title: Detecting transcription profile associated to mammosphere medium

status: Public on Nov 30 2013

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Mammosphere medium (Grange et al. Neoplasia 2008;10(12):1433-43) contains epidermal growth factor (EGF), insulin and basic fibroblast growth factor (bFGF) that may influence transcript expression in a way not necessarily related to the assembly of mammspheres. To identify the set of genes associated mammosphere cell growth medium we analyzed two prototypic situations in triplicate experiments: TUBO cells (a mouse breast cancer cell line derived by Balb-neuT mice) grown in DMEM under adherent conditions (TDA), TUBO cells grown in Mammosphere medium under adherent conditions (TMA).

overall_design: Two prototypic situations in triplicate experiments were analysed: TUBO cells (Rovero et al. Gene Ther 2001;8(6):447-52) grown in DMEM under adherent conditions (TDA), TUBO cells grown in Mammosphere medium under adherent conditions (TMA).

first: Laura

last: Conti

first: Stefania

last: Lanzardo

first: Federica

last: Cavallo

first: Guido

last: Forni


title: Expression data from cultured mouse BALB 3T3 cells containing bacterial plasmid gene mucAB

status: Public on Dec 01 2013

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

summary: The gene mucAB has an error-prone activity in bacteria. We introduced mucAB into mouse 3T3 cells with an expression vector and found drastic increase of spontaneous transformation, accompanied by increase of expression of eight oncogenes, i. e., Gpnmb, Foxml, Maff, Myc, Aurka, Aukb, Fosl1, and Anxa8 and decrease of expression in two oncogenes, i. e., Lrig1 and RhoX in order of the magnitude of change, as compared with those in non-treated 3T3 cells.

overall_design: Transformation of cultured mouse BALB 3T3 cells was used as an indicator of cellular oncogenesis. We examined effects of introduction of foreign bacterial plasmid gene into mouse cells on spontaneous transformation frequency, accompanied by change of expression of known oncogenes. To do this, 3T3 cells with or without mucAB were compared for expression of known genes, using the microarray method.

first: Hiroshi

last: Tanooka


title: Genome-wide analysis of gene expression in jnk1-/-jnk2-/- immortalized mouse embryonic fibroblasts compared to wildtype counterparts co-cultivated with differentiating keratinocytes

status: Public on Nov 26 2013

city: Heidelberg

first: Peter

last: Angel

address: Im Neuenheimer Feld 280

department: Signal Transduction and Growth Control

country: Germany

institute: German Cancer Research Center

summary: Analysis of JNK-dependent fibroblast-derived soluble factors at gene expression level. The hypothesis tested in the present study was that loss of c-Jun N-terminal kinases 1 and 2, JNK1 and JNK2, in MEFs causes a strong alteration of the gene expression program coding for soluble factors, which promote an efficient keratinocyte differentiation. Results provide important information of the repertoire of fibroblast transcripts encoding secreted proteins, which is severely disarranged upon loss of JNK activity under the in vitro co-culture conditions applied.

overall_design: In vitro transwell co-culture experiments were performed using jnk1-/-jnk2-/- or wildtype immortalized mouse embryonic fibroblasts (MEFs) and differentiating primary normal human epidermal keratinocytes (NHEK) over a time course of 6 days. Every second day, fibroblast-loaded inserts were changed resulting in 3 triads (triads 1, 2, and 3). Total RNA was obtained from jnk1-/-jnk2-/- and wildtype immortalized mouse embryonic fibroblasts (MEFs) prior to co-cultivation (day 0) and of each triad 1, 2, or 3.

first: Marion

last: Schumacher

first: Bettina

last: Füssel

first: Zbigniew

last: Rogon


title: DIFFERENTIAL GENE EXPRESSION OF MEDULLARY THYROID CARCINOMA REVEALS SPECIFIC MARKERS ASSOCIATED WITH GENETIC CONDITIONS.

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: Transcriptional analysis of 49 primary medullary thyroid carcinoma tumors. Comparisons MTCM918T vs MTC634 and MTCM918T vs MTCWT.

overall_design: 49 (52 hybridized tumors with 3 replicates) primary Medullary Thyroid Carcinoma (MTC) cases were hybridized onto a cDNA microarray in order to identify the unique markers for specific genetic classes of MTC.

first: A

last: Maliszewska

first: L

middle: J

last: Leandro-Garcia

first: E

last: Castelblanco

first: G

last: Goméz-López

last: Inglada-Pérez

first: C

last: Alvarez-Escola

last: Macià

last: De la Vega

first: R

last: Letón

last: Gómez-Graña

first: I

last: Landa

last: De Cubas

last: Cascón

last: Rodriguez Antona

first: S

last: Borrego

first: M

last: Zane

first: F

last: Schiavi

last: Merante Boschin

last: Encinas

middle: R

last: Pelizzo

first: D

middle: G

last: Pisano

last: Opocher

first: X

last: Matias-Guiu


title: IL6 Related Cytokines Augment Angiogenesis in Nascent and Mature Human Endothelium Via JAK2 Signaling

status: Public on Dec 14 2013

city: Buffalo

first: Thomas

last: Cimato

state: New York

address: Clinical and Translational Research Center

department: Medicine/Cardiovascular Medicine

country: USA

institute: SUNY at Buffalo School of Medicine and Biomedical Sciences

summary: While therapeutic angiogenesis holds promise for vascular diseases, progress has been limited due to discrepancies in defining adult endothelial progenitors. We have identified and characterized a population of pluripotent derived NRP1+CD34+ nascent endothelial cells, immediately diverged from NRP1+CD34- mesodermal cells. We contrasted the transcriptional profile of NRP1+ CD34+ nascent endothelial cells against undifferentiated human pluripotent stem cells and human umbilical vein endothelial cells (HUVECs) to gain insights into the pathways that are uniquely activated in formation of new endothelium. We found significant upregulation of IL-6 related growth factor receptors, including ciliary neurotrophic factor receptor (CNTFR), and their downstream JAK/STAT signaling components in NRP1+CD34+ endothelial cells. When exposed to CNTF, angiogenic sprouting of NRP1+CD34+ was induced in Matrigel, which was abolished with JAK2 inhibition. Furthermore, we found evidence of JAK2 dependent cytokine signaling in more mature endothelium, highlighting the significance of the IL6R/JAK2 pathway, well known in hematopoiesis, in vascular biology. The findings identify a novel group of growth factor receptors and downstream signaling components that may be targeted to modulate angiogenesis and vasculogenesis.

overall_design: 7 samples analyzed, 2 replicates for NRP1+CD34+, 3 replicates for NRP1+CD34-

first: Jennifer

middle: K

last: Lang

first: Fraser

last: Sim


title: DCLK1 Marks a Morphologically Distinct Subpopulation of Cells with Stem Cell Properties in Pre-invasive Pancreatic Cancer

status: Public on Nov 16 2013

city: Baltimore

last: Bailey

state: MD

address: 733 N. Broadway MRB 472

department: Surgery

institute: Johns Hopkins University

summary:
As in other tumor types, progression of pancreatic cancer may require a functionally unique population of cancer stem cells. Although such cells have been identified in many invasive cancers, is not clear whether they emerge during early or late stages of tumorigenesis. Using mouse models and human pancreatic cancer cell lines, we investigated whether pre-invasive pancreatic neoplasia contains a subpopulation of cells with distinct morphologies and cancer stem cell like properties.
Whole transcriptome anlaysis of AcTub Hi vs AcTub Low cells. Cells were labeled with an acetylated alpha tubulin antibody that recognized epitopes on the cell surface (AAT+).  AcTub Hi vs Low cells were FACS sorted from the human pancreatic cancer cell lines CFPAC and AsPC1

overall_design: CFPAC and AsPC1 cells were labeling with AcTub (acetylated alpha tubulin antibody) and then FACS sorted based on high or low levels of AcTub, and microarray analyses were run on biological replicates.

first: Steven

last: Leach


title: Gene expression profiles in vitiligo lesional skin

status: Public on Dec 12 2013

city: Worcester

first: John

last: Harris

state: MA - Massachusetts

address: 364 Plantation St

department: Medicine - Dermatology

institute: UMass Medical School

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

middle: E


title: Gene expression in human umbilical cord endothelial cells following FoxP1 knockdown

status: Public on Nov 12 2013

city: Freiburg

first: Sebastian

last: Grundmann

address: Hugstetter Str. 55

institute: University Hospital Freiburg

summary: To search for genes regulated by the transcription factor Forkhead box Protein P1 (FoxP1)  in endothelial cells, we transfected human umbilical cord endothelial cells (HUVECs) with a combination of three siRNA oligonucleotides directed against human FoxP1 . Human umbilical vein endothelial cells (HUVECs) were isolated from donated umbilical cords, pooled from two donors and cultivated up to passage 5. For transfection with FoxP1-siRNA cells were cultured to 70% confluence and transfected with a combination of three FoxP1-targeting siRNAs or an irrelevant control oligonucleotide (all from invitrogen) using Lipofectamin RNAiMax (Invitrogen) according to the manufacturers instructions. Total RNA was isolated 48h after transfection.

overall_design: Three individual samples per condition were analyzed.

last: Moser


title: Alteration of peripheral blood monocyte gene expression in humans following diesel exhaust inhalation

status: Public on Nov 17 2013

city: Piscataway

first: Howard

last: Kipen

state: NJ

address: 170 Frelinghuysen Road

institute: University of Medicine and Dentistry-Robert Wood Johnson Medical School

summary:
Background: Epidemiologic associations between acutely increased cardiorespiratory morbidity and mortality and particulate air pollution are well-established, but the effects of acute pollution exposure on human gene expression changes are not well understood.

Objectives: In order to identify potential mechanisms underlying epidemiologic associations between air pollution and morbidity, we explored changes in gene expression in humans following inhalation of fresh diesel exhaust (DE), a model for particulate air pollution.

Methods: 14 ethnically homogeneous (white males), young, healthy subjects underwent sixty minute inhalation exposures on 2 separate days with clean air (CA) or freshly generated and diluted DE at a concentration of 300 μg/m3 PM2.5. Prior to and 24 hours following each session, whole blood was sampled and fractionated for PBMC isolation, RNA extraction, and generation of cDNA, followed by hybridization with Agilent Whole Human Genome (4X44K) arrays.

Results: Oxidative stress and the ubiquitin proteasome pathway, as well as the coagulation system, were among hypothesized pathways identified by analysis of differentially expressed genes. Nine genes from these pathways were validated using real-time PCR comparing fold change in expression between DE exposed and clean (CA) days. Quantitative gene fold changes generated by real-time PCR were consistent with the directional fold changes from the microarray analysis.

