title: An antibody leukocyte capture microarray in diagnosis of Systemic Lupus Erythematosus

status: Public on Feb 21 2013

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

summary: The diagnosis of Systemic Lupus Erythematosus (SLE) is challenging due to its heterogeneous clinical presentation and lack of robust biomarkers for laboratory testing to distinguish it from other autoimmune or infectious diseases. Current diagnostic criterion relies on a combination of clinical examination and laboratory tests, and it does not readily distinguish between those with active clinical disease from those that are clinically quiescent. Several groups have attempted to apply emerging high throughput profiling technologies to diagnose SLE. Despite showing promising diagnostic potential, many of them are expensive and technically challenging for routine clinical uses. Here we report a pilot study of applying a technically simple and highly customisable leukocyte capture antibody microarray to profile healthy (n=24) and SLE patients (n=60) of various disease activities. Our analysis reveals a set of surface antigen biomarkers that have significant association with SLE. In addition, we present a computational method to calculate a score from the entire microarray profile to obtain a score that correlate most reliably with SLE disease activity. Although the current version of our microarray alone does not match the discriminatory power of the standard laboratory tests (serum dsDNA, complements C3 and C4), the combination of the two yields a test with significantly increased discriminatory ability than what can be achieved individually. This work paves the way for a customised SLE-specific antibody microarray for accurate diagnosis and monitoring of SLE that can be readily translated to routine clinical use.

overall_design: Blood samples were collected from 60 patients of Systemic Lupus Erythematosus (SLE) of different disease activity (11 active, 16 semi-active, and 33 inactive), and compared it with blood samples from 24 healthy blood donors. For each subject, we extracted PBMCs and apply them to a leukocyte capture antibody microarray. The microarray was then scaned by a DotScan™ slide reader (Medsaic; Eveleigh, NSW, Australia). The number of immobilized cells was proportional to the light scattered at each antibody spot. Binding of PBMCs to each antibody dot was monitored by light scatter and averaged between the duplicate spots on each slide. We then performed statistical analysis to identify CD antigen markers that are associated with SLE, as well as determining the potential diagnostic ability of this microarray for SLE.

first: Ming-Wei

last: Lin

middle: W

first: Leonard

last: Harrison

first: Cristobal

last: dos Remedios

first: Stephen

last: Adelstein


title: Long noncoding RNAs expression data from Atm+/+ and Atm-/- mouse embryonic fibroblasts  after DNA damage at various time point

status: Public on Jan 17 2013

city: Houston

first: Guohui

last: Wan

state: TX

address: 7777 Knight Road

department: Cancer Biology

country: USA

institute: The University of Texas M.D. Anderson Cancer Center

summary: Atm+/+ and Atm-/- mouse embryonic fibroblasts were treated with or without DNA damaging agent neocarzinostatin (NCS), and cells were harvested after 4 hours and 8 hours for the microarray analyses of whole-genome long noncoding RNAs.

overall_design: To examine how long noncoding RNAs are regulated in the DNA damage response, we assessed the genome-wide long noncoding RNA expression in Atm+/+ and Atm-/- littermate mouse embryonic fibroblasts (MEFs) treated with or without DNA damage


title: Sodium metavanadate exhibits carcinogenic tendencies in vitro in immortalized human bronchial epithelial cells [DEG.ABC]

status: Public on Jan 19 2013

city: Tuxedo

first: Lisa

last: Passantino

state: New York

address: 57 Old Forge Road

department: School of Medicine

institute: New York University

summary: Pentavalent vanadium compounds induce intracellular changes in vitro that are consistent with those of other carcinogenic substances, including alteration of transcription factor levels, promotion of oxidative stress, inflammation, DNA damage, stimulation of mitogenic signals, and suppression of apoptosis. While there is no clear evidence that vanadium compounds cause cancer in humans, vanadium pentoxide causes lung cancer in rodents after long-term inhalation exposures and in turn IARC has categorized it as a group 2B possible human carcinogen. The goal of this study was to investigate the carcinogenicity of NaVO3 in the human immortalized bronchial epithelial cell line, Beas-2B.  Cells were treated with 10 µM NaVO3 for 5 weeks, with or without recovery time, followed by gene expression microarray analysis. In a separate experiment, cells were exposed to 1-10 µM NaVO3 for 4 weeks and then grown in soft agar to test for anchorage-independent growth. A dose-dependent increase in the number of colonies was observed. NaVO3-transformed clones could repair a wound faster than controls during the scratch test. In a gene expression microarray analysis of soft agar clones there were 2010 differentially expressed genes (DEG) (adjusted p-value ≤ 0.05) in NaVO3-transformed clones relative to control clones. DEG from this experiment were compared with the DEG of 5 week NaVO3 exposure with or without recovery, all with adjusted p-values <0.05, and 469 genes were altered in the same direction for transformed clones, 5 week NaVO3-treated cells, and the recovered cells; a subset of these changes were validated by QRT-PCR. The data from this study imply that chronic exposure to NaVO3 causes changes that are consistent with cellular transformation including anchorage- independent growth, enhanced migration ability, and gene expression changes that were epigenetically inherited through cell division.

overall_design: Beas-2B cells were chronically exposed to sodium metavanadate in growth media for 4 weeks. Then, one set of exposed cells and unexposed control cells were grown in soft agar for 3 weeks in the absence of vanadate. Transformed colonies (arising from vanadate-exposed cells) and control colonies (spontaneously grew from unexposed cells) were extracted from soft agar and expanded in the absence of vanadate, then processed for gene expression analysis . A second set of exposed cells continued treatment for a total of 5 weeks exposure. A third set of cells recovered for 1 week after the 4 week long exposure. The gene expression of 5 transformed clones, 3 control clones, 2 5 week exposures, 2 recovery, and 2 unexposed control cells, and 1 parental Beas-2B cell samples were analyzed (15 total samples) with an Affymetrix GeneChip Human Exon 1.0 ST array.

first: Alexandra

middle: B

last: Muñoz

first: Max

last: Costa


title: Synthetic Lethality (SLAM) Project Data

status: Public on Feb 28 2013

city: Baltimore

first: Jef

last: Boeke

address: 733 N BROADWAY # 339

institute: Johns Hopkins U

summary: Synthetic lethality is a type of genetic interaction in which two non-lethal mutations acting together result in a loss of viability. Such interactions are important for the insights they may offer into how gene functions are organized into distinct cellular processes. The datasets in this Series represent an effort to identify synthetic lethal genetic interactions in the yeast Saccharomyces cerevisiae on a genome-wide scale.

overall_design: Please see the Pubmed IDs in the individual Sample annotations.

first: Pamela

last: Meluh

first: Daniel

middle: S

last: Yuan

first: Jasmeet

last: Sethi

first: Ou

last: Chen

first: Katrina

middle: J

last: Foelber

first: Abid

last: Khan

first: Emily

last: Kleinhans

first: Sharon

last: Sookhai-Mahadeo

first: Carol

last: Tiffany

first: Xiaoling

last: Wang

first: Yu

middle: Y

first: Xuewen

last: Pan

first: Brian

middle: D

last: Peyser

first: Yan

last: Qi

first: Bill

last: Shi

first: Cheryl

last: Warren

first: Ping

last: Ye

first: Forrest

middle: A

last: Spencer

first: Joel

last: Bader

first: Rafael

last: Irizarry


title: Real-time quantitative PCR analysis of human plasma miRNA expresson

status: Public on Dec 29 2012

city: Shanghai

first: Qifeng

address: NO 270,Dongan Road

country: China

institute: Cancer Hospital, Fudan University

summary: Plasma samples from 10 colonrectal cancer patients (CRCs) (including 5 stage II and 5 stage III patients) and 10 normal controls.An amount of 5 to 10 milliliters of whole blood were obtained from each participant.The plasma was obtained by centrifugation at 1200g for 10min at 4°C.To complete the removal of residual cellular components, plasma samples were recentrifuged at 12,000g for a further 10min at 4°C.A volume of 600μL of each plasma samples from CRC group or normal control group was picked out and uniformly mixed.

overall_design: qPCR miRNA expression profiling. Plasma samples form 10 colonrectal cancer patients(CRCs) (including 5 stage II and 5 stage III patients) and 10 normal controls were used and treated as indicated in the summary. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

last: WANG


title: Neuropsychiatric and clinical correlates to miRNA expression in the frontal cortex of HIV-infected individuals

status: Public on Jan 01 2013

city: La Jolla

first: Erick

middle: T

last: Tatro

state: CA

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California San Diego

summary: Objective: To elucidate molecular mechanisms of neurocognitive dysfunction in long-term HIV-infected individuals by assessing the microRNA (miR) profile and determining clinical and neurocognitive correlates to miR expression.    Design: Analysis of miR profile in frontal cortex of retrospectively-identified autopsy cases of longitudinally-followed subjects with HIV-infection and age/sex-matched controls. HIV-subjects had semi-annual neuropsychiatric and clinical testing, at autopsy, tissue was archived.    Methods: MiR repertoires were profiled from frontal cortices. Analysis of variance (ANOVA) and Tukey Honestly Sigificant Difference (HSD) tests with Benjamini-Hochberg correction for multiple comparisons were used to compare expression among the three groups. Pairwise correlations were used to identify neuropsychiatric variable that correlatee with expression of miRs.    Results: MiRs were significantly different by HIV-status: miR-103, miR-125a, miR-380, miR-422a, miR-515, miR-520b, miR0618, miR-886, and miR-9. Many miRs correlated with neuropsychiatric outcomes like Learning, Memory, Executive, Verbal, and Motor deficit scores.     Conclusions: MiRs are clearly dysregulated in the frontal cortex of HIV-positive individuals. Only a few miRs were significantly dysregulated in only the methamphetamine group. Our study identifies miRs that form rational targets for further inquiry on biochemical mechanisms of HIV-related neurocognitive deficits. Learning deficit score correlates with expression of more miRs than other parameters.

overall_design: A total of 11 HIV positive individuals were analyzed, 5 of which had a past history of methamphetamine ABUSE, and 5 age-matched HIV-negative normal Controls. Technical duplicates are included. Included are clinical and neuropsychiatric data from most recent visit before time of death. This is a retrospective autopsy study of longitudinally-followed subjects on miRNA levels in the frontal cortex.

first: Stephanie

last: Shumaker

first: David

last: Moore

first: Benchawanna

last: Soontornniyomkij

first: Cristian

middle: L

last: Achim


title: Intracellular Brucella melitensis gene expression

status: Public on Dec 27 2012

city: College Station

first: Leslie

middle: Garry

last: Adams

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

summary:
Brucella spp. is an intracellular pathogen in vivo. The intracellular B. melitensis transcriptome was determined by initially enriched and then amplified B. melitensis RNA from total RNA of B. melitensis-infected HeLa cells. Analysis of microarray results identified 161 and 115 genes differentially expressed at 4 and 12 h p.i., respectively.  Most of the genes (78%) differentially expressed were down-regulated at the earliest time point, but up-regulated (75%) at 12 h p.i. The analysis of the results indicates that Brucella undergo an adaptation period during the first 4 h p.i. that is overcome by 12 h p.i., permitting Brucella to replicate intracellularly. Specific genes and biological processes identified in this study will further help elucidate how Brucella act during the early infectious process to their eventual benefit and to the detriment of the naïve host.

