title: Placenta environment induces the differentiation of macrophages into multinucleated giant cells

status: Public on Dec 07 2012

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

institute: URMITE

summary:
A major population of placenta macrophages represented throughout the pregnancy consists of CD14+ macrophages, but their characteristics remain badly understood. Here we purified from placentas at term CD14+ macrophages using positive selection. The phenotyping of CD14+ macrophages performed using flow cytometry revealed that placenta CD14+ macrophages expressed a series of markers distinct of those of circulating monocytes monocyte-derived macrophages.
Placenta CD14+ macrophages spontaneously matured in multinucleated giant cells (MGCs) as demonstrated by size, number of nuclei display and specific cytoskeleton organization. Placenta CD14+ macrophages and MGCs were phagocytic cells but the potential of MGCs to mount an inflammatory response was lower than that of their precursors.
Placenta CD14+ macrophages and MGCs stimulated with interferon and interleukin-4 were not polarized into typical M1 or M2 profiles. Placenta macrophages exhibited specific activation transcriptional programs. Indeed, principal component analysis and hierarchical clustering show that placental macrophages formed a distinct group from circulating monocytes and monocyte-derived macrophages. Among placenta macrophages, it was also possible to distinguish CD14+ macrophages and MGCs. In addition, networks based on gene interactions were clearly different in CD14+ macrophages and MGCs.
Finally, the microenvironment of placenta CD14+ macrophages governs their differentiation into MGCs because CD14+ macrophages incubated with trophoblasts exhibited exarcerbated characteristics of MGCs and because the co-incubation of circulating monocytes from working women with trophoblast supernatants resulted into the formation of MGCs whereas monocytes from non-pregnant women incubated with trophoblast supernatants did not differentiate into MGCs. Taken together, these results clearly demonstrated specific feaures of placenta CD14+ macrophages.

overall_design:
Three replicates of each of the following:
1. Placental macrophages just after isolation (CD14+ macrophages)
2. Placental macrophages after 9 days in culture (MGCs)
3. CD14+ cells isolated from PBMC which are extracted from the whole human blood of healthy donors (Monocytes)
4. Macrophages derived from monocytes (MDMs)

first: Amira

middle: B

last: Amara

first: Laurent

last: Gorvel

first: Christel

last: Verollet

first: Abdoulaye

last: Barry

first: Adil

last: El-Filali

first: Christophe

last: Buffat

first: Florence

last: Bretelle

first: Isabelle

last: Maridonneau-Parini

first: Christian

last: Capo

first: Eric

last: Ghigo

first: Jean-Louis

last: Mege


title: Epigenetic and genetic influences on DNA methylation variation in maize populations

status: Public on Aug 12 2013

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

type: Methylation profiling by genome tiling array

summary: DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals.  However, other genetic changes such as transposon insertions also can lead to changes in DNA methylation levels.  Genome-wide profiles of DNA methylation levels for 20 maize inbreds were used to discover differentially methylated regions (DMRs).  The methylation level for each of these DMRs was also assayed in 31 additional maize genotypes resulting in the discovery of 1,966 common DMRs and 1,754 rare DMRs.  Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable.  A local association scan found that nearly half of the DMRs with common variation are significantly associated with SNPs found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the DNA methylation variation. The analysis of gene expression in the same samples used for DNA methylation profiling identifies over 300 genes with expression patterns that are significantly associated with the DNA methylation variation among genotypes.  Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic variation is often stably inherited and can influence expression level of genes in the population.

overall_design:
Methylation profiles in seedling tissue of a panel of 51 maize inbred lines using a custom 2.1M or 1.4M feature NimbleGen array.

Methylation profiles in seedling tissue of maize inbred lines, teosinte and recombinant inbred lines (RILs) derived from B73 and Mo17 using a custom 12x270K NimbleGen array. Inbred lines B73 and Mo17 each had 3 biological replicates, the other sample had 1 replicate.

first: Steven

first: Roman

last: Briskine

first: Jawon

last: Song

first: Qing

last: Li

first: Ruth

last: Swanson-Wagner

first: Peter

middle: J

last: Hermanson

first: Amanda

last: Waters

first: Evan

last: Starr

first: Patrick

middle: T

last: West

last: Tiffin

first: Chad

middle: L

last: Myers

first: Mattew

middle: W

last: Vaughn

first: Nathan

middle: M

last: Springer


title: Molecular characterization of Nodal marginal zone lymphoma [Gene Expression]

status: Public on Sep 21 2011

city: Toledo

first: Alberto

last: Arribas

state: Toledo

address: Avda Barber, 30

department: Molecular Pathology Research Unit

country: Spain

institute: Hospital Virgen de la Salud

summary: Nodal marginal zone lymphoma (NMZL) is a small B cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile and copy number data from 15 NMZL cases. For comparison, 16 follicular lymphomas, 9 extranodal marginal zone lymphomas, 8 reactive lymph nodes and B-cell subtypes were included. The results were validated by qRT-PCR in an independent series including 61 paraffin-embedded NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NF-kB and TGF-Beta; and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82 and CDC42EP5. Genes linked to G2/M and germinal center were downregulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1, TGFB1 and TACI in NMZL, and BCL6, LMO2 and CD10 in FL. NMZL displayed increased expression of miR-221, miR-223 and let-7f, while FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL.

first: J

middle: A

first: Y

last: Campos-Martín

first: C

last: Gómez-Abad

first: P

last: Algara

first: M

last: Sánchez-Beato

middle: S

last: Rodriguez-Pinilla

first: S

last: Montes-Moreno

first: N

last: Martinez

last: Alves-Ferreira

last: Piris

last: Mollejo


title: Gene expression modulation by paraquat-induced oxidative stress conditions in P. brasiliensis

status: Public on Jun 14 2013

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

summary: Paracoccidioides brasiliensis is a thermodimorphic fungus associated with paracoccidioidomycosis (PCM), the most common systemic mycosis in Latin America. The infection is initiated by inhalation of environmental dispersed conidia produced by the saprophytic phase of the fungus. In the lungs, P. brasiliensis assumes the parasitic yeast form and must cope with the adverse conditions imposed by cells of the host immune system, which includes a harsh environment highly concentrated in reactive oxygen species (ROS). In this work, we used the ROS-generating agent paraquat to experimentally simulate oxidative stress conditions in order to evaluate the stress-induced modulation in gene expression of cultured P. brasiliensis yeast cells using a microarray hybridization approach.

overall_design:
Microarray hybridizations were carried out with RNA obtained from cells treated with paraquat (0.5 or 5.0 mM) for 5 hours. The RNA obtained from cells unexposed to paraquat was taken as reference. Each treatment was analyzed with four independent hybridizations (two pairs of dye-swapped hybridizations), using RNA from two biological replicas.
The data has been filtered, normalized and adjusted as described in the "data processing" box for each individual sample. Dye swap consistency checking has been performed between equivalent experimental pairs with the aid of the software TIGR MIDAS v2.19 and inconsistent spots have been flagged and excluded from further analyses. The values obtained from each dye swap pair have been averaged and consolidated into a single data file, generating a total of 8 hybridization files (four from each treatment concentration). These files have been loaded into the software TIGR Multi-Experiment Viewer, v.3.01. Experiments were then normalized and genes that displayed statistically significant modulation were identified by one-way ANOVA, considering p < 0.01 as a cutoff value.
A list of statisticaly significant, modulated genes was created, showing the average log ratio for each one of these genes, within each time point

first: Marcus

middle: V

last: Oliveira

first: Ana

middle: F

first: Claudio

last: Shida

first: Regina

middle: C


title: Genome-wide SNP analysis of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients

status: Public on Feb 06 2013

city: Leiden

first: Harry

last: Vrieling

address: Einthovenweg 20

department: Toxicogenetics, S4-P

country: Netherlands

institute: Leiden University Medical Center

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

summary: The risk of developing cutaneous squamous cell carcinoma (SCC) is markedly increased in organ transplant recipients (OTRs) compared to the normal population. Next to sun exposure, the immunosuppressive regimen is an important risk factor for SCC development in OTRs. Various gene mutations (e.g. TP53) and genetic alterations (e.g. CDKN2A loss, RAS amplification) have been found in SCCs. The aim of this study was to identify genomic alterations that are consistently involved in the formation of SCCs and their precursor lesions, actinic keratoses (AKs). To perform the analysis in an isogenic background, DNA was isolated from SCC and AK from each of 13 OTRs. Tumor samples and their matching normal control (peripheral blood) were analyzed on the Illumina HumanHap550V3_duo genotyping beadchips. In contrast to previous studies, genome-wide SNP analysis showed very few copy number variations in AKs and SCCs, and these variations had no apparent relationship with observed changes in mRNA expression profiles (GSE32628). Other molecular mechanisms, such as DNA methylation or miRNA alterations, may affect gene expression in SCCs of OTRs.

overall_design:
Patients were selected from the group of OTRs that are regularly seen at the dermatology clinic of the Leiden University Medical Center. Patients with clinically suspected SCC were informed on the study and after informed consent was obtained, fresh frozen samples were obtained from SCCs (n=15, including 2 repeats) and AKs (n=11). Peripheral blood was taken as normal control. DNA was isolated and SNP profiles were obtained using HumanHap550V3_duo Genotyping BeadChips (Illumina).    Both the log R ratio and the B allele frequency (BAF) were investigated to identify copy number alterations and loss of heterozygosity (LOH)

The tumor DNA samples are from the same tumor samples as the RNA samples in GSE32628.

first: Liesbeth

last: Hameetman

first: Suzan

last: Commandeur

first: Jan

middle: N

last: Bouwes Bavinck

first: Hermina

last: Wisgerhof

first: Frank

last: de Gruijl

first: Rein

last: Willemze

first: Leon

last: Mullenders

first: Cornelis

middle: P

last: Tensen


title: Caco-2 cells:  cycling vs 21-days differentiated cells

status: Public on Apr 25 2011

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: Transcriptional profile of 21-days differentiated Caco-2 cells compared to Caco-2 cycling cells. Goal was to demonstrate the ability of Caco-2 cells to express most of the markers typical of differentiated enterocytes. A novel protocol of line maintenance was used.

