title: Genetic Loci that Regulate Ectopic Calcification in Response to Knee Trauma in LG/J by SM/J Advanced Intercross Mice

status: Public on Jan 09 2015

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary:
Ectopic calcification in synovial tissues is devastating to diarthrodial joints. While some forms of synovial ectopic calcification have genetically simple basis, most cases manifest as complex traits with environmental and multigenic components. The location of causal loci or the physiological processes affected by allelic variants is poorly understood. Here, we report on genetic susceptibility to ectopic calcification in the LG/J and SM/J advanced intercross mice. Using 347 mice in 98 full-sibships, destabilization of medial meniscus was performed to induce joint injury. We performed quantitative trait locus (QTL) analysis to map calcification phenotypes to discrete genomic locations. To validate the functional significance of the selected QTL candidate genes, we compared mRNA expression between parental LG/J and SM/J inbred strains.
Our findings showed that joint destabilization instigated ectopic calcifications as detected and quantified by micro-CT. Overall, we detected 20 QTLs affecting synovial and meniscus calcification phenotypes with 11 QTLs linked to synovial calcification. Functional and bioinformatic analyses of single nucleotide polymorphism identified functional classifications relevant to angiogenesis (Myo1e, Kif26b, Nprl3, Stab2, Fam105b), bone metabolism/calcification (Tle3, Tgfb2, Lipc, Nfe2l1, Ank, Fam105b), arthritis (Stab2, Tbx21, Map4k4, Hoxb9, Larp6, Col1a2, Adam10, Timp3, Nfe2l1, Trpm3), and ankylosing-spondylitis (Ank, Pon1, Il1r2, Tbkbp1) indicating that ectopic calcification involves multiple mechanisms. Furthermore, the expression of 11 candidate genes was significantly different between LG/J and SM/J. Correlation analysis showed that Aff3, Fam81a, Syn3, and Ank were correlated with synovial calcification. Our findings of multiple genetic loci affecting the phenotype suggest the involvement of multiple genes contributing to its pathogenesis.

overall_design: We collected tissue lysates from the formalin-fixed paraffin-embedded sections from mouse knee joints and analyzed the expression of several genes by Affymetrix QuantiGene Plex assay.

first: Muhammad

middle: F

first: Eric

last: Schmidt

first: Shingo

last: Hashimoto

first: James

middle: M

last: Cheverud

first: Linda

last: Sandell


title: Transcriptomic analysis of an iron-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

status: Public on Sep 11 2014

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

summary:
Iron-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering selection strategy. The mutant obtained “M8FE” is much more resistant to iron stress than the reference strain which was used to select this mutant. Mutant can resist up to 35mM Iron* stress whereas the reference strain cannot.
Whole-genome microarray analysis might be promising to identify the iron resistance mechanisms and stress response upon high levels of iron in the yeast cells. Iron-resistant mutant is also cross resistant to Cobalt, Chromium and Nickel but sensitive to Zinc. * refers to [NH4]2[Fe][SO4]2 and FeCl2.

overall_design: The reference Saccharomyces cerevisiae strain and the iron-resistant mutant were grown in minimal medium to an Optical Density (OD600) of 1.00 which correspond to the logarithmic growth phase of the yeast cells. Cultures were harvested and whole RNA isolation was carried out. The experiment was repeated three times.

first: B

middle: G

last: Balaban

first: C

last: Alkım

first: U

last: Yılmaz

first: H

middle: I

last: Kısakesen

first: Z

middle: P

last: Cakar


title: Host cell gene expression in Influenza A/duck/Malaysia/F59/04/1998 (H5N2) infected CEF cells at 10 hour post infection

status: Public on Aug 10 2014

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: Divison of Molecular and Cell Biology

country: Singapore

institute: Nanyang Technological University

summary: We used the microarray data to analyze host cells response on CEF cells infected with A/duck/Malaysia/F59/04/1998(H5N2)

overall_design: A/duck/Malaysia/F59/04/1998(H5N2) infected CEF cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F59/04/1998(H5N2) infection.

last: Sutejo

first: Hui

last: Chen

first: Boon

middle: H

last: Tan


title: Effect of acute and chronic social stress on hippocampal transcriptome in mice.

status: Public on Jul 04 2014

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

summary:
We investigated gene expression in mice subjected to acute and chronic social stress of different duration. Microarray data showed that chronic stress affected genes involved in function of vascular system (Alas2, Hbb-b1, Hba-a2, Hba-a1), injury response (Vwf, Mgp, Cfh, Fbln5, Col3a1, Ctgf) and inflammation (Isg20, Ctla2a, Ctla2b,Lcn2, Lrg1, Rsad2,S100a8, S100a9). Review of the literature revealed that the most frequently regulated genes (up or down) were Igfbp2, Igf2, Prlr, App, Cdh1, Col1A1, Clic6, Enpp2, Sostdc1,Itgb6, Mef2c, Spp1, and Zeb2. Obtained results suggest that stress may affect brain functions through the stress-induced dysfunction of the vascular system. Some of the key genes revealed by the review of published data participate both in the response to injury and in the mechanism of learning and memory. These genes may constitute a link between stress and stress-induced memory impairments. An important issue raised by our work is also the risk of tissue contamination with choroid plexus. Such contamination would result in consistent up- or down-regulation of genes, such as Ttr, Igf2, Igfbp2, Prlr, Enpp2, Sostdc1, 1500015O10RIK (Ecrg4), Kl, Clic6, Kcne2, F5, Slc4a5, and Aqp1.

The study was supported by Grant N N311 604938, 2011/03/N/NZ29/05222 and partially by IP2011 030371. Statistical analysis of microarray data was supported with Grant N N519 657940.

overall_design: This is analysis of 24 hippocampal RNA samples. Each sample consisted of equal amounts of total RNA from 3 mice subjected to the same experimental condition. Comparisons: acute stress vs. acute control (unstressed), stress-8 days vs. control-8 days, stress-13 days vs. control-13 days, stress-13 days+5 days of rest vs. control-13 days+5 days of rest. 3 biological replicates in each comparison. Dye swap (technical replicate) was included for each biological replicate.

first: Joanna

last: Goscik

first: Katarzyna

last: Gruba

first: Alicja

last: Majewska

first: Artur

last: Swiergiel

first: Grzegorz

middle: R

last: Juszczak

first: Pawel

last: Lisowski


title: MicroRNA profiling of Acute Lymphoblastic Leukemia (ALL)

status: Public on Jul 09 2014

city: Hyderabad

first: Lekha

middle: Dinesh

last: Kumar

state: Andhra Pradesh

address: Uppal road, habshiguda

department: Cancer biology

country: India

institute: Centre for cellular and molecular biology

summary: Total RNA was isolated from Peripheral blood (PB) and Bone Marrow (BM) samples using mirVana kit and RNA integrity number (RIN) was determined in Agilent Bioanalyzer (2100) to assess the suitability for microarray assays. Fifty samples were individually analyzed using miRCURY™ LNA arrays version 11.0 (Exiqon, Denmark). The LNA array slides were scanned using Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and image analysis was carried out using ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 14 and normalized using global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm.

overall_design: Three condition experiment T-ALL vs Healthy Individuals (normals),  B-ALL vs normals, T-ALL vs B-ALL; Biological replicates: 6, T-ALL replicates and 5 B-ALL replicates; Control replicates-5.139 is the BM of individual 136

middle: D

first: Rekha

middle: A

last: Nair


title: Host cell gene expression in Influenza A/duck/Malaysia/F59/04/1998 (H5N2) infected MDCK cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on MDCK cells infected with A/duck/Malaysia/F59/04/1998(H5N2)

overall_design: A/duck/Malaysia/F59/04/1998(H5N2) infected MDCK cells were harvested at 10 hpi for harvesting and and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F59/04/1998(H5N2) infection.


title: Epigenomic Alterations Define Lethal CIMP-positive Ependymomas of Infancy

status: Public on Mar 25 2014

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

country: USA

institute: Baylor College of Medicine

summary: 1) Illumina 450K methylation profiles-48 posterior fossa ependymomas

middle: C

last: Mack


title: Host cell gene expression in Influenza A/duck/Malaysia/F59/04/1998 (H5N2) infected A549 cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on A549 cells infected with A/duck/Malaysia/F59/04/1998(H5N2)

overall_design: A/duck/Malaysia/F59/04/1998(H5N2) infected A549 cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F59/04/1998(H5N2) infection.


title: Medicago abi3 mutant analysis

status: Public on May 09 2014

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

summary: Comparison of transcriptomes of WT and abi3 mutant lines at 32 and 40 days after pollination

overall_design: Transcriptome of Medicago WT lines (3 replicates) compared with Medicago abi3 mutant lines (NF6003) using Medicago_v1 NimbleGen chip

first: David

last: Lalanne

first: Jérôme

last: Verdier

first: Julia

last: Buitink


title: Genome response to tissue plasminogen activator in experimental ischemic stroke

status: Public on Mar 29 2014

city: Sacramento

first: Glen

last: Jickling

state: CA

institute: University of California Davis

summary:
To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke.
Forty-two Sprague-Dawley rats were subjected to: 2 hours of middle cerebral artery occlusion (MCAO); a permanent-MCAO; or were used as controls.  tPA was administered to half of the rats in each group at 3hours. Whole blood was drawn at 24 hours, and isolated RNA levels measured on Affymetrix Rat Genome 230 2.0 GeneChip microarrays to examine the entire RNA transcriptome.

