title: Rat superior olivary complex

summary:
The superior olivary complex (SOC) is an essential auditory brainstem structure involved in sound localization. In order to identify the genetic program underlying its maturation, we profiled the transcriptome of the rat SOC at postnatal days (P)0, P4, P16, and P25, using genome-wide microarrays (41,012 sequences). Differences in gene expression between two consecutive stages were highest between P4 versus P16 (3.6%), but dropped to 0.06% between P16 versus P25. To identify SOC-related genetic programs, we also profiled the brain at P4 and P25. Differentially expressed sequences between SOC and brain almost doubled from P4 (4.4%) to P25 (7.6%). These datademonstrate considerable molecular specification around hearing onset, which is rapidly finalized. Prior to hearing onset, several transcription factors associated with the peripheral auditory system were up-regulated, likely coordinating auditory system development. Additionally, serotonin-related genes and crystalline-gamma subunits were highly expressed. The molecular repertoire of mature neurons was sculpted by SOC-related up- and down-regulation of several protein categories, among which voltage-gated channels and myelination were prominent. Comparison with the brain revealed a significant enrichment of deafness-related oligos in the SOC-related genetic program (26 in the SOC, only 11 in the brain). Furthermore, 29 out of 453 SOC-related oligos mapped within 19 genetic intervals associated with hearing impairment. Together, we identified sequential genetic programs in the SOC, thereby pinpointing candidates which may guide its development and ensure proper function. The enrichment of deafness-related genes in the SOC may have implications for restoring hearing, as central auditory structures might be more severely affected than previously appreciated.

This SuperSeries is composed of the SubSeries listed below.

overall_design: The genome wide expression during the postnatal development of the SOC was investigated at four different time points: at postnatal (P) day 0, P4, P16 and P25. Concerning the brain, P4 and P25 were used. Samples were hybridized onto two color platforms. At least 6 up to nine biological replicates per sample were performed.


title: Comparative microarray analyses between the rat superior olivary complex and the brain

status: Public on Jul 31 2013

city: Oldenburg

first: Hans Gerd

last: Nothwang

state: Lower Saxony

address: Carl von Ossietzky Str. 9-11

department: Neurogenetics

country: Germany

institute: University of Oldenburg

summary:
To investigate the participation of deafness genes in the genetic program of the superior olivary complex (SOC), a prominent auditory brainstem center, we performed a comparative genome-wide microarray based gene expression analysis of the rat SOC and the rat brain at postnatal days (P) P4 and P25. Data were validated by qRT-PCR. Statistical analyses revealed 912 oligos up-regulated in the SOC at P4 and 1609 at P25. A total of 453 oligos were up-regulated in the SOC at both developmental stages. Subsequently, a list of 138 transcripts associated with hearing-impairment was extracted from publically available databases and literature. 26 of these transcripts were present in SOC-related gene signature lists, whereas only 11 were present in brain-related gene signature lists. Furthermore, in all 3 SOC-related gene signature lists, transcripts associated with hearing impairment were significantly enriched. Finally, there was a tendency of the SOC-related genes to map to human deafness loci with unknown etiology.
Altogether, our study identified a tight genetic link between the SOC-related genetic program and deafness genes.

overall_design: The genome wide expression during the postnatal development of the SOC and the brain was investigated at two different time points: at postnatal (P) day 4 (before hearing onset) and at P25 (after hearing onset). Samples were hybridized onto two color platforms. At least 6 up to nine biological replicates per sample were performed.

first: Heike

last: Ehmann

first: Hans-Gerd

first: Christian

last: Salzig


title: Disruption of immune responses hindered cardiac repair in zebrafish

status: Public on Jun 24 2013

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

summary: We investigated the role and programming of early immune responses during zebrafish heart regeneration. We found zebrafish treated with anti-inflammatory steroid, beclomethasone, would suffer significantly reduction of its heart regenerative ability, leading to excessive collagen deposition in wound. Microarray approach was used to evaluate the differential expression of heart transcriptome between normal and impaired healing zebrafish, which provides an overall assessment of significant genes that were important for triggering regeneration in the hemostasis-inflammation phase.

overall_design: Three sets of samples each containing 10 zebrafish hearts were used: sham operation, DMSO-1dpa, beclomethasone-1dpa. (dpa= days post amputation) Objects were pre-exposed to water containing 0.25μM beclomethasone or DMSO for 1 day. After ventricular resection surgery, objects were sacrificed with their ventricles harvested at the next day (i.e. 1dpa)

first: Wei-Chang

last: Huang


title: Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling

status: Public on Jun 28 2013

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

summary: Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants of unclear pathogen significance are found in the families, constituting an increasing clinical challenge. New methods are therefore needed to improve the detection rate and aid the interpretation of the clinically uncertain variants. In this study we analyzed a series of 33 BRCA1, 22 BRCA2, and 128 sporadic tumors by RNA profiling to investigate the classification potential of RNA profiles to predict BRCA1/2 mutation status. We found that breast tumors from BRCA1 and BRCA2 mutation carriers display characteristic RNA expression patterns, allowing them to be distinguished from sporadic tumors. The majority of BRCA1 tumors were basal-like while BRCA2 tumors were mainly luminal B. Using RNA profiles, we were able to distinguish BRCA1 tumors from sporadic tumors among basal-like tumors with 83% accuracy and BRCA2 from sporadic tumors among luminal B tumors with 89% accuracy. Furthermore, subtype-specific BRCA1/2 gene signatures were successfully validated in two independent data sets with high accuracies. Although additional validation studies are required, indication of BRCA1/2 involvement (“BRCAness”) by RNA profiling could potentially be valuable as a tool for distinguishing pathogenic mutations from benign variants, for identification of undetected mutation carriers, and for selecting patients sensitive to new therapeutics such as PARP inhibitors.

overall_design: Gene expression profiling of 183 breast tumor samples. Breast tumors from hereditary breast cancer patients carrying a pathogenic BRCA1 (n=33) or BRCA2 (n=22) germ-line mutation were included in the study. Serving as a representative control group, primary breast tumor samples (n=128) were randomly selected. The study was conducted using Agilent-029949 Custom SurePrint G3 Human GE 8x60K Microarray platform. For cross-platform validation, a subset of the tumor samples (92 of the 183 samples) were analyzed by our in-house spotted microarray platform.

middle: J

first: Torben

middle: A

last: Kruse

first: Qihua

last: Tan

first: Anne-Vibeke

last: Lænkholm

last: Bak

first: Anne

middle: E

last: Lykkesfeldt

first: Kristina

middle: P

last: Sørensen

first: Thomas

middle: O

last: Hansen

first: Bent

last: Ejlertsen

first: Anne-Marie

last: Gerdes

first: Mads

last: Thomassen


title: DNA Methylation Biomarkers for Noninvasive Diagnosis of Colorectal Cancer

status: Public on May 27 2013

city: L'Hospitalet del Llobregat

first: Antonio

last: Berenguer-Llergo

state: Barcelona

address: Gran Via 199-203

department: Cancer Prevention Program

country: Spain

institute: Catalan Institute of Oncology (ICO)

summary: DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed.

overall_design: Bisulphite converted DNA from 92 colorectal tumor samples and paired adjacent normal mucosa were hybridised to the Illumina GoldenGate Methylation Cancer Panel I. Additionally, replicates were hybridised for five tumor tissue and their corresponding normal mucosa for reproducibility purposes, totalling 194 samples. Three samples (SAMPLEs 49, 51, and 162) and 50 loci did not reach the quality criteria required regarding the signal-to-noise ratio and were therefore excluded from further analysis. One additional non-tumoral sample (SAMPLE 15) was removed because it exhibited a methylation pattern quiet different from that shown by the rest of normal specimens, which could be indicative of hybridization errors. These Samples and loci are included in the raw data matrix to allow other investigators to use them if different criteria are applied. They have been also included in the Sample tables with missing values in order to preserve the structure of the data across records/files (See 'data processing' section for more details).

first: V

last: Moreno

first: M

last: Esteller


title: Gene expression in brain and antennae of starved and fed Drosophilla adult

status: Public on Jun 20 2013

city: Jena

first: Abu

last: Farhan

state: Thuringia

address: Hans-knol-str 8

department: Evolutionary Neuroethology

institute: MPI for chemical ecology

summary: We found in our behavior experiment clearly distinnct olfactory responses in fed vs starved flies in response to differrent odors.To investigate the molecular basis of the starvation mediated olfactory modulation process, we compared gene expression at the level of the antenna and the brain for fed and starved flies.

overall_design: Gene expression in brain and antennae was measured at 0hr and 28 hours starved.  Four independent experiments were performed at each time using different flies for each experiment.

first: Jyotasana

last: Gulati

first: Ewald

last: Große-Wilde

first: Heiko

last: Vogel

first: Bill

middle: S

last: Hansson

first: Markus

last: Knaden


title: Piriformospora indica on Arabidopsis and barley root material

status: Public on Jul 22 2013

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

summary: Broad-host root endophytes establish long-term interactions with a large variety of plants, thereby playing a significant role in natural and managed ecosystems and in evolution of land plants. To exploit plants as living substrates and to establish a compatible interaction with morphologically and biochemically extremely different hosts, endophytes must respond and adapt to different plant signals and host metabolic states. Here we identified host-adapted colonization strategies and host-specific effector candidates of the mutualistic root endophyte Piriformospora indica by a global investigation of fungal transcriptional responses to barley and Arabidopsis at different symbiotic stages. Additionally we examined the role played by nitrogen in these two diverse associations. Cytological studies and colonization analyses of a barley mutant and fungal RNAi strains show that distinct physiological and metabolic signals regulate host-specific lifestyle in P. indica. This is the foundation for exploring how distinct fungal and host symbiosis determinants modulate biotrophy in one host and saprotrophy in another host and, ultimately, gives hints into the mechanisms underlying host adaptation in root symbioses.

