title: Array CGH of Drosophila compound chromosomes on heterochromatin custom array.

first: Bing

last: He

summary: Mapping the Drosophila melanogaster centromeric heterochromatin by CGH analysis of embryos lacking specific chromosomes or chromosome arms.

overall_design: Nine chromosome or chromosome arm deletions were tested: embryos lacking the entire second chromosome (2En-), 2L (2L-), 2R (2R-), the entire third chromosome (3En-), 3L (3L-), 3R (3R-), the entire fourth chromosome (4En-), the X chromosome (X-), or both X and Y chromosomes (XY-). Control: Blastoderm stage wild type Oregon R embryos. For each experiment 100-150 embryos of the appropriate genotype were collected. DNA from randomly staged 0-8 hr wild type Oregon R embryos was used as reference for all experiments. Embryos with no X chromosome were obtained by crossing attached-X/Y females (C(1)DX, y f) to X/Y males. Embryos with no X and Y chromosomes were obtained by crossing attached-X/Y females (C(1)RM, y2suwawa) to attached-XY males (YSX YL, In(1)EN, y B). The compound II chromosomes RM(2L); RM(2R)=C(2)v and the compound III chromosomes RM(3L); RM(3R)=C(3)se were used to generate 2L- and 2R-, and 3L- and 3R- embryos, respectively. The compound II C(2)EN and compound III C(3)EN st1 cu1es stocks were used to generate embryos deficient for the entire second and third chromosome, respectively. The compound IV C(4)RM, ci1eyR/0 were used to generate embryos deficient for the fourth chromosome. Embryos deficient for chromosome 4 were identified by their defects in denticle belt patterning during late embryogenesis, whereas embryos deficient for other chromosome/chromosome arm were recognized based on their specific phenotypic defects during early embryonic development. All embryos were collected at room temperature.


title: Highly Parallel Genome-Wide Expression Analysis of Single Mammalian Cells (Performance Metrics)

status: Public on Feb 27 2012

city: San Diego

first: Craig

last: April

state: CA

address: 9885 Towne Centre Drive

country: USA

institute: Illumina, Inc.

summary: Assay Performance Metrics for Low RNA Inputs and Single Cells

overall_design: Low Input Total RNA and Isolated Single Mammalian Cells

middle: S


title: Genipin inhibits LPS-induced acute systemic inflammation in mice

status: Public on Feb 25 2012

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: Genipin is a natural blue colorant in food industry. Inflammation is correlated with human disorders, and nuclear factor-κB (NF-κB) is the critical molecule involved in inflammation. In this study, the anti-inflammatory effect of genipin on the lipopolysaccharide (LPS)-induced acute systemic inflammation in mice was evaluated by NF-κB bioluminescence-guided transcriptomic analysis. Transgenic mice carrying the NF-κB-driven luciferase genes were administered intraperitoneally with LPS and various amounts of genipin. Bioluminescent imaging showed that genipin significantly suppressed LPS-induced NF-κB-dependent luminescence in vivo. The suppression of LPS-induced acute inflammation by genipin was further evidenced by the reductions of cytokine levels in sera and organs. Microarray analysis of these organs showed that the transcripts of 79 genes were differentially expressed in both LPS and LPS/genipin groups, and one third of these genes belonged to chemokine ligand, chemokine receptor, and interferon (IFN)-induced protein genes. Moreover, network analysis showed that NF-κB played a critical role in the regulation of genipin-affected gene expression. In conclusion, we newly identified that genipin exhibited anti-inflammatory effects in a model of LPSinduced acute systemic inflammation via downregulation of chemokine ligand, chemokine receptor, and IFN-induced protein productions.

overall_design: A total of 25 transgenic mice (female, 6 to 8 weeks old) were randomly divided into five groups of five mice: (1) mock, no treatment; (2) LPS (4 mg/kg), (3) LPS plus genipin (1 mg/kg), (4) LPS plus genipin (10 mg/kg), and (5) LPS plus genipin (100 mg/kg). Mice were challenged intraperitoneally with LPS and then with genipin 10 min later. Four hours later, mice were imaged for the luciferase activity, and subsequently sacrificed for ex vivo imaging, RNA extraction, and immunohistochemical staining.

first: Chia-Cheng

last: Li

first: Hsin-Yi

last: Lo

first: Fu-Tzu

last: Pai

first: Shih-Lu

last: Wu

first: Tin-Yun

last: Ho


title: Yeast Colony Differentiation

status: Public on Feb 17 2012

city: Prague

first: Michal

last: Cap

address: Vinicna 5

department: genetics and microbiology

country: Czech Republic

institute: Faculty of Science, Charles University in Prague

summary: Transcription profile of different layers from S.cerevisiae colonies in day 15 and day 20.

overall_design:
Lower layer (L-cells) vs upper layer (U-cells). 3 biological replicates for day 15 and two replicates for day 20 were used for the total of 4 and 3 technical replicates, respectively.
Spotted oligonucleotide microarray slides contain double genome of S. cerevisiae.
Dye-swap was performed in replicates

first: Cap

last: Michal

first: Palkova

last: Zdena


title: miRNA expression profiling in Adult T-cell Leukemia (ATL) cells and in Normal CD4+ T-cells

status: Public on Feb 23 2012

city: Tokyo

first: Kazumi

last: Nakano

address: 4-6-1, Sirokanedai, Minatoku

department: Department of Medical Genome Sciences, Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

summary: HTLV-1 infected individuals stay as carriers for their lifetimes, while the rest of 5% are killed by ATL. ATL leukemogenesis is a complex process involving accumulation of multiple genetic abnormalities in HTLV-1 infected cells. To clarify genetic events underlying ATL leukemogenesis, we conducted comprehensive miRNA expression profiling in 40 ATL patients and in 22 healthy volunteers.

overall_design: Total RNA samples from PBMC of ATL patients (mostly HTLV-1 inefcted CD4+ T-cells) and from CD4+ T-cells from healthy donors were subjected to Cy-3 labeling followed by miRNA expression microarray analyses.

first: A

last: Tsutsumi

first: Y

last: Kagami

first: K

first: M

last: Yamagishi

last: Uchimaru

last: Utsunomiya

last: Yamaguchi

first: T

last: Watanabe


title: Alteration of gene expression in mouse mammary tissue upon E. coli infection

status: Public on Feb 28 2012

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

summary: Mastitis is a multietiological complex disease, which is defined as inflammation of parenchyma of mammary glands. Bacterial infection is the predominant cause of mastitis, though fungal, viral and mycoplasma infections also have been reported. Based on severity of the disease, mastitis can be classified into- subclinical, clinical and chronic forms. Bacterial pathogens from the fresh cow milk were isolated and classified by standard microbiological tests and multiplex PCR. Epidemiological studies have shown that Escherichia coli is the 2nd largest mastitic pathogen after Staphylococcus aureus in India. Based on Enterobacterial Repetitive Intergenic Consensus (ERIC) -PCR profile and presence of virulence genes, a field isolate of E. coli was used for intramammary inoculation in lactating mice. Histopathological examination of H&E stained sections showed severe infiltration of polymorphonuclear neutrophils (PMNs), mononuclear inflammatory cells in the alveolar lumen and also in interstitial space and necrosis of alveolar epithelial cells after 24h. Western blot and immunohistochemical analysis of the mice mammary tissues have shown significant hyperacetylation at histone H3Lys14 residue of both mammary epithelial cells and migrated inflammatory cells. Quantitative real-time PCR and genome-wide gene expression profile in the E. coli infected mice mammary tissue revealed differential expression of genes related to inflammation, immunity, antimicrobial peptide expression, acute phase response and oxidative stress response. Expression levels of milk proteins were also suppressed. ChIP assay from the paraffinized tissues have shown selective enrichment of acetylated histone H3K14 and H4K8 at the promoters of over expressed genes.  These data suggests that E. coli infection in the mice mammary tissue leads to histone hyperacetylation at the immune gene promoters which is pre-requisite for expression of inflammatory genes to mount drastic immune response.

overall_design: Abdominal mammary glands of 7 Day post partum lactating female Swiss albino mice was challenged with a pure culture of E. coli isolated from cow milk. Mammary tissues were harvested after 24h of infection. Total RNA was isolated by Qiagen RNeasy mini columns and used for global gene expression and RT-PCR analysis. For RT-PCR, cDNAs corresponding to total mRNAs were synthesized using Oligo-dT primer. Global gene expression analysis were done by single colour labelling of total RNA and hybridization to Agilent 8x60k mouse Microarray.

first: Rahul

last: Modak

middle: K

first: Bibek

middle: R

last: Shome

first: Suswetha

last: Das Mitra


title: Expression Profiling of Early Myogenesis - Illumina Dataset

status: Public on Mar 21 2012

city: Montreal

first: Saravanan

last: Sundararajan

state: Quebec

address: 740, Dr Penfield Ave

department: Human Genetics

country: Canada

institute: McGill University

summary: Myogenesis is a tightly controlled process involving the transcriptional activation and repression of thousands of genes. Although many components of the transcriptional network are known for the later phases of myogenesis, relatively little work has described the transcriptional landscape within the first 24 hours, when myoblasts commit to differentiate. Through dense temporal sampling of differentiating C2C12 myoblasts, we identify 266 transcriptional regulators (TRs) whose expression is altered within the first 12 hours of myogenesis. A high-content shRNA screen of 76 TRs involving 427 stable lines identified 48 genes whose knockdown significantly inhibits differentiation of C2C12 myoblasts. These include known regulators of myogenesis (Myod1, Myog and Myf5), as well as 26 regulators not previously associated with the process. Of the TRs differentially expressed within the first 24 hours, two-thirds inhibited differentiation when knocked down. Surprisingly, a similar proportion (67%) of shRNAs targeting TRs whose expression did not change during differentiation also inhibited myogenesis, suggesting that both stably and differentially expressed TRs are essential for this complex differentiation program. This implies that microarray-based approaches that concentrate functional validation studies on differentially-expressed genes will fail to identify many genes that are critically implicated in complex biological processes.

overall_design: C2C12 myoblasts were differentiated into myotubes and sampled at various timepoints for gene expression measurement on Illumina Mouse WG-6v1.1 arrays.  Cells grown in separate plates were harvested at 12 different timepoints: t_0h, t_1h, t_1.5h, t_2h, t_3h, t_6h, t_9h, t_12h, t_24h, t_48h, t_96h, t_144h.  All harvests were performed in triplicate using growths from successive passages.

