title: Comparison of linear and exponential amplification techniques for expression profiling at the single-cell level

status: Public on Jun 27 2006

city: London

first: Tatiana

last: Subkhankulova

address: 4 Newark Street

department: Neuroscience

institute: Queen Mary University London

summary:
We tested the performance of three methods for amplifying single-cell amounts of RNA under ideal conditions: T7-based in vitro transcription; switching mechanism at 5' end of RNA template (SMART) PCR amplification; and global PCR amplification. All methods introduced amplification-dependent noise when mRNA was amplified 108-fold, compared with data from unamplified cDNA. PCR-amplified cDNA demonstrated the smallest number of differences between two parallel replicate samples and the best correlation between independent amplifications from the same cell type, with SMART outperforming global PCR amplification. SMART had the highest true-positive rate and the lowest false-positive rate when comparing expression between two different cell types, but had the lowest absolute discovery rate of all three methods. Direct comparison of the performance of SMART and global PCR amplification on single-cell amounts of total RNA and on single neural stem cells confirmed these findings. Under the conditions tested, PCR amplification was more reliable than linear amplification for detecting true expression differences between samples. SMART amplification had a higher true-positive rate than global amplification, but at the expense of a considerably lower absolute discovery rate and a systematic compression of observed expression ratios.
Keywords: Oliginucleotide expression microarrays, T7-based linear amplification; SMART PCR-based amplification;  global PCR amplification

overall_design: Total RNA was isolated from two mouse cell lines, an ovary epithelial cell line (OV) and 3T3 fibroblasts (3T3). Unamplified targets (cDNA) were synthesized from 100 μg of total RNA by reverse transcription. RNA (starting with 10 ng) was amplified by using linear T7 based- (cRNA) or exponential PCR-based amplifications (switching mechanism at 5' end of RNA template (SMART) PCR amplification; modified SMART  (SM37) and global PCR amplification (GA). Synthesized DNA/cRNA samples were indirectly labeled with Cy3/Cy5 dyes. Labeled targets were co-hybridized on oligonucleotide arrays. Self-self control hybridizations were performed to estimate the levels of technical noise. Labeled DNA/cRNA were divided in two parts and each was coupled with either Cy3 or Cy5 NHS-esters followed by co-hybridization on the same slide Replicate hybridizations were performed to estimate the variability in expression data due to amplification techniques. Pairs of technical replicates synthesized from ovarian cell line total RNA by each amplification method or by reverse transcription (unamplified cDNA) were compared in two dye-swaps hybridizations. Comparison of gene expression between two different cell lines was performed to estimate the rate of true outliers for each amplification method in four hybridizations of cDNAs amplified by the same technique. Similarly, we compared the precision of SMART and GA amplification techniques at the 10 pg input RNA level in four hybridizations of the targets obtained from the same cell lines.

middle: N

first: Frederick

last: Livesey


title: Xenobiotic response in Drosophila melanogaster: sex dependence of P450 and GST gene induction

status: Public on Jun 29 2006

city: Sophia-Antipolis

first: Gaelle

last: LE GOFF

address: 400 route des Chappes

country: France

institute: INRA

summary:
The effect of xenobiotics (phenobarbital and atrazine) on the expression of Drosophila melanogaster CYP genes encoding cytochromes P450, a gene family generally associated with detoxification, was analyzed by DNA microarray hybridization and verified by real time RT-PCR in adults of both sexes. Only a small subset of the 86 CYP genes was significantly induced by the xenobiotics. Eleven CYP genes and three GST genes were significantly induced by phenobarbital, seven CYP and one GST gene were induced by atrazine. Cyp6d5, Cyp6w1, Cyp12d1 and the ecdysone-inducible Cyp6a2 were induced by both chemicals. The constitutive expression of several of the inducible genes (Cyp6a2, Cyp6a8, Cyp6d5, Cyp12d1) was higher in males than in females, and the induced level similar in both sexes. Thus, the level of induction was consistently higher in females than in males. The female-specific and hormonally-regulated yolk protein genes were significantly induced by phenobarbital in males and repressed by atrazine in females. Our results suggest that the numerous CYP genes of Drosophila respond selectively to xenobiotics, providing the fly with an adaptive response to chemically adverse environments. The xenobiotic-inducibility of some CYP genes previously associated with insecticide resistance in laboratory-selected strains (Cyp6a2, Cyp6a8, Cyp12d1) suggests that deregulation of P450 gene expression may be a facile way to achieve resistance. Our study also suggests that xenobiotic-induced changes in P450 levels can affect insect fitness by interfering with hormonally-regulated networks.
Keywords: induction by phenobarbital and atrazine in adults drosophila melanogaster of both sex.

overall_design: Three independent biological repeat were done for each condition (control, atrazine treatment, phenobarbital treatment). For each microarray experiment, the Cy3 and the Cy5 were swapped between conditions to account for the potential differences in labelling efficiency.

last: Le Goff

first: Frederique

last: Hilliou

first: Blair

middle: S

last: Siegfried

first: Sam

last: Boundy

first: Eric

last: Wajnberg

first: Luc

last: Sofer

first: Pascaline

last: Audant

first: Richard

middle: H

last: ffrench-Constant

first: Rene

last: Feyereisen


title: Gene expression in degenerated rat supraspinatus tendon

status: Public on Jun 21 2006

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

country: Australia

institute: St Vincent's Centre for Applied Medical Research

summary:
Microarray of exercised (degenerated) rat supraspinatus versus non-exercised (normal)
Keywords: Disease state analysis

overall_design: rats were subjected to exercise that consisted of running on a 10˚ decline at 17m/min for 1 hour per day, 5 days per week. This regimen equates to approximately 7500 strides per day. After four weeks of running, rats were sacrificed by CO2 inhalation and both supraspinatus tendons were collected. 12 non-exercised rats were used as controls.


title: PPARalpha Agonists Induce a Fiber-Type Selective Transcriptional Response in Rat Skeletal Muscle

status: Public on Jun 20 2006

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

country: USA

institute: Merck & Co.

summary:
In rodents, treatment with peroxisome proliferator-activated receptor alpha (PPARalpha) agonists results in peroxisome proliferation, hepatocellular hypertrophy and hepatomegaly. Drugs in the fibrate class of PPARalpha agonists have also been reported to produce rare skeletal muscle toxicity. Although target-driven hepatic effects of PPARalpha treatment have been extensively studied, a characterization of the transcriptional effects of this nuclear receptor/transcription factor on skeletal muscle responses has not been reported. In this study we investigated the effects of PPARalpha agonists on skeletal muscle gene transcription in rats. Further, since statins have been reported to preferentially effect type II muscle fibers we compared PPARalpha signaling effects between type I and type II muscles. By comparing the transcriptional responses of agonists that signal through different nuclear receptors and, using a selection/deselection analytical strategy based on ANOVA, we identified a PPARalpha activation signature that is evident in type-I (soleus) but not type II (quadriceps femoris) skeletal muscle fibers. The fiber-type selective nature of this response is consistent with increased fatty acid uptake and beta-oxidation, which represent the major clinical benefits of the hypolipidemic compounds used in this study, but does not reveal any obvious off-target pathways that may drive adverse effects.
Keywords: drug response

overall_design: Please refer to associated publication (PMID: 16707586)


title: MT1-MMP induces malignant transformation in Mammary cells

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary:
Expression of the MT1-MMP gene induces a significant upregulation of of oncogenes and tumorignenic genes in 184B5-MT1 cells.
Keywords: Genetic modification

overall_design: Three biological replicates of untransfected Mammary cell line compared to MT1-MMP transfected Mammary cell line. Singel channel data from the illumina platform. After normalisation and t-tests differential gene expression was determined between the two groups using p-values and fold change.

first: Vladislav

last: Golubkov


title: EGF treated SCN versus intra-animal control at two circadian times

city: Philadelphia

first: Gregory

last: Miller

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

summary:
Background:

Identifying the gene regulatory networks governing physiological signal integration remains an important challenge in circadian biology.  Epidermal growth factor receptor (EGFR) has been implicated in circadian function and EGFR is expressed in the suprachiasmatic nucleus (SCN), the core circadian pacemaker.  The transcription networks downstream of EGFR in the SCN are unknown, but by analogy to other SCN inputs we expect the response to EGFR activation to depend on circadian timing and thus be “circadian context–dependent”.

Results:
We have undertaken a systems level analysis of EGFR circadian context–dependent signaling in the SCN.  We collected gene expression profiles to study how the SCN response to EGFR activation depends on circadian timing.  Mixed–model analysis of variance (ANOVA) was employed to identify genes with circadian context–dependent EGFR regulation. The expression data was integrated with transcription factor (TF) binding predictions through gene group enrichment analyses to generate robust hypotheses about TFs responsible for the circadian phase–dependent EGFR responses.

Conclusions:
The analysis results suggest that the transcriptional response to EGFR signaling in the SCN may be partly mediated by established EGFR signaling regulated TFs (AP1, Ets1), TFs involved in circadian clock entrainment (CREB), and by core clock TFs (Rorα).  qRT-PCR measurements of several TF expression levels support a model in which circadian context-dependent EGFR responses are partly achieved by circadian regulation of upstream signaling components.  Our study suggests an important role for EGFR signaling in SCN function and provides an example for gaining physiological insights through systems-level analysis.
Keywords: dose response; repeat sample

sample_organism:
Rattus norvegicus
synthetic construct

overall_design:
A 2X2 factorial experimental design was used to investigate differences between "day" (8 hours after lights on) and "night" (2 hours after lights off) SCN gene expression responses to EGFR activation induced by EGF treatment (20 nM, 1 hr).