overall_design: Two-condition experiment: cycling Caco-2 cells and 21-days differentiated Caco-2 cells. Two biological replicates of each condition in dye-swap configuration

first: Rossella

last: Brandi

first: Mara

last: D'Onofrio

first: Armando

last: Felsani

first: Manuela

last: Natoli


title: Selective Targeting of the Proliferating Compartment in Chronic Lymhocytic Leukemia by Inhibition or Downregulation of Aurora Kinases

status: Public on Jul 26 2011

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

summary: Chronic lymphocytic leukemia (CLL) B-cells receive signals from the lymph node and bone marrow (BM) microenvironments that regulate their survival and proliferation. These signals and the pathways that propagate them to the interior of the cell represent potential targets for therapeutic intervention. To characterize the pathways that are activated by the BM microenvironment in CLL cells in vivo, we performed gene expression profiling of tumor cells purified from BM and peripheral blood. Functional classification analysis revealed that the most frequently upregulated genes in BM-CLL cells are genes involved in cell cycle and mitosis. Among the most significantly overexpressed were the Aurora A and B kinases. To investigate whether these kinases could represent potential therapeutic targets in CLL, we performed RNA interference experiments in the CLL cell lines MEC1 and EHEB. Downregulation of Aurora A and B inhibited the proliferation and induced apoptosis in these cells. Similar effects were observed with the pan-Aurora kinase inhibitor VX-680 in primary CLL cells induced to proliferate by CpG-ODN and IL-2. VX-680 also inhibited leukemia growth in vivo in a mouse model of CLL. These data suggest that inhibition of Aurora kinases could represent a potential strategy to selectively target the proliferating compartment in CLL.

overall_design: To identify gene expression related to microenvironmental stimuli in B-cell Chronic Lymphocytic Leukemia (CLL) cells in vivo, expression profiles of CLL cells purified (>95%) from bone marrow (BM) and peripheral blood (PB) were compared. Paired BM and PB samples from 6 individuals were used for this analysis.

first: Francisco

last: Careta

first: Stefania

last: Gobessi

first: Engin

last: Bojnik

first: Fabio

first: Daniel

last: Matos

first: Roberto

last: Falcão

first: Luca

last: Laurenti

first: Marco

last: Zago

first: Dimitar

middle: G

last: Efremov


title: NDRG2 transcriptional inactivation is involved in tumoral progression and worse clinical outcome of oligodendroglial tumors

status: Public on Feb 09 2011

city: TOLEDO

first: Barbara

last: Melendez

address: AVDA. BARBER 30

department: UNIDAD DE INVESTIGACION DE PATOLOGIA MOLECULAR

institute: HOSPITAL VIRGEN DE LA SALUD

summary:
Purpose: The most clearly established genetic hallmark in oligodendroglial tumors (OTs) is the combined loss of 1p/19q, a molecular alteration characteristic of tumors responding to therapy. Markers of tumoral progression have not yet been studied.
Experimental Design: Novel markers of tumoral progression in OTs were sought through gene expression profiling analysis.
Results: Unsupervised hierarchical cluster analysis classified OTs into two main groups associated with tumoral grade, independent of histological subtype and 1p/19q status. Differential gene expression analysis between low- and high-grade OTs revealed that only cell cycle-related genes were significantly upregulated in high-grade OTs. Among the deregulated genes, NDRG2 downregulation was detected in high-grade OTs with combined loss of 1p/19q. Expression analysis revealed low transcript levels of NDRG2 relative to non-tumoral brain tissue in 45% (9/20) of high-grade OTs. Furthermore, the low transcript levels of NDRG2 were significantly associated with a worse clinical outcome in patients. Transcript levels of NDRG2 were associated with promoter hypermethylation, which was detected in 38.4% (10/26) of high-grade OTs. The treatment of glioma cell lines T98 and LN18 with demethylating agents increased the mRNA expression levels of NDRG2 relative to the control cell line. Additionally, cell proliferation was significantly reduced and cell cycle was arrested in G1 phase after treatment with demethylating agents.
Conclusions: Taken together, our results suggest that NDRG2 is a candidate tumor suppressor gene in OTs whose inactivation could be involved in tumoral progression and worse patient survival.

overall_design: The microarray study involved 28 glioma samples including oligodendrogliomas and oligoastrocytomas WHO grade II and III. Six non-tumoral brain tissues were used as controls, two of which were purchased from Stratagene (La Jolla, CA) and Clontech (Mountain View, CA). RNAs from several cell lines (Universal Human RNA, Stratagene, La Jolla, CA) was used as a standard reference in all hybridizations

first: Yolanda

last: Ruano

first: Angel

last: Rodriguez de Lope

first: Teresa

last: Ribalta

first: Concepción

last: Fiaño

first: Juan-Fernando

last: García

last: Campos-Martín

first: Elisa

last: Pérez-Magán

first: Paula

last: Ferrara

first: José-Luis

last: Hernández-Moneo

last: Mollejo

first: Bárbara

last: Meléndez


title: Gene expression profiles of oral normal fibroblasts (NFs) and oral carcinoma-associated fibroblasts (CAFs)

status: Public on Jan 26 2012

city: Hefei

first: Wei

last: Lan

state: Anhui

address: 96#, Jinzhai Road

department: School of Life Science

country: China

institute: University of Science and Technology of China

summary: This study aims to identify genes differentially expressed in oral CAFs with respect to their normal counterparts, i.e. oral NFs. We collected oral normal mucosal tissues and oral squamous cell carcinoma (OSCC) tissues from 12 healthy people and 12 OSCC patients, respectively, at West China Hospital of Stomatology, Sichuang University, P. R. China. The tissues were isolated, cultured and purified using standard protocols to obtain oral NFs and CAFs. Agilent 4×44K Whole Genome Oligo Microarrays were used to measure the gene expression profiles of the samples. Sample preparation and hybrid reactions were performed according to the manufacture’s instructions. RNA samples from NFs and CAFs were pooled respectively before hybridization. The chips were scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software (version 10.5.1.1). Raw data were normalized in the Agilent GeneSpring GX software (version 11.0) using the Agilent FE one-color scenario (mainly median normalization).

overall_design: Oral NFs and CAFs were obtained from tissues derived from 12 healthy people undergoing plastic surgery and 12 OSCC patiens undergoing surgical resection. RNA samples from NFs and CAFs were pooled respectively before hybridization.

first: Yun

last: Wu

first: Zhi

last: Liang

first: Hongmei

last: Zhou


title: Major Depressive Disorder blood gene expression

status: Public on Oct 05 2011

city: Amsterdam

first: sabine

last: Spijker

address: De Boelelaan 1085

department: Center for Neurogenomics and Cognitive Research

institute: Neuroscience Campus Amsterdam

summary:
Background: Major Depressive Disorder (MDD) is a moderately heritable disorder with a high lifetime prevalence. At present, laboratory blood tests to support MDD diagnosis are not available.

Methods: We used a classifier approach on blood gene expression profiles of a unique set of non-medicated subjects (MDD patients and controls) to select genes of which expression is predictive for disease status. To reveal blood gene expression changes related to MDD disease, we applied a powerful ex vivo stimulus to the blood, i.e. incubation with lipopolysaccharide (LPS; 10 ng/ml blood).

Results: Based on LPS-stimulated blood gene expression using whole-genome microarrays in 42 subjects (primary cohort; 21 MDD patients (mean age 42.3 years), 21 healthy controls (mean age 41.9 years)), we identified a set of genes (CAPRIN1, CLEC4A, KRT23, MLC1, PLSCR1, PROK2, ZBTB16) that serves as a molecular signature of MDD. These findings were validated for the primary cohort using an independent quantitative PCR method (P = 0.007). The difference between depressive patients and controls was confirmed (P = 0.019) in a replication cohort of 13 patients with MDD (mean age 42.8 years) and 14 controls (mean age 45.6 years). The MDD-signature score comprised of expression levels of 7 genes could discriminate depressive patients from controls with sensitivity of 76.9% and specificity of 71.8%.

Conclusions: We show for the first time that molecular analysis of stimulated blood cells can be used as an endophenotype for MDD diagnosis, which is a milestone in establishing biomarkers for neuropsychiatric disorders with moderate heritability in general. Our results may provide a new entry point for following and predicting treatment outcome, as well as prediction of severity and recurrence of MDD.

overall_design:
In total, 33 MDD patients and 34 healthy controls were analyzed using basal gene expression in whole blood, and gene expression from whole blood that was stimulated with LPS for 5-6 h, using microarrays.

Patients were arbitrarily selected from all patients to serve as primary cohort (nMDD = 21 (MDD01-MDD21); nControls = 21 (Con01-Con21)), or replication cohort (nMDD = 12 (MDD22-MDD35); nControls = 13 (Con22-Con37)) using microarrays.

This submission does not include Samples CON21_LPS or CON30_LPS.

first: Sabine

first: Jeroen

last: van Zanten

first: Simone

last: de Jong

first: Brenda

last: Penninx

first: Richard

last: van Dyck

first: Frans

last: Zitman

first: Jan

middle: H

last: Smit

first: Bauke

last: Ylstra

first: August

middle: B

first: Witte

last: Hoogendijk


title: A new gene expression signature, the ClinicoMolecular Triad Classification, may improve prediction and prognostication of breast cancer at the time of diagnosis

status: Public on Sep 29 2011

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

summary: When making treatment decisions, oncologists often stratify breast cancers into a low-risk group (ER+, low grade); an intermediate-risk group (ER+, high grade); and a high-risk group that includes Her2+ and triple-negative (ER-/PR-/Her2-) tumors. None of the currently available gene signatures correlates to this clinical classification. We aimed to develop a test that is practical for the oncologists, that offers both molecular characterization of BCs, and improved prediction of prognosis and treatment response. We investigated the molecular basis of such clinical practice by grouping Her2+ and triple-negative breast cancers together during clustering analyses on the genome-wide gene expression profiles of our training cohort, mostly derived from fine needle aspiration biopsies (FNABs) of 149 consecutive evaluable Breast cancers. The analyses consistently divided these tumors into a three-cluster pattern, similar to clinical risk-stratification groups, that was reproducible in published microarray databases (n=2487) annotated with clinical outcomes. The clinicopathologic parameters of each of these three molecular groups were also similar to clinical classification. The low-risk group had good outcomes and benefited from endocrine therapy. Both intermediate- and high-risk groups had poor outcomes and were resistant to endocrine therapy. The latter demonstrated the highest rate of complete pathological response to neoadjuvant chemotherapy; the highest activities in MYC, E2F1, Ras, β-Catenin and IFN-γ pathways; and poor prognosis predicted by 14 independent prognostic signatures. Based on a multivariate analysis, this new gene signature, termed ClinicoMolecular Triad Classification, predicted recurrence and treatment response better than all pathologic parameters and other prognostic signatures.

overall_design:
149 invasive breast cancers from the 172 specimens contained 161 tumors were used in this study. Expression data of the 11 tumors with replicate was separately combined before analysis.