first: Harry

last: Zuzan

first: Rob

last: Sladek

first: Thomas

middle: J

last: Hudson


title: A genome-wide genetic interaction screen reveals metabolic roles of human histone deacetylase 1

status: Public on Feb 10 2012

city: Taipei

first: Yu-yi

last: Lin

address: R809, No.1 Jen-Ai Road Section 1

institute: National Taiwan University College of Medicine

summary: Dynamic acetylation of metabolic proteins has emerged as a ubiquitous post-translational modification of human metabolic proteins. However, the corresponding modifying enzymes and the functions of the modification await exploration. Using a genome-wide synthetic lethality screen, we constructed a genetic interaction network of human histone deacetylases (HDACs) and discovered many metabolic substrates of these enzymes. We further confirmed that the adenosine monophosphate-activated protein kinase (AMPK) catalytic subunit is acetylated and deacetylated by EP300 and HDAC1, respectively. Deacetylation of AMPK catalytic subunit enhances physical interaction with the upstream kinase LKB1, and leads to AMPK phosphorylation and activation. These findings highlight the importance of genetic interaction profiling to identify specific substrates of individual HDACs and elucidate how cells use protein (de)acetylation to coordinate nutrient availability and cellular energy status.

overall_design:
To study the functional specificity of individual HDAC, we developed a genome-wide genetic interaction profiling technology in cultured human cells by RNAi using pooled TRC (The RNAi Consortium) 75k human shRNA library and complexity deconvolution by high-density microarray with a half-hairpin barcode design. The HCT116 colon cancer cell line was chosen as the screen platform because of its quasinormal diploid karyotype. The performance of the customized microarray we designed was first evaluated by the receiver operating characteristic (ROC) curve showing high sensitivity (89%), specificity (94%) and area under curve (0.95), as well as a control hybridization without DNA sample showing low background signal. Both results suggest that the fluorescent signals were generated by specific hybridization reactions. The high correlation of signal between Cy5 and Cy3 channel as well as dye-swap experiments indicated that biases between the two labeling fluorophores during competitive hybridization were negligible. Moreover, correlation between technical and biological replicates confirmed the high reproducibility of the methodology.
        In the screen, we used stable polyclonal cells expressing shRNA constructs targeting firefly luciferase (shLuciferase) as control. We checked the knockdown efficiency in protein or RNA level of individual shRNA constructs for 12 human HDAC genes (HDAC1~4, HDAC6~9, SIRT1~3 and SIRT5) by immunoblotting or quantitative PCR, and generated stable polyclonal query cell lines expressing two shRNA constructs with the highest knockdown efficiency for each HDAC gene. After transduction by TRC shRNA lentiviral pools, benchmark samples were harvested prior to puromycin selection, and the remaining cells were propagated under selection and harvested again after 18 population doublings as the end samples. Half-hairpin barcode library of the benchmark and end samples was recovered from genomic DNA respectively by PCR with Cy5 and Cy3-labeled primers, gel purified, and hybridized to the microarray. For each shRNA construct, the Z-score of the log2(Cy5/Cy3) was computed, and Z-score difference was calculated by subtracting the Z-score of the control sample from that of the query sample. Z-score differences larger than 1.5 and less than -1.5 were used as arbitrary thresholds to define candidate negative and positive genetic interactions, respectively.

first: Jef

middle: D

last: Boeke

first: Samara

last: Kiihl

first: Yasir

last: Suhail

first: Shang-Yun

last: Liu

first: Jin-ying

last: Lu

first: Yi-hsuan

last: Chou

first: Kuang

last: Zheng

first: Chin-Ni

last: Khor

first: Chi-Long

first: Joel

last: Bader

first: Rafael

last: Irizarry


title: Random monoallelic expression in the mouse: SNP array data

city: Boston

first: Alexander

last: Gimelbrant

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Random monoallelic expression is defined by the allele-specific expression of genes, and by the fact that for an individual cell this monoallelic expression is neither obligate nor necessarily coordinated with the allelic expression in other cells. In order to find novel examples of random monoallelic expression in mouse, we did a transcriptome-wide survey of allele-specific gene expression in two different immortalized cell types. Lymphoblast cell lines and fibroblast cell lines were established (both clonal and nonclonal) and were used as a source of both nuclear RNA and genomic DNA. These samples were assessed for allele-specific gene expression using a custom-designed Mouse SNP Chip. A large number of genes (over 10% of those that were assessed in lymphoblast clones) displayed random monoallelic expression.

overall_design: For each cell line, two replicate samples of ds-cDNA were assessed for monoallelic expression, while genomic DNA was assessed as a control for possible LOH events. Nonclonal samples were used as controls for cis-acting allelic bias.

first: Lillian

middle: M

last: Zwemer

middle: A

first: Andrew

last: Chess


title: Array CGH of Drosophila polytene chromosomes on heterochromatin custom array.

status: Public on Mar 06 2012

city: Princeton

first: Bing

last: He

state: NJ

address: Washington Rd

department: Molecular Biology

institute: Princeton University

summary: CGH analysis of Drosophila polytene chromosomes.

overall_design: Drosophila polytene chromosomes were isolated from whole salivary glands dissected from roaming third-instar larvae or from ovaries dissected from adult females. Salivary gland has two biological repeats.


title: Long non-coding RNA expression in Human tissues and cell lines

status: Public on Feb 01 2012

city: Barcelona

first: Rory

last: Johnson

state: Catalonia

address: Calle Dr Aiguader, 88

department: Bioinformatics and Genomics

country: Spain

institute: Centre for Genomic Regulation

summary: We designed a custom microarray to profile the expression and used it to measure the expression of 9929 human lncRNAs manually-annotated by the GENCODE group as part of the ENCODE consortium.

overall_design: One microarray hybridisation per biological sample.

first: Roderic

last: Guigo


title: Microarray profiling of monocytic differentiaion reveals miRNA-mRNA intrinsic correlation (gene expression)

status: Public on Feb 02 2012

city: Beijing

first: jing

last: wang

address: Tsinghu University

country: China

institute: Medical Systems Biology Research Center School of Medicine Tsinghua University

summary: Since the expression profile of miRNAs is specific in different tissues or under different physiological conditions, the correlations between miRNAs and mRNAs could vary under different biological circumstances. This is a study also used expression profiles of miRNA and mRNA during monocytic differentiation to explore the correlations between the expression levels of miRNAs and mRNA, either negative or positive.

overall_design: After treatment of TPA, U937 cells present functional differentiation markers as well as specific cell morphology, which were confirmed by flow cytometric analysis and Wright-Giemsa staining.Here we use genome-wide microarray analysis to profile the expression levels of mRNA in normal U937 cells and differentiated U937 cells. For each differentiated and control sample, two hybridizations were performed by using a reversal fluorescent strategy.

first: Jing

last: Wang

first: Yuxiang

last: Zhou


title: Differential gene expression in adipose tissue from obese human subjects during weight loss and weight maintenance

status: Public on Jan 31 2012

city: Malmö

first: Anders

last: Danielsson

state: Skåne

address: Jan Waldenströms gata 35

department: Medical Faculty, Clinical Sciences

country: Sweden

institute: Lund University

summary: Background. Differential gene expression in adipose tissue during diet-induced weight loss followed by a weight stability period is not well characterized. Markers of these processes may provide a deeper understanding of the underlying mechanisms.  Objective. To identify differentially expressed genes in human adipose tissue during weight loss and weight maintenance after weight loss.  Design. RNA from subcutaneous abdominal adipose tissue from nine obese subjects was obtained and analyzed at baseline, after weight reduction on a low calorie diet (LCD), and after a period of group therapy in order to maintain weight stability.  Results. Subjects lost 18.8 + 5.4% of their body weight during the LCD and maintained this weight during group therapy. Insulin sensitivity (HOMA) improved after weight loss with no further improvement during weight maintenance. Cyclin-dependent kinase inhibitor 2B (CDKN2B) and JAZF zinc finger 1 (JAZF1), associated with type 2 diabetes, were downregulated. We could also confirm the downregulation of candidates for obesity and related traits, such as tenomodulin (TNMD) and matrix metallopeptidase 9 (MMP9), with weight loss. The expression of other candidates, such as cell death-inducing DFFA-like effector A (CIDEA) and stearoyl-CoA desaturase (SCD) were upregulated during weight loss but returned to baseline levels during weight maintenance.  Conclusion. Genes in the adipose tissue are differentially expressed during weight loss and weight maintenance after weight loss. Genes that show sustained regulation may be of potential interest as markers of the beneficial effects of weight loss whereas others seem to be primarily involved in the process of weight loss itself.

overall_design: Nine participants were prescribed a low calorie diet (LCD) containing 1200 kcal/day for approximately three months (101 ± 26 days). Following the weight reduction phase the participants attended a six month follow-up period (167 ± 37 days). By protocol design, subjects were eligible to enter the study if they had lost at least 10% of their initial body weight during the LCD-period and maintained this weight (+5%) after group therapy. Subcutaneous adipose tissue samples were obtained at three time-points: (i) at baseline, (ii) after weight reduction when subjects were no longer losing weight, and (iii) after the group therapy weight maintenance phase.

first: Lovisa

middle: E

last: Johansson

middle: P

first: Hemang

last: Parikh

first: Maria

last: Klintenberg

first: Fredrik

last: Norström

first: Leif

last: Groop

first: Martin

last: Ridderstråle


title: Microarray profiling of monocytic differentiaion reveals miRNA-mRNA intrinsic correlation

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Surface Functionalities of Gold Nanoparticles (AuNPs) Impacts Embryonic Gene Expression Responses

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary: Investigation of whole genome expression pattern of 24 and 48 hours post fertilization Danio Rerio embryos exposed to 1.5nm MES- and TMAT- AuNPs. TMAT is a positively charged (cationic) ligand, and MES is a negatively charged (anionic) ligand.

overall_design: Embryos were exposed to 10ug/mL of 1.5nm TMAT-AuNPs, 50ug/mL of 1.5nm MES-AuNPs or control from 6hpf to 24 or 48 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

first: L

last: Truong

first: S

middle: C

last: Tilton

first: T

last: Zaikova

first: E

last: Richman

first: K

last: Waters

first: J

last: Hutchison

first: R


title: Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue

status: Public on Jan 17 2012

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array


title: Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae [Array Data]

status: Public on Jan 20 2012

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

type: Genome binding/occupancy profiling by genome tiling array

summary: The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function.  The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure.  Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing.  Forkhead regulation of origin timing is independent of local levels or changes of transcription.  Instead, we show that Fkh1 and Fkh2 are required for the clustering of early origins and their association with the key initiation factor Cdc45 in G1-phase, suggesting that Fkh1 and Fkh2 selectively recruit origins to emergent replication factories.  Fkh1 and Fkh2 bind Fkh-activated origins, and interact physically with ORC, providing a plausible mechanism to cluster origins.  These findings add a new dimension to our understanding of the epigenetic basis for differential origin regulation and its connection to chromosomal domain organization.

