title: Gene expression profile of Nurse-Like Cells (NLC) derived from chronic lymphocytic leukemia

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

institute: INSERM

summary:
The study of the roles of macrophages in the microenvironment of cancer cells (tumor-associated macrophages, TAM) has gained deep insight over the recent years. Here, we describe gene expression profile of chronic lymphocytic leukemia (CLL)-associated macrophages, also called nurse-like cells (NLC), derived from in vitro co-cultures system.
We define these NLC as M2-oriented, TAM-like specific subset of macrophages, with very few inter-individual variations in gene expression profiles.

overall_design: CLL patients PBMC were isolated and cultured for 15 days in vitro. NLC were then isolated, mRNA were purified and hybridized on Affymetrix U133 plus 2.0 chips. Data were normalized by RMA5

first: Loic

last: Ysebaert

first: Jean-Jacques

last: Fournié


title: Whole mouse genome analysis of LCMV-specific CD4 and CD8 T cells throughout acute and chronic LCMV infection.

status: Public on Dec 12 2012

city: Philadelphia

first: Alison

last: Crawford

state: PA

address: 421 Curie Blvd, BRB

department: Microbiology

country: USA

institute: University of Pennsylvania

summary: CD4 and CD8 T cells display functional defects during chronic infection such as loss of certain cytokines. Recent studies have suggested that CD4 T cells may actually gain other functions, however. Here, we analyzed gene expression profiles from LCMV-specific CD4 and CD8 T cells throughout the response to either acute LCMV or chronic LCMV infection. This alllowed us to identify CD4-specific changes during chronic infection compared to acute infection but also revealed shared core regulators between CD4 and CD8 T cells.

overall_design: LCMV-specific CD4 and CD8 T cells were isolated 6, 8, 15 and 30 days post infection with LCMV Armstrong or LCMV clone 13. Naïve CD4 and CD8 T cells were also isolated from naïve mice as comparisons. Four replicates of each sample were hybridized. The only exception is LCMV-specific CD4 T cells isolated 6 days post infection with LCMV-Arm where only three replicates were hybridized.

first: Jill

middle: M

last: Angelosanto

first: E

middle: J

last: Wherry


title: Expression data from dsDNA-stimulated mouse embryonic fibroblasts

status: Public on Dec 08 2012

city: Cambridge

first: Mark

last: Lee

state: MA

address: 7 Cambridge Center

department: MIT

institute: Broad Institute

summary:
Transfection of dsDNA into many mammalian cell types indues the production of type I interferons and interferon-stimulated genes.  We performed an siRNA screen to identify genes involved in this innate immune response, and identified Abcf1.
We used microarrays to determine which genes are regulated by ABCF1 following dsDNA stimulation.

overall_design: We treated p53-/- mouse embryonic fibroblasts (MEFs) with siRNAs targeting Abcf1 or Irf3 (positive control) or a negative control siRNA (siCtrl), and then stimulated the cells with 45-base pair dsDNA for 6 hrs or left the cells unstimulated.  We then lysed the cells and hybridized the RNA to Affymetrix microarrays.

middle: N

first: Nir

last: Hacohen


title: A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma:An Integrated Analysis at the Genetic and Expression Levels

status: Public on Dec 10 2012

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

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

summary: Previous studies have reported that the tumour cells of nasopharyngeal carcinoma (NPC) exhibit both recurrent chromosome abnormalities and changes in the expression of numerous genes. However, it is not known to what extent changes in the copy number of individual genes are associated with the observed expression changes. To address this, a genome wide analysis of chromosome copy number and gene expression was performed in tumour cells micro-dissected from the same NPC biopsies. Significant gene expression changes were identified in tumour suppressor genes (TSGs) and in tumour-promoting genes (TPGs) but almost 60% of these can be either upregulated or downregulated in different types of cancer. This suggests that the simplistic classification of genes as TSGs or TPGs may not be entirely appropriate and that the concept of onco-suppressors may be more extensive than previously recognised. Several genomic regions showing frequent copy number gain or loss were identified. Whereas TSGs were significantly enriched within regions of frequent loss, no significant enrichment of TPGs was observed in regions of frequent gain. However, on a gene by gene basis little correlation was found between DNA copy number and alterations in gene expression except for loss of expression from homozygous deletions and a single highly amplified segment which showed enhanced gene expression.

overall_design: Gene expression and DNA copy number of nasopharyngeal carcinoma was compared with those of normal controls.

first: Chunfang

last: Hu

first: Xiaoyi

last: Chen

first: Ciaran

middle: B

last: Woodman

first: Yunhong

last: Yao

first: John

last: Nicholls

first: Irène

last: Joab

first: Sim

middle: K

last: Sihota

first: Jian-Yong

last: Shao

first: Dalia

last: Derkaoui

first: Aicha

last: Amari

first: Stephanie

middle: L

last: Maloney

first: Andrew

middle: I

last: Bell

first: Paul

middle: G

last: Murray

first: Christopher

middle: W

last: Dawson

first: Lawrence

middle: S

last: Young

middle: R

last: Arrand


title: Filarial nematode AsnRS interacts with interleukin 8 receptors in iDCs but causes different gene expression patterns compared to iDCs stimulated by interleukin 8.

city: Milwaukee

first: Michael

middle: Andrew

last: Kron

state: Wisconsin

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

summary: Nematode derived  substances are known to down regulate host immune responses in order to survive in the human host. Brugia malayi is a parasitic nematode responsible for long lasting and disabling infection known as lymphatic filariasis in humans.  The therapeutic benefit of a controlled parasitic nematode infection on the course of inflammatory bowel disease (IBD) has been demonstrated in both animal and human models.  However the inability of individual purified nematode proteins to recreate this beneficial effect has limited the application of component immunotherapy to human disease. This experiment addresses the hypothesis that the genes regulated by IL8 and recombinant Brugia malayi AsnRS (rBmAsnRS) are different even though it is known that both molecules interact with IL-8 receptors. Furthermore, we theorize that the signal transduction pathways activated by IL-8 and rBmAsnRS are different because it is known that the extracellular G protein loops utilized by IL-8 and rBmAsnRS to activate IL8 receptors, are different.   These results obtained with a single recombinant nematode protein, rBmAsnRS, share immunological features with those observed in a whole nematode infection and include desirable features for treatment of idiopathic inflammatory diseases, such as IBD.

overall_design: The immune reaction of human host in response to most abundant nematode expressed protein Asparaginyl t RNA Synthetase was compared with reaction of human immature dendritic cells to IL-8 stimulation or no stimulation.

first: Sanja

last: Vodanovic-Jankovic


title: Expression data from IFNbeta-stimulated 293T cells

first: Mark

last: Lee

summary: We used microarrays to determine which genes are upregulated by IFNbeta stimulation in 293T cells.

overall_design: We treated 293T cells with recombinant IFNbeta for 12 hrs or left the cells unstimulated.  We then lysed the cells and hybridized the RNA to Affymetrix microarrays.

first: Nir

last: Hacohen


title: Microarray gene expression profiling of kinase-dependent and kinase-independent effects of GRK2

status: Public on Dec 06 2012

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary: The ubiquitously expressed G-protein-coupled receptor kinase 2 (GRK2, ADRBK1) is an indispensable kinase involved in growth, differentiation and development. Exaggerated GRK2 activity plays a major pathophysiological role in the development of cardiovascular diseases such as heart failure and hypertension. GRK2 exerts its functions by kinase-dependent and kinase-independent effects. To assess the differential impact of GRK2 on cellular signalling we established HEK cell clones with over-expression of comparable protein levels of GRK2 or the kinase-deficient GRK2-K220R mutant, respectively. HEK cells were either cultured in vitro or expanded in vivo, in immunodeficient NOD.Scid mice to discriminate between in vitro and in vivo effects of GRK2. Whole genome microarray gene expression profiling was performed of cultured HEK cells and of NOD.Scid mouse-expanded HEK clones. As an additional control, cells were re-cultured in vitro after expansion in NOD.Scid mice.

overall_design: Whole genome microarray gene expression profiling was performed with three different study groups: (i) NOD.Scid mouse-expanded HEK clones expressing GRK2 or GRK2-K220R, (ii) cultured HEK cell clones expressing GRK2 or GRK2-K220R, and (iii) cell clones expressing GRK2 or GRK2-K220R, which were re-cultured after NOD.Scid mouse expansion.

first: Joshua

last: Abd Alla


title: Epigenetic analysis of normal colon epithelium and colon adenocarcinoma

city: Moscow

first: Vladimir

last: Naumov

address: Malaya Pirogovskaya 1a

department: Molecular Biology

country: Russia

institute: Research Institute of Physico-Chemical Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiles were obtained from colon adenocarcinoma samples (22), corresponding normal colon tissue (22) and cancer-unrelated normal colon tissue using Illumina HumanMethylation450 BeadChips. Approximately 485000 CpG sites were measured in every sample.

overall_design: Bisulphite-converted DNA from the 63 samples were hybridised to the Illumina HumanMethylation450 BeadChip.

middle: A

first: Eduard

middle: V

last: Generozov


title: Controlling Reoxygenation During Cardiopulmonary Bypass is Associated with Reduced Transcriptomic Changes in Cyanotic Patients with Tetralogy of Fallot Undergoing Heart Surgery

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

institute: University of Bristol

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

overall_design: Refer to individual Series


title: Transcription profile in patients with cyanotic Tetralogy of Fallot undergoing corrective surgery using controlled reoxygenation cardiopulmonary bypass

summary: To determine cardiac transcription profile in cyanotic Tetralogy of Fallot patients subjected to conrolled reoxygenation cardiopulmonary bypass, we collected myocardial samples at the end of the ischemic time. The transcriptional profile of the mRNA in these samples was measured with gene array technology

overall_design: Myocardial samples were collected at the end of ischemic time from cyanotic Tetralogy of Fallot patients undergoing corrective surgery using conrolled reoxygenation cardiopulmonary bypass


title: Transcription profile in patients with cyanotic Tetralogy of Fallot undergoing corrective surgery using hyperoxic/standard cardiopulmonary bypass

summary: To determine cardiac transcription profile in cyanotic Tetralogy of Fallot patients subjected to hyperoxic/standard cardiopulmonary bypass, we collected myocardial samples at the end of the ischemic time. The transcriptional profile of the mRNA in these samples was measured with gene array technology

overall_design: Myocardial samples were collected at the end of ischemic time from cyanotic Tetralogy of Fallot patients undergoing corrective surgery using hyperoxic/standard cardiopulmonary bypass

middle: T

first: Gianni

middle: D

last: Angelini

first: Massimo

last: Caputo


title: Transcription profiling of mouse liver cells during the circadian cycle at 4 hour time resolution

city: Lausanne

first: Nouria

last: Hernandez

state: Vaud

address: Dorigny

department: CIG

institute: UNIL

summary: Cyclic regulatory systems are ubiquitous in cells and tissues. In the liver rhythms in mRNA expression are determined by the homeostatic regulation that operates on daily circumstances. In particular the specific response to nutrients, as well as systemic and peripheral circadian oscillators, contribute to the set up of the hepatic homeostasis at different phases of the day. In this series we used microarrays to detail the global program of gene expression in the mouse liver under physiological daily variations, determined by both the feeding and the circadian cycles.