Conclusions: Changes in gene expression connected with key oxidative stress, protein degradation, and coagulation pathways are likely to underlie observed physiologic and clinical outcomes and suggest specific avenues and sensitive time points for further physiologic exploration.

overall_design: Diesel exhaust inhalation exposure-induced human gene expression changes were measured in peripheral blood mononuclear cells. 14 white males subjects were seated in a controlled environment facility for 2 separate 60 minute inhalation exposures which occurred at least 1 week apart to either clean air and freshly generate or diluted diesel exhaust (300ug/m3 PM2.5) .Blood collection occurred immediately prior to and 24 hours following exposures. Two microarrays per subject were completed using Agilent Whole Human Genome (4X44K) arrays. Genes that were of interest to our research group were verified using Real Time PCR analysis.

first: Ashley

middle: P

last: Pettit

middle: M


title: Pre-Collaborative Cross lung gene expression after allergen challenge

status: Public on Nov 15 2013

city: Chapel Hill

first: Samir

last: Kelada

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina

summary: The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. These mice were initially described in the following reference. Genome Research 2011 Aug;21(8):1213-22 (PMID: 21406540).  The goal of this specific project was to identify gene expression QTL using lung tissue from pre-CC mice that were sensitized and challenged with house dust mite allergen (namely, Der p 1).

overall_design: We analyzed whole lung RNAs from 138 pre-Collaborative Cross mice using Illumina WG6v2 arrays. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 5-12 generations. One animal was sampled from 138 unique pre-CC strains, each designated by the prefix OR which denotes Oak Ridge National Laboratory as the original source of these mice. The parental strains are not part of this submission. Hybridizations were performed at the National Human Genome Research Institute’s Gene Expression Core Facility.The resulting data were initially processed using Illumina Genome Studio software and then imported into R (v2.9.2) for post-processing. Normalization was conducted using RMA with quantile normalization and log2 transformation.

middle: N

first: Danielle

last: Carpenter

first: David

middle: L

last: Aylor

first: Peter

last: Chines

first: Elissa

middle: A

last: Chessler

first: Gary

last: Churchill

first: Fernando

last: Pardo-Manuel de Villena

last: Schwartz

first: Francis

middle: S

last: Collins


title: A growth differentiation factor 9 (GDF9) motif regulates follicle-stimulating hormone b-subunit (FSHb) gene expression: involvement of activin receptor-like kinase receptors 4/5 (ALK4/5) in the induction of FSHb by GDF9

status: Public on Nov 22 2013

city: New York

first: Soon Gang

last: Choi

state: NY

address: One Gustave L. Levy Place

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Gonadotropin-releasing hormone (GnRH) is secreted in brief pulses from the hypothalamus.  GnRH regulates follicle-stimulating hormone b-subunit (FSHb) gene expression in pituitary gonadotropes in a frequency-sensitive manner that is central to reproductive physiology. The mechanisms underlying the preferential and paradoxical induction of FSHb by low frequency GnRH pulses are incompletely understood. Here, we identify growth differentiation factor 9 (GDF9) as a novel autocrine inducer of FSHb gene expression. GDF9 gene expression was preferentially suppressed by high frequency GnRH pulses due to reduced transcription. Exogenous GDF9 induced FSHb mRNA expression and knockdown or immunoneutralization of GDF9 reduced FSHb gene expression. Treatment with GDF9 stimulated Smad2/3 phosphorylation. The activin receptor-like kinase (ALK) receptor inhibitor SB-505124 antagonized GDF9-induced Smad2/3 phosphorylation and FSHb mRNA induction. Smad2 and Smad3 knockdown studies indicated that the induction of FSHb by GDF9 involves both Smad2 and Smad3. GDF9 and GnRH synergistically induced FSHb mRNA expression and high frequency GnRH pulses suppressed GDF9. We hypothesized that GDF9 contributes to a regulatory loop that tunes the GnRH frequency-response characteristics of the FSHb gene. To test this, we determined the effects of GDF9 knockdown on FSHb induction at different GnRH pulse frequencies using a parallel perifusion system. Reduction of GDF9 shifted the characteristic pattern of GnRH pulse frequency sensitivity. These results identify GDF9 as contributing to an incoherent feed-forward loop, comprised of both intracellular and secreted elementscomponents, that regulates FSHb expression in response to activation of the cell surface GnRH receptor. LbT2 microarray datasets as well as RNA-Seq data (GSE42120) were interrogated to determine the levels of expression of ALK4/5/7.

overall_design:
LβT2 cells were transfected with either scrambled siRNA or Gas siRNA for 48 h. RNA samples were snap-frozen in dry ice prior to whole-genome expression profiling analysis using MouseWG-6 v2.0 Expression BeadChip (Illumina, San Diego, CA). A total of 6 concentrated conditioned media samples were independently prepared: 3 replicates from control siRNA-treated cells, and 3 replicates from Gas siRNA-treated cells.

This submission represents the microarray component of study.

first: Soon

first: Qian

last: Wang

first: Jingjing

last: Jia

first: Hanna

last: Pincas

first: Judith

last: Turgeon

first: Stuart

middle: C

last: Sealfon


title: Differentially expressed genes analysis between Eupolyphaga sinensis Walker (ESW) and Taspine derivate

status: Public on Nov 21 2013

city: Xi’an

first: yanmin

last: zhang

state: Shaanxi

address: No. 76, Yanta Weststreet, #54

country: China

institute: School of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province

summary: To gain insights into the mechanisms of Eupolyphaga sinensis Walker (ESW) and taspine derivate on inhibition to HCC, we have employed whole genome microarray expression profiling as a discovery platform to identify different genes between ESW-treated sample and control. At the same time, the differences were investigated between taspine derivate and the same control. SMMC-7721 cells were cultivated in the absence or presence of 0.1mg/mL ESWE and  Taspine derivate of 2.5x10-5mol/L for 48 h, followed by the Agilent Whole Human Genome Oligo Microarray. The PLG, PKCβ and IL3RA genes confirmation of Microarray analysis was confirmed by Real-time PCR.

overall_design: SMMC-7721 cells were cultivated in the absence or presence of 0.1mg/mL Eupolyphaga sinensis Walker extract (ESWE) and  Taspine derivate of 2.5x10-5mol/L for 48 h, followed by the Agilent Whole Human Genome Oligo Microarray

first: Yanmin

last: Zhang

first: Bingling

last: Dai


title: From mouse to humans: detecting preventing vaccination targets associated to breast cancer stem cells. Gene-level analysis

first: Raffaele

last: Calogero

summary: The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of TuBo epithelial cell and three mammosphere passages (P1, P2 and P3). This analysis allowed the identification of two new breast cancer CSC OAs: TMPRSS4 and xCT. Both genes are linked to invasion, migration and metastasis. These results were achieved integrating data derived by the analysis of transcription profile of CSCs derived by BALB-neuT mouse breast cancer model with meta-analyses of seven large independent breast tumour data sets.

overall_design: TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres (three independent experiments for each experimental condition). Transcription profiling was done using MouseWG-6 v2.0 Illumina beadchips. After normalization and removal of non significant probes (i.e. those not expressed and those not changing) differential expression between epithelial and mammospheres, was assessed using regularized t-test comparing each mammosphere passage with respect to TuBo cells using a FDR ≤ 0.05  together with an |log2(fold-change)|≥1. The union of the three sets of differentially expressed transcripts produced a total of 495 transcripts.

first: Stefania

last: Lanzardo

first: Laura

last: Conti

first: Guido

last: Forni

first: Daniela

last: Cantarella

first: Federica

last: Cavallo

first: Hedwige

last: Pinto


title: Whole genome expression profile of 120 human glioma samples

status: Public on Nov 07 2013

city: Beijing

first: Tao

last: Jiang

address: Tiantan Xili No.6, Dongcheng District

department: Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

summary: We performed whole genome expression profile for 120 human glioma samples to explore significantly aberrantly expressed genes.

overall_design: Grade 2, 3 and 4 gliomas are included in our experiment.

first: Zheng


title: Expression analysis of Baz1a-deficient spermatocytes and spermatids

first: Scott

last: Keeney

address: 1275 York Ave

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Acf1 was isolated almost 15 years ago from Drosophila embryo extracts as a subunit of several complexes that possess chromatin assembly activity. Acf1 binds to the ATPase ISWI (SNF2H in mammals) to form the ACF/CHRAC chromatin remodeling complexes. Studies in Drosophila and in human and mouse cell culture implicate Acf1 in many cellular processes including transcriptional repression, heterochromatin formation and replication, and DNA damage checkpoints and repair. However, the in vivo function of Acf1 in mammals is unknown. We generated mice deficient for Baz1a, the mammalian homolog of Drosophila Acf1. In contrast to partially penetrant lethality of the mutation in flies, Baz1a-deficient mice are viable. The mutant mice show no obvious defects in B or T cell lineages, class switch recombination in cultured B cells, or meiotic recombination. Thus, BAZ1A is dispensable in vivo for the survival and differentiation of cells that require the repair of developmentally programmed DNA double-strand breaks (DSBs). However, Baz1a-/- male mice are sterile because of a severe defect in spermiogenesis that results in fewer and non-motile sperm with morphological defects. Baz1a-deficient round spermatids display widespread perturbation of gene expression. The mutant cells faithfully execute the widespread reprogramming of gene expression that normally accompanies the developmental transition from meiosis to postmeiotic differentiation, but overlaid on this normal developmental program is mis-regulation of a large number of additional genes. The inappropriate expression of this eclectic group of genes is likely the cause of the pleiotropic spermiogenesis defects in the mutant. We propose that the dramatic changes in chromatin composition that occur in late meiotic prophase and early spermiogenesis create a window of vulnerability during which BAZ1A-targeted chromatin assembly functions are needed to prevent inappropriate transcription changes. This appears to be the sole essential function of the ACF and CHRAC complexes in mouse.

overall_design: total RNA isolated from FACS-enriched pachytene/diplotene spermatocytes and round spermatids from three littermate pairs of Baz1a-/- and Baz1a-/+ animals. Data from all samples are provided, but expression data for one Baz1a-/- spermatocyte sample (683_PD) was censored because of inferred high degree of contamination with round spermatids

first: James

last: Dowdle


title: Gene expression in kidney following UUO +/- anti-miR-214

status: Public on Nov 05 2013

city: Glasgow

last: Denby

address: 126 University Place

department: BHF GCRC

country: United Kingdom

institute: University of Glasgow

summary: Animals were sc dosed with 5mg/kg anti-miR-214 or control anti-miR, had UUO performed and were sacrificed at 7 days.

overall_design: n=4 animals per group, 2 groups


title: From mouse to humans: detecting preventing vaccination targets associated to breast cancer stem cells

summary:
The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. In this experiment we used a cell line (TuBo) derived by the mouse breast cancer model BALB-neuT and its CSC subpupolation, enriched by mean of mammosphere formation. Integrating data derived by gene and exon-level transcription profiling of the above experiments with public available normal and tumor datasets we identified two new breast cancer CSC OAs: TMPRSS4 and xCT. Both genes are linked to invasion, migration and metastasis. Furthermore, we observed that alternative splicing events discriminating TuBo cells, grown in adherent medium, with respect of TuBo mammospheres, produced growing in no-adherent medium, are very limited. We detect only one clear splcing event characterizing the beta-isoform of Rabgap1l gene.

