title: Gene expression in cardiac tissues from infants with idiopathic conotruncal defects

status: Public on Jan 20 2011

city: Kansas City

first: Douglas

middle: C

last: Bittel

state: MO

address: 2401 Gillham Rd

department: Genetics research

institute: Childrens Mercy Hospital

summary:
Tetralogy of Fallot (TOF) is the most commonly seen type of conotruncal congenital heart defect. Treatment of these patients has evolved dramatically in the last few decades, yet a genetic explanation for the failure of cardiac development is lacking for the majority of children with TOF.  Our goal was to examine genome wide gene expression to characterize expression patterns in cardiovascular tissue (right ventricle, pulmonary valve and pulmonary artery) obtained at the time of reconstructive surgery from 19 children with tetralogy of Fallot.  We employed genome wide gene expression microarrays to characterize cardiovascular tissue (right ventricle, pulmonary valve and pulmonary artery) obtained at the time of reconstructive surgery from 19 children with tetralogy of Fallot (16 idiopathic and 3 with 22q11.2 deletions) and compared gene expression patterns to normally developing subjects.

We detected a signal from approximately 26,000 probes (ranging from 35% to 49% of array probes in the three tissues), reflecting expression from about half of all genes.  More than 1000 genes had a 2-fold change in expression in the right ventricle (RV) of children with TOF compared to RV from matched control infants.  Most of these genes were involved in compensatory functions (e.g., hypertrophy, cardiac fibrosis and cardiac dilation).  However, two canonical pathways involved in spatial and temporal cell differentiation (WNT, p = 0.017 and Notch, p = 0.003) appeared to be generally suppressed.  The suppression of developmental networks may be a remnant of a broad malfunction of regulatory pathways leading to inaccurate boundary formation and improper structural development in the embryonic heart.  We suggest that small tissue specific genomic and/or epigenetic fluctuations could be cumulative, leading to regulatory network disruption and failure of proper cardiac development.

overall_design:
Analyzed RNA extracted from right ventricle of 16 idiopathic TOF patients and 5 controls.

This submission represents the right ventricle component of the study.

first: Nataliya

last: Kibiryeva


title: Expression profiling of human umbilical cord mesenchymal stem cell line hMSCs, human esophageal carcinoma cell line EC9706 and their hybrids EMFs.

status: Public on Jan 21 2011

city: Beijing

first: Antican

last: Wang

state: Beijing

address: #17 Pan Jia Yuan Nan Li, Chao Yang District.

department: State Key Lab of Molecular Oncology, Department of Etiology and Carcinogenesis

country: China

institute: Cancer Institute and Hosital, Chinese Academy of Medical Sciences.

summary: Our findings demonstrate that hMSCs can inhibit the malignant phenotypes of ECs through induced cell fusion without potentially cancerous reprogramming. To further understand the differences between before-after cell fusion and the mechanism of suppression, we used gene expression profiling technology from Capitalbio to find out the differences between EC cells, hMSCs and their derived heterokaryons.

overall_design: Six dual channel Capitalbio 22K Human oligo arrays was used to hybrid six paired samples (EC9706-cy3+EMF1-cy5, EC9706-cy3+EMF2-cy5, EC9706-cy3+EMF3-cy5, EMF1-cy3+hMSCs-cy5, EMF3-cy3+hMSC-cy5, hMSC-cy3+EMF2-cy5).One replicate per array.

first: Bing

last: Zhou


title: KYSE170 transfected with ncRNA or miR-210

status: Public on Jan 05 2011

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

country: Japan

institute: Kumamoto University

summary: MicroRNAs are small non-coding RNA species, some of which are playing important roles in malignancies. However, roles of miR-210 in cancer have yet to be unknown and controversial. Here, we found the expression level of miR-210 is downregulated in human esophageal squamous cell carcinoma and its cell lines. Additionally, we demonstrate that miR-210 inhibits cancer cell survival and proliferation through upregulation of cell death and induction of cell cycle arrest at G1/G0 and G2/M phases. However, candidate target mRNAs of miR-210 and the mechanism behind observed phenomena is uncertain. Then, we performed comprehensive gene expression analysis to identify candidate target mRNAs and understand their mechanisms.

overall_design: KYSE-170 cells were transfected with oligoribonucleotides for miR-210 or ncRNA (Ambion, Austin, TX) using Hiperfect (Qiagen, Valencia, CA) according to the provider’s protocol for overexpression. Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method and was labeled and prepared for hybridization to human Oligo chip 25k (Toray, Kamakura, Japan) using standard methods.


title: Benign prostate epithelial cell gene expression after four weeks of treatment with daily transdermal DHT or placebo gel

status: Public on Jan 19 2011

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

summary: Significant increases in serum DHT do not increase intraprostatic levels of DHT, PSA, prostate volume, or prostate epithelial cell androgen-regulated gene expression in healthy men. Changes in serum androgen concentrations are not necessarily mimicked within the prostate.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile benign prostate epithelium from twenty-seven men, twelve of which were treated for four weeks with daily transdermal DHT and 15 which were placebo gel treated controls. All samples were laser-capture microdissected and total RNA isolated and amplified prior to hybridization against a reference reference prostate cell line pool.

first: Stephanie

middle: T

last: Page

first: Daniel

middle: W

last: Lin

first: Elahe

last: Mostaghel

first: Brett

last: Marck

first: Jonathan

last: Wright

first: John

middle: K

last: Amory

first: Alvin

middle: M

last: Matsumoto


title: Genes regulated by Sox2 in glioma cancer cell line

status: Public on Jan 10 2011

city: HangZhou

first: Biaoyang

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

institute: ZheJiang University

summary:
Knockdown of Sox2 in LN229 gliomal cancer cells decrease their growth rates in vitro.
We used microarrays to detail the global programme of gene expression in Sox2 Knockdown LN229 cells compared with mock knockdown LN229 cells

overall_design: Sox2 knockdown LN229 cells and and mock knockdown LN229 cells were cultured in DMEM cell culture media for RNA extraction and hybridization on  Applied Biosystems Human Genome Survey Microarrays . We sought to obtain the genes regulated by Sox2 in glioma cell line.

first: Xuefeng

last: Fang


title: Gene expression comparisons of megakaryocyte-erythrocyte progenitors isolated from wild type and c-MybTG/c-MybTG mice

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

institute: Tohoku University Graduate School of Medicine

summary:
Transgene insertion in proximity to the c-Myb gene disrupts c-Myb expression in megakaryocyte-erythrocyte progenitors (MEPs), resulting in skewed commitment to megakaryocyte lineage.
To understand the genes regulated by c-Myb at the megakaryocyte-erythrocyte bifurcation,  MEPs of c-MybTG/c-MybTG mice were examined.  Detailed analysis on c-MybTG/c-MybTG is descried in the paper by Mukai et al, Mol Cell Biol 2006.

overall_design: The IL-7R-Lin-Sca-1–c-Kit+ fraction was subdivided into FcR loCD34+, FcRloCD34-, and FcRhiCD34+ populations.  Among them, FcRloCD34- fraction was use as MEPs.  MEPs from 16 wild type mice and those from 32 c-MybTG/c-MybTG mice were pooled and used for RNA purification.

first: Y

middle: H

last: Mukai

first: T

last: Kohno

first: H

first: M

last: Yamamoto


title: Expression profiling of rat MHC and NKC genes in skin explant assays reveals genes that are regulated in GVHD

status: Public on Jan 04 2011

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary:
Expression profiling of rat major histocompatibility complex and natural killer complex genes in skin explant assays reveals genes that are regulated in graft versus host disease.
The major histocompatibility complex (MHC) is the most important genomic region that contributes to the genetic risk of graft rejection and graft versus host disease (GVHD) after haematopoietic stem cell transplantation. Therefore, MHC matching is most essential for the success of clinical transplantations. However, the MHC contains in addition to MHC class I and class II genes that are genotyped for selection of donors further so far unidentified genes that also contribute significantly to the risk to develop acute GVHD. It is difficult to identify these MHC genes by genetic association studies alone due to linkage disequilibrium in this region. Therefore, we aimed to identify MHC genes that might be involved in the pathohysiology of GVHD by expression profiling. To reduce the complexity of our model, we used genetically well-defined inbred rat strains (PVG and BN) and skin explant assays, an in-vitro-model of graft versus host reaction (GVHR), to analyse the expression of MHC and natural killer complex (NKC) genes in a cutaneous GVHR by a custom microarray. A higher percentage of genes in these immunologically highly important genomic regions were regulated than in the rest of the genome. We observed a statistically significant regulation of 25 MHC and 6 NKC genes and 168 other genes (i.e., 4.9%, 14.0%, and 6.6%, respectively) in rat skin explants cultured in the presence of pre-stimulated allogeneic lymphocytes compared to control samples cultured in the presence of syngeneic lymphocytes. Seven MHC and 3 NKC genes were selected for analysis by quantitative real-time polymerase chain reaction PCR. Most of the results of the microarray were confirmed in the same experimental set that was used for the microarray analysis and in a second independent experimental set of skin explant samples. In addition, GVHD-affected skin lesions of transplanted rats were analysed and similar regulations of most of the selected MHC and NKC genes were observed. Thus, our skin explant model of GVHR is informative for the gene regulation during GVHD. Interestingly, the human homologues of several of the regulated genes are polymorphic and could therefore contribute to the genetic risk of GVHD. These genes include RT1-Dmb, C2, Aif1, Spr1, Ubd, and Olr1. The human homologues of these genes might be useful for risk assessment and diagnosis of GVHD in patients.

overall_design: Two-condition experiment, Stimulated vs. NonSimulated cells. 12 Biological replicates, 2 Technical Replicates (Dye Swap) per Biological Replicate.

first: Anne

last: Dickinson


title: Genome-wide expression analysis comparing SKOV3ip1 and the taxane-resistant SKOV3TRip2

status: Public on Jan 01 2011

city: Birmingham

first: Charles

last: Landen

state: AL

address: 1825 University Blvd Rm 505

department: Obstetrics and Gynecology

institute: University of Alabama at Birmingham

summary: We sought to compare mRNA expression profiles between the parental SKOV3ip1 and taxane-resistant SKOV3TRip2 in order to determine what genes are mediating taxane resistance

overall_design:
3 separate collections of each cell line were made, with cells at 75-80% confluence growing on 2-dimentional culture plates, and RNA extracted with RNAeasy kit

Authors were unable to retrieve raw data.