An additional validation dataset of 340 FNABs from a prospective breast cancer cohort can be found at GEO Accession: GSE45725.

first: Dong

middle: Y

first: Wey

last: Leong


title: Expression analysis of Antirrhinum majus cv. Maryland True Pink (snapdragon) petals and sepals at different stages of flower development

status: Public on Jun 07 2012

city: West Lafayette

first: Natalia

last: Dudareva

state: Indiana

address: 625 Agriculture Mall Drive

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary:
Investigation of gene expression level changes in snapdragon petals and sepals during flower development
The flower developmental stages analyzed in this study are representative of distinct developmental events: (i) preanthesis, (ii) anthesis, (iii) maturation and (iv) presenescence and are further described in the accompanying article.

overall_design: A 24 chip study using total RNA recovered from samples of petal and sepal tissue of Antirrhinum majus cv. Maryland True Pink harvested at four different stages of flower development, namely (i) preanthesis (three days before flower opening=d-3), (ii) anthesis (day of flower opening=d1), (iii) maturation (four days after flower opening=d4) and (iv) presenescence (seven days after flower opening=d7). Three separate samples were extracted per tissue and developmental stages. Each chip measures the expression level of 11,959 ESTs from Antirrhinum majus cv. Maryland True Pink with up to six 60-mer probes per target.

first: Joëlle

middle: K

last: Muhlemann

first: Hiroshi

last: Maeda


title: ChIP-chip from 48h hemin induced K562 cells with GATA-1, EKLF, and NF-E2 antibodies

status: Public on Dec 31 2011

city: Bei Jing

first: Jia

last: Yu

address: Dong Dan San Tiao #5

department: Biochemistry

institute: Peking Union Medical College

type: Genome binding/occupancy profiling by array

summary:
The transcription factor GATA-1, EKLF and NF-E2 promotes erythroid differentition by regulating their target genes, however, the intricate interplays between these key TFs and microRNA genes are largely unknown.
Chromatin immunoprecipitation (ChIP) of GATA-1, EKLF and NF-E2 together with microRNA genomic promoter profiling by ChIP-on-chip analysis demonstrated that GATA-1, EKLF and NF-E2 collaborately regulate a series of microRNA genes.

overall_design: Comparison of microRNA promoter arrays of GATA-1 VS EKLF VS NF-E2 in K562 cells suffering with hemin induced erythroid differentiation

first: Fang


title: Genotyping SAX1 Mouse Human Hybrid

status: Public on Aug 27 2010

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

summary: Genotyping SAX1 Mouse Human Hybrid to identify haplotypes of chromosomes 7 and X

sample_organism:
Homo sapiens
Mus musculus

overall_design: Single sample prepared from SAX1 cells


title: miR-K10a expression and inhibition

status: Public on Nov 10 2010

city: Bethesda

first: Joseph

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary:
Transcriptional profiling of BJAB cells expressing miR-K10a and BCBL cells treated with miR-K10a inhibitor.
To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under three sets of conditions in which KSHV miRNAs were expressed or inhibited.

overall_design:
Cells transfected with negative control miRNA compared to miR-K10a or negative miRNA inhibitor compared to miR-K10a inhibitor.
The publication associated with this data set is about human TNFRSF12A/TWEAKR being targeted by KSHV miR-K10a.

first: Don

last: Ganem


title: CrkII transgene induces atypical mammary gland development and tumorigenesis

status: Public on Jul 18 2011

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Goodman Cancer centre

institute: McGill

summary: The v-Crk protein was originally isolated as the oncogene fusion product of the CT10 chicken retrovirus. Cellular homologues of v-Crk include Crk, which encodes two alternatively spliced proteins (CrkI and CrkII), and CrkL. Though CrkI/II proteins are elevated in several types of cancer, including breast, the question of whether these Crk adaptor proteins can promote breast cancer has not been addressed. We created a transgenic mouse model that allows the expression of CrkII through the hormonally responsive mouse mammary tumor virus promoter. During puberty, transgenic mice were found to have delayed ductal outgrowth, characterized by increased collagen surrounding the terminal end buds. In post-pubertal mice, precocious ductal branching was observed and associated with increased proliferation. Focal mammary tumors appeared in a subset of animals, with a latency of approximately 15 months. Mouse mammary tumor virus/CrkII tumors showed high levels of Crk protein as well as various cytokeratin markers characteristic of their respective tumor pathologies. This study demonstrates that the precise expression of CrkII is critical for integrating signals for ductal outgrowth and branching morphogenesis during mammary gland development. Furthermore, this study provides evidence for a potential role of CrkII in integrating signals for breast cancer progression in vivo, which has important implications for elevated CrkII observed in human cancer.

overall_design: Two T47D-CrkII samples vs two T47D samples.

first: Morag

last: Park

first: Kelly

last: Fathers


title: Characterization of the human host response to Encephalitozoon cuniculi infection

status: Public on Dec 07 2010

city: Saint Nazaire

first: goncalves

last: olivier

address: 37, boulevard de l'Université

country: France

institute: CNRS

summary: In order to study the molecular response of human foreskin fibroblast (HFF) cells to E. cuniculi parasite infection, kinetics microarray experiments targeting human genes expression have been performed during the parasite whole infection cycle. Infected HFF cells (IHFF; t=4h, 16h, 48h, 72h and 120h ) were systematically compared with control uninfected HFF cells (UHFF; t=0h).

overall_design: Time-dependent experiment comparing two conditions, IHFF vs. UHFF cells (data points: t=4h/0h, t=16h/0h, t=48h/0h, t=72h/0h, t=120h/0h).

first: Stéphanie

last: Bornes

first: Olivier

last: Gonçalves

first: Muriel

last: Bonnet

first: Anne

last: Moné

first: Sébastien

last: Déjean

first: Eric

last: Peyretaillade

first: Pierre

last: Peyret


title: Gene expression data for two xenograft models representing luminal-like and basal-like breast cancer

status: Public on Dec 08 2010

city: Oslo

first: Eldrid

last: Borgan

address: Ullernchausseen 70

department: Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

summary:
Choline (reference 1) and glucose (reference 2) was studied using HR MAS MR spectroscopy data and 105 and 38 gene transcripts were selected respectively from the microarray data to study differences between two xenograft models.
Reference 1: Moestue SA et al, Distinct choline metabolic profiles are associated with differences in gene expression for basal-like and luminal-like breast cancer xenograft models, BMC Cancer 2010 Aug 17;10:433 (PMID: 20716336).
Reference 2: Grinde et al., NMR Biomed. 2011 Dec;24(10):1243-52. doi: 10.1002/nbm.1683. (PMID: 21462378)

overall_design: The microarray data from the luminal-like and basal-like xenograft models were compared for selected genes, using Limma Bioconducotr package

first: Siver

last: Moestue

first: Maria

middle: T

last: Grinde

first: Else

last: Huuse

first: Evita

last: Lindholm

first: Beathe

last: Sitter

first: Oystein

last: Risa

first: Anne-Lise

last: Børresen-Dale

first: Olav

last: Engebraaten

first: Gunhild

last: Mælandsmo

first: Ingrid

last: Gribbestad


title: Cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients

first: Harry

last: Vrieling

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

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

overall_design: Refer to individual Series


title: The transcriptional profile of Langhans-like multinucleated giant macrophages: Collapse of the inflammatory and immune responses

status: Public on Dec 07 2012

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

institute: URMITE

summary: Monocytes/macrophages have the ability to fuse in multinucleated giant cells (MGCs). Except for osteoclasts that resorb bones on large surfaces, the function of other macrophage-derived MGCs, which appear under pathological situations associated with granulomatous inflammation such as tuberculosis, is not understood. Here we deciphered functions and gene expression profiles of MGCs obtained after stimulation of human monocytes with IFN-g and concanavalin A. First, we show that the competence of MGCs in phagocytosis and O2- production was similar to those of monocytes-derived macrophages (MDMs) and that MGCs exhibited a M1 polarization. Second, we analyzed the transcriptional profile of MGCs using gene categories and the building of gene networks. The signature of MGCs was markedly distinct from that of resting or stimulated MDMs. It consisted of the up-regulation of genes involved in adhesion and cytoskeleton organization while genes associated with immune response were down-regulated. Hence,  MGC formation was associated with a profound and original modulation of gene expression repertoire suggesting that macrophage immune were not prominent in MGC. This expression gene repertoire may be instrumental to understand the specific function of this giant macrophages in human pathologies

overall_design: 9 samples of monocytes-derived macrophages and 3 samples of mulitnucleated giant cells. 3 samples of MDM treated with concanavalin A, 3 samples of MDM treated with IFN-g, and 3 control MDM.

first: Christel

last: Vérollet

first: Amira

last: Amara

first: Adil

last: El Filali

first: Isabelle

last: Maridonneau-Parini

first: Jean-Louis

last: Mege


title: Molecular characterization of Nodal marginal zone lymphoma

status: Public on Sep 21 2011

city: Toledo

first: Alberto

last: Arribas

address: Avda Barber, 30

institute: Hospital Virgen de la Salud

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

first: J

first: Y

last: Campos-Martín

first: C

last: Gómez-Abad

first: P

last: Algara

first: M

last: Sánchez-Beato

last: Rodriguez-Pinilla

first: S

last: Montes-Moreno

first: N

last: Martinez

last: Alves-Ferreira

last: Piris

last: Mollejo


title: Innate signature induced in human mDCs by dengue vaccine candidates

status: Public on Jan 03 2011

city: Marcy l'Etoile

first: Bruno

last: Guy

address: 1541 Av M Mérieux

department: Discovery

institute: sanofi pasteur

summary: Sanofi Pasteur is developing a tetravalent YFV 17D vaccine-based chimeric dengue vaccine (TV CYD), which is currently in clinical phase 3 development. DNA microarrays were used to assess the innate gene signature in human mDCs infected with the four CYDs alone or in combination, with a wild type dengue serotype 3 virus, or with a classically attenuated serotype 3 virus (VDV3) shown to be reactogenic in humans. We observed a very reproducible signature for each of the 4 CYDs, involving stimulation of Type I IFN genes and associated genes, together with genes encoding chemokines and other mediators involved in the initiation of adaptive responses. In contrast, the wt DEN3 virus induced a predominantly inflammatory profile, while VDV3 appeared to induce a blunted response, which may have contributed to its clinical outcome.

overall_design: All oligochip experiments were performed in dye swap. For each experiment, the gene expression profile of infected cells was compared with the corresponding profile of uninfected cells. 2 biologicals replicates were performed for each virus.

first: Claire

last: Balas

first: Audrey

last: Kennel

first: Florence

last: Deauvieau

first: Regis

last: Sodoyer

first: Nadege

last: Arnaud-Barbe

first: Jean

last: Lang


title: Identification of IL4 dependent genes involved in reinforcement stage of Th2 differentiation

status: Public on Mar 30 2010

city: Turku

first: Ubaid Ullah

last: Sheikh

state: Turku

address: Tykistökatu

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

summary: T helper cells differentiate to many different subclasses depending upon the stimulus and the microenvironment where the cells were stimlated. IL4 is known to polarize the cells towards Th2 differentiation pathway. In this study we aim to identify IL4 dependent genes during late stage of Th2 differentiation.