overall_design: We examined 7 samples, each consisting in a pool of RNAs extracted from the whole liver of 5 mice. Samples were collected at times ZT2, ZT6, ZT10 ,ZT14, ZT18, ZT22, ZT26 (ZT0/24 and ZT12 are the times when the lights are switched on and off, respectively)

first: Gilardi

last: Federica

first: Canella

last: Donatella

first: Gwendal

last: Le Martelot

first: Eugenia

last: Migliavacca

first: Ueli

last: Schibler

first: Nicolas

last: Guex

first: Béatrice

last: Desvergne


title: Gene expression profiles of renin producing cells in the adult kidney (captopril treated animals) isolated from Renin-YFP transgenic mice using FACS (GUDMAP Series ID:46).

status: Public on Dec 05 2012

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney.  The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

overall_design: Renin-YFP transgenic mice were utilized to isolate renin producing cells from the kidneys of Adult mice treated with captopril, which was provided in the drinking water at a concentration of 0.5mg/ml. In addition, mice were given low-salt chow.   Mice were treated for two weeks before renin producing cells were isolated from the kidney by fluorescent activated cell sorting (FACS).  RNA was isolated from FACS sorted cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

summary: The aim of the dataset was to study on genome-wide level the effect of PIM kinase (PIM1+PIM2+PIM3) knockdown in gene expression on early differentiation of human cord blood derived CD4+ T cells cultured under Th1 (Act+IL12) polarizing conditions.

overall_design: Total RNA from PIM1+PIM2+PIM3 siRNA treated cord blood CD4+ T cells 6 hours after culturing the cells in activating (antiCD3+antiCD28) plus IL-12 (Th1) or IL-4 (Th2) conditions was compared to total RNA from nonspecific control siRNA treated cells. Samples from 3 biological replicates were analysed.

first: Johanna

last: Tahvanainen

first: Minna

last: Kyläniemi

first: Bhawna

last: Gupta

first: Hanna

last: Lähteenmäki

first: Teemu

last: Kallonen

first: Anna

last: Rajavuori

first: Omid

last: Rasool

first: Päivi

last: Koskinen

first: Kanury

last: Rao

first: Harri

last: Lähdesmäki

first: Riitta

last: Lahesmaa


title: Expression data of FFPE peritumoral neocortex tissue

status: Public on Dec 11 2012

city: Duarte

first: Charles

last: Wang

state: CA

address: 1710 Flower Ave

department: Functional Genomics Core

institute: City of Hope

summary:
Epilepsy is a common cause of morbidity affecting approximately one third of patients with primary brain tumors. However, the molecular mechanism underlying the tumor induced epileptogenesis is poorly understood. The alteration in peritumoral microenvironments is believed to play a significant role in inducing epileptogenesis.
We hypothesize that the change of gene expression in neighboring astrocytes and neurons may contribute to the increased neuronal excitability and epileptogenesis.

overall_design: Genome-wide gene expression profiling was conducted using Affymetrix HG U133 plus 2.0 arrays and RNAs derived from formalin-fixed paraffin embedded (FFPE) peritumoral cortex tissue slides from 5-paired (seizure vs. non-seizure) low grade brain tumor patients.

middle: E

last: Niesen


title: Bcl6-deficient regulatory T cells

city: Indianapolis

first: Alexander

last: Dent

state: IN

address: 950 W. Walnut St. R2 302, Walther Oncology Center

institute: Alexander Dent

summary:
gene expression data from wild-type and Bcl6-/- regulatory T cells
in order to find genes regulated by Bcl6 in Treg cells

overall_design: FoxP3+ Tregs were sorted from wild-type (WT) and Bcl6-/- (KO) mice-- 8 samples, 2 from each type of Treg, 2 WT and 2 KO

first: Deepali

last: Sawant


title: Stress response in the yajL (DJ-1 homolog) mutant of Escherichia coli

status: Public on Dec 04 2012

city: paris

first: gilbert

last: richarme

state: ile de france

address: 15 rue helene brion

country: France

institute: Institut Jacques Monod

summary: YajL is the most closely related Escherichia coli homolog of Parkinsonism-associated protein DJ-1, a protein with a yet undefined function in the oxidative stress response. YajL protects cells against oxidative stress-induced protein aggregation and functions as a covalent chaperone for the thiol proteome, including FeS proteins. To clarify the cellular responses to YajL deficiency, transcriptional profiling of the yajL mutant was performed. As compared to the parental strain, the yajL mutant overexpressed genes coding for chaperones, proteases, chemical chaperone transporters, superoxide dismutases, catalases, peroxidases, components of thioredoxin and glutaredoxin systems, iron transporters, ferritins and FeS cluster biogenesis enzymes, DNA-repair proteins, RNA chaperones and small regulatory RNAs. It also overexpressed the RNA polymerase stress sigma factors sigma S (multiple stresses) and sigma 32 (protein stress) and activated the OxyR and SoxRS oxidative stress transcriptional regulators, which together trigger the global stress response. The yajL mutant also overexpressed genes involved in septation and adopted a shorter and rounder shape characteristic of stressed bacteria. Biochemical experiments showed that this upregulation of many stress genes resulted in increased expression of stress proteins and improved biochemical function. Thus, protein defects resulting from the yajL mutation trigger the onset of a robust and global stress response in a prokaryotic model of DJ-1-associated Parkinsonism.

overall_design: We performed microarray analysis of the transcriptome response of the yajL mutant and its parental strain in the exponential phase of growth (grown in aerobiosis in LB medium to OD600 = 0.3) in the absence of any exogenous stress. Two replicates per strain (wild type, yajL mutant).

first: Gilbert

last: Richarme


title: Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma and other tumors

status: Public on Dec 19 2012

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam


title: Cellular senescence reprograms human NK cells to promote vascular remodeling

status: Public on Dec 03 2012

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Natural killer (NK) cells are lymphocytes that participate in immune responses through their cytotoxic activity and secretion of cytokines and chemokines. They can be activated by interaction with ligands on target cells or by soluble mediators such as cytokines. In addition, soluble HLA-G, a major histocompatibility complex molecule secreted by fetal trophoblast cells during early pregnancy, stimulates resting NK cells to secrete proinflammatory and proangiogenic factors. Human NK cells are abundant in uterus, where they remain after implantation. Soluble HLA-G is endocytosed into early endosomes of NK cells where its receptor, CD158d, initiates a signaling cascade through DNA-PKcs, Akt and NF-kB3. The physiological relevance of this endosomal signaling pathway, and how the fate and function of NK cells during early pregnancy is regulated, is unknown. Here we show that soluble agonists of CD158d trigger DNA damage response signaling and p21 (CIP1/WAF1) expression to promote senescence in primary NK cells. CD158d engagement resulted in morphological alterations in cell size and shape, chromatin remodeling, and survival in the absence of proliferation, all hallmarks of senescence. Microarray analysis revealed a senescence signature of upregulated genes upon sustained activation through CD158d. The proinflammatory and proangiogenic factors secreted by these metabolically active NK cells are part of a senescence associated secretory phenotype (SASP) that promoted tissue remodeling and angiogenesis as assessed by functional readouts of vascular permeability and endothelial cell tube formation. We propose that ligand-induced senescence is a molecular switch for the sustained activation of NK cells in response to soluble HLA-G for the purpose of remodeling the maternal vasculature in early pregnancy.

overall_design: Time series (4 hr, 16 hr, 64 hr) of NK cells treated with agonist (anti-CD158d mAb) or control. NK cells were from 4 donors.

first: Sumati

last: Rajagopalan

first: Eric

middle: O

last: Long


title: Gene expression profiles of E11.5 metanephric mesenchyme and Adult Juxtaglomerular Complex cells or renal cortex from the kidneys of Crym-GFP or Ren1c-YFP transgenic mice using FACS or single-cell isolation techniques (GUDMAP Series ID:47).

first: GUDMAP

last: Developers

overall_design: YFP & GFP transgenic lines have been used to isolate several cell types including the metanephric mesenchyme, Juxtaglomerular Complex cells or renal cortex from the kidneys of either E11.5 embryos or adult mice.  The various cell types were isolated from the kidney using microdissection and single-cell isolation techniques.  RNA was isolated from cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Ariel

last: Gomez

last: Brunskill


title: Liver Regeneration Gene Signature in Hepatitis B virus (HBV)-Associated Acute Liver Failure Identified by Gene Expression Profiling

status: Public on Dec 01 2012

city: Bethesda

first: Patrizia

last: Farci

state: MD

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The liver has inherent regenerative capacity via mitotic division of mature hepatocytes. However, if the hepatic loss is massive or mature hepatocyte proliferation is impaired by chronic liver injury, HSPC are activated to support liver regeneration. Access to liver tissue from 4 patients who underwent liver transplantation for hepatitis B virus (HBV)- associated acute liver failure (ALF) provided us with the opportunity to investigate the molecular mechanisms of liver regeneration in humans by means of gene expression profiling and immunohistochemistry (IHC). Gene expression profiling of 17 liver specimens from the 4 ALF cases and individual liver specimens from 10 liver donors documented a distinct gene signature for ALF. However, unsupervised multidimensional scaling and hierarchical clustering identified two-well defined clusters that segregated according to the histopathological severity, i.e. massive hepatic necrosis (MHN; 2 patients) and submassive hepatic necrosis (SHN; 2 patients). We found that ALF is characterized by a strong hepatic stem/progenitor cell (HSPC) gene signature, as also confirmed by IHC, along with ductular reaction, both of which are more prominent in MHN. Interestingly, no evidence of further lineage differentiation was seen in MHN, whereas in SHN we detected cells with hepatocyte-like morphology.  Strikingly, ALF was associated with a strong tumorigenesis gene signature. MHN had the greatest upregulation of cancer stem cell genes (EpCAM, CK19 and CK7), whereas the most upregulated genes in SHN were related to cellular growth and proliferation (AKR1B10, NQO1, RRM2, SFN, TOP2A, CCNB1, CDC20, ANLN and KI67). The extent of liver necrosis correlated with an overriding fibrogenesis gene signature, reflecting the wound healing process. Conclusion:  Our data provide evidence of marked HSPC cell activation and fibrogenesis in HBV-associated ALF, which positively correlate with the extent of liver necrosis. Moreover, we detected a strong tumorigenesis gene signature in ALF, which underlines the relationship between liver regeneration and liver cancer.