middle: N

first: Lance

middle: D

last: Miller


title: Mouse infections with Neospora caninum

city: Sydney

last: Ellis

state: NSW

address: Broadway

department: Medical & Molecular Biosciences

country: Australia

institute: University of Technology Sydney

summary: Transcriptional responses occurring in the spleen in response to N. caninum infection compared to uninfected mice

overall_design: Two conditions: infected and un-infected mice; Biological replicates: three (or four) infected and three uninfected mice. One control and one infected per array

first: Duncan

last: Sinclair


title: Pathology and Protective Immune Response in Pigs Infected with Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) of High and Low Virulence

status: Public on Jan 15 2011

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

summary:
Porcine reproductive and respiratory disease (PRRS) is the most important disease in swine industry worldwide. However, strategies such as vaccination and good biosecurity are not consistently successful to eliminate PRRSV. Though some interesting pathways have been tentatively examined recently, host molecular pathways utilized by PRRSV and the protective immune responses in resistant to PRRSV are largely unknown. In order to answer these questions, we herein characterize changes in global gene expressions in multiple tissues [tonsil, tracheobronchial lymph nodes (TBLN), Cranial lung (CR Lung), and distal lung (D Lung)] in response to PRRSV of high and low virulence. Both vaccinated and unvaccinated pigs are used for this study.
Based on Ingenuity Pathway Analysis (IPA), molecule bases of some “black boxes” underlying immune responses are further identified. Our results indicate that cross talks among these pathways and immune balances/competition between host and virus are always happened during the pathogenesis of PRRS.

overall_design: connected loop design was used to accommodate samples from 4 treatment groups.

first: Juan

middle: P

last: Steibel

first: Joan

last: Lunney


title: Microarray for density study of mouse Adipose-derived Stromal Cells (ASCs)

status: Public on Jan 16 2011

city: Stanford

first: Michael

last: Longaker

state: CA

address: 257 Campus Drive

department: Department of Surgery

institute: Stanford University

summary: Cytoskeletal tension is an intracellular mechanism through which cells convert a mechanical signal into a biochemical response, including production of cytokines and activation of various signaling pathways.  Adipose-derived stromal cells (ASCs) were allowed to spread into large cells by seeding them at a low-density (1,250 cells/cm2), which was observed to induce osteogenesis.  Conversely, ASCs seeded at a high-density (25,000 cells/cm2) featured small cells that promoted adipogenesis.  RhoA and actin filaments were altered by changes in cell size.  Blocking actin polymerization by Cytochalasin D influenced cytoskeletal tension and differentiation of ASCs.  To understand the potential regulatory mechanisms leading to actin cytoskeletal tension, cDNA microarray was performed on large and small ASCs.  Connective tissue growth factor (CTGF) was identified as a major regulator of osteogenesis associated with RhoA mediated cytoskeletal tension.  Subsequently, knock-down of CTGF by siRNA in ASCs inhibited this osteogenesis.  Therefore, we conclude that cytoskeletal tension is important for CTGF-regulated ASC osteogenic differentiation.

overall_design: Computed

first: Yue

last: Xu


title: aCGH study of lobular carcinoma in situ (LCIS) and invasive lobular carcinoma (ILC)

status: Public on Dec 31 2010

city: Toronto

first: Susan

last: Done

state: ON

address: 200 Elizabeth Street, 11E444

country: Canada

institute: University Health Network

summary: The identification of lobular caricnoma in situ (LCIS) in a patient's specimen confers and appreciable increased risk of development of future invasive mammary carcinoma. However the study of LCIS presents a challenge as it is usually only recognized in fixed specimens and no good in vivo or in vitro models currently exist. Recent advances in high throughput genomics have made possible comprehensive copy number analysis of lesions such as this. We have characterized LCIS on microdissected cases of archival patient samples using aCGH. We used 4 cases of LCIS with adjacent ILC.

overall_design: Histological sections from 4 cases of LCIS and 4 cases of ILC microdissected, DNA extracted and subjected to whole genome amplification, and aCGH.

middle: J

first: Danh

last: Tran-Thanh


title: Investigation of extra-telomeric effects of hTERT in neoplastic transformation of IMR90 cells

city: Singapore

first: Tan

last: Wei Han

address: 21 Lower Kent Ridge Road

country: Singapore

institute: National University of Singapore

summary: The complexity and heterogeneity of cancer cells are under-represented by the current experimental models which revolve around primary tumor cells, cancer cell lines, and rodent models. We used the transformed cell model in our studies. IMR90 and BJ fibroblast cells were transformed by three oncogenic genetic factors, SV40 Large-T antigen, H-Ras and human telomerase (hTERT). These transformed cells can grow under anchorage independent conditions, are self-sufficient in growth signals, have decreased sensitivity to apoptosis, and showed recurrent chromosomal abnormalities. Further characterization of transformed cells through cell cycle profiling and mass spectrometry analysis also revealed an increased fraction in the G2/M phase, and an up-regulation of Ku70. Furthermore, transformed cells exhibited increased telomerase activity that was not accountable by hTERT overexpression alone. Microarray results revealed that hTERT overexpression promoted cell migration and the initiation of DNA damage responses; two cellular processes that are important in cancer progression. Collectively, these data imply that IMR90 transformed cell model is an invaluable tool for cancer studies. Our results in the systematic study of this model helped us identify possible early events in cancer transformation and reveal the extra-telomeric effects of telomerase in cell migration and DNA damage initiation.

overall_design: IMR90 and BJ fibroblast cells were transformed by three oncogenic genetic factors, SV40 Large-T antigen, H-Ras and human telomerase (hTERT). Through microarray analysis, gene expression of transformed cells were compared against control cells.

first: Dashayini

last: Mahalingam

first: Zhicong

last: Luo

first: Wei

last: Tan

first: Xueyi

last: Huang

first: Yoon

last: Lim

first: Lih-Wen

last: Deng

first: Valere

last: Cacheux-Rataboul

first: Edison

last: Liu

first: Elizabeth

last: Blackburn

first: Xueying

last: Wang


title: Array CGH between GK and Wistar Rats for Detecting Copy Number Variations

city: Shanghai

first: Zhi-Qiang

last: Ye

address: No. 320 of Yueyang Road

institute: Shanghai Institutes for Biological Sciences

type: Genome variation profiling by genome tiling array

summary:
The Goto-Kakizak (GK) rat, a nonobese animal model of Type 2 diabetes (T2D), were developed by repeated inbreeding of glucose-intolerent individuals selected from Wistar rats. During their development, GK rats suffer from reduced beta-cell mass and insulin resistance spontaneously (T2D phenotype), which are supposed to be caused by loci holding different genotypes between GK and Wistar rats.
This array CGH experiment can detect loci which show different copy numbers (genotype) between GK and Wistar rats. These loci serve as a valuable repository for mining candidates contributing to the pathogenesis of T2D.

overall_design: The genomic DNA taken from 3 male GK rats as 3 test samples while pooled genomic DNA from 8 male Wistar rats as the common referrence. For each of the hybridization, a dye-swap was designed as well.

first: Rong-Xia

last: Li

first: Yang

last: Yu

first: Yuan-Yuan

first: Shen

last: Niu


title: Gene Expression Profiling Data of African Malaria Vector Anopheles gambiae Aging

city: Irvine

first: Mei-Hui

address: 3501B Hewitt Hall UCI

institute: UC irvine

summary: Senescence is a biological phenomenon experienced by all living eukaryote organisms. Genome-wide gene expression associated with aging has been explored in model organisms such as Drosophila melanogaster and Caenorhabditis elegans, but this has not been well understood in African malaria vector, Anopheles gambiae. Gene expression profiling using DNA microarray allows for simultaneous study of changes in mRNA levels for thousands of genes. This study examined genome-wide gene expression during aging process in An. gambiae. The influence of blood feeding on gene expression was also examined.  The data can be used to further our understanding of mosquito senescence and identify biomarkers for mosquito age grading.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Transcriptional profiles of Anopheles gambiae female mosquitoes were determined at 1, 4, 10, 19 and 28 days post adult eclosion. Additionally mosquitoes that had access to blood meals were compared to those that were maintained with access to only water and sugar.

first: Osvaldo

last: Marinotti

first: A

middle: A

last: Jame

first: E

last: Walker

first: G

last: Yan


title: Elucidating Host-Pathogen Interaction in Acute Systemic Candidiasis in a Mouse Model Using Genomic Approach

city: Serdang

first: Phelim

last: Yong

state: Selangor

address: Faculty of Medicine and Health Sciences

department: Biomedical Sciences

country: Malaysia

institute: Universiti Putra Malaysia

summary: Candida species is a common fungus that had evolved as both commensal and opportunistic pathogen in humans. The rise in human morbidity and mortality caused by Candida species sparked an alarming concern.  However, the thin line between commensalism and infection as well as the analysis of Candida host-pathogen interactions has not been completely elucidated prior to the birth of global gene expression technologies. Gene expression analysis of host response upon systemic candidiasis had been carried out using Beadarray and validated by using GenomeLab™ GeXP multiplex PCR. Whole blood from infected mouse was isolated, globin mRNA depleted through subtractive hybridization and its RNA purified. Results from microarray data demonstrated increased expression of genes involved in the pathogen recognition, signal transduction, inflammation, microbial killing and in antigen processing. Interestingly, we also discovered possible increment of erythropoiesis in our animal model and this lead us to believe that Candida tropicalis might possess potent haemolytic factors to sequester iron from the host erythrocytes.  Taken together, our data also suggest novel genes such as syndecans and dendritic cell immunoreceptor which might be exploited by Candida tropicalis in its pathogenesis in the host. Nevertheless, the challenge ahead is to understand the specific roles of these genes that underlies in Candida tropicalis pathogenesis.

overall_design: For gene expression analysis, BALB/c mice (six-week-old female weighing 20-25g) were used and the animals were randomized, assigned to the control, sublethal infection and lethal infection groups. At the time of killing, mice were anesthetized and exsanguinated by cardiac puncture. Approximately 200 µl of whole blood was collected and added into 2 ml tubes preloaded with RNAlater (Sigma-Aldrich CO, USA) and stored in -80 °C.

first: V

first: P

last: Chong


title: The expression profiles of 82 novel and 245 known human imsRNAs

status: Public on Dec 21 2010

first: Shunmin

last: He

address: 15 Datun Road, Chaoyang District

department: National Laboratory of Biomacromolecules

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The expression profiling of 245 known and 82 novel imsRNAs (intermediate-size noncoding RNAs, 50-500nt, which were identified from human fetal brain tissue) across different human fetal tissues (brain, heart, liver, lung and spleen at the 24-week gestation stage), different fetal brain gestational stages (13w, 14w, 20w, and 24w) and two human brain tumor cell lines (SHSY-5Y and U251).

overall_design: The analysis was based on the loop design method, in which all combinations of two samples  were simultaneously hybridized to a microarray, each of the two sample labeled with a different fluorescent probe (Cy3 or Cy5).

first: Dongsheng

first: Dandan


title: The effects of 3OC12-HSL on global gene expression in primary human aortic endothelial cells (HAEC).

status: Public on Dec 30 2010

city: Los Angeles

first: Juyong

middle: Brian

last: Kim

address: 675 Charles Young Dr.

