title: Characterisation of the mouse megakaryocyte transcriptome

status: Public on Feb 03 2007

city: Birmingham

first: Michael

middle: Graham

last: Tomlinson

state: West Midlands

address: Wolfson Drive

department: Division of Medical Sciences

institute: University of Birmingham

summary:
This study aims to identify all genes expressed in primary mouse megakaryocytes
Keywords: Megakaryocyte, SAGE, transcriptome analysis

overall_design: Mouse megakaryocytes were grown in vitro from bone marrow progenitors.  Mature, polyploid (approximately 95% 64n and 128n) differentiated megakaryocytes were used to generate RNA for SAGE library construction.

first: Victoria

middle: L

last: Heath

first: Stephanie

last: Dumon

first: Jon

last: Frampton

first: Steve

last: Watson


title: Male and female embryonic chicken livers (arnol-affy-chick-445002)

status: Public on Mar 20 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

country: USA

institute: Translational Genomics

summary:
The study is relevant to an understanding of the forces that lead to sex differences in the brain. Many neural and psychiatric diseases affect men and women differently, so the understanding of sex differences in brain function impacts on our understanding of why the male and female brain differ in their susceptibility to disease.
Using Affymetrix chicken arrays, we will measure the gene expression in male and female embryonic chicken liver to compare with previous studies of brain.
Gene expression differs in the male and female embryonic chicken liver.  Z-linked genes are expressed higher in males than females, in a manner similar to Z-linked genes in the brain.  The comparison of brain and liver will demonstrate which sex differences are specific to brain and which are general.
20 male and 20 female chicken embryos will serve as source of brain tissue. In late stage embryos, we will remove the liver and extract total RNA. Four birds will comprise each individual sample. Thus, we will have 5 biologically independent male samples, and an equal number of female samples.
Keywords: dose response

first: Arthur

middle: P

last: Arnold


title: Mouse Brain Voxelation, Voxels

status: Public on Jul 12 2007

city: Los Angeles

first: Mark

middle: H.

last: Chin

state: CA

address: 650 Charles E. Young Dr

department: Human Genetics

institute: UCLA

summary:
Transcriptional profiling of mouse brain voxels from a single coronal slice of the mouse brain comparing each voxel to whole mouse brain RNA.  Goal was to determine the gene expression profiles for the mouse genome in a coronal slice of the mouse brain.
Keywords: Genetic modification

overall_design: Two-condition experiment, Voxel vs. Whole Brain RNA. Biological replicates: 3 independent datasets from mouse brains, independently harvested. One voxel replicate per array.

middle: H

first: Alex

middle: B

last: Geng

first: Arshad

last: Khan

first: Wei-Jun

last: Qian

first: Vladislav

middle: A

last: Petyuk

first: Shawn

last: Levy

middle: W

last: Toga

first: Richard

middle: D

last: Smith

middle: M

last: Leahy

first: Desmond

middle: J


title: Tumor and Non Tumor Associated Skin Fibroblasts

status: Public on Oct 10 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Fibroblast cells were cultured from human skin, either tumor (basal cell carcinoma) or non-tumor tissue.  Cells were propagated for several passages in culture, then switched to low (0.1%) serum conditions for 48 hours prior to mRNA harvest.  Reference for all arrays was Stratagene Universal Human Reference RNA.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Julie

last: Sneddon


title: Polyanion binding proteins data for five cellular polyanionic samples

status: Public on Nov 30 2006

city: cambridge

first: Nazila

last: Salamat-Miller

state: MA

address: 700 main street

institute: Shire

summary:
The existence of interactions between many cellular proteins and various polyanionic surfaces within a cell is now well-established.  The functional role of such interactions, however, remains to be clearly defined.  The existence of protein arrays, with a large selection of different kinds of proteins, provides a way to better address a number of aspects of this question.  We have therefore investigated the interaction between five cellular polyanions (actin, tubulin, heparin, heparan sulfate (HS), and DNA) and approximately 5,000 human proteins using protein microarrays in an attempt to better understand the functional nature of such interaction(s).  We demonstrate that a large number of polyanion binding proteins exist which contain multiply positively-charged regions, are often disordered, are involved in phosphorylation processes, and appear to play a role in protein-protein interaction networks.  Considering the crowded nature of cellular interiors, we propose that polyanion binding proteins (PABPs) interact with a wide variety of polyanionic surfaces in cells in a functionally significant manner.
Keywords: Protein-Protein, protein-polyanion Interaction

sample_organism:
Sus scrofa
Bos taurus

overall_design: Experiments were conducted according to the manufacturer’s protocol.  Briefly, protein arrays were probed with 120 ul of 50 ug/ml of each polyanion (actin, tubulin, heparin, heparan sulfate, and DNA) in the presence and absence of 0.15 M NaCl in the probing solution.  After subsequent washings, the arrays were exposed to strepavidin-Alexa Fluor® 647.  The arrays were then washed, dried, and scanned with the GenePix®4000B at 635 nm to acquire a fluorescence image.  The resultant files were produced using GenePix® Pro 5.0 software.  Each image was analyzed using the appropriate grid downloaded from the Invitrogen Inc. website.  For all of the scanned images, a program available through Invitrogen Inc. (ProtoArray™ Prospector, v. 3.1.1) was used to obtain the identity of the proteins which demonstrated significant interaction with the probes.

first: Jianwen

last: Fang

first: Christopher

last: Seidel

first: Yassen

last: Assenov

first: Mario

last: Albrecht

first: CRussell

last: Middaugh


title: Contrasting patterns of expression divergence in early and late stages of population divergence in mice

status: Public on Dec 13 2006

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary:
We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis.
Keywords: multi-species comparison

sample_organism:
Mus musculus
Mus spretus

overall_design: The design we employed is a reference design. All tissues were hybridized against a pool of that same tissue from 9 C57BL6 mice. All mice were roughly 12 weeks of age. To control for biological variation, we have used several individual males from each sub-species. RNA was isolated from three different organs, namely brain, liver/kidney and testis.

first: Diethard

last: Tautz

first: Ludwig

last: Eichinger

first: Patrick

last: Farbrother

first: Bettina

last: Harr


title: Transcriptional changes associated with woolliness during fruit ripening in Prunus persica

status: Public on Apr 30 2007

city: Santiago

first: Mauricio

last: Gonzalez

state: Region Metropolitana

address: Santa Rosa 11610

country: Chile

institute: Instituto de Investigaciones Agropecuarias

summary:
During ripening of fruits stored under low temperatures, a number of physiological alterations which are manifested in a reduction of juice content take place, resulting in the apparition of woolly fruits. Modifications in cell wall structure during the ripening process are proposed to be key to determine the decreasing of juice content in woolly fruits. Under the assumption that changes in relative abundance of genes related to cell wall metabolism would be involved in woolliness development, in this work we present an analysis of the expression of multiple genes, which serves as an approximation to uncover the mechanisms behind this physiological alteration.
The expression of 847 genes was examined using macroarrays hybridizations. Membranes were  hybridized with 32P-labeled cDNAs synthesized from mRNAs of juice and woolly peaches. The results showed that 67.5% of the clones (n = 573) fulfilled all filter criteria and they were selected for sequence analysis. Our analysis indicate that 45% of transcripts which present a consistent expression level in all biological replicates are activated exclusively in juice condition, and only 15% in woolly fruits. In the resting 40% (transcripts common to both conditions,) only 5% presents an abundance increase in woolly samples.
Keywords: Analysis of physiological disorder in peaches

overall_design: Macroarrays experiments were performed in six independent labeling/hybridization events (experimental replicates) of six distinct biological replicates (three juicy fruits and three woolly fruits). Therefore, a total of 36 membranes containing 960 spots that include the selected clones (847 cDNAs) plus control genes were obtained six intensity values/spot were recovered for each sample/fruit, and used to calculate the expression ratios.

last: González-Agüero

first: Leonardo

last: Pavez

first: Freddy

last: Ibáñez

first: Igor

last: Pacheco

first: Reinaldo

last: Campos-Vargas

first: Lee

last: Meisel

first: Ariel

last: Orellana

first: Julio

last: Retamales

first: Herman

last: Silva

last: González

first: Verónica

last: Cambiazo


title: Human Leukocytes SAGE

status: Public on Sep 16 2006

city: Tokyo

first: Shinichi

last: Hashimoto

address: 7-3-1 Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

summary:
This series represents the human leukocyte SAGE library collection.
Keywords: Human Leukocytes, Blood, SAGE

overall_design: Leukocytes are classified as myelocytic or lymphocytic, and each class of leukocytes consists of several types of cells that have different phenotypes and different roles. To define the gene expression in these cells, we have performed SAGE using human leukocytes and have provided the gene database for these cells not only at the resting stage but also at the activated stage.