overall_design: Liver samples were obtained from explanted liver of four patients with HBV-associated acute liver failure (4-5 samples per liver) and 10 individual normal liver donors and gene expression profiling was used to establish a molecular definition of this disease.

first: Oriel

last: Nissim

first: Marta

last: Melis

first: Giacomo

last: Diaz

first: David

last: Kleiner

first: Ashley

last: Tice

first: Giovanni

last: Fantola

first: Fausto

last: Zamboni

first: Lopa

last: Mishra


title: Expression data from AK4 overexpression in CL1-0 lung cancer cell line and AK4 knockdown in CL1-5 lung cancer cell line

city: Taipei

first: Michael

last: Hsiao

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary:
We demonstrate that AK4 down-regulation shRNAs significantly reduced cell migration and invasion in highly invasive lung cancer cell lines in vitro, as well as in lung metastases in vivo
We used microarrays to analyze the AK4 regulated gene expression underlying invasion-metastasis cascade.

overall_design: CL1-0 lung adenocarcinoma cells with AK4 overexpression and CL1-5 cells with AK4 knockdown were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yi-Hua

last: Jan


title: Myocardial gene expression profiles and cardiodepressant autoantibodies predict response of patients with dilated cardiomyopathy to immunoadsorption therapy

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

summary:
Background: Immunoadsorption with subsequent IgG substitution (IA/IgG) represents a novel therapeutic approach in treatment of dilated cardiomyopathy (DCM) which leads to improvement of left ventricular ejection fraction (LVEF). However, response to this therapeutic intervention shows wide inter-individual variability. In this pilot study, we tested the value of clinical, biochemical and molecular parameters for prediction of the response of patients with DCM to IA/IgG.
Methods & Results: Forty DCM patients underwent endomyocardial biopsies (EMBs) before IA/IgG. In 8 patients with normal LVEF (controls) EMB were obtained for clinical reasons. Clinical parameters, negative inotropic activity (NIA) of antibodies on isolated rat cardiomyocytes and gene expression profiles of EMBs were analyzed. DCM patients displaying improvement of LVEF (≥ 20% relative and ≥ 5% absolute) six month after IA/IgG were considered responders. Compared to non-responders (n=16), responders (n=24) displayed shorter disease duration (p=0.006), smaller LV internal diameter in diastole (LVIDd) (p=0.019) and stronger NIA of antibodies. Antibodies obtained from controls were devoid of NIA. Myocardial gene expression patterns were different in responders and non-responders for genes of oxidative phosphorylation, mitochondrial dysfunction, hypertrophy, and ubiquitin proteasome pathway. Integration of scores of NIA and expression levels of four genes allowed robust discrimination of responders from non-responders at baseline (sensitivity of 100 % (95% CI, 85.8%-100%); specificity up to 100% (95 % CI, 79.4%-100%, cut-off value: -0.28), and was superior to scores derived from antibodies, gene expression or clinical parameters only.
Conclusion: Combined assessment of NIA of antibodies and gene expression patterns of DCM patients at baseline predicts response to IA/IgG therapy and may enable appropriate selection of patients who benefit from this therapeutic intervention.

overall_design: EMBs of 40 DCM patients at baseline (before IA/IgG), as well as 8 controls, were used for transcriptional profiling using Affymetrix HGU 133 Plus 2.0.

first: Lars

last: Herda

first: Elke

last: Hammer

first: Leif

last: Steil

first: Alexander

last: Teumer

first: Christiane

last: Trimpert

first: Marcus

last: Dörr

first: Heyo

last: Kroemer

first: Karin

last: Klingel

first: Rainhard

last: Kandolf

first: Uwe

last: Völker

first: Stephan

last: Felix


title: Rituximab plus chlorambucil as initial treatment for elderly patients with chronic lymphocytic leukemia: effect of pretreatment biologic characteristics and gene expression patterns on response to treatment

city: Rome

first: Sabina

last: Chiaretti

address: Via Benevento, 6

department: Cellular Technologies and Hematology

country: Italy

institute: Division of Hematology

summary: Evaluation of pretreatment gene expression profiling features in elderly CLL patients; correlation with clinical outcome

overall_design: Evaluation of pretreatment gene expression profiling features in elderly CLL patients enrolled in a clinical trial; correlation with clinical outcome

first: Silvia

last: Bonina

first: Simona

last: Tavolaro


title: Expression data from treatment of human melanocytes with phenolic compounds

city: New York

first: Siavash

last: Toosi

state: NY

address: 522 First Ave, R401

department: Dermatology

institute: New York University School of Medicine

summary: Vitiligo, an acquired disorder characterized by depigmented skin patches, results from loss of epidermal melanocytes. Etiology of vitiligo is not clearly understood but environmental, biochemical, genetic, and immune factors play a role in its pathogenesis. There is evidence that melanocyte death is perpetuated by an autoimmune response that causes lesions to spread. 4-tertiary butyl phenol (4TBP) and monobenzyl ether of hydroquinone (MBEH) are phenolic compounds that are known as environmental causes of vitiligo. We used microarray to detail the global gene expression that occurs following exposure of melanocytes to 4-TBP or MBEH to identified distinct classes of up-regulated genes that may contribute to melanocyte loss in vitiligo. We show that human melanocytes exposed to 4-TBP and MBEH show increased production of some  inflammatory cytokines. Interleukin-6 (IL6) and IL8, in particular, are expressed at the periphery of vitiligo lesions and may contribute to recruitment of immune components to the areas, perpetuating melanocyte loss.

overall_design: Cultured human epidermal melanocytes were treated with 4TBP or MBEH for 3, 6, or 24 hours and gene expression were compared with untreated cells.

first: Seth

middle: J

last: Orlow

first: Prashiela

last: Manga


title: Expression data from the hepatitis E virus capsid protein

city: Rostock

first: lijo

last: john

state: Mecklenberg Vorpomen

address: Schillingallee 69

institute: Universitätsklinikum Rostock

summary: The hepatitis E virus (HEV), a non enveloped RNA virus, causes viral hepatitis. The viral open reading frame 2 (ORF2) protein represents the capsid protein of HEV which is known to cause endoplasmic reticulum stress in ORF2 expressing cells. The initiation of endoplasmic reticulum stress induced apoptosis mainly involves the transcriptional activation of pro-apoptotic gene CHOP which will further trigger the major apoptotic pathways. However, the activation of CHOP by ORF2 protein in this study does not induce apoptotic markers such as Bax translocation to mitochondria. We have used the Affymetrix microarray platform to screen the pro-apoptotic effects induced by the expression of ORF2 protein in human hepatic cell lines (Huh7). The Huh7 cells were transduced either with recombinant adenovirus encoding the HEV ORF2 (Ad-ORF2) or an adenovirus encoding the green fluorescent protein (Ad-GFP). The array results consistently showed an ORF2 specific induction of mRNA corresponding to the chaperones Hsp72, Hsp70B’ and co-chaperone Hsp40. These studies provide further mechanisms of the ER stress mediated pro apoptotic effects caused by the ORF2 protein and its potential role for the activation of anti-apoptotic activity of the host cell.

overall_design:
We used microarray to screen the host genes were regulated by the expression of the hepatitis E virus capsid protein.
Huh7 cells transduced with Ad-GFP (control) or with Ad-HEV ORF2.

first: Lijo

last: John

first: Saijo

last: Thomas


title: Conversion of human fibroblast to endothelial cell by defined factors

city: beijing

first: jun

last: li

address: heqinglu haidianqu

country: China

institute: tsinghua university

summary: Transient pluripotency-factor-based signaling-directed (TPS) transdifferentiation  approach could be further applied to generate functional induced endothelial (iEnd) cells  from human fibroblasts with only two factors: Oct4 and Klf4 (OK). The iEnd cells exhibit  characteristic endothelial cell phenotype in vitro and in vivo and are capable of functionally  promoting vascular regeneration and blood perfusion in a murine model of PAD.

overall_design: Human fibroblasts were transfected with Oct4 and Klf4 then changed to endothelial cell culture media with growth factors. iENDs were purified by FACS and enriched in EGM2 media.

first: Jun

last: Li

first: Sheng

last: Ding

first: Ngan

last: Huang


title: Expression profiling of Notch constitutive activation induced HCC in mice

city: Barcelona

first: Clara

last: Alsinet

state: Catalonia

address: Rosselló 153

country: Spain

institute: IDIBAPS - Hospital Clínic

summary: Notch intracellular domain (NICD) is the active form of the Notch receptor. In this mouse model, NICD is inserted in the Rosa26 locus downstream of a loxP-STOP-LoxP (lsl) sequence and therefore NICD expression is dependant on Cre recombinase expression. These mice are crossed with the AFP-Cre strain that expresses Cre in hepatoblasts due to its regulation by the AFP promoter and albumin enhancer. Mice from 6 to 12 months are sacrificed and liver RNA samples from control monotransgenic Rosa26-lsl-NICD and confirmed HCC lesions from bitransgenic AFP-Cre/Rosa26-lsl-NICD (AFP-NICD) are obtained. Exon expression profiling of these samples are submitted.

overall_design: Four liver samples from monotransgenic mice (control) and five hepatocellular carcinoma samples from bitransgenic mice are analyzed using the Affymetrix GeneChip Mouse Gene 1.0 ST Array platform. Array data was preprocessed and analyzed using GenePattern software and R.

first: Augusto

last: Villanueva

first: Kilangsungla

last: Yanger

first: Yujin

last: Hoshida

first: Yiwei

last: Zong

first: Sara

last: Toffanin

first: Leonardo

last: Rodriguez-Carunchio

first: Manel

last: Sole

first: Swan

last: Thung

first: Ben

middle: Z

last: Stanger

first: Josep

middle: M

last: Llovet


title: Gene expression profile after dexamethasone in chronic lymphocytic leukemia cells according to IGHV/ZAP-70 status

first: Maria Joao

last: Baptista

address: Pg de la Vall d’Hebron 119-129

department: Department of Hematology

institute: Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron

summary:
Glucocorticoids are part of the therapeutic armamentarium of chronic lymphocytic leukemia where it has been suggested that cells with unmutated IGHV genes exhibit higher sensitivity. The mechanisms by which glucorticoids are active in CLL are not well elucidated.
We used microarrays to detail the global programme of gene expression underlying dexamethasone differential activity according to the prognostic subgroups mutated IGHV genes / low ZAP-70 expression and unmutated IGHV genes / high ZAP-70 expression. We aimed to ascertain the molecular mechanisms that are influencing the diffferential response to this drug.