Keywords: Time course study of intracellular B. melitensis gene expression

overall_design: Gene expression of the intracellular Brucella melitensis was determined at 4 and 12 h p.i. We generated the following samples: A) B. melitensis total RNA enriched and amplified from total RNA of B. melitensis-infected HeLa cells at 4  h p.i.; B) Total RNA isolated from B. melitensis-infected HeLa cells at 4 h p.i.; C) B. melitensis total RNA enriched and amplified from total RNA of B. melitensis-infected HeLa cells at 12 h p.i.; D) Total RNA isolated from B. melitensis-infected HeLa cells at 12 h p.i.  B. melitensis total RNA was initially enriched and then amplified from total RNA of B. melitensis-infected HeLa cells at 4 and 12 h p.i. in quadruplicate, indirectly labeled and co-hybridized against B. melitensis gDNA to a custom 3.2K B. melitensis oligo-array (n = 8). As there was a possibility that some HeLa transcripts cross-hybridize with probes on B. melitensis microarrays, the original total RNA from B. melitensis-infected HeLa cells were also co-hybridized against B. melitensis gDNA to B. melitensis oligo-arrays (n = 8), and any oligospots with signals were considered non-specific and eliminated from all analysis to avoid false positive gene detection. The intracellular B. melitensis gene expression was compared to the gene expression of the inoculum (n = 2). Every Brucella melitensis open reading frame was printed in triplicate on each microarray, thereby providing three technical replicates for each biological replicates. Each replicate was normalized against labeled Brucella melitensis genomic DNA.

first: Carlos

last: Rossetti

first: Cristi

last: Galindo

first: Harold

middle: R

last: Garner

first: L

middle: G


title: Brucella melitensis-infected HeLa cells gene expression

summary:
In a time course study, we characterized global gene expression profile of B. melitensis-infected epithelium-like cells at the onset of infection. B. melitensis-infected HeLa cells exhibited a down-regulated expression profile at 4 h (48 up- and 109 down-regulated genes) that transitioned to an activated transcriptional profile at 12 h post-infection (733 up- and 224 down-regulated genes).  The analysis of the results indicates that infected cells undergo an adaptation period during the first 4 h p.i. that is overcome by 12 h p.i., permitting Brucella to replicate intracellularly while minimally affecting host physiological processes. Specific genes and biological processes identified in this study will further help elucidate how both host and Brucella interact during the early infectious process to the eventual benefit of the pathogen and to the detriment of the naïve host.

Keywords: Time course study of gene expression profile of Brucella melitensis-infected HeLa cells

overall_design: We generated 4 different samples: A) RNA isolated from Brucella melitensis-infected HeLa cells at 4 h p.i.; B) RNA isolated from non-infected HeLa cells at 4 h p.i. of the A samples; C) RNA isolated from Brucella melitensis-infected HeLa cells at 12 h p.i., and D) RNA isolated from non-infected HeLa cells at 12 h p.i. of the D samples. The B. melitensis-infected HeLa cells gene expression was compared with gene expression from non-infected HeLa cells treated similarly. There are four biological replicates of each sample and time point (n=16). ORFs were single spotted on each microarray. Each replicate was normalized against labeled universal human reference RNA.

first: Kenneth

last: Drake


title: Deficiency in hematopoietic phosphatase Ptpn6/Shp1 hyperactivates the innate immune system and impairs control of bacterial infections in zebrafish embryos

status: Public on Dec 31 2012

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

country: Netherlands

institute: Institute of Biology, Leiden University

summary: Deficiency in the protein-tyrosine phosphatase SHP1/PTPN6 is linked with hematological malignancies and chronic inflammatory diseases. Here we exploited the embryonic and larval stages of zebrafish as an animal model to study ptpn6 function in the sole context of innate immunity. We show that ptpn6 knockdown induces a spontaneous inflammation-associated phenotype at the late larval stage, which was microbe-independent and enhanced instead of suppressed by glucocorticoids. When challenged with Salmonella typhimurium or Mycobacterium marinum at earlier stages of development, the innate immune system was hyperactivated to a contra-productive level that impaired the control of these pathogenic bacteria. These results demonstrate the crucial regulatory function of ptpn6 in preventing host-detrimental effects of inflammation by imposing a tight control over the level of innate immune response activation.

overall_design: This microarray study was designed to determine the effect of morpholino knockdown of the ptpn6 gene on the innate immune response of zebrafish embryos during infection with Salmonella typhimurium. Three independent infection experiments were performed using mixed egg clutches of wild type zebrafish, which were a cross of the AB and TL strains. Each experiment consisted of the following four treatment groups: (1) uninfected control embryos, (2) S. typhimurium-infected control embryos, (3) uninfected ptpn6 knockdown embryos, and (4) S. typhimurium-infected ptpn6 knockdown embryos. Knockdown of ptpn6 was performed by micro-injecting embryos at the 1-2 cell stage with the ptpn6 morpholino, and control embryos were mock-injected with buffer. Embryos were grown at 28.5–30°C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200-250 colony forming units (CFU) of S. typhimurium SL1027 bacteria into the caudal vein, or were mock-injected with buffer as a control.  After injections embryos were transferred into fresh egg water and incubated for 8 h at 28°C. After the incubation period, pools of 15-20 embryos per treatment group were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. All treatment groups were analyzed using a common reference approach.

first: Z

last: Kanwal

first: A

last: Zakrzewska

first: J

last: den Hertog

first: H

middle: P

last: Spaink

first: M

last: Schaaf

middle: H


title: Protein Determinants of Meiotic DNA Break Hotspots

status: Public on Dec 26 2012

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Human Macrophage Response to Leishmania (Viannia) panamensis Infection: Evidence for an Early Inflammatory Response

status: Public on Dec 25 2012

city: New Haven

first: Diane

last: McMahon-Pratt

state: Ct

address: 60 College St

department: Epidemiology of Microbial Diseases

institute: Yale School of Public Health

summary: Transcriptional profile of human monocyte-derived macrophages infected with L.(V.)panamensis was compared to the profile of uninfected cells to delineate transcriptional activation triggered by the infection.

overall_design: two condition experiment: human monocyte-derived macrophages infected with L.(V.)panamensis. 6-5 donors per time point. 3 times point. 1-3 replicates per donor-time point.

first: C

last: Ramirez

first: Y

last: Díaz

last: Tellez

first: T

middle: M

last: Castilho

first: R

last: Rojas

first: I

last: Tikhonova

first: N

last: Alexander

last: Hager

last: Wilson

last: Ettinger

last: Lin

last: Zhao

last: Saravia

first: D


title: Common molecular signature of two neuroprotective agents

status: Public on Dec 23 2012

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: The current lack of proven pharmacological treatment options for traumatic brain injury (TBI) patients reflects the poor translation of successful preclinical studies in clinical trials. This may be due to poor choice of therapeutic agents based on incomplete knowledge of critical elements of neuroprotection. Our goal is to expedite discovery and translation of therapeutic agents that can improve functional outcome by identifying the common molecular profile of neuroprotective drugs. Since damage to the hippocampus is associated with TBI-induced deficits in learning and memory, we analyzed of the hippocampal transcriptional profiles of TBI rats treated with two clinically used drugs metyrapone and carbenoxolone, which have been shown to improve cognitive deficits in previous studies. Despite their different structures, we found that MT and CB have similar effects on several known biological pathways. The neuroprotective effects of these drugs are associated with a distinctive molecular signature which is characterized not by changes in expression of any individual gene but by a common global effect on multiple cell signaling pathways. These data suggest that drug treatments that induce a coordinated attenuation of multiple injury-induced cell signaling networks, both deleterious and protective, have high translational potential.

overall_design: There were 16 samples for array analysis, two biological replicates each for control (4 and 24 hour), TBI (4 and 24 hour), TBI plus MT (4 and 24 hour) and TBI plus CB (4 and 24 hour). Each biological sample, which is a pooled RNA sample (laser captured CA3 pyramidal neurons) from the hippocampus of 3-6 rats, was hybridized to duplicate arrays so that there were 32 gene arrays in this study.

first: Helen

last: Hellmich

first: Donald

last: Prough

first: Daniel

last: Rojo

first: Brent

last: Masel

first: Douglas

last: DeWitt

first: Deborah

last: Boone

first: Jeanna

last: Crookshanks

first: Bridget

last: Capra

first: Kristine

last: Eidson


title: Real-time quantitative PCR analysis of mRNA from lungs of WT and Pglyrp1-/- mice sensitized with HDM

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

summary: Wild type (WT) and Pglyrp1-/- mice were treated with PBS or sensitized 5 days/week for 3 or 5 weeks with 10 µl per application of 2.5 mg/ml of purified house dust mite allergen. 3 days after the last sensitization the lungs were removed and homogenized, and RNA was isolated from the right lobes using the TRIZOL method. Quantitative reverse transcription real-time PCR (qRT-PCR) was used to quantify the amounts of mRNA in the lungs using custom RT2 Profiler PCR Arrays designed by us and manufactured by Qiagen/SA Biosciences.

