title: Kidney transplantation (Agilent set)

status: Public on Dec 26 2012

first: Minnie

last: Sarwal

state: CA

address: 703 Welch Road

department: Pediatric Nephrology

summary: In this study, we examined transcriptional profiles from 3 different microarray platforms, across 103 peripheral blood samples with and without acute rejection, to find a critical gene-set for the diagnosis of acute renal rejection that matched biopsy diagnosis, irrespective of patient demographics, clinical confounders, concomitant infection, immunosuppression usage or sample processing methods. We hypothesized that changes in peripheral blood expression profiles correlate with biopsy-proven rejection, and that these changes could be used as biomarkers for the diagnosis and prediction of acute rejection.

overall_design:
We performed cross-sectional microarray analysis of 103 matched peripheral blood samples collected at a single time point, timed with a biopsy where acute rejection was either confirmed as present (60 AR samples) or absent (62 STA samples). The samples were hybridized to one of 3 microarray platforms: Affymetrix (n=75 the 54K HG-U133_Plus2 Array), Agilent (n=26, 44K oligo Array) and cDNA array (n=21, ~30K cDNA).  Of 103 samples, 14 were used on both Affy and Agilent arrays; 1 was used in cDNA and Agilent array and 2 were used across 3 array platforms.   Microarray data generated from 3 array platforms were cross-compared, by mapping common and overlapping transcripts to Human Gene Organization (HUGO) gene names. Significant gene lists on each platform were identified using Significant Analysis of Microarray (SAM, ref) with a common significance threshold of a false discovery rate (FDR) of <10%. This set contains the data for samples hybridized to Agilent arrays.
Disease State: Acute Rejection (AR#sampleid) or Stable (S#sampleid) samples


title: Locust flight muscle: hypoxia-treated vs control

status: Public on Dec 12 2012

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

country: USA

institute: Yale School of Medicine

summary: Background: Hypoxia can affect aerobic organisms profoundly. Biological responses to extreme hypoxia have been well studied. However, it is not well characterized how living organisms respond to mild hypoxia, and how they distinguish different levels of hypoxia. Results: We examined the transcriptional responses of locusts using microarrays to reveal their strategies to cope with mild hypoxia. Mitochondrial activities were systemically suppressed, mainly involving energy production and mitochondrial biogenesis. The functions of endoplasmic reticulum were activated to clear the dysfunctional proteins and rescue newly synthesized proteins. Glucose in cytosol was shunted from glycolysis to pentose phosphate pathway probably to tackle the oxidative stress by enhancing the production of reductive forces. Conclusions: Locusts’ responses to mild hypoxia differ from that to severe hypoxia . In severe hypoxia, glucose resources are shunted to glycolysis to produce ATP and tackle energy crisis; however, in mild hypoxia, they are diverted to produce reductive forces and deal with oxidative stress. Locusts are capable of distinguishing different levels of hypoxia and initiating proper defenses.

overall_design: Simulated 4km altitude hypoxia treatment vs. normoxia control;direct comparison on 6 separate microarrays; each microarray compares one biological replicate of treatment and control; each biological replicate contains 10 individuals

first: Le

last: Kang

first: De-Jian


title: Chromosomal changes in primary human uveal melanomas [UCSF]

status: Public on Dec 06 2012

city: Saint Louis

first: Michael

middle: D

last: Onken

state: MO

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

type: Genome variation profiling by genome tiling array

summary: Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris.  Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal.  One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis.  We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk.  Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3.  For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling.  Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported.

overall_design: Total genomic DNA was obtained from tumor samples that were collected at the time of treatment.  Samples were analyzed by the Microarray Shared Resource at the Comprehensive Cancer Center, University of California, San Francisco or by the Microarray and Genomics Facility of the Roswell Park Cancer Institute.


title: Chromosomal changes in primary human uveal melanomas

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

overall_design: Refer to individual Series


title: Profiling of copy-number variation between BN and M520 rats

status: Public on Dec 31 2012

city: Utrecht

first: Victor

last: Guryev

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and M520 rats

overall_design: Comparison of single BN against single M520 individual in a dye-swap experiment

first: Michal

last: Mokry


title: Chromosomal changes in primary human uveal melanomas [RPCI]


title: Interplay between HIV-1 infection and host microRNAs

status: Public on Dec 05 2012

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Using microRNA array analyses of in vitro HIV-1-infected CD4+ cells, we find that several host microRNAs are significantly up- or downregulated around the time HIV-1 infection peaks in vitro. While microRNA-223 levels were significantly enriched in HIV-1-infected CD4+CD8− PBMCs, microRNA-29a/b, microRNA-155 and microRNA-21 levels were significantly reduced. Based on the potential for microRNA binding sites in a conserved sequence of the Nef-3′-LTR, several host microRNAs potentially could affect HIV-1 gene expression. Among those microRNAs, the microRNA-29 family has seed complementarity in the HIV-1 3′-UTR, but the potential suppressive effect of microRNA-29 on HIV-1 is severely blocked by the secondary structure of the target region. Our data support a possible regulatory circuit at the peak of HIV-1 replication which involves downregulation of microRNA-29, expression of Nef, the apoptosis of host CD4 cells and upregulation of microRNA-223.

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

overall_design: Time course of HIV infection on CD4 cells

first: Guihua

last: Sun

first: Haitang

last: Li

first: John

last: Rossi


title: The Warburg effect alters histone acetylation in cancer cells by influencing the utilization of HDAC and HAT mechanisms.

status: Public on Dec 01 2012

city: Chapel Hill

first: Dallas

middle: Ross

last: Donohoe

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

summary: Microarray transcriptome analysis of siMock and siACL HCT116 cells treated with 0, 0.5, 2.0, and 5.0 mM butyrate over three days.

overall_design: Gene expression is measured at control cells (siMock) and ACL-depleted (siACL) cells with 4 dosages (0, 0.5, 2.0, and 5.0 mM) of butyrate treatments

first: Scott

last: Bultman


title: Hepatic gene expression in chinook salmon (Oncorhynchus tshawytscha) exposed to sewage

city: Burnaby

first: Heather

last: Osachoff

state: BC

address: 8888 University Way

department: Biological Sciences

country: Canada

institute: Simon Fraser University

summary: Hepatic transcriptional profiling of fish exposed to sewage to evaluate temporal and concentration trends.

sample_organism:
Oncorhynchus mykiss
Oncorhynchus tshawytscha

overall_design: Two experiments (Year 1 and 2), each with 6 concentrations (0%, 0.05%, 0.1%, 0.7%, 2% and 5/10%) of sewage diluted in seawater at 4 timepoints (1, 4, 8 and 16 days).

first: Graham

last: van Aggelen

first: Tom

last: Mommsen

first: Chris

last: Kennedy


title: Microarray analysis of gene expression changes during non-climacteric pineapple fruit ripening

status: Public on Nov 30 2012

city: Brisbane

first: Jonni

last: Koia

address: Mansfield Place

department: School of Agriculture and Food Sciences

country: Australia

institute: University of Queensland

summary: Pineapple is a non climacteric fruit. This study investigates changes in gene expression between the mature green fruit and mature yellow fruit ripening stages

overall_design: Pineapple 3 (mature green) and Pineapple 9 (mature yellow) fruit total RNA were labelled with either Cy3 or Cy5 and hybridised to the pineapple microarray.

first: Richard

middle: L

last: Moyle

middle: H

first: Jose

middle: R

last: Botella


title: Genome wide transcriptional portrait of Actinobacillus pleuropneumoniae during invasive disease reveals new strategies for survival and persistence in the host

city: Copenhagen

first: Kirstine

last: Klitgaard

address: Bulowsvej 27

country: Denmark

institute: National Veterinary Institute, Technical University of Denmark

summary: The transcriptional profile of the porcine lung pathogen, Actinobacillus pleuropneumoniae, was monitored during the acute phase of infection in its natural host. Bacterial expression profiles of A. pleuropneumoniae isolated from lung lesions of 25 infected pigs were compared in samples taken 6, 12, 24 and 48 hours post infection.

overall_design: A 84 chip study using total RNA recovered from A. pleuropneumoniae serotype 2 (4226) and serotype 6 (7712640) isolated from infected pig lung tissue during the first 48 of infection. Samples were taken 6, 12, 24 and 48 hours post infection, respectively. Before hybridization the samples were enriched for bacterial RNA and submitted to linear amplification. Each chip measures the expression level of 4,876 target genes from A. pleuropneumoniae with each gene covered by an average of 26.7 probes. Three biological replicates per sample. Microarray data from 3 pigs (no. 39, no. 43 and no. 72) were omitted from the final analysis due to poor signal intensity. A total of 75 microarrays were included in the final analysis.

first: Carsten

last: Friis

first: Tim

middle: K

last: Jensen

first: Oystein

last: Angen

first: Mette

last: Boye


title: A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae

status: Public on Dec 04 2012

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: The goal of our microarray experiments was twofold: 1) Compare the gene expression profile of acaricide resistant spider mite strains (MAR-AB and MR-VP) with that of a susceptible spider mite strain (London); 2) Study gene expression changes in spider mites from the London strain upon transfer from bean, a suitable host, to tomato, a less favorable host. These gene expression changes upon host change were measured for three timepoints (2 hour on tomato (Tomato-2h), 12 hour on tomato (Tomato-12h) and 5 generations on tomato (Tomato-5G)).

overall_design: 23 samples were analyzed: 6 biological replicates for MR-VP, 5 biological replicates for MAR-AB and four biological replicates each for Tomato-2h, Tomato-12h and Tomato-5G

first: Nicky

last: Wybouw

first: Stephane

last: Rombauts

first: Thomas

last: Van Leeuwen


title: Transcriptional regulation of brain gene expression in response to a territorial intrusion

status: Public on Nov 21 2012

city: Urbana

first: Yibayiri

middle: Osee

last: Sanogo

state: IL

address: 505 S. Goodwin

department: Integrative Biology

institute: University of Illinois at Urbana-Champaign

summary: We investigated the transcriptomic response to territorial intrusion in four regions of the brain (telencephalon, diencephalon, cerebellum and brain stem) of a teleost fish, the threespined stickleback (Gasterosteus aculeatus). We tested the hypothesis that gene regulatory networks modulate the transcriptional response to territorial intrusion in the different brain regions and thereby aggressive behavior. Indeed, transcription regulatory network analysis identified cis-regulatory transcription factor motifs enriched in upregulated genes in one brain region and downregulated in the others. We further validated our findings by showing that many of the differentially expressed genes in the diencephalon were positively correlated with levels of aggression in individual males.