Two SCN were obtained from each rat and served as EGF–treated and vehicle-treated samples. Pairing control and treated samples from the same rat permitted detection of EGF effects in the presence of substantial animal-to-animal variability. SCN from two rats were experimentally treated at each circadian time, yielding a total of eight biological samples. Since our goal was a preliminary characterization of EGFR response clock phase dependency, samples were hybridized to one microarray each.  A universal reference design was used for the microarrays themselves.

first: Daniel

middle: E

last: Zak

first: Haiping

last: Hao

first: Rajanikanth

last: Vadigepalli

first: Babatunde

middle: A

last: Ogunnaike

first: James

last: Schwaber


title: The function of CEBiP in the chitin elicitor signaling in rice cells

status: Public on Jun 13 2006

city: tsukuba

first: Chiharu

last: Akimoto-Tomiyama

address: 2-1-2 kannonndai

country: Japan

institute: NIAS

summary:
To see the function of CEBiP in the chitin elicitor signaling in rice cells, a plasmid for the gene-specific knock-down by RNA interference (RNAi) was constructed by using a sequence for the 3’-terminal region of CEBiP and transformed into the rice cells by using Rhizobium radiobacter (Agrobacterium tumefaciens). chitinoligomer was added (or not added) to the medium.
For the control of them, rice cells that non transformed wild type was used.
Keywords: genetic modification

overall_design:
We compared chitinoligomer treated rice cells with non treated on a same plate.
Dye-swaps was done for transfomed or non transformed rice cells individually.

first: Hanae

last: Kaku

first: Nishizawa

last: Yoko

first: Naoko

last: Ishii-Minami

first: Eiichi

last: Minami

first: Naoto

last: Shibuya


title: Exposure to phenolic acids

city: LUBBOCK

first: Michael

last: San Francisco

state: TX

address: Flint and Main St

department: Biological Sciences

institute: Texas Tech University

summary:
Exposure of Erwinia chrysanthemi 3937 to a combination of phenolic acids (salicylic, benzoic and t-cinnamic) each at a concentration of 0.078 mM resulted in activation of genes encoding efflux pumps and those involved in oxidative stress resistance.
Keywords: phenolic acid exposure gene response

overall_design:
Flasks with pre-warmed 15 ml LB were inoculated with approximately 10^6 cells/ml of E. chrysanthemi cells from an overnight culture and grown shaken at 150 rpm at 300C to mid-exponential growth (OD600 of 0.4) before addition of inducer phenolic acids (0.078 mM each of SA, BA, TC) (PA) or DMSO as a control.  RNA was harvested from these cultures after 90 min as described below.  For the microarray, RNA was prepared from three replicates of each inducer and control cultures.
The E. chrysanthemi 3937 coding sequences (CDSs) and a subset of the intergenic regions were selected and an initial set of candidate oligonucleotide probes designed using ArrayDesignerTM 1.17 (Premier Biosoft Intl).  For all consecutive runs, the parameters were kept with constant values, which Hairpin MaxDG was 5, SelfDimer MaxDG was 6, and Run/Repeat (dinucleotide) max length was 5.  The final probes of 3937 were spotted using the inkjet array technology to generate a 60-mer E. chrysanthemi 11K customer array (Agilent, Inc), which contained 5862 probes from the E. chrysanthemi genome (the entire ORF complement of Ech 3937), 20 Lucidea spike (Lucidea Universal ScoreCard, Amersham Biosciences) and internal controls.  Most of the probes were spotted twice onto a single array.


status: Public on Jun 15 2006

city: Toronto

first: Chung-Hae

last: Lee

state: ON

address: 9th Floor Rm. 717, 610 University Ave

department: Applied Molecular Oncology

country: Canada

institute: Ontario Cancer Institute, Princess Margaret Hospital

summary:
Background
Identification of the molecular determinants of invasion and metastatic potential may guide the development of a rational strategy for devising specific therapies that target the pathways leading to osteosarcoma.

Methods
In this study, we used pathway-focused GEarrays to screen for candidate genes related to tumor progression.  Expression patterns of the selected genes were validated by real time PCR on 61 osteosarcoma patient tumor samples and correlated with clinical and pathological data.

Results
THBS3, SPARC and SPP1 were identified with pathway-focused GEarrays as genes differentially expressed in osteosarcoma.  In particular, THBS3 was expressed at significantly high levels (p=0.0001) in biopsies from patients with metastasis at diagnosis, which is a predictor of worse overall survival, event-free survival and relapse free survival at diagnosis.  After chemotherapy, patients with tumors over-expressing THBS3 have worse relapse free survival. High SPARC expression was found in 51 of 55 (96.3%) osteosarcoma samples and correlated with the worst event-free survival (p=0.03) and relapse free survival (p=0.07).  Overexpression of SPP1 was found in 47 of 53 (89%) osteosarcomas correlating with better overall survival, event-free survival and relapse free survival at diagnosis.

Conclusion
With pathway-focused Gearrays, we identified three genes, which interestingly all encode for proteins involved in extracellular remodeling suggesting potential roles in osteosarcoma progression.  This is the first report on the THBS3 gene working as a stimulator of tumor progression.  Higher levels of THBS3 maintain the capacity of angiogenesis.  High levels of SPARC are not required for tumor progression but are necessary for tumor growth and maintenance.  SPP1 is not necessary for tumor progression in osteosarcoma and may be associated with inflammatory response and bone remodeling, functioning as a good biomarker.
Keywords: disease state analysis using Superarray Pathway focused arrays

overall_design:
see paper:
Cristiane Arruda Dalla-Torre et al. (2006). Effects of THBS3, SPARC and SPP1 expression on biological behavior and survival in patients with osteosarcoma. BMC Cancer.


title: Effect of post-translational modifications of SATB1 on global gene expression in Jurkat T cells

city: Pune

first: Sanjeev

last: Galande

address: Ganeshkhind

country: India

institute: National Centre for Cell Science

summary:
Gene profiling studies using RNA from cells overexpressing point mutants of SATB1 defective in phosphorylation or acetylation unequivocally demonstrated the importance of these modifications towards the ability of SATB1 to act as a global regulator of gene expression in Jurkat T cells. Jurkat cells express SATB1 endogenously, and therefore we monitored the effect of overexpression of SATB1. Under this situation, the overexpressed mutants will compete with the endogenously expressed wild type SATB1 and therefore the effect on gene expression may differ from SATB1 non-expressing non T cell line such as HeLa.
Keywords: cDNA array

overall_design: Total RNA from untransfected Jurkat cells was taken as reference and was labeled with Cy3. Total RNA from Jurkat cells stably transfected individually with wild-type, S185A, or K136A mutant of SATB1 were taken as experimental sample and labeled with Cy5.

first: Pavan

last: Kumar

first: Dimple

last: Notani

first: Chandan


title: Effect of posttranslational modifications of SATB1 on its ability to regulate global gene expression in HeLa Cells

summary:
Gene profiling studies using RNA from HeLa cells overexpressing point mutants of SATB1 defective in phosphorylation or acetylation unequivocally demonstrated the importance of these modifications towards the ability of SATB1 to act as a global regulator of gene expression. HeLa cells were chosen as a representative of non-T cells, and do not express SATB1 endogenously.
Keywords: cDNA array

overall_design: Total RNA from untransfected HeLa cells was used as reference and was labeled with Cy5. Total RNA from HeLa cells stably transfected with wild type, or S185A, or K136A mutant SATB1 expressing construct was used as experimental sample and was labeled with Cy3.


title: Oxidative metabolism and PGC-1 attenuate macrophage-mediated inflammation

status: Public on Jun 07 2006

city: Stanford

first: Justin

last: Odegaard

address: 269 Campus Dr

department: CCSR 3110

institute: Stanford University

summary:
Total RNA was prepared from three independent experimental replicates using Trizol reagent (Invitrogen) and validated by northern blot.   Microarray experiments were performed with 20-25 ?g of total RNA, which was labelled with fluorescent nucleotides and hybridized to murine cDNA slides.  Hybridized slides were interrogated via an Agilent scanner.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Complex


title: Comparison of testes gene expression of D. melanogaster species and their hybrids

status: Public on Jun 12 2006

city: Hamilton

first: Rama

middle: S.

last: Singh

state: Ontario

address: 1280 Main Street West

department: Biology Department

institute: McMaster University

summary:
Males hybrids from the crosses between species of the D. simulans clade are steriles as the females are fertiles. Hybrid male sterility is due to severe defects in spermatogenesis and phenotypic differences are observed between the different hybrids involving D. simulans, D. sechellia and D. mauritiana.
In this study we are comparing gene expression in the testes of hybrids involving the female D. simulans and the males D. melanogaster, D. mauritiana, or D. sechellia to the gene expression in species testes.
Keywords: Comparative genomic hybridization

sample_organism: Drosophila sechellia x Drosophila simulans

overall_design:
4 species (D. melanogaster, D. simulans, D. sechellia, D. mauritiana) and 3 different hybrids were used in this study.
RNA extracted from whole D. melanogaster males was used as a reference.
Hybridizations were perfomed using RNA extraxted from a pool of 200 testes from a sample with RNA extracted from whole D. melanogaster males.
At least three independent replicates per hybridizations were performed

first: Wilfried

last: Haerty

first: Heidi

last: Muster


status: Public on Jun 09 2006

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary:
ChIP-on-chip analyses of JmjC protein Epe1  in fission yeast.
Keywords: ChIP-on_chip

overall_design: ChIP-on-chip analyses using custom Agilent 44K in situ 60mer DNA microarray that tiles the entire Schizosaccharomyces pombe genome every 300 bp alternately on both strands were used to interrogate Swi6/HP1 and Epe1 in fission yeast genome.

first: Martin

last: Zofall

first: Hugh

middle: P

last: Cam

middle: I


title: Gene expression of RAW 264.7 cells treated with LPS, IFG, 2MA, LPS PLUS IFG, and LPS PLUS 2MA

status: Public on Jun 06 2006

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

summary:
LPS plus IFG and LPS plus 2MA had non-additive effects on gene expression in RAW 264.7 cells
Keywords: time course

overall_design: total RNA from RAW 264.7 cells (macrophages) treated with Lipopolysaccharide (LPS), Interferon-gamma (IFG), 2-Methyl-thio-ATP (2MA), LPS PLUS IFG, and LPS PLUS 2MA vs total RNA from time_matched_control RAW 264.7 cells (macrophages) cultured in media, 1 h, 2 h, and 4 h time course with triplicates, with dyeSwap measurements on custom Ailgent Oligo arrays

first: Xiaocui

last: Zhu

first: MiSook

last: Chang

first: Robert

last: Hsueh

first: Ron

last: Taussig

first: Kelly

middle: D

last: Smith

first: Mel

last: Simon


title: A small RNA mechanism distinct from the RNAi and microRNA pathways silences selfish genetic elements in Drosophila.