overall_design: These files contain BrdU-IP-chip files from a BrdU-Pulse experiment (7 timepoints for each strain; 2 strains totall). These files also contain BrdU-IP-chip data from HU-arrested cells (1 replicate for 2 strains). These files also contain chIP-chip data of ORC (1 replicate 4 strains), MCM (1 replicate 2 strains), Cdc45 (1 replicate 2 stains), Fkh1 (1 replicate 2 strains). Finally, these files also contain 4C data (2 replicates 2 stains).

first: Jared

last: Peace

first: A

middle: Z

last: Ostrow

first: Yan

last: Gan

first: Alexandra

last: Rex

first: Christopher

last: Viggiani

last: Tavare

first: Oscar

last: Aparicio


title: The Co-regulated Genes by Ectopic Expression of MiR-371-372-373 Cluster in HepG2 Cells

status: Public on Jan 15 2012

first: Hongyan

last: Guo

address: Chengfu

department: School of Medcine

institute: Tsinghua University

summary: MicroRNAs are important cellular regulators and their dysfunctions are associated with various disease. miR-371/372/373 was found co-regulated in HBV-producing HepG2.2.15 cells when compared to its non-HBV producing maternal HepG2 cells. To obtain a glimpse of the potential influence of the enforced miR-371-372-373 cluster in HepG2 gene expression, a two-color Capitalbio 70-mer oligo microarray platform, which contained 21,329 well-characterized human gene probes, was used to identify the differentially expressed genes between miR-371-372-373-HepG2 and mock-HepG2 in two independent biological replicate.

overall_design: miR-371-372-373-HepG2 vs. mock-HepG2

first: Mingyong

last: Luo


title: Genomic copy number profiling of different generations of Atm-/-TERT-ER T-cell lymphomas and associated resistant tumors following telomerase inhibition

city: Houston

first: Jian

last: Hu

state: TX

address: 1515 Holcombe Blvd

department: Cancer Biology

institute: MD Anderson Cancer Center

summary:
Genomic copy numbers of various generations of  Atm-/-TERT-ER mice treated with 4-OHT or vehicle were profiled.
Genomic copy numbers of transplanted G3 Atm-/-TERT-ER T-cell lymphomas with telomerase or ALT

overall_design: T-cell lymphomas were developed in various generations of Atm-/-TERT-ER mice with 4-OHT or vehicle treatment. These tumors were profiled with aCGH. G3 Atm-/-TERT-ER tumors were transplanted into SCID mice treated with 4-OHT or vehicle. Cells maintained on vehicle eventually developed ALT-dependent resistance. We used aCGH to profile telomerase+ tumors vs. ALT+ tumors from the same parental lines.

first: Ron

last: DePinho


title: Sox11 inhibits osteoblast differentiation of adipose tissue derived mesenchymal stem cell

status: Public on Jan 05 2012

city: seoul

first: Mi Kyung

last: Choi

address: daehyundong

country: South Korea

institute: Ewha womans university

summary: we analyzed the expression level change of transcription factors in adipose derived stem cells during osteogenic differentiation and found a candidate target gene, Sox11. We defined that Sox11 suppresses osteogenic differentiation through overexpression and knock down of Sox11.

overall_design: total RNA obtained from adipose derived stem cells subjected to 1,3,6,10 or 14 days in osteogenic differentiation compared to undifferentiated control adipose derived stem cells.

first: Mi

first: Sun

last: Kang

first: Jae

last: Kim


title: Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue [Agilent]

summary: Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH.   Aim of the present study is to compare aCGH platforms suitable for copy number analysis using FFPE derived DNA. Two dual channel aCGH platforms (Agilent and NimbleGen) and a single channel SNP based platform (Affymetrix), were evaluated using seven FFPE colon cancer samples, median absolute deviation (MAD), deflection, signal-to-noise ratio (SNR) and DNA input requirements were used as quality criteria.  Large differences were observed in MAD values and deflection between platforms; Agilent and NimbleGen showed better MAD values (0.13 for both) compared to Affymetrix (0.22). Contrary, Affymetrix showed a better deflection of 0.94, followed by 0.71 for Agilent and 0.51 for NimbleGen. Since the deflection compensates for the MAD the Signal to Noise Ratios (SNR) were comparable; Agilent ranks first, Affymetrix second and NimbleGen third with SNRs of 3.9, 3.6 and 3.3 respectively.  DNA input amounts of 40ng are sufficient for high quality profiles with Affymetrix. For Agilent DNA input amounts of 50ng are sufficient for high quality profiles. For results of similar quality NimbleGen requires at least 100ng.  Copy number analysis using DNA derived from FFPE archival material is feasible and shows reproducible results on high-resolution copy number platforms. Input amounts of DNA from FFPE material lower than recommended still yield high quality profiles without additional amplification steps.

overall_design:
Overall study comprises 6 samples analyzed across three platforms with an additional dilution range (5 concentrations) of a seventh sample on two platforms.
This Series represents Agilent platform-derived data.

last: Krijgsman

first: Danielle

last: Israeli

first: Josien

last: Haan

first: Hendrik

middle: F

last: van Essen

first: Serge

last: Smeets

first: Paul

last: Eijk

first: Renske

last: Steenbergen

first: Klaas

last: Kok

first: Sabine

last: Tejpar

first: Gerrit

last: Meijer

first: Bauke

last: Ylstra


title: Global gene expression profiling of human osteosarcomas of primary and metastatic origin reveals alterations in chemokine pattern

status: Public on Jan 01 2012

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

summary:
Global gene expression analysis was performed on a panel of 23 osteosarcoma samples of primary and metastatic origin using the Applied Biosystems Gene Expression Array System. When comparing the primary tumours with the metastases, we found a significantly increased expression of genes involved in immunological processes, e.g. coding for cytokines and chemokines, in the metastatic samples, suggesting that these signal molecules play an important role in promoting metastasis.
In addition, a comparison of the gene expression in primary samples from patients with or without metastases demonstrated that patients who later developed metastases had high expression of the chemokine (C-X-C motif) receptor 4 (CXCR4), similar to the metastatic samples. Increased knowledge of mechanisms and interactions between specified molecular signalling pathways in osteosarcomas could lead to a more rational strategy for development of targeted therapy.

overall_design: Total RNA was isolated from tumor tissue of osteosarcoma patients. Gene expression patterns of metastatic versus primary samples were compared, as well as primary samples from patients who did or did not later develop metastases.

first: Christoph

last: Müller

first: Stine

middle: H

last: Kresse

first: Jørn

last: Henriksen

first: Rita

last: Holdhus

first: Gunnar

last: Sæter

first: Oyvind

last: Bruland

first: Bodil

last: Bjerkehagen

first: Vidar

last: Steen

first: Ola

last: Myklebost


title: Human lung minimally invasive adenocarcinoma (MIA): lepidic growth (LG) cancer cell pool vs. micro-invasion (MI) cancer cell pool

status: Public on Jan 02 2012

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profiling of human lung minimally invasive adenocarcinoma cells comparing control lepidic growth (LG) cell pool with micro-invasion (MI) cell pool.

overall_design: Two-condition experiment, LG vs. MI cell pools. Biological replicates: 1 control LG cancer cell, 1 MI cancer cell in an individual MIA tumor. One replicate per array.

first: Akihiko

last: Ito

first: Takahiro

last: Mimae


title: Role of bHLH93 in controlling flowering time in Arabidopsis

status: Public on Dec 31 2011

city: Austin

first: Enamul

last: Huq

address: 24th St. and Whitis BIO labs ,

department: MCDB

institute: University of Texas at Austin

summary: Flowering in plants is a very dynamic and synchronized process where various cues including age, day-length, temperature and endogenous hormones fine-tune the timing of flowering for reproductive success. Arabidopsis thaliana is a facultative long day plant where long-day (LD) photoperiod promotes flowering. Arabidopsis still flowers under short-day (SD) conditions, albeit much later than LD conditions. Although, factors regulating the photoperiodic LD pathway have been extensively investigated, the SD pathway is much less understood. Here we identified a critical transcription factor called bHLH93 (basic Helix-Loop-Helix 93) that is essential to induce flowering specifically under SD conditions in Arabidopsis. bhlh93 mutants do not flower from primary meristem under SD conditions, but flowers similar to wild type under LD conditions. The late flowering phenotype is rescued by exogenous application of GA, suggesting that bHLH93 acts upstream of GA pathway to promote flowering. Double mutant studies showed that bhlh93 is epistatic to phyB and soc1 genes under SD conditions. bHLH93 is expressed at the meristematic regions and its expression peaks at 8 hours after dawn under SD conditions. As expected, the bHLH93 is localized in the nucleus. Taken together, these data suggest that bHLH93 is a key transcription factor necessary for Arabidopsis thaliana to evolve as a facultative plant.

overall_design: Stratified Col-0 and bhlh93-1 mutants seeds in cold for 4 days. Transferred to Short Day (8h light and 16h dark) chamber and harvested samples after 10days. Tissue was harvested 0 and 4 hour after light was turned on.

first: Nidhi

last: Sharma

first: Scott

last: Hunicksmith


title: Differential analysis of transcriptomes regulated upon ischemic preconditioning and postconditioning versus ischemia-reperfusion protocols in the mouse heart in vivo

status: Public on Jan 06 2012

city: Montpellier Cedex 05

first: Stéphanie

last: Barrère

address: 141 rue de la cardonille

country: France

institute: CNRS

summary: Ischemic preconditioning (PreC) and postconditioning (PostC) are the most potent cardioprotective strategies inhibiting ischemia-reperfusion (IR) injuries.The aim of our study was to identify the gene profiles regulated upon preconditioning and postconditioning in the mouse heart in vivo.

overall_design: Analysis used myocardial ischemia-reperfusion (IR) RNA as control samples for comparison to the experimental samples taken after an ischemic preconditioning (PreC), a postconditioning (PosC) or a 30min delayed PostC (Post30) treatment. Comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

last: Barrere-Lemaire


title: Array comparative genomic hybridization (aCGH) study of formalin-fixed paraffin-embedded (FFPE) small gastrointestinal stromal tumors (GISTs) less than 1 cm in greatest diameter (microGISTs)

first: Cher-wei

last: Liang

address: 7 Chung-Shan S. Rd.