overall_design:
2 conditions: control fish and fish that experienced intrusion into their territory,  Biological replicates 5.Four brain regions.
Sample 4BS was excluded from the analysis during data preprocessing because it was an outlier.

middle: O

first: Mark

last: Band

first: Charles

last: Blatti

first: Saurabh

last: Sinha

first: Alison

middle: M

last: Bell


title: C. elegans daf-10(m79) mutants vs wild-type worms

status: Public on Nov 01 2012

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

summary:
Transcriptional profiling of whole day 1 adult C. elegans, comparing animals carrying the m79 mutation in the daf-10 gene and wild-type isogenic animals. Genes that act downstream of sensory neurons to influence longevity, dauer formation and pathogen responses in Caenorhabditis elegans
Manuscript abstract:

overall_design: Two-condition experiments, daf-10 vs wt, 3 biological repeats of each grown in parallel, verified lifespan increase in daf-10 mutant animals

first: Seung-Jae

last: Lee


title: Monocyte-like THP-1 Cells: Trichosporon asahii Infected vs Control

status: Public on Nov 03 2012

city: Beijing

first: Lin

last: Cong

address: 5 Nanmencang, Dongcheng District

country: China

institute: General Hospital of Beijing Military Command

summary: Transcriptional profiling of Monocyte-like THP-1 Cells   with Trichosporon asahii Infected THP-1 Cells comparing  untreated THP-1 cells

overall_design: Two-condition experiment,Trichosporon asahii Infected THP-1 Cells  vs  THP-1 Cells.  Biological replicates: 3  infected THP-1 Cells, independently grown and harvested.One replicate per array.

first: Rong

middle: Y

last: Yang


title: The Ciliated Cell Transcriptome: Ciliated Mouse Tracheal Epithelial Cells vs Control Non-ciliated Mouse Tracheal Epithelial Cells during in Vitro Differentiation

status: Public on Nov 29 2012

city: Stanford

last: Stearns

address: Lorry Lokey Chem/Bio, 337 Campus Drive

department: Biology

institute: Stanford University

summary: Transcriptional profiling of ciliating mouse tracheal epithelial cells compared to non-ciliating cells at two timepoints, ALI+4 and ALI+12, during differentiation in vitro.  These cells are obtained from a transgenic mouse expressing GFP from a human FOXJ1 promoter, so that cells destined to become ciliated can be sorted by FACS based on their expression of GFP.  Likewise, the control non-ciliated cells are identified by their lack of GFP expression.  Ciliated cells were compared to Universal Reference RNA, and non-ciliated cells were compared to Universal Reference RNA.

overall_design: Two-color arrays were used to compare non-ciliated cells, or ciliated cell samples taken at 4 days or 12 days after establishment of the air-liquid interface (ALI), to a Universal Reference RNA. Ciliated cells vs. Universal Reference RNA or Non-ciliated cells vs. Universal Reference RNA.  3 biological replicates from independently grown and harvested cell cultures were performed for non-ciliated cells, 5 biological replicates were performed for a ciliated cell samples at ALI+12, and 3 biological replicates plus 2 technical replicates were performed for ciliated cell samples at ALI+4.

first: Ramona

middle: A

last: Hoh


title: Transient fetal defects in islet architecture caused by pancreas-specific deletion of Bmpr1a led to ageing glucose intolerance

status: Public on Nov 26 2012

city: Perth

first: Abdul

last: Baten

state: WA

address: Level 6, Rear 50 Murray Street

department: WAIMR

institute: The University of Western Australia

summary: Microarray raw data were generated from RNA extracted from isolated islets of 12-week wild type or Pdx1-controled bone morphogenetic protein receptor 1a gene knockout mice

overall_design: Analysis were performed on data generated from RNA extracted from isolated islets of 12-week wild type or Pdx1-controled bone morphogenetic protein receptor 1a gene knockout mice

first: FX

last: Jiang

first: Yuji

last: Mishina

first: Akma

first: Gaetano

last: Naselli

first: Grant

last: Morahan

first: Leonard

middle: C

last: Harrison


title: Expression profiling of early lymphoid progenitors deficient for Ebf1 and Foxo1

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

summary:
Foxo1 and Ebf1 deficiency leads to a similar disruption of normal B-cell development at the level of the common lymphoid progenitor (CLP). Both mouse strains display the existance of LY6D+ CLPs but a marked/complete lack of proB cells.
To investigate similarities of the developmental defects observed we generated gene expression profiles from both genotypes (with corresponding WT controls). This illustrated a shared gene expression signature in Ebf1/Foxo1 deficient CLPs.

overall_design: Gene expression profiling was done using highly purified (FACS sorted) progenitor cells. Cells were purified from bone marrow of wild-type, Foxo1 deficient and Ebf1 deficient mice. Ebf1 deficient bone marrow was aquired by transplantation of Ebf1 deficient progenitors into irradiated hosts. Populations analysed were CLP LY6D-, CLP LY6D+ and proB cells.

first: R

last: Mansson

first: E

last: Welinder

first: J

last: Åhsberg

first: M

last: Sigvardsson

first: C

last: Murre


title: Zebrafish ectonucleoside triphosphate/diphosphohydrolase 5 (entpd5) mutants compared to siblings at 7 dpf

first: Leonie

last: Huitema

state: Utrecht

department: Schulte-Merker group

summary: This microarray was performed in attempt to find genes that are related to the presence of entpd5 during embryonic development

overall_design: Embryos were raised in standard E3 medium at 28 degrees Celcius. At 6 dpf  mutant were separated from siblings by an in vivo skeletal staining (incubating embryos 5 minutes in 0.05% alizarin red in E3 medium where after they are extensively washed with E3 medium) as mutants fail to mineralize their skeleton. At 7 dpf, total RNA from (n=30) entpd5 mutants versus sibling embryos was isolated using the Rnaesy mini kit (Qiagen) according to the manufactures protocol.

first: Stefan

last: Schulte-Merker

first: Ive

last: Logister


title: Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

institute: University of Arkansas

summary: The Crabtree effect, in which fermentative metabolism is preferred at the expense of respiration, is a hallmark of budding yeast’s glucose response and a model for the Warburg effect in human tumors.  While the glucose-responsive transcriptional repressors Mig1p and Mig2p play well-characterized roles in the Crabtree effect, little function for the related Mig3p transcription factor has been uncovered despite numerous investigations of laboratory yeast strains.  Here we studied a wild isolate of Saccharomyces cerevisiae to uncover a critical role for Mig3p that has been lost in S288c-derived laboratory strains.   We found that Mig3p affects the expression of hundreds of glucose-responsive genes in the oak strain YPS163, both during growth under standard conditions and upon ethanol treatment.  Our results suggest that Mig3p may act as a multifunctional activator/repressor that plays separate roles under standard versus stress conditions, but this function has been largely lost in the lab strains.  Population analysis suggests that the lab strain, and several wild strains, harbor mutations that diminish Mig3p function.  Thus, by expanding our attention to multiple genetic backgrounds, we have uncovered an important missing link in a key metabolic response.

overall_design: We performed a series of microarray experiments comparing the gene expression response of unstressed or EtOH stressed wild-type or mig3∆ strains in either the BY4741 or YPS163 background (biological triplicates).  We also compared gene expression for in reciprocal hemizygous strains (YPS163/BY4741mig3∆ and YPS163mig3∆/BY4742; biological duplicates).  Lastly, we measured the gene expression of BY4741 over-expressing BY_MIG3 via galactose induction (biological triplicates).

first: Audrey

middle: P

last: Gasch


title: Benefit of a second opinion, intrapulmonary metastases or multiple primary tumors?

status: Public on Nov 20 2012

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: The presence of bilateral pulmonary nodules in lung cancer usually means distant metastases (M1a). We present an extraordinary example that challenges to look beyond this classification, and illustrates the potential benefits of a multidisciplinary re-evaluation in such a case.

overall_design: FFPE DNA from a patient with three primary tumors. Test samples were compared to normal tissue.

first: Marleen

middle: J

last: Avest

first: Romane

last: Schook

first: Pieter

middle: E

last: Postmus

first: Katrien

last: Grünberg

first: Marinus

last: Paul

first: Bauke

last: Ylstra


title: Substrate-specific gene expression in the amphibian chytrid pathogen

city: Berkeley

first: Thomas

last: Poorten

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

summary: Determining the mechanisms of host-pathogen interaction is critical for understanding and mitigating infectious disease. Mechanisms of fungal pathogenicity are of particular interest given the recent outbreaks of fungal diseases in wildlife populations. Our study focuses on Batrachochytrium dendrobatidis (Bd), the chytrid pathogen responsible for amphibian declines around the world. Previous studies have hypothesized a role for several specific families of secreted proteases as pathogenicity factors in Bd, but the expression of these genes has only been evaluated in laboratory growth conditions. Here we conduct a genome-wide study of Bd gene expression under two different nutrient conditions. We compare Bd gene expression profiles in laboratory growth media and in host tissue (i.e., frog skin). A large proportion of genes in the Bd genome show increased expression when grown in host tissue, indicating the importance of studying pathogens in their infection environment. A number of gene classes show particularly high levels of expression in host tissue, including three families of secreted proteases (metallo-, serine- and aspartyl-proteases), adhesion genes, lipase-3 encoding genes, and a group of phylogenetically unusual crinkler-like effectors. We discuss the roles of these different genes as putative pathogenicity factors and discuss what they can teach us about Bd's metabolic targets, host invasion, and pathogenesis.

sample_organism:
Batrachochytrium dendrobatidis
Batrachochytrium dendrobatidis JAM81

overall_design: One 12-plex chip was analyzed from 12 RNA samples extracted from Batrachochytrium dendrobatidis grown in 2 substrates. Six biological replicates were used for each substrate - sterile frog skin and tryptone nutrient broth. The same dye, Cy5, was used for all samples.

first: T

middle: B

last: Rosenblum

last: Settles

first: S

last: Joneson


title: Expression profiling of B.subtils SMY wild-type vs. (p)ppGpp0 cells upon amino acid starvation.