department: Department of Medicine

institute: UCLA School of Medicine

summary:
Analysis of the effect of a bacterial quorum sensing molecule on in-vitro culture of human endothelial cells at gene expression levels.
Objective: Chronic infection has long been postulated as a stimulus for atherogenesis. Pseudomonas aeruginosa infection has been associated with increased atherosclerosis in rats, and the bacteria produce a quorum sensing molecule 3-oxo-dodecynoyl-homoserine lactone (3OC12-HSL) that is critical for colonization and virulence.  Paraoxonase 2 (PON2) hydrolyzes 3OC12-HSL and also protects against the effects of oxidized phospholipids thought to contribute to atherosclerosis.  We now report the response of human aortic endothelial cells (HAEC) to 3OC12-HSL and oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (Ox-PAPC) in relation to PON2 expression.
Methods and Results: Using expression profiling and network modeling, we identified the unfolded protein response (UPR), cell cycle genes, and the MAPK signaling pathway to be heavily involved in the HAEC response to 3OC12-HSL. The network also showed striking similarities to a network created based on HAEC response to Ox-PAPC, a major component of minimally-modified LDL.  HAEC in which PON2 was silenced by siRNA showed increased pro-inflammatory and UPR responses when treated with 3OC12-HSL or Ox-PAPC.
Conclusion: 3OC12-HSL and Ox-PAPC influence similar inflammatory pathways.   Quorum sensing molecules such as 3OC12-HSL contribute to the pro-atherogenic effects of chronic infection and the anti-atherogenic effects of PON2 include destruction of quorum sensing molecules.

overall_design: 4 HAEC lines from different donors were treated with 3-O-C12 HSL or control (medium).

middle: B

first: Diana

last: Shih


title: Transcriptome of mouse primary muscle cultures upon dystrophin knockdown by RNAi.

city: Egham

first: George

last: Dickson

address: Royal Holloway University

department: School of Biological Sciences

country: United Kingdom

institute: Royal Holloway University

summary: Dystrophin was knocked down in primary muscle cultures prepared from C57Bl/10 neonate mice using siRNA targeting dystrophin. Also in parallel, primary muscle cultures treated with siRNA targting luciferase were used as controls. The experiment was designed so that the same cell populations were used for both test and control conditions. This helped avoid the heterogeneity associated with the previous studies where test and control cell populations were non-identical. The experiment resulted in a clear transcriptome of dystrophin deficiency and demonstrated dystrophin as a major organizer of myogensis. Moreover, several interesting experimental targets were identified which can potentially open new lines of investigations.

overall_design: 18 primary muscle cell cultures were prepared on 4 occasions. 7 cultures were treated with siRNAs targeting dystrophin, 7 received siRNA targeting firefly GL2 luciferase (treatment controls) and 4 remained untreated (untreated controls). RNAs were extracted 48 hours after differentiation induction for expression profiling analysis.

first: Mohammad

last: Seno

first: Capucine

last: Trollet

first: Ian

middle: R

last: Graham

first: Takis

last: Athanasopoulos

first: Pingzhao

last: Hu


title: Profiles of gene expression in skeletal muscle in sheep from the middle gestation to postnatal stages

status: Public on Dec 20 2010

city: Beijing

first: Lixin

last: Du

address: 2 # Yuanmingyuan West Rd

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

summary: Texel and Ujumqin sheep show obvious differences in muscle and fat growth, so they are ideal models not only to understand the molecular mechanism in prenatal skeletal muscle development, but to identify the potential target genes of myostatin. To elucidate the phenotypic variation between the two sheep breeds and the dynamic characteristics of gene expression in skeletal muscle during the development, we examined the development of skeletal muscle in transcriptome-wide level at 70, 85,100,120 , 135 days post coitus (dpc),birth, 1 month and 2 month. Using the specialized and standardized sheep transcriptome-wide oligo DNA microarray (Agilent), we analyzed the transcriptomic profiles of longissmuss dorsi muscle from fetuses of Texel and Ujumqin sheep. We characterized dynamic transcriptome-wide profiles that accompany the prenatal skeletal muscle and fat development in Texel and Ujumqin sheep respectively, and compared the difference in profiles of gene expression between the two sheep breeds at the same developmental stage.Some potential myostatin target genes and other genes controlling the growth of skeletal muscle and adipose were identified for further examinations. Our findings not only contribute to understand the molecular mechanism of prenatal skeletal muscle development in large precocial species, but also provide some clues for human myopathy and obesity at prenatal stages. Moreover, we also can identify putative candidate genes for meat quality traits in farm animals.

overall_design: Longissimus dorsi muscles were sampled from five prenatal development stages (70, 85, 100, 120 and 135 day of gestation) in Texel and eight development stages (at 70, 85, 100, 120, 135 days post coitus (dpc), birth, 1 month and 2 month) in Ujumqin sheep. There were at least three replicates at each development time in each breed. Two gene expression experiments were conducted with a total of 40 hybridizations.

first: Hangxing

last: Ren

first: Li

last: Li

first: Hongwei

last: Su

first: Lingyang

last: Xu

first: Caihong

last: Wei

last: Zhang

first: Hongbin

first: Wenzhong

last: Liu


title: Genome wide transcriptome profiling of a murine acute melioidosis model reveals new insights into how Burkholderia pseudomallei overcome host innate immunity

status: Public on Dec 23 2010

city: Bangi

first: Sheila

last: Nathan

address: Jalan Universiti

department: Faculty of Science & Technology

institute: Universiti Kebangsaan Malaysia

summary:
The purpose of this study was to develop a comprehensive picture of the host transcriptional response during the acute stage of melioidosis.
To adress this, we compared the transcriptome of infected liver and spleen with uninfected tissues over an infection period of 42 hr (16 hpi, 24 hpi and 42 hpi, respectively) to identify genes whose expression is altered in response to an acute infection.

overall_design: The microarray experimental design included 3 biological replicates for each time point and both liver and spleen were harvested for RNA extraction (except the liver 0 hpi only has 2 biological replicates). The microarray data from each time point was compared relative to uninfected mice.

first: Chui-Yoke

last: Chin


title: PFOS and PFHxS decrease lipoprotein production

city: Zeist

first: MJ

last: van Erk

address: PO Box 360

country: Netherlands

institute: TNO Quality of Life

type:
Expression profiling by array
Third-party reanalysis

summary: The effect of perfluoroalkyl sulfonates on lipoprotein metabolism was investigated in APOE*3-Leiden.CETP mice with a humanized lipoprotein profile. Perfluorohexane sulfonate and perfluorooctane sulfonate markedly reduced both plasma TG and TC by decreasing nonHDL-C and HDL-C accompanied by a reduction in apoAI. Mechanistic studies showed that these effects were mainly caused by impaired lipoprotein production.

overall_design: Male E3L.CETP mice on a C57Bl/6 background were fed a Western-type diet, containing 0.25% (w/w) cholesterol, 1% (w/w) corn oil and 14% (w/w) bovine fat (Western-type diet) (Hope Farms, Woerden, The Netherlands) for 4 to 6 weeks in three independent experiments. Upon randomization according to total plasma cholesterol (TC) and TG levels, mice received the Western-type diet without or with PFBS (30 mg/kg/day), PFHxS (6 mg/kg/day) or PFOS (3 mg/kg/day) during 4-6 weeks. The effects of these PFAS on plasma lipids and lipoproteins were determined. In addition, PFAS levels were determined in plasma and livers were isolated for hepatic lipid analysis and hepatic gene expression analysis using an Affymetrix technology platform and Affymetrix GeneChip® mouse genome 430 2.0 arrays.

first: Silvia

last: Bijland

first: Patrick

last: Rensen

first: Elsbet

last: Pieterman

first: Annemarie

last: Maas

first: José

last: van der Hoorn

first: Marjan

first: Louis

last: Havekes

first: Ko

last: Willems van Dijk

first: Shu-Ching

last: Chang

first: David

last: Ehresman

first: John

middle: L

last: Butenhoff

first: Hans

last: Princen


title: Comparisons of the global gene profile between CLDN4-overexpressing and CLDN4-silencing ovarian cancer cells.

status: Public on Dec 15 2010

city: Boston

first: Zhijian

last: Gao

state: MA

address: Longwood 221

institute: BWH, Harvard Medical School

summary: A microarray analysis was performed to compare the global gene expression profile between CLDN4-overexpressing (Control) and CLDN4-silencing SKOV-3 ovarian cancer cells.

overall_design: CLDN4 gene was knocked down by CLDN4 siRNA lentivirus. Total RNA was extracted and microarray was perfomed to compare the gene profiling changes between CLDN4-overexpressing (Control) and CLDN4-silencing cells. The experiment was performed in triplicate.


title: Transcriptome analysis of muscle in horses suffering from recurrent exertional rhabdomyolysis revealed energetic pathway alterations and disruption in the cytoplasmic calcium regulation

city: EVRY

first: ERIC

last: BARREY

address: 3bis Christophe Colomb

country: France

institute: INSERM-INRA

summary:
The purpose of this study was to compare the gene expression profile of  recurent exercise rhabdomyolysis vs control muscles in French Trotter to determine any metabolic or structural disorder.
Transcriptome analysis revealed 191 genes significantly modulated in rhabdomyolysis vs control muscles (p<0.05).  Many genes involved in the fatty acid oxidation, the TCA cycle  and the mitochondrial respiratory chain were severely down-regulated. The muscle fibers were under hypoxia and oxidative stress conditions which stimulated glycolysis. The muscle fiber calcium homeostasis was greatly affected towards an increase of cytoplasmic calcium and a depletion of the sarcoplasmic reticulum calcium.  Gene expression analysis revealed an alteration of the aerobic ATP synthesis with a severe mitochondrial dysfunction which could explain the disruption of the cytoplasmic calcium regulation and a muscular relaxation disorder.

overall_design: Total RNA was extracted from the gluteal medius and longissimus lumborum  muscles after biopsies in 15 French Trotter horses including 10 controls and 5 RER horses affected by rhabdomyolysis with high plasmatic muscular enzyme activities. Gene expression analysis was performed on the muscle biopsies using a 25K oligonucleotide microarray.

first: E

last: Barrey

first: L

last: Jayr

last: Mucher

first: S

last: Gospodnetic

first: F

last: Joly

first: P

last: Benech

first: X

last: Gidrol

last: Mata

first: A

last: Vaiman

first: G

last: Guérin


title: Gene regulation by full length human adiponectin

status: Public on Dec 09 2010

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary:
Transcriptionnal profiling of 4 human cell lines treated during 3 hours with human adiponectin

Keywords: transcriptionnal analysis

overall_design: Four human cell lines (Hela, HepG2, Panc-1, Hek293) were grown until confluence. These cell lines were serum depleted during 2 hours and then treated with human adiponectin (2,5 µg/ml) during 3 hours. Each adiponectin stimulated cell line was compared to depleted cell line. Depleted cell line was considered as control.