This SuperSeries is composed of the SubSeries listed below.

overall_design: The adherent TuBo epithelial cells were generated from a mammary carcinoma arising in a BALB/c mouse female transgenic for the activated rat ErbB2 oncogene (BALB-neuT) and were cultured in DMEM supplemented with 20% FCS. Single TuBo cells were plated in ultra low attachment flasks in serum-free DMEM-F12 medium supplemented with bFGF, EGF and insulin. Nonadherent spherical clusters of cells, named mammospheres, were collected by gentle centrifugation after 7 days and dissociated enzymatically and mechanically, using trypsin and pipetting, respectively.


title: Transcriptome profiling of GATA4 depleted hepatocytes

city: Philadelphia

first: Rena

last: Zheng

state: PA

address: 3615 Civic Center Blvd. Abramson Research Center 315A

institute: Children's Hospital of Philadelphia

summary: Analysis of changes in gene expression following hepatocyte specific deletion of GATA4 in adult mice.  Results showed that the subset of differentially expressed genes had liver specific ontologies.

overall_design: Total RNA isolated from hepatocytes of AAV8-Tbg-Cre injected GATA4 fl/fl mice was compared to total RNA isolated from AAV-Tbg-GFP injected GATA4 fl/fl mice.

first: Boris

last: Rebolledo-Jaramillo


title: Differential gene expression in mouse kidney following 72 hours of colistin exposure by Illumina WG-6_V2 array

city: Indianapolis

first: Michael

middle: Thomas

last: Eadon

state: IN

address: 950 W. Walnut St R2 202

department: Medicine

institute: Indiana University

summary: Colistin sulfate (polymixin E) is an antibiotic prescribed with resurging frequency for multidrug resistant gram negative bacterial infections. It is associated with nephrotoxicity in humans in up to 33% of cases.  Little is known regarding genes involved in colistin nephrotoxicity. A murine model of colistin-mediated kidney injury was developed.  C57/BL6 mice were administered saline or colistin at a dose of 16mg/kg/day in 2 divided doses. An Illumina gene expression array was performed on kidney RNA harvested 72 hours after first colistin dose to identify differentially expressed genes early in drug treatment. Array platform was MouseWG-6, 48,000 probes. Drug given intraperitoneal.

overall_design: Total RNA was isolated from mouse kidneys which were harvested upon sacrifice. 12 total 10 week old C57 bl6 mice were analyzed. Six mice were administered 0.1% saline twice daily, six mice were given colistin at 16 mg/kg/day in 2 divided doses. The 2 groups were randomized to 2 different MouseWG-6_V2_0_R2_11278593 and groups were compared.

middle: T

first: Patrick

last: Cunningham

first: Riyue

last: Bao

first: Bradley

last: Hack


title: Transcriptome profiling of GATA4,6 double depleted hepatocytes

summary: Analysis of changes in gene expression following hepatocyte specific deletion of GATA4 and GATA6 in adult mice.  Results showed that the subset of differentially expressed genes had liver specific ontologies.

overall_design: Total RNA isolated from hepatocytes of AAV8-Tbg-Cre injected GATA4,6 fl/fl mice was compared to total RNA isolated from AAV-Tbg-GFP injected GATA4,6 fl/fl mice.


title: Rip-Chip profiling of HnRNP A1 nuclear complexes in HuR WT and HuR KO cells

status: Public on Nov 01 2013

city: Athens

first: Olga

last: Papadodima

address: 48, Vasileos Konstantinou av.

country: Greece

institute: National Hellenic Research Foundation

summary: Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP)-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO) mouse embryonic fibroblast (MEF) cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced) with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart) within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle) indicative of their concerted function in mRNA metabolism.

overall_design: Ribonucleoprotein Immunoprecipitation (RIP) using hnRNP A1 specific antibody was performed in nuclear extracts from HuR WT and HuR KO Mouse Embryonic Fibroblasts (MEFs). RNA isolated from these IPs together with nuclear RNA from the two cell types, was subjected to microarray analysis. Three biological replicates, representing three independent experiments, are available for each condition except in the case of nuclear RNA isolated from HuR WT MEFs that one replicate didn’t pass the quality control.

first: Aristotelis

last: Chatziioannou

first: Meropi

last: Georgoula

first: Fragiskos

last: Kolisis

first: Vasiliki

last: Pletsa

first: Apostolia

last: Guialis


title: Human breast cancer cells: parental v.s lapatinib-resistant clone

status: Public on Oct 31 2013

city: Taichung

first: Wei-Chien

last: Huang

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

summary: Transcriptional profiling of human HER2-positive BT474 breast cancer cells comparing control untreated cancer cells with lapatinib-resistant clone established by chronic treatment with lapatinib

overall_design: Two-condition experiment, parental cells vs. lapatinib-resistant (LR) clone.


title: mRNA expression profiles of antigen-specific CD8+ T cells induced by DNA prime-DNA boost and DNA prime-VACV boost immunization regimen

status: Public on Oct 30 2013

city: Shanghai

first: Hu

last: Zhidong

address: 2901 Caolang Road, Jinshan district

institute: Shanghai public health clinical center

summary: Similar with others, our data proved that antigen-specific CD8+ T cells from mice primed with DNA and boosted by VACV were much more sensitive to antigen stimulation than those from DNA-boost. Since the mechanisms of in vivo tuning of antigen sensitivity (also termed functional avidity) is still not defined, we compared this two vaccination regimen at gene expression level. Results provide important information of which genes were selectively activated by VACV boost vaccination. For example, data shows that the expression levels of genes involved in Cancer and Wnt signaling pathways is more higher in DNA prime-VACV boost regimen that DNA prime-DNA boost vaccination.

overall_design: To obtain sufficient of antigen-specific cells for microarray analysis, the OVA-specific CD8+ T cells from OT-1 mice were adoptively transferred into wild type mice and then immunized by DNA and VACV vaccine encoding OVA. Four week later, mice were scarificed and antigen-specific CD8+ T cells were emriched by CD45.1-PE antibody and anti-PE MicroBeads from splenocytes.Total RNA was extracted by the RNeasy Mini Kit (QIAGEN, Germany). Followed by amplification and biotin labeling, the samples were hybridized using Illumina Total Prep RNA Amplification Kit (Ambion, USA). Mouse WG-6v2 Expression BeadChips were used for analysis of transcriptome.

first: Zhidong

last: Hu

first: Chao

last: Qiu

first: Jianqing

last: Xu


title: Increases in Insulin Sensitivity among Obese Youth are Associated with Gene Expression Changes in Whole Blood.

status: Public on Nov 04 2013

city: Phoenix

first: Gabriel

last: Shaibi

state: AZ

address: 411 N. Central Avenue

institute: Arizona State University

summary: Lifestyle intervention can improve insulin sensitivity in obese youth yet few studies have examined the biological mechanisms underlying improvements. Therefore, the purpose of this study was to explore biological pathways associated with intervention-induced improvements in insulin sensitivity. Fifteen (7M/8F) overweight/obese (BMI percentile=96.3±1.1) Latino adolescents (15.0±0.9 years) completed a 12-week lifestyle intervention that included weekly nutrition education and 180 minutes of moderate-vigorous exercise per week. Insulin sensitivity, estimated by an oral glucose tolerance test and the Matsuda Index, increased 29.2% post intervention (2.4±0.3 to 3.1±0.3, p=0.01). Global microarray analysis profiling from whole blood was performed to examine changes in gene expression and to explore biological pathways that were significantly changed in response to the intervention. A total of 1,459 probes corresponding to mRNA transcripts (717 up, 742 down) were differentially expressed with a fold change≥1.2 and P<0.05. Among the genes identified were hexokinase 3 (HK3), ATPase, H+ transporting V0 subunit e2 (ATPV0E), and sterol regulatory element binding transcription factor 1 (SREBF1), and endothelial cell adhesion molecule  (ESAM). There were 8 pathways identified that met the criteria for significance, including insulin signaling, type 1 diabetes, and glycerophospholipid metabolism. Participants that increased insulin sensitivity exhibited five times the number of significant genes altered compared to non-responders (1,144 vs. 230). These findings offer insight into the molecular mechanisms underlying health improvements among high-risk Latino youth. Lifestyle interventions may contribute to improved insulin sensitivity through pathways related to insulin signaling and immune response. Further, genetic factors may mediate response to lifestyle intervention.

overall_design: Fifteen (7M/8F) overweight/obese Latino Youth Whole blood RNA samples evaluated pre and post intervention.

first: Danielle

last: Miranda

first: Dawn

last: Coletta

first: Lawrence

last: Mandarino

middle: Q


title: Illumina  Human1Mv1_C array CGH on NCI-60 cancer cell lines

city: Princeton

first: Sudhir

last: Varma

address: 1215 Wessex Pl

institute: HiThru Analytics

summary: The NCI-60 cancer cell lines have been used for studying cancer pathogenesis and for drug discovery. This dataset adds to the growing number of datasets on various genomic platforms that have been made public on Cellminer (http://discover.nci.nih.gov/cellminer/)

overall_design: 60 cell lines (including PR:DU145 and its drug resistant derivative PR:RC01) were arrayed. Four cell lines were done in duplicate CNS:SF_295, LC:HOP_92, ME:SK_MEL_28 , OV:OVCAR_3, while CO:HT29 was not assayed.

first: William

last: Reinhold

first: John

last: Weinstein


title: Gene expression profile of endothelial cells maturated into brain-like endothelial cells

status: Public on Oct 18 2013

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

summary: To understand the molecular mechanisms during the maturation of cord blood-derived endothelial cells into blood brain barrier capillary endothelial cells (BCECs), we have employed whole genome microarray expression profiling to identify genes responsible for the maturation process. Hematopoietic stem cells were isolated from cord-blood samples and differentiated into endothelial cells. The endothelial cells were further maturated into BCECs by co-culturing with blood-brain barrier (BBB) specific cells (pericytes) for 3 days and 6 days.

overall_design: The gene expression in human hematopoietic stem cell-derived endothelial cells was measured at 3 and 6 days after co-culture with pericytes. Three independent experiments were performed at each time (3 or 6 days). The RNA obtained from different experiments were pooled together for each group before microarray studies.