overall_design: qRT-PCR gene expression profiling

first: Shin

last: Park

first: Dipika

last: Gupta


title: Detection of mutant NPM1 mRNA in acute myeloid leukemia (AML) using custom gene expression arrays

city: Rotterdam

first: Martin

middle: van

last: Vliet

address: Lichtenauerlaan 40

department: Bioinformatics

institute: SkylineDx


title: Protein Determinants of Meiotic DNA Break Hotspots (dataset 1)

first: Kyle

last: Fowler

summary: Meiotic recombination, crucial for proper chromosome segregation and genome evolution, is initiated by programmed DNA double-strand breaks (DSBs) in budding and fission yeasts and likely all sexually reproducing species. In fission yeast, DSBs occur up to several hundred times more frequently at special sites, called hotspots, than in other regions of the genome. What distinguishes hotspots from cold regions is a major unsolved problem, although transcription factors determine some hotspots. We report here the discovery that three coiled-coil proteins -- Rec25, Rec27, and Mug20 -- bind essentially all hotspots with unprecedented, high specificity even without DSB formation. These small proteins are components of linear elements, are related to synaptonemal complex proteins, and are essential for nearly all DSBs at most hotspots. Our results indicate that these hotspot determinants activate or stabilize the DSB-forming protein Rec12 (Spo11 homolog) rather than promote its binding to hotspots. We propose here a new paradigm for hotspot determination and crossover control by linear element proteins.

overall_design: Meiotic DSB analysis by immunoprecipitation of Rec12 covalently linked to DNA (no exogenous crosslinking agent used) in WT and various mutants; one mutant repeated.

first: Gerald

last: Smith


title: Linkage of genomic biomarkers to whole organism endpoints in a Toxicity Identification Evaluation (TIE)

status: Public on Dec 21 2012

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

institute: US Environmental Protection Agency

summary: Aquatic organisms are exposed to many toxic chemicals and interpreting the cause and effect relationships between occurrence and impairment is difficult.  Toxicity Identification Evaluation (TIE) provides a systematic approach for identifying responsible toxicants. TIE relies on relatively uninformative and potentially insensitive toxicological endpoints.  Gene expression analysis may provide needed sensitivity and specificity aiding in the identification of primary toxicants.  The current work aims to determine the added benefit of integrating gene expression endpoints into the TIE process.  A cDNA library and a custom microarray were constructed for the marine amphipod Ampelisca abdita.  Phase 1 TIEs were conducted using 10% and 40% dilutions of acutely toxic sediment.  Gene expression was monitored in survivors and controls. An expression-based classifier was developed and evaluated against control organisms, organisms exposed to low or medium toxicity diluted sediment, and chemically selective manipulations of highly toxic sediment.  The expression-based classifier correctly identified organisms exposed to toxic sediment even when little mortality was observed, suggesting enhanced sensitivity of the TIE process.  The ability of the expression-based endpoint to correctly identify toxic sediment was lost concomitantly with acute toxicity when organic contaminants were removed.  Taken together, this suggests that gene expression enhances the performance of the TIE process.

overall_design: Wild-collected Ampelisca abdita were exposed to either control (from sites in Long Island Sound, labeled LIS) sediment, toxic (from site on Elizabeth River, labeled ER) sediment, a series of mixtures of LIS and ER sediment, sediments manipulated to alter toxin bioavailability, or toxicant amended sediments. Lethality was scored, and survivors were subjected to mRNA expression analysis via oligo microarray.

first: Adam

last: Biales

first: Mitchell

last: Kostich

first: Robert

last: Burgess

first: Kay

last: Ho

first: David

middle: C

last: Bencic

last: Flick

first: Lisa

last: Portis

first: M

last: Pelletier

first: Monique

last: Perron

first: Mark

last: Reiss


title: Variant acute promyelocytic leukemia (APL) bone marrow aCGH

status: Public on Dec 19 2012

city: Seoul

first: Eul-Ju

last: Seo

address: 88, Olympic-ro, 43-gil, Songpa-gu

department: Laboratory Medicine

country: South Korea

institute: Asan Medical Center

type: Genome variation profiling by genome tiling array

summary: CGH microarray in a patient with variant APL

overall_design: 1 sample hybridized to the Whole Human Genome CGH microarray 244K


title: CGH-arrays ovarian serous carcinomas.

status: Public on Dec 20 2012

city: Oslo

first: Aslaug

last: Helland

address: Hospital Radiumhospitalet

department: Dept of Genetics

country: Norway

institute: Institute for Cancer Research, Oslo University

summary: The samples were collected after the Regional ethical review board approval (Reference No: S-01127). Seventy four samples were successfully analyzed by cDNA microarray based CGH. Clinicopathological characteristics of the patients included in this study have previously been published {Wang, 2004 907 /id}.

overall_design: comparative genomic hybridization by array

first: Yun

last: Wang


title: Ribonucleotides in DNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: We report here the consequences of loss of Saccharomyces cerevisiae RNase H2 by comparing mRNA expression profiles in wild type yeast versus a strain lacking the RNH201 gene, encoding the catalytic subunit.  Deleting RHN201 alters mRNA expression for hundreds of genes. Expression changes were based on seven biological replicates (3 from one batch and 4 from another batch) and are seen for many genes involved in stress responses and genome maintenance, consistent with a role of RNase H2 in removing ribonucleotides incorporated into DNA during replication. Differentially expressed genes include, those involved in ribosomal RNA processing and biogenesis and in tRNA modification, supports a role for RNase H2 in resolving R-loops formed during transcription of rRNA and tRNA. Other differentially expresses genes include putative or known helicases and nucleases maintenance of dsRNA viruses, which could be relevant to how mammalian RNase H2 dysfunction elicits an innate immune response leading to neurodegeneration.

overall_design: We examine the consequences of loss of Saccharomyces cerevisiae RNase H2 by comparing mRNA expression profiles in wild type yeast versus a strain lacking the RNH201 gene encoding the catalytic subunit. Expression changes were based on seven biological replicates (3 from one batch and 4 from another batch). For strain reference please see S.A. Nick McElhinny, et al, Genome instability due to ribonucleotide  incorporation into DNA, Nat Chem Bio 6, 774-781 (2010).

first: Mercedes

middle: E

last: Arana

first: Robnet

last: Kerns

first: Kevin

last: Gerrish

first: Laura

last: Wharey

first: Pierre

last: Bushel

first: Thomas

last: Kunkel


title: miRNAs expression in kidney tissues of systemic lupus erythematosus (SLE) individuals

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

institute: Renji Hospital, JiaoTong University School of Medicine

summary:
MicroRNAs (miRNAs) have been implicated as fine-tuning  regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including inflammatory autoimmune diseases.
By using high-throughput microRNA profiling analysis, we identified a series of miRNAs dysregulated in local inflammatory lesions of human patients with autoimmune diseases such as SLE.

overall_design: We isolated the renal biopsy samples from eight SLE patients as well as tumor adjacent kidney tissues from four kidney cancer patients as controls for comparison. Total RNA was extracted for the TaqMan® Low Density Assay v3.0

first: Wen

last: Pan

first: Shu

last: Zhu

first: Youcun

last: Qian


title: miRNAs expression in synovial tissues of rheumatoid arthritis (RA) individuals

summary:
MicroRNAs (miRNAs) have been implicated as fine-tuning  regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including inflammatory autoimmune diseases.
By using high-throughput microRNA profiling analysis, we identified a series of miRNAs dysregulated in local inflammatory lesions of human patients with autoimmune diseases such as RA.

overall_design: We isolated the synovial tissues from four RA patients as well as from two normal people (victims of accidental injury) and two osteoarthristis (OA) patients as controls for comparison. Total RNA was extracted for the TaqMan® Low Density Assay v3.0


title: miRNAs expression in spinal cords of experimental autoimmune encephalomyelitis (EAE) mice

summary:
MicroRNAs (miRNAs) have been implicated as fine-tuning regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including inflammatory autoimmune diseases.
By using high-throughput microRNA profiling analysis, we identified a series of miRNAs dysregulated in local inflammatory lesions of human patients with autoimmune diseases, as well as their relevant mouse models such as EAE.

overall_design: We isolated the spinal cords pooled from six EAE mice or from six naïve control mice. Total RNA was extracted for the TaqMan® Low Density Assay v3.0


title: An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in Uterine Leiomyomas

city: Botucatu

first: Priscila

middle: Daniele Ramos

last: Cirilo

state: SP

address: Distrito de Rubião Junior S/N

department: Genética

country: Brazil

institute: Instituto de Biociências de Botucatu

summary: Copy number alterations data and transcriptional profiling of uterine leiomyomas tumor samples for integrative analysis. Goal was to determine identify genomic gains and/or losses  associated with up and/or down expressed genes, respectively. After, it was applied GSEA and CONEXIC algorithm to integrate the data. Protein-Protein interactions also was building and the data were validated using qRT-PCR and IHC techniques.

overall_design: Experiment condition, 51 uterine leiomyoma DNA samples obtained from patients at secretory and proliferative menstrual cycle phases were labeled with Cy5 or Cy3 and commercial reference samples (Promega) were labled with Cy5 or Cy3. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 4x44 platform. See GSE43027 for the gene expression component.

first: Fábio

last: Marchi


title: Protein Determinants of Meiotic DNA Break Hotspots (dataset 2)

first: Kyle

last: Fowler

overall_design: 16 ChIP-chip arrays of meiotic proteins at various times in meiosis and in several mutant backgrounds. Two protein pull-downs (Rec27 and Rec25) were repeated.

first: Gerald

last: Smith


title: miRNAs expression in kidneys tissues of MRL/lpr mice

summary:
MicroRNAs (miRNAs) have been implicated as fine-tuning regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including inflammatory autoimmune diseases.
By using high-throughput microRNA profiling analysis, we identified a series of miRNAs dysregulated in local inflammatory lesions of human patients with autoimmune diseases, as well as their relevant mouse models such as MRL/lpr.

overall_design: We isolated the kidneys tissues pooled from six female MRL/lpr mice or from three control mice. Total RNA was extracted for the TaqMan® Low Density Assay v3.0


title: miRNAs expression in joint of Collagen-induced arthritis (CIA)

summary:
MicroRNAs (miRNAs) have been implicated as fine-tuning regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including inflammatory autoimmune diseases.
By using high-throughput microRNA profiling analysis, we identified a series of miRNAs dysregulated in local inflammatory lesions of human patients with autoimmune diseases, as well as their relevant mouse models such as CIA.

overall_design: We isolated joint samples pooled from six CIA mice or from six naïve control mice. Total RNA was extracted for the TaqMan® Low Density Assay v3.0


title: S. coelicolor M145 SMM medium time course study (Culture # 3)

city: Minneapolis

first: Marlene

last: Castro-Melchor

state: MN

address: 421 Washington Ave SE

department: Department of Chemical Engineering and Materials Science

institute: University of Minnesota

summary: Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants.

