title: Microarray Studies in the Laser Capture Microdissected SNc after a Single Administration of MPTP in Common Marmosets

status: Public on Jun 29 2006

city: Kagoshima

first: Shin-ichi

last: Iwata

state: Kagoshima

address: Sakuragaoka 8-35-1

department: Pharmacology

institute: Kagoshima University

summary:
We have previously detected cyclin D1-initiated and p53-related (PERP; p53 apoptosis-associated target) cell death in a striatal 6-hydroxydopamine (6-OHDA)-treated Parkinsonian mouse model by adaptor-tagged competitive PCR (ATAC-PCR) (Synapse 51, 279-286, 2004). In order to establish the mechanism of dopaminergic cell death in Parkinson’s disease, various Parkinsonian animal models should be studied. Therefore, the time-course alteration of gene expression in the substantia nigra pars compacta was investigated after a single administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) in common marmosets. In the MPTP model, gene expression of neither cyclin D1 nor PERP was altered. There were also few common alterations in gene expression between the MPTP and 6-OHDA models. This suggests that the mechanism of cell death may differ between these models, and extensive study in various Parkinsonian models should be performed to elucidate the mechanisms of dopaminergic cell death in Parkinson’s disease.
Keywords: time course

overall_design:
Materials and methods
1. Animals
Five 3-year-old male common marmosets (Callithrix jacchus) weighing 350–400 g were used. A single marmoset was used as a vehicle-treated control, with the rest being administered MPTP. A microarray experiment and an immunohistochemical study were performed in the same animals. They were colonized in the Center for Life Science Resources in Kagoshima University, Japan. Animals were housed with free access to standard food in an air-conditioned room under a constant 12 h light/dark cycle (lights on at 7:00 a.m.) at a temperature of 25–27°C and 45–55% humidity. All efforts were made to minimize animal suffering, and to reduce the number of animals used. The present experiments were carried out after obtaining permission from the Committee of Animal Experimentation, Kagoshima University Graduate School of Medical and Dental Sciences, Japan.

2. MPTP administration
A single dose of MPTP was administered intravenously (i.v.) to the animals in order to examine the time-course alteration in gene expression. As in our previous study, the dose of MPTP was 2.5 mg/kg (Nomoto et al., 1997). At this dose, animals exhibit immobility during an entire day, while doses greater than 2.5 mg/kg can induce death. MPTP hydrochloride (Sigma, St. Louis, MO, USA) was dissolved in 0.9% saline, and administered under intraperitoneal pentobarbital anesthesia (40 mg/kg). Under deep anesthesia with pentobarbital, the animals were decapitated either at 2 h, 6 h, 1 day or 14 days after MPTP administration. All experiments using MPTP were performed in accordance with safety guidelines (Przedborski et al., 2001).

3.  Laser capture microdissection
The midbrain of each marmoset was dissected on an ice-cold glass plate, and mounted on a specimen block with O.C.T. compound (Tissue-Tek, Sakura Finetechnical, Tokyo, Japan). The midbrains were frozen by covering them with very finely powdered dry ice. Sections (8 μm thickness) were cut on a cryostat (Microm HM500S, Carl Zeiss Japan, Tokyo, Japan), and mounted on ice-cold, membrane-coated glass slides (Carl Zeiss Japan). The membranes on the glass slides were coated with poly-L-lysine (P8920; Sigma). Immediately after mounting, slides were cooled on dry ice and stored at –80°C for less than 3 days. Slides were fixed in ethanol/acetate solution (19:1) at 4°C for 3 min, and washed with PBS at 4°C for 1 min. Slides were stained with 0.1% toluidine blue at room temperature for 10 s, washed with PBS at 4°C for 10 s, and then air-dried for 5 min. Immediately after staining, slides were processed for laser capture microdissection (LCM).
A Leica AS LMD (Leica Microsystems, Wetzlar, Germany) was used for LCM. SNc sections corresponded to level A4.5 of the brain atlas (Stephan et al., 1980). These sections contained transverse sections of the oculomotor nerve. A strip of the unilateral SNc was dissected (Fig. 1). The SNcs from two slides were collected and placed in a PCR tube containing 10 μl extraction buffer of the PicoPure RNA Isolation Kit (Arcturus Bioscience, Mountain View, CA, USA).

4. Microarray experiments
Total RNA was extracted by the PicoPure RNA Isolation Kit, and eluted in approximately 10 μl buffer, according to the manufacturer’s protocol. In order to obtain a sufficient amount of amplified RNA (aRNA) for the microarray experiments, total RNA was amplified using two rounds of in vitro transcription. The first round of amplification was performed using the RiboAmp HS RNA Amplification Kit (Arcturus). The second round of amplification used the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA, USA) and cyanine-3 or cyanine-5 labeling. The labeled aRNA was hybridized with Agilent whole human genome oligo microarray G4112A. In order to correct the buffer composition in the second round of amplification using the Low RNA Input Fluorescent Linear Amplification Kit, cDNA (11 μl) that was purified in the round 2 procedure by the RiboAmp HS RNA Amplification Kit, was added to the modified transcription buffer of the Agilent kit.  Each sample contained 4 μl of 5 X first strand buffer, 20 μl of 4 X transcription buffer, 6 μl 0.1 M DTT, 8 μl NTP mix, 6.4 μl 50% PEG, 0.5 μl RNase inhibitor (RNase Out; Invitrogen, Carlsbad, CA, USA), 0.6 µl inorganic pyrophosphatase, 0.8 μl T7 RNA polymerase, 2.4 μl cyanine (PerkinElmer Life Sciences, Boston, MA, USA; cyanine-3 for controls and cyanine-5 for MPTP-treated marmosets), and 20.3 μl DW. Labeled aRNA was synthesized according to the instructions for the Agilent kit.
An Agilent 2100 bioanalyzer and an RNA 6000 Pico LabChip Kit were used to examine the length distribution of labeled aRNAs. A preliminary experiment using the protocol found in the appendices of the HistoGene LCM Immunofluorescence Staining Kit (Arcturus) was performed to determine the degree of degradation of total RNA that occurred during tissue staining.


title: Gene Expression in the Rice Blast Fungus, Magnaporthe grisea, During Nitrogen Starvation

status: Public on May 26 2006

city: Raleigh

first: Huaqin

last: Pan

state: NC

country: USA

institute: North Carolina State University

summary:
This experiment was designed to analyze transcriptional changes that occur when the fungal plant pathogen M. grisea is shifted from a complete media to a nitrogen-starved media. Comparisons were made in the following way between fungal mycelial grown in minimal media supplemented with a nitrogen source (MM+N) and minimal media without a nitrogen source (NS)
Keywords: parallel sample

first: Nicole

middle: M

last: Donofrio

first: Yeon Yee

last: Oh

first: R

last: Lundy

first: Jun Seop

last: Jeong

first: Sean

last: Coughlan

first: Thomas

middle: K

last: Mitchell

first: Ralph

middle: A

last: Dean


title: CCAT regulated gene expression

status: Public on May 05 2006

city: Stanford

first: Ricardo

last: Dolmetsch

state: CA

address: 299 Campus Drive, D227

department: Neurobiology

institute: Ricardo Dolmetsch

summary:
Voltage gated calcium channels play a central role in regulating the electrical and biochemical properties of neurons and muscle cells.  Cells coordinate the expression of voltage gated calcium channels with the expression of other proteins that regulate membrane potential and calcium homeostasis.  We report that the C-terminus of CaV 1.2, an L-type calcium channel (LTC) contains a C-terminal fragment that translocates to the nucleus and regulates transcription.  This calcium channel associated transcription factor (CCAT) associates with transcriptional co-regulators such as p54nrb/NonO and binds to endogenous promoters.  CCAT regulates the expression of gap junctions, sodium calcium exchangers, NMDA receptors, potassium channels and other proteins that regulate neuronal signaling.  Electrical activity and developmental processes regulate the nuclear localization of CCAT, suggesting that the CCAT integrates information about the number of LTCs with information about the developmental history and electrical activity of a cell.  These findings provide the first evidence that voltage gated calcium channels can directly activate transcription and suggest a novel mechanism linking voltage gated channels to the function and differentiation of excitable cells.
Keywords: Genetic modification Analysis

overall_design: The goal of these experiments was to identify the genes that are regulated by CCAT, a novel transcription factor derived from the C-terminus of CaV1.2.  Neuro2A neuroblastoma cells were transfected with the last 503 AA of CaV1.2 which is full length CCAT (CCAT FL) or with the last 280 AA of CaV1.2, a form of CCAT that lacks the transcriptional activation domain (CCAT DTA).  The mRNA from either CCAT FL or CCAT DTA expressing cells was hybridized to Agilent mouse genome microarrays along with mRNA from untransfected neuro2A cells (CCAT FL or DTA A series). Subsequent investigation revealed that transfection with the PA1 plasmid by itself increases the expression of some genes.  To control for this effect we compared Neuro2A cells transfected with full length CCAT (in PA1) with Neuro2A cells transfectected with PA1 alone (CCAT FL B series).   The microarray data was analyzed with the Rossetta Luminator gene expression data analysis system.