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Cells constantly adjust their metabolism in response to environmental conditions, yet major mechanisms underlying survival remain poorly understood. We discover a post-transcriptional mechanism that integrates starvation response with GTP homeostasis to allow survival, enacted by the nucleotide (p)ppGpp, a key player in bacterial stress response and persistence. We reveal that (p)ppGpp activates global metabolic changes upon starvation, allowing survival entirely by regulating GTP. Combining metabolomics with biochemical demonstrations, we find that (p)ppGpp directly inhibits the activities of multiple GTP biosynthesis enzymes. This inhibition results in robust and rapid GTP regulation in Bacillus subtilis, which we demonstrate is essential to maintaining GTP levels within a range that supports viability even in the absence of starvation. Correspondingly, without (p)ppGpp, gross GTP dysregulation occurs, revealing a vital housekeeping function of (p)ppGpp; in fact, loss of (p)ppGpp results in death from rising GTP, a severe and previously unknown consequence of GTP dysfunction.

overall_design: Four-condition experiment: wt, wt+RHX, (p)ppGpp0, (p)ppGpp0+RHX. Biological replicates: 3 for each sample. Reference: a mixture of wt RNA from different growth phases and wt backgrounds.

first: Allison

last: Kriel

middle: D


title: Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia

city: Groningen

first: Bea

last: Wisman

address: PObox 30001

department: Gynecologic Oncology

institute: University Medical Center Groningen

type: Methylation profiling by genome tiling array

summary: Epigenetic modifications, such as aberrant DNA promoter methylation is frequently observed in cervical cancer. Identification of hypermethylated regions maybe useful for discrimination between normal cervical epithelium and high-grade cervical intraepithelial neoplasia (CIN2/3) or worse may improve current cervical cancer population-based screening programs. In this study, the DNA methylome of high-grade CIN lesions were characterised using genome-wide methylation screening to identify potential biomarkers for early diagnosis of cervical neoplasia.   Methyl-DNA Immunoprecipitation (MeDIP) combined with DNA microarray was used to compare DNA methylation profiles of epithelial cells derived from high-grade CIN lesions with normal cervical epithelium resulting in the identification of hypermethylated differentially methylated regions (DMRs). Validation of 9 selected DMRs by MSP or BSP in cervical tissue revealed methylation in 63.2-94.7% high-grade CIN and in 59.3-100% cervical carcinomas. QMSP for the two most significant high-grade CIN-specific methylation markers was applied exploring test performance in a large series of cervical scrapings. Frequency and relative level of methylation were significantly different between normal and cancer samples (p<0.001). Clinical validation of both markers in cervical scrapings from patients referred with an abnormal cervical smear, confirmed that frequency and relative level of methylation were related with increasing severity of the underlying CIN lesion (p<0.001) and the ROC analysis was discriminative (p<0.005). These possible methylation markers represent COL25A1 and KATNAL2 promoters and their observed increased methylation upon progression is in agreement with their biological function (cytoskeleton regulation).   In conclusion, our newly identified hypermethylated DMRs represent specific DNA methylation patterns in high-grade CIN lesions and could be potential biomarkers for early detection.  Epigenetic modifications, such as aberrant DNA promoter methylation is frequently observed in cervical cancer. Identification of hypermethylated regions maybe useful for discrimination between normal cervical epithelium and high-grade cervical intraepithelial neoplasia (CIN2/3) or worse may improve current cervical cancer population-based screening programs. In this study, the DNA methylome of high-grade CIN lesions were characterised using genome-wide methylation screening to identify potential biomarkers for early diagnosis of cervical neoplasia.   Methyl-DNA Immunoprecipitation (MeDIP) combined with DNA microarray was used to compare DNA methylation profiles of epithelial cells derived from high-grade CIN lesions with normal cervical epithelium resulting in the identification of hypermethylated differentially methylated regions (DMRs). Validation of 9 selected DMRs by MSP or BSP in cervical tissue revealed methylation in 63.2-94.7% high-grade CIN and in 59.3-100% cervical carcinomas. QMSP for the two most significant high-grade CIN-specific methylation markers was applied exploring test performance in a large series of cervical scrapings. Frequency and relative level of methylation were significantly different between normal and cancer samples (p<0.001). Clinical validation of both markers in cervical scrapings from patients referred with an abnormal cervical smear, confirmed that frequency and relative level of methylation were related with increasing severity of the underlying CIN lesion (p<0.001) and the ROC analysis was discriminative (p<0.005). These possible methylation markers represent COL25A1 and KATNAL2 promoters and their observed increased methylation upon progression is in agreement with their biological function (cytoskeleton regulation).   In conclusion, our newly identified hypermethylated DMRs represent specific DNA methylation patterns in high-grade CIN lesions and could be potential biomarkers for early detection.

overall_design: MeDIP with subsequent microarray analysis was performed on DNA isolated from frozen macrodissected epithelial tissue of CIN3 lesions (n=15) and normal cervices (n=10).

first: Agnes

last: Lendvai

first: Frank

last: Johannes

first: Christina

last: Grimm

first: Jasper

last: Eijsink

first: René

last: Wardenaar

first: Haukeline

middle: H

last: Volders

first: Harry

middle: G

last: Klip

last: Hollema

first: Ritsert

last: Jansen

first: Ed

last: Schuuring

first: G

first: Ate

last: van der Zee


title: Characterization of Nicotiana attenuata plants with reduced expression of HSPRO (ir-hspro plants).

status: Public on Nov 06 2012

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of transcripts that change expression in roots of Nicotiana attenuata plants with reduced expression of HSPRO and in association with Piriformospora indica.

overall_design: Gene expression in roots of Nicotiana attenuata wild type and ir-hspro seedlings was measured at 14 days after inoculation with Piriformospora indica. Three independent experiments were performed with wild type plants and three independent experiments were performed with ir-hspro plants.

first: Stefan

last: Schuck

first: Gustavo

last: Bonaventure


title: DNA copy number profiling of 20 pancreatic cancer cell lines

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

institute: BC Cancer Research Centre

summary: Genome wide copy number profiling of 20 PDAC cell lines to facilitate identification of novel tumor suppressor genes using an integrative genomics approach.

overall_design: Profiling of 20 commonly used PDAC cell lines

first: Wan

last: Lam


title: Toxicity of atrazine and nonylphenol in juvenile rainbow trout (Oncorhynchus mykiss): Effects on general health, disease susceptibility and gene expression

city: Nanaimo

first: Shaorong

last: Li

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

institute: Fisheries and Oceans Canada

summary: Atrazine (ATZ) and nonylphenol (NP) are commonly identified contaminants in aquatic habitats; however, relatively few studies have considered the impact of these endocrine disrupters on immune function.  This study examined the immunotoxicological effects of ATZ and NP at multiple levels of biological organization.  Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to a solvent control (0.00625 % v/v anhydrous ethanol), 59 µg/L ATZ, 555 µg/L ATZ, 2.3 µg/L NP or 18 µg/L NP (measured concentrations) for 4 d.  At the end of exposure, fish were assessed for general health indicators (liver somatic index (LSI), spleen somatic index (SSI), hematocrit), biochemical endpoints (plasma cortisol concentrations, lysozyme activity, and protein content), a cellular endpoint (blood leukocyte differential counts), and an integrated immune response at the organism level (host resistance challenge with Listonella anguillarum).  Additionally, liver gene expression was assessed using a salmonid microarray (cGRASP, 32K version 1) for fish exposed to the (solvent) control, high ATZ (555 µg/L) and high NP (18 µg/L) treatments.  Fish exposed to the high ATZ concentration exhibited elevated plasma cortisol, a decrease in SSI, and decreased lymphocytes and increased monocytes in peripheral blood, with suppression of early immune system processes apparent at the molecular level.  In contrast, fish exposed to the high NP concentration showed physiological (e.g. elevated LSI) and gene expression changes (e.g. induction of vitellogenin) consistent with estrogenic effects, as well as decreased lymphocytes in the peripheral blood and more limited alteration in immune system related pathways in the liver transcriptome.  Fish exposed to high ATZ or NP concentrations suffered higher mortality than the control group following disease challenge with L. anguillarum.  Microarray analysis of the liver transcriptome revealed a total of 211 unique, annotated differentially-regulated genes (DRGs) following high ATZ exposure and 294 DRGs following high NP exposure, with signatures that included alterations to a number of immune-system related processes and pathways.  Functional (enrichment) analysis revealed effects on immune system function, metabolism, oxygen homeostasis, cell cycle, DNA damage, and other processes affected by ATZ or NP exposure.  Overall this study provides evidence at multiple levels of biological organization that both ATZ and NP are immunotoxic and highlights the potential risk posed by these chemicals to wild fish populations.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Total of 24 microarrays.  1 experimental sample and 1 pooled reference sample per microarray.  Total of 8 individual samples (replicates) per treatment group.  Three (3) treatment groups:  control, atrazine (ATZ, 555 ug/L) and nonylphenol (NP, 18 ug/L).

first: Lesley

middle: K

last: Shelley

first: Peter

middle: S

last: Ross

first: Kristina

last: Miller

first: Karia

last: Kaukinen

first: Christopher

last: Kennedy


title: CpG island methylation in colorectal cancer

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

summary: To globally define methylation-’prone’ and -’protected’ CpG islands in cancer, we analyzed the methylation status of 23,000 CpG islands of the human genome in 19 colorectal carcinoma samples as well as normal colon using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step.

overall_design: CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from colorectal carcinoma samples was compared to the enriched material from normal colon to identify aberrantly methylated regions.

first: Claudia

last: Gebhard


title: Transcriptional profiling of the Δmak-1 strain

status: Public on Oct 24 2012

city: College Station

first: Lindsay

last: Bennett

state: TExas

institute: Texas A&M University

summary:
The MAK-1 pathway is the least characterized MAP kinase pathway in Neurospora. Microarray analyses were carried out to identify genes with altered expression in Δmak-1 as compared to wild type strains.
Mycelial mats of wild type and  Δmak-1 strains were grown in constant light (LL) at 25C for 2 and 6 days, respectively,  in 1X Vogel’s, 2% glucose, 0.5% Arginine HCl, pH 6.0.
A cork borer was used to cut plugs to inoculate 75mL of the same liquid media and cultures were grown in LL at 25C for 24h, transferred to constant darkness (DD) 25C for 24 h before being harvested and total RNA extracted.

overall_design: One-condition experiment of the Δmak-1 mutant strain compared to the wild type strain. Cy3 and Cy5 dye swaps were performed.

first: Phillip

last: Berremand

first: Terry

last: Thomas

first: Deborah

last: Bell-Pedersen


title: First Development, Characterization and Experimental Validation of sunflower (Helianthus annuus L.) 44 K Agilent gene expression microarray

status: Public on Oct 31 2012

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

summary: We describe the design, cleaning and annotation of the gene index for sunflower and the construction of the microarray platform. In addition, we validate this tool by means of the analysis of global changes in gene expression profiles in response to water deficit as a physiological event which induces senescence, taken as a model experiment, for which reference genes have also been identified and validated (Fernandez et al., 2011). Our results show that Helianthus annuus L. microarray is suitable for a functional genomics approach across many different possible treatments and conditions to be carried out. Actually, it is already being used for other experiments showing a precise and accurate level of trustability along different gene expression profiles.