overall_design: The time-course study involved analysis of 8 samples (14hr, 14.5hr, 15.5hr, 17.5hr, 18.5hr, 20hr, 34hr, 40hr). Sample 14hr was analyzed on 5 arrays. Sample 14.5hr was analyzed on 3 arrays. Sample 20hr was analyzed on 2 arrays. Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.

first: Eriko

last: Takano

first: Wei-Shou

last: Hu


title: S. coelicolor M145 SMM medium time course study (Culture # 1)

overall_design: The time-course study involved analysis of 9 samples (14hr, 15hr, 16hr, 17hr, 18hr, 19hr, 20hr, 21hr, 40hr). Samples (14hr, 15hr, 17hr, 20hr, 40hr) were analyzed on 2 arrays. Samples (18hr, 19hr, 21hr) were analyzed on 3 arrays. Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.


title: S. coelicolor LY2517 R5- medium time course study (Culture # 1)

summary: Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) deltaSCO2517::kan mutant strain (LY2517) and compare it to the wild-type M145 strain. SCO2517 is a putative two-component system response regulator.

overall_design: The time-course study involved analysis of 6 samples (15h, 22h, 24h, 26h, 35h, 43h). All samples were analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.


title: S. coelicolor M145 SMM medium time course study (Culture # 2)

overall_design: The time-course study involved analysis of 8 samples (15.5hr, 17hr, 19hr, 20.5hr, 22.5hr, 23.5hr, 25hr, 42hr). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.


title: S. coelicolor LY2517 R5- medium time course study (Culture # 2)

overall_design: The time-course study involved analysis of 13 samples (14h, 16h, 18h, 20h, 22h, 24h, 26h, 28h, 30h, 32h, 34h, 37h, 39h). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.


title: Global microRNA profiling of aTC1-6 and bTC1 before and after treatment with cytokines

status: Public on Dec 18 2012

city: Catania

first: Michele

last: Purrello

email: purrello@unict.it, dbarbaga@unict.it

address: Via S. Sofia, 87

country: Italy

institute: University of Catania

summary: The study sought to determine the global miRNA profiles of mouse pancreatic cell lines aTC1-6 and bTC1 at steady state and after treatment with a cocktail of pro-inflammatory cytokines (IL1b; IFNg and TNFa) for a time course of 24 and 48 hours. Inflammatory cocktail contains IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml. MicroRNA expression profiles in both cell lines during the different experimental conditions were determined using TaqMan® Rodent miRNA A+B Cards Set v2.0 (TLDA, Life Technologies). MicroRNA profiles were measured in 3 independent biological replicates.

overall_design: qRT-PCR analysis of microRNAs of aTC1-6 treated with cytokines for 24 and 48 h and of their respective not-treated controls as well as of βTC1 cells not treated with cytokines. 180 ng RNA of each sample was reverse transcribed through Megaplex™ RT Rodent Primer Pool sets A and B, and preamplified through Megaplex™ PreAmp Rodent Primer Pool sets (Lifetechnologies™). Complementary DNA (cDNA) was amplified usingTaqMan® Rodent miRNA A+B Cards Set v2.0 (Life Technologies™) with TaqMan Universal PCR Master Mix on an ABI 7900HT Sequence Detection System.

first: Davide

last: Barbagallo

first: Salvatore

last: Piro

first: Angelo

last: Condorelli

first: Loriana

last: Mascali

first: Francesca

last: Urbano

first: Nunziatina

last: Parrinello

first: Adelina

last: Monello

first: Luisa

last: Statello

first: Marco

last: Ragusa

first: Agata

last: Rabuazzo

first: Cinzia

last: Di Pietro

first: Francesco


title: AURATUS goldfish environmental genomics projects: dopamine agonists

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

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

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design: Refer to individual Series


title: Chick Otic Placode Induction Arrays

status: Public on Dec 12 2012

city: Houston

first: Andrew

last: Groves

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The inner ear develops from a patch of thickened cranial ectoderm adjacent to the hindbrain called the otic placode. Studies in a number of vertebrate species suggest that the initial steps in induction of the otic placode are regulated by members of the Fibroblast Growth Factor (FGF) family, and that inhibition of FGF signaling can prevent otic placode formation. To better understand the genetic pathways activated by FGF signaling during otic placode induction, we performed microarray experiments to estimate the proportion of chicken otic placode genes that can be up-regulated by the FGF pathway in a simple culture model of otic placode induction. Surprisingly, we find that FGF is only sufficient to induce about 15% of chick otic placode-specific genes in our experimental system. However, pharmacological blockade of the FGF pathway in cultured chick embryos showed that although FGF signaling was not sufficient to induce the majority of otic placode-specific genes, it was still necessary for their expression in vivo. These inhibitor experiments further suggest that the early steps in otic placode induction regulated by FGF signaling occur through the MAP kinase pathway. Although our work suggests that FGF signaling is necessary for otic placode induction, it demonstrates that other unidentified signaling pathways are required to co-operate with FGF signaling to induce the full otic placode program.

overall_design: 8 samples were analyzed. These contain two replicates of each of the following four catergories: Otic ectoderm, Non-Otic (lateral) ectoderm, Trigeminal Ectoderm cultured - FGF, Trigeminal Ectoderm cultured + FGF

first: Raj

last: Ladher


title: SABiosciences Human miRNA PCR array assay of normal respiratory epithelia and lung cancer cells with or without treatment of CSC

city: Frederick

first: Jigui

last: Shan

address: 430 Miller Dr

institute: NCI-Frederick

summary: MicroRNAs are critical mediators of stem cell pluripotency, differentiation and malignancy.  Limited information exists regarding microRNA alterations that facilitate initiation and progression of human lung cancers.  In this study, array techniques were used to evaluate microRNA expression in normal human respiratory epithelia and lung cancer cells cultured in the presence or absence of cigarette smoke condensate (CSC).  Under relevant exposure conditions, CSC significantly repressed miR-487b in these cells.  Subsequent experiments demonstrated that miR-487b directly targets SUZ12, BMI1, Wnt5a, c-Myc and K-ras.  Repression of miR-487b correlated with over-expression of these targets in primary lung cancers, and coincided with DNA methylation, de-novo nucleosome occupancy, and decreased H2AZ and TCF1 levels within the miR-487b genomic locus.  Deoxyazacytidine de-repressed miR-487b, and attenuated CSC-mediated silencing of miR-487b.  TGF-β1 recapitulated CSC-mediated repression of miR-487b.  Constitutive expression of miR-487b abrogated Wnt signaling; inhibited in-vitro proliferation and invasion of lung cancer cells mediated by CSC or over-expression of miR-487b targets, and decreased growth and metastatic potential of lung cancer cells in-vivo.  Collectively, these findings indicate that miR-487b is a novel tumor suppressor microRNA silenced by epigenetic mechanisms during tobacco-induced pulmonary carcinogenesis, and suggest that DNA demethylating agents may be useful for activating miR-487b for lung cancer therapy.

overall_design: MicroRNA PCR array analysis.  Human RT2 miRNA PCR Arrays (MAH-3100E-12) were obtained from SA Biosciences.  Two hundred ng of isolated miRNA was used for reverse transcription and the entire first strand cDNA was diluted and distributed amongst the 384 wells of the super-array plate. The reactions were performed with RT² SYBR Green / ROX PCR Master Mix (SABiosciences).  Results were analyzed using software provided by the vendor (http://www.sabiosciences.com/pcr/arrayanalysis.php).

first: Sichuan

last: Xi

first: Hong

last: Xu

first: David

middle: S

last: Schrump


title: Real-time based miRNA array for MCF10 derived cell series with different metastatic potentials

status: Public on Dec 13 2012

city: Durham

first: Yun

last: Zhang

state: North Carolina

address: 308 Research Dr., C215 LSRC

department: Pharmacology and Cancer Biology

institute: Duke University

summary: MCF10AT1 (M-II), MCF10CA1h (M-III) and MCF10CA1a.cl1 (M-IV) are a set of human breast cancer cell lines that derived from the same parent cell line MCF10 but display distinct phenotypes in metastatic potential in the form of xenografts in immune-compromised mice. From M-II to M-IV, the metastatic potential is gradually increased. Using a self-designed real-time PCR based miRNA array containing 242 genes, we tested the miRNA expression levels in these cell lines in order to identify metastasis-related miRNAs.

overall_design: qPCR gene expression profiling.  Equal amount total RNA from each cell line was pooled prior to gene expression analysis.

first: Pengyuan

last: Yang


title: Variation in the transcriptional response of threatened coral larvae to elevated temperatures

city: University Park

first: Nicholas

last: Polato

state: PA

address: 208 Mueller Lab

institute: Penn State University

summary: Coral populations have declined worldwide largely due to increased sea surface temperatures. Recovery of coral populations depends in part upon larval recruitment. Many corals reproduce during the warmest time of year when further increases in temperature can lead to low fertilization rates of eggs and high larval mortality. Microarray experiments were designed to capture and assess variability in the thermal stress responses of Acropora palmata larvae from Puerto Rico. Transcription profiles showed a striking acceleration of normal developmental gene expression patterns with increased temperature. The transcriptional response to heat suggested rapid depletion of larval energy stores via peroxisomal lipid oxidation and included key enzymes that indicated the activation of the glyoxylate cycle. High temperature also resulted in expression differences in key developmental signalling genes including the conserved WNT pathway that is critical for pattern formation and tissue differentiation in developing embryos. Expression of these and other important developmental and thermal stress genes such as ferritin, heat shock proteins, cytoskeletal components, cell adhesion and autophagy proteins also varied among larvae derived from different parent colonies. Disruption of normal developmental and metabolic processes will have negative impacts on larval survival and dispersal as temperatures rise. However, it appears that variation in larval response to high temperature remains despite the dramatic population declines. Further research is needed to determine whether this variation is heritable or attributable to maternal effects.

overall_design: Hybridization followed a dual channel loop design using two biological replicates (dye-swapped) from each treatment that maximized power to detect differential expression in contrasts between temperatures and batches (within time-points) as well as the amount of data obtained from each slide (Simon and Dobbin 2003). A total of 18 arrays on two 12 plex slides were used (Table S1). Additional samples from other sub-batches (b3/b4) were included in the microarray experiment but are not used in this analysis. Each array measures the expression level of 135,185 genes from the elkhorn coral (Acropora palmata) transcriptome (Polato et al. 2011). Two 60-mer probes were designed for each contig (n = 85,260), and a single probe was designed for each singleton sequence (n = 45,390). Two additional probes each were developed for sequences associated with annotation information relating to calcium metabolism and stress response (n = 4,798). Replicate probes for individual sequences from the assembled transcriptome were not identical; rather they represented multiple different 60-mer sequences from the original template.

