


title: Plasticity of transcriptional regulation under antibiotic stress

city: Szeged

first: Balazs

last: Bogos

address: Temesvári krt. 62-64

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre of the Hungarian Academy of Sciences

summary:
Evolution of antibiotic resistance in microbes is frequently achieved by acquisition of spontaneous mutations during antimicrobial therapy. Here we demonstrate that inactivation of a central regulator of iron homeostasis (fur) facilitates laboratory evolution of ciprofloxacin resistance in Escherichia coli. To decipher the underlying molecular mechanisms, we first performed a global transcriptome analysis and demonstrated a substantial reorganization of the Fur regulon in response to antibiotic treatment. We hypothesized that the impact of Fur on evolvability under antibiotic pressure is due to the elevated intracellular concentration of free iron and the consequent enhancement of oxidative damage-induced mutagenesis. In agreement with expectations, over-expression of iron storage proteins, inhibition of iron transport, or anaerobic conditions drastically suppressed the evolution of resistance, while inhibition of the SOS response-mediated mutagenesis had no such effect in fur deficient population. In sum, our work revealed the central role of iron metabolism in de novo evolution of antibiotic resistance, a pattern that could influence the development of novel antimicrobial strategies.
We used microarrays to identify genotype specific transcriptional changes under severe DNA damaging conditions (antibiotic ciprofloxacin).

overall_design: We treated Escherichia coli cells with a highly toxic level of ciprofloxacin (gyrase inhibitor) for RNA extraction and hybridization on Affymetrix microarrays. We planned to find genotype specific transcriptional responses using WT control (BW25113) and fur-knockout mutant (selected from the KEIO collection) strains during antibiotic treatments. For each treatment type we used two biological replicates.

first: Orsolya

last: Méhi

first: Balázs

first: Bálint

last: Csörgő

first: Ákos

last: Nyerges

first: Ferenc

last: Pál

last: Papp

first: Csaba


title: Multi-Omic Integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in type 2 diabetic obesity [Methylation data]

status: Public on Sep 10 2014

city: Wellington

first: David

last: Rowlands

state: Wellington

address: 63 Wallace St Mt Cook

department: Institute of Food, Nutrition and Human Health

country: New Zealand

institute: Massey University

summary: Analysis of skeletal muscle DNA methylation from type 2 diabetic volunteers before and after 16 weeks of chronic exercise training (two groups, one undergoing aerobic excercise and the other resistance training exercise)

overall_design: A biopsy was collected from the right Vastus Lateralis under local anaesthesia andGenomic DNA was extracted from 5-10 mg muscle, Bisulphite conversion (Illumina) was checked using methylation specific PCR. 4 μl of bisulphite-converted DNA was used for hybridization on Infinium Human Methylation 450 BeadChip (Illumina)

first: Mamta

last: Giri


status: Public on Sep 13 2014

city: Exeter

first: Jonathan

last: Mill

address: RD&E NHS Foundation, Trust Campus, Barrack Rd

department: Medical School, RILD Building

institute: University of Exeter

summary: Background: Schizophrenia is a severe neuropsychiatric disorder that is hypothesized to result from disturbances in early brain development, and there is mounting evidence to support a role for developmentally-regulated epigenetic variation in the molecular etiology of the disorder. Here, we describe a systematic study of schizophrenia-associated methylomic variation in the adult brain and its relationship to changes in DNA methylation across human fetal brain development.      Results: We profile methylomic variation in matched prefrontal cortex and cerebellum brain tissue from schizophrenia patients and controls, identifying disease-associated differential DNA methylation at multiple loci, particularly in the prefrontal cortex, and confirming these differences in an independent set of adult brain samples. Our data reveal discrete modules of co-methylated loci associated with schizophrenia that are enriched for genes involved in neurodevelopmental processes and include loci implicated by genetic studies of the disorder. Methylomic data from human fetal cortex samples, spanning 23 to 184 days post-conception, indicates that disease-associated differentially methylated positions are significantly enriched for loci at which DNA methylation is dynamically altered during human fetal brain development.     Conclusions: Our data support the hypothesis that schizophrenia has an important early neurodevelopmental component, and suggest that epigenetic mechanisms may mediate these effects.

overall_design: 33 post-mortem brain (prefrontal cortex) samples (18 schizophrenia cases and 15 controls)  were obtained from Douglas Bell-Canada Brain Bank (DBCBB), Montreal, Canada. Bisulfite converted DNA from these samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.0.

first: Ruth

last: Pidsley

first: Joana

last: Viana

first: Eilis

last: Hannon

first: Helen

last: Spiers

first: Claire

last: Troakes

first: Safa

last: Al-Saraj

first: Naguib

last: Mechawar

first: Gustavo

last: Turecki

first: Leonard

last: Schalkwyk

first: Nicholas

last: Bray


title: Multi-Omic Integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in type 2 diabetic obesity

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: mRNA expression data from whole trachea dissected from either wild-type mice or Scnn1b-Tg mice at post-natal days 0, 3, 10, and 42

city: Chapel Hill

first: Hong

last: Dang

state: NC

address: 7027 Thurston-Bowles Bldg. CB#7248

department: CF Center

institute: UNC Chapel Hill

summary:
Scnn1b-Tg mice overexpress the beta subunit of the epithelial sodium channel (Scnn1b) in airway Club cells.  The general phenotype of these mice is described in three published manuscripts (Mall et al. 2004, Nature Medicine, 10(5):487-93;  Mall et al. 2008, Am J Respir Crit Care Med. 177(7):730-42; Livraghi-Butrico et al. 2012, Physiol. Genomics 44(8):470-84; and Livraghi-Butrico et al. 2012, Mucosal Immunology 5(4):397-408). Briefly, overexpression of the Scnn1b transgene in airway Club cells leads to hyperabsorption of sodium from the airway surface liquid, which causes airway surface liquid and mucus dehydration, resulting in reduced mucus clearance and airway mucus obstruction.  The data provided here represents mRNA expression data from dissected whole trachea (distal and proximal ends were cut 3-4 cartilage rings below the larynx and just above the bifurcation, respectively) from male WT and Scnn1b-Tg littermates (C57Bl/6N Tac background) at 4 time points [postnatal days (PND) 0, 3, 10, and 42].  Histologically, PND 0 trachea are normal, a tracheal mucus plug/obstruction develops around PND 3 and typically recedes to the intrapulmonary airways after PND 10, and the trachea is again histologically normal by PND 42.  The data from the WT mice provides a global look at mRNA post-natal developmental changes, while the data from the Scnn1b-Tg line provides mRNA data that allows differential gene expression due to airway mucus obstruction to be queried.
The data presented for the trachea is part of a larger body of work evaluating gene expression in whole lung, trachea, and purified macrophages.