overall_design: 42 samples, 7 groups in total ( 2 treatmented disease, 2 untreated disease, and  3 control groups), each group had 6 replicates


title: Digital Genomic Footprinting by Dnase I of fetal liver derived erythroid cells

status: Public on Mar 05 2014

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Base-pair level resolution of DNase susceptibility of the native chromatin state. These  maps represent and are dependent upon the nature and the specificity of interaction of the DNA with the regulatory/modulatory proteins binding at specific loci in the genome; thus they represent the native chromatin state of the genome under investigation. The deep sequencing approach has been used to define the footprint landscape of the genome by identifying DNA motifs that interact with known or novel DNA-binding proteins

overall_design: 2 replicates of the erythroid cells were generated and profiled by Dnase I.

first: Kai-Hsin

last: Chang

first: Hao

last: Wang

first: Xiangdong

last: Fang

first: Fyodor

last: Urnov

first: Richard

last: Sandstrom


title: Applied Biosystems Human TaqMan Low Density Array (TLDA) in HCC tumor and adjacent non-tumor tissues

status: Public on Feb 08 2014

city: New York

first: Jing

last: Shen

address: 650 W. 168th St. Black Building Rm.1608

institute: Columbia University

summary: MicroRNAs (miRNAs) are aberrant expressed in hepatocellular carcinoma (HCC) tissue and play a central role in diverse biological processes. We conducted a genome-wide miRNAs screening in 10 pairs of HCC tumor and adjacent non-tumor tissues to test the hypothesis that dysregulation of miRNAs in HCC tumor tissue are partially due to aberrant methylation in relevant miRNAs host genes. Taqman low density arrays were used to examine miRNA profiles in paired HCC tissues, and quantitative RT-PCR was used to validate candidate miRNAs for both discovery and validation sets.

overall_design: A cross-sectional study was conducted in 10 HCC tumor tissues and 10 adjacent non-tumor tissues in Columbia University Medical Center (CUMC), which is approved by the Institutional Review Board.


title: COL11A1 promotes tumor progression and predicts poor clinical outcome in ovarian cancer.

status: Public on Jan 01 2014

city: Taipei

first: Tzu-Hao

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

summary: Biomarkers that predict disease progression might assist the development of better therapeutic strategies for aggressive cancers, such as ovarian cancer. Here, we investigated the role of collagen type XI alpha 1 (COL11A1) in cell invasiveness and tumor formation and the prognostic impact of COL11A1 expression in ovarian cancer. Microarray analysis suggested that COL11A1 is a disease progression-associated gene that is linked to ovarian cancer recurrence and poor survival.

overall_design: Whole tumor gene expression profiling was conducted on tissue samples from 60 ovarian cancer patients, and characteristics and clinico-pathological features of the patients are provided. We used several steps to analyze the expression profiles of the samples to identify the genes whose expression values correlate with survival, recurrence and advanced disease stage. First, using hazard ratios from univariate Cox regression analysis, the top 200 survival-related genes were evaluated for intersection with the top 200 recurrence-related genes, and 44 genes were obtained. Second, we examined the 44 genes that met the criteria of fold-change values between advanced stage and early stage samples of greater than 2 or less than 0.5. Ultimately, 17 genes were identified. A heat map of the 17 genes is depicted in the associated publication. Gene ontology and pathway enrichment analyses of the 17 genes were performed using Database for Annotation, Visualization and Integrated Discovery (DAVID). The major cellular component, biological process and molecular function of the 17 genes are associated with the extracellular region, intracellular signaling cascade, and protein binding and bridging, respectively. Two genes, COL11A1 and COL4A6, are involved in ECM-receptor interaction pathways. Notably, COL11A1 displayed the highest fold-change value in ovarian cancer disease progression; therefore, we selected COL11A1 for further experimental analysis.

first: Yi-Hui

last: Wu

first: Yu-Fang

last: Huang

first: Hsien-Da

first: Cheng-Yang

last: Chou


title: Expression data from three human cancer cell lines (PC-3, SK-OV-3, WM793B) exposed to  experimental cycling and chronic hypoxa in vitro

status: Public on Dec 06 2013

city: Gliwice

first: Magdalena

last: Olbryt

address: Wybrzerze AK 15

department: Center for Translational Research and Molecular Biology of Cancer

institute: Cancer Center and Institute of Oncology

summary: One of the most important features of tumor microenvironment, imposing adverse effect on patient prognosis, is low oxygen tension. There are two types of hypoxia that may occur within tumor mass: chronic and cycling. Preliminary studies point at cycling hypoxia as being more relevant in induction of aggressive phenotype of tumor cells and radioresistance though little is known about the molecular mechanism of this phenomenon. Analysis of gene expression profile of human prostate (PC-3), ovarian (SK-OV-3) and melanoma (WM793B) cancer cells to expermental cycling (interchanging conditions of 1% and 21% oxygen) or chronic (1% oxygen) for 72 hours. Gene expression profiles were analyzed using U133 Plus 2.0 Array (Affymetrix) oligonucleotide microarrays. Data analysis revealed that globally gene expression profiles induced by the two types of hypoxia are similar and they strongly depend on the cell type.However, cycling hypoxia changes expression of lower number of genes in comparison to chronic one ( 3767 vs. 5954 probesets (p<0.001)) and to lower extent (lower fold changes). Analysis of hypoxia-regulated gene lists obtained using  Random Variance Model t-test  identified 253 probe sets (FC>2, p<0.001) common to all three cell lines, though no universal (changed throughout all analyzed cell lines) genes specifically influanced only by cycling hypoxia was selected. On the other hand, we identified such genes within particular one or two cell lines. Among them those related with EGF pathway seemed to be overrepresented (i.e. EPHA2, AREG, and HBEGF) and together with PLAU and IL-8 were mostly validated by Q-PCR.

overall_design: We investigated transcriptional activity of prostate and ovarian cancer cells as well as melanoma cells cultured for 72h under chronic hypoxic (nominal 1% oxygen; 3 experimental samples for each cell type), cycling hypoxia (interchanging periods of nominal 1% and 21% oxygen; 3 samples for each line) and control conditions (21% oxygen; 3 samples for each cell lines).

first: Anna

last: Habryka

first: Michał

last: Jarząb

first: Sebastian

last: Student

first: Tomasz

last: Tyszkiewicz

first: Katarzyna

last: Lisowska


title: Medicago truncatula seed development at 20/18°C 16 h light/dark in osmotic stress conditions: -0.1 Mpa

status: Public on Dec 05 2013

first: Sandra

last: Pelletier

summary: Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 20/18°C 16 h light/dark, in osmotic stress conditions (-0.1 Mpa). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

overall_design: Seeds of Medicago truncatula grown at 20/18°C 16 h light/dark  in osmotic stress conditions of -0.1 Mpa, were collected at different developmental stages, 7 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment corresponding to the later developmental stage. For each repetition 4 hybridisation were made: 12DAP vs 15DAP, 20DAP vs 25DAP, 30DAP vs Abs, DS (Rep1 and Rep2) vs 12DAP (Rep3 and Rep4). For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.

first: Karima

last: Righetti

first: Julia

last: Buitink


title: Medicago truncatula seed development at 14/11°C 16 light/dark

status: Public on Dec 18 2013

summary: Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 14/11°C, 16h light/dark. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

overall_design: Seeds of Medicago truncatula grown at 14/11°C, 16h light/dark  were collected at different developmental stages, 10 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment, corresponding to the later developmental stage. For each repetition 5 hybridisation were made: 22DAP vs 28DAP, 34DAP vs 40DAP, 46DAP vs 52DAP, 58DAP vs 65DAP,Abs vs DS. For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.


title: Medicago truncatula seed development at under greenhouse conditions

summary: Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at variable light and temperature conditions under greenhouse environment (period March-June). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

overall_design: Seeds of Medicago truncatula were collected at different developmental stages, 9 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment corresponding to the later developmental stage. For each repetition 5 hybridisation were made: 16DAP vs 20DAP, 24DAP vs 28DAP, 32DAP vs 36DAP, 40DAP vs Abs, DS (Rep1 and Rep2) vs 16DAP (Rep3 and Rep4). For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.


title: Medicago truncatula seed development at 26/24°C 16 h light/dark

summary: Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 26/24°C 16 h light/dark. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

overall_design: Seeds of Medicago truncatula grown at 26/24°C 16 h light/dark were collected at different developmental stages, 8 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment corresponding to the later developmental stage. For each repetition 4 hybridisation were made: 7DAP vs 9DAP, 11DAP vs 14DAP, 17DAP vs 20DAP, Abs vs DS. For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.


title: Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos

status: Public on Dec 13 2013

city: Blacksburg

first: Delasa

last: Aghamirzaie

state: VA

address: 101L Price Hall, Virginia Tech

department: GBCB

institute: virginia Tech

type: Expression profiling by high throughput sequencing

summary: Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on    guilt-by-association    relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.

