title: Differential gene expression in circulating leukocytes from chronically lonely individuals

status: Public on Mar 16 2011

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

institute: UCLA School of Medicine

summary:
Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 93 older adults participating in the Chicago Health Aging and Social Relations Study (CHASRS).  The primary research question is whether gene expression differs in participants who are chronically lonely.

Keywords: Risk prediction


title: Oncogene activation induces metabolic transformation resulting in insulin independence in human breast cancer cells

status: Public on Mar 18 2011

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

country: USA

institute: Karmanos Cancer Inst., Wayne State University

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

overall_design: Refer to individual Series


title: Comparison of the testicular transcriptome of chromosomes 2, X, Y and the mitochondrial genome between two mouse species

status: Public on Feb 16 2011

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

type: Expression profiling by genome tiling array

summary: We used tiling arrays to compare the testicular expression of chromosomes 2, X, Y and the mitochondrial genome between Mus m. domesticus and Mus spretus. We found an excess of dysregulated non-coding RNAs on chromosome 2. This group consists of intronic antisense RNAs, intergenic RNAs and also premature forms of PIWI-interacting RNAs (piRNAs). The unique transcriptional regulation in spermatogenesis is a characteristic of chromosome X. It is subject to meiotic transcriptional silencing, which is accompanied by generating X-chromosomal retrogenes on autosomes. We found striking dysregulation of the G6pdx - G6pd2 parental-retrogene pair between the mouse species. The postmeiotic expression of G6pdx in Mus spretus points out the continuous evolution of X chromosome silencing and provides clue for regulatory changes, which accompanies the out-of-X gene flow.

sample_organism:
Mus musculus domesticus
Mus spretus

overall_design:
Comparison between 3 samples of Mus spretus and 3 samples of Mus m. domesticus (C57BL/6J, B6).

The supplementary file 'GSE19633_Spr_v_B6.bed' contains the chromosomal localizations of the probes together with logFC and adjusted P values.

first: David

last: Homolka

first: Jiri

last: Forejt

first: Petr

last: Jansa


title: Comparison of B6/D2 Whole Brain Alternative Splicing

status: Public on May 10 2011

city: Portland

first: Ted

last: Laderas

state: OR

address: 3181 SW Sam Jackson Rd CR145

department: OHSU Knight Cancer Institute

institute: Oregon Health & Science University

summary: This dataset consists of whole brain samples from 10 B6 and 12 D2 mice, in order to assess the amount of strain-specific alternative splicing.

overall_design: This design consists of whole brain total RNA samples from 10 B6 and 12 D2 mice

last: Hitzemann

first: Kari

last: Buck


title: Genome-wide analysis of time-dependent gene expression in SUM-225 cells treated with the HER-2-specific inhibitor CP724,714 for 45 hours

summary: Results of blocking the HER-2 oncogene kinase function in SUM-225 cells by treatment with CP724,714 and measuring gene expression as a function of time provides information as to what genes are regulated by HER-2 in this breast cancer cell line.

overall_design: SUM-225 cells were treated with the HER-2-specific small molecule kinase inhibitor CP724,714 for 45 hours.  Total RNA was collected every 3 hours from parallel cultures throughout the 45 hour duration of treatment and genome-wide analysis of expression was performed on RNA from each time point (total 16 time points, starting at 0 hours treatment).

first: Stephen

middle: P

last: Ethier


title: IL-6-mediated activation of STAT3α prevents trauma/hemorrhagic shock-induced liver inflammation

city: Houston

middle: Andrew

last: Thacker

state: TX

address: One Baylor Plaza  BCM 286, Room N1319

department: Medicine, Section of Infectious Disease

institute: Baylor College of Medicine

summary:
We previously demonstrated in rodents that T/HS results in liver injury that can be prevented by IL-6 administration at the start of resuscitation, however the mechanism(s) for the IL-6 protective effect is not fully known.
We used microarrays to detail the global gene expression in response to T/HS and the effect of IL-6 on this model with and without pharmacologic blockade of Stat3-mediated IL-6 and identified distinct members of the inflammasome de-regulated  during T/HS that normalized with IL-6 administration during resuscitation.

overall_design: Adult male rats were subjected to either sham procedure, a trauma plus hemorrhagic shock (T/HS) procedure, T/HS with IL-6 versus PBS during resuscitation, or pretreatment with pharmacologic blockade of Stat3-mediated IL6 via GQ-ODN and after procedural completion, animals were sacrificed and livers were taken and homegenized for RNA extraction and microarray analysis using Affymetrix Rat 230A GeneChip® array

first: Ana

last: Moran

middle: A

middle: J

last: Tweardy

first: Mary-Ann

last: Mastrangelo

first: Ayse

last: Arikan

first: Yong

last: Wu

first: Bi

last: Yu


title: ChIP-on-Chip data from Rh30 cells +/- rapamycin treatment

status: Public on Jan 05 2011

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

institute: Vanderbilt University Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary:
p73 is a p53 family transcription factor that plays critical roles during development and tumor suppression.  We analyzed p73 activity using a combination of ChIP-on-Chip and gene expression profiling, both at baseline and after treatment with the mTOR inhibitor rapamycin.
We report the first comprehensive analysis of p73 binding across the genome.  Furthermore, we re-analyzed this p73 cistrome after perturbation with rapamycin, an inhibitor of mTOR and inducer of p73.  Multiple determinants of p73 binding, activity, and function were evident, and were modulated by mTOR.

overall_design: Rh30 rhabdomyosarcoma cells were treated with vehicle or 40 nM rapamycin for 24 h, then cross-linked and harvested.

middle: M

last: Rosenbluth


title: Runx2 Transcriptome of Prostate Cancer Cells: Insights into Invasiveness and Bone Metastasis

status: Public on Dec 26 2010

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

summary:
Background: Prostate cancer (PCa) cells preferentially metastasize to bone at least in part by acquiring osteomimetic properties. Runx2, an osteoblast master transcription factor, is aberrantly expressed in PCa cells, and promotes their metastatic phenotype. The transcriptional programs regulated by Runx2 have been extensively studied during osteoblastogenesis, where it activates or represses target genes in a context-dependent manner. However, little is known about the gene regulatory networks influenced by Runx2 in PCa cells. We therefore investigated genome-wide mRNA expression changes in PCa cells in response to Runx2.

Results: We engineered a C4-2B PCa sub-line called C4-2B/Rx2dox, in which  doxycycline (Dox) treatment stimulates Runx2 expression from very low levels to levels observed in other PCa cells. Transcriptome profiling using whole genome expression array followed by in silico analysis indicated that Runx2 upregulated a multitude of genes with prominent cancer-associated functions. They included secreted factors (CSF2, SDF-1), proteolytic enzymes (MMP9, CST7), cytoskeleton modulators (SDC2, Twinfilin, SH3PXD2A), intracellular signaling molecules (DUSP1, SPHK1, RASD1) and transcription factors (Sox9, SNAI2, SMAD3) functioning in epithelium to mesenchyme transition (EMT), tissue invasion, as well as homing and attachment to bone. Consistent with the gene expression data, induction of Runx2 in C4-2B cells enhanced their invasiveness. It also promoted cellular quiescence by blocking the G1/S phase transition during cell cycle progression. Furthermore, the cell cycle block was reversed as Runx2 levels declined after Dox withdrawal.

Conclusions: The effects of Runx2 in C4-2B/Rx2dox cells, as well as similar observations made by employing LNCaP, 22RV1 and PC3 cells, highlight multiple mechanisms by which Runx2 promotes the metastatic phenotype of PCa cells, including tissue invasion, homing to bone and induction of high bone turnover. Runx2 is therefore an attractive target for the development of novel diagnostic, prognostic and therapeutic approaches to PCa management. Targeting Runx2 may prove more effective than focusing on its individual downstream genes and pathways.

overall_design: C4-2B/Rx2dox cells were subjected to microarray gene expression analysis after one and two days of treatment with either Dox or vehicle in biological quadruplicates (a total of 16 samples).

first: Sanjeev

middle: K

last: Baniwal

first: Omar

last: Khalid

first: Yankel

last: Gabet

first: Ruchir

middle: R

last: Shah

first: Daniel

last: Purcel

first: Alice

middle: E

last: Kohn-Gabet

first: Yunfan

last: Shi

first: Gerhard

last: Coetzee

first: Baruch

last: Frenkel


title: Comparative analysis of hESCs and iPSCs-derived hepatocyte-like cells reveals current drawbacks and possible strategies for improved differentiation

status: Public on Jan 20 2011

city: Berlin

first: Justyna

last: Jozefczuk

address: Ihnestrasse 63

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Two independent protocols for deriving HLCs from hESCs and iPSCs were adopted and further characterization included immunocytochemistry, real-time RT-PCR, and in vitro functional assays. Comparative microarray-based gene expression profiling was conducted on these cells and compared to the transcriptomes of human fetal liver and adult liver progenitors. HLCs derived from hESCs and hiPSCs showed significant functional similarities, similar expression of genes important for liver physiology and common pathways. However, specific differences between the two cell types could be observed.

overall_design: Total RNA obtained from undifferentiated hESCs, iPSCs, HLCs (hepatocyte-like cells)-derived from hESCs and iPSCs, fetal forskin fibroblasts and fetal liver.

first: Jozefczuk

last: Justyna


title: A human iPSC model of Hutchinson Gilford Progeria Syndrome reveals a possible mesenchymal stem cell defect

status: Public on Dec 23 2010

city: Singapore

first: FAN

last: ZHOU

address: 8A Biomedical Grove

country: Singapore

institute: Institute of Medical Biolog

summary:
Hutchinson Gilford Progeria Syndrome (HGPS) is a rare, sporadic genetic disease caused by mutations in the nuclear lamin A gene. In most cases the mutation creates an efficient donor-splice site that generates an altered transcript encoding a truncated lamin A protein, progerin.  In vitro studies have indicated that progerin can disrupt nuclear function. HGPS affects mainly mesenchymal lineages but the shortage of patient material has precluded a tissue-wide molecular survey of progerin’s cellular impact.
We report here a new, induced pluripotent stem cell (iPSC)-based model for studying HGPS. HGPS dermal fibroblasts were reprogrammed into iPSC lines using a cocktail of the transcription factor genes, OCT4, SOX2, KLF4 and C-MYC. The iPSC cells were differentiated into neural progenitors (NPs), endothelial cells (ECs), fibroblast-like cells and mesenchymal stem cells (MSCs). Progerin levels in the different cell types followed the pattern MSC≥ fibroblast>EC>>NP.  Functionally, we detected a major impact of progerin on MSC function. We show that HGPS-MSCs are vulnerable to the ischemic conditions found in a murine hind limb recovery model and an in vitro hypoxia assay, as well as showing enhanced sensitivity in a serum starvation assay. Since there is widespread consensus that MSCs reside in low oxygen niches in vivo, we propose that these conditions lead to an accelerated depletion of the MSC pool in HGPS patients with consequent accretion of mesenchymal tissue.

