title: Acetaminophen (APAP) Rat Blood Test Gene Expression Data Set

summary:
Gene expression test data set from rat blood samples exposed to either 150, 1500 or 2000 mg/kg of APAP for 3, 6 or 24 hours.

The Supplementary file (appended below) contains the mapping for the decoding of blinded samples.
Keywords: Dose response, Time course, Microarray, Gene expression

overall_design:
Male F344/N rats, 10-12 weeks old, were exposed to 0 (vehicle only), 150, 1500 or 2000 mg/kg APAP in 0.5% ethyl cellulose by oral gavage in two doses to increase absorption. The animals were sacrificed after 3, 6, or 24 hours. Equal amounts of RNA from the blood from each of six vehicle-only treated control animals were pooled at each time point and compared to individual control and treated animals at each dose and time period.  The samples were hybridized in duplicate for each individual rat for a total of 12 (test set) microarray chips per dose and time period.

Experiments were performed according to the guidelines established in the NIH Guide for the Care and Use of Laboratory Animals and an approved Animal Study Protocol was on file prior to initiation of the study.


title: Gene expression in the Antarctic fish Trematomus bernacchii shows a muted response to heat stress

status: Public on Dec 14 2007

city: Portland

first: Brad

last: Buckley

state: OR

address: 1719 SW 10th Ave

department: Biology

country: USA

institute: Portland State University

summary:
The goal of this study was to measure the effect of heat stress on the transcriptome of a cold-adapted fish (Trematomus bernacchii) and compare it to a temperate species (Gillichthys mirabilis).

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Gillichthys mirabilis
Trematomus bernacchii

overall_design:
In the first experiment (Gillichthys mirabilis), three control fish are compared to three heat-shocked fish.

In the second experiment (Trematomus bernacchii), three control fish are compared to 3 heat-shocked fish, 3 short-term recovery fish and 3 longer term recovery fish.

first: Bradley

middle: A

first: George

middle: N

last: Somero


title: Phenotypically concordant and discordant monozygotic twins display different DNA copy number variation profiles

status: Public on Dec 11 2007

city: Birmingham

first: Jan

middle: P

last: Dumanski

state: AL

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Blood and liver exposed to acetaminophen (APAP)

status: Public on Sep 19 2007

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

summary:
The Supplementary files (appended below) contain the mapping for the decoding of blinded samples.

This SuperSeries is composed of the SubSeries listed below.


title: Ras Affects Filamentous Growth in Saccharomyces cerevisiae Solely Through Regulation of Protein Kinase A

status: Public on Aug 18 2007

city: Princeton

first: Cemile

middle: Gokce

last: Guldal

state: NJ

address: Washington Road, Lewis Thomas Lab

department: Molecular Biology

institute: Princeton University

summary:
To assess the relative contributions of the PKA and MAPK pathways in Ras stimulation of filamentation, we examined the change in transcriptional profile following activation of Ras in strains in which one of these two pathways has been severed. These arrays contain the experiments involving WT strain with glucose addition, Ras2G19V strain with galactose induction, tpk2-w strain as a control, and RasG19V activation in the tpk2-w background. Activation of Ras in the Σ1278b background – by galactose addition to a gal1 PGAL10-RAS2G19V strain - causes a massive restructuring of the transcription pattern of the cell, which closely resembles the changes induced by addition of glucose. To assess the extent to which these Ras-induced changes depended on signaling through PKA, we compared the expression profile following induction of activated Ras in a wild type background to that following induction of activated Ras in the bcy1 tpk1 tpk3 tpk2V218G.
Keywords: time course

overall_design: RNA from strains grown as described was extracted using the RNeasy Mini Kit (Qiagen, California, USA) with mechanical disruption. RNA labeling and hybridization to Agilent oligonucleotide microarrays were done according to manufacturer’s instructions (Agilent Technologies, California, USA). RNA and cRNA concentrations were measured with NanoDrop (NanoDrop Technologies, Delaware, USA). 250ng labeled cRNA was used for each hybridization. The zero minute time point samples were labeled with Cy3 and others with Cy5. At least two technical replicates of each hybridization were performed. Hybridized microarrays were scanned with Agilent Microarray Scanner G2505B and the images were prepared for data analysis with Feature Extraction Software version 7.5 (Agilent Technologies, California, USA). Data were filtered and analyzed using PUMAdb based on the Stanford Microarray Database package.

middle: G

first: Holly

middle: K

last: Koblish

first: Lisa

last: Schneper

first: Ying

last: Wang

first: Corey

last: Davis

first: James

middle: R

last: Broach


title: Genome-wide gene expression profile analysis of MCL1 over-expressing B-NHL cells

status: Public on Aug 23 2007

city: Madrid

first: Antonio

last: Ruiz-Vela

state: Madrid

address: Melchor Fernández Almagro

country: Spain

institute: CNIO

summary:
To get insight into the mechanisms of MCL1-induced survival and transformation, we screened 41,000 human genes in a genome-wide gene expression profile analysis of MCL1 over-expressing B-NHL cells.
Keywords: MCL1-induced gene expression

overall_design: Two-color (Cy5-CTP/ Cy3-CTP) microarray-based gene expression formats presenting high-density oligonucleotide probes printed on a single glass slide were used (Agilent technologies, Cat No# G4112A whole human genome 41K). Total RNAs from MCL1 over-expressing RAMOS RA-1 and Z-138 B-cells were labeled with Cy5-CTP, whereas RNAs from references (empty vector/ RAMOS RA-1 and empty vector/ Z-138 B-cells) were labeled with Cy3-CTP. After competitive hybridization [RNA-Cy5 from MCL1 over-expressing RAMOS RA-1 or MCL1 over-expressing Z-138 versus RNA-Cy3 from either empty vector/ RAMOS RA-1 or empty vector/ Z-138 respectively] gene expression data were pre-processed using Feature Extraction software and GEPAS tools (http://gepas.bioinfo.cipf.es/).