platform_organism:
Arabidopsis thaliana
Serendipita indica

overall_design: Arabidopsis and barley roots were inoculated with Piriformospora indica and grown for 14 days. Additionally P. indica was grown on 1/10 PNM medium alone. Samples were taken 3 and 14 dpi (Arabidopsis), 14 dpi (barley) and 3dpi (1/10 PNM). Each experiment was performed in three independent biological repetitions.  Piriformospora indica  gene expression examined only.

first: Yi

last: Ding

first: Alga

last: Zuccaro


title: The effect of HO-1 overexpression on microRNA transcriptome in NCI-H292 lung cancer cells

status: Public on Apr 27 2013

city: Krakow

first: Klaudia

last: Skrzypek

address: ul. Gronostajowa 7

department: Department of Medical Biotechnology

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

summary:
The aim was to determine the effect of heme oxygenase-1 (HO-1) overexpression on microRNA transcriptome in human non-small cell lung carcinoma cell line (NCI-H292).
Since the cells of different HO-1 genotypes were used (cells are after retroviral transduction with empty vector with normal level of HO-1 or retroviral transduction with vector harboring HO-1), it is possible get the comprehensive answer which microRNAs are regulated by HO-1.

overall_design: Confluent NCI-H292 cells that contain EV-ctrl or overexpressing HO-1.  Pool of reference cells are cells  untreated and treated with 10 ng/ml TNF-α for 6 hours before RNA isolation.  The samples are biological triplicates - three independent experiments were performed at different time points for all cell lines. Total number of the presented samples is 6.

first: Jozef

last: Dulak

first: Claudine

last: Kieda


title: Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum

status: Public on May 06 2013

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

country: USA

institute: University of Notre Dame

type: Expression profiling by genome tiling array

summary:
Using a tiled whole-genome microarray, we found that 58.2% of Tribolium castaneum genes are maternally loaded into eggs.  Comparison of known Drosophila melanogaster maternal genes to our results showed widespread conservation of maternal function with T. castaneum.  We also found many T. castaneum genes with previously identified gender or tissue specific expression were also maternally loaded into eggs.  The microarray design also allowed the detection of 2315 and 4060 novel transcriptionally active regions greater in length than 100 bp in unfertilized and fertilized T. castaneum eggs, respectively.
The primary objective of this study was to identify expressed regions of the Tribolium castaneum genome in unfertilized and fertilized eggs using a whole-genome tiled microarray.

overall_design: The whole RNA of 3 samples of virgin laid eggs and 3 samples of fertilized eggs were compaired.

first: Kevin

middle: M

last: Preuss


title: Structurally distinct polycyclic aromatic hydrocarbons induce differential transcriptional responses in developing zebrafish

status: Public on May 15 2013

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary: Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment as components of fossil fuels and by-products of combustion. These multi-ring chemicals differentially activate the Aryl Hydrocarbon Receptor (AHR) in a structurally-dependent manner, and induce toxicity via both AHR-dependent and -independent mechanisms. PAH exposure is known to induce developmental malformations in zebrafish embryos, and recent studies have shown cardiac toxicity induced by compounds with low AHR affinity. Unraveling the potentially diverse molecular mechanisms of PAH toxicity is essential for understanding the hazard posed by complex PAH mixtures present in the environment. We analyzed transcriptional responses to PAH exposure in zebrafish embryos exposed to benz(a)anthracene (BAA), dibenzothiophene (DBT) and pyrene (PYR) at a concentration that induces developmental malformations by 120 hours post-fertilization (hpf). Whole genome microarray analysis of mRNA expression at 24 and 48 hpf identified genes that were differentially regulated over time and in response to the three PAH structures. PAH body burden was analyzed at these time points using GC-MS, and demonstrated differences in PAH uptake into the embryos. This was important for discerning dose-related differences from those that represented unique molecular mechanisms. While BAA misregulated the smallest number of transcripts, it caused strong induction of cyp1a and other genes known to be downstream of the AHR, which were not induced by the other two PAHs. Analysis of functional roles of misregulated genes and their predicted regulatory transcription factors also distinguished the BAA response from regulatory networks disrupted by DBT and PYR exposure. These results indicate that systems approaches can be used to classify the toxicity of PAHs based on the networks perturbed following exposure and may provide a path for unraveling the toxicity of complex PAH mixtures.

overall_design: Gene expression was measured in zebrafish embryos after exposure to PAHs. Embryos were batch-exposed in groups of 40 to 25 μM BAA, 25 μM DBT, 25 μM PYR or 1% DMSO vehicle control starting at 6 hpf and collected at 24 or 48 hpf. Four independent biological replicates were prepared for each treatment. The reference was a pool of zebrafish embryos exposed to DMSO control until 24 and 48 hpf.

middle: C

first: Robert

middle: L

last: Tanguay


title: Plasma miRNA Expression Profiling Using Human TaqMan Low Density Array Cards

status: Public on Apr 13 2013

city: Kyoto

first: Koichi

last: Murata

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

country: Japan

institute: Kyoto University

summary: Our study was designed to identify plasma miRNAs specific for rheumatoid arthritis (RA) by a comprehensive array approach. We performed a array-based miRNA analysis on plasma samples from three RA patients and three healthy controls (HCs).

overall_design: TaqMan Low-Density Array (TLDA) using human miRNA version 3.0A and version 2.0B cards (Applied Biosystems) were applied to examine the global change of miRNA expression levels in plasma from patients with RA and healthy controls. A total of 756 mature miRNA updated in the Sanger miRBase v.15.0 were quantified according to the manufacturer's instructions as previously described. Normalization was carried out with the average Ct value of all miRNAs. Relative quantification of miRNA expression was calculated with the 2−ΔΔCt Ct method. The data was presented as log10 of the relative quantity of each miRNA.

first: K

first: H

last: Yoshitomi


title: Genomic signatures predict poor outcome in Undifferentiated Pleomorphic Sarcomas and Leiomyosarcomas

status: Public on May 20 2013

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

type: Genome variation profiling by genome tiling array

summary: Array-based comparative genomic hybridization (array CGH) analyses was used to analyze 20 UPS and 17 LMS samples from untreated patients. The data were validated using quantitative PCR.

overall_design: Experiment condition, 20 UPS and 17 LMS DNA samples obtained from untreated patients were laleled with Cy5 and commercial reference samples (Promega) were labled with Cy3. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 4x44 platform.

first: Sara

last: Silveira

first: Fábio


title: Transcriptional profiling of CD8 cells laser captured from skin biopsies at dermal-epidermal junction and at deeper dermal area near blood vessel during the healed phase of mucocutaneous HSV-2 reactivation

status: Public on Apr 11 2013

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

summary: We aim to get a comprehensive analysis on gene expression of CD8a+ T-cells during the post healed phases of HSV-2 reactivation at different anatomic location (CD8a+ cells at dermal-epidermal junction versus CD8a+ cells in deeper dermal area near blood vessel). Our hypothesis is that JC_CD8 cells may function as a resident effector-like T-cells while BV_CD8 cells may be infiltrating cells from circulation.

overall_design: CD8 cells were immunofluorescently stained and laser captured from genital skin biopsies at dermal-epidermal junction at 2 and 8 weeks post healed (JC_2wks_CD8 and JC_8wks_CD8) and at deeper dermal area near blood vessel (BV_2wks_CD8 and BV_8wks_CD8); total RNA were purified from captured cells and cDNA were amplified from the total RNA using NuGEN pico kits


title: Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma [tumor]

status: Public on May 22 2013

city: San Diego

first: Kai

last: Wang

state: CA

address: 10646 Science Center Dr

department: Oncology Research

institute: Pfizer

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Cancer is a genetic disease with frequent somatic alterations in DNA. Study of recurrent copy number aberrations (CNAs) in human cancers would enable the elucidation of disease mechanisms and the identification of key oncogenic drivers with causal roles in oncogenesis. We have comprehensively and systematically characterized CNAs and accompanied gene expression changes in the tumors and their matched non-tumor liver tissues from 286 hepatocellular carcinoma (HCC) patients. Our analysis identified 29 recurrently amplified regions and 22 deleted regions with a high level of copy number changes, harboring established oncogenes and tumor suppressors, including CCND1, MET, CDKN2A and CDKN2B, as well as many other genes not previously reported to be involved in liver carcinogenesis. Cis-acting genes in the amplification and deletion peaks were enriched in core cancer pathways, including cell cycle, p53, PI3K, MAPK, Wnt and TGFβ signaling in large proportions of HCCs. We further validated two candidate driver genes, BCL9 and MTDH, from the recurrent focal amplification peaks and showed that they play a significant role in HCC growth and survival. In summary, we have demonstrated that characterizing the CNA landscape in HCC will facilitate the understanding of disease mechanisms and the identification of oncogenic drivers that may serve as potential therapeutic targets for the treatment of this devastating disease.

overall_design: Two hundred and eighty-six hepatocellular carcinoma tumors and their matched non-tumor adjacent liver tissue samples were genotyped using Illumina HumanOmni1-Quad BeadChip to estimate their somatic copy number profiles.

first: Stephanie

last: Shi

first: Jeeyun

last: Lee

first: Shibing

last: Deng

first: Paul

last: Rejto

first: Mao

last: Mao

first: Cheol-Keun

last: Park

first: Jiangchun

last: Xu


title: Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma [cell line]

overall_design: Thirty hepatocellular carcinoma cell lines were genotyped using Illumina HumanOmni1-Quad BeadChip to estimate their copy number profiles relative to pooled Hapmap samples.

first: Yuli


title: Cryptococcus neoformans gene expression in YPD and Minimal Media of Wild type (WT) and ALL1 mutant cells

status: Public on Apr 01 2013

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: To examine the comparative transcription profile of WT and ALL1 mutant cells in in vitro conditions to determine genes resposible for hypervirulent phenotype of ALL1 mutant cells. Using transcriptional profiling, we determined that many genes involved in oxidation reduction processes and iron homeostasis were differentially transcribed between the wild type and the mutant strain

overall_design: For arrays, total RNA was isolated from WT and ALL1 mutant using Qiagen RNeasy Kit. For RNA extraction, Wt and ALL1 mutant were grown in two different culture medium conditions including minimal media and YPD broth. Cells were grown for overnight, diluted 1:100 and then again grown overnight or up to an OD of 0.6-0.7 with agitation (150rpm) at 37°C.