overall_design: 24 Total tracheal samples were analyzed;  three from each timepoint.  In our manuscript, we were most interested in changes between WT and Scnn1b-Tg mice, however, the data can also be used to evaluate changes in gene expression across time (PND 0, 3, 10, and 42).  It should be noted that a significant difference in RNA expression quality parameters was noted for the 10 day trachea data.

first: Yogesh

last: Saini

first: Alessandra

last: Livraghi-Butrico

first: Wanda

last: O'Neal

first: Richard

last: Boucher


title: Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration [left lobe only]

summary:
Scnn1b-Tg mice overexpress the beta subunit of the epithelial sodium channel (Scnn1b) in airway Club cells.  The general phenotype of these mice is described in three published manuscripts (Mall et al. 2004, Nature Medicine, 10(5):487-93;  Mall et al. 2008, Am J Respir Crit Care Med. 177(7):730-42; Livraghi-Butrico et al. 2012, Physiol. Genomics 44(8):470-84;  and Livraghi-Butrico et al. 2012, Mucosal Immunology 5(4):397-408). Briefly, overexpression of the Scnn1b transgene in airway Club cells leads to hyperabsorption of sodium from the airway surface liquid, which causes airway surface liquid and mucus dehydration, resulting in reduced mucus clearance and airway mucus obstruction.  The data provided here represents mRNA expression data from disseccted whole lung from male WT and Scnn1b-transgenic littermates (C57Bl/6NTac background) at 4 time points [postnatal days (PND) 0, 3, 10, and 42].  Histologically, PND 0 lungs are normal, at PND 3 the intrapulmonary airways exhibit transient and spotty Club cell necrosis, and by PND 10 airway mucus obstruction is evident in the proximal portion of the intrapulmonary main stem bronchus. At PND 42, Scnn1b-Tg lungs are charactyerized by chronic low level inflammation, with activated macrophages, neutrophilia, eosinophilia and increased incidence of bronchus-associated lymphoid tissue.  The data from the WT mice provides a global look at mRNA post-natal developmental changes, while the data from the Scnn1b-transgenic line allows differential gene expression due to airway surface liquid dehydration and mucus obstruction to be queried.
The data presented for the lung is part of a larger body of work evaluating gene expression in lung (left lobe only), trachea, and purified macrophages (from bronchoalveolar lavage fluid).

overall_design: 24 Total lung (left lobe only) samples were analyzed;  three from each timepoint for each genotype (wild type and Scnn1b-transgenic).  In our manuscript, we were most interested in changes between WT and Scnn1b-Tg mice, however, the data can also be used to evaluate changes in gene expression across time (PND 0, 3, 10, and 42).  We generated the following pairwise comparisons: Scnn1b-Tg vs WT mice for each PND time point; Intra-strain comparison between PND 3, or 10, or 42 vs PND 0.


title: mRNA expression data from either wild-type mice or Scnn1b-transgenic mice at post-natal days 0, 3, 10, and 42


title: Colorectal cancer classification based on gene expression is not associated with FOLFIRI response

city: Madrid

first: Manuel

last: Hidalgo

state: Madrid

address: C/Melchor Fernandez Almagro 3

department: Clinical Research Programme

institute: CNIO

summary: Sadanandam et al. (2013) recently published a study based on the use of microarray data to classify colorectal cancer (CRC) samples. The classification claimed to have strong clinical implications, as reflected in the paper title: “A colorectal cancer classification system that associates cellular phenotype and responses to therapy”. They defined five subtypes: (i) inflammatory; (ii) goblet-like; (iii) enterocyte; (iv) transit-amplifying; and (v) stem-like. Based on drug sensitivity data from 21 patients, they also reported that the so-called stem-like subtype show differential sensitivity to FOLFIRI. This is the key result in their publication, since it implies a direct relation between the subtype and the choice of CRC therapy (i.e. FOLFIRI response). However, our analyses using the same drug sensitivity data and results from additional patients showed that the CRC classification reported by Sadanandam et al. is not predictive of FOLFIRI response.

overall_design: We used the classification algorithm to obtain CRC subtypes from our samples. Then we tested the subtype-drug response association performing a retrospective study.

first: Raquel

last: Martínez-García

first: Alfonso

last: Valencia


title: A cancer associated fibroblasts (CAFs) specific gene signature in high grade serous ovarian cancer

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Ovarian cancer is the most lethal malignancy in the United States. In the year 2012, there will be an estimated 22,280 new cases and 15,500 deaths from ovarian cancer in the country (Siegel et al., 2012). While studies on ovarian cancer pathogenesis were mainly focused on the epithelial component of the tumor, understanding in the role of cancer associated fibroblasts (CAFs) in ovarian cancer progression is limited. We hypothesized that comparing the gene expression profiles of different components from laser capture microdissected ovarian tissue will allow us to identify an ovarian CAFs specific gene signature which accounts for the supportive role of CAFs in ovarian cancer progression. In this study, gene expression profiling was completed for 31 cancer stroma samples and 32 samples of epithelial component from high grade serous ovarian cancer patients. 8 microdissected normal ovarian stroma and 6 normal human ovarian surface epithelium (HOSE) samples were also included in the study. By comparing the expression data from cancer stroma against that from normal stroma, cancer cells and HOSE, we identified a set of differential expressed genes in ovarian CAFs which showed correlation with cancer patient survival. Further study on these genes can reveal their roles in ovarian cancer progression and pathogenesis. Ultimately, ovarian CAFs specified genes identified in this study may aid in the classification and enhancement of patient outcome.

overall_design: Transcriptome profiling analyses were performed on 31 laser microdissected cancer associated stroma samples, 32 epithelial tumor samples from high grade serous ovarian cancer patients, 8 microdissected normal ovarian stroma samples and 6 ovarian surface epthelium (HOSE) samples using the Affymetrix human genome U133 Plus 2.0 microarray.