first: Emmanuelle

last: Meugnier

first: Sandra

last: Pesenti

last: Danty

first: Hubert

last: Vidal


title: Agilent_E. coli O157 response to Chrysanthemum herba

status: Public on Dec 14 2010

city: Aurora

first: Ki-Suk

last: Kim

state: CO

department: Pediatrics

institute: University of Colorado Anschutz Medical Campus

summary: According to our study, Chrysanthemum lavandulifolum extract showed excellent antibiotic effects on Escherichia coli O157:H7. A notable point is that the antibiotic efficacy of the herb extract is on the all three proven targets for main antibiotic drugs that are bacterial cell wall biosynthesis, bacterial protein synthesis and bacterial DNA replication and repair.  This multi-target efficacy of the herbal antibiotics may be used as more effective and safe drugs that substitute existing antibiotics.

overall_design: Up- or downregulated gene expressions in E. coli O157:H7 (EDL932) which exposure to Chrysanthemum lavandulifolum (CL) methyl chloride (MC) fraction for 24 hours was measured.

first: Hyeung-Jin

last: Jang


title: Transcription profiling of Drosophila melanogaster SSDP target genes

city: Tel-Aviv

first: Revital

last: Bronstein

address: Ramat Aviv

department: Molecular microbiology and biotechnology

country: Israel

institute: Tel-Aviv University

summary: Transcription profiling of third instar male larvae of two different heteroallelic combinations of ssdp hypomorphic alleles, ssdp[neo48]/ssdp]BG1663] and ssdp[31]/ssdp[BG1663] were compared to each of the corresponding single heterozygotes

overall_design: 22 hybridizations were conducted, these include biological repeats and dye swaps as technical controls.

first: Liron

last: Levkovitz

first: Nir

last: Yosef

first: Eytan

last: Ruppin

first: Roded

last: Sharan

first: Heinrich

last: Westphal

first: Brian

last: Oliver

first: Daniel

last: Segal


title: Gene expression in vitamin K2-induced HepG2 cells

status: Public on Dec 01 2010

city: Tokyo

first: Motoyuki

last: Otsuka

department: Department of Gastroenterology

institute: University of Tokyo

summary: Human hepatocellular carcinoma cells, HepG2 , cultured in DMEM containing 10% fetal calf serum. To study gene expression changes induced by Vitamin K2, total RNA was isolated following the Isogen procedure (Nippon-gene, Tokyo, Japan) from HepG2 cells with and without 50 microM of Vitamin K2 treatment for three days. The cDNA microarrays Human Oligo Chip 30K “AceGene” subset A was purchased from Hitachi Software Engineering Co. (Yokohama-City, Japan). This array contains 10368 kinds of gene-specific 50 mer sense oligonucleotides. Subset A contains mainly known function ORF oligo probes. Preparation of fluorescent cDNA targets by an indirect labeling approach was performed using PowerScript reverse transcription kit (Clontech). First-strand cDNAs were synthesized from 30 microg of total RNA from HepG2 cells treated with or without Vitamin K2 using random primer and PoweScript Fluorescent Labelling Kit. Monofunctional, N-hydroxysuccinimide-activated fluorescent dyes (Cy3 and Cy5; Amersham) were coupled to the cDNAs by reaction with the amino functional groups. Untreated cells were labeled with Cy3 as a control and treated cells with Cy5 as a sample. After free dyes were removed using MinElute Purification kit (Qiagen), the targets were mixed together and added to the microarrays, and then incubated overnight (16 hours) at 42?C. The slides were washed at 30?C in each with 2x SSC, 0.1% SDS and 2x SSC for 10 min and 5 min, respectively, and washed in 1x SSC for 5 min. Fluorescent images of the hybridized microarrays were scanned with a fluorescence laser confocal slide scanner (Affymetrix 428 Array Scanner, Affymetrix, Santa Clara, CA). The Cy3 and Cy5 intensities with background subtraction were determined by ImaGene 4.2 software (BioDiscovery, Marina Del Rey, CA). The expression data were then filtered based on their channel intensities, spot size and flag (missing or inaccurate data), and the Cy5/Cy3 ratios were calculated and normalized by median-centering the log-ratio of all genes.

overall_design: This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.


title: Genome-wide analysis of gene expression regulated by calcineurin-NFAT signaling in mouse embryonic stem cells

first: Xiang

last: Li

state: Shanghai

address: 225 South Chongqing Road

institute: Institute of Health Sciences

summary: Self-renewal and pluripotency are hallmarks of embryonic stem cells (ESCs). However, signaling pathways triggering their transition from self-renewal to differentiation are not well defined. Here, we report that the calcineurin-NFAT signaling pathway is both necessary and sufficient to switch ESCs from an undifferentiated state to early differentiation.To gain an insight into the function of calcinerin-NFAT signaling in ESC lineage commitment, we examined the repertoire of genes changed after LIF withdrawal alone, LIF withdrawal in the presence of cyclosporine A (CsA), a specific inhibitor of calcinerin and forced expression of active forms of calcineurin (deltaCnA) in the presence of LIF,and identified distinct classes of up and down regulated genes by calcineurin-NFAT signaling in mouse embryonic stem cells.

overall_design: Total RNA obtained from CGR8 ES cells under the following conditions: withdrawal of LIF for 0, 1 and 3 days; withdrawal of LIF for 0, 1 and 3 days in the presence of CsA, and induced expression of deltaCnA by withdrawal of Tc for 0, 1 and 4 days in ideltaCnAES cells.Hybridized to Illumina Sentrix Mouse-6 v1.1 Beadhips

first: Lili

last: Zhu

first: Yin

last: Jin


title: JNK3 null vs. wild type hippocampi

city: Barcelona

first: Felix

last: Junyent

address: Avda/Diagonal

country: Spain

institute: Universitat de Barcelona

summary: JNK is a member of the mitogen-activated protein kinase (MAPK) family and there are three genes that encode for JNK1, JNK2 and JNK3 respectively. JNK3 is mainly expressed in the central nervous system and it plays a crucial role in neuronal death in several neurodegenerative diseases, including epilepsy, Alzheimer’s disease, Parkinson’s disease and Huntington’s disease. By contrast, the isoforms JNK1 and JNK2 seem to be involved in brain development. The lack of Jnk3 gene confers neuroprotection, although the specific mechanism underlying this has yet to be elucidated. The present study analyze the gene expression profiling in mice lacking Jnk3, comparing them to wild-type mice. The microarray analysis showed that 22 genes are differentially expressed in Jnk3 null mice. Of these we focused in pik3cb, since it is directly related to the pro-survival PI3K/AKT pathway. Results from Jnk3 null mice showed an increase in pik3cb transcript, together with an increase in PI3K activity and hyperphosphorylation of AKT. By contrast, these changes were not observed in Jnk1 null mice, indicating that activation of PI3K/AKT pathway is specifically related to the lack of JNK3. The data obtained in this study demonstrates activation of the PI3K/AKT pathway in Jnk3 null mice through the increase of pik3cb transcript.

overall_design: We performed arrays from Jnk3 null mice respect wilde-type mice. For each experiment (sample) a RNA pool from hippocampus form three different mice were used. Moreover, a second independent hybridization were done with new sample of RNA (sample 2). The genes differentially expressed were determined based on the results from both samples.


title: CC10 gene deletion: Effect on gene expression in the sinonasal mucosa

city: wuhan

first: heng

last: wang

address: jiefang avenue 1095#

institute: tongji hospital

summary: Comparative analysis of gene expression in murine sinonasal mucosa in wild-type and CC10-knockout littermates with allergic eosinophilic chronic rhinosinusitis. The data provide a comprehensive overview of genes expressed in the mouse sinonasal mucosa and show that the expression of several known and unidentified genes is modified by disruption of the CC10 gene.

overall_design: Total RNA isolated from sinonasal mucosae of 6- to 8-week-old mice, C57BL/6 strain, was used for this comparison. Three groups: wild-type control, wild-type with allergic eosinophilic chronic rhinosinusitis, and CC10-knockout with allergic eosinophilic chronic rhinosinusitis.

first: H

last: Wang

first: L

last: Zheng


title: Genes regulated by T cell and B cell derived TNF in naive lymph nodes

status: Public on Dec 07 2010

city: Frederick

first: Sergei

middle: I

last: Grivennikov

state: MD

address: P.O. Box B

institute: National Cancer Institute

summary:
We present a RNA microarray analysis of RNA`s extracted from naive mesenterial lymph nodes of mice with specific inactivation of tumor necrosis factor only in B cells (B-TNf mice) or in T- and B-cells  (TB-TNF mice). Several genes are cooperatively regulated by T cell derived and B cell derived TNF
Keywords: cell type comparison design

overall_design: For 1 independent sample 3 mice of one genotype have been sacrificed, mesenterial lymph nodes were isolated and pooled together. Lymph nodes were immediately frozen in luquid N2  and RNA was prepared using Tri-reagent. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in DEPC dH2O.

first: Alexei

middle: V

last: Tumanov

first: Andrei

last: Kruglov

first: Yury

last: Shebzukhov

first: Yulan

last: Piao

first: Chang-Yi

last: Cui

first: David

last: Schlessinger

first: Dan

last: Littman

first: Dmitry

last: Kuprash

last: Nedospasov


title: Interindividual comparison of methylation profiling by MSAM

city: Houston

first: Robert

last: Waterland

state: TX

address: 1100 Bates St.,

institute: Baylor College of Medicine

type: Methylation profiling by genome tiling array

summary: Interindividual variation in methylation profiling of human DNA samples were detected using two-tissue screening by MSAM. 0.5ug of DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification

overall_design: HF (hair follicle) and PBL (Peripheral Blood Leukocyte) DNA samples for 8 different individuals, two-color experiment, interindividual paired comparison (same sex and age)

first: Richard

last: Kellermayer

first: JieXin

last: Zhang

first: Ronald

last: Harris

first: Wenjuan

first: Lanlan

last: Shen


title: Gene expression profiling of human mammary artery media during aging

city: Paris

first: Sophie

last: Nadaud

address: 91 Bd de l'hopital

institute: INSERM

summary: Our goal was to better understand the genes and pathways implicated during arterial media aging. We therefore compared the gene expression profile of human mammary artery media between Young (<60, 8 patients) and old (>75, 7 patients) patients. The microarray data, generated using the Illumina sentrix Ref8-V2 platform, was normalized and analyzed using the IlluminaGUI package (Eggle and Schultze, 2007).

overall_design: We used 8 samples from the "Young" groups and 7 samples from the "old" group. No technical replicates were used.