first: Shin-ichi

first: Takuji

last: Suzuki

first: Shigenori

last: Nagai

first: Aya

last: Obata

last: Morishita

first: Kouji

last: Matsushima


title: Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae

status: Public on Jun 23 2006

city: Haren

first: Sacha

last: van Hijum

address: Kerklaan 30

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary:
Several genes involved in nitrogen metabolism are known to contribute to the virulence of pathogenic bacteria. Here, we studied the function of the nitrogen regulatory protein GlnR in the Gram-positive human pathogen Streptococcus pneumoniae. We demonstrate that GlnR mediates transcriptional repression of genes involved in glutamine synthesis and uptake (glnA, glnPQ), glutamate synthesis (gdhA), and the gene encoding the pentose phosphate pathway enzyme Zwf, which forms an operon with glnPQ. Moreover, the expression of gdhA is also repressed by the pleiotropic regulator CodY. The GlnR-dependent regulation occurs through a conserved operator sequence and is responsive to the concentration of glutamate, glutamine and ammonium in the growth medium. By means of in vitro binding studies and transcriptional analyses we show that  the regulatory function of GlnR is dependent on GlnA. Mutants of glnA and glnP displayed significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells, suggesting a role for these genes in the colonization of the host by S. pneumoniae. Thus, our results provide a thorough insight into the regulation of glutamine and glutamate metabolism of S. pneumoniae as mediated by both GlnR and GlnA.
Keywords: genetic modification

overall_design: Each amplicon was spotted twice (technical replicates) on the DNA microarray. These replicates are indicated in the platforms and DNA microarray data by the addition of _rep1, _rep2, etc. The RNA for wild-type and mutant strains was isolated in 3 independent biological replicates which were hybridized in (partly dye-swap) to the 3 slides for glnA and 3 slides for glnR.

first: Tomas

middle: G

last: Kloosterman

first: Wouter

middle: T

last: Hendriksen

first: Jetta

last: Bijlsma

first: Hester

last: Bootsma

first: Jan

last: Kok

first: Peter

last: Hermans

first: Oscar

last: Kuipers


title: Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions.

status: Public on May 23 2006

last: Stanford Microarray Database

summary:
DNA microarray analysis was used to profile gene expression in a commercial isolate of Saccharomyces cerevisiae grown in a synthetic grape juice medium under conditions mimicking a natural environment for yeast: High-sugar and variable nitrogen conditions. The high nitrogen condition displayed elevated levels of expression of genes involved in biosynthesis of macromolecular precursors across the time course as compared to low-nitrogen. In contrast, expression of genes involved in translation and oxidative carbon metabolism were increased in the low-nitrogen condition, suggesting that respiration is more nitrogen-conserving than fermentation. Several genes under glucose repression control were induced in low-nitrogen in spite of very high (17%) external glucose concentrations, but there was no general relief of glucose repression. Expression of many stress response genes was elevated in stationary phase. Some of these genes were expressed regardless of the nitrogen concentration while others were found at higher levels only under high nitrogen conditions. A few genes, FSP2, RGS2, AQY1, YFL030W, were expressed more strongly with nitrogen limitation as compared to other conditions.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Joe

last: DeRisi


title: Sobel-1R01NS046414-01

status: Public on Jun 07 2006

first: Winnie

last: Liang

summary:
Multiple sclerosis (MS) begins as an inflammatory/demyelinating disease but axon injury and neurodegeneration underlie chronic progression.  Extracellular matrix (ECM) heparan sulfate proteoglycans (HSPG) are catabolized in acute inflammatory MS lesions and HSPG catabolic products may contribute to failure of neuron repair.  Neurite outgrowth and axon elongation of PC12 cells are inhibited when these cells are grown on heparanase-digested HSPG.  This inhibition of differentiation is counteracted by nerve growth factor (NGF) but failure to completely reverse inhibition may be due to loss of other growth factors affected by HSPG breakdown.  To understand effects of the digested ECM in this model, expression of genes that control differentiation in PC12 cells grown on digested and undigested HSPG will be analyzed.  This will permit identification of new potential therapeutic targets for specifically counteracting inhibitory effects of ECM breakdown on neuron regrowth/regeneration in MS.
We will compare gene expression patterns of PC12 cells grown on undigested and digested HSPG in the presence and in the absence of NGF over a two week time course to identify the alterations induced by the catabolized HSPG on expression of genes involved in their acquisition of a neuronal phenotype and to determine which genes are and are not targeted by NGF.
We are studying ECM HSPG breakdown in human and experimental demyelinating diseases and have developed an in vitro model of ECM catabolism-induced inhibition of neuronal differentiation.  Our data indicate that: 1) the numbers of PC12 cells that exhibit neurite outgrowth are decreased when the ECM contains digested, as opposed to intact HSPG; and 2) in the presence of NGF, neurite outgrowth inhibition is counteracted, but complete axonal growth/elongation is not achieved.  We will use gene microarray analysis to identify the specific gene expression alterations that digested ECM HSPG induces in PC12 cells in this model of inhibition of neural differentiation.  We hypothesize that the genes that are critical for PC12 cell differentiation will be altered by the pathologically altered ECM.
Rat pheochromocytoma PC12 cell lines are widely used for analyzing neuronal differentiation.  Microarray analyses have identified gene expression patterns associated with their differentiation and response to growth factors.  We developed a model of catabolized HSPG inhibition of PC12 cell differentiation that mimics the ECM in MS lesions.  HSPG coated on tissue culture dishes is digested with heparanases prior to plating of the PC12 cells.  Cells grown on digested ECM without NGF show inhibition of neuronal differentiation (decreased numbers with neurite outgrowth) from days 7 to 14.  NGF can partially, but not completely counteract the inhibition, suggesting that signaling pathways in addition to those affected by NGF may be affected by the ECM HSPG digestion.   Therefore, we will compare gene expression patterns in samples of cells grown on digested and undigested HSPG ECM both in the presence and absence of NGF. The cells are plated on washed, undigested or digested HSPG-coated 100 mm Petri dishes and grown with or without NGF.  Total RNA will be extracted from cells grown in the 4 conditions (w/without digestion; w/without NGF) on 100mm Petri dishes using the RNeasy extraction kit (Qiagen).  We propose:  2 duplicate samples/culture condition (8 samples) per time point X 5 time points (days 1, 5, 7, 10, and 14 of culture) = 40 samples/experiment.  The RNA will be sent to the Microarray Consortium center for QC check and microarray analysis.  Previous analyses of PC12 cells have used the NIA Mouse 15K cDNA clone set scanned with the Agilent Oligo array platform (Vaudry, 2002; Grumolato, 2003).  Therefore, this methodology will be useful for comparisons to published studies.  (Number of experiments to be determined). Vaudry D, et al, 2002. J Neurochem 83:1272-1284 Grumolato L, et al, 2003. Endocrinology 144:2368-2379
Keywords: time-course

first: Raymond

last: Sobel


title: Differential gene expression of Appresorium vs Vegetative mycelium of Magnaporthe using oligoarray

status: Public on Aug 18 2006

city: Columbus

first: Mohan

last: Raghupathy

email: mohanbabu_r@yahoo.com, wang.620@osu.edu

state: OH

address: 201 Kottman Hall, 2021 Coffey Rd

department: Department of Plant Pathology

institute: The Ohio State University

type:
Expression profiling by array
Expression profiling by SAGE

summary:
Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants at the transcriptome level. To identify all
the expressed genes encoded in the fungal genome, we have analyzed the mycelium and appressorium transcriptomes using MPSS, RL-SAGE and oligoarray methods.
Keywords: RL-SAGE, oligoarray

overall_design: The M. grisea oliogoarray chip containing 60-mer oligos representing a total of 21,885 probes was obtained from Agilent (G4137A; Wilmington, Delaware). Of the 21,885 probes, 13,666 are from the annotated genes of M. grisea and 7,144 probes are from the rice ESTs (http://www.chem.agilent.com/scripts). The remainder 1,075 probes include quality controls, positive controls and negative controls.The oligoarray hybridization experiments included six technical replicates, of which three were dye-reversal.

first: Guo-Liang

last: Wang

first: Malali

last: Gowda

first: Venu

last: Reddychennavari


title: Gene expression profile of extraskeletal myxoid chondrosarcoma.

status: Public on Mar 15 2006

summary:
Abstract: Extraskeletal myxoid chondrosarcoma (EMC) is a soft tissue tumour that occurs primarily in the extremities and is characterized by a balanced translocation most commonly involving t(9;22) (q22;q12). The morphological spectrum of EMC is broad and thus a diagnosis based on histology alone can be difficult. Currently, no systemic therapy exists that improves survival in patients with EMC. In the present study, gene expression profiling has been performed to discover new diagnostic markers and potential therapeutic targets for this tumour type. Global gene expression profiling of ten EMCs and 26 other sarcomas using 42,000 spot cDNA microarrays revealed that the cases of EMC were closely related to each other and distinct from the other tumours profiled. Significance analysis of microarrays (SAM) identified 86 genes that distinguished EMC from the other sarcomas with 0.25% likelihood of false significance. NMB, DKK1, DNER, CLCN3, and DEF6 were the top five genes in this analysis. In situ hybridization for NMB gene expression on tissue microarrays (TMAs) containing a total of 1164 specimens representing 62 different sarcoma types and 15 different carcinoma types showed that NMB was highly expressed in 17 of 22 EMC cases and very rarely expressed in other tumours and thus could function as a novel diagnostic marker. High levels of expression of PPARG and the gene encoding its interacting protein, PPARGC1A, in most EMCs suggest activation of lipid metabolism pathways in this tumour. Small molecule inhibitors for PPARG exist and PPARG could be a potential therapeutic target for EMC.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Matt

last: Van De Rijn


title: Determination of stromal signatures in breast carcinoma

summary:
Abstract: Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patterns of expression of extracellular matrix genes and growth factors. Using immunohistochemistry and in situ hybridization on a tissue microarray, we found that genes specific for these two tumors have mutually specific expression in the stroma of nonneoplastic tissues. We defined a set of 786 gene spots whose pattern of expression distinguishes SFT from DTF. In an analysis of DNA microarray gene expression data from 295 previously published breast carcinomas, we found that expression of this gene set defined two groups of breast carcinomas with significant differences in overall survival. One of the groups had a favorable outcome and was defined by the expression of DTF genes. The other group of tumors had a poor prognosis and showed variable expression of genes enriched for SFT type. Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells.
Soft tissue tumor gene expression of 10 cases of DTF (blue), 13 cases of SFT (orange), and 35 other previously examined soft tissue tumors (black) based expression profiling on 42,000 -element cDNA microarrays.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Keywords: clinical_history_design