institute: National Taiwan University Hospital

summary: To investigate the cytogenetic and large-scale chromosomal changes in involuted or non-involuted microGISTs using post-whole genome amplification (WGA) FFPE DNA materials

overall_design:
Sixteen patients, total 19 FFPE tumor samples (block storage time 4 months to 9 years), including 16 microGISTs and 3 GISTs larger than 1 cm from the same patients harboring microGISTs.
All FFPE tumor samples underwent DNA extraction and WGA (modified degenerate oligonucleotide PCR (DOP) method, provided by Sigma). For each tumor sample, a post-WGA DNA extract from the normal tissue in the same block (or block from the same patient with a block storage time differences less than 2 years) was obtained for tumor sample DNA co-hybridization.
Tumor and normal areas of interest were marked and collected from 5- to 10-micron unstained or hematoxylin-stained sections by manual or laser (PixCell IITM, Arcturus Bioscience, CA, USA) microdissection. DNAs were then extracted. WGA was performed using GenomePlex® Tissue Whole Genome Amplification WGA5 kit (Sigma, Saint Louis, MO, USA; http://www.sigmaaldrich.com/) in parallel in accordance with the manufacturer's protocols.
At least four independent experiments were concurrently performed per template amplification. Four separate WGA reaction products were pooled for each sample.

first: Jonathan

last: Fletcher

first: Alexei

last: Protopopov


title: Molecular Mechanisms of Diabetic Neuropathy: A Transcriptional Profling Study of db/db Mouse Sciatic Nerve

city: Ann Arobr

first: Manjusha

last: Pande

address: 2800 Plymouth Rd.

department: BRCF

institute: University of Michigan

summary:
The mechanisms of diabetic neuropathy (DN) development and progression  are not fully understood. We examined global gene expression in the  sciatic nerve (SCN) of BKS-db/db mice at 8 and 24 weeks of age to  identify genetic pathways altered in peripheral nerves at early and  advanced stages of DN. The sets of differentially expressed genes were  analyzed to identify enriched biological functions and regulated  genetic pathways. Our results suggest that carbohydrate metabolism and  lipid metabolism pathways are dysregulated in the db/db SCN at 8 weeks  of age. Impairment of Schwann cell-extracellular matrix interaction  and axon guidance occurs early in the development of DN, while  neurotrophic support, neurotransmitter transport and axonogenesis are  impaired at the advanced stage of DN. Gene expression changes also  suggest that oxidative stress- and inflammation-mediated nerve damage occurs by 8 weeks.
Our analysis identified mechanisms regulated in the early stages of DN. Additionally, interactions between genes from different pathways provide insight into potential relationships among the regulated pathways.

overall_design: RNA extracted from the SCN of four groups of mice: (8 week old db/db (n=8) or db/+ (n=8), and 24 week old db/db (n=6) or db/+ (n=7)) was hybridized to Affymetrix GeneChip microarrays. Gene expression for the two genotypes (db/db vs. db/+) was compared at each age. Gene expression at the early and advanced stages of DN (8 weeks vs. 24 weeks) was also compared for each genotype.


title: Response to immunotherapy in melanoma metastasis

city: Granada

first: Rafael

last: Carretero

address: Avenida del Hospicio

institute: Universidad de Granada

summary: We have study 15 melanoma metastasis obtained from 2 different patients. Five metastases were obtained from patient 1 after M-VAX treatment (2 regressing and 3 progressing). Ten were obtained from patient 2, five after interferon treatment (1 progressing and 4 regreesing) and another 5 after M-VAX treatment (1 progressing and 4 regressing)

first: Ena

last: Wang

first: Maria

last: Ascierto

first: Teresa

last: Cabrera

first: Francesco

last: Marincola

first: Federico

last: Garrido


title: Assessment of host responses to ionizing radiation

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

summary: The aim of this study was to analyze the host responses to ionizing radiation by nuclear factor-κB (NF-κB) bioluminescence imaging-guided transcriptomic tool. Transgenic mice, carrying the NF-κB-driven luciferase gene, were exposed to a single dose of 8.5 Gy total-body irradiation. In vivo imaging showed that a maximal NF-κB-dependent bioluminescent intensity was observed at 3 h after irradiation and ex vivo imaging showed that liver, intestine, and brain displayed strong NF-κB activations. Microarray analysis of these organs showed that irradiation altered gene expression signatures in an organ-specific manner. Pathway analysis showed that pathways associated with metabolism and immune system were altered primarily in liver and intestine. the upregulation of fatty acid binding protein 4, serum amyloid A2, and serum amyloid A3, which are participated in both inflammation and lipid metabolism, suggesting that irradiation might affect the cross pathways of metabolism and inflammation. Moreover, The upregulation of chemokine (CC-motif) ligand 5, chemokine (CC-motif) ligand 20, and Jagged 1 genes suggested that these genes might contribute to the radiation enteropathy.

overall_design: Male transgenic mice (6 to 8 weeks old) were exposed to a single dose of whole-body X-rays generated at 6 MV (Clinac® 21EX medical linear accelerator, Varian, Palo Alto, CA, USA) and at a dose rate of 4 Gy/min. Mice were imaged at 0 h, 1 h, 3 h, 9 h, 24 h, 48 h, or 72 h, or on 7 d or 14 d after irradiation with 8.5 Gy. RNAs were extracted at 3 h after irradiation.

first: Chung-Ta

last: Chang

first: Chia-Cheng

last: Li

first: Hsin-Yi

last: Lo

first: Shih-Lu

last: Wu

first: Ji-An

first: Tin-Yun

last: Ho


title: miRNA profiling of HPCX1 linked prostate cancer patients and their healthy brothers

city: Tampere

first: Henna

last: Mattila

address: Biokatu 8

department: Institute of Medical Technology

country: Finland

institute: University of Tampere

summary: MicroRNA expression levels in the lymphoblastic cells of prostate cancer patients and their healthy brothers from HPCX1 linked prostate cancer families were analyzed to trace variants that might alter miRNA expression  and explain partly an inherited  genetic predisposion to prostate cancer.

overall_design: MicroRNA expression levels in lymphoblastoid cell lines were detected using an Agilent Human miRNA V2 Oligo Microarray Kit (Agilent Technologies).100 ng of total RNA was used as a starting material, and miRNAs were labeled using the Agilent miRNA Labeling Kit. Labeled RNA was hybridized to Agilent miRNA arrays with eight identical arrays per slide, with each array containing probes directed against 723 human and 76 human viral miRNAs. Slides were scanned (Agilent microarray scanner) after hybridization and data was extracted using Feature Extraction software, version 9.5.1. (Agilent Technologies). Altogether 14 cancer patients and 15 healthy brothers from 11 families were included with no replicates.

first: Martin

last: Schindler

first: Jarkko

last: Isotalo

first: Tarja

last: Ikonen

first: Mauno

last: Vihinen

first: Hannu

last: Oja

first: Teuvo

last: Tammela

first: Tiina

last: Wahlfors

first: Johanna

last: Schleutker


title: MiR-21 involves in cervical squamous cell tumorigenesis and regulates CCL20

city: guangzhou

first: yao

last: tingting

address: yanjiangxi road 107

institute: sun yat-sen memorial hospital,sun yat-sen university

summary: MicroRNA 21 (miR-21) has been implicated in various aspects of carcinogenesis. However, the function and molecular mechanism of miR-21 in cervical squamous carcinoma has not been studied. Using TaqMan quantitative real-time PCR and Northern blot, we confirmed that miR-21 is significantly overexpressed in human cervical squamous cancer tissues and cell lines. Remarkably, we showed that the level of miR-21 correlates with the nodal status and differentiation by ISH. Furthermore, we demonstrated that miR-21 regulates cervical squamous cells proliferation, apoptosis, and migration which are HPV16 positive. In order to identify the candidate target genes for miR-21, we used gene expression profiling. By luciferase reporter assay, we confirmed the CCL20 gene is one of its targets, which is relative to the HPV16 oncogenes E6 and E7. Our results suggest that miR-21 may be involved in the cervical squamous cell tumorigenesis.

overall_design: Total RNA of cells transfected with anti-miR-21 or scrambled RNA oligonucleotide was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip_ Porcine Genome Array (Affymetrix) at CapitalBio Corporation (Beijing, China) in which GeneChip microarray service was certificated by Affymetrix.

first: Tingting

last: Yao

first: Zhongqiu

last: Lin


title: Genome level identification of direct Ubx targets from third-instar imaginal discs

status: Public on Dec 22 2011

city: Pune

first: Pavan

last: Agrawal

state: Maharashtra

address: First floor, Central Tower, Sai Trinity Building, Pashan

department: Biology

institute: Indian Institute of Science Education and Research (IISER)

summary: Hox proteins are transcription factors and key regulators of segmental identity along the anterior posterior axis across all bilateral animals. Despite decades of research, mechanism by which Hox proteins select their targets and specify segmental identity remains elusive. To address this question we carried out whole genome ChIP-chip experiments to identify direct targets of Hox protein Ultrabithorax (Ubx) during haltere development in Drosophila. When mis-expressed in wing segment (T2) Ubx converts its identity to that of haltere segment (T3).  We used CbxHm/+ wing discs ectopically expressing Ubx in the pouch region of discs to obtain chromatin. This helped us focus on targets of Ubx involved in pouch development without mixing with the targets involved in notum development. Polyclonal Ubx antibodies against N-terminal region (excluding homeodomain) were generated in our lab and used to pull down Ubx bound regions from CbxHm/+ wing discs. Mock DNA (No antibody) was used as control.

