title: Gene expression profiles of amiodarone, valproic acid, and tetracycline induced steatosis in C57BL/6 mice

status: Public on Feb 25 2014

city: Bilthoven

first: Alexa

last: Vitins

address: P.O. Box 1

institute: RIVM

summary: Toxicogenomics (tgx) is used as a tool to identify mechanisms and markers of steatosis in C57BL/6 mice treated by oral gavage using amiodarone (AMD), valproic acid (VPA), and tetracycline (TET). Critical doses for tgx analysis were derived from a 25 day dose range finding study.  For tgx analysis, livers of mice were collected after 1, 4, and 11 days of repeated treatment with 6.7, 20, and 60 mg/kg bw for AMD; 125, 250, and 500 mg/kg bw for VPA; and 14.8, 44, and 133 mg/kg bw for TET.

overall_design: For each treatment (compound and vehicle) in the toxicogenomics study samples were as follows: four at the high dose 1 and 4 day time point, and five at the low, medium, and high dose at 11 days. One set of vehicle controls were used for AMD and VPA (PBS), and TET had its own vehicle controls (milli-q water with ascorbic acid). The total number of samples was 95.

first: Anne

middle: S

last: Kienhuis

first: Ewoud

middle: N

last: Speksnijder

first: Marianne

last: Roodbergen

first: Leo

middle: T

last: van der Ven


title: Impact of maternal diet supplemented with selenium (Se) and vitamin B6 during pregnancy on gene expression of porcine expanded blastocysts (EB)

status: Public on Sep 28 2013

city: Edmonton

first: Stephen

last: Tsoi

address: 4-32G Agriculture/Forestry Centre

department: AFNS

country: Canada

institute: University of Alberta

summary: Transcriptional profiling of porcine expanded blastocysts comparing control (EB obtained from 4 sows treated with basal diet) with either inorganic Se + B6 (EB obtained from 4 sows treated with basal diet plus inorganic Se and B6) or organic Se + B6 (EB obtained from 3 sows treated with basal diet plus organic Se and B6).

overall_design: Three-condition experiment, EB without and with maternal diet supplemented B6 plus either inorganic Se or organic Se. Four biological replicates for inorganic Se and three biological replicates and one technical replicate for organic Se. Pooled of four biological replicates for control group.

middle: C

first: Danyel

middle: B

last: Dalto

first: Michael

middle: K

last: Dyck

first: Matte

middle: J

last: Jacques


title: Gene expression profiles of individual blastomeres of early Ciona embryos

status: Public on Oct 29 2013

city: Kyoto

first: Yutaka

last: Satou

state: Kyoto

address: Kitashirakawa Oiwake-tyo, Sakyo-ku

department: Department of zoology, Graduate School of Science

country: Japan

institute: Kyoto University

summary: We examined gene expression profiles of individual blastomeres of early Ciona embryos using microarrays.

overall_design: We examined gene expression profiles of individual blastomeres of the 8-cell, 16-cell and 32-cell embryos by dissecting with a fine glass needle. We also examined gene expression profiles of unfertilized eggs and embryos from the 1- to 32-cell stages.

first: Terumi

last: Matsuoka


title: Gene Expression on Profiles of Early Ciona intestinalis Embryos

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

overall_design: Refer to individual Series


title: Gene expression regulation by angiotensin II in late gestation fetal sheep

status: Public on Aug 09 2013

city: Iowa City

first: Timothy

middle: Marvin

last: Bahr

state: IA

department: Pediatrics

country: USA

institute: University of Iowa

summary: We undertook a transcriptome-wide discovery approach to provide information on the involved gene regulatory responses to change in fetal cardiac mass in response to chronic infusion of angiotensin II or losartan.

overall_design: One of each of 8 twin fetus pairs was infused with either angiotensin II or losartan daily for five days in utero.  A portion of the left ventricular free wall of treatment and control fetuses was excised, homogenized in a reagent, and then total RNA was then isolated and assayed on the agilent microarray

middle: M

first: Jeffrey

middle: L

last: Segar

first: Andrew

middle: W

last: Norris


title: Transcriptomics of mycobacterial microaggregates

status: Public on Feb 15 2014

city: Muttenz

first: Laura

last: Sutter-Dick

state: Basel-Land

address: Hofackerstrasse 30

department: Institute of Chemistry and Bioanalytics

country: Switzerland

institute: FHNW

summary: During initial colonization of the airways, MAH form microaggregates composed of 3-20 bacteria on human respiratory epithelial cells, which provides an environment for phenotypic changes leading to efficient mucosal invasion.  DNA microarray was employed to identify genes associated with the microaggregate phenotype.

overall_design: Bacteria were incubated with Hep-2 epithelial cells for 24 hrs to form microaggregates or incubated in tissue culture media alone as the control (planktonic bacteria). Bacterial RNA was isolated, purified using MicrobeEnrich, and amplified using Abmbion's Bacterial MessageAMP kit. RNA was hybridized to Affymetrix custom made mycobacterium avium 104 microarrays

first: Lmar

last: Babrak

first: Luiz

last: Bermudez


title: The polycomb repressive complex PRC2 regulates proliferation and neurogenesis in the Xenopus retina, and is governed by Wnt/beta-catenin signaling

status: Public on May 30 2013

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

summary: The histone methyltransferase complex PRC2 controls key steps in developmental transitions and cell fate choices. However, its roles in vertebrate eye development remain unknown. Here we report that in Xenopus PRC2 regulates the progression of retinal progenitors from proliferation to differentiation. We show that the PRC2 core components are enriched in retinal progenitors and downregulated with differentiation. Knockdown of the PRC2 core component Ezh2 leads to reduced retinal progenitor proliferation in part due to upregulation of the cdk inhibitor p15Ink4b. In addition, while PRC2 knockdown does not alter eye patterning, retinal progenitor gene expression or expression of the neural competence factor Sox2, it does cause suppression of proneural bHLH gene expression, indicating that PRC2 is critical for the initiation of neural differentiation in the retina. Consistent with this, knocking down or blocking PRC2 function constrains the generation of most retinal neural cell types and promotes a Mueller glial cell fate decision. We also show that Wnt/β-catenin signaling acting through the receptor Frizzled 5, but independent of Sox2, regulates expression of key PRC2 subunits in the developing retina. This is consistent with a role for this pathway in coordinating proliferation and the transition to neurogenesis in the Xenopus retina. Our data establishes PRC2 as a regulator of proliferation and differentiation during eye development.

overall_design: Xenopus embryos were injected at the 8-cell stage with 5ng Ezh2 ATG MO or 5ng control MO (scrambled sequence of Ezh2 ATG MO) together with 400 pg mRNA for GFP as a lineage tracer. At stage 27, GFP-positive eyes were isolated by microdissection. Pools of 20-25 eyes were used to prepare total RNA for each sample on the microarray. 4 control and 4 Ezh2 ATG MO samples were hybridized to Agilent 1-color microarrays.