last: Piris

first: Orlando

last: Dominguez

first: Paloma

last: de la Cueva


title: Distinct ErbB-2-coupled signalling pathways promote mammary tumors with unique pathological and transcriptional profiles

status: Public on Aug 15 2007

city: Montreal

first: Daniela

last: Cernea

state: Quebec

address: 3775 University Street, Room 332

department: Computer Science

country: Canada

institute: McGill

summary:
ErbB-2 overexpression and amplification occurs in 15 - 30% of human invasive breast  carcinomas associated with poor clinical prognosis. Previously, we have demonstrated that four  ErbB-2/Neu tyrosine-autophosphorylation sites within the cytoplasmic tail of the receptor recruit  distinct adaptor proteins and are sufficient to mediate transforming signals in vitro. Two of these  sites representing the Grb2 (Neu-YB) and Shc (Neu-YD) binding sites can induce mammary  tumourigenesis and metastasis. Here we show that Neu-YC and Neu-YE transgenic mice develop  metastatic mammary tumours. A detailed comparison of pathological and transcriptional profiles  among all Neu mutant mouse models revealed that Neu-YC, -YD and -YE mammary tumours  shared similar pathological and transcriptional features correlating with their capacity to signal  through a common adaptor like Shc. In contrast, the Neu-YB mouse model displayed a unique  pathology with a high metastatic potential that correlates with a distinct transcriptional profile.  We identified genes specifically expressed in YB-induced mammary tumours, including  CXCL12/SDF-1α that promotes malignant tumour progression. Furthermore, Neu-YB tumour  epithelial cells showed abundant intracellular CXCL12/SDF-1α protein, which may reflect the  more aggressive phenotype among all Neu mutant mouse models. These findings indicate that  activation of distinct Neu-coupled signalling pathways has a deep impact on the biological  behaviour of Neu-induced tumours.
Keywords: genetic modification, Neu mutant mouse models, mammary tumor

overall_design: Total RNA was isolated from 10 individual flash frozen mammary tumour samples  derived from our MMTV/neundl-NYPD, -YB, -YC, -YD, -YE and the parental MMTV/neu  NDL2-5 strains. Two RNA pools, containing equal  amount of total RNA from five individual tumours, were generated from each strain and  functioned as a biological repeat. Five hundred nanograms of total RNA from each pool was  subjected to one round of T7 linear amplification using the Amino Allyl MessageAmpTM aRNA  Kit (Ambion, Austin, Texas). Ten micrograms of the resulting aRNA was labelled with Cy3 and  Cy5 dyes.  Each of the 12 Samples represents a dyeswap pair.

first: Babette

last: Schade

first: Sonya

middle: H

last: Lam

first: Virginie

last: Sanguin-Gendreau

first: Robert

middle: D

last: Cardiff

first: Boonim

middle: L

last: Jung

first: Michael

last: Hallett

first: William

middle: J

last: Muller


title: Coordination of Growth Rate, Cell Cycle, Stress Response and Metabolic Activity in Yeast

status: Public on Aug 21 2007

first: John

middle: Charles

last: Matese

address: Washington Rd.

department: Lewis-Sigler Institute

summary:
We studied the relation between growth rate and genomewide gene expression, cell cycle progression, and glucose metabolism in 36 steady state continuous cultures limited by one of six different nutrients (glucose, ammonium, sulfate, phosphate, uracil or leucine).  The expression of more than a quarter of all yeast genes is linearly correlated with growth rate, independently of the limiting nutrient.  The subset of negatively growth-correlated genes is most enriched for peroxisomal functions, whereas positively correlated genes mainly encode ribosomal functions.  Many (not all) genes associated with stress response are strongly correlated with growth rate, as are genes that are periodically expressed under conditions of metabolic cycling.  We confirmed a linear relationship between growth rate and the fraction of the cell population in the G0/G1 cell cycle phase, independent of limiting nutrient.  Cultures limited by auxotrophic requirements wasted excess glucose, whereas those limited on phosphate, sulfate or ammonia did not; this phenomenon (reminiscent of the "Warburg effect" in cancer cells) was confirmed in batch cultures.  Using an aggregate of gene expression values, we predict (in both continuous and batch cultures) an "instantaneous growth rate".  This concept is useful in interpreting the systemlevel connections among growth rate, metabolism, stress and the cell cycle.
Keywords: growth condition design

overall_design: Yeast cultures were grown in chemostats under 36 different continuous culture conditions, namely six different limiting nutrients (glucose, ammonia, sulfate, phosphate, uracil, or leucine) each at six different dilution rates. The dilution rates (and therefore the culture's average exponential growth rate μ) ranged from about 0.05hr-1 (corresponding to a cell doubling time of about 14hr) to more than 0.3hr-1 (doubling time of about 2hr).

first: Matthew

last: Brauer

first: Curtis

last: Huttenhower

first: Edoardo

middle: M

last: Airoldi

first: Rachel

last: Rosenstein

middle: C

first: David

last: Gresham

first: Viktor

last: Boer

first: Olga

last: Troyanskaya

last: Botstein


title: Rice plants infested with planthoppers

city: Koshi

first: Masaru

last: Satoh

state: Kumamoto

country: Japan

institute: National Agricultural Research Center for Kyushu Okinawa Region

summary:
Infestation with white-backed planthopper (WBPH) to rice caused induced resistance to rice pathogens but brown planthopper (BPH) infestation induce weaker resistance to rice pathogens. We compared changes in gene expression in rice plants infested with WBPH and BPH to gain some insight into the WBPH-induced resistance to rice pathogens.
An analysis, using microarrays, of gene expression in rice plants infested with these planthoppers revealed that WBPH infestation caused high induction of many defense-related genes including pathogenesis-related (PR) genes than BPH infestation. Furthermore, hydroperoxide lyase 2 (OsHPL2) which is an enzyme to produce C6 volatiles was induced by WBPH infestation, but not by BPH infestation.
Keywords: response to herbivory; induced resistance

overall_design: Agilent rice oligo microarray was used to investigate the gene expression profiling in rice plants infested with WBPH or BPH. Total RNA was extracted from pooled leaf blades infested with WBPH or BPH for 24 h and from mock-treated pooled leaf blades. Total RNA (200 ng) was labeled with Cy-3 or Cy-5 using an Agilent low RNA input linear amplification kit. Fluorescently labeled targets were hybridized to Agilent rice oligo microarrays. Hybridization and wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent DNA microarray scanner. Agilent Feature Extraction software was employed for the image analysis and data extraction processes. Fold changes in expression level in each treatment were compared with those of the respective mock-treated controls. In each treatment, the experiment was performed independently three times.