overall_design: Test Vs. Mock experiment. CbxHm/+ discs for Chromatin source. Biological replicates: 3 [Agilent two-color ChIP-on-Chip experiment,Organism: Drosophila melanogaster  ,Drosophila Whole Genome ChIP-on-Chip Set 244K Microarray 1 of 2  (AMADID: 014816 and 014817)]

first: Farhat

last: Habib

first: Ramesh

last: Yelagandula

first: L

middle: S

last: Shashidhara


title: HPCX1 linked prostate cancer

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

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

overall_design: Refer to individual Series


title: Arsenic-induced Changes in L2 Cells

status: Public on Dec 23 2011

city: Stillwater

last: Weng

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary:
Arsenic is a carcinogen that is known to induce cell transformation and tumor formation.  Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic alters gene expression leading to carcinogenesis in the lung.
In this study, we examined global gene expression in response to 0.75 µM arsenic treatment for 1-7 days in a rat lung epithelial cell line (L2) using an in-house 10k rat DNA microarray. One hundred thirty one genes were identified using the one-class statistical analysis of microarray (SAM) test. Of them, 33 genes had a fold change of ≥ 2 at least between two time points. These genes were then clustered into 5 groups using K-means cluster analysis based on their expression patterns. Seven selected genes, all associated with cancer, were confirmed by real-time PCR. These genes have functions directly or indirectly related to metabolism, glycolysis, cell proliferation and differentiation, and regulation of transcription, all of which may be involved in neoplastic transformation of cells.
Our findings provide important insight for the future studies of arsenic-mediated lung cancer.
Keywords: Lung, aresenic, L2, micorarray

overall_design: L2 cells were exposed with 0.75 uM of arsenite for 0, 1, 3, 5, and 7 days (C, D1, D3, D5 and D7). The samples were arranged for hybridization using a loop design. For each paired sample, dye flip and three biological replications were performed for each sample.

first: Tisha

last: Posey

first: Zhongming

last: Chen

first: Narendranath

last: Chintagari

first: Pengcheng

last: Wang

first: Nili

last: Jin

first: Heidi

last: Strikcer

first: Lin

last: Liu


title: Genome-wide Transcriptional Analysis of Genes Associated with Desiccation Stress in Anopheles gambiae

city: Irvine

first: Mei-Hui

address: 3501B Hewitt Hall UCI

institute: UC irvine

summary:
Anopheles gambiae mosquitoes play an important role in malaria transmission. In sub-Saharan Africa, the dry season can last several months. The mechanisms for mosquito population to survive through the dry season are poorly understood.  One possible mechanism is that adults increase their desiccation tolerance over the dry season. Genetic analyses have shown that inversions 2La, 2Rb, 2Rc, 2Rd and 2Ru are associated with aridity resistance, however little is known about the transcriptional response of genes in response to desiccation.
The results of the present study demonstrate that desiccation affects expression of genes associated with several mosquito physiological mechanisms, including those that protect against water loss, but all structural related genes decreased their expression. The identified differentially expressed genes in response to desiccation stress can lay a foundation for better understanding of molecular mechanisms underling dry-season survival of An. gambiae mosquitoes, so it may provide a different option for malaria vector control.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Transcriptional profiles of Anopheles gambiae female mosquitoes were exposed to 70% (standard) or 30% (desiccated) RH without any access to sugar and water at 0hr, 18hr or 36hr.


title: Delayed activation of host innate immune pathways in streptozotocin-induced diabetic hosts leads to more severe disease during infection with Burkholderia pseudomallei

status: Public on Dec 30 2011

city: Bangi

first: Sheila

last: Nathan

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary:
The purpose of this study was to develop a comprehensive picture of the STZ-diabetic host transcriptional response during the acute stage of melioidosis and investigate the interplay between the diabetic host response and Burkholderia pseudomallei.
To adress this, we compared the transcriptome of infected STZ-diabetic liver and spleen with uninfected STZ-diabetic 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. The microarray data from each time point was compared relative to uninfected diabetic mice. In addition, the transcriptome of uninfected STZ-diabetic liver and spleen were also compared with uninfected buffer (sodium citrate) control mice.

first: Chui-Yoke

last: Chin


title: Angiotensin receptor blockade attenuates cigarette smoke-induced lung injury and rescues lung architecture in a murine model

city: baltimore

first: chris

last: cheadle

state: MD

address: 5200 Eastern Ave

department: SOM

institute: JHU

summary: TGFβ inhibition attenuates chronic cigarette smoke induced lung injury and rescues lung architecture.

overall_design: AKR/J mice were exposed to Cigarette Smoke (CS) for a period of two months.  Some animals received a treatment of Losartan (.6gr/L) orally while exposed (CS Los).  These two groups are to be compared to animals that remained in Room Air (RA) and Room Air plus Losartan(0.6g/L) (RA Los) for any changes.

first: Chris

last: Cheadle

first: Alan

last: Berger


title: Pathway simulations in common oncogenic drivers of leukemic and rhabdomyosarcomatic cells: a systems biology approach

status: Public on Dec 20 2011

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

summary: A part of current research has intensively been focused on the proliferation and metabolic processes governing biological systems. Since the advent of high throughput methodologies like microarrays, the load of genomic data has increased geometrically and along with that the need for computational methods which will interpret these data. In the present work we study in vitro the common proliferation and metabolic processes, which are combined to the common oncogenic pathways, as far as gene expression is concerned, between the T-cell acute lymphoblastic leukemia (CCRF-CEM) and the rhabdomyosarcoma (TE-671) cell lines. We present a computational approach, using cDNA microarrays, in order to identify commonalities between diverse biological systems. Our analysis predicted that JAK1, STAT1, PIAS2 and CDK4 are the driving forces in the two cell lines. This type of analysis can lead to the understanding of the common mechanisms that transform physiological cells to malignant, as well as it reveals a new holistic way to understandthe the dynamics of tumor onset as well as the mechanistics of oncogenic drivers.

overall_design:
The present work is concerned with the common expressional profile of two cell lines: the T-cell acute lymphoblastic leukemia (CCRF-CEM) and the rhabdomyosarcoma (TE-671) cell lines. Our investigation was focused on the identification of genes that share a common expression profile between the two cell lines. Both cell lines are characterized by the fact that their differentiation has stopped at an early stage, before they mature to their final cell type. Normally, these cells would have matured and progressed into differentiated cells, constituting blood and muscle cells, respectively. At some unknown point, normal differentiation ceased for these cells and they became malignant. From that point on, to the first manifestation of symptoms of malignancy, there is a lack of knowledge regarding the mechanisms underlying oncogenesis.
From these observations, the question whether two distinct cell types destined to fulfill different functions, manifest similar mechanisms of growth and progression due to their malignant character, arises. The present study was focused on the identification of the differential expression profiles underlying the two cell lines. A previous report studied the expression profile of seven ARMS cell lines possessing the PAX3-FKHR fusion gene, along with other cell lines of different tumor types (22). To our knowledge, this is the first time that a comparison between two totally different types of neoplasia, such as the CCRF-CEM and TE-671 cell lines, is attempted. These mechanisms are examined with purpose to identify common drivers that lead to the progression of tumor cells. We hereby propose a new computational approach for the investigation of common oncogenic drivers.


title: Altered gene expression profiles  in the hippocampus and prefrontal cortex of type 2 diabetic rats

status: Public on Dec 15 2011

city: Budapest

first: Omar

last: Abdul-Rahman

address: Tüzoltó utca 37-47

department: Department of Medical Chemistry, Molecular Biology and Pathobiochemistry

country: Hungary

institute: Semmelweis University

summary: There has been an incresing body of epidemiologic and biochemical evidence implying the role of cerebral insulin resistance in Alzheimer-type dementia. For a better understanding of the insulin effect on the central nervous system we performed microarray-based gene expression profiling in the hippocampus, striatum and prefrontal cortex of streptozotocin-induced and spontaneously diabetic Goto-Kakizaki rats as model animals for type 1 and type 2 diabetes, respectively. Following pathway analysis and validation of gene lists by RT-PCR, 30 genes from hippocampus, such as the inhibitory neuropeptide galanin, synuclein gamma and uncoupling protein 2, and 22 genes from the prefrontal cortex, e.g. galanin receptor 2, protein kinase gamma and epsilon, ABCA1, CD47 and the RET protooncogene, were found to exhibit altered expression levels in type 2 diabetic model animals in comparison to non-diabetic control animals. These gene lists proved to be partly overlapping and encompassed genes related to neurotransmission, lipidmetabolism, neuronal development, insulin secretion, oxidative damage and DNA repair. On the other hand, no significant alterations were found in the transcriptomes of the corpus sriatum in the same animals. Changes in the cerebral gene expression profiles seemed to be specific for the type 2 diabetic model, as no such alterations were found in streptozotocin-treated animals. According to our knowledge this is the first characterization of the whole-genome expression changes of specific brain regions in a diabetic model. Our findings shed light on the complex role of insulin signaling in fine-tuning brain functions, and provide further experimental evidence in support of the recently elaborated theory of type 3diabetes.

overall_design: Experiments were performed with 9 animals from each group. Wistar rats (control), streptoztocin-treated Wistar rats (type 1 diabetes) and Goto-Kakizaki rats (type 2 diabetes). The brain was removed and the striatum, hippocampus and prefrontal cortex were dissected. Samples from 3-3 identically treated animals were pooled. That means, 3 biological parallels were prepared from each brain region of type 1 or type 2 diabetic and control animals, amounting to a total of 27 different pooled samples.

first: Maria

last: Sasvari-Szekely

first: Agota

last: Ver

first: Klara

last: Rosta

first: Bernadett

middle: K

last: Szasz

first: Eve

last: Kereszturi

first: Gergely

last: Keszler


title: Transcription profiling of Density-dependent of Xanthomonas oryzae pv. oryzae PXO99A and PXO99∆ax21

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

country: USA

institute: University of California, Davis

summary:
Xanthomonas oryzae pv. oryzae strain PXO99A, so called Xoo, is disable to infect in rice cultivar carrying Xa21 gene. A set of experiments indicated that Ax21 is quorum sensing factor in PXO99 strain. To observe fine-tuned details how Ax21 controls expression of PXO99 in response to change of cell population density, transcriptional profiling analysis was perform by using published two channel oligo Xo microarray platform (Seo et al.,2008 BMC microbiology).