first: Micheal

last: Birrer

first: Samuel

last: Mok

first: Kwong-Kwok

last: Wong


title: DNA methylation from severely obese samples in liver, muscle, visceral adipose tissue and  subcutaneous adipose samples

first: Lude

last: Franke


title: Global DNA methylation alterations reveal multiple pathways in the initiation and progression of colorectal cancer

status: Public on Sep 08 2014

city: Seattle

first: Yanxin

last: Luo

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Genetic and epigenetic alterations are a fundamental aspect of colorectal cancer formation.  There is considerable heterogeneity between colorectal cancers regarding the mutations and methylated genes they carry, and this heterogeneity may arise early in the polyp-cancer sequence.  However, our understanding of the epigenetic alterations and gene mutations in colon adenomas and their relation to colorectal cancer is incomplete.  Thus, we have assessed the methylome in normal colon mucosa, tubular adenomas, and colorectal adenocarcinomas and have determined the relationship of these findings between adenomas and cancer in the colon. Genome-wide alterations in DNA methylation were found in the normal colon mucosa adjacent to colorectal cancer, tubular adenomas, and colorectal cancer.  Three subgroups of CRCs and two subgroups of adenomas were identified on the basis of their DNA methylation patterns.  The adenomas separated into a high-frequency methylation class (Adenoma-H) and a low-frequency methylation class.  The adenoma-H polyps have a methylated DNA signature similar to non-CIMP CRCs, whereas those of the Adenoma-L class have a similar methylation pattern to normal colon mucosa.  The CpGs that account for these signatures are located in intragenic/intergenic regions, which suggests that these two groups of adenomas arise from different stem cell populations.

overall_design:
We conducted genome-wide array-based studies and comprehensive data analyses of aberrantly methylated loci in 41 normal colon samples, 42 colon adenomas, and 64 colorectal cancers.

Supplementary file 'GSE48684_Matrix_signal_intensities_1.txt.gz': includes the unmethylated and methylated signal intensities from Samples GSM1183439-GSM1183561.
Supplementary file 'GSE48684_Matrix_signal_intensities_2.txt.gz': includes the unmethylated and methylated signal intensities from Samples GSM1235135-GSM1235158.

first: William

last: Grady


title: Profile the RNA composition of cell-free saliva and salivary exosomes

city: los angeles

first: jieping

last: yang

address: 10833 Le Conte Ave

institute: UCLA

summary: We compared the transcriptomic content of salivary exosomes vs. whole saliva via microarray (Affymetrix HU133 plus 2.0).

overall_design: Unstimulated saliva samples and derived exosome-like microvesicles were obtained from 3 healthy volunteers and processed for RNA isolation and microarray analysis.

first: Jieping

last: Yang

first: David


title: Airway Basal Cells of Healthy Smokers Express an Embryonic Stem Cell Signature Relevant to Lung Cancer

status: Public on Sep 09 2014

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Activation of the human embryonic stem cell (hESC)-signature genes has been observed in various epithelial cancers. In this study, we found that the hESC signature is selectively induced in the airway basal stem/progenitor cell population of healthy smokers (BC-S), with a pat-tern similar to that activated in all major types of human lung cancer. We further identified a subset of 6 BC-S hESC genes, whose coherent overexpression in lung AdCa was associated with reduced lung function, poorer differentiation grade, more advanced tumor stage, remarkably shorter survival and higher frequency of TP53 mutations. BC-S shared with hESC and a consid-erable subset of lung carcinomas a common TP53 inactivation molecular pattern which strongly correlated with the BC-S hESC gene expression. These data provide transcriptome-based evi-dence that smoking-induced reprogramming of airway BC towards the hESC-like phenotype might represent a common early molecular event in the development of aggressive lung carci-nomas in humans.

overall_design: Affymetrix arrays were used to assess gene expression data of genes realted to human embryonic stem cells in large airway epithelium obtained by fiberoptic bronchoscopy of 21 healthy non-smokers and 31 healthy smokers, basal cell culture of large airway epithelium obtained by fiberoptic bronchoscopy of 4 healthy nonsmokers and 4 healthy smokers and cells obtained from tumor tissues of 4 individuals.

first: Renat

last: Shaykhiev

first: Rui

last: Wang

first: Rachel

last: Zwick

first: Neil

middle: R

last: Hackett

first: Ronald

last: Leung

first: Malcolm

middle: A

last: Moore

first: Camelia

last: Sima

first: IonWa

last: Chao

first: Robert

last: Downey

middle: G

first: Jacqueline

last: Salit

last: Crystal


title: MicroRNAs control the apoptotic threshold in primed pluripotent stem cells through regulation of BIM

status: Public on Sep 06 2014

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

institute: NHLI Imperial College London

summary:
Mammalian primed pluripotent stem cells have been shown to be highly susceptible to cell death stimuli due to their low apoptotic threshold, but how this threshold is regulated remains largely unknown. Here we identify miRNA-mediated regulation as a key mechanism controlling apoptosis in the post-implantation epiblast. Moreover, we find that three miRNA families, miR-20, miR-92 and miR-302, control the mitochondrial apoptotic machinery by fine-tuning the levels of expression of the pro-apoptotic protein BIM. These families therefore represent an essential buffer needed to maintain cell survival in stem cells that are not only primed for differentiation but also for cell death.
We used microarrays to compare the gene expression profiles of Dicer conditional Epiblast stem cells (Dicer fx/fx EpiSCs, used as control cells) and Dicer deleted epiblast stem cells (Dicer-/- EpiSCs) five days after the induction of Dicer deletion

overall_design: Dicer fx/fx EpiSCs were left untreated (control cells) or treated with 0.3uM of 4-OH-Tamoxifen for three days and without Tamoxifen for two further days, until day 5 when RNA was extracted and used for microarray analysis. Three independent deletion experiments including a Dicer fx/fx sample and a Dicer -/- sample were analyzed as biological replicates.

first: Barbara

last: Pernaute


title: Codeletion of 1p and 19q Determines Distinct Gene Methylation and Expression Profiles in IDH-mutated Oligodendroglial Tumors

city: TOLEDO

last: Melendez

address: AVDA. BARBER 30

department: UNIDAD DE INVESTIGACION DE PATOLOGIA MOLECULAR

institute: HOSPITAL VIRGEN DE LA SALUD

summary: Genome wide DNA methylation profiling of oligodendroglial tumors (OTs) and five non tumoral brain tissue (NTBT) samples. The Illumina Infinium Human DNA methylation 450k Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumoral samples. Samples included 46 OTs and 5 NTBT.