title: Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation

status: Public on Sep 28 2006

city: College Park

first: Jocelyne

last: DiRuggiero

state: MD

address: 3221 H.J. Patterson Hall

department: Cell Biology and Molecular Genetics

institute: University of Maryland

summary:
The remarkable survival of the hyperthermophilic archaeon Pyrococcus furiosus to ionizing radiation was previously demonstrated. Using a time course study and whole-genome microarray analyses of mRNA transcript levels, the genes and regulatory pathways involved in the repair of lesions produced by ionizing irradiation (oxidative damage and DNA strand breaks) in P. furiosus were investigated. Data analyses showed that radA, encoding the archaeal homolog of the RecA/Rad51 recombinase, was moderately up regulated by irradiation and that a putative DNA-repair gene cluster was specifically induced by exposure to ionizing radiation. This novel repair system appears to be unique to thermophilic archaea and bacteria and is suspected to be involved in translesion synthesis. Genes that encode for a putative Dps-like iron-chelating protein and two membrane-bound oxidoreductases were differentially expressed following gamma irradiation, potentially in response to oxidative stress. Surprisingly, the many systems involved in oxygen detoxification and redox homeostasis appeared to be constitutively expressed. Finally, we identified several transcriptional regulators and protein kinases highly regulated in response to gamma irradiation.
Keywords: time course

overall_design:
P. furiosus cultures grown to approximately 5 · 10^6 cells/ml were chilled to 4 C and exposed to 2,500 Gy of gamma radiation using a 26,000- curie (9.6 · 1014 Bq) 60Co gamma source at the University of Maryland College Park Gamma Test Facility, at a dose rate of 73 Gy/min. Cultures were further incubated at 90 C and samples for RNA extraction were taken at 0, 20, 40, 60, 120 and 240 min after the temperature
of the cultures reached 90 C.

first: Ernest

last: Williams

first: Todd

last: Lowe

first: J

last: Savas


title: Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers

status: Public on Feb 25 2006

summary:
This 58 arrays are the basis of our hypoxia story published in PLoS Medicine. The cell type, oxygen tension and time points are indicated.
Abstract: BACKGROUND: Inadequate oxygen (hypoxia) triggers a multifaceted cellular response that has important roles in normal physiology and in many human diseases. 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-1alpha protein. Despite the ubiquity and importance of hypoxia responses, little is known about the variation in the global transcriptional response to hypoxia among different cell types or how this variation might relate to tissue- and cell-specific diseases. METHODS AND FINDINGS: We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells, breast epithelial cells, smooth muscle cells, and endothelial cells with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This heightened response was associated with a uniquely high level of HIF-1alpha RNA in renal cells, and it could be diminished by reducing HIF-1alpha expression via RNA interference. 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 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. CONCLUSIONS: The transcriptional response to hypoxia varies among human cells. Some of this variation is traceable to variation in expression of the HIF1A gene. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis in breast and ovarian cancer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Jen-Tsan

last: Chi


title: Iron- and Irr-regulated genes in Bradyrhizobium japonicum

city: Buffalo

first: Mark

middle: R.

last: O'Brian

state: NY

address: 140 Farber Hall

department: Biochemistry

institute: State University of New York at Buffalo

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

overall_design: Refer to individual Series


title: Genome-Scale Identification of Membrane-Associated Human mRNAs

summary:
The subcellular localization of proteins is critical to their biological roles. Moreover, whether a protein is membrane-bound, secreted, or intracellular affects the usefulness of, and the strategies for, using a protein as a diagnostic marker or a target for therapy. We employed a rapid and efficient experimental approach to classify thousands of human gene products as either membrane-associated/secreted (MS) or cytosolic/nuclear (CN). Using subcellular fractionation methods, we separated mRNAs associated with membranes from those associated with the soluble cytosolic fraction and analyzed these two pools by comparative hybridization to DNA microarrays. Analysis of 11 different human cell lines, representing lymphoid, myeloid, breast, ovarian, hepatic, colon, and prostate tissues, identified more than 5,000 previously uncharacterized MS and more than 6,400 putative CN genes at high confidence levels. The experimentally determined localizations correlated well with in silico predictions of signal peptides and transmembrane domains, but also significantly increased the number of human genes that could be cataloged as encoding either MS or CN proteins. Using gene expression data from a variety of primary human malignancies and normal tissues, we rationally identified hundreds of MS gene products that are significantly overexpressed in tumors compared to normal tissues and thus represent candidates for serum diagnostic tests or monoclonal antibody-based therapies. Finally, we used the catalog of CN gene products to generate sets of candidate markers of organ-specific tissue injury. The large-scale annotation of subcellular localization reported here will serve as a reference database and will aid in the rational design of diagnostic tests and molecular therapies for diverse diseases.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Max

last: Diehn


title: Comparison of Bradyrhizobium japonicum parent strain LO with irr mutant strain LODTM5

summary:
The purpose of the study is to identify Irr-responsive genes in the bacterium Bradyrhizobium japonicum. Parent strain LO was compared to irr mutant strain LODTM5 by whole genome microarray analysis. Both cell types were grown in iron-limited media.
Keywords: Comparison of B. japonicum wild type and mutant cells

overall_design: RNA was isolated from three biological replicates for each cell type, and prepared for microarray analysis using Affymetrix chips. A complete description of these experiments are found in Yang et al., (2006) Mol. Microbiol. 60:427-437.

first: Jianhua

last: Yang

first: Indu

last: Sangwan

first: Andrea

last: Lindemann

first: Felix

last: Hauser

first: Hauke

last: Hennecke

first: Hans-Martin

last: Fischer

middle: R


title: High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH

status: Public on Feb 21 2006

city: Bethesda

first: William

middle: Wallace

last: Lockwood

address: 50 South Drive

institute: National Human Genome Research Institute

type: Genome variation profiling by genome tiling array

summary:
Chromosomal regions harboring tumor suppressors and oncogenes are often deleted or amplified.  Array comparative genomic hybridization (CGH) detects segmental DNA copy number alterations in tumor DNA relative to a normal control.  The recent development of a bacterial artificial chromosome (BAC) array, that spans the human genome in a tiling path manner with >32,000 clones, has facilitated whole genome profiling at an unprecedented resolution.  Using this technology, we comprehensively describe and compare the genomes of 28 commonly used non-small cell lung carcinoma cell models, derived from 18 adenocarcinomas, 9 squamous cell carcinomas, and 1 large cell carcinoma.  Analysis at such resolution not only provided a detailed genomic alteration template for each of these model cell lines, but revealed novel regions of frequent duplication and deletion.  Significantly, a detailed analysis of chromosome 7 identified 6 distinct regions of alterations across this chromosome implicating the presence of multiple novel oncogene loci on this chromosome. As well, a comparison between the squamous and adenocarcinoma cells revealed alterations common to both subtypes, such as the loss of 3p and gain of 5p, in addition to multiple hotspots more frequently associated with only one subtype.  Interestingly, chromosome 3q, which is known to be amplified in both subtypes, showed two distinct regions of alteration, one frequently altered in squamous and one more frequent altered in adenocarcinoma.  In summary, our data demonstrates the unique information generated by high resolution analysis of NSCLC genomes and uncovers the presence of genetic alterations prevalent in the different NSCLC subtypes.
Keywords: array CGH, amplification, segmental copy number, NSCLC, Lung cancer, genetic alterations

overall_design: Whole genome tiling path array CGH profiles of 28 NSCLC Cell Lines

first: Cathie

last: Garnis

first: Emily

last: Vucic

first: Yong

last: Ge

first: Luc

last: Girard

first: John

last: Minna

first: Adi

middle: F

last: Gazdar

first: Stephen

last: Lam

first: Calum

last: MacAulay

first: Wan

last: LAM


title: devellis-5U24NS043562-02

status: Public on Feb 14 2006

first: Winnie

last: Liang

summary:
Nicotinic receptors (nAChR) are widely distributed in the adult brain where they mediate excitatory postsynaptic transmission and presynaptic release of other neurotransmitters. Functional nicotinic receptors are also present in the embryonic brain. Several studies have suggested a role for nAChRs in cognitive functions (learning and memory) and cellular events such as degeneration and survival. In vitro, activation of nAChR can differentially modulate neuritic outgrowth, and enhance early gene expression prior to neuronal differentiation. Furthermore, several reports have shown that nicotine can prevent cell death induced by activation of glutamatergic receptors, NMDA-subtype. Little is known of these events in the cerebral cortex. Knowledge of the genes activated by exposure of cortical neurons to nicotine or to an excitotoxic agent such as the glutamatergic agonist NMDA could potentially lead to new strategies for adult brain protection and repair.
The effect of nicotine and the cembranoid 4R, a novel nicotinic receptor non competitive antagonist, will be analyzed in primary cultures of cortical neurons, in the presence or the absence of NMDA, to identify which genes affected by NMDA receptor activation are modulated nicotine or 4R.
We hypothesize that the neuroprotective effect of nAChRs is mediated by modulation of the changes in gene expressions elicited by NMDA.
In order to detect early changes in gene expression, primary culture of cortical neurons prepared from 16 day old Sprague Dawley rat embryos at 11 days in culture will be treated for different times (10, 30, 60, 180, 360, min) with 1 mM NMDA and then harvested. In a second set of experiments, neuronal cultures will be treated with NMDA for 10, 30 and 60 min then the drug will be washed out and the cells will be harvested 24 h later. It was reported that 8-24 h pretreatment of neurons with 10 micromolar nicotine is neuroprotective, therefore we will treat separate cultures with either 10 micromolar nicotine or 2 micromolar 4R for 18 h and then with NMDA for 30 min or 1 h. The cells will be either harvested soon after NMDA treatment or the drugs will be washed out and the cells harvested 24 h later. We will also examine sample treated only with either 4R or nicotine for 15 min or 18 h in order to determine which genes are differentially regulated by these drugs. These experiments will allow us to detect any change in gene expression elicited soon by each treatment or with some delay. The samples in Trizol will be kept at -70 until all the 3 or 5 replicates are harvested and then the RNA will be purified. RNA from 3-5 independent experiments for each different protocol or treatment together with controls will be sent to the facility.
Keywords: time-course

