title: Interactions between Saccharomyces cerevisiae WW domains and proteins discovered using protein microarrays

status: Public on Feb 08 2006

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary:
A total of 12 WW domains from Saccharomyces cerevisiae were expressed and purified as fusion proteins to either GST or MBP.  The fusion proteins were chemically biotinylated and applied to duplicate protein microarrays.  Data processing revealed a total of 587 interactions between the domains and 207 proteins.  Most of these interactions have not been previously observed.
Keywords: Protein microarray analysis of yeast WW domains

overall_design: We analyzed a total of 12 WW domains from S.cerevisiae, each on duplicate protoarrays.

middle: R

first: John

last: Miller


title: Tenosynovial giant-cell tumor and pigmented villonodular synovitis

status: Public on Feb 25 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary:
Tenosynovial giant-cell tumor (TGCT) and pigmented villonodular synovitis (PVNS) are related conditions with features of both reactive inflammatory disorders and clonal neoplastic proliferations. Chromosomal translocations involving chromosome 1p13 have been reported in both TGCT and PVNS. We confirm that translocations involving 1p13 are present in a majority of cases of TGCT and PVNS and show that CSF1 is the gene at the chromosome 1p13 breakpoint. In some cases of both TGCT and PVNS, CSF1 is fused to COL6A3 (2q35). The CSF1 translocations result in overexpression of CSF1. In cases of TGCT and PVNS carrying this translocation, it is present in a minority of the intratumoral cells, leading to CSF1 expression only in these cells, whereas the majority of cells express CSF1R but not CSF1, suggesting a tumor-landscaping effect with aberrant CSF1 expression in the neoplastic cells, leading to the abnormal accumulation of nonneoplastic cells that form a tumorous mass.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Matt

last: Van De Rijn


title: Regulation of signaling genes by TGFbeta during entry into dauer diapause in C. elegans

status: Public on Feb 03 2006

summary:
BACKGROUND: When resources are scant, C. elegans larvae arrest as long-lived dauers under the control of insulin/IGF- and TGFbeta-related signaling pathways. : We have identified genes that show different levels of expression in a comparison of wild-type L2 or L3 larvae (non-dauer) to TGFbeta mutants at similar developmental stages undergoing dauer formation. Many insulin/IGF pathway and other known dauer regulatory genes have changes in expression that suggest strong positive feedback by the TGFbeta pathway. In addition, many insulin-like ligand and novel genes with similarity to the extracellular domain of insulin/IGF receptors have altered expression. We have identified a large group of regulated genes with putative binding sites for the FOXO transcription factor, DAF-16. Genes with DAF-16 sites upstream of the transcription start site tend to be upregulated, whereas genes with DAF-16 sites downstream of the coding region tend to be downregulated. Finally, we also see strong regulation of many novel hedgehog- and patched-related genes, hormone biosynthetic genes, cell cycle genes, and other regulatory genes.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

last: Wang


title: mRNA tagging (intestine)

summary:
For each experiment (as described in Pauli et al. 2006): Channel 1: whole worm lysate from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 Channel 2: mRNA immunoprecipitated from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1  mRNA was amplified and hybridized to C. elegans DNA arrays from the Stuart Kim lab
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate, mRNA tagging

overall_design:
Biological Replicate
Computed

first: Min

last: Jiang


title: Renal Cell Carcinoma

status: Public on Feb 01 2006

summary:
Renal cell carcinoma comprises several histological types with different clinical behavior. Accurate pathological characterization is important in the clinical management of these tumors. We describe gene expression profiles in 41 renal tumors determined by using DNA microarrays containing 22,648 unique cDNAs representing 17,083 different UniGene Clusters, including 7230 characterized human genes. Differences in the patterns of gene expression among the different tumor types were readily apparent; hierarchical cluster analysis of the tumor samples segregated histologically distinct tumor types solely based on their gene expression patterns. Conventional renal cell carcinomas with clear cells showed a highly distinctive pattern of gene expression. Papillary carcinomas formed a tightly clustered group, as did tumors arising from the distal nephron and the normal kidney samples. Surprisingly, conventional renal cell carcinomas with granular cytoplasm were heterogeneous, and did not resemble any of the conventional carcinomas with clear cytoplasm in their pattern of gene expression. Characterization of renal cell carcinomas based on gene expression patterns provides a revised classification of these tumors and has the potential to supply significant biological and clinical insights.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

first: Rajesh

last: Shinghal


title: Pooled B-Cell C441MC-C442MC

status: Public on Feb 18 2006

city: Oklahoma City

first: Parima

last: Pathipvanich

state: OK

address: 755 Research Parkway, Suite 464

department: Arthritis/Immunology

institute: Oklahoma Medical Research Foundation

summary:
A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis.
Keywords: Rheumatoid Arthritis, B-cells

overall_design: RNA from B-cells was seperately pooled from 8 RA patients and 8 controls, hybridized to long oligonucleotide microarrays in order to identify disease related differentially expressed genes.

first: Peter

last: Szodoray

first: Philip

last: Alex

first: Mark

middle: B

last: Frank

first: Mary

last: Turner

first: Sean

first: Nicholas

last: Knowlton

first: Craig

last: Cadwell

first: Igor

last: Dozmorov

first: Yuhong

last: Tang

first: Patrick

middle: C

last: Wilson

first: Roland

last: Jonsson

first: Michael

last: Centola


title: Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source

last: Stanford Microarray Database

summary:
Two time courses after pulses of 0.2 g/l  and 2 g/l glucose on cells growing in chemostat with galactose as the carbon source. The reference is sample from the chemostat at time 0.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

overall_design: Using regression correlation

first: Michal

last: Ronen


title: The response of E. coli to exposure to the biocide polyhexamethylene biguanide

city: Plymouth

middle: James

last: Allen

address: Prospect Place

country: United Kingdom

institute: Plymouth Marine Laboratory

summary:
The global response of E. coli tot he broad spectrum biocide polyhexamethyelene biguanide (PHMB) was investigated using transcriptional profiling.
Keywords: dose response

overall_design: E. coli was grown until early exponential phase and (t=2.5 hrs) then exposed to PHMB (7.5 mg/l). RNA was extracted (3.75 hrs) from triplicate exposed cultures and triplicate unexposed cultures.

middle: J

first: Graham

middle: F

last: White

first: Andrew

middle: P

last: Morby


title: Combinatorial regulation of estrogen receptor alpha-responsive promoters

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

type: Genome binding/occupancy profiling by genome tiling array

summary:
In breast cancer and normal estrogen target tissues, estrogen receptor alpha (ERalpha) signaling results in establishment of spatiotemporal patterns of gene expression. A time-course series of ChIP-chip experiments were performed to identify direct ERalpha target genes and determine whether these targets were transcriptionally activated or repressed by ERalpha.
Keywords: Time-course ChIP-chip

overall_design: A total of 24 samples were analyzed. MCF7 cells were treated with E2 for 0 (control), 3, 12 and 24 hours. ChIP assays were performed using antibodies against ERalpha and specific histone modifications (acetyl-H3-K9 and dimethyl-H3-K9). The immunoprecipitated DNA was used to probe the 12K CGI microarray. Two independent experiments were performed for each time-point treatment and antibody.


title: Mouse ventilator-induced lung injury experiment

status: Public on Feb 12 2006

city: Pittsburgh

first: Tamas

last: Dolinay

state: PA

department: Pulmonary, Allergy and Critical Care

institute: Univerisity of Pittsburgh Medical Center

summary:
Gene expression analysis of BALB/c mouse lung tissue following  LPS, high pressure ventilation and LPS+high pressure ventilation treatment
Keywords: VILI, gene expression profiling, ARDS

overall_design: BALB/c mice control (C) (low pressure ventilation), S. suis LPS treatment (LPS), high pressure ventilation (OV) and LPS+OV (OVLPS)

first: Naftali

last: Kaminski

first: Martina

last: Felgendreher

first: Hong

last: Kim

first: Paul

last: Reynolds

first: Simon

last: Watkins

first: Doerte

last: Karp

first: Stefan

last: Uhlig

first: Augustine

middle: M

last: Choi


title: GEP associated with drug resistance in adult AML

summary:
Acute myeloid leukemia (AML) patients are primarily resistant to induction chemotherapy in 20-50%. Previously it has been shown that resistance to the first cycle of induction chemotherapy is an independent prognostic factor. We investigated whether resistance to chemotherapy can be represented by gene-expression profiling, and which genes are associated with resistance. cDNA microarrays containing ~41.000 features were used to compare the gene-expression profile of AML blasts between 33 patients with good or poor response to induction chemotherapy. Data generated by cDNA-arrays were confirmed by quantitative RT-PCR. Using Significance Analysis of Microarrays, we identified a characteristic gene-expression profile which distinguished good- from poor-response AML samples. In hierarchical clustering analysis poor responders clustered together with normal CD34+ cells. Moreover, 13/40 (32.5%) genes highly expressed in poor responders are also overexpressed in hematopoietic stem/progenitor cells. Prediction analysis using 10-fold crossvalidation revealed 80% overall accuracy. Using the treatment response signature to predict the outcome in an independent test set of 104 AML patients, samples were separated into two subgroups with significantly inferior response rate (43.5% vs. 66.7%, P=.044), significantly shorter event-free and overall survival (P=.01 and P=.03, respectively) in the poor-response compared to the good-response signature group. In multivariate analysis, the treatment-response signature was an independent prognostic factor (hazard ratio, 2.1, 95 percent-confidence interval 1.2 to 3.6, P=.006). Resistance to chemotherapy in AML can be identified by gene-expression profiling before treatment and seems to be mediated by a transcriptional program active in hematopoietic stem/progenitor cells.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Doris

last: Steinemann

first: Joan

last: Hebert


title: Hepatoma cell lines vs. Universal control 3

status: Public on Jan 31 2006

city: Daejeon

first: Heun-Sik

last: Lee

address: 52 Eoeun-dong, Yuseong-gu

country: South Korea

institute: Korea Reaearch Institute of Bioscience and Biotechnology

summary:
Gene expression profiles in hepatoma cells
Keywords: Cell type comparison

overall_design:
Quadrant experiment.
Hepatoma cell lines vs. Universal control


title: Cholinergic Receptor and Cyclic Stretch-Mediated Inflammatory Gene Expression in Intact Airway Smooth Muscle

status: Public on Feb 23 2006

city: Boston

first: Marc

middle: E.