status: Public on Jun 30 2006

city: Worcester

first: Hervé

last: Seitz

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

summary:
In flies, repeat-associated small interfering RNAs (rasiRNAs) ensure genomic stability by silencing endogenous selfish genetic elements such as retrotransposons and repetitive sequences. Here, we show that while small interfering RNAs (siRNAs) derive from both the sense and antisense strands of their double-stranded RNA precursors, rasiRNAs arise mainly from the antisense strand. rasiRNA production appear not to require Dicer-1, which makes microRNAs, or Dicer-2, which makes siRNAs, and rasiRNAs lack the 2´,3´ hydroxy termini characteristic of animal siRNA and miRNA. Unlike siRNAs and miRNAs, rasiRNAs function through the Piwi, rather than the Ago, Argonaute protein subfamily. Thus, rasiRNAs define a third RNA silencing pathway distinct from both the miRNA and RNAi pathways.
Keywords: gene silencing; post-transcriptional gene regulation; short RNAs; RNAi; rasiRNAs; rasiRNA; microRNAs; microRNA; siRNAs; siRNA

overall_design:
Short RNAs homologous to several selfish genetic elements (including Su(Ste) and roo), as well as a transgenic inverse-repeat made of white exon 3, were detected using custom-made tiling microarrays. These arrays also detect microRNAs. We used them to quantify rasiRNAs and siRNAs in various genetic backgrounds.
Su(Ste) rasiRNAs were quantified in crystal mutants vs. wt (two arrays, with color-reversal; wt samples for both arrays were prepared independently, as well as cry samples); in armitage mutants vs. wt (two arrays, with color-reversal; the same

first: Vasily

middle: V

last: Vagin

first: Alla

last: Sigova

first: Chengjian

last: Li

first: Vladimir

last: Gvozdev

first: Phillip

last: Zamore


title: in vivo binding of su(Hw) in the Drosophila genome

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

summary:
There is considerable evidence that insulator elements are likely to play a key role in the organisation of the regulatory architecture of the genome.  In Drosophila, one of the best studied insulator elements is the gypsy insulator in the gypsy retrotransposon whose function is dependent on the Su(Hw) Zn-finger DNA binding protein.  Although there are several hundred Su(Hw) sites in the genome which are proposed to act as endogenous insulator elements, analysis of the role of the Su(Hw) protein has focussed on the gypsy insulator and few endogenous sites have yet been identified.  We have used chromatin immunopurification coupled to genomic microarray analysis to identify Su(Hw) binding sites within a representative region of the Drosophila genome; the 3MB Adh region on chromosome 2L.  We have located about 60 Su(Hw) binding sites across this region and this has enabled us to construct a robust new  Su(Hw) binding site consensus based on these in vivo sites.  In contrast to the gypsy insulator which contains 12 Su(Hw) binding sites within 340bp, the endogenous sites are not present in clusters.  We identify two key features of these endogenous Su(Hw) sites.  Firstly, in contrast to most analyses of DNA binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy.  Secondly, examination of Su(Hw) binding site occupancy in 0-20hr embryos, 3rd larval instar brains or 3rd larval imaginal discs reveals a constant pattern of Su(Hw) binding indicating that most , if not all Su(Hw) sites are constitutively occupied.   These two features support a constant genomic architectural role for the Su(Hw) protein.
Keywords: ChIP-chip

overall_design: Chromatin prepared from 3 different Drosophila tissues (embryo, larval brain and larval wing disc) was immunopurified with anti-su(hw) (or anti-GFP from flies carrying a GFP-tagged su(hw)) and compared with control immunopurifications using normal serum.  Enrichemnt for su(hw) binding sites in a 3Mb region of the fly genome was identified via a tiling microarray containing a seriese of 1kb amplicons.  Each immunopurification was dye swapped (technical replicate) and several independent biological replications were performed.

first: Boris

last: Adryan

first: Gertrude

last: Woerfel

first: Ian

last: Birch-Machin

first: Shan

last: Gao

first: Marie

last: Quick

first: Steven

last: White


title: Analysis of heart tissue from 2 and 15-16 month old Wt and Taut -/- Mice

city: Duesseldorf

first: Birgit

last: Andree

address: Moorenstr. 5

country: Germany

institute: BMFZ

summary:
Taurine is the most abundant free amino acid in heart muscle and protects against heart failure. In the present study, the consequences of hereditary taurine deficiency on cardiac gene expression were examined in 2 and 15-16 months old taurine transporter knockout (taut-/-) mice by using a mouse-specific DNA oligonucleotide microarray which was developed with probes for 251 genes with relevance for heart.
Keywords: Comparison, knock out, wildtype

overall_design:
Heart tissue from 5 mice (2 month old) and from 4 mice (15ß16 month old) were used respectively. Dual channel analysis with dye swap was performed. The oligos were printed in duplicates and the grid was repeated twice on the array. Wt1-1 is the analysis for the first grid and Wt1-2 for the second grid.

2 month old mice: GSM108518 - GSM108527

15 - 16 month old mice: GSM108509 - GSM108517

first: Ulrich

last: Warskulat

first: Karl

last: Koehrer

first: J

last: Lusebrink

first: Dieter

last: Haussinger


title: VI-28 treatment induced alteration of gene expression in human lymphocytes

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

summary:
The aim of the present study was to evaluate whether Chinese herbs VI-28 has any potential effect on the immune system in a human cell culture system. An inflammatory cDNA array was used in the study to analyze the profile of gene expression in cells treated by VI-28.
Keywords: other

first: Sicheng

last: Wen

first: lennart

last: Hammarström


title: Regulation of 22q11 orthologous genes during mouse development

status: Public on Jun 14 2006

city: Roma

first: Francesca

last: Amati

address: Via Montpellier 1

department: Biomedicine and Prevention

country: Italy

institute: University of Rome Tor Vergata

summary:
22q11-deletion syndrome (22q11DS) is a developmental anomaly caused by a microdeletion on human chromosome 22q11. Although mouse models indicated Tbx1 as the gene responsible of the syndrome, the phenotypic spectrum of del22q11 patients is complex suggesting that gene-gene and gene-environment interactions, probably during embryonic development, are crucial in delineating the pathogenesis of 22q11DS. In order to define cis-acting regulatory effects of 22q11Ds haploinsufficiency during development we analysed the expression pattern of MM16 mouse genes, that is the syntenic region to 22q11, in RNA from total embryos at different stages (from 4.5 dpc to 14.5 dpc; corresponding to pharyngeal development) by a low density microarray (22q11DS-chip).
Keywords: time-course

overall_design:
Deletion of 22q11.2 chromosomal region causes the most common microdeletion syndrome in man with an incidence of approximately 1:4000 live births (Scambler, 2000). The major malformations include congenital heart defects such as truncus arteriosus (TA) and interrupted aortic arch type B (IAA-B), hypo/aplasia of the parathyroid glands, hypo/aplasia of the thymus gland, and craniofacial dysmorphism. However more than 180 clinical symptoms are due to 22q11 microdeletion (Ryan et al, 1997); in particular the psychiatric disorders are one of the more prevalent phenotype in adult patients (Basset et al., 2003). An unsolved question regarding 22q11 deletions is whether the associated congenital defects are caused by a single dose-dependent 22q11 gene or rather by the combined loss of multiple linked genes that may act in a common pathway or in parallel during a critical period of pharyngeal development.
In order to answer to this question we have turned out our attention at analysing the expression level of 68 murine genes, 39 hortologues to human 22q11 genes and 29 mapping outside. The expression level of these 68 genes was analysed in mouse embryos at different stages (from 4.5 dpc to 14.5 dpc), corresponding to the pharyngeal development. The RNA reference used in this study was obtained by pooling different CD1 mouse embryos at 18.5 dpc; total RNA was isolated by the TRIZOL standard protocol (Invitrogen).

first: Michela

last: Biancolella

first: Alessio

last: Farcomeni

first: Daniela

last: Minella

first: Susana

last: Bueno

first: Stefania

last: Giallonardi

first: Lucia

last: Vecchione

first: Giovanni

last: Chillemi

first: Alessandro

last: Desideri

first: Giuseppe

last: Novelli


title: A role for TFIIIC transcription factor complex in genome organization

first: Shiv

last: Grewal

summary:
ChIP-chip analyses of TFIIIC subunit, Sfc6, and RNA Polymerase III subunit, Rpc130, across the S. pombe genome.
Keywords: ChIP-chip

overall_design: Chromatin immunoprecipitated DNA recovered with either Sfc6 or Rpc130 antibody from wild-type asynchronous growing fission yeast cells and DNA from whole cell extracts were amplified by random priming and respectively labeled with Cy5 and Cy3.  Labeled DNA were mixed and hybridized onto a 44k pombe Agilent oligo array.  Data were processed using Agilent scanner and Feature Extraction software.

first: Ken-ichi

last: Noma

first: Hugh

last: Cam

first: Richard

middle: J

last: Maraia


title: Evaluation of technical (array-to-array) reproducibility of L. vannamei microarray

status: Public on Jun 01 2006

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

summary:
Five aliquots of the same RNA sample were labeled and hybridized in parallel to the L. vannamei microarray, in order to assess the technical reproducibility of the tool
Keywords: technical validation

overall_design: A sample of gill total RNA was divided in 5 identical aliquots, and each aliquot was labeled and hybridized to an array. The co-relation among the global expression profiles obtained was assessed.

first: Javier

last: Robalino

first: David

last: McKillen

first: Harold

middle: F

last: Trent

first: Yian

last: Chen

first: Craig

last: Browdy

first: Jonas

last: Almeida

first: Paul

last: Gross

first: Robert

middle: W

last: Chapman

first: Gregory

last: Warr


title: Sex and line specific gene expression and alternative splicing in Drosophila revealed

city: Gainesville

first: Lauren

middle: M.

last: McIntyre

state: FL

department: Dept. of Molecular Genetics and Microbiology

institute: University of Florida

summary:
Many multi-exon genes are subject to alternative splicing, which is thought to increase phenotypic complexity by allowing a single locus to produce multiple functionally distinct proteins.  However, genetic and developmental variation in alternative splicing has never been examined systematically.  We therefore undertook a genome-wide analysis of sex- and genotypic-specific splicing in Drosophila in conjunction with sex- and line-specific transcription.
Keywords: microarray, sexual dimorphism, alternative splicing, genetical genomics, genetic variation

overall_design: Experiments were conducted on flies from two standard strains of D. melanogaster: Oregon R [79] and 2b3 [80], and six randomly chosen recombinant inbred (RI) lines derived from these parental lines [81].  Each of the 8 lines was grown in four separate replicates of small mass-matings containing on average 20 adults, with a sex ratio of 1.  We analyzed four independent biological replicates for each line and sex combination with a Cy3/Cy5 dye swap on the sexes.