first: Alexandre

last: Marchand

first: Fabrice

last: Atassi

first: Pascal

last: leprince

first: Claude

last: Lefeuvre

first: Anne-Marie

last: Lompre


title: Expression data from SPAK transfected Caco2-BBE cells

status: Public on Nov 30 2010

city: Atlanta

first: Yutao

last: Yan

state: Georgia

address: 615 Michael St, WHB/265

department: Medicine

institute: Emory University

summary:
Ste20-related proline/alanine rich kinase (SPAK) is involved in diverse function, such as the pathogenesis of inflammatory bowel diseases. It is very important to study the underlying mechanisms by which SPAK regulates the progress of IBD.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: We transfected colon cancer modified cell line Caco2-BBE cells with SPAK plasmid and vector for RNA extraction and hybridization on VMSR Human 30k oligonucleotide microarrays.

first: Didier

last: Merlin


title: microRNA expression and opioid regulation in the zebrafish

city: Minneapolis

first: Xiaoxiao

address: 312 Church St. SE

institute: University of Minnesota

summary: We examined morphine responsing miRNAs in Zebrafish embroys. Microarray studies revealed morphine can change microRNA expression in Zebrafish embroys.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 18 arrays: 9 untreated, 9 morphine, 3 time points

first: Yan

last: Zeng

first: Raque

middle: E

last: Rodriguez

first: Fatima

last: Sanchez-Simon

first: Ping-yee

last: Law


title: Study on differences in the pathology, T cell subsets and gene expression in susceptible and non-susceptible hosts infected with Schistosoma japonicum

city: Shanghai

first: Weibin

last: Jiang

address: 518,Ziyue ARd

institute: Shanghai Institute of Veterinary Research, Chinese Academy of Agricultural Sciences

summary:
More than 40 kinds of mammals in China are known to be naturally infected with Schistosoma japonicum (S. japonicum); Microtus fortis (M. fortis), a species of vole, is the only mammal in which the schistosomes cannot mature or cause significant pathogenic changes. In the current study, we compared the differences in pathology by Hematoxylin-eosin staining and in changes in the T cell subsets with flow cytometry as well as gene expression using genome oligonucleotide microarrays in the lung and liver, before challenge and 10 days post-infection with schistosomes in a S. japonicum-susceptible mouse model of infection, a non-susceptible rat model and the non-permissive host, M. fortis. The results demonstrated that S. japonicum promoted a more intensive immune response and more pathological lesions in M. fortis and rats than in mice. Hematoxylin-eosin staining revealed that the immune effector cells involved were mainly eosinophilic granulocytes supplemented with heterophilic granulocytes and macrophages. The analysis of splenic T cell subsets showed that CD4+ T cell subsets and the CD4+/CD8+ ratio were increased while the CD8+ T cell subsets decreased remarkably in rats; whereas the CD8+ T cell subsets were increased but the CD4+/CD8+ ratio was decreased significantly in mice. The analysis of the pattern of gene expression suggested that some immune-associated genes and apoptosis-inducing genes upregulated while some development-associated genes were downregulated in the infected M. fortis compared to the uninfected controls; the three different hosts have different response mechanisms to schistosome infection. The results of this study will be helpful for identifying the key molecules in the immune response to S. japonicum in M. fortis and for understanding more about the underlying mechanism of the response, as well as for elucidating the interaction between S. japonicum and its hosts.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Mus musculus
Rattus norvegicus
Alexandromys fortis

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Mouse - lung and liver

summary: More than 40 kinds of mammals in China are known to be naturally infected with Schistosoma japonicum (S. japonicum); Microtus fortis (M. fortis), a species of vole, is the only mammal in which the schistosomes cannot mature or cause significant pathogenic changes. In the current study, we compared the differences in pathology by Hematoxylin-eosin staining and in changes in the T cell subsets with flow cytometry as well as gene expression using genome oligonucleotide microarrays in the lung and liver, before challenge and 10 days post-infection with schistosomes in a S. japonicum-susceptible mouse model of infection, a non-susceptible rat model and the non-permissive host, M. fortis. The results demonstrated that S. japonicum promoted a more intensive immune response and more pathological lesions in M. fortis and rats than in mice. Hematoxylin-eosin staining revealed that the immune effector cells involved were mainly eosinophilic granulocytes supplemented with heterophilic granulocytes and macrophages. The analysis of splenic T cell subsets showed that CD4+ T cell subsets and the CD4+/CD8+ ratio were increased while the CD8+ T cell subsets decreased remarkably in rats; whereas the CD8+ T cell subsets were increased but the CD4+/CD8+ ratio was decreased significantly in mice. The analysis of the pattern of gene expression suggested that some immune-associated genes and apoptosis-inducing genes upregulated while some development-associated genes were downregulated in the infected M. fortis compared to the uninfected controls; the three different hosts have different response mechanisms to schistosome infection. The results of this study will be helpful for identifying the key molecules in the immune response to S. japonicum in M. fortis and for understanding more about the underlying mechanism of the response, as well as for elucidating the interaction between S. japonicum and its hosts.

overall_design:
Genes Differentially Expressed in lung and liver before challenge and 10 days post-infection with Schistosoma japonicum.
Total RNA from the control tissue and infected tissue were used to generate target cDNA, and then hybridized to 36k Mouse Genome Array Genechips, representing about 25000 characterized murine genes.

first: Jiaojiao

last: Lin


title: The role of vimentin in regulating genes related to EMT

status: Public on Nov 18 2010

city: Turku

first: Karoliina

last: Vuoriluoto

address: Itäinen pitkäkatu 4C

country: Finland

institute: VTT Medical Biotechnology

summary: To study the biological and functional role of vimentin in maintenance of the mesenchymal phenotype of mammary epithelial cells, vimentin was silenced in the non-transformed MCF10A cells and vimentin-dependent changes in gene expression were analyzed.

overall_design: Scrambled is the siScr-transfected control with two replicates; KD the sample with vimentin knockdown, also two replicates.

first: Johanna

last: Ivaska


title: Protease activated receptor 2 (PAR2) on HEK293 activated by trypsin or 2f-LIGRLO-NH2

status: Public on Nov 19 2010

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

summary: Human embryonic kidney cell (HEK293) were treated with PAR2 peptide agonist 2f-LIGRLO-NH2 (1.5h, 3h, 6h and 12h) or trypsin (6h). Comparison of genes similarly regulated by both treatments allowed better characterization of PAR2 induced response as both agonists had been reported as non-specific for PAR2.

overall_design: Six conditioned experiments with 3 replicates each. Individual grown and harvested.

first: Jacky

middle: Y

last: Suen

first: Brooke

last: Gardiner

first: Sean

last: Grimmond

first: David

last: Fairlie


title: Profiles of JARID1B target genes in MCF-7 cell line

status: Public on Nov 10 2010

city: Beijing

first: Shang

last: Yongfeng

address: Hai dian district,38# Xue Yuan Road

department: Biochemistry and Molecular Biology

institute: Peking University

type: Genome binding/occupancy profiling by array

summary: Using ChIP-DSL technology from AVIVA SYSTEMS BIOLOGY to find out the targets of JARID1B on whole genome.

overall_design: Enriched DNA from Chromatin IP of JARID1B was analyzed by arrays, normal IgG was used as negative control.

first: Y

last: Shang


title: Gene expression analysis of the human glioma cell line U87MG

status: Public on Nov 11 2010

city: Heidelberg

first: Ulrike

middle: Mareike

last: Litzenburger

state: Baden-Württemnberg

address: INF 280

department: neuroimmuology

institute: DKFZ

summary: Identification of genes and pathways regulated by kynurenine in human glioma cells

overall_design: Total RNA from U87MG cells was extraced after 8h or 24h of treatment with 100µM kynurenine and compared to untreated control.

first: Christiane

last: Opitz

middle: M


title: TAF6 orchestrates transcription programs and apoptosis in the absence of p53

status: Public on Nov 27 2010

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

summary:
The decision of metazoan cells to live or undergo programmed cell death hinges on the balance between the levels of pro- versus anti-apoptotic gene products. The general RNA polymerase II (Pol II) transcription factor, TFIID, plays a central role in the regulation of gene expression through its core promoter recognition and co-activator functions. The core TFIID subunit TAF6 is a co-activator for the pro-apoptotic p53 tumour suppressor protein. Our previous studies identified a specialized isoform of TAF6, termed TAF6 that can specifically be induced in apoptosis. To elucidate the impact of TAF6 on gene expression and cell death, we employed modified antisense oligonucleotides to enforce expression of endogenous TAF6. The induction of endogenous TAF6 triggered apoptosis in several cancer cell lines. Importantly, TAF6 also induces apoptosis in tumor cell lines devoid of p53, placing TAF6 function downstream of p53. Microarray experiments uncovered a TAF6-induced transcriptome landscape displaying enhanced expression of genes of the Notch, oxidative stress, integrin, p53 and apoptosis pathways. Our data show that the TAF6 pathway is a pivotal signalling nexus that controls pro-apoptotic gene expression programs.
Keywords: Treatment with splice site switching antisense oligonucleotides, induction of apoptosis

overall_design: Biological triplicates, 3 conditions: control oligonucleotide, Taf6 oligonucleotide, specificity control Bcl-x oligonucleotide

first: Emmanuelle

last: Wilhelm

first: François-Xavier

last: Pellay

first: Brendan

last: Bell


title: Profiling of growth and differentiation factor 15 regulated genes in hepatoma cells

first: Wei

last: Yang

address: 6 Rong Jing Dong Jie

institute: Chinese Academy of Medical Sciences

summary: To systematically profile the GDF15-regulated genes in hepatoma cells and to elucidate the possible role of GDF15 on biological processes, high-density oligonucleotide microarrays were hybridized with samples prepared from GDF15- or PBS-treated Huh7.5.1 cells. We found that a total of 894 genes were differentially expressed in response to GDF15 treatment based on the 2-fold cut-off range, and a majority (828 genes, about 92.6%) of the genes is up-regulated. According to the descriptions outlined by the Gene Ontology Biological Process, the differentially expressed genes were found to belong to a variety of functional categories.

overall_design: Two samples were included in the experiment. They are Huh7.5.1 cells treated with PBS, and Huh7.5.1 cells treated with recombinant human growth and differentiation factor 15. Twenty four hours post treatment, the total RNA was isolated from the cells. The microarray hybridization and analysis were performed by CapitalBio Corporation using the 22K Human Genome Array. Two-channel hybridizations microarray assay was performed.

first: Xiuying

last: Liu

first: Youhui

last: Si

first: Maorong

last: Wang

first: Min

last: Cheng

first: Qiaoling

last: Gong

first: Yang

first: Tianyi


title: Toxoplasma gondii response to monensin

status: Public on Nov 06 2010

city: Moscow

first: Mark

last: Lavine

address: Department MMBB

institute: University of Idaho

summary: In order to better understand how the coccidiocide monensin affects T. gondii, we analyzed the effect of monensin on gene expression of intracellular parasites through microarrays.