last: Lenburg

state: MA

address: 715 Albany Street, E613B

department: Genetics and Genomics

institute: Boston University School of Medicine

summary:
We tested the hypothesis that cholinergic stimulation (via treatment with carbachol) and cyclic stretch regulate inflammatory gene expression in intact airway smooth muscle by measuring mRNA expression in bovine tracheal smooth muscle.
Keywords: response to stress and drug

overall_design: Airway smooth muscle from 5 animals was treated with 4 treatments (+/- stretch, +/- carbachol).  RNA from these 20 samples were split into two:  one labeled with Cy3 and one labeled with Cy5.  These 40 labeled RNA samples were then hybridized to 20 custom oligonucleotide arrays containing a number of genes known to be involved in airway smooth muscle function

first: Jeannette

last: Kanefsky

first: Chi-Ming

last: Hai


title: Interferon alfa regulated gene expression in patients initiating interferon treatment for chronic hepatitis C

last: Stanford Microarray Database

summary:
Interferon alfa (IFN-alpha) is an approved therapeutic agent for chronic hepatitis C. To directly characterize the effects of IFN-alpha in humans, we used microarrays to profile gene expression in peripheral blood mononuclear cells (PBMCs) from hepatitis C patients treated with IFN-alpha. Seven patients were studied using two strategies: (1) in vivo: PBMCs were collected immediately before the first dose of IFN-alpha, and 3 and 6 hours after the dose; (2) ex vivo: PBMCs that were collected before the first IFN-alpha dose were incubated with IFN-alpha for 3 and 6 hours. The microarray datasets were analyzed with significance analysis of microarrays (SAM) to identify genes regulated by IFN-alpha. We identified 516 named genes up-regulated at least 2-fold, at a false discovery rate (FDR) of less than 1%. In vivo and ex vivo studies generated similar results. No genes were identified as regulated differently between these 2 experimental conditions. The up-regulated genes belonged to a broad range of functional pathways and included multiple genes thought to be involved in the direct antiviral effect of IFN-alpha. Of particular interest, 88 genes directly relating to functions of immune cells were up-regulated, including genes involved in antigen processing and presentation, T-cell activation, lymphocyte trafficking, and effector functions, suggesting that IFN-alpha up-regulates multiple genes involving different aspects of immune responses to enhance immunity against hepatitis C virus. In conclusion, IFN-alpha-inducible genes can be identified in human PBMCs in vivo as well as ex vivo. Signature changes associated with different treatment outcomes may be found among these genes.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Xuhuai

last: Ji


title: Rapid alteration of microRNA levels by histone deacetylase inhibition

city: Research Triangle Park

first: Michael

middle: D.

last: Mattie

state: NC

address: Five Moore Drive

department: Genomics Research

institute: GlaxoSmithKline

summary:
Comparison of miRNA expression profiles in SKBr3 breast cancer cells treated with HDAC inhibitor LAQ-824 vs. untreated SKBr3 cells.
Keywords: Expression profiling of pharmacological response to HDAC inhibitor

overall_design:
MicroRNA expression was compared between treated/untreated SKBr3 breast cancer cells to examine the effects of the HDAC inhibitor LAQ-824 on miRNA expression.

SKBr3 control (untreated breast cancer cell line)
SKBr3 treated (breast cancer cell line treated with 20 uM LAQ-824 for 5 hours)
Both cell lines were grown to ~70% confluency and harvested for enriched miRNAs using the mirVana miRNA Isolation kit from Ambion per the manufacturers instructions.  Untreated SKBr3 cell miRNA was labeled with Cy3 and treated SKBr3 treated cell miRNA was labeled with Cy5.

first: Gary

middle: K

last: Scott

middle: D

first: Crystal

middle: E

last: Berger

first: Stephen

last: Benz

first: Christopher


title: Sir-2.1 low copy transgenic

status: Public on Jan 25 2006

summary:
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Genotype: unc-119+ transgenic worm
Keywords: all_pairs

first: Min

last: Jiang


title: Drug resistance in glioblastoma

status: Public on Jan 27 2006

first: Markus

last: Bredel

institute: Stanford University School of Medicine

type:
Expression profiling by array
Genome variation profiling by array

summary:
Combined model of in vitro and in vivo resistance to alkylating agents (BCNU and Temozolomide) in glioblastoma multiforme. Three matched pairs of surgical specimens from initial (DI, ME, LX) and repeat (DIR, MER, LXR) tumor resection were used to establish cell lines. Patients received BCNU chemotherapy between the two operations, which rendered the sublines from repeat surgery more resistant to BCNU than those from initial surgery. Each the pre-chemotherapeutic set and the post-chemotherapeutic set of cell lines was selected in vitro for resistance to either BCNU or Temozolomide. 9 in vitro selected sublines were established. Of those 4 (2 selected for BCNU [ME-BCNU, DI-BCNU] and 2 selected for Temozolomide [ME-TMZ, LX-TMZ) were generated from the parental/sensitive pre-chemotherapeutic set and 5 (2 selected for BCNU [DIR-BCNU, MER-BCNU] and 3 selected for Temozolomide [DIR-TMZ, MER-TMZ, LXR-TMZ) from the in vivo resistant post-chemotherapeutic set. The model included a total of 15 sublines. Genome-wide high-resolution gene copy number profiling was performed on each subline using 42,000-feature cDNA microarrays. Utilizing the same microarray platform genome-wide gene expression profiles were generated. Biostatistical tools were employed to identify signatures of resistance to alkylating agents both at the genetic as well as at the transcriptomic levels.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Series_type = Logical Set
Keywords: other


title: Mechanism of the anti-inflammatory effect of colchicine in rheumatic diseases

summary:
Objective. Colchicine is an alkaloid that is used to alleviate acute gout and to prevent acute attacks of familial Mediterranean fever (FMF). However, it is not beneficial when given during the occurrence of an acute episode of FMF. It is believed that colchicine exerts its anti-inflammatory effect through direct interaction with microtubules. We aim to study the molecular basis of colchicine action by analysing the effect of this drug on global gene expression of HUVEC (human umbilical vein endothelial cell line) cells. Methods. HUVEC cells were exposed to various concentrations of colchicine and were harvested at different time points. Ribonucleic acid was extracted, amplified, reverse transcribed and hybridized to complementary deoxyribonucleic acid microarrrays containing more than 40,000 probes to human expressed sequence tags. This approach enabled us to have a global look at the transcriptional response induced by colchicine treatment. Results. Colchicine changed the expression of many genes in HUVEC cells following exposure to a concentration of 100 ng/ml or higher. Following short exposure (30 or 120 min), colchicine affected genes known to be involved in the cell cycle and its regulation. However, change in expression of genes involved in neutrophil migration or other inflammatory processes were observed mainly after 12 to 24 h. Conclusions. The anti-inflammatory effect of colchicine may be mediated not only through direct interaction with microtubules but also through changes at the transcriptional level. This latter effect apparently requires a higher concentration and a longer time to occur. This can explain the observation that colchicine does not have an immediate effect when given during an acute attack of FMF.
A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s).
Keywords: dose_response_design

first: Eldad

last: Ben-Chetrit


title: Hepatoma cell lines vs. Universal control 2

status: Public on Jan 26 2006

overall_design:
Duplicate experiment.
Hepatoma cell lines vs. Universal control


title: Temporal expression profiling of beta- and gamma-sarcoglycan deficient mice

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
Temporal expression profiling of hindlimb muscle of beta- and gamma-sarcoglycan deficient mice aged 1, 2.5, 4, 6, 8, 10, 12, 14 and 20 weeks.
Keywords: time course

overall_design: 4 closed loop-designs where subsequent time points are co-hybridised. Two closed loops per strain. Two individuals per strain per time point.

first: Peter

middle: A

last: 't Hoen


title: The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens

city: Seattle

first: Renata

middle: Fava

last: Ditt

state: WA

address: Hitchcock Hall Box 355325

institute: University of Washington

summary:
The pathogen Agrobacterium tumefaciens infects a broad range of plants, introducing the T-DNA into their genome. Contrary to all known bacterial phyto-pathogens, Agrobacterium lacks the hypersensitive response-inducing HRP genes although it introduces numerous proteins into the plant cell through a type IV secretion system. To understand the timing and extent of the plant transcriptional response to this unusual pathogen, we used an Arabidopsis 26-thousand gene oligonucleotide microarray. We inoculated Arabidopsis cell cultures with an oncogenic strain of Agrobacterium and analyzed four biological replicates to identify two robust sets of regulated genes, one induced and the other suppressed. In both cases, the response was distinct at 48 hours after infection, but not at 24 hours or earlier. The induced set includes genes encoding known defense proteins, the repressed set is enriched with genes characteristic of cell proliferation even though a growth arrest was not visible in the inoculated cultures. The analysis of the repressed genes revealed that the conserved upstream regulatory elements Frankiebox (a.k.a. “site II”) and Telobox are associated with the suppression of gene expression. The regulated gene sets should be useful in dissecting the signaling pathways in this plant-pathogen interaction.
Keywords: Time-course of Agrobacterium infection

overall_design: Time-course of Agrobacterium-inoculated Arabidopsis cell cultures. Four biological replicates of mock- and Agrobacterium-inoculated samples collected at 4h, 12h, 24h and 48h after inoculation were compared to a reference RNA in a oligonucleotide array.