first: Neena

last: Jain

first: Bettina

last: Fries


title: Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma

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

overall_design: Refer to individual Series


title: Affymetrix expression data from GTEx

status: Public on Apr 09 2013

city: Cambridge

first: Kristin

last: Ardlie

state: MA

address: 7 Cambridge Center

institute: The Broad Institute of MIT and Harvard

summary:
The Genotype-Tissue Expression (GTEx) project is a collaborative effort that aims to identify correlations between genotype and tissue-specific gene expression levels that will help identify regions of the genome that influence whether and how much a gene is expressed. GTEx is funded through the Common Fund, and managed by the NIH Office of the Director in partnership with the National Human Genome Research Institute, National Institute of Mental Health, the National Cancer Institute, the National Center for Biotechnology Information at the National Library of Medicine, the National Heart, Lung and Blood Institute, the National Institute on Drug Abuse, and the National Institute of Neurological Diseases and Stroke, all part of NIH.
This series of 837 samples represents multiple tissues collected from 102 GTEX donors and 1 control cell line. In total, 30 tissue sites are represented including Adipose, Artery, Heart, Lung, Whole Blood, Muscle, Skin, and 11 brain subregions. RNA-seq expression data, robust clinical data, pathological annotations, and genotypes are also available for these samples from dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v2.p1) and the GTEx portal (www.broadinstitute.org/gtex). While GTEx is no longer generating Affymetrix expression data, donor enrollment continues and is expected to reach 1,000 by the end of 2015. Updates to the GTEx data in dbGaP and the GTEx Portal will be made periodically.
contributor: GTEx Laboratory, Data Analysis, and Coordinating Center (LDACC)
contributor: The Broad Institute of MIT and Harvard (LDACC PIs: Kristin Ardlie and Gaddy Getz)

overall_design: GTEx samples are collected from deceased donors at low post-mortem intervals and preserved in PAXgene fixative prior to DNA and RNA extraction.


title: M. sedula transcriptional response under "strict" carbon-limited autotrophy compared to carbon "rich" autotrophy and heterotrophy

status: Public on Mar 05 2013

city: Raleigh

first: Aaron

last: Hawkins

state: North Carolina

address: 840 Main Campus Dr

department: Chemical and Biomolecular Engineering

institute: North Carolina State Universit

summary: Metallosphaera sedula is an extremely thermoacidophilic archaeon that grows heterotrophically on peptides, and chemolithoautotrophically on hydrogen, sulfur, or reduced metals as energy sources. During autotrophic growth, carbon dioxide is incorporated into cellular carbon via the 3-hydroxypropionate /4-hydroxybutyrate cycle (3HP/4HB). To date, all of the steps in the pathway have been connected to enzymes encoded in specific ORFs, except for the one responsible for ligation of coenzyme A (CoA) to 4-hydroxybutyrate (4HB). While several candidates for this step have been identified through bioinformatic analysis of the M. sedula genome, none have been shown to catalyze this biotransformation. Transcriptomic analysis of cells grown under strict H2-CO2 autotrophy was used elucidate additional candidate genes involved in carbon fixation and identify the genes which encode for 4HB-CoA synthetase.

overall_design: Three slide loop for Mse cells includes 3 conditions tested in duplicate (biological repeats from tandem fermentors): autotrophic carbon limited (ACL), autotrophic carbon rich (ACR), and heterotrophic (HTR). Half of an RNA sample for one condition was labeled with Cy3 while the other half was labeled with Cy5. The two differently labeled samples were run on different slides. Each probe is spotted on each slide 5 times (5 replicates; spot intensities for all replicates on slide provided in associated raw data file).

first: Yejun

last: Han

first: Robert

middle: K

last: Bennett

first: Michael

middle: W

last: Adams

last: Kelly


title: Toxicogenomic analyses of Ruditapes philippinarum by DNA microarray: new tools for anthropogenic impact assessment on the Venice Lagoon.

status: Public on Feb 15 2013

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum sampled in four seasons in 4 different areas of Venice Lagoon. For each tissue, total RNA was extracted from four (4) independent biological replicates of digestive gland, each consisting of tissue pools of five (5) animals.

overall_design: In this study, we analyzed 64 samples (pools of 5 digestive gland). Gene expression profiling was performed using the Agilent-027304 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni


title: Development of gene expression signatures for senecionine exposure

status: Public on Feb 08 2013

city: shanghai

first: aizhen

last: xiong

address: cailun road 1200

country: China

institute: shanghai university of traditional chinese medicine

summary: Senecionine is among the most well-studied pyrrolizidine alkaloids, which have caused intense and lasting attention for their significant hepatotoxicity. To develop gene expression approach to senecionine exposure, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to be biomarkers after senecionine exposure. Rat liver tissues after 36 h of senecionine treatment (i.g., 35 mg/kg body weight) were collected and analyzed comparing with control samples (i.g., sodium chloride solution). Differentially expressed genes were identified through Fold-change filtering and subjected to GO term using gene ontology project (http://www.geneontology.org/) to uncover the co-expression network on the basis of biological process and molecular function. By setting the fold change at ≥ 2 and p value ≤0.05, 46 down-regulated signaling pathways and 50 up-regulated pathways were found, including bile secretion, primary bile acid biosynthesis, and ABC transporters. Expression of 13 genes referred to bile acids metabolism was quantified from the same tissue samples by real-time PCR, confirming senecionine exposure after 36 h could result in compromised bile acid homeostasis.

overall_design: Senecionine exposure induced gene expression in rat liver was measured at 36 h after exposure to that of control sample. Three tissue samples from each group were pooled as a mixture. And two independent experiments were performed (control and 36 h after senecionine exposure).

first: Aizhen

last: Xiong

first: Li

last: Yang

first: Zhengtao

last: Wang


title: Expression data from Zea mays developmental series.

status: Public on Mar 01 2013

city: Guelph

first: Gregory

last: Downs

address: 50 Stone Road E

country: Canada

institute: University of Guelph

summary: Through hierarchical clustering of transcript abundance data across a diverse set of tissues and developmental stages in maize, we have identified a number of coexpression modules which describe the transcriptional circuits of maize development.

overall_design:
We examined transcript abundance data at 50 developmental stages/tissues of maize, from embryogenesis to senescence, using a custom Affymetrix Unigene array.
The VE stage is germination and emergence
Vn leaf stage refers to when the collar of the nth leaf is visible.


title: Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma

status: Public on Mar 26 2013

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

institute: DKFZ

type:
Genome variation profiling by array
Expression profiling by array


title: Assessing global transcriptomic changes in response to South African cassava mosaic virus [ZA-99] infection in susceptible Arabidopsis thaliana

status: Public on Jan 07 2013

city: Braamfontein

first: Chrissie

last: Rey

state: Johannesburg, Gauteng

address: 1 Jan Smuts Avenue

department: School of Molecular and Cell Biology

country: South Africa

institute: University of the Witswatersrand

summary: In susceptible plant hosts, co-evolution has favoured viral strategies to evade host defenses and utilize resources to their own benefit. The degree of manipulation of host gene expression is dependent on host-virus specificity and certain abiotic factors. In order to gain insight into global transcriptomic changes for a geminivirus pathosystem, South African cassava mosaic virus [ZA:99] (SACMV-ZA:99]) and Arabidopsis thaliana, 4 x 44K Agilent microarrays were adopted. After normalization, a 2-fold change filtering of data (p<0.05) identified 1,820 differentially expressed genes in apical leaf tissue. A significant increase in differential gene expression over time (451 genes at 14 dpi, 742 genes at 24 dpi, and 1011 genes at 36 dpi) was observed. This increase in expression, correlated with an increase in SACMV accumulation as virus copies were 5-fold higher at 24 dpi and 6-fold higher at 36 dpi than at 14 dpi (1.1x104 virus copies present at 14 dpi, 5.7x104 copies at 24 dpi, and 6.3x104 copies at 36 dpi). Many 2-fold genes were primarily involved in stress and defense responses, phytohormone signalling pathways, cellular transport, cell-cycle regulation, transcription, oxidation-reduction, and other metabolic processes. Forty-one genes (2.3%) were shown to be continuously expressed across the infection period, indicating that the majority of genes were transient and unique to a particular time point. Plant signalling networks were disrupted and manipulated by SACMV-[ZA:99] in order to affect homeostasis and antagonize host’s defense responses. At the same time, an adaptive response was initiated to reprogramme metabolism and divert energy from growth-related processes to defense, all leading to disruption of normal biological host processes. Comparisons between SACMV-[ZA:99] with plant-infecting RNA and DNA viruses revealed similarities and differences in expression patterns among viruses, showing either general defense or virus-specific responses. Within the Geminiviridae family in particular, similarities in cell-cycle regulation and gene expression patterns correlated between SACMV-[ZA:99] and Cabbage leaf curl virus (CaLCuV) but differences were also evident. For instance, CaLCuV showed antagonistic interactions between Salicyclic Acid (SA) and Jasmonic Acid (JA) pathways, whereas SACMV displayed synergism. Differences in gene induction, repression and outcome between the two geminiviruses clearly demonstrated host-specific interactions with SACMV-[ZA:99] leading to infection. To our knowledge this is the first geminivirus study identifying differentially expressed transcripts across 3 time points

overall_design: A three time-point (14, 24, and 36 dpi) study was carried out to identify differentially expressed genes in SACMV-[ZA:99] infected Arabidopsis leaf cells using a direct comparison design against mock-inoculated controls. Three biological replicates and 1 technical replicate for both SACMV-[ZA:99]-infected and mock-inoculated controls were conducted at each time point.

first: Erica

last: Pierce

first: M


title: Expression analysis of systemically infected Nicotiana benthamiana infected by South African cassava mosaic virus (SACMV)

status: Public on Jan 17 2013

summary:
Micrarray analysis was used to identify gene expression changes associated with disease development  and virus movement in N.benthamina plants induced by infection with the SACMV