first: Iliana

middle: B

last: Baums

first: Naomi

last: Altman


title: A Genome-wide Transcriptional Analysis of Morphology Determination in Candida albicans

city: San Antonio

last: Kadosh

address: 7703 Floyd Curl Drive

department: Microbiology and Immunology

institute: University of Texas Health Science Center at San Antonio

summary: Candida albicans, the most common cause of human fungal infections, undergoes a reversible morphological transition from yeast to pseudohyphal and hyphal filaments, which is required for virulence. For many years, the relationship between global gene expression patterns associated with determination of specific C. albicans morphologies has remained obscure. Using a strain that can be genetically manipulated to sequentially transition from yeast to pseudohyphae to hyphae in the absence of complex environmental cues and upstream signaling pathways, we demonstrate by whole-genome transcriptional profiling that genes associated with pseudohyphae represent a subset of those associated hyphae and are generally expressed at lower levels; interestingly, no genes appeared to be expressed exclusively in pseudohyphae. Our results also strongly suggest that in addition to dosage, extended duration of filament-specific gene expression is sufficient to drive the C. albicans yeast-pseudohyphal-hyphal transition. Finally, we describe the first transcriptional profile of the C. albicans reverse hyphal-pseudohyphal-yeast transition and demonstrate that this transition not only involves down-regulation of known hyphal-specific genes but also differential expression of additional genes which have not previously been associated with the forward transition, including many involved in protein synthesis. These findings provide new insight into genome-wide mechanisms important for determining fungal morphology and suggest that in addition to similarities, there are also fundamental differences in global gene expression as pathogenic filamentous fungi undergo forward and reverse morphological transitions.

overall_design: The Dosage Experiment (13 arrays) was performed twice (two biological replicates). MBY38 cells were treated with various concentrations of Doxycycline (Dox): 20 (n=3), 0.4 (n=1), 0.35 (n=1), 0.3 (n=1), 0.25 (n=1), 0.2 (n=1), 0.15 (n=1), 0.1 (n=1), 0.05 (n=1), 0.02 (n=1) and 0 µg/mL (n=1). Each 20 ug/ml sample was used for 3 technical replicate arrays, one of which was labeled using reverse fluors. The reference sample consisted of equal aliquots of the experimental samples. The Forward Transition Experiment (23 arrays) was performed twice (two biological replicates). MBY38 cells were grown in the presence (n=10) or absence (n=10) of 1.0 ug/ml Dox and subsequently harvested at time points between 1 and 10 hours. Each 1.0 ug/mL Dox treated sample was collected at 0 hours and used for 3 technical replicate arrays, one of which was labeled using reverse fluors. The reference sample consisted of equal aliquots of all 21 experimental samples. The Reverse Transition Experiment (26 arrays) was performed twice (two biological replicates). MBY38 cells were grown in the presence (n=10) or absence (n=10) of 20.0 ug/ml Dox and subsequently harvested at time points between 1 and 10 hours. Each 20.0 ug/mL sample was collected at 0 hours and used for 3 technical replicate arrays, one of which was labeled using reverse fluors. Each untreated (no Dox) sample was collected at 0 hours and used for 3 technical replicate arrays, one of which was labeled using reverse fluors. The reference sample consisted of equal aliquots of all 22 experimental samples. The Dox Control Experiment consisted of 12 arrays. PCY87 cells were grown in the presence (n=5) or absence (n=5) of 20.0 ug/ml Dox overnight to create 5 pairs of biological replicates. Three pairs of biological replicates were labelled normally (one of which was repeated as a technical replicate using reverse fluors) and 2 pairs of biological replicates were labeled using reverse fluors. The Dosage Experiment reference was used as the reference sample.

first: Patricia

last: Carlisle


title: Effects of miR-126/126* of cytokine/chemokine expression in tumor-derived 4T1 cells

summary:
In order to test the effects of metastasis suppressive miR-126/126* on primary tumor microenvironment, we designed a real-time PCR-based mouse cytokine/chemokine array containing 95 cytokines/chemokines and their receptors. Considering the possibility that production of cytokines/chemokines may be dependent on the interactions among different cell types within the tumor mass, we inoculated GFP-labeled 4T1 cells with a control vector or 4T1 cells with pri-miR-126 overexpression into the fat pad of BALB/c mice. 10 days later, we harvested the primary tumors, isolated GFP-positive cancer cells,
and analyzed the expression levels of different cytokines/chemokines and their receptors in the cancer cells at the mRNA level using the cytokine array.


title: Methylome profiling reveals distinct alterations in phenotypic and mutational subgroups of myeloproliferative neoplasms (MPN)

status: Public on Dec 05 2012

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Even though mutations in epigenetic regulators frequently occur in myeloproliferative neoplasms, their effects on the epigenome have not been well studied. Furthermore, even though primary myelofibrosis (PMF) has a markedly worse prognosis compared to essential thrombocytosis (ET) or polycythemia vera (PV), the molecular distinctions between these subgroups are not well elucidated. We performed the HELP (HpaII tiny fragment enriched by LM-PCR) assay to study genome-wide methylation in PV, ET and PMF samples compared with healthy controls. We determined that PV and ET are characterized by aberrant promoter hypermethylation while PMF is an epigenetically distinct subgroup characterized by both aberrant hyper and hypomethylation. Aberrant hypomethylation in PMF was seen to occur in non CpG island loci, demonstrating further qualitative differences between the disease subgroups. The differentially methylated genes in PV and ET were involved predominantly in cell signaling pathways and were enriched for binding sites of GATA1 and other transcription factors. In contrast, aberrantly methylated genes in PMF were involved in inflammatory pathways and were enriched for NF1 (NFI), LEF1 and other transcription factors. Within the PMF subgroup, cases with ASXL1 disruptions formed an epigenetically distinct subgroup with relatively increased methylation. Cases of MPNs with TET2 mutations demonstrated decreased levels of hydroxymethylation and distinct set of hypermethylated genes. In contrast, the JAK2V617F mutation did not drive epigenetic clustering within MPNs. Finally, the significance of aberrant methylation was demonstrated by sensitivity of MPN derived cell lines to decitabine. These results demonstrate epigenetic differences between PMF and PV/ET and reveal methylomic signatures of ASXL1 and TET2 mutations.

overall_design: The study population consisted of 26 MPN patients (6 cases of ET, 8 cases of PV and 12 cases of PMF) and 3 healthy controls. Individual HpaII restriction digest profiles were compared to an internal MspI digest control, to yield differentially methylated fragments for every sample. The purpose of this study was to assess genome wide patterns of DNA methylation across the MPN stratified by disease class.

first: S

last: Nischal

first: A

last: Verma


title: ChIP-chip profiles of MLE,  MSL3 and MOF in Drosophila S2 cells

status: Public on Dec 11 2012

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

overall_design: MLE, MSL3 amd MOF ChIP in Drosophila S2 cells. 1-5 biological replicates per experiment. dye-swaps as indicated in sample description

first: T

last: Mitterweger

first: G

middle: D

last: Gilfillan

first: C

last: Feller

first: P

last: Becker


status: Public on Dec 07 2012

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

summary: Time-course in rice plants of the day length shift experiment in a growth chamber.

overall_design: Rice plants (cv. Norin 8) were collected at every 2h from dusk to noon on the day 0, 1, and 5 from the day length shift (a long-day conditon to a short-day condition).

first: Hironori

last: Itoh


title: Gene expression changes in 786-O cells in response to 5DC treatment.

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

summary: Inactivation of the von Hippel-Lindau tumor suppressor gene, VHL, is an archetypical tumor-initiating event in clear cell renal carcinoma (ccRCC) that leads to the activation of hypoxia-inducible transcription factors (HIFs). However, VHL mutation status in ccRCC is not correlated with clinical outcome. Here we show that during ccRCC progression, cancer cells exploit diverse epigenetic alterations to empower a branch of the VHL-HIF pathway for metastasis, and the strength of this activation is associated with poor clinical outcome. By analyzing metastatic subpopulations of VHL-deficient ccRCC cells, we discovered an epigenetically altered VHL-HIF response that is specific to metastatic ccRCC. Focusing on the two most prominent pro-metastatic VHL-HIF target genes, we show that loss of polycomb repressive complex 2 (PRC2)-dependent histone H3 Lys27 trimethylation (H3K27me3) activates HIF-driven chemokine (C-X-C motif) receptor 4 (CXCR4) expression in support of chemotactic cell invasion, whereas loss of DNA methylation enables HIF-driven cytohesin 1 interacting protein (CYTIP) expression to protect cancer cells from death cytokine signals. Thus, metastasis in ccRCC is based on an epigenetically expanded output of the tumor-initiating pathway.

overall_design: Gene expression data from 786-O cells after 3-day treatment with 100uM 5’-aza-deoxycytidine (5DC) or vehicle (DMSO).

first: Joan

last: Massagué


title: Gene expression changes in response to VHL-reintroduction in metastatic 786-M1A cells.

overall_design: Gene expression data from metastatic 786-M1A cells with and without reintroduced HA-VHL. The empty vector, pBabe-puro, was used as control.


title: Gene expression changes in 786-O cells in response to SUZ12 knockdown.

overall_design: The effects of SUZ12 knockdown on 786-O cells were investigated by  comparing the gene expression profiles of control (pGIPZ) cells with  SUZ12sh1 and SUZ12sh2 cells. The controls were done in triplicate and  both kd cells in duplicate.


title: Spatial Congregation of STAT Binding Directs Selective Nuclear Architecture During T Cell Functional Differentiation

status: Public on Dec 03 2012

city: Bethesda

first: Myong-Hee

last: Sung

state: MD

address: 41 Library Dr

department: NCI

institute: NIH

summary: Although higher-order genome organization is tissue-specific, its functional relevance and mechanistic basis are poorly understood.  Here we analyzed the dynamics of chromatin interactions for lineage-specific cytokine loci during T helper (Th) differentiation.  The naive-to-effector transition is accompanied by a profound shift from promiscuous to highly selective and functionally enriched genome-wide contacts.  Despite the establishment of divergent interactomes and global reprogramming of transcription in Th1 versus Th2 commitment, the overall expression status of the contact genes is surprisingly similar between the two lineages.  Importantly, the genomic contacts are retained and strengthened precisely at DNA binding sites of the specific lineage-determining STAT transcription factor.  The global aggregation of STAT binding loci from genic and non-genic regions highlights a new role for differentiation-promoting transcription factors in direct specification of higher-order nuclear architecture through interacting with regulatory regions.  Such subnuclear environments have implications for efficient functioning of the mature effector lymphocytes.