overall_design: There are in all 10 samples, two replicates of each 5. Two samples, namely U_1 and U_2 (replicates of one) are control. Cells have been cultured for either five days or six days. For each of these, we have two groups, one where we add IL4 and IL4R neutralizing antibodies either on days 3 and 4 (For five day culture) [D5ABS_1 and D5ABS_2] or on days 3,4 and 5 (For six day culture) [D6ABS_1 and D6ABS_2] and next where we don't add neutralizing antibodies [D5_1 & D5_2 and D6_1 & D6_2].

first: Parul

last: Tripathi

first: Ubaid

last: Ullah

first: Naresh

last: Sahoo

first: Henna

last: Jarvenpaa

first: Amita

last: Suneja

first: Riitta

last: Lahesmaa

first: Kanury

last: Rao


title: Mammographic density and genetics - A study of breast biopsies in relation to mammoraphic density

status: Public on Aug 13 2010

first: Vilde

middle: Drageset

last: Haakensen

address: Montebello

department: Dept of Genetics

institute: The Norwegian Radium Hospital

summary:
Introduction
Mammographic density (MD), as assessed from film screen mammograms, is determined by the relative content of adipose, connective and epithelial tissue in the female breast. In epidemiological studies, a high percentage of MD confers a four to six fold risk elevation of developing breast cancer, even after adjustment for other known breast cancer risk factors. However, the biologic correlates of density are little known.

Methods
Gene expression analysis using whole genome arrays was performed on breast biopsies from 143 women; 79 women with no malignancy (healthy women) and 64 newly diagnosed breast cancer patients, both included from mammographic centres. Percent MD was determined using a previously validated, computerized method on scanned mammograms. Significance analysis of microarrays (SAM) was performed to identify genes influencing MD and generalized regression models were used to assess the independent contribution from different variables to MD.

Results
SAM-analysis identified 24 genes differentially expressed between samples from breasts with high and low MD. These genes included three uridine 5'-diphospho-glucuronosyltransferase (UGT) genes and the oestrogen receptor gene (ESR1). These genes were down-regulated in samples with high MD compared to those with low MD. The UGT gene products, which are known to inactivate oestrogen metabolites, were also down-regulated in tumour samples compared to samples from healthy individuals. Several single nucleotide polymorphisms (SNPs) in the UGT genes associated with the expression of UGT and other genes in their vicinity were identified.

Conclusions
Three UGT enzymes were lower expressed both in breast tissue biopsies from healthy women with high MD and in biopsies from newly diagnosed breast cancers. The association was strongest among young women and women using hormonal therapy. UGT2B10 predicts MD independently of age, hormone therapy and parity. Our results indicate that down-regulation of UGT genes in women exposed to female sex hormones is associated with high MD and might increase the risk of breast cancer.

overall_design: Gene expression analysis of breast biopsies from 143 women, 79 non-cancer (healthy women with no cancer who had a mammogram taken) and 64 breast cancer.

first: Alaug

last: Helland

first: Anne-Lise

last: Borresen-Dale

first: Giske

last: Ursin

first: Vessela

last: Kristensen

first: Marit

last: Holmen

first: OleChristian

last: Lingjaerde

first: Ying

last: Chen

first: Linda

last: Romundstad

first: Jan-Ole

last: Frantzen

first: Dina

last: Navjord

first: Margarethe

last: Biong

middle: D

first: Torben

last: Lüders

first: Ida

last: Bukholm


title: Effect of lactation on transcriptomic expression in bovine adipose tissue

status: Public on Apr 29 2010

city: Pullman

first: John

last: McNamara

state: WA

address: 233 Clark Hall

department: Animal Sciences

institute: Washington State University

summary:
The objective was to study the transcriptomic changes in adipose tissue in the early stages of lactation, specifically in Bos Taurus, Holstein dairy cattle as a function of milk production and genetic merit.
Chip quality backgrounds averaged below 50 units, and 3’/5’ bias on control genes < 2.0. Correlations among replicates were > 0.85.

overall_design: The design was a simple paired sampling, with time (30 d prepartum and 14 d postpartum as the sampling times.  There was no dietary manipulation.  Animals were all first calving Holstein heifers, all raised on the same farm on the same diet

first: J

middle: M

last: Sumner

last: Vierck


title: Transcriptional networks regulated by drugs of abuse in mouse striatum

status: Public on Apr 14 2010

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary:
In summary, we characterized genomic signatures of response to drugs of abuse and we found positive correlations between the drug-induced expression and various behavioral effects. These signatures are formed by two dynamically inducible transcriptional networks: (1) CREB/SRF-dependent gene pattern that appears to be related to drug-induced neuronal activity, (2) the pattern of genes controlled at least in part via release of glucocorticoids and androgens that are associated with rewarding and harmful drug effects. The discovery of co-expressed networks of genes allowed for the identification of master-switch controlling factors involved in molecular response to the drugs. Finally, using the pharmacological tools we were able to dissect and inhibit particular gene expression patterns from genomic profile.
Type: Drug response, Time-course, Gene expression profiling with Illumina Microarrays
Keywords: Addiction, Drugs of abuse, Time-course, Immediate Early Genes, Glucocorticoid receptor dependent genes, Cocaine, Heroin, Nicotine, Ethanol, Morphine, Methamphetamine

overall_design:
The microarray experiment was performed to analyze time-course of drug-induced transcriptional response in C57BL/6J mouse striatum. Six the most addictive and harming drugs of abuse (morphine 20 mg/kg, heroin 10 mg/kg, ethanol 2 g/kg, nicotine 1 mg/kg, methamphetamine 2 mg/kg or cocaine 25 mg/kg, i.p.) were selected for the comparison. Drug doses were previously reported as rewarding in mice and further tested in our laboratory. To analyze dynamics of early, intermediate and relatively late changes of mRNA abundance the experiment was performed in four time points (1, 2, 4 and 8h after drug administration). To exclude influence of drug injection and circadian rhythm on gene expression profile, control groups of saline treated and naïve animals were prepared for each time point. Design of the experiment assumed pooling of two animals per each array and using of three independent arrays per group. To provide appropriate balance in the whole dataset groups were equally divided between the array hybridization batches.

'Complete' normalized data and non-normalized data (containing control rows not represented in Platform GPL6105) are linked below as supplementary files.

first: Michal

last: Korostynski


title: Acute myeloid leukemia presenting with leukopenia: a distinct entity

status: Public on Mar 01 2010

city: atlanta

first: leon

last: bernal

state: GA

address: 1365 clifton road, bulding C

department: Hematolog and medical oncology

institute: Emory University

summary: Patients with acute myeloid leukemia and low circulating white count have a different gene expression profile compared those with high white count

overall_design: Bone marrow of ten patients( 5 patients with high and 5 patients with low peripheral blood white count) with blast count higher than 80% were selected for RNA extraction. RNA was used for gene expression analysis

first: Leon

last: Bernal-Mizrachi

first: Xiangxue

last: Guo


title: Whole Genome Sequencing Informs Therapeutic Selection for Pancreatic Cancer

status: Public on Feb 27 2015

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

summary: Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole genome sequencing and CNV analysis of 100 pancreatic ductal adenocarcinomas. Chromosomal rearrangements leading to gene disruption were frequent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A, ROBO2) and novel candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation classified PDAC into 4 subtypes with potential clinical utility: stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3, and PIK3CA), but at low individual frequency. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2, PALB2 or RPA1), and a mutational signature of DNA damage repair deficiency. This subgroup was associated with response to platinum-based therapy and defines candidate biomarkers of therapeutic responsiveness.

overall_design: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA) (HumanOmni1-Quad or HumanOmni2.5-8 BeadChips). SNP arrays were scanned and data was processed using the Genotyping module (v1.8.4) in Genomestudio v2010.3 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and logR values. GenoCN4 and GAP5 were used to call somatic regions of copy number change – gain, loss or copy neutral LOH. Recurrent regions of copy number change were determined and genes within these regions were extracted using ENSEMBL v70 annotations. Significant regions of gain and loss were identified by GISTIC6.

first: Nicola

last: Waddell

first: Marina

last: Pajic

first: Ann-Marie

last: Patch

first: David

last: Chang

first: Karin

middle: S

last: Kassahn

first: Peter

last: Bailey

first: Amber

middle: L

last: Johns

last: Miller

first: Kelly

last: Quek

first: Michael

last: Quinn

first: Alan

last: Robertson

first: Muhammad

last: Fudlullah

first: Timothy

middle: J

last: Bruxner

first: Angelika

last: Christ

first: Ivon

last: Harliwong

first: Senel

last: Idrisoglu

first: Suzanne

last: Manning

first: Craig

last: Nourse

first: Ehsan

last: Nourbakhsh

first: Shivangi

last: Wani

last: Wilson

first: Emma

last: Markham

first: Nicole

last: Cloonan

first: Matthew

last: Anderson

last: Fink

first: Oliver

last: Holmes

first: Stephen

last: Kazakoff

first: Conrad

last: Leonard

first: Felicity

last: Newell

first: Sarah

last: Song

first: Darrin

last: Taylor

first: Nick

first: Scott

last: Wood

first: Qinying

last: Xu

first: Jianmin

last: Wu

first: Mark

last: Pinese

last: Cowley

first: Marc

last: Jones

first: Emily

last: Colvin

first: Adnan

last: Nagrial


title: Candidate driver genes in focal chromosomal aberrations of stage II colon cancer

status: Public on Apr 19 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary: Chromosomal instable colorectal cancer is marked by specific large chromosomal copy number aberrations. Recently, focal aberrations of 3Mb or smaller have been identified as a common phenomenon in cancer. Inherent to their limited size, these aberrations harbour one or few genes. The aim of this study is to identify recurrent focal chromosomal aberrations and their candidate driver genes in a well defined series of stage II colon cancers and assess their potential clinical relevance.  High resolution DNA copy number profiles were obtained from 38 formalin fixed paraffin embedded colon cancer samples with matched normal mucosa as a reference using array comparative genomic hybridization. In total, 81 focal chromosomal aberrations were identified that harboured 177 genes. Statistical validation of focal aberrations and identification of candidate driver genes was performed by enrichment analysis and mapping copy number and mutation data of colorectal-, breast-, pancreatic cancer and glioblastomas to loci of focal aberrations in stage II colon cancer. This analysis demonstrated a significant overlap with previously identified focal amplifications in colorectal cancer, but not with cancers from other sites. In contrast, focal deletions seem less tumour type specific since they also show significant overlap with focal deletions of other sites. Focal deletions detected are significantly enriched for cancer genes and genes frequently mutated in colorectal cancer. The mRNA expression of these genes is significantly correlated with DNA copy number status, supporting the relevance of focal aberrations. Loss of 5q34 and gain of 13q22.1 were identified as independent prognostic factors of survival in this series of patients.   In conclusion, focal chromosomal copy number aberrations in stage II colon cancer are enriched in cancer genes which contribute to and drive the process of colorectal cancer development. DNA copy number status of these genes correlate with mRNA expression and some are associated with clinical outcome.