Slides were originally designed as a collaboration between Prof. Steven A. Lommel's research group and NimbleGen. Should you require any additional information regarding this array, kindly contact Prof. Lommel.

http://plantpath.cals.ncsu.edu/faculty/steven-lommel

overall_design: 1-Plex , 385K array Nicotiana benthamiana (NimbleGen design name: 110121_N_benthamiana_60mer_exp) was used in this study to monitor changes in gene expression levels in SACMV- infected leaf tissue. Three biological replicates were used for infected leaf tissue and one pooled mock-inoculated sample was used as a control/reference.

first: Farhahna

last: Allie


title: Development of a porcine (Sus scofa) embryo-specific microarray: array annotation and validation

status: Public on Feb 25 2013

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

institute: University of Alberta

summary: Background  The domestic pig is an important livestock species for meat production worldwide and is becoming an established biomedical research model. As a result, there is a strong interest in the factors that affect the efficient production of viable embryos and offspring in this species using either in vivo or in vitro production methods. A limited understanding of the molecular mechanisms involved in this critical physiological process has inhibited our ability to fully elucidate these factors. The use of next generation deep sequencing and microarray technology are powerful tools for delineation of molecular pathways during early embryonic development of mammals. Here, we report on the assessment of a porcine-embryo-specific microarray platform created from a large expressed sequence tag (EST) analysis generated by Roche/454 next-generation sequencing of cDNAs constructed from critical stages of in vivo or in vitro porcine preimplantation embryos.  Results  Two cDNA libraries constructed from in vitro and in vivo produced preimplantation porcine embryos were normalized and sequenced using the 454 Titanium pyrosequencing technology. Treatment of cDNA libraries with BAL 31 nuclease digestion resulted in a 2 fold improvement of sequencing quality compared with untreated libraries. Over one million high quality EST sequences were obtained from this process and used to create an augmented porcine genome catalogue. Using the resulting dataset the EMbryogene Porcine Version 1 (EMPV1) microarray was developed and is composed of 43,795 probes printed onto a 4 × 44 K Agilent array. Based on the initial probe sequences annotation, the EMPV1 featured 17,409 protein-coding, 473 pseudogenes, 46 retrotransposed, 2,359 non-coding RNA (snRNA, snoRNA, etc.), 4,121 splice variants in 2,862 genes and a total of 12,324 Novel Transcript Regions (NTR). After re-annotation, the total unique genes increased from 11,961 to 16,281 and 1.9% of them belonged to a large olfactory receptor (OR) gene family. Quality control of EMPV1 was performed using porcine cumulus–oocyte complexes (COC) as well as early developmental stages of embryos. This revealed an even distribution of ten clusters of spike-in control spots and array to array (dye-swap) correction was 0.97. Further bioinformatics analysis revealed that our microarray probes hybridized with more developmental related transcripts from embryonic labelled targets when compared to COC.   Conclusions  Using next-generation deep sequencing we have produced a large EST dataset to provide the selection of probe sequences for the development of the EMPV1 microarray platform. The quality of this embryo- specific array was confirmed with the high level of reproducibility using current Agilent microarray technology. Despite the current limitations for full NTR annotation, due to the incomplete porcine genome sequencing project, a significant number of NTR were annotated using Version 10 of porcine genome and human RefSeq RNA database to enrich the orthologous genes with unique gene symbol (GS) for Gene Ontology (GO) search. GO terms confirmed that many are related relevant developmental processes. With more than an estimated 20 thousands unique genes represented on the EMPV1, this platform will provide the foundation for future research into the in vivo and in vitro factors that affect the viability of the porcine embryos, as well as the effects of these factors on the live offspring that result from these embryos.

overall_design: Two biological samples.


title: Gene expression analysis on Hydrangea macrophylla sepal pigmentation due to aluminum accumulation

status: Public on Dec 20 2012

city: Nagoya

first: Takashi

last: Negishi

state: Aichi

address: Furo-cho, Chikusa-ku

institute: Nagoya University Graduate School

summary: Most blue color in flowers is due to anthocyanin, and considerable proportion of blue coloration can be attributed to metal-complexed anthocyanins. Recently, we reported vacuolar localized iron-transporter in blue petal cells of Tulipa gesneriana. However the mechanism of another metal ion transporters and subsequent flower color development has yet to be fully explored. In Hydrangea macrophylla, Al3+ is involved in blue coloration and the anthocyanin is formed Al3+-complex in vacuoles. To identify the molecular mechanism of blue coloration in hydrangea flowers, we tried to isolate the related genes transporting metal ion into vacuoles. From the sepal cDNA library we read the sequences of ca. 12000 genes, then a microarray analysis was carried out. From the sequences information, we chose several genes that might localize vacuolar membrane and transport Al3+. By using Al3+-sensitive yeast strain, we could identify the gene transporting Al3+ into vacuole. From the functional similarity and predicted localization, we could also identify the gene transporting Al3+ into cytosol. We will report the Al3+ mobilization from out of cell into vacuole in the sepal of Hydrangea macrophylla.

overall_design: Three sepal pigmentation stages were chosen: S1=no pigmentation-sepal closed; S2=started pigmentation-sepal opening; and S3=pigmentation complete-sepal opened.  One pooled sepal sample per stage was prepared and gene expression pattern was analyzed by custom-designed Hydrangea oligo DNA microarray (CombiMatrix 12K).  The genes that were expressed >2-fold or <0.5-fold in S3 compared with S1 and S2 were selected as potential players involved in sepal pigmentation due to aluminum accumulation.

first: Kumi

last: Yoshida

first: Kenshiro

last: Oshima

first: Masahira

last: Hattori


title: Gene expression signatures following nerve injury in a rat model (0h-9h)

city: Shanghai

first: Guohui

last: Ding

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: We used microarrays to distinguish the gene expression differences among different time points after injury.

overall_design: We generated proximal sciatic nerve (SN) tissues (0.5cm) at 0h, 0.5h, 1h, 3h, 6h and 9h after sciatic nerve resection.

first: Bin

last: Yu

first: Xiaosong

last: Gu


title: Gene Expression Analyses of Subchondral Bone in Early Experimental Osteoarthritis by Microarray

status: Public on Dec 11 2012

city: Guangzhou

first: DaoZhang

last: Cai

state: GuangDong

institute: The Third Affiliated Hospital of Sun Yat-sen University

summary: Osteoarthritis (OA) is a complex degenerative joint disease, which is not only a cartilage but also a bone disease. A better understanding of the early molecular mechanism changes of subchondral bone in vivo may contribute to elucidating the pathogenesis of OA. We used microarray technology to investigate the time-course molecular changes of subchondral bone just beneath damaged cartilage in early stage of experimental osteoarthritis, and found 2,234 differentially expressed (DE) genes at 1 week, 1,944 at 2 weeks and 1,517 at 4 weeks postsurgery.Further analysis of dysregulated genes indicated that subchondral bone remodeling occurred sequentially and in a time-dependent manner at the gene expression level. Some known dysregulated genes suspected roles in influencing bone development or bone remodeling, such as Alp, Igf1, Tgf β1, Postn, Mmp3, Tnfsf11, Acp5, Bmp5, Aspn and Ihh, were confirmed by real-time PCR, and results indicated that our microarray data could accurately reflect gene expression patterns of early OA. Subsequently, to validate the results of our microarray analysis at protein level, immunohistochemistry staining was introduced to investigate the translational level of genes Mmp3 and Aspn in tissue sections, and results showed that the level of Mmp3 protein expression was totally matched the results of microarray and real-time PCR analysis. Nevertheless, the expression of Aspn protein was not observed differentially expressed at any time point.

overall_design: Ninety 10-week-old male Sprague-Dawley rats, weighing 300-325g, were used in the study. Animals were equally divided into two groups: experimental group (E-Group) and sham-operated group (S-Group). The E-Group rats underwent open surgery, involved in both medial meniscectomy and medial collateral ligament (MCL) transaction with micro-scissors. The S-Group rats were carried out with a sham operation, via a similar incision, without operations of the medial meniscus and the medial collateral ligament.Animals were killed at 1, 2, and 4 weeks postsurgery, and 15 animals were put into use per-timepoint in each treatment group. 5 animals were used for histological analysis and immunohistochemistry, and others were used for microarray study and Real-time polymerase chain reaction (PCR) analysis equally at each timepoint.

first: Rong-Kai

last: Zhang

first: Hang

last: Fang

first: Yu-Xian

last: Chen

first: Jun

last: Shen

first: Hua-Ding

last: Lu

first: Chun

last: Zeng

first: Jian-Hua

last: Ren

first: Hua

first: Zhi-Fu

last: Li

first: Shao-Ming

first: Dao-Zhang

first: Qing

last: Zhao


title: Thrombopoietin (TPO) protects against heart damage induced infarction in rat model

status: Public on Dec 01 2012

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: In order to examine the mechanism of TPO on cardiac protection against myocardial infarction damage (MI), we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to delineate the TPO cardioprotective mechanism against infarction.

overall_design: MI and TPO induced gene expressions in rat heart were measured at week 4. Two biological replicates were performed for each treatment group.

first: Li

last: Karen

first: Sung

last: Rita


title: Integrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia [mRNA profiling]

status: Public on Nov 27 2012

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: We performed DNA methylation (HELP array) and gene expression profiling in 215 samples of adult B-lineage acute lymphoblastic leukemia (ALL) and 12 normal preB samples. Adult B-lineage acute lymphoblastic leukemia (B-ALL) is an aggressive disease with <40% long-term survival. Genetic alterations such as BCR/ABL, E2A/PBX1 and MLL rearrangement (tMLL) define distinct B-ALL subtypes, which are associated with poor clinical outcome. It has been shown that these B-ALL subtypes have distinct expression profiles. However, the role of the epigenome in shaping these expression profiles and how the aberrant epigenetic gene regulation contributes to the biological and clinical features of those ALL subtypes is largely unknown. To address this question, we performed genome-wide DNA methylation and gene expression profiling on a large cohort of 215 well-characterized adult B-ALL specimens from the ECOG E2993 phase III clinical trial and a cohort of normal precursor B (preB) cells from 12 healthy bone marrows. The integrative analysis of these profiles led to the identification of key gene networks deregulated at the epigenetic and transcriptional levels within each subtype. In BCR/ABL, we identified a network centered on IL2RA(CD25), which is itself hypomethylated and overexpressed in most BCR/ABL B-ALL and confers poor clinical outcomes.  In the tMLL subtype, we uncovered aberrant epigenetic and transcriptional activities that include hypomethylation and upregulation of FLT3 and BCL6. After showing that MLL/AF4 fusion protein binds to these genes as well as other hypomethylated and overexpressed genes in tMLL ALL cells, we showed that a specific BCL6 inhibitor, RI-BPI, kills tumor cells in both tMLL ALL cell lines and patient samples. BCL6 inhibition may therefore represent a novel therapeutic strategy for B-ALL patients with MLL translocations.