first: Kenji

last: Gomi

first: Yuko

last: Ohashi

first: Junji

last: Takabayashi


title: Molecular Characterization of the Human and Mouse Parotid Gland

status: Public on Aug 13 2007

city: Rochester

first: Alaka

last: Srivastava

state: NY

address: 601 Elmwood Avenue

department: Oral Biology

institute: University of Rochester Medical Center

summary:
Gene expression of 4 human parotid gland samples were comapred with 4 mouse parotid gland samples.
Keywords: Comparative Gene Expression

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human and mouse parotid gland gene expression was screened using custom-designed targeted cDNA containing probes for 198 genes which encode for ion/water transporter (75 genes) and receptor/regulatory (101 genes) proteins potentially involved in the fluid secretion mechanism, as well as 11 secretory protein genes and 11 control genes

first: James

middle: E

last: Melvin


title: Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains

city: Albany

first: Robert

last: Osuna

address: 1400 Washington Avenue

institute: University at Albany


title: Identity of the human cancer cell DNA hypermethylome revealed by gene expression profiling

status: Public on Aug 08 2007

city: Baltimore

first: Wayne

last: Yu

state: MD

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

summary:
Altered gene expression is a hallmark of human cancers and arises in part through abnormal epigenetic regulation of gene transcription. The best characterized epigenetic alteration involves tumor suppressor gene inactivation via transcriptional repression associated with aberrant DNA hypermethylation of promoter region CpG islands1. Despite characterization of a growing number of such genes, the majority have yet to be identified.  We now describe a genome wide microarray gene expression approach for human colorectal cancer cells, which can efficiently identify hundreds of hypermethylated genes for any cancer type. We compared isogenic cells altered pharmacologically versus genetically to induce genomic demethylation, to pinpoint genes activated by DNA demethylation, but not by inhibition of class I and II histone deacetylases (HDACs).  We achieve an 82% success rate in predicting genes with densely hypermethylated CpG islands and complete gene silencing. The genes are similarly hypermethylated in primary tumors and have previously undetected tumor suppressor functions.  Our approach provides the first highly efficient, comprehensive, platform for defining the cancer “DNA hypermethylome"
Keywords: gene expression profiling of pharmacological and genetic human cancer cells

overall_design:
Cell culture and treatment.  HCT116 cells and isogenic genetic knockout derivatives were maintained as previously described14. For drug treatments, log phase HCT116 cells were cultured in McCoys 5A media (Invitrogen) containing 10% BCS and 1x penicillin/streptomycin with 5 uM 5aza-deoxycytidine (DAC) (Sigma; stock solution: 1mM in PBS) for 96 hours, replacing media and DAC every 24 hours.  Cell treatment with 300nM Trichostatin A (Sigma; stock solution: 1.5mM dissolved in ethanol) was performed for 18 hours. Control cells underwent mock treatment in parallel with addition of equal volume of PBS or ethanol without drugs.
Microarray analysis.  Total RNA was harvested from log phase cells using the Qiagen kit according to the manufacturers instructions, including a DNAase step.  RNA was quantified using the NanoDrop ND-100 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies).  RNA concentrations for individual samples were greater than 200ng/ul, with 28s/18s ratios greater than 2.2 and RNA integrity numbers of 10 (highest).  Sample amplification and labeling procedures were carried out using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturers instructions.  The labeled cRNA was purified using the RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification.  0.75 microgram of samples labeled with Cy3 or Cy5 were mixed with control targets (Agilent Technologies), assembled on Oligo Microarray, hybridized, and processed according to the Agilent microarray protocol.  Scanning was performed with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies.
Data analysis. All arrays were subject to quality checks recommended by the manufacturer.  Images were visually inspected for artifacts and distributions of signal and background intensity of both red and green channels were examined to identify anomalous arrays.  No irregularities were observed, and all arrays were retained and used.  All calculations were performed using the R statistical computing platform37 and packages from Bioconductor bioinformatics software project38.  The log ratio of red signal to green signal was calculated after background-subtraction and LoEss normalization as implemented in the limma package from Bioconductor39,40. Individual arrays were scaled to have the same inter-quartile range (75th percentile -25th percentile) Log fold changes were averaged over dye-swap replicate microarrays to produce a single set of expression values for each condition.

first: Kornel

last: Schuebel

first: Wei

last: Chen

first: Leslie

last: Cope

first: Steve

middle: B

last: Baylin


title: SuperSeries for the study of expression analysis of the T. thermophilus CRP (TTHA1437)

status: Public on Aug 05 2007

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute


title: Identification of Primary Transcriptional Regulation of Cell-Cycle-Regulated Genes upon DNA Damage

status: Public on Aug 01 2007

city: Morrisville

first: Tong

last: Zhou

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

institute: Gentris Corperation

summary:
The changes in global gene expression in response to DNA damage may derive from either direct induction or repression by transcriptional regulation or indirectly by synchronization of cells to specific cell cycle phases, such as G1 or G2.  We developed a model that successfully estimated the expression levels of >400 cell-cycle-regulated genes in normal human fibroblasts based on the proportions of cells in each phase of the cell cycle. By isolating effects on the gene expression associated with the cell cycle phase redistribution after genotoxin treatment, the direct transcriptional target genes were distinguished from genes for which expression changed secondary to cell synchronization. Application of this model to ionizing radiation (IR)-treated normal human fibroblasts identified 150 of 406 cycle-regulated genes as putative direct transcriptional targets of IR-induced DNA damage. Changes in expression of these genes after IR treatment derived from both direct transcriptional regulation and cell cycle synchronization.
Keywords: Microarray, Cell cycle, Ionizing radiation, Human fibroblasts, EPIG