overall_design:
38 Stage II colorectal cancer (CRC) tissue samples (FFPE) of which 19 were done on expression arrays.
One sample (Stage II colorectal cancer tissue samples (FFPE) 26) was also done on the 135K NimbleGen array.
Fresh frozen and FFPE of the same CRC stage I sample was done on 105K agilent. The fresh frozen was across array in silico set out against a pool of blood of 18 healthy females.

first: Rebecca

last: Brosens

first: Josien

last: Haan

first: Beatriz

last: Carvalho

first: François

last: Rustenburg

first: Heike

last: Grabsch

first: Philip

last: Quirke

first: Alexander

middle: F

last: Engel

first: Miquel

middle: A

last: Cuesta

first: Nicola

last: Maughan

first: Marcel

last: Flens

first: Gerrit

last: Meijer

first: Bauke

last: Ylstra


title: Comparative transcriptional profiling of Limbal Epithelial Crypts with rest of the ocular surface epithelial regions.

status: Public on Mar 24 2010

city: Nottingham

first: Patrick

middle: Jason

last: Tighe

state: Nottinghamshire

address: University Hospital

department: School of Molecular Medical Sciences

institute: The University of Nottingham

summary:
Recently we had discovered a solid cord like structure at the limbus of human eyes, termed as the Limbal Epithelial Crypt (LEC).  It arises from the undersurface of the interpalisade rete ridges and extends towards the conjunctiva over the conjunctival stroma.
Anatomical and immunohistochemical studies have shown it to be potentially a Stem Cell Niche.  To confirm this hypothesis we conducted comparative gene expression profile of LEC with pathway and Geneontology studies in comparison with other ocular surface epithelial regions such as cornea, limbus, LEC stroma and conjunctiva.
Frozen tissue blocks of corneoscleral buttons dissected from cadaver eyes were cryosectioned. These tissue sections from different ocular surface regions were laser microdissected. Extracted RNA was amplified & hybridized to 30,000k Human spotted cDNA  microarray chips. Raw data obtained with Genepix Pro6 software was filtered, normalized & analysed on BASE & Jexpresspro software. Unpaired T-Test, Significance Analysis of Microarrays  were performed on the data.  Database for Annotation, Visualisation, and Integrated Discovery (DAVID)  (http://www.DAVID.niaid.nih.gov) and Ingenuity Pathway Analysis (IPA) was used to determine the enriched GO terms and pathways in the differentially expressed genes.  Quantitative gene expression analysis (qPCR) and immunohistochemistry was performed on the genes of interest.  Statistical analysis for real time PCR was performed on SPSS16 to determine the normalised expression of gene of interest on ocular surface regions.

overall_design: Samples were prepared from five human ocular surface epithelial regions such as Cornea, Limbus, LEC, LEC Stroma, Conjunctiva. There were four replicates in each groups except Cornea and Conjunctiva with 3 each. The Standard Probe (SP) was prepared from mixing equal amount of Corneal and conjunctival epithelial RNA followed by ethanol precipitation. Samples were labelled with Cy5 dye and Standard Probe with Cy3 Dye.  These were mixed in equal amount to prepare hybrid probes which were then hybridised to microarray slide.

first: Bina

last: Kulkarni

first: Harminder

last: Dua


title: miR-30e* induced gene expression alteration in glioma cells

status: Public on Feb 17 2010

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

institute: Sun Yat-sen University

summary: This experiment is designed to evaluate gene expression alteration following miR-30e* transfection in glioma cells. We find a significant elevation of NF kappa B transcriptional targets.

overall_design: Total RNA were extracted from SNB-19 and U-87MG glioma cells transfected with miR-30e* mimic oligo or miRNA mimic negative control 36 hours after transfection, two biological replications for each treatment.

first: Zhe

last: Ying

first: Jun


title: Regulatory divergence in Drosophila melanogaster and D. simulans: a genome-wide analysis of allele-specific expression

status: Public on Aug 05 2009

city: Gainesville

first: Rob

last: Kulathinal

state: FL

address: 1376 Mowry Road

department: Department of Biology

institute: University of Florida

type: Expression profiling by genome tiling array

summary: Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits.  A better understanding of the evolutionary forces which shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids.  Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genome-wide in female adult heads of D. melanogaster, D. simulans and their F1 hybrids.  A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level.  Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy.  In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila sp. (in: flies)

overall_design: Females heads from two species, D. melanogaster and D. simulans, and their F1 hybrid were compared.  Genomic DNA was used as a control.

first: Rita

last: Graze

first: Lauren

last: McIntyre

first: Brad

last: Main

first: Marta

last: Wayne

first: Sergey

middle: V

last: Nuzhdin


title: Osteosarcoma is characterized by impaired osteoclastogenesis and antigen presentation compared to normal bone

status: Public on Jan 31 2010

city: Woolloongabba

first: Liliana

middle: Beatriz

last: Endo-Munoz

state: Queensland

address: TRI, 37 Kent St

department: Diamantina Institute

institute: University of Queensland

summary:
Osteosarcoma is characterized by reduced expression of markers of impaired osteoclastogenesis and antigen presentation compared to normal bone
Osteosarcoma (OS) is the most common primary bone tumour in children and young adults, and the second highest cause of cancer-related death in this age group. In spite of aggressive chemotherapy, disease-free survival has not improved significantly in the past 20 years, and 50% of patients subsequently develop fatal pulmonary metastasis. We have performed gene expression profiling of primary osteosarcoma biopsies and compared the results to gene expression profiling of non-malignant bone to identify differentially expressed genes unique to OS in the context of the bone micorenvironment.

Keywords: Comaprison between disease status (OS) and normal; comparison between good and poor response to chemotherapy

overall_design: Two-colour experiment. 23 samples of OS analyzed in duplicate (dye-swaps); 3 samples of good responders, 20 of poor responders analyzed in duplicate (dye-swaps); 5 samples of non-malignant bone analyzed individualy, no dye-swaps (i.e. 5 biological replicates).

first: Andrew

last: Cumming

first: Scott

last: Sommerville

first: Ian

last: Dickinson

first: Nicholas

last: Saunders


title: Monocyte Transmigration

status: Public on Nov 16 2009

city: Snellville

first: Marcie

middle: R

last: Williams

address: 2300 Country Walk 3427

department: Biomedical Engineering

institute: Georgia Institute of Technology

summary: We investigated the hypothesis that transmigration drives monocyte transcriptional changes.  Using Agilent Whole Human Genome Microarrays, we identified over 600 differentially expressed genes (2x, p<0.05) in freshly isolated human monocytes following 1.5 h of transmigration across IL1beta-stimulated ECs compared to untreated monocytes.  Genes up-regulated by monocyte transmigration belong to a number of overrepresented functional groups including immune response, and inhibition of apoptosis.  qRT-PCR confirmed increased expression of monocyte chemotactic proteins 1 and 3 and of NLR family apoptosis inhibitory protein  (NAIP) following monocyte transmigration.  In addition, quantification of annexin V binding revealed a reduction in apoptosis following monocyte transmigration.  Comparison of gene expression in transmigrated monocytes to additional controls (monocytes which failed to transmigrate and monocytes incubated beneath stimulated ECs) revealed 89 differentially expressed genes which were controlled by the physical process of diapedesis.  Functional annotation of these genes showed down-regulation of antimicrobial genes (e.g. alpha-defensin down 50x, cathelicidin down 9x, and cathepsin G down 3x).  qRT-PCR confirmed down-regulation of these genes.  Immunoblots confirmed that monocyte transmigration down-regulates alpha-defensin protein expression.  Overall, these data indicate that exposure of monocytes to stimulated ECs promotes further monocyte recruitment and inhibits monocyte apoptosis.  Unexpectedly, following transmigration monocytes displayed reduced anti-microbial expression.

overall_design: Monocytes were allowed to transmigrate across IL1b stimulated HUVEC.  Monocytes which transmigrated and monocytes which failed to transmigrate were collected after 1.5 hours from 3 experimental replicates of different human donors.  Untreated monocytes were collected as a control from 4 human donors.  Monocytes incubated beneath stimulated HUVEC for 1.5 hours were also collected from four human donors as a control.

first: Yumiko

last: Sakurai

first: Suzanne

middle: G

last: Eskin

first: Larry

last: McIntire


title: Changes in gene expression of granulocytes during in vivo G-CSF/dexamethasone mobilization.

status: Public on Sep 09 2009

first: Agata

last: Drewniak

address: Plesmanlaan 125

department: Blood Cell Research

institute: Sanquin Research

summary:
Treatment of healthy donors with G-CSF and dexamethasone, results in sufficient number of circulating granulocytes to prepare granulocyte concentrates for clinical purposes. Granulocytes obtained this way demonstrate relatively normal functional behavior combined with a prolonged life span. To study the influence of mobilizing agents on granulocytes, we used oligonucleotide microarrays to identify genes that are differentially expressed in mobilized granulocytes as compared to control ones.