overall_design: Analysis of global changes in gene expression profiles in response to water deficit, 44K Agilent one color array

first: Marcelo

last: Soria

first: David

last: Blesa

first: Julio

last: Di Rienzo

first: Sebastian

last: Moschen

first: Dario

last: Principi

first: Guillermo

last: Dosio

first: Luis

last: Aguirrezabal

first: Francisco

last: Garcia

first: Ana

last: Conesa

first: H

last: Hopp

first: Joaquin

last: Dopazo

first: Ruth

last: Heinz

first: Norma

last: Paniego


title: Genome-wide analysis of miRNA-associated transcriptome profiles in multiple cell models

city: Callaghan

first: Adam

last: Carroll

state: NSW

address: Ring Road

institute: University of Newcastle

summary: Schizophrenia-associated miRNA were bidirectionally modulated in HEK-293, HeLa, and SH-SY5Y cell models. Results provide important insights into the current understanding of miRNA function in various cellular environments.

overall_design: Total RNA was obtained from HEK-293, HeLa, and SH-SY5Y cells at 24hrs post-transfection with either synthetic miRNA (miR overexpression) or anti-miR inhibitor (miR inhibition) oligonucleotides.


title: Methylation analysis of cancer and control samples.

city: Detroit

first: Michael

last: Tainsky

state: MI

address: 110 E. Warren

department: Department of Oncology, Molecular Biology and Genetics

institute: Wayne State University School Of Medicine

summary: DNA methylation profiling of cancer and control samples. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across 1,505 CpG sites CpGs distributed across 807 genes in blood DNA specimens.

overall_design: DNA samples were extracted from blood specimens, bisulfite treated  and subsequently used for GoldenGate Methylation Cancer Panel I Array (Illumina) according to manufacturer’s protocol together with normalization methylated, hemimethylated and unmethylated DNA controls (Qiagen).


title: Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection

city: Moncada

first: Gema

last: Ancillo

state: Valencia

address: Ctr. Moncada-Naquera Km 4.5

department: Protección Vegetal y Biotecnología

country: Spain

institute: Instituto Valenciano de Investigaciones Agrarias (IVIA)

summary: The main objective of the present study was to analyze the effect of a severe isolate of CEVd on gene expression of Etrog citron plants was performed not only in late (post-symptomatic) stages of infection but also in early (pre-symptomatic) stages. A genome-wide 20K cDNA mycroarray of citrus was used.

overall_design: Four replicates for each sample category (time-point 0: healthy plants; time-point 1: infected plants at the symptomless stage; time-point 2: infected plants at the symptomatic stage) were generated and compared by a reference design .

first: Serena

last: Rizza

first: José

last: Juarez

first: Antonino

last: Catara

last: Navarro

first: Nuria

last: Duran-Vila


status: Public on Oct 30 2012

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

institute: Cell Signaling Group, IRB Barcelona

summary:
Hog1 bypasses stress-mediated downregulation of transcription by PolII redistribution and chromatin remodeling
Keyword: genetic modification

overall_design: Three independent 200 ml cultures of wild-type strain were grown to mid-log phase in YPD rich medium at 30ºC

first: Mariona

last: Nadal

first: Eulàlia

last: de Nadal


title: Ten percent of aberrant cells is sufficient for detection of DNA copy number alterations (part 3)

status: Public on Oct 21 2012

first: Daoud

last: Sie

summary: Array Comparative Genomic Hybridization (aCGH) is a widely used technique to assess chromosomal copy number alterations. Chromosomal content, however, is often not uniform throughout cell populations.  The aim of our present study is to evaluate to what extent aCGH can detect DNA copy number alterations in a heterogeneous cell population. Reported detection limits are a compound of analytical software and laboratory technique whilst systematic evaluation is lacking, despite the importance in diagnostics and research. Detection limits were explored with DNA isolated from a patient with intellectual disability (ID) and from tumor cell line BT474. Both were diluted with increasing amounts of normal DNA to simulate different levels of cellularity. Samples were hybridized on CGH arrays containing 180880 oligonucleotides evenly distributed over the genome (space ~17kb). The ID sample has a single copy number gain of 4Mb and a single copy number loss of 7.5Mb that could both be detected with 10% mosaicism. The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample and could be detected with 15% tumor cells. The diagnostic validity of these findings was verified using two clinical mosaic samples with alterations in 20% (40Mb) and 14% (34Mb) of cells. Both alterations could be accurately detected using t-statistics.  In conclusion, single copy number gains and losses, down to 4Mb in as little as 10% of a cell population, can be detected by aCGH.

overall_design: Dilution range of DNA from a patient with an intellectual disabillity (ID) used to test the detection limits of array CGH.

first: Oscar

last: Krijgsman

first: Danielle

last: Israeli

first: Hendrik

middle: F

last: van Essen

first: Paul

last: Eijk

first: Michel

last: Berens

first: Clemens

last: Mellink

first: Aggie

middle: W

last: Nieuwint

first: Marjan

last: Weiss

first: Renkse

last: Steenbergen

first: Gerrit

last: Meijer

first: Bauke

last: Ylstra


title: Genome-wide analysis of unbalanced chromosomal changes in colorectal carcinoma

first: Michael

last: Rehli

summary:
Colorectal carcinoma (CRC) is often characterized by chromosomal instability (CIN) which has been associated with a poor prognosis. Disease-related de novo methylation often causes gene repression that may complement chromosomal losses or mutations. To compare CpG island methylation and chromosomal abnormalities in colorectal cancer, we determineded unbalanced chromosomal changes by aCGH of CRCs that were also profiled for aberrant de novo DNA methylation at 23,000 CpG islands of the human genome (Gebhard et al. 2010; and unpublished data).

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Ten percent of aberrant cells is sufficient for detection of DNA copy number alterations (part 1)

overall_design: Dilution range of breast cancer cell line BT474 used to test the detection limits of array CGH.


title: Gene expression profiles in white blood cells of volunteers exposed to a 50 Hz electromagnetic field

city: Cambridge

first: James

last: Metcalfe

address: 80 Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

summary: Consistent and independently replicated laboratory evidence to support a causative relationship between environmental exposure to extremely low frequency electromagnetic fields (ELF-EMF) at power line frequencies and the associated increase in risk of childhood leukaemia has not been obtained. In particular, although gene expression responses have been reported in a wide variety of cells, none have emerged as robust, widely replicated effects. DNA microarrays facilitate comprehensive searches for changes in gene expression without a requirement to select candidate responsive genes. To determine if gene expression changes occur in white blood cells of volunteers exposed to an ELF-EMF, each of 17 pairs of male volunteers age 20-30 was subjected either to a 50 Hz EMF exposure of 62.0 ± 7.1 μT for 2 h or to a sham exposure (0.21 ± 0.05 μT) at the same time (11:00-13:00).  The alternative regime for each volunteer was repeated on the following day and the two-day sequence was repeated 6 days later except that a null exposure (0.085 ± 0.01 μT) replaced the sham exposure. Five blood samples (10 ml) were collected at 2 h intervals from 9:00 to 17:00 with five additional samples during the exposure and sham or null exposure periods on each study day at 11.05, 11.10, 11.20, 11.40 and 12.20. RNA samples were pooled for the same time points on each study day for the 17 volunteers that were subjected to the ELF-EMF exposure/sham or null exposure sequence and were analysed on Illumina microarrays. Time courses for 16 mammalian genes previously reported to be responsive to ELF-EMF exposure, including immediate early genes, stress response, cell proliferation and apoptotic genes were examined in detail. No genes or gene sets significantly expressed on the arrays showed consistent response profiles to repeated ELF-EMF exposures. A stress response was detected as a transient increase in plasma cortisol at the onset of either exposure or sham exposure on the first study day. The cortisol response diminished progressively on subsequent exposures or sham exposures and was attributable to mild stress associated with the experimental protocol.

overall_design:
The study design described in the summary gave a total of 40 pooled RNA samples (10 for each study day) using equal amounts of RNA  from the 17 volunteers exposed to ELF-EMF on study days 1 and 3, a sham exposure on study day 2 and a null exposures on study day 4. The pooled sample from 11:00 on Day1 (immediately prior to ELF-EMF exposure) was used as a reference sample that was amplified and labelled 4 times with the other samples from each of the 4 study days (titled as replicates 1 to 4).
Each replicate was hybridised twice (titled replicates  a and b for each day ( e.g. 1a, 1b) to give a total of 8 arrays from the reference RNA sample (Sample names 2 and 41-47, i.e.GSM879110-GSM879117).

first: Heide

last: Kirschenlohr

first: Peter

last: Ellis

first: Robin

last: Hesketh


title: Genome-wide Tinman binding sites in early and late Drosophila embryos

status: Public on Oct 17 2012

first: Boris

last: Adryan

address: Tennis Court Road

department: Cambridge Systems Biology Centre

type: Genome binding/occupancy profiling by genome tiling array

summary:
The Drosophila transcription factor Tinman (Tin) is involved in embryonic heart development. We have analyzed genomic binding sites for Tin using a ChIP-chip strategy, making use of our high-quality antibody and Affymetrix Drosophila Tiling Arrays. We sampled to time points (early: 3-5.5h AEL and late: 5-8h AEL) that see distinct Tin expression in the embryo. Our data analysis yielded 2548 binding events in early and 988 binding events in late embryos.
Our results are described in Jin et al. "Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures"; submitted to PLoS Genetics

overall_design: Drosophila whole embryos, ChIPed with anti-Tin antibody or IgG control, hybridised to Affymetrix Drosophila tiling arrays, data analysed using MAT

first: Hong

last: Jin

first: Robert

last: Stojnic

first: Anil

last: Ozdemir

first: Angelike

last: Stathopoulos

first: Manfred

last: Frasch


title: miRNA array for LPS-activated tnc+/+ and tnc-/- macrophages

status: Public on Oct 18 2012

city: London

first: Kim

middle: S.