overall_design: Nineteen arrays total: Eighteen microarrays from individual biological replicates, one microarray from a pool of two biological replicates.

first: Gordon

last: Hager

first: Ofir

last: Hakim


title: Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer

summary:
Inactivation of the von Hippel-Lindau tumor suppressor gene, VHL, is an archetypical tumor-initiating event in clear cell renal carcinoma (ccRCC) that leads to the activation of hypoxia-inducible transcription factors (HIFs). However, VHL mutation status in ccRCC is not correlated with clinical outcome. Here we show that during ccRCC progression, cancer cells exploit diverse epigenetic alterations to empower a branch of the VHL-HIF pathway for metastasis, and the strength of this activation is associated with poor clinical outcome. By analyzing metastatic subpopulations of VHL-deficient ccRCC cells, we discovered an epigenetically altered VHL-HIF response that is specific to metastatic ccRCC. Focusing on the two most prominent pro-metastatic VHL-HIF target genes, we show that loss of polycomb repressive complex 2 (PRC2)-dependent histone H3 Lys27 trimethylation (H3K27me3) activates HIF-driven chemokine (C-X-C motif) receptor 4 (CXCR4) expression in support of chemotactic cell invasion, whereas loss of DNA methylation enables HIF-driven cytohesin 1 interacting protein (CYTIP) expression to protect cancer cells from death cytokine signals. Thus, metastasis in ccRCC is based on an epigenetically expanded output of the tumor-initiating pathway.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

last: Massague


title: Gene expression data from the 786-O renal cell carcinoma cell line and its metastatic derivatives.

overall_design: Gene expression profiles of 786-O renal cell carcinoma cells and metastatic subpopulations isoloated by in vivo selection in immunocomrpmized mice. The derivatives are significantly enriched in the metastatic propensity as measure by experimental metastasis assays.


title: An extensive investigation of sulfur metabolism in the yeast Yarrowia lipolytica

status: Public on Dec 01 2012

city: Thiverval-Grignon

first: Jean-Marie

last: Beckerich

address: Campus Agroparistech

country: France

institute: INRA

summary: A comparison between high and low sulfur source supplies, i.e., sulfate, methionine or cystine, was carried out in order to identify key steps in the biosynthetic and catabolic pathways of the sulfur amino acids.

overall_design: Two conditions experiment, high versus low sulfur conditions (sulfate, cystine or methionine with a ratio of 1 to 1000). Three biological experiments with a dye swap for each for  cystine and sulfate. Two biological experiments with a dye swap for each for methionine.

first: Agnès

last: Hébert

first: Marie-Pierre

last: Forquin

first: Aurélie

last: Roux

first: Julie

last: Aubert

first: Christophe

last: Junot

first: Valentin

last: Loux

first: Jean-François

last: Heilier

first: Pascal

last: Bonnarme

first: Sophie

last: Landaud


title: Expression analysis of aging cardiac tubes in Drosophila

city: Marseille

first: Laurent

last: Perrin

address: Campus de Luminy

institute: CNRS

summary: Investigation of the whole genome expression levels from dissected adult cardiac tubes at 10 days and 40 day. We describe a functional genomic investigation of the genetic control of cardiac senescence in Drosophila. Molecular signatures of heart aging were identified by differential transcriptome analysis followed by a detailed bio-informatic analysis. This approach implicated the JNK/dJun pathway and the transcription factor Vri/dNFIL3 in the transcription regulatory network involved in cardiac senescence and suggested the possible involvement of oxidative stress (OS) in the aging process.

overall_design: 4 biological replicates for each time point (10 days and 40 days) were used. Dye-swap replications, in which each hybridization is done twice, with dye assignments reversed in the second hybridization, were used with a design which allows direct comparison between time points . This method allows technical replicates and eliminates variation that might result from differences in fluorescence dye intensities.


title: Differential Expression of Iron Acquisition Genes by Brucella melitensis and Brucella canis During Macrophage Infection (part 3)

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: Brucella melitensis and Brucella canis differ by ~75 genes yet B. melitensis is highly virulent for humans while B. canis is considered rarely pathogenic.  No identified bacterial factors or mechanisms account for this difference in virulence.  To identify functional differences of these two bacteria, gene transcription was examined during infection of murine macrophages and compared to bacteria grown in broth.  Our analysis identified transcriptional differences in macrophage infection between B. melitensis and B. canis genes involved in iron transport.  Increased transcription of the TonB, enterobactin, and ferric anguibactin transport systems were observed in B. canis but not B. melitensis during infection of macrophages. Therefore, iron appears as an important requirement during the first 24h of infection by B. canis but not for B. melitensis and provides strategies for controlling these pathogens.

overall_design: comparison of total bacterial RNA from Brucella  canis infected murine macrophages and broth grown bacteria

first: Linda

last: Eskra

first: Jill

last: Covert

first: Jeremy

last: Glasner


title: High resolution aCGH of the FGFR3-TACC3 locus in glioblastoma patients

city: Tampere

first: Matti

last: Annala

address: Korkeakoulunkatu 1

institute: Tampere University of Technology

summary: Targeted high resolution array comparative genomic hybridization of the 4p16.3 locus in seven glioblastoma patients

overall_design: A custom Agilent CGH microarray based on the 105A backbone was designed with high probe coverage for 4p16.3. Tumor tissue from four FGFR3-TACC3 positive patients and three negative patients was hybridized onto the microarray for the purposes of identifying a tandem duplication causing the fusion gene.

first: Brittany

last: Parker

middle: J

first: David

last: Cogdell

first: Kirsi

last: Granberg

first: Yan

last: Sun

first: Ping

last: Ji

first: Xia

last: Li

first: Joy

last: Gumin

first: Hong

last: Zheng

first: Limei

last: Hu

first: Olli

last: Yli-Harja

first: Hannu

last: Haapasalo

first: Tapio

last: Visakorpi

first: Xiuping

last: Liu

first: Chang-gong

first: Raymond

last: Sawaya

first: Gregory

middle: N

last: Fuller

first: Kexin

last: Chen

first: Frederick

last: Lang

last: Nykter

first: Wei

last: Zhang


title: Differential Expression of Iron Acquisition Genes by Brucella melitensis and Brucella canis During Macrophage Infection (part 1)

first: Gary

last: Splitter

overall_design: Comparison of total bacterial RNA from Brucella melitensis infected murine macrophages to broth grown bacteria

first: Linda

last: Eskra

first: Jill

last: Covert

first: Jeremy

last: Glasner


title: Dissecting the Molecular Relationship Between Cardiac And Bone Marrow-Derived Progenitor Cells

city: Stanford

first: Leng

last: Han

address: 265 Campus Dr

institute: Stanford University

summary:
Baseline gene expression of mouse Cardiac Progenitor Cells (CPC)
We used microarrays to analyze the global gene expression of mouse CPCs.

overall_design: Compare the gloable gene expression of mouse CPCs and Cardiomyocytes. Although the chip is two color, we only used Cy5 as the data channel.

first: Devaveena

last: Dey

first: Joseph

last: Wu


title: Differential Expression of Iron Acquisition Genes by Brucella melitensis and Brucella canis During Macrophage Infection

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

sample_organism:
Brucella canis
Brucella melitensis bv. 1 str. 16M

platform_organism:
Brucella ovis
Brucella melitensis

overall_design: Refer to individual Series


title: Transcriptome analysis of the Salmonella enterica OmpR regulon

city: norwich

last: Rowley

address: Norwich Research Park

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

summary: Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and ompR mutant grown to mil-exponential phase in LB. The goal was to define the ompR-regulated genes.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Two strains (wild type, ompR mutant), 4 biological replicates of each. Each sample was hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference, which also acted as a control for spot quality.

first: Jay

last: Hinton


title: Expression data from Burkholderia cepacia IST408 bceE and bceF mutants

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

summary: The bacterial tyrosine (BY) kinase family comprises the major group of bacterial enzymes endowed with tyrosine kinase activity. We have previously shown that the BceF protein from Burkholderia cepacia IST408 belongs to this BY kinase family and is involved in the biosynthesis of the exopolysaccharide cepacian. However, little is known about the extent of regulation in the cell by this kinase protein. In order to examine this, we performed a comparative transcriptome profile between the bceF mutant and the wild-type B. cepacia IST408. As a control, the transcriptome of another exopolysaccharide-deficient mutant, which had a mutation in the bceE gene, was also determined.

platform_organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616

overall_design:
For expression profiling, overnight cultures of the Burkholderia cepacia IST408 wild-type strain and the isogenic mutants bceE::Tp and bceF::Tp grown in LB medium were diluted to an initial OD640 nm of 0.1 into S medium. Triplicate samples were cultured at 30ºC with 250 r.p.m. agitation for 12 h, and RNA was extracted from the bacterial isolates.