first: Issam

last: Aldiri

first: Kathryn

last: Moore

first: David

middle: A

last: Hutcheson

first: Jianming

last: Zhang

first: Monica

last: Vetter


title: CINCINNATA Controls Surface Curvature of Antirrhinum Leaf by Coordinated and Direct Activation of Cytokinin and Auxin Signaling

status: Public on May 01 2013

city: Bangalore

first: Mainak

last: Das Gupta

state: Karnataka

address: C.V. Raman Avenue

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary: Mutations in the CINCINNATA gene in Antirrhinum and its orthologues in Arabidopsis cause negative surface curvature in leaves due to excess marginal growth. CIN-like genes code for TCP transcription factors and are expressed in a broad zone of a growing leaf somewhat distal to the proliferation zone. Although a few TCP targets are known, the role of CIN-like TCP genes in regulating leaf curvature has remained unclear. We have compared the global transcription profile of wild type and cincinnata mutant to identify its targets. By combining DNA-protein interaction, chromatin immunoprecipitation and RNA in situ hybridization, we show that CIN maintains surface flatness by regulating signaling or level of major plant hormones. CIN promotes cytokinin signaling directly and GA level indirectly, in accelerating maturity in leaf cells along the tip-to-base direction. In addition, CIN suppresses auxin signaling more at the margin than centre by establishing a margin-to-medial expression gradient of a homologue of the auxin suppressor IAA3. Our results uncover an underlying mechanism in a developing leaf that controls maturity of leaf and its surface curvature. Considering the conservation of CIN-like genes and their function in leaf morphogenesis in multiple plant species, it is likely that such mechanism is evolutionarily conserved.

sample_organism:
Arabidopsis thaliana
Antirrhinum majus

platform_organism:
Arabidopsis thaliana
Antirrhinum majus

overall_design: Two color Experiment, Organism: Arabidopsis thaliana and Antirrhinum. Arrays Used: 1. Agilent Arabidopsis  thaliana Gene expression Microarray 22k (AMADID: 013324) 2. Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226) 3. Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) designed by Genotypic Technology Private Limited.

middle: D

last: Gupta

first: Pooja

last: Aggarwal

first: Utpal

last: Nath


title: Evaluating the endocrine disrupting impacts of paper mill exposure on the Eastern Mosquitofish (Gambusia holbrooki) by gene expression analysis

status: Public on Nov 01 2013

city: Gainesville

first: Erica

middle: Karin

last: Brockmeier

state: FL

address: 2187 Mowry Road

institute: University of Florida

summary: Masculinized female Eastern Mosquitofish (Gambusia holbrooki) have resided downstream of paper mills in Florida since the 1980's. The potential impacts of this effluent on the mosquitofish endocrine system are unknown. The objective of this study was to evaluate gene expression patterns of endocrine system genes and global gene expression patterns in female G. holbrooki from a paper mill-impacted site. Masculinized female G. holbrooki were collected from a paper mill-impacted site (Fenholloway River) and from a reference site (Econfina River) and microarray analysis in livers was conducted. Hepatic microarray analysis revealed an increase in the expression of metabolic genes at the Fenholloway, with similarities in individual genes and biological processes compared to G. holbrooki exposed to androgens. These data indicate G. holbrooki from the Fenholloway may be impacted by a mixture of endocrine-active chemicals, including androgens.

overall_design: During the summer of 2012, G. holbrooki were captured from one site downstream of the Buckeye Pulp and Paper Mill (Taylor County, Perry, FL, USA) on the Fenholloway River (GPS coordinates: N 30 058.341’, W 83 588.569’) and one site in the Econfina conservation area (GPS coordinates: N 30 08.549', W 83 51.962') . Only sexually mature G. holbrooki (females > 15cm standard length and with the presence of the gravid spot near the vent) were collected. A 1/8 mesh seine was used for sample collection. Female G. holbrooki were transferred to 5 gallon aerated buckets filled with site water and were processed at the site immediately after collection. Fish were anesthetized using Tricaine-S (Western Chemical, Ferndale, USA) and sacrificed via spinal transection. Oocyte development was assessed upon dissection and livers were removed and stored in RNAlater (Qiagen, Hilden, Germany) overnight at 4 C before storage at -80 C. RNA was isolated from the livers using TRIzol (Invitrogen, Grand Island, USA), hydrated using RNAsecure (Ambion, Grand Island, USA), and DNase treated using the Turbo DNA-free kit (Ambion, Grand Island, USA). Four oocyte-development stage-matched RNA samples per treatment were evaluated for RNA integrity using the 2100 BioAnalyzer (Agilent, Santa Clara, USA). The range of RIN values was 7.8-8.9.

first: Nancy

last: Denslow


title: Aspergillus nidulans : Control (Wt) vs. ΔcnaA or alcApkcAΔcnaA

status: Public on Jul 04 2013

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

summary: Transcriptional profiling of A. nidulans comparing the mutant strain alcApkcA ΔcnaA and ΔcnaA grown on alcA inducing conditions. The main objective was to identifiy genes related to ΔcnaA phenotype supression by pkcA overexpression. The experiment was further validated by real-time PCR.

overall_design: Two-condition experiment : A. nidulans strains grown during 24 and 48 h at 37oC in glycerol 2% threonine 100mM.

first: A

last: Colabardini

first: G

middle: H

last: Goldman


title: Hepatic transcriptome profiles differ among maturing beef heifers supplemented with different forms of dietary selenium

status: Public on Jun 01 2013

city: Lexington

first: Jennifer

middle: Denyse

last: Patterson

state: KY

address: 215 WP Garrigus

department: Animal and Food Sciences

institute: University of Kentucky

summary: Little is known regarding the relationship between Selenium (Se) concentrations in the liver and liver gene expression. Because most cow-calf operations in Se-poor soils provide enough Se in mineral mixes to avoid deficiency, the aim of this study was to determine the effects of 4 Se form supplementation strategies (none or inorganic, organic, or 1:1 inorganic:organic mix) on liver gene expression profiles using a Se-adequate model. Microarray analysis was conducted using the custom WT Btau 4.0 Array (version 1; GeneChip, Affymetrix, Inc., Santa Clara, CA, USA) to determine if dietary Se supplementation form differentially affects the hepatic gene expression profiles of maturing beef heifers.

overall_design: Sodium selenite was used as the source of inorganic Se and Se-enriched yeast was the source of organic selenium. Thirty-six Angus heifers (BW 400 ± 9.0 kg) were ranked on the Se concentration of their biopsied (day -14) liver sample and randomly assigned to one of four dietary Se treatments: Control (Ctrl) group received no exogenous dietary Se supplementation; inorganic (ISe) treatment group received daily dietary Se supplementation at 3 mg/ animal of the ISe form; organic (OSe) treatment group received daily dietary Se supplementation of 3 mg/ animal of OSe form; and the mix (1:1 ISe:OSe) received daily dietary Se supplementation of 3 mg/ animal of 50:50 mix of ISe and OSe forms. RNA was extracted from biopsied liver samples taken 168 days after initiation of Se supplementation and microarray analyses were conducted.