overall_design: Normal human fibroblasts were synchronized and harvested at G0, G1, S G2 and M cell cycle phase, and logarithmically growing cells were treated with 1.5 Gy IR or sham, and harvested at 2, 6 or 24 h after the treatment. Total RNA was isolated using Qiagen RNeasy kit. The quality of all RNA samples was confirmed using an Agilent 2100 Bioanalyzer. Microarray analysis was then performed: briefly, 1 µg of sample RNA and global reference RNA (Stratagene) were converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with either Cy3-dUTP or Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization. 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven (Robbins Scientific Model 400, 1040-60-1AG) at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap. Following hybridization, the arrays were scanned using the Agilent DNA Microarray Scanner with SureScan® Technology and microarray images were analyzed using Agilent Feature Extraction Software (v7.1). The gene expression level was presented as ratio of sample intensity against reference intensity.

first: Jeff

last: Chou

first: Thomas

last: Mullen

first: Yingchun

first: William

last: Kaufmann


title: Effects of renal ischemia on angiogenic gene expression

city: Indianapolis

first: David

last: Basile

state: IN

address: 635 Barnhill Drive

department: Cellular & Integrative Physiology

institute: Indiana University


title: Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes

status: Public on Aug 29 2007

city: Vienna

first: J. Andrew

last: Pospisilik

address: Dr. Bohr-gasse 3

country: Austria

institute: IMBA


title: Yeast carbon source comparison

status: Public on Aug 22 2007

city: Hattiesburg

first: Kellie

last: Barbara

state: MS

address: 118 College Dr. #5018

department: Biological Sciences

institute: Univ. of Southern MS

summary:
This experiment compares the transcriptional profiles of a WT yeast strain grown in either 2% glucose or 3% pyruvate.  The goal was to identify genes whose expression is either induced or repressed by glucose (catabolite repression).
Keywords: nutrient response

overall_design: This experiment used dye-swap replicates.


title: Comparison of expression in Arabidopsis mutant tdt-1 and wild type

status: Public on Jul 31 2007

city: Salt Lake City

last: Goeres

state: UT

institute: University of Utah

summary:
The object of this study was to explore whether the loss of mRNA decapping in the Arabidopsis mutant tdt-1 resulted in global dfferences of RNA profiles, as compared to wild type.
Keywords: Genetic modification affect on gene expression

overall_design: In this experiment we compared expression in tdt-1 and wild type 3 day whole seedlings.  We performed three biological replicates, in which one experiment was dye-swapped.

last: Sieburth

first: Brian

last: Dalley

first: Brett

last: Milash


title: Ductal and lobular breast carcinomas in situ array CGH

status: Public on Jul 27 2007

city: Cambridge

first: Mitchell

last: Guttman

state: MA

address: 7 Cambridge Center

institute: Broad Institute


title: Genomic integrity of P493 cells

first: Jonathan

last: Pevsner

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

summary:
We compared the genomic integrity of human P493 cells grown in vitro with those recovered from xenografts of P493 cells.
Keywords: single nucleotide polymorphism, array comparative genomic hybridization

overall_design: We used control, parental P493 cell lines (P493-parent and P493-luc expressing a luciferase construct for array CGH; P493-TR with tetracycline resistance for the SNP assays) and compared them to P493 cells recovered from xenografts.


title: Defective cell cycle checkpoint functions in melanoma are associated with altered patterns of gene expression

status: Public on Jul 01 2007

summary:
Defects in DNA damage responses may underlie genetic instability and malignant progression in melanoma. Cultures of normal human melanocytes (NHMs) and melanoma lines were analyzed to determine whether global patterns of gene expression could predict the efficacy of DNA damage cell cycle checkpoints that arrest growth and suppress genetic instability.  NHMs displayed effective G1 and G2 checkpoint responses to ionizing radiation-induced DNA damage. A majority of melanoma cell lines (11/16) displayed significant quantitative defects in one or both checkpoints. Melanomas with B-RAF mutations as a class displayed a significant defect in DNA damage G2 checkpoint function. In contrast the epithelial-like subtype of melanomas with wildtype N-RAS and B-RAF alleles displayed an effective G2 checkpoint but a significant defect in G1 checkpoint function. RNA expression profiling revealed that melanoma lines with defects in the DNA damage G1 checkpoint displayed reduced expression of p53 transcriptional targets, such as CDKN1A and DDB2, and enhanced expression of proliferation-associated genes, such as CDC7 and GEMININ. A Bayesian analysis tool was more accurate than significance analysis of microarrays for predicting checkpoint function using a leave-one-out method. The results suggest that defects in DNA damage checkpoints may be recognized in melanomas through analysis of gene expression.
Keywords: Melanoma, checkpoint, microarry

overall_design: Normal human melanocyte and melanoma cell lines w/wo mutations in B-raf or N-ras were treated with 1.5 Gy IR irridiartion for G1 and G2 checkpoint determination. RNA was isolated from exponentially growing cultures and applied for microarray hybridizaton with Agilent 44 K (G4112A) array.