overall_design: Analysis of iPSCs, hESCs and parental fibroblasts at the gene expression level. The comparison analysis in the present study was expected to show the similarity between iPSCs, hESCs and parental fibroblasts. Results provide important information of the differences between iPSCs, hESCs and parental fibroblasts. Total RNA was obtained from different samples (iPSCs, hESCs, and fibroblasts) separately.

first: Jinqiu

last: Zhang

first: Qizhou

last: Lian

first: Guili

last: Zhu

first: Fan

last: Zhou

first: Lin

last: Sui

first: Cindy

last: Tan

first: Rafidah

last: Mutalif

first: Raju

last: Navasankari

first: Yuelin

first: Hung-Fat

last: Tse

first: Colin

last: Stewart

first: Alan

last: Colman


title: Multi-tissue, selective PPARγ modulation of insulin sensitivity and metabolic pathways in obese rats

status: Public on Feb 11 2011

city: La Jolla

first: Gene

last: Hsiao

state: CA

address: 9500 Gilman Dr

institute: UCSD

summary:
We characterized the insulin sensitivity and multi-tissue gene expression profiles of lean and insulin resistant, obese Zucker rats untreated or treated with one of four PPARγ ligands (pioglitazone, rosiglitazone, troglitazone, and AG035029). We analyzed the transcriptional profiles of adipose tissue, skeletal muscle, and liver from the rats and determined whether ligand insulin-sensitizing potency was related to ligand-induced alteration of functional pathways.  Ligand treatments improved insulin sensitivity in obese rats, albeit to varying degrees.
Male Zucker fatty (fa/fa) and lean (fa/+) rats (Charles River, Wilmington, MA) were received at 6 weeks of age. Fatty rats were weight-matched upon arrival and randomly divided into one of five experimental groups.  The fatty rat groups varied by the type of chow they were fed - normal chow alone or with a PPARγ ligand admixture:  normal chow (fatty control, FC), rosiglitazone-treated (Rosi), pioglitazone-treated (Pio), troglitazone-treated (Tro), or AG035029-treated (AG). Lean control (LC) rats were all fed normal chow. Rats groups were maintained on the diets for 21 days.

overall_design: Adipose tissue (epididymal), skeletal muscle (gastrocnemius), and liver were harvested from lean (LC) and insulin resistant, obese Zucker rats untreated (FC) or treated with one of four PPARγ ligands (pioglitazone [Pio], rosiglitazone [Rosi], troglitazone [Tro], and AG035029 [AG]).

first: Justin

last: Chapman

first: Jachelle

last: Ofrecio

first: Jason

last: Wilkes

first: Jamie

middle: L

last: Resnik

first: Divya

last: Thapar

first: Shankar

last: Subramaniam

first: Dorothy

middle: D

last: Sears


title: Comparison of exon profiles before and after hormone induction

status: Public on Dec 21 2010

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary: Exon array analysis component. Development, differentiation, and response to environmental stimuli are characterized by sequential changes in cellular state initiated by the de novo binding of induced or temporally regulated transcriptional factors to their cognate genomic sites. The mechanism whereby a given regulatory factor selects a limited number of in vivo targets from myriads of potential genomic binding sites is undetermined. Here we show that up to 95% of induced de novo genomic binding by the glucocorticoid receptor, a paradigmatic ligandactivated transcription factor, is targeted to preexisting foci of accessible chromatin. Factor binding invariably potentiates chromatin accessibility. Cellselective de novo genomic occupancy patterns appear to be comprehensively predetermined by cellspecific differences in baseline chromatin accessibility patterns, with secondary contributions from local sequence features. The results define a novel framework for understanding regulatory factorgenome interactions, and provide a molecular basis for the tissueselectivity of steroid pharmaceuticals and other agents that intersect the living genome.

overall_design: Time course of dexamethasone treatment of 2 cell types from a zero hour untreated control, 2 hour, 4 hour and 8hr treatment times. This is part of a larger study: Chromatin accessibility predetermines de novo steroid receptor binding. There are 2 replicates per cell line per time point except in the case of 8hr Dex treated AtT-20 where a second replicate was unavailable.

first: S

last: John

first: J

first: G

last: Hager


title: Growth Factor Stimulation Induces a Distinct ERα Cistrome Underlying Breast Cancer Endocrine Resistance

status: Public on Dec 29 2010

city: Lebanon

first: Mathieu

last: Lupien

state: NH

address: One Medical Center Drive

department: Genetics

institute: Norris Cotton Cancer Center/Dartmouth Medical School

summary: Estrogen receptor alpha (ERα) expression in breast cancer is predictive of response to endocrine therapy, however resistance is common in ERα-positive tumors that over-express the growth factor receptor ERBB2. Even in the absence of estrogen, ERα can be activated by growth factors including the epidermal growth factor (EGF). EGF induces a transcriptional program distinct from estrogen, however the mechanism of the stimulus-specific response is unknown. Here we show that the EGF-induced ERα genomic targets, its cistrome, are distinct from those induced by estrogen in a process dependent on the transcription factor AP-1. The EGF-induced ERα cistrome specifically regulates genes found over-expressed in ERBB2-positive human breast cancers. This provides a potential molecular explanation for the endocrine therapy resistance seen in ERα-positive breast cancers that over-express ERBB2. These results suggest a central role for ERα in hormone-refractory breast tumors dependent on growth factor pathway activation and favors the development of therapeutic strategies completely antagonizing ERα as opposed to blocking its estrogen responsiveness alone.

overall_design: ChIP-Chip against ERa in MCF7 breast cancer cells treated with Epidermal Growth Factor (EGF) for 90 min and expression profile analysis (mRNA) in MCF7 cells treated with EGF (3h or 12h) or pre-treated with ICI182,780 and then with EGF from 3h.

first: Clifford

last: Meyer

first: Shannon

middle: T

last: Bailey

first: Jérôme

last: Eeckhoute

first: Jennifer

last: Cook

first: Thomas

last: Westerling

first: Xiaoyang

middle: S

last: Carroll

first: Daniel

last: Rhodes

first: X

last: Liu

first: Myles

last: Brown


title: Comprehensive Characterization of 3D Models for Prostate Cancer Growth and Invasion in Laminin-rich Extracellular Matrix

status: Public on Dec 06 2010

city: Turku

first: Matthias

last: Nees

address: Itäinen Pitkäkatu 4C

department: Medical Biotechnology

country: Finland

institute: VTT Technical Research Centre of Finland

summary:
Full title: Comprehensive Characterization of Three-Dimensional Models for Prostate Cancer Growth and Invasion in Laminin-rich Extracellular Matrix
Prostate Cancer (PrCa) cells undergo acinar morphogenesis and spheroid formation in three-dimensional (3D) culture, supported by laminin-rich extracellular matrix (lrECM, Matrigel). We developed miniaturized 3D model systems that facilitate investigation of morphogenesis and invasion of normal and PrCa cell lines in lrECM. Primary and non-transformed cell lines formed round structures with strong cell-cell contacts and epithelial polarization, lumen and a complete basal lamina (BL). In contrast, most PrCa cell lines formed either defective, “mass” spheroids with incomplete BL, or invasive “stellate” structures. The bioinformatic analyses of genome-wide mRNA expression data revealed massive alteration of key functional and signaling pathways in 3D cultures, with lipid and steroid metabolism, epigenetic reprogramming, and differentiation-related transcription factors induced across all cell lines by lrECM. In invasive cells, AKT, PI3Kinase, mTOR, and hedgehog signaling pathways were most highly activated, validated by small molecule inhibitors compounds specifically targeting key regulatory molecules. Compounds against AKT and PI3kinase pathways were significantly more effective in invasive cells, compared to mass or round/normal phenotype spheroids, and monolayer culture. A severe morphologic conversion was observed in PC-3 and PC-3M cells, transforming initially round, normal-appearing epithelial spheroids into rapidly invading cell masses. Markers for EMT (epithelial-mesenchymal transition) were highly expressed already in early stage, round spheroids prior to invasive conversion, and were not further increased in invasive cells. This indicates that PrCa cells can display extraordinary plasticity. EMT may be involved in providing a metastable genotype that allows morphological transformation, but is not be required for invasive processes themselves.

overall_design: Total RNA was obtained from non-transformed prostate epithelial cells and prostate cancer cells cultured in monolayer and three-dimensional laminin-rich extracellular matrix (growth factor-reduced Matrigel).

first: Ville

last: Härmä

first: Johannes

last: Virtanen

first: Rami

last: Mäkelä

first: Antti

last: Happonen

first: John-Patrick

last: Mpdindi

first: Matias

last: Knuuttila

first: Pekka

last: Kohonen

first: Jyrki

last: Lötjönen

first: Olli

last: Kallioniemi


title: Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors Whole Genome DASL

status: Public on Dec 20 2010

city: Rochester

first: Keith

last: Anderson

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: HER2-positive and HER2-negative samples are compared within this Whole Genome Platform

overall_design: Two-class comparison

first: Monica

last: Reinholz

first: Jeanette

last: Eckel-Passow

first: S

first: Yan

middle: W

last: Asmann

first: Michael

last: Zschunke

first: Ann

last: Oberg

last: McCullough

first: Amylou

middle: C

last: Dueck

first: Beiyun

last: Chen

first: Craig

last: April

first: Eliza

last: Wickham-Garcia

first: Robert

last: Jenkins

first: Julie

last: Cunningham

first: Jin

last: Jen

first: Edith

last: Perez

first: Jian-Bing

last: Fan

first: Wilma

last: Lingle


title: Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors

first: Keith

last: Anderson


title: Reprogramming of human primary somatic cells by OCT4 and chemical compounds

status: Public on Dec 03 2010

first: Saiyong

last: Zhu

address: 10550 North Torrey Pines Road,

institute: The Scripps Research Institute

summary:
Human induced pluripotent stem cells (hiPSCs) can be practically derived from neonatal human epidermal keratinocytes (NHEKs) transduced with OCT4, by a novel cocktail of small molecules including 5 μM PS48, 0.25 mM NaB, 0.5 μM A-83-01 and 0.5 μM PD0325901. These iPSCs are morphologically, molecularly and functionally similar to pluripotent hESCs.
NHEKs were cultured in a 100 mm tissue culture dish and transduced 3 times (3-4 hours each transduction) with freshly produced lentivirus supernatants. 1,000,000 transduced NHEKs were seeded on the irradiated x-ray inactivated CF1 MEF feeder cells in a 100-mm dish and cultured in KCM and treated with 5 μM PS48, 0.25 mM NaB (Stemgent) and 0.5 μM A-83-01 (Stemgent) for 2 weeks, followed by changing half volume of media to hESCM and supplementing with 5 μM PS48, 0.25 mM NaB and 0.5 μM A-83-01 for another 2 weeks. Then cell culture media were changed to hESCM and supplemented with 5 μM PS48, 0.25 mM NaB, 0.5 μM A-83-01 and 0.5 μM PD0325901 (Stemgent) for additional four weeks.The culture was split by Accutase (Millipore) and treated with 1 μM Thiazovivin (Stemgent) in the first day after splitting. The iPSC colonies stained positive by Alexa Fluor 555 Mouse anti-Human TRA-1-81 antibody (BD Pharmingen) were picked up for expansion on feeder cells in hESCM and cultured routinely.