last: Midwood

address: 65 Aspenlea Road

institute: Kennedy Institute of Rheumatology

summary: Endogenous molecules generated upon pathogen invasion or tissue damage serve as danger signals that activate host defence, however their precise immunological role remains unclear. Tenascin-C is an extracellular matrix glycoprotein that is specifically induced upon injury and infection. We have shown that its expression is required to generate an effective immune response to bacterial lipopolysaccharide (LPS) during experimental sepsis in vivo. Tenascin-C enables macrophage translation of pro-inflammatory cytokines upon LPS activation of toll-like receptor 4 (TLR4) and suppresses the synthesis of anti-inflammatory cytokines. It mediates post-transcriptional control of a specific subset of inflammatory mediators via induction of the microRNA miR-155. Thus tenascin-C plays a key role in regulating the inflammatory axis during pathogenic activation of TLR signaling. The data deposited here include the analysis of miRNA profile of  tnc+/+ and tnc-/- bone marrow-derived macrophages (BMDMs) following stimulation with LPS for 8 hours.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Bone marrow-derived macrophages (BMDMs) were cultured in complete DMEM medium, non-stimulated or stimulated for 8 hours with 100ng/ml LPS and total RNA was extracted. Samples were analysed with TaqMan Low Density Arrays (Applied Biosystems).

first: Anna

middle: M

last: Piccinini


title: Identifying changes in host responses to Yersinia infection in the presence or absence of YopM virulence factor

status: Public on Oct 16 2012

city: Chapel Hill

first: June

last: Brickey

address: 450 West Drive

institute: UNC

summary: Transcriptional profiling of total splenic RNA isolated from Yersinia pestis infected mice, comparing samples from YopM-competent parental strain (D27) infected mice to infected mice with YopM-deficient strain (M') at 1hr and 16hr post infection

overall_design: 4 groups. Biological replicates per group: n=3. One replicate per array.

first: W

first: Jenny

last: P-Y Ting

first: Annette

last: Uittenbogard

first: Tanya

last: Myers-Morales

first: Lakshman

last: Chelvarajan

first: Susan

middle: C

last: Straley


title: Tumor-infiltrating monocytic myeloid-derived suppressor cells mediate CCR5-dependent recruitment of regulatory T cells favoring tumor growth

city: Heidelberg

first: Christian

last: Eisen

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Analysis of MDSC subsets from naive blood and RMA-S blood and RMA-S tumor, respectively. Tumor-infiltrating MO-MDSCs changed their expression pattern compared to blood and exhibited high levels of chemokines

overall_design: Total RNA obtained from PMN-MDSCs and MO-MDSCs from naive blood or from blood and tumor of RMA-S bearing mice

first: Eva

last: Schlecker

first: Ana

last: Stojanovic

last: Quack

first: Christine

last: Falk

first: Viktor

last: Umansky

first: Adelheid

last: Cerwenka


title: Systematic Evaluation of Medium-Throughput mRNA Abundance Platforms

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

summary: Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we present ABI's OpenArray and qPCR systems.

overall_design: TCDD-sensitive (Long-Evans) and TCDD-resistant (Han/Wistar) rats were used in both time-course and dose response studies to asses the transcriptomic response to TCDD-insult. The time-course experiment saw animals recieve a single dose of 100ug/kg TCDD or corn oil vehicle followed by euthanasia and tissue collection at various time-points. Animals in the dose-response experiment recieved a single dose of TCDD at varying concentrations or corn oil vehicle, followed by euthanasia and tissue collection 19 hours post-treatment. Each treatment group contained 4-5 biologicial replicates.

first: John

last: Watson

first: Daryl

last: Waggott

first: Ashley

last: Smith

first: Alexander

last: Wu

first: Allan

last: Okey

first: Raimo

last: Pohjanvirta

first: Paul

last: Boutros


title: Transcriptional profiling of somatic cells differentiation throughout oocyte competence acquisition in the xenopus ovarian follicles.

status: Public on Oct 14 2012

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

summary:
Somatic cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes).
NC1 samples were collected from immature stage IV follicles, C1 samples from immature stage VI follicles, and C2 samples from in vitro matured stage VI follicles.

overall_design: Global transcriptional profiling was performed using somatic cells collected from xenopus ovarian follicles during in vivo oocyte developmental competence acquisition. Somatic cells were collected at 3 stages of oogenesis: early stage follicles (stage IV, vitellogenic, prophase I arrested oocytes, meiotically competent but developmentally incompetent, n=5), late stage follicles (stage VI, post-vitellogenic, prophase I arrested oocytes, meiotically competent and developmentally competent, n=5) and ovulatory follicles collected after in vitro maturation induction with hCG of post-vitellogenic follicles (metaphase II arrested oocytes, developmentally fully competent, n=5).

first: Cathy

last: Charlier

first: Svetlana

last: Uzbekova

first: Franck

last: Chesnel


title: Comparison of gene expression between wild type and FUL1/2 knockdown tomato fruits

status: Public on Oct 13 2012

city: Wageningen

first: Ruud

middle: A

last: de Maagd

address: PO Box 619

institute: Plant Resarch International

summary: We compared gene expression by microarray analysis between wild type and transgenic sibling progeny from two primary transgenic lines containing a construct for knocking down expression of both tomato fruitfull orthologs, FUL1/TDR4 and FUL2/MBP7.

overall_design: 2 replicate samples each were taken from wild type progeny of primary transformed line 1-10, transgenic progeny of line 1-10, wild type progeny of transformed line 1-30, and transgenic progeny of line 1-30.

first: Marian

last: Bemer

first: Rumyana

last: Karlova


title: Microarray analysis of juvenile and mature cuttings of Eucalyptus grandis revealed developmental regulation of nitrate reductase which potentially influences nitric oxide production and adventitious root formation

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

country: Israel

institute: Agricultire Research Organization

summary: The loss of rooting capability following the transition from the juvenile to the mature phase is a known phenomenon in woody plant development. Eucalyptus grandis was used here as a model system to study the differences in gene expression between juvenile and mature cuttings.  RNA was prepared from the base of the two types of cuttings before root induction and hybridized to a DNA microarray of E. grandis. In juvenile cuttings, 363 transcripts were specifically upregulated, enriched in enzymes of oxidation/reduction processes. In contrast, in mature cuttings, 245 transcripts were specifically upregulated, enriched in transcription factors involved in the regulation of secondary metabolites. A gene encoding for nitrate reductase (NIA), an enzyme that is known to be involved in nitric oxide (NO) production, was among the genes that were upregulated in juvenile cuttings.  Concomitantly, a transient burst of NO upon excision was higher in juvenile cuttings than in mature ones. Treatment with a NO donor improved rooting of both juvenile and mature cuttings. A single NIA gene was found in the newly released E. grandis genome sequence, the cDNA of which was isolated, overexpressed in Arabidopsis plants and shown to increase NO production. Therefore, higher levels of NIA in E. grandis juvenile cuttings might lead to their better ability to produce NO and form adventitious roots. The Arabidopsis transgenic plants did not exhibit significantly increased lateral or adventitious roots, suggesting that spatial and temporal rather than a constitutive increase in NO is favorable for root formation.

overall_design: E. grandis seedlings were grown from seeds to the age of 6-7 months. The seedlings were pruned either at 10-15 cm or at 150-200 cm above the ground. The newly developed shoots were used as cuttings. To induce rooting, auxin (6000 ppm of K-IBA), was applied by quick dipping (20 sec). Stem cuttings taken from low-pruned seedlings were found to be easy-to root, exhibiting 45% rooting after 14 days and 60% after 35 days. These cuttings were defined as juvenile (RNA from two biological replicates was extracted). In contrast, stem cuttings taken from high pruned seedlings, barely rooted (5%) after 35 days, and were defined as mature (RNA from two biological replicates was extracted). The two biological replicates was used to dye swap experimental design.

first: Einat

last: Sadot


title: TGF-beta-mediated microRNA expression in breast cancer cells

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Road, Rm 2404

institute: Case Western Reserve University

summary: We utilized 3D-organotypic cultures whose physical properties were altered by inclusiong of type I collagen to create biomechanically rigid microenvironments that approximated those typically observed in primary mammary tumors.  Compliant 3D-organotypic cultures were also generated to recapitulate the biomechanical properties of pulmonary microenvironments typically encountered by disseminated breast carcioma cells.  The murine 4T1 progression series represents an established model of triple negative breast cancer development and metastasis and consists of isogenically-derived nonmetastatic 67NR, systemically invasive 4TO7, and highly metastatic 4T1 cells that were propagated for 6 days in the absense or presense of TGF-beta in either rigid or compliant 3D-cultures.  Afterward, total RNA was extracted and subjected to miRNA profiling.

overall_design: two replicates of each growth and treatment condition for each cell line.

first: Molly

last: Taylor

first: Khalid

last: Sossey-Alaoui

first: Cheryl

last: Thompson

first: David

last: Danielpour

middle: P


title: Expression data from TSA-treated Plasmodium

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

state: CA

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

summary:
Variation of surface adhesins is a critical mediator of virulence and immune evasion in many medically important microbes. Phenotypic switching has been linked to transcriptional changes and the function of chromatin proteins, but the determinants of the rate of phenotypic switching remain poorly defined. We analyzed epigenetic switching of the Plasmodium falciparum erythrocyte invasion ligand PfRh4. By introducing a prokaryotic Dam methylase, we demonstrate that parasites selected for in vivo PfRh4 activation show a reversible increase in promoter accessibility while exhibiting perinuclear repositioning of the locus from a silent to a conserved activation domain. Forced activation of a proximal gene results in a similar level of repositioning of the PfRh4 locus into this domain and a concomitant increase in PfRh4 activation in a sub-population of parasites, with promoter accessibility occurring only at actively transcribed loci. Thus, we reveal two distinct epigenetic mechanisms regulating the expression of a malaria virulence gene.