Keywords: Comparative transcription profiling between low cell density and high cell density with same genetic background

platform_organism: Xanthomonas oryzae pv. oryzae KACC 10331

overall_design: Three biological and dye-swap replicates, total six samples for each dataset. Two datasets contained; (i) PXO99 at 106 CFU/ml vs 108 CFU/ml, and (ii) PXO99∆ax21at 106 CFU/ml vs PXO99∆ax21 108 CFU/ml. 106 CFU/ml and 108 CFU/ml are cell density used in this study as representation of low and high cell density. All bacteria cultures were grown in PS (Peptone sucrose) broth media.

first: Pamela

last: Ronald


title: Bmp signaling regulates a dosage dependent transcriptional program to control facial skeletal development.

status: Public on Dec 17 2011

city: Houston

first: Margarita

last: Bonilla

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

summary: Conditional Bmp4 overexpression (Bmp4 OE), using a tetracycline regulated Bmp4 gain of function allele, resulted in facial skeletal changes that were most dramatic after an E10.5 Bmp4 induction. We identified a number of genes predominantly transcriptional regulators controlling self-renewal, osteoblast differentiation, and negative Bmp autoregulation whose expression were change after Bmp4 overexpression in the cranial neural crest cells.

overall_design: We performed expression profiling using RNA extracted from E11.5 Bmp4 OE mandibles that were induced with dox for 24 hours. Using a 2-fold change (p< 0.05) as threshold, we identified 144 down-regulated and 120 up-regulated genes.

last: Bonilla-Claudio


title: miRNA expression in thyroid cancer cells

status: Public on Dec 06 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS


title: Caulobacter strains ET163 and ET166 vs. CB15N (wild-type)

status: Public on Dec 01 2011

city: Boston

first: Mark

last: Umbarger

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: The goal of this study was to compare the expression profiles of inversion strains ET163 and ET166 to that of wild-type.  To this end we performed transcriptional profiling of Caulobacter crescentus swarmer cells from strains ET163, ET166, and CB15N (WT).

sample_organism:
Caulobacter vibrioides
Caulobacter vibrioides CB15

overall_design: Two strain experiment.  ET163 vs. WT and ET166 vs. WT.  Biological replicates: 2 ET163, 2 ET166, and 3 Wild-type


title: Analysis of p53 target genes in melanoma part 1

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

country: Australia

institute: University of Newcastle

summary: Although mutations in p53 are infrequent in human melanoma, its function is abnormal. In this study, whole genome bead arrays were used to examine the expression of p53 target genes in extracts from 82 metastatic melanoma samples, compared to extracts derived from diploid human melanocytes, to provide a global assessment of aberrant p53 function.

overall_design: Total RNA extracted from 82 tumour samples and 8 melanocyte cell lines was analysed. Metastatic melanomas were compared to melanocyte cell lines.

last: Avery-Kiejda

first: Nikola

last: Bowden

first: Carla

last: Kairupan

first: Amanda

last: Croft

first: Katie

last: Ashton

first: Lyndee

last: Scurr

first: Bente

last: Talseth-Palmer

first: Helen

last: Rizos

first: Xu

last: Zhang

first: Rodney

last: Scott

first: Peter

last: Hersey


title: Gene expression study for effectiveness of nicotinamide using chemically-induced mouse bladder cancer model

status: Public on Dec 12 2011

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary:
The objective of this study was to evaluate the efficacy of nicotinamide in a N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN)-induced urinary bladder cancer model in mice, and to identify through gene expression profiling the molecular signatures of cancer prevention by nicotinamide. We used 20 mice for microarray experiments: five mice with normal bladders (group I), five with nicotinamide-treated bladders (group II), five with BBN-induced mouse bladder tumors (group III), and five with non-tumorigenic bladders treated with BBN and nicotinamide (group IV).

Keywords: Gene expression, Mouse bladder cancer, Cancer prevention

overall_design: Total RNA was isolated using TRIzol reagent (Life Technologies, NY), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Five-hundred nanograms of total RNA were used for labeling hybridization according to the manufacturer’s protocols (Illumina Mouse-6 BeadChips, version 1.0). Arrays were scanned with an Illumina Bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions. After scanning, the microarray data were normalized using quantile normalization. Measured gene expression values were log2 transformed and median-centered across genes and samples.

first: Sun-Hee

last: Leem

first: Min-Ju

first: Wun-Jae


title: Met mutations in MEFs

status: Public on Nov 20 2011

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary:
Tyrosine kinase-activating mutations in Met have been observed in hereditary papillary renal carcinomas as well as in other cancers. These mutations have been examined in several in vitro systems, where they cause constitutive Met activation, focus formation, and cell motility, and are tumorigenic in xenografts. To determine the influence of these mutations on tumorigenesis in vivo, we generated mice with targeted mutations in the murine met locus. Five mouse lines with mutant Met were created: wt, D1226N, Y1228C, M1248T, and M1248T/L1193V. These mouse lines develop a wide range of sarcomas, lymphomas, and carcinomas. To determine if mutationally activated forms of Met have altered signaling specificity we utilized gene expression analysis. Mouse embryonic fibroblasts (MEFs) were isolated from the mutant Met lines and here we present data for wild type and M1248T (M833). Our results indicate that Met activating mutations have unique gene expression signatures.
Keywords: mutant analysis

overall_design: Color swapped replicates with common reference


title: Gene expression profile of decidual macrophages and different in vitro M1 and M2 macrophage populations

status: Public on Nov 22 2011

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary: Uterine (decidual) macrophages (M) are believed to play an important role in fetal tolerance during pregnancy, but the factors that regulate them are not known. In this study we investigated the potential role of several factors (M-CSF, GM-CSF, IL-4/13, IL-10, progesterone and estradiol) to drive the differentiation and polarization of human decidual M by using an in vitro M differentiation model. To estimate the similarity of the in vitro differentiated M with decidual M, we used the present gene expression array. The array consisted of 420 M-related genes, including 100 genes highly regulated in decidual M based on the gene expression profile previously reported (Gustafsson et al, 2008, PLoS ONE. 3(4): e2078). The analysis focused on the 100 decidual M-associated genes.

overall_design: Comparative expression analysis of CD14+ cells isolated from blood (3 samples) or decidua (3 samples) from pregnant women, CD14+ cells isolated from non-pregnant women (14 samples) and different types of in vitro-generated macrophages (55 samples). A total of 75 samples were anlayzed.

first: R

first: J

last: Svensson


title: Regulation of hTERT by BCR-ABL at multiple levels in K562 cells

city: Singapore

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: To investigate the mechanism of telomerase regulation in BCR-ABL positive cells due to its clinical value, we studied the catalytic component of telomerase, TERT. Our results suggest that BCR-ABL plays an important role in regulating hTERT in K562 (BCR-ABL positive human leukemia) cells. When Gleevec inhibited the tyrosine kinase activity of BCR-ABL, phosphorylation of hTERT was downregulated, therefore suggesting a positive correlation between BCR-ABL and hTERT. Gleevec treatment inhibited hTERT at the mRNA level and significantly reduced telomerase activity (TA) in K562 cells, but not in HL60 or Jurkat cells. TRAP assay also revealed that Gleevec treatment significantly reduced TA specifically in K562 cells. Furthermore, translocation of hTERT from nucleoli to nucleoplasm was observed in K562 cells induced by Gleevec. Although Gleevec down-regulated hTERT mRNA level, the protein level of hTERT remained unchanged. Therefore, Gleevec-induced-TA decrease is not due to the alteration in telomerase subunits expression. It could be presumably due to posttranslational modification of hTERT, possibly through multiple signaling pathways. We have found that Gleevec reduced the tyrosine phosphorylation of hTERT by BCR-ABL, which is associated with the nucleoplasm localization of hTERT from nucleoli sequesters. These findings reveal unknown functions and regulations of telomerase by BCR-ABL.

overall_design: Using cRNA microarray, gene expression of Gleevec-treated and non-treated K562 (BCR-ABL positive) cells were compared against Gleevec-treated and non-treated HL60 (BCR-ABL deficient) cells.

first: Juin

last: Chai

first: Yong

first: Wei

last: Tan

first: Wee

last: Chng

first: Baojie

last: Li

first: Xueying


title: Systemic Comparison of Heat Shock Response Induced by Heat Shock and a Proteasome Inhibitor in Mouse Fibrosarcoma Cells and Their Thermotolerant Counterparts

status: Public on Nov 09 2011

city: Seoul

first: Kong-Joo

last: Lee

address: Seodaemun-gu

department: College of Pharmacy

institute: Ewha Womans Univ.

summary: Heat shock response (HSR) is a cellular defense mechanism against various stresses. Both heat shock and proteasome inhibitor MG132 cause the induction of heat shock proteins, a distinct feature of HSR. To better understand the molecular basis of HSR, we subjected the mouse fibrosarcoma cell line, RIF-1, and its thermotolerant variant, TR-RIF-1 cells, to heat shock and MG132. We compared mRNA expressions using microarray analysis during recovery after heat shock and MG132 treatment. This study led us to group the 3,245 up-regulated genes by heat shock and MG132 into three families: genes regulated 1) by both heat shock and MG132 (e.g. chaperones); 2) by heat shock (e.g. DNA-binding proteins including histones); and 3) by MG132 (e.g. innate immunity and defense-related molecules).

overall_design: RIF-1 and TR cells were heat shock treated or MG132 treated and harvested after various times of recovery. mRNA expressions were compared to untreated samples. Biological replication was done.

first: Hee-Jung


title: Analysis of Gene Expression changes in human intestinal endothelial-to-mesenchymal transition

status: Public on Nov 02 2011

city: Cleveland

first: Florian

last: Rieder

state: OH

address: 9500 Euclid Avenue

department: Dept of Pathobiology

institute: Cleveland Clinic


title: RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls

city: Charlestown

first: Mikkel

last: Noerholm

address: 149 13th Street

department: Neurology

institute: MGH

summary: Comparative expression analysis of RNA isolated from microvesicles from serum from glioblastoma multiforme (GBM) patients and normal healthy individuals.

overall_design:
Background
RNA from exosomes and other microvesicles contain transcripts of tumour origin. In this study we sought to identify biomarkers of glioblastoma multiforme in microvesicle RNA from serum of affected patients.

Methods
Microvesicle RNA from serum from patients with de-novo primary glioblastoma multiforme (N = 9) and normal controls (N = 7) were analyzed by microarray analysis. Samples were collected according to protocols approved by the Institutional Review Board. Differential expressions were validated by qRT-PCR in a separate set of samples (N = 10 in both groups).

Results
Expression profiles of microvesicle RNA correctly separated individuals in two groups by unsupervised clustering. The most significant differences pertained to down-regulated genes (121 genes > 2-fold down) in the glioblastoma multiforme patient microvesicle RNA, validated by qRT-PCR on several genes. Overall, yields of microvesicle RNA from patients was higher than from normal controls, but the additional RNA was primarily of size < 500 nt. Gene ontology of the down-regulated genes indicated these are coding for ribosomal proteins and genes related to ribosome production.