first: Jean

last: Devellis


title: Iron uptake experiments in yeast

status: Public on Feb 08 2006

last: Stanford Microarray Database

summary:
The budding yeast S. cerevisiae responds to depletion of iron in the environment by activating Aft1p, the major iron-dependent transcription factor, and by transcribing systems involved in the uptake of iron. Here we have studied the transcriptional response to iron deprivation, and have identified new Aft1p target genes. We find that other metabolic pathways are regulated by iron: biotin uptake and biosynthesis, nitrogen assimilation, and purine biosynthesis. Two enzymes active in these pathways, biotin synthase and glutamate synthase, require an iron-sulfur cluster for activity. Iron deprivation activates transcription of the biotin importer and simultaneously represses transcription of the entire biotin biosynthetic pathway. Multiple genes involved in nitrogen assimilation and amino acid metabolism are induced by iron deprivation, while glutamate synthase, a key enzyme in nitrogen assimilation, is repressed. A CGG palindrome within the promoter of glutamate synthase confers iron-regulated expression, suggesting control by a transcription factor of the binuclear zinc cluster family. We provide evidence that yeast subjected to iron deprivation undergo a transcriptional remodeling, resulting in a shift from iron-dependent to parallel, but iron-independent, metabolic pathways.
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: Tracy

last: Ferea


title: Diverse and specific gene expression responses to stresses in cultured human cells.

summary:
TT3 and TN are cell cycle time courses and should be centered or transformed before clustering or computing fourier scores.  The preferred method is SVD centering preceded by KNNImpute missing-value estimation, although mean-centering is a viable alternative.     Hela Heat 42 degrees time course has 2 zeroes (the second is labeled "Cold 25 degrees 0h").  Normalization is by centering or zero transformation (average 2 zeroes)  WI38 Crowding (1-3 days) was by plating cells at ~50%? confluence and allowing to age.  The zeroes are the same as for WI38 Heat Shock (there are 2)  Other time courses should be self-explanatory.  They have 1-4 zeroes each and can be treated either by centering or zero-transforming. WI38
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Michael

last: Whitfield

last: Murray


title: Comparison of Bradyrhizobium japonicum parent strain LO grown under low or high iron conditions

first: Mark

last: O'Brian

summary:
The purpose of the study is to identify iron-responsive genes in the bacterium Bradyrhizobium japonicum. Parent strain LO was grown under iron limitation or under iron sufficiency and compared to each other by whole genome microarray analysis.
Keywords: Comparison of cells grown under low or high iron conditons

overall_design: RNA was isolated from three biological replicates for each condition, and prepared for microarray analysis using Affymetrix chips. A complete description of these experiments are found in Yang et al., 2006, Mol. Microbiol. 60: 427-437.

first: Jianhua

last: Yang

first: Indu

last: Sangwan

first: Andrea

last: Lindemann

first: Felix

last: Hauser

last: Hennecke

last: Fischer


title: Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme

status: Public on Jan 19 2006

summary:
Glioblastoma multiforme (GBM) is the most common form of malignant glioma and is characterized by marked genetic instability, extensive intra-tumoral histopathological variability, and unpredictable variation in its clinical behavior. We investigated global gene expression in surgical samples of primary brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower grade oligodendroglial tumors. Extensive differences in gene expression were found among GBMs, particularly in genes involved in angiogenesis, immune cell infiltration, and extracellular matrix re-modeling. Significantly, we found that the global gene expression patterns in paired specimens from the same GBM invariably were more closely related to each other than to any other tumor, even when the paired specimens had strikingly divergent histologies. Survival analyses revealed a set of approximately 70 genes that were more highly expressed in rapidly progressing tumors and which stratified GBMs into two groups that differed by more than four-fold in median duration of survival. We further investigated one gene from the group, FABP7, and confirmed its association with survival in two unrelated cohorts totaling 105 patients. Expression of FABP7 enhanced the motility of glioma-derived cells in vitro. Our analyses thus provide a series of prognostic markers and suggest that their expression may enhance the invasive potential of tumor cells.
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: Max

last: Diehn


title: Clinical pediatric acute lymphoblastic leukemia samples after in vitro exposure to  L-asparaginase

status: Public on Jan 21 2006

summary:
Samples of pediatric acute lymphoblastic leukemia.  All samples contain at least 90% blasts.  Each sample was split into two flasks, one of which was exposed to 2IU/ml of L-asparaginase.  The other flask served as a control.  Cells were lysed at the times indicated.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Bernard

last: Fine


title: Gastrointestinal stromal tumors (GISTs) with KIT and PDGFRA mutations

status: Public on Jan 10 2006

summary:
Abstract: Most GISTs require oncogenic activation of the KIT or PDGFRA receptor tyrosine kinase proteins, and the genomic mechanisms of oncogene activation are heterogeneous. Notably, the kinase mutation type correlates with both tumor biology and imatinib response. For example, GISTs with KIT exon 11 mutations are typically gastric and have excellent imatinib response, whereas those with KIT exon 9 mutations generally arise in the small bowel and are less responsive to imatinib. To identify genes that might contribute to these biological differences, we carried out gene expression profiling of 26 GISTs with known KIT and PDGFRA mutational status. Expression differences were then evaluated further by RNA in situ hybridization, immunohistochemistry, and immunoblotting. Unsupervised hierarchical clustering grouped tumors with similar mutations together, but the distinction between the different groups was not absolute. Differentially expressed genes included ezrin, p70S6K, and PKCs, which are known to have key roles in KIT or PDGFRA signaling, and which might therefore contribute to the distinctive clinicopathological features in GISTs with different mutation types. These gene products could serve as highly selective therapeutic targets in GISTs containing the KIT or PDGFRA mutational types with which they are associated.
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: Matt

last: Van De Rijn


title: Host response to smallpox

status: Public on Jan 11 2006

summary:
Smallpox has played an unparalleled role in human history and remains a significant potential threat to public health. Despite the historical significance of this disease, we know little about the underlying pathophysiology or the virulence mechanisms of the causative agent, variola virus. To improve our understanding of variola pathogenesis and variola-host interactions, we examined the molecular and cellular features of hemorrhagic smallpox in cynomolgus macaques. We used cDNA microarrays to analyze host gene expression patterns in sequential blood samples from each of 22 infected animals. Variola infection elicited striking and temporally coordinated patterns of gene expression in peripheral blood. Of particular interest were features that appear to represent an IFN response, cell proliferation, immunoglobulin gene expression, viral dose-dependent gene expression patterns, and viral modulation of the host immune response. The virtual absence of a tumor necrosis factor /NF-B-activated transcriptional program in the face of an overwhelming systemic infection suggests that variola gene products may ablate this response. These results provide a detailed picture of the host transcriptional response during smallpox infection, and may help guide the development of diagnostic, therapeutic, and prophylactic strategies.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Kate

last: Rubins


title: Expression profiling of human primary breast cancer tissue before treatment with gemcitabine, epirubicine and docetaxel

city: Heidelberg

first: Olaf

last: Thuerigen

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

country: Germany

institute: German Cancer Research Center

summary:
Gene expression profiles of human breast cancer tissues from 100 different patients treated with primary systemic chemotherapy  (Gemcitabine, Epirubicin and Docetaxel)
Keywords: expression profiling

overall_design: Human breast cancer tissues from 100 patients have been used to perform expression profiling analysis.

first: Andreas

last: Schneeweiss

first: Grischa

last: Toedt

first: Patrick

last: Warnat

first: Axel

last: Benner

first: Meinhard

last: Hahn

first: Peter

last: Lichter


title: A comprehensive analysis of copy number variations in the human genome

status: Public on Dec 06 2006

city: Vancouver

first: Kendy

last: Wong

state: British Columbia

address: 675 West 10th Avenue

department: Cancer Genetics

country: Canada

institute: BC Cancer Research Center

summary:
Segmental copy number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to human diseases.  More importantly, these variations may represent a major genetic component of our phenotypic diversity.  In this study, using a whole genome array CGH assay, we identified 3,654 autosomal segmental CNVs, of which 800 appeared at a frequency of at least 3%.  77% of these frequent CNVs are novel.  In the 95 individuals analyzed, the most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content.  Approximately 68% of the 800 polymorphic regions overlap with genes, reflecting human diversity in senses (smell, hearing, taste, and sight), Rhesus phenotype, metabolism, and disease susceptibility.  Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of microRNAs’ contribution to phenotypic diversity in humans.  This in depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics.
Keywords: array CGH, segmental copy number variations (CNVs)

overall_design: Whole genome tiling path array CGH of 95 DNA samples against a single male reference genomic DNA; control hybridizations include repeat and dyeswap experiments