overall_design: Peripheral blood mononuclear cells from chronic lymphocytic leukemia patients were obtained. Samples were split in two for control and incubation with dexamethasone for 6 hours. RNA was extracted and processed for further hybridization on Affymetrix microarrays.

first: Maria

first: Susana

last: Kalko

first: Francesc

last: Bosch


title: Sox2 ablation in the DP alters its gene expression signature

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary: Using Tbx18Cre to target embryonic DP precursors, we ablate Sox2 early and efficiently, resulting in diminished hair shaft outgrowth. Transcriptional profiling of Sox2 null DPs reveals increased Bmp6 and decreased Bmp inhibitor Sostdc1, a direct Sox2 transcriptional target.

overall_design: FACS sort to isolate Sox2GFP/Integrin-alpha 9 double-positive DP cells from Sox2 HET and cKO P5 skin for transcriptional profiling

first: Carlos

last: Clavel


title: Ankylosing spondylitis vs control synovial biopsies

city: Woolloongabba

first: Gethin

last: Thomas

state: QLD

address: Princess Alexandra Hospital

country: Australia

institute: University of Queensland Diamantina Institute

summary: We have compared synovial biopsies from ankylosing spondylitis and undifferentiated spondylitis patients with healthy controls and osteoarthritis patients  Objective:  In spondylarthropies, whole-genome gene expression profiling studies have been limited to peripheral blood to date. By undertaking a study in knee synovial biopsies from spondylarthropy (SpA) and ankylosing spondylitis (AS) patients we aimed to identified joint-specific candidate genes and pathways. These pathways may mediate systemic inflammation driven joint damaging processes and more specifically, the osteoproliferation that is characteristic of these conditions.  Methods: RNA was extracted from six seronegative SpA, two AS, three osteoarthritis (OA) and four normal control knee synovial biopsies. Whole genome expression profiling was undertaken using the Illumina DASL system, which assays 24000 cDNA probes. Differentially expressed candidate genes were then validated using quantitative PCR and immunohistochemistry.   Results: 416 differentially expressed genes were identified that clearly delineated between AS/SpA and control groups. Pathway analysis showed altered gene-expression in oxidoreductase activity, osteoblast activity, B-cell associated, matrix catabolic, and metabolic pathways. The inflammatory mediator, MMP3, was strongly upregulated in AS/SpA samples and the Wnt pathway inhibitors DKK3 and Kremen1 were downregulated.  Conclusion: Pathways mediating both systemic inflammation as well as local tissue changes were identified. This suggests initial systemic inflammation in spondylarthropies transfers to and persists in the local joint environment, subsequently mediating changes in genes directly involved in the destructive tissue remodelling.

overall_design: Fifteen knee synovial biopsy tissue samples consisting of six seronegative spondyloarthropy (SpA), two ankylosing spondylitis (AS), three osteoarthritis (OA) and four normal control biopsies were obtained from the Synovial Tissue Bank at the Repatriation General Hospital in Adelaide, South Australia with the appropriate ethical approval (Supplementary Table 1). All patients provided informed written consent.


title: Identification of human miR-22-responsive transcripts in MCF7 cells

city: Beijing

first: Jianhua

last: Xiong

address: Jinguang Life Science Building,Peking University,No.5 Yiheyuan Road

institute: Peking University

summary:
To examine the expression patterns of human miR-22-responsive transcripts in estrogen receptor alpha positive cell line MCF7, we transfected miR-22 duplex or negative control RNA duplex into MCF7 cells. Gene expression patterns were then evaluated using Affymetrix Human Genome U133 Plus 2.0 Array microarrays.

Keywords: comparision of expression patterns in MCF7 cells with or without  human miR-22 overexpression.

overall_design: Total RNA was collected from two groups MCF7-NC (MCF7 cells transfected with negative control RNA duplex) and MCF7-miR (MCF7 cells transfected with miR-22 duplex) and hybridized to Affymetrix microarrays. Each group has three repeat samples.

first: Zicai

last: Liang


title: Molecular fingerprint of the podocyte reveals novel gene  regulatory networks

status: Public on Nov 30 2012

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: The thorough characterization of the transcriptome of endogenous podocytes   has been hampered by low yields of cell isolation procedures.   Here we introduce a double fluorescent reporter mouse model combined   with an optimized bead perfusion protocol and efficient single cell   dissociation yielding more than 500,000 podocytes per mouse allowing for   global, unbiased downstream applications.   Combining mRNA  transcriptional profiling revealed programs of highly   specific gene regulation tightly controlling cytoskeleton,   cell differentiation, endosomal transport and peroxisome function in podocytes.   Strikingly, the analyses further predict that these podocyte-specific gene   regulatory networks are accompanied by alternative splicing of respective genes.   In summary, the presented ‘omics’ approach will facilitate the discovery   and integration of novel gene, protein and organelle regulatory   networks that deepen our systematic understanding of podocyte biology.

overall_design: To compare gene expression of glomerulus podocytes versus non-podocytes  5 replicates of 4 pooled mice were used. Data were normalized by robust multi-chip analysis. Exon expression values were summarised to the core meta probesets, as defined by Affymetrix, using the oligo library from R.

first: Melanie

last: Boerries

first: Florian

last: Grahammer

first: Sven

last: Eiselein

first: Moritz

last: Buck

first: Charlotte

last: Meyer

first: Markus

last: Goedel

first: Wibke

last: Bechtel

last: Krüger

first: Stefan

last: Zschiedrich

first: Dietmar

last: Pfeifer

first: Denis

last: Laloe

last: Arrondel

last: Goncalves

first: Scott

last: Harvey

first: Joern

last: Dengjel

first: Tobias

middle: B

last: Huber


title: 450k Analysis of 3 FF HPV+ and 3 FF HPV- HNSCC samples

city: London

first: Matthias

last: Lechner

address: Gower Street

department: UCL Cancer Institute

institute: University College London

summary: The methylation analysis of 3 FF HPV+ HNSCC samples and 21 FP HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

overall_design: Analysis of 6 450k methylation profiles, comprising 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

first: Tim

last: Fenton

first: James

last: West

first: Gareth

last: Wilson

first: Andrew

last: Feber

first: Christina

last: Thirlwell

first: Harpreet

middle: K

last: Dibra

first: Amrita

last: Jay

first: Lee

last: Butcher

first: Fiona

last: Gratrix

first: Nirali

last: Patel

first: Francis

last: Vaz

first: Paul

last: O'Flynn

first: Nicholas

last: Kalavrezos

last: Teschendorff

first: Chris

last: Boshoff

first: Stephan

last: Beck


title: Hypermethylation of miR-34b is associated with CREB overexpression and Myeloid Cell Transformation

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary: Increased CREB levels and upregulation of its target genes expression resulted in increased myelopoiesis and colony formation.

overall_design: Class comparison between MDS patients at diagnosis and evolution in AML

first: Silvia

last: Bresolin

first: Martina

last: Pigazzi


title: Transcriptional profile of EHEC 86-24 fusK (HK) and fusR (RR) mutants

city: Dallas

first: Alline

middle: Roberta

last: Pacheco

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: The goals of this experiment was to obtain a transcriptional profile of EHEC 86-24 upon deletion of fusK or fusR genes.

overall_design: The samples were grown in DMEM until late logaritmic phase then RNA was extracted using the TriZol method.


title: Oral Cavity Cancer Compared to Adjacent "Normal" Tissue [Validation Set]

city: Stanford

first: Floyd

middle: Christopher

last: Holsinger

address: 875 Blake Wilbur Drive, CC-2227

department: Head and Neck srugery

institute: Stanford University School of Medicine, Stanford Cancer Center

summary: Oral Cavity Cancer

overall_design: Comparative analysis of gene expression using Affymetrix U133 plus 2.0 microarrays to compare differences between oral cancer samples (most HPV-) and adjacent "normal" mucosa.   We have 24 matched pairs of tumor and normal from the same patient


title: 450k Analysis of 24 HNSCC cell lines

first: Matthias

last: Lechner

summary: The methylation analysis of HPV+ HNSCC cell lines and HPV- HNSCC cell lines as well as clones from an infected HPV- cell line by Infinium HumanMethylation450 BeadChip

overall_design: Analysis of 24 450k methylation profiles, comprising 3 HPV+ HNSCC cell lines and 3 HPV- HNSCC cell lines (in duplicate each) and 12 infected HPV- HNSCC cell line clones

first: Tim

last: Fenton

first: James

last: West

first: Gareth

last: Wilson

first: Andrew

last: Feber

last: Thirlwell


title: FF and FFPE HPV+ and HPV- HNSCC and HNSCC cell lines

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

overall_design: Refer to individual Series


title: Expression data from YAP-S127A Villin-rtTA crypts

status: Public on Nov 29 2012

city: Boston

first: Fernando

last: Camargo

address: 1 Blackfan Circle

institute: Children's Hospital Boston

summary: We overexpressed YAP in the intestinal epithelium by adding doxycycline to the drinking water of experimental mice. Mice were given dox for 2 days, and referred to as Tg (transgenic).

overall_design: Mice were given dox for 2 days, sacrificed, and crypts were isolated for RNA extraction and analyzed by Affymetrix microarrays.

first: Evan

last: Barry


title: RSpondin1 treatment of control and Yap cKO mice

summary: RSpondin1 adenovirus was administered to mice and intestine was isolated for expression analysis 1 week later.

overall_design: Yap control and cKO mice were given Rspondin virus and sacrificed 1 week later.


title: Methylation of the Proximal, Distal and Core Promoter of CEBPA in 572 Cases with Normal Karyotpye AML and 44 with t(8;21) Disclosed Different Frequencies but no Impact on Prognosis

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

institute: Munich Leukemia Laboratory

summary: The clinical impact of aberrant CEBPA promoter methylation (PM) in AML is controversial discussed. The aim of this study was to clarify the significance of aberrant CEBPA PM with regard to clinical features in a cohort of 572 de novo AML with wildtype CEBPA and normal karyotype. The distal promoter was methylated in 54/572 cases (9.41%) whereas proximal PM was never detected. Methylation of the core promoter was detected in only 8 of 326 cases (2.45%) and thus seems to be a rare event in AML. There was no correlation between CEBPA distal PM, age, sex, white blood cell (WBC) count or Hb levels at diagnosis. We also were not able to detect a significant correlation between the presence of CEBPA distal PM and molecular mutations such as FLT3-ITD, NPM1, AML1, MLL-PTD and IDH1. Solely the frequency of IDH2R140 mutations was significantly reduced in CEBPA distal PM positive compared to CEBPA distal PM negative cases (p=0.01). Furthermore, analysis of CEBPA mRNA expression level revealed no difference between CEBPA distal PM positive and CEBPA distal PM negative cases, suggesting that CEBPA distal PM has no influence on CEBPA expression. CEBPA distal PM did not show impact on overall survival (OS), event free survival (EFS) or incidence of relapse. Also when other mutations were taken into regard no prognostic impact of CEBPA distal PM could be shown. In contrast, a distinct expression profile of CEBPA distal PM positive cases compared to CEBPA mutated and CEBPA distal PM negative cases was observed. In addition, a significantly higher frequency of CEBPA distal PM was detected in RUNX1-RUNX1T1 positive AML compared to the CEBPA witdtype cases. We conclude that the presence of aberrant CEBPA PM has no clinical relevance and is therefore a negligible prognostic marker in de novo AML with normal karyotype.