Keywords: mobilized granulocytes, G-CSF/dexamethasone treated granulocytes

overall_design: Granulocytes were isolated from three individuals before (control situation) and 18 hours after treatment with G-CSF&dexamethasone; part of the control cells was cultured overnight in HBSS medium with or without addition of G-CSF and dexamethasone. Total RNA from each experimental condition was compared to pooled RNA of control granulocytes.

first: A

first: B

last: van Raam

first: J

last: Geissler

last: J Tool

first: O

last: F Mook

first: T

last: van den Berg

first: F

last: Baas

middle: W

last: Kuijpers


title: Population genomics in a disease targeted primary cell model

status: Public on Apr 16 2009

city: Montreal

first: Elin

last: Grundberg

address: 740 Dr Penfield Avenue

institute: McGill University and Genome Quebec Innovation Centre

summary: The common genetic variants associated with complex traits typically lie in non-coding DNA and may alter gene regulation in a cell-type specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an eQTL study of primary human osteoblasts (HOb) derived from unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. We combined our data with publicly available information from a genome-wide association study (GWAS) of bone mineral density (BMD). The top BMD-associated SNPs  were tested for cis-association of gene expression in HObs and in lymphoblastoid cell lines (LCLs) using publicly available data and showed that HObs have a significantly greater enrichment of converging cis-eQTLs as compared to LCLs. The top BMD loci with SNPs showing strong cis-effects on gene expression in HObs were selected for further validation using a staged design in two cohorts of Caucasian male subjects. All  variants were tested in the Swedish MrOs Cohort (n=3014), providing evidence for two novel BMD loci. These variants were then tested in the Rotterdam Study (n=2100), yielding converging evidence for BMD association at one locus. The cis-regulatory effect was further fine-mapped to the proximal promoter of the gene. Our results suggest that primary cells relevant to disease phenotypes complement traditional approaches for prioritization and validation of GWAS hits for follow-up studies.

overall_design: Total RNA obtained from 95 unrelated donors of Swedish origin each represented by two biological replicates

first: Tony

last: Kwan

first: Bing

last: Ge

first: Kevin

middle: C

last: Lam

first: Vonda

last: Koka

first: Andreas

last: Kindmark

first: Hans

last: Mallmin

first: Joana

last: Dias

first: Dominique

last: Verlaan

first: Manon

last: Ouimet

first: Daniel

last: Sinnett

first: Fernando

last: Rivadeneira

first: Karol

last: Estrada

first: Joyce

last: van Meurs

first: André

last: Uitterlinden

first: Patrick

last: Beaulieu

first: Alexandru

last: Graziani

first: Eef

last: Harmsen

first: Osten

last: Ljunggren

first: Claes

last: Ohlsson

first: Dan

last: Mellström

first: Magnus

last: Karlsson

first: Olle

last: Nilsson

first: Tomi

last: Pastinen


title: Array CGH analysis in primary human renal tumors, categorized by VHL genotype and HIF-alpha expression

status: Public on Dec 27 2008

city: Philadelphia

first: Bradley

last: Wubbenhorst

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvannia

summary:
Human renal cell carcinomas (RCC) have differential expression of HIF-1alpha and HIF-2alpha, depending on VHL genotype and other events.
Here, we have divided a series of RCC samples based on HIF-alpha expression, in order to examine levels of genomic DNA aberration.

Keywords: Patient Sample Study

overall_design: A total of 57 frozen RCC samples were stained for HIF-1alpha and HIF-2alpha, and genotyped for VHL. 10 VHL-deficient/HIF-1alpha+/HIF-2alpha+ and 11 VHL-deficient/HIF-2alpha+ tumors were selected for array CGH.

first: John

last: Gordan

first: Priti

last: Lal

first: Vijat

last: Dondeti

first: Richard

last: Letrero

first: Krishna

middle: N

last: Parekh

first: C

middle: E

last: Oquendo

first: Roger

last: Greenberg

first: Keith

last: Flaherty

first: W

middle: K

last: Rathmell

first: Brian

last: Keith

first: M

last: Simon

first: Katherine

last: Nathanson


title: Regulation of androgen receptor transcriptional activity and specificity by RNF6

status: Public on Apr 06 2009

city: Baltimore

first: Hegang

last: Chen

address: 660 West Redwood Street

institute: University of Maryland School of Medicine

summary: The androgen receptor (AR) plays a critical role in prostate cancer. We identified an ubiquitin E3 ligase RNF6 as one of AR-associated proteins in a proteomic screening. RNF6 induces AR ubiquitination and promotes AR transcriptional activity. Specific knockdown of the endogenous RNF6 alters expression of a subset of AR target genes and diminishes recruitment of AR and its coactivators to androgen responsive elements (AREs) present in the regulatory region of these genes. Furthermore, RNF6 is overexpressed in human hormone-refractory prostate cancer tissues and required for prostate cancer cell growth under androgen-depleted conditions. Our work has provided a novel mechanism by which AR transcriptional activity and specificity is regulated, and identified RNF6 as a potential new target for prostate cancer treatment.

overall_design: Total RNA was extracted from LNCaP cells treated with (1) No Treatment (NT-DHT) (2) shCon-DHT, (3) shRNF6-DHT, (4) NT+DHT, (5) shCon+DHT, (6) shRNF6+DHT, respectively. Total RNA from each of 5 treated LNCaP cells was labeled with Cy5 dye. RNA from LNCaP cells that received no DHT (NT-DHT) was also labeled with Cy3 dye and served as a common reference, with which each of the five labeled test samples were cohybridized in a classical two-color hybridization scheme.


title: NIAS Rice Project

status: Public on Aug 13 2009

city: Tsukuba

first: Shoshi

last: Kikuchi

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

country: Japan

institute: National Institute of Agrobiological Sciences

summary:
[to be updated]
Keywords: other

sample_organism:
Matthiola incana
Bromus secalinus
Hordeum vulgare
Oryza sativa
Triticum aestivum
Zea mays
Bromus inermis

first: Junshi

last: Yazaki

first: Zenpei

last: Shimatani

first: Shinozaki

last: Kazuko

first: Yosiyuki

last: Tanaka

first: Noboru

last: Endoh

first: Masahiro

last: Ooshima

first: Naoki

last: Kishimoto

first: Hisako

last: Ohtubo

first: Sigeru

last: Iida

first: Etuo

last: Shimosaka

first: Konishi

last: Tomokazu

first: Tomokazu

last: Konishi

first: Saito

last: Akira

first: Toshiaki

last: Tadano

first: Tooru

last: Fujiwara

first: Masamichi

last: Nishiguchi

first: Eiichi

last: Minami

first: Setuko

last: Komatu

first: Isomaro

last: Yamaguchi

first: Kazuhiko

last: Sugimoto

first: Masaya

last: Ishikawa

first: Yuko

last: Oohashi

first: Youko

last: Nisizawa

first: Tomoya

first: Ryouzou

last: Imai

first: Yutaka

last: Sato

first: Hiroyuki

last: Oota

first: Tukaho

last: Hattori

first: Naoko

first: Kenichi

last: Ogawa

first: Nobuhiro

last: Tutumi

first: Hideo

last: Matumura

first: Jyunji

last: Hashimoto

first: Masaaki

last: Umeda

first: Tetuji

last: Kakutani

first: Toshiki

last: Mine

first: Yasunari

last: Hagiwara

first: Noritoshi

last: Inagaki

last: Niki

first: Makoto

last: Kawase

first: Makiko

last: Kawagisi

first: Sakiko

last: Takahashi

first: Masao

last: Iwamoto

last: Takano


title: Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer

status: Public on Dec 24 2010

first: Sean

last: Cory

address: 3649 Promenade Sir William Osler

institute: McGill

summary: Ductal carcinoma in situ (DCIS) is a non-invasive form of breast cancer where cells restricted to the ducts exhibit an atypical phenotype. Some DCIS lesions are believed to rapidly transit to invasive ductal carcinomas (IDCs), while others remain unchanged. Existing classification systems for DCIS fail to identify those lesions that transit to IDC. We studied gene expression patterns of 31 pure DCIS, 36 pure invasive cancers and 42 cases of mixed diagnosis (invasive cancer with an in situ component) using Agilent Whole Human Genome Oligo Microarrays 44k. Six normal breast tissue samples were also included as controls. qRT-PCR was used for validation. All DCIS and invasive samples could be classified into the intrinsic molecular subtypes defined for invasive breast cancer. Hierarchical clustering establishes that samples group by intrinsic subtype, and not by diagnosis. We observed heterogeneity in the transcriptomes among DCIS of high histological grade and identified a distinct subgroup containing seven of the 31 DCIS samples with gene expression characteristics more similar to advanced tumours. A set of genes independent of grade, ER-status and HER2-status was identified by logistic regression that univariately classified a sample as belonging to this distinct DCIS subgroup. qRT-PCR of single markers clearly separated this DCIS subgroup from the other DCIS, and contains samples from several histopathological and intrinsic molecular subtypes. The genes that differentiate between these two types of DCIS suggest several processes related to the re-organisation of the microenvironment. This raises interesting possibilities for identification of DCIS lesions both with and without invasive characteristics, which potentially could be used in clinical assessment of a woman's risk of progression, and lead to improved management that would avoid the current over- and under-treatment of patients.

overall_design: Breast cancer samples, 31 pure DCIS patients, 36 IDC patients, 42 mixed and 6 normal.

first: Michael

last: Hallett

first: Aslaug

last: Muggerud


title: Differential Genetic and Functional Markers of Second Neoplasias in Hodgkin´s Disease Patients

status: Public on Dec 01 2008

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

institute: CNIO (Spanish National Cancer Center)

summary: The mechanisms involved in the appearance of a second neoplasia in patients with Hodgkin´s disease (HD) may be probably related with the genomic damage induced by the administrated treatments and its repair. Evaluate using the Comet Assay whether baseline, induced and unrepaired DNA damage differ in HD patients who did not develop a second neoplasia (HD-NST), HD patients who developed a second tumor (HD-ST) and healthy individuals, and to identify, through cDNA microarray hybridization, an expression signature of genes which could discriminate among the three groups. Baseline, induced and unrepaired DNA damage was higher in HD-ST than in HD-NST and in the latest group higher than in healthy donors. The genomic approach revealed two set of genes that discriminated between healthy subjects and patients and among the 3 sets of individuals. Hsp40, RAD50, TPMT, Rap2a, E2F2, EPHX2, TBX21 and BATF were validated by RT-PCR. Functional and genomics techniques revealed that alterations in cell cycle, repair, detoxifying and stress response pathways could be involved in the development of HD and in the occurrence of a primary second neoplasia in these patients. Both approaches may be useful as biological markers in the clinical setting.

overall_design:
We have measured the relative abundance of RNA species in plasma through microarray hybridization, by comparing RNA isolated and amplified from 3 samples classes:
- 9 patients with Hodgkin´s Disease who did not develop a second neoplasia (HD-NST)
- 9 patients with Hodgkin´s disease who developed a second tumor against (HD-ST)
- 9 healthy donors.
For each population’s series (healthy individuals, HD-ST and HD-NST), 3 different pooled samples were obtained by mixing equal amounts of RNA from three individual samples of each series.
Each pooled sample was competitively hybridized against a common reference formed by a pool of samples from the 9 healthy donors.


title: miR-K5 expression and inhibition

status: Public on Oct 01 2008

city: San Francisco

first: Don

last: Ganem

state: CA

address: 513 Parnassus Ave

department: G.W. Hooper

institute: University of California, San Francisco

summary:
Transcriptional profiling of BJAB cells expressing miR-K5 and BCBL cells treated with miR-K5 inhibitor.
To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under four sets of conditions in which KSHV miRNAs were expressed or inhibited.