overall_design:
Expression profiling in 191 samples of adult B-lineage acute lymphoblastic leukemia (ALL) and 3 normal preB samples

This submission represents transcriptome component of study.

first: Olivier

last: Elemento

first: Ari

last: Melnick


title: Integrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia [methylation profiling]

type: Methylation profiling by genome tiling array

overall_design: DNA methylation profiling in 215 samples of adult B-lineage acute lymphoblastic leukemia (ALL) and 12 normal preB samples, using DNA promoter methylation array (HELP array).


title: H3K27me3 profiles along the length of the  X chromosome in trophoblast stem (TS) cells, ChIP-chip

status: Public on Nov 02 2012

city: Paris

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

country: France

institute: UMR7216-Epigenetics and stem cell

type: Genome binding/occupancy profiling by genome tiling array

summary: This analysis includes H3K27me3 profiles along the length of the X-chromosome in male (F2) and female (K4) TS cells and in female TS cells showing local reversals of imprinted X-chromosome inactivation (K4GFP). Data also includes H3K27me3 ChIP-chip profiles in Eed-/- mutant male and female TS cells obtained from Magnuson laboratory (Kalantry S. et al., Nat Cell Biol, 2006).

overall_design: Analysis of H3K27me3 profiles in five different cell populations. Three independent biological replicates for each wild-type female cell population and two independent biological replicates for the wild-type male cell population are provided. The ChIP-chip analysis was also carried out in Eed-/- male and female TS cells lacking H3K27me3 for comparison (one replicate). The array includes approx. 162,5 Mb of the X chromosome and approx. 14,6 Mb of chromosome 17 as a control.

first: Agnes

last: Dubois

first: Pablo

last: Navarro

first: Sarra

last: Merzouk

first: Sylvain

last: Pichard

first: Anne

last: Louise

first: Danielle

last: Arnaud

first: Philip

middle: R

last: Avner

first: Jane

last: Deuve


title: Comparison of the effects of Tris (2-ethylhexyl) trimellitate (TOTM) on gene expression associated with testicular maldevelopment (TMD) in male rat foetal testes by transcription profiling

status: Public on Oct 30 2012

city: Dundee

first: Mark

middle: Peter

last: Chamberlain

state: Tayside

address: 2 James Lindsay Place

department: MCT

country: United Kingdom

institute: CXR Biosciences

summary:
The purpose of this study is to assess the potential of TOTM to induce testicular maldevelopment in the rat. We studied the effects of TOTM on the expression of genes in pathways involved in steriodogenesis and testes development.
Certain phthalate esters have previously been shown to be involved in the induction of rat testicular mal-development (TMD) through effects on the expression of genes in pathways involved in steroidogenesis and testes development. In order to assess the effects of a potential alternate plasticizer, tris(2-ethylhexyl)trimellitate (TOTM), rats were exposed daily, in utero, to TOTM in order to assess the potential of this compound to induce developmental effects on the fetal testes. Pregnant rats were exposed between gestational day 12 and 19 and fetal testes RNA was analysed using whole genome microarrays. The effects of TOTM on the expression of genes in pathways involved in steroidogenesis and testes development were examined. The effects of TOTM were also compared with di(2-ethylhexyl)phthalate (DEHP), mono(2-ethylhexyl)phthalate (MEHP), an active metabolite of DEHP, and 2-ethylhexanol (2-EH), which were used as positive and negative controls, respectively. MEHP & DEHP (500mg/kg) caused a repression of genes in TMD pathways involved in cholesterol synthesis and transport (HMGCS, HMGCR, StAR, SCARB1, FDFT1, FDPS), steroidogenesis (Cyp11a, HSD3B1, SC4MOL) and testes development (INSL3, INHA). 2-EH caused minor repression of some of the genes in the TMD pathway. This was rationalised on the basis that 2-EH, a DEHP metabolite, is also a weak PPARα agonist. It has been shown that in utero treatment with DBP will repress the genes from fetal testes involved in steroidogenesis and that this effect is associated with direct DBP-mediated binding of PPARα to the promoters of these genes (Plummer et. al. 2010). TOTM did not cause a significant repression of genes in the TMD pathway.  Based on these data, it is highly unlikely that TOTM will cause testicular dysgenesis in rats.

overall_design: Rats were exposed to TOTM in utero by the administration of daily oral gavage doses to pregnant dams between gestational day 12 and 19. The foetal testes were obtained by micro-dissection and prepared to facilitate the isolation of RNA, which was subsequently analysed using whole rat genome microarrays.

first: Simon

last: Plummer

first: David

last: Farrar

first: Clifford

last: Elcombe

first: Christopher

first: Joanne

last: Quinney


title: Modulation of colonic inflammation in Mdr1a-/- mice by green tea polyphenols and their effects on the colon transcriptome and proteome

status: Public on Oct 18 2012

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

country: New Zealand

institute: Plant and Food Research Ltd.

summary:
This study tested the anti-inflammatory potential of a green tea extract rich in polyphenols (GrTP) in the colon of the multi-drug resistance targeted mutation (Mdr1a-/-) mouse model of IBD.
A colonic histological injury score was determined for each mouse to establish the effect of GrTP on inflammation. Insights into mechanisms responsible for changes in inflammation were gained using transcriptome (microarray) and proteome (2-D gel electrophoresis and LCMS protein identification) analyses.

overall_design: A total of 24 male Mdr1a-/- mice purchased from Taconic (Hudson, NY, USA) at 4-5 weeks of age were used for this study. 12 mice were randomly assigned to each of two different dietary groups: control (AIN-76A powdered diet), or GrTP (AIN-76A + 0.6% green tea polyphenol). At 21 and 24 weeks of age, mice were euthanized and colon samples taken for histological and microarray analyses. The total histology score (HIS) in the colon was determined according to previously described criteria. Total RNA was isolated using TRIzol reagent. Colon RNA from four Mdr1a-/- mice on the GrTP diet (with low HIS) was compared with colon RNA from four Mdr1a-/- mice on the AIN-76A diet (with high HIS). All individual RNA samples were hybridized against a common reference RNA on separate slides. The reference RNA was prepared using equimolar RNA extracts from small intestine, colon, kidney and liver of normal healthy growing Swiss mice plus RNA extracts from Swiss mouse fetuses.

first: Matthew

last: Barnett

first: Janine

last: Cooney

first: Yvonne

last: Dommels

first: Katia

last: Nones

first: Diane

middle: T

last: Brewster

first: Zaneta

last: Park

first: Christine

last: Butts

first: Warren

last: McNabb

first: William

last: Laing

first: Nicole

last: Roy


title: Candidate pathways for promoting differentiation and quiescence of oligodendrocyte progenitor-like cells in glioblastoma

status: Public on Oct 04 2012

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: The mature CNS contains PDGFRA+ ‘oligodendrocyte progenitor cells’ (OPC) which may remain quiescent, proliferate, or differentiate into oligodendrocytes. In human gliomas, rapidly proliferating Olig2+ cells resembling OPCs are frequently observed. We sought to identify, in vivo, candidate pathways uniquely required for OPC differentiation or quiescence. Using the bacTRAP methodology, we generated and analyzed mouse lines for translational profiling the major cells types (including OPCs), in the normal mouse brain. We then profiled oligodendoglial (Olig2+) cells from a mouse model of Pdgf-driven glioma. This analysis confirmed that Olig2+ tumor cells are most similar to OPCs, yet, it identified differences in key progenitor genes - candidates for promotion of differentiation or quiescence.

overall_design: There are two datasets here. One characterizes the normal translational profiles of neurons, astrocytes, mature and immature oligodendrocytes. Each cell type was profiled in triplicate, from pools of at least two mice, and total RNA controls were collected in parallel. The second dataset includes translational profiles of Olig2 positive cells from tumors form several variations of a murine model of glioma. Each variation was collected at least in triplicate, and total RNA controls were analyzed in parallel. All translational profiles were generated using the Translating Ribosome Affinity Purification protocol.

first: Elena

last: Fomchenko

first: Eric

last: Schmidt

last: Holland

first: Ana

last: Milosevic


title: Fish oil alters tamoxifen-modulated expression of genes related to differentiation, proliferation, metastasis, and immune response in rat mammary tumors

status: Public on Oct 16 2012

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

institute: Barretos Cancer Hospital

summary: Herein, we evidence that tamoxifen treatment modifies gene expression of mammary tumors depending upon the type of dietary fat fed to the animals. Rats initiated with MNU and treated with tam were fed a diet rich in corn oil (CO) or fish oil (FO). After 8 weeks, tumors of the same histological type (cribriform) were collected and comprehensive analysis of messenger RNA expression was performed. The mRNA expression of genes such as SerpinB10, Wisp2 and Apod in tumors from FO-treated rats is indicative of highly differentiated tumors. Decreased expression of H19 and Igf2 mRNA in tam-treated groups, and Thrsp and Wnt5b mRNA in FOtam group may be related to tumor growth impairment and lower metastatic capacity. Increased Irf7, RT1-CE3, RT1-CE16 transcript levels in FO-treated animals suggests an improved immune response against tumors (Th1 pattern) whereas decreased mRNA of Fcer1a, Hdc, Ms4a2, Slp1, Mcpt1 and Mcpt2 may indicate a shift of the immune response towards Th2 pattern.