overall_design: Global gene expression analysis of hiPSCs

first: Sheng

last: Ding


title: Murine Histone Methyltransferase Mll5, is involved in Male Gametogenesis

status: Public on Sep 30 2010

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

country: Canada

institute: British Columbia Cancer Agency

summary:
Male mice but not female Mll5 -/- mice are infertile. This study showed that post-meiotic spermatogenic maturation is impaired in Mll5 -/- mice. In order to investigate the role of Mll5 in spermatogenesis, a transcriptome analysis of whole testes from Mll5 knock out and wildtype mice was performed.
Affymetrix Mouse Exon chips were hybridized with testes material from three individual male mice from each wild-type or Mll5 -/- genotype, in order to identify gene regulation differences attributed to the loss of Mll5.

overall_design: One-way ANOVA: wildtype vs. Mll5-/-

first: Damian

last: Yap

first: David

last: Walker

first: Gulisa

last: Turashvili

first: Katrin

last: Mooslehner-Allen

first: Teresa

last: de Algara

first: Leah

last: Prentice

first: John

last: Fee

first: Xavier

last: d'Anglemont de Tassigny

first: William

middle: H

last: Colledge

first: Samuel

last: Aparicio


title: Whole genome mapping of p73 binding sites in ME180 human cervical carcinoma cells

status: Public on Sep 10 2010

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

summary: Using chromatin immunoprecipitation and high-resolution tiling arrays covering the human genome, we render a genome-wide map of p73 DNA binding sites in ME180 human cervical carcinoma cells.

overall_design: Crosslinked chromatin from ME180 cells was immunoprecipitated with anti-p73 monoclonal antibody (AKp73).

first: Annie

last: Yang

first: Zhou


title: Improved Innate and Adaptive Immunostimulation by Genetically Modified HIV-1 Protein Expressing NYVAC Vectors

city: port st-lucie

first: Ali

last: Filali

state: Florida

address: 11350 SW Village Parkway, 3rd Floor

institute: Vaccine & Gene Therapy Institute of Florida

summary: Attenuated poxviruses are safe and capable to express foreign antigens. Poxviruses are applied in veterinary vaccination and explored as candidate vaccines for humans. However, poxviruses express multiple genes encoding proteins that interfere with components of the innate and adaptive immune response. This manuscript describes two strategies aimed to improve the immunogenicity of the highly attenuated, host-range restricted poxvirus NYVAC: deletion of the viral gene encoding type-I interferon-binding protein and development of attenuated replication-competent NYVAC. We evaluated these newly generated NYVAC mutants, encoding HIV-1 env, gag, pol and nef, for their ability to stimulate HIV-specific CD8 T-cell responses from blood mononuclear cells of HIV-infected subjects. The new vectors were evaluated and compared to the parental NYVAC vector in dendritic cells (DCs), RNA expression arrays, HIV gag expression and direct and cross-presentation assays in vitro. Deletion of type-I interferon-binding protein enhanced expression of interferon and interferon-induced genes in DCs, and increased maturation of infected DCs. Restoration of replication competence induced activation of pathways involving antigen processing and presentation. Also, replication-competent NYVAC showed increased Gag expression in infected cells, permitting enhanced cross-presentation to HIV-specific CD8 T cells and proliferation of HIV-specific memory CD8 T-cells. The recombinant NYVAC combining both modifications induced interferon-induced genes and genes involved in antigen processing and presentation, as well as increased Gag expression. This combined replication-competent NYVAC is a promising candidate for the next generation of HIV vaccines.

overall_design:
RNA expression obtained from  DCs  infected by NYVAC-C-dB19R and NYVAC-C-KC-dB19R compared to RNA expression obtained from  DCs infected by NYVAC-C
Supplementary file 'normalized_data_Human_V3_V2.txt' reports data for ILMN identifiers common to platforms HumanRef8V2 and HumanRef8V3.

first: Esther

last: Quakkelaar

first: Anke

last: Redeker

first: Elias

last: Haddad

first: Alexandre

last: Harari

first: Stella

last: McCaughey

first: Thomas

last: Duhen

first: Abdelali

last: Filali-Mouhim

first: Jean-Phillipe

last: Goulet

first: Nikki

last: Loof

first: Ferry

last: Ossendorp

first: Beatrice

last: Perdiguero

first: Paul

last: Heinen

first: Carmen

last: Gomez

first: Karen

last: Kibler

last: Koelle

first: Rafick

last: Sékaly

first: Federica

last: Sallusto

first: Antonio

last: Lanzavecchia

first: Giuseppe

last: Pantaleo

first: Mariano

last: Esteban

first: Jim

last: Tartaglia

first: Bertram

last: Jacobs

first: Cornelis

last: Melief


title: RNA degradation in proliferating and differentiated C2C12 muscle precursor cells analyzed on Affymetrix exon arrays

status: Public on Sep 22 2010

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
Steady-state RNA levels are a result of RNA synthesis and degradation. The importance of transcription-factor mediated induction or repression of mRNA synthesis is well established, but the role and mechanisms of RNA degradation are less well understood. We globally evaluated the RNA decay rates in proliferating and differentiated mouse myoblasts on whole-genome Affymetrix exon arrays, allowing for the assessment of directionality of RNA degradation and the detection of splice variant-specific differences in RNA decay rates. We found large differences in decay rates. mRNAs coding for proteins involved in signal transduction and transcriptional regulation have shortest half lives, whereas mRNAs coding for DNA replication enzymes and muscle contraction proteins are among the most stable. Many genes differentially expressed between proliferating and differentiated myoblasts demonstrate major differences in RNA decay rates. Quantitative PCR experiments confirmed the higher stability of transcripts with increased expression levels. RNA degradation has no apparent preferential directionality. RNA degradation appears to affect the ratio of different splice variants. For example, Itga7 isoforms with higher abundance in differentiated than in proliferating cells are more stable in differentiated cells, despite the sharing of a common 3’ untranslated region. Thus, where it was previously thought that the abundance of different splice isoforms was mainly controlled by tissue-specific splicing factors, we now demonstrate that isoforms may be produced at comparable levels but degraded with different efficiencies, depending on the differentiation status of the cells. Our results indicate that control of RNA degradation rates contributes significantly to the differentiation stage-dependent differences in abundance of transcripts and splice variants.

Keywords: total RNA expression profiling; cultured cells

overall_design: We analyzed proliferating C2C12 cells and C2C12 cells differentiated into myotubes by serum starvation (8 days after induction of differentiation). We analyzed 7 time points after addition of actionmycin D (0, 10, 20, 30, 60, 150, 480 minutes). There were two biological replicates per condition.


title: Mesenchymal stromal cells from neonatal tracheal aspirates demonstrate a pattern of gene expression consistent with a lung origin

status: Public on Oct 08 2010

city: Ann Arbor

first: Marc

last: Hershenson

address: 1150 W Medical Center Dr

department: Pediatrics

institute: University of Michigan Medical School

summary: Expression profiling of lung derived mesenchymal stromal cells to lung fibrblasts and cord blood derived mesenchymal stromal cells

overall_design: We have previously isolated mesenchymal stromal cells (MSCs) from the tracheal aspirates of premature neonates with respiratory distress.  While isolation of MSCs correlates with the development of bronchopulmonary dysplasia, the physiologic role of these cells remains unclear.  To address this, we further characterized the cells, focusing on the issues of gene expression, origin and cytokine expression.  Microarray comparison of early passage neonatal lung MSC gene expression to cord blood MSCs and human fetal and neonatal lung fibroblast lines demonstrated that the neonatal lung MSCs differentially expressed 971 gene probes compared to cord blood MSCs, including the transcription factors Tbx2, Tbx3, Wnt5a, FoxF1 and Gli2, each of which have been associated with lung development.  Compared to lung fibroblasts, 710 gene probe transcripts were differentially expressed by the lung MSCs, including IL-6 and IL-8/CXCL8.  Further, neonatal lung MSCs exhibited a pattern of Hox gene expression distinct from cord-blood MSCs but similar to human fetal lung fibroblasts, consistent with a lung origin.  Together, these data suggest that MSCs isolated from neonatal tracheal aspirates originate in the lung and are distinct from lung fibroblasts.

last: Bozyk

first: Antonia

last: Popova

first: J

last: Bentley

first: Adam

last: Goldsmith

first: Marisa

last: Linn

first: Daniel

last: Weiss


title: Expression data from Control and Six1 expressing MCF7 cells

status: Public on Aug 21 2010

city: Aurora

first: Heide

last: Ford

state: CO

address: 12800 E 19th Ave RC1 North, Room 5102

department: OB/Gyn

institute: University of Colorado at Denver

summary: Inappropriate activation of developmental pathways is a well-recognized tumor-promoting mechanism. Here we show that overexpression of the homeoprotein Six1, normally a developmentally restricted transcriptional regulator, increases Transforming Growth Factor-beta (TGF-beta) signaling in mammary carcinoma cells and induces an epithelial to mesenchymal transition (EMT) that is in part dependent on its ability to increase TGF-beta signaling. TGF-beta signaling and EMT have been implicated in metastatic dissemination of carcinoma. Using spontaneous and experimental metastasis mouse models, we demonstrate that Six1 overexpression promotes breast cancer metastasis.  In addition, we show that, like its induction of EMT, Six1-induced experimental metastasis is dependent on its ability to activate TGF-beta signaling. Importantly, in human breast cancers Six1 significantly correlates with nuclear Smad3, and thus increased TGF-beta signaling. Further, breast cancer patients whose tumors overexpress Six1 have a shortened time to relapse and metastasis, and an overall decrease in survival. Finally, we show that the effects of Six1 on tumor progression likely extend beyond breast cancer, since its overexpression correlates with adverse outcomes in numerous other cancers, including brain, cervical, prostate, colon, kidney, and liver, amongst others. Our findings argue that Six1, acting through TGF-beta signaling and EMT, is a powerful and global promoter of cancer metastasis.

