title: Differences between CD44+/CD24- and CD44-/CD24+ subpopulation of immortalized human mammary epithelial cells

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary:
CD44+/CD24- subpopulation of normal and cancerous breast epithelial cells are suggested to have stem cell properties. The goal of this study was to identify gene expression differences between CD44+/CD24- and CD44-/CD24+ subpopulation of cells from a same cell lines. We selected MCF-10A cells, which are immortalized derived from a fibrocystic breast disease. These cells are immortalized but not transformed and express basal cell markers.
Cells were from a single sort but plated into four 100 mm plates. RNA was prepared from each plate separately for the analysis.

overall_design: Comparison of gene expression between 2 groups ( CD44+/CD24- and CD44-/CD24+) 4 replicates each.

first: Harikrisha

first: Poornima

last: Bhat-Nakshatri

first: Howard

middle: J

last: Edenberg


title: In-transit extremity melanoma II

status: Public on Feb 26 2010

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

country: USA

institute: Duke University Medical Center

summary:
An evaluation of biopsies from patients with in-transit extremity melanoma who have been treated with melphalan in the setting of isolated limb infusion
Gene expression profiles were obtained from 52 lesions across 28 patients and evaluated for expression values that correlated with response to melphalan isolated limb infusion

overall_design: Chemotherapy response analysis: complete response - CR; partial response - PR; stable disease - SD; progressive disease - PD. 52 samples.

middle: K

first: Douglas

middle: S

last: Tyler


title: expression data from pediatric primary intracranial germ cell tumor

city: Taipei

first: Yu Hsuan

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

summary: Intracranial pediatric germ cell tumors (GCTs) have different histological differentiations, prognosis and clinical behaviors. Prognosis of patients with germinoma and mature teratoma is good, while patients with other types of GCTs, termed as nongerminomatous malignant germ cell tumors (NGMGCTs), require more extensive drug and irradiation treatment regimen. The mechanisms underlying different prognosis of various GCT subgroups remain elusive. We presented a distinct mRNA profile correlating with GCT histological differentiation and prognosis.

overall_design: 13 central nervous system GCT cases with different histological subtypes are subjected to transcriptome analysis. The histological subtypes are germinoma, mixed GCT of germinoma and mature teratoma , immature teratoma , mixed GCTs of NGMGCTs category,  yolk sac tumor, immature teratoma, and embryonal carcinoma.

first: Yu-Hsuan

first: Hsei-Wei

last: Wang


title: Altered gene expression in normal breast and ovarian epithelial cells from BRCA1 and BRCA2 mutation carriers

status: Public on Mar 01 2010

city: philadelphia

first: suraj

last: peri

state: PA

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

summary:
Early genetic changes during cancer initiation may provide targets for agents that delay, or even prevent, cancer.  We hypothesized that cells bearing a single inherited “hit” in a tumor suppressor gene express an altered mRNA repertoire that may identify targets for measures that could delay or even prevent progression to carcinoma.  Here, we report on the transcriptomes of primary breast and ovarian epithelial cells cultured from BRCA1 and BRCA2 mutation-carriers and controls.  Our comparison analyses identified multiple changes in gene expression, in both tissues for both mutations that were independently validated by real-time RT-PCR analysis.  Several of the differentially expressed genes had been previously proposed as cancer markers including, mammaglobin in breast cancer and serum amyloid in ovarian cancer.  These findings demonstrate that heterozygosity for a mutant tumor suppressor gene can alter the expression profiles of phenotypically normal epithelial cells in a gene-specific manner, and that these detectable effects of “one-hit” represent early molecular changes in tumorigenesis that may serve as novel biomarkers of cancer risk and as targets for chemoprevention
Using affymetrix U133 plus2 chips, we compare the transcriptome of primary breast and ovarian epithelial cultures derived from subjects predisposed to cancer, bearing monoallelic BRCA1 or BRCA2 mutations, with corresponding cultures from control individuals that do not have mutations.

overall_design: For both breast and ovarian samples, epithelial cell cultures were generated from 6 subjects that have both BRCA1 or BRCA2 mutations and 6 subjects that do not have mutations. Affymetrix U133 plus 2 chips were used to profile the transcriptome of BRCA1 or BRCA2 mutant and wild type.  In total 36 chips were used to profile 18 samples from both breast and ovary, 6 mutant (BRCA1 and BRCA2) and 6 wild type.

first: Alfonso

last: Bellacosa

first: Suraj

last: Peri

first: Alfred

last: Knudson Jr


title: Ectopic Myc expression

status: Public on Feb 25 2010

city: Baltimore

first: Chi

middle: V.

last: Dang

state: MD

address: 720 Rutland Ave, Ross 1032

department: Medicine

institute: Johns Hopkins University, School of Medicine

summary:
Ectopic Myc Expression in P493-6 B-cells at three levels:
High Myc, Low Myc and No Myc

overall_design: High Myc, Low Myc and No Myc expressions


title: Expression data from CD34+ hematopoietic progenitor cells

status: Public on Feb 24 2010

city: Bethesda

first: Amrita

last: Ghosh

address: 49 Convent Drive, 3B-07

department: Genetics and Molecular Biology

institute: National Human Genome Research Institute (NHGRI), NIH

summary:
Gene transfer vectors based on gamma-retroviruses target actively transcribing genes indicating that the cellular gene expression profile can be predictive of their integration pattern.  Therefore, different culture conditions leading to different transcriptional activity may translate into differences in the profile of targeted genes in cells transduced with these vectors.  Recent data from two gene therapy trials for SCID-X1 conducted in France and the UK suggested that small differences between in vitro stimulation conditions could explain the disparity in the frequency of common integrations sites observed in the two studies.
We set out to compare the transcriptional activity of human CD34+ bone marrow-derived cells cultured under the French (S1) or British (S2) culture conditions.

overall_design: RNA was extracted from human CD34+ bone marrow-derived cells from 3 donors stimulated under the French (S1) conditions (X-vivo 10, 4% fetal calf serum, 300 ng/ml stem cell factor [SCF], 100 ng/ml thrombopoietin [TPO], 60 ng/ml interleukin-3 [IL3], and 300 ng/ml Flt3 ligand [FL]) and under the British (S2) conditions (X-vivo 10, 1% human serum albumin, 300 ng/ml SCF, 100 ng/ml TPO, 20 ng/ml IL3, and 300 ng/ml FL).  Extracted RNA was amplified with random hexamer primer reverse transcription strategy.  Lastly, amplified RNA was labeled and hybridized to HG U133 Plus 2.0 Affymetrix microarrays.  Four time points during cytokine stimulation were analyzed, corresponding to 0 hr and three transduction time points in the French and British SCID-X1 gene therapy clinical trials (48 h, 72 h, and 96 h).  Samples are referred to as donor, stimulation condition, and time point (e.g., Don 1 S1-48 for donor 1 of 3, S1 stimulation conditions, and 48 h after stimulation was begun).

first: Ghosh

last: Amrita

first: Wang

last: Chenwei

first: Elkalhoun

last: Abdel

first: Fabio

last: Candotti


title: Transcription profile in patients with acyanotic or cyanotic Tetralogy of Fallot

status: Public on Feb 23 2010

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

country: United Kingdom

institute: University of Bristol

summary: To determine cardiac transcription profiles, we collected myocardial samples immediately after institution of cardiopulmonary bypass from acyanotic or cyanotic Tetralogy of Fallot patients undergoing corrective surgery. The transcriptional profile of the mRNA in these samples was measured with gene array technology.

overall_design: Myocardial samples were collected, immediately after institution of cardiopulmonary bypass from acyanotic or cyanotic Tetralogy of Fallot patients undergoing corrective surgery.


title: Transcription profile in patients with cyanotic Tetralogy of Fallot

summary: To determine cardiac transcription profile in cyanotic Tetralogy of Fallot patients, we collected myocardial samples immediately after institution of cardiopulmonary bypass from cyanotic Tetralogy of Fallot patients undergoing corrective surgery. The transcriptional profile of the mRNA in these samples was measured with gene array technology.

overall_design: Myocardial samples were collected, immediately after institution of cardiopulmonary bypass from cyanotic Tetralogy of Fallot patients undergoing corrective surgery.

middle: T

first: Myriam

last: Cherif

first: EmmaJ

last: Jenkins

first: Amir

last: Mokhtari

first: Gianni

middle: D

last: Angelini

first: Massimo

last: Caputo


title: Comparison of gene expression data between wild-type and DM1-affected undifferentiated hES cells.

city: Evry

first: Genevieve

last: PIETU

address: 1 rue de l'Internationale

country: France

institute: INSERM

summary:
Analysis of genes that were differentially expressed in mutant VUB03_DM1 as compared to controls VUB01 and SA01 undifferentiated hES cells

Embryonic stem (ES) cell lines provide, theoretically, unlimited access to any needed amount of any specific cell phenotype of an organism, due to their unique capacities at indefinite self-renewal and pluripotency (Smith 2001; Trounson 2006). These properties allow using the progeny of ES cell lines to model human pathologies (Martinat, Shendelman et al. 2004; Lerou and Daley 2005; Ben-Nun and Benvenisty 2006). In particular, human ES cell lines derived from embryos characterized as gene-carriers following pre-implantation genetic diagnosis (PGD) for any one of major monogenic diseases (Pickering, Minger et al. 2005; Mateizel, De Temmerman et al. 2006) may be considered as perfect cellular replicas of those diseases, as they exhibit the exact genotypes associated to them. Here, we confirm this hypothesis by demonstrating that the cell progeny of an ES cell line derived from an embryo with myotonic dystrophy type 1 (DM1) displayed the morphological stigma associated to the expression of the mutant gene –so-called intranuclear foci- as well as abnormal alternate splicing of the insulin receptor, a characteristic feature of DM1. Further differential transcriptomic analysis of the DM1 gene-carrying cells with phenotypically similar populations from native ES cell lines revealed abnormal expression of 89 genes, among which 48 were down-regulated and 39 over-expressed. This study demonstrates that DM1, though a disease with relatively late clinical onset, is associated with expression of genetic defects early on during development. It underlines the value of PGD-derived ES cell lines as a tool to decipher molecular mechanisms of genetic diseases.
Ben-Nun, I. F. and N. Benvenisty (2006). Human embryonic stem cells as a cellular model for human disorders. Mol Cell Endocrinol 252(1-2): 154-9.
Lerou, P. H. and G. Q. Daley (2005). Therapeutic potential of embryonic stem cells. Blood Rev 19(6): 321-31.
Martinat, C., S. Shendelman, et al. (2004). Sensitivity to oxidative stress in DJ-1-deficient dopamine neurons: an ES- derived cell model of primary Parkinsonism. PLoS Biol 2(11): e327.
Mateizel, I., N. De Temmerman, et al. (2006). Derivation of human embryonic stem cell lines from embryos obtained after IVF and after PGD for monogenic disorders. Hum Reprod 21(2): 503-11.
Pickering, S. J., S. L. Minger, et al. (2005). Generation of a human embryonic stem cell line encoding the cystic fibrosis mutation deltaF508, using preimplantation genetic diagnosis. Reprod Biomed Online 10(3): 390-7.
Smith, A. G. (2001). Embryo-derived stem cells: of mice and men. Annu Rev Cell Dev Biol 17: 435-62.
Trounson, A. (2006). The production and directed differentiation of human embryonic stem cells. Endocr Rev 27(2): 208-19.
Keywords: disease state analysis

overall_design: Two controls cell lines (VUB01 and SA01) and one mutant cell line (VUB03_DM1), with three biological replicats for each


title: Comparison of gene expression data between wild-type and DM1-affected cells