first: Jamie

last: Matthews

first: Walter

middle: R

last: Burris

first: Jim

last: Boling

first: Zhi


title: DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA

status: Public on May 22 2012

city: St. John's

first: Ryan

middle: G

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

department: Biology

institute: Memorial University

type:
Expression profiling by array
Genome variation profiling by array

summary: Rhodobacter capsulatus produces a gene transfer agent (GTA) called RcGTA. RcGTA is a phage-like particle that packages R. capsulatus DNA and transfers it to other R. capsulatus cells. Low-resolution techniques suggested RcGTA packages random DNA. Analysis of the RcGTA terminase sequence revealed a distant relationship to the phage T4 terminase protein, which can also perform sequence-independent packaging. We quantified the relative frequency of packaging for each gene in the genome by hybridization of DNA from RcGTA particles to an R. capsulatus microarray. All genes were found within the RcGTA particles, and random packaging was observed at a genome-wide scale. However, the genes encoding the RcGTA particle were under-packaged compared to other regions. Single-cell expression analysis demonstrated that RcGTA gene expression is not uniform within a culture. We propose a mechanism by which high levels of RcGTA gene transcription in the most active RcGTA producing cells hinders access of the packaging machinery to these genes, which causes a reduction in their packaging frequency. This sub-population gene expression phenomenon likely explains the lack of observed cell lysis in RcGTA producing cultures.

overall_design: DNA extracted from within RcGTA particles produced by DE442, an RcGTA overproducer, was hybridized to an Affymetrix genechip custom array in order to quantify the relative frequency with which any given gene was packaged within the particles. These data were MAS5 normalized. An underlying packaging bias was suspected to be transcription related, so these frequencies were compared to expression levels within the population, as determined by hybridization of late-stationary RNA samples of DE442 and of the wildtype (SB1003) to the same custom array. These data were RMA normalized.

first: Alexander

middle: P

last: Hynes

middle: E

last: Watton

first: Colleen

last: Buckley

first: Andrew

middle: S

last: Lang


title: Effects of ploidy and sex-locus genotype on gene expression patterns in the fire ant Solenopsis invicta [pupa]

status: Public on Dec 06 2012

city: Lausanne

first: Mingkwan

last: Nipitwattanaphon

address: Biophore Building, UNIL-Sorge

department: Department of Ecology and Evolution

institute: University of Lausanne

summary:
In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion.
Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene

overall_design:
Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study).
Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.

first: John

last: Wang

first: Kenneth

last: Ross

first: Oksana

last: Riba-Grognuz

first: Yannick

last: Wurm

first: Chitsanu

last: Khurewathanakul

first: Laurent

last: Keller


title: Effects of ploidy and sex-locus genotype on gene expression patterns in the fire ant Solenopsis invicta [1d]


title: C.elegans exposed to P. aeurigonsa: Colonized vs Non colonized animals

status: Public on Jul 20 2012

city: Berkeley

first: Michael

last: Shapira

state: CA

address: 3060 Valley Life Sciences Bldg room 5163

department: Integrative Biology

institute: UC Berkeley

summary:
Transcriptional profiling of adult C.elegans exposed to E.coli or to GFP-expressing P. aeruginosa (strain PA14).
For P. aeruginosa exposure, worms were separated into 2 groups - fully colonized (green) or non-colonized (dark).

overall_design:
Three conditions (E.coli, P. aeurginosa colonized, and P. aeurginosa non-colonized).
2-color arrrays, each sample co-hybridized with the same reference RNA sample from mixed stage C.elegans cultures
Each condition includes 3 biological replicates - 2 using the wormsorter (WS) to separate colonized from non-colonized and one hand picked (HP) under a fluorescent stereoscope

first: Kwame

last: Twumasi-Boateng


title: Gene expression profiles for onset and progression of Cyclosporin A-induced cholestasis in C57BL/6 mice

status: Public on Jul 11 2013

first: Anne

middle: Susan

last: Kienhuis

address: A. van Leeuwenhoeklaan 9

country: Netherlands

summary: Mechanism-based toxicogenomics (tgx) is used as a tool to identify markers reflective of the onset and progression of cholestasis in C57BL/6 mice using Cyclosporin A (CsA) as a model compound. Critical doses for tgx analysis were derived from a dose range finding study in which increase of serum cholesterol, total bile acids, and total bilirubin as well as induction of hepatocyte vacuolization 25 days upon repeated CsA administration through oral gavage were considered as critical effects. For tgx analysis to find early markers, livers of mice repeatedly treated with 3 mg/kg BW, 8.9 mg/kg BW, and 26.7 mg/kg BW for one, four, and eleven days were collected.

overall_design: 60 samples are analyzed; per treatment duration (1, 4, 11 days), time-matched vehicle (olive oil) controls and three dose groups (3, 8.9, 26.7 mg/kg BW) were included; each group consisted of 5 replicates; 3 arrays were excluded, 2 because of quality control restrictions, 1 because of outlier properties.  2 that failed QC are omitted.  Final data consists of 58 CEL files.

first: Jeroen

last: Pennings

first: Tessa

last: Pronk

first: Ewoud

middle: N

last: Speksnijder

first: Marianne

last: Roodbergen

first: Leo

middle: T

last: van der Ven


title: Streptococcus mutans UA159 vs. fabT mutant strain, pH5 vs. pH7

status: Public on Jun 01 2012

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

summary: Transcriptional analysis of the regulator FabT in S. mutans

overall_design: RNA was extracted from 4 replicate samples of S. mutans UA159 and MU1591 (∆fabT) grown in continuous culture to steady-state pH values of 7 and 5.  RNA was labeled with Cy3.  For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.

first: Cory

middle: J

last: Hubbard

first: Robert

last: Quivey


title: Rice stem at early stage growth: Control vs.Chromosome segment substitution lines (SLs) from a cross the Koshihikari (japonica) and Habataki (indica)

status: Public on Apr 01 2012

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

institute: Nagoya University

summary: By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, qEPD1 and qEPD2, responsible for modulating plant height and/or leaf sheath length. To narrow down the number of candidate genes of each QTL, we conducted transcriptional profiling using RNAs isolated from the vegetative stem of Koshihikari and its two substituted lines (SL) with the Habataki qEPD1 or qEPD2 allele.

overall_design: Expression profiling with the rice 44K-Agilent microarray (Agilent-028517) was conducted using RNAs extracted from the 30-day-old vegetative stem of the corresponding lines. Each dataset was obtained from three biological replicates.

first: Makoto

last: Matsuoka


title: Effects of ploidy and sex-locus genotype on gene expression patterns in the fire ant Solenopsis invicta

first: Mingkwan

last: Nipitwattanaphon


title: Effects of ploidy and sex-locus genotype on gene expression patterns in the fire ant Solenopsis invicta [11d]

first: John

last: Wang

first: Kenneth

last: Ross

first: Oksana

last: Riba-Grognuz

first: Yannick

last: Wurm


title: Soybean fast neutron genotyping: 700k Reverse genetics

status: Public on Aug 03 2011

city: Saint Paul

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

type: Genome variation profiling by genome tiling array

summary: CGH was used to compare induced structural variation among soybean fast neutron lines, developed in background M92-220.