overall_design: Sprague-Dawley rats received one injection of MNU and were distributed in 4 different groups. G1 received corn oil diet (CO); G2 received CO and tamoxifen; G3 received fish oil diet (FO) and G4 received FO an tamoxifen. After 8 weeks of treatment, diet- and/or tamoxifen-induced transcriptomic changes were evaluated in cribriform tumors of three different rats/group.

first: Ricardo

last: de Cicco

first: Johana

last: Vanegas

first: Julia

last: Pereira

first: John

last: Vanden Heuvel

first: Sharlene

last: Washigton

first: Cesar

last: Aliaga

first: Haifang

last: Xu

first: Irma

middle: H

last: Russo

first: Andrea

last: Manni

first: Karam

last: El-Bayoumy

first: Jose


title: Transcriptomic analysis of an evolutionary strain of Saccharomyces cerevisiae resistant to cobalt 10mM

status: Public on Aug 01 2012

city: Toulouse

first: Laurent

last: Benbadis

address: 135 Av de Rangueil

institute: LISBP INSA CNRS UMR5504

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes implicated in the resistance to cobalt in Saccharomyces cerevisiae.
The evolved strains and the wild type were harvested in exponential phase

overall_design: WT (CEN.PK), the evolved strain (CI25E) and the evolved strain delta Cot1 harvested in exponential phase (DO 600nm=3) ; three independant replicate for each.

first: L

first: C

last: Alkim


title: Comprehensive gene expression analysis of cerebral cortices from mature rats after neonatal hypoxic-ischemic brain injury

status: Public on Jun 28 2012

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary: Neonatal hypoxic-ischemic (HI) encephalopathy can lead to severe brain damage and is a common cause of neurological handicaps in adulthood. To elucidate the molecular events occurring in cerebral cortices of mature rats (8 weeks old) after neonatal HI brain insult, we performed comprehensive gene expression and gene network analyses using a DNA microarray system (Agilent 4x44K). A rat model of neonatal HI encephalopathy (Rice model) was obtained by unilateral ligation of the common carotid artery of 7-day-old rats with hypoxia (exposure to 8% oxygen). Due to the HI insult-related breakdown of the ipsilateral hemisphere in the brain, RNAs were prepared from the contralateral cerebral cortices of 8-week-old rats and analyzed by DNA microarray. Biofunctional analysis of differentially regulated genes revealed that many upregulated genes were related to cell death signaling, such as the arachidonic acid cascade. In contrast, many downregulated genes were related to gene expression, reflecting progressive damage by the HI insult, even within the contralateral cerebral hemisphere.

overall_design: Seven-day-old Wistar rats were assigned to two groups: the control group and the Rice group (four pups in each group). HI brain insult was not induced in the control group rats. The Rice group rats were subjected to a modified Levine’s procedure to induce HI brain injury. The Rice group rats were anesthetized with ether, and the left carotid artery was sectioned between double ligatures with 4-0 surgical silk. The rats were allowed to recover for 1–2 h and then exposed to 1 h of hypoxia in a plastic chamber that was perfused with a mixture of humidified 8% oxygen balanced with nitrogen. The temperature inside the chamber was maintained at 33 °C, the usual temperature generated when pups huddle with the mother.  The cerebral cortexes contralateral to the HI brain insult and those of the same side of the control animals were used for the experiment.

first: Yuto

last: Ueda

first: Akira

last: Sato

first: Hiroshi

last: Sameshima

first: Tsuyomu

last: Ikenoue


title: New insights into the molecular mechanisms of 1,3-dinitrobenzene-induced testicular toxicity

status: Public on Jul 14 2012

city: Sophia Antipolis

first: Sophie

last: Ludwig

address: 355 Rue Dostoievski BP 153

department: Toxicology Research

institute: Bayer Cropscience

summary: Several studies have shown that 1,3-dinitrobenzene (DNB) causes injury to Sertoli cells and induces apoptosis in the surrounding germinal cells in male laboratory rats ; however, the mechanisms by which DNB functions are not well understood. In this context, we have conducted studies using standard parameters and molecular tools to better understand the pathogenesis of the testicular effects produced by DNB, as well as its mode of action. Wistar rats were orally exposed to 0.1-8 mg DNB/kg/day for 4 days. Testosterone concentrations were not affected at any dose level, but marked histopathological lesions in the testes were recorded at 4 mg/kg/day. Global transcriptomic analysis of rat testes revealed cell cycle and cell death as the major biological processes affected. In particular, we identified an alteration in the expression of genes associated with cell cycle progression (mitotic roles of polo-like kinase).

overall_design: Dinitrobenzene was administered in suspension to rats (7 weeks old at start of treatment) by oral gavage at a daily dose of 0 (control, 0.5% methylcellulose in sterilized water), 0.1, 1, and 4  mg/kg body weight, for 4 consecutive days. Dose-related changes in gene expression were determined in the testes using whole genome oligonucleotide microarrays.

first: Helen

last: Tinwell


title: Comparison of the global gene expression of choroid plexus and meninges and associated vasculature under control conditions and after pronounced hyperthermia or amphetamine toxicity

status: Public on Aug 02 2012

city: Jefferson

first: John

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

summary: These tissue were harvested to complement and extend the studies that generated GSE23093.  They served 3 purposes; 1) identify genes important to choroid plexus function and compare them with those important for meninges and associated vasculature (MAV) function, 2) determine genes in the choroid plexus and sensitivity hyperthermia and amphetamine toxicity, 3) identify the important gene expression changes related to the immune system in MAV, choroid plexus and trunk' blood

overall_design: Gene mRNA expression patterns in choroid plexus and trunk blood were determined under control conditions as well as after (3 hr and 1day) exposure to either environmentally-induced hyperthermia or neurotoxic doses of amphetamine.  This data was analyzed and compared to data from meninges and associated vasculature previously deposited in GEO.  The data gathered under control conditions was used to further understand how the choroid plexus and meninges and associated vasculature might function to generate and regulate the cerebrospinal fluid.  The expression patterns in the choroid plexus after environmentally-induced hyperthermia or neurotoxic doses of amphetamine was determine its damage and protective responses.  The expression patterns after environmentally-induced hyperthermia or neurotoxic doses of amphetamine were compared among choroid plexus, meninges and associated vasculature and blood were analyzed to determine immune system responses.

middle: F

first: Upasana

last: Saini

first: Tucker

middle: A

last: Patterson

first: Nysia

middle: I

last: George

first: James

middle: J

last: Chen

first: Monzy

last: Thomas


title: Expression data from LCM-captured Zea mays root cells after challenge with Meloidogyne incognita

status: Public on Apr 28 2012

city: Gainesville

first: Lauren

last: McIntyre

state: FL

address: 2033 Mowry Rd

department: Department of Molecular Genetics and Microbiology

institute: University of Florida

summary: The differentiation of specialized feeding sites in Zea mays root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Zea mays root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation.

overall_design: Each time point (14 day and 21 day) consisted of three biological replicates per treatment (control root cells or giant cells). Control cells were captured from an area ~13,000,000 um2 in size and giant cells were captured from an area ~5,000,000 um2 in size. RNA samples were isolated using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA amplifications were carried out with the NuGEN WT-Ovation Pico kit.

first: Alison

middle: M

last: Morse

first: Heather

last: Marella

first: Christopher

middle: G

last: Taylor


title: Expression profile of PC12 cells stimulated by nerve growth factor measured by Agilent microarray

status: Public on Apr 25 2012

city: Minato-ku

first: Yuzuru

last: Otsuka

state: Tokyo

department: Department of Nutrition

institute: Toita Women's College

summary: We analyzed the comprehensive gene expression changes by nerve growth factor (NGF) in PC12 cells using Agilent microarrays. The genes of 1920 NGF treated were up-regulated and 2670 genes were down-regulated significantly compared with the control group. The expression level of genes involved in cell structure and proteolysis were up-regulated. On the other hand, the genes of cell cycle and some metabolism were rather down-regulated. Therefore, it is suggested that it is necessary to stop the cell cycle and down-regulate metabolism to neurite outgrowth.

overall_design: Gene regulation associated with the differentiation program in PC12 cells still needs to be elucidated. We analyzed the genes expression with Agilent microarrays after 6 hours of NGF treatment by the one-color method, and found 2099 genes were up-regulated and 2781 genes were down-regulated.

first: Kouko

last: Nakajima


title: Transport of influenza A virus neuraminidase to host cell surface and virus replication are regulated by ARHGAP21 and Cdc42

status: Public on Apr 04 2012

city: Beijing

first: Song

last: Wang

email: wscookie@163.com, chenjl@im.ac.cn

address: West Beichen Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

type: Non-coding RNA profiling by genome tiling array

summary:
Influenza virus neuraminidase (NA), a type II transmembrane glycoprotein, is transported to the virus assembly site at the plasma membrane and is a major viral envelope component that plays a critical role in the release of progeny virions and in determination of host range restriction. Although signals/sequences in NA for translocation, sorting and raft association have been identified, little is known about the host factors that are involved in regulating the intracellular and cell surface transport of NA. In this report, we have investigated the involvement of Rho family GTPases in NA transport to the cell surface. We found that expression of constitutively active or inactive mutants of RhoA or Rac1 did not significantly affect the amount of NA that reached the cell surface. Interestingly, expression of constitutively active Cdc42 or depletion of the Cdc42-specific GAP, ARHGAP21, promoted the transport of NA to the plasma membranes. By contrast, cells expressing shRNA targrting Cdc42 or overexpressing ARHGAP21 exhibited a significant decrease in the amount of cell surface-localized NA. Furthermore, silencing of Cdc42 or ARHGAP21 had significant effects on influenza A virus replication. Together, our results reveal that ARHGAP21 and Cdc42-based signaling regulates the NA transport and thereby impacts virus replication.
This microarray experiment was carried out to find out whether Cdc42 and ARHGAP21 expression levels in A549 cell were changed after WSN infection.