title: Treatment of prostate cancer cell lines DU-145 and LNCaP with zebularine

status: Public on Oct 24 2013

city: Berlin

first: Hans

last: Krause

address: Charitéplatz 1

department: Klinik für Urologie

institute: Charité - Universitätsmedizin Berlin

summary: Cultures of DU-145 cells and of LNCaP cells were treated for 216 hours with 100µM zebularine (SIGMA) in three independent biological experiments. Zebularine acts as a DNA methyltransferase (DNMT) inhibitor thereby upregulating genes that are inactivated by e.g. promotor hypermethylation. The experiment aimed to search for upregulated transcripts to provide new targets for biomarker development and therapeutic use.

overall_design: Total RNA of untreated and treated (100µM zebularine) DU-145 cells (experiment HK_21_DU_145-HK_26_DU_145), and of untreated and treated (100µM zebularine) LNCaP cells (experiment HK_27_LNCaP-HK_32_LNCaP), were subjected to Affymetrix array analysis to detail the overall expression changes after treatment with a DNMT inhibitor. Treated cells showed no obvious signs of zebularine-induced cytotoxicity as revealed by XTT assays.

first: Odiljon

last: Ikromov


title: Transcriptome analysis of adipose tissues of A. actinomycetemcomitans- and C. pneumoniae-infected apoE-deficient mice

status: Public on Oct 28 2013

city: Helsinki

first: Kati

last: Hyvärinen

address: Biomedicum Helsinki 1, Haartmaninkatu 8

country: Finland

institute: Institute of Dentistry, University of Helsinki

summary: The 14-week experiment included three groups: 1) the Acute Cpn group, with one C. pneumoniae inoculation at the age of 9 wks; 2) the Chronic Cpn group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; and 3) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks. The mice were sacrificed at the age of 14 wks. The 24-week experiment included four groups: 1) the recurrent A. actinomycetemcomitans infection group, with ten  A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; 2) the chronic C. pneumoniae infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; 3) the combined chronic C. pneumoniae and recurrent A. actinomycetemcomitans infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks, and ten A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; and 4) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks, and ten 0.9% NaCl inoculations once a week from the age of 14 to 23 wks. The mice were sacrificed at the age of 24 wks.Epididymal and inguinal AT gene expression was analyzed using an Illumina Mouse WG-6 v2.0 platform.

overall_design: Total RNA obtained from inguinal and epididymal adipose tissues, samples from infected animals were compared to vehicle-inoculated controls.

first: Pirkko

last: Pussinen


title: WIP1 controls global heterochromatin silencing via ATM/BRCA1-dependent DNA methylation

status: Public on Oct 19 2013

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

summary: WIP1 phosphatase is emerging as an important regulator of tumorigenesis, but no unifying mechanistic network has been proposed. Here we found that WIP1 plays a key role in the transcriptional regulation of heterochromatin-associated DNA sequences in germ-line and cancer cells. WIP1 was required for epigenetic remodeling of repetitive DNA elements within the heterochromatin, including L1 LINE retrotransposons. Mechanistically, WIP1regulated an ATM-dependent increase in BRCA1 occupancy on L1 LINEs, resulting in closed chromatin without ubiquitination of histone H2A. This mechanism appeared to be dependent on the ability of BRCA1 to bind the heterochromatin protein HP1, the recruitment of DNA methyltransferases, and subsequent DNA methylation. Attenuation of ATM, in turn, reversed heterochromatin methylation in both germ-line and cancer cells. DNA methylation plays a central role in the generation of mutations in human tumors and we found that WIP1 levels strongly correlated with C-to-T substitutions and a total mutation load in primary breast cancers. We propose that WIP1 plays an important role in the regulation of DNA methylation and global heterochromatin silencing, and thus is critical in maintaining genome integrity during development and in cancer.

overall_design: Total RNA was extracted from control spermatids, Wip1-/- and Wip1-/- Atm+/- spermatids. The final cRNA samples were hybridized in triplicates to Illumina Mouse WG-6 v2.0 Expression arrays.

first: Doria

last: Filipponi

first: Dmitry

last: Bulavin


title: Transcriptome of mouse pluripotent embryonic stem cells (mESC) cultured in R2i, 2i, PD and SB conditions

status: Public on Oct 21 2013

city: Tehran

first: Hossein

last: Baharvand

address: Hafez St., Bani Hashem St.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

summary:
In this study we have analyzed the global gene expression of naïve mouse embryonic stem cells in different culture conditions including R2i (PD0325901+SB431542), 2i (PD0325901+CHIR99021), and also PD0325901+LIF and SB431542+LIF to show the similarities and differences between the conditions in maintaining pluripotency.
Since the first generation of mouse embryonic stem (ES) cells, extrinsic regulation of pluripotency has been at the focus of attention. Here we show that suppression of transforming growth factor β (TGFβ) signaling could have impressive effects on self-renewal and pluripotency of mouse ES cells. We introduce a chemically defined medium with inhibitors of TGFβ and mitogen-activated protein kinase (MAPK) kinase, designated here as R2i (Royan 2 inhibitors), for highly efficient establishment of ES cell lines from various mouse strains. R2i also supports homogenous expression of Nanog and Dppa3 proteins in ES cells and shows minimal differentiation leakage. Our results uncover an appropriate condition for ES cell generation from single blastomeres of various cleavage-stage embryos. Further, the high accuracy of genome integrity after long-term cultivation in R2i illustrates an optimal condition for ES cell culture. Global transcriptomic analysis of R2i cells demonstrates that bone morphogenetic protein 4 (BMP4) signaling becomes overrepresented pursuant to TGFβ repression, which may confer further robustness to pluripotency through shielding cells from differentiation stimuli. These findings point to a new facet of ground state pluripotency by blocking differentiation pathways, without influencing the pluripotency regulatory circuitry of mouse ES cells.

overall_design: Whole gene expression study of 4 different mouse embryonic stem cell lines maintained under 4 different chemically defined conditions: R2i, 2i, PD and SB

first: Sayedeh

last: Hassani

first: Mehdi

last: Totonchi

first: Ali

last: Sharifi-Zarchi

first: Sepideh

last: Mollamohammadi

first: Mohammad

last: Pakzad

first: Sharif

last: Moradi

first: Azam

last: Samadian

first: Najmesadat

last: Masoudi

first: Shahab

last: Mirshahvaladi

last: Farrokhi

first: Boris

last: Greber

first: Marcos

last: Araúzo-Bravo

first: Davood

last: Sabour

last: Sadeghi

first: Ghasem

middle: H

last: Salekdeh

first: Hamid

last: Gourabi

last: Schoeler


title: Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy [GPL6983]

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

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

summary: STAG2 is a novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy

overall_design: Gene copy number analyses of STAG2 in urinary bladder tumors. R values were extracted from beadstudio and normalised using the pounds method. Log R Ratios were calculated using an average value of R from 200 cases and controls from the Epicuro study. WaviCGH was used to generate copy number calls and log R ratios in the region of STAG2 on the X chromosome were also visualised manually to determine STAG2 loss.

first: Francisco

middle: X

last: Real

first: Stephen

last: Chanock

first: Daniel

last: Rico

first: Kevin

last: Jacobs

first: Julie

last: Earl

first: David

last: Pisano

first: Alfonso

last: Valencia

first: Nuria

last: Malats


title: Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy

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

overall_design: Refer to individual Series


title: Gene expression in an EMT model using an immortalized bronchial epithelial cell line induced by TGF-β1

status: Public on Oct 06 2013

first: Bangrong

last: Cao

address: NO.17 Panjiayuannanli, Chaoyang District, Beijing, P.R.China

institute: Cancer Institute & Hospital, Chinese Academy of Medical Sciences

summary: This study aimed to establish an epithelial-mesenchymal transition (EMT) model with an immortalized human bronchial epithelial cell line, M-BE, and to identify an EMT signature gene set. The TGF-β1-induced M-BE cells got spindle-shaped fibroblast-like morphology and lost the cell-cell contact, with down-regulated expression of epithelial marker E-cadherin and up-regulated expression of mesenchymal markers N-cadherin and Vimentin. Examined by microarray, there were 2628 genes identified as significant EMT-related, including 1490 up-regulated genes (FC > 2, fdr < 0.01) and 1138 down-regulated genes (FC < 0.5, fdr < 0.01) in TGF-β1-induced M-BE cells.

overall_design: M-BE cells were treated with human recombinant TGF-β1 (5ng/ml) for six days. M-BE cells cultured without TGF-β1 were considered the controls. Three replicates of each were carried out for this investigation. Agilent 4x44K Human Whole Genome expression microarray (G4112F) analysis was applied to the RNA samples of the TGF-β1-treated M-BE cells and the controls.

first: Lin

last: Feng

first: Dan

last: Lu

first: Suping

last: Guo

first: Shujun

last: Cheng

first: Yanning

last: Gao

first: Kaitai

last: Zhang


title: Cyclic-Di-Nucleotides Trigger ULK1 (ATG1) Phosphorylation of STING to Prevent Sustained Innate Immune Signaling

status: Public on Oct 10 2013

city: Silver Spring

first: BIJU

last: ISSAC

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

summary: Activation of the STING (Stimulator of Interferon Genes) pathway by microbial or self-DNA, as well as cyclic di nucleotides (CDN), results in the induction of numerous genes that suppress pathogen replication and facilitate adaptive immunity. However, sustained gene transcription is rigidly prevented to avoid lethal STING-dependent pro-inflammatory disease by mechanisms that remain unknown. We demonstrate here that after autophagy-dependent STING delivery of TBK1 (TANK-binding kinase 1) to endosomal/lysosomal compartments and activation of transcription factors IRF3 (interferon regulatory factors 3) and NF-κB (nuclear factor kappa beta), that STING is subsequently phosphorylated by serine/threonine UNC-51-like kinase (ULK1/ATG1) and IRF3 function is suppressed. ULK1 activation occurred following disassociation from its repressor adenine monophosphate activated protein kinase (AMPK), and was elicited by CDN’S generated by the cGAMP synthase, cGAS. Thus, while CDN’s may initially facilitate STING function, they subsequently trigger negative-feedback control of STING activity, thus preventing the persistent transcription of innate immune genes.

overall_design: Total RNA obtained from primary STING deficient mouse embryonic fibroblast reconstituted with mSTING (W), S365A variant (A), or S365D variant (D). These cells were transfected with dsDNA (ISD) for 3 hours.