first: Natalia

last: Gomez-Ospina

first: Fuminori

last: Tsuruta

first: Linda

last: Hu

middle: E


title: Genomic and genetic characterization of rice Cen3 reveals evolutionary remnants of a complex centromere

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

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

overall_design: Refer to individual Series


title: Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests

status: Public on May 20 2006

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Abstract: Vibrio cholerae, the etiological agent of the diarrheal illness cholera, can kill an infected adult in 24 h. V.cholerae lives as an autochthonous microbe in estuaries, rivers and coastal waters. A better understanding of its metabolic pathways will assist the development of more effective treatments and will provide a deeper understanding of how this bacterium persists in natural aquatic habitats. Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium. We report here experimental evidence supporting the computationally predicted pathways. The evidence comes from microarray gene expression studies of V.cholerae in the stools of three cholera patients [D. S. Merrell, S. M. Butler, F. Qadri, N. A. Dolganov, A. Alam, M. B. Cohen, S. B. Calderwood, G. K. Schoolnik and A. Camilli (2002) Nature, 417, 642-645.], from gene expression studies in minimal growth conditions and LB rich medium, and from clinical tests that identify V.cholerae. Expression data provide evidence supporting 92 (53%) of the 171 pathways. The clinical tests provide evidence supporting seven pathways, with six pathways supported by both methods. VchoCyc provides biologists with a useful tool for analyzing this organism's metabolic and genomic information, which could lead to potential insights into new anti-bacterial agents. VchoCyc is available in the BioCyc database collection (http://BioCyc.org).

This SuperSeries is composed of the SubSeries listed below.


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

status: Public on Jun 15 2006

city: Pune

first: Sanjeev

last: Galande

address: Ganeshkhind

country: India

institute: National Centre for Cell Science


title: cDNA microarray analysis of human skeletal muscle after eccentric or endurance exercise

status: Public on Apr 15 2006

city: Ottawa

first: Douglas

middle: Joseph

last: Mahoney

state: ON

address: 401 Smyth Rd

department: Apoptosis Research Center

country: Canada

institute: CHEO Research Institute


title: Cotton Fiber Development

status: Public on Apr 12 2006

city: Shanghai

first: Xiao-Ya

last: Chen

address: No. 300, Fenglin Road

department: Institute of Plant Physiology and Ecology

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences


title: Transcriptional reprogramming during reloading of atrophied rat soleus muscle

status: Public on Mar 17 2006

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

country: Switzerland

institute: University of Berne


title: Transcriptional profiling of Entamoeba histolytica trophozoites

status: Public on Mar 08 2006

summary:
Abstract: We have developed an Entamoeba histolytica genomic DNA microarray and used it to develop a transcriptional profile of 1,971 E. histolytica (HM-1:IMSS) genes. The arrays accurately detected message abundance and 31-47% of amebic genes were expressed under standard tissue culture conditions (levels detectable by Northern blot analysis or RT-PCR respectively). Genes expressed at high levels ( approximately 2% of total) included actin (8.m00351), and ribosomal genes (20.m00312). Moderately expressed genes ( approximately 14% of total) included cysteine proteinase (191.m00117), profilin (156.m00098), and an Argonaute family member (11.m00378). Genes with low-level expression ( approximately 15% of total) included Ariel1 (160.m00087). Genes with very low expression ( approximately 16% of total) and those not expressed ( approximately 52% of total) included encystation-specific genes such as Jacob cyst wall glycoprotein (33.m00261), chitin synthase (3.m00544), and chitinase (22.m00311). Transcriptional modulation could be detected using the arrays with 17% of genes upregulated at least two-fold in response to heat shock. These included heat shock proteins (119.m00119 and 279.m00091), cyst wall glycoprotein Jacob (33.m00261), and ubiquitin-associated proteins (16.m00343; 195.m00092). Using Caco-2 cells to model the host-parasite interaction, we verified that host cell killing was dependent on live ameba. However, surprisingly these events did not appear to induce major transcriptional changes in the parasites.

This SuperSeries is composed of the SubSeries listed below.


title: Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures

summary:
Abstract: We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this "diauxic shift." Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift.

This SuperSeries is composed of the SubSeries listed below.


title: Cell-specific analysis of mRNA synthesis and decay

summary:
Abstract: Standard microarrays measure mRNA abundance, not mRNA synthesis, and therefore cannot identify the mechanisms that regulate gene expression. We have developed a method to overcome this limitation by using the salvage enzyme uracil phosphoribosyltransferase (UPRT) from the protozoan Toxoplasma gondii. T. gondii UPRT has been well characterized because of its application in monitoring parasite growth: mammals lack this enzyme activity and thus only the parasite incorporates (3)H-uracil into its nucleic acids. In this study we used RNA labeling by UPRT to determine the roles of mRNA synthesis and decay in the control of gene expression during T. gondii asexual development. We also used this approach to specifically label parasite RNA during a mouse infection and to incorporate thio-substituted uridines into the RNA of human cells engineered to express T. gondii UPRT, indicating that engineered UPRT expression will allow cell-specific analysis of gene expression in organisms other than T. gondii.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Toxoplasma gondii
Homo sapiens

platform_organism:
Toxoplasma gondii
Homo sapiens


title: A role for SIR-2.1 regulation of ER stress response genes in determining C. elegans life span

summary:
Abstract: C. elegans SIR-2.1, a member of the Sir-2 family of NAD(+)-dependent protein deacetylases, has been shown to regulate nematode aging via the insulin/IGF pathway transcription factor daf-16. Treatment of C. elegans with the small molecule resveratrol, however, extends life span in a manner fully dependent upon sir-2.1, but independent of daf-16. Microarray analysis of worms treated with resveratrol demonstrates the transcriptional induction of a family of genes encoding prion-like glutamine/asparagine-rich proteins involved in endoplasmic reticulum (ER) stress response to unfolded proteins. RNA interference of abu-11, a member of this ER stress gene family, abolishes resveratrol-mediated life span extension, and overexpression of abu-11 extends the life span of transgenic animals. Furthermore, SIR-2.1 normally represses transcription of abu-11 and other ER stress gene family members, indicating that resveratrol extends life span by inhibiting sir-2.1-mediated repression of ER stress genes. Our findings demonstrate that abu-11 and other members of its ER stress gene family are positive determinants of C. elegans life span.

This SuperSeries is composed of the SubSeries listed below.


title: Characterization of E2F1 in HeLa and MCF7 cells

status: Public on Mar 09 2006

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

type: Genome binding/occupancy profiling by genome tiling array

relation:
SuperSeries of: GSE4306
SuperSeries of: GSE4319
SuperSeries of: GSE4355


title: In vitro response to l-asparaginase in acute lymphoblastic leukemia

summary:
Abstract: To investigate the effect of l-asparaginase on acute lymphoblastic leukemia (ALL), we used cDNA microarrays to obtain a genome-wide view of gene expression both at baseline and after in vitro exposure to l-asparaginase in cell lines and pediatric ALL samples. In 16 cell lines, a baseline gene expression pattern distinguished l-asparaginase sensitivity from resistance. However, for 28 pediatric ALL samples, no consistent baseline expression pattern was associated with sensitivity to l-asparaginase. In particular, baseline expression of asparagine synthetase (ASNS) was not predictive of response to l-asparaginase. After exposure to l-asparaginase, 5 cell lines and 10 clinical samples exhibited very similar changes in the expression of a large number of genes. However, the gene expression changes occurred more slowly in the clinical samples. These changes included a consistent increase in expression of tRNA synthetases and solute transporters and activating transcription factor and CCAAT/enhancer binding protein family members, a response similar to that observed with amino acid starvation. There was also a consistent decrease in many genes associated with proliferation. Taken together, the changes seem to reflect a consistent coordinated response to asparagine starvation in both cell lines and clinical samples. Importantly, in the clinical samples, increased expression of ASNS after l-asparaginase exposure was not associated with in vitro resistance to l-asparaginase, indicating that ASNS-independent mechanisms of in vitro l-asparaginase resistance are common in ALL. These results suggest that targeting particular genes involved in the response to amino acid starvation in ALL cells may provide a novel way to overcome l-asparaginase resistance.