overall_design: To detect underlying common differences in their gene expression profiles, we investigated 9 CEBPA methylated (unmutated), 8 CEBPA single-mutated, 10 CEBPA double-mutated, and 10 non-methylated/non-mutated cases (Affymetrix HG-U133 Plus 2.0 microarrays; Santa Clara, CA). The microarray sample preparation assay was performed as previously reported. Gene expression raw data were processed according to the manufacturer’s recommendations.

first: Annette

last: Fasan

first: Tamara

last: Alpermann

first: Christiane

last: Eder

first: Vera

last: Grossmann

last: Kowarsch

first: Claudia

last: Haferlach

first: Wolfgang

last: Kern

first: Torsten

first: Susanne

last: Schnittger


title: Yap role in intestine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A new classification of chromosome instability (CIN) phynotype, CIN-high and CIN-low (validation dataset)

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

summary: Samples were taken from colorectal cancers in surgically resected specimens in 33 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for CIN phynotype

overall_design:
Specimens from 33 consecutive stage II and stage III patients who had undergone surgical resection of CRC were studied. Patients with familial adenomatous polyposis and HNPCC were excluded from the study. Specimens from tumors and corresponding normal tissues in surgically resected specimens were snap-frozen in liquid nitrogen and stored at -80degreesC until use. Parallel tumor specimens were formalin fixed and paraffin embedded for histological examination. DNA and RNA was extracted from paired tumor and normal tissue using frozen samples. The patients provided written, informed consent to the collection of specimens, and the local Ethics Committee approved the study protocol. MSI and LOH phenotype analysis were done as follows;
Using DNA, we performed the polymerase chain reaction (PCR) and determined the MSI status. In addition to five microsatellite markers recommended by the National Cancer Institute workshop, we also used TP53, D18S46, D18S363 and D18S474.9 We determined LOH status in non–MSI-high tumors, because LOH is rare in MSI-high tumors and also interpretation of LOH is difficult in MSI-high tumors. We defined LOH at each locus as a 50% reduction in the height of one of two allele peaks in tumor DNA relative to non-neoplastic control DNA. LOH was defined as present if any of the markers on the same chromosome show LOH. In order to evaluate the severity of chromosomal instability based on the actual frequency of LOH among evaluable loci, we defined the LOH Ratio (%) as:
LOH Ratio (%) = Total number of chromosomes with LOH / Total number of chromosomes that could be evaluated for LOH × 100. Depending on the LOH Ratio, we classified tumors as having high levels of chromosomal instability (CIN-high) (33% < LOH Ratio < 100%) or low levels of chromosomal instability (CIN-low) (0% < LOH Ratio <33%). Furthermore, CIN-high tumors were divided into two subgroups; CIN-high (mild type) (33% < LOH Ratio < 75%) and CIN-high (severe type) (75% < LOH Ratio <100%).

first: Takashi

last: Kobunai


title: Expression data of EZH2-dependent genes in prostate cancer cell lines

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary:
EZH2 is frequently over-expressed in aggressive and metastatic solid tumors, including castration resistant prostate cancer (CRPC). We sought to determine EZH2-dependent gene expression programmes in prostate cancer progression, and found an intriguing functional switch of EZH2 from a repressor to an activator during CRPC development.
We used microarrays to detail the global profiling of gene expression that are differentially regulated upon EZH2 depletion in two different prostate cancer cell lines.

overall_design: The androgen-dependent prostate cancer cell line LNCaP and the LNCaP-derived androgen-independent cell line LNCaP-abl (abl) were used for this study, as their transcription profiles strongly resemble that of clinical androgen-dependent and castration resistant prostate tumors, respectively. EZH2 was silenced by specific siRNAs in both cell lines, and total RNA was extracted and hybridized on Affymetrix microarrays.

first: Zhenhua

last: Wu


title: Role of FOXP3 in human Jurkat T cells

status: Public on Nov 26 2012

city: Braunschweig

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research

type: Genome binding/occupancy profiling by genome tiling array


title: Expression data from control and colicin M treated E. coli MG1655 culture

city: ljubljana

first: simona

last: kamensek

address: večna pot 111

department: department of biology

country: Slovenia

institute: university of ljubljana, biotechnical faculty

summary: Among colicin producing E. coli, colicin M producing strains are the most frequently present in natural populations. Bacteria must be able to sense and respond to unfavourable conditions, resulting in adaptive responses. To gain insight into colicin M ecological role and the purposes related to antimicrobial therapy, the effects of subinhibitory concentrations of colicin M on E. coli whole genome transcription was investigated. We used microarray analysis to follow differential gene expression in E. coli upon colicin M exposure. Colicin M inhibits peptidoglycan synthesis altering expression of genes involved in envelope stress, osmotic and other stresses, exopolysaccharide prodoction, biofilm formation, and cell motility.

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

overall_design: A sub-lethal concentration of colicin M was used to treat E. coli MG1655 cultures at an early logarithmic phase. The experiments were performed  in parallel with untreated control E. coli MG1655 cultures. Total RNA was extracted after 30 min and 60 min  treatment with colicin M and used for hybridization on Affymetrix microarrays.

first: Darja

last: Žgur-Bertok

first: Simona

last: Kamenšek


title: Longitudinal expression data from CD8+ T cells responding to LCMV-Armstrong or LCMV-Clone 13

status: Public on Nov 23 2012

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

institute: University of Pennsylvania

summary: During acute viral infections, naïve CD8+ T cells differentiate into effector CD8+ T cells and, after viral control, into memory CD8+ T cells. Memory CD8+ T cells are highly functional, proliferate rapidly upon reinfection and persist long-term without antigen. In contrast, during chronic infections, CD8+ T cells become “exhausted” and have poor effector function, express multiple inhibitory receptors, possess low proliferative capacity, and cannot persist without antigen. To compare the development of functional memory T cells with poorly functional exhausted T cells, we generated longitudinal transcriptional profiles for each.

overall_design: Naive CD44Lo CD8+ T cells were isolated and sorted from uninfected C57BL/6 mice and H2-Db GP33-specific CD8+ T cells were sorted using MHC-I tetramers at d6, 8, 15, and 30 p.i. with either LCMV Arm or LCMV clone 13. RNA from these CD8+ T cells was processed, amplified, labeled, and hybridized to Affymetrix GeneChip MoGene 1.0 st microarrays

first: Alison

last: Crawford

first: Jill

last: Angelosanto


title: Expression data of hepatocytes isolated from chimeric mouse livers repopulated with human hepatocytes and from normal human livers

status: Public on Nov 27 2012

city: Tokyo

first: Fuyuki

last: Miya

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

institute: Keio University

summary:
We generated chimeric mice with livers that were predominantly repopulated with human hepatocytes. Hepatocytes were isolated from the chimeric mouse livers and their gene expressions were compared with hepatocytes isolated from normal human livers . Cluster and principal components analyses showed that gene expression profiles of hepatocytes from the chimeric mice and those from normal human livers were extremely closed.
Additionally, we performed microarray experiments to examine gene expression in human tissues. This data was used for comparison with hepatocytes.
A total of 22 tissues (bone marrow, cerebellum, colon, cortex, fetal brain, heart, kidney, liver, lung, pancreas, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea and uterus) were examined.

overall_design:
The chimeric mice were generated by transplantation of 2 different donor hepatocytes. Hepatocytes were isolated from the mouse livers and normal human livers, and their cDNAs were used for microarray analysis.
Total RNA isolated from human tissues and cell cultures were labeled and hybridized to the GeneChip Human Genome U133 Plus 2.0 Array according to the manufacturer's protocol.

first: Chise

last: Tateno

first: Miho

last: Kataoka

first: Asato

last: Tachibana

first: Toshiyuki

last: Itamoto

first: Toshimasa

last: Asahara

first: Yusuke

last: Nakamura

first: Tatsuhiko

last: Tsunoda

first: Katsutoshi

last: Yoshizato


title: H2A.Z inheritance during the cell cycle [expression array]

city: Singapore

first: Rohan

last: Williams

address: Medical Drive

country: Singapore

institute: SCELSE-NUS

summary:
While it has been clearly established that well positioned H2A.Z-containing nucleosomes flank the nucleosome depleted region (NDR) at the transcriptional start site (TSS) of active mammalian genes 1,2, how this chromatin-based information is transmitted through the cell cycle is unknown. We show here that in trophoblast stem (TS) cells, the level of H2A.Z at promoters decreases during S phase coinciding with homotypic (H2A.Z/H2A.Z) nucleosomes flanking the TSS becoming heterotypic (H2A.Z/H2A). Surprisingly, these nucleosomes remain heterotypic at M phase. At the TSS, we identify an unstable heterotypic H2A.Z-containing nucleosome in G1 which, strikingly, is lost following DNA replication. These dynamic changes in H2A.Z at the TSS mirror a global expansion of the NDR at S and M which, unexpectedly, is unrelated to transcriptional activity. Coincident with the loss of H2A.Z at promoters, it is targeted to the centromere when mitosis begins.
We surveyed whole genome expression using microarrays, in combination with H2A.Z ChIP-Seq (Illumina) data, to study the H2A.Z distribution on promoters of coding genes in different stages of the cell cycle in Trophoblast Stem (TS) cells. These data are published in Nekrasov et al., H2AZ inheritance during the cell cycle and it's impact on promoter organization and dynamics, Nature Structural and Molecular Biology (in press: accepted for publication on 24 Sep 2012).

overall_design: Mouse Trophoblast stem (TS) cells were grown in cell culture medium. By adding specific drugs cells were arrested at particular stages of the cell cycle: G1; S and M. Total RNA was extracted from TS cells arrested at G1; S and M stages of cell cycle using TRizol (Invitrogen) extraction protocol and purified further the by RNAeasy Extraction Kit (Qiagen). RNA quality was assesed on Bioanalyzer total RNA  chip. RNA samples were reverse transcribed and resulted cDNA samples were subjected to DNA microarray analysis (in triplicate) using the GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Robust Multichip Average (RMA) correction and probe set summaries were obtained using Affymetrix Power Tools software annotation (Affymetrix) based on the mm9 mouse genome. Unless otherwise stated, all subsequent expression analyses (see Supplementary Methods) were performed in the R statistical computing environment (version 2.11.1).