first: Lisa

last: Bono

first: Anne

last: Genissel

first: Rick

last: Westerman

first: Damion

last: Junk

first: Marina

last: Telonis-Scott

first: Larry

last: Harshman

first: Marta

middle: L

last: Wayne

first: Artyom

last: Kopp

first: Sergey

last: Nuzhdin


title: Gene Expression in Granulosal Cells From Persistent Follicles

city: Morgantown

first: Brandon

last: Lingenfelter

state: WV

address: G058 Agricultural Sciences Bldg

department: Animal & Veterinary Sciences

institute: West Virginia University

summary:
Granulosa cells form highly specialized membrane connections with the oocyte and each other, allowing the passage of regulatory molecules and metabolites between cells. These connections must be maintained for oocyte growth in vitro and have been implicated in oocyte aging both in vivo and in vitro. Changes in gene expression in granulosa cells from persistent follicles may adversely affect oocyte development. Previous studies have reported changes in gene expression in oocytes and high embryonic loss associated with persistent follicles. Cows were assigned randomly to two groups; growing follicles on day 8 (young cells) and persistent follicles on day 15 (aged cells) of the estrous cycle (estrus = d 0). Cows were super-stimulated with Folltropin-V® on day 1 to 4 and received 25 mg PGF2α on day 6. Cows in P15 group received progesterone from CIDR-B devices on day 4 through 13. Follicles were aspirated immediately after colpotomy. Granulosa cells were collected from each aspirate, pelleted, and stored at -80° until total RNA isolation. Three biological replicates, after linear amplification, were used in a direct comparison microarray experiment using a bovine oligo array. Microarray data were analyzed using GenePix AutoProcessor (GPAP 3.2; http://darwin.biochem.okstate.edu/gpap32/). The analysis revealed up regulation of 272 genes (M-value ≥ 0.9, q ≤ 0.05) and down regulation of 203 genes (M-value ≤ -0.9, q ≤ 0.05) in granulosa cells from persistent follicles (aged cells) in comparison to growing follicles (young cells). Grouping of these genes into themes revealed down regulation of many genes involved in protein metabolism, amino acid transport, and mitosis regulation and an up-regulation of apoptotic genes. However, there was no change in the expression of gap junction genes. These data suggest that aged cells have a reduced capacity to regulate mitosis and provide amino acids to the oocyte. Supported by project Hatch 427 (NE 1007) of the WV Agricultural and Forestry Experiment Station.
Keywords: direct comparison, cell type comparison

overall_design: This experiment employed a direct comparison between day 8 and day 15 granulosa cells. There are two technical replicates per slide and a total of 5 biological replicates were used for each sample (5 from day 8 and 5 from day 15). Three day 8 samples were labeled with Cy3 and two with Cy5. Two day 15 samples were labeled with Cy3 and three samples with Cy5.

last: Dailey

first: Keith

last: Inskeep

first: Michael

last: Vernon

first: Daniel

last: Poole

first: Justin

last: Rhinehart

first: Jianbo

last: Yao


title: Expression data from untreated and IAA treated cells

city: Napoli

first: Roberto

last: Defez

address: via Castellino 111

department: Institute of Genetics and Biophysics

institute: National Research Council

summary:
We investigated the physiological changes induced by indoleacetic acid (IAA) treatment in the totally sequenced Escherichia coli K-12 MG1655.
We used DNA macroarrays to measure the mRNA levels for all the 4,290 E. coli protein-coding genes and observed that 50 genes (1.1 %) exhibited significantly different expression profiles. In particular, genes involved in the tricarboxylic acid cycle (TCA), glyoxylate shunt, and amino acid biosynthesis (leucine, isoleucine, valine and proline) were up-regulated, whereas the fermentative adhE gene was down-regulated. To confirm the indications obtained from the macroarray analysis we measured the activity of 33 enzymes involved in the central metabolism and found an activation of the TCA cycle and the glyoxylate shunt.
Keywords: treatment

overall_design:
Gene expression levels for control and IAA-treated cells were monitored by using DNA macroarray membranes containing the whole E. coli K-12 MG1655 genome.To identify ORFs whose expression was altered by addition of IAA, the two growth conditions (with and without IAA addition) were compared by determining the ratio of the corresponding intensities of each pair of ORF-specific spots on two blots. These ratios represent the relative transcript levels of each E. coli ORF under the same growth condition. Each ORF-specific spot was present in duplicate, and the mean of the normalised intensity values of the duplicate spots of each gene was used for further analysis.

Cells were grown aerobically at 37 °C in M9 minimal medium containing 0.4 % L-arabinose as carbon source. Exponentially growing E. coli K-12 (MG1655) cultures (OD600 = 0.6) were split into two aliquots; to the first one, an IAA solution was added to a final concentration of 0.5 mM and the other was left untreated (control). After two hours (OD600 = 1.2 for both cultures) different cell batches, taken from IAA-treated and untreated cells, were aliquoted, frozen in liquid nitrogen for 5 min and stored at –80 °C for use in experiments. After RNA purification, probe synthesis, labelling, arrays (Panorama E. coli gene arrays) hybridisation and washing steps were performed using the protocol provided by the manufacturer (Sigma-Genosys Biotechnologies Inc.).
The exposed phosphorimager screens were scanned and were analysed to determine the signal intensities for each spot by summing the value of each pixel within the boundaries of the spot using Image-Quant (version 3.0) software (Molecular Dynamics). Background values were measured in the surrounding region of the four corner grids containing E. coli genomic DNA, as a positive control, and empty spots.  The intensity values for each spot were exported from ImageQuant to Microsoft Excel spreadsheet. Each ORF-specific spot was present in duplicate, and the mean of the normalised intensity values of the duplicate spots (a and b) of each gene was used for further analysis. To avoid extreme intensity ratio for genes close to or below the detection limit, signal intensity values corresponding to a signal-to-background (S/B) ratio < 2.0 were scaled up to a value corresponding to the normalised background means. To identify ORFs whose expression was altered by addition of IAA, the two growth conditions (with and without IAA addition) were compared by determining the ratio of the corresponding intensities of each pair of ORF-specific spots on two blots. These ratios represent the relative transcript levels of each E. coli ORF under the same growth condition. Ratios were calculated such that the log2 of the absolute value of the expression ratio was positive for intensities that were higher in IAA-treated cells and negative for intensities that were higher in control cells. A gene was considered significantly regulated when the relative intensity was least two times greater than the background expression threshold and the log2 expression ratio was greater than or equal to 0.8 (up-regulated) or less than or equal to -0.8 (down-regulated) and greater than 4 times standard deviation from the mean.

first: Carmen

last: Bianco

first: Esther

last: Imperlini

first: Raffaele

last: Calogero

first: Beatrice

last: Senatore

first: Piero

last: Pucci


city: Davis

first: Sharon

last: Squazzo

address: 4617 GBSF, 451 E. Health Sci. Dr.

department: Pharmacology

institute: UC Davis Genome Center

summary:
Suz12 samples are biological replicates from F9 cells crosslinked on different days.  EZH2 and H3me3K27 samples are from the same batch of crosslinked cells as Suz12 replicate 2. For each sample matched total was prepared in parallel. Amplicons were made and hybridized on custom genomic tiling arrays.
Keywords: ChIP-chip

overall_design: Goal was determination of Suz12, EZH2 and H3me3K27 binding sites in F9 cells using a custom genomic tiling array from Nimblegen.


summary:
For each sample a matched total was produced in parallel.  Amplicons were made from each and hybridized on human 5.0 kb promoter arrays from Nimblegen.
Keywords: ChIP-chip

overall_design: Goal was to determine Suz12 target promoters in Ntera, MCF7 and SW480 cells using ChIP-chip methodology.


title: Operon/Compugen experiments for cross-platform study

city: Boston

first: Winston

middle: Patrick

last: Kuo

address: 188 Longwood Avenue

department: Genetics

institute: Harvard Medical School

summary:
Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than “in-house” arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
Keywords: cross platform microarrays

overall_design:
RNA samples used were aliquoted from two pools of samples: C57/B6 adult mouse retina (MR) and Swiss-Webster postnatal day one (P1) mouse cortex (MC). The mouse cortex was used as a reference sample for the dual-dye platforms.Five replicates of each sample were used to assess the degree of variation in the expression data within each platform.

In this case probes from Operon and Compugen were spotted onto the same slide.


title: Gene expression of RAW 264.7 cells treated with LPS, ISO, PGE2, LPS PLUS ISO, and LPS PLUS PGE2

first: Sangdun

last: Choi

summary:
LPS plus ISO and LPS plus PGE2 had non-additive effects on gene expression in RAW 264.7 cells
Keywords: time course

overall_design: total RNA from RAW 264.7 cells (macrophages) treated with Lipopolysaccharide (LPS), Isoproterenol (ISO), Prostaglandin E2 (PGE2), LPS PLUS Iso, and LPS PLUS PGE2 vs total RNA from time_matched_control RAW 264.7 cells (macrophages) cultured in media, 1 h, 2 h, and 4 h time course with triplicates, with dyeSwap measurements on custom Ailgent Oligo arrays

first: Xiaocui

last: Zhu

first: MiSook

last: Chang

first: Robert

last: Hsueh

first: Ron

last: Taussig

first: Kelly

last: Smith

first: Mel

last: Simon


title: MWG BioTech experiments for cross-platform study

overall_design: RNA samples used were aliquoted from two pools of samples: C57/B6 adult mouse retina (MR) and Swiss-Webster postnatal day one (P1) mouse cortex (MC). The mouse cortex was used as a reference sample for the dual-dye platforms.Five replicates of each sample were used to assess the degree of variation in the expression data within each platform.


title: Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1(E2F)does not require LIN-35(pRB)

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

institute: Yale University School of Medicine

summary:
Microarray-based expression profiling of dissected gonads from efl-1, dpl-1 and lin-35 mutants reveals that EFL-1 and DPL-1 promote expression of an extensively overlapping set of target genes, consistent with the expectation that these two proteins function as a heterodimer.  Regulatory regions upstream of many of these target genes have a canonical E2F binding site, suggesting that their regulation by EFL-1/DPL-1 is direct.  Many EFL-1/DPL-1 responsive genes encode proteins required for oogenesis and early embryogenesis, rather than cell cycle components.  By contrast, LIN-35 appears to function primarily as a repressor of gene expression in the germ line, and the genes that it acts on are for the most part distinct from those regulated by EFL-1 and/or DPL-1
Keywords: Mutant analysis of dpl-1, efl-1, and lin-35 in dissected C. elegans gonads

overall_design: We isolated dissected gonads from dpl-1, efl-1 and lin-35 mutant adults and compared each to control dissected gonads.  RNA was linearly amplified prior to labeling for all genotypes.  Each comparison was done in triplicate (dpl-1 and lin-35) or in quadruplicate (efl-1) on independently grown and isolated animals.


title: cDNA (Cepko BMAP) experiments for cross-platform study


title: GE Healthcare (Amersham) experiments for cross-platform study including site 2 data

overall_design:
RNA samples used were aliquoted from two pools of samples: C57/B6 adult mouse retina (MR) and Swiss-Webster postnatal day one (P1) mouse cortex (MC). The mouse cortex was used as a reference sample for the dual-dye platforms.Five replicates of each sample were used to assess the degree of variation in the expression data within each platform.