overall_design: This study has two parts: the first part compared three Control and three Six1 expressing MCF7 clones.  Total RNA was isolated from each clone on two separate occassions and hybridized to Affymetrix arrays. The second part compared MCF7-control and Six1 expressing cell lines expressing either GFP control or TbetaRIIDN.  Total RNA was isolated from each cell line on two separate occassions and hybridized to Affymetrix arrays

first: Douglas

last: Micalizzi


title: Chromatin Immunoprecipitation Analysis of Aryl Hydrocarbon Receptor Binding in a Mouse B-cell Line (CH12.LX) Activated with Lipopolysaccharide and Treated with 2,3,7,8-Tetrachlorodibenzo-p-dioxin

status: Public on Sep 01 2010

first: Russell

middle: Scott

last: Thomas

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary: The aryl hydrocarbon receptor (AHR) agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) alters differentiation of B cells and suppresses antibody production.  The objectives of this study was to use a combination of whole genome, microarray-based chromatin immunoprecipitation (ChIP-on-chip) and time course gene expression microarray analysis on the mouse B-cell line CH12.LX following exposure to lipopolysaccharide (LPS) or  LPS and TCDD to identify the primary and downstream  transcriptional elements of B-cell differentiation that are altered by the AHR.

overall_design: CH12.LX cells (1X10^5 cells/ml, 25ml in P150s) were treated with either 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)(10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR (Biomol, Plymouth Meeting, PA, Catalog #: SA210-0100). After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.  The ChIP studies were performed in triplicate (n = 3) with the cells for each replicate treated and harvested on separate days.

first: Nadira

last: De Abrew

first: Norbert

last: Kaminski


title: mCG-PML-RARA alters multipotent hematopoiesis.

status: Public on Oct 21 2010

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

summary: Acute promyelocytic leukemia (APL) is associated with PML-RARA expression and late myeloid maturation arrest. The myeloid restriction of PML-RARA dependent leukemia has been recapitulated in multiple mouse models of APL, including PML-RARA expressed from the Ctsg locus (mCG-PR). However, we report here that Ctsg expression is not limited to promyelocytes (as had previously been thought); Ctsg RNA is detectable in KLS cells, and mCG-PR mice express PML-RARA within the same compartment, an event that alters multilineage hematopoiesis. However, these animals only develop myeloid leukemia (consistent with the myeloid restriction of human PML-RARA-associated leukemia). Our results suggest that APL is shaped by myeloid- and development-specific factors that define the ultimate leukemic phenotype rather than PML-RARA acting in a committed myeloid precursor.

overall_design: Bone marrow from individual mice expressing PML-RARA from the murine Ctg locus (mCG-PR) and littermate controls was harvested from both femurs and tibia. Standard cell lysis was performed and total RNA was extracted from the flow sorted KLS and SLAM cells. A total of 13 specimens including 3 x mCG-PR_KLS_6wks, 2 x mCG-PR_KLS_13wks,2 x mCG-PR_SLAM_7wks, 4 x WT_KLS_12-13wks (control) and 2 x WT_SLAM_6wks (control) were analyzed using Affymetrics Mouse Exon 1.0 ST platform.

first: John

last: Welch

first: Lukas

last: Wartman

first: Geoffrey

last: Uy

first: Rakesh

last: Nagarajan

first: Timothy

last: Ley


title: Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls: Exon array data

status: Public on Aug 04 2010

city: New York

first: Chaolin

last: Zhang

state: NY

address: 1230 York Ave

department: Molecular Neuro-Oncology

institute: Rockefeller University

summary: The control of RNA alternative splicing is critical for generating biological diversity. Despite emerging genome-wide technologies to study RNA complexity, reliable and comprehensive RNA-regulatory networks have not been defined. Here we used Bayesian networks to probabilistically model diverse datasets and predict the target networks of specific regulators. We applied this strategy to identify ~700 alternative splicing events directly regulated by the neuron-specific factor Nova in the mouse brain, integrating RNA-binding data, splicing microarray data, Nova-binding motifs, and evolutionary signatures. The resulting integrative network revealed combinatorial regulation by Nova and the neuronal splicing factor Fox, interplay between phosphorylation and splicing, and potential links to neurologic disease. Thus we have developed a general approach to understanding mammalian RNA regulation at the systems level.

overall_design: RNA from the whole brain or spinal cord of 4 wild type and 4 Nova1/2 double KO (dKO) E18.5 CD1 mice. One array per biological replicate.

first: Taesun

last: Eom

first: Matteo

last: Ruggiu

last: Fak

first: Robert

middle: B

last: Darnell


title: COP1 siRNA knockdown in human Hepatocellular carcinoma cells

status: Public on Nov 01 2010

city: Bethesda

first: Daekwan

last: Seo

state: MD

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

summary: Development of targeted therapeutics for hepatocellular carcinoma (HCC) remains a major challenge. We have previously demonstrated that constitutively photomorphogenic 1 (COP1), which regulates p53 activity by ubiquitination, is frequently overexpressed in human HCC. Here we examined whether molecular targeting of COP1 by small interfering (si) RNA can affect the course of HCC progression. COP1-1 was selected as the most effective target siRNAs in terms of growth inhibition and apoptotic induction in several HCC cell lines. Interestingly, the growth inhibition occurred both in HCC cells that retain wild-type p53 or express mutant p53 (Y220C or R249S). Next we have determined to investigate the molecular mechanisms underlying the phenotypic changes. Given the recent findings that COP1 functions as a negative regulator of p53, we addressed whether the phenotypic changes caused by COP1 silencing were due to alterations in p53 and/or p21 status. Indeed, in COP1-depleted HepG2 cells expressing wild type p53, induction of apoptosis was associated with restoration of p53 function as judged by a marked increase in the levels of p53 and its target p21, suggesting that cell death was p53-dependent. However, the COP1 silencing in Huh7 cells, which carry Y220C mutation, caused a strong induction of apoptosis without changing p53 levels. To further address this issue, we next looked for the global transcriptional changes underlying the antitumor effects of COP1 silencing in HCC cells [with different p53 status]. For this purpose, Huh7 and HepG2 were treated with NCsiRNA and COP1-1siRNA for 48 hours and subjected to illumina microarray analysis. We found that the number of differentially expressed genes which displayed more than a 2-fold change (P < 0.01 by Bootstrap t-test) was 462 (167 up- and 295 down-regulated genes) and 522 (179 up- and 343 down-regulated genes) in COP1siRNA-treated Huh7 and HepG2 cells, respectively. As expected, the expression levels of RFWD2 (COP1) mRNA were significantly reduced in both treated HCC cell lines. Consistent with phenotypic changes, COP1-depleted Huh7 cells also displayed changes in p53-associated group of genes functionally involved in regulation of apoptosis, growth and differentiation including CASP6, GLIPR1, FHL2, GADD45A, HMOX1 BCL6, FOXO3, GDF15, and SCNN1A genes. Finally, we generated the common COP1 knockdown gene signature which included 78 genes. The Ingenuity Pathway Analysis analysis revealed that the 5 top putative networks with high score (>19) were strongly associated with NF-κB, HNF4α, TNF, and p53 pathways, suggesting that a common subset of molecular alterations in the diverse oncogenic pathways may cooperatively result in growth inhibition of HCC cells with wild type and mutant p53. Analysis of COP1 knockdown gene expression signatures by microarray revealed that the anti-proliferative effect was driven by a common subset of molecular alterations including p53-associated functional network. Systemic delivery of a modified COP1siRNA by stable-nucleic-acid-lipid-particles (SNALP) significantly suppressed neoplastic growth in liver, without unwanted immune response in an orthotopic xenograft model. These findings provide the first proof of principle that COP1 is a promising target for systemic therapy of HCC.

overall_design: Microarray was performed on human Ref-8v3 microarrays (illumina) as recommended by the manufacture. In detail, total RNAs were isolated 48 h after the transfection of NCsiRNA or COP1-1siRNA to Huh7, HepG2 or Hep3B cells. Biotin-labeled cRNA was linearly amplified according to manufacturer’s specification (AMIL1791; Ambion, Austin, TX). As input, 200 ng total RNA from tumor was used for the in vitro transcription (IVT) reactions which were incubated for 16 h at 37 ºC. The efficiency of this single round amplification was measured by NanoDrop (ND1000, Thermo Scientific). Hybridization, washing, detection (Cy3-streptavidin, Amersham Biosciences, GE Healthcare) and scanning were performed on an Illumina iScan system (Illumina) using reagents and following protocols supplied by the manufacturer. Briefly, the biotinylated cRNA (750 ng/sample) was hybridized on Sentrix whole genome beadchips human Ref-8v3 for 18 h at 58ºC while rocking (5 rpm). The beadchip covers ~ 24,000 RefSeq transcripts. Image analysis and data extraction were performed automatically using Illumina GenomeScan Software. To explore the functional relationships among the genes with altered expression in the HCC cells treated with COP1-1siRNA, a pathway analysis was carried out with the Ingenuity Pathway Analysis tool (Ingenuity Systems). Using the approach, we examined functional associations among genes and generated the gene networks with high significance on the basis that they had more of the interconnected genes present than would be expected by chance. The significance of each network was estimated by scoring system provided by Ingenuity. The scores are determined by the number of differentially expressed genes within each of the networks and the strength of the associations among network members. Once over-represented genes that are functionally relevant in gene networks are identified, we validated their functional association by using the independent pathway analysis tool PathwayStudio (Ariadne Genomics).

first: Yun-Han

last: Lee

first: Deakwan

first: Jesper

last: Andersen

first: Jens

middle: U

last: Marquardt

first: Snorri

last: Thorgeirsson


title: RARA haploinsufficiency modestly influences the phenotype of APL.