Keywords: Experimental treatment versus control treatment

overall_design: Cells transfected with negative control miRNA compared to miR-K5 or negative miRNA inhibitor compared to miR-K5 inhibitor or stable cells transduced with empty vector compared to stable cells transduced to express miR cluster K1,2,3,4,5.

first: Joseph

last: Ziegelbauer


title: Supervised Lowess normalization of comparative genome hybridization data: application to lactococcal strain comparisons.

status: Public on Jul 20 2008

city: Haren

first: Sacha

last: van Hijum

address: Kerklaan 30

institute: University of Groningen

summary:
Background
Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. In aCGH data, systematic errors are comparable to those occurring in transcriptome data. However, especially for microbes, an additional source of variation exists: differences in hybridization due to gene sequence divergence between the strains hybridized. Current normalization methods do not take this source of variation into consideration.
Results
We present Supervised Lowess, or S-Lowess, an application of the subset Lowess normalization method that does take difference in genomic content into account. The performance of S-Lowess was assessed on aCGH experiments in which differentially labeled genomic DNA fragments of Lactococcus lactis IL1403 and L. lactis MG1363
strains were hybridized to IL1403 microarrays. Since both genome sequences are known (they have only on average 85 % sequence identity), the success rate in detecting deletions in the MG1363 genome of different aCGH normalization methods can be compared. S-Lowess detects 97% of the deletions, whereas other aCGH normalization methods detect up to only 60% of the deletions.
Conclusions
S-Lowess removes systematic errors from dual-dye aCGH data in two steps: (i) determination of likely homologous genes (LHG); and (ii) estimation of correction factors for systematic errors from spots of LHG and subset Lowess normalization of the remaining spots using these correction factors. It is implemented in a user-friendly web-tool accessible from http://bioinformatics.biol.rug.nl/websoftware/s-lowess. We demonstrate that it outperforms existing normalization methods and maximizes the number of detectable genomic deletions or duplications from microbial aCGH data.
Keywords: comparative genome hybridisation

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: In this study, 4 aCGH comparisons (slides) between L. lactis MG1363 and L. lactis IL1403 were performed (including dye swap with biological replicates; see also supplementary materials). The resulting aCGH slide signals were normalized using the different 'likely homologous gene' (LHG) sets (see above) yielding ratios of signals of labelled DNA of MG1363 over those of IL1403. A maximum of 8 ratios per amplicon (gene) were obtained for the 4 hybridized slides (each with 2 replicate spots per amplicon). Only genes with at least 5 measurements were used in this study. The normalization methods evaluated in this study are: a) no normalization, b) total signal normalization, c) grid-based Lowess (implemented in PreP; f = 0.7) [García de la Nava, J et al. 2003. Bioinformatics 19:2328-2329], and d) S-Lowess using different subsets of conserved lactococcal genes (for details see above). Results with the MANOR R package (spatial normalization; standard parameters) [Neuvial P, et al. 2006. BMC Bioinformatics 7:264; Liva S, et al. 2006. Nucleic Acids Res 34:W477-W481] are shown in our supplementary materials.

first: Richard

last: Baerends

first: Aldert

last: Zomer

first: Harma

last: Karsens

first: Victoria

last: Martin-Requena

first: Oswaldo

last: Trelles

first: Jan

last: Kok

first: Oscar

middle: P

last: Kuipers


title: Comparison of the costimuli anti-CD28 and IL-2 on the activation of purified naïve human T cells

status: Public on Dec 17 2009

city: Heidelberg

first: Maximilian

last: Aigner

address: Im Neuenheimer Feld 280

country: Germany

institute: Deutsches Krebsforschungszentrum (DKFZ)

summary:
The aim of the study was to compare the two different costimuli anti-CD28 (costimulus 2a) and IL-2 (costimulus 2b) – in the presence of a suboptimal anti-CD3 signal (signal 1) – on the de novo activation of freshly purified human naive T cells.
To this end, purified human naive T cells were co-incubated for seven days with a tumor vaccine which consisted of gamma-irradiated and Newcastle Disease Virus (NDV)-infected MCF-7 cells (a well-defined mammacarcinoma cell line). The gamma-irradiation dose was 200 Gray (Gy) to suppress the proliferation capacity of the vaccine cells (although the vaccine cells are not killed by such a procedure but still survive for several days); NDV-infection was performed at a dose of 100 hemagglutination units (HU) per 10^7 vaccine cells. The latter led – among others – to the upregulation of the viral surface molecules hemagglutinin neuraminidase (HN) and the fusion protein (F), both of which can serve for the attachment of fusion proteins delivering the activation signals to the naive T cells.
The bispecific (bs) fusion proteins used in this study were of the single chain (scFv) format, binding with one arm to the viral HN molecule (for the attachment to the vaccine cells), and with the other arm either to the T cell receptor (TCR)-associated CD3 complex [as a surrogate of a major histocompatibility complex (MHC)-presented peptide recognized by the TCR] (bsHN-CD3), or to the costimulatory molecule CD28 (bsHN-CD28). Furthermore, a bispecific fusion protein containing the human interleukin (IL)-2 (bsHN-IL-2, a so-called immunocytokine) was used.
The gene expression analysis of the differentially activated naive T cells revealed that in the presence of a suboptimal dose of anti-CD3 the two costimuli anti-CD28 (sample d7-S2_280705) and IL-2 (sample d7-S3_280705) led to a highly redundant pattern of gene upregulation in comparison to control samples in which naive T cells received only anti-CD3 (sample d7-S4_280705), anti-CD28 (sample d7-S5_280705) or IL-2 (sample d7-S6_280705) signals alone, or no signal at all (i.e. only vaccine cells; sample d7-S7_280705). All signals were compared to the reference sample which consisited of freshly isolated, non-activated naive T cells (sample d0-S1_280705).
Global analysis of the gene expression showed that full naive T cell activation by anti-CD3/anti-CD28 and anti-CD3/IL-2 led to a significant upregulation of 76 and 71 genes, respectively (upregulation was considered to be significant if the relative gene expression was more than 5-fold than in the reference sample). However, the suboptimal anti-CD3 stimulus alone upregulated only 31 genes, the anti-CD28 stimulus alone only 6 genes, and the IL-2 stimulus alone only 22 genes. Naive T cells that reveived virus-modified vaccine cells alone upregulated 18 genes.
Equally upregulated genes in anti-CD3/anti-CD28 and anti-CD3/IL-2 activated naive T cells comprised genes coding for both (i) signalling and (ii) effector molecules. Concerning signalling molecules, both costimuli induced the nuclear factor (NF)-kappa B and nuclear factor of activated T cells (NF-AT) pathway via the key enzymes protein kinase C (PKC)-theta and phospholipase C (PLC)-gamma 1, respectively. Of special note was that signalling molecules of the CD28-mediated stress-activated protein kinase (Sapk) pathway, namely Vav-1, Rac-1 and Jnk-2, were also upregulated by IL-2 costimulation. Upregulated genes coding for effector molecules could be classified into different functional groups: namely regulators of apoptosis, cell adhesion, receptors/ligands and cytokines/chemokines. Some examples of effector molecule-coding genes similarly upregulated in anti-CD3/anti-CD28 and anti-CD3/IL-2 stimulated naive T cells, respectively, were for instance the cell adhesion molecules LFA-1 and CD2, or members of the TNF and TNF receptor superfamilies such as CD27, CD70, CD40 ligand, Fas ligand, as well as TNF-alpha and TNF-beta (and their corresponding receptors). Among apoptosis-related genes, the anti-apoptotic gene bcl-XL as well as the pro-apoptotic gene caspase 9 were upregulated. The latter – together with the observed upregulation of cytotoxic T lymphocytes-associated protein (CTLA)-4 – might be interpreted as an indication of cellular events occurring seven days after stimulation which are aiming at termination of the response. Furthermore, the microarray analysis also revealed and upregulation of the receptor for interferon (IFN)-gamma inducible protein of 10 kDa (IP-10), namely CXCR3, of the IL-12 receptor beta-chain and of the IL-15 receptor alpha-chain; these are often seen in close association with T cell activation in general, with T cell proliferation and with generation of memory T cells. It is also of interest to mention the upregulation of beta-actin which is required for a re-organization of the cytoskeleton and the 40-fold upregulation of the metabolic enzyme glyceraldehye-3-phosphate dehydrogenase (GAPDH) which provides ATP necessary for the increased metabolism of the activated cells. A summary of the interesting gene subset is attached as a supplementary table (including the pairwise compared normalized data).
In summary, these data suggest a synergism and cross-talk between the two costimulatory pathways mediated by anti-CD28/CD28 and IL-2/IL-2 receptor, respectively.
Keywords: Human naive T cells, activation, costimulation, anti-CD28, IL-2, signal transduction, tumor vaccine, immunocytokine

overall_design:
A complete and exhaustive experimental design is given in the "Sample description" section of each sample.
In total, seven samples were analyzed in parallel: one reference sample (d0-S1_280705: freshly isolated, purified naive T cells), two samples of fully activated naive T cells (d7-S2_280705: anti-CD3/anti-CD28 activation; d7-S3_280705: anti-CD3/IL-2 activation) and four control samples (d7-S4_280705: anti-CD3 alone; d7-S5_280705: anti-CD28 alone; d7-S6_280705: IL-2 alone; d7-S7_280705: vaccine cells alone).


title: CMV infection induces a rapid and sustained change in the expression of Natural Killer Cell Receptors on CD8+ T Cells

status: Public on Aug 28 2008

first: Amber

last: van Stijn

address: Meibergdreef 9

department: Experimental Immunology

institute: Academic Medical Center

summary:
The CD8+ T cell compartment of human cytomegalovirus (CMV) seropositive individuals characteristically contains a high proportion of cells that expresses Natural Killer Cell Receptors (NKR) which may contribute to the surveillance of virus-infected cells. To test if this enhanced expression is a direct and immediate result of CMV infection we used DNA microarrays to analyse putative changes in RNA-expression level of 39 NKRs in CMV-specific CD8+ T cells of renal transplant recipients experiencing primary CMV infection. Already in the acute phase of infection 29 NKRs were induced of which 19 remained high 1 year after cessation of viral replication. Activating and inhibitory NKRs were induced to a similar extent. Detailed longitudinal flowcytometric analyses confirmed NKR changes at the protein level. Strikingly, a strong induction of CD94 on CD3+ T cells was observed with surface expression of activating CD94dimNKG2C dimers appearing before inhibitory CD94brightNKG2A ones. After the acute phase of infection, the balance between inhibitory and activating receptors did not change. Thus, CMV infection induces a rapid and lasting change in the expression of NK receptors on human CD8+ T cells.