first: Norman

last: Sharpless


title: Profiling of mucosal derived bovine ab and gd T cells during Salmonella enterica serovar typhimurium enterocolitis

status: Public on Jun 30 2007

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

summary:
gd T cells have an important yet incompletely defined role in inflammation associated with a variety of infectious and autoimmune conditions.  To better understand the precise roles of gd T cells relative to ab T cells in a specific infection, we utilized Salmonella Enterica Serovar Typhimurium (S. typhimurium) infection in cattle as it is a leading cause of disease in cattle and closely approximates S. typhimurium-induced enterocolitis in humans.  To best represent phenotype and gene expression changes occurring in the gut mucosa early in S. typhimurium infection, gd and ab T cells were collected directly from the mesenteric lymphatic ducts and analyzed by FACS or immediately sorted and processed for microarray analysis.  Gene expression profiles were compared at intervals during infection within T cell subsets.  The majority of gene expression changes in both subsets occurred 48 hours after infection.  In response to S. typhimurium infection there was an increase in expression of several genes in gd T cells which were indicative of activation, proliferation and innate function, whereas in ab T cells gene expression changes suggested a lack of S. typhimurium-specific response.  This work represents the first focus on gene expression trends in tissue-derived T lymphocytes in an in vivo model that is highly relevant to human S. typhimurium-induced enterocolitis.
Keywords: Comparison of ab and gd T cells in bovine lymphatic fluid time course after salmonella or mock infection

overall_design:
For one mock infection (calf 156) and two experimental S. typhimurium infections (calves 112 and 162), gd and ab  lymphatic T cells were stained with GD3.8 directly conjugated to FITC, washed, and sorted on a Vantage SE cell sorter (BD Immunocytometry Systems) as previously described.  Sorted gd and ab T cells were collected directly into TRIzol reagent (Invitrogen; calf 112) and lysed or suspended in Buffer RLT (Qiagen; calves 156 and 162) and lysed using Qiashredder columns, then frozen at -80oC. RNA was extracted following the manufacturer’s protocol for Trizol (Invitrogen) extraction, or RNeasy (Qiagen) column purification, assessed on a Bioanalyzer 2100 (Agilent Technologies), and amplified either using Affymetrix Two-cycle (calf 112) target labeling protocol with 100 ng total RNA or the One-cycle protocol (calves 156 and 162) with approximately 1.6 micrograms of total RNA as described in the GeneChip® Expression Analysis Technical Manual (June 2004).  Hybridizations to Genechip® Bovine Genome Arrays (Affymetrix) were performed with 15 micrograms biotin labeled cRNA.  Washing and staining was performed in the GeneChip® Fluidics Station 450 using the Midi_euk2v3 protocol.  Chip scans were performed on the Affymetrix GeneChip® Scanner 3000.  GeneChip® Operating Software (GCOS v.1.1, Affymetrix) was used for data collection.

Table I represents annotated genes of potential interest that changed 2 fold or greater in expression between 0 and 48 hours post-Salmonella infection (calves 112 and 162) or mock-infection (calf 156) in T cell subsets.

middle: F

first: Diana

last: Buckner

first: Kerri

last: Rask

first: Larissa

middle: O

last: Jackiw

first: Theresa

last: Trunkle

middle: W

last: Pascual

first: Mark

middle: A

last: Jutila

first: Hannah

last: Kerns


title: Analysis of MYC- and PIM1-dependent genes

city: siena

first: alessio

last: zippo

address: via fiorentina 1

country: Italy

institute: university of siena

summary:
It has been estimated that about 11% of cellular genes present a functional E box to which MYC can associate on the genome. MYC silencing demonstrated that MYC recruits PIM1 at specific MYC binding sites and confocal microscopy following growth factor treatment, showed an elevated degree of nuclear co-localization of PIM1 with nascent transcripts and with MYC suggesting that PIM1 is recruited by MYC to a large number of sites. To understand the actual extension of PIM1 and MYC co-operation in gene transcription we performed expression profile analysis of 293 cells silenced either for MYC or PIM1 at 120 minutes after serum treatment. MYC silencing affected the expression of 1026 genes of which 818 were up-regulated and 208 were down-regulated. Comparison of genes regulated by MYC with those regulated by PIM1, by RNAi silencing, showed that PIM1 contributes to the regulation of 207 genes out of the 1026 MYC-regulated genes. Thus, a subset of 20% of MYC-regulated genes, are also regulated by PIM1. The co-regulated includes genes involved in cell metabolism, protein synthesis, cycle progression, and oncogenesis. Interestingly, a large number of genes are transcriptional factors, which suggests that PIM1 participates in MYC-dependent regulatory networks.
Keywords: expression profiles

overall_design: The gene expression analysis was performed by hybridizing RNA samples to the Whole Human Genome Oligo Microarray from Agilent Technologies. Samples were obtained from 293 cells, treated with serum for 120 minutes, expressing either two independent MYC shRNA (shMYC#1 and shMYC#2) or their relative scrambled shRNA (shsM#1 and shsM#2) for MYC expression analysis; two independent PIM1 shRNA (shPIM1#1 and shPIM1#2) or their relative scrambled shRNA (shsP#1 and shsP#2) for PIM1 expression analysis.

first: Alessio

last: Zippo

first: Salvatore

last: Oliviero


title: ZAS3-null vs wild-type whole mouse thymus

status: Public on Jul 11 2007

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:
The HIVEP/ZAS/Schnurri genes encode large zinc finger proteins that regulate gene expression through DNA binding to the kappaB motif. The ZAS proteins have also been shown to associate with signaling molecules to regulate the TNFa and TGFb signaling pathways. Because ZAS3 transcript and protein expression is rapidly abrogated in primary lymphocytes upon tissue culture, we have generated a ZAS3-null mouse model to study the physiological function of ZAS3. Mice with targeted disruption of ZAS3 are viable with life span comparable to controls. Additionally, the gross anatomy and histology of the major organs, proliferation rates of splenocytes and thymocytes, and the diversity of the TCRb chains of ZAS3 mice are comparable to wild-type. However, compared to wild-type mice, there are decreased CD3+CD4+ and CD3+CD4+CD69+ thymocyte populations.   Additionally, CD44hi/CD62Llo subset and CD25 and CD69 expression are increased in splenocytes of ZAS3 mice. Microarray analysis validated by  real time PCR revealed changes in the expression level of specific transcripts in ZAS3-null thymus, including several proteins in the G-protein coupled olfactory receptor family. Furthermore, EMSA shows that disruption of ZAS3 results in varying changes in binding activities towards NF-kB and AP1 binding sites. Other phenotypes observed in the ZAS3 mice include generalized increased bone density in older animals and infertility in females. As with ZAS2/shn-2 mice, disruption of ZAS3 is not lethal and does not grossly affect development or homeostasis. We propose that the ZAS proteins likely have overlapping functions, which may be uncovered with deletion of multiple ZAS genes in a single animal.
Keywords: Gene knock-out mouse model