overall_design: Total mRNA profiles of 10 time course samples of Soybean developing embryos with three replicates per sample were generated by deep sequencing, using Illumina HiSeq 2000

first: Eva

last: Collakova

first: Ruth

last: Grene


title: EZH2-mediated H3K27 trimethylation mediates neurodegeneration in ataxia-telangiectasia

status: Public on Oct 25 2013

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: The symptoms of ataxia-telangiectasia (A-T) include a progressive neurodegeneration caused by ATM protein deficiency. We previously found that nuclear accumulation of histone deacetylase-4, HDAC4, contributes to this degeneration; we now report that increased histone H3K27 trimethylation (H3K27me3) mediated by polycomb repressive complex 2 (PRC2) also plays an important role in the A-T phenotype. Enhancer of zeste homolog 2 (EZH2), a core catalytic component of PRC2, is identified as a new ATM kinase target, and its S734 phosphorylation reduces protein stability. Thus, PRC2 formation is elevated along with H3K27me3in ATM deficiency.  ChIP-sequencing shows a significant increase in H3K27me3 ‘marks’ and a dramatic shift in their location. The change of H3K27me3 chromatin-binding pattern is directly related to cell cycle re-entry and cell death of ATM-deficient neurons. Lentiviral knockdown of EZH2 rescues Purkinje cell degeneration and behavioral abnormalities in Atm /  mice, demonstrating that EZH2-mediated H3K27me3 is another key factor in A-T neurodegeneration.

overall_design: Two samples each were run of brain total RNA from Atm+/+ and Atm-/- mice.

first: Jiali

last: Li

first: Karl

last: Herrup


title: Medicago truncatula seed development under different growth conditions

status: Public on Dec 19 2013

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

overall_design: Refer to individual Series


title: The transcriptional network for cell cycle regulation in prostate cancer

status: Public on Nov 25 2013

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

summary: Several compounds were treated on the PC-3 cell line to investigate cell cycle regulation in prostate cancer through gene expression profile data. Our study demonstrated that several compounds induced cell cycle regulation in the CRPC (Castration-Resistant Prostate Cancer) cell model.

overall_design: Compounds (menthol, cineol, geraniol, icilin, linalool) were dissolved in ethanol as a vehicle at 0.1% working concentration and treated in PC-3 cells in triplicate. Vehicle-treated PC-3 cells in triplicate were used as a control.

first: Jung

last: Chun

first: Sanghoon

last: Lee

first: Su-Hwa

last: Kim

first: Insuk

last: So


title: Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis

status: Public on Oct 15 2013

city: New Haven

first: JOSE

middle: DAVID

last: HERAZO MAYA

state: CT

address: 300 Cedar Street

department: Medicine

institute: Yale University

summary:
Background:  In this study we aimed to identify peripheral blood mononuclear cell (PBMC) gene expression profiles predictive of poor outcomes in idiopathic pulmonary fibrosis (IPF)
Methods:  Microarray analyses of PBMC were performed in 120 patients from discovery (n=45) and replication cohorts (n=75).  Genes and pathways associated with transplant-free survival (TFS) were identified and confirmed by qRT-PCR.
Findings:  52 genes were predictive of TFS in a discovery cohort (FDR<5%, Cox score above 2.5 or below -2.5). Clustering the replication cohort samples using these genes distinguished two patient groups with significantly different TFS (hazard ratio 1.96, 95%CI 1.01-3.8, P=0.018). Decreased expression of “The co-stimulatory signaling during T cell activation” Biocarta pathway and in particular CD28, ICOS, LCK and ITK was associated with shorter TFS times in each cohort (FDR<5%). qRT-PCR expression of CD28, ICOS, LCK and ITK correlated with the microarray results in the discovery cohort (P<0.05) and their decreased expression was predictive of shorter TFS in the replication cohort (P<0.05).  A genomic and clinical model demonstrated an area under the ROC curve of 78.5% at 2.4 months for death and lung transplant prediction.
Interpretation:  Our results suggest that CD28, ICOS, LCK and ITK are outcome biomarkers in IPF.

overall_design:
The 'GeneID_matched_gene_expression_dataset_of_IPF_cohorts.txt' supplementary data file contains the matched gene expression data of the subseries GSE28042 with the subseries GSE27957 by gene ID (details in the readme.txt)

This SuperSeries is composed of the SubSeries listed below.


title: Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis [Affymetrix]

summary:
Background:  In this study we aimed to identify peripheral blood mononuclear cell (PBMC) gene expression profiles predictive of poor outcomes in idiopathic pulmonary fibrosis (IPF)
Methods:  Microarray analyses of PBMC were performed in 120 patients from discovery (n=45) and replication cohorts (n=75).  Genes and pathways associated with transplant-free survival (TFS) were identified and confirmed by qRT-PCR.
Findings:  52 genes were predictive of TFS in a discovery cohort (FDR<5%, Cox score above 2.5 or below -2.5). Clustering the replication cohort samples using these genes distinguished two patient groups with significantly different TFS (hazard ratio 1.96, 95%CI 1.01-3.8, P=0.018). Decreased expression of “The co-stimulatory signaling during T cell activation” Biocarta pathway and in particular CD28, ICOS, LCK and ITK was associated with shorter TFS times in each cohort (FDR<5%). qRT-PCR expression of CD28, ICOS, LCK and ITK correlated with the microarray results in the discovery cohort (P<0.05) and their decreased expression was predictive of shorter TFS in the replication cohort (P<0.05).  A genomic and clinical model demonstrated an area under the ROC curve of 78.5% at 2.4 months for death and lung transplant prediction.
Interpretation:  Our results suggest that CD28, ICOS, LCK and ITK are outcome biomarkers in IPF.  They should be further evaluated for patient prioritization for lung transplantation and stratification in drug studies.

overall_design: This submission represents the Affymetrix component of the study (discovery cohort)

first: Shwu-Fan

last: Ma

first: Yong

last: Huang

first: Imre

last: Noth

first: Joe

last: Garcia


title: The gene expression profiling array of LncRNA between tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma

status: Public on Aug 10 2013

city: Shanghai

first: Wang

last: Kang

state: Shanghai

address: 225 Changhai Road

country: China

institute: Eastern Hepatobiliary Surgery Hospital Second Military Medical University

summary: Investigation of whole genome gene expression level changes of LncRNAs in tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma. The different expression genes were further analysised.

overall_design: The human LncRNA microarray analysis of the 10 samples (5 non-tumor tissues and 5 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C.  Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples.

first: Kang

last: Wang

first: Wei-xing

last: Guo


title: Host cell gene expression in Human respiratory syncytial virus (HRSV) infected mouse macrophage cells at 4, 24 hours post infection

status: Public on Aug 16 2013

first: Richard

last: Sugrue

summary: We used the microarray data to analyze host cells response on mouse macrophage cells infected with HRSV

overall_design: The HRSV infected mouse macrophage cells were harvested at 4 and 24 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host cell response to HRSV infection.

last: Sutejo

first: Hui

last: Chen

first: Boon

last: Tan


title: Xenoestrogen Dose-dependent Transcriptomal Changes in MCF-7 Human Breast Cancer Cells

status: Public on Sep 10 2013

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary:
Transcriptome analysis of MCF-7 cells exposed for 48 hours to various concentrations of xenoestrogen chemicals.
Although biological effects of endocrine disrupting chemicals (EDCs) are often observed at unexpectedly low doses with occasional non-monotonic dose-response characteristics, transcriptome-wide profiles of sensitivities or dose-dependent behaviors of the EDC responsive genes have remained unexplored. Here, we describe expressome analysis for the comprehensive examination of dose-dependent gene responses and its applications to characterize estrogen responsive genes in MCF-7 cells. Transcriptomes of MCF-7 cells exposed to varying concentrations of representative natural and xenobiotic estrogens for 48 hours were determined by microarray and used for computational calculation of interpolated approximations of estimated transcriptomes for 300 doses uniformly distributed in log space for each chemical. The entire collection of these estimated transcriptomes, designated as the expressome, has provided unique opportunities to profile chemical-specific distributions of ligand sensitivities for large numbers of estrogen responsive genes, revealing that at low concentrations estrogens generally tended to suppress rather than to activate transcription. Gene ontology analysis demonstrated distinct functional enrichment between high- and low-sensitivity estrogen responsive genes, supporting the notion that a single EDC chemical can cause qualitatively distinct biological responses at different doses. Expressomal heatmap visualization of dose-dependent induction of Bisphenol A-inducible genes showed a weak gene activation peak at a very low concentration range (ca. 0.1 nM) in addition to the main, strong gene activation peak at and above 100 nM. Thus, expressome analysis is a powerful approach to understanding the EDC dose-dependent dynamic changes in gene expression at the transcriptomal level, providing important information on the overall profiles of ligand sensitivities and non-monotonic responses.

overall_design: Subconfluent density of MCF-7 cells were exposed to various concentrations of xenoestrogen chemicals for 48 hours and then subjected to transcriptomal analysis using Affymetrix U133 version 2 plus microarray.

first: Toshi

first: Noël

last: Rosenthal

first: Kathryn

last: Coser

first: Mizuki

last: Suto

first: Mukta

last: Phatak

first: Mario

last: Medvedovic

first: Vincent

last: Carey

first: Kurt

last: Isselbacher


title: A Hybrid Mechanism of Action for BCL6 in B Cells Defined by Formation of Functionally Distinct Complexes at Enhancers and Promoters

status: Public on Aug 05 2013

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

summary:
BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore BCL6 mechanism in normal and malignant B-cells. Surprisingly, BCL6 assembled distinct complexes at enhancers vs. promoters. At enhancers BCL6 preferentially recruited SMRT, which mediated H3K27 deacetylation through HDAC3, antagonized p300 activity and repressed transcription, but without decommissioning enhancers. This provides a biochemical
basis for toggling enhancers from the active to poised state. Virtually all SMRT was bound with BCL6 suggesting that in B-cells BCL6 uniquely sequesters SMRT from other factors. In promoters BCL6 preferentially recruited BCOR, but most potently repressed promoters where it
formed a distinctive ternary complex with SMRT and BCOR. Promoter repression was associated with decreased H3K36me3, H3K79me2 and Pol II elongation, linking BCL6 to transcriptional pausing.