This SuperSeries is composed of the SubSeries listed below.


title: Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines

type:
Expression profiling by array
Genome variation profiling by array

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

This SuperSeries is composed of the SubSeries listed below.


title: Genome-wide Analysis of Re-replication Reveals Inhibitory Controls that Target Multiple Stages of Replication Initiation

status: Public on Mar 20 2006

city: Cambridge

first: Stephen

last: Bell

state: MA

address: 77 Massachusetts Ave

department: Biology

institute: MIT

type: Genome variation profiling by genome tiling array

summary:
DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-Replicative Complex (pre-RC) assembly outside of the G1 phase of the cell cycle. We have analyzed the effects of re-replication on the S. cerevisiae genome using a combination of Comparitive Genomic Hybridization (CGH) of re-replicating strains and Genome-Wide Location Analysis of pre-RC components. These data indicate which sites in the genome assemble pre-RCs under re-replication conditions, which sites undergo re-initiation and the extent of re-replication.
Keywords: comparative genomic hybridization, ChIP-chip, re-replication, DNA replication, pre-RC

overall_design:
We used strain SB1507 which contains a number of mutations that confer sensitivity to re-replication to monitor the effects of re-replication on the S. cerevisiae genome. Cells were induced to re-replicate with galactose and collected after either 45 minutes (for genome-wide location analysis) or three hours (for CGH). For comparision for pre-RC assembly, we also performed genome-wide location analysis for wild type cells during the G1 phase of the cell cycle.  All of the above samples were hybridized to high-resolution, tiled DNA microarrays.

We also showed that origin and origin-proximal DNA is sufficient to direct re-replication at an ectopic locus.  For these experiments we used strains that had a re-replicating origin integrated at an endogenous locus. The strains were induced to re-replicate as described above for CGH.  The resulting genomic DNAs were co-hybridized with G1-phase DNA to ORF DNA microarrays.

Each experiment was performed with three experimental replicated per experiment.

first: Robyn

last: Tanny

first: David

last: MacAlpine

first: Hannah

middle: G

last: Blitzblau

middle: P


title: Reverse engineering of industrial pharmaceutical-producing actinomycete strains

summary:
Abstract: Transcript levels in production cultures of wildtype and classically improved strains of the actinomycete bacteria Saccharopolyspora erythraea and Streptomyces fradiae were monitored using microarrays of the sequenced actinomycete S. coelicolor. Sac. erythraea and S. fradiae synthesize the polyketide antibiotics erythromycin and tylosin, respectively, and the classically improved strains contain unknown overproduction mutations. The Sac. erythraea overproducer was found to express the entire 56-kb erythromycin gene cluster several days longer than the wildtype strain. In contrast, the S. fradiae wildtype and overproducer strains expressed the 85-kb tylosin biosynthetic gene cluster similarly, while they expressed several tens of other S. fradiae genes and S. coelicolor homologs differently, including the acyl-CoA dehydrogenase gene aco and the S. coelicolor isobutyryl-CoA mutase homolog icmA. These observations indicated that overproduction mechanisms in classically improved strains can affect both the timing and rate of antibiotic synthesis, and alter the regulation of antibiotic biosynthetic enzymes and enzymes involved in precursor metabolism.

This SuperSeries is composed of the SubSeries listed below.


title: Global analysis of Escherichia coli RNA degradosome function

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

This SuperSeries is composed of the SubSeries listed below.


title: Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

summary:
Abstract: Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of RNA-binding proteins in Saccharomyces cerevisiae and DNA microarrays to comprehensively identify the associated mRNAs. Distinct groups of 40-220 different mRNAs with striking common themes in the functions and subcellular localization of the proteins they encode are associated with each of the five Puf proteins: Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. We identified distinct sequence motifs in the 3'-untranslated regions of the mRNAs bound by Puf3p, Puf4p, and Puf5p. Three-hybrid assays confirmed the role of these motifs in specific RNA-protein interactions in vivo. The results suggest that combinatorial tagging of transcripts by specific RNA-binding proteins may be a general mechanism for coordinated control of the localization, translation, and decay of mRNAs and thus an integral part of the global gene expression program.

This SuperSeries is composed of the SubSeries listed below.


title: Systemic and cell type-specific gene expression patterns in scleroderma skin

summary:
Abstract: We used DNA microarrays representing >12,000 human genes to characterize gene expression patterns in skin biopsies from individuals with a diagnosis of systemic sclerosis with diffuse scleroderma. We found consistent differences in the patterns of gene expression between skin biopsies from individuals with scleroderma and those from normal, unaffected individuals. The biopsies from affected individuals showed nearly indistinguishable patterns of gene expression in clinically affected and clinically unaffected tissue, even though these were clearly distinguishable from the patterns found in similar tissue from unaffected individuals. Genes characteristically expressed in endothelial cells, B lymphocytes, and fibroblasts showed differential expression between scleroderma and normal biopsies. Analysis of lymphocyte populations in scleroderma skin biopsies by immunohistochemistry suggest the B lymphocyte signature observed on our arrays is from CD20+ B cells. These results provide evidence that scleroderma has systemic manifestations that affect multiple cell types and suggests genes that could be used as potential markers for the disease

This SuperSeries is composed of the SubSeries listed below.


title: Gene expression analysis of peritoneal mesotheliomas following chemical treatment in F344 rats

status: Public on Apr 20 2006

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
This study was performed to characterize the gene expression profile of rat peritoneal mesothelioma (RPM) formation following treatment of Fischer 344 rats with o-nitrotoluene (o-NT) or bromochloracetic acid (BCA).
Keywords: Rat, Mesotheliomas, Bromochloractetic acid, o-Nitrotoluene, Carcinogenesis, Microarray

overall_design: Four mesotheliomas from o-NT-treated rats and four mesotheliomas from BCA-treated rats were selected for microarray analysis.  At necrosy, the tumors were collected, minced and flash frozen in liquid nitrogen.  A non-transformed mesothelial cell line, Fred-PE (passage eight), was used as a source of reference RNA.  Total RNAs from tumor tissue and Fred-PE were isolated with the RNeasy kit and 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.  For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5), using default for all parameters.  Two arrays for each comparison were used, incorporating a fluor reversal.

first: Yongbaek

last: Kim

first: Thai-Vu

last: Ton

first: Anthony

middle: B

last: DeAngelo

first: Kevin

last: Morgan

first: Theodora

middle: R

last: Devereux

first: Colleen

last: Anna

first: Jennifer

last: Collins

first: Richard

middle: S

last: Paules

first: Lynn

last: Crosby

first: Robert

middle: C

last: Sills


title: Universal Reference RNA as a standard for microarray experiments

last: Stanford Microarray Database

summary:
Abstract: BACKGROUND: Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR), developed with the goal of providing hybridization signal at each microarray probe location (spot). Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment.
RESULTS: Human, mouse and rat URR (UHRR, UMRR and URRR, respectively) were prepared from pools of RNA derived from individual cell lines representing different tissues. A variety of microarrays were used to determine percentage of spots hybridizing with URR and producing signal above a user defined threshold (microarray coverage). Microarray coverage was consistently greater than 80% for all arrays tested. We confirmed that individual cell lines contribute their own unique set of genes to URR, arguing for a pool of RNA from several cell lines as a better configuration for URR as opposed to a single cell line source for URR. Microarray coverage comparing two separately prepared batches each of UHRR, UMRR and URRR were highly correlated (Pearson's correlation coefficients of 0.97).
CONCLUSION: Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation. This type of reference provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and laboratories.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The Vibrio cholerae chitin utilization program

summary:
Abstract: Chitin, an insoluble polymer of GlcNAc, is an abundant source of carbon, nitrogen, and energy for marine microorganisms. Microarray expression profiling and mutational studies of Vibrio cholerae growing on a natural chitin surface, or with the soluble chitin oligosaccharides (GlcNAc)(2-6), GlcNAc, or the glucosamine dimer (GlcN)2 identified three sets of differentially regulated genes. We show that (i) ChiS, a sensor histidine kinase, regulates expression of the (GlcNAc)(2-6) gene set, including a (GlcNAc)2 catabolic operon, two extracellular chitinases, a chitoporin, and a PilA-containing type IV pilus, designated ChiRP (chitin-regulated pilus) that confers a significant growth advantage to V. cholerae on a chitin surface; (ii) GlcNAc causes the coordinate expression of genes involved with chitin chemotaxis and adherence and with the transport and assimilation of GlcNAc; (iii) (GlcN)2 induces genes required for the transport and catabolism of nonacetylated chitin residues; and (iv) the constitutively expressed MSHA pilus facilitates adhesion to the chitin surface independent of surface chemistry. Collectively, these results provide a global portrait of a complex, multistage V. cholerae program for the efficient utilization of chitin.