overall_design: 11 different soybean fast neutron lines were hybridized against the parental reference genotype M92-220. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.

first: William

last: Haun


title: Gene expression analysis of Merkel Cell Carcinoma

status: Public on Dec 15 2010

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

summary: Merkel cell carcinoma (MCC) is a polyomavirus-associated skin cancer that is frequently lethal and lacks established prognostic biomarkers. The purpose of this study was to use gene expression analysis to identify biomarkers that may improve prognostic accuracy and provide insight into MCC biology.

overall_design: We profiled 35 tumors from 34 patients. Tumors were macrodissected from surrounding stroma. RNA isolation was performed with RNeasy or Allprep Mini kits (Qiagen, Alameda, CA), and RNA quality assessed by Agilent Bioanalyzer analysis. RNAs were profiled on the Human Rosetta Custom Affymetrix 2.0 chip.

first: Kelly

last: Paulson

first: Jayasri

last: Iyer

first: Janell

last: Schelter

first: James

last: Hardwick

first: Paul

last: Nghiem


title: Systems analysis identifies an essential role for SHARPIN in macrophage TLR2 responses (Agilent)

status: Public on Aug 31 2011

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

summary: Our systems analysis reported here demonstrates that TLR-responses in macrophages are markedly impaired by SHARPIN deficiency, and that SHARPIN controls expression of a subset of TLR2-induced, NF-kB and AP-1 dependent genes that overlaps with those affected by the hypomorphic panr2 mutation in NEMO.

overall_design:
46 total RNA samples from murine bone marrow derived macrophages were analyzed (32 by Agilent array, 14 by Affymetrix Exon array)

On Agilent array, the responses of macrophages to 12hr stimulation with the TLR2 ligand PAM3CSK4 (300ng/mL) were analyzed in biological duplicates for five mutant mouse strains and respective controls: Sharpin(cpdm), Ikbkg(panr2), Atf3(KO), Il10(KO), and Nfkb1(KO).

first: Frank

last: Schmitz

first: Bruce

last: Beutler

first: Alan

last: Aderem


title: Systems analysis identifies an essential role for SHARPIN in macrophage TLR2 responses

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

overall_design: Refer to individual Series


title: The singing genome: Core and region enriched gene expression define behaviorally regulated gene networks

status: Public on Dec 13 2012

city: Durham

first: Andreas

middle: Robert

last: Pfenning

state: NC

address: Duke University Medical Center, Box 3209, Department of Neurobiology

department: Neurobiology

institute: Duke University

summary: Studies of transcriptional networks in multi-cellular organisms usually focus on isolated cells and typically assume that the discovered gene networks represent those present in connected cells within a complex organ like the brain. However, similar cell types connected in diverse anatomical networks could differentially influence transcriptional networks. Here, we used laser capture microdissection, expression arrays, genome mapping, and computational inference to explore behaviorally regulated gene networks in the brains of awake, behaving songbirds producing a skilled motor behavior, singing. We found that at baseline, in the absence of singing, a large proportion of genes (17%, >3000) are differentially expressed in the different brain regions of the neural circuit that controls singing. These genes predominantly code for cell communication and connectivity proteins, and non-coding RNAs. Remarkably, the act of singing was associated with differential regulation of ~10% of the coding and non-coding genome. However, less than 1% of genes were singing-regulated in most brain regions and these were largely immediate early genes (IEGs), which peaked early, including the inducible transcription factors EGR1 and FOS. The remaining vast majority of behaviorally regulated gene expression was specific to one or a subset of brain regions, which peaked later. Promoters of the baseline, common, and diverse singing regulated gene clusters were enriched for different combinations of post-translationally activated transcription factors, like CREB, SRF, MEF2, MZF, and the IEG transcription factors. The results suggest that diverse cell-to-cell interactions and differential combinatorial binding of a small group of transcription factors may influence regional diversity of gene networks in seemingly similar cell types. Thus, in highly integrated neural circuits of intact behaving animals, transcriptional network diversity appears to be the rule, rather than the exception.

overall_design: Gene expression in Area X, HVC, LMAN, and Ra was measured before singing (0) or after singing for 0.5, 1, 2, 3, 4, 5, 6, and 7hours.  Four-Six independent experiments were performed at each of the 9 timepoints.

first: Whitney

last: Osceola

first: Pfenning

last: Andreas

first: Howard

last: Jason

first: Blatti

last: Charles

first: Ward

last: James

first: Hartemink

last: Alexander

first: Sinha

last: Saurabh

first: Jarvis

last: Erich


title: Soybean fast neutron genotyping: 700k Forward genetics

status: Public on Aug 02 2011

first: Robert

last: Stupar

overall_design: 114 different soybean fast neutron lines were hybridized against the parental reference genotype M92-220. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.

first: Pudota

middle: B

last: Bhaskar

first: William

last: Haun

first: Jean-Michel

last: Michno


title: microRNA/UCR expression profiling of human Barrett's carcinogenesis

status: Public on Jan 30 2010

city: Padova

first: Matteo

last: Fassan

state: PD

address: via Gabelli 61

department: Department of Diagnostic Sciences & Special Therapies

country: Italy

institute: University of Padova

summary: To test the hypothesis that there are specific miRNA/UCR expression signature which characterizes Barrett's esophagus development and progression, we performed miRNA/UCR microarray analysis comparing normal esophageal squamous epithelium with all the phenotypic lesions seen in the Barrett's carcinogenic process

platform_organism:
Homo sapiens
Mus musculus

overall_design: miRNA/UCR microarray analysis was performed in a series of 14 normal esophageal squamous epithelium samples, 14 Barrett's mucosa samples, 7 low-grade intra-epithelial neoplasia samples, 5 high-grade intra-epithelial neoplasia samples and 11 Barrett's adenocarcinoma samples

first: Stefano

last: Volinia

first: Jeff

last: Palatini

first: Carlo

last: Croce

first: Raffaele

last: Baffa

first: Marco

last: Pizzi

first: Ermanno

last: Ancona

first: Massimo

last: Rugge

last: Galasso

first: Giovanni

last: Zaninotto


title: Targetted Microarray Testing for Intellectual Disability Provides Diagnoses and Identifies Novel Candidate Genes

status: Public on Jul 24 2012

city: vancouver

first: Farah

last: Zahir

state: BC

address: Box 153, 4500 Oak Street

institute: UBc

summary: We designed a microarray to test at exonic resolution for genomic imbalance for genes representative of all known chromosomal microdeletion/microduplication syndromes, all known causative genes for ID, all known genes encoding glutamate receptors and their known encoding proteins and all known genes encoding proteins with epigenetic regulatory function. We found 36 de novo copy number variants affecting 35 children in this study.

overall_design: 167 trios, each comprising an affected child and both its normal parents were analyzed by conducting two comparative hybridizations; child vs. mother and child vs. father, and only selecting a CNV if it appeared in both hybridizations, i.e., was de novo. De novo CNVs were independantly validated using quantitative PCR.