overall_design: Bisulphite converted DNA from the 51 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Pilar

last: Mur

first: Manuela

last: Mollejo

first: Yolanda

last: Ruano

first: Ángel

last: Rodríguez de Lope

first: Concepción

last: Fiaño

first: Juan

last: García

first: Javier

last: Castresana

first: Aurelio

last: Hernández-Lain

last: Rey

first: Bárbara

last: Meléndez


title: Expression data from mammary epithelial cells harvested from 8-9 week old C3H female mice - various isolation conditions

status: Public on Sep 05 2014

city: Nashville

first: Ian

last: Macara

state: TN

address: 465 21st Avenue South U

department: Cell and Developmental Biology

institute: Vanderbilt University

summary:
Numerous lineage analysis studies have used FACS sorting as a separation technique prior to measuring mRNA expression patterns. To assess if FACS sorting causes non-specific changes in gene expression, we collected a heterogeneous population of mammary epithelial cells from three biological replicates. We then performed gene expression analysis on each replicate either prior to trypsin digestion, immediately following trypsin digestion, or following both the trypsin digestion and a mock FACS sort.
In this dataset, we include gene expression data obtained from isolated murine mammary epithelial cells either prior to trypsin digestion, immediately following trypsin digestion, or following the trypsin digestion and a mock FACS sort.

overall_design: Nine total samples were analyzed (3 biological replicates of three experimental conditions).  Using LIMMA packages gene-wise comparisons were made between untrypsinized and trypsinized replicates as well as between trypsinized and mock FACS sorted replicates using and P≤0.05 and a ≥1.5-fold difference between conditions.

first: Graham

middle: M

last: Richardson


title: Expression data from human monocyte derived dendritic cells infected with adenovirus expressing HIV-1 Vpr

city: Toronto

first: Muhammad

middle: Atif

last: Zahoor

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

summary:
HIV-1 Vpr protein is a multifunctional protein which perturbs human transcriptome and interacts with a number of cellular proteins. In this study, we have attempted to explore the efffects of Vpr on human transcriptome and have identified several genes which are involved in innate immune responses.
We used the microarray analysis to elucidate the differnetail expression pattern of differnet genes in human dendritic cells infected with HIV-1 Vpr. As result we found that HIV-1 Vpr protein leads to the induction of various interferon stimualted genes (ISGs) in human monocyte derived dendritic cells.

overall_design: Human monocytes-derived dendritic cells (MDDCs) were isolated from peripheral blood mononuclear cells (PBMCs) from two healthy donors and were infected with recombinant adenoviruses either expressing HIV-1 Vpr or ZsGreen1 as a control. At 48 hours post-infection, RNA was isolated and subjected to microarray analysis.

first: Guangai

last: Xue

first: Keisuke

last: Fukumoto

first: Aida

last: Yoko


title: Expression data from normal urothelial cells with exogenous expression of mutant FGFR3

status: Public on Sep 12 2014

city: Leeds

first: Erica

last: di Martino

address: Becket Street

department: Experimental Oncology

institute: University of Leeds

summary:
Activating mutations of FGFR3 are found in a high proportion of bladder tumours. The molecular consequences of FGFR3 mutation in urothelial cells and the mechanisms by which mutant FGFR3 may drive bladder tumourigenesis are largely unknown.
We used expression arrays to identify downstream targets of mutant FGFR3 signalling in normal urothelial cells.

overall_design: TERT-immortalized normal urothelial cells stably transduced to express the most common FGFR3 mutation (S249C) were compared with control cells transduced with the empty vector (pFB).

first: Margaret

last: Knowles

first: Gavin

last: Kelly


title: Gene expression profiling of LCM captured breast cancer cells

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: The purpose of this study is to obtain comprehensive gene expression profiles in breast cancer. Mammary gland cells were specifically isolated from 433 clinical tissue samples by laser capture microdissection (LCM). Total RNAs were extracted from LCM captured samples. We investigated gene expression profiles in 417 patients with breast cancer and 16 non-tumor tissues as a normal control using an Affymetrix GeneChip.

overall_design: Mammary gland cells were captured from clinical tissues of breast cancer patient by LCM. Gene expression profilings for 417 tumor and 16 non-tumor samples were acquired using GeneChip Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA). Microarray datasets were normalized and transformed to log2 values using robust multi-array average (RMA) method with R statistical software and BioConductor package.

first: Yoshio

last: Miki

first: Masaaki

last: Matsuura

first: Tetsuo

last: Noda


title: Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients

city: Kelvin Grove

first: Joanne

last: Voisey

state: Queensland

address: 60 Musk Ave

department: IHBI

country: Australia

institute: Queensland University of Technology

summary: Recent studies suggest that genetic and environmental factors do not account for all the schizophrenia risk and epigenetics also plays a role in disease susceptibility.  DNA methylation is a heritable epigenetic modification that can regulate gene expression.  Genome-Wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls.  DNA methylation was assessed at over 485 000 CpG sites using the Illumina Infinium Human Methylation450 Bead Chip.  After adjusting for age and post-mortem interval (PMI), 4 641 probes corresponding to 2 929 unique genes were found to be differentially methylated.  Of those genes, 1 291 were located in a CpG island and 817 were in a promoter region.  These include NOS1, AKT1, DTNBP1, DNMT1, PPP3CC and SOX10 which have previously been associated with schizophrenia.  More than 100 of these genes overlap with a previous DNA methylation study of peripheral blood from schizophrenia patients in which 27 000 CpG sites were analysed.  Unsupervised clustering analysis of the top 3 000 most variable probes revealed two distinct groups with significantly more people with schizophrenia in cluster one compared to controls (p = 1.74x10-4).  The first cluster was composed of 88% of patients with schizophrenia and only 12% controls while the second cluster was composed of 27% of patients with schizophrenia and 73% controls.  These results strongly suggest that differential DNA methylation is important in schizophrenia etiology and add support for the use of DNA methylation profiles as a future prognostic indicator of schizophrenia

first: L

last: Wockner

first: E

last: Noble

first: B

last: Lawford

first: R

last: Young

first: C

last: Morris

first: V

middle: L

last: Whitehall

first: J


title: DNA methylation analysis during in vitro myogenic differentiation

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: DNA methylation has been considered to play an important role in myogenic differentiation. In terminal differentiation of myoblasts, a chronological pattern of DNA methylation changes has been poorly understood. Using Infinium HumanMethylation450 BeadChips, we obtained and evaluated the genome-wide DNA methylation profiles of human myoblast differentiation in vitro.