first: K

middle: K

first: R

last: deLeeuw

first: N

middle: S

last: Dosanjh

first: L

last: Kimm

first: Z

last: Cheng

first: D

middle: E

last: Horsman

first: C

last: MacAulay

last: Ng

last: Brown

first: E

last: Eichler

first: W

middle: L

last: Lam


title: L-asparaginase exposure in acute lymphoblastic leukemia cell lines time series

last: Stanford Microarray Database

summary:
Time series of in vitro 2 IU/ml L-asparaginase exposure in acute lymphoblastic leukemia cell lines.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Bernard

last: Fine


title: Listeria host responses

status: Public on Jan 07 2006

summary:
This logical set encompases several 8hr timecourses (0,1,2,4,8 hrs) and their replicates.  All correspond to treatments of bone marrow derived macrophages.
Abstract: Innate and adaptive immunity depends critically on host recognition of pathogen-associated molecules. Toll-like receptors (TLRs) are key mediators of pathogen surveillance at the cell or phagocytic vacuole surface. However, mechanisms underlying recognition of pathogens in other cellular compartments remain unclear, and responses elicited by cytosolic challenge are poorly characterized. We therefore used mouse cDNA microarrays to investigate gene expression triggered by infection of bone marrow-derived macrophages with cytosol- and vacuole-localized Listeria monocytogenes (Lm), a model cytosolic pathogen. The resulting gene expression program included two basic categories of induced genes: an "early/persistent" cluster consistent with NF-kappaB-dependent responses downstream of TLRs, and a subsequent "late response" cluster largely composed of IFN-responsive genes (IRGs). The early/persistent cluster was observed upon infection with WT, heat-killed, or mutant Lm lacking listeriolysin O, the pore-forming hemolysin that promotes escape from phagocytic vacuoles. However, the IRG cluster depended on entry of WT Lm into the cytosol. Infection with listeriolysin O-expressing, cytosolic Bacillus subtilis (Bs) strikingly recapitulated the expression profile associated with WT Lm, including IRG induction. IRG up-regulation was associated with MyD88-independent induction of IFN-beta transcription and activity. Whereas Staphylococcus aureus (Sa) lipoteichoic acid treatment confirmed that many late-response genes could also be stimulated through TLRs, our study identified a cytosol-specific transcriptional program independent of TLR signaling through MyD88. Further characterization of cytosolic surveillance pathway(s) and their points of convergence with TLR- and IFN-dependent pathways will enhance our understanding of the means by which mammals detect and respond to pathogens.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Paul

last: Fawcett


title: Clinical acute lymphoblastic leukemia samples (untreated) with known asparaginase LC50 values

summary:
Samples of pediatric acute lymphoblastic leukemia obtained from patients at diagnosis.  All samples contain at least 77% blasts.  Asparaginase LC50 values were determined for each of these samples. (LC50 was determined on a different aliquot of the same sample.)
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Puf3delta vs. wild type comparison

status: Public on Jan 04 2006

summary:
Three independent experiments: S. cervisiae wild-type (BY4741) and Puf3 mutant cells were grown in minimal medium supplemented with 3% glycerol. Cells were harvested in mid-log phase by centrifugation and total RNA was prepared by hot-phenol extraction. cDNA was prepared with oligo-dT and using a mixture of amino-allyl dUTP and dNTPs, fluorescently labeled (Cy3= wild-type, Cy5 = mutant) and hybridize on S. cerevisiae DNA microarray.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Andre

last: Gerber


title: Identification of Xenotropic MuLV-related virus

status: Public on Jan 01 2006

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
This series includes 20 microarrays used to identify Xenotropic MuLV-related virus (XMRV) in a set of human prostate tumors associated with R462Q RNASEL variant (Urisman, et al. 2006).
Keywords: viral detection

overall_design: The series includes 19 prostate tumor samples (VP) and a cell line control (HeLa).

first: Anatoly

last: Urisman

first: Nicole

last: Fischer

first: Ross

last: Molinaro

first: Robert

middle: H

last: Silverman

first: Don

last: Ganem

first: Joseph


title: Fibroblast Serum Stimulation Time Course

status: Public on Dec 31 2005

summary:
Foreskin fibroblasts CRL 2091 (ATCC) were serum starved for 48 hours, and harvested at the indicated time points after switching to media with 10% FBS essentially as described (Iyer et al., 1999). RNA from all of the sampled time points were pooled as reference RNA to compare with RNA from individual time points as described (Iyer et al., 1999).
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Ruchira

last: Sood


title: de novo childhood AML patients and FLT3 mutations.

summary:
This data set was used to study FLT3 wild type and mutants in childhood AML samples from the Pediatric Oncology Group Study 9421.
Abstract: Fms-like tyrosine kinase 3 (FLT3) mutations are associated with unfavorable outcomes in children with acute myeloid leukemia (AML). We used DNA microarrays to identify gene expression profiles related to FLT3 status and outcome in childhood AML. Among 81 diagnostic specimens, 36 had FLT3 mutations (FLT3-MUs), 24 with internal tandem duplications (ITDs) and 12 with activating loop mutations (ALMs). In addition, 8 of 19 specimens from patients with relapses had FLT3-MUs. Predictive analysis of microarrays (PAM) identified genes that differentiated FLT3-ITD from FLT3-ALM and FLT3 wild-type (FLT3-WT) cases. Among the 42 specimens with FLT3-MUs, PAM identified 128 genes that correlated with clinical outcome. Event-free survival (EFS) in FLT3-MU patients with a favorable signature was 45% versus 5% for those with an unfavorable signature (P = .018). Among FLT3-MU specimens, high expression of the RUNX3 gene and low expression of the ATRX gene were associated with inferior outcome. The ratio of RUNX3 to ATRX expression was used to classify FLT3-MU cases into 3 EFS groups: 70%, 37%, and 0% for low, intermediate, and high ratios, respectively (P < .0001). Thus, gene expression profiling identified AML patients with divergent prognoses within the FLT3-MU group, and the RUNX3 to ATRX expression ratio should be a useful prognostic indicator in these patients.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Keywords: clinical_history_design

first: Norman

last: Lacayo


title: Gene expression in the normal adult human kidney

status: Public on Dec 30 2005

summary:
This set of arrays was published in Molecular Biology of the Cell. The manuscript was released electronically on 12/01/2003 and the hard copy version in February 2004. The FT number indicates the kidney from which the component parts were dissected.
Abstract: The kidney is a highly specialized organ with a complex, stereotyped architecture and a great diversity of functions and cell types. Because the microscopic organization of the nephron, the functional unit of the kidney, has a consistent relationship to the macroscopic anatomy of the kidney, knowledge of the characteristic patterns of gene expression in different compartments of the kidney could provide insight into the functions and functional organization of the normal nephron. We studied gene expression in dissected renal lobes of five adult human kidneys using cDNA microarrays representing approximately 30,000 different human genes. Total RNA was isolated from sections of the inner and outer cortex, inner and outer medulla, papillary tips, and renal pelvis and from glomeruli isolated by sieving. The results revealed unique and highly distinctive patterns of gene expression for glomeruli, cortex, medulla, papillary tips, and pelvic samples. Immunohistochemical staining using selected antisera confirmed differential expression of several cognate proteins and provided histological localization of expression within the nephron. The distinctive patterns of gene expression in discrete portions of the kidney may serve as a resource for further understanding of renal physiology and the molecular and cellular organization of the nephron
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: John

last: Higgins


title: Independent repeat hybridizations

city: Singapore

first: Jianhua

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary:
GIS 10K S. pombe oligonucleotide array
Keywords: repeat sample

first: Juntao

last: Li

first: Zhaoqing

last: Chu

first: Krishna

last: Karuturi

first: Kui

last: Lin

first: Edison


title: Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

last: Stanford Microarray Database

summary:
We developed a 'Virtual Northern' method, using DNA microarrays for genome-wide systematic analysis of mRNA lengths. We used this method to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the S. cerevisiae genome, with high precision and accuracy (measurement errors 1 6-7%). We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences. Analysis of genes deviating from that relationship identified ORFs with annotation errors, ORFs that appear not to be bona fide genes, and potentially novel genes. Interestingly, we found that systematic differences in the total length of the untranslated sequences in mRNAs were related to the functions of the encoded proteins.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Evan

last: Hurowitz


title: Gene expression profiling of bundle sheath and mesophyll cell types of wild-type maize seedlings.