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

overall_design: Refer to individual Series


title: Comparison of gene expression data between wild-type and DM1-affected Neural Precursors Cells (NPC)

summary:
Analysis of genes that were differentially expressed in mutant VUB03_DM1 as compared to controls VUB01 and SA01 Neural Precursor cells

Embryonic stem (ES) cell lines provide, theoretically, unlimited access to any needed amount of any specific cell phenotype of an organism, due to their unique capacities at indefinite self-renewal and pluripotency (Smith 2001; Trounson 2006). These properties allow using the progeny of ES cell lines to model human pathologies (Martinat, Shendelman et al. 2004; Lerou and Daley 2005; Ben-Nun and Benvenisty 2006). In particular, human ES cell lines derived from embryos characterized as gene-carriers following pre-implantation genetic diagnosis (PGD) for any one of major monogenic diseases (Pickering, Minger et al. 2005; Mateizel, De Temmerman et al. 2006) may be considered as perfect cellular replicas of those diseases, as they exhibit the exact genotypes associated to them. Here, we confirm this hypothesis by demonstrating that the cell progeny of an ES cell line derived from an embryo with myotonic dystrophy type 1 (DM1) displayed the morphological stigma associated to the expression of the mutant gene –so-called intranuclear foci- as well as abnormal alternate splicing of the insulin receptor, a characteristic feature of DM1. Further differential transcriptomic analysis of the DM1 gene-carrying cells with phenotypically similar populations from native ES cell lines revealed abnormal expression of 89 genes, among which 48 were down-regulated and 39 over-expressed. This study demonstrates that DM1, though a disease with relatively late clinical onset, is associated with expression of genetic defects early on during development. It underlines the value of PGD-derived ES cell lines as a tool to decipher molecular mechanisms of genetic diseases.
Ben-Nun, I. F. and N. Benvenisty (2006). Human embryonic stem cells as a cellular model for human disorders. Mol Cell Endocrinol 252(1-2): 154-9.
Lerou, P. H. and G. Q. Daley (2005). Therapeutic potential of embryonic stem cells. Blood Rev 19(6): 321-31.
Martinat, C., S. Shendelman, et al. (2004). Sensitivity to oxidative stress in DJ-1-deficient dopamine neurons: an ES- derived cell model of primary Parkinsonism. PLoS Biol 2(11): e327.
Mateizel, I., N. De Temmerman, et al. (2006). Derivation of human embryonic stem cell lines from embryos obtained after IVF and after PGD for monogenic disorders. Hum Reprod 21(2): 503-11.
Pickering, S. J., S. L. Minger, et al. (2005). Generation of a human embryonic stem cell line encoding the cystic fibrosis mutation deltaF508, using preimplantation genetic diagnosis. Reprod Biomed Online 10(3): 390-7.
Smith, A. G. (2001). Embryo-derived stem cells: of mice and men. Annu Rev Cell Dev Biol 17: 435-62.
Trounson, A. (2006). The production and directed differentiation of human embryonic stem cells. Endocr Rev 27(2): 208-19.
Keywords: disease state analysis

overall_design: Two controls hES-derived NPC (VUB01 and SA01) and one mutant hES-derived NPC (VUB03_DM1), with three biological replicats for each


title: Changes in gene expression of Imr90 cells with age and senescence under 3% and 20% oxygen growth conditions

city: Blacksburg

first: Bernd

middle: Robert

last: Stab II

state: VA

address: Life Sciences 1 Washington Str

department: Biochemistry

institute: Virginia Tech

summary:
Senescent is an irreversible form of cell cycle arrest initiated by damaged cell constituents and subsequent pro-oncogenic signaling.  Replicative senescence in vitro can be considered a model for human aging.  When fibroblasts are cultured under atmospheric oxygen conditions of 20%, typical of normal tissue culture procedure, fibroblasts generally reach their replicative capacity at 50-60 population doublings (PDs).  When fibroblasts are cultured under normal physiological oxygen conditions of 3%, PDs increase about 30% relative to atmospheric levels.  Hence while oxygen is a requirement for normal aerobic respiration, it can contribute to the total amount of oxidative stress to which cells are exposed to, leading to a long-term adverse effect in vitro.  Inasmuch, cultures maintained under hyperoxic and hypoxic conditions provide a convenient model system for assessing the relationship between oxygen/oxidative stress and senescence.
We used microarrays to profile the changes in global gene expression during aging and senescence of Imr90 cells under growth oxygen conditions of 3% and 20%.

overall_design: Imr90 cells at various population doubling timepoints (young, old, and senescent) grown seperately under 3 and 20% oxygen growth conditions were selected for RNA extraction and hybridization on Affymetrix microarrays.  Timepoints from cells grown under 3% and 20% oxygen conditions were age matched via population doublings to ensure accurate cross sample comparison.

middle: R

last: Stab

first: Richard

middle: F

last: Helm


title: Molecular Classification of AIDS-Related Lymphomas

city: Omaha

first: Karen

last: Deffenbacher

state: NE

address: 987660 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary:
Gene expression profiling (GEP) of ARL patient samples was done to determine whether gene expression signatures derived from HIV- lymphomas retained their ability to molecularly classify HIV+ lymphomas. The GEP-based predictors robustly classified ARL tumors, distinguishing molecular Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), as well as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) molecular subtypes of DLBCL.
Gene expression profiles were used to identify coordinately regulated gene sets and pathways that differ between HIV+ and HIV- lymphomas of corresponding molecular subtype.

overall_design: Frozen tumor biopsies were obtained from 20 HIV-positive patients with an AIDS-defining lymphoma. Cases were ascertained at the University of Nebraska Medical Center and through the NCI AIDS and Cancer Specimen Resource tumor bank. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on 17 ARL cases.  Details of all 20 HIV-positive patients can be found in the supplementary file below.

middle: E

first: Wing

middle: C

last: Chan


title: E. coli K-12 hha hns: pCA24N-hnsK57N vs pCA24N-hns biofilm

status: Public on Feb 22 2010

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: The global regulator, H-NS, controls genes related to stress response, biofilm formation, and virulence expression by recognizing the curved DNA and silences gene transcription acquired from lateral gene transfer.  Here, we rewired H-NS to control biofilm formation using protein engineering.  One H-NS variant, H-NS K57N was obtained to reduce biofilm formation 10-fold compared to H-NS wild-type. Whole-transcriptome analysis (BW25113 hha hns / pCA24N-hns K57N vs. BW25113 hha hns / pCA24N-hns) revealed that H-NS K57N represses biofilm formation through the interactinon with other nucleoid proteins, Cnu and StpA.  Remarkably, H-NS K57N enhanced the excision of defective prophage Rac while H-NS wild-type represses it, and H-NS controlled only Rac excision among E. coli prophages.  These results imply that the repression of Rac excision is one of the silencing manner for foreign genes by H-NS.  Also, the prophage excision not only led to the change of biofilm formation but also resulted in cell lysis through the expression of toxin protein HokD with reduced viability, which are important for cell physiology in response to the change of environmental conditions.  Hence, H-NS regulatory system may be evolved easily with specialized functions in terms of biofilm formation, prophage control, and cell lysis.

overall_design: For the whole transcriptome study of BW25113 hha hns / pCA24N-hns K57N versus BW25113 hha hns / pCA24N-hns, cells were grown in 250 mL LB containing 1 mM IPTG for 7 h with 10 g of glass wool (Corning Glass Works, Corning, N.Y.) in 1 L Erlenmeyer flasks to form a robust biofilm.  Biofilm cells were obtained by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C, and RNALater buffer® (Applied Biosystems, Foster City, CA) was added for RNA stabilization and protection during the RNA preparation steps.  Total RNA was isolated from biofilm cells.  The E. coli GeneChip Genome 2.0 array (Affymetrix, Lot# 4059655) containing 10,208 probe sets for four E. coli strains (MG1655, CFT073, O157:H7-Sakai, and O157:H7-EDL933) was used for DNA microarray.  cDNA synthesis, fragmentation, and hybridizations were performed.

first: SeokHoon

last: Hong

first: Xiaoxue

last: Wang


title: Time course expression data from early Bovine embryo, Human embryo, and Mouse embryo

status: Public on Feb 20 2010

city: Urbana

first: Dan

last: Xie

state: IL

address: 3215 Digital Computer Lab, MC-278, 1304 W. Springfield Ave

department: Bioengineering

institute: University of Illinois at Urbana and Champaign

summary:
The process of early development of mammals is subtly and accurately controlled by the regulation networks of embryo cells. Time course expression data measured at different stages during early embryo development process can give us valuable information by revealing the dynamic expression patterns of genes in genome wide scale. In this study, bovine embryo expression data were generated  at oocyte, one cell stage, two cell stage, four cell stage, eight cell stage, sixteen cell stage, morula, and blastocyst; Human embryo expression data were generated at one cell stage, two cell stage, four cell stage, eight cell stage, morula, and blastocyst; Mouse embryo expression data were generated at one cell stage, two cell stage, four cell stage, eight cell stage, morula, and blastocyst.