first: Hiroyasu

last: Konno

first: Keiko

first: Glen

last: Barber


title: A strong anti-inflammatory signature revealed by liver transcription profiling of Tmprss6-/- mice

status: Public on Oct 09 2013

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

institute: IRCCS, Ospdale San Raffaele

summary: Tmprss6 is the master inhibitor of hepcidin and its inactivation causes iron refractory iron deficiency anemia both in human and in mice. Mice with iron deficiency anemia (IDA)-low hepcidin show a pro-inflammatory response that is blunted in iron deficienct-high hepcidin Tmprss6 null mice. We investigated the transcriptional response associated with chronic hepcidin overexpression by comparing whole genome transcription profiling of the liver of Tmprss6 KO mice and IDA animals, irrespective of iron deficiency.

overall_design: Total liver RNA obtained from Tmprss6 KO mice were compared to wild type (iron deficient) animals, under basal conditions and after LPS challenge

first: Marco

last: Rausa

first: Melissa

last: Sorosina

first: Davide

last: Cittaro

first: Jose

last: Garcia Manteiga

first: Filippo

last: Martinelli Boneschi

first: Antonella

last: Nai

first: Alessia

last: Pagani

first: Elia

last: Stupka

first: Clara

last: Camaschella

first: Laura

last: Silvestri


title: Transcription profile of adipose derived mesenchymal stem cells separated by cell surface protein N-cadherin.

status: Public on Oct 29 2013

city: Tsukuba

first: Hisako

last: Ishimine

state: Japan Ibaraki

address: higashi1-1-1 Tsukuba central 4

department: Research Center for Stem Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

summary: Mesenchymal stem cells (MSCs) are one of most promising stem cell sources for regenerative medicine. MSCs have a differention ability into several tissues. However, their differentiation efficiency is considered quite limited. Especially, the differentiation efficiency into cardiomyocytes is very low. N-cadherin is one of the cell surface protein that is expressed in developing and adult cardiomyocytes. We found that cell surface expression of N-cadherin in MSCs shows good correlation with the cardiomyogenic differentiation ability. We also analyzed the expression profiles of N-cadherin-positive and N-cadherin-negative fraction by microarray. We found that N-cadherin-positive MSCs show higher expression of some of the cardiomyogenesis-related genes than N-cadherin-negative MSCs.

overall_design: The ASCs were maintained in MesenPRO RSTM Medium. The ASCs were harvested in a cell dissociation buffer. The ASCs were incubated with biotinylated anti N-cadherin antibody and next incubated with streptavidin –APC. Subsequently cells were incubated with anti-APC microbeads. Immunomagnetic separation of N-cadherin+ cells were performed with autoMACSTMPro separator applying the separation program ‘depl025’

first: Akira

last: Kurisaki

first: Makoto

last: Asashima


title: Gene signature of the embryonic meniscus

status: Public on Oct 01 2013

city: Boston

first: Dorothy

last: Pazin

state: MA

address: 188 Longwood Ave. REB513

department: Developmental Biology

institute: Harvard School of Dental Medicine

summary:
Analysis of gene expression in E16 mouse meniscus, articular cartilage, and cruciate ligaments
Limbs were dissected from E16 CD-1 mice. Samples were frozen in OCT and cryosectioned. Meniscus, articular carilage, and cruciate ligament were isolated using laser capture microdissection.  Total RNA was isolated from these tissues, amplified, and gene expression was analyzed using microarrays. Three biological replicates were analyzed for each tissue type.

overall_design: Total RNA extracted from E16 mouse meniscus, articular cartilage, and cruciate ligaments

first: Vicki

last: Rosen


title: Gene expression profiling of normal mouse hepatocyte, premalignant hepatocytes and fully malignant HCC

status: Public on Oct 11 2013

city: la jolla

first: Michael

last: Karin

address: 9500 gilman dr

institute: UCSD

summary: Gene expression was analyzed and compared of normal mouse hepatocyte, premalignant hepatocytes and fully malignant HCC cells. The results provide valuable information about the gene expression alterations during the chronic process of liver cancer development.

overall_design: HCC in age-matched male mice were induced by DEN injection. Normal mouse hepatocyte, premalignant hepatocytes and fully malignant HCC were freshly isolated and RNA extracted.

first: Guobin

last: He

first: Joan

last: Font-Burgada


title: Expression data from control and mutant TIFIACaMKCreERT2

status: Public on Sep 28 2013

city: Krakow

first: Grzegorz

last: Kreiner

address: Smetna 12

department: Dept. Brain Biochemistry

country: Poland

institute: Institute of Pharmacology

summary:
We inhibited RNA polymerase I by genetic ablation of the basal transcription factor TIF-IA in adult hippocampal neurons. Nucleolar stress resulted in progressive neurodegeneration, although with a differential vulnerability within the CA1, CA3 and dentate gyrus.
Here, we investigate the consequences of nucleolar stress on learning and memory. The mutant mice do not show any impairment in the behavioral memory tests, suggesting the activation of adaptive mechanisms. In fact, we observe a significantly enhanced learning and re-learning corresponding to the initial inhibition of rRNA transcription and accompanied by aberrant synaptic plasticity.

overall_design: To explore the putative molecular mechanisms underlying these adaptative changes we profiled global gene expression of control and TIFIACaMKCreERT2 mutant mice (5-6 mice/genotype) 4 weeks after induction of the mutation (injection of tamoxifen).

first: Jan

last: Parkitna

first: Rosanna

last: Parlato


title: Whole blood transcriptomics to define adaptive biochemical pathways of exercise during aging

status: Public on Sep 27 2013

city: Kingston

first: Colin

middle: D.

last: Funk

state: Ontario

address: 18 Stuart Street

department: Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

summary: The aim of the current study was to characterize the genetic adaptive pathways altered by exercise in veteran athletes and age-matched untrained individuals. Two groups of 50-60 year old males: competitive cyclists and untrained, minimally active individuals were examined. All participants completed an acut bout of submaximal endurance exercise and blood samples pre- and post-exercise were analyzed for gene expression changes utilizing genome-wide DNA microarray analysis. Our results indicate distinct differences in gene expression involving energy metabolism, lipids, insuling signaling and cardiovascular function between the two groups. These findings may lead to new insights into beneficial signaling pathways of healthy aging and help identify surrogate markers for monitoring exercise and training load.

overall_design: Blood samples from the control and athlete groups were analyzed at three time-points: T1 (before exercise); T2 (immediately after exercise) and T3 (24 hours after exercise). There were n = 4 samples in each of control and athlete group at T1 and T3; and n = 7 for control group and n = 8 for athlete group at T2. One athlete sample (Sample # 010201) at time - point T2 had a technical replicate.

middle: D


title: The TLR2 pathway is required for self-renewal of mammary cancer initiating cells

status: Public on Nov 30 2013

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary:
In the past few years, mammary cancer initiating cells (CICs) have been identified in mouse and human as a subpopulation of tumor cells that selectively posses tumor initiation and self-renewal capacity and the ability to give rise to bulk populations of non-tumorigenic cancer cells progeny through differentiation. They could also be responsible for tumor progression, metastasis, resistance to therapy and recurrence. Thus, the understanding of the pathways regulating CIC self-renewal, differentiation and tumorigenicity represents an important task in the development of effective anticancer therapies.
To detect the set of genes associated to CIC in our mouse breast cancer model we analysed three prototypic situations: TUBO cells grown in DMEM under adherent conditions (called TDA in GSE26517 and epithelial bulk in GSE21451), TUBO cells grown in mammosphere medium under adherent conditions (called TMA  in GSE26517), TUBO cells grown in mammosphere medium under low-attachment conditions (called mammospheres p1 in GSE21451), i.e. the conditions used to support the formation of mammospheres.
This analysis led to the identification of growth factors and immune system-related genes, including toll-like receptor 2 (TLR2). The inhibition of TLR2 signaling pathway strongly impaired mammosphere generation, demonstrating the involvement of TLR2 in CSC self-renewal.

overall_design:
We profiled on MouseWG‐6 v2.0 Illumina beadchips two independent experiments: ADHERENT (GSE26517) made by the comparison between TDA and TMA and SOSPENSION (part of GSE21451) made by the comparison between epithelial bulk and mammospheres p1.
Mammosphere medium contains epidermal growth factor (EGF), insulin and basic fibroblast growth factor (bFGF) that may influence transcript expression in a way not necessarily related to the assembly of mammospheres. Therefore, following normalization and removal of those transcripts not expressed and not changing, we used the Integrative Correlation coefficient (IC, Parmigiani et al. Clin Cancer Res 2004, 10:2922–2927) as filter to remove genes only associate to growth factors present in the mammosphere medium under adherent growth conditions, i.e IC > 0.1. Differential gene expression was then assessed by regularized t‐test (Smyth GK. Stat Appl Genet Mol Biol 2004, 3:Article3) comparing mammospheres p1 with respect to epithelial bulk, using an uncorrected p-value ≤ 0.05, together with an absolute log2 fold change threshold ≥1.

last: Conti

first: Stefania

last: Lanzardo

first: Guido

last: Forni

first: Roberta

last: Porporato

first: Federica

last: Cavallo


title: Gene regulation by CBP-p300 in the lens placode - E9.5

status: Public on Sep 24 2013

city: Saint Louis

first: David

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

summary: Wild type or CBP/p300 fx/fx; Le-Cre-positive (CBP/p300-/-) surface ectoderm from E9.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified, pooled for each genotype and triplicate samples were reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6 v2.0 bead arrays.

overall_design: Three wild type and three knockout embryos were used. The RNA from embryos of the same genotype was purified and pooled and triplicate samples were amplified and used for microarray analysis.

first: Jie

last: Huang

first: Ying

last: Liu


title: Gene regulation by CBP-p300 in the lens placode - E10.5

status: Public on Sep 23 2013

summary: Wild type or CBP/p300 fx/fx; Pax6-Cre-positive (CBP/p300-/-) surface ectoderm from E10.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified, pooled for each genotype and triplicate samples were reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6v2.0 bead arrays.


title: Histone posttranslational modifications and cell fate determination: Lens induction requires the lysine acetyltransferases CBP and p300


title: Cytokine-dependent dendritic cell differentiation in the splenic microenvironment

status: Public on Sep 19 2013

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: The dendritic cell (DC)-derived chemokine CCL17, a ligand of CCR4, has been shown to promote various inflammatory diseases such as atopic dermatitis, atherosclerosis, and inflammatory bowel disease. Under steady state conditions, and even after systemic stimulation with lipopolysaccharide, CCL17 is not expressed in resident splenic DC as opposed to CD8-CD11b+ lymph node (LN) DC, which produce large amounts of CCL17, in particular after maturation. Upon systemic NKT cell activation through alpha-galactosylceramide stimulation, however, CCL17 can be upregulated in both CD8- and CD8+ splenic DC subsets and enhances cross-presentation of exogenous antigens. Based on genome wide expression profiling, we now show that splenic DC are susceptible to Interferon-gamma (IFNgamma) mediated suppression of CCL17, whereas LN DC are much less responsive to IFNgamma and downregulate the IFNgamma receptor. Under inflammatory conditions, particularly in the absence of IFNgamma signaling in IFNgamma receptor deficient mice, CCL17 expression is strongly induced in a major proportion of splenic DC by the action of granulocyte-macrophage colony stimulating factor (GM-CSF) in concert with interleukin (IL)-4. Our findings demonstrate that the local cytokine milieu and differential cytokine responsiveness of DC subsets regulate lymphoid organ specific immune responses at the level of chemokine expression.