first: Kathleen

last: Kerr

first: Paul

last: de Figueiredo

first: Jeff

last: Delrow

first: Luca

last: Comai

first: Eugene

last: Nester


title: Mechanical shear effects on flexor tendon cells

status: Public on Jan 28 2006

last: Stanford Microarray Database

summary:
Adhesion formation after flexor tendon repair remains a clinical problem. Early postoperative motion after tendon repair has been demonstrated to reduce adhesion formation while increasing tendon strength. It is hypothesized that during mobilization, tendon cells experience mechanical shear forces that alter their biology in a fashion that reduces scar formation but also activates key genes involved in tendon healing. To test this hypothesis, primary intrinsic tenocyte cultures were established from flexor tendons of 20 Sprague-Dawley rats and sheared at 50 rpm (0.41 Pa) using a cone viscometer for 6 and 12 hours. Total RNA was harvested and compared with time-matched unsheared controls using cDNA microarrays and Northern blot analysis. Microarray analysis demonstrated that mechanical shear stress induced an overall "antifibrotic" expression pattern with decreased transcription of collagen type I and collagen type III. Shear stress down-regulated profibrotic molecules in the platelet-derived growth factor, insulin-like growth factor, and fibroblast growth factor signaling pathways. In addition, shear stress induced an overall decrease in transforming growth factor (TGF)-beta signaling pathway molecules with down-regulation of TGF-beta2, TGF-beta3, TGF-RI, and TGF-RII expression. Moreover, sheared tendon cells increased expression of matrix metalloproteinases and decreased expression of tissue inhibitors of metalloproteinase, an expression pattern consistent with an antifibrotic increase in extracellular matrix degradation. However, up-regulation of genes implicated in tendon healing, specifically, vascular endothelial growth factor-A and several bone morphogenetic proteins. Interestingly, the known mechanoresponsive gene, TGF-beta1, also implicated in tendon healing, was differentially up-regulated by shear stress. Northern blot validation of our results for TGF-beta1, TGF-beta2, TGF-beta3, and collagen type I demonstrated direct correlation with microarray data.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Kenton

last: Fong


title: brca1_brca2_controls_Vs_universal_RNA

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

summary:
Comparison of the expression profiles of normal cells from 10 BRCA1 and 10 BRCA2 mutation carriers to 10 non-carrier control samples after radiation induced DNA damage
Keywords: dose response

overall_design: 60 samples  - all samples compared to universal human reference RNA. There are 3 subsets of samples: brca1, brca2 and controls.

first: Zsofia

last: Kote-Jarai

first: Lucy

last: Matthews

first: Ana

last: Osorio

first: Susan

last: Shanley

first: Francois

last: Moreews

first: Imogen

last: Locke

first: Mark

last: Girolami

first: Richard

last: Williams

first: Colin

last: Campbell

first: Ros

last: Eeles


title: N2 worms treated with Resveratrol

summary:
Eggs were isolated by hypochlorite treatment and allowed to hatch in the absence of food as L1 stage arrested worms in S-buffer. Worms were then transferred to large plates containing NGM alone or NGM+ resveratrol and allowed to grow till young adult stage (ca 40 hours). Worms were harvested and total RNA extracted using Trizol reagent. Poly-A+ RNA was isolated using Qiagen midi-prep kit and used for microarray hybridization.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Compound Based Treatment: Resveratrol
Keywords: compound_treatment_design

first: Mohan

last: Viswanathan


title: DpiA overexpression

summary:
The dpiA and dpiB genes of Escherichia coli, which are orthologs of genes that regulate citrate uptake and utilization in Klebsiella pneumoniae, comprise a two-component signal transduction system that can modulate the replication of and destabilize the inheritance of pSC101 and certain other plasmids. Here we show that perturbed replication and inheritance result from binding of the effector protein DpiA to A+T-rich replication origin sequences that resemble those in the K. pneumoniae promoter region targeted by the DpiA ortholog, CitB. Consistent with its ability to bind to A+T-rich origin sequences, overproduction of DpiA induced the SOS response in E. coli, suggesting that chromosomal DNA replication is affected. Bacteria that overexpressed DpiA showed an increased amount of DNA per cell and increased cell size-both also characteristic of the SOS response. Concurrent overexpression of the DNA replication initiation protein, DnaA, or the DNA helicase, DnaB-both of which act at A+T-rich replication origin sequences in the E. coli chromosome and DpiA-targeted plasmids-reversed SOS induction as well as plasmid destabilization by DpiA. Our finding that physical and functional interactions between DpiA and sites of replication initiation modulate DNA replication and plasmid inheritance suggests a mechanism by which environmental stimuli transmitted by these gene products can regulate chromosomal and plasmid dynamics.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Christine

last: Miller


title: Expression profiling of five different xenobiotics using a C. elegans microarray

summary:
Using a C. elegans whole genome DNA microarray in this study, the effects of five different xenobiotics on the gene expression of the nematode were investigated. The exposure time for the following five applied compounds beta-NF (5 mg/l), Fla (0.5 mg/l), atrazine (25 mg/l), clofibrate (10 mg/l) and DES (0.5 mg/l) was 48+/-5 h. The analysis of the data showed a clear induction of 203 genes belonging to different families like the cytochromes P450, UDP-glucoronosyltransferases (UDPGT), glutathione S-transferases (GST), carboxylesterases, collagenes, C-type lectins and others. Under the applied conditions, fluoranthene was able to induce most of the induceable genes, followed by clofibrate, atrazine, beta-naphthoflavone and diethylstilbestrol. A decreased expression could be shown for 153 genes with atrazine having the strongest effect followed by fluoranthene, diethylstilbestrol, beta-naphthoflavone and clofibrate. For upregulated genes a change ranging from approximately 2.1- till 42.3-fold and for downregulated genes from approximately 2.1 till 6.6-fold of gene expression could be affected through the applied xenobiotics.  Sample Treatments (by exptids) Clofibrate: 14317, 16443, 16505 Fluoranthene: 33664, 33667, 33669, 23484 beta-Naphthoflavone: 6844, 14320, 14316 Atrazin: 33672, 33674, 23487, 23486 DES: 33671, 23485
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Keywords: compound_treatment_design

first: Ralph

last: Menzel


title: Sporulation_transfer_to_YPA2

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

country: Israel

institute: Weizmann Institute

summary:
We have used genome-wide expression profiling to investigate how budding yeast cells become committed to sporulation. Sporulating cells were transferred to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately down-regulated upon the transfer, even in committed cells that continued to sporulate. The metabolic-related transcription response of pre-committed cells or of mature spores transferred to growth medium was essentially the same as that of vegetative cells exposed to glucose. In contrast, committed cells elicited a unique, and dramatically different response. Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their information processing in an active manner that may optimize sporulation in an environment-specific manner.
Keywords: Time course

overall_design: Wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPA. Each YPA culture was monitored 20, 80 and 140 minutes after the transfer.


title: Resveratrol treatment of daf-16 mutant C. elegans

last: Stanford Microarray Database

summary:
Eggs were isolated by hypochlorite treatment and allowed to hatch in the absence of food as L1 stage arrested worms in S-buffer. Worms were then transferred to large plates containing NGM alone or NGM+ resveratrol and allowed to grow till young adult stage (ca 40 hours). Worms were harvested and total RNA extracted using trizol reagent. Poly-A+ RNA was isolated using Qiagen midi-prep kit and used for microarray hybridization.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Compound Based Treatment: Resveratrol
Keywords: compound_treatment_design


title: Sporulation_sum1_del_transfer_to_YPD

overall_design: sum1 deleted SK1 cells (JPY214) were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight.   The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At 6 hours of the sporulation process, cells were kept for RNA extraction. Part of the culture was centrifuged and resuspended in YPD, and was monitored 20 and 40 minutes after the transfer.


title: Sporulation_transfer_to_glucose

overall_design: wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in glucose solution (4%). Each glucose culture was monitored immediately after the transfer, after 20 and 40 minutes.