This SuperSeries is composed of the SubSeries listed below.


title: 24 hour time course: regulation of uterine genes by estradiol in ovariectomized mice

status: Public on Apr 14 2006

summary:
Using microarray technology, we compared the global expression pattern of uterine RNA from ovariectomized control mice to those of ovariectomized mice treated with estradiol for various intervals between 30 minutes and 24 hours.
Keywords: estrogen, uterus, genomic, mouse

overall_design: Mice (C57 BI/6) were treated with sesame oil or estradiol and uteri were collected at 30 minutes, two hours, 6 hours, 12 hours and 24 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.  Two arrays for each time point were used, incorporating a fluor reversal.

first: Kenneth

last: Korach

first: Sylvia

last: Hewitt

first: Bonnie

middle: J

last: Deroo

first: Sherry

middle: F

last: Grissom


title: Estren Behaves as a Weak Estrogen Rather than a Non-genomic Selective Activator in the Mouse Uterus

status: Public on Apr 07 2006

summary:
A proposed membrane-mediated mechanism of rapid non genomic response to estrogen has been the intense focus of recent research.  Estren (Es), a synthetic steroid, is reported to act selectively through a rapid membrane-mediated pathway, rather than through the classical nuclear estrogen receptor (ER)-mediated pathway, to maintain bone density in ovaierectomized mice without uterotropic effects. To further evaluate the mechanism and physiological effects of Es we studied responses in adult ovariectomized mice.
Keywords: estrogen receptor, nongenomic steriod action, uterus

overall_design:
Mice were treated with sesame oil vehicle (Sigma), E2 (Steraloids; 1 µg/mouse) estren (300 µg/mouse), or dihydrotestosterone (DHT, Steraloids; 50 µg/mouse) and uteri were collected 2 or 24 hours after treatment and snap frozen in liquid nitrogen. Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent (Invitrogen, Carlsbad CA) and the RNeasy clean up protocol (Qiagen Valencia CA). Gene expression profiling was conducted using Agilent Mouse Oligo arrays with ~20,000 genes represented (Agilent Technologies, Palo Alto, CA).  Five hundred ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to manufacturer’s protocol.  For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner (Agilent Technologies, Wilmington, DE).  Each sample pair was hybridized on 2 replicate chips.
Data was obtained using the Agilent Feature Extraction software (v7.5, v8.1), using defaults for all parameters.

first: Katherine

last: Hamilton


title: Near naked hairless, Hr(n), and Hr(Rh-R) mice

status: Public on Apr 18 2006

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta University

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


title: Gene expression patterns associated with recurrent chromosomal translocations in acute lymphoblastic leukemia

summary:
Abstract: We obtained a global view of gene expression in both cell lines and pediatric acute lymphoblastic leukemia (ALL) samples that harbor one of several selected chromosomal abnormalities. When the cell lines were studied alone, we found that these chromosomal abnormalities were associated with the predominant variation in transcriptional programs across the set of cell lines studied. When cell lines and clinical samples were studied together, we found that each chromosomal abnormality (TEL/AML1, BCR/ABL, or MLL abnormalities) was associated with a characteristic gene expression signature that was shared by both cell lines and clinical samples. However, BCR/ABL was associated with a much more heterogeneous pattern of expression than were TEL/AML1 and MLL abnormalities. This observation has important implications for the study of BCR/ABL ALL. In addition, we systematically identified genes whose expression was associated with TEL/AML1, BCR/ABL, or MLL abnormalities in both clinical samples and cell lines. Although some of these genes have previously been described, many have not previously been reported to be associated with one of these chromosomal abnormalities. Notably, we found that the erythropoietin receptor (EPOR) is consistently highly expressed in TEL/AML1 ALL compared with BCR/ABL or MLL.

This SuperSeries is composed of the SubSeries listed below.


title: RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli

summary:
Abstract: Ribonuclease E (RNase E) has a key role in mRNA degradation and the processing of catalytic and structural RNAs in E. coli. We report the discovery of an evolutionarily conserved 17.4 kDa protein, here named RraA (regulator of ribonuclease activity A) that binds to RNase E and inhibits RNase E endonucleolytic cleavages without altering cleavage site specificity or interacting detectably with substrate RNAs. Overexpression of RraA circumvents the effects of an autoregulatory mechanism that normally maintains the RNase E cellular level within a narrow range, resulting in the genome-wide accumulation of RNase E-targeted transcripts. While not required for RraA action, the C-terminal RNase E region that serves as a scaffold for formation of a multiprotein degradosome complex modulates the inhibition of RNase E catalytic activity by RraA. Our results reveal a possible mechanism for the dynamic regulation of RNA decay and processing by inhibitory RNase binding proteins.

This SuperSeries is composed of the SubSeries listed below.


title: Repeated observation of breast tumor subtypes in independent gene expression data sets

summary:
Abstract: Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be distinguished by their distinct patterns of gene expression. A total of 115 malignant breast tumors were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into one basal-like, one ERBB2-overexpressing, two luminal-like, and one normal breast tissue-like subgroup. The genes used for classification were selected based on their similar expression levels between pairs of consecutive samples taken from the same tumor separated by 15 weeks of neoadjuvant treatment. Similar cluster analyses of two published, independent data sets representing different patient cohorts from different laboratories, uncovered some of the same breast cancer subtypes. In the one data set that included information on time to development of distant metastasis, subtypes were associated with significant differences in this clinical feature. By including a group of tumors from BRCA1 carriers in the analysis, we found that this genotype predisposes to the basal tumor subtype. Our results strongly support the idea that many of these breast tumor subtypes represent biologically distinct disease entities.

This SuperSeries is composed of the SubSeries listed below.


title: Senescence-specific gene expression fingerprints

status: Public on Mar 07 2006

summary:
Abstract: Replicative senescence is the state of irreversible proliferative arrest that occurs as a concomitant of progressive telomere shortening. By using cDNA microarrays and the gabriel system of computer programs to apply domain-specific and procedural knowledge for data analysis, we investigated global changes in gene transcription occurring during replicative senescence in human fibroblasts and mammary epithelial cells (HMECs). Here we report the identification of transcriptional "fingerprints" unique to senescence, the finding that gene expression perturbations during senescence differ greatly in fibroblasts and HMECs, and the discovery that despite the disparate nature of the chromosomal loci affected by senescence in fibroblasts and HMECs, the up-regulated loci in both types of cells show physical clustering. This clustering, which contrasts with the random distribution of genes down-regulated during senescence or up-regulated during reversible proliferative arrest (i.e., quiescence), supports the view that replicative senescence is associated with alteration of chromatin structure.

This SuperSeries is composed of the SubSeries listed below.


title: Variation in gene expression patterns in follicular lymphoma and the response to rituximab

summary:
Abstract: Analysis of the patterns of gene expression in follicular lymphomas from 24 patients suggested that two groups of tumors might be distinguished. All patients, whose biopsies were obtained before any treatment, were treated with rituximab, a monoclonal antibody directed against the B cell antigen, CD20. Gene expression patterns in the tumors that subsequently failed to respond to rituximab appeared more similar to those of normal lymphoid tissues than to gene expression patterns of tumors from rituximab responders. These findings suggest the possibility that the response of follicular lymphoma to rituximab treatment may be predicted from the gene expression pattern of tumors.

This SuperSeries is composed of the SubSeries listed below.


title: Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of DNA

status: Public on Mar 15 2006

summary:
Abstract: Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of fresh-frozen and formalin-fixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens.

This SuperSeries is composed of the SubSeries listed below.


title: Arbuscular mycorrhizal symbioses

status: Public on Mar 08 2007

city: Ithaca

first: Maria

middle: J.

last: Harrison

state: NY

address: Tower Road, Cornell Campus

institute: Boyce Thompson Institute for Plant Research

sample_organism:
Medicago truncatula
Rhizophagus intraradices
Gigaspora gigantea


title: Genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome

summary:
Abstract: BACKGROUND: Androgen insensitivity syndrome (AIS) comprises a range of phenotypes from male infertility to complete feminization. Most individuals with AIS carry germline mutations of the androgen receptor (AR) that interfere with or ablate its function. As genital fibroblasts retain expression of the AR in vitro, we used genital skin fibroblasts from normal males and 46,XY females with complete AIS due to known AR mutations to gain insights into the role of the AR in human genital differentiation.
RESULTS: Using DNA microarrays representing 32,968 different genes, we identified 404 transcripts with significant differences in transcription levels between genital skin fibroblasts cultured from normal and AIS-affected individuals. Gene-cluster analyses uncovered coordinated expression of genes involved in key processes of morphogenesis. On the basis of animal studies and human genetic syndromes, several of these genes are known to have specific roles in genital differentiation. Remarkably, genital fibroblasts from both normal and AIS-affected individuals showed no transcriptional response to dihydrotestosterone treatment despite expression of the AR.
CONCLUSIONS: The results suggest that in addition to differences in the anatomic origin of the cells, androgen signaling during prenatal development contributes to setting long-lasting, androgen-independent transcriptional programs in genital fibroblasts. Our findings have broad implications in understanding the establishment and the stability of sexual dimorphism in human genital development.

This SuperSeries is composed of the SubSeries listed below.


title: Gene expression during the life cycle of Drosophila melanogaster

summary:
Abstract: 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.

This SuperSeries is composed of the SubSeries listed below.


title: Intestinal epithelial cells transfected with Ras and treated with TGF-beta-1

status: Public on Dec 01 2005

city: Houston

first: Carl

last: Allen

state: TX

address: 6621 Fannin St

department: Pediatrics

institute: Texas Children's Cancer Center/Baylor College of Medicine

summary:
RIE (rat intestinal epithelial) cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells. The experiment was performed under identical conditions four times: RIE vs RIE - TGF-beta #1-#4.