first: Tracy

last: Tucker

first: Malachi

last: Griffith

first: Allen

last: Delaney

first: David

last: Chai

first: Erica

last: Tsang

first: Emmanuelle

last: Lemyre

first: Sylvia

last: Dobrzeniecka

last: Marra

first: Patrice

last: Eydoux

first: Sylvie

last: Langlois

first: Fadi

middle: F

last: Hamdan

first: Jacques

middle: L

last: Michaud

first: Jan

last: Friedman


title: A genomic approach highlights common and diverse effects and determinants of susceptibility on the yeast Saccharomyces cerevisiae exposed to distinct antimicrobial peptides

status: Public on Nov 11 2010

city: PATERNA

first: MONICA

last: GANDIA

state: VALENCIA

address: AVDA. AGUSTIN ESCARDINO 7

department: CIENCIA DE LOS ALIMENTOS

country: Spain

institute: IATA

summary:
The mechanism of action of antimicrobial peptides (AMPs) was initially correlated with peptide membrane permeation properties. However, recent evidences indicate that action of a number of AMPs is more complex and involves specific interactions at cell envelopes or with intracellular targets. In this study, a genomic approach was undertaken on the model yeast Saccharomyces cerevisiae to characterize the antifungal effect of two unrelated AMPs.

Two differentiated peptides were used: the synthetic cell-penetrating PAF26 and the natural cytolytic melittin. Transcriptomic analyses demonstrated distinctive gene expression changes for each peptide. Quantitative RT-PCR confirmed differential expression of selected genes. Gene onthology (GO) annotation of differential gene lists showed that the unique significant terms shared by treatment with both peptides were related to the cell wall (CW). Assays with mutants lacking CW related genes, including those of MAPK signaling pathways, revealed genes having influence on sensitivity to peptides. Fluorescence microscopy and flow cytometry demonstrated PAF26 interaction with cells and internalization that correlated with cell killing in sensitive CW-defective mutants such as ∆ecm33 or ∆ssd1. GO annotation also showed differential responses between peptides, which included ribosomal biogenesis, ARG genes from the metabolism of amino groups (specifically induced by PAF26), or the reaction to unfolded protein stress. Susceptibility of deletion mutants confirmed the involvement of these processes. Specifically, mutants lacking ARG genes from the metabolism of arginine pathway were markedly more resistant to PAF26 and had a functional CW. In the deletant in the arginosuccinate synthetase (ARG1) gene, PAF26 interaction occurred normally, thus uncoupling peptide interaction from cell killing. The previously described involvement of the glycosphingolipid gene IPT1 was extended to the peptides studied here.

Reinforcement of CW is a general response common after exposure to distinct AMPs, and likely contributes to shield cells from peptide interaction. However, a weakened CW is not necessarily indicative of a higher sensitivity to AMPs. Additional processes modulate susceptibility to specific peptides, exemplified in the involvement of the metabolism of amino groups in the case of PAF26. The relevance of the response to unfolded protein stress or the sphingolipid biosynthesis, previously reported for other unrelated AMPs, was also independently confirmed.

overall_design: We carried out the characterization of the transcriptome of S. cerevisiae after exposure to PAF26 and melittin peptides. The global transcriptome response to peptides was undertaken by treating S. cerevisiae FY1679 cells in the logarithmic growth phase to sub-lethal concentrations (5 µM) of either PAF26 (PAF samples) or melittin (MEL samples) for 3 hours. Control treatment (CTR samples) consisted in cells exposed to buffer in the absence of peptide. Three biological replicates were conducted for each treatment. DNA macroarrays representing 6,020 yeast genes were hybridized with labelled cDNAs from cells.

first: Mónica

last: Gandía

first: Jose

last: Marcos


title: Transcriptome and proteome analyses of the CtrA regulon and growth-phase regulation in Rhodobacter capsulatus

status: Public on Apr 08 2010

first: Ryan

last: Mercer

summary: The samples in this series were used to analyze the transcriptome of the CtrA regulon using wild type (SB1003) and ctrA mutant (SBRM1) strains of Rhodobacter capsulatus. As well, the transcriptome of growth phase regulation in R. capsulatus SB1003 between log and stationary phases was determined.

overall_design: This study included wild type and mutant samples from both log and stationary growth phases. Three biological replicates of each sample were used, yielding a total sample size (including replicates) of 12. Results compared wild type and mutant cultures in both log and stationary phase, as well as comparison between log and stationary phase of wild type.

first: Stephen

last: Callister

first: Mary

last: Lipton

first: Ljiljana

last: Pasa-Tolic

first: Hynek

last: Strnad

first: Vaclav

last: Paces

first: J.

last: Beatty

first: Andrew

last: Lang


title: Genetic background effect on Scn5a mutant cardiac right ventricle gene expression

status: Public on Jan 12 2010

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: Conduction slowing of the electric impulse that drives the heartbeat may evoke lethal cardiac arrhythmias. Mutations in SCN5A, which encodes the pore-forming cardiac sodium channel alpha subunit, are associated with familial arrhythmia syndromes based on conduction slowing. However, disease severity among mutation carriers is highly variable. We hypothesized that genetic modifiers underlie the variability in conduction slowing and disease severity. With the aim of identifying such modifiers, we studied the Scn5a(1798insD/+) mutation in 2 distinct mouse strains, FVB/N and 129P2. In 129P2 mice, the mutation resulted in more severe conduction slowing particularly in the right ventricle (RV) compared to FVB/N. Pan-genomic mRNA expression profiling in the 2 mouse strains uncovered a drastic reduction in mRNA encoding the sodium channel auxiliary subunit beta4 (Scn4b) in 129P2 mice compared to FVB/N. This corresponded to low to undetectable beta4 protein levels in 129P2 ventricular tissue, whereas abundant beta4 protein was detected in FVB/N. Sodium current measurements in isolated myocytes from the 2 mouse strains indicated that sodium channel activation in myocytes from 129P2 mice occurred at more positive potentials compared to FVB/N. Using computer simulations, this difference in activation kinetics was predicted to explain the observed differences in conduction disease severity between the 2 strains. In conclusion, genetically determined differences in sodium current characteristics on the myocyte level modulate disease severity in cardiac sodium channelopathies. In particular, the sodium channel subunit beta4 (SCN4B) may constitute a potential genetic modifier of conduction and cardiac sodium channel disease.

overall_design:
For micro-array analysis, RNA from Right Ventricle samples of wildtype and mutant mice of both 129P2 and FVB/NJ strains were compared (4 experimental groups, n=3 in each group) using Applied Biosystems Mouse Genome Survey Microarrays, containing probes
representing approximately 32,000 mouse genes from the public and Celera databases.