overall_design: We identified the binding patterns of BCL6, SMRT, NCOR and BCOR corepressors in normal germinal center B cells and a DLBCL cell line (OCI-Ly1) using ChIP-seq. Additionally we treated lymphoma cells with siRNA against BCL6 and a non-targeted siRNA (NT control) and performed RNA-seq to identify the genes bound and repressed by BCL6. RNA-seq experiments were performed at 24h and 48h after siRNA treatments. Additional biological triplicate RNA-seq experiments were performed at 48h after BCL6 knockdown. Furthermore, a series of histone mark ChIP-seq and RNA polymerase ChIP-seq (total, Ser5-P and Ser2-P) were preformed to capture the chromatin states associated with the formation of BCL6 corepressor complexes.

first: Olivier

last: Elemento

first: Ari

last: Melnick


title: Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis [Agilent]

first: JOSE

last: HERAZO MAYA

overall_design: PBMC from 75 patients with the diagnosis of IPF were obtained within 30 minutes from blood draw. Total RNA was extracted, labeled and hybridized to Agilent Whole Human Genome Oligo Microarray, 4 x 44K. Patients were followed from blood draw until death, transplant or last follow up. Hierarchical clustering and gene-set analysis with censored outcome data were used to study the association of gene expression and outcome in this cohort (replication cohort)

first: Jose

last: Herazo Maya


title: Expression data from peripheral blood in pancreatic ductal adenocarcinoma (PDAC) patients

status: Public on Aug 12 2013

city: Jaen

first: Octavio

last: Caba

state: Jaen

address: Paraje de las Lagunillas

department: Health Sciences

country: Spain

institute: University of Jaen

summary:
The presence of some malignancies, such as cancer, impacts on peripheral blood mononuclear cells (PBMCs) gene expression profiling, suggesting the potential suitability of these genes as diagnostic and prognostic markers.
The objective of this study was to identify new markers in peripheral blood that differentiate between PDAC patients and healthy controls as a means of facilitating fast detection of the disease.

overall_design: 18 patients with unresectable PDAC were recruited. The diagnosis of PDAC was based on clinical evaluation and imaging studies, which were histologically confirmed by surgery or imaging-guided biopsy. 18 gender, age, and habits matched healthy controls were also included. Whole genome cDNA microarray hybridization of PBMC samples was performed to identify potential PDAC markers.

last: Prados

first: Raúl

last: Ortiz

first: Consolación

last: Melguizo

first: Cristina

last: Jiménez-Luna

first: Pablo

last: Álvarez

first: Juan

last: Delgado

first: Antonio

last: Irigoyen

first: Ignacio

last: Rojas

first: Javier

last: Pérez-Florido

first: Sonia

last: Perales

first: Carolina

last: Torres

first: Ana

last: Linares

first: Antonia

last: Aránega


title: Co-regulated gene expression by estrogen receptor-a and liver receptor homolog-1 is a feature of the estrogen response in breast cancer cells

status: Public on Aug 01 2013

city: Amsterdam

first: Koen

last: Flach

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: Our findings establish a key role for LRH-1 in the regulation of ERa target genes in breast cancer cells and identify a mechanism in which co-operative binding of LRH-1 and ERa at estrogen response elements controls the expression of estrogen responsive g

overall_design: Examination of ERα, with or without LRH-1 knockdown, and HA-LRH-1 in MCF-7 cells

first: Wilbert

last: Zwart

first: Simak

last: Ali

first: Arno

last: Velds

first: Laki

last: Buluwela


title: Gene expression profiling in the cerebral cortex of patients with cirrhosis with and without hepatic encephalopathy

status: Public on May 01 2013

city: Düsseldorf

first: Boris

last: Goerg

address: Moorenstrasse 5

department: Clinic for Gastroenterology, Hepatology and Infectiology

country: Germany

institute: Heinrich-Heine Universität Düsseldorf

summary: Hepatic encephalopathy (HE) is a frequent complication of liver cirrhosis and is seen as the clinical manifestation of a low grade cerebral edema associated with oxidative-nitrosative stress, however, comprehensive data on HE-associated molecular derangements in human brain are lacking. In the present study we used a whole human genome micro-array approach for gene expression profiling in post mortem brain samples from cirrhotic patients with or without HE and non-cirrhotic controls. Altered expression levels were found for a total of 1012 genes in liver cirrhotic patients without and with HE and HE-characteristic gene expression changes were identified. Genes with altered expression pattern in HE were related oxidative stress, microglia activation, inflammatory signalling pathways, cellular proliferation and apoptosis. Despite an up-regulation of genes associated with microglia activation, pro-inflammatory cytokine mRNA profiles remained unchanged in the brain of patients with liver cirrhosis and HE as compared to controls. Interestingly, many genes counteracting pro-inflammatory signalling and inflammatory cytokine expression were up-regulated in the cerebral cortex of patients with liver cirrhosis and HE. It is concluded that pathogenetic mechanisms of HE deduced from cell culture and animal experiments, such as oxidative stress, altered Zn2+-homeostasis and microglia activation also apply to human brain from cirrhotic patients with HE.  The study also revealed a not yet recognized increased expression of genes antagonizing pro-inflammatory signalling and inflammatory cytokine expression.

overall_design: The dataset comprises 19 samples divided into three sample groups each representing a certain liver disease condition of humans.

last: Görg

first: Hans

last: Bidmon

first: Dieter

last: Häussinger


title: EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation

status: Public on May 13 2013

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently suppress GC B-cell differentiation. Somatic mutations reinforce these physiological effects through enhanced silencing of EZH2 targets in B-cells, and in human B-cell lymphomas. Conditional expression of mutant EZH2 in mice induces GC hyperplasia and accelerated lymphomagenesis in cooperation with BCL2. GCB-type DLBCLs are mostly addicted to EZH2, regardless of mutation status, but not the more differentiated ABC-type DLBCLs, thus clarifying the therapeutic scope of EZH2 targeting.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA sequencing and H3K27me3 ChIP sequencing of human DLBCL cell lines and murine BCL1 cell line. RNA sequencing, H3K27me3 and H3K4me3 ChIP sequencing of B cells from de-identified human tonsills.

first: Wendy

last: Béguelin

first: Olivier

last: Elemento

first: Ari

last: Melnick


title: Adipose tissue gene expression associated with weight gain in kidney transplant recipients

status: Public on Oct 04 2013

city: Memphis

first: Ansley

last: Stanfill

state: TN

address: 920 Madison Ave

institute: University of Tennessee Health Sciences Center

summary:
The aim of this study was to investigate the association of gene expression profiles in subcutaneous adipose tissue with percent of total body weight change in 26 kidney transplant recipients.
Using multivariate linear regression analysis controlled for race and gender, expression levels of 1553 genes were significantly (p<0.05) associated with weight change.

overall_design: A secondary data analysis was done on a subgroup (n=26) of existing clinical and gene expression data from a larger prospective longitudinal study examining factors contributing to weight gain in transplant recipients.

first: Ann

middle: K

last: Cashion

first: Fridtjof

last: Thomas

first: Lijing

last: Xu

first: Thomas

last: Sutter

first: James

last: Eason

first: Mang

last: Ensell

first: Ramin

last: Homayouni


title: Cell transcriptional state alters genomic patterns of DNA double-strand break repair in human astrocytes

status: Public on Sep 01 2013

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: The misrepair of DNA double-strand breaks in close spatial proximity within the nucleus can result in chromosomal rearrangements that are important in the pathogenesis of hematopoietic and solid malignancies.  It is unknown why certain epigenetic states, such as those found in stem or progenitor cells, appear to facilitate neoplastic transformation.  Here we show that altering the transcriptional state of human astrocytes alters patterns of DNA damage repair from ionizing radiation at a gene locus-specific and genome-wide level.  Astrocytes induced into a reactive state exhibited increased DNA repair, compared to non-reactive cells, in actively transcribed chromatin domains after irradiation.  In mapping these sites of repair, we identified misrepair events and repair hotspots that were unique to each state.  The precise characterization of genomic regions susceptible to mutation in specific epigenetic transcriptional states provides new opportunities for addressing clonal evolution in solid cancers, particularly those where double-strand break induction is a cornerstone of management.

overall_design: Primary astrocyte cells were cultured to confluency and went through a linear monolyer scratch or no scratch.

first: Abdel

first: Raymund

middle: L

last: Yong

first: Weiwei

last: Wu


title: Rho transcription inhibitor CCG-1423 effect on PC-3 cells

city: Ann Arbor

first: Richard

middle: R.

last: Neubig

state: MI

address: 1150 W. Med. Ctr. Dr.

department: Pharmacology

institute: University of Michigan

summary: Analysis of serum starved PC-3 cells treated with CCG-1423, Latrunculin B, or the transcription elongation inhibitor DRB for 2 or 24 hours. Results provide insights to potential therapeutic approaches to cancer metastasis.

overall_design:
Twenty one samples in triplicate were analyzed and compared to the DMSO-treated control. The primary condition tested was the effect of the Rho-transcription pathway inhibitor, CCG-1423
As a biologically related control, the actin polymerization inhibitor, Latrunculin B, that also blocks Rho-stimulated gene transcription was tested.
As a control for non-specific transcription inhibition, DRB was used. All samples, 2-hr and 24-hr treated samples were compared to the 24-hr DMSO sample.