Keywords: time course

sample_organism:
Homo sapiens
Bos taurus
Mus musculus

platform_organism:
Homo sapiens
Bos taurus
Mus musculus

overall_design: Bovine, Human, and Mouse embryos were harvested at successive stage from oocyte to blastocyste. Total RNAs were extracted, amplified and hybridized onto Affymetrix microarrays.


title: Transcription profile in patients with acyanotic Tetralogy of Fallot

summary: To determine cardiac transcription profile in acyanotic Tetralogy of Fallot patients, we collected myocardial samples immediately after institution of cardiopulmonary bypass from acyanotic Tetralogy of Fallot patients undergoing corrective surgery. The transcriptional profile of the mRNA in these samples was measured with gene array technology.

overall_design: Myocardial samples were collected, immediately after institution of cardiopulmonary bypass from acyanotic Tetralogy of Fallot patients undergoing corrective surgery.

first: Emma


title: Exposure of SKGT4 and HET-1A cell lines to deoxycholic acid (DCA)

city: Dublin

first: Shane

middle: P

last: Duggan

address: TCD Health Sciences Building, St James Hospital,

department: Clinical Medicine

country: Ireland

institute: Institute of Molecular Medicine


title: Metabolic and transcriptional response to cofactor perturbations in Escherichia coli

status: Public on Feb 18 2010

city: Göteborg

first: Goutham

middle: N

last: Vemuri

address: Kemivagen 10

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Towards this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli to lower the level of NADH and ATP, respectively. We used a systems biology approach to study the response to these perturbations by measuring global transcription profiles, metabolic fluxes and the metabolite levels. We integrated information from the different measurements using network-based methods to identify high-scoring networks in a global interaction map that included protein interactions, transcriptional regulation and metabolism. The results revealed that the action of many global transcription factors such as ArcA, Fnr, CRP and IHF commonly involved both NADH and ATP while others were influential only in one of the pertubations. In general, overexpressing NADH oxidase invokes response in widespread aspects of metabolism involving the redox cofactors (NADH and NADPH) while ATPase has a more focused response to restore ATP level by enhancing proton translocation mechanisms and repressing biosynthesis. Interestingly, NADPH played a key role in restoring redox homeostasis through the concerted activity of isocitrate dehydrogenase and UdhA transhydrogenase. We present a reconciled network of regulation that illustrates the overlapping and distinct aspects of metabolism controlled by NADH and ATP. Our study contributes to the general understanding of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli.

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

overall_design: The experimental design involves measuring transcriptome in three strains (in triplicates) of E. coli during mid-exponential phase of growth on MOPS media supplemented with glucose. The three strains are:  1. REF: MG1655/pAK80 (MG1655 transformed with a plasmid with no insert)  2. NOX: MG1655/pAC06 (MG1655 transformed with a plasmid containing NADH oxidase)  3. ATPase: MG1655/pCP41 (MG1655 transformed with a plasmid containing soluble ATPase)  RNA was extracted using Qiagen RNeasy kit and processes according to Affymetrix® guidelines. The quality of RNA was verified using BioAnalyzer (Agilent BioSystems) and the electropherograms are shown in the file “RNA quality.pdf”. Samples 1-3 are REF, Samples 4-6 are NOX and Samples 7-9 are ATPase. The fragmented cRNA was hybridized to E. coli Genome 2.0 chips.


title: Array-based bioinformatic analysis on pediatric primary central nervous system germ cell tumors

first: Yu Hsuan

last: Wu

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


title: Expression data of human decidual NK cells from gravid uteri and NK cells from cycling endometrium

city: Boston

first: Hernan

last: Kopcow

state: MA

address: 330 Brookline Ave RN359

institute: Beth Israel  Deaconess  Medical Center

summary: Human NK cells from the decidua basalis of gravid uteri (dNK) and from  cycling endometrium  (eNK) of women undergoing hysterectomy were isolated and compared by gene expression profiling using  Affymetrix  microarrays with probes representing ~47,400 transcripts. Substantial differences indicate that these two types of NK cells represent distinct subsets.

overall_design: Freshly isolated NK cells were obtained by FACS sorting. 4 dNK and 5 eNK samples were obtained form independent donors. dNK cells were isolated from the decidua basalis of first trimester placentas and sorted  as CD3-, CD16-, CD56+ cells. eNK cells  were  obtained from non-affected regions  of cycling endometrium   of donor women undergoing   hysterectomy and were sorted as CD45+, CD56+, CD3-  cells . The preliminary patient diagnoses included genital prolapse, fibroids, cervical dysplasia, or menorrhagia. All cycling endometrium  samples were from the secretory phase  of the cycle with exception of sample eNK_S6 that was from the  proliferative phase.

first: Charles

last: Sentman

first: Jack

middle: L

last: Strominger


title: Expression data of LCM-dissected retina layers

status: Public on Feb 19 2010

city: Basel

first: Jacek

last: Krol

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: We have analyzed the transcript expression in different LCM-dissected cell layers isolated from mouse retinas adapted to light or dark in order to identify transcripts potentially targetted by retinal microRNAs which are regulated in response to light treatment

overall_design: Retinas were isolated from adult mice adapted to light or dark following LCM dissection of photoreceptors (ONL+OS/IS), inner nuclear layer (INL), inner plexiform layer (IPL), ganglion cell layer (GCL) and whole retina samples. Experiments were performed in duplicates. Total RNA was extracted and hybridization on Affymatrix array was performed.

first: Volker

last: Busskamp

first: Botond

last: Roska

first: Witold

last: Filipowicz


title: Exposure of squamous esophageal cell line HET-1A to deoxycholic acid (DCA)

summary: The involvment of bile acids such as deoxycholic acid (DCA) in gastro-esophageal reflux disease and subsequent Barrett’s metaplsia has been postulated. This study examines gene expression induced by exposure to DCA in esophageal cells and may be utilised in cross-comparisions with data derived from gene expression studies of Barrett’s esophagus and associated adenocarcinoma. Additionally this study may be used to assess divergence in response to bile acids by comparisons with similar study performed in SKGT4 barrett''s assocaited adenocarcinoma cell line.

overall_design: HET-1A cells were exposed to 300um DCA over 24 hours in duplicate experiments including matched timepoint controls


title: Effects of Cigarette Smoke on the Human Oral Mucosal Transcriptome

status: Public on Feb 15 2010

city: New York

first: Zeynep

middle: H.

last: Gumus

state: NY

address: 1300 York Ave

department: Physiology and Biophysics

institute: Cornell University

summary:
40 current smokers and 40 age- and gender- matched never smokers underwent buccal biopsies.The study had four objectives: (a) to define the effects of smoking on the transcriptome of oral epithelial cells; (b) to determine if any of the effects of tobacco smoke on the transcriptome are gender-dependent; (c) to compare the effects of tobacco smoke exposure on the transcriptome in oral v. bronchial epithelium and (d) to identify agents with the potential to suppress the effects of tobacco smoke on the transcriptome.
We used microarrays to provide new insights into the carcinogenic effects of tobacco smoke and offer insights that may prove useful in developing preventive strategies.

overall_design: 40 never smokers (<100 cigarettes per lifetime) and 40 active smokers (≥ 15 pack year exposure) were recruited. Subjects were age- and gender-matched. Eligible subjects were healthy volunteers recruited from the community and the hospital. Subjects were excluded if they had gross evidence of oral inflammation a history of heavy alcohol consumption or recent use of nonsteroidal anti-inflammatory drugs or other anti-inflammatory medications. The study was approved by the Weill Cornell Medical College Institutional Review Board and the Clinical and Translational Research Center. All subjects provided written informed consent for participation. After topical anestesia 5-mm punch biopsies were obtained from grossly normal appearing buccal mucosa. One sample was excluded from the study based on a quality measure leaving 79 for analysis and deposited here.

middle: H


title: Silencing of C2TA reveals the autonomous role of medullary thymic epithelial cells in central CD4 T cell tolerance

status: Public on Feb 11 2010

city: Munich

first: Maria

last: Hinterberger

address: Goethestr. 31

department: Institut für Immunologie

country: Germany

institute: LMU

summary:
[original title] Tissue-specific silencing of C2TA reveals the autonomous role of medullary thymic epithelial cells in central CD4 T cell tolerance.

Medullary thymic epithelial cells (mTECs) serve an essential function in central tolerance through expressing peripheral tissue-antigens. Because these antigens may be transferred to and presented by Dendritic Cells, it is unclear whether, besides being an ‘antigen reservoir’, mTECs also fulfill a critical antigen presenting cellfunction. We found that reducing MHC class II-levels on mTECs through transgenic expression of a C2TA-specific ‘designer miRNA’ resulted in an enlarged polyclonal CD4 single-positive compartment. Less CD4+ thymocytes specific for model-antigens expressed in mTECs were deleted, whereas more antigen-specific Foxp3+ regulatory T cells (Treg) emerged. Our data suggest a substantial autonomous contribution of mTECs to both dominant and recessive mechanisms of CD4 T cell tolerance and support an avidity model of Treg development versus deletion.

overall_design: Three conditions: Wild-type, C2TA knockdown, and C2TA knock-out. For each condition three replicates and in total 9 arrays.

first: Martin

last: Aichinger

first: David

last: Voehringer

first: Olivia

last: Prazeres da Costa

first: Reinhard

last: Hoffmann

first: Ludger

last: Klein


title: Expression data from healthy controls and early stage CRC patient's tumor

city: Singapore

first: Yi

last: Hong

email: hong.yi@sgh.com.sg, fbap8570@yahoo.com

address: Outram Road

department: Colorectal Surgery

country: Singapore

institute: Singapore General Hospital

summary:
Metastasis is the major cause of cancer mortality. Up to 25% of early stage sporadic colorectal cancer (CRC) patients succumb to metastasis after curative surgery.
We used microarrays to detail  gene expression and identified a metastasis-prone signature for early stage CRC.
Keywords: RNA expression

overall_design: Tumors from age- and ethnicity-matched 70 patients and biopsies from 12 healthy controls were used. We aimed to find a metastasis-prone signature for early stage CRC by genome-wide expression profiling of age- and ethnicity-matched patients and healthy controls using the Affymetrix U133 Plus 2 array.


title: Expression data from human ovarian cancer cells induced by IL-6 and CNTO328

first: Zhenfeng

last: Duan

address: 100 Fruit St

institute: Massachusetts General Hospital

summary: The SKOV-3 and Caov-3 ovarian cancer cell lines where seeded onto the 100mm cell culture plate for overnight.  The cells were then incubated with IL-6 (30ng/ml) alone for one hour or pre-treated with siltuximab for four hours and then treated with IL-6 for one hour. Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 in the first and most comprehensive whole human genome expression array.  This array completes coverage of the whole human Genome with over 47,000 transcripts.   The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. GeneSifter was used to analyze the microarray data (http://www.genesifter.net/web/). Fold change in expression between sensitive and resistant cell lines was evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

overall_design: Evalutate the effect of CNTO328 on IL-6 induced gene expression in ovarian cancer cells

first: Yuqi

last: Guo


title: Exposure of Barrett's associated adenocarcinoma cell lines SKGT4 to deoxycholic acid (DCA)

first: Shane

last: Duggan

summary: The involvment of bile acids such as deoxycholic acid (DCA) in gastro-esophageal reflux disease and subsequent Barrett’s metaplsia has been postulated. This study examines gene expression induced by exposure to DCA in esophageal cells and may be utilised in cross-comparisons with data derived from gene expression studies of Barrett’s esophagus and associated adenocarcinoma.

overall_design: SKGT4 cells were exposed to 300um DCA over 24 hours in duplicate experiments including matched timepoint controls. RNA samples were taken at 4, 8, 12 and 24 hours from DCA (DCA) exposed and resting (REST) timepoint controls.


title: Salivary Transcriptomic and Proteomic Biomarkers for Breast Cancer Detection

city: Los Angeles

first: Lei

last: Zhang

state: CA

address: 10833 Le Conte Ave., CHS 73-029

institute: UCLA Dental Research Institute

summary:
A sensitive assay to identify biomarkers that can accurately diagnose the onset of breast cancer using non-invasively collected clinical specimens is ideal for early detection. In this study, we have conducted a prospective sample collection and retrospective blinded validation (PRoBE design) to evaluate the performance and translational utilities of salivary transcriptomic and proteomic biomarkers for the non-invasive detection of breast cancer. The Affymetrix HG U133 Plus 2.0 Array and 2D-DIGE were used to profile transcriptomes and proteomes in saliva supernatants respectively. Significant variations of salivary transcriptomic and proteomic profiles were observed between breast cancer patients and healthy controls. Eleven transcriptomic biomarker candidates and two proteomic biomarker candidates were selected for a preclinical validation using an independent sample set. Transcriptomic biomarkers were validated by RT-qPCR and proteomic biomarkers were validated by quantitative protein immunoblot. Eight mRNA biomarkers and one protein biomarker have been validated for breast cancer detection, yielding ROC-plot AUC values between 0.665 and 0.959. This report provides proof of concept of salivary biomarkers for the non-invasive detection of breast cancer. The salivary biomarkers’ discriminatory power paves the way for a PRoBE-design definitive validation study.