status: Public on Jul 29 2010

summary: RARA haploinsufficiency is an invariable consequence of t(15;17) reciprocal translocations in acute promyelocytic leukemia (APL). Furthermore, retinoids and RARA activity have been implicated in hematopoietic self-renewal, lineage commitment and neutrophil maturation. We and others therefore predicted that RARA haploinsufficiency would contribute to APL pathogenesis. To test this hypothesis we crossed RARA+/- mice with mice expressing PML-RARA from the Cathepsin G locus (mCG-PR). We found that RARA haploinsufficiency cooperated with PML-RARA, only modestly influencing the pre-leukemic and leukemic phenotype. Bone marrow from mCG-PR+/- x RARA+/- mice had decreased numbers of mature myeloid cells, increased ex vivo myeloid cell proliferation and an increased competitive advantage following transplantation. RARA haploinsufficiency did not alter mCG-PR dependent leukemic latency or penetrance, but did influence the distribution of leukemic cells; mCG-PR+/- x RARA+/- mice presented more commonly with low to normal white blood cell counts and with myeloid infiltration of lymph nodes. APL arising in these mice was responsive to ATRA, and had virtually no differences in expression profiling compared to tumors arising in mCG-PR+/- x RARA+/+ mice. These phenotypes were dependent on PML-RARA activity, since they were not detected in RARA+/- mice in the absence of the mCG-PR transgene. These data show that RARA haploinsufficiency (like PML haploinsufficiency and RARA-PML) can cooperate with PML-RARA to influence the pathogenesis and phenotype of APL in mice, but that PML-RARA is the driver of t(15;17) APL.

overall_design: RARA+/- mice were crossed with mice expressing PML-RARA from Cathepsin G locus (mCG-PR). Five leukemic mice were chosen from each of the mCG-PR+/-RARA+/- and mCG-PR+/-RARA+/+ strains and total RNA extracted from the spleen samples were analyzed using Affymetrics Mouse Exon 1.0 platform

first: Jeffery

last: Klco

first: Pierre

last: Chambon


title: Expression profile in bone marrow Nestin-GFP cells

status: Public on Jul 15 2010

city: Bronx

first: Paul

last: Frenette

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: Expression profile analysis in steady-state bone marrow-derived GFP+ cells obtained from transgenic mice in which GFP expression is regulated under the nestin gene promoter

overall_design: Three replicates


title: Genome-wide analysis of gene expression response upon infection with Toxoplasma gondii

status: Public on Aug 01 2010

city: Spokane

first: Lucia

last: Peixoto

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

summary:
The in vitro effect of infection with different strains of Toxoplasma gondii was tested 24 hours after infection of Human Foreskin Fibroblasts (HFF)
The strains tested include RH, VEG, and transgenic strains of RH overexpressing ROP38 or ROP21

overall_design: Total RNA of Toxoplasma gondii infected HFF cell was compared to uninfected cells

last: Davis

first: David

last: Roos


title: Genome-wide methylation analysis in HPV(-) and HPV(+) squamous cell carcinoma cell lines

status: Public on Dec 01 2010

first: Jung

last: Kim

address: 1420 Washington Heights

institute: University of Michigan

type: Methylation profiling by genome tiling array

summary: HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. To assess the genome-wide methylation changes in HPV(+) and HPV(-) tumors, we analyzed DNA methylation and expression patterns in two HPV(+) and two HPV(-) cell lines. HPV(+) tumors have overall higher DNA methylation in genic and LINE1 regions than HPV(-) tumors, and polycomb repressive complex 2 (PRC2) targets tend to be much more highly methylated in HPV(+) cells.

overall_design:
MeDIP-ChIP performed with GenPathway using 4mg of DNA.  Cell lines analyzed: UM-SCC-4, UM-SCC-47, UM-SCC-74A, and CaSki. Methylated DNA was compared to mock-immunoprecipitated input DNA.

The BED files with "HPVpos" in the name contain the regions more highly methylated in the HPV(+) samples, and the BED files with "HPVneg" in the name contain the regions more highly methylated in the HPV(-) samples.

first: Maureen

last: Sartor

first: Dana

last: Dolinoy

first: Thomas

last: Carey

first: Tamara

last: Jones

first: Justin

last: Colacino

first: Laura

last: Rozek


title: Type 2 Diabetes mellitus: mRNA and miRNA profiling

status: Public on Dec 18 2010

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

institute: National University of Singapore

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

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: Normal rat diaphragm vs sternohyoid

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

summary: Normal young adult Sprague Dawley rats (male)

overall_design: 6 diaphragm muscle samples are compared with 6 sternohyoid muscle samples -- each sample is one muscle from one rat


title: Gene expression changes in multiple sclerosis relapse suggest activation of T and non-T cells

status: Public on Jun 30 2010

city: Houston

first: John

middle: William

last: Lindsey

address: 6431 Fannin, Suite 7.044

department: Neurology

institute: University of Texas Health Science Center at Houston

summary:
paired comparison of RNA expression in peripheral blood mononuclear cells in the same group of 14 multiple sclerosis patients while stable and while in relapse.
A defining feature of multiple sclerosis is the occurrence of clinical relapses separated by periods of clinical stability.  Better understanding of the events underlying clinical relapse might suggest new approaches to treatment.  We used microarrays to measure mRNA expression in the peripheral blood of 14 MS patients during clinical relapse and while stable.  Seventy-one transcripts changed expression at the p<0.001 significance level.  The most notable finding was decreased expression of transcripts with regulatory function, expressed primarily in non-T cells.  Transcripts with increased expression were primarily expressed in T cells.  Pathways analysis suggested involvement of the cytokine network, coagulation and complement cascades, IL-10 signaling, and NF-?B signaling.

overall_design: total RNA from PBMC in relapse and while stable from 14 multiple sclerosis patients

first: J


title: Genome-wide analysis of fetal adrenocortical cells gene expression after 48 h ACTH treatment

status: Public on Jun 16 2010

city: Augusta

first: yewei

last: xing

state: GA

address: 1120 15th street

department: Physiology

institute: Medical College of Georgia

summary: Analysis of ACTH-regulation on adrenocortical cells at gene expression level. The hypothesis tested in the present study was that ACTH increases chronic cell growth and steroidogenesis in adrenal glands by changing the gene expression profile. Results provide important information on the changes of gene expression of adrenocortical cells after chronic ACTH treatment.

overall_design: Total RNA obtained from primary cultured fetal adrenal cells subjected to 48 hours in vitro treatment of ACTH compared to untreated control cell.

first: Yewei

last: Xing

first: William

last: Rainey

first: Richard

last: Parker


title: A distinctive DNA damage response in human hematopoietic stem cells reveals an apoptosis independent role for p53 in self-renewal

status: Public on Jun 29 2010

city: Toronto

first: Michael

last: Milyavsky

state: Ontario

address: 101 College street

department: Department of Stem Cell and Developmental Biology

institute: Ontario Cancer Institute, Toronto General Research Institute, University Health Network

summary: Analysis of differentially expressed genes in human Cord Blood cells cultured for 4 days and sorted into CD34+CD90+ and CD34+CD90- fractions. The objective for the experiment was to identify genes related to p53 and DNA damage response pathways

overall_design: Total RNA  was isolated from at least 10000 cells after 4 days of culture and sorting

last: Dick


title: Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma (CGH)

status: Public on Jun 10 2010

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

summary: Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). Array-CGH results was validated by FISH using tumors showing HER2/neu gene amplification and expression profiling was confirmed using qPCR for 16 transcripts.

overall_design: Genomic DNA was isolated from fresh-frozen tissue samples

middle: Z

first: Anna

last: Danielsson

first: Szilard

last: Nemes

first: Anikó

last: Kovács

first: Ulla

last: Delle

first: Ghita

last: Fallenius

first: Elin

last: Möllerström

first: Per

last: Karlsson

first: Khalil

last: Helou


title: The Androgen Receptor Modulates Expression of Genes with Critical Roles in Muscle Development and Function

status: Public on Jul 08 2010

city: Collegeville

first: Yuchen

last: Bai

state: PA

address: 500 Arcola Road, S2316

department: CIBB

institute: Pfizer

summary:
Androgen signaling through the androgen receptor (AR), a ligand-dependent transcription factor within the steroid receptor superfamily, plays an important role in the development and maintenance of many tissues. In muscle, androgens act as anabolic agents that increase both muscle mass and strength; however, a key unanswered question is the mechanism through which AR-mediated gene expression leads to these effects. To gain further insight into the mechanism of AR action in muscle, we identified AR binding sites in primary human muscle cells using chromatin immunoprecipitation followed by tiling microarray detection (ChIP-on-Chip).
Through this analysis, we identified 32,518 potential AR binding sites throughout the genome that were enriched upon androgen treatment. Sequence analysis of these regions indicated that approximately 90% possess a consensus androgen response element or half-site. Among the identified AR binding sites are genes known to be directly regulated by AR, confirming the validity of our methodology. Additionally, we identified a number of novel AR targets, including genes and microRNAs implicated in muscle differentiation and function, suggesting a direct role for AR-mediated transcription in muscle development. Intriguingly, binding sequences for the Mef2 family of transcription factors were enriched in the AR-bound regions, and we show that several Mef2c-dependent genes are direct targets of AR, suggesting a functional interaction between Mef2c and AR in skeletal muscle. Our results provide new insights into the mechanisms by which androgens promote muscle growth, and validate AR as a potential therapeutic target for sarcopenia, muscle wasting, and other androgen-related muscle disorders.

overall_design: Primary human muscle cells treated with 5alpha-dihydrotestosterone (DHT) or vehicle ChIPed with AR antibody vs. IgG and Input

first: Anastasia

last: Wyce

first: Sunil

last: Nagpal

first: Catherine

last: Thompson


title: Blood microRNA profiles and upregulation of hsa-miR-144 in males with type 2 diabetes mellitus.