status: Public on Dec 24 2005

city: Ithaca

first: Ruairidh

last: Sawers

address: Tower Rd

institute: Boyce Thompson Institute

summary:
A number of taxa utilize C4 photosynthesis, to limit the impact of photorespiration upon photosynthetic performance. In order to achieve a local elevation of CO2 concentration, maize plants possess two photosynthetic cell types. Rubisco accumulation is restricted to bundle sheath (BS) cells that surround the leaf veins. Carbon fixation occurs initially in adjacent mesophyll (ME) cells. C4 compounds are transported into the BS cells where they are subsequently decarboxylated, releasing CO2. Although the major components of the C4 pathway have been well characterized, less is known about further metabolic partitioning in the maize leaf. Microarray hybridizations have been performed in order to further investigate metabolic differences between BS and ME cell types. BS strands and ME protoplasts were isolated from the leaves of 10 day old maize seedlings by mechanical disruption and enzymatic digestion respectively. To control for differences arising from these different protocols, total leaf (TO) and total leaf stress (ST) samples were also isolated. The ST sample was subjected to the same treatments as the ME sample, with the omission of cell-wall degrading enzymes. Leaves for the TO sample were harvested as for the BS strand sample. An interwoven loop design was used to compare the four treatment groups. A biological group consisted of a growth of plants from which pooled individuals were taken for the four treatments. Six biological replicates (groups) were used. Labeling was performed using the Genisphere Array 900-MPX kit according to the manufacturer's protocol. Post hybridization washes were performed according to the recommendations of the Maize Oligo Array Project. Scan settings were used for detection of moderate to high expression signals (gain ~ 60%. power 90%). Following hybridization with TO cDNA, ~1/3 of features provided signal above twice background and below saturation.
A number of taxa utilize C4 photosynthesis, to limit the impact of photorespiration upon photosynthetic performance. In order to achieve a local elevation of CO2 concentration, maize plants possess two photosynthetic cell types. Rubisco accumulation is restricted to bundle sheath (BS) cells that surround the leaf veins. Carbon fixation occurs initially in adjacent mesophyll (ME) cells. C4 compounds are transported into the BS cells where they are subsequently decarboxylated, releasing CO2. Although the major components of the C4 pathway have been well characterized, less is known about further metabolic partitioning in the maize leaf. Microarray hybridizations have been performed in order to further investigate metabolic differences between BS and ME cell types. BS strands and ME protoplasts were isolated from the leaves of 10 day old maize seedlings by mechanical disruption and enzymatic digestion respectively. To control for differences arising from these different protocols, total leaf (TO) and total leaf stress (ST) samples were also isolated. The ST sample was subjected to the same treatments as the ME sample, with the omission of cell-wall degrading enzymes. Leaves for the TO sample were harvested as for the BS strand sample. An interwoven loop design was used to compare the four treatment groups. A biological group consisted of a growth of plants from which pooled individuals were taken for the four treatments. Six biological replicates (groups) were used. Labeling was performed using the Genisphere Array 900-MPX kit according to the manufacturer's protocol. Post hybridization washes were performed according to the recommendations of the Maize Oligo Array Project. Scan settings were used for detection of moderate to high expression signals (gain ~ 60%. power 90%). Following hybridization with TO cDNA, ~1/3 of features provided signal above twice background and below saturation.
Keywords: Gene expression profiling of bundle sheath and mesophyll cell types

first: Thomas

last: Brutnell


title: Dermatofibrosarcoma protuberans

type:
Expression profiling by array
Genome variation profiling by array

summary:
Dermatofibrosarcoma protuberans (DFSP) is an aggressive spindle cell neoplasm. It is associated with the chromosomal translocation, t(17:22), which fuses the COL1A1 and PDGFbeta genes. We determined the characteristic gene expression profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative genomic hybridization (array CGH). Fresh frozen and formalin-fixed, paraffin-embedded samples of DFSP were analyzed by array CGH (four cases) and DNA microarray analysis of global gene expression (nine cases). The nine DFSPs were readily distinguished from 27 other diverse soft tissue tumors based on their gene expression patterns. Genes characteristically expressed in the DFSPs included PDGFbeta and its receptor, PDGFRB, APOD, MEOX1, PLA2R, and PRKCA. Array CGH of DNA extracted either from frozen tumor samples or from paraffin blocks yielded equivalent results. Large areas of chromosomes 17q and 22q, bounded by COL1A1 and PDGFbeta, respectively, were amplified in DFSP. Expression of genes in the amplified regions was significantly elevated. Our data shows that: 1) DFSP has a distinctive gene expression profile; 2) array CGH can be applied successfully to frozen or formalin-fixed, paraffin-embedded tumor samples; 3) a characteristic amplification of sequences from chromosomes 17q and 22q, demarcated by the COL1A1 and PDGFbeta genes, respectively, was associated with elevated expression of the amplified genes.
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: Matt

last: Van De Rijn


title: Puf proteins, RNA co-immunopurification

summary:
RNA-coimmunopurifications with TAP-tagged Puf proteins from Saccharomyces cereviseae. Untagged strain  (BY4741) served as a control. Cells were grown to midlog phase and harvested by centrifugation. TAP-tagged Puf proteins were affinity purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input)and from purified protein samples by phenol-chloroform extraction. RNA samples were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/ dNTP mixture. cDNAs were fluorescently labeled and hybridized on yeast DNA microarrays over night at 65 degrees. For a detailed procedure see http://microarray-pubs.stanford.edu/yeast_puf and also Gerber AP et al. PLoS Biology, 2004.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Andre

last: Gerber


title: ALL Cell Lines

status: Public on Dec 21 2005

summary:
Collection of leukemia cell lines selected because they contain one of several recurrent chromosomal translocations commonly seen in acute lymphoblastic leukemia.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Bernard

last: Fine


title: Effects of rraA deletion on transcription

status: Public on Dec 20 2005

summary:
Effects of rraA deletion on the global transcript profile of E. coli. This experiment set contains primary data for Figure 5B, Lee et. al. Cell 2003.
An RNA stablity experiment design type examines stability and/or decay of RNA transcripts.
Keywords: RNA_stability_design

first: Kangseok

last: Lee


title: Endothelial cell diversity revealed by global expression profiling

summary:
The vascular system is locally specialized to accommodate widely varying blood flow and pressure and the distinct needs of individual tissues. The endothelial cells (ECs) that line the lumens of blood and lymphatic vessels play an integral role in the regional specialization of vascular structure and physiology. However, our understanding of EC diversity is limited. To explore EC specialization on a global scale, we used DNA microarrays to determine the expression profile of 53 cultured ECs. We found that ECs from different blood vessels and microvascular ECs from different tissues have distinct and characteristic gene expression profiles. Pervasive differences in gene expression patterns distinguish the ECs of large vessels from microvascular ECs. We identified groups of genes characteristic of arterial and venous endothelium. Hey2, the human homologue of the zebrafish gene gridlock, was selectively expressed in arterial ECs and induced the expression of several arterial-specific genes. Several genes critical in the establishment of left/right asymmetry were expressed preferentially in venous ECs, suggesting coordination between vascular differentiation and body plan development. Tissue-specific expression patterns in different tissue microvascular ECs suggest they are distinct differentiated cell types that play roles in the local physiology of their respective organs and tissues.
A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.
Keywords: development_or_differentiation_design

first: Jen-Tsan

last: Chi


title: Embryonic stem cells and pluripotent germ cell tumors

status: Public on Dec 29 2005

summary:
Remarkably little is known about the transcriptional profiles of human embryonic stem (ES) cells or the molecular mechanisms that underlie their pluripotency. To identify commonalties among the transcriptional profiles of different human pluripotent cells and to search for clues into the genesis of human germ cell tumors, we compared the expression profiles of human ES cell lines, human germ cell tumor cell lines and tumor samples, somatic cell lines, and testicular tissue samples by using cDNA microarray analysis. Hierarchical cluster analysis of gene expression profiles showed that the five independent human ES cell lines clustered tightly together, reflecting highly similar expression profiles. The gene expression patterns of human ES cell lines showed many similarities with the human embryonal carcinoma cell samples and more distantly with the seminoma samples. We identified 895 genes that were expressed at significantly greater levels in human ES and embryonal carcinoma cell lines than in control samples. These genes are candidates for involvement in the maintenance of a pluripotent, undifferentiated phenotype.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Xin

last: Chen

first: Howard

last: Chang

first: Sunita

last: Jones


title: Microarray Analysis of Gene Expression during Bacteriophage T4 Infection

status: Public on Nov 18 2005

city: Chicago

first: Yakov

middle: N.

last: Kogan

state: IL

address: 2201 W. Campbell Park Dr.

institute: Integrated Genomics, Inc.

summary:
Genomic microarrays were used to examine the complex temporal program of gene expression exhibited by bacteriophage T4 during the course of development.The microarray data confirm the existence of distinct early, middle, and late transcriptional classes during the bacteriophage replicative cycle.This approach allows assignment of previously uncharacterized genes to specific temporal classes.The genomic expression data verify many promoter assignments and predict the existence of previously unidentified promoters.
Keywords: time course

overall_design: The present study used microarrays to identify temporal classes of RNA produced during T4 infection of E. coli.  Briefly, the data were produced from time course studies from T4 infections of E. coli B. Samples were isolated at various time points throughout the course of infection. Samples were analyzed using Integrated Genomics T4 genomic arrays.


title: Gene expression profiling of children affected by Alveolar Rhabdomyosarcoma (ARMS)

status: Public on Oct 25 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary:
We analyzed the expression signatures of 10 tumor biopsies from children affected by alveolar rhabdomyosarcoma (ARMS) to identify genes correlating to biological features of this tumor. Five of these patients were positive for the PAX3-FKHR fusion gene and five were negative. We used a cDNA platform containing a large majority of probes derived for muscle tissues.
The comparison of transcription profiles of tumor samples with normal fetal skeletal muscle identified 171 differentially expressed genes common to all ARMS patients. The functional analysis of altered genes led to the identification of a group of transcripts (BCOR, DDX5, LGALS1, BIN1) that may be relevant for the tumorigenic processes leading a normal muscle cell to become a malignant rhabdomyoblast.
The muscle-specific platform was able to distinguish PAX3-FKHR positive and negative ARMS through the expression pattern of a limited number of genes (RAC1, CFL1, CCND1) that might be biologically relevant for the different clinical behavior and aggressiveness of the two ARMS subtypes. Expression levels for selected candidate genes were validated by quantitative real-time reverse-transcription PCR.
Keywords: human fetal skeletal muscle, alveolar rhabdomyiosarcoma, gene expression profiling, PAX3-FKHR

overall_design: We compared the transcription profiles of ARMS samples by microarray competitive hybridization against an arbitrary total RNA reference prepared from a pool of 5 human fetal skeletal muscles. Two replicates of each experiment were performed using different microarray slides, in which sample and reference RNAs, labeled either with Cy3 or Cy5 fluorochromes, were crossed in both combinations (dye-swapping procedure).