overall_design: DNA methylation profiles of human myoblasts (day1, day3, day8, day15), human mesenchymal stem cells (1 sample) and human skeletal muscle tissues (2 samples) were obtained using Infinium HumanMethylation450 BeadChips (Illumina).

first: Kohei

last: Miyata

first: Tomoko

first: Hiroshi

last: Asahara


title: Migration and invasion of 5 glioblastoma cell lines

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary: Glioblastoma cells are characterized by a highly invasive behavior whose mechanisms are not yet understood. Using the wound healing and Boyden chamber assays we compared in the present study the migration and invasion abilities of 5 glioblastoma cell lines (DK-MG, GaMG, U87-MG, U373-MG, SNB19) differing in p53 and PTEN status. We also analyzed by Western blotting the expression of PTEN, p53, mTOR and several other marker proteins involved in cell adhesion, migration and invasion. Among 5 cell lines, GaMG cells exhibited the fastest rate of wound closure, whereas U87-MG cells showed the most rapid chemotactic migration in the Boyden chamber assay. In DK-MG and GaMG cells, F-actin mainly occurred in the numerous stress fibers spanning the cytoplasm, whereas U87-MG, U373-MG and SNB19 cells preferentially expressed F-actin in filopodia and lamellipodia. Moreover, the two glioblastoma lines mutated in both p53 and PTEN genes (U373-MG and SNB19) were found to exhibit the fastest invasion rates through the Matrigel matrix.

overall_design: Here, we performed a gene expression profiling of the five glioblastoma cell lines to examine the molecular framework of differences in invasive behavior to find possible targets for chemo- and radiation therapy.

first: Cholpon

last: Djuzenova

first: Vanessa

last: Fiedler

first: Simon

last: Memmel

first: Astrid

last: Katzer

first: Susanne

last: Hartmann

first: Madlen

last: Staus

first: Musga

last: Qureischi

first: Georg

last: Krohne

first: Heiko

last: Zimmermann

middle: J

first: Michael

last: Flentje

first: Vladimir

last: Sukhorukov


title: Effect of methylphenidate on gene expression profiles of Attention Deficit Hyperactivity Disorder patients and unaffected controls.

summary:
Attention deficit hyperactivity disorder (ADHD) is a common psychiatric condition of children with a prevalence of 5-10% worldwide. Up to 30% of adults with a history of childhood ADHD maintain symptoms in later life; these adult ADHD patients  are severely impaired in social and professional life due to persistence of ADHD core symptoms like impulsivity, attention deficit and hyperactivity as well as frequently observed co-morbidities like alcohol and drug abuse, major depression, bipolar and personality disorders.
Pharmaceutical treatment options include methylphenidate (MPH), which is amongst others an inhibitor of the dopamine transporter and therefore increases dopamine levels in the brain. However, not all ADHD patients are MPH responders with clinical features to distinguish responders and non-responders being not at hand so far. Likewise, neurobiological reasons for drug response are still elusive.

overall_design: Here, we examined the global transcriptional response of MPH on lymphoblastoid cell lines (LCLs) derived from ADHD patients and unaffected controls.

first: Ricarda

last: Schwarz

first: Heike

last: Weber

first: Andreas

last: Reif

first: Sarah

last: Kittel-Schneider


title: Gene expression profiling of human breast cancer during pregnancy

city: Brussels

first: Sylvain

last: Brohée

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

summary: Using a dataset of 54 pregnant and 113 age/stage-matched non-pregnant breast cancer patients with complete clinical and survival data; we evaluated the pattern of hot spot somatic mutations and performed transcriptomic profiling using Sequenom® and Affymetrix®, respectively. Breast cancer molecular subtypes were defined using PAM50 and 3-Gene classifiers. We performed Gene set enrichment analysis (GSEA) to evaluate pathways associated with diagnosis during pregnancy. We investigated the differential expression of cancer-related genes and published gene sets according to pregnancy. We finally investigated genes associated with disease-free survival.

overall_design: We identified 65 patients who were diagnosed with breast cancer during pregnancy. Moreover, for each case, two breast cancer patients who were not diagnosed during pregnancy or lactation, but who were matched according to age (±2 years), tumors size, nodal status, year of surgery (±2 years) and whether neoadjuvant chemotherapy was received were selected. Messenger RNA from tumor tissue has been extracted and hybridized on Affymetrix microarrays. However, due to experimental issues, 54 pregnant and 113 non-pregnant patients were remaining and used in our study.

first: Hatem

last: Azim

first: Fedro

last: Peccatori

first: Christine

last: Desmedt

first: Sherene

last: Loi

first: Diether

last: Lambrechts

first: Patrizia

last: Dell’Orto

first: Samira

last: Majjaj

first: Vinu

last: Jose

first: Nicole

last: Rotmensz

first: Michail

last: Ignatiadis

first: Giancarlo

last: Pruneri

first: Martine

last: Piccart

first: Giuseppe

last: Viale

first: Christos

last: Sotiriou


title: IL-5-mediated gene expression in LDBM cells

city: Cincinnati

first: Patricia

middle: C.

last: Fulkerson

state: OH

address: 3333 Burnet Ave, ML 7028

institute: Cincinnati Children's Hospital Medical Center

summary: Transcriptome analysis of LDBM cells stimulated with IL-5

overall_design: LDBM cells were stimulated in liquid cultures with SCF and FLT3L to expand progenitors, then stimulated with IL-5 to promote eosinophil differentiation. Cultured LDBM cells were harvested after 4 days and 10 days of IL-5 stimulation.