title: DNA methyltransferase inhibitor 5-aza-dC-treated prostate cancer cell lines

summary:
This microarray dataset accompanies the publication by Kim et al, "The retinoic acid synthesis gene ALDH1a2 is a candidate tumor suppressor in prostate cancer".  The dataset comprises four prostate cancer cell lines treated with the DNA methyltransferase inhibitor 5-aza-dC.  For each cell line, gene expression in treated (channel 2; Cy5) and untreated (channel 1; Cy3) cells is directly compared by hybridization to the same DNA microarray.  Further details on the treatment conditions are provided in the manuscript.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Keywords: compound_treatment_design

first: Hanna

last: Kim


title: Fibroblast-like synoviocytes derived from patients with rheumatoid arthritis

status: Public on Jan 19 2006

summary:
Fibroblast-like synoviocytes (FLS) were cultured from synovial tissues from 19 RA patients. RNA was isolated using the Fast Track 2.0 kit (Invitrogen, Carlsbad, California)from the FLS cultures. Fluorescent cDNA probes were prepared from 1 ug experimental mRNA by oligo dT-primed polymerization using Superscript II reverse transcriptase in the presence of Cy5 labeled dCTP.  A common reference mRNA sample (CRE) that consists of a mixture of mRNAs isolated from 11 different cell-lines, was labeled with Cy3. The Cy5 and Cy3 labeled cDNAs were pooled and hybridized to a 24,000 cDNA microarray.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Using regression correlation

first: Cornelis

last: Verweij


title: Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

summary:
Background: The autism spectrum includes a set of complex multigenic developmental disorders that severely impact the development of language, non-verbal communication, and social skills, and are associated with odd, stereotyped, repetitive behavior and restricted interests. To date, diagnosis of these neurologically based disorders relies predominantly upon behavioral observations often prompted by delayed speech or aberrant behavior, and there are no known genes that can serve as definitive biomarkers for the disorders.
Results: Here we demonstrate, for the first time, that lymphoblastoid cell lines from monozygotic twins discordant with respect to severity of autism and/or language impairment exhibit differential gene expression patterns on DNA microarrays. Furthermore, we show that genes important to the development, structure, and/or function of the nervous system are among the most differentially expressed genes, and that many of these genes map in silico to chromosomal regions containing autism susceptibility genes or quantitative trait loci.
Conclusions: Our present results provide compelling evidence that candidate genes for autism may be expressed in lymphoid cell lines from individuals with autism spectrum disorders.  This finding further suggests the possibility of developing a molecular screen for autism using peripheral blood lymphocytes, an easily accessible tissue. In addition, gene networks are identified that may play a role in the pathophysiology of autism.
Keywords: DNA microarrays, comparison expression profiling, relation to autistic phenotype

overall_design: The experimental strategy used in the study reported here was designed to tease out differences in gene expression among genetically identical individuals with ASD which might relate to observed differences in degree of expression of autistic symptoms.  To determine whether lymphoblastoid cell lines (LCL) derived from individuals with autism exhibit patterns of gene expression that may be relevant to autism spectrum disorders (ASD), gene expression profiling was performed on LCL derived from 5 sets of male monozygotic twins, in which the co-twins (twin siblings) differed with respect to diagnosis of autism, or the severity of language impairment.  Two of twin pairs had an unaffected sibling and these were also used for comparison with their respective twin siblings. All of these assays employed a experimental design in which RNA from the co-twins (or from a twin and his nonautistic sibling) were cohybridized on two-color spotted microarrays containing 39,936 human cDNA elements.  Each microarray experiment involved dye-reversal replicates, and was performed in duplicate or, in one case, triplicate for the different sets of twins.

middle: W

first: Bryan

last: Frank

first: Normal

middle: H

last: Lee

first: John

last: Quackenbush


title: Sporulation_SPS4_NDT80_transfer_to_YPD

overall_design: SK1 cells, in which NDT80 is expressed under the promoter of SPS4 (GF18), were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight.   The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At 5.5 hours of the sporulation process, cells were kept for RNA extraction. Part of the culture was centrifuged and resuspended in YPD, and was monitored immediately, 20 and 40 minutes after the transfer.


title: Sporulation_transfer_to_YPA1

overall_design: Wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPA. Each YPA culture was monitored immediately after the transfer, after 20 and 40 minutes.


title: Mouse Alt-Splice Tissue Panel (Brain vs Non-Brain)

city: Santa Cruz

first: Charles

last: Sugnet

address: Sinsheimer Labs

department: MCD

institute: UC Santa Cruz

summary:
22 Normal adult mouse tissues on custom alternative transcript sensitive Affymetrix microarray used to address differeneces in tissue specific alternative splicing.

Abstract:
Alternative splicing contributes to both gene regulation and protein diversity.  To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome.  In a set of 22 adult tissues, we observe expression of RNA containing at least two alternative splice junctions for about a third of the 3200 alternative events we could detect.  Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues, and another 28 exons whose splicing is different in muscle.  A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons.  By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation.  Of note is a motif strikingly similar to the branchpoint consensus, but which is located downstream of the 5' splice site of exons included in muscle.  Analysis of three paralogous membrane-associated guanylate kinase (MAGUK) genes reveals that each contains a paralogous tissue regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families.
Keywords: Alternative splicing isoform specific, adult mouse tissues

overall_design: 22 Normal tissues with at least 3 replicates each. Custom Affymetrix microarrays with probes specific to different alternative splicing events, including splice junction probes. Perfect match probes only.

first: Mannny

last: Ares


title: pp65 mutant human cytomegalovirus infected human fibroblasts

summary:
Abstract: We have identified a cytomegalovirus virion protein capable of modulating the rapid induction of an interferon-like response in cells that follows virus binding and penetration. Functional genomics revealed a role for the major cytomegalovirus structural protein, pp65 (ppUL83), in counteracting this response. The underlying mechanism involves a differential impact of this structural protein on the regulation of interferon response factor 3 (IRF-3). In contrast, NF-{kappa}B is activated independent of pp65, and neither STAT1 nor STAT3 becomes activated by either virus. pp65 is sufficient to prevent the activation of IRF-3 when introduced alone into cells. pp65 acts by inhibiting nuclear accumulation of IRF-3 and is associated with a reduced IRF-3 phosphorylation state. Thus, this investigation shows that the major structural protein of cytomegalovirus is committed to the modulation of the IRF-3 response, a primary mediator of the type I interferon response. By subverting IRF-3, the virus escapes throwing a central alarm devoted to both immediate antiviral control and regulation of the immune response.
Polyadenylated RNA from 107 confluent HFs was purified by using Oligotex (QIAGEN, Valencia, Calif.) from Trizol (Invitrogen)-extracted total RNA. This RNA was prepared, reverse transcribed, labeled with Cy3-dUTP or Cy5-dUTP (Amersham, Little Chalfont, Buckinghamshire, United Kingdom) by random primed synthesis with DNA pol I Klenow (Amersham Life Science, Inc., Cleveland, Ohio), and hybridized to spotted, human cDNA microarrays as previously described. Sequence-verified human cDNA microarrays (HE and HG series, 31,000 spots; HD51 series, 17,000 spots) were produced at Stanford. Images were collected by using a GenePix 4000B microarray scanner, manually flagged to eliminate poor spots and analyzed by GenePix Pro 2.0 (Axon, Union City, Calif.).
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Keywords: disease_state_design, pathogenicity_design

overall_design: User Defined

first: Davide

last: Abate


title: Sporulation_transfer_to_YPD

overall_design: Wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. Part of that culture was used as reference for all hybridizations preformed in this study. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPD. Each YPD culture was monitored immediately after the transfer, after 20 and 40 minutes.


title: Gene expression associated with chicken resistance to infectious bursal disease virus (IBDV)

status: Public on Jan 21 2006

city: Ames

first: Susan

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
Infectious Bursal Disease Virus (IBDV) causes highly contagious, immunosuppressive disease that leads to high mortality in young chickens. Chicks of a F2 generation of two lines divergently selected for high (HH) or low (LL) antibody (Ab) response to Escherichia coli vaccination, were challenged with virulent IBDV. Viral load in infected bursae was used to determine resistant (R) and susceptible (S) birds. By using a 13K chicken cDNA microarray, and pooled spleens of R, S and non-challenged, control (C) chicks, several genes were identified with differential expression associated with host resistance to IBDV. These genes were also subjected to RT-PCR on individual samples to verify the results obtained from microarrays. The major finding was the co-upregulation of 7 genes – coding for Ets2, H963, RGS1, ABIN-2, CREM/ICER, DUSP1 and CXCR4 – in several R, but not S or C, individuals, and characterized by very high correlations of expression levels. Resistance also generally coincided with reduced transcript levels of acute-phase serum amyloid A (A-SAA) and increased levels of IL-8. Based on reported functions of these genes, our findings suggest that resistance was mediated by the activation of specific cellular mechanisms, indicated by increased activity of splenic macrophages and T-lymphocytes 3d post-challenge. Early and intense innate responses may enhance the formation and activity of germinal centers in the spleen of resistant birds, and the transition to acquired cellular response. The migration of activated cells towards the bursa is presumably important for resistance to occur.
Keywords: host-resistance analysis

overall_design: Male and female chicks (N = 183) were grown under routine management conditions. At 13 days of age, chicks were housed in isolators. At age 21d, 160 chicks were IBDV-challenge and the remaining 23 were grown under the same conditions in a separate isolator and served as non-challenged controls (C). At age 24d (3d PC), all chicks were weighed, bled and euthanized. Spleens and bursae were harvested. Viral load in infected bursae was used to determine resistant (R) and susceptible (S) birds. S, R and C groups were divided into 4 sub-groups (S1-S4, R1-R4 and C1-C4) with similar representation of viral-load scores, so that they were considered biological replicas. These sub-groups were of 2 birds each, except S1 and R1 which were single individuals. Overall, 22 birds were used (7 from R group, 7 from S and 8 from C). Each sub-group was used to create a RNA pool, forming 4 sets of replicated comparisons. Each set consisted of 3 comparisons: R vs. S, R vs. C and S vs. C (overall: 12 comparisons/microarrays). Cy3- and Cy5-labellings of two compared groups were switched in same comparisons in different sets (dye-swaps).

first: Eyal

last: Koren

first: Huaijun

last: Zhou

first: Avigdor

last: Cahaner

first: Dan

last: Heller

first: Jacob

last: Pitcovski


title: Phi29-based amplification of fresh-frozen and FFPE tumor DNA

summary:
Corresponds to Bredel et al 2005 Figure 1
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Markus

last: Bredel


title: ATM Requirement in Gene Expression Responses to Ionizing Radiation in Human Lymphoblasts and Fibroblasts

status: Public on Jan 15 2006

city: DURHAM

first: Cynthia

last: Innes

address: 111 ALEXANDER DR

department: NCT

institute: NIEHS

summary:
Investigation of ATM-dependent and dose-dependent, or -independent, responses were examined in human lymphoblast cells 6 hr following exposure to either 1 or 5 Gy ionizing radiation.
Keywords: cDNA, dual-channel

overall_design: Human lymphoblast cells from "apparently healthy" individuals and individuals with Ataxia telangiectasia were exposed to 1 Gy or 5 Gy ionizing radiation.  Gene expression responses 6 hr following IR were examined.  Untreated samples were hybridized together with their matched treated samples.