overall_design: We compared RNA collected either from RH strain tachyzoites 24 hrs after invasion of human foreskin fibroblasts, or 24 hrs after invasion followed by 24 hrs exposure to 2.5ng monensin/ml in tissue culture medium.

first: Gustavo

last: Arrizabalaga


title: Identifying putative candidate genes and pathways involved in immune responses to porcine reproductive and respiratory syndrome virus (PRRSV) infection

status: Public on Nov 05 2010

city: East Lansing

first: juan

last: steibel

address: 1205 I Anthony Hall

institute: Michigan State University

summary: This study compares differences in gene expression between RNAs from lung and bronchial lymph node (BLN) tissue of high (H), low (L) PRRSV burden pigs or a pooled reference (R) using the swine protein-annotated long oligonucleotide microarray. Pathway analyses were carried out on a large scale to determine biological processes, pathways and networks that differ between the H, L and R responses.

overall_design: Samples corresponding to animals with High and Low response to PRRSV infection were hyridized in a common reference design

first: Juan

last: Steibel

first: Joan

middle: K

last: Lunney


title: Mandibular precursor at E13.5 in Ts65Dn Down syndrome mouse

status: Public on Nov 02 2010

city: Indianapolis

first: Randall

middle: J.

last: Roper

state: IN

address: 723 W. Michigan Street., SL306

department: Biology

institute: Indiana University-Purdue University Indianapolis

summary: Gene expression of mandibular precursor from embryonic day 13.5 trisomic and euploid embryos from the Ts65Dn Down syndrome mouse model. Results provide insight into importance of non-trisomic genes in organogenesis.

overall_design: Total RNA isolated from mandibular precursor of 13 trisomic and 11 euploid E13.5 embryos.


title: Genome-wide analysis of IFNa response in WT and STAT3KO MEFs

status: Public on Nov 04 2010

city: Taipei

first: Chien-Kuo

last: Lee

address: No. 1, Jen-Ai Road, Section 1, Rm 513

department: Graduate Institute of Immunology

country: Taiwan

institute: National Taiwan University College of Medicine

summary: Analysis of gene expression profiles in MEF cell lines in the absence or presence of STAT3 following IFNa stimulation. This study is to unveil possible role of STAT3 during type I IFN-mediated gene induction and functions.

overall_design: Total RNA obtained from WT or STAT3KO MEFs stimulated without or with IFNa 1000 U/ml for 2 h.

first: Wei-Bei


title: Genomic profiling of Imatinib resistance in CD34+ cell populations from chronic myeloid leukaemia patients using Agilent-014698 Whole Human Genome 105K microarrays.

status: Public on Nov 15 2010

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: To ascertain genomic alterations associated with Imatinib resistance in chronic myeloid leukaemia, we performed high resolution genomic analysis of CD34+ cells from 25 Imatinib (IM) resistant and 11 responders CML patients. Using patients' T-cells as reference, we found significant association between number of acquired cryptic copy number alterations (CNA) and disease phase (p=0.036) or loss of IM response for patients diagnosed in chronic phase (CP) (p=0.04). Recurrent cryptic losses were identified on chromosomes 7, 12 and 13. On chromosome 7, recurrent deletions of the IKZF1 locus were detected, for the first time, in four patients in CP.

overall_design: Patients suffering from chronic myeloid leukaemia were compared using CD34+ cells and T cells as reference and hybridized on Agilent-014698 Whole Human Genome 105K microarrays.

first: Catherine

last: Roche-Lestienne


title: Immunological responses unique to virulent F. tularensis Schu4 in the mouse model of infection

status: Public on Nov 01 2010

city: Fort Collins

first: Luke

last: Kingry

address: 2025 IDRC at Foothills Campus Delivery

institute: Colorado State University

summary: Francisella tularensis is a category A select agent based on its infectivity and virulence but disease mechanisms in F. tularensis infection remain poorly understood.  A murine pulmonary model of infection was therefore employed to characterize the host immune response to F. tularensis infection and to discern differences in responses to infection with the highly virulent Type A F. tularensis strain Schu4 and to the less virulent Type B live vaccine strain (LVS).  Mice were infected intranasally with F. tularensis Schu4 or LVS and organ lesions were assessed 48 and 120 hours after infection.  Experiments were also conducted to assess and compare the host immune response to infection using global transcriptional analysis.  Mice were infected via low dose aerosol with F. tularensis Schu4 or LVS strains, and transcriptional response in the lungs and spleen was monitored using full mouse genome microarrays at 12, 24, 48, and 120 hours after infection.  We found differential and temporal differences in expression of cytokine and chemokine genes, CD molecules, apoptosis, leukocytes and adhesion receptors, and immunological signaling between infection with Schu4 and LVS strains.  The transcriptional differences coincided with marked differences in the timing and extent of organ lesions in mice infected with the LVS and Schu4 strains.  Thus, these studies revealed both temporal and qualitative differences in the host immune response to infection with virulent F. tularensis Schu4 compared to infection with LVS.

overall_design: 18 mice total, 2 uninfected controls, 2 mice per time point, time points were 12 hour/24 hour/48 hour/ 120 hour post infection, 2 infection groups: LVS and Schu4 infection.  Lung and spleen were harvested at each time point, poly A RNA was extracted, converted to cDNA, labeled and hybridized in triplicate

middle: C

first: Richard

last: Slayden


title: Whole blood gene expression in Vietnamese dengue patients

status: Public on Oct 29 2010

city: Ho Chi Minh

first: Long

last: Hoang

address: 190 Ben Ham Tu

country: Viet Nam

institute: OUCRU

summary: Dengue is a pan-tropic public health problem. In children, dengue shock syndrome (DSS) is the most common life-threatening complication. Predicting patients who may develop DSS may improve triage and treatment. To this end, we conducted a nested case-control comparison of the early host-transcriptional features in 24 DSS patients and 56 sex-, age-, virus serotype-matched uncomplicated dengue patients. In the first instance we defined the “early dengue” profile. The transcriptional signature in acute versus convalescent samples (≤72hrs post illness-onset) was defined by an over-abundance of interferon-inducible transcripts (31% of the 551 over-abundant transcripts), and canonical gene ontology terms that included response to virus, immune response, innate immune response and inflammatory response. Pathway and network analysis identified STAT1, STAT2, STAT3, IRF7, IRF9, IRF1, CEBPB and SP1 as key transcriptional factors mediating the early response. Strikingly, the only differences in the transcriptional signatures of early DSS and uncomplicated dengue cases was the greater abundance of several neutrophil-associated transcripts in patients who progressed to DSS, a finding supported by higher plasma concentrations of several canonical proteins associated with neutrophil-degranulation (BPI, ELA2,  DEF1A). Elevated levels of neutrophil-associated transcripts were independent of the neutrophil count and also the genotype of the infecting virus, as genome-length sequences of DENV-1 (n=15) and DENV-2 (n=3) viruses sampled from DSS patients were phylogenetically indistinguishable from those sampled from uncomplicated dengue patients (32 DENV-1 and 9 DENV-2).  Collectively, these data suggest an hitherto unrecognised association between neutrophil activation, pathogenesis and the development of DSS and point to future strategies for guiding prognosis.

overall_design: 112 patients: 80 with uncomplicated dengue, 32 with dengue shock syndrome

first: David

last: Lynn

first: Matt

last: Henn

first: Bruce

middle: W

last: Birren

first: Niall

last: Lennon

first: Phuong

middle: T

last: Le

first: Kien

last: Duong

first: Tham

last: Nguyen

first: Lanh

middle: N

last: Mai

first: Jeremy

last: Farrar

first: Martin

last: Hibberd

first: Cameron

middle: P

last: Simmons


title: Custom microchip analysis identifies differentially expressed non-coding RNAs in Epstein-Barr virus-infected B cells

status: Public on Oct 30 2010

city: Innsbruck

first: Roland

last: Hutzinger

address: Fritz-Pregl-Str. 3

country: Austria

institute: Biocenter Innsbruck

summary: Upon Epstein-Barr virus (EBV) infection of human B lymphocytes non-coding RNAs (ncRNAs) regulate expression of viral and cellular genes. In this study, we generated a specialized cDNA library from EBV-immortalized cells and subjected it to deep sequencing. We identified 631 unique ncRNA genes, comprised of 321 potential novel differentially expressed ncRNA candidates. Subsequently, we investigated differential expression of known and potential novel ncRNA candidates by custom-designed microchips by comparing expression of ncRNA genes of EBV-immortalized versus non-infected control cells. Among the differentially expressed candidates from chip analysis, differential expression of six novel ncRNA candidates was verified by northern blot analysis. In addition, microchip analysis resulted in observation of increased expression levels of a significant number of potential ncRNA candidates that were preferentially derived from genomic loci annotated as Alu repetitive elements. Alu elements are members of the repeat subfamily of short interspersed nuclear elements (SINE) and were reported to be transcribed upon stress stimulation. While EBV infection significantly up-regulated expression of Alu-derived RNA transcripts, no significant increase in expression of these transcripts was observed under additional tested stress conditions. By employing deep sequencing followed by custom microchip analysis, we identified six novel differentially expressed ncRNAs as well as significantly increased expression levels of Alu-derived RNA transcripts. These transcripts might be involved in crucial functions upon infection by EBV.

platform_organism:
Homo sapiens
Human herpesvirus 4 strain B95-8

overall_design: 5 biological replica of non-infected BL2 samples were compared to 5 biological replica of LCL 197/2 EBV immortalized samples

first: Sonja

last: Vorwerk

first: Alexander

last: Hüttenhofer


title: acLDL-induced gene expression in wildtype and IRAK4 KI mouse macrophages

status: Public on Oct 23 2010

city: Cleveland

first: Tae Whan

last: Kim

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary: Exciting discoveries related to IL-1R/TLR signaling in development of atherosclerosis plaque have triggered intense interest in the molecular mechanisms by which innate immune signaling modulates the onset and development of atherosclerosis.  Previous studies have clearly shown the definitive role of proinflammatory cytokine IL-1 in the development of atherosclerosis.  Recent studies have provided direct evidence supporting a link between innate immunity and atherogenesis.  While it is still controversial about whether infectious pathogens contribute to cardiovascular diseases, direct genetic evidence indicates the importance of IL-1R/TLR signaling in atherogenesis. In this study, we examined the role of IRAK4 kinase activity in modified LDL-mediated signaling using bone marrow-derived macrophage as well as in vivo model of atherosclerosis. First, we found that the IRAK4 kinase activity was required for modified LDL-induced NFκB activation and expression of a subset of proinflammatory genes, but not for the activation of MAPKs in bonemarrow-derived macrophage. IRAK4 kinase inactive knock-in (IRAK4KI) mice were bred onto ApoE-/- mice to generate IRAK4KI/ApoE-/- mice. Importantly, the aortic sinus lesion formation was impaired in IRAK4KI/ApoE-/- mice compared to that in ApoE-/- mice. Furthermore, proinflammatory cytokine production was reduced in the aortic sinus region of IRAK4KI/ApoE-/- mice compared to that in ApoE-/- mice. Taken together, our results indicate that the IRAK4 kinase plays an important role in modified LDL-mediated signaling and the development of atherosclerosis, suggesting that pharmacological inhibition of IRAK4 kinase activity might be a feasible approach in the development of anti-atherosclerosis drugs.

overall_design: To identify global changes in gene expression, we examined gene expression profiles of macrophages from wild-type and IRAK4 kinase-inactive knock-in mice in response to acLDL stimulation using the Illumina microarray with probes for 23,000 transcripts.  Bone marrow-derived macrophages from wild-type and IRAK4 kinase-inactive knock-in mice were treated with acLDL for 24 hours.

first: TaeWhan

first: Xiaoxia

last: Li

first: Pieter

last: Faber


title: Cell type-specific induction of mRNA in human B cells and monocytes by IFN-beta

status: Public on Oct 20 2010

first: Anette

middle: H.

last: van Boxel-Dezaire

address: 9500 Euclid Avenue

department: Molecular Genetics

institute: Cleveland Clinic Foundation

summary:
Compared to primary human monocytes in whole blood cultures, few B cells activated STAT1 in response to stimulation of 2000 IU/ml IFN-beta for 45 minutes.  Because activation of STAT1 leads to apoptosis induction, we tested the hypothesis that less pro-apoptotic genes are induced in B cells as compared to monocytes.