Keywords: primary cytomegalovirus infection, human, CD8+ T cells, NKR, latent infection, chronic infection

overall_design: CMV-specific CD8+ T cells were isolated at three different stages (peak, 1 year p.i, latent) from three CMV seropositive individuals. Total RNA for each stage was pooled and compared with pooled RNA of naive CD8+ T-cells from healthy controls. For quality control naive CD8+ T-cells were compared with naive CD8+ T-cells. The experiment was performed in dye-swap.

first: Perry

middle: D

last: Moerland

first: Ajda

middle: T

last: Rowshani

first: Sila

last: Yong

first: Frank

last: Baas

first: Ineke

last: ten Berge

first: René

last: van Lier


title: Evaluation of Wpa-generated amplicons for SNP typing (allele bias), locus bias, and detection of known CNVs

status: Public on Sep 24 2008

city: New Haven

first: Xinghua

last: Pan

state: CT

address: 300 Cedar Street, TAC-S320

department: Department of Genetics

institute: Yale University School of Medicine

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

overall_design: Refer to individual Series


title: Illumina HapMap (550duo)

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

summary: HapMap samples

overall_design: 120 samples from Human550duo_1Megt_Final_FinalReport.txt


title: Evaluation of the amplicons for SNP typing (allele bias) and locus bias using Illumina 550-Duo BeadChip

summary:
Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a procedure using phi29 DNA polymerase and trehalose and optimized control of amplification to create micrograms of specific amplicons without TIPs from down to sub-femtograms of DNA. The amplicons from 5 ng and 0.5 ng DNA, which were from originally good quality of gDNA (05-050), or partially degraded gDNA (04-018), were validate with Illumina HumanHap550-Duo Genotyping Beadchip. As seen in (Suppl. Table 5a), the call rates (97.30% to 99.07%) and accuracy or concordance ( > 99.85% for the SNPs called in both amplicon and natural reference) for 5 ng derived amplicons with both Wpa and Gv2 were close to each other and close to native gDNA (call rate: 98.3% to 99.75%). These call rates were better than a recent report (amplicon 95.9% vs. un-amplified 98.5%), in which the early kit Repli-g 625S was applied, and re-genotyping was performed when the performance was low and duplicate samples were filtered for the highest call rate. The genotyping accuracy of Wpa was actually in the same range as the variation in technical replicates with similar SNP typing arrays (99.87% and 99.88%, replicated Affymetrix array, or between Affymetrix and Illumina arrays). Importantly, the genotyping concordance for amplicons generated from 0.5 ng with Wpa (99.88% and 99.69%) were also close to the technical replicates. In this case, the call rates of Wpa were slightlyreduced compared to that with 5 ng input, but the call rate for the partially degraded sample 04-018, was modestly improved over Gv2 (92.06 % vs. 90.53%).  Wpa data also showed some amplification non-uniformity among different locations, resulting in some “artificial CNVs” similar to Gv2 (exampled as in Suppl. Fig. 5 and Suppl. Table 6), with the outputs obtained by taking unamplified gDNAs as their reference. This imbalance however was consistent and reproducible for each method but different between Wpa and Gv2. These artificial CNVs can be efficiently cancelled if pair-wise amplified test and reference are compared, as observed in CGH result (Fig. 4 and Suppl. Fig. 4), also supported by others {Pugh 2008}. It is interesting to note that the representation of chromosomal terminal sequences was greatly improved with Wpa compared with Gv2 (Fig. 5), and that some of these regions were significantly under-amplified or even lost with Gv2 (Suppl. Fig. 5 and Suppl. Table 6, 7), as also independently reported recently {Pugh 2008}. This occurred especially in the terminal 3 to 5 Mb and sometimes extended to 10 Mb in many chromosome termini, and was particularly serious when low levels or degraded DNA was as input. An analysis for 5 Mb termini is shown (Suppl. Table 5b calculated all involved SNPs as a cohort. Fig. 5 and Suppl. Tables 6 and 7 were the result for each chromosome terminus). Importantly, the SNP typing was also greatly improved, outstandingly exemplified by the amplicons of 0.5 ng input for the partially degraded 04-018, with Wpa versus Gv2 call rate of 91.9% vs. 84.45% and accuracy of 99.57% vs. 98.62%. The result also showed that these terminal regions underrepresentation in Gv2 was not absolutely associated with the distance-to-end, but possibly was a sequence related issue.

Keywords: Whole-pool amplification, whole genome SNP typing

overall_design: The overall goal of the part of study was a validation of the quality of the amplicons from different amounts (5ng and 0.5 ng) of original starting gDNA, good quality (sample 05-050) or partially degraded gDNA (sample 04-018), with our new procedure Wpa, and with native gDNA as control, in terms of the call rate and accuracy (allele bias) in addition to the uniformity of the sequence amplified (sequence representation or sequence bias). Amplified or native genomic DNA isolated from patients was in-parallel analyzed/genotyped with the same experimental platform, of which the native genomic DNAs were used as the standard controls. For the sequence representation, the two alleles of the SNPs’ signal of a panel of multiple native DNAs’ signal provided by the experimental platform (Illumina) was used as the reference, so that an abstract signal for sequence representation of each SNP and for all SNPs was obtained.

first: Alexander

last: Urban

first: Dean

last: Palejev

first: Vincent

last: Schulz

first: Fabian

last: Grubert

first: Yiping

last: Hu

first: Michael

last: Snyder

first: Sherman

middle: M

last: Weissman


title: C. elegans SAGE

status: Public on Jun 11 2004

city: Vancouver

first: Kim

last: Wong

state: BC

address: 600 West 10th Avenue

institute: British Columbia Cancer Agency

summary:
The SAGE libraries were built from total mRNA populations in specific tissues, cells, mutation-specific populations, and all developmental stages of C. elegans.  Tissue- and cell-specific libraries were generated from FACS-sorted cells marked by expression of specific promoter::GFP fusions
Keywords = SAGE
Keywords = LongSAGE
Keywords = Caenorhabditis elegans
Keywords = development
Keywords = dauer
Keywords: other

first: David

middle: L

last: Baillie

first: Steven

middle: J

last: Jones

first: Marco

last: Marra

first: Sheldon

last: McKay

first: Donald

last: Moerman

first: James

last: McGhee

last: Riddle

first: Anatoli

last: Pouzyrev

first: Victor

last: Velculescu

first: LaDeana

last: Hillier

first: Sean

last: Eddy

first: Shawn

last: Stricklin

first: Robert

last: Waterston


title: GBM invasion transcriptiome

status: Public on Oct 19 2008

city: Phoenix

first: Brock

last: Armstrong

state: AZ

address: 445 N. 5th Street

department: Cancer and Cell Biology

institute: TGen

summary: Glioblastoma multiforme (GBM), the most advanced form of a large subset of brain tumors collectively known as glioma, is the most aggressive and invasive type of brain tumor.  Patients usually experience a median survival range of 9 to 12 months.  GBMs are extremely difficult to manage because of the tumor cells’ tendency to migrate and pervade into adjacent tissues.  Surgical resection of GBMs generally only slows disease progression because any remaining tumor cells proceed to migrate through brain tissues and reform a new tumor mass.  It is hypothesized that the invasive phenotype of these tumor cells may be attributable to unique gene expression.  Stationary core and invasive rim tumor cells were collected separately by laser capture microdissection (LCM) from 19 biopsy samples.  Identification of differentially expressed genes in the tumor core and invasive rim can give valuable insight to the genes and pathways potentially involved with the invasive phenotype.  This information can then be used to generate possible biomarkers, diagnostic markers, or drug targets.

overall_design:
Human glioblastoma tumor samples were obtained from patients who underwent primary therapeutic brain tumor resection. All specimens were collected and submitted to the study under institutional review board approved protocols. None of the patients had been subjected to chemotherapy or radiotherapy prior to resection, in order to avoid genetic signatures that are due to exposure to alkylating agents and/or ionizing radiation. All specimens were verified as GBMs by a neuropathologist.
Tumors are embedded in OCT, then sectioned in a cryostat at -20C, to a thickness of 8-10 um and placed onto HistoGene slides. Sections to be microdissected are removed from the -80C fixed and stained with an abbreviated Hematoxylin and Eosin protocol. Two thousand tumor core and invasive cells are dissected onto separate caps using the PixCell II instrument using CapSure™ Macro LCM Caps. The CapSure™ Macro LCM Caps LCM 0211 should be used with the AutoPix instrument. Cells in the tumor core are identified by nuclear atypia and size and captured using the larger spot sizes. Tumor cells immediately adjacent to necrotic areas, cortical areas, cells with small regular nuclei, endothelial and blood cells should be avoided. Individual white matter invading GBM cells can be identified by means of their nuclear atypia and heteropyknotic staining, which is consistent with that of the cells within the tumor core. They should be microdissected using the 7.5 um laser spot size and the initial power settings recommended by the PixCell II manual.
After microdissection all harvested material should immediately be lysed on the cap by applying the lysis buffer (XB) from the PicoPure RNA Isolation Kit according to the PicoPure protocol and stored -80C. Cell populations harvested on different caps can be pooled at the time of RNA isolation. RNA integrity is varified by identification of distinct 28S and 18S ribosomal bands with an Agilent Bioanalyzer using the RNA 6000 Nano LabChip kit.
Total RNA was isolated from 2000 LCM cells (to ensure at least 500 ng total RNA) using the PicoPure RNA solation Kit, following manufacturers protocol. mRNA is reverse transcribed with the RiboAmp RNA Amplification kit.

500 ng total RNA is amplified with the RiboAmp RNA Amplification kit, following manufacturer’s instructions. The total yield that can be expected falls between 30 and 60 µg copy RNA. The size of the copy RNA should be verified by gel electrophoresis. Approximately 500ng of copy RNA can be separated on a 1% agarose gel in TAE buffer. A smear of amplified material should be seen between 200 and 3000bp. Six µg amplified RNA are labeled in a RT with SuperScriptIII in the presence of dUTP Cy5 utilizing 6 µg random hexamers as primers. Universal reference RNA is amplified one round in the same manner and labeled with Cy3 dUTP. Labeled cDNA is hybridized overnight onto cDNA microarray. Following hybridization, arrays are washed, scanned and quantitated with the Axon GenePix 4000 microarray reader (Axon Instruments). Gene expression results are analyzed using GeneSpring (Silicon Genetics) software. Intensity dependent normalization is applied, where the ratio is reduced to the residual Lowess fit of the intensity versus ratio curve. The measured intensity of each gene is divided by its reference channel (signal from the universal reference RNA) in each sample. When the reference channel is below 10, the data point is considered uninformative. The ratios (sample over reference) for the tumor core experiments and invasive rim experiments are averaged and compared. Genes that are more than two-fold differentially regulated in the majority of the matched core/invasive rim sets are selected.

last: Berens

first: Tim

last: Demuth

first: Linsey

last: Reavie

first: Dominique

last: Hoelzinger