middle: L

first: Alexandra

middle: N

last: Heinloth

first: Kristina

middle: G

last: Flores

first: Stella

middle: O

last: Sieber

first: Paula

middle: B

last: Deming

first: Pierre

middle: R

last: Bushel

first: William

last: Kaufmann

first: Richard

middle: S

last: Paules


title: Hypoxia

status: Public on Jan 24 2006

first: Edwin

last: Rodriguez

address: Beckman, B439

institute: UC Stanford

summary:
All mammalian cells need oxygen. Inadequate oxygen (hypoxia) triggers cellular responses for survival and the maintenance of homeostasis. A transcription factor, hypoxia-inducible factor (HIF), plays a central role in the hypoxia response; its activity is regulated by the oxygen-dependent degradation of the HIF-1a protein. Despite the ubiquity and importance of hypoxia responses, very little is known about the variation in the global transcriptional response to hypoxia among different cell types and its links to tissue and cell-specific diseases. We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells (RPTECs), breast epithelial cells, smooth muscle (SMs), and endothelial cells (ECs) with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This exaggerated response was associated with a uniquely high level of HIF-1a RNA in renal cells and could be diminished by reducing HIF-1a expression via RNA interference (RNAi). A gene-expression signature of the hypoxia response, derived from our studies of cultured mammary and renal tubular epithelial cells, showed coordinated variation in several human cancers, and was a strong predictor of clinical outcomes in both breast and ovarian cancers.  In an analysis of a large, published gene-expression dataset from breast cancers, we found that the prognostic information in the hypoxia signature was virtually independent of that provided by the previously reported wound signature and more predictive of outcomes than any of the clinical parameters in current use.
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
Keywords: stimulus_or_stress_design

overall_design: Using regression correlation

last: Chi

first: Zhen

last: Wang


title: DNA copy number changes in prostate cancer cell lines

status: Public on Jan 12 2006

last: Stanford Microarray Database

institute: Stanford Microarray Database (SMD)

summary:
Abstract: BACKGROUND: The aim of this study was to characterize gene expression and DNA copy number profiles in androgen sensitive (AS) and androgen insensitive (AI) prostate cancer cell lines on a genome-wide scale. METHODS: Gene expression profiles and DNA copy number changes were examined using DNA microarrays in eight commonly used prostate cancer cell lines. Chromosomal regions with DNA copy number changes were identified using cluster along chromosome (CLAC). RESULTS: There were discrete differences in gene expression patterns between AS and AI cells that were not limited to androgen-responsive genes. AI cells displayed more DNA copy number changes, especially amplifications, than AS cells. The gene expression profiles of cell lines showed limited similarities to prostate tumors harvested at surgery. CONCLUSIONS: AS and AI cell lines are different in their transcriptional programs and degree of DNA copy number alterations. This dataset provides a context for the use of prostate cancer cell lines as models for clinical cancers.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Hongjuan

last: Zhao


title: Gene expression variations in prostate cancer cell lines


title: Hmo1 ChIP-chip

first: Joseph

last: Wade

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

summary:
Yeast Hmo1 ChIP-chip in triplicate with single untagged control
Keywords: ChIP-chip

overall_design: Yeast Hmo1 ChIP-chip was performed in yDH419 (Hmo1-3myc) in triplicate using anti-myc (9E10 monoclonal antibody). A control experiment was performed using the untagged isogenic strain, BY4742

first: Daniel

last: Hall

middle: T

first: Kevin

last: Struhl


title: Genome-Wide Gene Dosage Representation in Phi29-Amplified DNA

summary:
Corresponds to Bredel et al 2005 Figure 2
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Young

last: Kim


title: EBV-Host interaction in nasal NK/T lymphoma and chronic acvtive EBV infection

status: Public on Jan 11 2006

city: Tokyo

first: Junko

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

country: Japan

institute: Tokyo Medical University

summary:
Extranodal NK/T-cell, nasal type (hereinafter, nasal T/NK lymphoma), is a distinct clinicopahtologic entity highly associated with EBV.  Among nasal T/NK lymphoma, some cases are developed from the long-lasting EBV infection termed chronic active EBV (CAEBV) infection.The clonal expansion of EB infected T- or NK cell are seen in patients with both nasal T/NK lymphoma and CAEBV infection, suggesting that two diseases might partly share the similar mechanism by which EBV affect host cellular genes. Question has thus arisen why a subset of patients with CAEB infection develop into nasal T/NK lymphoma. This study aimed to investigate the virus-host interaction in EBV-associated lymphoma.

Keywords = nasak NK/T lymphoma
Keywords = chronic active EBV infection
Keywords: other

overall_design:
For dual color analysis, normal human lymphocyte mRNA was purchased from Ambion (Austin, TX, USA), and utilized as a reference, and then cellular gene expression were compared among SNK/T cells.
(1) We first investigated the common molecular signature of SNK/T cells.
(2) We next compared the gene expression pattern between two groups, one with cells from NK/T lymphoma and the other from CAEBV infection.

first: Yu

last: Zhang


title: A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue.

status: Public on Jan 10 2006

city: Stanford

address: 300 Pasteur Drive

summary:
Background  To identify the spectrum of malignant attributes maintained outside the host environment, we have compared global gene expression in primary breast tumors and matched short-term epithelial cultures.  Results  In contrast to immortal cell lines, a characteristic 'limited proliferation' phenotype was observed, which included over expressed genes associated with the TGFbeta signal transduction pathway, such as SPARC, LOXL1, RUNX1, and DAPK1. Underlying this profile was the conspicuous absence of hTERT expression and telomerase activity, a significant increase in TGFbeta receptor2, its cognate ligand, and the CDK inhibitor, p21CIP1/WAF1. Concurrently, tumor tissue and primary cultures displayed low transcript levels of proliferation-related genes, such as, TOP2A, ANKT, RAD51, UBE2C, CENPA, RRM2, and PLK.  Conclusions  Our data demonstrate that commonly used immortal cell lines do not reflect some aspects of tumor biology as closely as primary tumor cell cultures. The gene expression profile of malignant tissue, which is uniquely retained by cells cultured on solid substrates, could facilitate the development and testing of novel molecular targets for breast cancer.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Youngran

last: Ji


title: Human Breast Tumor SNPs

status: Public on Feb 09 2006

first: Andrea

last: Richardson

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

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

summary:
Genotype calls for 78 human breast tumor cases.
Keywords: Human Breast tissue

overall_design: Genotype calls by Affymetrix GeneChip Mapping 10K Array


title: Expression profiles of Salmonella typhi inside human macrophages (THP-1) compared to supernatant

city: Montreal

first: Sébastien

middle: P

last: Faucher

state: QUEBEC

address: C.P. 6128 Succ. Centre-Ville

department: Microbiology and Immunology

country: Canada

institute: University of Montreal

summary:
Global expression profiles of Salmonella typhi grown in the supernatant of infection and within human macrophages at 0h, 2h, 8h and 24h were obtained. Stringent analytical methods were used to compare Salmonella typhi cDNAs and revealed that known virulence factors, such as the SPI-1 and SPI-2 encoded type III secretion systems, were found to be expressed as predicted during infection by Salmonella. Intracellular Typhi expressed many genes encoding antimicrobial peptides, used the glyoxylate bypass for fatty acid utilization, and, did not induce the SOS response or the oxidative stress response. Genes coding for the flagellar apparatus, chemotaxis and the iron transport system were down-regulated in vivo. The combined use of SCOTS and microarray is an effective way to determine global bacterial gene expression profiling in the context of host infection, without the need of increasing the multiplicity of infection beyond what is seen in nature.
Keywords: Time course

sample_organism: Salmonella enterica subsp. enterica serovar Typhi

platform_organism:
Salmonella
Salmonella enterica

overall_design: cDNA was prepared by 3 round of SCOTS from the Supernatant of infection of THP-1 human macrophages and at 0h, 2h, 8h and 24h post-infection. 6 replicates were recorded for each conditions (Supernatant, 0h, 2h, 8h and 24h). Genomic DNA was used as a reference channel on each slide.

first: Sebastien

first: Steffen

last: Porwollik

first: Charles

middle: M

last: Dozois

first: Michael

last: McClelland

first: France

last: Daigle


title: Consequences of a deletion in dspA on transcript accumulation in Synechocystis sp. strain PCC6803.