status: Public on Apr 24 2010

first: Kandiah

last: Jeyaseelan

department: Biochemistry

summary:
In this study, we compared the expression profiles of miRNAs in blood samples from Impaired Fasting Glucose (IFG) and T2D male patients. Healthy adult males with no past history of T2D (n=158) and with desirable cholesterol and blood pressure profiles were enrolled in this study. They were then classified according to fasting glucose levels to have T2D, IFG or as healthy controls (CTL), for comparison of miRNA expression profiles. Employing miRNA microarray, we identified ‘signature miRNAs’ in peripheral blood samples that distinguished IFG and T2D. Eight selected miRNAs were further validated using stem-loop real-time RT-PCR. miR-144 expression was found to be dysregulated in Type 2 Diabetes, wherein its expression was significantly higher than in healthy controls. Insulin receptor substrate 1 (IRS1) has been predicted to be a potential target of miR-144. Consistent with this observation, IRS1 mRNA and protein levels, verified by quantitative real-time PCR and western blotting respectively, were found to be down-regulated.
Dysregulation in expression of microRNAs (miRNAs) in various tissues has been linked to a wide spectrum of diseases, including Type 2 Diabetes mellitus (T2D). In this study, we compared the expression profiles of miRNAs in blood samples from Impaired Fasting Glucose (IFG) and T2D male patients. Healthy adult males with no past history of T2D (n=158) and with desirable cholesterol and blood pressure profiles were enrolled in this study. They were then classified according to fasting glucose levels to have T2D, IFG or as healthy controls (CTL), for comparison of miRNA expression profiles. Employing miRNA microarray, we identified ‘signature miRNAs’ in peripheral blood samples that distinguished IFG and T2D. Eight selected miRNAs were further validated using stem-loop real-time RT-PCR. miR-144 expression was found to be dysregulated in Type 2 Diabetes, wherein its expression was significantly higher than in healthy controls. Insulin receptor substrate 1 (IRS1) has been predicted to be a potential target of miR-144. Consistent with this observation, IRS1 mRNA and protein levels, verified by quantitative real-time PCR and western blotting respectively, were found to be down-regulated. Using luciferase assay, we further demonstrated that miR-144 directly targets IRS1 and showed its effects on protein expression via immunocytochemistry. From this cross-sectional study in humans, we have identified signature miRNAs which could explain the pathogenesis of T2D. Whether miRNAs like miR-144 could be potential therapeutic targets for management of T2D will need to be explored by further mechanistic and functional studies.

overall_design: Total RNA (plus miRNAs) was isolated using a modification of the RiboPure™-Blood kit from Ambion (Austin,TX) according to the manufacturer’s protocol. The concentration of total RNA and integrity were determined by using Nano-Drop ND-1000 Spectrophotometry (NanoDrop Tech, Rockland, Del) and gel electrophoresis respectively.

first: DwiSetyowati

last: Karolina

first: Arunmozhiarasi

last: Armugam

first: Tavintharan

last: Subramaniam


title: The effect of ERG overexpression and ERG knockdown by shRNA in RWPE1 and VCAP cells, respectively

status: Public on Aug 26 2010

city: Turku

first: Santosh

middle: Kumar

last: Gupta

address: 4th floor pharma city

department: University of Turku

institute: VTT medical biotechnology

summary: The goal of this project was to analyze the global gene expression profiles of RWPE1 and VCAP cells following transfection of GFP, GFP-ERG at 48 and 72hrs time points and stable ERG shRNA, scramble shRNA, respectively.

overall_design: RWPE1 cells were transfected with GFP or GFP-ERG. VCAP cells were transfected with ERG lenti-shRNA or scramble shRNA. Transfections were performed in duplicate. Total cellular RNA was isolated with Trizol and quality analysed by the bioanalyser kit.

first: Iljin

last: Kristiina

first: Sara

last: Henri

first: Nees

last: Matthias


title: Most “dark matter” transcripts are associated with known genes

status: Public on May 18 2010

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: A series of reports over the last few years have indicated that a much larger portion of the mammalian genome is transcribed than can be accounted for by currently annotated genes, but the quantity and nature of these additional transcripts remains unclear. Here, we have used data from single- and paired-end RNA-Seq and tiling arrays to assess the quantity and composition of transcripts in PolyA+ RNA from human and mouse tissues. Relative to tiling arrays, RNA-Seq identifies many fewer transcribed regions (‘‘seqfrags’’) outside known exons and ncRNAs. Most nonexonic seqfrags are in introns, raising the possibility that they are fragments of pre-mRNAs. The chromosomal locations of the majority of intergenic seqfrags in RNA-Seq data are near known genes, consistent with alternative cleavage and polyadenylation site usage, promoter- and terminator-associated transcripts, or new alternative exons; indeed, reads that bridge splice sites identified 4,544 new exons, affecting 3,554 genes. Most of the remaining seqfrags correspond to either single reads that display characteristics of random sampling from a low-level background or several thousand small transcripts (median length = 111 bp) present at higher levels, which also tend to display sequence conservation and originate from regions with open chromatin. We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Genome-wide expression profiling of human and mouse total and polyA+ RNA from four different tissue sources (brain, heart, liver, testes) was performed using Affymetrix tiling microarrays (Human & Mouse tiling 2.0R array set; 7 arrays per genome).

BAR files: HBP - Human Brain PolyA+ RNA; HBT - Human Brain Total RNA; HLP - Human Liver PolyA+ RNA; HLT - Human Liver Total RNA; HHP - Human Heart PolyA+ RNA; HHT - Human Heart Total RNA; HTP - Human Testes PolyA+ RNA; HTT - Human Testes Total RNA; MBP - Mouse Brain PolyA+ RNA; MBT - Mouse Brain Total RNA; MLP - Mouse Liver PolyA+ RNA; MLT - Mouse Liver Total RNA; MHP - Mouse Heart PolyA+ RNA; MHT - Mouse Heart Total RNA; MTP - Mouse Testes PolyA+ RNA; MTT - Mouse Testes Total RNA

last: vanBakel

first: Corey

last: Nislow

first: Benjamin

middle: J

last: Blencowe

first: Timothy

last: Hughes


title: 5-azacytidine treatment reorganizes genomic histone modification patterns

status: Public on Apr 09 2010

city: Seattle

first: Vitalina

last: Komashko

address: 1100 Fairview Ave N

institute: Sage Bionetworks

summary: Methylation of DNA in combination with histone modifications establishes an epigenetic code that ensures the proper control of gene expression. Although DNA methyltransferases have been shown to interact with histone methyltransferases such as EZH2 (which methylates histone H3 on lysine 27) and G9a (which methylates histone H3 on lysine 9), the relationship between DNA methylation and repressive histone marks has not been fully studied. In cancer cells, promoters of genes are often aberrantly methylated. Accordingly, 5-azacytidine (a DNA demethylating drug) is used for treating patients with myelodysplastic syndrome. However, no genome-scale studies of the effects of this drug have been reported. In this work, we report the effects of 5-azacytidine on global gene expression and analyze ~24,000 human promoters using ChIP-chip to determine how 5-azacytidine treatment effects H3K27me3 and H3K9me3 levels. We found that (1) 5-azacytidine treatment results in large changes in gene regulation with distinct functional categories of genes showing increased (e.g. C2H2 zinc finger transcription factors) and decreased (e.g. genes involved in regulation of mitochondria and oxidoreductase activity) levels; (2) most genes that show altered expression are not regulated by promoters that display DNA methylation prior to the treatment; (3) certain gene classes switch their repression mark upon treatment with 5-azacytidine (from H3K27me3 to H3K9me3 and vice versa); and (4) most changes in gene expression are not due to relief of repression mediated by DNA or histone methylation.

overall_design:
5 ChIP-chip arrays.
6 gene expression samples: 3 treatments with 2 biological replicates per treatment.

middle: M

first: Peggy

last: Farnham


title: Microarray analysis of normal and tumor-like bone cells from neonatal-onset multisystem inflammatory disease (NOMID)

status: Public on May 15 2010

first: Madson

middle: Q

last: Almeida

address: 10 Center Drive, MSC 1103

department: Section on Genetics and Endocrinology / NICHD

summary: We analyzed the whole transcriptome profiling of NOMID normal and tumor-like bone cells

overall_design: Total RNA obtained from NOMID bone tumor culture was compared to NOMID normal cartilage cells established from the same patient.

first: M

first: R

last: Goldback-Mansky

first: C

middle: A

last: Stratakis

last: Cheadle

first: T

last: Watkins


title: Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Ovarian Tumor Tissue Samples: Dilutions

status: Public on Jan 13 2010

city: San Diego

first: Craig

last: April

address: 9885 Towne Centre Drive

institute: Illumina, Inc.

summary: Performance assayed with formalin-fixed, paraffin-embedded (FFPE) ovarian tumor tissues.

overall_design:
Total RNA obtained from two human ovarian FFPE tumors (DFCI 120, DFCI 129) using six different RNA input amounts (250 pg, 1 ng, 5 ng, 10 ng, 50 ng, 200 ng).

The supplementary file 'GSE18769_nonorm_nobkgd.txt' contains non-normalized data for Samples GSM465821-GSM465844.


title: Whole-Genome Gene Expression of Formalin-Fixed, Paraffin-Embedded Intact and Artificially Degraded Tissue Samples

summary: Assay performance comparison between intact and artificially degraded RNA samples

overall_design: Total RNA obtained from two human cancer cell lines, intact and artificially degraded


title: Gene expression in hepatocytes and bile ducts from ANIT-treated rats

status: Public on Feb 24 2010

city: Research Triangle Park

first: Neal

middle: F

last: Cariello

state: NC

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

institute: GlaxoSmithKline

summary: Acute toxic responses to a single 50 mg/kg oral dose of 1-napthylisothiocyanate (ANIT) were evaluated by microarray analysis of laser capture-microdissected rat biliary epithelium or hepatic parenchyma at 2 and 6 hours post-dose. Selective and dramatic differences between the biliary epithelium and the hepatic parenchyma were evident as soon as 2 hours at which time 375 genes were altered in biliary epithelium, but only a nominal 38 genes were altered in the hepatic parenchyma. Gene expression analysis revealed increased expression of genes involved in the unfolded protein response and ER stress in biliary epithelial cells, but no alteration of these genes in hepatocytes. By 6 hours post dose, 620 genes showed altered expression in biliary epithelium while there were only 32 genes altered in hepatic parenchyma. At this timepoint, analysis of the biliary epithelium revealed decreased expression of genes involved in the unfolded protein response compared to the 2 hour time point, and increased expression at 6 hours of genes involved in protein degradation such as proteasome-ubquination pathways, and genes associated with cell death. Our analysis revealed early loss of biliary epithelial integrity and attempts at repair of damage with subsequent activation of protein degradation and cell fate decisions leading to death pathways within a 6 hour time course. During this same time interval, hepatic parenchymal gene expression changed little and mainly reflected a decrease in enterohepatic circulation of bile acids and an increase in ribosomal proteins which may signal an adaptive change to reduced bile acid delivery to the liver and an increased demand for bile acids and glutathione-mediated transport of ANIT. This versatile approach provides a precise evaluation of distinct cell populations, biliary epithelium and hepatic parenchyma, in situ. (Cullen et.al., Toxicologic Pathology 2010)

overall_design: Rat were exposed to a single dose of 1-napthylisothiocyanate (ANIT) or vehicle. Laser capture-microdissection was used to isolate rat biliary epithelium or hepatic parenchyma at 2 and 6 hours post-dose. Affymetrix GeneChips and Rosetta Resolver were used to determine differential gene expression.