Keywords: Salivary biomarker, Breast cancer, Early detection, Salivary transcriptome, Salivary proteome

overall_design: This study, which was approved by the UCLA and Cedars-Sinai Medical Center Institutional Review Boards (#06-07-043 and #3870, respectively), started sample collection in February 2007. The sample collection followed the PRoBE principle (prospective specimen collection). The saliva bank for breast cancer project at the UCLA Dental Research Institute in collaboration with Cedars Sinai Medical Center has collected 200 saliva samples since 2007 with all subjects recruited from the Saul and Joyce Brandman Breast Cancer Center. Of these, 113 samples, including 41 breast cancer patients and 72 healthy control individuals, were selected for the discovery and validation phase of this study. Inclusion criteria of cancer patients consisted of a confirmed diagnosis of breast cancer. Exclusion criteria of cancer patients included therapy/surgery and/or a diagnosis of other malignancies within 5 years prior to saliva collection. Exclusion criteria of control patients included a diagnosis of any malignancies within 5 years prior to saliva collection. Written informed consents and questionnaire data sheets were obtained from all patients who agreed to serve as saliva donors. Unstimulated saliva samples were consistently collected, stabilized, and preserved as previously described. The sample supernatants were reserved at -80 C prior to assay. This study consisted of a discovery phase, followed by an independent preclinical validation phase. Of the 113 samples, 10 breast cancer samples and 10 healthy control samples were chosen for the discovery phase. All breast cancer cases are invasive ductal carcinoma (IDC), the most common type of breast cancer. Biomarkers identified from the discovery studies were first verified using the discovery sample set. An independent sample set, including 31 breast cancer patients and 62 healthy control subjects, was used for the biomarker validation phase.

first: Hua

last: Xiao

first: Scott

last: Karlan

first: Hui

last: Zhou

first: Jenny

last: Gross

first: Ziding

last: Feng

last: Elashoff

last: Akin

first: Xinmin

last: Yan

last: Chia

first: Beth

last: Wong


title: Expression data from EBER1-overexpressing Hodgkin lymphoma cell lines KM-H2 and L428

status: Public on Feb 13 2010

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

institute: National Taiwan University

summary: Epstein-Barr virus (EBV)- encoded RNAs (EBERs) are aboundance in all EBV lantency, it was  found that EBERs may contribute to the oncogenesis. To study the role of EBV-encoded small RNAs (EBERs) in Hodgkin lymphoma, we transfected Hodgkin lymphoma cell lines, KMH2 and L428, with EBER1 and screen with microarrays to verify what is the possible role of the EBER1 in Hodgkin lymphoma.

overall_design: We deliver EBER1-expressing plasmid (p9362-EBER1) or control plasmid (p9362) into the Hodgkin lymphoma, KM-H2 and L428,  and selected with GENETICIN to establish 4 stable clones: the EBER1-positive cell lines were named KE & LE, and the vector-only cell lines were named K9 & L9. We performed the microarray to show the effect of EBER1 on Hodgkin lymphoma. The data of KE was compare with K9 and LE was compare with L9.

first: Ting-Yun

last: Liu

first: Mi-Shin

last: Huang

first: Fai-Yun

last: Lo


title: Expression data from embryonic stem cells (ESCs) and re-derived cell lines

status: Public on Feb 10 2010

city: Tianjin

first: Yueying

last: Li

address: 288 Nanjing Road

country: China

institute: Institute of Hematology and Blood Diseases Hospital

summary:
Our recovered cell lines, derived from bone marrow (BM), expressed all markers known for embryonic stem cells and were able to differentiate into three germ layers although germ line transmission is yet to be further defined.
No germline transmission of the re-derived cell lines indicated their pluripotency decreased. We used gene array to compare the gene-expression of ESCs and re-derived cell lines.

overall_design: We derived two cell lines, Sorted (D10) and No.2 (D5) cell lines, from bone marrow at two different time points after C57OG2 ESCs (oGFP+ ESCs) transplantation.


title: p120ctn mouse expression data

city: Philadelphia

first: Anil

middle: K

last: Rustgi

address: 415 Curie Blvd, 600 CRB

department: Medicine-Gastroenterology

institute: University of Pennsylvania

summary:
Loss of p120ctn results in dysplasia and invasive cancer in the mouse esophagus and squamous forestomach.
We used microarray expression analysis to identify gene expression changes in pre-tumorigenic esophagus samples and in tumors of the squamous forestomach.

overall_design: L2-Cre/p120 flox/flox tissue samples were compared to L2-Cre tissues.  Epithelium was separated from whole tissue samples by dispase treatment and used for analysis.

first: Douglas

middle: B

last: Stairs


title: Comparison of gene expression data between wild-type and DM1-affected Mesodermal Precursors Cells (MPC)

first: Genevieve

last: PIETU

address: 1 rue de l'Internationale

institute: INSERM

summary:
Analysis of genes that were differentially expressed in mutant VUB03_DM1 as compared to controls VUB01 and SA01 Mesodermal Precursors Cells.

Embryonic stem (ES) cell lines provide, theoretically, unlimited access to any needed amount of any specific cell phenotype of an organism, due to their unique capacities at indefinite self-renewal and pluripotency (Smith 2001; Trounson 2006). These properties allow using the progeny of ES cell lines to model human pathologies (Martinat, Shendelman et al. 2004; Lerou and Daley 2005; Ben-Nun and Benvenisty 2006). In particular, human ES cell lines derived from embryos characterized as gene-carriers following pre-implantation genetic diagnosis (PGD) for any one of major monogenic diseases (Pickering, Minger et al. 2005; Mateizel, De Temmerman et al. 2006) may be considered as perfect cellular replicas of those diseases, as they exhibit the exact genotypes associated to them. Here, we confirm this hypothesis by demonstrating that the cell progeny of an ES cell line derived from an embryo with myotonic dystrophy type 1 (DM1) displayed the morphological stigma associated to the expression of the mutant gene –so-called intranuclear foci- as well as abnormal alternate splicing of the insulin receptor, a characteristic feature of DM1. Further differential transcriptomic analysis of the DM1 gene-carrying cells with phenotypically similar populations from native ES cell lines revealed abnormal expression of 89 genes, among which 48 were down-regulated and 39 over-expressed. This study demonstrates that DM1, though a disease with relatively late clinical onset, is associated with expression of genetic defects early on during development. It underlines the value of PGD-derived ES cell lines as a tool to decipher molecular mechanisms of genetic diseases.
Ben-Nun, I. F. and N. Benvenisty (2006). Human embryonic stem cells as a cellular model for human disorders. Mol Cell Endocrinol 252(1-2): 154-9.
Lerou, P. H. and G. Q. Daley (2005). Therapeutic potential of embryonic stem cells. Blood Rev 19(6): 321-31.
Martinat, C., S. Shendelman, et al. (2004). Sensitivity to oxidative stress in DJ-1-deficient dopamine neurons: an ES- derived cell model of primary Parkinsonism. PLoS Biol 2(11): e327.
Mateizel, I., N. De Temmerman, et al. (2006). Derivation of human embryonic stem cell lines from embryos obtained after IVF and after PGD for monogenic disorders. Hum Reprod 21(2): 503-11.
Pickering, S. J., S. L. Minger, et al. (2005). Generation of a human embryonic stem cell line encoding the cystic fibrosis mutation deltaF508, using preimplantation genetic diagnosis. Reprod Biomed Online 10(3): 390-7.
Smith, A. G. (2001). Embryo-derived stem cells: of mice and men. Annu Rev Cell Dev Biol 17: 435-62.
Trounson, A. (2006). The production and directed differentiation of human embryonic stem cells. Endocr Rev 27(2): 208-19.
Keywords: disease state analysis

overall_design: Two controls hES-derived MPC (VUB01 and SA01) and one mutant hES-derived MPC (VUB03_DM1), with three biological replicats for each


title: Expression analysis of lymphoblast cells lines in Parkinson's disease

status: Public on Feb 04 2010

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Genome-wide transcriptome analysis of expression changes in EBV transformed cell lines from the Coriell Cell Repository in Parkinson and Control subjects.

overall_design: 8 Parkinson cell lines versus 8 control cell lines.

first: Richard

last: Davis


title: Expression analysis of dissected GPi in Parkinson's disease

summary: Genome-wide transcriptome analysis of expression changes in Globus Pallidus interna (GPi) from Parkinson's disease brain tissue versus control brain tissue.

overall_design: Post-mortem brain expression analysis performed in 10 PD brain samples and 10 control brain samples.

first: Peter

last: Kim

first: Yanli

last: Zhang-James


title: SOX2 is a new oncogene activated by the recurrent 3q26.3 amplifications in lung Squamous Cell Carcinoma

status: Public on Feb 09 2010

city: ILLKIRCH

first: Thomas

last: Hussenet

address: 1 rue Laurent Fries

department: Cancer Biology Department

institute: IGBMC

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Stanislas

last: du Manoir


title: Minicircle-derived iPS cells - Affymetrix Data

status: Public on Feb 01 2010

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

type:
Expression profiling by array
Third-party reanalysis

summary: Owing to the risk of insertional mutagenesis, viral transduction has been increasingly replaced by nonviral methods to generate induced pluripotent stem (iPS) cells. We report the use of ‘minicircle’ DNA, a vector type that is free of bacterial DNA and capable of high expression in cells. Here we use a single minicircle vector to generate transgene-free iPSCs from adult human adipose stem cells. (Note: Our Nature Methods publication included analysis of array data from GSM378832 (Foreskin),  GSM378833-GSM378838 (JT-iPSC), and GSM378817-GSM378820 (H1, H7, H9, H13, H14) in conjunction with this series).