Manuscript titled: Major differences in the responses of primary human leukocyte subsets to IFN-beta.

Abstract: Treatment of cell lines with type I IFNs activates the formation of ISGF3 (STAT1/STAT2/ IRF9), which induces the expression of many genes.  To study this response in primary cells, we treated fresh human blood with IFN-beta and used flow cytometry to analyze phosphorylated STATs1, 3 and 5 in CD4+ and CD8+ T cells, B cells, and monocytes.  The activation of STAT1 was remarkably different among these leukocyte subsets.  In contrast to monocytes, CD4+ and CD8+ T cells, few B cells activated STAT1 in response to IFN-beta, a finding that could not be explained by decreased levels of IFNAR2 or STAT1 or enhanced levels of SOCS1 or relevant protein tyrosine phosphatases in B cells.  Micro-array and real-time PCR analyses revealed the induction of STAT1-dependent pro-apoptotic mRNAs in monocytes but not in B cells.  These data show that ISGF3 or STAT1 homodimers are not the main activators of gene expression in primary B cells of healthy humans.  Notably, in B cells and especially in CD4+ T cells, IFN-beta activated STAT5 in addition to STAT3, with biological effects often opposite from those driven by activated STAT1.  These data help to explain why IFN-beta increases the survival of primary human B cells and CD4+ T cells, but enhances the apoptosis of monocytes, and also to understand how leukocyte subsets are differentially affected by endogenous type I IFNs during viral or bacterial infections, and by type I IFN treatment of patients with multiple sclerosis, hepatitis or cancer.

overall_design: Undiluted whole blood of 2 healthy individuals (HI) was used, and either stimulated with IFN-beta or left untreated (control) for 3 hrs. After 3 hrs, both B cells and monocytes were isolated from whole blood of the first healthy individual, and only B cells were isolated from whole blood of the second healthy individual.

middle: H

first: Yaomin

last: Xu

first: George

last: Stark


title: Her2/Neu breast cancer mouse model transcriptome

status: Public on Oct 18 2010

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary:
Purpose:  We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer.  This report makes these data publicly available in raw and processed forms, as a resource to the community.  Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens.
Experimental design:  Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast).  Cases and controls were rigorously paired to avoid bias.
Results:  In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate ≤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively.  Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue.
Conclusions and clinical relevance:  These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for MRM-MS.  The availability of these datasets will contribute positively to clinical proteomics.

overall_design: Custom Agilent 44K whole mouse genome expression oligonucleotide microarrays were used to profile breast tumors from three Her2/Neu mice compared to normal breast epithelium from two control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice. All samples were laser-capture microdissected and total RNA isolated and amplified prior to hybridization against a reference pool of normal adult mouse tissues.

first: Regine

last: Schoenherr

first: Karen

middle: S

last: Kelly-Spratt

first: ChenWei

last: Lin

first: Jeffrey

middle: R

last: Whiteaker

first: Tao

last: Liu

first: Ted

last: Holzman

first: Li-Chia

last: Feng

first: Travis

middle: D

last: Lorentzen

first: Alexei

middle: L

last: Krasnoselsky

first: Pei

last: Wang

first: Yan

first: Kay

last: Gurley

first: Lynn

last: Amon

first: Athena

middle: A

last: Schepmoes

first: Ronald

middle: J

last: Moore

first: David

middle: G

last: Camp II

first: Lewis

last: Chodosh

first: Richard

last: Smith

first: Peter

last: Nelson

last: McIntosh

first: Christopher

last: Kemp

first: Amanda

last: Paulovich


title: Gene expression analysis of Rip1Tag2 spontaneous tumors treated by sEphB4-Alb or PBS

status: Public on Oct 09 2010

city: Los Angeles

first: ren

last: liu

address: 1441 Eastlake Avenue

institute: University of Southern California

summary: Rip1Tag2 mice spontaneously develop tumors. Mice were treated with sEphB4-Alb or PBS for 3.5 weeks. RNA was isolated from harvested tumors and subjected to global gene expression analysis.

overall_design:
The transgenic Rip1Tag2 mice of C57/BL6 background were used as spontaneous tumor model. These transgenic mice express the oncogenic SV40 large T antigen (Tag) under the transcriptional control of the insulin promoter. In these mice, the entire course of tumor development can be closely followed. They develop hyperplastic/dysplastic islets that eventually become angiogenic, form invasive carcinomas, and metastasize.
The Rip1Tag2 mice were fed standard laboratory diet and water ad libitum. From 12 weeks of age, all RT2 mice received 5% sugar in their water to relieve the hypoglycemia induced by the insulin-secreting tumors. From 10 weeks of age, mice (6 per group) were treated with either PBS or 10 mg/kg sEphB4-Alb intraperitoneally 3 times a weekk. The treatment continued until mice were 13.5-week-old. Tumors were harvested at week 13.5. Total RNA was then isolated from 2 tumors per group and used for global gene expression analysis with Illumina MouseRef-8 v2.0 Expression BeadChip. The gene expression  level in PBS and sEphB4-Alb treated tumors were compared.

first: Antonio

last: Duarte

first: Parkash

last: Gill

first: Ren

last: Liu


title: Effects of Genistein on LNCaP Gene Expression

city: Stanford

first: James

last: Brooks

address: 300 Pasteur Drive

department: Department of Urology, Room S287

institute: Stanford University Medical Center

summary: Gene expression profiling to identify genes significantly modulated by low and high doses of genistein in LNCaP cells. Significant genes were identified using StepMiner analysis and significantly altered pathways with Ingenuity Pathways analysis.  Genistein significantly altered expression of transcripts involved in cell growth, carcinogen defenses and steroid signaling pathways.  The effects of genistein on these pathways were confirmed by directly assessing dose-related effects on LNCaP cell growth, NQO-1 enzymatic activity and PSA protein expression.

overall_design:
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
SUBMITTER_CITATION: Suvarna Bhamre, Debashis Sahoo, Robert Tibshirani, David L. Dill and James D. Brooks. Gene expression changes induced by genistein in the prostate cancer cell line LNCaP. The Open Prostate Cancer Journal. 3: 86-98, 2010

first: Suvarna

last: Bhamre

first: Sunita

last: Jones

first: Hongjuan

last: Zhao


title: Integration of metabolism and virulence by Clostridium difficile CodY

city: Boston

first: Abraham

last: Sonenshein

address: 136 Harrison Avenue

department: Molecular Biology & Microbiology

institute: Tufts University

summary: CodY, a global regulatory protein that monitors the nutrient sufficiency of the environment by responding to the intracellular levels of GTP and the branched-chain amino acids, was previously shown to be a potent repressor of toxin gene expression in Clostridium difficile during growth in rich medium. In the intestinal tract, such derepression of toxin synthesis may lead to destruction of epithelial cells and the liberation of potential nutrients for the bacterium. CodY is likely to play an important role in regulating overall cellular physiology as well. In this study, DNA microarray analysis and affinity purification of CodY-DNA complexes were used to identify and distinguish the direct and indirect effects of CodY on global gene transcription. A codY null mutation resulted in >4-fold overexpression of 146 genes (organized in 82 apparent transcription units) and underexpression of 19 genes. In addition to the toxin genes, genes for amino acid biosynthesis, nutrient transport, fermentation pathways, membrane components and surface proteins were overexpressed in the codY mutant. Genome-wide analysis identified more than 350 CodY binding regions, many of which are likely to correspond to sites of direct CodY-mediated regulation. About 60%  of the CodY-repressed transcription units were associated with binding regions. Several of these genes were confirmed to be direct targets of CodY by gel mobility shift and DNase I footprinting assays.

overall_design: The experiment was designed to compare gene expression in codY+ and codY mutant strains grown to mid-exponential phase. Three two-color arrays, representing three biological replicates. Each array compares two strains: JIR8094 (pSD21) and JIR9084::pSD21.

first: Sean

last: Dineen

first: Shonna

middle: M

last: McBride


title: Differential gene expression profiles of human promyelocytic leukemia cell line exposed to benzene toluene, and o-xylene

status: Public on Oct 27 2010

city: Seoul

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

country: South Korea

institute: Korea Institute of Science and Technology

summary: The gene expression profiles of HL-60 cells were determined with IC50 doses of 3 chemicals (benzene, toluene, and o-xylene) at a 3 h time point. Assays were performed in triplicate for each chemical/dose, and individual gene-expression profiles were determined for each chemical at the tested concentration doses.

overall_design: Three independent experiments were performed for each chemical (N = 3), simultaneously. Labeling and hybridization were performed using the instructions of the Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). This was followed by the coupling of the Cy3 dye for the controls (DMSO) and Cy5 dye for the treated samples. Hybridization was performed in a hybridization oven at 62 oC for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58 oC, 1× SSC for 2 min at RT and 0.2× SSC for 3 min at RT), the slide was dried by centrifugation at 800 rpm for 3 min at RT. Hybridization images on the slides were scanned by ScanArray Lite (PerkinElmer Life Sciences, USA). Scanned images were analyzed with GenePix 3.0 software (Axon Instruments, USA) to obtain gene expression ratios.