first: James

middle: G

last: Falls

first: John

last: Cullen


title: Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples - dilution series

state: CA

summary: Assay performance with low RNA inputs

overall_design: Total RNA obtained from two human cancer cell lines, input dilution series (100 ng to 10 pg)

middle: S


title: Coativator Function Defines the Active Estrogen Receptor Alpha Cistrome

status: Public on Dec 09 2009

city: Lebanon

first: Mathieu

last: Lupien

address: One Medical Center Drive

department: Genetics

institute: Norris Cotton Cancer Center/Dartmouth Medical School

summary: Genome-wide ChIP-on-Chip against RNA Pol II in untreated MCF7 cells (phenol-red free media) and H3R17me2 in untreated and estrogen (45 min) treated cells.

overall_design: MCF7 breast cancer cells were grown in phenol-red free media, cross-linked and processed as in (Carroll et al 2005). DNA was hybridized to GeneChip® Human Tiling 2.0R Array Set.


title: Whole-Genome Gene Expression Profiling of FFPE in Normal and Tumor Lung Tissue Samples

summary: Comparison between fresh-frozen and Formalin-Fixed, Paraffin-Embedded tissues

overall_design: Total RNA obtained from normal and tumor human lung tissues, fresh-frozen and FFPE


title: Genome-wide analysis of miRNA-targeted cellular NMD substrates in HeLa cell

status: Public on Mar 08 2010

city: Seoul

first: Junho

last: Choe

address: Sungbuggu Anam 5ga

department: korea University

country: South Korea

institute: School of Life science and Biotechnology

summary:
Analysis of miRNA-targeted cellular NMD substrates in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates containing long 3' untranslated region may targeted for miRNA. Results provide important information expanding the roles of miRISC in the posttranscriptional regulation of gene expression: a new cross-talk between miRNA-mediated gene silencing and NMD.
ABSTRACT: Imperfect base-pairing between microRNA (miRNA) and the 3’-untranslated region (3’UTR) of target mRNA triggers translational repression of the target mRNA. Here, we provide evidence that human Argonaute 2 (Ago2) targets cap-binding protein (CBP)80/20- and exon junction complex (EJC)-bound mRNAs and inhibits nonsense-mediated mRNA decay (NMD), which is tightly restricted to CBP80/20-bound mRNAs. Furthermore, microarray analyses reveal that a subset of cellular transcripts, which are expected to be targeted for NMD, is stabilized by miRNA-mediated gene silencing. The regulation of NMD by miRNAs will shed light on a new post-transcriptional regulation mechanism of gene expression in mammalian cells

overall_design: Total RNA obtained from HeLa cells with downregulation of Ago2 or Ago2/UPF1 by siRNA. The up- or down-regulated transcripts were compared to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication.

first: Hana

last: Cho


title: Whole-Genome Gene Expression Profiling of FFPE Raji and MCF-7 Mixed Ratio Tissue Samples

summary: Assay performance with mixed RNA samples

overall_design: Total RNA obtained from two human cancer cell lines, mixed at different ratios


title: DNA methylation of developmental genes in pediatric medulloblastomas identified by DAMD

status: Public on Dec 05 2009

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

institute: Fred Hutchinson Cancer Research Center

summary: DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary medulloblastomas in critical developmental regulatory pathways, including Sonic hedgehog (Shh), Wingless (Wnt), retinoic acid receptor (RAR), and bone morphogenetic protein (BMP). One of the commonly methylated loci is the PTCH1-1C promoter, a negative regulator of the Shh pathway that is methylated in both primary patient samples and human medulloblastoma cell lines. Treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dC) increases the expression of PTCH1 and other methylated loci. Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1, and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. This finding warrants strong consideration for DNA demethylating agents in future clinical trials for children with this disease.

overall_design: Genome-wide DNA methylation profiles generated using the Denaturation Analysis of Methylation Differences (DAMD) assay. Samples analyzed: Colo320DM vs. HDF; HCT116 vs. DKO; and 4 primary human medulloblastoma samples vs. adult normal cerebellum

first: Jamie

last: Guenthoer

first: Linda

middle: N

last: Geng

first: Sarah

middle: E

last: Mahoney

first: Michael

last: Marotta

last: Olson

first: Hisashi

last: Tanaka

first: Stephen

last: Tapscott


title: Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Ovarian Tumor Tissue Samples: Ratios

overall_design:
Total RNA obtained from two human ovarian FFPE tumors (DFCI 121, DFCI 123) using seven different RNA input mixes (100% 121 / 0% 123, 75% 121 / 25% 123, 66% 121 / 33% 123, 50% 121 / 50% 123, 33% 121 / 66% 123, 25% 121 / 75% 123, 0% 121 / 100% 123).

The supplementary file 'GSE18767_nonorm_nobkgd.txt' contains non-normalized data for Samples GSM465767-GSM465808.


title: Complementary proteomics and transcriptomics sheds light on drug detoxifying proteins of the endoplasmic reticulum

status: Public on Nov 24 2009

first: Paul

middle: C

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
The hepatic endoplasmic reticulum contains a series of enzymes that oxidize and conjugate lipid and steroids. Together, these enzymes form a molecular machine that plays key roles in the metabolism of both endogenous and xenobiotic compounds. To characterize this molecular machine, we used quantitative proteomics to assess the frequency of occurrence of detected peptides within each primary sequence, leading to the assessment of the relative abundances of 137 of these proteins. These 137 proteins include over 38 different cytochrome P450s, 11 glucuronosyltransferases, and 9 carboxylesterases. Our sensitive approach was able to detect P450 allelic isoforms which differ by only a single amino acid and clearly resolved 4 splice variants of the glucuronosyltransferases. We identified a cytosolically-exposed DID motif for 3 cytochrome P450s that were located with high abundance in the Golgi apparatus as well the lack of a C-terminal HXEL motif for the sole carboxylesterase highly abundant in the Golgi. Using gene expression microarrays, we also characterized the hepatic transcriptome, and a comparison of proteomics and transcriptomics indicated a requirement for both technologies in order to provide insight into protein families of drug detoxification. In this way, a major hurdle of hepatotoxicity related to drug development may be overcome.
Keywords: steady-state mRNA levels

overall_design: Four replicate Sprague-Dawley rats were assessed, each on an individual microarray.

first: Ivy

middle: D

last: Moffat

first: Raimo

last: Pohjanvirta

first: Allan

middle: B

last: Okey

first: Souad

last: Lesimple

first: Alex

middle: W

last: Bell

first: Catherine

last: Au

last: Hallet

first: Robert

last: Kearney

last: Bergeron


title: Rat Semi-Circular Canal Duct Gene Expression Studies

status: Public on Apr 14 2010

city: Manhattan

first: Daniel

last: Marcus

state: KS

address: 228 Coles Hall

department: Anatomy & Physiology

institute: Kansas State University

summary:
The goal was to screen for the expressed genes in Semi-Circular Canal Duct (SCCD) that are related to ion transport and its regulation.  The objectives was to discover which genes changed expression levels in response to glucocorticoids.
Keywords: drug response

overall_design: Primary cultures were incubated for 24 hours in the presence or absence of 100 nM dexamethasone.  Four independent cultures from each group were processed for total RNA and submitted for gene array analysis.  Although two Samples out of four in each group were done at different time points, we found that there was not much variation between the datasets (by cluster analysis).

first: Nithya

last: Raveendran

first: Satyanarayana

middle: R

last: Pondugula


title: Dioxin lethality: aryl hydrocarbon receptor (AHR)-mediated gene expression in a rat resistant model

summary:
Major toxicities of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) result from dysregulation of gene expression mediated by the aryl hydrocarbon receptor (AHR).  Dioxin-like chemicals alter expression of numerous genes in liver but the specific genes whose dysregulation leads to toxicities such as wasting, hepatotoxicity and lethality have not been identified.  We searched for genes that are most likely to be key to dioxin toxicity by using gene expression arrays to contrast hepatic gene expression after TCDD treatment in dioxin-sensitive rats (that carry wildtype AHR) with gene expression in H/W(Kuopio) rats which are highly resistant to dioxin toxicity due to a major deletion in the AHR's transactivation domain (TAD).  The total number of TCDD-responsive genes was smaller in rats with the AHRH/W genotype than in rats with wildtype AHR.  However, genes in the classic AH gene battery such as CYP1A1, CYP1A2 and CYP1B1 remained fully responsive to TCDD in AHRH/W rats; thus the TAD deletion selectively interferes with expression of a subset of hepatic genes rather than abolishing global AHR-mediated responses. Genes in the following functional categories differ in response to TCDD between dioxin-sensitive rats and dioxin-resistant rats: fatty acid  oxidation, metabolism (xenobiotic, alcohol, amino  acid,  and fatty  acid), phosphate transport, regulation of  steroid  biosynthesis, nitrogen compound  catabolism, and generation of  precursor  metabolites  and  energy.  Many of these differentially-responsive genes are integral parts of pathways such as: protein degradation and synthesis, fatty acid metabolism and synthesis, cytokinesis, cell growth, and apoptosis which may be part of mechanisms which lead to TCDD-induced wasting, hepatotoxicity, tumors, and death. These differentially-responsive genes are worthy candidates for further mechanistic studies to test their role in mediating or protecting from major dioxin toxicities.
Keywords: Treatment-Control, Inter-Strain, Time-Course

overall_design: Four strains of rats were either treated with 100 ug/kg TCDD or cornoil vehicle and profiled at 19 hours, each with four replicates. Two strains were also analyzed at 3 hours, each with four replicates.

first: Jouni

middle: T

last: Tuomisto


title: mRNA Levels in the Rat Liver Display Strain-Specific, Hereditary and AHR-Dependent Components

summary:
Background
The rat is a major model organism in toxicogenomics and pharmacogenomics, and the use of steady-state hepatic mRNA levels to predict and understand drug toxicity and mechanism is well-established. Surprisingly, the inter- and intra-strain variability of rat mRNA expression has not been evaluated, nor has the extent of its hereditability been established. We address these issues by studying three rat strains (Long-Evans, Hans/Wistar, and Sprague-Dawley) and two F2 lines derived from Long-Evans x Hans/Wistar crosses.
Results
Using three independent techniques – variance analysis, linear modelling, and unsupervised pattern recognition – we characterize large amounts of both intra- and inter-strain variability in mRNA levels. Importantly, both sources of variability are highly non-random, and are enriched for specific functional groups. Specific transcription-factor binding-sites are enriched in their promoter regions, and these genes occur in “islands” throughout the rat genome. Using the two F2 crosses we study the hereditability of hepatic mRNA levels and show that the majority of rat genes appear to exhibit directional genetics, with only a small fraction having evidence for interacting loci. Finally, a comparison of inter-strain heterogeneity between mouse and rat orthologs shows more heterogeneity in rats than mice, and find that rat and mouse heterogeneity are uncorrelated.
Conclusions
Our results establish that hepatic mRNA levels are relatively homogeneous within rat strains, but highly variable between them. This variability may be related to increased activity specific transcription-factors, and has clear functional consequences. Future toxicogenomic and pharmacogenomic studies may take advantage of this phenomenon by surveying panels of rat strains.
Keywords: Inter-Strain Comparison

overall_design: We profiled the basal mRNA levels in three strains and two lines of rat, each using four biological replicates.