first: Cristiano

last: De Pitta

first: Lucia

last: Tombolan

first: Giada

last: Albiero

first: Francesca

last: Sartori

first: Chiara

last: Romualdi

first: Giuseppe

last: Jurman

first: Modesto

last: Carli

first: Cesare

last: Furlanello

first: Angelo

last: Rosolen


title: Guided differentiation of mouse embryonic stem cell

status: Public on Nov 01 2005

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

summary:
The mouse embryonic stem cell’s differentiation was guided by several treatments, and each stage of differentiation was examined.
Keywords: development stage

overall_design: EBs were dissociated and plated onto tissue culture dishes in the serum-free medium containing Insulin/Transferrin/Selenium/Fibronectin (ITSF). After 6 days, the cells were expanded and plated onto polyornithine (15 mg ml-1) and laminin-coated plates (Becton Dickinson Labware, Bedford, MA) with the N2 medium (Johe, 1996) supplemented with laminin, bFGF (R&D Systems, Minneapolis, MN), murine N-terminal fragment of SHH and murine FGF8 isoform b (R&D Systems) (stage 4) . Finally the cells were induced to differentiated into DA neurons by removal of bFGF. The differentiation medium consisted of N2 medium supplemented with laminin in the presence or absence of cAMP, AA (Sigma, St. Louis, MO). The cells were incubated under differentiation conditions for 6–15 days.

first: Woong-Yang

first: Dae-Hyun

last: Jun

first: Chang-Il

last: Hwang


title: NHGRI_Sarcoma_Baird

status: Public on Oct 11 2005

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

summary:
Sarcomas are a biologically complex group of tumors of mesenchymal origin. By using gene expression microarray analysis, we aimed to find clues into the cellular differentiation and oncogenic pathways active in these tumors as well as potential biomarkers and therapeutic targets. We examined 181 tumors representing 16 classes of human bone and soft tissue sarcomas on a 12,601-feature cDNA microarray. Remarkably, 2,766 probes differentially expressed across this sample set clearly delineated the various tumor classes. Several genes of potential biological and therapeutic interest were associated with each sarcoma type, including specific tyrosine kinases, transcription factors, and homeobox genes. We also identified subgroups of tumors within the liposarcomas, leiomyosarcomas, and malignant fibrous histiocytomas. We found significant gene ontology correlates for each tumor group and identified similarity to normal tissues by Gene Set Enrichment Analysis. Mutation analysis done on 275 tumor samples revealed that the high expression of epidermal growth factor receptor (EGFR) in certain tumors was not associated with gene mutations. Finally, to further the investigation of human sarcoma biology, we have created an online, publicly available, searchable database housing the data from the gene expression profiles of these tumors (http://watson.nhgri.nih.gov/sarcoma), allowing the user to interactively explore this data set in depth.

Keywords = sarcoma
Keywords = cDNA
Keywords = tumor profiling
Keywords: other

overall_design: Common reference, multiclass gene profiling

first: Kristin

last: Baird

first: Paul

last: Meltzer


title: Murine fast-twitch muscle: two-week progression of denervation atrophy

status: Public on Sep 21 2005

first: Paolo

last: Laveder

address: via U.Bassi 58/B

department: Department of Biology

institute: CRIBI Biotechnology Center

summary:
The right legs of 3 months old CD1 mice were denervated by unilaterally cutting the sciatic nerve at the level of trochanter, resulting in a permanent denervation of the lower hindleg. At the indicated times, animals were killed by cervical dislocation and tibialis anterior (TA) muscles were dissected out and frozen in liquid nitrogen. The expression analysis was carried out at five time points, namely just after denervation (time 0) and 1, 3, 7 and 14 days after nerve interruption. The contralateral, left TA muscle from the same individual served as innervated control. We reversed labeling of denervated and contralateral samples in each experiment, thus carrying out two separate hybridizations for each time point.
Keywords = mouse
Keywords = fast-twitch muscle
Keywords = denervation
Keywords = atrophy
Keywords: time-course

first: Anna

last: Raffaello

first: Luana

last: Toniolo

first: Elena

last: Germinario

first: Daniela

last: Danieli

first: Aram

last: Megighian

first: Carlo

last: Reggiani

first: Gerolamo


summary:
Embryoid Bodies were dissociated and plated onto tissue culture dish in DMEM with fetal bovine serum and antibiotics for 4, 8, 12, 15, 21 day.
Keywords: development stage

overall_design: Random differentiation of mouse embryonic stem cell with time series


title: Eyes absent mutant adults

status: Public on Sep 10 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
Eyes absent mutant adult flies collected 0-24 hours after eclosion, with N=2 biological collections for males and females each.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Farhad

last: Imam


title: Unfertilized eggs

summary:
Four separate biological collections of unfertilized eggs laid by wildtype females mated with sterile males, eggs dechorionated and snap-forzen in liquid nitrogen 0-1 hour after egg lay.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Human 32 MPSS samples

status: Public on Nov 29 2005

city: Hayward

first: Lynx

last: Lynx

address: 25861 Industrial Blvd.

institute: Lynx Therapeutics, Inc.

summary:
This series represents a very deep survey of all transcripts expressed in a wide range of human tissues and cells by Massively Parallel Signature Sequencing (MPSS). These datasets have been generated and donated to the scientific community by Lynx Therapeutics, Inc in Hayward, CA.

The data contained in this submission is described in the following publication:
'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Abstract of the publication:
'We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of over 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences between cell and tissue types are largely determined by the expression of a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little over half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the notion that most human genes have been mapped, if not functionally characterised. This dataset should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance.'
Keywords: other

first: Christian

last: Haudenschild

first: Daixing

last: Zhou

first: Irina

last: Khrebtukova

first: Tom

last: Vasicek


title: Genetic diversity study for Entamoeba strains

status: Public on Aug 26 2005

summary:
Little is known about the extent of genetic variability among Entamoeba strains and potential genotypic associations with virulence.  Variable phenotypes have been identified for Entamoeba strains.  E. histolytica is invasive and causes colitis and liver abscesses, but only in 10% of infected individuals; 90% of subjects remain asymptomatically colonized.  E. dispar, a closely related species, appears to be incapable of causing invasive disease.  In order to determine the extent of genetic diversity among Entamoeba strains we have developed an E. histolytica genomic DNA microarray and used it to genotype strains of E. dispar and E. histolytica.  Based on the identification of divergent genetic loci, all six strains (four EH and two ED) had unique genetic fingerprints.  Genomic regions with unusually high levels of divergence were identified indicating that structural or evolutionary pressures are molding selective regions of the Entamoeba genome.  Comparison of divergent genetic regions allowed us to readily distinguish between EH and ED, identify novel genetic regions that may be used for strain and species typing, and identity a number of novel potential virulence determinants.  Among these are Androgen Inducible Gene1, a CXXC receptor kinase, a peroxiredoxin 1-related gene, a Ras family member gene, a Rab geranylgeranyltransferase, and a gene with a UPF0034 domain.  Among the four EH strains, an avirulent strain EH (Rahman) was the most divergent and phylogenetically distinct raising the intriguing possibility that genetic subtypes of E. histolytica may be at least partially responsible for the observed variability in clinical outcomes.  Our approach shows the utility of a microarray-based genotyping assay to identify genetic variability between Entamoeba isolates and can readily be applied to the study of clinical isolates.
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
Keywords: genotyping_design

overall_design: User Defined

first: Preetam

last: Shah


title: Adaptation to famine

summary:
Bacterial adaptation to nutrient limitation and increased population densities is central to survival and virulence. Surprisingly, <3% of Escherichia coli genes are known to play roles specific to the stationary phase. There is evidence that the leucine-responsive regulatory protein (Lrp) may play an important role in stationary phase, so this study used microarrays representing >98% of E. coli genes to more comprehensively identify those controlled by Lrp. The primary analysis compared isogenic Lrp(+) and Lrp(-) strains in cells growing in steady state in glucose minimal medium, either in the presence or absence of leucine. More than 400 genes were significantly Lrp-responsive under the conditions used. Transcription of 147 genes was lower in Lrp(+) than in Lrp(-) cells whether or not leucine was present; most of these genes were tightly coregulated under several conditions, including a burst of synthesis on transition to stationary phase. This cluster includes 56 of 115 genes already known to play roles in stationary phase. Our results suggest that the actual number of genes induced on entrance into stationary phase is closer to 200 and that Lrp affects nearly three-quarters of them, including genes involved in response to nutrient limitation, high concentrations of organic acids, and osmotic stress.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Arkady

last: Khodursky


title: Drosophila Life Cycle

summary:
Molecular genetic studies of Drosophila melanogaster have led to profound advances in understanding the regulation of development. Here we report gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes
A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.
Keywords: development_or_differentiation_design


title: Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16

status: Public on Aug 10 2005

summary:
To identify DAF-16-dependent transcriptional alterations that occur in a long-lived C. elegans strain, we used cDNA microarrays and genomic analysis to identify putative direct and indirect DAF-16 transcriptional target genes.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Joshua

last: Mcelwee


title: Improved statistical analysis of budding yeast TAG microarrays

status: Public on Sep 02 2005

city: Frederick

first: Brian

middle: D.