first: Chris

last: Evelyn

first: Susan

middle: M

last: Wade

first: Andrew

last: Haak

first: Craig

middle: N

last: Johnson

first: Elizabeth

last: Lawlor


title: The Cellular and Genomic Response of  Dopaminergic Neurons (N27) to Commericial “Capped” Nanosilver

status: Public on Jun 20 2013

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

summary: Global gene expression indicated that N27 neurons exposed to each nanoAg material (1.0 ppm, 18 hr) responded primarily to PVP coated nanoAg of both sizes with affected pathways largely associated with mitochondrial dysfunction (PVP 75 nm nanoAg) and Nrf-2 mediated oxidative stress (PVP 10 nm nanoAg) pathways.

overall_design: N27 rat dopaminergic neurons were exposed to non-cytoxic (0.5-5.0 ppm) concentrations of nanoAg of different sizes (10 nm, 75 nm) and “cappings” (PVP, citrate).

first: Bellina

last: Veronesi

first: Brian

last: Chorley

first: Beena

last: Valant

first: Stephen

last: Simmons

first: Alan

last: Tennant


title: An evaluation of analysis pipelines for DNA methylation profiling using the Illumina Human Methylation 450k platform

status: Public on Mar 14 2013

city: Stockholm

first: Francesco

last: Marabita

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

type: Methylation profiling by genome tiling array

summary: Abstract The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina Human Methylation 450k BeadChip is widely used to quantify DNA methylation, nevertheless the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate datasets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished datasets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. The blood samples included individuals with Multiple Sclerosis (MS). We evaluated the performance of different analysis pipelines and demonstrated that a) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; b) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); c) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive dataset suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450k arrays.

overall_design: DNA samples from peripheral blood or CD14+ monocytes of individuals with Multiple Sclerosis (MS), were included in the study. DNA methylation levels were profiled using Illumina 450K arrays. Specifically, 50 biological sample replicates from PB and 36 biological sample replicates from monocytes were randomly assigned to 8 BeadChips with technical replicates and processed in one run (a total of 96 DNA samples). Eight samples were technically replicated in pairs, while one sample was represented in a trio of replicates. Different analysis pipelines were compared, however, the file uploaded refers to the best scored. In our publication we used this one to make all analyses and conclusions.

first: David

last: Gomez-Cabrero

first: Jesper

last: Tegnér

first: Maja

last: Jagodic

first: Tomas

last: Ekström


title: Involvement of transcription factor early growth response 4 (EGR4) in lung cancer bone metastasis

status: Public on Apr 01 2013

city: Tokushima

first: Le

middle: Tan

last: Dat

state: Tokushima

address: 3-18-15, Kuramoto-cho

department: Genome center

country: Japan

institute: Tokushima university

summary: EGR4 (early growth response 4), a transcription factor, was previously shown to be up-regulated in lung cancer bone metastasis, compared with its expression in metastasis in other organs, using a multiorgan metastasis model of human small-cell lung cancer cells (SBC-5) in NK cell-depleted SCID mice (Kakiuchi S et al. Mol Cancer Res 2003). Here we show that EGR4 was essential for survival cancer cells, and migration ability. Next, in searching of downstream genes regulated by EGR4, we analyzed the changes in transcriptomes of SBC-5 cells at different time-points (24, 48 and 72 hr) when knockdown of EGR4 by siRNA. Lots of genes were identified either up-regulated or down-regulated in siEGR4 samples compared with control siRNA. Among these genes, there were genes with roles in metastasis or bone biology. The fact that EGR4 knockdown led to up-regulation or suppression of these genes also indicated dual roles of EGR4 in transcriptional regulation, which is consistent with previous reports: EGR4 may repress its own promoter (Zipfel PF et al. Biochim Biophys Acta. 1997) or activate certain inflammatory genes (Decker EL et al. Nucleic Acids Res. 2003; Wieland GD et al. J Cell Sci. 2005).

overall_design: SBC-5 cells were cultured at 1x10^6 cells/2 ml in 3.5 cm plate. After seeding 24 hours, cells were transfected either siEGR4 or siEGFP (for control), using Lipofectamin. At 24, 48 and 72 hours after starting of siRNA, we extracted RNA from these cells, and subjected these RNAs to microarray analysis. The labeling, amplification, hybridization and microarray data analysis were described previously (Dat LT et al. Int J Oncol, 40: 1455-1469 2012).

middle: T

first: Taisuke

last: Matsuo

first: Tetsuro

last: Yoshimaru

first: Takuya

last: Kuramoto

first: Masaki

last: Hanibuchi

first: Hisatsugu

last: Goto

first: Soji

last: Kakiuchi

first: Atsushi

last: Mitsuhashi

first: Yasuhiko

last: Nishioka

first: Saburo

last: Sone

first: Toyomasa

last: Katagiri


title: Medicago truncatula seed development at 21-19°C

status: Public on Jul 31 2013

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary: Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 21-19°C, 16h light. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

overall_design: Seeds of Medicago truncatula grown at 21-19°C were collected at different developmental stages, 15 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment, corresponding to the later developmental stage. For each repetition 8 hybridisation were made: 8DAP vs 11DAP, 14DAP vs 17DAP, 20DAP vs 23DAP, 26DAP vs 29DAP,32DAP vs 35DAP, 38DAP vs 41DAP, 44DAP vs Abs, DS (Rep1 and Rep2) vs 8DAP (Rep3 and Rep4). For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.

first: Karima

last: Righetti

first: Julia

last: Buitink


title: Lung tissues in systemic sclerosis have gene expression patterns unique to pulmonary fibrosis and pulmonary hypertension

status: Public on Jun 21 2013

city: Pittsburgh

first: Carol

last: Feghali-Bostwick

state: PA

address: MONF 628NW Pittsburgh

institute: University of Pittsburgh

summary: Objective: Pulmonary complications in systemic sclerosis (SSc), including pulmonary fibrosis (PF) and pulmonary arterial hypertension (PAH), are the leading cause of mortality. We compared the molecular fingerprint of SSc lung tissues and matching primary lung fibroblasts to those of normal donors, and patients with idiopathic pulmonary fibrosis (IPF) and idiopathic pulmonary arterial hypertension (IPAH).     Methods: Lung tissues were obtained from 33 patients with SSc who underwent lung transplantation. Tissues and cells from a subgroup of SSc patients with predominantly PF or PAH were compared to those from normal donors, patients with IPF, or IPAH. Microarray data was analyzed using Efficiency Analysis for determination of optimal data processing methods. Real time PCR and immunohistochemistry were used to confirm differential levels of mRNA and protein, respectively.    Results: We identified a consensus of 242 and 335 genes that were differentially expressed in lungs and primary fibroblasts, respectively. Enriched function groups in SSc-PF and IPF lungs included fibrosis, insulin-like growth factor signaling and caveolin-mediated endocytosis. Functional groups shared by SSc-PAH and IPAH lungs included antigen presentation, chemokine activity, and IL-17 signaling.     Conclusion: Using microarray analysis on carefully phenotyped SSc and comparator lung tissues, we demonstrated distinct molecular profiles in tissues and fibroblasts of patients with SSc-associated lung disease compared to idiopathic forms of lung disease. Unique molecular signatures were generated that are disease- (SSc) and phenotype- (PF vs PAH) specific. These signatures provide new insights into pathogenesis and potential therapeutic targets for SSc lung disease.


title: Overexpression of MtABI3 in transgenic Medicago truncatula roots

status: Public on Feb 14 2013

summary: ABI3 is a B3-domain transcription factor that acts as a master regulator of seed maturation. To identify genes that are regulated by this transcription factor in the model legume Medicago truncatula, Medicago hairy roots were generated using Agrobacterium rhizogenes transformed with the genomic sequence of the ABI3 gene of Medicago. Using the Medicago NimbleGen chip, a transciptomic analysis was performed to identify differentially expressed genes compared to the GUS expressed control.

overall_design: Two-condition experiment, GUS versus genomic. Biological replicates: 3 control (35S::GUS), 3 treatment (35S::Genomic ABI3 sequence), independently grown and harvested. One replicate per array.

first: David

last: Lalanne


title: Wee1 Inhibition sensitizes prostate cancer cells to Hsp90 inhibitor to activate the intrinsic apoptotic pathway

status: Public on Jan 10 2013

city: Bethesda

first: Mehdi

last: Mollapour

state: MD

address: 9000 Rockville Pike

department: UOB

institute: NCI-NIH

summary:
Heat shock protein 90 (Hsp90) is an essential evolutionarily conserved molecular chaperone in eukaryotes. Cancer cells rely on Hsp90 to chaperone activated oncoproteins, and its involvement in numerous signaling pathways makes it an attractive target for drug development. Surprisingly, however, the impact of Hsp90 inhibitors on cancer cells is most commonly cytostatic, and efforts to enhance the anti-tumor activity of Hsp90 inhibitors in the clinic remain a significant challenge. In this study, we show that dual inhibition of Wee1 tyrosine kinase and Hsp90 causes prostate cancer cells to undergo apoptosis. Gene-expression profiling revealed that induction of the intrinsic apoptotic pathway by this drug combination coincided with transcriptional down-regulation of Survivin and Wee1, an outcome not seen in cells treated separately with either agent. At the translational level, expression of these two proteins as well as activated Akt was completely abrogated. Similar results were obtained in prostate cancer xenografts. These data establish a novel therapeutic strategy to enhance the efficacy of Hsp90 inhibitors in prostate cancer, and they provide a mechanistic rationale for stimulating the pro-apoptotic activity of Hsp90 inhibitors.
In order to explore the mechanism underlying the enhanced cell death caused by Wee1 inhibitorII and 17-AAG combination, we performed microarray analysis using PC3 cells treated with Wee1 inhibitorII alone, 17-AAG alone, or the two drugs in combination.