title: Exon-based clustering of tumor transcriptomes reveals alternative exons associated with metastasis in breast cancer

status: Public on Nov 19 2009

city: lyon

first: didier

last: auboeuf

address: 28 rue Laenec

country: France

institute: inserm

summary: Exonic profiling is an emerging topic in disease-associated transcriptome analysis, but is still facing major limitations. In this study, we performed a microarray-based analysis of the transcriptome at the exon level of mouse primary mammary tumors having different abilities to give rise to metastases. First, we developed a bioinformatics platform and used a stringent algorithm to identify 679 genes with differentially expressed exons in primary tumors of the 4T1 mouse model of mammary tumor progression. We tested 152 alternative exons by RT-PCR and validated 97 of them as being differentially expressed across primary tumors with different metastasis capability. Many of the 679 identified genes are involved in cellular morphology and movement. This analysis not only pointed to genes involved in cellular functions relevant to tumor progression, but also hinted to protein features targeted by variations at the exon level. Second, we developed a novel exon-based clustering analysis of tumor transcriptomes and identified alternative exons associated with the ability of cells to disseminate from primary mammary tumors into the lungs. A large set of these alternatively spliced exons was differentially expressed across normal tissues and/or conserved during evolution. These data indicated that the splicing events identified by comparing primary tumors were not aberrant events. Finally, we demonstrated that a set of differentially expressed variants, which we identified in the murine model, were associated with poor prognosis in a large cohort of breast cancer patients. In conclusion, this approach constitutes a valuable resource for both the understanding and the development of prognosis/diagnosis markers of tumor metastatic potential.

overall_design: 12 Total samples were analyzed: 3 x 67NR primary tumors; 3 x 168FARN primary tumors; 3 x 4T07 primary tumors; 3 x 4T1 primary tumors;

first: Martin

last: Dutertre

first: Magali

last: Lacroix-Triki

first: Keltouma

last: Driouch

first: Pierre

last: de la Grange

first: Lise

last: Gratadou

first: Samantha

last: Beck

first: Stefania

last: Millevoi

first: Jamal

last: Tazi

first: Rosette

last: Liderau

first: Stephan

last: Vagner

first: Didier

last: Auboeuf


title: Diaphragm in Diabetes

status: Public on Nov 13 2009

first: Erik

last: van Lunteren

address: 10701 East Boulevard

institute: Cleveland VA Medical Center

summary:
8 week old rats injected with streptozotocin or buffer alone at age of 8 weeks, diaphragm muscle obtained at age of 12 weeks (thus animals were diabetic for 4 weeks)
Keywords: Disease state analysis (diabetes)

overall_design:
Three control rats (normal diaphragm #1, 2, 3)
Three diabetic rats (diabetic diaphragm #1, 2, 3)

first: Michelle

last: Moyer


title: Whole-Genome Gene Expression Profiling of FFPE Tissue Samples with WG-DASL and IVT-based assays

first: Craig

last: April

summary: Cross-platform comparison between WG-DASL and IVT-based assays

overall_design: Total RNA obtained from two human cancer cell lines, compared using WG-DASL and Direct Hyb assays


title: Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Ovarian Tissue Samples

summary: Performance assayed with FFPE tissues

overall_design: Total RNA obtained from four human ovarian FFPE tumors using two different RNA inputs (200 ng and 50 ng)


title: JMJ and PRC2 ChIP-chip data from mouse embryonic stem cells

status: Public on Dec 29 2009

city: Boston

first: Xiaohua

last: Shen

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

type: Genome variation profiling by genome tiling array

summary:
We used ChIP-chip to reveal genome-wide locationation of JMJ and Polycomb proteins including EZH2, SUZ12 and EED in undifferentiated wild-type (CJ7) embryonic stem (ES) cells.

Keywords: ChIP-chip

overall_design: DNA fragments pulled down by chromatin immunoprecipitation, amplified and hybridization on Affymetrix tiling arrays.

first: Stuart

last: Orkin


title: Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples

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

overall_design: Refer to individual Series


title: Wild type vs. Nova2 KO mouse: Exon array data

status: Public on Nov 04 2009

first: Donny

last: Licatalosi

address: 10900 Euclid Ave

institute: Case Western Reserve University

summary: To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP).  HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo.  HITS-CLIP revealed a large number of Nova-RNA interactions in 3’ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.

overall_design: RNA from the cortex of 4 wild type and 4 Nova2 KO P10 CD1 mice.  One array per biological replicate.

first: Robert

last: Darnell


title: The relationship between brain mRNA levels and behaviour among inbred Lewis rats: Experiment 1

first: Paul

last: Boutros

summary:
Behaviour is derived from complex molecular interactions within the brain, in response to specific environmental stimuli. In some rare cases, the direct causes of behaviour have been attributed to the interactions of a single or small group of gene transcripts and proteins. We conducted two experiments with the hope of defining some of the molecular interactors for four separate behaviours: sugar feeding, locomotor activity in a novel field, and acoustic startle reflex, and prepulse inhibition of the acoustic startle reflex, which have been linked to prefrontal cortex dopaminergic function or as predictors of sensorimotor gating in diseases such as schizophrenia. Rats with high and low response phenotypes were selected to determine the differences between these two extremes of behaviour. From our analyses, transcripts of Homer1, a neuronal scaffolding protein which interacts with group1 metabotropic glutamate receptors, were found to be significantly correlated with array data in both experiments, and with behaviour data across three separate tests in the second experiment, indicating that this gene's transcripts and probably downstream protein interactions have a significant correlation with behaviour phenotype in the inbred Lewis rat. Future areas of pursuit for this data should involve modification of the expression of Homer1 in an isolated fashion to determine a pharmacological threshold for differences in behaviour.

Keywords: Phenotype-Association Study

overall_design: Nine rats with varying behavioural phenotypes were analyzed.  Three behavioural tests: SF, locomotion, and ASR.

first: Laura

last: Feldcamp

first: Susan

last: Rotzinger

first: Mawahib

middle: O

last: Semeralul

first: Franco

last: Vaccarino

first: Arturas

last: Petronis

first: Albert

middle: H

last: Wong


title: Wild type vs. Nova2 KO mouse P10 cortex RNA

type: Genome binding/occupancy profiling by array

summary:
To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP).  HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo.  HITS-CLIP revealed a large number of Nova-RNA interactions in 3’ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Adult and Neonatal dorsal horn gene expression 7 day post sciatic nerve SNI injury

status: Public on Oct 30 2009

city: London

first: Caroline

middle: Emma

last: Johnston

address: 125 Coldharbour Lane

country: United Kingdom

institute: Kings College London

summary:
As rats do not develop neuropathic pain like hypersensitivity as neonates post nerve injury but do as adults we have used these arrays to help define the processes involved in this process.
Rat spinal cord (ipsilateral dorsal horn) was assayed 7 days post SNI injury to the sciatic nerve relative to sham injury. Two age groups of animals were tested Neonates (P10) and Adult (8-12wks).

Keywords: Two way analysis of differential regulation

overall_design: Six biologically indepenedent arrays were hybridized per assay point.  Dorsal horn total RNA was prepared using standard Affymetrix protocols. Affymetrix Rat Expression 230A array used.

first: Michael

last: Costigan

first: Andrew

last: Moss


title: Expression data from rat (Sprague Dawley) brain subjected to MCAo.

status: Public on Sep 04 2009

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

institute: National University of Singapore

summary:
Middle cerebral artery occlusion (MCAo) in rat represent the ischemic stroke in human. Rodents subjected to MCAo and treated with venom phospholipase A2 showed reduction in infarct volume after 24hours of stroke.
We studied the global gene expression of the reduction in infarct volume using Affymetrix Gene Chips. We analysed all the genes that were up or down regulated in the study.

overall_design: Total RNA isolated from sham, MCAo and MCAo+nPLA rat brains, was pooled to minimize inter-individual variation and hybridized to each array of the RAE-230A or U34A GeneChipTM according to protocols described in the GeneChipTM expression analysis package (Affymetrix, CA).

first: Arunmozhiarasi

last: Armugam


title: Molecular variability of FLT3/ITD mutants and their impact on the differentiation program of 32D cells

status: Public on Sep 12 2009

city: Basel

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University of Basel

summary:
FLT3 is the most frequently mutated gene in AML – up to 40% of AML harbor an activating mutation within FLT3 gene. Though AML is a relatively rare disease, such a high mutability rate, as observed with FLT3 gene, is striking. To elucidate the molecular background of this phenomenon, we have established nine unique FLT3/ITD - carrying 32D cell lines and a set of controls, and subjected them to whole genome expression analysis and 2DE LC/MS proteomics. Data obtained on this so far largest set of ITD mutants indicates that in comparison to the wild type FLT3 expressing 32D cells and transduction controls, FLT3/ITD positive cells exhibit less mature expression profiles resembling ST-HSC and MkEP/CMP/LMPP progenitors. We hypothesize that FLT3/ITD might contribute not only to the proliferative advantage of FLT3/ITD positive cells, but also to their reprogramming towards less differentiated stages, thus strengthening their malignant properties. This finding might explain the pronounced mutation rate of the aberrantly expressed FLT3 gene in AML, and, also, the inferior prognosis of FLT3/ITD positive AML patients. Moreover, the microarray data has revealed biological differences among individual ITD variants – a finding supporting the recent clinical data on the prognostic impact of the size of individual ITDs.

Keywords: genetic modification

overall_design: Nine stable 32D cell lines harboring unique human FLT3/ITD mutants, two parental 32 cell lines, two 32D stable cell lines harboring cloning vector only, and two 32D cell lines stably expressing human wild type FLT3 were subjected to the microarray analysis.

first: Sona

last: Pekova

first: Michal

last: Dvorak

first: Sabrina

last: Rueggeberg

first: Stefan

last: Leicht

first: Tomas

last: Kozak

first: Jiri

last: Vrba

last: Schwarz

first: Petr

last: Cetkovsky

first: Miroslav

last: Prucha