Conclusions
Serum microvesicle RNA from patients with glioblastoma multiforme has significantly down-regulated levels of RNAs coding for ribosome production, compared to normal healthy controls, but a large overabundance of RNA of unknown origin with size < 500 nt.

first: Leonora

last: Balaj

first: Tobias

last: Limperg

first: Afshin

last: Salehi

first: Fred

last: Hochberg

first: Bob

last: Carter

first: LinDan

last: Zhu

first: Xandra

middle: O

last: Breakefield

first: Johan

last: Skog


title: Microarray profiling reveals Integrated Stress Response is activated by Halofuginone in mammary epithelial cells

status: Public on Oct 18 2011

first: Yana

middle: George

last: Kamberov

address: 77 Ave Louis Pasteur

institute: Harvard University

summary: The small molecule Halofuginone (HF) is a potent regulator of extracellular matrix (ECM ) gene expression and is unique in its therapeutic potential.  While the basis for HF effects is unknown, inhibition of TGFb signaling and activation of the AAR have been linked to HF transcriptional control of a number of ECM components and amelioration of fibrosis and alleviation of autoimmune disease by regulation of Th17 cell differentiation, respectively.  The aim of this study was to generate a global expression profile of HF targets in epithelial cells to identify potential mediators of HF function in this cell type.  We report that HF modulation of the ECM remodeling protein Mmp13 in epithelial cells is separable from previously reported effects of HF on TGFß signal inhibition, and use microarray expression analysis to correlate this with transcriptional responses characteristic of the Integrated Stress Response (ISR).  Our findings suggest a common mechanism underlying HF anti-fibrotic and anti-angiogenic effects in parenchymal cells and HF effects on Th17 differentiation.  Moreover, our results point away from a central role of TGFb signaling in the HF mechanism of action and suggest a new approach to small molecule based regulation of the ECM transcriptional program in vivo.

overall_design: NMuMG mammary epithelial cells were treated with 10 nM Halofuginone or 10 nM MAZ1310 (a non-functional analog of Halofuginone used as a control) for 8 hours.  Each treatment was performed in biological triplicate.  Following RNA extraction, we used Phalanx Mouse Whole Genome OneArray to measure mRNA abundance of Halofuginone-treated and MAZ1310 control samples.  Each array was performed in triplicate. Expression of transcripts in Halofuginone versus MAZ1310 treated cells was examined.

middle: G

first: Malcolm

middle: R

last: Whitman

first: Kim

last: Jihoon


title: A conserved transcriptional regulator governs fungal morphology in widely diverged species [expression data]

status: Public on Oct 04 2011

city: san francisco

first: Chris

last: Cain

address: 600 16th street

institute: UC San Francisco

summary: In this paper, we examine orthologs of a transcriptional regulator in three fungal species, Saccharomyces cerevisiae, Candida albicans, and Histoplasma capsulatum. We show that, despite an estimated 600 million years since those species diverged from a common ancestor, Wor1 in C. albicans, Ryp1 in H. capsulatum, and Mit1 in S. cerevisiae recognize the same DNA motif. Previous work established that Wor1 regulates white-opaque switching in C. albicans and that its ortholog Ryp1 regulates the yeast to mycelial transition in H. capsulatum. Here we show that the ortholog Mit1 in S. cerevisiae also regulates a morphological transition, in this case pseudohyphal growth. Full genome chromatin immunoprecipitation experiments show that Mit1 binds to the control regions of approximately 94 genes including the previously known regulators of pseudohyphal growth. Through a comparison of full genome chromatin immunoprecipitation experiments for Mit1 in S. cerevisiae, Wor1 in C. albicans, and Wor1 ectopically expressed in S. cerevisiae, we conclude that genes controlled by the orthologous regulators overlap only slightly between these two species. We suggest that the ancestral Wor1/Mit1/Ryp1 protein controlled aspects of cell morphology and that evolutionary movement of genes in and out of the Wor1/Mit1/Ryp1 regulon is responsible, in part, for the differences of morphological forms among these species. Consistent with this idea, ectopic expression of C. albicans Wor1 or H. capsulatum Ryp1 can drive the pseudohyphal growth program in S. cerevisiae.

overall_design: Replicate experiments for each of four strains compared with reference sample - WT, a Mit1 deletion haploid A strain, a Yhr177w deletion haploid A strain, and a double deletion haploid A strain. All were in the sigma 2000 background.

first: C

middle: W


title: Identification of copy number variants in horses

status: Public on Oct 08 2011

city: College Station

first: Ryan

last: Doan

state: Texas

address: 4467 TAMU

institute: Texas A&M University

summary: Custom exon aCGH analysis of copy number across the genomes of 16 horse breeds

overall_design: Two-condition experiment, All breed samples were compared to a single Thoroughbred reference, Reference was then compared to Twilight (DNA from horse used for reference genome assembly)

first: Scott

last: Dindot

first: Noah

last: Cohen

first: Jessica

last: Nerren

first: Kylee

last: Veazey

first: Rytis

last: Juras

first: Gus

last: Cothran


title: Y. pestis KIM6+ TraSH Microarray Analysis After Intracellular Replication

status: Public on Nov 30 2011

city: Stony Brook

first: Hana

middle: S.

last: Fukuto

address: CMM rm350, Stony Brook University

department: Microbiology and Molecular Genetics/Center for Infectious Diseases

institute: Stony Brook University

summary: The transposon site hybridization (TraSH) technique (Sassetti, CM et al. 2001. PNAS 98:12712-7) was utilized to identify genes important for the survival of Y. pestis within murine macrophages.  A transposon library was created with ~31,500 Y. pestis KIM6+ insertion mutants.  A portion of the Y. pestis transposon insertion mutant library was used to infect BMMs and the surviving bacteria (output pool) were recovered.  TraSH was used to compare the output pool to a portion of the library that was not subjected to selection (input pool) in order to identify Y. pestis genes important for survival in macrophages.  Each end of the transposon used for mutagenesis contains an outward-reading T7 RNA polymerase promoter.  RNAs transcribed from the T7 promoters are complementary to the chromosomal DNA flanking each transposon in the library, so the RNAs can be used as “targets” to identify the approximate position of each transposon insertion in the mutant pool.   Differentially labeled targets generated from the output and input pools are competitively hybridized to the 70-mer oligonucleotide microarrays obtained from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute.  Genes important for survival of Y. pestis in macrophages are identified by determining the ratio of the signal intensities for the output and input targets hybridizing to a given probe.

overall_design: A transposon library was created with ~31,500 Y. pestis KIM6+ insertion mutants.  A portion of the Y. pestis transposon insertion mutant library was used to infect BMMs and the surviving bacteria (output pool) were recovered.  TraSH was used to compare the output pool to a portion of the library that was not subjected to selection (input pool).  Each end of the transposon used for mutagenesis contains an outward-reading T7 RNA polymerase promoter.  RNAs transcribed from the T7 promoters are complementary to the chromosomal DNA flanking each transposon in the library, so the RNAs was used as “targets” to identify the approximate position of each transposon insertion in the mutant pool.   Differentially labeled targets generated from the output and input pools are competitively hybridized to the 70-mer oligonucleotide microarrays obtained from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute.  Genes important for survival of Y. pestis in macrophages are identified by determining the ratio of the signal intensities for the output and input targets hybridizing to a given probe.

first: Kathryn

middle: A

last: Klein

first: Mark

last: Pelletier

first: Galina

last: Romanov

first: Jens

last: Grabenstein

first: Lance

middle: E

last: Palmer

first: Robert

last: Ernst

first: James

middle: B

last: Bliska


title: miRNA array in  colorectal carcinoma

status: Public on Nov 29 2011

city: Shanghai

first: Sun

last: Y

address: 180 Fenglin Road

institute: Fudan University

summary: To search for potential miRNAs associated with prognosis in colorectal carcinoma, miRNA expression profiles were analyzed in patients with stage III colorectal carcinoma. miRNA expression levels were compared between long and short time survival after surgery with standard chemotherapy.

overall_design: Two groups of colorectal carcinoma tissues for miRNA array. Long time (L) survival (≥5 years) group and short time survival (S) (<5 years) group.


title: Characterization of Nicotiana attenuata plants with reduced expression of lectin receptor kinase 1 (ir-lecRK1 plants).

status: Public on Nov 23 2011

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of transcripts that change expression in Nicotiana attenuata plants with reduced expression of lectin receptor kinase 1 after elicitation with oral secretions of Manduca sexta larvae.

overall_design: Gene expression in leaves of Nicotiana attenuata wild type and ir-lecRK1 plants was measured at 1 hour after elicitation with oral secretions of Manduca sexta larvae. Three independent experiments were performed with wild type plants and three independent experiments were performed with ir-lecRK1 plants. A total of 148 genes were identified as differentially regulated in ir-lecRK1 plants compared to wild type plants.

first: Paola

last: Gilardoni

first: Gustavo

last: Bonaventure


title: Transcriptome and translational signaling following endurance exercise in trained skeletal muscle: impact of dietary protein

status: Public on Nov 21 2011

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: Impact of protein ingestion following 1 h intense cycling on the induced transcriptome and signaling in biopsy samples from endurance-trained men, relative to isocaloric control

overall_design: Single blind, randomized, crossover design comprising two experimental blocks. During the blocks, exercise and diet were controlled and the intervention consisted of the ingestion of a protein-enriched and control beverage, with outcome measures obtained from skeletal muscle tissue collected following a bout of intense cycling. Total RNA were obtained from quadriceps. Each of the two serves were isocaloric and provided 0.2 g/kg fat (freeze dried canola oil) with either 1.2 g/kg carbohydrate (1:1 maltodextrin:fructose) and 0.4 g/kg protein (2:1 milk protein concentrate:whey isolate); or 1.6 g/kg carbohydrate (1:1 maltodextrin:fructose).

first: David

last: Rowlands

first: Jasmine

last: Thomson

first: Brian

last: Timmons

first: Frédéric

first: Andreas

last: Fuerholz

last: Mansourian

first: Marie-Camille

last: Zawhlen

first: Sylviane

last: Métairon

first: Elisa

last: Glover

first: Trent

last: Stellingwerff

last: Tarnopolsky


title: Avian arcopallium

city: Durham

first: Erina

last: Hara

state: NC

address: Rm 449 Bryan Research Building

institute: Duke University Medical Center

summary: To determine what kind of genes are involved in vocal learning ability, we performed microarray experiments using 3 vocal learning species (zebra finch, budgerigar, Anna's hummingbird) and 2 non-vocal learning species(ring dive, and Japanese quail) from bird group. All of the animals are adult males. They were isolated over night and had 1hour light exposure at morning. Birds who did not sing were used in this experiment.