overall_design: There are 12 samples in total. There are three experimental replicate. Samples 1, 5 and 9 are control (C)  (untreated PC3- prostate cancer cells). Samples 2, 6, and 10 are cells treated with Wee1 inhibitor II (W). Samples 3, 7, and 11 are treated with 17-AAG (A), (an Hsp90 inhibitor). Samples 4, 8, and 12 are treated with both Wee1 inhibitorII and 17-AAG (WA). Samples 5 was removed from our analysis due to weak signal.

first: Aki

last: Iwai

first: Dimitra

last: Bourboulia

last: Jensen-Taubman

first: Sunmin

last: Lee

first: Alison

last: Donnelly

first: Soichiro

last: Yoshida

first: Shinji

last: Tsutsumi

first: Naoto

last: Miyajima

first: Armine

last: Smith

last: Sun

first: Xiaolin

last: Wu

first: Brian

middle: S

last: Blagg

first: Jane

middle: B

last: Trepel

first: William

middle: G

last: Stetler-Stevenson

first: Len

last: Neckers


title: Host cell gene expression in Influenza A virus (A/Singapore/478/2009 (pH1N1)) infected A549 cells at 2, 4, 6, 8 and 10 hours post infection

status: Public on Jan 03 2013

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: Divison of Molecular and Cell Biology

institute: Nanyang Technological University

summary: We used the microarray data to analyze host cells response on A549 cells infected with Influenza A virus (A/Singapore/478/2009 (pH1N1))

overall_design: The Influenza A virus (A/Singapore/478/2009 (pH1N1)) infected A549 cells were harvested at 2, 4, 6, 8 and 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A virus (A/Singapore/478/2009 (pH1N1)) infection.

last: Sutejo

first: Hui

last: Chen

first: Boon

middle: H

last: Tan


title: Host cell gene expression in Influenza A/duck/Malaysia/F119/3/1997 (H5N3) infected MDCK cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on MDCK cells infected with A/duck/Malaysia/F119/3/1997(H5N3)

overall_design: A/duck/Malaysia/F119/3/1997(H5N3) infected MDCK cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F119/3/1997(H5N3) infection.


title: Host cell gene expression in Influenza A/WSN/33 (H1N1) infected MDCK cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on MDCK cells infected with A/WSN/33 (H1N1)

overall_design: A/WSN/33 (H1N1) infected MDCK cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/WSN/33 (H1N1) infection.


title: Host cell gene expression in Influenza A/duck/Malaysia/F189/07/2004 (H5N2) infected MDCK cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on MDCK cells infected with A/duck/Malaysia/F189/07/2004(H5N2)

overall_design: A/duck/Malaysia/F189/07/2004(H5N2) infected MDCK cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F189/07/2004(H5N2) infection.


title: Host cell gene expression in Influenza A/WSN/33 (H1N1) infected MDCK cells at 2, 4 and 6 hours post infection

overall_design: A/WSN/33 (H1N1) infected MDCK cells were harvested at 2, 4, and 6 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/WSN/33 (H1N1) infection.


title: Host cell gene expression in Influenza A/Duck/Malaysia/01 (H9N2) infected MDCK cells at 2, 4, 6, 8 and 10 hours post infection

summary: We used the microarray data to analyze host cells response on MDCK cells infected with A/Duck/Malaysia/01 (H9N2)

overall_design: A/Duck/Malaysia/01 (H9N2) infected MDCK cells were harvested at 2, 4, 6, 8 and 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/Duck/Malaysia/01 (H9N2) infection.


title: Host cell gene expression in Influenza A/duck/Malaysia/F189/07/2004 (H5N2) infected CEF cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on CEF cells infected with A/duck/Malaysia/F189/07/2004(H5N2)

overall_design: A/duck/Malaysia/F189/07/2004(H5N2) infected CEF cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F189/07/2004(H5N2) infection.


title: Host cell gene expression in Influenza A/duck/Malaysia/F118/08/2004 (H5N2) infected CEF cells at 2, 4, 6, 8, and 10 hours post infection

summary: We used the microarray data to analyze host cells response on CEF cells infected with A/duck/Malaysia/F118/08/2004(H5N2)

overall_design: A/duck/Malaysia/F118/08/2004(H5N2) infected CEF cells were harvested at 2, 4, 6, 8 and 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F118/08/2004(H5N2) infection.


title: Host cell gene expression in Influenza A/WSN/33 (H1N1) infected CEF cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on CEF cells infected with A/WSN/33 (H1N1)

overall_design: A/WSN/33 (H1N1) infected CEF cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/WSN/33 (H1N1) infection.


title: Host cell gene expression in Influenza A/duck/Malaysia/F119/3/1997 (H5N3) infected CEF cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on CEF cells infected with A/duck/Malaysia/F119/3/1997(H5N3)

overall_design: A/duck/Malaysia/F119/3/1997(H5N3) infected CEF cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F119/3/1997(H5N3) infection.


title: Host cell gene expression in Influenza A/duck/Malaysia/F189/07/2004 (H5N2) infected A549 cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on A549 cells infected with A/duck/Malaysia/F189/07/2004(H5N2)

overall_design: A/duck/Malaysia/F189/07/2004(H5N2) infected A549 cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F189/07/2004(H5N2) infection.


title: Host cell gene expression in Influenza A/duck/Malaysia/F118/08/2004 (H5N2) infected A549 cells at 2, 4, 6, 8, and 10 hours post infection

summary: We used the microarray data to analyze host cells response on A549 cells infected with A/duck/Malaysia/F118/08/2004(H5N2)

overall_design: A/duck/Malaysia/F118/08/2004(H5N2) infected A549 cells were harvested at 2, 4, 6, 8 and 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F118/08/2004(H5N2) infection.


title: Host cell gene expression in Influenza A/Duck/Malaysia/01 (H9N2) infected CEF cells at 2, 4, 6, 8 and 10 hours post infection

summary: We used the microarray data to analyze host cells response on CEF cells infected with A/Duck/Malaysia/01 (H9N2)

overall_design: A/Duck/Malaysia/01 (H9N2) infected CEF cells were harvested at 2, 4, 6, 8 and 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/Duck/Malaysia/01 (H9N2) infection.


title: Host cell gene expression in Influenza A/duck/Malaysia/F119/3/1997 (H5N3) infected A549 cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on A549 cells infected with A/duck/Malaysia/F119/3/1997(H5N3)

overall_design: A/duck/Malaysia/F119/3/1997(H5N3) infected A549 cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F119/3/1997(H5N3) infection.


title: A comprehensive gene expression analysis of resistance formation upon metronomic cyclophosphamide therapy

status: Public on Jan 23 2013

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: Resistance formation is one of the major hurdles in cancer therapy. Metronomic anti-angiogenic treatment of xenografted prostate cancer tumors in SCID mice with cyclophosphamide (CPA) results in the appearance of resistant tumors. To investigate the complex molecular changes occurring during resistance formation, we performed a comprehensive gene expression analysis of the resistant tumors in vivo. We observed a multitude of differentially expressed genes, e.g., PASD1, ANXA3, NTS or PLAT, when comparing resistant to in vivo passaged tumor samples. Furthermore, tumor cells from in vivo and in vitro conditions showed a significant difference in target gene expression. We assigned the differentially expressed genes to functional pathways like axon guidance, steroid biosynthesis and complement and coagulation cascades. Most of the genes were involved in anti-coagulation, indicating its possible importance. Upregulation of anti-coagulatory ANXA3 and PLAT and downregulation of PLAT inhibitor SERPINA were validated by qPCR. In contrast, coagulation factor F3 was upregulated, accompanied by the expression of an altered gene product. These findings give insights into the resistance mechanisms of metronomical CPA treatment suggesting an important role of anti-coagulation in resistance formation.

overall_design: 4 cell lines * 2 treatments * 4 replicates = 32 arrays. One sample (C3-T) was identified as an outlier and was omitted from further analysis; it is not included here.

first: Rebekka

last: Kubisch

first: Lilja

last: Meissner

first: Helmut

last: Blum

first: Michael

last: Günther

first: Andreas

last: Roidl

first: Ernst

last: Wagner


title: Host cell gene expression in Influenza A/duck/Malaysia/F118/08/2004 (H5N2) infected MDCK cells at 2, 4, 6, 8, and 10 hours post infection

summary: We used the microarray data to analyze host cells response on MDCK cells infected with A/duck/Malaysia/F118/08/2004(H5N2)

overall_design: A/duck/Malaysia/F118/08/2004(H5N2) infected MDCK cells were harvested at 2, 4, 6, 8 and 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/duck/Malaysia/F118/08/2004(H5N2) infection.


title: Host cell gene expression in Influenza A/WSN/33 (H1N1) infected A549 cells at 10 hour post infection

summary: We used the microarray data to analyze host cells response on A549 cells infected with A/WSN/33 (H1N1)

overall_design: The A/WSN/33 (H1N1) infected A549 cells were harvested at 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/WSN/33 (H1N1) infection.


title: Host cell gene expression in Influenza A/Duck/Malaysia/01 (H9N2) infected A549 cells at 2, 4, 6, 8 and 10 hours post infection

summary: We used the microarray data to analyze host cells response on A549 cells infected with A/Duck/Malaysia/01 (H9N2)

overall_design: The A/Duck/Malaysia/01 (H9N2) infected A549 cells were harvested at 2, 4, 6, 8 and 10 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/Duck/Malaysia/01 (H9N2) infection.