overall_design: Total RNA from human adipose stem cells (hASC, n = 3 replicate samples),  hASC-derived iPS cells using lentiviral factors (lenti-iPSC, n = 3 replicate samples), and minicircle-derived human iPS cells (mc-iPSC, n = 3 subclones from adipose tissue of three individual patients) was hybridized to nine Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays.

first: Fangjun

last: Jia

first: Ning

last: Sun


title: Stage II and stage III colorectal cancer

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Distant metastasis is the major causes of death in colorectal cancer (CRC) patients. In order to identify genes influencing the prognosis of patients with CRC, we compared gene expression in primary tumors with and without distant metastasis using an oligonucleotide microarray. We also examined the expression of the candidate gene in 100 CRC patients by quantitative real-time reverse transcription PCR and studied the relationship between its expression and the prognosis of patients with CRC. As a result, we identified MUC12 as a candidate gene involved in metastasis processes by microarray analysis. Quantitative real-time reverse transcription PCR showed that MUC12 expression was significantly lower in cancer tissues than in adjacent normal tissues (P < 0.001). In stage II and stage III CRC, patients with low expression showed worse disease-free survival (P = 0.038). Multivariate analysis disclosed that MUC12 expression status was an independent prognostic factor in stage II and stage III CRC (relative risk, 9.532; 95% confidence interval, 2.303-41.905; P = 0.002).   This study revealed the prognostic value of MUC12 expression in CRC patients. Moreover, our result suggests MUC12 expression is a possible candidate gene for assessing postoperative adjuvant therapy for CRC patients.

overall_design: Total of 111 microarray datasets (77 for LCM samples, and 17 pairs for homogenized samples from tumor and adjacent tissues) were normalized using robust multi-array average (RMA) method under R 2.6.2 statistical software together with BioConductor package, as described previously. Then, the gene expression levels were log2-transformed, and 62 control probe sets were removed for further analysis.  In order to identify a set of genes associated with development of metastatic recurrence, we performed Wilcoxon rank-sum test for gene expression differences of 54,613 probe sets between recurrence and non-recurrence groups. Similarly, Wilcoxon singed-rank test was conducted to select genes which showed significant expression difference between tumor and adjacent tissue. Then, we selected a set of genes that satisfied both of above two criteria.

first: Takatoshi

last: Matsuyama

first: Toshiaki

last: Ishikawa

first: Tsuyoshi

last: Yoshida

first: Satoru

last: Iida

first: Hiroyuki

last: Uetake

first: Hiroshi

last: Mizushima

last: Tanaka

first: Kenichi

last: Sugihara


title: Expression Profiling Reveals Unexpected Targets and Functions of the Human Steroid Receptor RNA Activator (SRA) Gene

city: Houston

first: Charles

last: Foulds

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: The human steroid receptor RNA activator (SRA) gene encodes both non-coding RNAs (ncRNAs) and protein-generating isoforms. However, the breadth of endogenous target genes that might be regulated by SRA RNAs remains largely unknown. To address this, we depleted SRA RNA in two human cancer cell lines (HeLa and MCF-7) with small interfering RNAs, then assayed for changes in gene expression by microarray analyses using Affymetrix HGU133+2 arrays. We also tested if SRA depletion affects estradiol-regulated genes in MCF-7 breast cancer cells.

overall_design: We transiently transfected HeLa or MCF-7 human cancer cell lines with with non-targeting (NT) or SRA-targeting siRNAs. Six total HeLa RNA samples were analyzed on an Affymetrix HGU133+2 array, representing three biological triplicates. Likewise, 12 total MCF-7 RNA samples were analyzed on Affymetrix HGU133+2 arrays, representing biological trilplicates for both NT and siSRA transfected cells and with/without 10 nM estradiol (E2) for 6 hours.

first: Anna

last: Tsimelzon

first: Weiwen

last: Long

first: Andrew

last: Le

first: Sophia

middle: Y

last: Tsai

first: Ming-Jer

first: Bert

middle: W

last: O'Malley


title: Gene Expression in Frontal Cortex in Major Depression and HIV

city: La Jolla

first: Erick

middle: T

last: Tatro

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California San Diego

summary:
Major depressive disorder (MDD) is a clinically defined entity with little understanding as to the underlying pathological substrate.  Biologically, MDD is characterized by disruption of neurotransmitters, especially serotonin and noradrenaline, which are the main targets of antidepressants.  We previously demonstrated significant reduction of glial cell number in the cingulate and dorsolateral prefrontal cortical regions.  Unfortunately, individuals living with HIV still have very high rates of MDD, despite the fact that mortality rates have fallen sharply with effective antiretroviral treatment.  It is possible that in this treatment era, living with chronic HIV infection may result in long-term neuropathological changes that predispose to MDD.  For example, it is known that HIV is associated with a range of inflammatory pathologies, neuronal loss, and dendrite-synaptic damage.  In HIV, these neurodegenerative changes have been linked to neurocognitive impairments, however it is also possible that these changes potentiate MDD.
In the current study, we sought to determine whether there are changes in gene expression in the MDD brain in the frontal cortex in HIV-context.  We identify a large number of genes dysregulated at p<0.05 significance.

overall_design: Retrospective gene expression analysis of autopsy brain tissue.  Four HIV/MDD subjects are identified and age-matched HIV patients without neuropsychiatric conditions are compared as controls.

first: Shahid

last: Salaria

first: Gursharan

last: Chana

last: Scott

first: Timothy

last: Nguyen

first: Eliezer

last: Masliah

first: Cristian

last: Achim

first: Ian

last: Everall


title: Gene expression analysis of TSC-tubers reveals increased expression of adhesion and inflammatory factors

status: Public on Feb 02 2010

city: Amsterdam

first: Floyd

last: Wittink

address: Kruislaan 318

department: MAD

country: Netherlands

institute: Universiteit van Amsterdam

summary: Cortical tubers in patients with tuberous sclerosis complex (TSC) are associated with cognitive disability and intractable epilepsy. While these developmental malformations are believed to result from the effects of TSC1 or TSC2 Gene mutations, the molecular mechanisms leading to tuber formation during brain development as well as the onset of seizures remain largely unknown. We used the Affymetrix Gene Chip platform as a genome-wide strategy to define the Gene expression profile of cortical tubers resected during epilepsy surgery compared to histologically normal perituberal tissue (adjacent to the cortical tuber) from the same patients or autopsy control tissue.

overall_design: Gene expression profiles of cortical tubers were compared with autopsy control specimens and perituberal tissue from the same patients.

first: Karin

last: Boer

first: Jan

last: Gorter

first: Peter

last: Crino

first: Mark

last: Nellist

first: Floor

last: Jansen

first: Wim

middle: G

last: Spliet

last: van Rijen

middle: R

first: Timo

middle: M

last: Breit

first: Dirk

last: Troost

first: Wytse

middle: J

last: Wadman

first: Eleonora

last: Aronica


title: Rac1-Induced Connective Tissue Growth Factor regulates Connexin 43 and N-Cadherin Expression in Atrial Fibrillation

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

summary:
Objectives: We studied the signal transduction of atrial structural remodelling that contributes to
the pathogenesis of atrial fibrillation (AF).
Backround: Fibrosis is a hallmark of arrhythmogenic structural remodelling but the underlying
molecular mechanisms are incompletely understood.
Methods: We performed transcriptional profiling of left atrial myocardium (LA) from patients
with AF and sinus rhythm (SR) and applied cultured primary cardiac cells and transgenic mice
with overexpression of constitutively active V12Rac1 (RacET) who develop AF at old age to
characterize mediators of the signal transduction of atrial remodeling.
Results: LA from patients with AF showed a marked upregulation of connective tissue growth
factor (CTGF) expression compared SR patients. This was associated with increased fibrosis,
NADPH-oxidase-, Rac1- and RhoA activity, upregulation of N-cadherin and connexin 43 (Cx43)
expression and increased angiotensin II tissue concentration. In neonatal rat cardiac myocytes and
-fibroblasts, a specific small molecule inhibitor of Rac1 or simvastatin completely prevented the
angiotensin II induced upregulation of CTGF, Cx43 and N-cadherin expression. Transfection
with small-inhibiting CTGF RNA blocked Cx43 and N-cadherin expression. RacET mice
showed upregulation of CTGF, Cx43 and N-cadherin protein expression. Inhibition of Rac1 by
oral statin treatment prevented these effects, identifying Rac1 as a key regulator of CTGF in vivo.
Conclusion: The data identify CTGF as an important mediator of atrial structural remodelling
during AF. Angiotensin II activates CTGF via activation of Rac1 and NADPH oxidase, leading
to upregulation of Cx43, N-cadherin and interstitial fibrosis and therefore contributing to the
signal transduction of atrial structural remodelling.

overall_design: Array design study consists of 5 Atrial Fibrillation patients and  matched 5 samples of patients in sinus rhythm (controls).

first: Oliver

last: Adam

first: Daniel

last: Lavall

first: Katharina

last: Theobald

first: Mathias

last: Hohl

first: Markus

last: Grube

last: Sussman

first: Stephan

last: Rosenkranz

first: Heyo

last: Kroemer

first: Hans-Joachim

last: Schäfers

first: Michael

last: Böhm

first: Ulrich

last: Laufs


title: Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-Infected Brain

first: Erick

last: Tatro

type:
Expression profiling by array
Expression profiling by RT-PCR
Non-coding RNA profiling by array
Other


title: Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies

city: Baltimore

first: Yanqin

last: Yang

address: 600 N. Wolfe Street

institute: The Johns Hopkins University

summary:
Expression data comparing typical E.coli colonies grown on BHI and BHI+Sucrose+MgSO4 to L-form colonies grown on BHI+Sucrose+MgSO4+Penicillin G.