RIE-Ras cells were established by stable transfection of the parental cells with pSV2-H-Ras(12V) which contain human sequences encoding the constitutively active H-Ras(12V) protein. RIE-Ras cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells. The experiment was performed four times under identical conditions (RIE-Ras vs RIE-RAS TGF-beta #1-#4).
Keywords = TGF-beta
Keywords = rat
Keywords = intestinal epithelial cells
Keywords: parallel sample

first: John

last: Barnard


title: Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

summary:
Abstract: BACKGROUND: T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays.
RESULTS: Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3-3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification.
CONCLUSION: T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays.

This SuperSeries is composed of the SubSeries listed below.


title: Low level of pathogenesis-related protein1 mRNA expression in 15-day-old Arabidopsis cer6-2 and cer2 eceriferum mutants.

status: Public on Dec 20 2005

city: bordeaux

first: bertrand

last: garbay

address: 146 rue leo saignat

department: estbb

country: France

institute: university bordeaux2

summary:
RNA from the aerial parts of 15-day-old eceriferum cer6-2 mutant and control plants were used in microarray experiments to screen for differentially expressed genes. Among those which were down regulated in the mutant, several were known to be involved in various plant defense mechanisms. The most remarkable difference was measured for the transcripts encoding the pathogenesis-related protein1 (PR-1), which is a marker of the systemic acquired resistance (SAR) pathway, with a 100-fold decrease in the cer6-2 mutant. Further Q-PCR experiments showed that the PR-1 transcript levels were low in two other eceriferum mutants, representing 1/200th and 1/25th of the normal values in the aerial part of 15-day-old cer2 and cer1-1 mutants, respectively. Interestingly, PR-1 mRNA levels were closed to the normal values in the cer3-1 and cer6-2R mutant, the latter being a plant where the synthesis of the very-long chain fatty acids, which is deficient in the cer6-2 plants, is partially restored. Altogether, these results strongly suggested that the amount of PR1-mRNA was not directly correlated to the amount of epicuticular wax on the leaves, but was rather correlated to the presence or absence of some particular lipid-constituents in the epicuticular wax layer.

Related publication:

Garbay B, Tautu MT, Costaglioli P. Low level of pathogenesis-related protein 1 mRNA expression in 15-day-old Arabidopsis cer6-2 and cer2 eceriferum mutants. Plant Science 2007
Volume 172, Issue 2, Pages 299-305

Keywords: Effect of eceriferum mutation

overall_design: Total RNA was purified from the aerial parts of 2-week-old plants (20 plants were pooled for each genotype). Arabidopsis plants were grown under long-day conditions (16 h light:8 h dark) at 22°C and 80% relative humidity. The control plants and the cer mutant were cultivated in the same phytotron, and the Petri dishes were placed randomly on the same shelf. This was done to avoid any difference in plant growth conditions between the mutants and the control plants. The microarrays used were Agilent Arabidopsis2. GSM87735 represents the direct experiment (cer6-2 Cy3, Ler-0 Cy5), and GSM88340 represents the dye-swap (Ler-0 Cy3, cer6-2 Cy5)

first: Bertrand

last: Garbay

first: Michel

middle: T

last: Tautu

first: Patricia

last: Costaglioli


title: In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone

summary:
Abstract: Thyroid hormones are key regulators of metabolism that modulate transcription via nuclear receptors. Hyperthyroidism is associated with increased metabolic rate, protein breakdown, and weight loss. Although the molecular actions of thyroid hormones have been studied thoroughly, their pleiotropic effects are mediated by complex changes in expression of an unknown number of target genes. Here, we measured patterns of skeletal muscle gene expression in five healthy men treated for 14 days with 75 µg of triiodothyronine, using 24,000 cDNA element microarrays. To analyze the data, we used a new statistical method that identifies significant changes in expression and estimates the false discovery rate. The 381 up-regulated genes were involved in a wide range of cellular functions including transcriptional control, mRNA maturation, protein turnover, signal transduction, cellular trafficking, and energy metabolism. Only two genes were down-regulated. Most of the genes are novel targets of thyroid hormone. Cluster analysis of triiodothyronine-regulated gene expression among 19 different human tissues or cell lines revealed sets of coregulated genes that serve similar biologic functions. These results define molecular signatures that help to understand the physiology and pathophysiology of thyroid hormone action.

This SuperSeries is composed of the SubSeries listed below.


title: Detection of Transposon Mutants That Cannot Survive in Macrophages and Mice.

status: Public on Aug 24 2005

summary:
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
We have adapted a microarray-based transposon tracking strategy for use with a Salmonella enterica serovar Typhimurium cDNA microarray in order to identify genes important for survival and replication in RAW 264.7 mouse macrophage-like cells or in the spleens of BALB/cJ mice. A 50,000-CFU transposon library of S. enterica serovar Typhimurium strain SL1344 was serially passaged in cultured macrophages or intraperitoneally inoculated into BALB/cJ mice. The bacterial genomic DNA was isolated and processed for analysis on the microarray. The novel application of this approach to identify mutants unable to survive in cultured cells resulted in the identification of components of Salmonella pathogenicity island 2 (SPI2), which is known to be critical for intracellular survival and replication.
Keywords: all_pairs

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Computed

first: Kaman

last: Chan


title: Comparison of miR-181a transfected K562 cells and mock transfected K562 cells

status: Public on Nov 18 2005

city: Guangzhou

first: Jueyu

last: Zhou

state: Guangdong

address: Southern Medical University

department: Institute of genetic engineering

institute: Southern Medical University

summary:
This series consists of samples taken from two groups of K562 cells(miR-181a transfected group and control group ) and harvested 48 hours later.
We used Agilent human 1A oligo microarray identified the changes in gene expression profile of K562 cells after miR-181a transfection experiment. Further studies aimed to find target mRNA of miR-181a in mammalian cells and its biological function.
Keywords = miR-181a
Keywords = microarray
Keywords = K562

Keywords: microRNA transfection analysis

overall_design:
The K562 cells in our research were divided into tranfected group and mock-transfected control according to Lim et al.

To transfect, we diluted 60 pmol miR-181 a duplex into 12 µL Opti-Mem each well, then we diluted 3 µL Oligofectamine(Invitrogen) into 48 µL Opti-Mem  for each sample, incubated for 5 min at room temperature and  add 10 µL of diluted transfection mixture to wells and incubate for another 20 min at room temperature. We next added 100 µL of diluted cells suspension mixture containing 50000 cells on top of the complex. Four hours after transfection, FBS was added to the cells at a final concentration of 10% and the cells were incubated for 48 hours. And control group was transfected only with Oligofectamine but no RNA. Each individual transfection experiment was performed in 10 replicate wells.

After transfection experiments, total RNAs from above two group K562 cells were purified using the RNeasy mini kit (Qiagen, Heidelberg, Germany) in accordance with the manufacturer’s protocols. RNA concentration and purity were estimated spectrophotometrically and the quality further assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
Total RNA from control group and transfected group were respectively reverse transcription, in vitro transcribed and labeled (Cy3 and Cy5) according to the Agilent Low RNA Input Fluorescent Linear Amplification Kit Protocol, green is control group, red is transfected group. The array hybridization, washing, and scanning procedures were performed in our lab according to Agilent 60-mer oligo microarray processing protocol using 0.75 µg samples of labeled, fragmented cRNA on Agilent Human 1A oligo microarray with 22575 probes (Agilent Technologies). Labeled cRNA is incubated with the microarray in a hybridization chamber at 60ºC for 17 hours, 4 rpm/min. The microarray was scanned using Agilent 2565BA DNA microarray scanner (Agilent Technologies). Data collection was performed by Agilent DNA microarray scanner. Using the Agilent Feature Extraction Software(v.7.5), spots were identified, measured for fluorescence intensity, local background, and arraywide parameters used to normalize the signals. Outliers and saturated spots were rejected according to 1.42xIQR, and local backgroud subtracted from the signals. Signals were then normalized to remove dye bias and arraywide drift in flourescence.
The following two tests are performed to determined the significance of a feature: (1) Log ratio P-value of the red over green processed signals was calculated using two-sided t-test with P<0.01 considered significant, and (2) a boolean flag of 1 indicated that the feature BGSubSignal is well above background and passes the IsPosAndSignif test.