To examine the correlation between changes in gene expression induced by treatment with a high dose of trichostatin A (TSA) and the associated changes in chromatin accessibility.

overall_design: Plasmodium falciparum was treated (or not, control) with 100nm or 500nm TSA, and then the expression profiles were analyzed.

first: Micah

middle: J

last: Manary


title: Genome-wide identification and analysis of gene expression in brains of mice infected with FJDRV, a street rabies virus with high virulence, and ERA, a laboratory-adapted virus with lower virulence

status: Public on Oct 10 2012

city: Changchun

first: Pingsen

last: Zhao

state: Jilin

address: No. 666 Liuying Xilu

department: The research centre for canine diseases

institute: Institute of Military Veterinary Academy of Military Medical Sciences

summary: Host-virus interaction was analyzed at gene expression level. The hypothesis tested in the present study was that rabies virus (RABV) infection affects the gene expression in brains of mice and RAB with different virulence induce distinct expression pattern in host. Results provide important information that RABV infection led to alteration of gene expression in brains of mice and FJDRV, a street rabies virus with highly virulence isolated from brain of rabid dog in Fujian provice of China, or ERA, a laboratory-adapted rabies virus with lower virulence induced different expression pattern, including immune-related and cellular signaling-related genes.

overall_design: An eighteen chip study was performed using total RNA isolated from brains in Treatment 1, three BALB/c mice infected with FJDRV, Treatment 2, three BALB/c mice infected with ERA, and Control, three BALB/c mice non-infected and all treatments were performed with two technical replicates.

first: Lili

first: Songtao

last: Yang

first: Xianzhu

last: Xia


title: Expression Profiling of Primary Human Proerythroblasts (ProEs) After IRF2, IRF6, and MYB shRNA Knockdown

status: Public on Oct 05 2012

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

summary: IRF2, IRF6, and MYB are candidate regulators of human erythropoiesis. We here examine primary CD34+ hematopoietic stem/progenitor cells (HSPCs)-derived erythroid progenitors with control, IRF2, IRF6, or MYB shRNA lentiviral transduction prior to differentiation. Gene expression microarray profiling datasets for MYB shRNA and control shRNA were obtained from Gene Expression Omnibus (GEO) under accession number GSE25678. The data were analyzed together with the datasets obtained in this study.

overall_design: Primary maturing adult erythroblasts were generated ex vivo from CD34+ hematopoietic stem/progenitor cells (HSPCs) using a serum-free two-phase liquid culture system. CD34+ HSPCs were transduced with lentiviruses containing shRNAs against IRF2 or IRF6 gene, selected and differentiated to proerythroblasts (ProEs). Cells were harvested at day 5 of differentiated and total RNA were extracted. This was used to hybridize to Affymetrix expression arrays using the HG-U133 Plus 2.0 platform.

first: Zhen

last: Shao

first: Stuart

last: Orkin


title: Genome-wide identification and analysis of miRNA and mRNA expression in brains of mice infected with FJDRV and ERA

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

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

overall_design: Refer to individual Series


title: Gene expression changes in murine ileum during inflammation: Controls vs. intestinal schistosomiasis and TNBS-ileitis.

city: Antwerp

first: Leela Rani

last: Avula

state: Antwerp

address: Groenenborgerlaan 171

department: Dept of Veterinary Sciences

institute: University of Antwerp

summary:
Background: Although a number of intestinal inflammatory conditions pertain to the ileum, whole-genome gene expression analyses on ileal inflammation in animal models are lacking to date. Therefore, we aimed to identify and characterize alterations in gene expression in the acutely inflamed ileum of two murine models of intestinal inflammation, namely intestinal schistosomiasis and TNBS-induced ileitis, using Agilent whole-genome microarrays followed by bioinformatics analysis to detect enrichment of Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology categories.
Results: When compared with healthy control mice, of almost all known mouse genes and transcripts represented on the array, intestinal schistosomiasis and TNBS-induced ileitis yielded 207 and 1417 differential genes respectively, with 48 overlapping genes (adj.p.value<0.1 and log2FC>1 or <1). Complement and coagulation cascades, extracellular matrix-receptor interaction, Fc epsilon receptor I signaling pathways and protein activation cascade, cell adhesion categories were enriched for differential genes in intestinal schistosomiasis. Antigen processing and presentation, cell adhesion molecules, ABC transporters, Toll-like receptor signaling pathways and response to chemical stimulus categories were enriched for differential genes in TNBS-induced ileitis. Although cytokine-cytokine receptor interaction, intestinal immune network for immunoglobulin A production, focal adhesion pathways and immune, inflammatory and defense response categories were enriched for differential genes in both inflammation models, the vast majority of the associated differential genes were unique to each model.
Conclusions: This study characterized the two diverse models of ileal inflammation at a whole-genome level and outlined their underlying molecular heterogeneity. The results indicate that intestinal schistosomiasis involves Th2 responses, enhanced tissue repair and complement activation, while TNBS-induced ileitis involves Th17 responses, defective antigen processing and presentation and altered Toll-like receptor-mediated responses. Epithelial barrier impairment seems to occur in both inflammation models. Moreover, the comprehensive differential gene-list provided by this study would be helpful as a starting point to explore a specific novel pathway in more detail dealing with small bowel inflammation.

overall_design: A total of 9 biological samples containing 3 each of Control, S.mansoni-infected and TNBS-treated were included in the study. A reference design was used including a reference sample containing a pool of equimolar amounts of all Control samples. The design consisted totally of 11 arrays which included 3 biological replicates each of Control (labeled in Cy5),  S.mansoni-infected (labeled in Cy3) and  TNBS-treated tissue samples(labeled in Cy5) as well as two dye flipped technical replicates of a Control  and a  S.mansoni-infected  tissue sample. The reference was labeled with either Cy5 or Cy3, depending on the labeling of the test sample.

first: Leela

middle: R

first: Dries

last: Knapen

first: Roeland

last: Buckinx

first: Lucia

last: Vergauwen

first: Dirk

last: Adriaensen

first: Luc

last: Van Nassauw

first: Jean-Pierre

last: Timmermans


title: Genome-wide identification and analysis of microRNA expression in brains of mice infected with FJDRV, a street rabies virus with high virulence, and ERA, a laboratory-adapted virus with lower virulence

summary: Host-virus interaction was analyzed at microRNA expression level. The hypothesis tested in the present study was that rabies virus (RABV) infection affects the microRNA expression in brains of mice and RABV with different virulence induce distinct microRNA expression pattern in host. Results provide important information that RABV infection led to alteration of microRNA expression in brains of mice and FJDRV, a street rabies virus with highly virulence isolated from brain of rabid dog in Fujian provice of China, or ERA, a laboratory-adapted rabies virus with lower virulence induced different microRNA expression pattern, and some them may involved in host defense and immune-related function.

overall_design: An nine chip study was performed using total RNA isolated from brains in Treatment 1, three BALB/c mice infected with FJDRV, Treatment 2, three BALB/c mice infected with ERA, and Control, three BALB/c mice non-infected.


title: Zur regulon of Neisseria meningitidis

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

summary: The zur regulon in Neisseria meningitidis was elucidated in the strain MC58 using a zur knockout strain and conditions which activate Zur ( zinc supplementation in the medium)

overall_design: Common reference design, zur knock out strain was used as the common reference and the samples wild type strain grown in RPMI and in RPMI with Zinc supplementation were compared to the common reference.

first: Marie-Christin

last: Pawlik

first: Kerstin

last: Hubert

first: Biju

last: Joseph

first: Heike

last: Claus

first: Chrisoph

last: Schoen

first: Ulrich

last: Vogel


title: Expression Profiling of Primary Human Fetal and Adult Hematopoietic Stem/Progenitor Cells (HSPCs) and Differentiating Proerythroblasts (ProEs)

first: Jian

last: Xu

summary: To facilitate comparative genomic analyses of human fetal and adult cells undergoing erythropoiesis, we employed a serum-free two-phase liquid culture system to expand and differentiate primary human CD34+ hematopoietic stem/progenitor cells (HSPCs) ex vivo. In this experimental context, highly enriched populations of stage-matched, differentiating, primary proerythroblasts (ProEs) were generated. We selected four time points (day 0, CD34+ HSPCs; day 3, 5, and 7, differentiating ProEs) that represented similar stages differentiation for gene expression profiling using microarrays.

overall_design: Primary maturing fetal or adult erythroblasts were generated ex vivo from CD34+ hematopoietic stem/progenitor cells (HSPCs) using a serum-free two-phase liquid culture system. Total RNA from primary fetal and adult HSPCs (day 0) and differentiating proerythroblasts (ProEs; day 3, 5, and 7) were extracted and used to hybridize to Affymetrix expression arrays using the HG-U133 Plus 2.0 platform.

first: Zhen


title: Spontaneous Nf1 deletion and recurrent copy number alterations in mammary tumorigenesis

status: Public on Oct 01 2012

city: Ithaca

first: John

last: Schimenti

state: NY

department: Biomedical Sciences

institute: Cornell University

summary:
Breast cancer is the most prevalent cancer in women 1, and most cases are believed to have a sporadic, rather than heritable basis 2.  To identify breast cancer driver genes, we exploited the C3H-Mcm4Chaos3/Chaos3 (“Chaos3”) mouse model that, by virtue of bearing a defective DNA replicative helicase subunit that causes elevated genomic instability (GIN), sustains somatic alterations ultimately causing mammary adenocarcinomas 6.  Array Comparative Genomic Hybridization (aCGH) analysis of Chaos3 mammary tumors revealed recurrent copy number alterations (CNAs), most notably deletion of the Neurofibromin 1 (Nf1) tumor suppressor gene in all cases.  NF1, a negative regulator of RAS, is traditionally recognized for its role in driving the development of neurofibromas in the context of the human disease Neurofibromatosis Type 1, but not breast cancer.
Genomic DNA from tumor and reference samples were hybridized to NimbleGen 3x720K mouse CGH arrays.  Two reference samples were used independently.  CNAs were visualized using Nimblegen, IGV, and KCsmart software 32.  Select genes were validated via qPCR.  Critical regions within each Chaos3 CNA were identified as the region with the greatest overlap across multiple Chaos3 tumors.

overall_design: Recurring Copy Number Variations (CNVs) for 12 Chaos3 tumors and 2 MMTV-Neu mammary tumors analyzed by aCGH are indicated.  Samples analyzed are primary tumors except where indicated.

first: Marsha

last: Wallace

first: Lishuang

last: Shen

first: Adrian

last: McNairn

first: Ethan

last: Cerami

first: Adam

last: Pfefferle

first: Barbara

last: Fallon

first: Vera

last: Rinaldi

first: Charles

last: Perou


title: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HT-12 samples]

status: Public on Oct 02 2012

city: Herston

first: Amy

middle: McCart

last: Reed

state: Queensland

address: Royal Brisbane & Women's Hospital Campus

department: UQ Centre for Clinical Research

institute: University of Queensland

summary: We performed an expression profiling study of 168 primary breast tumors, lymph node metastases, and autopsy samples of primary breast tumours and metastases to liver, chest wall, lymph node, lung, and spleen, as well as positive and negative RNA controls, with technical replicates, to assess quality control methodology and probe-level reproducibility of the Illumina DASL microarray assay.  The experiment included both Illumina DASL HumanRef-v3 and DASL HT-12; this series includes only the 48 HT12 samples .

overall_design: This series includes 48 samples in total: 9 positive controls, 4 negative controls, and 35 primary breast tumors and metastatic lymph nodes.