overall_design: 15 h after pretreatment with 100 µg LPS, spleens and LN (MLN and PLN) from CCL17E/+ mice were harvested and DC-enriched cell suspensions of the respective organs were stained for NK1.1, CD8alpha, CD11c and CD11b. For isolation of LN DC, NK1.1-CD8alpha-CD11c+CD11b+ cells expressing CCL17/EGFP were sorted (FACSAria). Splenic DC were sorted in parallel from the same mice, but only CCL17/EGFP-negative cells expressing the same markers were selected. After the sort, cells were immediately lysed in Trizol (Invitrogen) before storage at -80°C for RNA isolation.

first: T

last: Globisch

first: V

last: Lukacs-Kornek

first: D

last: Degrandi

first: P

last: Dresing

first: J

last: Alferink

first: R

last: Lang

first: K

last: Pfeffer

first: M

last: Beyer

first: H

last: Weighardt

first: C

last: Kurts

last: Ulas

first: I

last: Förster


title: Dnmt3L-dependent regulation of DNA methylation promotes stem cells differentiation toward primitive germinal cells [Expression array]

first: Francesco

last: Neri

state: Italy

summary: The de novo DNA methyltransferase 3-like (Dnmt3L) is a catalytically inactive DNA methylase that has been previously shown to cooperate with Dnmt3a and Dnmt3b to methylate DNA. Dnmt3L is highly expressed in mouse embryonic stem cells (ESC) but its function in these cells is unknown. We here report that Dnmt3L is required for the differentiation of ESC into primordial germ cells (PGC) through activation of the homeotic gene Rhox5. By genome-wide analysis we found that Dnmt3L is a positive regulator of methylation at gene bodies of housekeeping genes and a negative regulator of methylation at promoters of bivalent genes. We demonstrate that Dnmt3L interacts with the Polycomb PRC2 complex in competition with the DNA methyl transferases Dnmt3a and Dnmt3b to maintain low the methylation level at H3H27me3 regions. Thus in ESC, Dnmt3L counteracts the activity of de novo DNA methylases to keep low the level of DNA methylation at developmental gene promoters.

overall_design: Total RNA extracted from shGFP or shDnmt3L (three different) embryonic stem cells. A duplicate was performed for each point. Cells were transfected with shRNA and selected with Puromicin for 3 days before RNA extraction

first: Salvatore

last: Oliviero


title: Gene expression profiling in leiomyosarcomas and undifferentiated pleomorphic sarcomas: SRC as a new diagnostic marker

status: Public on Sep 15 2013

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

summary: Transcriptional profiling of leiomyosarcomas (LMS) and undifferentiated pleomorphic sarcomas (UPS) aiming to identify molecular biomarkers. Data were validated using RT-qPCR. To assess the relevance of the gene signature, a meta-analysis was performed using five published studies. SRC protein immunolabeling was performed for 38 UPS and 52 LMS.

overall_design: Experiment condition, 22 LMS vs. 22 UPS. Total RNA extracted from tumors was labeled with Cy5, while a custom reference sample (combination of equal amounts of total RNA obtained from 15 different human cell lines) was labeled with Cy3. Samples Cy3 and Cy5 were mixed and hybridized on a two-Color Human GE 4X44K Microarray platform (Agilent Technologies, Palo Alto, CA, USA).

first: Rolando

middle: R

last: Villacis


title: Microarray analysis of PC3 prostate tumor-initiating cells (PC3 holoclones)

status: Public on Nov 07 2013

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: BACKGROUND: Cancer stem-like cells are proposed to sustain solid tumors by virtue of their capacity for self-renewal and differentiation to cells that comprise the bulk of the tumor, and have been identified for a variety of cancers based on characteristic clonal morphologies and patterns of marker gene expression. METHODS: Single cell cloning and spheroid culture studies were used to identify a population of cancer stem-like cells in the androgen-independent human prostate cancer cell line PC3. RESULTS: We demonstrate that, under standard culture conditions, ~10% of PC3 cells form holoclones with cancer stem cell characteristics. These holoclones display high self-renewal capability in spheroid formation assays under low attachment and serum-free culture conditions, retain their holoclone morphology when passaged at high cell density, exhibit moderate drug resistance, and show high tumorigenicity in scid immunodeficient mice. PC3 holoclones readily form spheres, and PC3-derived spheres yield a high percentage of holoclones, further supporting their cancer stem cell-like nature. We identified one gene, FAM65B, whose expression is consistently up regulated in PC3 holoclones compared to paraclones, the major cell morphology in the parental PC3 cell population, and two genes, MFI2 and LEF1, that are consistently down regulated. This molecular profile, FAM65Bhigh/MFI2low/LEF1low, also characterizes spheres generated from parental PC3 cells. The PC3 holoclones did not show significant enriched expression of the putative prostate cancer stem cell markers CD44 and integrin α2β1. PC3 tumors seeded with holoclones showed dramatic down regulation of FAM65B and dramatic up regulation of MFI2 and LEF1, and unexpectedly, a marked increase in tumor vascularity compared to parental PC3 tumors, suggesting a role of cancer stem cells in tumor angiogenesis. CONCLUSIONS: These findings support the proposal that PC3 tumors are sustained by a small number of tumor-initiating cells with stem-like characteristics, including strong self-renewal and pro-angiogenic capability and marked by the expression pattern FAM65Bhigh/MFI2low/LEF1low. These markers may serve as targets for therapies designed to eliminate cancer stem cell populations associated with aggressive, androgen-independent prostate tumors such as PC3. (Mol Cancer. 2010 Dec 29;9:319. doi: 10.1186/1476-4598-9-319; PMID: 21190562; PMCID: PMC3024252).

overall_design: Four PC3 cell-derived holoclones, selected based on their clear and unambiguous holoclone morphology and designated holoclones 2H10, 2G7, 1A8 and 5A2, were used for global transcriptome/microarray analysis in direct comparison to parental PC3 cells. Total RNA was prepared from each of four sequential cell passages for each PC3-derived holoclone, and from four passages of parental PC3 cells, 48 h after seeding the cells at 100,000 cells per well of a 6-well plate. For each sample (holoclones or parental PC3 cells), a pool of RNA was prepared by combining equal amounts of RNA from each passage to minimize the effects of passage number and inter-sample variability on gene expression profiles. All RNAs had an RNA integrity number >8.0, determined using an Agilent Bioanalyzer 2100 instrument. cDNAs transcribed from pools of RNA for each holoclone, and for parental PC3 cells, were labeled with Alexa 647 or Alexa 555 dyes in a fluorescent reverse pair (dye swap) design for competitive hybridization to Agilent Whole Human Genome Microarrays.

first: Kexiong

last: Zhang

middle: J


title: Human exosomal placenta-specific miRNAs modulate expression of target genes in maternal immune cells during pregnancy

status: Public on Sep 13 2013

city: Sendagi, Tokyo

first: Kazuya

last: Yuge

institute: Nippon Medical School

summary: We investigated placenta-specific miRNA miR-517a (miR-517a-3p) functions in Jurkat cells. For this purpose, we identified candidate target mRNAs of the placenta-specific miRNAs using DNA microarray analysis. Transfection of Jurkat cells with miR-517a significantly downregulated 123 genes. Among the 123 genes identified, we searched for potential direct targets of miR-517a using the online software MicroCosm Targets. Seven genes, ALDH1B1, ANP32E, DHFR, FAT2, IGSF5, PRKG1, and RSPO3, had at least one potential miR-517a binding site in their 3’-UTRs. Furthermore, we revealed that PRKG1, one of the seven genes, was a miR-517a target using an in vitro experimental validation system.

overall_design: We compared gene expression pattern of miR-517a–overexpressing Jurkat cells with that of negative control.

first: Toshihiro

last: Takizawa


title: Effect of tumor conditioned medium of human mesenchymal stem cell (MSCs)

status: Public on Sep 11 2013

city: Riyadh

first: Nehad

middle: M

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

summary: We have employed whole genome microarray  to identify changes in gene expression in human MSCs exposed to tumor conditioned medium

overall_design: Human MSC line (hMSC-TERT) was exposed to tumor conditioned medium (CM) from FaDu hypo pharyngeal cancer cell line for 7 day. Subsequently, RNA was extracted using Roche MagNA Pure automated nucleic acid purification system. Control RNA was collected from the same batch of MSCs exposed to normal medium. Extracted RNA was labeled and then hybridized to the one-color Agilent Human GE 4x44K v2 Microarray chip.


title: CD5 alters gene transcription in Jok-1 B cells

city: Brest

first: soizic

last: garaud

address: 2 avenue Foch

country: France

institute: Laboratory of Immunology and Immunotherapy

summary: To assess the impact of CD5 on the transcriptome in B cells, we studied changes in mRNA levels in Jok-E1A/Jok-E1B cells compared with Jok-1 cells.

overall_design: Gene expression was performed in untransfected CD5-negative hairy B cell leukemia line (Jok-1), transfected with cDNA for either the membrane isoform of CD5 (E1A; Jok-E1A) or the cytoplasmic E1B isoform (Jok-E1B). Three biological replicates  were performed.

first: Soizic

last: Garaud


title: Gene expression in human peripheral blood 48 hours after exposure to ionizing radiation

city: New York

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

summary: Analysis of human peripheral blood 48 hours after irradiation ex vivo with graded doses of gamma rays.  Results have been used in building and testing classifiers to predict exposure dose for use in radiological triage, and also provide insight into immune cell responses.  Results were compared with those from earlier times and from patients exposed in vivo.

overall_design: Peripheral blood from 5 healthy donors was exposed ex vivo to 0. 0.5, 2, 5, or 8 Gy gamma-rays and gene expression was analyzed up to 48 hours after exposure.

first: Sunirmal

last: Paul


title: Developmental equivalence of epiblast stem cells (EpiSCs)

city: Westmead

first: Yoji

last: Kojima

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

summary: Epiblast stem cells (EpiSCs) were derived from the epiblast or the ectoderm (epi/ect) of pre-gastrula stage to late-bud stage mouse embryos. To identify if the EpiSCs retain any original stage specific characteristics or which developmental stage of epi/ect they most closely related to, we performed microarray analysis to compare the gene expression profile of multiple EpiSC lines with that of epi/ect of 7 different stages.