first: Max

last: Nekrasov


title: Comparative transcriptomic profiling of liver tissue from wild-type C57BL-6 mice fed a high-fat diet (HFD) supplemented with the probiotic (P) Bifidobacterium pseudocatenulatum  CECT 7765.

status: Public on Nov 20 2012

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

institute: CEBAS-CSIC

summary: We used Affymetrix microarrays to investigate gene expression changes in the liver of wild-type C57BL-6 mice exposed to a high-fat diet that might have been caused by the oral consumption of the probiotic B. pseudocatenulatum CECT 7765.

overall_design:
The aim of this work was to determine whether the daily intake (by oral gavage) of the probiotic (P) B. pseudocatenulatum for seven weeks exerted any modulatory effects, at the level of gene expression, in the liver of C57BL-6 male mice exposed to a high-fat diet (HFD). Male mice were randomly assigned to four experimental groups (n= 5 animals per group) as follows: (1) control group, fed a standard diet (SD); (2) obese group, fed a high-fat diet (HFD); (3) a group that received the SD and a daily dose of the probiotic (1×109 CFU B. pseudocatenulatum CECT 7765) (SD+P); and (d) an obese group that was fed the HFD and a daily dose of the probiotic (1×109 CFU B. pseudocatenulatum CECT 7765) (HFD+P). At the end of the experimental procedure total RNA was extracted from the liver to compare differential gene expression between the groups.
Liver differential gene expression after 7 weeks of supplementation between: 1) the HFD group and the SD group (effects of the high-fat diet); 2) the HFD+P and the HFD (effects of the probiotic on the consumption of a high-fat diet) and 3) the SD+P group and the SD (direct effects of the probiotic on the liver of animals consuming a normal diet).

first: Angela

last: Moya-Pérez

first: Yolanda

middle: S

last: Herranz


title: Expression analysis of cancer of unknown primary (CUP) 1

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

institute: Kinki university School of Medicine

summary:
Biopsies (lymph nodes, ascites or hydrothorax) from 60 patients with cancer of unknown primary origin were analyzed.
Results provide insight into the molecular pathogenesis of CUP.

overall_design: 60 samples; 1 array per sample

first: Kazunari

last: Kurahashi

first: Kazuto

last: Nishio


title: JmjD2d-dependence of LPS-induced genes

status: Public on Nov 19 2012

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

summary: In dendritic cells, expression of the H3K9me3 demethylase JmjD2d is upregulated by LPS stimulation.  To identify genes whose induction by LPS depends on JmjD2d activity, we performed a microarray analysis of wild-type and JmjD2d-knockdown dendritic cells, before and after stimulation with LPS.

overall_design: RNA was extracted from three independent cultures of wild-type and JmjD2d-knockdown dendritic cells, before and 4h after stimulation with 100ng/ml LPS.  The unstimulated and stimulated wild-type samples, and the stimulated JmjD2d-knockdown samples, were used for microarray analysis.

first: Yina

last: Zhu

first: Simona

last: Saccani


title: Gene expression from lamina propria of olfactory mucosa from Human

status: Public on Nov 15 2012

city: San Diego

first: Ignacio

last: Sancho-Martinez

state: California

address: 110 North Torrey Pines Road

department: Gene Expression Laborartory-B

institute: Salk Institute for Biological Studies

summary: The establishment of induced pluripotent stem (iPS) cells methodologies has widened the possibilities of stem cell related clinical therapies. However, safety concerns over current reprogramming technologies as well as lack of efficient protocols for differentiation raise serious questions over their usage in clinical settings.  Direct lineage conversion may represent a safer technology for cell-therapy. Here, we identify Sox2 as a factor able to transdetermine human mesenchymal stem cells (MSCs) to hematopoietic progenitor cells (HPCs), recapitulating the molecular events during in vivo hematopoiesis. This technology offers an efficiency of up to 70% HPC generation in less than 8 days under feeder-free conditions. With the goal of devising ways for transplantation into diseased patients we developed two different methodologies that avoid exogenous DNA integration or viral infections. The first, by transduction of recombinant Sox2 protein, and the second by functional replacement of Sox2 by inhibition of TGFß signaling. The DNA integration-, virus-, and feeder-free transdetermination system here described may complement and enhance current approaches for autologous as well as heterologous HPC transplantation in humans.

overall_design: Mesenchymal Stem Cells were transdifferentiated towards the hematopoietic lineage.

first: Leo

last: Kurian

first: Emmanuel

last: Nivet

last: Martinez

first: JC

last: Belmonte

first: Francoise

last: Feron

first: Sachin

last: Kumar


title: Gene expression data from T cells and NK cells with and without treatment with Hsp90 inhibitor (Geldanamycin)

status: Public on Nov 14 2012

first: Aditya

last: Munshi

state: MA

address: 44 Binney St

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

summary: Hsp90 is critical for regulation of the phenotype and functional activity of human T lymphocytes and natural killer (NK) cells.

overall_design: Analysis of human T cells (CD4, CD8) and NK cells treated with Hsp90 inhibitor.

first: Jooeun

last: Bae


title: Nitric Oxide-releasing prodrug triggers cancer cell death through deregulation of cellular redox balance

status: Public on Nov 17 2012

city: Bethesda

first: Robert

last: Cheng

address: 10 Center Drive

department: CCR

institute: NCI

summary: JS-K, a NO donor which capable to induce cancer apopotosis, it's killing mechanism was investigated in this study. We found out that JS-K induce apopotosis via deregulating the GSH/GSSG redox couple.

overall_design: Leukemia cells were treated with JS-K and then assayed for metabolic changes by LC/MS and gene expression alterations by microarray.

first: Anna

last: Maciag

middle: Y


title: Expression data from in vitro derived dendritic cells generated in the presence of FLT3-L from wt and miR-142-/- BM cells

status: Public on Nov 16 2012

city: Rehovot

first: Alexander

last: Mildner

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary:
2 types of dendritic cells (DCs) can be generated in vitro in the presence of Flt3-L: CD4+ equivalent CD24- DCs and CD8+ equivalent CD24+ DCs. miR-142-/- mice show a severe defect in the generation of CD4+ equivalent CD24- DCs. To understand the underlying mechanism, RNA expression was analyzed by Affymetrix microarray from the 2 in vitro subtypes of DCs derived from miR-142+/+ and miR-142-/- bone marrow cells.
We used microarrays to detail the global programme of gene expression in the presence or absence of miR-142 in in vitro derived DCs.

overall_design: Bone marrow cells from miR-142+/+ and miR-142-/- C57Bl/6 mice were isolated and incubated in the presence of Flt3-L for 8 days. in vitro derived wt and ko dendritic cells were devided into CD4+ and CD8+ equivalent DCs by FACS and sorted with a FACS-Aria. RNA was isolated and gene expression was investigated

first: Steffen

last: Jung


title: Expression data from WT and VAChT KDHOM ventricles

city: London

first: David

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

summary:
VAChT KDHOM mice have a 70% decrease in the vesicular acetylcholine transporter (VAChT) and this leads to a systemic decrease in ACh release and cardiac dysfunction.
We used this microarray to determine whether there were transcriptional alterations in the hearts of mutant mice as a result of this long-term decrease in cholinergic tone.

overall_design: We isolated whole hearts from 3-month-old WT and VAChT KD mice and used them for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogenous populations for each sample and, as such, pooled together two RNA samples to generate one microarray sample.

first: Prado

last: Marco A.M.

first: Gros

last: Robert


title: High-time-resolution dynamic analysis of human regulatory T cell (Treg) / CD4+ T-effector cell (Teff) activation

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary:
Human FOXP3+CD25+CD4+ regulatory T cells (Tregs) play a dominant role in the maintenance of immune homeostasis. Several genes are known to be important for murine Tregs, but for human Tregs the genes and underlying molecular networks controlling the suppressor function still largely remain unclear. We here performed a high-time-resolution dynamic analysis of the transcriptome during the very early phase of human Treg/ CD4+ T-effector cell activation. After constructing a correlation network specific for Tregs based on these dynamic data, we described a strategy to identify key genes by directly analyzing the constructed undirected correlation network. Six out of the top 10 ranked key hubs are known to be important for Treg function or involved in autoimmune diseases. Surprisingly, PLAU (the plasminogen activator urokinase) was among the 4 new key hubs. We here show that PLAU was critical for expression regulation of FOXP3, EOS and several other important Treg genes and the suppressor function of human Tregs. Moreover, we found Plau inhibits murine Treg development and but promotes the suppressive function. Further analysis unveils that PLAU is particularly important for memory Tregs and that PLAU mediates Treg suppressor function via STAT5 and ERK signaling pathways. Our study shows the potential for identifying novel key genes for complex dynamic biological processes using a network strategy based on high-time-resolution data, and highlights a critical role of PLAU in both human and murine Tregs. The construction of a dynamic correlation network of human Tregs provides a useful resource for the understanding of Treg function and human autoimmune diseases.
The high-time-resolution time-series transcriptomic data during the very early phase of human Treg/Teff activation could be generally used for further mechanistic analysis of human Treg function. These data could be further used for biological network analysis, dynamic analysis, modeling by experimental researchers, bioinformaticians, computational biologists and systems biologists.

overall_design: We have measured the genome-wide expression of 38,500 genes (probes) by performing a high-time-resolution time-series analysis during the activation process of human regulatory T cells /CD4+ T-effector cells at 19 time points for the first 6h with an equal interval of 20 min. We have also overexpressed the GARP gene in human effector T cells and measured the genome-scale expression for the GARP-overexpressed cells and ThGFP cells at time point 0, 100 and 360min following activation. The stimulation source used in this work is a combination of anti-CD3/-CD28 Dynal beads with IL2 100U/ml.

last: He

first: Hairong

last: Chen

first: Michael

last: Probst-Kepper

last: Geffers

first: Klaus

last: Schughart

first: An-Ping

last: Zeng

first: Rudi

last: Balling


title: Effect of FTO overexpression and knockdown on transcriptome of HEK293 cells

status: Public on Nov 13 2012

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
To gain insight into FTO function, we knocked down and overexpressed FTO in HEK293 cells.Genetrail analyses of expression profiles pointed to the RNA splicing and processing machinery. Intriguingly, using immunocytochemistry and confocal laser scanning microscopy, we observed strong enrichment of FTO in nuclear speckles and - to a lesser extent - in nucleoli, but not in other known nuclear bodies. We also studied RNA samples of Fto knockout and wild type mice with regard to content of methylated and unmethylated nucleosidesand observed that ratios of modified and unmodified uracil and adenine were different depending on the presence of FTO. Taken together, our data suggest that FTO is involved in RNA processing and modification.
We used microarrays to investigate global gene expression changes depending on the level of FTO

overall_design: We compared FTO overexpressing and FTO depleted cells to cells with endogeneus level of FTO to determine global gene expression changes.