last: Peyser

address: 1425 Porter St

department: Bacteriology

institute: USAMRIID

summary:
Yeast knockout collection TAG microarrays are an emergent platform for rapid, genome-wide functional characterization of yeast genes. We describe a method for analyzing two-color array data to efficiently represent differential knockout strain representation across two experimental conditions. Using a fully defined spike-in pool, we show that the sensitivity and specificity of this method exceed typical current approaches.
Keywords: Saccharomyces cerevisiae, yeast, self_vs_self, spike-in pools

overall_design:
Two pools were created (“A” and “B”) such that 94 heterozygous yeast
knockout strains were differentially represented between the two. The
94 differentially represented strains were diluted 1:1, 1:8, or 1:64 (High, Medium, or Low representation), then added to Pool B. Each strain was then diluted again from 1:2^0.33 to 1:2^5 and added to pool A. One set of strains from each representation group was not added to
pool A (dilution 1:2^inf). All other strains are at equivalent representation between the two pools.

first: Rafael

middle: A

last: Irizarry

first: Carol

middle: W

last: Tiffany

first: Ou

last: Chen

first: Daniel

last: Yuan

first: Jef

last: Boeke

first: Forrest

last: Spencer


title: Bacillus PerR set

status: Public on Aug 16 2005

last: Stanford Microarray Database

summary:
Comparison between perR and wild type Bacillus
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Paul

last: Fawcett


title: Bacillus Stress Responses

summary:
Bacillus subtilis exhibits a complex adaptive response to low levels of peroxides. We used global transcriptional profiling to monitor the magnitude and kinetics of changes in the mRNA population after exposure to either hydrogen peroxide (H2O2) or tert-butyl peroxide (t-buOOH). The peroxide stimulons could be largely accounted for by three regulons controlled by the PerR, B, and OhrR transcription factors. Three members of the PerR regulon (katA, mrgA, and zosA) were strongly induced by H2O2 and weakly induced by t-buOOH. The remaining members of the PerR regulon were only modestly up-regulated by peroxide treatment. Overall, the magnitude of peroxide induction of PerR regulon genes corresponded well with the extent of derepression in a perR mutant strain. The B regulon was activated by 58 µM H2O2 but not by 8 µM H2O2 and was strongly activated by either t-buOOH or, in a control experiment, tert-butyl alcohol. Apart from the B regulon there was a single gene, ohrA, that was strongly and rapidly induced by t-buOOH exposure. This gene, controlled by the peroxide-sensing repressor OhrR, was not induced by any of the other conditions tested.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element

status: Public on Jul 22 2005

first: Sacha

last: van Hijum

address: Kerklaan 30

institute: University of Groningen

summary:
CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of several genes encoding proteins of the proteolytic system. DNA microarray analysis, comparing the expression profiles of L. lactis MG1363 and an isogenic strain in which codY was mutated, was used to determine the CodY regulon. In peptide-rich medium and exponentially growing cells, where CodY exerts strong repressing activity, the expression of over 30 genes was significantly increased upon removal of codY. The differentially expressed genes included those predominantly involved in amino acid transport and metabolism. In addition, several genes belonging to other functional categories were derepressed, stressing the pleiotropic role of CodY. Scrutinizing the transcriptome data with bioinformatics tools revealed the presence of a novel overrepresented motif in the upstream regions of several of the genes derepressed in L. lactis MG1363codY. Evidence is presented that this 15-bps cis-sequence, AATTTTCWGAAAATT, serves as a high-affinity binding site for CodY, as shown by electrophoretic mobility shift assays and DNaseI footprinting analyses. The presence of this CodY-box is sufficient to evoke CodY-mediated regulation in vivo. A copy of this motif is also present in the upstream region of codY itself. It is shown that CodY regulates its own synthesis and requires the CodY-box and branched-chain amino acids to interact with its promoter.
Keywords: genetic modification

overall_design: Each amplicon was spotted twice (technical replicates) on the DNA microarray. The RNA for wild-type and dCodY strains was isolated in 4 biological replicates which were hybridized in (partly dye-swap) to the 5 slides.

first: Chris

middle: D

last: Den Hengst

last: Van Hijum

first: Jan

middle: M

last: Geurts

first: Arjen

last: Nauta

last: Kok

first: Oscar

middle: P

last: Kuipers


title: Gene expression profiling in dysferlinopathies using a dedicated muscle microarray

status: Public on Jul 28 2005

first: Gerolamo

last: Lanfranchi

summary:
We have performed expression profiling to define the molecular changes in dysferlinopathy using a novel dedicated microarray platform made with 3’-end skeletal muscle cDNAs. Eight dysferlinopathy patients, defined by western blot, immunohistochemistry and mutation analysis, were investigated with this
technology. The expression profiles of patients with different clinical traits were independently obtained and hierarchical clustering was applied to discover patient-specific gene variations. MHC class I genes and genes involved in protein biosynthesis were up-regulated in relation to muscle histopathological
features. Conversely, the expression of genes codifying the sarcomeric proteins titin, nebulin and telethonin was down-regulated. Neither calpain-3 nor caveolin, a sarcolemmal protein interacting with dysferlin, was consistently reduced. There was a major up-regulation of proteins interacting with calcium, namely S100
calcium-binding proteins and sarcolipin, a sarcoplasmic calcium regulator.
Keywords: Dysferlinopathies, limb-girdle muscular dystrophy type 2B,biopsy, cDNA microarray

overall_design:
Five dysferlinopathy patients, defined by western blot, immunohistochemistry and mutation analysis, were investigated with microarray technology.
These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 1.0). Two replicates of each experiment were performed using different microarray slides, in which sample and reference RNAs, labeled either with Cy3 or Cy5 fluorochromes, were crossed in both combinations (dye-swapping procedure).

first: Stefano

last: Campanaro

first: Chiara

last: Romualdi

first: Marina

last: Fanin

first: Barbara

last: Celegato

first: Beniamina

last: Pacchioni

first: Silvia

last: Trevisan

first: Paolo

last: Laveder

first: Cristiano

last: De Pittà

first: Elena

last: Pegoraro

first: Yukiko

last: Hayashi

first: Giorgio

last: Valle

first: Corrado

last: Angelini


title: Nutritional homeostasis in batch and steady-state culture of yeast.

status: Public on Jul 16 2005

last: Stanford Microarray Database

summary:
This data file contains all the data used to produce Figure 4 of Saldanha, Brauer and Bostein. The limiting nutrient is indicated by the letter followed by the timecourse number. S= sulfate, P=phosphate, U=uracil, L=leucine. The chemostat comparisons are prefixed by CC. Channels are as noted in the individual arrays, and are consistent for a given timecouse, but may vary between time courses.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

overall_design: Using regression correlation

first: Alok

last: Saldanha


title: CommercialWineYeastStrainsCGH

summary:
Microarray karyotyping (aCGH) of three independent isolates each of four different commerical wine yeast strains was performed.  Duplicate arrays (labeled "A" and "B") were performed for each isolate.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

last: Dunn


title: The Ankrd2, Cdkn1c and Calcyclin Genes are Under the Control of MyoD During Myogenic Differentiation

summary:
Skeletal muscle development requires the coordinated expression of numerous transcription factors to control the specification of the muscle fate in mesodermal cells and the differentiation of the committed myoblasts into functional contractile fibers. The bHLH transcription factor MyoD plays a key role in these processes, since its forced expression is sufficient to induce the myogenesis in a variety of non-muscle cells in culture. Consistent with this observation, the majority of skeletal muscle genes requires MyoD to activate their own transcription. In order to identify novel MyoD-target genes we generated C2C12 MyoD-silenced clones, and used a muscle-specific cDNA microarray to study the induced modifications of the transcriptional profile. Gene expression was analyzed at three different stages in differentiating MyoD(-)C2C12 myoblasts. These microarray data sets identified many additional uncharacterized downstream MyoD transcripts that may play important functions in muscle cell differentiation. Among these genes, we concentrated our study on the cell cycle regulators Cdkn1c and calcyclin and on the muscle-specific putative myogenic regulator Ankrd2. Bioinformatic and functional studies on the promoters of these genes clarified their dependence on MyoD activity. Clues of other regulatory mechanisms that might interact with the principal bHLH transcription factor have been revealed by the unexpected up regulation in MyoD(-) cells of these novel (and other) target transcripts, at the differentiation stage in which MyoD became normally down regulated.
Keywords: MyoD, cell cycle regulation, cDNA microarray, myogenic differentiation, gene regulation

overall_design: RNAs purified from C2C12 MyoD(-)cl.A8 at one, three and six myogenic differentiation time-points were compared with RNA from C2C12 control cells at the corresponding differentiation stages. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 1.0). Two replicates of each experiment were performed using different microarray slides, in which sample and reference RNAs, labeled either with Cy3 or Cy5 fluorochromes, were crossed in both combinations (dye-swapping procedure).

first: Camilla

last: Bean

first: Michela

last: Salamon

first: Anna

last: Raffaello

first: Alberto

last: Pallavicini


title: Host Response Malaria

status: Public on Jul 09 2005

summary:
Subjects are children from Kilifi District Hospital, Kenya, recruited in 2001 malaria season. total RNA extracted from PaxGene tubes, total RNA  and Stratagene Universal reference RNA underwent linear amplification (Message Amp, Ambion). Amplified RNA directly labelled Cy5 and Cy3 and hybridised to 'lymphochip' arrays (print run - lc36n). Scanned on Axon 4000B scanner using GenePix 4.0 software. Clinical sample ID provided in 'Disease State Description' corresponds with Sample ID in Table 1 "Clinical Information for the micro-array samples" in the associated publication.
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: Michael

last: Griffiths


title: HSF1 Mouse Fibroblast Heat Shock - Scanner7

status: Public on Aug 05 2005

summary:
Mouse HSF1+/+ and HSF1-/- Fibroblasts Heat Shock Time Courses Scanned on Scanner 7 (Axon 4000B)
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: John

last: Murray