middle: E

last: McCart Reed

first: Peter

middle: T

last: Simpson

first: Ana

last: Vargas

first: Margaret

last: Cummings

first: Sunil

last: Lakhani

first: Levi

last: Waldron


title: Nucleosome occupancy microarray for WT and jhd2-delete strains though sporulation

first: Mengshu

last: Xu

state: ON

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

summary: WT (MMY718) and jhd2∆ (MMY1879) sporulating cell cultures were profiled for global nucleosome occupancy using Affymetrix high-resolution tiling arrays.

overall_design: MNase-treated mono-nucleosomes from WT and jhd2∆ cultures in rich media, and sporulation timepoints at 0h, 4h, 6h, 8h, 10h, 12h, and 16h were microarrayed.

first: Marc

middle: D

last: Meneghini


title: Comparison of the response to bile of Lactobacillus casei BL23 and its derivative strain TC01

city: Paterna

first: Manuel

last: Zúñiga

address: Avda. Profesor Agustín Escardino 7

department: Biotecnología

institute: Instituto de Agroquímica y Tecnología de Alimentos

summary: The response to  bile of Lactobacillus casei BL23 and its derivative strain TC01 was investigated. TC01 strain carries a complete deletion of gene LCABL_02080 which encodes a two component signal transduction response regulator.

overall_design: Lactobacillus casei BL23 and TC01 strains were grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The cultures were then two fold diluted with prewarmed MRS medium (control) or MRS supplemented with 0.2% bovine bile (treatment) and incubation continued for 45 min. Cells were then harvested and total RNA purified.

first: Cristina

last: Alcántara


title: X-linked CNV burden and male infertility

city: Florence

first: Chiara

last: Chianese

address: viale Pieraccini. 6

country: Italy

institute: Univerity of Florence

summary: Male factor infertility affects about 7% of men in the general population and it can be related to a number of different etiologic factors, including genetic anomalies. Both sex chromosomes are enriched in genes prevalently or exclusively expressed in the testis. Nevertheless only the Y chromosome-linked Copy Number Variants (CNVs) and Y-linked genes have been demonstrated as important contributors to impaired sperm production in humans  Data on the potential role of X-linked gene products in spermatogenesis derives mainly from model organisms. X-linked genes seem to be expressed both in pre-meiotic and post-meiotic germ cells in the mouse testis and interestingly those expressed in the post-meiotic cells belong to multicopy gene families. The apparent paucity of X-linked factors in male infertility is most likely related to the scarcity of studies, which focused only on a total of seven genes. No pathogenic mutations causing infertility have, thus far, been described in these genes, with the exception of AR gene  In order to advance in the understanding of the role of X-linked CNVs and genes in male infertility, we applied an innovative approach based on high resolution X chromosome specific CGH array. Given that such a detailed analysis of the X chromosome has not been published so far and the testicular function of subjects included in the Genomic Variant Database is unknown (except for 24 X-linked CNVs reported in the recent paper by Tuttelmann), our is the first study providing a detailed analysis of X-linked losses and gains in several hundreds of subjects with known sperm parameters.

overall_design:
The study was approved by the local Ethical Committees of the University Hospital Careggi (Italy) and the Fundacio Puigvert (Spain). All participants signed an informed consent. 96 infertile subjects with different grade of spermatogenic impairment (74 azoospermic, 6 mild oligozoospermia and 16 severe oligozoospermic men) and 103 normozoospermic men have been analyzed with aCGH. All known causes of impaired spermatogenesis have been excluded in the patients and testis histology was available for 47 men. The ethnic composition was similar in the controls and patients groups (40% Spanish and 60% Italians). A customized array-CGH platform (custom 8 x 60K, Agilent Technologies) was generated using the eArray software (http://earray.chem.agilent.com/); probes, selected from those available in the Agilent database, covered the whole X chromosome, including Xp and Xq  pseudoregions, with an average resolution of 4 Kb. As a reference DNA, we used the same normozoospermic subject for the entire study population. This control DNA was already characterized for CNV content in previous array-CGH experiments against different (8)  normospermic controls. In the second part of the study, we performed a case-control study on 31 selected CNVs which appeared to be specific for infertile men after the aCGH analysis. For these selected losses a total of 359 patients and 370 normozoospermic controls were studied. With regard to the gains, 270 patients and 325 controls were analyzed (further phenotypic data are provided in supplementary tables 1a-e). Deletions were analyzed by PCR plus/minus, whereas loss 31 and all the gains have been analyzed with  Real Time PCR using TaqMan Copy Number Assay.

CNV code Loss or Gain Region Size (kb) Start End
1a GAIN Xp22.33 224,83 1544 226372
4.A GAIN Xp22.33 237,08 153373 390452
5 GAIN Xp22.33 160,10 302644 462740
5.A GAIN Xp22.33 241,98 674222 916206
5.B LOSS Xp22.33 12,63 701071 713696
5.C GAIN Xp22.33 420,72 747358 1168080
11 GAIN Xp22.33 39,73 1347599 1387328
12 GAIN Xp22.33 17,30 1693897 1711194
12.A GAIN Xp22.33 6,61 1693897 1700511
12.B GAIN Xp22.33 683,74 1716023 2399766
14 GAIN Xp22.33 1,40 1896197 1897608
15 LOSS Xp22.33 1,40 1896197 1897608
15.A GAIN Xp22.33 27,94 2382699 2410643
15.B GAIN Xp22.33/22.32 280,09 4206493 4486580
16 LOSS Xp22.32 7,76 4250413 4258174
16.A GAIN Xp22.31 1609,42 6487238 8096662
17 LOSS Xp22.31 31,70 6594834 6626533
18 LOSS Xp22.31 82,00 6756310 6838310
19 GAIN Xp22.31 245,03 7002649 7247676
19.A GAIN Xp22.31 129,96 7961788 8091751
19.B GAIN Xp22.31 177,54 8411159 8588699
20 GAIN Xp22.2 602,10 11104518 11706614
20.A GAIN Xp22.2 665,88 14590604 15256487
20.B GAIN Xp22.13 13,34 18018894 18032238
22 LOSS Xp22.11 24,35 22969648 22993997
23 LOSS Xp21.3 6,69 25274024 25280712
24 LOSS Xp21.3 67,33 26891769 26959101
25 GAIN Xp21.3 60,40 27277529 27337933
25.A LOSS Xp21.2 9,69 31282923 31292613
25.B LOSS Xp21.1 28,26 33953232 33981492
25.C GAIN Xp21.1 185,02 34931807 35116827
25.D GAIN Xp21.1 215,00 35269628 35484626
26 GAIN Xp21.1 88,57 37168387 37256960
27 GAIN Xp21.1 9,61 37242364 37251969
30 GAIN Xp11.3 81,13 47766391 47847516
31 LOSS Xp11.3 81,13 47766391 47847516
31.A GAIN Xp11.23 78,87 48021982 48100848
32 LOSS Xp11.22 4,15 52065798 52069943
33.A LOSS Xp11.21 58,89 56403390 56462278
34.A GAIN Xp11.12 48,06 56870427 56918489
35 GAIN Xp11.1 117,14 57318438 57435573
36.A GAIN Xq11 716,03 63925948 64641977
38 GAIN Xq13.2 8,98 72202996 72211976
38.A GAIN Xq13.2 192,04 74375875 74567915
38.B GAIN Xq13.3 153,23 75123387 75276621
39 GAIN Xq21.1 21,98 76992067 77014050
40 GAIN Xq21.1 5,28 80112246 80117526
49 GAIN Xq22.1 5,30 100942190 100947490
50 LOSS Xq22.1 45,36 101803578 101848935
51 GAIN Xq22.2 34,69 103152319 103187013
53.A LOSS Xq24 170,73 118278913 118449646
54 LOSS Xq24 44,85 118281024 118325874
55 GAIN Xq24 206,90 118691020 118897917
55.A GAIN Xq25 53,80 120385787 120439584
56 LOSS Xq25 86,07 124632886 124718959
57 LOSS Xq25 188,03 124929673 125117699
58 GAIN Xq25 9,68 125143278 125152957
58.A LOSS Xq25 12,68 125198109 125210792
59.A GAIN Xq26.3 24,69 134151039 134175725
60 GAIN Xq26.3 42,30 134585636 134627936
60.A LOSS Xq26.3 50,84 134801361 134852198
60.B GAIN Xq26.3 13,45 136050422 136063872
60.C GAIN Xq26.3 91,26 137089527 137180783
60.D LOSS Xq27.1 217,83 140175103 140392930
61 LOSS Xq27.2 4,67 140773893 140778561
64 LOSS Xq27.3 3,92 143436347 143440268
66 LOSS Xq27.3 7,35 145030566 145037917
66.A LOSS Xq28 37,12 147393583 147430698
67 LOSS Xq28 5,42 148456474 148461889
68 GAIN Xq28 105,66 148686631 148792286
69 LOSS Xq28 11,77 154044877 154056645
71 LOSS Xq28 290,99 154586913 154877901
71.A LOSS Xq28 122,36 154755542 154877901


title: DNA copy number changes in colorectal flat adenomas

status: Public on Oct 04 2012

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary:
Background & aim: Flat adenomas form a specific phenotype of colorectal adenomas that has been associated with more severe molecular changes and consequently a more aggressive clinical behavior compared to their polypoid counterparts. In the present study we set out to compare one of the molecular changes most explicitly associated with adenoma to carcinoma progression, i.e. chromosomal instability, between flat and polypoid colorectal adenomas.
Methods: Consecutive series of 83 flat and 35 polypoid adenomas were analyzed for DNA copy number changes using a high resolution arrayCGH platform as well as for mutations in the adenomatous polyposis coli (APC) gene. Gene ontology on the genes located on the significantly different regions was performed.
Results: Overall, flat adenomas show similar DNA copy number changes as polypoid adenomas. Patterns of DNA copy number changes differed between the two phenotypes with significantly more frequently loss of 5q14.3 and 5q15-q23.3 in flat adenomas, while loss of 1p36.32-p35.3, 10q25.2-q25.3, 17p12 and chromosome 18 were more frequent in polypoid adenomas. The 5q15-q23.3 region harbors the APC locus, therefore mutation status of APC was investigated, showing significantly less mutations in flat adenomas. Pathway analysis and datamining linked the 5q region to inflammation.
Conclusion: These results provide evidence that flat and polypoid adenomas have partly overlapping DNA copy number changes, while alterations more specific to flat adenomas have associations with inflammation. Loss of 5q has been associated with aggressive behavior and this could serve as an explanation for a more aggressive clinical behavior of flat lesions.

overall_design: FFPE colorectal tissue samples of 35 polypoid adenomas and 83 flat adenomas. Test samples were compared to an external pool of normal male/female reference DNA.