first: L

first: T

last: Berulava


title: Gene expression profile of Human tissues and cells

status: Public on Nov 12 2012

first: Fuyuki

last: Miya

summary:
We performed microarray experiments to examine gene expression in human tissues. This data was used for comparison with our humanized mouse study (GEO ID GSE33846) and threshold determination of our tiling array data (GEO ID GSE18490, public in the near future).
A total of 22 tissues (bone marrow, cerebellum, colon, cortex, fetal brain, heart, kidney, liver, lung, pancreas, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea and uterus) and 2 cell lines (HeLa and SH-SY5Y) were examined.

overall_design: Total RNA isolated from Human tissues and cell cultures were labeled and hybridized to the GeneChip Human Genome U133 Plus 2.0 Array according to the manufacturer's protocol.

first: Yusuke

last: Nakamura

first: Tatsuhiko

last: Tsunoda


title: Mapping  and genome-wide profiling of human NKp46+ cells

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary: Understanding Natural Killer (NK) cell anatomical distribution is key to dissect the role of these unconventional lymphocytes in physiological and disease conditions. In mouse, NK cells have been detected in various lymphoid and non-lymphoid organs, while in humans the current knowledge of NK cell distribution at steady state is mainly restricted to lymphoid tissues. The translation to humans of findings obtained in mice is facilitated by the identification of NK cell markers conserved between these two species. The Natural Cytotoxicity Receptor (NCR) NKp46 is a marker of the NK cell lineage evolutionary conserved in mammals. In mice, NKp46 is also present on rare T cell subsets and on a subset of gut Innate Lymphoid Cells (ILCs) expressing the retinoic acid receptor-related orphan receptor gammat (RORgammat) transcription factor. Here, we documented the distribution and the phenotype of human NKp46+ cells in lymphoid and non-lymphoid tissues isolated from healthy donors. Human NKp46+ cells were found in splenic red pulp, in lymph nodes, in lungs and gut lamina propria, thus mirroring mouse NKp46+ cell distribution. We identified a novel cell subset of CD56dimNKp46low cells that includes RORgammat+ILCs with a lineage-CD94-CD117brightCD127bright phenotype.We also included data regarding the genome-wide transcriptional profiles of human healthy colonic NK cells and  RORgammat+ILCs.The use of NKp46 thus contributes to establish the basis for analyzing quantitative and qualitative changes of NK cell and ILC subsets in human diseases.

overall_design: Human colonic CD56-NKp46lowCD117brightCD127bright cells = LTi cells and CD56+NKp46+CD117-CD127- cells =NK cells were isolated from macroscopically unaffected areas of colon of patients with colon cancer. Indicated populations were sorted and immediately lysed in RLT buffer supplemented with 10% beta-mercaptoethanol (Quiagen, France). Lysates of three distinct donors were pooled and RNA was isolated by using RNAeasy Microkit (Quiagen, France). Duplicates were performed for each cell type. cRNA were obtained after double amplification using the MessageAmp II aRNA Amplification Kit (Ambion, France). cRNA were then hybridized on Human Genome HG_U133 +2.0 Affymetrix chips. Chip images were generated using Affymetrix AGCC 3.2 software, then expression data were extracted and normalized using Affymetrix Expression console 1.1 with the algorithm RMA. Data obtained were expressed as log2.

first: Elena

last: Tomasello

first: Nadia

last: Yessaad

first: Emilie

last: Gregoire

first: Kelly

last: Hudspeth

first: Carmelo

last: Luci

first: Domenico

last: Mavilio

first: Jean

last: Hardwigsen

first: Eric

last: Vivier


title: Gene expression profiling of pancreatic epithelial cells in response to tissue contextual changes

city: Tainan City

first: Wei-Yu

last: Wang

address: 2F., No. 367, Shengli Road

institute: National Health Research Institutes

summary: To understand the molecular process associated with tissue morphogenesis of pancreatic epithelial cells, we profiled the transcriptomes of normal or malignant pancreatic organoids formed in three-dimenstional reconsitututed basement membrance (rBM). Cell monolayers cultured on rBM-coated culture plastics were used as controls.

overall_design: HPDE (immortalized pancreatic epithelial cells) and PANC-1 cells (pancreatic cancer cells) were seeded on reconstituted basement membrane (rBM)-coated culture plastics or cultured on top of three-dimensional (3D) rBM gels. Total RNA samples were collected from cell monolayers or 3D cell clusters (formed at day 2), pancreatic tubules or tumor spheroids (formed at day 6) in the rBM culture, followed by global gene expression profiling.

first: J-M

last: Su

first: K-C

last: Tsai


title: Gene expression profile of conventional T cells (Tconv) and regulatory T cells (Treg) stimulated with anti-costimulatory molecule antibodies

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

summary: Co-stimulatory molecules of the CD28 family on T lymphocytes integrate cues from innate immune system sensors, and modulate activation responses in conventional CD4+ T cells (Tconv) and their FoxP3+ regulatory counterparts (Treg). To better understand how costimulatory and co-inhibitory signals might be integrated, we profiled the changes in gene expression elicited in the hours and days after engagement of Treg and Tconv by anti-CD3 and either anti-CD28, -CTLA4, -ICOS, -PD1, -BTLA or -CD80.

overall_design: Total CD4+ T cells were stimulated by anti-CD3 and either anti-CD28, -CTLA4, -ICOS, -PD1, -BTLA or -CD80 antibodies for 1, 4, 20 and 48 hrs and Tconv and Treg were separated by flowcytometry. The 1 and 4 hr lysates were pooled [the 'early' samples] before RNA purification and profiling, as were the 20 and 48 hr samples [the 'late' samples] (note; for Treg cells, only the 20 hr sample was used). RNA was amplified, labeled and hybridized to Mouse Gene 1.0 ST arrays with the data generation and quality control pipeline of 19 the Immunological Genome Project (www.immgen.org), in biological triplicates (duplicates only for ICOS and CD80). Raw data were background-corrected and normalized using the RMA algorithm.

first: Ei

last: Wakamatsu

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Global expression analysis of DLBCL and SMZL cell lines

status: Public on Nov 10 2012

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

institute: University of Navarra/ Clínica Universidad de Navarra

summary: The multifunctional protein lipopolysaccharide-induced TNFalpha factor (LITAF) induces the secretion of inflammatory cytokines in monocytes and regulates protein degradation in neural cells. In B-cell lymphomas, LITAF is frequently inactivated by epigenetic mechanisms, but beyond these data little is known about its regulation and function. Immunohistochemical and gene expression profiling analyses of normal and malignant B-cells revealed that LITAF and BCL6 exhibited opposite expression patterns. Accordingly, chromatin immunoprecipitation and luciferase experiments showed that LITAF is transcriptionally repressed by BCL6 in germinal center (GC) lymphocytes and in B-cell lymphoma cells. Gain- and-loss-of-function assays demonstrated that LITAF does not exert any of its previous roles. Conversely, LITAF co-localized with autophagosomes in B-cells whereby activated autophagic responses, which were abrogated upon LITAF silencing. Therefore, BCL6-mediated transcriptional repression of LITAF may contribute to an appropriate GC reaction by suppressing autophagy in GC lymphocytes, whereas constitutive repression of autophagic responses may promote B-cell lymphoma development.

overall_design: 39 diffuse large B-cell lymphoma (DLBCL) and 3 splenic marginal zone lymphoma (SMZL) untreated cell lines were analyzed for global gene expression with the GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). SMZL cell lines were hybridized in duplicate, resulting in a total of 45 microarrays.

first: Victor

last: Segura

first: Jose

middle: A

last: Martinez-Climent

first: Carolina

last: Gomez-Municio


title: Expression data from HIV exposed and uninfected women

status: Public on Nov 11 2012

city: winnipge

first: binhua

last: liang

address: 1015 Arlington Street

institute: National Microbiology Laboratory

summary:
We carried out a global whole blood genome wide expression profiling of HIV exposed and uninfected women from Nairobi to  identify host factors which may be a key contribution to HIV resistance phenomenon.
To identify novel biomarkers for HIV resistance including pathways that may be critical in anti-HIV vaccine design, we carried out a gene expression analysis on blood samples obtained from HIV Exposed and uninfected volunteers from a commercial sex worker cohort in Nairobi and compared their profiles to HIV susceptible negative controls. Whole blood samples were collected from 43 HIV resistant and a similar number of HIV negative antenatal clinic attendees and total RNA extracted and hybridized to the affymetrix HUG 133 Plus 2.0 micro arrays (Affymetrix, Santa Clara CA). More than 2,274 probe sets   were differentially expressed in the HIV resistant women as compared to the control group (fold change   ≥1.3; p value ≤ 0.0001, FDR <0.05) . Unsupervised hierarchical clustering of the differentially expressed genes readily distinguished EUs from susceptible controls. Pathway analysis of the differentially expressed genes through the KEGG signaling revealed a majority of the impacted pathways (13 of 15, 87%) were significantly down expressed. The most down expressed pathways were glycolysis/gluconeogenesis, pentose phosphate, Phosphatidyl inositol, Natural Killer cell cytotoxicity and T-cell receptor signaling. Ribosomal protein synthesis and tight junction genes were up expressed. We infer that the hallmark of HIV resistance is down regulation of genes in key signaling pathways that HIV depends on for infection and suggest that an anti-HIV vaccine design may need to incorporate components that switch down specific immune activating factors.

overall_design: Whole blood samples were collected from 43 HIV resistant and a similar number of HIV negative women and total RNAs were extracted and hybridized on Affymetrix microarrays. We sought to compare gene expression patterns between two groups of women and infer the genes which may be involved in key signaling patheways that HIV depending on for infection.

first: Ben

last: Liang

first: Martin

last: Songok


title: Loss of p53 in enterocytes facilitates an inflammatory microenvironment enabling invasion and metastasis of carcinogen-induced colorectal tumors

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

summary: Here, we examined the role of intestinal epithelial specific tumor suppressive function of 53. We provide evidence that p53 plays a dual role during carcinogen-induced tumorigenesis. At the initiation stage, p53 controls DNA damage and survival of initiated epithelia. In contrast, at later stages, loss of p53 is associated with the formation of an inflammatory microenvironment that is linked to epithelial mesenchymal transition, invasion and metastasis and the activation of NF-kappaB and Stat3. Thus, we propose a novel p53 controlled tumor suppressive function during the progression stage of colorectal cancer that is independent of its well-established role in cell cycle regulation, apoptosis and senescence.

overall_design: 6 samples were analyzed. We compared 3 wt colon tumor samples and 3 p53-knockout tumor samples.