We used Agilent human 1A oligo microarray identified the changes in gene expression profile of K562 cells after miR-181a transfection experiment.
Further studies aimed to find target mRNA of miR-181a in mammalian cells and the function of miR-181a in cancers.

first: Wenli

last: Ma

first: Dapeng

last: Ding

first: Rong

last: Shi

first: Li

last: Jiang

first: Wenling

last: Zheng


title: NST1 over-expression vs wild type

status: Public on Sep 29 2005

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary:
In plants, secondary wall thickenings play important roles in various biological processes, although the factors regulating these processes remain to be characterized. We show that expression of chimeric repressors derived from NAC SECONDARY WALL THICKENINGS PROMOTING FACTOR1 (NST1) and NST2 in Arabidopsis resulted in an anther dehiscence defect due to loss of secondary wall thickening in anther endothecium. Plants with double, but not single, T-DNA-tagged lines for NST1 and NST2, had the same anther-indehiscent phenotype as transgenic plants that expressed the individual chimeric repressors, indicating that NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls. The activity of the NST2 promoter was particularly strong in anther tissue, while that of the NST1 promoter was detected in various tissues in which lignified secondary walls develop. Ectopic expression of NST1 or NST2 induced ectopic thickening of secondary walls in various above-ground tissues. Epidermal cells with ectopic thickening of secondary walls had structural features similar to those of tracheary elements. However, among genes involved in the differentiation of tracheary elements, only those related to secondary wall synthesis were clearly upregulated. None of the genes involved in programmed cell death was similarly affected. Our results suggest NAC transcription factors as possible regulators of secondary wall thickening in various tissues.
Keywords: transgenic vs wt comparison

overall_design: Total RNA was extracted from rosette leaves of two independent 2-week-old T1 plants over-expressing NST1 driven by 35S promoter and the whole transcriptome was compared with that of wild-type plant.

first: Motoaki

last: Seki

first: Kazuo

last: Shinozaki

first: Masaru

last: Ohme-Takagi


title: Whole-blood samples from women exposed to hormone replacement therapy

status: Public on Oct 25 2005

city: Tromsoe

first: Vanessa

last: Dumeaux

address: University of Tromsoe

country: Norway

institute: "The Norwegian Women and Cancer project"

summary:
The American Women’s Health Initiative study published in July 2002 caused considerable concern among hormone replacement therapy (HRT) users and prescribers in many countries. This study is an exploratory research comparing the genome wide expression profile in whole blood samples according to HRT use.
Within the Norwegian Women and Cancer study, 100 postmenopausal women (50 HRT users and 50 non-HRT users) born between 1943 and 1949 with normal to high body mass index and no other medication use were selected. After total RNA extraction, amplification and labelling, the samples were hybridized together with a common reference (Universal human reference RNA, Stratagen) to Agilent Human 1A oligoarrays (G4110b, Agilent Technologies, Palo Alto, CA) containing 20,173 unique genes. Differentially expressed genes were used to build a classifier using the nearest shrunken centroids method (PAM). Then, we tested the significant changes in single genes by different methods like t-test, Significance Analysis of Microarrays (SAM) and Bayesian ANOVA analysis (BAM).
Results did not reveal any distinct gene list which predicted accurately HRT exposure (error rate = 0.45). Classifier performance slightly improved (error rate = 0.29) including only women who were using continuous combined HRT treatment. According to the small amplitude of expression alterations observed after HRT use in whole blood, large sample sizes are needed to identify significant single genes differentially expressed. However, significant enrichments in biologic process of genes with small changes after HRT use were observed (e.g. receptor and transporter activities, immune response, frizzled signalling pathway, actin filament organization, glycogen metabolism).
Keywords: gene expression profile and exposure

overall_design:
Indirect design with Startagen reference
47 non HRT users and 42 HRT users
No technical replicates

first: Jostein

last: Johansen

first: Anne-Lise

last: Borresen-Dale

first: Eiliv

last: Lund


title: Differential expression of genes in cells mutant for Wrn and/or PARP-1 compared to wild type cells

status: Public on Dec 21 2005

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

institute: Centre de Recherche du CHU de Québec

summary:
Werner syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS is believed to be involved in different aspects of transcription, replication, and/or DNA repair. The poly(ADP-ribose) polymerase-1 (PARP-1) enzyme is also involved in DNA repair and is known to affect transcription of several genes. In this study, we examined the expression profile of cells lacking the normal function of either or both enzymes. All mutant cells exhibited altered expression of genes normally responding to oxidative stress. Interestingly, more than 58% of misregulated genes identified in double mutant cells were not altered in cells with either the Wrn or PARP-1 mutation alone. Consequently, the impact on gene expression profile when both Wrn and PARP-1 are mutated was greater than a simple addition of individual mutant genotype. In addition, double mutant cultured cells showed major misregulation of genes involved in apoptosis, cell cycle control, embryonic development, metabolism, and signal transduction. More importantly, in vivo analyses of double mutant mice have confirmed the increased apoptosis and the developmental defects in embryos as well as the major increase in intracellular phosphorylation and oxidative DNA damage in adult tissues. They also exhibited a progressive increase in oxidative stress with age. Thus, a major result of this study is that changes in expression of several genes and physiological functions identified in vitro were confirmed in mouse embryonic and adult tissues.
Keywords: Genetic modification

overall_design: Microarray analyses were performed on cell cultures at the second passage (10 population doublings). For each genotype, asynchronously dividing cells derived from three healthy 15.5 day embryos from one litter were pooled at the second passage and cytoplasmic RNA was extracted. Cytoplasmic RNA was used in these experiments to avoid contamination with heterogeneous nuclear RNA and genomic DNA. (Note that DNAse treatment was also applied to all samples). This pool of RNA was labeled sample number 1 for each genotype. Pooling of embryonic cells was performed to minimize the effect of inter-individual biological differences. A second pool of embryonic cells was also created from a separate dam (second litter) for each genotype (called samples number 2). This strategy allowed obtaining samples in duplicate for each genotype. The cRNA from wild type cells were synthesized with Cy-5 labeled nucleotides and cRNAs from Wrn mutant, PARP-1 null, and PARP-1 null/Wrn mutant cells were synthesized with Cy-3 labeled nucleotides. Hybridization was performed on Mouse Agilent 60-mer Oligo Microarray chips  by mixing wild type labeled cRNA (baseline expression levels) with either Wrn mutant, PARP-1 null, or PARP-1 null/Wrn mutant cRNA. Hybridization experiments were done in duplicates.

first: Francois

last: Deschenes

first: Laurent

last: Massip

first: Chantal

last: Garand


title: Global transcriptional response of Bacillus subtilis to peroxide stress

city: Stanford

last: Stanford Microarray Database

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


title: Comparison of bovine gd and ab T cell clones

status: Public on Aug 23 2005

city: Pullman

first: Kevin

middle: Karl

last: Lahmers

state: WA

department: Veterinary Microbiology and Pathology

institute: Washington State University

summary:
Comparison of gd T cell clones with ab T cell clones that responded to the same antigen.  Clones were identically stimulated with ConA/IL-2 and analyzed with two separate microarrays.
Keywords: other

first: Jodi

last: Hedges

first: Mark

last: Jutila

first: Mingqi

last: Deng

first: Mitchell

last: Abrahamsen

first: Wendy

last: Brown


title: Gene expression profiling of Acute Promyelocytic Leukemia identifies two subtypes mainly associated with FLT3 ITD

status: Public on Oct 06 2005

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

summary:
In this series we described the gene expression profiles of 18 APL patients using a high density DNA-oligonucleotide microarray (Agilent) representing about 20.000 genes demonstrating the presence of a very uniform expression pattern of APL cases among which two mainly types of gene profiles were recognized by unsupervised analysis. Relationship between these two subgroups and the different clinical, haematological and molecular APL features, comprising FLT3 status,  were investigated.
To identify biologically meaningful subsets of APL, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer?s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP and Human Universal Reference (Stratagene) with 3-CTP in each experiment. Samples were hybridized on Agilent Human 1A Oligo Microarray (V2), ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features).
Fluorescence data were analysed with Feature Extraction Software v.7.5 (Agilent Technologies). Log10 ratio of the dye-normalized Cy3 and Cy5 channel signals were calculated. Raw signal intensities from each scan were imported into the gene expression analysis software Luminator (Rosetta Biosoftware). Two-dimensional clustering analysis was performed with Rosetta Luminator using an agglomerative algorithm with average link heuristics and correlation with mean subtraction. Supervised classification of APL samples into categories based on gene expression profiles was performed using Bayesian classifier implemented by Rosetta Biosoftware.
Resultant gene expression profiles were first analyzed using an unsupervised, agglomerative hierarchical clustering. The matrix view clearly evidenced the high grade of uniformity in gene expression pattern among APL patients being the majority of genes expressed at high (red colour) or low (green colour) levels relative to reference in all APL cases analyzed. This appearance of unsupervised matrix reflects the homogeneous nature of acute promyelocytic leukemia whose gene expression pattern definitely distinguishes it from all other types of acute myeloid leukemia.
Beside the homogeneous pattern, subtle differences in gene expression had the strength to distinguish three clusters of APL patients (designed I, II, III). Comparisons between cluster I and cluster II patients clearly revealed a preferential distribution of FLT3 gene mutated cases in cluster I. Again, cluster I was related to microgranular morphology (M3v) (p=0.035) and short-type PML-RAR isoform (bcr3) (p=0.044). Furthermore cluster I was significantly associated with higher presentation circulant blast cell percentage (p=0.030) as well as hyperleucocitosis (p=0.009).
To identify those genes distinguishing the FLT3-ITD leukemic cells from FLT3-WT, we applied a Bayesian classifier. 147 genes, significantly different among classes based on t-tests, were selected and included into the classifier. Among them, 92 genes were up-regulated in FLT3-ITD class and 55 were down-regulated. FLT3 internal tandem duplication gene expression signature consisted of several high expressed genes, among them we found genes that are involved in cytoskeleton organization, cell adhesion and migration, in proliferation and coagulation/inflammation pathways as well as down-regulated genes of myeloid granules and  differentiation suggesting a role of  FLT3 mutations in the pathogenesis and clinical manifestation of  an APL subtype.