overall_design: Five independent microarray hybridizations were performed with thymocytes isolated from sex- and age-matched mutant and wild-type littermates at 6-8 weeks of age. The Agilent Whole Mouse Genome Oligo Microarray (G4121A) containing over 20,000 60-mer oligonucleotide probes representing mouse genes, ESTs and EST clusters was used (Agilent, Cincinnati, OH). Probe labeling and hybridization were preformed by the Microarray Core Faculty (Columbus Children’s Research Institute) following the manufacturer's protocols. Briefly, cDNA probes were synthesized with Superscript III, oligo-dT primers and dNTPs supplemented with amino-allyl-UTP to improve hybridization characteristics and stability. After purification, cDNA samples from mutant or control mice were labeled with Cy3 or Cy5, respectively, and hybridized to the microarray for 14 hours at 48o C.  Slide image was acquired using an Affymetrix 428 scanner with gain settings set so that 95% of spots were below saturation to yield the maximum dynamic range within an experiment.  Images were converted into “.gpr” files using GenePix software (Axon, Union City, CA).  Data were analyzed using GeneTraffic 2.6 software (Iobion, La Jolla, CA).  Lowess-global normalization was applied to all experiments.  Flagging parameters were set as spot intensity lower than the intensity of local spot background, spot intensity lower than average background, and raw spot intensity less than 100.  Flagged spots were not included in normalization or aggregate calculations.  Only genes that were induced or repressed 1.5-fold in at least four of the five independent analyses and hybridization were targeted for potential further study.

first: Lai-Chu

last: Wu


title: Developmental Exposure to DES Alters Uterine Gene Expression That Maybe Associated with Neoplasia Later in Life

status: Public on Jun 14 2007

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
 Previously, we described a mouse model where the well-known reproductive carcinogen, diethylstilbestrol (DES), caused uterine adenocarcinoma following neonatal treatment. Tumor incidence was dose-dependent reaching >90% by 18 mo. following 1000 µg/kg/day of DES.  These tumors followed the initiation/promotion model of hormonal carcinogenesis with developmental exposure as the initiator, and exposure to ovarian hormones at puberty as the promoter. To identify molecular pathways involved in DES-initiation events, uterine gene expression profiles were examined in prepubertal mice exposed to DES (1, 10 or 1000 µg/kg/day) on days 1-5 and compared to age-matched controls.  Of more than 20,000 transcripts, approximately 3% were differentially expressed in at least one DES treatment group compared to controls; several transcripts demonstrated dose-responsiveness. Assessment of gene ontology annotation revealed alterations in genes associated with cell growth, differentiation, and adhesion.  When expression profiles were compared to published studies of uteri from 5 day old DES-treated mice, or adult mice treated with 17β estradiol, similarities were seen suggesting persistent differential expression of estrogen responsive genes following developmental DES exposure.  Moreover, several significantly altered genes have been identified in human uterine adenocarcinomas.  Four altered genes [Lactotransferrin (Ltf), Transforming growth factor beta inducible (Tgfβ1), Cyclin D1 (Ccnd1), and Secreted frizzled-related protein 4 (Sfrp4)], selected for real time RT-PCR analysis, correlated well with the directionality of the microarray data. These data suggest altered gene expression profiles observed two weeks after treatment ceased, were imprinted at the time of developmental exposure and maybe related to the initiation events resulting in carcinogenesis.
Keywords: dose reponse

overall_design: There were 3 DES doses (1, 10 and 1000 ug/kg/day) administered to neonates on days 1-5.  RNA was pooled for 10 mice, with each dose having its own matching control (corn oil).  Dye-flipped hybridizations were performed for each paired comparison.

first: Retha

last: Newbold

first: Wendy

middle: N

last: Jefferson

first: Sherry

last: Grissom

first: Elizabeth

last: Padilla-Banks

first: Ryan

last: Snyder

first: Edward

last: Lobenhofer


title: A. nidulans transcriptome analysis

status: Public on Jul 25 2007

city: Ribeirão Preto

first: Gustavo

middle: Henrique

last: Goldman

state: São Paulo

address: Av do Café, s/n

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirão Preto

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

overall_design: Refer to individual Series


title: Effects of Phenylethyl Isothiocyanate on N-Nitrosomethylbenzylamine-induced Cytotoxicity in Rat Esophagus

status: Public on Jul 18 2007

city: Columbus

first: Gary

last: Stoner

state: OH

address: 2001 Polaris Pkwy

department: The Ohio State University

institute: Department of Internal Medicine

summary:
To date, there is little information on early molecular events in the development of N-nitrosomethylbenzylamine (NMBA) induced esophageal tumorigenesis and of the effects of chemopreventive agents on these events. In this study, we identified genes in rat esophagus that were differentially expressed in response to short–term NMBA-treatment and modulated by co-treatment with phenethylisothiocyanate (PEITC). Rats were fed AIN-76A diet or AIN-76A diet containing PEITC for three weeks. During the third week of dietary treatment, they were administered three s.c. doses of NMBA (0.5 mg/kg b.w.). Rats were sacrificed 24 h after the last treatment, esophagi excised and processed for histological grading, microarray and real-time PCR analysis. Our histopathological data showed that treatment of rats with PEITC had protective effect on NMBA-induced preneoplastic lesions in the rat esophagus. We identified 2261 genes that were differentially expressed in the NMBA-treated vs. control esophagi and 1936 genes in the NMBA+PEITC- vs. NMBA-treated esophagi. The intersection of these two sets resulted in the identification of 1323 genes in NMBA-treated esophagus that were modulated by PEITC to near-normal levels of expression. The measured changes in the expression levels of 10 selected genes were validated using real-time PCR. Principle components analysis (PCA) was applied to all twelve microarrays in the study, which suggested that in terms of global gene expression, PEITC treatment had a genome-wide modulating effect on NMBA-induced gene expression. Samples obtained from animals treated with PEITC alone or co-treated with NMBA were more similar to controls than they were to NMBA treatment alone.
Keywords: Toxicogenomics,reference design