Additionally there were five replicates of each sample to assess the degree of variation in the expression data across different sites (site 2).


title: SNP Analysis of Primary Glioblastoma Cell Lines

status: Public on Jun 16 2006

city: Los Angeles

first: Cho-Lea

last: Tso

address: 10833 Le Conte Avenue

department: Surgery

institute: University of California, Los Angeles

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

summary:
Genomic abnormalities that are associated with mesecnhmal phenotype of GBM were detected in glioblastoma cell lines.
Keywords: SNP array analysis of glioblastome cell lines.

overall_design: Whole genomic DNA of GBM cell lines (W-98, D431, F-502, and S-496) and the fibroblast cell line were evaluated for allelic imbalances and chromosomal copy number abnormalities by using a highdensity single-nucleotide polymorphic (SNP) array analysis (Affymetrix XbaI 131 Array).

first: Cho-lea

first: Peter

last: Shintaku

first: James

last: Chen

first: Zugen

first: Koji

last: Yoshimoto

first: Paul

last: Mischel

first: Timothy

last: Cloughesy

first: Linda

last: Liau

first: Stanley

last: Nelson


title: ABI experiments for cross-platform study

first: Winston

last: Kuo


title: Gene expression changes in feeding female and male lone star ticks, Amblyomma americanum (L)

status: Public on Jun 08 2006

city: Stillwater

first: Richard

middle: C.

last: Essenberg

state: OK

address: 246 NRC

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

summary:
A collection of 1145 clones from an EST project on female tick salivary gland genes was hybridized on glass slides to RNA extracted from several feeding stages of adult female tick salivary glands, including unfed and replete, and from adult male ticks, either unfed or fed in the presence or absence of female ticks. In the female ticks, the early fed (<50 mg) and partially fed (30-200 mg) groups were very similar.  The fast feeding (350-500 mg) and replete ticks were similar to each other, but different from the partially fed.  The unfed ticks were more similar to the fast feeding – replete groups than the early fed-partially fed groups.  In the males, there were differences between the males fed in the presence or absence of females, but overall, these groups were very similar. The unfed ticks were significantly different from the fed ticks.  Males showed clear differences with females in expression, as well.  The unfed females had high levels of genes involved in protein synthesis, while genes possibly involved in survival on the host, such as anticoagulants, seemed to be most expressed in the early and partially fed states.  By contrast, in the males, the protein synthesis genes were expressed more in all three groups, while the putative secreted genes for survival were expressed less.
Keywords: time course, effect of feeding, sex, effect of presence of females

overall_design: All samples were compared to the partially fed females.  Females consisted of five groups: unfed, early fed, partially fed, fast feeding and replete.  Four or five biological replicates were done of each, with the dyes used in both possible ways.  In the males, three groups were used: unfed, feeding in the presence of females, and feeding in the absence of females.  Two biological replicates were done of the feeding males, and one of extracts was hybridized twice  for the males fed in the presence of females.  Unfed males used one RNA sample, extracted from a large pool of ticks.

first: Majd

middle: N

last: Aljamali

first: Vijay

middle: G

last: Ramakrishnan

last: Tucker

first: Hua

last: Weng

first: Patricia

last: Ayoubi

first: John

middle: R

last: Sauer

middle: C


title: Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

summary:
Xylella fastidiosa is a phytopathogenic bacterium responsible for diseases in many economically important crops. Although different strains have been studied, little is known about X. fastidiosa stress responses. One of the best characterized stresses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation, and to promote degradation of the irreversibly denatured polypeptides. To investigate X. fastidiosa genes involved in the heat shock response, we performed a whole genome microarray analysis in a time-course experiment. Globally,
261 genes were induced (9.7%) and 222 genes were repressed (8.3%). The expression profiles of the differentially expressed genes were grouped and their expression patterns were validated by quantitative RT-PCR experiments. As expected, genes that presented the higher induction rates encoded chaperones and proteases. We determined the transcription start site of six heat shock inducible genes and analyzed their promoter regions, which allowed us to propose a putative consensus for 32 promoters in Xylella and suggest additional genes as putative members of this regulon. Besides the induction of classical heat shock protein genes, we observed the up-regulation of virulence-associated genes such as vapD, hemagglutinins, hemolysin and xylan degrading enzymes, which may indicate the importance of heat stress to bacterial pathogenesis. In addition, we observed the repression of genes related to fimbriae, aerobic respiration, protein biosynthesis, and the induction of genes related to the extracytoplasmic stress response and some phage-related genes, revealing the complex network of genes that work together in response to heat shock.
Keywords: stress response; heat shock response

overall_design: Direct comparison between heat-shock condition and control (29oC) condition. Some hybridizations are dye-swaped. There are at least 3 biological replicates (independent harvest) and 2 technical replicates of each array (L - left and R - right).

first: Suely

last: Gomes


title: Gastric Cancer Gene Expression Profiling

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary:
This series studied the patterns of gene expression among different types of gastric tumors. Gastric tumors and adjacent non-tumor normal tissues were obtained from 50 gastric cancer patients of diverse stages (IA, IB, II, IIIA, IIIB, and IV), tumor types (intestinal, diffuse, or mixed), and degree of tumor differentiation (moderately or poorly differentiated).
Keywords: Cancer patient samples

overall_design: We obtained both tumor and normal tissue samples from the same patient and hybridized them together to remove any individual biological variations unrelated to gatric cancer progression. We hybridized each patient's sample twice with dye swapping.

first: Jeong-Hwan

first: Heun-Sik

last: Lee

first: Seung-Moo

last: Noh

first: Kyu-Sang

last: Song

first: June-Sik

last: Cho

first: Hyun-Yong

last: Jeong

first: Woo-Ho

first: Young-Il

last: Yeom

first: Nam-Soon

first: Sangsoo

first: Hyang-Sook

last: Yoo

first: YongSung


title: Heat Shock response of the phytopathogenic bacteria Xylella fastidiosa

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

summary:
This is the study of the Heat Shock response of phytopathogenic bacteria Xylella fastidiosa. This series keeps the 25 minutes 40oC stimulus response (Aug 2005).
Keywords: stress response; heat shock response


title: Saccharomyces cerevisiae alpha factor cell cycle

first: Tata

last: Pramila

address: 1100, Fairview Avenue N

department: Basic Sciences

institute: FHCRC

summary:
Yeast cell cycle microarray to identify global trancription profile.
Keywords: cell cycle time course

overall_design: Cells were synchronized with alpha factor and sampled every 10 min across 2 cell cycles. A total of 13 samples were analyzed. No replicates were included. cDNA of the cell cycle samples were labelled with Cy5. For Cy3 labelling, asynchronous yeast population was used.


title: set2, set2sir4 transcription profiles

city: San Francisco

first: Rachel

last: Tompa

department: Biochemistry

institute: UC San Francisco

summary:
Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type
Keywords: quadruplicate mutant:WT analysis, with dye-swapping

overall_design: mutant and wild-type grown to log phase, YPAD, 30C, purified mRNA, reverse-transcribed to cDNA, labelled with Cy5/Cy3, hybridized to whole genome ORF microarrays


title: Auratus goldfish genome project: Gene expression profiling in the brain of male goldfish exposed to 17α-EE2

status: Public on May 31 2006

first: Christopher

middle: Joseph

last: Martyniuk

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary:
A goldfish brain enriched cDNA combined with a carp microarray (Gracey et al., 2004). Experiment exposed adult male goldfish to 17-alpha ethinylestradiol for two weeks (two doses - 30 ng/L and 300 ng/L)
Keywords: estrogenic exposure, dose response,

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design:
4 arrays per group
30 ng/L = slide 3, 15, 31, 41 (n=4)