DNA-based probe-selection was performed using a CEL file derived from a hybridization of genomic DNA, and Xspecies DNA hyb CDF batchmaker v3.2, available here: http://affymetrix.arabidopsis.info/xspecies/. An optimal signal cutoff of 80 and minimum number of probes per probe set of 7 were determined empirically, resulting in the masking of 24223 of the original 226576 probes on the array and the exclusion of 156 probe sets. The new cdf file created (Bcc1sa520656F_Xspecies.CEL80.cdf) was used in DNA-Chip Analyzer 2008 for the subsequent gene expression analyses.

first: Ana

last: Ferreira

first: Inês

last: Silva

first: Jorg

last: Becker


title: Gene expression profile of the stomach from an AGR2 null mouse

first: Anson

middle: W

last: Lowe

address: 300 Pasteur Drive

department: Medicine

summary: The in vivo function of AGR2 was examined by generating an AGR2 null mouse.  The mice died prematurely due to hyperplasia and dysplasia of the glandular stomach. Gene expression profiling was performed to compare differences in transcription between wild-type and null AGR2 mice.

overall_design: Female AGR2 wild-type and knockout mice were sacrificed at the age of 26 weeks and the glandular stomachs were removed.  Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA). The RNA was was reverse transcribed, labeled, and hybridized to mouse oligonucleotide DNA microarrays (Illumina MouseRef-8 v2 Expression BeadChip)

first: Aparna

last: Gupta


title: Differential Expression of Iron Acquisition Genes by Brucella melitensis and Brucella canis During Macrophage Infection (part 2)

overall_design: Comparison of total bacterial RNA from Brucella canis infected murine macrophages at 5 and 24h


title: Differential Expression of Iron Acquisition Genes by Brucella melitensis and Brucella canis During Macrophage Infection (part 4)

overall_design: Comparison of total bacterial RNA from Brucella canis infected murine macrophages to broth grown bacteria


title: A splice isoform signature of Parkinson’s disease in peripheral blood

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

summary: In these studies, we used splice variant-specific microarrays manufactured by the ExonHit company ( www.exonhit.com) on the Affymetrix platform. The goal was to identify splice isoforms whose expression is altered in whole blood of early-stage Parkinson’s disease patients compared to healthy and neurodegenerative disease controls. The study included 19 cases of Parkinson’s disease (PD) samples, 4 of multiple system atrophy (MSA), 4 progressive supranuclear palsy (PSP) and 10 healthy controls. Thirteen splice variants were confirmed in quantitative polymerase chain reactions and used to classify blinded samples from Parkinson’s disease patients and controls with 90% accuracy and 94% sensitivity.

overall_design: In these studies, we used splice variant-specific microarrays manufactured by the ExonHit company ( www.exonhit.com) on the Affymetrix platform. The study included 19 cases of Parkinson’s disease (PD) samples and 20 control samples including 4 cases of multiple system atrophy (MSA), 4 progressive supranuclear palsy (PSP) and 12 healthy controls. Splice isoforms differentially expressed in PD vs any other control group were identified and validated using real-time quantitative PCR on two independent sets of 33 coded and 53 blinded samples.

middle: A

first: Judith

last: Potashkin


title: Gene expression in Citrus sinensis fruit tissues harvested from huanglongbing-infected trees: comparison with girdled fruit

city: Lake Alfred

first: Hui-Ling

last: Liao

state: Florida

address: 700 Experiment Station Road

department: Horticulture sciences

institute: University of Florida

summary: In this data set, we reported for the first time that huanglongbing disease (HLB) induces major changes in the expression of global genes in flavedo, vascular and juice vesicle tissues of citrus fruit.

overall_design: 68 Total samples were analyzed. cDNA generation, array analysis, and statistical tests were performed as a service at the Interdisciplinary Center for Biotechnology Research (ICBR) Microarray Core facility at the University of Florida (Gainesville, FL). The linear models were used for array analysis (Smyth GK et al. Bioinformatics, 2005, 2067-2075). The linear models were firstly used to assess differential expression, and then an empirical Bayes method was used to moderate the standard errors. 13 comparisons were performed for the study. The comparisons in Citrus sinensis cv. Hamlin included: SC vs. CC (genes that respond to infection in symptomatic vascular core); SJV vs. CJV (genes that respond to infection in symptomatic juice vesicle); SS vs. CS (genes that respond to infection in symptomatic seed); SP vs. CP (genes that respond to infection in symptomatic peel). The comparisons in Citrus sinensis cv. Valencia included: SP vs. HP (genes that respond to infection in symptomatic peel); ASP vs. HP (genes that respond to infection in asymptomatic peel); SP vs. ASP (genes that respond to infection in symptomatic peel compared to asymptomatic peel); SC vs. HC (genes that respond to infection in symptomatic vascular core); ASC vs. HC (genes that respond to infection in asymptomatic vascular core); SC vs. ASC (genes that respond to infection in symptomatic vascular core compared to asymptomatic vascular core); SJV vs. HJV (genes that respond to infection in symptomatic juice vesicle); ASJV vs. HJV (genes that respond to infection in asymptomatic juice vesicle); SJV vs. ASJV (genes that respond to infection in symptomatic juice vesicle compared to asymptomatic juice vesicle). ESTs with significant expression changes (P value <0.001; false discovery rate <0.01 with equal or higher than 2-fold changes in expression) were selected for further analysis.

first: Jacqueline

middle: K

last: Burns


title: Rbfox1 downregulation and altered Calpain 3 splicing by FRG1 in a mouse model of facioscapulohumeral muscular dystrophy (FSHD).

city: Santa Cruz

first: Lily

last: Shiue

state: CA

address: 1156 High Street

department: MCD Biology

institute: UCSC

summary:
FRG1 over-expression results in an FSHD-like phenotype in mice.
Muscles (vastus lateralis and biceps brachii) from wild type and FRG1 over-expressing mice were compared at 4 and 13 weeks of age by splicing sensitive microarray.

overall_design: Comparisons at 4 different time points/muscles were performed between groups of 3 each FRG1 and WT mice.

first: D

last: Gabellini

first: M

last: Pistoni

first: L


title: Comparative microarray analysis of microRNA expression profiles in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases and benign melanocytic naevi

status: Public on Nov 02 2012

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

summary: Perturbations in microRNA (miRNA) expression profiles has been reported for cutaneous malignant melanoma (CMM). With regards to a rapidly growing number of newly discovered miRNA sequences, the availability of up-to-date miRNA expression profiles for primary cutaneous malignant melanoma (PCMM), cutaneous malignant melanoma metastases (CMMM) and benign melanocytic naevi (BMN) is limited. Patients with PCMM (n=9), CMMM (n=4) and BMN (n=8) were included in the study. Specimens were obtained during surgery from the center of the tumors (lesional). An exploratory microarray analysis was performed by miRNA expression profiling based on miRBase V.16. Additionally, the expression levels of selected miRNA candidates were confirmed by TaqMan real-time quantitative polymerase chain reaction (RT-PCR). New miRNA candidates previously not described to be associated with CMM were found to be potentially dysregulated in CMM.

overall_design: Nine patients with PCMM (PCMM1-PCMM9), four patients with CMMM (CMMM1-CMMM4) and eight patients with BMN (BMN1-BMN8) were enrolled in the present study. All cutaneous specimens were harvested in the operating room, immediately stored in RNAlater (Quiagen, Hilden, Germany) and kept at - 80 °C until RNA isolation. Total RNA including miRNAs was isolated using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA concentration and purity was determined by NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). RNA integrity control (RIN) was determined by means of capillary electrophoresis with the 2100 Bioanalyzer and the RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA). To be further considered for Microarray analysis a RIN ≥ 7.0 indicating medium to good RNA quality was defined as inclusion criteria.  For assessment of labeling and hybridization efficiencies total RNA samples were spiked with in-vitro synthesized oligonucleotides by using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). A total of 100 ng total RNA per sample were introduced into a labeling reaction. The  spiked  total  RNA  was  treated  with  alkaline  calf  intestine  phosphatase  (CIP).  The dephosphorylated RNA was labeled with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions using T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (pCp). The Cyanine-3-labeled miRNA samples were prepared for One-Color based hybridization with Complete miRNA Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions. Labeled miRNA samples  were  hybridized  at  55°C  for  20  hrs  on  separate  Human  miRNA  Microarrays Release 16.0 (8x60K format, (Agilent Technologies, Santa Clara, USA). Afterwards, microarrays  were  washed  with  increasing  stringency  using  Gene  Expression Wash Buffers  (Agilent Technologies, Santa Clara, USA) followed by drying with acetonitrile  (Sigma-Aldich, St.Louis, USA). Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). All the steps described were carried out according to the manufacturer´s instructions.

first: Marina

last: Skrygan

first: Daniel

first: Dimitrios

last: Georgas

first: Thilo

last: Gambichler

first: Stephan

last: Hahn

first: Peter

last: Altmeyer

first: Falk

middle: G

last: Bechara


status: Public on Nov 19 2012

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: In plants, basic helix-loop-helix (bHLH) transcription factors play important roles in the control of cell elongation. Two bHLH proteins, PACLOBTRAZOL RESISTANCE1 (PRE1) and Arabidopsis ILI1 binding bHLH1 (IBH1), antagonistically regulate cell elongation in response to brassinosteroid and gibberellin signaling, but the detailed molecular mechanisms by which these factors regulate cell elongation remain unclear. Here, we identify the bHLH transcriptional activators for cell elongation (ACEs) and demonstrate that PRE1, IBH1, and the ACEs constitute a triantagonistic bHLH system that competitively regulates cell elongation. In this system, the ACE bHLH transcription factors directly activate the expression of enzyme genes for cell elongation by interacting with their promoter regions. IBH1 negatively regulates cell elongation by interacting with the ACEs and thus interfering with their DNA binding. PRE1 interacts with IBH1 and counteracts the ability of IBH1 to affect ACEs. Therefore, PRE1 restores the transcriptional activity of ACEs, resulting in induction of cell elongation. The balance of triantagonistic bHLH proteins, ACEs, IBH1, and PRE1, might be important for determination of the size of plant cells. The expression of IBH1 and PRE1 is regulated by brassinosteroid, gibberellins, and developmental phase dependent factors, indicating that two phytohormones and phase-dependent signals are integrated by this triantagonistic bHLH system.

overall_design: Two-condition experiment, 35S:AtIBH1-SRDX Arabidopsis vs. wild type. Biological replicates: 3 for both.

last: Ikeda

first: N

last: Ohme-Takagi


title: Cyanothece 51142 grown under high CO2 conditions: 0.03% CO2 vs. 8% CO2

status: Public on Oct 30 2012

city: St Louis

first: Thanura

last: Elvitigala

state: MO

address: 1 Brookings Drive, Campus Box 1137

institute: Washington University

summary: Cyanobacteria are oxygenic photoautotrophs notable for their ability to utilize atmospheric CO2 as the major source of carbon. The prospect of using cyanobacteria in converting solar energy and high concentrations of CO2 (e.g. flue gas from coal power plants) efficiently into biomass and renewable energy sources is of interest to many research fields. In order to guide further advances in this area, a better understanding about the metabolic changes that occur under conditions of high CO2 is important. The objective of this study is to utilize genome-wide microarray expression profiling in the unicellular diazotrophic cyanobacterium Cyanothece 51142 grown in 8% CO2-enriched air and to determined the impact of high CO2 on cyanobacterial cell physiology and growth.