first: Connie

last: Bezzina


status: Public on Mar 28 2007

city: Inage-ku

first: Hiroshi

last: Watanabe

state: Chiba-shi

address: Anagawa 4-9-1

institute: National institute of radiological sceiences

summary:
Gene expression profiles of oral tongue squamous cell carcinoma tissues.
Keywords: human tongue cancer, brachytherapy,  biopsy sample, primary tissues

overall_design: For investigations of oral squamous cell carcinoma, pre-therapeutic biopsy sample tissues were taken from the patients suffering with tongue cancer. All the patients was treated by brachytherapy using 137Cs, 192Ir or 198Au source. Oligonucleotide microarray analysis-duplicate hybridization was carried out to total RNA of these samples.

first: Shuhei

last: Noda


title: Investigation of pneumococcal two-component signal transduction system RR/HK06 in TIGR4

status: Public on Dec 17 2006

city: Adelaide

first: Alistair

last: Standish

address: North Terrace

department: School of Molecular and Biomedical Sciences

country: Australia

institute: University of Adelaide

summary:
We wanted to identify genes regulated by the two-component signal transduction system RR/HK06 in Streptococcus pneumoniae. We used microarray in order to discover regulated genes, investigating the effects of the over-expression of RR06 in TIGR4 (serotype 4).
Keywords: Gene Regulation

overall_design: The RNA used for microarray analysis was extracted from S. pneumoniae TIGR4 over-expressing RR06 and TIGR4 containing over-expression vector without insert. RNA used was from three biological replicates with dye-swap performed for each.

first: Uwe

middle: H

last: Stroeher

first: James

last: Paton


title: Angiotensin II early regulated genes in H295R human adrenocortical cells

status: Public on Nov 19 2004

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

department: Biochemistry

institute: University of Mississippi Medical Center

summary:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Keywords: parallel sample

overall_design:
H295R human adrenocortical cells (a generous gift from Dr. W. Rainey) were grown in complete media containing DMEM:F12 (1:1) supplemented with 2% Ultroser G (Biosepra, Villeneuve-la-Garenne, France), ITS-Plus (Discovery Labware, Bedford, MA) and antibiotic/antimycotic mix (Invitrogen, Carlsbad, CA). Cells were grown in 175-cm2 flasks to about 95% confluence. The RNA for the microarrays was obtained from cells incubated for 3 h with 100 nM ANG II.
Total RNA samples were labeled with Cy3 and Cy5 dyes using an indirect aminoallyl-dUTP method. Briefly, 10 μg total RNA was reverse transcribed with 5 μg T12VN, 2 μl SuperScript II (200 U/μl) (Invitrogen), and 0.5 mM of each deoxynucleotide and a dUTP:aminoallyl-dUTP ratio of 1:1. The reaction was incubated at 37°C; after 1 h, an additional 2 μl was added, and the incubation continued for an additional hour. RNA was degraded by acid treatment and separated from labeled cDNA by Microcon-30 filtration (Millipore, Billerica, MA). Aminoallyl-labeled cDNA was coupled with monofunctional NHS-ester Cy3 or Cy5 (Amersham, Piscataway, NJ), quenched with hydroxylamine, cleaned by filtration, then ethanol precipitated. Control and treated labeled samples were combined, resuspended in DIG Easy HYB solution containing 0.5 mg/ml yeast tRNA (Sigma) and 0.5 mg/ml calf thymus DNA (Sigma), heated for 5 min at 65°C, and allowed to cool to room temperature. The samples were hybridized with cDNA-spotted microarrays containing 19,000 human genes (Microarray Center, University Health Network, Toronto, Canada) and incubated overnight at 37°C. Slides were washed three times in 1× SSC containing 0.1% SDS for 10 min at 50°C. Finally, slides were extensively washed in 1× SSC at room temperature and dried. Hybridizations were performed in sextuplicates with dye swap. Slides were immediately scanned using a ScanArray (Packard Biosciences, Boston, MA) and spot quantified with QuantArray (Packard Biosciences). Spot intensities on each slide were normalized using the rank invariant method followed by Loess regression. Statistical analysis of regulated genes was done using the statistical analysis of microarray data (SAM) software using the one-class protocol with k-nearest neighbor method for missing data estimation and the maximum number of permutations allowed.

first: Maria

last: Plonczynski

first: Gaston

middle: R

last: Vergara

first: Elise

last: Gomez-Sanchez


title: Gene category-specific regulation of transcription elongation across the yeast genome

status: Public on Aug 24 2009

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

type: Genome binding/occupancy profiling by array

summary:
Analysis of genome-wide differences of transcription using Genomic run-on (GRO),  RNApol II ChIP-on-Chip, cDNA analysis and ChIP-on-Chip.

This SuperSeries is composed of the SubSeries listed below.

first: Vicent

last: Pelechano

first: Silvia

last: Jimeno-Gonzalez

first: Alfonso

last: Rodriguez-Gil

last: Garcia-Martinez

first: Sebastian

last: Chavez


title: Transcriptional effects of the IWR1 deletion

status: Public on Oct 13 2009

first: Paco

last: Estruch

address: Dr. Moliner, 50

department: Dpt. Bioquimica i Biologia Molecular

summary: Analysis of the genome-wide transcrptional effects caused by the deletion of the IWR1 gene by comparing the transcriptional profile of a iwr1 mutant strain with the isogenic wild type strain when cells were exponentially grown in YPD medium.

overall_design: Three independent cultures for the wt and the iwr1 mutant were used for the whole genome transcription analysis and they were grown in YPD at the early exponential phase. Total RNA was isolated and cDNA synthesis and labeling, filter hybridization and quantification/normalization of hybridization signals were performed as described in Garcia-Martinez, J., Aranda, A. and Perez-Ortin, J.E. (2004) Mol Cell 15(2),303-313.

first: Francisco

first: Lorena

last: Peiro


title: Consensus Preprocessing of GEO and ArrayExpress Normal and Diseased Lung Tissue Microarray Data

status: Public on Sep 18 2014

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

type:
Expression profiling by array
Third-party reanalysis

summary: The Affymetrix oligonucleotide microarrays measure gene expression by quantifying intensity of fluorescently labeled gene fragments that bind to sets of 25-mer oligonucleotide probes on the chip with specific sequences tailored to be complementary to the target genes. Each gene is associated with a "probe set" containing several pairs (usually 11) of "perfect match" (perfectly complementary to target sequence) and "mismatch" (different base at position 13 of 25) probes. The raw measurements of each probe set consist of a set of intensities from the probes, which require in silico preprocessing by (1) correcting for background variability, (2) normalizing intensities across samples, and (3) summarizing intensities across the probe set into a single expression value. The output of the summarization step corresponds to the background-adjusted value for the mRNA of interest. We preprocess using GCRMA, which corrects for background variability by accounting for optical noise, probe affinity, and mismatch probe adjustment; normalizes intensities by quantile normalization; and summarizes intensities using a median polish method. To minimize preprocessing batch effects, it is desirable to preprocess all samples in the dataset together. However, preprocessing across multple platforms requires  a consolidation of probes with identical sequences, precluding global preprocessing on datasets with multiple platforms using the standard preprocessing pipelines. To address this problem, we have developed and applied a custom preprocessing pipeline to combine the raw .CEL files from multiple platforms that share the same probe sets.