Keywords: one time point

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design: DNA microarray analysis of E.coli colonies grown on BHI and BHI+Sucrose+MgSO4 (controls) with L-form colonies grown on BHI+Sucrose+MgSO4+Penicillin G (experimental). An isolated colony of fresh W3110 was grown for 5hrs to log phase, dilutions of the inoculmn were spread onto three media: BHI, BHI+Sucrose+MgSO4, and BHI+Sucrose+MgSO4+Penicillin G to yield isolated colonies. Isolated control colonies which grow overnight were harvested the next day while isolated L-form colonies which do not grow until 48-72 hrs were harvested after 72hrs. All colonies were harvest with a PBS moistened sterile swab and dipped into a sterile microcentrifuge tube containing 500ul of PBS. RNA was isolated from pelleted cells using MasterPure RNA Purification Kit and reverse transcribed for making probes for array hybridization on E.coli Genome 2.0 Affymetrix microarrays.


title: Expression data from ERBB2 over-expression and EGF stimulation in MCF10A cells

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

overall_design: The cells were transduced with retroviruses encoding vector control (pBabe) or pBabe-ErbB2. After infection cells were switched to assay medium supplemented with only 2% horse serum and no EGF. For EGF stimulation, cells transduced with empty vector were treated with EGF at 50 ng/ml for 2 hours before harvesting.

first: A

last: Wolfer

first: B

middle: S

first: D

last: Irimia

first: R

last: Flavin

first: M

last: Lupien

first: N

last: Gunawardane

first: C

last: Meyer

first: E

last: Lightcap

first: P

last: Tamayo

first: J

last: Mesirov

first: X

last: Liu

first: T

last: Shioda

last: Toner

last: Loda

last: Brown

last: Brugge

first: S

last: Ramaswamy


title: Gene expression profiles from osteosarcpma samples

city: Tsukiji

first: Eisuke

last: Kobayashi

state: Chuou-ku Tokyo

department: Chemotherapy Division

institute: National Cancer Center Research Institute

summary:
Osteosarcoma patients with development of pulmonary metastasis have still poorer prognosis in spite of aggressive treatment. However, molecular mechanism of metastasis is still unknown.
We analysed the expression levels of 54,613 probe sets in  surgical 27 samples of osteosarcoma with GeneChip Human Genome U133 Plus 2.0 arrays.

Keywords: gene expression array-based, count

overall_design: Total RNA was extracted from 27 fresh frozen tumour specimens. We analysed the global gene exprssion profiles of these osteosarcoma cases in order to clarify the genomic basis behind the development of pulmonary metastasis.

first: Robert

last: Nakayama

first: Hitoshi

last: Ichikawa

first: Reiko

last: Satow

first: Tesshi

last: Yamada


title: Expression data from DHT stimulation vs. control in LNCaP cells

first: Ben

last: Wittner

overall_design: LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran stripped FCS for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours

first: A

last: Wolfer

first: B

last: Irimia

last: Flavin

last: Lupien

last: Gunawardane


title: DNA microarrays time course of a MaF pre-iPSC clone (C9) untreated or treated with Vc

status: Public on Jan 31 2010

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

summary: Treatment with vitamin C (Vc) on MaF pre-induced pluripotent stem cells (pre-iPSCs) induced a rapid conversion into full-iPSCs within a few passages. We used microarrays to identify changes induced by Vc in the MaF pre-iPSC clone.

overall_design: MaF pre-iPSCs were cultured in mESC medium with or without Vc. TRIZOL cell lysates were prepared from D3, D4, D5 and D6 of Vc treated or untreated cells.

first: Baoming

last: Qin

first: Wenzhi

last: He


title: DNA microarrays time course of SKO-infected MEFs and MaF pre-iPSCs treated with Vc


title: Regulation of Fibroblast Growth Factor-2 by an endogenous antisense RNA and by Argonaute-2

status: Public on Jan 28 2010

city: Halifax

first: Paul

last: Murphy

state: Nova Scotia

address: 5850 College Street

country: Canada

institute: Dalhousie University

summary: We have previously reported that elevated fibroblast growth factor-2 (FGF-2) expression is associated with tumor recurrence and reduced survival after surgical resection of esophageal cancer, and that these risks are reduced in tumors co-expressing an endogenous antisense (FGF-AS) RNA. In the present study we examined the role of the endogenous FGF-AS transcript in the regulation of FGF-2 expression in the human lung adenocarcinoma cell line, Seg-1. FGF-2 and FGF-AS were temporally and spatially co-localized in the cytoplasm of individual cells, and knock-down of either FGF-2 or FGF-AS by target specific siRNAs resulted in dose-dependent up-regulation of the complementary transcript and its encoded protein product. Using a luciferase reporter system we show that these effects are mediated by interaction of the endogenous antisense RNA with the 3’UTR of the FGF-2 mRNA. Deletion mapping identified a 392 nt sequence in the 5823 nucleotide FGF-2 untranslated tail which is targeted by FGF-AS. siRNA-mediated knockdown of either FGF-AS or FGF-2 significantly increased the stability of the complementary partner mRNA, demonstrating that these mRNAs are mutually regulatory. Knockdown of FGF-AS also resulted in reduced expression of argonaute-2 (AGO-2) and a number of other elements of the endogenous microRNA/RNAi pathways. Conversely, siRNA-mediated knockdown of AGO-2 significantly increased the stability of the FGF-2 mRNA transcript, and the steady-state levels of both FGF-2 mRNA and protein, suggesting a role for AGO-2 in the regulation of FGF-2 expression.

overall_design: Gene expression in Seg-1 cells transfected with FGF-AS siRNA was compared to gene expression in Seg-1 cells transfected with negative control siRNA using Affymetrix Human Genome U133 Plus 2.0 arrays

first: Leigh-Ann

last: MacFarlane

first: Ying

last: Gu

first: Alan

last: Casson


title: Dynamic Innate Immune Responses of Human Bronchial Epithelial Cells against SARS-CoV and DOHV infection

city: Galveston

first: Tomoki

last: Yoshikawa

address: 301 University BLVD

institute: University of Texas Medical Branch

summary: Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection causes an immune-mediated disease. We have recently shown that SARS-CoV-induced epithelial Calu-3 cytokines could exacerbate and dampen host inflammatory and T cell responses, respectively, through modulating the functions of macrophages and dendritic cells, thereby suggesting that not only are lung epithelial cells the primary cells of SARS-CoV infection,  but they also involve in initiating and orchestrating the host innate and adaptive immunity. Comprehensive evaluation of the complex epithelial signaling to SARS-CoV is, thus, crucial for paving the way to better understand SARS pathogenesis and develop the innovative therapeutics against SARS. Here, based on the microarray-based functional genomics, we reported that 2B4 cells, a clonal derivative of Calu-3 cells, elicited a temporal and spatial activation of nuclear factor (NF)kappaB, activator protein (AP)-1 (ATF2/c-Jun), and interferon regulatory factor (IRF)-3/-7 at 12-, 24-, and 48-hrs post infection (p.i.), respectively, resulting in the activation of many antiviral genes, including interferon (IFN)-β, -λs, SARS-related inflammatory mediators, and various IFN-stimulated genes (ISGs). While elevated responses of IFN-β and IFN-λs were not detected until 48-hrs p.i., as a consequence of a delayed IRF-3/-7 activation, we showed, for the first time, that both types of IFNs exerted previously under-described non-redundant, complementary, and/or synergistic effects on the epithelial defense against SARS-CoV. Collectively, our results highlight the molecular mechanisms of the sequential activation of virus- and IFN-dependent signaling of lung epithelial cells against SARS-CoV and identify novel cellular targets for future studies, aiming at advancing strategies against SARS.

overall_design:
DNA microarrays were performed in the Molecular Genomics (MG) Core Facilities at UTMB. The detailed information about the procedures of microarray analysis has been posted on the MG Core Facilities website (genomics@scms.utmb.edu). To characterize the dynamic, spatial, and temporal changes of the gene expression induced by SARS-CoV, confluent 2B4 cells grown in T-75 flasks were infected with SARS-CoV (MOI=0.1) or remained uninfected (as control) for 12, 24, and 48hrs. Because 2B4 cells were also permissive to the productive infection of Dhori virus (DHOV), a member of the Orthomyxoviridae family within the Thogotovirus genus, resulting in robust responses of IFNs and other pro-inflammatory mediators, we also established parallel cultures of DHOV-infected 2B4 cells (MOI=0.1) for the comparative analysis of global gene expression elicited by SARS-CoV- versus DHOV-infected 2B4 cells. To meet the minimal number required for application of statistical algorithms, we performed the study in triplicate at each time point for mock-, SARS-CoV-, and DHOV-infected cultures, yielding a total of 27 arrays.
Briefly, supernatants were harvested from differentially treated cultures at 12-, 24-, and 48-hrs p.i. for subsequent analyses of viral yields and cytokine profiling, whereas the cells were subjected to total RNA extraction by using an RNAqueous-4PCR kit and following the protocol recommended by the manufacturer (Ambion, Austin, TX). Purified RNA samples were sent to our core facility for conversion to cDNA, biotin-labeled, and hybridized to 27 Affymetrix Human Genome U133 Plus 2.0 “Gene Chips” each of which contained 54,675 probe set identifiers representing more than ~47,400 transcripts that identify ~38,500 well-characterized genes, and various internal controls (Affymetrix, Santa Clara, CA). Mock-infected cells were compared to cells infected with SARS-CoV or DHOV at each time point.

first: Terence

middle: E

last: Hill

first: Naoko

last: Iwata

first: Clarence

last: Peters

first: Chien-Te

last: Tseng


title: Heterogeneity of gene expression in stromal fibroblasts of human breast carcinomas and normal breast

status: Public on Jan 29 2010

city: Madison

first: Andreas

last: Friedl

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin

summary: Twenty-one genes (27 probe sets) were up-regulated in CAF, as compared with NF. Known functions of these genes relate to paracrine or intracellular signaling, transcriptional regulation, extracellular matrix and cell adhesion/migration. Ten genes (14 probe sets) were down-regulated in CAF, including the pluripotency transcription factor KLF4. Quantitative RT–PCR analysis of 10 genes validated the array results. Immunohistochemical staining for three gene products confirmed stromal expression in terms of location and relative quantity. Surprisingly, the variability of gene expression was slightly higher in NF than in CAF, suggesting inter-individual heterogeneity of normal stroma.

overall_design: Paired CAF and NF were isolated from six primary human breast carcinoma specimens. RNA was extracted from low-passage cultures of CAF and NF and analyzed with Affymetrix Human Genome U133 Plus 2.0 arrays. The array data were examined with an empirical Bayes model and filtered according to the posterior probability of equivalent expression and fold difference in expression.

first: Maret

last: Bauer

first: Gui

last: Su

first: Charlie

last: Casper

first: Rong

first: William

last: Rehrauer


title: Loss-of-function mutations in REP-1 affect intracellular vesicle transport in fibroblasts and monocytes of CHM patients

status: Public on Jan 27 2010

city: Bethesda

first: Jennifer

last: Barb

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: Choroideremia (CHM) is a progressive X-linked retinopathy caused by mutations in the CHM gene, which encodes Rab escort protein-1 (REP-1), an escort protein involved in the prenylation of Rabs. Under-prenylation of certain Rabs, as a result of loss of function mutations in REP-1, could affect vesicular trafficking, exocytosis and secretion. To evaluate this hypothesis, intracellular vesicle transport, lysosomal acidification and rates of proteolytic degradation were studied in monocytes (CD14+ fraction) and primary skin fibroblasts from the nine age-matched controls and thirteen CHM patients carrying 10 different loss-of-function mutations.