summary:
Abstract: A sensor histidine kinase of Synechococcus sp. strain PCC7942, designated nblS, was previously identified and shown to be critical for the acclimation of cells to high-light and nutrient limitation conditions and to influence the expression of a number of light-responsive genes. The nblS orthologue in Synechocystis sp. strain PCC6803 is designated dspA (also called hik33). We have generated a dspA null mutant and analyzed global gene expression in both the mutant and wild-type strains under high- and low-light conditions. The mutant is aberrant for the expression of many genes encoding proteins critical for photosynthesis, phosphate and carbon acquisition, and the amelioration of stress conditions. Furthermore, transcripts from a number of genes normally detected only during exposure of wild-type cells to high-light conditions become partially constitutive in the low-light-grown dspA mutant. Other genes for which transcripts decline upon exposure of wild-type cells to high light are already lower in the mutant during growth in low light. These results suggest that DspA may influence gene expression in both a positive and a negative manner and that the dspA mutant behaves as if it were experiencing stress conditions (e.g., high-light exposure) even when maintained at near-optimal growth conditions for wild-type cells. This is discussed with respect to the importance of DspA for regulating the responses of the cell to environmental cues.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Keywords: strain_or_line_design

first: Chao-Jung

last: Tu


title: Analysis of genomic differences between Salmonella typhi ISP1820 and CT18

summary:
Genomic DNA from Strain ISP1820 and CT18 were compared to identify missing genes in strain ISP1820.
Keywords: Comparative Genomic Hybridization

overall_design: 3 replicates were recorded


status: Public on Jan 13 2006

first: Heun-Sik

last: Lee

institute: Korea Reaearch Institute of Bioscience and Biotechnology

summary:
Gene expression profiles in hepatoma cells
Keywords: Cell type comparison

overall_design:
Duplicate experiment.
Hepatoma cell lines vs. Universal control


title: Transcriptional profiling of ADPKD placentas

status: Public on Jan 17 2006

city: Baltimore

first: Erica

last: Allen

state: MD

institute: Johns Hopkins University

summary:
The goal of this microarray study was to determine genes whose transcriptional profile was altered in the absence of polycystin-1 expression.  Placentas from knockout and wild-type littermates were compared at the latest viable timepoints (14.5d and 15.5dpc) and genes with a fold change > 1.5 were identified.
Keywords: other

first: Greg

last: Germino


title: Induction of Senescence in Diterpene Ester-Treated Melanoma Cells via PKC-dependent Hyperactivation of the MAPK Pathway

status: Public on Jan 20 2006

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

summary:
The diterpene ester PEP005 is a novel anticancer agent that activates PKC and cures subcutaneous murine melanoma by topical application.  We now describe the in vitro cytostatic effects of PEP005 and the diterpene ester TPA, observed in 20% of human melanoma cell lines.  Primary cultures of normal human neonatal fibroblasts were uniformly resistant to growth arrest, indicating a potential for tumor selectivity.  Sensitive cells were induced to senesce and exhibited a G1 and G2/M arrest.  There was sustained expression of p21WAF1/CIP1, irreversible dephosphorylation of the retinoblastoma gene product (Rb) and transcriptional silencing of E2F-responsive genes in sensitive cell lines.  Activation of MEK1/2 by PKC was required for diterpene ester-induced senescence.  Expression profiling revealed that the MAPK inhibitor HREV107 was expressed at a higher transcript level in resistant compared to sensitive cell lines.  We propose that activation of PKC over-stimulates the Ras/Raf/MEK/ERK pathway, resulting in sustained induction of p21WAF1/CIP1, dephosphorylation of Rb and transcriptional silencing of E2F-responsive genes required for DNA synthesis and mitosis.
Keywords: expression profile following treatment

overall_design: To investigate the molecular changes associated with the senescent phenotype, we examined the unique transcriptional changes occurring in sensitive melanoma cell lines treated with TPA or PEP005.  Initially a time-course cDNA microarray analysis was conducted on one sensitive and one resistant cell line treated with 1 µg/ml of TPA for 6, 24 h and 24 h recovery following 24 h treatment, to determine the earliest time point at which the most significant changes in transcription occurred.  The results provided support for conducting array experiments with 24 h treatment, in which three sensitive and four resistant melanoma cell lines were treated with 1 µg/ml of either diterpene ester.  Our primary objective was to identify those genes which were uniquely up or down-regulated in sensitive or resistant cell lines in response to treatment, which could reflect the phenotypic outcome.  Through applying a series of stringent selective criteria (see Material and Methods) we found that the most significant changes occurred in the transcriptional repression of genes required for DNA synthesis and mitosis in cell lines sensitive to treatment (Table 1).  To confirm that these changes were reflected at the protein level, western blot analysis was conducted on three sensitive and three resistant cell lines following 6 and 24 h treatment with TPA or PEP005.  We also included a 24 h recovery time point to determine the irreversibility of the change.

first: Sarah-Jane

last: Cozzi

first: Peter

last: Parsons

first: Julie

last: Pedley

first: Steven

last: Ogbourne


title: si RNA interference of Hepatitis B viral gene expression

status: Public on Jan 07 2006

last: Stanford Microarray Database

department: Stanford University, School of Medicine

summary:
Gene expression profiling comparisons of HepG2.2.15 or PLC/PRF/5 cells either mock (M) transfected or transfected with 0.2 microM S2 RNA or Scrambled (SCR) siRNA were carried out in duplicate 48 hours after transfection. The experiments were carried out in duplicate (a and b). The following combinations of RNA were used on 2 slides each: 1. 2.2.15 cells: mock transfection (reference) versus S2 treatment (test) 2. 2.2.15 cells: mock transfection (reference) versus Scr treatment (test) 3. 2.2.15 cells: Scr treatment (reference) versus S2 treatment (test) 4. PLC/PRF/5 cells: mock transfection (reference) versus S2 treatment (test) 5. PLC/PRF/5 cells: mock transfection (reference) versus Scr treatment (test) 6. PLC/PRF/5 cells: Scr treatment (reference) versus S2 treatment (test)
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
Keywords: stimulus_or_stress_design

first: Shanthi

last: Wasser


title: Cadaveric vs. live donor kidneys

summary:
Recipients of live donor transplant kidneys (LIV) exhibit a significantly longer allograft half-life compared with cadaveric donor organs (CADs). The reasons are incompletely understood. Therefore this study sought to elucidate the genome-wide gene expression profiles in microdissected transplant kidney biopsies obtained from five cadaveric and five matched live donors before transplantation. cDNA microarrays were used to determine the transcripts in isolated glomeruli (G) and the tubulointerstitial (TI) compartment. Data were subjected to hierarchical clustering, maxT adjustment and a jackknife procedure to ensure robustness of reported findings; validation was performed by independent analysis of split biopsies and TaqMan-PCR. One hundred and thirteen sequences representing 62 unique genes (17 redundant features), and 34 ESTs separated G from TI. No difference in gene expression was found in G between LIV and CAD kidneys, but nine genes (two represented twice) and three ESTs were abundantly expressed in the CAD TI compared with LIV. The main biological function of these genes is counter regulation of oxidative stress. Promoter analysis of significant features suggested coregulated gene groups. These data suggest that CAD kidneys exhibit a distinctly different set of transcripts in the TI compartment but not in the G compartment when compared with LIV kidneys.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Timothy

last: Meyer


title: Sensory ray genes

status: Public on Jan 06 2006

summary:
These experiments were undertaken with the goal of identifying genes whose expression is enriched in or restricted to the sensory rays of the C. elegans male tail. We constructed two mutant strains in which ray development is either compromised (EM672) or enhanced (EM673), and harvested mRNA from adult males. Labeled cDNAs were compared on seven arrays (representing three different sets of mRNA preps). In all experiments, Channel 1 (green) represents the EM672 expression profile and Channel 2 (Red) corresponds to EM673. Ray-enriched genes would therefore generally be expected to have higher intensities in Channel 2 than in Channel 1. Experimental details and results from these studies are available in D.S. Portman and S.W. Emmons (2004) Identification of C. elegans sensory ray genes using whole-genome expression profiling.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Douglas

last: Portman


title: Polarized T84 Cells Response to H. pylori infection

summary:
All arrays use the same reference, which is cDNA generated from RNA harvested from uninfected polarized T84 monolayers.  Infections were done on two seperate days.  Numbers following the name of each array designate the time point post H. pylori infection.  Data for time course one is named such that only this timepoint is listed, while data for time course two (wildtype and mock) is named such that the time point is followed by the designation "-2".
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

last: Merrell


title: mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains

summary:
mRNA decay in E. Coli degradosome mutants and their parental strains following transcriptional arrest with rifampicin.
Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes.
An RNA stablity experiment design type examines stability and/or decay of RNA transcripts.
Keywords: RNA_stability_design

first: Sue

last: Lin-Chao


title: S. typhimurium Bile regulated genes

summary:
Bile treatment 30 and 60 minutes regulation of genes by PmrA and UblA, 30 and 60 minutes
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
Keywords: stimulus_or_stress_design