300 ng/L = slide 13, 18, 32, 49 (n=3)
-slides 13 and 18 are dye swaps

first: Huiling

last: Xiong

first: Kate

last: Crump

first: Suzanne

last: Chui

first: Ravinder

last: Sardana

first: Ashlie

last: Nadler

first: Emily

last: Gerrie

first: Xuhua

last: Xia

first: Vance

last: Trudeau


title: Profiling of WSSV infection in hepatopancreas of shrimp

first: MarineGenomics

last: Project

summary:
Profiles of gene expression in hepatopancreas isolated from shrimp experimentally infected with White Spot Syndrome Virus were compared to those of un-infected controls
Keywords: response to viral disease

overall_design: Two groups of eight shrimp were compared in terms of hepatopancreas gene expression, 40 hours after challenge with White Spot Syndrome Virus

first: Javier

last: Robalino

first: David

last: McKillen

first: Harold

last: Trent

first: Yian

middle: A

last: Chen

first: Craig

last: Browdy

first: Jonas

middle: S

last: Almeida

first: Paul

last: Gross

first: Robert

last: Chapman

first: Gregory

last: Warr


title: GAP aflR- vs WT timecourse

city: Lynchburg

first: Michael

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

summary:
The carcinogen aflatoxin is synthesized by a cluster of genes that are regulated by the transcriptional factor, AflR.  Most, but not all of these genes, have a consensus binding site for AflR in their 5’ untranslated region.  Because aflR resides within the biosynthetic cluster, is has been suggested that it regulates only genes within the cluster.  The objective of this study was to identify those genes transcriptionally regulated by AflR and to determine if any of those genes reside outside the aflatoxin biosynthetic cluster.  To address this objective, we employed a cDNA microarray of 5,002 genes from Aspergillus flavus to monitor the expression of genes in a wild type and an aflR deletion strain of A. parasiticus.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = regulation
Keywords = secondary metabolism
Keywords: time-course

first: Jiujiang

last: Yu

first: William

last: Nierman

first: Stanley

last: Kim

first: Bethan

last: Pritchard

first: Deepak

last: Bhatnagar

first: Thomas

middle: E

last: Cleveland

first: Gary

last: Payne


title: Tissue-specific expression profiles in L. vannamei

first: MarineGenomics

last: Project

summary:
RNA from different tissues of Litopenaeus vannamei was used to test the ability of the microarray to discriminate tissue-specific gene expression profiles
Keywords: validation, tissue comparison

overall_design: RNA from circulating hemocytes, gills, hepatopancreas, or muscle (3 biological replicates each) was hybridized to the L. vannamei microarray. The number of hybridizing genes was noted and the relationships among the global profiles in each sample were determined by cluster analysis

first: Javier

last: Robalino


title: Effect of ppGpp on Salmonella Typhimurium gene expression

status: Public on May 30 2006

city: Norwich

first: Arthur

last: Thompson

state: Norfolk

address: Colney Lane

department: Food Safety Science

institute: Institute of Food Research

summary:
The expression profile of an S. Typhimurium mutant strain unable to synthesise ppGpp (relAspoT deletions) was compared to the wild-type strain. The effect of ppGpp on virulence gene expression was studied under 4 different growth conditions that induce virulence gene expression.
Keywords: genetic modification

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

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

overall_design: Study comprised 4 separate experiments (with 2 strains and 4 replicates for each strain per growth condition).  The experiments were indirect comparisons using Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

first: Sacha

last: Lucchini

first: Jay

last: Hinton

first: Karsten

last: Tedin

first: Matthew

last: Rolfe


title: Genomic and genetic characterization of rice Cen3 reveals evolutionary remnants of a complex centromere (mRNA data)

status: Public on May 26 2006

city: St. Louis

first: Blake

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division.  In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping.  Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3.  Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO.  Cen3 includes a ~1,851-kb domain associated with CENH3, the centromere-specific histone H3 variant.  This CENH3-associated chromatin domain is embedded within a 3,083-kb region that lacks genetic recombination.  We detected several active genes within the CENH3-binding domain based on a comprehensive annotation and a survey for matches with mRNA signatures.  However, the gene density in the CENH3-binding domain is significantly lower than in the pericentromeric domains.  In contrast, the CENH3-binding domain contains a higher percentage of repetitive DNA sequences than the pericentromeric regions.  These results suggest that Cen3 is in the process of evolving from a genic region toward an accumulation of satellite repeats and transposable elements that is more characteristic of centromeres in most complex eukaryotic species.
Keywords: MPSS, mRNA, transcriptome, rice, centromere, Cen3, chromosome 3

overall_design: MPSS was performed to sequence small RNAs that derived from 16 untreated and 6 abiotic-treated diverse tissue libraries.  The method for the MPSS sequencing of mRNAs is described in Brenner et al. (Nat Biotechnol. 2000 18:630).


title: Translation State Array Analysis of Thrombin Stimulated Human Endothelial Cells

city: Salt Lake City

first: Douglas

middle: I.

last: Schmid

state: UT

department: HMBG

institute: University of Utah

summary:
Confluent human umbilical vein endothelial cells (HUVECs) were exposed to Thrombin (2 U/mL) for 2 hours.  Ribosomal profiling via gradient centrifugation and fractionation was used to separate monosome, or under-translated, and polysome, or actively translated, mRNA species that were then used to probe cDNA arrays, a process known as Translation State Array Analysis (TSAA).  Four samples were obtained from these experiments, Control Monosome, Control Polysome, Thrombin Monosome, and Thrombin Polysome.  Using the normalized signal intensities from the GeneFilters, we calculated a translation index, or measure of movement of an mRNA molecule from the monosome to the polysome fraction upon stimulation.  This calculation was made as follows:  (thrombin polysome/thrombin monosome)/(control polysome/control monosome).  Translational indices greater than 2.5 (upregulated) or lower than 0.4 (downregulated) were chosen for further study.  TSAA data suggests that JunB is translationally regulated by thrombin stimulation.  Immunocytochemistry, western blotting and RT-PCR were used to verify the results of TSAA.
Keywords: Translation State Array Analysis

overall_design:
Polysome Profiling.  HUVECs were stimulated with thrombin (2 U/mL) for 2 hours.  Cycloheximide (CHX) was added to a final concentration of 100 ng/mL for 5 minutes and cells were then rinsed with cold HBSS containing CHX (100 ng/mL) and scraped from the dish and pelleted by centrifugation (2000 x g, 5 minutes).  The supernatant was removed and cells were carefully resuspended in 375 microL Low Salt Buffer (LSB; 20 mM Tris, 10 mM NaCl, 3 mM MgCl2, pH 7.4) + RNasin (40 U/mL) + DTT (10 nM) for 3 minutes on ice.  125 microL LSB Lysis buffer (LSB containing 200 mM sucrose and 1.2% Triton-X100) was then added and cells disrupted by pipetting.  The mixture was then transferred to 1.7 mL microfuge tubes and centrifuged (20,000 x g, 1 minute, 4 degrees C) to remove nuclei and cellular debris.  The supernatant was transferred to a new tube containing 50 microL LSB + RNasin (40 U/mL) + DTT (10 nM) and 15 microL 5M NaCl.  This mixture was then layered onto prepoured gradients (15-50% sucrose in LSB).  Gradients were spun at 43,700 rpm for 90 minutes (4 degrees C) and then run on a density gradient flow cell fractionator (Isco) to obtain ribosomal profiles.  Ribosomal fractions corresponding to monosomes (M) and polysomes (P) (Figure 1) were collected into Trizol LS (Invitrogen) and total RNA isolated according to the directions of the manufacturer.  Total RNA was reverse transcribed using oligo dT primers in the presence of 33P dCTP to generate labeled cDNA probes from the M and P associated mRNA fractions of control and stimulated cells and these probes used to detect specific array elements on four identical Research Genetics (ResGen) Named Human Gene cDNA GeneFilters (GF 211, Invitrogen).  These filters were washed using high stringency conditions and exposed to phosphorimaging screens for analysis using Pathways 3, proprietary software included with the ResGen filters.
Hybridization signals were normalized to the average intensity of the hybridization signals from the particular array filter to correct for differing global hybridization efficiencies between filters.  To determine if a particular hybridization signal was significantly above background levels, an initial screen of the array elements was conducted by dividing the hybridization signal of an individual cDNA spot by the background signal on particular filter.  Background signal levels were determined using the Pathways 3 analysis software that measures the signal intensity of the area between cDNA spots and averages that signal over the area of the entire array.  Array elements were considered to be distinguishable from background if the hybridization signal/background ratio was greater than 1.1.  Signal intensities from each filter were normalized by dividing the raw signal intensity of the cDNA spot by the average signal intensity for the entire filter.  The translation state (TS) of each qualifying array element was determined by dividing the normalized signal intensity of the element in the polysome fraction by the normalized signal intensity of the element in the monosome fraction:  TS=P/M.  The Translation Index (TLI), a measure of the change of translation states of individual genes, was determined by calculating the ratio of the treated cell TS to the control cell TS; TLI = TSe/TSc where e represents experimental or treated conditions and c represents controls.  In this scenario, a gene that is not regulated by translation would have a TLI value of 1, actively translated genes would have a TLI value greater than 1, whereas a poorly translated or under-translated gene would have a TLI value less than 1.  Arbitrary TLI values of 2.5 and 0.4 were used to categorize individual array elements as being translationally regulated.
A measure of transcriptional activity was also determined from the signal intensities of the array elements.  Summing the normalized signal intensities from the M and P fractions of the experimental cells and dividing that value by the sum of the normalized signal intensities from the control fractions calculated the Transcription Index (TCI).  Therefore, TCI = (Me + Pe)/(Mc + Pc).  If transcript levels for a specific gene do not change, the TCI value for that gene will be 1.  Genes that are transcribed upon stimulation of the cells will have a TCI value greater than 1, while genes that are not transcribed or transcription is down-regulated upon stimulation will have a TCI value less than 1.  Arbitrary values of 2 and 0.5, a doubling or halving of the amount of mRNA for that element, respectively, were used to categorize individual array elements as being transcriptionally regulated.

middle: I

first: Huimiao

last: Jiang

first: Andrew

last: Weyrich

middle: M

last: McIntyre

first: Guy

last: Zimmerman

first: Larry

last: Kraiss


title: Large scale copy number variation (CNV) at 14q12 is associated with the presence of genomic abnormalities in neoplasia.

status: Public on May 25 2006

city: Toronto

first: Chung-Hae

last: Lee

address: 9th Floor Rm. 717, 610 University Ave

department: Applied Molecular Oncology

institute: Ontario Cancer Institute, Princess Margaret Hospital

type: Genome variation profiling by genome tiling array

summary:
Background:  Advances made in the area of microarray comparative genomic hybridization (aCGH) have enabled the interrogation of the entire genome at a previously unattainable resolution.  This has lead to the discovery of a novel class of alternative entities called large-scale copy number variations (CNVs).  These CNVs are often found in regions of closely linked sequence homology called duplicons that are thought to facilitate genomic rearrangements in some classes of neoplasia.  Recently, it was proposed that duplicons located near the recurrent translocation break points on chromosomes 9 and 22 in chronic myeloid leukemia (CML) may facilitate this tumor-specific translocation.  Furthermore, ~15-20% of CML patients also carry a microdeletion on the derivative 9 chromosome (der(9)) and these patients have a poor prognosis.  It has been hypothesised that der(9) deletion patients have increased levels of chromosomal instability.
Results:  In this study aCGH was performed and identified a CNV (RP11-125A5, hereafter called CNV14q12) that was present as genomic gain or loss in 10% of control DNA samples derived from cytogenetically normal individuals.  CNV14q12 was the same clone identified by Iafrate et al. as a CNV.  Real-time polymerase chain reaction (Q-PCR) was used to determine the relative frequency of this CNV in DNA from a series of 16 CML patients (both with and without a der(9) deletion) together with DNA derived from 36 paediatric solid tumors in comparison to the incidence of CNV in control DNA.  CNV14q12 was present in ~50% of both tumor and CML DNA, but was found in 72% of CML bearing a der(9) microdeletion. Chi square analysis found a statistically significant difference (p ≤ 0.001) between the incidence of this CNV in cancer and normal DNA and a slightly increased incidence in CML with deletions in comparison to those CML without a detectable deletion.
Conclusions:  The increased incidence of CNV14q12 in tumor samples suggests that either acquired or inherited genomic variation of this new class of variation may be associated with onset or progression of neoplasia.
Keywords: CML, array CGH, aCGH, BAC array

overall_design: Cy5 -labelled genomic DNA were cohybridized with Cy3-labelled control XY genomic DNA onto Spectral Genomics human BAC arrays or BC Cancer Agency SMRT arrays and processed for aCGH analysis. Normalization and analysis were performed with NormalizeSuite V2.