overall_design: expression data were collected from 6 CHM patients' monocytes and 4 CHM primary fibroblasts cultures, monocytes or FB from 5 normal age-matched subjects were used as a control

first: Natalia

middle: V

last: Strunnikova

first: Peter

last: Munson

first: Ian

last: MacDonald


title: MYC regulation of a "poor prognosis" metastatic cancer cell state

first: Ben

last: Wittner

institute: Massachusetts General Hospital

first: Anita

last: Wolfer

first: Daniel

last: Irimia

first: Richard

last: Flavin

first: Mathieu

last: Lupien

first: Ruwanthi

middle: N

last: Gunawardane

first: Clifford

last: Meyer

first: Eric

last: Lightcap

first: Pablo

last: Tamayo

first: Jill

middle: P

last: Mesirov

first: X.

last: Liu

first: Toshi

last: Shioda

first: Mehmet

last: Toner

first: Massimo

last: Loda

first: Myles

last: Brown

first: Joan

last: Brugge

first: Sridhar

last: Ramaswamy


title: Expression analysis of laser-dissected SNpc neurons in Parkinson's disease

first: Frank

last: Middleton

summary: Genome-wide transcriptome analysis of expression changes in laser-dissected SNpc neurons from Parkinson's disease brain tissue versus control brain tissue.

overall_design: Post-mortem brain expression analysis performed in 10 PD brain samples and 8 control brain samples.

first: Peter

middle: D

last: Kim

first: Yanli

last: Zhang-James

middle: L

last: Davis


title: DNA microarrays time course of SKO-infected MEFs treated with Vc

first: Duanqing

last: Pei

summary: In order to understand the global gene expression changes resulting from the addition of vitamin C (Vc) to SKO (sox2, klf4 and oct4)-transduced mouse embryonic fibroblasts (MEFs), we used microarray to compare the gene expression profile at different time points with or without Vc.

overall_design: MEFs were infected at Day 0 (D0) with SKO or GFP retroviruses (control), and TRIZOL cell lysates were prepared from D3 of GFP-MEFs, and D3, 4, 5, 6, 8 and 10 of SKO-MEFs, with or without Vc.

first: Tao

last: Wang

first: Baoming

last: Qin

first: Wenzhi

last: He


title: MEK5D-transfected HUVEC

status: Public on Jun 16 2010

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

summary: We expressed a constitutively active mutant of MEK5 (MEK5D) in human primary endothelial cells (EC) to study the transcriptional and functional responses to Erk5 activation under static conditions.

overall_design: HUVEC were infected with either empty vector or constitutively active MEK5D and RNA was processed for microarray analysis 40 h post infection.

first: Nils

last: Ohnesorge

first: Nicole

last: Endres

first: Désirée

last: Spiering

first: Mirco

last: Schmolke

first: Stephan

last: Ludwig

first: Johannes

last: Roth

first: Matthias

last: Goebeler

first: Marc

last: Schmidt


title: Gene expression profiles of adult renal medullary endothelial cells isolated from TIE2-GFP transgenic mice using FACS. (GUDMAP Series ID: 35)

status: Public on Jan 26 2010

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

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

overall_design: Tie2  transgenic mice were utilized to isolate the endothelial cells from the adult  kidneys.  Endothelial cells were isolated from the kidney using collagenase treatment and FACS.   RNA was isolated and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Effect of mesalazine on Caco2 cells

status: Public on Jan 23 2010

city: MODENA

first: Alexis

last: Grande

address: via Campi n 287

department: Department of Biomedical Sciences

country: Italy

institute: University of Modena and Reggio Emilia

summary: Several reports indicate that mesalazine (5-aminosalicylic acid or 5-ASA) is a promising candidate for the chemoprevention of Colo-Rectal Cancer (CRC) due to its ability to reach the purpose, yet avoiding at the same time the side effects that are usually determined by prolonged administrations of Non Steroidal Anti-Inflammatory Drugs. This activity of 5-ASA is probably the consequence of a number of effects determined on colon cancer cells and consisting of reduced proliferation, increased apoptosis and activation of cell cycle checkpoints. A recent observation has suggested that these effects could be mediated by the capacity of 5-ASA to interfere with the nuclear translocation of beta-catenin, in turn responsible for the inhibition of its transcription activity. The aim of our study was to better characterize the molecular mechanism by which 5-ASA inhibits the beta-catenin signaling pathway. To address this issue we assessed, by means of the Affymetrix microarray methodology, the transcriptome changes determined on Caco2 cells by a 96 h treatment with 20 mM mesalazine.

overall_design: We used the Affymetrix microarray methodology to assess the transcriptome changes determined on Caco2 cells by a 96 h treatment with 20 mM mesalazine. One sample was treated with mesalazine, and one sample was left untreated.

first: Sandra

last: Parenti

first: Fabrizio

last: Ferrarini

first: Roberta

last: Zini

first: Monica

last: Montanari

first: Lorena

last: Losi

first: Brenno

last: Canovi

first: Sergio

last: Ferrari


title: SOX2 overexpression effect on human lung squamous cells

city: ILLKIRCH

first: Thomas

last: Hussenet

address: 1 rue Laurent Fries

institute: IGBMC

summary: We have identified SOX2 as a new oncogene and a likely driver of recurrent 3q26.3 amplifications in lung Squamous Cell Carcinoma.  SOX2 is a crucial transcription factor implicated in Embryonic and Neural Stem Cells, that we found widely activatd in human lung SCC. This part of the study aimed at analyzing the transcriptomic consequences of SOX2 overexpression in a simple in vitro model (human lung squamous immortalized cells).

overall_design: Human lung squamous BEAS-2B cells were transduced for Control or SOX2 expression, and their transcriptomes compared using Affymetrix arrays.

first: Christelle

last: Thibault

first: Stanislas

last: du Manoir


title: E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

status: Public on Jan 20 2010

city: State College

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells.

platform_organism:
Escherichia coli
Escherichia coli K-12

overall_design:
Strains: E. coli K-12 BW25113 wild type, ompA mutant
Medium: LB
Cell type: Biofilm cells grown on glasswool and polystyrene surfaces
Time: 15 h

Temperature: 37C
Strains: BW25113 ompA/pCA24N_ompA and ompA/pCA24N
Medium: LB
Time: 7 h
Temperature: 37C
Cell type: suspension cells, induced by 0.1 mM IPTG

first: Qun

last: Ma

middle: K


title: p53 regulates the Wnt signaling pathway in murine embryonic stem cells

status: Public on Jan 19 2010

first: Jing

last: Huang

institute: National Cancer Institute

summary:
Genome-wide analysis of gene expression changes in murine embryonic stem cells (R1E cells) treated with Ultraviolet and adriamycin
Both p53 and the Wnt signaling pathways play important roles in tumorigenesis and development. However, few studies, particularly on a genome-wide scale, have linked these two pathways. Here we show that p53 directly regulates the Wnt signaling pathway in murine embryonic stem cells (mESCs) using an integrated genome-wide approach. A chromatin-immunoprecipitation-based microarray assay (ChIP-chip) reveals that the Wnt signaling pathway is significantly over-represented in p53 bound genes.  Using gene expression microarray and real-time PCR, we demonstrate that the expressions of many Wnts are robustly induced by various stresses, including DNA damage and hypoxia that activate p53. Importantly, the activation of p53 is a prerequisite for the induction of Wnts. Moreover, conditional medium (CM) collected from ultraviolet (UV)-treated mESCs contains an anti-differentiation activity, which can be lowered by either the addition of Wnt signaling inhibitors into the CM or the reduction of p53 levels in UV-treated mESCs. These results suggest that stressed mESCs utilize the p53-Wnt signaling axis to signal neighboring mESCs to delay the differentiation. Together, our results uncover a novel connection between p53 and the Wnt signaling pathways in mediating cell-to-cell communication in mESCs, and provide insights into the functions of these two pathways in tumorigenesis and development.

overall_design: We analyzed R1E cells treated with mock (control), adriamycin or Ultraviolet using Affymetrix Mouse Gene ST 1.0 arrays. Four replicates for each treatment were performed.

first: Li

last: Mangmang

first: Lee

last: Kyoung-Hwa

first: Michalowski

last: Aleksandra

first: Zhang

last: Xinyue

first: Liao

last: Hongling

first: Chen

last: Lingyi

first: Wu

last: Xiaolin

first: Huang

last: Jing


title: Transcriptome of Bacillus anthracis lethal toxin (LT)-intoxicated HUVECs monolayers

city: Nice

first: emmanuel

last: lemichez

address: 151 route Saint Antoine de Ginestière

department: Microbiology

institute: INSERM

summary: We have analyzed the variation of transcriptome of HUVECs intoxicated by the lethal toxin of Bacillus anthracis at 4 and 8 hours

overall_design: Three experimental conditions with two biological replicates for the control condition corresponding to untreated HUVEC monolayer. RNA were extracted before labeling and hybridizations on Human U133A Plus 2.0 Affymetrix GeneChip

first: Monica

last: Rolando

first: Gilles

last: Flatau

first: Patrick

last: Munro

first: Caroline

last: Stéfani

first: Emmanuel

last: Lemichez


title: The Effects of Static Magnetic Fields on Human Embryonic Cells

status: Public on Jan 18 2010

city: baltimore

first: zhiyun

last: wang

address: 3400 N Charles St

department: Biomedical Engineering

institute: Johns Hopkins Univesity

summary: This study provides a framework describing how magnetic exposure is transduced from the most-plausible molecular-level ‘biosensor’ (lipid membranes) to cell-level responses that include differentiation toward neural lineages. In addition, SMF provided a stimulus that uncovered new relationships – that exist even in the absence of magnetic fields – between gangliosides, the time dependent regulation of IL-6 signaling by these glycolipids, and the fate of embryonic cells.

overall_design: Subconfluent (70%-80%) undifferentiated LVECs (passage 11) were resuspended at 500k cells in 10 ml culture medium (day 0) and cultured in the presence or absence of static magnetic field. Four conditions were investigated: A) Control (without exposure); B) One day exposure (Exposed on day 6 without recovery); C) Continuous exposure (day 2 to day 5) followed by one day recovery; D) Continuous exposure (day 2 to day 6) without recovery. Cells are harvested on day 7. mRNA was isolated from the cells and microarray analysis was done using the Affymetric Human Genome U133 2.0 Plus Chip.

first: Kevin

last: Yarema

first: Zhiyun

last: Wang

first: Pao-Lin

last: Che

first: Anshu

last: Sarje


title: Expression data from E protein deficient double-positive (DP) thymocytes

status: Public on Jan 16 2010

city: La Jolla

first: Louise

last: D'Cruz

address: 9500 Gilman Drive

institute: UCSD

summary:
We wanted to test the role of mammalian E proteins E2A and HEB in the development of T cells.
Using a conditional deletion system in which these proteins are deleted at the DP stage of T cell development, we compared DP thymocytes deficient for E2A, HEB or both to wild-type thymocytes

overall_design: We sorted DP thymocytes from wild-type, E2A-deficient, HEB-deficient or E2A/HEB-deficient mice for RNA extraction and hybridization on Affymetrix microarrays.  Cells we sorted using fluorescent activated cell sorting and purity was verified as greater that 98%. Approximately 1000000 cells were sorted per sample.