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Igor

last: Brodsky


title: Molecular targets of doxazosin in human prostatic stromal cells

summary:
BACKGROUND: We used cDNA microarray analysis to obtain insights into the mechanisms of action of doxazosin, an alpha(1)-adrenergic receptor antagonist used to treat benign prostatic hyperplasia (BPH). METHODS: Hierarchical clustering analysis and significance analysis of microarray (SAM) were performed to identify genes differentially expressed between untreated stromal cells cultured from normal tissue and BPH, and changes in gene expression induced by doxazosin. Transcript levels of selected genes were validated by real-time reverse-transcription polymerase chain reaction (RT-PCR). : Hierarchical clustering analyses separated untreated normal and BPH cells. Sixty-seven genes whose expression varied at least twofold after doxazosin treatment in both normal and BPH cells were identified, as were 93 genes differentially regulated in normal versus BPH cells. Molecular targets consistent with tumor necrosis factor (TNF)-alpha-related activity were identified. CONCLUSIONS: Normal versus BPH stromal cells differ in global gene transcription. Doxazosin induced gene expression changes relevant to proliferation/apoptosis, immune defense, cell-cell signaling/signal transduction, and transcriptional regulation.
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
Keywords: stimulus_or_stress_design

first: Hongjuan

last: Zhao


title: PLA2G2A and human gastric cancers

summary:
We analyzed gene expression patterns in human gastric cancers by using cDNA microarrays representing approximately 30,300 genes. Expression of PLA2G2A, a gene previously implicated as a modifier of the Apc(Min/+) (multiple intestinal neoplasia 1) mutant phenotype in the mouse, was significantly correlated with patient survival. We confirmed this observation in an independent set of patient samples by using quantitative RT-PCR. Beyond its potential diagnostic and prognostic significance, this result suggests the intriguing possibility that the activity of PLA2G2A may suppress progression or metastasis of human gastric cancer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Xin

last: Chen


title: Aging time course

summary:
Transcriptional Profile of Aging in C. elegans  Whole-genome analysis of gene expression during chronological aging of the worm provides a rich database of age-specific changes in gene expression and represents one way to distinguish among these models. Using a rigorous statistical model with multiple replicates, we find that a relatively small number of genes (only 164) show statistically significant changes in transcript levels as aging occurs (<1% of the genome). Expression of heat shock proteins decreases, while expression of certain transposases increases in older worms, and these findings are consistent with a higher mortality risk due to a failure in homeostenosis and destabilization of the genome in older animals. Finally, a specific subset of genes is coordinately altered both during chronological aging and in the transition from the reproductive form to the dauer, demonstrating a mechanistic overlap in aging between these two processes.
Groups of assays that are related as part of a time series.
Age: Age of organism
Keywords: time_series_design

first: Jim

last: Lund

first: Pat

last: Tedesco


title: Microarray Coverage of Universal Human Reference RNA on microarrays with yeast controls

status: Public on Jan 05 2006

summary:
Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye.
A reference experiment design type is where all samples are compared to a common reference.
Keywords: reference_design

first: Charles

last: Perou


title: Comparative Transcriptome Profiling of Maize Lines

status: Public on Jan 01 2006

first: Jiong

last: Ma

address: 385 Serra Mall

department: Biological Sciences

institute: Stanford University

summary:
Four tissues (leaves, 1 mm anthers, 1.5 mm anthers, pollen) from one hybrid and one inbred maize line were hybridized with the W23 inbred on Agilent oligonucleotide microarrays with 21K elements. Tissue-specific gene expression patterns were documented with leaves having the most tissue-specific transcripts. Haploid pollen expresses about half as many genes as the other samples. High overlap of gene expression was found between leaves and anthers. Anther and pollen transcript expression showed high conservation among the three lines while leaves had more divergence. Antisense transcripts represented about 6 to 14 percent of total transcriptome by tissue type but were similar across lines. Gene Ontology (GO) annotations were assigned and tabulated. Enrichment in GO terms related to cell cycle functions was found for the identified antisense transcripts. Microarray results were validated via quantitative real time PCR and by hybridization to a second oligonucleotide microarray platform.
Keywords: genetic background comparison

overall_design: We analyzed 4 tissues from 3 maize lines, each with 3 biological replicates, with W23 as a reference, and hybridized to 24 arrays.

first: Darren

middle: J

last: Morrow

first: John

last: Fernandes

first: Virginia

last: Walbot


title: Contribution of unique genes by individual cell lines to Universal Human Reference RNA

summary:
Total RNA isolated from 10 individual human cell lines were reverse-transcribed to cDNA, labeled with Cy5 and co-hybridized with Cy3-labeled UHRR onto 43,000-spot cDNA microarrays (Stanford University). The data was analyzed using GeneTraffic software. Approximately 6000-8000 spots out of 43,000 (14-18 %) were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics in only one cell line was determined.
A reference experiment design type is where all samples are compared to a common reference.
Keywords: reference_design

first: Natalia

last: Novoradovskaya


title: Comparative expression studies of a complex phenotype: cord formation in Mycobacterium tuberculosis

last: Stanford Microarray Database

summary:
Abstract: The aggregation of mycobacteria into structures known as cords is an intrinsic property of the human tubercle bacillus. This property is thought to be determined by the lipid composition of the bacterial cell surface and may contribute to the virulence of the organism. Using microarray technology, we compared the pattern of gene expression of H37Rv, a virulent, cording strain of Mycobacterium tuberculosis, with H37Ra, an avirulent, non-cording strain derived from the same original patient isolate, under five different nutrient combinations and growth conditions. Under all of these conditions, H37Rv formed cords and H37Ra did not. By focusing our analysis only on genes that were differentially expressed under all conditions, we hoped to enrich the resulting gene list for genes associated with cording. We identified 22 genes that were consistently expressed at higher levels in H37Rv than in H37Ra under all conditions tested. Genes involved in lipid metabolism and the cell membrane were significantly enriched in our gene list, indicating that the cell wall and the cell membrane may be the major sites of difference between these two strains. This work represents a new strategy for enriching gene lists for relevant genes, which may also be applicable for other types of problems.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Strain Name: H37Ra or H37Rv
Media: 7H9 (Roll or Shake), Dubos, Sauton, or Youman
Keywords: replicate_design

first: Qian

last: Gao


title: cDNA array expression profile of wild-type and fl-mutant upland cotton ovules

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

summary:
Comparison of gene expression profiles of wild-type and fl-mutant upland cotton ovules
Keywords: repeat samples

overall_design:
Data for six replicate experiments performed with  biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+5-Cy5 wt+3-Cy3
Set 1 (dye swap): wt+5-Cy3 wt+3-Cy5
Set 2: wt+5-Cy5 wt+3-Cy3
Set 2 (dye swap): wt+5-Cy3 wt+3-Cy5
Set 3: wt+5-Cy5 wt+3-Cy3
Set 3 (dye swap): wt+5-Cy3 wt+3-Cy5

GSM63341, GSM63342, GSM63343, GSM63344, GSM63345, GSM63346

Data for 3 replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+3-Cy5 vs wt+3-Cy3
Set 2: wt+3-Cy3 vs wt+3-Cy5
Set 3: wt+3-Cy5 vs wt+3-Cy3

GSM63365, GSM63366, GSM63367

Data for six replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+3-Cy5 wt-3-Cy3
Set 1 (dye swap): wt+3-Cy3 wt-3-Cy5
Set 2: wt+3-Cy5 wt-3-Cy3
Set 2 (dye swap): wt+3-Cy3 wt-3-Cy5
Set 3: wt+3-Cy5 wt-3-Cy3
Set 3 (dye swap): wt+3-Cy3 wt-3-Cy5

GSM63368, GSM63369, GSM63370, GSM63371, GSM63372, GSM63373

Data for six replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: 0wt-Cy5 wt+3-Cy3
Set 1 (dye swap): 0wt-Cy3 wt+3-Cy5
Set 2: 0wt-Cy5 wt+3-Cy3
Set 2 (dye swap): 0wt-Cy3 wt+3-Cy5
Set 3: 0wt-Cy5 wt+3-Cy3
Set 3 (dye swap): 0wt-Cy3 wt+3-Cy5

GSM63374, GSM63375, GSM63376, GSM63377, GSM63378, GSM63379

Data for six replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+3-Cy5 fl+3-Cy3
Set 1 (dye swap): wt+3-Cy3 fl+3-Cy5
Set 2: wt+3-Cy5 fl+3-Cy3
Set 2 (dye swap): wt+3-Cy3 fl+3-Cy5
Set 3: wt+3-Cy5 fl+3-Cy3
Set 3 (dye swap): wt+3-Cy3 fl+3-Cy5

GSM63391, GSM63392, GSM63393, GSM63394, GSM63395, GSM63396

Data for six replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+10-Cy5 fl+10-Cy3
Set 1 (dye swap): wt+10-Cy3 fl+10-Cy5
Set 2: wt+10-Cy5 fl+10-Cy3
Set 2 (dye swap): wt+10-Cy3 fl+10-Cy5
Set 3: wt+10-Cy5 fl+10-Cy3
Set 3 (dye swap): wt+10-Cy3 fl+10-Cy5

GSM63397, GSM63398, GSM63399, GSM63400, GSM63401, GSM63402

Data for six replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+10-Cy5 wt+3-Cy3
Set 1 (dye swap): wt+10-Cy3 wt+3-Cy5
Set 2: wt+10-Cy5 wt+3-Cy3
Set 2 (dye swap): wt+10-Cy3 wt+3-Cy5
Set 3: wt+10-Cy5 wt+3-Cy3
Set 3 (dye swap): wt+10-Cy3 wt+3-Cy5

GSM63403, GSM63404, GSM63405, GSM63406, GSM63407, GSM63408

Data for six replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+15-Cy5 wt+3-Cy3
Set 1 (dye swap): wt+15-Cy3 wt+3-Cy5
Set 2: wt+15-Cy5 wt+3-Cy3
Set 2 (dye swap): wt+15-Cy3 wt+3-Cy5
Set 3: wt+15-Cy5 wt+3-Cy3
Set 3 (dye swap): wt+15-Cy3 wt+3-Cy5

GSM63409, GSM63410, GSM63411, GSM63412, GSM63413, GSM63414

Data for six replicate experiments performed with biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1: wt+20-Cy5 wt+3-Cy3
Set 1 (dye swap): wt+20-Cy3 wt+3-Cy5
Set 2: wt+20-Cy5 wt+3-Cy3
Set 2 (dye swap): wt+20-Cy3 wt+3-Cy5
Set 3: wt+20-Cy5 wt+3-Cy3
Set 3 (dye swap): wt+20-Cy3 wt+3-Cy5