title: Transcriptome analysis of A. nidulans growing in different carbon sources

city: Kgs. Lyngby

first: Ana Paula

last: Oliveira

address: Building 223

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary:
Aspergillus nidulans is a model organism for aspergilli, an important group of filamentous fungi that encompasses human and plant pathogens, as well as industrial cell factories. Aspergilli have a highly diversified metabolism and both in connection with their biotechnological application as well as their interaction with other cells (humans or plants), it is valuable to understand how their metabolism is regulated. We therefore performed genome-wide transcription analysis of A. nidulans grown on three different carbon sources (glucose, glycerol, and ethanol) with the objective to identify global regulatory structures. We furthermore reconstructed the complete metabolic network of this organism, and this resulted in linking of 666 genes with metabolic functions, as well as assigning metabolic roles to 472 genes that had not been annotated earlier. Through combinations of the reconstructed metabolic network and the transcription data, we identified subnetwork structures that pointed to coordinated regulation of genes involved in many different parts of the metabolism.
Keywords: carbon sources, metabolism, comparative genomics

overall_design: Aspergillus was grown in three different carbon sources - glucose, ethanol and glycerol. Cultivations were run in triplicate, and each biological replicate was load on a different chip. Therefore, we analyzed nine arrays (3 carbon sources x 3 biological replicates).

first: Helga

last: David

first: Gerald

last: Hofmann

first: Ana

first: Hanne

last: Jarmer

first: Jens

last: Nielsen


title: F8 broiler by Leghorn and broiler by Fayoumi spleen at day 7 and 8 after challenge with SE

city: Ames

first: Susan

middle: J

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
In the two F8 advanced crosses of broiler by Leghorn and broiler by Fayoumi, birds at day 1 were challenged with Salmonella enteritidis (SE). Spleen were collected at day 7 and 8. SE bacterial load in spleen were measured. Based on the bacterial load, birds were divided into high and low SE load groups.
Keywords: Salmonella enteritidis challenge

overall_design: At each line cross and each day time point, three pair comparisons among high SE load, low SE load, and non-SE were used for the loop design, and two biological replicates were used.

first: Huaijun

last: Zhou

first: Dan

last: Nettleton


title: TLR7 gene duplication accelerates autoimmunity and promotes nucleolar-specific B cells

city: Rockville

first: Prapaporn

last: Pisitkun

address: 12441 Parklawn Drive, TW2, Room 217

department: NIAID

institute: NIH

summary:
Systemic autoimmune diseases such as lupus and scleroderma are characterized by the loss of tolerance to nuclear antigens, but the mechanisms by which specific autoantibodies are selected are unclear.  Here we report that B cells containing the Y-linked autoimmune accelerator (Yaa) locus are intrinsically biased towards nucleolar antigens due to a duplication of TLR genes in the pseudoautosomal region that makes them more responsive to TLR7 ligands and augments the Btk-dependent signaling pathway.  These findings provide genetic evidence that naturally occurring differences in expression of TLR7 have a dramatic impact on antigen selection in autoimmunity.
Keywords: genetic modification, Yaa locus

overall_design: Follicular B cells were isolated from spleen of C57BL/6 male and C57BL/6.Yaa male. Four mice from each group using in this analysis were 2 months old. Dye swab labeled RNA had been done in one mice from each group.


title: Growth in minimal media with maltose

status: Public on May 20 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose versus growth in rich LB media
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Media: M9 minimal media with 0.5% maltose
Keywords: Logical Set

overall_design: Computed

first: Nadia

last: Dolganov


title: Transcriptional p of B. burgdorferi containing a unique bosR allele identifies a putative oxidative stress regulon

city: College Station

first: Jenny

last: Hyde

state: TX

address: 407 Reynolds Medical Building

department: MMPA

institute: Texas A&M University HSC

summary:
Borrelia burgdorferi regulates gene expression in response to environmental conditions, including temperature, pH, redox potential, and host factors.  B. burgdorferi encodes a PerR homologue designated BosR which presumably serves as a global regulator of genes involved in the oxidative stress response.  Infectious B. burgdorferi strain B31 is resistant to oxidative stressors in vitro whereas our non-infectious isolate is sensitive due, in part, to a point mutation that converts an arginine to a lysine at residue 39 of BosR.  Subsequent insertional inactivation of this bosRR39K allele (bosRR39K::kanR) restores resistance to oxidative stressors.  These observations suggest that the B. burgdorferi non-infectious bosRR39K::kanR strain may transcribe genes that are also expressed in infectious B. burgdorferi cells, but are repressed in the bosRR39K background, thus explaining the different oxidative stress phenotypes observed between these isolates.  To test this hypothesis, macroarray technology and quantitative RT-PCR was utilized to compare the transcriptional profiles from the isogenic bosRR39K and bosRR39K::kanR isolates.  Array data indicated that 88 ORFs were significantly expressed in the absence of BosRR39K.  Since most genes affected mapped to the chromosome, it is likely that these genes define an important physiologic response for B. burgdorferi.  Included within the genes identified was the detoxification gene sodA as well as other loci not overtly linked to oxidative stress.  These results suggest that a putative BosR regulon, as defined by the bosRR39K allele, is required to combat toxic oxidative intermediates, but may also be involved in adaptive strategies that are independent of reactive oxygen species.
Keywords: genetic modification

overall_design: JS167, containing bosRR39K::kanR allele, and CHP100, containing bosRR39K allele, were labeled with P33 and hybridized to nylon membrane arrays.  The arrays were spotted in duplicate and the experiment was performed in triplicate resulting in 6 data points for each ORF spotted.


title: Growth in minimal media with lactate

summary:
Growth to mid exponential phase in M9 minimal media supplemented with 0.5% lactate versus growth in rich LB media
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Media: M9 minimal media with 0.5% lactate
Keywords: Logical Set


title: Mapping of hns sites in Typhimurium 14028 using a tiling oligo array

status: Public on May 23 2006

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

summary:
The NimbleGen array contains 387,000 46~50-mer oligos, including 377,230 salmonella probes whose sequences only hit genome once. The probes were designed based on Salmonella typhimurium LT2 (NC_003197) genome, with a moving window of about 12 bases. Raw intensities were normalized by the median intensity in each channel and the ratios were calculated by log base 2 (hns-bound DNA / genomic DNA) after the normalization.
Keywords: ChIP-chip

overall_design: Two arrays were hybridized with Typhimurium 14028genomic DNA and hns-bound DNA from a chromatin immunoprecipitation with a Dye swap.

first: William

middle: W

last: Navarre

first: Steffen

last: Porwollik

first: Michael

last: McClelland

first: Nina

last: Salama

first: Henry

last: Rosen

first: Stephen

last: Libby

first: Ferric

last: Fang


title: CC2_Navarre_14028srpoSlowhns-_IP_pHNStagged_antiHA

status: Public on May 24 2006

city: Irvine

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

type: Genome binding/occupancy profiling by array

summary:
array analysis of immunoprecipitated DNA from tagged HNS proteins in 14028s mutant strain (rpoS low, hns minus)
Keywords: ChIP-chip

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: four slides, FLAG-tagged HNS versus gDNA and HA-tagged HNS versus gDNA IP'd using anti-HA, including dye-swaps

first: Pui

last: Cheng

first: Steve

first: YiPeng


title: Grass shrimp SAGE libraries

status: Public on May 18 2006

city: Ocean SPrings

first: Joe

last: Griffitt

state: MS

address: 703 East BEach Drive

department: Coastal Sciences

institute: University of Southern Mississippi

summary:
Adult male grass shrimp were exposed for 96 hours to LC50 concentrations of either Fipronil, Endosulfan, or Cadmium, as well as a Carrier Control exposure.  RNA was extracted from whole-body homogenates using the RNABee kit.  Tags were clustered to identify tags diagnostic of the different exposures.
Keywords: SAGE, Grass shrimp, ecotoxicogenomics

overall_design: 3 randomly selected shrimp were pooled for each library.  Libraries were constructed using the I-SAGE long kit from Invitrogen.

first: Robert

first: George

middle: T

last: Chandler

last: Quattro

first: Thomas

last: Greig


title: Indicators of exposure to biological threat agents using host gene profiles in peripheral blood mononuclear cells

status: Public on May 19 2006

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

summary:
gene expression host responses to biological threat agents in human PBMC
Keywords: pathogen response

overall_design: PBMC were exposed to various pathgens at different time points

first: Yan

first: Marti

last: Jett


title: Prostate Cancer CGH in a single large family

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

summary:
For sample information see "High-Density, Genome-Wide Linkage and Gene Copy Number Analyses of a Six-Generation Prostate Cancer Family." by Fitzgerald et al, Cancer Research.