first: Ananda

last: Goldrath


title: Gene expression profiles after RNAi-mediated suppression of RB, p107 or p130 in growing, quiescent or ras-induced senescent IMR90 cells

status: Public on Jan 15 2010

city: Cold Spring Harbor

first: Agustin

last: Chicas

address: One Bungtown Road

institute: Memorial Sloan Kettering

summary: The action of RB as a tumor suppressor has been difficult to define, in part, due to the redundancy of the related proteins p107 and p130. By coupling advanced RNAi technology to suppress RB, p107 or p130 with a genome wide analysis of gene expression in growing, quiescent or ras-senescent cells, we identified a unique and specific activity of RB in repressing DNA replication as cells exit the cell cycle into senescence, a tumor suppressive program.

overall_design: Expression profiles of IMR90 cells before and after RNAi-mediated supppression of RB, p107 or p130 in growing, quiescent or ras-induced senescent conditions. RNA was extracted from growing, low serum (0.1% FBS), confluent, or ras-senescent cells.

first: Scott

last: Lowe


title: Expression data from E161K LMNA mutant heart and control

status: Public on Jan 30 2010

city: Chicago

first: Stephanie

last: Mewborn

address: 5841 S Maryland Ave

department: Medicine

institute: University of Chicago

summary:
Over 180 LMNA gene mutations have been identified in human diseases including cardiac and skeletal myopathies, lipodystrophies, and premature aging syndromes.  Postulated mechanisms by which these mutations result in different phenotypes include perturbation of normal nuclear structure and chromosome organization, and gene activity.

We investigated whether a cardiomyopathic LMNA mutation, E161K, displayed abnormal gene expression.  We compared the gene expression profile in the E161K LMNA-mutant heart to that of an end stage LMNA-normal heart.

overall_design: We compared the gene expression levels between two end-stage cardiomyopathic hearts in order to detect the gene expression differences more likely to reflect the LMNA mutation state.   A region of left ventricle tissue that was grossly less fibrotic and contained cardiomyocytes of the LMNA-mutant heart was selected for RNA isolation.  A region of a male heart that was also end-stage dilated cardiomyopathy, but LMNA-normal and also devoid of obvious fibrosis was selected for RNA isolation.  Two technical replicates were performed for each sample, and data were analyzed using two different normalization strategies (Mas5 and RMA).

first: Elizabeth

last: McNally


title: Expression data from gastric cancer

status: Public on Jan 12 2010

city: Shanghai

first: zhihai

last: peng

state: Shanghai

address: 85 Wujin Road

department: Department of General Surgery

institute: Shanghai Jiao Tong University Affiliated First People's Hospital

summary:
We used microarrays to detail the global program of gene expression between Chinese gastric cancer and its adjacent noncancer tissues and identified some key differential expression genes in cancer.
Gene expression profiling is a valuable tool for identifying differentially expressed genes in studies of gastric cancer. However, it remains difficult to assign biological significance to the vast number of genes. There is an increasing awareness of gene expression profile as an important part of the contextual molecular network at play in cancer initiation and progression. The key pathways or genes might be the target for our clinical curement.

overall_design: This study analysed the transcriptional profiles commonly activated at different stages of gastric cancers using an integrated approach combining gene expression profiling of 12 adjacent normal/tumor-matched gastric tissues to form a gene regulatory coexpression map. We sought to obtain homogeneous populations of cancer tissues at each TNM stage in order to increase the accurateness of expression profiles.In addition we performed this test in 3 normal tissues in order to get data for further study.


title: Expression data from human lymphoma endothelium and reactive lymph node-derived endothelium

status: Public on Jan 14 2010

city: wuhan

first: ding

last: ma

address: jiefang avenue 1095#

institute: cancer biology research center, tongji hospital, tongji medical college, huazhong university of science and technology

summary:
Angiogenesis plays a key role in tumor metastasis. Many genes may act in this process including formation of vessels, immune evasion,etc. Different gene expression profiles between lymphoma endothelium cells and reactive lymph node-derived endothelium cells may uncover these genes. And intensive mechanism researches on such key genes may explain the mechanisim of tumor-specific angiogenesis and help to explore effective treatment strategies to prevent/reverse tumor metastasis.
We use microarrays to detail gene expression profiles of human lymphoma endothelium and reactive lymph node-derived endothelium.

overall_design: Lymph nodes were taken from surgery samples of cases pathologically diagnosed DLBCL (diffuse large B-cell lymphoma), PTL (peripheral T cell lymphoma) and reactive lymph nodes. The pure endothelium cells were isolated by LCM after immunohistochemical staining of CD34. We found Tim-3 was preferentially expressed on lymphoma-derived ECs via different expression profiles between lymphoma ECs and reactive lymph node-derived ECs. Intensive researches were carried out on Tim-3-expressing -ECs and we found that Tim-3 -expressing-Ecs may play important role on EC-mediated tumor evasion.

first: Xiaoyuan

last: Huang

first: Xiangyang

last: Bai

first: Yang

last: Cao


title: Down's syndrome with acute lymphoblastic pediatric leukemia (DS-ALL)

status: Public on Jan 13 2010

city: Rehovot

first: Libi

last: Hertzberg

address: Herzel 145

country: Israel

institute: Weizmann Institute of Science

summary:
DS-ALL is a highly heterogeneous disease with predominance of an aberrant exp. of CRLF2 cooperating with mutated JAK2

Acute lymphoblastic pediatric leukemia specimens of Down's syndrome are examined for gene expression profiles and specific genetic aberrations. Gene expression profiling and specific genetic variation analysis identify novel pathways involved in DS-ALL pathogenesis.

overall_design: Gene expression profile analysis and specific genetic data are integrated to find characteristics of DS-ALL's

last: Herzberg

first: Geertruy

last: te Kronnie

first: Jean

last: Bourquin

first: Helena

last: Kempski


title: Expression profiling of PaTu8988s and PaTu8988t cell lines

status: Public on Jan 10 2010

city: London

first: yaohe

last: Wang

address: Charterhouse Square

institute: Institute of Cancer

summary:
We used microarray to look at the genes deregulated in PaTu8988s (adenovirus insensitive) and PaTu8988t (adenovirus sensitive) cell lines
PaTu8988s and PaTu8988t are pancreatic cell lines derived from the same patient and show significant responses to oncolytic adenoviruses. The different response to adenovirus in these cell lines is not related to the previously known mechanisms that affect adenovirus infection. The two cell lines represent represent a "suitable" model to screen tumour-associated genes affecting the potency of aoncolytic adenovirus.

overall_design: RNA was extracted and hybridized on Affymetrix microarrays.

first: Yaohe

first: Nicholas

last: Lemoine


title: In vivo actin cross-linking induced by type VI secretion system is associated with intestinal inflammation

city: Boston

first: Amy

last: Ma

address: 200 Longwood Ave D1-411

institute: Harvard Medical School

summary:
To determine whether the Vibrio cholerae type VI secretion system (T6SS) is functional during animal infection, derivatives of V52 were used to infect infant mice.  In this infection model, a diarrheal response occurred and effector translocation could be detected.  These host responses were dependent on a functional T6SS and on the actin cross-linking effector domain of VgrG-1.
Gene expression and histological studies showed innate immune activation and immune cell infiltration in the intestinal lumen.

overall_design: 3 infection groups (mock, V52, ACD), 3 biological replicates per group.

first: John

last: Mekalanos


title: Expression data from different grades (WHO) of astrocytomas (ACM)

status: Public on Jan 05 2010

city: Luoyang

first: Zhiqiang

last: Yao

state: Henan

address: No.288, Zhongzhou Road

department: Neurosurgery

institute: No.150 Military Central Hospital

summary: The aim of the study was to identify significant alterations in genes and molecular functional pathways in comparison with normal and ACM tissue, and detect the marker genes to differentiate the different stage astrocytomas

overall_design:
Total RNA was isolated from Seventeen tumor tissue of patients, which included two WHO grade I(T1) and five WHO grade II(T2), III(T3) and IV(T4) samples, and four pooled normal tissue samples. The genome-wide expression analysis was first performed by directly comparing the expression profile of highly enriched different grade astrocytomas and pooled normal tissues, we then applied various data-mining methods to process the 15 different grades tumor tissues sample. Paired T-test and Q-cluster method was performed to explore mark genes validated by qRT-PCR.
This study utilized a pathway-specific enrichment analysis of the microarray data and quantified the gene expression difference between astrocytomas tumor and pooled normal tissues. BioCarta and KEGG pathways of the ACM compared to normal tissue were identified through enrichment tests on gene lists obtained using SAM, while GO is organized into hierarchical annotations in the context of normal cellular function, the BioCarta and KEGG database organizes the genes(gen products) into pathway reaction maps and functional complexes, including some disease-specific pathway

first: Zhongyu

last: Liu


title: Expression data from 290 primary colorectal cancers

status: Public on Jan 08 2010

city: Parkville

first: Oliver

last: Sieber

state: Victoria

address: 6th floor, Centre for Medical Research,  Royal Melbourne Hospital,  Royal Parade

department: Melbourne Tumour Biology Branch

country: Australia

institute: Ludwig Institute for Cancer Research

summary:
Samples were taken from colorectal cancers in surgically resected specimens in 290 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. The training set of our prognosis classifier included the stage A and D samples. Validation used our stage B and C samples.

Keywords: Expression profiling by array

overall_design: mRNA from 290 primary colorectal tumour samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. The MAS5.0 procedure was used to make calls of expression. Data from the Stage A and D samples were quantile normalized and used with microarray data from the expO set to build a classifier. The Stage B and C samples were were quantile normalized with reference to a training set prior to application of our prognosis classifier.


title: HPV16 E7 expression effect on expression profile mediated by tumor necrosis factor

city: Sao Paulo

first: Enrique

last: Boccardo

state: Sao Paulo

address: R. João Julião, 245 1º andar

country: Brazil

institute: Ludwig Institute for Cancer Research Ltd

summary: Acute expression of E7 oncogene from HPV-16 or HPV-18 is sufficient to overcome tumor necrosis factor-alfa (TNF) cytostatic effect on primary human keratinocytes. In the present study we investigated the molecular basis of E7-induced TNF resistance through a comparative analysis of the effect of this cytokine on the proliferation and global gene expression of organotypic cultures of normal and E7(wild type or mutant)-expressing keratinocytes.

overall_design: In order to determine the effects of E7 expression on TNF response, we performed 3 independent experiment for each cell line. Organotypic cultures of normal and E7(wild type or mutant)-expressing keratinocytes were treated with 2 nM TNF for 72 hours, or left untreated.

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