GSM63415, GSM63416, GSM63417, GSM63418, GSM63419, GSM63420

first: Yong-Hui

last: Shi

first: Liang

last: Zhang

first: Jing

last: Cheng


title: Rat Normal Cochlear Nucleus

city: Milwaukee

first: David

last: Friedland

state: WI

address: 8701 Watertown Plank Rd

department: Otolaryngology and Communication Sciences

institute: Medical College of Wisconsin

summary:
The cochlear nucleus is the first central pathway involved in the processing of peripheral auditory activity.  It is heterogeneous in neuronal populations and physiologic responses and is organized in three major subdivisions: the anterior ventral cochlear nucleus (AVCN), the posterior ventral cochlear nucleus (PVCN) and the dorsal cochlear nucleus (DCN).  Although each region demonstrates multiple cell types and functions, there are predominant populations of neurons in each region that underlie the principal role each subdivision plays in auditory processing.  Little is known of the underlying genetic contribution to these properties.  This study sought to identify genes expressed in the subdivisions of the cochlear nucleus that may account for the anatomical and physiological characteristics of each subdivision. These data provide a genetic basis for understanding normal auditory processing in the cochlear nucleus and a template for investigating changes that may occur with hearing loss, the generation and percept of tinnitus, and central processing disorders.
Keywords: normal, comparative

overall_design: Brown Norway rats (n=40, female, 45days) were anesthetized and decapitated.  Brains were rapidly removed and the subdivisions of the cochlear nucleus (AVCN, PVCN and DCN) dissected on dry ice.  Total RNA was extracted and tested for concentration and purity by spectrophotometry and integrity by gel electrophoresis.  SAGE was performed using the NlaIII enzyme and Invitrogen SAGE kit.  Concatemers were commercially sequenced and imported into eSAGE (Margulies and Innis, 2000) for tag extraction and frequency.

first: Rebecca

last: Eernisse

first: Paul

last: Popper

first: Joseph

last: Cioffi


title: Genome-wide transcriptional dependencies on TAF1 functional domains

city: University Park

first: Jordan

middle: D

last: Irvin

address: 452 N Frear

department: Biochemistry

institute: Penn State University

summary:
TFIID plays a central role in regulating the expression of most eukaryotic genes. Of the 14 TAF subunits that compose TFIID, TAF1 is one of the largest and most functionally diverse.  Yeast (Saccharomyces cerevisiae) TAF1 reportedly possesses at least four distinct activities including a histone acetyltransferase, and TBP, TAF, and promoter binding.  Establishing the importance of each region in gene expression through deletion analysis has been hampered by the cellular requirement of TAF1 for viability.  To circumvent this limitation we introduced galactose-inducible deletion derivatives of previously defined functional regions of TAF1 into a temperature sensitive taf1ts2 yeast strain.  After galactose-induction and temperature inactivation of the temperature-sensitive allele, we examined the properties and phenotypes of the mutants, including their impact on genome-wide transcription.  Virtually all TAF1-dependent genes, which comprise ~90% of the yeast genome, displayed a strong dependency upon all regions of TAF1 that were tested.  This might reflect the need for each region of TAF1 to stabilize TAF1 against degradation or that all TAF1-dependent genes require the many activities of TAF1.  Paradoxically, deletion of the region of TAF1 that is important for promoter binding interfered with the expression of many genes that are normally TFIID-independent/SAGA-dominated, suggesting that this region normally prevents TAF1 (TFIID) from interfering with the expression of SAGA-regulated genes.
Keywords: genetic modification

overall_design: Experiment contains 14 total hybridizations.  Yeast cDNA dual channel (Cy3/Cy5) cohybridization.  All experiments performed in duplicate (dye swap).  Homotypic (reference vs reference) sample included with each hybridization.  Dye swap data was mode normalized using "R" software package and then corrected by B. subtilis spiking controls (added to each culture based on OD600 units).  Platform GPL1220: non-commercial nucleotide arrays. PCR amplified yeast (Saccharomyces cerevisiae) genomic DNA chip with ResGen Primer Pairs.  Amplification as described at http://cmgm.stanford.edu/pbrown/protocols/2_DNA.html.  Printed on aminosaline glass slides by the Penn State University Microarray facility


title: Lineage-specific gene duplication and loss in human and great ape evolution

summary:
Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.
A species experiment design type assays differences between distinct species.
Keywords: species_design

overall_design: Using regression correlation, arrayCGH, acCGH

first: Young

last: Kim


title: Chronic Helicobacter pylori Infection with Sydney Strain 1 and Mouse-Adapted Sydney Strain 2000

summary:
This experiment set contains the raw data for 8 arrays that were used in the genomic typing of the pre- and post-mouse H. pylori strains SS1 and SS2000. 10700 is the pre-mouse clinical isolate of SS1 and PMSS2000 is the pre-mouse clinical isolate of SS2000. gDNA from these strains were labeled and hybridized to H. pylori microarrays as described in Salama et al. {Salama et al. 2000 PNAS 97:14668-73}. In each case the test gDNA sample was labeled with Cy5 (red) and this was hybridized with Cy3 (green) labeled reference DNA of equal amount. The reference DNA consisted of equal amounts of gDNA from the two H. pylori strains used to make the H. pylori microarray, 26695 and J99.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Lucinda

last: Thompson

first: Nina

last: Salama


title: Analysis of SCOTS effect on transcript population

first: Sébastien

last: Faucher

summary:
The cDNA obtained before and after each round of SCOTS (first, second and third) from 2 h post-infection were hybridized to analyse the effect of SCOTS round on transcripts population. The number of detected genes increase with the numer of round of SCOTS. Because the cDNA prepared by 3 round of SCOTS gave the best results, three round of SCOTS were used in the preparation of the other samples.
Keywords: Evaluation of SCOTS round

overall_design: 6 replicates for each sample (cDNA, 1XSCOS, 2XSCOTS amd 3XSCOTS) were analysed to monitor the effect of the round of SCOTS on transcripts population.

first: Sebastien

first: Steffen

last: Porwollik

first: Charles

last: Dozois

first: Michael

last: McClelland

first: France

last: Daigle


title: IRES containing mRNAs and mitotic cell cycle

status: Public on Dec 31 2005

last: Stanford Microarray Database

summary:
A cell synchronization protocol was established in which global and individual mRNA translational efficiencies could be examined. While global translational efficiency was reduced in mitotic cells, approximately 3% of mRNAs remained predominantly associated with large polysomes during mitosis, as determined by cDNA microarray analyses. The 5 noncoding regions of six mRNAs were shown to contain internal ribosome entry sites (IRES). However, not all known mRNAs that contain IRES elements were actively translated during mitosis, arguing that specific IRES sequences are differentially regulated during mitosis.
A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
Keywords: cell_cycle_design

overall_design: User Defined

first: Peter

last: Sarnow


title: Six diploid strains grown in four conditions

city: Florence

first: Duccio

last: Cavalieri

address: Viale Pieraccini 6

department: Department of Pharmacology

country: Italy

institute: University of Florence

summary:
Six strains of Saccharomyces cerevisiae were grown in four different environments representing a continuum of rich and poor natural conditions
Keywords: Stress response, genetic diversity

overall_design:
Some hybridizations were performed in duplicates on the same microarrays. Two complete sets of PCR products were printed on the same glass slide and under a single cover slip. These duplicates are labeled Array_A and Array_B. Since these are not complete technical replicates, they were averaged in Landry et al. (Gene, accepted) following the normalization and prior to statistical analysis.Replicate indicates a complete independent hybridization.
Strains were grown in YPD (laboratory conditions), synthetic wine must (SWM) simulating fermentation conditions, or in low-nitrogen, proline-supplemented SWM (SWM_NS). The standard nutrient medium for yeast cultivation (YPD) is composed of 1% yeast extract, 2% peptone, and 2% dextrose. SWM contains 0.17% yeast nitrogen base, without amino acids and (NH4)SO4, 0.15% casamino acids, 0.05% NH4Cl, 0.60% DL-malic acid, 0.02% citric acid, 0.15% L-tartaric acid, 21% glucose, and 0.20% anaerobic factors ergosterol–Tween 80 (total 10 mg/L ergosterol, 0.5 ml/L Tween 80). The pH was adjusted to 3.3 with KOH. SWM has a total nitrogen concentration of 247.2 mg/L. The nitrogen starvation medium (SWM_NS) was composed of 0.17% yeast nitrogen base, 0.1% L-proline, 0.60% DL-malic acid, 0.02% citric acid, 0.15% L-tartaric acid, 21% glucose, and 0.20% ergosterol Tween 80 (10 mg/L ergosterol, 0.5 ml/L Tween 80). The pH was adjusted to 3.3. SWM_NS has a total nitrogen concentration of 123 mg/L. All cells were grown at 28°C. For YPD, cells were grown aerobically in a shaker at 200 rpm and harvested at an optical density (OD) of 0.8 (A600). SWM and SWM_NS: Strains were grown aerobically overnight in SWM. Cells were then diluted to 0.2 OD in SWM and left to grow to 0.8 OD in a shaker at 50 rpm. Anaerobic conditions were established by locked fermentation flasks with CO2 outlets filled with water. For growth under nitrogen starvation, cells were then pelleted (3000 g, 5 min), washed with sterile water, resuspended in SWM_NS medium, and left to grow for 4 (NS_4) or 24 (NS_24) hours under the same conditions. For all conditions, cells were harvested by centrifugation (3000 g, 10 min) at then flash frozen using liquid nitrogen. The hybridization protocol is described in Townsend et al. (2003). Hybridization Spots were visually inspected and flawed ones were flagged (negative values).


title: Primate Comparison Study

city: New Haven

first: Yoav

last: Gilad

state: CT

address: 333 Cedar St.

department: Genetics

institute: Yale

summary:
Comparing different primates to Human; treated vs.untreated
Keywords: other

sample_organism:
Macaca mulatta
Pan troglodytes
Pongo pygmaeus
Homo sapiens