Keywords: other

first: Liesel

last: FitzGerald

first: Jim

last: Stankovich

first: Jesper

last: Brohede

last: Quinn

first: Russell

last: Thomson

first: David

last: Challis

first: Christopher

last: Wilkinson

first: John

last: Slavin

first: Annette

last: Banks

first: Kris

last: Hazelwood

last: Mackey

first: Garry

last: Hannan

first: Terence

last: Dwyer

first: Joanne

middle: L

last: Dickinson

first: Deon

last: Venter

first: James

middle: D

last: McKay


title: Spo13 facilitates monopolin recruitment to kinetochores and regulates maintenance of centromeric cohesion

status: Public on May 16 2006

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

summary:
	BACKGROUND: Cells undergoing meiosis perform two consecutive divisions after a single round of DNA replication. During the first meiotic division, homologous chromosomes segregate to opposite poles. This is achieved by (1) the pairing of maternal and paternal chromosomes via recombination producing chiasmata, (2) coorientation of homologous chromosomes such that sister chromatids attach to the same spindle pole, and (3) resolution of chiasmata by proteolytic cleavage by separase of the meiotic-specific cohesin Rec8 along chromosome arms. Crucially, cohesin at centromeres is retained to allow sister centromeres to biorient at the second division. Little is known about how these meiosis I-specific events are regulated. RESULTS: Here, we show that Spo13, a centromere-associated protein produced exclusively during meiosis I, is required to prevent sister kinetochore biorientation by facilitating the recruitment of the monopolin complex to kinetochores. Spo13 is also required for the reaccumulation of securin, the persistence of centromeric cohesin during meiosis II, and the maintenance of a metaphase I arrest induced by downregulation of the APC/C activator CDC20. CONCLUSION: Spo13 is a key regulator of several meiosis I events. The presence of Spo13 at centromere-surrounding regions is consistent with the notion that it plays a direct role in both monopolin recruitment to centromeres during meiosis I and maintenance of centromeric cohesion between the meiotic divisions. Spo13 may also limit separase activity after the first division by ensuring securin reaccumulation and, in doing so, preventing precocious removal from chromatin of centromeric cohesin.
Keywords: Meiosis, Cell cycle, Saccharomyces cerevisiae, Chromosome VI tiling array, Spo13, ChIP-chip

overall_design:
•	Experimental factors
	Distribution of the Spo13 at Meiosis I. Experiment was performed in Saccharomyces cerevisiae SK1 strain.
•	Experimental design
	ChIP analysis: Hybridization data for ChIP fraction was compared with that of SUP (supernatant) fraction. Cerevisiae chromosome VI array was used.

•	Quality control steps taken
	Checking of the ChIP fraction by Western blotting. Mock hybridisation of samples immunoprecipitated from cells containing no tag recognized by antibody used. Sup swapping.

Samples used, extract preparation and labelling:
•	The origin of each biological sample
	Saccharomyces cerevisiae (SK1).
•	Manipulation of biological samples and protocols used
	Chromatin immunoprecipitation (ChIP) and hybridization to Affimetrix high-density oligonucleotide arrays of S. cerevisiae chromosome VIwere performed essentially as previously described (Katou et al., 2003, nature) (Lengronne et al., 2004, nature).
•	Technical protocols for preparing the hybridization extract
	The chromatin-immunprecipates were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp. After Dnase I inactivation at 95ºC. DNA fragments were end-labeled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) for 1 hour at 37ºC as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.
•	Hybridization procedures and parameters:
	Hybridization, blocking and washing were carried out as previously described (Lengronne et al. Nature 2004). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3’biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100ºC for 10 minutes, and then put on ice before being hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).
•	Measurement data and specifications:

	Arrays were scanned using the Genechip Scanner3000 7G following the library array description. All the cel files data and processed data files can be downloaded from GEO database. The primary analysis of tiling chip data was performed following exactly the statistical algorithm used for Affymetrix GeneChip Operating Software (GCOS). The detailed information for the algorithm used can be downloaded from the Affymetrix web site. The analysis is available on request. For the ChrVI array, one unit for analysis (locus) was set to 300bp. Fold change value, change p-value, and detection p-value for each locus were obtained by primary analysis. For the discrimination of positive and negative signals for the binding, we used three criteria as follows. First, the reliability of the signal strength was judged by detection p-value of each locus (p-value≤0.025). Secondly, reliability of binding ratio was judged by change p-value (p-value≤0.0025). Thirdly, clusters consisting of at least 900bp contiguous loci that satisfied the above two criteria were selected, because it is known that a single site of protein-DNA interaction resulted in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors.

•	Array Design:

		General array design: in situ synthesized arrays by Affymetrix
		Availability of arrays: commercially available from Affymetrix
		Location and ID of each spot on arrays: available from Affymetrix on 			request
		Probe type: oligonucleotide
		The arrays used in this study can be purchased from Affymetrix:
			Chromosome VI S.cerevisiae: rikDACFC6, P/N# 510636
GSM108198 was used for normalization of GSM108511.

first: Vittorio

last: Katis

first: Saori

last: Mori

first: Kim

last: Nasmyth


title: miRNA-Targeted and siRNA-Mediated mRNA Degradation Regulated by Argonaute, Dicer and RdRP

status: Public on May 17 2006

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

summary:
Microarray expression profiles of wild-type, ago1-10, ago1-11, and dcl1-9 Arabidopsis thaliana ec. Landsberg erecta seedling at 9, 21, and 35 days after germination.
Keywords: mutant response

overall_design: Reference design, wild-type vs mutants, multiple biological replicates

first: Michael

last: Ronemus

first: Robert

last: Martienssen


title: Skin layer-specific transcriptional profiles in normal and recessive yellow (Mc1r/Mc1r) mice

last: Stanford Microarray Database

summary:
Total RNA was extracted from three partially overlapping dorsal skin layers derived from P2.5 normal (E+/E+) and recessive yellow (e/e) mice, as well as from an immortalized mouse melanocyte cell line (melan-a). Replicate samples (cy5) were labelled and co-hybridized with a reference RNA sample (cy3) to a 26K mouse cDNA microarray.
A reference experiment design type is where all samples are compared to a common reference.
Keywords: reference_design

first: Craig

last: April


title: Limbal and Central Corneal Epithelia

status: Public on May 15 2006

city: Bethedsa

first: Hagit

last: Ulanovsky

address: 7 Memorial Dr, room 135

institute: NEI

summary:
Limbal and central regoins of the rat cornea epithelium were used to constract 2 SAGE libraries, in order to identify candidate genes to distinguish stem cell from differentiated central cornea epithelium cells.
Keywords: gene expression SAGE-based, count

overall_design: cornea epithelium was scraped from central cornea and limbal Epithelium regions of 6 week male Wister rat 16 and 48 eye (respectively).

first: Wakoko

last: Adachi

first: Barbara

last: Norman

first: Yan

last: Li

first: Janine

last: Davis

first: Joram

last: Piatigorsky


title: The effects of chronic immune stimulation on muscle growth in rainbow trout

status: Public on May 13 2006

city: Hagerman

first: Ken

last: Overturf

state: ID

address: 3059-F National Fish Hatchery Road

department: ARS

institute: USDA

summary:
Successful production of aquaculture species depends on efficient growth with low susceptibility to disease. Therefore, selection programs have focused on rapid growth combined with disease resistance. However, chronic immune stimulation diminishes muscle growth (a syndrome referred to as cachexia), and decreases growth efficiency in production animals, including rainbow trout. In mammals, recent results show that increased levels of pro-inflammatory cytokines, such as those seen during an immune assault, specifically target myosin and MyoD and inhibit muscle growth. This suggests that increased disease resistance in fish, a desired trait for production, may actually decrease the growth of muscle, the main aquacultural commodity. To test this possibility, a rainbow trout model of cachexia was developed and characterized.   A six-week study was conducted in which rainbow trout were chronically immune stimulated by repeated injections of LPS.  Growth indices were monitored, and whole body and muscle proximate analyses, real-time PCR, and immunohistochemistry were conducted to examine the resulting cachectic phenotype.  Muscle ratio was decreased in fish chronically immunostimulated, however expression levels of MyoD2 and myosin were not decreased compared to fish that were not immunostimulated, indicating that while muscle accretion was altered, the mechanism by which it occurred was somewhat different than that characterized in mammals.  Microarray analysis was used to compare gene expression in fish that had been chronically immunostimulated versus those that had not to identify possible alternative mechanisms of cachexia in fish.
Keywords:  muscle, cachexia, rainbow trout, chronic immune stimulation

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design:
Fish of approximately 60g were separated into either an experimental group receiving an LPS injection or a control group receiving a sterile PBS injection.  The LPS group was injected with 10 mg/kg bw (body weight) LPS in a volume of 0.1ml sterile PBS, and the PBS group was injected with an equal volume of sterile PBS. Liver, and muscle tissue were harvested from 10 fish from (saline and LPS injected) at day 43 of the experiments.  During the experiment, fish were fed to satiation once daily with a commercial feed (Silver Cup, Murray, UT), and feed consumption was recorded daily.  In the first week following injection, fish injected with LPS consumed 45-70% of the amount of feed consumed by the saline-injected fish.  The following week, LPS-injected fish consumed 80-90% of the amount of feed consumed by the saline-injected fish.Total RNA from either muscle or liver was pooled by treatment (saline- or LPS-injected, 9 fish per treatment).  cDNA was prepared and either Cy3- or Cy5-labeled using Superscript II Reverse Transcriptase (Invitrogen) and Genisphere’s Array 50 Kit.Scanning was performed using a Perkin Elmer ScanArray 5000 and images and data were processed using ScanArray Express software (Perkin Elmer, Wellesley, MA).  The adaptive circle method was used for quantitation, and mean background of spots was subtracted and LOWESS normalization was performed.  Data was filtered by eliminating sequences that did not have a minimum of 2-fold difference in expression on at least one of the dye-flip slides and that did not have a spot mean minus background pixel intensity of at least 1000.

For the microarray work presented in the paper, only the samples from day 43 were analyzed, because day 43 is the relevant time point for testing the hypothesis that chronic immune stimulation suppresses muscle growth.

first: Katherine

last: Johansen

first: Wendy

last: Sealey


title: Normal blood cell subtypes

summary:
We used antibodies coupled to magnetic beads (MACS) to purify cell types out of whole blood from healthy donors (CD4+ T cells, CD8+ T cells, and B cells).  We also profiled whole blood (collected in Pax tubes) and Peripheral Blood Mononuclear cells obtained by Ficoll-Paque based separation.  RNA was extracted using Trizol, amplified linearly twice, labeled with Cy5 and co-hybridized with amplified Stratagene human reference (labeled with Cy3).
A reference experiement design type is where all samples are compared to a common reference.
Keywords: reference_design

overall_design: Using regression correlation

first: Chana

last: Palmer