title: Host cell gene expression in Influenza A/WSN/33 (H1N1) infected CEF cells at 2, 4, 6, and 8 hours post infection

overall_design: A/WSN/33 (H1N1) infected CEF cells were harvested at 2, 4, 6 and 8 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/WSN/33 (H1N1) infection.


title: Oxygen regulation of immunogenicity in primary human glioma cells

status: Public on Jan 01 2013

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Dendritic Cell (DC) vaccination is a powerful approach for cancer immunotherapy that has recently obtained regulatory approval, and tumor lysate-pulsed DC vaccines are being tested in clinical trials. Tumor cell lysates (TLs) are often generated from cells cultured in atmospheric oxygen (~20% O2), which is roughly four-fold higher than that of the tumor in situ. We analyzed the expression patterns of glioma cells cultured in 5% Oxygen, 20% Oxygen and the primary tumors which the cell cultures were derived.

overall_design: Total RNA from primary resected glioma tumors or tumor cells cultured in in either 5% oxygen or 20% oxygen


title: Identification of microRNA responsive to pathogen infection in sugarcane

status: Public on Nov 30 2012

city: Rio de Janeiro

first: Paulo

last: Ferreira

address: Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária

country: Brazil

institute: Universidade Federal do Rio de Janeiro

type: Non-coding RNA profiling by high throughput sequencing

summary: Sugarcane is a very efficient crop to produce ethanol. In recent years, extensive efforts have been made in order to increase sugarcane yields. To reach this goal, molecular biology tools have been used comprehensively, identifying genes, pathways and genetic polymorphisms. However, some important molecular components, like microRNAs, have not been deeply investigated. MicroRNAs are an important class of endogenous small, noncoding RNAs that regulate gene expression at the post-transcription level and play fundamental roles in diverse aspects of animal and plant biology. Plant genomes harbor numerous miRNA genes that regulate many protein-coding genes to influence key processes ranging from development, metabolism, and responses to abiotic and biotic stresses. There is wide range of pests and diseases that affect sugarcane, yet the mechanisms that regulate pathogen interactions with sugarcane have not been thoroughly investigated. To gain knowledge on the physiological responses to pathogens mediated by microRNAs in sugarcane, we screened the transcriptoma of sugarcane plants infected with Acidovorax avenae subsp avenae, the causal agent of red stripe disease in sugarcane, and detected several microRNAs modulated in the presence of the pathogen. Furthermore, we validated with qPCR a number of microRNA expression patterns observed by bioinformatics analysis. In addition, we observed high expression levels of several star microRNAs, in numbers larger than the mature microRNAs in some cases. Interestingly, sof-miR408 was consistently down-regulated in the presence of several pathogens, but not in the presence beneficial microbes. This result indicates that the sugarcane senses pathogenic or beneficial microorganisms differentially and triggers specific epigenetic regulatory mechanisms accordingly

overall_design: Screenning of sRNA transcriptome of sugarcane plants infected with Acidovorax avenae subsp avenae after seven days

first: Cristian

middle: A

last: Rojas

first: Flávia

last: Thiebaut

first: Clícia

last: Grativol

first: Barbara

last: Peixoto

first: Mariana

last: Carnavale-Bottino

first: Laurent

last: Farinelli

first: Adriana

last: Hemerly


title: Host cell gene expression in Influenza A/WSN/33 (H1N1) infected A549 cells at 2, 4 and 6 hours post infection

first: Richard

last: Sugrue

overall_design: The A/WSN/33 (H1N1) infected A549 cells were harvested at 2, 4 and 6 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host response to Influenza A/WSN/33 (H1N1) infection.

last: Sutejo

first: Hui

last: Chen

first: Boon

last: Tan


title: Expression from early pre-hematopoietic progenitors from mouse embryo

status: Public on Jul 03 2012

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary: Hematopoietic Stem Cells (HSC) are originated during embryonic development from endothelial-like cells located in the ventral side of the dorsal aorta around day E10-12 of murine development. This region is called AGM for Aorta/Gonad/Mesonephros and refers to the tissues around the hemogenic aorta. Cells that emerge from the endothelium and show hematopoietic traits can be distinguished by the expression of the c-kit receptor and finally acquire the CD45 marker.

overall_design: AGM regions were obtained from E11.5 embryos by dissection and digested with 0.1% collagenase. Cells were stained with anti-CD31, anti-ckit, anti-CD45 and anti-Ter119 antibodies. Sorting of the CD31+CD45-Ter119- population was performed, and cells were separated into c-kit+ and c-kit-. 3 replicates each of c-kit+ and c-kit- cells.

first: Jordi

last: Guiu

first: Cristina

last: Ruiz-Herguido

first: LLuis

last: Espinosa


title: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 4)

status: Public on Jun 30 2012

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

institute: National Institute for Occupational Safety and Health

summary: A proper understanding of the mechanisms underlying crystalline silica-induced pulmonary toxicity has implications in the management and potential prevention of the adverse health effects associated with silica exposure including silicosis, cancer and several auto-immune diseases. Human lung type II epithelial cells and rat lungs exposed to crystalline silica were employed as experimental models to determine global gene expression changes in order to understand the molecular mechanisms underlying silica-induced pulmonary toxicity. The differential gene expression profile induced by silica correlated with its toxicity in the A549 cells. The biological processes perturbed by silica exposure in the A549 cells and rat lungs, as identified by the bioinformatic analysis of the differentially expressed genes, demonstrated significant similarity. Functional categorization of the differentially expressed genes identified cancer, cellular movement, cellular growth and proliferation, cell death, inflammatory response, cell cycle, cellular development, and genetic disorder as top-ranking biological functions perturbed by silica exposure in the A549 cells and rat lungs. The involvement of oxidative stress and apoptosis in the silica-induced pulmonary toxicity was confirmed by ELISA and confocal microscopy analysis, respectively, of the silica-exposed A549 cells. Results of our study, in addition to confirming several previously identified molecular targets and mechanisms involved in silica toxicity, identified novel molecular targets and mechanisms potentially involved in silica-induced pulmonary toxicity. Further investigations, including those focused on the novel molecular targets and mechanisms identified in the current study, may result in a better management and, possibly, reduction and/or prevention of the potential adverse health effects associated with crystalline silica exposure.

overall_design: 10 samples were analyzed in this experiment. Exponentially growing human lung epithelial cells (1.5x10^5 cells) were cultured in 6-well cell culture plates. When the cells were approximately 70% confluent, they were treated with crystalline silica (0 or 200 µg/ml) in serum-free medium. Following 2 hours of culturing at 37oC, total RNA was isolated for gene expression studies.

first: Christina

last: Umbright

first: Shengqio

last: Li

first: Michael

last: Kashon

first: Joseph

last: Pius


title: Effect of NO-sulindac treatment on hypoxic prostate cancer cells

status: Public on Dec 01 2012

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

summary: The hypoxia response contributes to radio and chemo-resistance in cancer cells. Our previous work has shown that the nitric oxide donating non-steroidal anti-inflammatory drug (NO-NSAID) NO-sulindac is a potent inhibitor of the hypoxia response in prostate cancer cells and leads to increased susceptibilty to radiation. In this study we used microarrays to investigated the global impact of NO-sulindac on the hypoxia response in prostate cancer cells with a view to determining the mechanism of action.

overall_design: PC3 hormone-insensitive prostate cancer cells were grown under normoxic or hypoxic conditions and treated with NO-sulindac, unnitrated sulindac or vehicle control. Global gene expression in response to treatment was examined using microarrays and the bioconductor software suite. Gene set enrichment analysis (GSEA), Gene ontology (GO) analysis and pathway analysis were used to examine the biological impact of treatments.


title: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: DNA methylation contributes to natural human variation

status: Public on Jul 22 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

type:
Methylation profiling by array
Third-party reanalysis

summary: DNA methylation analysis using the Infinium HumanMethylation450 BeadChip platform (Illumina) of 96 Caucasian American, 96 Han Chinese American and 96 African American LCL samples determined differences in terms of differentially methylated sites. Importantly, the observed differences were confirmed in primary blood samples of 10 healthy Caucasian, 10 African American (GSE36064) and 10 Asian individuals. Genes associated to differentially methylated site suggest an influence of DNA methylation on phenotype differences. Interestingly, methylation differences could be partially traced back to genetic polymorphisms.

sample_organism:
Pan troglodytes
Homo sapiens
Pan troglodytes schweinfurthii
Pan troglodytes troglodytes
Pan troglodytes verus

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

first: Holger

last: Heyn

first: Sebastian

last: Salama


title: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 3)

overall_design: 10 samples were analyzed in this experiment. Exponentially growing human lung epithelial cells (1.5x10^5 cells) were cultured in 6-well cell culture plates. When the cells were approximately 70% confluent, they were treated with crystalline silica (0 or 50 µg/ml) in serum-free medium. Following 6 hours of culturing at 37oC, total RNA was isolated for gene expression studies.


title: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (rat lungs)

overall_design: 20 samples were analyzed in this experiment. RNA from rat lung samples was isolated for gene expression studies. Rats were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days) or air. Lung gene expression profiling was performed using rat lung samples, 8 for silica exposed and 12 for air-exposed controls at 0 weeks post-exposure time period.