overall_design:
We preprocessed as a single dataset gene expression data collected from 26 publicly available GEO and ArrayExpress studies by applying a custom preprocessing pipeline based on GCRMA. The assembled dataset contains 1489 microarray samples of human tissue that measure gene expression of normal lung (NORM) and 5 different lung diseases (lung adenocarcinoma (ADC), lung squamous cell carcinoma (SCC), large cell lung carcinoma (LCLC), asthma (AST), and chronic obstructive pulmonary disease (COPD)) in preparation for subsequent disease classification analysis. The studies included are: GSE994, GSE10072, GSE10245, GSE10445, GSE10799, GSE12345, GSE12667, GSE14814, GSE1643, GSE1650, GSE17475, GSE18842, GSE18965, GSE19188, GSE2109, GSE3141, GSE4302, GSE5058, GSE6253, GSE7368, GSE7670, GSE8545, GSE8581, E-TABM-15, E-MEXP-231, and E-MTAB-47. These studies collected the microarray data using 2 platforms: Affymetrix U133-A (GPL96) and Affymetrix U133-Plus-2 (GPL570).

The following are included in this reanalysis:

79_1 ArrayExpress study E-TABM-15 sample 1, ADC lung surgical resection GPL96
47_1 ArrayExpress study E-TABM-15 sample 2, ADC lung surgical resection GPL96
41_1 ArrayExpress study E-TABM-15 sample 3, ADC lung surgical resection GPL96
61_1 ArrayExpress study E-TABM-15 sample 4, ADC lung surgical resection GPL96
92_1 ArrayExpress study E-TABM-15 sample 5, ADC lung surgical resection GPL96
60_1 ArrayExpress study E-TABM-15 sample 6, ADC lung surgical resection GPL96
86_1 ArrayExpress study E-TABM-15 sample 7, ADC lung surgical resection GPL96
53_1 ArrayExpress study E-TABM-15 sample 8, ADC lung surgical resection GPL96
40_1 ArrayExpress study E-TABM-15 sample 9, ADC lung surgical resection GPL96
33_1 ArrayExpress study E-TABM-15 sample 10, ADC lung surgical resection GPL96
71_1 ArrayExpress study E-TABM-15 sample 11, ADC lung surgical resection GPL96
23_1 ArrayExpress study E-TABM-15 sample 12, ADC lung surgical resection GPL96
78_1 ArrayExpress study E-TABM-15 sample 13, ADC lung surgical resection GPL96
89_1 ArrayExpress study E-TABM-15 sample 14, ADC lung surgical resection GPL96
38_1 ArrayExpress study E-TABM-15 sample 15, ADC lung surgical resection GPL96
84_1 ArrayExpress study E-TABM-15 sample 16, ADC lung surgical resection GPL96
54_1 ArrayExpress study E-TABM-15 sample 17, ADC lung surgical resection GPL96
87_1 ArrayExpress study E-TABM-15 sample 18, ADC lung surgical resection GPL96
59_1 ArrayExpress study E-TABM-15 sample 19, ADC lung surgical resection GPL96
28_1 ArrayExpress study E-TABM-15 sample 20, ADC lung surgical resection GPL96
32_1 ArrayExpress study E-TABM-15 sample 21, ADC lung surgical resection GPL96
67_1 ArrayExpress study E-TABM-15 sample 22, ADC lung surgical resection GPL96
48_1 ArrayExpress study E-TABM-15 sample 23, ADC lung surgical resection GPL96
40_2 ArrayExpress study E-TABM-15 sample 24, NORM lung surgical resection GPL96
33_2 ArrayExpress study E-TABM-15 sample 25, NORM lung surgical resection GPL96
54_2 ArrayExpress study E-TABM-15 sample 26, NORM lung surgical resection GPL96
48_2 ArrayExpress study E-TABM-15 sample 27, NORM lung surgical resection GPL96
84_2 ArrayExpress study E-TABM-15 sample 28, NORM lung surgical resection GPL96
89_2 ArrayExpress study E-TABM-15 sample 29, NORM lung surgical resection GPL96
28_2 ArrayExpress study E-TABM-15 sample 30, NORM lung surgical resection GPL96
41_2 ArrayExpress study E-TABM-15 sample 31, NORM lung surgical resection GPL96
92_2 ArrayExpress study E-TABM-15 sample 32, NORM lung surgical resection GPL96
78_2 ArrayExpress study E-TABM-15 sample 33, NORM lung surgical resection GPL96
87_2 ArrayExpress study E-TABM-15 sample 34, NORM lung surgical resection GPL96
38_2 ArrayExpress study E-TABM-15 sample 35, NORM lung surgical resection GPL96
23_2 ArrayExpress study E-TABM-15 sample 36, NORM lung surgical resection GPL96
61_2 ArrayExpress study E-TABM-15 sample 37, NORM lung surgical resection GPL96
32_2 ArrayExpress study E-TABM-15 sample 38, NORM lung surgical resection GPL96
47_2 ArrayExpress study E-TABM-15 sample 39, NORM lung surgical resection GPL96
79_2 ArrayExpress study E-TABM-15 sample 40, NORM lung surgical resection GPL96
86_2 ArrayExpress study E-TABM-15 sample 41, NORM lung surgical resection GPL96
DL06 ArrayExpress study E-MEXP-231 sample 1, ADC lung surgical resection GPL96
DL01 ArrayExpress study E-MEXP-231 sample 2, ADC lung surgical resection GPL96
DL05 ArrayExpress study E-MEXP-231 sample 3, ADC lung surgical resection GPL96
DL14 ArrayExpress study E-MEXP-231 sample 4, ADC lung surgical resection GPL96
DL39 ArrayExpress study E-MEXP-231 sample 5, ADC lung surgical resection GPL96
DL34 ArrayExpress study E-MEXP-231 sample 6, ADC lung surgical resection GPL96
DL88 ArrayExpress study E-MEXP-231 sample 7, ADC lung surgical resection GPL96
DL09 ArrayExpress study E-MEXP-231 sample 8, ADC lung surgical resection GPL96
DL59 ArrayExpress study E-MEXP-231 sample 9, ADC lung surgical resection GPL96
DL65 ArrayExpress study E-MEXP-231 sample 10, ADC lung surgical resection GPL96
DL31 ArrayExpress study E-MEXP-231 sample 11, ADC lung surgical resection GPL96
DL45 ArrayExpress study E-MEXP-231 sample 12, ADC lung surgical resection GPL96
DL63 ArrayExpress study E-MEXP-231 sample 13, ADC lung surgical resection GPL96
DL36 ArrayExpress study E-MEXP-231 sample 14, ADC lung surgical resection GPL96
DL13 ArrayExpress study E-MEXP-231 sample 15, ADC lung surgical resection GPL96
T42-1 ArrayExpress study E-MEXP-231 sample 16, ADC lung surgical resection GPL96
DL68 ArrayExpress study E-MEXP-231 sample 17, ADC lung surgical resection GPL96
DL50 ArrayExpress study E-MEXP-231 sample 18, ADC lung surgical resection GPL96
DL46 ArrayExpress study E-MEXP-231 sample 19, ADC lung surgical resection GPL96
DL30 ArrayExpress study E-MEXP-231 sample 20, ADC lung surgical resection GPL96
DL40 ArrayExpress study E-MEXP-231 sample 21, ADC lung surgical resection GPL96
DL51 ArrayExpress study E-MEXP-231 sample 22, ADC lung surgical resection GPL96
DL08 ArrayExpress study E-MEXP-231 sample 23, ADC lung surgical resection GPL96
DL35 ArrayExpress study E-MEXP-231 sample 24, ADC lung surgical resection GPL96
DL58 ArrayExpress study E-MEXP-231 sample 25, ADC lung surgical resection GPL96
DL61 ArrayExpress study E-MEXP-231 sample 26, ADC lung surgical resection GPL96
DL33 ArrayExpress study E-MEXP-231 sample 27, ADC lung surgical resection GPL96
DL16 ArrayExpress study E-MEXP-231 sample 28, ADC lung surgical resection GPL96
DL37 ArrayExpress study E-MEXP-231 sample 29, ADC lung surgical resection GPL96
DL12 ArrayExpress study E-MEXP-231 sample 30, ADC lung surgical resection GPL96
DL67 ArrayExpress study E-MEXP-231 sample 31, ADC lung surgical resection GPL96
DL91 ArrayExpress study E-MEXP-231 sample 32, ADC lung surgical resection GPL96
DL54 ArrayExpress study E-MEXP-231 sample 33, ADC lung surgical resection GPL96
DL47 ArrayExpress study E-MEXP-231 sample 34, ADC lung surgical resection GPL96
DL57 ArrayExpress study E-MEXP-231 sample 35, ADC lung surgical resection GPL96
DL03 ArrayExpress study E-MEXP-231 sample 36, ADC lung surgical resection GPL96
DL41 ArrayExpress study E-MEXP-231 sample 37, ADC lung surgical resection GPL96
DL15 ArrayExpress study E-MEXP-231 sample 38, ADC lung surgical resection GPL96
DL66 ArrayExpress study E-MEXP-231 sample 39, ADC lung surgical resection GPL96
DL11 ArrayExpress study E-MEXP-231 sample 40, ADC lung surgical resection GPL96
DL44 ArrayExpress study E-MEXP-231 sample 41, ADC lung surgical resection GPL96
DL38 ArrayExpress study E-MEXP-231 sample 42, ADC lung surgical resection GPL96
DL56 ArrayExpress study E-MEXP-231 sample 43, ADC lung surgical resection GPL96
DL60 ArrayExpress study E-MEXP-231 sample 44, ADC lung surgical resection GPL96
DL48 ArrayExpress study E-MEXP-231 sample 45, ADC lung surgical resection GPL96
DL89 ArrayExpress study E-MEXP-231 sample 46, ADC lung surgical resection GPL96
DL42 ArrayExpress study E-MEXP-231 sample 47, ADC lung surgical resection GPL96
DL32 ArrayExpress study E-MEXP-231 sample 48, ADC lung surgical resection GPL96
DL55 ArrayExpress study E-MEXP-231 sample 49, ADC lung surgical resection GPL96
DL15N ArrayExpress study E-MEXP-231 sample 50, NORM lung surgical resection GPL96
DL50N ArrayExpress study E-MEXP-231 sample 51, NORM lung surgical resection GPL96
DL4_1N ArrayExpress study E-MEXP-231 sample 52, NORM lung surgical resection GPL96
DL4_17N ArrayExpress study E-MEXP-231 sample 53, NORM lung surgical resection GPL96
DL4_7N ArrayExpress study E-MEXP-231 sample 54, NORM lung surgical resection GPL96
DL4_11N ArrayExpress study E-MEXP-231 sample 55, NORM lung surgical resection GPL96
DL86N ArrayExpress study E-MEXP-231 sample 56, NORM lung surgical resection GPL96
DL79N ArrayExpress study E-MEXP-231 sample 57, NORM lung surgical resection GPL96
DL67N ArrayExpress study E-MEXP-231 sample 58, NORM lung surgical resection GPL96
Biopsy_07 ArrayExpress study E-MTAB-47 sample 1, NORM lung surgical resection GPL570
Biopsy_11 ArrayExpress study E-MTAB-47 sample 2, NORM lung surgical resection GPL570
Biopsy_06 ArrayExpress study E-MTAB-47 sample 3, NORM lung surgical resection GPL570
Biopsy_13 ArrayExpress study E-MTAB-47 sample 4, NORM lung surgical resection GPL570
Biopsy_10 ArrayExpress study E-MTAB-47 sample 5, NORM lung surgical resection GPL570
Biopsy_01 ArrayExpress study E-MTAB-47 sample 6, NORM lung surgical resection GPL570
Biopsy_22 ArrayExpress study E-MTAB-47 sample 7, NORM lung surgical resection GPL570
Biopsy_04 ArrayExpress study E-MTAB-47 sample 8, NORM lung surgical resection GPL570
Biopsy_20 ArrayExpress study E-MTAB-47 sample 9, NORM lung surgical resection GPL570
Biopsy_14 ArrayExpress study E-MTAB-47 sample 10, NORM lung surgical resection GPL570
Biopsy_02 ArrayExpress study E-MTAB-47 sample 11, NORM lung surgical resection GPL570
Biopsy_08 ArrayExpress study E-MTAB-47 sample 12, NORM lung surgical resection GPL570