first: Quirinus

last: Voorham

first: Beatriz

last: Carvalho

first: Angela

last: Spiertz

first: Nicole

last: van Grieken

first: Sandra

last: Mongera

first: Eveline

last: Rondagh

first: Mark

last: van de Wiel

first: Bauke

last: Ylstra

first: Martin

last: Kliment

first: Heike

last: Grabsch

first: Bjorn

last: Rembacken

first: Tomio

last: Arai

first: Adriaan

last: de Bruine

first: Silvia

last: Sanduleanu

first: Philip

last: Quirke

first: Chris

last: Mulder

first: Manon

last: van Engeland

first: Gerrit

last: Meijer


title: Oral Samples (HOMIM-v.02); A Characterization of the Oral Microbiome in Allogeneic Stem Cell Transplant Patients

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: The purpose of this study is to describe the effects of allogeneic stem cell transplant on oral microbiota and to examine differences in those patients who acquired respiratory complications. Forty-five patients were consented for the study and followed for 100 days post-transplant. Eleven patients represented by 115 speciment had specimens collected before and after transplant were subjected to further analysis. The Human Oral Microbe Identification Microarray was used for this analysis. In these 11 patients, five developed respiraotry complications after transplant and six did not develop this complication. Cluster analysis was used to identify patterns in the data.

overall_design: 115 specimens are included from 11 patients. These specimens were collected before and after transplant. There are no duplicate samples.

first: Nancy

last: Ames

first: Pawel

last: Sulima

first: Thoi

last: Ngo

first: Peter

last: Munson

first: Bruce

last: Paster

first: Thomas

last: Hart


title: Copy number analysis of familial and sporadic Epithelial Ovarian Carcinomas (EOC) from FFPE tissue on high resolution Agilent platform.

city: Madird

first: Maria

middle: Jose

last: García

state: Madrid

address: C/ Melchor Fernández Almagro 3

department: Human Cancer Genetics

institute: Centro Nacional de Investigaciones Oncológicas

summary: This study was conducted in order to characterize genomic instability level and pattern in hereditary and sporadic ovarian tumours and define common and/or distinct events occurring in the genesis and evolution of these neoplasms.

overall_design: Overall study comprises 68 epithelial ovarian cancer samples (53 familial and 15 sporadic cases) on high resolution 4x180K Agilent platform.

first: Marta

last: Kamieniak

first: Iván

last: Muñoz-Repeto

first: Daniel

last: Rico

first: Ana

last: Osorio

first: Miguel

last: Urioste

first: Jesus

last: Donas

first: Susana

last: Hernando

first: Luis

last: Robles

first: Teresa

last: Ramón y Cajal

first: Alicia

last: Cazorla

first: Raquel

last: Sáez

first: Jose

last: García-Bueno

first: Samuel

last: Domingo

first: Salud

last: Borrego

first: Eduardo

last: Mendoza

last: .Palacios

first: Mark

last: Van De Wiel

first: Bauke

last: Ylstra

first: Javier

last: Benítez


title: Process-sensitive sentinel genes as novel cell culture comparability metrics

city: Baltimore

first: Bhargavi

last: Kondragunta

address: 1000 Hilltop circle

department: Chemical and Biochemical Engineering

institute: University of Maryland Baltimore County

summary: Biotechnology-derived therapeutics manufacturing is highly regulated to assure product quality, safety and efficacy. Process conditions are closely monitored as they can influence product characteristics. Culture of mammalian cells at different scales is a vital part of biomanufacturing. Currently, scale up of bioreactors is largely done based on engineering parameters such as oxygen transfer and mixing characteristics. There is a lack of genomic translational studies in mammalian cell culture scale-up that can help delineate measurable cellular attributes for improved process understanding. These could be used for quantifying physiological response of cells due to changes in bioreactor environment. In this study, we identified 18 process-sensitive sentinel genes using microarray statistical analysis, which we further verified by qRT-PCR. These were differentially expressed transcripts between a typical 5 liter bench-scale bubble-aerated and impeller-agitated bioreactor and novel 35 mL high-throughput minibioreactors. Using expression changes and biochemical-pathway guidance of these sentinel genes, we were able to tune engineering parameters such that the improved scale-down resulted in both process parameter and sentinel gene profile convergence between the two systems, further solidifying the functionality evidence of these sentinel genes. This study serves as a starting point for developing qRT-PCR assays as comparability metrics that could be performed near-at-line during the cell culture process itself leading to enhanced process control. Additional broad applications of sentinel genes could be to validate different manufacturing facilities for the same product, and allow better process definition by fingerprinting the manufacturing process for more rapid biogenerics and vaccine approvals.

overall_design: We ran consecutive bioreactor (5L and HTCB) runs, each with an independent vial thaw, to achieve multiple biological replicates per time-point. Bioreactors were sampled approximately every 12 hours for RNA extraction. For the 5L bioreactors, microarray samples were run for day 1 (n=2), day 2 (n=2), day 3 (n=3), and day 3.5 (n=3). Here 2 or 3 of the three biological replicates run for each time-point were included in the analysis, based on >70% genes found. For the High-Throughput Controlled Minibioreactors (HTCB), microarray samples were run for day 1 (n=3), day 2 (n=3), day 3 (n=3), day 4 (n=2), and day 4.5 (n=2). Here 2 to 4 of the 4 biological replicate runs were included in the analysis, based on >70% genes found. We define early exponential as day 1, peak exponential as day 2 and day 3 and late stationary as day 3.5.


title: Genomic analysis for predicting cell culture status in a sparged bench-scale 5L bioreactor

summary: There is a great need for setting novel measurable attributes at the cell physiological level in a scalable biopharmaceutical production process to be able to predict the process outcomes and improve process understanding. In a biologic production process, changes in culture environment due to several factors such as shear and bubble induced damage from gas sparging and agitation are known to occur. There is a gap in the knowledge of cellular response due to varying bioreactor environment itself during the course of cell culture, from lag-phase to log-phase to stationary-phase in culture. With the emergence of micro-arrays as tools for exploring cell physiological changes, it opens the possibility for studying the effect of bioreactor culture environment itself on the cell substrate. Such information could be eventually used to designate gene transcripts as biomarkers for cell status in a controlled bioreactor system. A model 5L bench-scale bubble aerated and impeller agitated bioreactor system was used to study gene expression profiles of a hybridoma cell line during the time-course of batch culture. Gene expression profiles that were variable from early-to-late in batch culture, as well as invariant gene profiles were summarized using microarray findings. Typical cellular functions studied were oxidative stress response, DNA damage response, apoptosis, antioxidant activity, cellular metabolism, and protein folding. These findings were also verified with a more rigorous semi-quantitative RT-PCR technique. The results of this study suggest that under predefined bioreactor culture conditions, significant gene changes from lag to log to stationary phase could be identified, which could then be used to track the culture state.

overall_design: We ran consecutive 5L bioreactor runs, each with an independent vial thaw, to achieve multiple biological replicates per time-point. Bioreactors were sampled approximately every 12 hours for RNA extraction. For the 5L bioreactors, microarray samples were run for day 1 (n=2), day 2 (n=2), day 3 (n=3), and day 3.5 (n=3). Here 2 or 3 of the three biological replicates run for each time-point were included in the analysis, based on >70% genes found. We define early exponential as day 1, peak exponential as day 2 and day 3 and late stationary as day 3.5.


title: Affymetrix custom RNA microarray for WT and jhd2-delete strains in terminal spores (20h)

city: Toronto

first: Mengshu

last: Xu

type: Expression profiling by genome tiling array

summary: RNA transcript signals were profiled in WT (MMY718) and jhd2∆ (MMY1879) terminally sporulated cultures (20h of sporulation) using Affymetrix high resolution tiling microarrays.

overall_design: Total RNA was isolated, biotin labelled, and hybridized to custom Affymetrix Scerevisiae_tlg tiling arrays. The array contains 25nt probes covering the Watson strand of the yeast genome with 8nt tiling resolution, and another set of 25nt probes covering the Crick strand with 8nt resolution, with a 4nt offset from the Watson probes. This gives an overall tiling resolution of 4bp with a total of 6.5 million probes, and also allows detection of strand-specific RNA signals.

first: Marc

last: Meneghini

first: Maria

last: Soloveychik


title: Molecular insights on the peripheral and intra-tumoral effects of systemic high dose rIL-2 (Aldesleukin) administration for the treatment of metastatic melanoma

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: We have previously shown that within tumors, recombinant interleukin-2 (rIL-2, Aldesleukin) consistently activates tumor-associated macrophages and up-regulates interferon stimulated genes (ISGs) while inducing minimal migration, activation or proliferation of T-cells. These effects are independent of tumor response to treatment. Here, we prospectively evaluated transcriptional alterations induced by rIL-2 in peripheral blood mononuclear cells (PBMCs) and within melanoma metastases by serially comparing pre- to post-treatment samples in 13 patients. We also compared transcriptional differences among lesions displaying different responsiveness to therapy, focusing on 2 lesions decreasing in size and 2 remaining stable (responding lesions) compared to non-responding ones. As previously described, the effects of rIL-2 were dramatic within PBMC, while effects within the tumor microenvironment were lesion-specific and limited. However, distinct signatures specific to response could be observed in responding lesions pre-treatment that were amplified following rIL-2 administration. These signatures match the functional profile observed in other human or experimental models in which immune-mediated tissue-specific destruction (TSD) occurs underlying a common pathways leading to rejection. Moreover, the signatures observed in pre-treatment lesions were qualitatively similar to those associated with TSD underlining a determinism to immune responsiveness that depends upon the genetic background of the host or the intrinsic genetic makeup of individual tumors. This is the first prospectively collected insight on global transcriptional events occurring during high-dose rIL-2 therapy in melanoma metastases responding to treatment.

overall_design: Evaluated transcriptional alterations induced by rIL-2 in peripheral blood mononuclear cells (PBMCs) (n=34) and within melanoma metastases (n=30) by serially comparing pre- (n=34) to post-treatment (n=30) samples in 13 patients.


title: Study of the functional implication of altered nuclear morphology on global gene expression profile in Drosophila S2R+ cells

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: A probe of the coupling of gene expression and nuclear structure in Drosophila S2R+ cells was undertaken by a study of altered expression profile following a 6 day RNAi mediated genetic perturbation of Klaroid (CG18584), Lamin (CG6944) and Msp-300 (CG33715).

overall_design: Genotypic Technology designed  Custom  Gene Expression Drosophila 8x15k array ( Agilent-AMADID:020441)

first: R

middle: I

last: Lakshmi

first: Nisha

last: Ramdas

first: G

middle: V

last: Shivashankar