overall_design: Eighteen EpiSC lines established from R1-129 embryos of different stages and 1 line (EpiSC9) imported were harvested in triplicate cultured separately for 3 days. The * marks the subline thawed at a different time and harvested but originated from the same embryo. EpiSC9_T is an RNA sample provided by Dr Tesar. ESCs, iPSCs and MEFs were prepared accordingly. For the epiblast samples, in order to avoid the averaging effect by pooling samples, we linearly amplified the RNA starting from a single epiblast or ectoderm.

first: Patrick

middle: P

last: Tam


title: Protein sets define disease states and predict in vivo effects of drug treatment [Liver A]

status: Public on Sep 05 2013

city: Berlin

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

institute: Max Planck-Institute for Molecular Genetics

summary: Gaining understanding of common complex diseases and their treatments are the main drivers for life sciences. As we show here, comprehensive protein set analyses offer new opportunities to decipher functional molecular networks of diseases and assess the efficacy and side-effects of treatments in vivo. Using mass spectrometry, we quantitatively detected several thousands of proteins and observed significant changes in protein pathways that were (dys-) regulated in diet-induced obesity mice. Analysis of the expression and post-translational modifications of proteins in various peripheral metabolic target tissues including adipose, heart, and liver tissue generated functional insights in the regulation of cell and tissue homeostasis during high-fat diet feeding and medication with two antidiabetic compounds. Protein set analyses singled out pathways for functional characterization, and indicated, for example, early-on potential cardiovascular complication of the diabetes drug rosiglitazone. In vivo protein set detection can provide new avenues for monitoring complex disease processes, and for evaluating preclinical drug candidates.

overall_design:
Male C57BL/6 mice (age 6 wks) were fed for 12 weeks with high-fat diet (HFD) and than distributed into 3 groups. Mice were than fed over 3 weeks with HFD without compound ('HFD'), HFD with 4 mg/kg/d rosiglitazone ('HFD_RSG') or with 100 mg/kg/d amorfrutin 1 ('HFD_A1').

In parallel [GSE38854; Liver B], mice were fed for 15 weeks with low-fat diet (LFD) as healthy control subjects. In addition, a group of mice was treated with 37 mg/kg/d amorfrutin 1 during the whole 15 weeks of HFD feeding ('HFD+A1prev'). Finally, LIVER tissue was harvested and RNA extracted. --> 3-4 biological replicates (2 mice per each replicate, RNA of 2 mice always pooled).

liver_HFD_*A and _*B samples are from the same biological source material, but the cRNA preparation and hybridization to Illumina arrays were performed at different days (i.e. technical repeats).


title: Protein sets define disease states and predict in vivo effects of drug treatment [heart]

overall_design: Male C57BL/6 mice (age 6 wks) were fed for 12 weeks with high-fat diet (HFD) and than distributed into 3 groups. Mice were then fed over 3 weeks with HFD without compound ('HFD'), HFD with 4 mg/kg/d rosiglitazone ('HFD_RSG') or with 100 mg/kg/d amorfrutin 1 ('HFD_A1'). Finally, HEART tissue was harvested and RNA extracted. --> 3-4 biological replicates (2 mice per each replicate, RNA of 2 mice always pooled).


title: TPL-2;ERK1/2 signaling promotes host resistance against intracellular bacterial infection by negative regulation of type I interferon production [Set 2]

city: London

first: Fin

last: McNab

address: The Ridgeway, Mill Hill

institute: MRC NIMR

summary:
Analysis of Mtb infected murine macrophages derived from C57Bl/6 WT, TPL2KO, IFNARKO & TPL2IFNAR DKO mice [Set 2]

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), remains a leading cause of mortality and morbidity worldwide, causing approximately 1.4 million deaths per year. Key immune components for host protection during tuberculosis include the cytokines IL‐12, IL‐1 and TNF‐α, as well as IFN‐γ and CD4+ Th1 cells. However, immune factors determining whether individuals control infection or progress to active tuberculosis are incompletely understood. Excess amounts of type I interferon have been linked to exacerbated disease during tuberculosis in mouse models and to active disease in patients, suggesting tight regulation of this family of cytokines is critical to host resistance. In addition, the immunosuppressive cytokine IL‐10 is known to inhibit the immune response to Mtb in murine models through the negative regulation of key pro-inflammatory cytokines and the subsequent Th1 response. We show here, using a combination of transcriptomic analysis, genetics and pharmacological inhibitors that the TPL-2-ERK1/2 signaling pathway is important in mediating host resistance to tuberculosis through negative regulation of type I interferon production. The TPL-2-ERK1/2 signalling pathway regulated production by macrophages of several cytokines important in the immune response to Mtb as well as regulating induction of a large number of additional genes, many in a type I IFN dependent manner. In the absence of TPL-2 in vivo, excess type I interferon promoted IL-10 production and exacerbated disease. These findings describe an important regulatory mechanism for controlling tuberculosis and reveal mechanisms by which type I interferon may promote susceptibility to this important disease.

overall_design:
Macrophages were derived from C57Bl/6 WT, TPL2KO, IFNARKO & TPL2IFNARKO bone marrow, plated and infected with Mtb H37Rv (or not) in triplicate wells. The indicated samples were also treated with 5ng/ml IFNgamma at the time of infection. Samples were then harvested for RNA at time 0, 1hr and 6hr.

Please note that *Sample and *Medium control samples (e.g. '0hr TPL2-/-IFNabR-/- Sample' vs '0hr TPL2-/-IFNabR-/- Medium Control Sample') are the same sample group (i.e. uninfected) with one group being a repeat re-run of the other (indicated in the correponding SAMPLE description field).

first: Finlay

middle: W

first: John

last: Ewbank

first: Ricardo

last: Rajsbaum

first: Evangelos

last: Stavropoulos

first: Anna

last: Martirosyan

first: Paul

last: Redford

first: Xuemei

last: Wu

first: Christine

last: Graham

first: Margarida

last: Saraiva

first: Philip

last: Tsichlis

first: Damien

last: Chaussabel

first: Steven

last: Ley

first: Anne

last: O’Garra


title: Hypoxia-enhanced Derivation of iPSCs from Human Dental Pulp Cells

status: Public on Sep 03 2013

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

country: Japan

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

summary: Hypoxia enhances the reprogramming efficiency of human dermal fibroblasts to become induced pluripotent stem cells (iPSCs). Because we showed previously that the hypoxia facilitates the isolation and maintenance of human dental pulp cells (DPCs), we examined here whether it promotes the reprogramming of DPCs to become iPSCs.

overall_design: To investigate the effect of oxygen concentration on global gene expression, we compared DPCs cultured for 6 days under hypoxia and normoxia.

first: Kazuki

last: Iida

first: Tomoko

last: Kawaguchi


title: Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B [Illumina]

status: Public on Oct 17 2013

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

summary: The conversion of male germ cell chromatin to a nucleoprotamine structure is fundamental to the life cycle yet the underlying molecular details remain obscure. Here we show that an essential step is the genome-wide incorporation of TH2B, a histone H2B variant of hitherto unknown function. Using mouse models in which TH2B is depleted or C-terminally modified we show that TH2B directs the final transformation of dissociating nucleosomes into protamine-packed structures. Depletion of TH2B induces compensatory mechanisms that permit histone removal by up-regulating H2B and programming nucleosome instability through targeted histone modifications, including lysine crotonylation and arginine methylation. Furthermore, after fertilization, TH2B re-assembles onto the male genome during protamine-to-histone exchange. Thus, TH2B is a unique histone variant, which plays a key role in the histone-to-protamine packing of the male genome and guides genome-wide chromatin transitions that both precede and follow transmission of the male genome to the egg.

overall_design: Total RNA were obtained from testes from meiotic (spermatocytes) and post-meiotic (round spermatids) male germ cells from adult wt and Th2b+/tag mice (experiment 1: 6 biological replicates for each condition) and adult wt and th2bkd mice (experiment 2: 5 biological replicates for each condition). In each experiment, 5 or 6 replicates of each genotype and each cell type were used. Th2b+/tag mice expressed TH2B C-terminally fused to three consecutive affinity tags: His, Flag and Ha. Th2bkd mice did not express any TH2B.

first: Saadi

last: Khochbin

first: Emilie

last: Montellier

first: Alexandra

last: Debernardi

first: Matthieu

last: Gérard

first: Fayçal

last: Boussouar

first: Philippe

last: Guardiola


title: Protein sets define disease states and predict in vivo effects of drug treatment [WAT]

first: Christopher

last: Weidner

country: Germany

overall_design: Male C57BL/6 mice (age 6 wks) were fed for 12 weeks with high-fat diet (HFD) and than distributed into 3 groups. Mice were than fed over 3 weeks with HFD without compound ('HFD'), HFD with 4 mg/kg/d rosiglitazone ('HFD_RSG') or with 100 mg/kg/d amorfrutin 1 ('HFD_A1'). In parallel, mice were fed for 15 weeks with low-fat diet (LFD) as healthy control subjects. In addition, a group of mice was treated with 37 mg/kg/d amorfrutin 1 during the whole 15 weeks of HFD feeding ('HFD+A1prev'). Finally, visceral white adipose tissue (WAT) was harvested and RNA extracted. --> 2-4 biological replicates (2 mice per each replicate, RNA of 2 mice always pooled).


title: TPL-2;ERK1/2 signaling promotes host resistance against intracellular bacterial infection by negative regulation of type I interferon production

first: Fin

last: McNab

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

overall_design: Refer to individual Series

first: Finlay

first: John

last: Ewbank

first: Ricardo

last: Rajsbaum

first: Evangelos

last: Stavropoulos

first: Anna

last: Martirosyan

first: Paul

middle: S

last: Redford

first: Xuemei

last: Wu

first: Christine

last: Graham


title: Gene regulation by Pax6 in the lens placode - E9.5 (3)

status: Public on Sep 01 2013

first: David

last: Beebe

summary: Wild type or Pax6 fx/fx; Le-Cre-positive (Pax6-/-) surface ectoderm from E9.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified, pooled for each genotype and triplicate samples were reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6v2.0 bead arrays.

overall_design: Three wild type and three knockout embryos were used. The RNA from embryos of the same genotype was purified and pooled and triplicate samples were amplified and used for microarray analysis.

middle: C

first: Jie

last: Huang

first: Ying

last: Liu


title: Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (BeadChip)

status: Public on Sep 04 2013

city: Rochester

first: Jennifer

last: Westendorf

address: 200 1st St SW

institute: Mayo Clinic

summary: Suberoylanilidehydroxamic acid (SAHA) significantly increased the expression levels of 127 transcripts and suppressed expression of 130 genes by more than 2-fold within 3 standard deviations of the mean in differentiating MC3T3 sc4 osteoblasts

overall_design: Total RNA was obtained from differentiating MC3T3 sc4 cells treated with SAHA or vehicle (DMSO).