overall_design:
Study of metabolic and cellular adaptations to high CO2 conditions in the unicellular diazotrophic cyanobacterium Cyanothece 51142.
Two-condition experiment: 0.03% CO2 vs. 8% CO2. Biological replicates: 2; technical replicates: 3; Spots/ORF: 3 per Chip.
Samples were collected at 7 time points over a period of two days, namely, Day1_30minLight (30min), Day1_2hrsLight (2hr), Day1_6hrsLight (6hr), Day1_1hrsDark (13hr), Day1-6hrsDark (18hr), Day2_6hrsLight (30hr) and Day2_6hrsDark (42hr).

first: Jana

last: Stockel

first: Himadri

last: Pakrasi


title: Expression analysis of Salmonella typhimurium LT2 TA100 upon exposure to C60

status: Public on Sep 01 2012

city: Vicksburg

first: Dawn

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

summary:
Investigation of gene expression level changes in Salmonella typhimurium LT2 TA100 upon exposure to C60, compared to unexposed controls.  The mutations engineered into this strain make it susceptile to mutagenic compounds.
The Salmonella typhimurium TA100 strain used in this study is further described in Pedersen P, Thomsen E, Stern RM. 1983. Detection by Replica Plating of False Revertant Colonies Induced in the Salmonella Mammalian Microsome Assay by Hexavalent Chromium. Environmental health perspectives 51: 227-230.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: A 4 x 72K array study using total RNA recovered from triplicate cultures of Salmonella typhimurium LT2 TA100 exposed to C60 and triplicate cultures of controls that were not exposed to C60.  Each 72K array measures the expression level of 4,504 genes from Salmonella typhimurium LT2 with seven 45 to 60-mer probe pairs per gene.

first: Karl

last: Indest


title: Genome-wide copy number variant analysis in inbred lines of chickens with different susceptibility to Marek’s disease

city: College Park

first: Juan

last: Luo

address: RM1122, BLDG142, Animal & Avian Sciences

department: Animal & Avian Sciences

institute: University of Maryland

summary:
Marek’s disease virus (MDV) is an oncovirus causing tumor disease known as Marek’s disease (MD) in chicken. Breeding of chickens genetically resistant to MD is considered a vital augment to better control MD. To find the mechanism underlying the genetic resistance to MD, a genomic structural variation, copy number variation (CNV), was examined in inbred MD-resistant and -susceptible chicken lines by using the comparative genomic hybridization (CGH) technique. A total of 45 copy number variation regions (CNVRs) were found spanning across 3,297,038 bp in length of the chicken genome in 4 lines of chickens. Ten CNVRs were selectively confirmed with quantitative real-time PCR. The comparison between the resistant and susceptible chicken lines revealed 28 differentially presented CNVRs, which are functionally involved in immune response, cell proliferation in midbrain, G-protein coupled receptor signaling pathway, and protein-glutamine gamma-glutamyltransferase activity. Two CNVRs that are related with MD-resistance and –susceptibility were also found transmitted to descendent recombinant congenic lines that differ in susceptibility to MD. A positive correlation was identified between the CNVRs and gene expression, indicating the importance of gene expression dosage in disease resistance. We also found the overlapping between the CNVR region and the Marek’s disease trait related quantitative trait loci (QTLs). In conclusion, our data provided additional information elucidating one of possible mechanisms underlying of genetic resistance to MD. The findings may eventually lead to better strategies for genetic improvement of resistance to MD in poultry.
L63: highly resistant to MD; L72: highly susceptible to MD; RCS-L: moderate resistant to MD; RCS-M: moderate susceptible to MD

overall_design: Red blood cell DNAs were isolated from L63, L72, RCS-L and RCS-M and then labeled with Cy3. DNA from Red Junglefowl was labeled with Cy5 as reference and mixed with Cy3 labeled DNA, then hybridized to the 385K chicken tiling array. The hybridization, normalization and segmentation analysis were performed by NimbleGen Systems Inc. (Madison, USA). A detailed description of their technical specifics can be found on http://www.nimblegen.com/products/lit/lit.html. Briefly, the segments with five or more probes having a mean log2 ratio greater than ±0.5 (0.5_5) were chosen as candidate CNVs.

first: Ying

last: Yu

first: Shuang

last: Chang

first: Huanmin

last: Zhang

first: Jiuzhou

last: Song


title: Transcriptomic analysis of the voz1 voz2 double mutant

city: Tsukuba

summary: Plants adapt to abiotic and biotic stresses by activating abscisic acid-mediated (ABA) abiotic stress-responsive and salicylic acid-(SA) or jasmonic acid-mediated (JA) biotic stress-responsive pathways, respectively. Although the abiotic stress-responsive pathway interacts antagonistically with the biotic stress-responsive pathways, the mechanisms that regulate these pathways remain largely unknown. In this study, we provide insight into the function of vascular plant one-zinc-finger proteins (VOZs) that modulate various stress responses in Arabidopsis. The expression of many stress-responsive genes was changed in the voz1voz2 double mutant under normal growth conditions. Consistent with altered stress-responsive gene expression, freezing- and drought-stress tolerances were increased in the voz1voz2 double mutant. In contrast, resistance to a fungal pathogen, Colletotrichum higginsianum, and to a bacterial pathogen, Pseudomonas syringae, was severely impaired. Thus, impairing VOZ function simultaneously conferred increased abiotic tolerance and biotic stress susceptibility. In a chilling stress condition, both the VOZ1 and VOZ2 mRNA expression levels and the VOZ2 protein level gradually decreased. VOZ2 degradation during cold exposure was completely inhibited by the addition of the 26S proteasome inhibitor, MG132, a finding that suggested that VOZ2 degradation is dependent on the ubiquitin/26S proteasome system. In voz1voz2, ABA-inducible transcription factor CBF4 expression was enhanced significantly even under normal growth conditions, despite an unchanged endogenous ABA content. A finding that suggested that VOZs negatively affect CBF4 expression in an ABA-independent manner. These results suggest that VOZs function as both negative and positive regulators of the abiotic and biotic stress-responsive pathways, and control Arabidopsis adaptation to various stress conditions.

overall_design: voz1 voz2 double mutant and wild-type plants were grown on MS agar medium, and the transcriptomes of 14 day whole seedlings were compared. 4 replicates per genotype.

first: Yusuke

last: Nakai

first: Yoichi

last: Nakahira

first: Yuko

last: Takiguchi

first: Masa

middle: H

last: Sato


title: Microarray analysis of microRNA expression in cutaneous squamous cell carcinoma

status: Public on Oct 08 2012

first: Michael

last: Sand

summary: MicroRNAs (miRNAs) are a novel class of short RNAs which have shown to be dysregulated in a variety of cancers including squamous cell carcinoma (SCC) of the head&neck. Microarray based miRNA expression profiles of cutaneous SCC (cSCC) however have not been investigated so far. Seven patients with cutaneous SCC were enrolled in the study. Tumor biopsies (n=7) were taken from the center of the tumor. Adjacent healthy skin (n=7) was biopsied as a control (intraindividual control). miRNA expression profiles of all specimen were detected by mircroarray miRNA expression profiling based on miRBAse 16 and compared.

overall_design: In 7 patients biopsy specimens of cutaneous SCC and control specimens from an adjacent healthy skin site near the tumor border (intraindividual control) were obtained during surgical removal of the tumor. Specimes were immediately stored in RNAlater (Qiagen, HIlden, Germany) at -80 °C. Total RNA including miRNAs were isolated with miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s protocol. For RNA quality control purposes we determined RNA concentration, purity and RNA integrity number (RIN) with Agilent 2100 Bioanalyzer, RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA) and the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). All of the following steps described were carried out according to the manufacturer´s protocol. In order to enable assessment of labeling and hybridization efficiencies total RNA samples were spiked with MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). After treatment with calf intestine phosphatase (CIP), a labeling reaction was started with 100 ng total-RNA per sample. For labeling dephosphorylated RNA, T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (miRNA Complete Labeling and Hyb Kit, Agilent Technologies, Santa Clara, USA) was used. The Cyanine-3-labeled miRNA samples were then prepared for One-Color based hybridization (Complete miRNA Labeling and Hyb Kit, Agilent Technologies, Santa Clara, USA). Hybridization was performed at 55°C for 20 hrs with Human miRNA Microarrays Release 16.0, 8x60K format (Agilent Technologies, Santa Clara, USA). Microarray slides were washed (Gene Expression Wash Buffers, Agilent Technologies, Santa Clara) and dried with acetonitrile (Sigma-Aldich, St.Louis, USA). Fluorescent signal intensities were detected with Agilent DNA Microarray Scanner (Agilent Technologies, Santa Clara, USA) and Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA). Extraction of data was done by using the Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA).

first: Marina

last: Skrygan

first: Dimitrios

last: Georgas

first: Daniel

first: Stephan

last: Hahn

first: Thilo

last: Gambichler

first: Peter

last: Altmeyer

first: Falk

last: Bechara


title: Glucose-depletion time-course experiment in Saccharomyces cerevisiae wild-type cells.

status: Public on Jun 18 2012

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

summary: To investigate the glucose regulatory system in Saccharomyces cerevisiae, we conducted a time-course in which glucose-depleted wildtype (WT) cells were inoculated into fresh media (SC, 2% glucose). Their subsequent transcriptional output was monitored over a period of five hours by DNA microarrays: samples for gene expression profiling were taken immediately after, as well as 3, 7.5, 15, 30, 60, 110, 150, and 300 minutes after inoculation into fresh medium. Transcripts upregulated are involved in translational processes such as the GO biological processes “ribosome biogenesis” and “ribosome localization”. Transcripts downregulated are enriched for the GO biological processes “cellular respiration” and various metabolism related processes. The time-course was used to verify the physiological relevance of gene expression profiles determined for individual deletions of glucose regulatory system components. Importantly, transcripts up- or downregulated in WT cells upon the addition of glucose are similarly up- or downregulated in deletion mutants that each lack a component of the glucose regulatory system.

overall_design: RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used for each separate hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Two overnight WT cultures were used to inoculate 50 ml cultures at an OD600 of 0.15. These were depleted of glucose by growing for 24 hours and were used the next day to inoculate 500 ml cultures in fresh medium to an OD600 of 0.15. Samples for expression profiling were taken immediately after, as well as 3, 7.5, 15, 30, 60, 110, 150, and 300 minutes after inoculation into fresh medium.

first: Eva

last: Apweiler

first: Katrin

last: Sameith

first: Thanasis

last: Margaritis

first: Nathalie

last: Brabers

first: Loes

last: van de Pasch

first: Linda

last: Bakker

first: Dik

last: van Leenen

first: Frank

last: Holstege