middle: C

first: Kaila

last: Schollaert

first: Carine

last: Bouffi

first: Marc

middle: E

last: Rothenberg


title: Epigenetic silencing of miR-210 increases the proliferation of gastric epithelium during chronic Helicobacter pylori infection

status: Public on Sep 04 2014

city: Tokyo

first: Kotaro

last: Kiga

address: 4-6-1 Shirokanedai, Minato-ku

institute: University of Tokyo

summary: Persistent colonization of the gastric mucosa by Helicobacter pylori (Hp) elicits chronic inflammation and aberrant epithelial cell proliferation, which increases the risk of gastric cancer. We examined the ability of microRNAs to modulate gastric cell proliferation in response to persistent Hp infection and found that epigenetic silencing of miR-210 plays a key role in gastric disease progression. Importantly, DNA methylation of the miR-210 gene was increased in Hp-positive human gastric biopsies as compared to Hp-negative controls. Moreover silencing of miR-210 in gastric epithelial cells promoted proliferation. We identified STMN1 and DIMT1 as miR-210 target genes and demonstrated that inhibition of miR-210 expression augmented cell proliferation by activating STMN1 and DIMT1. Together, our results highlight inflammation-induced epigenetic silencing of miR-210 as a mechanism of induction of chronic gastric diseases, including cancer, during Hp infection.

overall_design: To identify miR-210 targets in gastric cells, whole transcriptome analysis of AGS and MKN45 cells transfected with pre-miR-210 was conducted using Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.


title: Nervous system developmental genes are altered in fetal hippocampus by ethanol.

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

summary:
Prenatal alcohol exposure can cause long-lasting changes in functional and genetic programs of the brain, which may underlie behavioral alterations found in FASD.
Here, we demonstrated that maternal binge alcohol consumption alters the expression of genes involved in nervous system development.

overall_design: Maternal binge alcohol consumption alters several important genes that are involved in nervous system development in the mouse hippocampus at embryonic day 18 (ED18)

first: KyoungHwa

last: Jung

first: YoungGyu


title: Expression data from Epithelial colon cancer cells treated with TGF-beta

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: Most available CRC cell lines have lost their TGF-beta response through the acquisition of mutations either in TGF-beta type II receptor (TGFBR2) or the intracellular mediator SMAD4 (Reviewed in Markowitz et al. 2002). To study the effect of TGF-beta in CRC epithelial cells, we restored wild-type TGFBR2 expression in the CRC cell line LS174T (LS). Ls174T cells are mutant for beta-catenin and therefore exhibit constitutive Wnt activity, which results in the expression of a genetic profile similar to that of intestinal epithelial progenitor cells (van de Wetering, Sancho et al. 2002). They thus reflect tumor cells at the initial stages of tumorogenesis.  In addition, Ls174T cells bear mutations in the TGF-beta receptor II (TGFBR2) sequence at the BATRII locus (Grady and Markowitz 2002). This mutation gives rise to a non-functional truncated form of the receptor lacking the transmembrane domain and the serine-threonine kinase domain (Parsons, Myeroff et al. 1995). We generated inducible clones of Ls174T cells, where the expression of TGFBR2 could be controlled at will by the presence or absence of doxycycline (LSTGFBR2 cell line).  Re-expression of wild-type receptor in Ls174T cells (LSTGFBR2) restored TGF-beta signalling resulting in strong phosphorylation of SMADs and activation of SMAD-binding reporter activity. Functionally, TGF-beta signalling in LSTGFBR2 resulted in a strong cytostatic response. By genome wide expression profiling using microarrays we investigated genes regulated by TGF-beta in this cell line.

overall_design: LsTGFBR2 inducible cells were generated by the Invitrogen T-Rex system following manufacturers instructions. LSTGFBR2 were seeded at 60% confluence in the presence or absence of Doxycycline and treated with TGF-β1 for 16 hours. Gene expression profiles were measured in duplicate using HG-U133 plus 2.0. We used RMA background correction, quantile normalization and RMA summarization (Gautier et al., 2004). A TGF-β response signature was obtained by selecting genes with limma P-value < 0.05 and at least two fold up-regulation in TGF-β treated LSTGFBR2 cells.

first: Elena

last: Sancho

first: Elisa

last: Espinet


title: Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (methylation array)

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

department: Human Genetics

country: USA

institute: University of Chicago

summary: Comparative studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. All lines are free of integration from exogenous reprogramming vectors, can be maintained using standard iPSC culture techniques, and have proliferative and differentiation potential similar to human and mouse lines. To begin demonstrating the utility of comparative iPSC panels, we collected RNA-seq data and methylation profiles from the chimpanzee iPSCs and their corresponding fibroblast precursors, as well as from 7 human iPSCs and their precursors, which were of multiple cell type and population origins. Overall, we observed much less regulatory variation within species in the iPSCs than in the somatic precursors, indicating that the reprogramming process has erased many of the differences observed between somatic cells of different origins. We identified 4,918 differentially expressed genes and 1,986 differentially methylated regions between iPSCs of the two species, many of which are novel inter-species differences and not observed between the somatic cells of the two species. Our panel will help realise the potential of iPSCs, and in combination with genomic technologies, transform studies of comparative evolution in primates.

sample_organism:
Pan troglodytes
Homo sapiens

overall_design: We obtained RNA sequencing and methylation profiles from 7 chimpanzee iPSCs and the fibroblasts used to generate them, as well as 7 human iPSCs and the LCLs and fibroblasts used to generate them.

first: Bryan

last: Pavlovic

last: Hernando-Herraez

first: Nicholas

last: Banovich

first: Courtney

last: Kagan

first: Jonathan

last: Burnett

first: Constance

middle: H

last: Huang

first: Amy

last: Mitrano

first: Claudia

middle: I

last: Chavarria

first: Inbar

last: Ben-Nun

first: Yingchun

last: Li

first: Karen

last: Sabatini

first: Trevor

last: Leonardo

first: Mana

last: Parast

first: Tomas

last: Marques-Bonet

first: Louise

last: Laurent

first: Jeanne

last: Loring

first: Yoav

last: Gilad


title: Expression data of neural progenitor cells differentiation from human embryonic stem cells

status: Public on Sep 03 2014

city: Shanghai

first: Weidong

last: Le

address: #197 Ruijin No.2 Road

country: China

institute: Institute of Health Sciences

summary:
Mocetinostat (MGCD) which is a kind of histone deacetylase inhibitors (HDACi) promotes human embryonic stem cells (hESCs) differentiation towards neural progenitor cells (NPCs). Application of HDAC inhibitors (HDACi) increased the expression of neuroectodermal markers once neural differentiation was initiated, thereby leading to more NPC generation.
We used  microarrays to detail the global gene expression during NPC differentiaton upon MGCD treatment and identified the transcript changes effected by MGCD during this process.