first: Amel

last: Dudakovic

first: Jared

last: Evans

last: Li

first: Sumit

last: Middha

first: Meghan

middle: E

last: McGee-Lawrence

first: Andre

last: van Wijnen


title: MyoD is a tumor suppressor gene in Medulloblastoma

city: Seattle

first: James

last: Olson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: While medulloblastoma, a pediatric tumor of the cerebellum, is characterized by aberrations in developmental pathways, the majority of genetic determinants remain unknown.  An unbiased Sleeping Beauty transposon screen revealed MyoD as a putative medulloblastoma tumor suppressor.  This was unexpected, as MyoD is a muscle differentiation factor and not previously known to be expressed in cerebellum or medulloblastoma.  In response to deletion of one allele of MyoD, two other Sonic hedgehog-driven mouse medulloblastoma models showed accelerated tumor formation and death, confirming MyoD as a tumor suppressor in these models.  In normal cerebellum, MyoD was expressed in the proliferating granule neuron progenitors that are thought to be precursors to medulloblastoma.  Similar to some other tumor suppressors that are induced in cancer, MyoD was expressed in proliferating medulloblastoma cells in three mouse models and in human medulloblastoma cases.  This suggests that although expression of MyoD in a proliferating tumor is insufficient to prevent tumor progression, its expression in the cerebellum hinders medulloblastoma genesis.

overall_design: The goal of the gene expression analysis was to determine whether the canonical myogenic differentiation program was involved in increased tumorigenicity following loss of MyoD in the SHH-driven mouse models of medulloblastoma. We compared MyoD+/+; SmoA2 (n=3) with MyoD+/- ;SmoA2 mouse medulloblastoma tumors (n=2).

first: Joyoti

last: Dey


title: Gene expression profile in the liver of insulin-deficient mice with icv leptin administration

city: Dallas

first: Teppei

last: Fujikawa

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern

summary: Analysis of gene expression in the liver of insulin-deficient mice regulated by icv leptin administration. Control group received icv PBS administration. Icv leptin administration ameliorates hyperglycemia in insulin-deficient mice. Our transcriptome data provides important aspects of the leptin’s anti-type 1 diabetes action.

overall_design: Mice were harvested 10 days after icv leptin administration (25ng/0.11uL/hour). Liver samples were quickly removed, frozen in liquid nitrogen and subsequently stored at –80ºC. RNAs were extracted by Qiagen mRNA extract kits (RNeasy plus). gDNA was eliminated in this procedure by gDNA eliminator column, which is included in Qiagen mRNA extract kits. Genomics and Microarray Core Facility at UT-Southwestern (http://microarray.swmed.edu/) checked RNA quality with Bioanalyzer Chip and processed the samples for hybridization with Illumina Mouse-6 V2 BeadChip (Illumina Inc., San Diego, CA).

first: Roberto

last: Coppari

first: Vishal

last: Patel

first: Pierre

last: Baldi


title: Protein sets define disease states and predict in vivo effects of drug treatment [Liver B]

first: Christopher

last: Weidner

overall_design:
Male C57BL/6 mice (age 6 wks) were fed for 12 weeks with high-fat diet (HFD) and than distributed into 3 groups. Mice were than fed over 3 weeks with HFD without compound ('HFD'), HFD with 4 mg/kg/d rosiglitazone ('HFD_RSG') or with 100 mg/kg/d amorfrutin 1 ('HFD_A1') [GSE38853; Liver A].

In parallel, mice were fed for 15 weeks with low-fat diet (LFD) as healthy control subjects. In addition, a group of mice was treated with 37 mg/kg/d amorfrutin 1 during the whole 15 weeks of HFD feeding ('HFD+A1prev'). Finally, LIVER tissue was harvested and RNA extracted. --> 3-4 biological replicates (2 mice per each replicate, RNA of 2 mice always pooled).

liver_HFD_*A and _*B samples are from the same biological source material, but the cRNA preparation and hybridization to Illumina arrays were performed at different days (i.e. technical repeats).


title: Protein sets define disease states and predict in vivo effects of drug treatment


title: Gene regulation by Pax6 in the lens placode - E9.5

last: Beebe


title: Gene regulation by Pax6 in the lens placode - E9.5 (2)

last: Huang


title: DOCK8 is critical for the survival and function of NKT cells [NKT_CD103+]

city: Oxford

first: Richard

last: Cornall

address: Roosevelt Drive

department: Centre of Cellular and Molecular Physiology

institute: University of Oxford

summary: Analysis of DOCK8 deficient animals revealed a novel marker of NKT cell development, the integrin CD103. The role of CD103 was further investigated by RNA microarray comparing CD103 negative versus positive NKT cells.

overall_design: Total RNA was extracted from 3 biological replicates of thymic, CD103positive NKT cells and compared using an Illumina microarray to CD103negative NKT cells.

first: Greg

last: Crawford

first: Uzi

last: Gileadi

first: Helen

last: Lockstone


title: DOCK8 is critical for the survival and function of NKT cells


title: DOCK8 is critical for the survival and function of NKT cells [DOCK8_CPM_NKT]

summary: Analysis of DOCK8 deficient animals revealed a key role for this protein the survival and maintenance of natural killer T cells. This work lead to the identification of genes regulated by the guanine exchange factor, DOCK8.

overall_design: Total RNA was extracted from 3 biological replicates of thymic, DOCK8 deficient NKT cells and compared using an Illumina microarray to WT NKT cells.


title: Gene expression profiles in 74 laser microdissected colorectal cancer tissues

status: Public on Aug 31 2013

city: Beppu

first: Koshi

last: Mimori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

institute: Kyushu university

summary: Tissues from another series of 74 patients with colorectal cancer were collected by laser micro-dissection with the Leica Laser Microdissection System (Leica Microsystems).

overall_design: Gene expression levels obtained from 74 microdissected colorectal tumors were compared with 5 microdissected normal colon epitheliums. We used the commercially available Human Whole Genome Oligo DNA Microarray Kit (Agilent Technologies). Labeled cRNAs were fragmented and hybridized to an oligonucleotide microarray (Whole Human Genome 4×44K Agilent G4112F). Fluorescence intensities were determined with an Agilent DNA Microarray Scanner and were analyzed using G2567AA Feature Extraction Software Version A.7.5.1 (Agilent Technologies).

first: Masaki

last: Mori

first: Daisuke

last: Okuzaki

first: Takehiko

last: Yokobori


title: Identification of a gene expression signature in colorectal adenocarcinoma in comparison with colorectal adenoma

status: Public on Aug 27 2013

first: Laurent

last: Corcos

address: 22, Avenue Camille Desmoulins

department: Faculty of Medicine

institute: INSERM U1078-ECLA

summary: We showed that a lot of genes were deregulated in colorectal adenocarcinomas in comparison with colorectal adenomas.

overall_design: 37 colorectal adenoma and 9 colorectal adenocarcinoma samples were analyzed. We generated a comparison between adenocarcinomas and adenomas.

first: Marine

last: Pesson

first: Alain

last: Volant

first: Kilian

last: Trillet

last: De La Grange

first: Mélanie

last: Daoulas

first: Michel

last: Robaskiewicz

first: Gérald

last: Le Gac

last: Morel

first: Brigitte

last: Simon


title: Molecular analysis of a case of renal cell carcinoma with t(6;11) (p21;q12) reveals a link to a lysosome-like structure

status: Public on Aug 16 2013

city: Yufu-city

first: Keiko

last: Matsuura

address: hasama-cho, Idaigaoka

institute: Oita University

summary: TFEB has been recently reported to be a key molecule for lysosomal regulation. Renal cell carcinoma (RCC) with t(6;11) (p21;q12) is known to be the only tumor in which TFEB is upregulated. Transcriptome analysis using a whole-genome expression array and pathway analysis using upregulated genes in tumor tissue revealed that the lysosome-associated pathways were significantly deregulated.

overall_design: Total RNA was extracted from non-tumor and tumor in patient of renal cell carcinoma with t(6;11) (p21;q12) and subjected to gene expression microarray analysis.


title: A Robust Method To Derive Functional Neural Crest Cells From Human Pluripotent Stem Cells

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary:
Neural crest (NC) cells contribute to the development of many complex tissues. The abnormal development of NC cells accounts for a number of congenital birth defects. Generating NC cells, and more specifically NC subpopulations such as cranial, cardiac, and trunk NC cells from human induced pluripotent stem (iPS) cells and human embryonic stem (ES) cells presents a valuable tool to model and study human NC development and disease.
Here we provide a robust, efficient, and reproducible protocol for the differentiation of human iPS and ES cells into NC cells. The protocol has been validated in multiple human pluripotent stem cell lines and yields relatively pure NC cell populations in eight days. The resulting cells can be propagated and retain NC marker expression over multiple passages. The NC cells show proper cell specification and can develop into NC-derived cell lineages including smooth muscle cells, peripheral neurons, and Schwann cells. Additionally, the NC cells are functional and migrate to appropriate chemoattractants such as SDF-1, Fgf8b, BMP2, and Wnt3a. Importantly, this method generates all NC subpopulations (cranial, cardiac, and trunk) providing a great advantage to readily available NC differentiation methods.

overall_design: Neural crest cells derived from human induced pluripotent stem cells were profiled using Affymetrix Gene 1.0 arrays to identify differential gene expression changes and alternative exons from the open-source software AltAnalyze. An FDR adjusted emperical Bayes moderated t-test p < 0.05 was used to identify differentially expressed Ensembl genes and GO-Elite used to identify biologically relevant, Ontology, pathway and gene-set categories. Alternative exons were obtained using the FIRMA analysis option and default thresholds. Other array neural crest array and RNA-Seq dataset were compared to this to identify common and distinct regulatory mechanisms.

first: Faith

last: Kreitzer

first: Alice

last: Sheehan

first: Miller

last: Huang

first: Matthew

last: Spindler

first: Jason

last: Park

first: Paweena

last: Lizarraga

first: Po-Lin

last: So

first: William

middle: A

last: Weiss

first: Bruce

last: Conklin


title: Effect of SRSF2 over-expression in a human lung carcinoma cell line

status: Public on Aug 30 2013

first: Laurent

last: Corcos

summary: We showed that the over-expression of the SR protein SRSF2 led to the regulation of transcript abundance of many genes.

overall_design: H358 cell line with 6 samples with SRSF2 over-expression and 6 samples as control.

first: Marine

last: Pesson

first: Béatrice

last: Eymin

first: Pierre

last: De La Grange