overall_design: Total RNAs were extracted from three different groups of A549 cells that had been infected with or without WSN for 10 h, using TRIzol reagent (Invitrogen, Carlsbad, CA). Samples were amplified and labeled using a NimbleGen One-Color DNA Labeling Kit.

first: S

first: H

last: Li

first: Y

last: Wei

first: J

last: Ouyang

middle: Q

last: Liu

first: G

last: Guo

middle: L


title: Effect of erythropoietin on cerebral ischemia-induced changes in gene expression in rats

status: Public on Jun 01 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Analysis of the gene expression profile in the cerebral cortex of rats 2h or 6h after middle cerebral artery occlusion with or without a single erythropoietin treatment

overall_design: 6 conditions with each 3 replicates, hybridized with 1 color.

first: Pietro

last: Ghezzi


title: Leptin dependent control of testosterone regulated hepatic lipid metabolism

status: Public on Sep 02 2012

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

summary:
Population based studies have established that androgen deficiency in males correlates with type 2 diabetes, visceral adiposity, and metabolic syndrome. Androgen therapy has been investigated as a possible treatment regime to combat these disorders. However, the molecular mechanism of androgen effects on these diseases still remain poorly understood. The zucker diabetic fatty (ZDF) rat, containing a mutation in the leptin receptor, is a well-investigated model of obesity and type 2 diabetes. Male rats are characterized as androgen deficient and spontaneously develop obese, hyperlipidemia, hyperglycemia and hyperinsulinemia. In this study, we used ZDF male rats as a model of metabolic syndrome to investigate the effects of testosterone administration on the development of the metabolic conditions.

Methods: Male ZDF rats at six week of age were randomly divided into two groups and administered testosterone undecanoate(TU) or vehicle alone every three days for three weeks. After three weeks, overnight fasted blood glucose and insulin concentrations were significantly higher and glucose tolerance and insulin sensitivity were impaired in TU treated ZDF rats compared to vehicle controls. Moreover, increased serum triglycerides and VLDL were observed in TU treated rats. To further explore the observed metabolic changes in TU treated ZDF rats, whole-genome microarray analysis were performed on isolated liver mRNA.

Results: Array analysis revealed that many hepatic lipogenic genes were increased in male ZDF rat livers treated with TU. Interestingly, SREBP-1c, a key transcriptional activator of lipogenic genes and PGC-1 , an activator of SREBP-1c were induced while small heterodimer partner, a transcriptional inhibitor of lipogenic genes was suppressed by TU treatment. Exploring signaling pathways for these effects, we observed that the hepatic activated forms of STAT3 and AMPK, two known inhibitors of hepatic lipogenesis, were decreased in TU treated rat. Moreover, we observed that DHT could block the induction of STAT3 and AMPK phosphorylation in treated primary human hepatocytes. Preliminarily, in the leptin receptor positive zucker diabetic lean male rats, we observed that TU treatment has an oppose effect on the hepatic lipogenic genes, suggesting that hepatic leptin signaling may influence androgen signaling. Further insight into the relationship between androgen deficiency and the leptin system may help improve treatment of the metabolic syndrome.  Population based studies have established that androgen deficiency in males correlates with type 2 diabetes, visceral adiposity, and metabolic syndrome. Androgen therapy has been investigated as a possible treatment regime to combat these disorders. However, the molecular mechanism of androgen effects on these diseases still remain poorly understood. The zucker diabetic fatty (ZDF) rat, containing a mutation in the leptin receptor, is a well-investigated model of obesity and type 2 diabetes. Male rats are characterized as androgen deficient and spontaneously develop obese, hyperlipidemia, hyperglycemia and hyperinsulinemia. In this study, we used ZDF male rats as a model of metabolic syndrome to investigate the effects of testosterone administration on the development of the metabolic conditions.

overall_design: Two-condition experiment. (1) lean ZDF rats (control) vs. lean ZDF rats (testosterone treated). (2) obese ZDF rats (control) vs. obese ZDF rats (testosterone treated). Biological replicates: 4 control replicates, 4 treated replicates.

first: Diego

last: Iglesias-Gato

first: Paolo

last: Parini

first: Konstantin

last: Svechnikov

first: Ewa

last: Ellis

first: Gunnar

last: Norstedt

first: Stefan

last: Arver

first: Amilcar

last: Flores-Morales

first: Petra

last: Tollet-Egnll

first: John

middle: N

last: Flanagan


title: Zeus Caf40 ChIP-chip

status: Public on May 01 2012

city: Cambridge

first: Sidi

last: Chen

department: Biology

institute: MIT

summary: Zeus Caf40 ChIP-chip with FLAG tag in D. melanogaster adult flies

overall_design: 3 biological replicates of ChIP vs input

first: Manyuan

last: Long

first: Kevin

last: White

first: Xiaochun

last: Ni


title: Mechanistic evaluation of the insulin response in H4IIE hepatoma cells: New endpoints for toxicity testing?

status: Public on Jun 18 2012

city: Antwerp

first: Tine

last: Hectors

address: Groenenborgerlaan 171

institute: University of Antwerp

summary:
Transcriptional profiling of insulin exposed H4IIE cells at different time points (6h-24h) to 100 nM insulin, with untreated solvent control cells (blanks). The central role of hepatic insulin resistance in pandemic metabolic diseases urges investigation of the underlying mechanisms of its development and pathogenesis. Besides genetic susceptibility and lifestyle factors, environmental pollutants are suggested risk factors. In order to appraise the role of the thousands of pollutants we are daily exposed to, stable, robust and high throughput cell-based systems should be developed. In this context, it is of paramount importance to select an in vitro system which mimics in vivo insulin responses as close as possible. Therefore, this study was designed to evaluate if the rat H4IIE hepatoma cell line is a physiologically relevant model to study hepatic insulin responses.

DNA microarray analysis, real-time PCR and flow cytometric cell cycle analysis were used to assess the relevance of the insulin response in H4IIE cells. Insulin dose dependently stimulated H4IIE growth. Time dependency of the insulin response was shown with real-time PCR for the known insulin responsive genes: Fasn, Pck1 and Irs2. Based on these results, microarray analysis was performed on H4IIE cells exposed to insulin (100 nM) for 6h and 24h. Genes related to carbohydrate (glycolysis and gluconeogenesis) and lipid metabolism (glycerolipid metabolism, cholesterol synthesis and fatty acid oxidation) were most profoundly afflicted, in accordance with in vivo insulin action in liver. Since changes in carbohydrate and lipid metabolism are pivotal in the pathogenesis of insulin resistance, the presence of a physiological relevant insulin response in H4IIE cells pleads for further testing of its potential use in research on pollutant-driven insulin resistance.

overall_design: Microarray analysis was performed on H4IIE cells exposed to insulin (100 nM) for 6h and 24h. A separate v+2 A-optimal hybridization design was used for each time-point. Using this design each exposure condition is represented by three biological replicates, with each biological replicate analysed in technical duplicate while applying the dye swap principle to correct for dye bias.

first: Caroline

last: Vanparys

first: Anna

last: Pereira-Fernandes

first: Dries

last: Knapen

first: Ronny

last: Blust


title: Identification of miR-181 target genes and a common prognostic gene signature in AML

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

summary:
Increased expression levels of miR-181 family members have been shown to be associated with favorable outcome in patients with cytogenetically normal acute myeloid leukemia. Here we show that increased expression of miR-181a and miR-181b is also significantly (P < .05; Cox regression) associated with favorable overall survival in cytogenetically abnormal AML (CA-AML) patients. We further show that up-regulation of a gene signature composed of 4 potential miR-181 targets (including HOXA7, HOXA9, HOXA11, and PBX3), associated with down-regulation of miR-181 family members, is an independent predictor of adverse overall survival on multivariable testing in analysis of 183 CA-AML patients. The independent prognostic impact of this 4-homeobox-gene signature was confirmed in a validation set of 271 CA-AML patients. Furthermore, our in vitro and in vivo studies indicated that ectopic expression of miR-181b significantly promoted apoptosis and inhibited viability/proliferation of leukemic cells and delayed leukemogenesis; such effects could be reversed by forced expression of PBX3. Thus, the up-regulation of the 4 homeobox genes resulting from the down-regulation of miR-181 family members probably contribute to the poor prognosis of patients with nonfavorable CA-AML. Restoring expression of miR-181b and/or targeting the HOXA/PBX3 pathways may provide new strategies to improve survival substantially.

In addition, this data set has been used to identify a common prognostic gene signature (Li Z. et al. unpublished).

overall_design: 65 human AML samples bearing various cytogenetic and molecular abnormalities are used to identify miR-181 target genes and a common prognostic gene signature.

first: Zejuan

last: Li

first: Hao

last: Huang

first: Yuanyuan

first: Michael

last: Radmacher

first: Xi

last: Jiang

first: Chunjiang

last: He

first: Kati

last: Maharry

first: Abdel

last: Elkahloun

first: Stephen

last: Arnovitz

first: Ping

first: Bob

last: Lowenberg

first: Ruud

last: Delwel

first: Konstanze

last: Dohner

first: Zhiyu

last: Zhang

first: Chen

last: Shen

first: Mary

middle: B

last: Neilly

first: Yanming

first: Richard

last: Larson

first: Michelle

last: Le Beau

last: Caligiuri

first: Lars

last: Bullinger

first: Peter

last: Valk

first: Paul

middle: P

last: Liu

first: Guido

last: Marcucci

first: Janet

last: Rowley

first: Clara

last: Bloomfield

first: Jianjun


title: Ceriporiopsis subvermispora gene expression in different media

status: Public on Mar 05 2012

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

summary: Transscript profiles of Ceriporiopsis subvermispora grown on different substrates were analyszed. Array design was based on the DoE's Joint Genome Institute's gene models for C. subvermispora version 1. The research goal is to identtify genes essential for lignocellulose depolymerization.