first: Sarah

last: Schwitalla


title: LITAF, a BCL6 target gene, regulates autophagy in mature B-cell lymphomas

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

overall_design: Refer to individual Series


title: Adenoviral shRNA-based knockdown of hepatic Hnf1b (Ad-shHnf1b)

city: Cologne

first: Jan-Wilhelm

last: Kornfeld

state: NRW

address: Zülpicher Strasse 47a

department: Department of Mouse Genetics and Metabolism

institute: Institute for Genetics

summary: Insulin resistance represents a hallmark during the development of type 2 diabetes mellitus (T2D) and in the pathogenesis of obesity-associated disturbances of glucose and lipid metabolism 1,2,3. MicroRNA (miR)-dependent posttranscriptional gene silencing has recently been recognized to control gene expression in disease development and progression including that of insulin-resistant T2D. MiRs, whose deregulation alters hepatic insulin sensitivity include miR-143, miR-181 and miR-103/107. Here we report that expression of miR-802 is increased in liver of two obese mouse models and of obese human subjects. Inducible transgenic overexpression of miR-802 in mice causes impaired glucose tolerance and attenuates insulin sensitivity, while reduction of miR-802 expression improves glucose tolerance and insulin action. We identify Hnf1b as a target of miR-802-dependent silencing and shRNA-mediated reduction of Hnf1b in liver causes glucose intolerance, impairs insulin signaling and promotes hepatic gluconeogenesis. In turn, hepatic overexpression of Hnf1b improves insulin sensitivity in db/db mice. Thus, the present study defines a critical role for deregulated expression of miR-802 in the development of obesity-associated impairment of glucose metabolism via targeting Hnf1b and assigns Hnf1b an unexpected role in the control of hepatic insulin sensitivity.

overall_design:
Adenoviruses (Ad5) encoding either GFP (Ad-Ctrl 1-3) or shHnf1b (Ad-shHnf1b 1-4) were injected into the tail vein of C57BL/6 mice at 1x10E10 viral particles (VP) per gram bodyweight.
Biotin-labeled cDNA was synthesized using GeneChip Whole Transcript Sense Labeling Assay (Affymetrix) according to vendor’s instructions. After fragmentation, cDNAs were hybridized for 17h at 45°C on Affymetrix Mouse Gene 1.0 ST Arrays. The Arrays were washed and stained in the GeneChip Fluidics Station 450 and scanned on a GeneChip Scanner 3000 7G (Affymetrix). Data intensities were log transformed and normalized with a quantile normalization method using Affymetrix Power Tools. Differentially expressed genes were identified according to statistical evidence indicated by Student's t-test and fold change statistics

first: Jens

middle: C

last: Brüning


title: Protein affects gene expression and prevents lipid accumulation in the liver in mice

status: Public on Nov 21 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Obesity and associated increased prevalence of non-alcoholic fatty liver (NAFLD) disease is suggested to be positively modulated by a high protein (HP) diet in humans and rodents. The aim was to detect mechanisms by which a HP diet prevents hepatic lipid accumulation by means of transcriptomics. To study the acute and long term effect of a high protein ingestion on hepatic lipid accumulation under both low and high fat (HF) conditions, mice were fed combinations of high (35%) or low (10%) fat and high (50%) or normal (15%) protein diets for 1 or 12 weeks. Body composition, liver fat, VLDL production rate and gene expression were investigated. Differences in metabolic processes and functions in the liver were identified using gene set enrichment analysis on microarray data. Mice fed the HP diets developed less adiposity and decreased hepatic lipid accumulation due a combination of induced processes mainly involved in protein catabolism such as transamination, TCA cycle and oxidative phosphorylation. Feeding a HP diet can successfully prevent the development of NAFLD by using ingested energy for oxidation instead of storage.

overall_design: Wild type mice were fed combinations of high (35%) or low (10%) fat and high (50%) or normal (15%) protein diets for 1 or 12 weeks. After the diet intervention period, the animals were killed and liver tissue was removed. Total RNA was isolated, pooled and subjected to gene expression profiling.

first: Jessica

last: Schwarz

first: Daniel

last: Tome

first: Annemarie

last: Baars

first: Michael

last: Müller


title: Expression data from intestinal mucosa of patients with UC

status: Public on Nov 09 2012

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

summary:
Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission.
We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls.

overall_design: Ulcerative colitis patients and non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria for UC patients were: age between 18 and 65, diagnosis of UC established at least 6 months before inclusion and exclusion of concomitant infection. Active disease was defined by endoscopic and histologic score: Mayo sub score >=2 and MATTS >=3 respectively . Inactive disease was also defined by endoscopic and histologic score: Mayo sub score =0 and MATTS <=2 respectively, and a remission state for a minimum of 5 month prior to biopsy collection, and remained inactive for at least 6 months after. Uninvolved mucosa from patients with active UC was defined as a colonic segment with completely normal endoscopic appearance, normal histology, and absence of any previous evidence of active disease. Finally, a total of 43 biopsies were analyzed: 13 healthy controls, 8 inactive UC, 7 non-involved active UC and 15 involved active UC.

first: Núria

last: Planell


title: An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation

city: Turku

first: Tapio

last: Lonnberg

address: P.O.Box 123

institute: University of Turku

summary: The aim of this dataset was to study in detail the transcription kinetics initiated by cytokines IL-12 and IL-4 in early differentiation of Th1 and Th2 cells, respectively.

overall_design:
Total RNA obtained from activated and IL-12 or IL-4 & anti-IL-12 treated cord blood CD4+ T cells, 12, 24, 48, and 72 hours after initiation of the cultures, compared to cells which were only activated. 37 samples were analyzed from three biological replicates of the culture.
Several (26) of the Samples in this Series represent a re-analysis of CEL files originally submitted as GEO Series GSE17974. Please see associations on each Sample record.

first: Tarmo

last: Äijö

first: Sanna

last: Edelman

last: Lönnberg

first: Antti

last: Larjo

first: Henna

last: Kallionpää

first: Soile

last: Tuomela

first: Emilia

last: Engström

first: Riitta

last: Lahesmaa

first: Harri

last: Lähdesmäki


title: Gene expression data from cultured cortical neurons.

city: La Jolla

first: Anton

last: Maximov

state: CA

address: 10550 North Torrey Pines DNC216

department: Cell Biology, Dorris Neuroscience Center

institute: The Scripps Research Institute

summary:
We used Affymetrix DNA arrays to investigate the extent to which nuclear HDAC4 accumulation affects neuronal gene expression.
Cultured neurons were infected with lentiviruses expressing either wildtype HDAC4 or the constitutuvely nuclear 3SA mutant under the control of neuronal Synapsin promoter.

overall_design: Neurons were infected at 5 days after plating (5DIV) and analyzed at 14 DIV.

first: Richard

last: Sando


title: Ly6Chi monocytes in the inflamed colon give rise to pro-inflammatory effector cells and migratory antigen presenting cells.

status: Public on Nov 08 2012

first: Gilgi

last: Friedlander

address: Hertzel st

summary:
We showed different function of monocyte derived cells in the lamina propria of the colon under steady state and inflammatory conditions.
We used microarrays to detail the global programme of gene expression and identified distinct clusters of  regulated genes during this process.

overall_design: Different subsets of mononuclear phagocytes were sorted from the colonic lamina propria as well as the spleen. Sorting was done in C57BL/6 mice in steady state and under inflammatory conditions (Dextran Sodium Sulphate induced colitis model)

first: Ehud

last: Zigmond

first: Chen

last: Varol

first: Julia

last: Farache

first: Elinor

last: Elmaliah

first: Ansuman

middle: T

last: Satpathy

first: Matthias

last: Mack

first: Nahum

last: Shpigl

first: Ivo

middle: G

last: Boneca

first: Ken

last: Murphy

first: Guy

last: Shakhar

first: Zamir

last: Halpern

first: Steffen

last: Jung


title: IKKe coordinates invasion and metastasis

first: Marianne

middle: Kwang-Hee

last: Kim

state: MD

address: 10 Center Dr. 4B55

department: Women's Malignancies Branch

institute: NIH/NCI

summary:
IKKe was identified previously as a breast cancer oncogene and was associated with poor clinical outcome in ovarian cancer.
In order to elucidate functional roles of IKKe, we used microarray analysis to identify genes changed upon IKKe shRNA knockdown and compared with genes affected in ovarian cancers

overall_design: IKKe was knockdowned by 2 different IKKe shRNAs in Ovcar5 in 6 replicates and candidate downstream targets were selected if changed by both shRNAs

first: Sarah

last: Hsu

first: Lidia

last: Hernandez

first: Valentina

last: Grajales

first: Anne

last: Noonan

first: Miriam

last: Anver

first: Ben

last: Davidson

first: Christina

last: Annunziata


title: Global expression analysis of DLBCL cell lines with LITAF over-expression or silencing

first: Raquel

last: Malumbres

overall_design: Analysis of global gene expression in the diffuse large B-cell lymphoma (DLBCL) cell lines KARPAS-231 and VAL treated with a specific siRNA for LITAF or a scrambled control, and analysis of global gene expression in the DLBCL cell lines RL and SC-1 stably transfected with a tetracycline-inducible LITAF expression vector in the presence or absence of 4 mg/ml doxycycline in the culture medium. The over-expression experiments were performed in duplicate and the silencing experiments in triplicate, resulting in a total of 20 microarrays.

first: Cristina

last: Bértolo

first: Sergio

last: Roa

first: Ainara

last: Sagardoy

first: Eloy

middle: F

last: Robles

first: Jose

middle: I

last: Martinez-Ferrandis

first: Xavier

last: Sagaert

first: Alberto

last: Orta

first: Izidore

last: Lossos

first: Salomon

last: Amar

first: Yaso

last: Natkunam

first: Javier

last: Briones

first: Ari

last: Melnick

last: Martinez-Climent


title: Expression data of PTK7+ and PTK7- cells from differentiated pluripotent stem cells (PSC), and expression data from undifferentiated PSC and definitive endoderm

status: Public on Nov 07 2012

city: Los Angeles

first: David

last: Chan

address: 621 Charles E Young Drive South

department: MCDB

institute: UCLA

summary:
As PSCs differentiate, they display characteristics of EMT as well as PTK7 expression.  We sought to discover novel markers and regulators of this process by comparing purified PTK7+ and PTK7- populations
We used microarrays to detail the global program of gene expression underlying this EMT process and identified distinct classes of up-regulated genes during this process.

overall_design: PTK7+ and PTK7- populations were purified by FACS and subjected to lysis and RNA extraction.  Undifferentiated PSCs and definitive endoderm were washed with PBS, then subjected to lysis and RNA extraction

middle: N

first: William

middle: E

last: Lowry