first: sailendra

middle: n

last: sarma

first: yong-jung

last: kim

first: Jae-Chun

last: ryu


title: ER stress impairs the insulin signaling pathway through mitochondrial damage in SH-SY5Y human neuroblastoma cells (part 1)

status: Public on Oct 07 2010

city: seoul

first: hyun-jung

last: koo

address: hoegi-dong,dongdaemun-gu

institute: Kyung Hee University

summary: To investigate thapsigargin or tunicamycin-induced transcriptomes in SH-SY5Y cells

overall_design: Total RNA was isolated from SH-SY5Y cells were treated with control vehicle (DMSO), thapsigargin (thap) or tunicamycin (tuni).

first: Hyun-Jung

last: Koo

first: Youngmi

middle: K

last: Pak


title: ER stress impairs the insulin signaling pathway through mitochondrial damage in SH-SY5Y human neuroblastoma cells

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

overall_design: Refer to individual Series


title: Deficiency in nucleotide excision repair (NER) family gene activity, especially ERCC3, is associated with non-pigmented hair fiber growth

city: Vancouver

first: Kevin

last: McElwee

state: BC

department: Dermatology and Skin Science

institute: University of British Columbia

summary: The hair follicle bulb is the only site of pigment production for the hair shaft and melanogenically active melanocytes are located in the upper hair matrix. We conducted a microarray study to discover gene expression patterns that may be implicated in the lack of melanogenesis in gray hair follicles (HF). Pigmented and non-pigmented HFs collected from the same individuals were micro-dissected into the lower one third including the hair bulb (HB) and the upper hair shaft and sheaths (HS) including the bulge region. Microarray data was verified with qPCR and immunohistochemistry. Target effects were evaluated in vitro on human epidermal melanocytes (HEMs). In comparison to pigmented HS and HBs, several nucleotide excision repair (NER) family genes exhibited statistically significant lower expression both in non-pigmented HS and non-pigmented HB. These genes were identified as ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, XPA, NTPBP, HCNP, DDB2 and POLH. Immunohistochemistry showed consistent results. By siRNA interference we also detected that a deficiency in ERCC3 in melanocytes reduced the ability to produce melanin in vitro. Our results suggest that loss of NER gene function may lead to DNA damage and mutation accumulation in melanocytes, which may possibly lead to cell death. Further, a loss of ERCC3 function may lead to reduced gene transcription and this in turn may lead to reduced melanin production ability. These results offer a new insight into the molecular changes that occur in non-pigmented HF and may also provide novel information with regard to melanogenesis and its regulation.

overall_design:
Samples of human hair follicles were collected from 4 mm scalp biopsies of normal individuals who presented with a combination of pigmented and non-pigmented gray hair. All samples were provided through the Department of Surgery and the Department of Dermatology and Skin Science, University of British Columbia, with approval from the University Clinical Research Ethics Board. Hair follicles (n=10-20 per sample group per subject) were microdissected to remove the sebaceous gland and upper hair follicle infundibulum. Hair follicles were separated into two sample groups; those with pigmentation, where the dermal papilla was hidden in a strongly pigmented hair bulb and pigment-activity was evident in the root sheath; and those where macroscopically no pigmented melanocytes could be detected in the hair bulb and the hair shaft appeared fully unpigmented. Pigmented and non-pigmented hair follicles were then sub-divided into the lower one third including the hair bulb, and into the keratinized hair shaft and root sheaths including the bulge region, for analysis.

Human Operon v.2.1 (21K) glass arrays were produced (based on human 70mers from Operon Biotechnologies Inc, Huntsville, AL) by the Microarray Facility of the Prostate Centre at Vancouver General Hospital, Vancouver, Canada. RNAs were amplified using the SenseAmp Plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. Total RNA from test samples and Universal Human Reference RNA (Stratagene, Cedar Creek, TX) were differentially labeled with Cy5 and Cy3, respectively, with the 3DNA array detection 350 kit (Genisphere Inc, Hatfield, PA) and cohybridized to cDNA microarrays. Following overnight hybridization and washing, arrays were imaged using a ScanArray Express scanner (PerkinElmer, Boston, MA).

first: Mei

last: Yu

first: Robert

last: Bell

first: Gigi

last: leung

first: Anne

last: Haegert

first: Nicholas

last: Carr

first: Jerry

last: Shapiro


title: Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: DEX, 24hr

status: Public on Oct 01 2010

city: Montreal

first: Elin

last: Grundberg

address: 740 Dr Penfield Avenue

institute: McGill University

summary: Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent to which environmental perturbation influences such traits has not been studied to date. We carried out large-scale induction experiments using primary human bone cells derived from 113 unrelated donors of Swedish origin harvested under 18 different conditions (seven treatments, two vehicles, each assessed at two time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t=2h), dexamethasone (DEX) (t=24h), and PGE2 (t=24h). Using these treatments, we performed expression profiling for 18,144 RefSeq transcripts applying biological replicates of the complete study cohort (ntotal=782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs. We found that 93% of cis-eQTLs at 1% FDR were replicated in at least one additional treatment and in fact, on average only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment, though treatment-specific cis-regulatory effects were 2-6-fold more abundant among up-or downregulated genes.  We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 and 250kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interaction between cellular environment and cis-variants are relatively rare (~1.5%), but that detection of such specific interactions can be achieved by combination of functional genomic tools.

overall_design:
Total RNA from cultured trabecular bone cells obtained from ~100 unrelated Caucasian donors treated under multiple different conditions and timepoints. Each sample represented by two or three biological replicates.

This dataset includes samples treated with dexamethasone (DEX) for 24 hours.

first: Veronique

last: Adoue

first: Tony

last: Kwan

first: Bing

last: Ge

first: Qing

last: Duan

middle: C

last: Lam

first: Vonda

last: Koka

first: Andreas

last: Kindmark

first: Scott

last: Weiss

first: Kelan

last: Tantisira

first: Hans

last: Mallmin

first: Timothy

last: Johns

first: Eric

last: Shoubridge

first: Osten

last: Ljunggren

first: Benjamin

last: Raby

first: Olle

last: Nilsson

first: Tomi

last: Pastinen


title: Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: control and variety of treatments, 2hr and 24hr

last: Grundberg

overall_design:
Total RNA from cultured trabecular bone cells obtained from ~100 unrelated Caucasian donors treated under multiple different conditions and timepoints. Each sample represented by two or three biological replicates.

This dataset includes samples treated with control vehicle (Ctrl), bone morphogenetic protein 2 (BMP2), dexamethasone (DEX), 1.25 VitD3 (VitD), insulin-like growth factor 1 (IGF1), prostaglandin E2 (PGE2), or tumor necrosis factor alpha (TNFalpha) for 2 or 24 hours.

first: Kevin

middle: T


title: Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: PGE2, 24hr

first: Elin

overall_design:
Total RNA from cultured trabecular bone cells obtained from ~100 unrelated Caucasian donors treated under multiple different conditions and timepoints. Each sample represented by two or three biological replicates.

This dataset includes samples treated with prostaglandin E2 (PGE2) for 24 hours.

last: Adoue


title: Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: BMP2, 2hr

overall_design:
Total RNA from cultured trabecular bone cells obtained from ~100 unrelated Caucasian donors treated under multiple different conditions and timepoints. Each sample represented by two or three biological replicates.

This dataset includes samples treated with bone morphogenetic protein 2 (BMP2) for 2 hours.

first: Veronique

last: Kwan


title: Genome-wide comparison of AML leukemic stem cells (LSCs) and normal human hematopoietic stem cells (HSCs).

status: Public on Sep 30 2010

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

summary: Gene expression analysis of AML LSCs vs normal HSCs

overall_design: Total RNA obtained from FACS-sorted AML-LSCs (n=12) and normal HSCs (n=5) were subjected to the microarray analysis

first: Koichi

last: Akashi


title: Transcriptional regulation through DNA bending by Nhp6A [Agilent]

status: Public on Sep 15 2010

first: Noah

middle: L.

last: Dowell

address: 615 Charles E. Young Drive South, BSRB 357

department: Biological Chemistry

country: USA

institute: UCLA

summary:
The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional HMGB family of chromatin-associated proteins.  Nhp6A binds DNA in vitro without sequence-specificity and bends DNA sharply, but its role in chromosome biology is poorly understood.  We show by whole genome ChIP-chip that Nhp6A is localized to specific regions of chromosomes that include about 23% of RNA polymerase II promoters.  Nhp6A binding functions to stabilize positioned nucleosomes within promoter and 5' coding regions of these genes.  Both genomic binding and transcript expression studies point to functionally-related groups of genes that are specifically bound by Nhp6A and whose transcription is altered by the absence of Nhp6.  Genomic analyses of Nhp6A mutants specifically defective in DNA bending reveals a critical role of DNA bending for co-regulation of transcription but not for targeted binding by Nhp6A.  We conclude that the chromatin environment, not DNA sequence recognition, localizes Nhp6A binding and that Nhp6A stabilizes chromatin structure and co-regulates transcription.
Two amino acid residues within the DNA binding interface of Nhp6A are critical for bending DNA .  Substitution of methionine 29 to alanine (M29A)  reduces the formation of 98 bp microcircles by 6-fold in vitro, but equilibrium binding to linear DNA is only reduced 2-fold.  The severe phenylalanine 48 to alanine (F48A) mutation abolishes formation of 98 bp microcircles, while again only lowering equilibrium binding to linear DNA by 2-fold (Masse et al. 2002; Dai et al. 2005).  We used these bending mutants to address if Nhp6A  bending activity is required for transcriptional regulation?  Specifically, genome-wide binding and transcript analysis was performed on nhp6A-M29A ∆nhp6B, nhp6A-F48A ∆nhp6B, and nhp6A-P18A ∆nhp6B cells.  Nhp6A-P18A was included to control for the modest decrease in DNA binding observed in the bending mutants because it also exhibits a 2-fold reduction of DNA binding but without a significant change of DNA bending (Yen et al. 1998; Allain et al. 1999).

overall_design: Transcription in four different genotypes (∆nhp6A ∆nhp6B, nhp6A-P18A ∆nhp6B, nhp6A-F48A ∆nhp6B, nhp6A-M29A ∆nhp6B) was compared to the same reference genotype (Nhp6A ∆nhp6B).  Biological replicates were performed for each comparison.

first: Reid

last: Johnson


title: Progressing vs regressing melanoma metastases

status: Public on Sep 11 2010

city: Granada

first: Rafael

last: Carretero

address: Avenida del Hospicio

institute: Universidad de Granada

summary: We documented the transcriptional pattern of 3 progressing and 2 regressing synchronous melanoma metastases from the same patient following M-VAX treatment.

overall_design: Two-condition experiment, Progressing vs regressing metastases. 3 progressing and 2 regressing metastases extracted from the same patient after M-VAX immunotherapy. One replicate per array.

first: Carretero

last: Rafael

first: Wang

last: Ena

first: Engle

last: Alyson

first: Ascierto

last: Maria

first: Liu

last: Hui

first: Camacho

last: Francisco

first: Marincola

last: Francesco

first: Garrido

last: Federico

first: Cabrera

last: Teresa