title: The Global Transcriptional Response of Fission Yeast to Hydrogen Sulfide

status: Public on Jun 15 2012

city: Shanghai

first: Xu

last: Jia

address: Yi Xue Yuan Road 138

department: School of Pharmacy, Institute of Biomedical Science

institute: Fudan University

summary:
Hydrogen sulfide (H2S) as an important gasotransmitter has fundamental roles in human diseases. The cellular effect of H2S has received lots of attention recently. H2S can affect ion channels, transcription factors and kinase in mammals. The mechanism of cellular effect of H2S is not completely understood.
We used fission yeast as a model organism to study the global transcriptional profile in response to H2S by microarray.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: The wild type S. pombe cells were grown in liquid medium to OD600=0.5. Then the cells were treated with or without 50μM of NaHS (Sigma, St Louis, MO, USA) for 30 min at 30℃.Total RNA was extracted from cells using a hot phenol method.The microarray experiments including RNA purification, cDNA probe preparation, hybridization, washing, scanning, image analysis, normalization and data processing were performed by Shanghai Biochip Co., Ltd. as described in the Affymetrix GeneChip_Expression Analysis Technical Manual. Three biological repeats were performed for the microarray experiments.

first: Weizhi

last: He

first: Alastair

middle: I

last: Murchie

first: Dongrong


title: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 5)

overall_design: 10 samples were analyzed in this experiment. Exponentially growing human lung epithelial cells (1.5x10^5 cells) were cultured in 6-well cell culture plates. When the cells were approximately 70% confluent, they were treated with crystalline silica (0 or 200 µg/ml) in serum-free medium. Following 24 hours of culturing at 37oC, total RNA was isolated for gene expression studies.


title: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 2)

overall_design: 20 samples were analyzed in this experiment. Exponentially growing human lung epithelial cells (1.5x10^5 cells) were cultured in 6-well cell culture plates. When the cells were approximately 70% confluent, they were treated with crystalline silica (0, 100, 200 and 400 µg/ml) in serum-free medium. Following 6 hours of culturing at 37oC, total RNA was isolated for gene expression studies.


title: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 1)

overall_design: 10 samples were analyzed in this experiment. Exponentially growing human lung epithelial cells (1.5x10^5 cells) were cultured in 6-well cell culture plates. When the cells were approximately 70% confluent, they were treated with crystalline silica (0 or 800 µg/ml) in serum-free medium. Following 6 hours of culturing at 37oC, total RNA was isolated for gene expression studies.


title: Erythroid-Specific Transcriptional Changes in PBMCs from Pulmonary Hypertension Patients

status: Public on Apr 30 2012

city: baltimore

first: chris

last: cheadle

address: 5200 Eastern Ave

department: SOM

institute: JHU

summary:
The hypothesis tested in this study was that chronic exposure of PBMCs to a hypertensive environment in remodeled pulmonary vessels would be reflected by specific transcriptional changes in these cells.
The transcript profiles of PBMCs from 30 idiopathic pulmonary arterial hypertension patients (IPAH), 19 patients with systemic sclerosis without pulmonary hypertension (SSc), 42 scleroderma-associated PAH patients (SSc-PAH), and 8 patients with SSc complicated by interstitial lung disease and PH (SSC-PH-ILD) were compared to the gene expression profiles of PBMCs from 41 healthy individuals.

overall_design: Gene expression is compared at a global level using total RNA from BPMC for pateints and controls using the Illumina microarray platform.

first: Chris

last: Cheadle

first: Berger

last: Alan


title: Gene expression of Tg 3×FLAG-Nanos2-deltaN10 mouse male gonad

status: Public on Apr 01 2012

city: Mishima

first: Rie

last: Saba

state: Shizuoka

address: Yata 1111

department: Genetic Strain Research Center

institute: National Institute of Genetics

summary: To investigate the biochemical function of NANOS2, we performed expression microarray analysis of the embyornic male gonad of Nanos2 hetero, Nanos2 KO, and Nanos2 KO_Tg 3×FLAG-tagged Nanos2-ΔN10, which is truncated form of Nanos2 in the N-terminal region, transgenic mice.

overall_design: 3×FLAG-tagged Nanos2-ΔN10 protein function was validated by rescue experiment in the Nanos2-null male gonad of mouse embryo at E14.5. Biological duplicates were examined at each genotype, Nanos2 hetero, Nanos2 KO, and Nanos2 KO_Tg 3×FLAG-tagged Nanos2-ΔN10 for each experiment.

first: Atsuhi

last: Suzuki

first: Yumiko

last: Saga


title: A Molecular Taxonomy of Urothelial Carcinoma

status: Public on May 24 2012

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

institute: Lund Univeristy

summary:
Even though urothelial cancer (UC) is the fourth common tumor type among males, progress in treatment development has been deficient. Pathological assessment provides the urologists with only a broad classification, complicated by frequent disagreement among pathologist and the co-existence of different grading systems. Consequently, there is a great need for an objective, reproducible and biologically relevant classification system to make treatment more efficient. In the present investigation we present a molecular taxonomy for UC stratification based on integrated genomics.
We used gene expression profiles from 308 UC to define seven molecular subtypes using step-by-step partitions and a bootstrap approach. Results were validated in three independent and publically available data sets. The subtypes differ significantly with respect to expression of cell cycle genes, of receptor tyrosine kinases particularity FGFR3, ERBB2 (HER2), and EGFR, of an FGFR3 associated gene expression signature, of cytokaratins, and of cell adhesion genes. The subtypes also differ significantly with respect to FGFR3, PIK3CA, and TP53 mutations. The expression of key proteins was validated by IHC on TMA. A further inspection indicated that the subtypes could be reduced to four major types of UC; Urobasal/D-driven, Genomically unstable/E-driven, Evolved urobasal, and Basal/SCC like, with characteristic and highly divergent molecular phenotypes. We show that the molecular subtypes cut across pathological classification and that tumors classified as one subtype maintain their characteristic molecular phenotype irrespective of pathological stage and grade. Available data from the Drugbank database and the Cochrane central registry of controlled trials indicate that susceptibility to specific drugs is more likely to be associated with the molecular stratification than with pathological classification.
The presented molecular taxonomy stratifies UC into subtypes with distinct molecular phenotypes and biological properties. We anticipate that the molecular taxonomy will be a useful tool in future clinical investigations.

overall_design:
Total RNA from fresh-frozen resection samples of 308 urothelial carcinomas was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip arrays (Illumina Inc) at the SCIBLU Genomics Centre at Lund University Sweden (http://www.lth.se/sciblu).

Supplementary files:
GSE32894_non-normalized_308UCsamples.txt file = Raw intensity values for 308 UC (urothelial tumor) samples subjected only to background correction.
GSE32894_reps_normals_preprocess*.txt files = Descriptive details and non-normalized data for technical replicates and normal samples that were used only in the preprocessing of the data.

This dataset partly overlaps with Series GSE32549. Names of the overlapping sample names are the same, but the title of each sample is unique to the hybridization.

last: Sjödahl

first: Martin

last: Lauss

first: David

last: Lindgren

first: Mattias

last: Höglund


title: Transcriptional and Proteomic Analysis of the Aspergillus fumigatus ΔprtT Protease-Deficient Mutant

status: Public on Nov 29 2011

city: Tel-Aviv

first: Nir

last: Osherov

address: Ramat Aviv Campus

department: Medical Microbiology and Immunology

country: Israel

institute: Tel-Aviv University

summary: Aspergillus fumigatus is the most common opportunistic mold pathogen of humans, causing invasive diseases in immunocompromised patients. In these patients, the fungus can invade the lungs and other organs, causing severe damage. Penetration of the pulmonary epithelium is a key step in the infectious process. A. fumigatus produces extracellular proteases to degrade the structural barriers of the host. The A. fumigatus transcription factor PrtT controls the expression of multiple secreted proteases. PrtT shows similarity to the fungal Gal4-type Zn(2)-Cys(6) DNA-binding domain of several transcription factors. In this work, we further investigate the function of this transcription factor by performing a transcriptional and a proteomic analysis of the ΔprtT mutant. The microarray analysis revealed several unexpected findings. In addition to a decrease in protease expression, expression of genes involved in iron uptake and ergosterol synthesis was dramatically decreased in the ΔprtT mutant. A second finding of interest is that deletion of PrtT resulted in the upregulation of four secondary metabolite clusters, including genes for the biosynthesis of pseurotin A. The proteomic analysis identified 15 proteins secreted by the A. fumigatus WT strain when grown on protein-rich skim-milk medium. Of these, the ΔprtT mutant expressed reduced levels of ALP1 protease, TppA tripeptidyl peptidase and a serine peptidase and increased levels of FAD-oxygenase, AspF chitosinase, EglC endoglucanase and Bgt1 glucanosyltransferase compared to the WT strain. This report highlights the complexity of gene regulation by PrtT.

overall_design: Three biological repeats of dual channel comparative transcriptome analysis between ΔprtT Protease-Deficient Mutant and wild type.

last: Amar

first: Shelly

last: Hagag

first: William

last: Nierman

first: Ron

last: Shamir


title: Liver protective effects of white button mushroom (Agaricus Bisporus)

status: Public on Mar 01 2012

city: Duarte

first: Noriko

last: Kanaya

address: 1500 East Duarte

department: Cancer Biology

institute: Beckman Research Institute at City of Hope

summary: To study the mechanism of protective effect by White Button Mushroom (WBM) for Nonalcoholic Fatty Liver Disease (NAFLD) in ovariectomized mice (model for postmenopausal women).

overall_design: The ovariectomized mice were fed WBM diet for 3 month, sacrificed to harvest liver. 4 mice for control diet and 4 mice for WBM diet.

first: Shiuan

last: Chen