We preprocess using the MATLAB implementation of GCRMA. To minimize preprocessing batch effects, it is desirable to preprocess all samples in the entire dataset together. Preprocessing requires microarray platform-specific chip specifications indicating the locations of each probe on the chip, precluding global preprocessing on meta-analyses that use multiple platforms. To address this problem, we developed and applied a preprocessing pipeline to combine the raw .CEL files from multiple platforms that share the same probe sets. Importantly, our pipeline maps the locations of probes containing identical sequences from the different platforms to enable grouping of these probes and subsequent processing. These "consensus datasets" are then preprocessed normally by applying the GCRMA algorithm. The output of this consensus preprocessing contains only the 22,227 probes that exist on both microarray platforms that we use; probes that only appear on one of the platforms are excluded from preprocessing. We also include "presence/marginal/absence" calls based on the MAS5 protocol, in which the measured values on the "perfect match" (perfectly complementary to target) probes are compared to the values on the "mismatch" (basepair mismatch at position 13 of 25) probes with Wilcoxon signed rank test. "Present" calls are made when the p-value of difference is less than 0.04; "marginal" calls are made when the p-value lies between 0.04 and 0.06, and "absent" calls are made when the p-value is greater than 0.06.
GCRMA signal

first: Jaeyun

last: Sung

first: Andrew

last: Magis

first: Yuliang

last: Wang

first: Donald

last: Geman

first: Nathan

middle: D

last: Price