overall_design: Undifferentiated H9 hESCs (D0), as well as H9 cells with or without MGCD treatment on day 3 (D3C and D3M) and on day 7(D7C and D7M) of NPC generation were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Juan

last: Yang

first: Yu

last: Tang


title: Gene expression profiling of KLF5, GATA4 and GATA6 knock down in YCC3/AGS/KATOIII cell lines

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

institute: Duke NUS Graduate Medical School

summary: Three transcription factors KLF5, GATA4 and GATA6 are recurrently amplified in multiple gastric cancer cohorts, representing one type of lineage-survival oncogenes in gastric cancer. ChIP-Seq analysis of these three factors in multiple cell lines revealed that significant number of genomic sites are co-occupied by KLF5 and GATA4 and/or GATA6. Integrative analysis of ChIP-Seq and gene expression identified several targets of the three transcription factors in both cell lines and primary tumors, including HNF4A. These results suggest that KLF5, GATA4 and GATA6 interact and co-operate to regulate HNF4A and other genes to promote tumorigenesis in gastric cancer.

overall_design: Gene expression profiling of KLF5, GATA4 and GATA6 knock down in YCC3/AGS/KATOIII cells

first: Na-Yu

last: Chia

first: Patrick

last: Tan


title: Heme-Bound Iron Activates Placenta Growth Factor via Erythroid Krüppel‐like Factor in Erythroid Cells

city: Bethesda

first: Yanqin

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: We have tested the effect of iron on the gene expression profile in human leukemia cells with properties of erythroid differentiation.

overall_design: 12 Total samples were analyzed. We compared the gene expression profiles of cells treated with iron mesoporphyrin to mesoporphyrin alone. DMSO vehicle was also tested as a control.

first: Xunde

last: Wang

first: Nalini

last: Raghavachari

first: Gregory

last: Kato


title: Expression profiling of peripheral blood of chronic HCV infection

status: Public on Sep 02 2014

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

institute: Erasmus MC

summary: In the present study, we studied chronic HCV patients who responded to IFN-based therapy as evidenced by absence of HCV RNA at the end of treatment, and focused on two issues that have not received much attention. Firstly, we evaluated whether specific genes or gene expression patterns in blood were able to distinguish responder patients with a viral relapse from responder patients who remained virus-negative after cessation of treatment. We found that chronic HCV patients who were sustained responders and relapsers to IFN-based therapy showed comparable baseline clinical parameters and immune composition in blood. However, at baseline, the gene expression profiles of a set of 18 genes predicted treatment outcome with an accuracy of 94%. Secondly, we examined whether patients with successful therapy-induced clearance of HCV still exhibited gene expression patterns characteristic for HCV, or whether normalization of their transcriptome was observed. We observed that the relatively high expression of IFN-stimulated genes (ISG) in chronic HCV patients prior to therapy was reduced after successful IFN-based antiviral therapy (at 24 weeks follow-up). These ISG included CXCL10, OAS1, IFI6, DDX60, TRIM5 and STAT1. In addition, 1428 differentially expressed non-ISG genes were identified in paired pre- and post-treatment samples from sustained responders, which included genes involved in TGF-β signaling, apoptosis, autophagy, and nucleic acid and protein metabolism. Interestingly, 1424 genes were identified with altered expression in responder patients after viral eradication in comparison to normal expression levels in healthy individuals. Additionally, aberrant expression of a subset of these genes, including IL-32, IL-16, CCND3 and RASSF1, was also observed at baseline.  Our findings indicate that successful antiviral therapy of chronic HCV patients does not lead to normalization of their blood transcriptional signature. The altered transcriptional activity may reflect HCV-induced liver damage in previously infected individuals.

overall_design: A genome-wide gene expression analysis was performed on a blood cohort of 59 chronic HCV patients and 20 healthy controls. The expression profiles of patients who responded to IFN-based therapy, who developed a viral relapse were compared respectively to the profiles of healthy controls. Pre- and post-treatment expression profiles of same responders were compared as well.

first: Jun

last: Hou

first: Gertine

last: van Oord

first: Zwier

last: Groothuismink

first: Mark

last: Claassen

first: Kim

last: Kreefft

first: Fatiha

last: Zaaraoui-Boutahar

first: Wilfred

last: van IJcken

first: Albert

last: Osterhaus

first: Harry

last: Janssen

first: Arno

last: Andeweg

first: Robert

last: de Knegt


title: Examination of gene expression in human breast cancer cells exposed to the HDAC inhibitor SAHA

status: Public on Sep 01 2014

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: The identification of proteins that change in response to a drug perturbation can shed light on the molecular mechanisms of the drug and its potential use in therapies. Histone deacetylases (HDACs) are targets for cancer therapy. Suberoylanilide hydroxamic acid (SAHA) is an FDA approved HDAC inhibitor used for the treatment of cutaneous T-cell lymphoma. ING2 is a non-catalytic component of the Sin3/HDAC complex. To obtain a better mechanistic understanding of the Sin3/HDAC complex in cancer, we extended its protein-protein interaction network and identified a mutually exclusive pair within the complex. We then assessed the effects of SAHA on the disruption of the complex network through six homologous baits. SAHA perturbs multiple protein interactions and therefore compromises the composition of large parts of the Sin3/HDAC network. A comparison of the effect of SAHA treatment on gene expression in breast cancer cells to a knockdown of the ING2 subunit indicated that a portion of the anticancer effects of SAHA may be attributed to the disruption of ING2's association with the complex.

overall_design: Cells from human breast cancer cell line MDA-MB-231 were treated with the HDAC inhibitor drug SAHA in duplicate and compared to a DMSO vehicle control in triplicate, for a total of 5 samples.

first: Karen

middle: T

last: Smith

first: Jerry

last: Workman

first: Mihaela

last: Sardiu

first: Brad

middle: D

last: Groppe

first: Joshua

last: Gilmore

first: Anita

last: Saraf

first: Rhonda

last: Egidy

first: Allison

last: Peak

first: Laurence

last: Florens

first: Michael

last: Washburn


title: Early life Lead exposure causes distinct gender specific changes in the DNA methylation profile of DNA extracted from dried blood spots