sample_organism:
Calypte anna
Melopsittacus undulatus
Taeniopygia guttata
Coturnix japonica
Streptopelia risoria

overall_design: We used 2-3 animals each species. We use arcopallium song nucleus for vocal learners and intermediate arcopallium for non-vocal learners. We used surrounding arcopallium as control area for both groups.

first: Erich

middle: D

last: Jarvis

middle: M

last: Ward

first: Miriam

middle: V

last: Rivas


title: Examination of Ollier Disease and Maffucci Syndrome using IDH Tiling Array

status: Public on Nov 05 2011

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

institute: LUMC

summary: Ollier disease and Maffucci syndrome are non-hereditary skeletal disorders characterized by multiple enchondromas (Ollier) combined with spindle cell hemangiomas (Maffucci). We found somatic heterozygous IDH1 mutations (R132C and R132H) in 83% of enchondromas, benign cartilage tumors, as well as in 40% of spindle cell hemangiomas, benign vascular lesions. In total, 33 of 42 (78%) patients with Ollier disease and 7 of 13 (54%) patients with Maffucci syndrome carried a mutation in at least one of their tumors. Twelve patients with multiple tumors at different locations displayed identical mutations in separate lesions. Immunohistochemical staining for the R132H IDH1 mutant protein suggested intraneoplastic as well as somatic mosaicism. IDH1 mutations were less frequent (63%) in high grade malignant cartilage tumors in Ollier disease, suggesting that IDH1 is less important for malignant transformation. IDH1 and IDH2 mutations were found in 36% of sporadic cartilage tumors and in four cell lines derived from sporadic chondrosarcomas.

overall_design: 16 samples were analyzed in two color experiment, using normal male or female as a reference sample (gender mismatched)


title: miRNA analysis of murine fibroblasts subjected to acute oxidative stress

status: Public on Nov 01 2011

city: PARIS

first: Fatima

last: Mechta-Grigoriou

address: 26 rue d'Ulm

department: INSERM U830

institute: Institut Curie

summary: Analysis of miRNA modulated by H2O2 treatment in murine fibroblasts. The hypothesis in the present study is that stress balance the level of some miRNAs. These particular miRNAs may target key proteins involved in stress and thus modulate cellular response to stress.

overall_design: Total RNA obtained from 2 independant fibroblasts clones treated for the indicated time with 400 uM H2O2


title: Rat hepatocytes: Advanced cirrhosis vs Control liver, Advanced cirrhosis vs Early cirrhosis

city: Pittsburgh

first: Taichiro

last: Nishikawa

state: PA

address: 530 45th Street

department: Surgery

institute: University of Pittsburgh

summary: Gene profiling of hepatocytes in early and advanced cirrhotic Rats

overall_design: Two-condition experiment, Advanced cirrhosis vs Control liver, Advanced cirrhosis vs Early cirrhosis. Biological replicates: 5 Advanced cirrhosis, 5 Early cirrhosis, 5 control liver. Each hepatocyte was isolated independently. One replicate per array.

first: Ira

middle: J

last: Fox


title: Genome-wide analysis of transfection of miR-141 or miR-200c in murine fibroblasts subjected to acute oxidative stress

summary: Analysis of abnormal cellular response to stress after overexpression of stress-induced microRNAs. The hypothesis tested in the present study was that miR-141 or miR-200c may influence transcription of stress-pathways related genes

overall_design: Total RNA obtained from fibroblasts transfected for 48h with Control, miR-141 or miR-200c. 2h hours before lysis, fibroblasts were stimulated with 400 uM H2O2.

first: Bogdan

last: Mateescu


title: IRF8-regulated genes in primary CD11 b cells

status: Public on Oct 20 2011

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

summary: Transcriptional profiling of IRF8-regulated genes in mouse CD11b-positive primary cells. CD11b-positive cells were isolated from spleens of age-matched wt and IRF8 KO mice, the compared for their gene expression profiles. The objective is to identify genes that are regulated by IRF8 in CD11b-positive primary cells.

overall_design: Two-condition experiments. Wt vs IRF8 KO cells. Biological replicates: 2 replicates for the comparison.


title: Glutathione-induced elicitation of defense responses in Lotus japonicus.

status: Public on Sep 16 2011

city: Fredriksberg

first: Dale

last: Shelton

address: Thorvaldsensvej 40

department: Dept. Plant Biology and Biotechnology

country: Denmark

institute: University of Copenhagen

summary: To identify transcription factors involved in the production of defense-related phytochemicals through co-expression studies.

overall_design: The changes in gene expression following GSH elicitation of leaves was followed over a time course.  Four biological replicates of the unelicited samples and three biological replicates were used for each time point.


title: Microarray analysis of Normal and MPS VII mouse aorta

status: Public on Oct 10 2011

city: Saint Louis

first: Katherine

middle: Parker

last: Ponder

state: MO

address: 660 S. Euclid Avenue

institute: Washington University St Louis

summary: Mucopolysaccharidosis VII (MPS VII) is due to mutations within the gene encoding the lysosomal enzyme beta-glucuronidase, and results in the accumulation of glycosaminoglycans.  MPS VII causes aortic dilatation and elastin fragmentation. In this study we performed microarray analysis of ascending aortas from normal and MPS VII mice, trying to find out possible genes responsible for the phenotype observed. In addition, during our breeding strategy, we noticed that some MPS VII mice had less dilated aortas, and we proposed that an yet-unidentified gene could be responsible for the difference observed. We therefore included in the analysis two MPS VII mice with aortas that were not dilated.

overall_design: Total RNA extracted from ascending aortas from 3 Normal mice, 3 MPS VII mice with dilated aortas and 2 MPS VII mice with aortas that were not dilated.

first: Guilherme

last: Baldo


title: Analysis of Gene Expression changes in human intestinal endothelial-to-mesenchymal transition - TRANSFORMED GROUP

first: Florian

last: Rieder

summary: Intestinal fibrosis is a well-known complication of inflammatory bowel disease (IBD) and has important clinical implications for both forms of IBD, Crohn's disease (CD) and ulcerative colitis (UC).  In addition to mesenchymal cells, endothelial cell contribute to organ fibrosis through the process of endothelial-to-mesenchymal transition (EndoMT).  Our aim was to investigate if human intestinal microvascular endothelial cells (HIMEC) can undergo EndoMT, produce extracellular matrix, and contribute to fibrosis in both forms of IBD.  Cellular transformation is a highly complex event involving drastic changes in multiple gene expression levels.  To assess global genomic changes accompanying HIMEC transformation, we performed microarray analysis comparing transformed to non-transformed/untreated HIMEC.  Consistent with the morphological, phenotypic and functional findings, transformed HIMEC downregulated the expression levels of genes typically expressed in endothelial cells and upregulated several genes of ECM molecules known to be increased in intestinal fibrosis.  Thus, it is evident that inflammatory stimuli induce transdifferentiation of HIMEC into matrix-producing mesenchymal cells. Because the conditions inducing transformation in vitro reproduce those found in vivo during active gut inflammation, the microvasculature may contribute to IBD-associated fibrosis through the novel process of EndoMT.  This series includes all treated or TRANSFORMED HIMEC samples (4).

overall_design: Surgically resected specimens were used for isolation of human intestinal microvascular endothelial cells (HIMEC).  HIMEC monolayers derived from intestinal mucosa of four different subjects – 2 controls, 1 ulcerative colitis, and 1 crohns were cultured in 75cm2 tissue culture flasks coated with fibronectin.  Cells were left untreated (unstimulated/non-transformed) or exposed to the combination of IL-1b 100 U/ml, TNF-a 100 U/ml and TGF-b1, 5ng/ml (TGFTNFIL1) for six days.  HIMEC medium was changed every 3 days.   Total ribonucleic acid (RNA) was extracted using a commercially available kit (Qiagen®). RNA was reverse transcribed into cRNA which was then hybridized to the Illumina HumanRef-8 v2 Expression BeadChip.  The raw gene expression datasets were processed to remove outliers, log2 transformed and quantile normalized using R lumi software.  Those genes that satisfied the FDR p-value threshold of < 0.05 or raw p-value of <0.001 were identified as significant for the functional pathway and network analysis.

first: Gail

last: West

first: Carol

last: de la Motte

first: Banu

last: Gopalan

first: Claudio

last: Fiocchi


title: Gene expression analysis of Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown

status: Public on Oct 14 2011

city: Atlanta

first: Ashley

last: Wood

address: 1510 Clifton Rd. RRC 1071B

institute: Emory University

summary: This study examines the changes in genes expression that occur in Drosophila melanogaster during the ecdysone response as well as during RNAi knockdown of the insulator protein, CP190.  Analysis was performed in Kc cells after 0, 3, and 48 hours of ecdysone treatment in the presence of either control or CP190 knockdown.

overall_design: Six conditions were analyzed, and each condition was performed for 2 biological replicates making a total of 12 chips.  Each chip measures the expression level of 16,637 genes from D.melanogaster with eight, 60-mer probes per gene.

first: Victor

last: Corces

first: Kevin

last: Van Bortle

first: Edward

last: Ramos


title: Analysis of Gene Expression changes in human intestinal endothelial-to-mesenchymal transition - UNTREATED/CONTROL GROUP

address: 9500 Euclid Avenue

institute: Cleveland Clinic

summary: Intestinal fibrosis is a well-known complication of inflammatory bowel disease (IBD) and has important clinical implications for both forms of IBD, Crohn's disease (CD) and ulcerative colitis (UC).  In addition to mesenchymal cells, endothelial cell contribute to organ fibrosis through the process of endothelial-to-mesenchymal transition (EndoMT).  Our aim was to investigate if human intestinal microvascular endothelial cells (HIMEC) can undergo EndoMT, produce extracellular matrix, and contribute to fibrosis in both forms of IBD.  Cellular transformation is a highly complex event involving drastic changes in multiple gene expression levels.  To assess global genomic changes accompanying HIMEC transformation, we performed microarray analysis comparing transformed to non-transformed/untreated HIMEC.  Consistent with the morphological, phenotypic and functional findings, transformed HIMEC downregulated the expression levels of genes typically expressed in endothelial cells and upregulated several genes of ECM molecules known to be increased in intestinal fibrosis.  Thus, it is evident that inflammatory stimuli induce transdifferentiation of HIMEC into matrix-producing mesenchymal cells. Because the conditions inducing transformation in vitro reproduce those found in vivo during active gut inflammation, the microvasculature may contribute to IBD-associated fibrosis through the novel process of EndoMT.  This series includes all untreated or CONTROL HIMEC samples (4).