overall_design: For each treatment we used a pooling strategy to enable the inclusion of samples from numerous animals. Three replicate microarrays were completed for each of the four treatments (control, PEITC, NMBA and NMBA+PEITC) for a total of twelve microarrays. Each microarray was hybridized using a pooled RNA sample, and each pool was created from equal amounts of total RNA from two or three independent RNA samples, representing individual animals. Each of these samples was obtained from a different animal, and no sample was included in more than one pool.  In total, samples from nine animals per group were pooled for control, NMBA, PEITC and NMBA+PEITC microarrays. To facilitate comparisons of gene expression across all treatments, we utilized a reference design in which each microarray was co-hybridized with a common reference sample labeled with Cy3, and RNA from the treatment pool was labeled with Cy5. Stratagene’s Universal Rat reference RNA (Stratagene, La Jolla, CA) was used as the common reference in all microarrays.

first: Rashmeet

middle: K

last: Reen

first: Alan

last: Dombkowski

first: Laura

last: Kresty

first: Daniela

last: Cukovic

first: Jennifer

last: Mele

first: Sridevi

last: Salagrama

first: Ronald

last: Nines


title: Tcf3 Targets in Mouse Embryonic Stem Cells E14

status: Public on Jul 10 2007

city: Singapore

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis Street

department: Stem Cell and Developmental Biology

country: Singapore

institute: GIS

type: Genome binding/occupancy profiling by genome tiling array

summary:
To determine the binding targets of Tcf3 in mouse ESCs,  ChIP combined with DNA microarray was carried out according to Agilent Mammalian ChIP-on-chip protocol (version 3)3. Briefly, immunoprecipitated (IP) DNA was blunted with T4 polymerase and ligated to linkers with T4 DNA ligase. For reference, 200 ng of input DNA was used. Ligated DNA was amplified with two rounds of PCR cycles. Two ug of each amplified sample were labeled with Cy5 for IP DNA, and Cy3 for input DNA using CGH labeling kit (Invitrogen). Four ug of each labeled sample was blocked with mouse Cot-1 DNA (Invitogen) and blocking agent (Agilent), and hybridized to DNA microarrays (G4490A, Agilent) for 40 h at 65oC. The microarrays were washed and stabilized with acetonitrile (Sigma), followed by stabilization and drying solution (Agilent). The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (G2567AA, version 9.1). The data was then analysed with ChIP Analytics 1.3 (G4477AA), according to the Whitehead Neighbourhood Model, P(Xbar)<0.001, with intra-array median normalization 3. Bound targets which was determined by the algorithm was validated by qPCR on a selected number of genes. The false positive rate was determined.
Keywords: ChIP-chip

overall_design:
ChIP assays with feeder-free E14 mouse ESCs were carried out as described previously{Zhang, 2006 #49}. Briefly, cells were cross-linked with 1% formaldehyde for 10 min at room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine. Chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using antibodies. The antibodies used for immunoprecipitation were Tcf3 (M-20), HA (Y-11), Tle2 (H-321), Tle3 (M-201), CtBP (H-440), GST (Z-5, all from Santa Cruz). For all ChIP experiments, quantitative PCR analyses were performed in real-time using the ABI PRISM 7900 Sequence Detection System and SYBR Green Master Mix as described previously {Zhang, 2006 #49}. Relative occupancy values were calculated by determining the apparent immunoprecipitation efficiency (ratios of the amount of immunoprecipitated DNA to that of the input sample) and normalized to the level observed.
            ChIP combined with DNA microarray was carried out according to Agilent Mammalian ChIP-on-chip protocol (version 3) {Boyer, 2005 #28}. Briefly, immunoprecipitated (IP) DNA was blunted with T4 polymerase and ligated to linkers with T4 DNA ligase. For reference, 200 ng of input DNA was used. Ligated DNA was amplified with two rounds of PCR cycles. Two ug of each amplified sample were labeled with Cy5 for IP DNA, and Cy3 for input DNA using CGH labeling kit (Invitrogen). Four ug of each labeled sample was blocked with mouse Cot-1 DNA (Invitogen) and blocking agent (Agilent), and hybridized to DNA microarrays (G4490A, Agilent) for 40 h at 65oC. The microarrays were washed and stabilized with acetonitrile (Sigma), followed by stabilization and drying solution (Agilent). The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (G2567AA, version 9.1). The data was then analysed with ChIP Analytics 1.3 (G4477AA), according to the Whitehead Neighbourhood Model, P(Xbar)<0.001, with intra-array median normalization {Boyer, 2005 #28}. Bound targets which was determined by the algorithm was validated by qPCR on a selected number of genes. The false positive rate was determined.

last: Tam


title: Identification of downstream genes regulated by OsMADS2

city: Bangalore

first: Shri Ram

last: Yadav

state: Karnataka

address: C. V. Raman Avenue

department: Department of Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary:
To gain mechanistic insights on OsMADS2 functions in rice spikelet development, we have employed global expression profilling to identify the genes regulated by OsMADS2. Transgenic rice panicle RNAs were compared with the wild type panicle RNA of similar developmental stage. Genes downregulated in transgenic lines will be those which expression requires functional OsMADS2 whereas upregulated genes will need OsMADS2 for their repression.
Keywords: Comparative expression profile analysis

overall_design: Two independent biological RNA pools of dsRNAiOsMADS2 transgenic panicles were compared with a single wild type RNA pool in two different hybridizations. A third hybridization was performed with reciprocally dye-lebeled wild type RNA and one of the mutant RNA.