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

summary: Study of influence of gender and Lead(Pb) exposure on DNA methylation for whole blood measured in dried blood spots for a Detroit cohort of child between the age of 3 months to 5years

overall_design:
DNA methylation profiling of dried blood spots for a Detroit cohort of child between the ages of 3 months to 5 years
Differential methylation study

first: Arko

last: Sen

first: Nicole

last: Heredia

first: Kurt

last: Hollacher

first: Marie-Claude

last: Senut

first: Mary

middle: O

last: Dereski

first: Matthew

last: Hess

first: Susan

last: Land


title: SAHA Induced Dynamics of a Human Histone Deacetylase Protein Interaction Network

first: Chris

last: Seidel

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

overall_design: Refer to individual Series


title: Examination of gene expression in response to ING2 knockdown by siRNA in human breast cancer cells

summary: The Sin3/HDAC multi-protein complex consists of at least 17 subunits and is known to have roles in diverse biological and cellular processes including transcription, chromatin structure, and the cell cycle. ING2 is a non-catalytic component of this complex. To obtain a better mechanistic understanding of the Sin3/HDAC complex in cancer, we extended its protein-protein interaction network and identified a mutually exclusive pair within the complex. Suberoylanilide hydroxamic acid (SAHA) is an FDA approved HDAC inhibitor used for the treatment of cutaneous T-cell lymphoma. We assessed the effects of SAHA on the disruption of the complex network through six homologous baits. SAHA perturbs multiple protein interactions and therefore compromises the composition of large parts of the Sin3/HDAC network. A comparison of the effect of SAHA treatment on gene expression in breast cancer cells to a knockdown of the ING2 subunit indicated that a portion of the anticancer effects of SAHA may be attributed to the disruption of ING2’s association with the complex.

overall_design: ING2 siRNA knockdowns in human breast cancer cell line MDA-MB-231 were compared to a non-targeting control in triplicate, for a total of 6 samples.

first: Karen

last: Smith

first: Jerry

last: Workman

first: Mihaela

last: Sardiu

middle: P


title: A Ferritin Mutant Induces Protective Immunity against Virulent Mycobacterium tuberculosis Infection

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren St, Rm# W250.Q

department: New Jersey Medical School,

institute: Rutgers Biomedical and Health Sciences, Rutgers The State University of NJ

summary: Iron plays a critical role in the pathogenesis of many organisms including Mtb. It is the preferred redox cofactor in many basic cellular processes but due to its insolubility and potential toxicity under physiological conditions is a limiting nutrient in the host environment.  Previously, we demonstrated that Mtb requires the iron storage protein ferritin (BfrB), for adaptation to both low and sufficient concentrations of environmental iron. We also showed that absence of bfrB compromises the ability of Mtb to overcome iron deficiency and prevent excess iron toxicity.  In this study, we tested whether vaccination with ∆bfrB could elicit host protective immune response against virulent Mtb infection.  The results show that immunization of mice with the ∆bfrB stimulates protective immunity associated with reduced immunopathology and better containment of the infection compared to vaccination with BCG.  Genome-wide transcriptome analysis showed a distinct expression pattern of significantly differentially expressed genes (SDEG) between the ∆bfrB and BCG-vaccinated, Mtb-infected mice lungs.  Our network/pathway analysis of SDEG revealed significant inhibition of inflammatory response genes and activation of fibrosis genes in the ∆bfrB, compared to BCG vaccinated, Mtb-infected mice lungs. The results provide a frame work for the study of mechanisms of protection relevant for the design of new and improved preventive strategies for TB.

overall_design: Female C57BL/6 mice were vaccinated subcutaneously with ∆bfrB or BCG .  At 8 weeks post-vaccination, mice were aerosol infected with Mtb H37Rv. At 4 weeks post infection, mice  were sacrificed and lungs were removed. Lung total RNA from vaccinated and Mtb-infected mice was extracted, purified  and were processed separately for microarray analysis.

first: G

last: Rodriguez


title: Methylation profiling data from medulloblastoma tumor samples

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

institute: The Hospital for Sick Children

summary:
Smoothened (SMO)-inhibitors recently entered clinical trials for sonic-hedgehog driven medulloblastoma (SHH-MB). Clinical response appears highly variable. To understand the mechanism(s) of primary resistance and to identify pathways co-operating with aberrant SHH-signaling, we sequenced a large cohort of SHH-MBs across all age groups by sequencing, DNA methylation and expression profiling. Our data show that most adults but only half of the pediatric patients with SHH-MB will respond to SMO inhibition as predicted by molecular analysis of the primary tumor and tested in the SHH-xenografts, demonstrating that the next generation of SMO-inhibitor trials should be based on these predictive biomarkers.
To further dissect the biological differences between the different age groups within SHH medulloblastomas, we looked at the DNA methylation profiles of SHH medulloblastoma samples.

overall_design: We investigated the DNA methylation profiles of 46 SHH medulloblastomas across all age groups using the Illumina 450k methylation array.

first: Florence

last: Cavalli

first: Volker

last: Hovestadt

first: Marcel

last: Kool

first: Stefan

last: Pfister

last: Taylor


title: Expression profiles in HMGN1-overexpressed neural precursor cells

city: Tokorozawa

first: Motoshi

last: Nagao

state: Saitama

address: 4-1 Namiki

department: Department of Rehabilitation for the Movement Functions

institute: Research Institute, National Rehabilitation Center for Persons with Disabilities

summary: Neural precursor cells (NPCs) are multipotent cells that can generate neurons, astrocytes, and oligodendrocytes in the mammalian central nervous system. Although high mobility group nucleosomal binding domain 1 (HMGN1) was highly expressed in NPCs, its functions in neural development are not fully understood. We performed microarray analysis to examine changes in gene expression between control and HMGN1-overexpressed NPCs.

overall_design: NPCs derived from E11.5 mouse forebrains were infected with control or HMGN1 retrovirus in the presence of fibroblast growth factor 2 (FGF2) and epidermal growth factor (EGF). Three days after infection, the virus-infected NPCs were dissociated and seeded on poly-D-lysine -coated dishes, and subsequently the cells were cultured for 1 day without  FGF2 and EGF.

first: Darin

last: Lanjakornsiripan

first: Yasuhiro

last: Itoh

first: Yusuke

last: Kishi

first: Toru

last: Ogata

first: Yukiko

last: Gotoh


title: Methylation data from medulloblastoma tumor samples

city: Heidelberg

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

overall_design: We investigated the DNA methylation profiles of 83 SHH medulloblastomas across all age groups using the Illumina 450k methylation array.