overall_design: From a data set of 12,125 unique gene models, each NimbleGen (Madison, WI) array targeted 12083 genes and featured 8 unique 60mers per gene, all in quadruplicate.   Total RNA was purified from 5-day old cultures containing microcrystalline cellulose (Avicel) or glucose or ball-milled Populus as sole carbon source. Three biological replicates per medium were used (9 separate arrays). In short, cultures were harvested by filtering through Miracloth (Calbiochem, EMD Biosciences, Gibbstown, NJ), squeeze dried and snap frozen in liquid nitrogen. Pellets were stored at -80 C until use. Extraction buffer was prepared by combining 10 ml 690 mM para-aminosalicylic acid (sodium salt) (Sigma-Aldrich, St. Louis, MO) with 10 ml 56 mM triisopropylnapthalene sulfonic acid (sodium salt) (Sigma-Aldrich), and placed on ice. To this was added 5 ml 5X RNB (1.0 M Tris, 1.25 M NaCl, 0.25 M EGTA). The pH of the 5X RNB was adjusted to 8.5 with NaOH. The mixture was kept on ice and shaken just before use.    Frozen fungal pellets were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. The ground mycelia were transferred to Falcon 2059 tubes (VWR International, West Chester, PA), and extraction buffer was added to make a thick slurry. The samples were vortexed vigorously and placed on ice until all samples were processed. One half volume TE-saturated phenol (Sigma-Aldrich) and ¼ volume chloroform (Sigma-Aldrich) were added to each sample and vortexed vigorously.  Samples were spun at 2940 x g in a fixed-angle rotor for five minutes.  The aqueous layer was removed to a new tube, and phenol:chloroform extractions were repeated until the interface between the aqueous and organic layers was clear. The final aqueous extractions were placed in clean 2059 tubes, to which was added 0.1 volume 3M sodium acetate, pH 5.2, (DEPC-treated) and two volumes absolute ethanol. The tubes were shaken vigorously and stored overnight at -20 0C.    The tubes were spun 1 hour at 2940 x g, the supernatants were decanted, and the pellets were resuspended in 4 ml RNase-free H2O. Total RNA was purified using the RNeasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol for RNA cleanup. RNAs were eluted from the RNeasy spin columns using two spins, for a final volume of 2 ml. The eluted RNAs were ethanol precipitated and stored overnight at -20C. The RNAs were spun one hour at 2940 x g, washed once with 70% ethanol, and resuspended in 50-100 μl RNase-free H2O. Three biological replicates per medium were used (nine separate arrays).    RNA was converted to double-strand cDNA using Invitrogen's ds cDNA Synthesis kit (Carlsbad, CA)  and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland).  In brief, 10 μg of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5 mM dNTPs, 100pM oligo T7 d(T)24  primer, and 400U of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2 mM dNTPs, 0.07 U/ul DNA ligase (Invitrogen, Carlsbad, CA), 0.27 U/ul DNA polymerase I (Invitrogen, Carlsbad, CA), 0.013 U/ul RNase H (Invitrogen), at 16°C for two hours. Immediately following, 10U T4 DNA polymerase (Invitrogen) was added for an additional five minute incubation at 16°C. Double-stranded cDNA was treated with 27 ng/ul of RNase A (EpiCentre Technologies, Madison, WI) for 10 min at 37°C. Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion/Life Technologies, Grand Island, NY), ethanol precipitated, washed with 80% ethanol, and resuspended in 20 μl water.  One μg of each cDNA sample was amplified and labeled with one unit per μl of Klenow Fragment (New England BioLabs, UK) and one OD unit of Cy3 fluorophore (TriLink Biotechnologies, Inc., San Diego, CA) for two hours at 37°C. Array hybridization was carried out with 6 μg of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C. Arrays were scanned on the Axon 4000B Scanner (Molecular Devices, Sunnyvale, CA) and data was extracted from the scanned image using NimbleScan v2.4. DNASTAR ArrayStar v4 (Madison, WI) software was used to quantify and visualize data. .


title: Comparative study of transcriptomes from four Trichoderma strains gene expression in early interaction with tomato plants

status: Public on Feb 27 2012

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

institute: University of Salamanca

summary:
A self-designed Trichoderma high density oligonuclotide (HDO) microarray  (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way  than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 14,081 EST-derived transcripts (Trichochip-1) and the genomes of T. reesei (9,129 genes) and T.  virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum), under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (Vizcaíno et al., 2006). This HDO microarray was used to analyze Trichoderma spp. transcriptomes after 20 h incubation in the presence of tomato plants.
The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032).

sample_organism:
Trichoderma harzianum
Trichoderma virens
Trichoderma hamatum
Trichoderma reesei

platform_organism:
Trichoderma virens
Trichoderma reesei

overall_design: Eight samples were analyzed as follows: Strain T. parareesei T6 grown in the presence or not of tomato plants, strain T. hamatum T7 grown in the presence or not of tomato plants, strain T. harzianum T34 grown in the presence or not of tomato plants and strain T. virens T87 grown in the presence or not of tomato plants. Three replicates for each samples were performed.

first: Belén

last: Rubio

first: Rosa

last: Hermosa


title: Cross-Species Comparisons of Transcriptomic Alterations in Human and Rat Primary Hepatocytes Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin: rat samples

status: Public on Feb 03 2012

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

institute: The Dow Chemical Company

summary: A toxicogenomics approach was used to qualitatively and quantitatively compare the gene expression changes in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Hepatocytes from five individual rats and five individual humans were exposed for 24 hours to 11 concentrations of TCDD ranging from 0.00001 nM to 100 nM and a vehicle control.  Gene expression changes were analyzed using whole genome microarrays.

overall_design: 60 microarrays representing primary hepatocytes from 5 rats, each exposed to 11 doses of TCDD and vehicle controls. Arrays were completed with a one-color design.

first: Alan

last: Dombkowski


title: miRNA Expression Profiling in Ovarian Cell Lines compared to pooled commercial RNA samples

status: Public on Feb 22 2012

city: St Leonards, Sydney

first: Casina

last: Kan

state: NSW

address: RNSH, Pacific Hwy

department: Hormones and Cancer Group

country: Australia

institute: Kolling Institute of Medical Research

summary:
We investigated whether levels of serum microRNAs (miRNAs) could discriminate women with high-grade serous ovarian epithelial cancer (SEOC) from age matched healthy volunteers.
miRNA expression profiling was performed on 4 SEOC cell lines and normal human ovarian surface epithelial cells (HOSE). miR-182, miR-200a, b and c were highly overexpressed in the SEOC cell lines.  miR-103, miR-92a and miR-638 displayed relatively invariant expression and with RNU48, were assessed, as putative serum miRNA normalizers. The 7 miRNA and RNU48 were assessed in serum from SEOC patients (n = 30) and age-matched healthy volunteers (n = 32) by qRT-PCR following pre-amplification.
No correlation between age and miRNA or RNU48 levels was observed (age range 30-79 years). miR-103 demonstrated the least variance and was chosen to normalize serum volume adjusted results. miR-200a, b and c were significantly elevated in SEOC serum (P = 0.002; 0.003; 0.0003 respectively) and a multivariate model was the best predictive classifier of SEOC (ROC-AUC = 0.806). A correlation between high miR-200b levels and residual macroscopic disease following cytoreductive surgery was identified (P = 0.006).
Our results suggest that serum miR-200a, b and c may have utility as diagnostic biomarkers for SEOC.

overall_design: miRNA expression was arrayed in 1 human surface epithelial cells (HOSE) and 4 ovarian cancer cell lines (OV167, OV202, OVCAR-3, PE01). HOSE cells were run in triplicate (including 1 dye-swap). Ovarian cancer cell lines were run in duplicate (including 1 dye-swap).

middle: W

first: Michael

last: Hahn

first: Jung-Yoon

last: Huh

first: Gregory

last: Gard

first: Jayne

last: Maidens

first: Deborah

last: Marsh

first: Viive

last: Howell


title: Expression data of Actinobacillus pleuropneumoniae 4074 in response to epinephrine and norepinephrine

status: Public on Mar 19 2012

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

summary: Bacteria can use host hormones as environment cue to modulate their pathogenic processes, which was discovered to play essential role in disease development. Actinobacillus pleuropneumoniae is one of the most important porcine respiratory pathogens causing great economic losses in the pig industry worldwide. Stress factors were found to contribute to the outcome of A. pleuropneumoniae infection. To test whether A. pleuropneumoniae could respond to host stress hormone catecholamines, the gene expression profiles after epinephrine (Epi) and norepinephrine (NE) treatment were compared with the untreated bacteria using microarray. Although the bacterial growth was not affected in the conditions tested, 157 and 104 genes associated with various function categories including many virulence factors were differentially expressed by Epi and NE treatment. 18 common genes were regulated by the two hormones, these genes included genes encoding virulence factors and potential responsors of Epi and NE. Further investigations on virulence traits demonstrated that cytotoxic activity was enhanced by Epi but repressed by NE in accordance with the regulations on apxIA. Biofilm formation was not affected by the two hormones despite that the biofilm formation gene pgaB was affected. Adhesion to host cells was induced by NE but not by Epi, possibly involving other putative adhesins affected by the hormones in addition to the autotransporter adhesin (APL_0443). Our study demonstrated that A. pleuropneumoniae could actively respond to catecholamines to control its virulence traits. The different regulated genes and effects caused by Epi and NE suggested A. pleuropneumoniae may have multiple responsive systems to sense different type of catecholamine hormones.

sample_organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

overall_design: Transcriptional profiles were analyzed using microarray to compared the epinephrine (Epi) or norepinephrine(NE) treated and untreated A. pleuropneumoniae. All samples were harvested from middle exponential phase (4 hours after sub-culture) at the OD600=1.435±0.065 for control, OD600=1.461±0.019 for Epi treated strain and OD600=1.545±0.115 for NE treated strain. Three biological replicates were conducted for each treatment. The total RNA were extracted and hybridized with the whole genome microarray of A. pleuropneumoniae. The signal intensities were normalized and transformed into log2 values. The genes with fold change ≥ 1.5 and P < 0.05 were selected as differentially expressed.

first: Zhuofei

last: Xu

first: Rui

last: Zhou

first: Huanchun

last: Chen