SUPPLEMENTARY DATA:1) Anova gene list ITD, 2)Anova gene list M3 morphology, 3)Anova gene list PML/RARalpha isoforms (bcr), 4)Intersection gene list ITD_M3, 5) Intersection gene list ITD_bcr, 6)Intersection gene list M3_bcr, 7)Bayesian classifier gene list for FLT3-ITD vs FLT3-wt, 8)Bayesian classifier gene list for bcr1 vs bcr3
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Keywords = expression profiling
Keywords: other

first: Roberto

last: Marasca

first: Patrizia

last: Zucchini

first: Ilaria

last: Castelli

first: Alessia

last: Saviola

first: Silvia

last: Martinelli

first: Marcella

last: Fontana

first: Angela

last: Ferrari

first: Sara

last: Ravanetti

first: Giuseppe

last: Torelli


title: Tachyzoite to bradyzoite differentiation.

status: Public on Aug 13 2005

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
Asexual development in Toxoplasma gondii is a vital aspect of the parasite's life cycle, allowing transmission and avoidance of the host immune response. Differentiation of rapidly dividing tachyzoites into slowly growing, encysted bradyzoites involves significant changes in both physiology and morphology. We generated microarrays of 4,400 Toxoplasma cDNAs, representing a minimum of 600 genes (based on partial sequencing), and used these microarrays to study changes in transcript levels during tachyzoite-to-bradyzoite differentiation. This approach has allowed us to (i) determine expression profiles of previously described developmentally regulated genes, (ii) identify novel developmentally regulated genes, and (iii) identify distinct classes of genes based on the timing and magnitude of changes in transcript levels. Whereas microarray analysis typically involves comparisons of mRNA levels at different time points, we have developed a method to measure relative transcript abundance between genes at a given time point. This method was used to determine transcript levels in parasites prior to differentiation and to further classify bradyzoite-induced genes, thus allowing a more comprehensive view of changes in gene expression than is provided by standard expression profiles. Newly identified developmentally regulated genes include putative surface proteins (a SAG1-related protein, SRS9, and a mucin-domain containing protein), regulatory and metabolic enzymes (methionine aminopeptidase, oligopeptidase, aminotransferase, and glucose- 6-phosphate dehydrogenase homologues), and a subset of genes encoding secretory organelle proteins (MIC1, ROP1, ROP2, ROP4, GRA1, GRA5, and GRA8). This analysis permits the first in depth look at changes in gene expression during development of this complex protozoan parasite.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: User Defined

first: Michael

last: Cleary


title: Pancreatic cancer drug treatment study

status: Public on Aug 01 2005

city: Phoenix

first: Hong

last: Wang

state: AZ

address: 445 N 5th Street

department: Translational Drug Development Division

institute: Translational Genomics Research Institute

summary:
Wildtype DPC4 or empty vector expressed in pancreatic cancer BxPC-3 cell lines
Keywords: other

first: Haiyong

last: Han

first: Daniel

middle: D

last: Von Hoff


title: Effect of inhaled anesthetic to cultured cortical neurons

status: Public on Jul 23 2005

city: Philadelphia

first: Roderic

last: Eckenhoff

state: PA

institute: University of Pennsylvania

summary:
Inhaled anesthetics produce many effects and bind to a large number of brain proteins, but it is not yet clear if this is accompanied by widespread changes in gene expression of the biological targets.  Such changes in expression might implicate functionally important targets from the large pool of binding targets. Isolated primary cortical neurons were exposed to anesthetics and DNA oligonucleotide microarrays were used to detect and quantify transcriptional changes in neuronal tissue.
Keywords: DNA Oligonucleotide Array

overall_design: Primary cortical neurons were treated with 1MAC, 3MAC Halothane and 3MAC Isoflurane, together with no drug control. Pool no drug control was used as Cy3 channel in all chips. The above drug treated and individual control samples were used in Cy5 channel.

first: Jonathan

middle: Z

last: Pan

first: Huafeng

last: Wei

first: James

last: Hecker

first: John

middle: W

last: Tobias

first: Maryellen


title: PPAR-gamma-activating Angiotensin Type 1 Receptor Blockers

status: Public on Apr 05 2005

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary:
expression pattern of adipocytes after telmisartan, pioglitazone or irbesartan treatment
Keywords: repeat sample

last: Schupp

first: Markus

last: Clemenz

first: Patricia

last: Ruiz

first: Ulrich

last: Kintscher


title: B-cell chronic lymphocytic leukemia gene expression profiles

status: Public on Feb 25 2006

first: Rossana

last: Maffei

summary:
B-cell chronic lymphocytic leukemia (B-CLL) shows an incredibly high heterogeneity in the clinical course, spanning from rapidly aggressive to completely indolent behaviour. In order to identify the correspondent gene expression variability, we investigated 29 cases of untreated B-CLL using microarray. Firstly, two robust CLL clusters were identified applying multiple unsupervised clustering algorithms. Their separation was mainly determined by the differential expression of several genes included into two gene groups designated OxPhos and Lyn clusters. OxPhos gene cluster, previously identified in a subset of diffuse large B-cell lymphomas, comprises genes coding  for some respiratory chain enzymes, ribosomal proteins and translation factors. Moreover, increased levels of genes involved in the regulation of apoptosis and in the proteasome-ubiquitin complex and the down-regulation of LYN gene, member of B-cell receptor pathway, characterized the OxPhos CLL subset. These B-CLL biological clusters did not reveal any preferential distribution of Ig mutated or Ig unmutated CLL prognostic groups. Furthermore, we applied another unsupervised algorithm (Subtractive Unsupervised Analysis) after the exclusion of genes characterizing the previously identified CLL subsets.  At this point, we could identify two new CLL clusters, showing a clear association to the Ig mutational status. In addition to the ZAP-70 and LPL genes, the patients with unmutated Ig expressed higher level of some interesting genes involved in B cell activation, cell cycle regulation, apoptosis resistance and angiogenesis. In conclusion,  we showed that B-CLL is characterized by an intrinsic heterogeneity in gene expression pattern, which overcomes the influence of the immunoglobulin mutational status on B-cell chronic lymphocytic leukemia profiles.
Keywords: chronic lymphocytic leukemia, gene expressione profile, immunuglobulin mutational status, clinical heterogeneity

overall_design:
Twenty-nine B-CLL patients, who have attended the haematology clinic of Modena Hospital, were enrolled in this study. Total RNA from mononuclear cells was isolated using RNeasy Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer’s instructions For all 29 specimens, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA) according to the manufacturer’s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Moreover, cRNA products were purified using RNeasy columns (Qiagen). 1 ug of Cy5-labelled cRNA was mixed with the same amount of Cy3-labelled reference cRNA and then mixed cRNAs were fragmented to an average size of ~50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized on Agilent Human 1A Oligo Microarray, ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features).33 After hybridization for 17 h at 60°C, slides were washed according to Agilent SSC protocol instructions and then scanned using a confocal laser scanner (Agilent Technologies).
Fluorescence data were analysed with Feature Extraction Software v.7.5 (Agilent Technologies). Log10 ratio of the dye-normalized Cy3 and Cy5 channel signals were calculated, then a p-value and a final error were obtained to establish the significance of each feature.

first: Roberto

last: Marasca

first: Patrizia

last: Zucchini

first: Ilaria

last: Castelli

first: Marcella

last: Fontana

first: Silvia

last: Martinelli

first: Elena

last: Morandi

first: Cinzia

last: Severini

first: Alessandro

last: Semeria

first: Paola

last: Silingardi

first: Angela

last: Ferrari

first: Rita

last: Santachiara

first: Annamaria

last: Colacci

first: Monica

last: Morselli

last: Serra


title: Differential regional gene expression from cardiac dyssynchrony

status: Public on Nov 03 2005

city: Germantown

first: Will

last: Ferguson

state: MD

department: Integrated Biology Solutions

institute: Agilent Technologies

summary:
Right ventricular free wall (RVFW) pacing results in left ventricular dyssynchrony with early septal shortening followed by late lateral contraction that reciprocally stretches the septum.  Dyssynchrony is disadvantageous to cardiac mechano-energetics, yet little is known about its molecular consequences.  We tested the hypothesis that dyssynchrony selectively alters regional gene expression in mice, employing a novel miniature implantable cardiac pacemaker.  Mice were subjected to 1-week overdrive RVFW pacing (720 min-1, baseline HR 520-620 min-1) to induce dyssynchrony  (pacemaker: 3V lithium battery, rate programmable, 0.8 grams, bipolar lead).  Electrical capture was confirmed by pulsed-wave Doppler at implantation and terminal study, and dyssynchrony by echocardiography.  Gene expression from left ventricular septal and lateral-wall myocardium were assessed by microarray (dual-dye method, Agilent) using oligonucleotide probes and dye swap.  Identical analysis was applied to 4 synchronously contracting controls.  Of 22,000 genes surveyed, only 18 genes displayed significant (p<0.01) differential expression between septal/lateral walls  exceeding 1.5-fold relative to any disparities in synchronous controls.  These changes were confirmed by qPCR with excellent correlations. Most (16) of the genes showed greater septal expression.  Of particular interest were 7 genes coding proteins involved with stretch responses, matrix remodeling, stem cell differentiation to myocyte lineage, and Purkinje fiber differentiation.  One-week cardiac dyssynchrony triggers regional differential expression differences in relatively few select genes.  Such analysis using a murine implantable pacemaker should facilitate molecular studies of cardiac dyssynchrony and help elucidate novel mechanisms by which stress/stretch stimuli due to dyssynchrony impact the normal and failing heart.
Keywords: Murine cardiac dyssynchrony and differential gene expression, Agilent, microarray, pacing

overall_design: Left ventricle segments from the mouse heart  - septal and lateral, were isolated from 4 dyssynchronous mice that were kept separate. RNA from the synchronous mice were pooled into a control septal and lateral sample.  Functional genomic analysis was conducted on these 10 RNA samples with fluorophore reversal, such that each sample was assayed on two different microarrays.  Corresponding septal and lateral samples from the same heart were paired on the same microarray to measure the relative differences in gene expression between the different regions of the heart then differences were compared across multiple mice to find overlapping genes that were affected by the pacememaker implantation.

first: Kenneth

last: Bilchick

first: Sudip

middle: K

last: Saha

first: Ed

last: Mikolajczyk

first: Leslie

last: Cope

first: Wayne

last: Yu

first: Steven

last: Girouard

first: David

middle: A

last: Kass


title: parous and AMV mammary gland before and after MNU treatment

status: Public on Jul 31 2005

city: Osaka

first: Norihisa

last: Uehara

institute: Kansai Medical University

summary:
Early full-term pregnancy affords lifetime protection against development of breast cancer. Parity-induced protection can be reproduced in a carcinogen-induced rat mammary carcinoma model. The molecular mechanisms of parity-induced protection against carcinogenic stimuli in rat mammary glands have not been fully characterized. In order to gain a better understanding of these molecular mechanisms, we performed gene expression analyses in parous and age-matched virgin (AMV) mammary glands of Lewis rats before and after carcinogen (N-methyl-N-nitrosourea; MNU) treatment.

Keywords: other

first: Akira

last: Unami

first: Yasuhiko

last: Kiyozuka

first: Nobuaki

last: Shikata

first: Yuji

last: Oishi

first: Airo

last: Tsubura


title: Human coronary artery study

status: Public on Jun 30 2005

city: Palo Alto

first: Jennifer

last: King

state: CA

department: Cardiovascular Medicine

institute: Stanford University

summary:
Study of atherosclerosis using 51 human coronary artery segments
Keywords: other


title: Testicular germ cell tumors and their histological subgroups

status: Public on Jul 01 2005

city: Oslo

first: Rolf

middle: I

last: Skotheim

department: Department of Cancer Prevention

institute: Rikshospitalet-Radiumhospitalet Medical Center, Institute for Cancer Research

summary:
Normal, premalignant and various histological subtypes of testicular germ cell tumor (TGCT) tissues were hybridized against Universal Human Reference RNA (Stratagene) onto Agilent 60mer oligo microarrays (GEO accession no GPL885). In vitro time series of two TGCT cell lines, NTERA2 and 2102Ep, treated with retinoic acid for 0, 3, and 7 days were also included. The data set (30 hybridizations) is particularly useful for comparisons between various histological subtypes of TGCT versus each other or versus normal testis.
Keywords = 2102Ep
Keywords = Agilent oligo microarrays
Keywords = carcinoma in situ
Keywords = choriocarcinoma
Keywords = development
Keywords = developmental biology
Keywords = differenciation
Keywords = embryogenesis
Keywords = embryonal carcinoma
Keywords = homo sapiens
Keywords = human
Keywords = human development
Keywords = intratubular germ cell tumor
Keywords = nonseminoma
Keywords = NTera2
Keywords = pluripotency
Keywords = pluripotent
Keywords = retinoic acid
Keywords = seminoma
Keywords = teratocarcinoma
Keywords = teratoma
Keywords = testis
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = totipotency
Keywords = totipotent
Keywords = undifferentiated
Keywords = universal human reference RNA (Stratagene)
Keywords = yolk sac tumor
Keywords: other

first: Guro

middle: E

last: Lind

first: Outi

last: Monni

first: Jahn

middle: M

last: Nesland

first: Vera

last: Abeler

first: Sophie

last: Fosså

first: Nur

last: Duale

first: Gunnar

last: Brunborg

first: Olli

last: Kallioniemi

first: Peter

last: Andrews

first: Ragnhild

last: Lothe


title: Global analysis of mRNA decay and abundance in Escherichia coli

status: Public on Mar 07 2006

last: Stanford Microarray Database

department: Stanford University, School of Medicine

summary:
Abstract: Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the approximately 4,300 predicted E. coli messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of E. coli, although approximately 80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in E. coli, nor the free energy of folding of 5' or 3' untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability.

This SuperSeries is composed of the SubSeries listed below.


title: Germination and appressorium formation in Magnaporthe grisea

status: Public on Nov 10 2004

city: Raleigh

first: Ralph

last: Dean

state: NC

institute: CIFR, North Carolina State University

summary:
This series examines differential gene expression during germination and appressorium formation by the rice blast fungus Magnaporthe grisea.  Conidia were germinated on either the hydrophobic (inductive) or hydrophilic (non-inductive) side of GelBond.  RNA was extracted from conidia and following incubation for 7 and 12 hours.  RNA from two biological replications of each treatment was pooled in equal amounts and labeled with both cy3 and cy5 dyes using the Agilent Technologies Low Input Linear Amplification Kit.  Hybridizations were performed on Agilent Technologies whole genome oligo rice blast arrays (product G4137A) using manufacturer prescribed protocols and reagents in an interlaced loop design in which each treatment was paired with every other.  This series contains a total of 10 hybridizations; each treatment was used in 4 hybridizations (2 with cy3 and 2 cy5).  Spot fluorescence was normalized using Lowess within and between microarray slides in Bioconductor and gene expression profiles analyzed in GeneSpring.
Keywords: other

first: Yeon Yee

last: Oh

first: Nicole

last: Donofrio

first: Huaqin

last: Pan

first: Sean

last: Coughlan

first: Thomas

last: Mitchell


title: Hepatic Gene Expression Changes Throughout the Day in the Fischer Rat

status: Public on Apr 15 2005

city: RTP

first: Gary

last: Boorman

department: Division of Intramural Research Environmental Toxicology Program

institute: NIEHS

summary:
One µg of total RNA from either an
individual rat or from a pooled sample was amplified and labeled with a
fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol. The amount and quality of the resulting fluorescently labeled cRNA was assessed using a Nanodrop ND-100 spectrophometer and an Agilent
Bioanalyzer. Equal amounts of Cy3- or Cy5-labeled cRNA were hybridized to the Agilent Rat Oligo Microarray (Agilent Technologies, Inc., Palo Alto, CA) for 17 hrs, prior to washing and scanning. Data was extracted from the resulting
images using Agilent’s Feature Extraction Software (Agilent Technologies, Inc., Palo Alto, CA). For day/night comparisons, two types of complementing hybridizations were performed: hepatic RNA from individual day rats was hybridized against a pool made up of RNA from 12 hour offset night rats, and RNA from individual night rats was hybridized against a pool made up of RNA from 12-hour offset day rats.

Specifically, hepatic RNA samples from three individual day rats collected ten hours after light on (CT10) were hybridized against a pooled RNA sample composed of equal aliquots of RNA from the livers of six night rats collected ten hrs after lights off (CT22); and RNA samples from three individual night rats collected at CT22 were hybridized against a pooled RNA sample composed of equal aliquots of RNA from the livers of six day rats collected at CT10. This was replicated in a second study for a total of 24 hybridizations of 12 hour offset samples.

For time of day comparisons, equal aliquots of RNA from the livers of six
rats collected at each of four different times of the circadian day (CT4, CT10, C16 and CT22) were pooled. The two replicate studies thus resulted in 8 pools (two replicate pools/time point times four time points); each pool was hybridized against a Universal Rat Reference RNA Standard (Stratagene, La Jolla, CA).
Keywords: time-course

first: Pamela

last: Blackshear

first: Joel

last: Parker

first: Edward

last: Lobenhofer

first: David

last: Malarkey

first: Molly

last: Vallant

first: Diane

last: Gerken

first: Richard

last: Irwin