first: Shri

middle: R

first: Kalika

last: Prasad

first: Usha

last: Vijayraghavan


title: Trimethylation of histone H3 lysine27 (H3K27me3) in Arabidopsis

status: Public on Jun 22 2007

city: Los Angeles

first: Steve

last: Jacobsen

state: CA

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles


title: Comparsion of different hESC line derived neural progenitor cells (hNPCs)

status: Public on Jul 04 2007

first: Yi

last: Sun

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

summary:
The self-renewal and differentiation potential of human embryonic stem cells (hESCs) suggests that hESCs could be used for regenerative medicine, especially for restoring neuronal functions in brain diseases. However, the functional properties of neurons derived from hESC are largely unknown. Moreover, since hESCs were derived under diverse conditions, the possibility arises that neurons derived from different hESC lines exhibit distinct properties, but this possibility remains unexplored. To address these issues, we developed a protocol that allows step-wise generation from hESCs of ~70-80% pure human neurons that form spontaneously active synaptic networks in culture. Comparison of neurons derived from the well-characterized HSF1 and HSF6 hESC lines revealed that HSF1- but not HSF6-derived neurons exhibit forebrain properties. Accordingly, HSF1-derived neurons initially form primarily GABAergic synaptic networks, whereas HSF6-derived neurons initially form glutamatergic networks. microRNA profiling revealed significant expression differences between the two hESC lines, suggesting that microRNAs may influence their distinct differentiation properties. These observations indicate that although both HSF1 and HSF6 hESCs differentiate into functional neurons, the two hESC lines exhibit distinct differentiation potentials, suggesting that they are pre-programmed. Information on hESC line-specific differentiation biases is crucial for neural stem cell therapy and establishment of novel disease models using hESCs.
Keywords: Gene expression profiling

overall_design:
We directly compared the transcriptome of hNPCs derived from HSF-1 and HSF-6 hESC lines under two different neural induction conditions (embryonic body formation in presence of caudalizing factors (retinoic acid and bFGF) and monolayer conversion in presence of BMP signaling inhibitor (Noggin)). Since HSF6 hESC cannot undergo efficient neural differentiation without caudalizing factors, we cannot obtain RNA samples for HSF6 (Noggin).
In summary, consistent with our immunostaining results, HSF1 hNPCs display more forebrain properties as compared to HSF6 hNPCs, indicated by expression of multiple forebrain specific markers. Conversely, HSF6 hNPCs show regional identity towards posterior central nervous system.

first: Hao

last: Wu

first: Weihong

last: Ge

first: Bruno

last: Blanchi

first: Kevin

last: Kim

first: Thomas

last: Südhof

first: Jun

last: Xu

first: Zhiping

last: Pang


title: Genome-wide analysis reveals determinants of redundant and specific binding within a transcription factor family

city: Bloomington

first: Peter

last: Hollenhorst

address: 1001 E Third St, Jordan Hall 104

summary:
A central question in transcription factor biology is how a specific member of a transcription factor family occupies a promoter in vivo, when all family members bind the same consensus site in vitro.  To uncover the mechanisms regulating DNA binding specificity within transcription factor families, we have used the techniques of chromatin immunoprecipitation coupled with genome-wide microarray analysis to query the occupancy of three members of the ETS transcription factor family in a human T-cell line.  Unexpectedly, redundant occupancy was frequently detected while specific occupancy was less likely.  An unbiased bioinformatics approach correlated redundant binding with consensus ETS binding sequences near transcription start sites, whereas specific binding sites diverged dramatically from the consensus, were coupled with a site for a cooperative binding partner, and were found further from transcription start sites.  The specific and redundant DNA binding modes illustrate the regulation of transcription factor specificity in vivo and suggest two distinct roles for members of the ETS transcription factor family.
Keywords: ChIP-chip

overall_design: Chromatin IP from uninduced asynchronous Jurkat T cells, or HT29 colon cells using antibodies to three ETS transcription factors (ETS1, ELF1, and GABPa) or the transcription factors RUNX1 or E2F4.  IP and whole input DNAs are amplified (WGA2 kit sigma) and labeled and compared by promoter microarrays (Agilent).  Each experiment requires 2 microarrays to cover the genome.  Proximal promoter arrays assay 1kb surrounding transcription start sites, extended promoter arrays assay 7kb surrounding transcription start sites.  Each microarray is performed as two biological replicates with the exception of ETS1 in HT29 proximal promoter array which were done once, and ETS1 in Jurkat proximal promoter array which was done three times.

first: Atul

last: Shah

first: Barbara

last: Graves


title: Generation of germ-line competent induced pluripotent stem cells

status: Public on Jun 07 2007

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary:
We have previously shown that pluripotent stem cells are induced from mouse fibroblasts by retroviral introduction of Oct3/4, Sox2, c-Myc and Klf4, and subsequent selection for Fbx15 expression. These iPS (induced pluripotent stem) cells are similar to embryonic stem (ES) cells in morphology, proliferation and teratoma formation. Fbx15-iPS cells, however, are different in gene expression and DNA methylation patterns and fail to produce adult chimeras. Here we show that selection for Nanog results in germ-line competent iPS cells, with more ES cell-like gene expression and DNA methylation patterns. The four transgenes were strongly silenced. We obtained adult chimeras from seven Nanog-iPS clones, with one clone transmitted through the germ-line to the next generation. Approximately 20% of the offspring developed tumors, where c-Myc transgene was reactivated. Thus iPS cells competent for germ-line chimeras can be obtained from fibroblasts, but retroviral introduction of c-Myc should be avoided for clinical application.
Keywords: cell type comparison

overall_design: Total RNA from Fbx15-null MEF (duplicate), Fbx15-null ES cells (duplicate), Fbx15-iPS cells (clone MEF4-7, duplicate), or Nanog-iPS cells (clones 20D -2, 16, 17, and 18) were labeled with Cy3. Samples were hybridized to a Mouse Oligo Microarray (Agilent) according to the manufacturer’s protocol. Arrays were scanned with a G2565BA Microarray Scanner System (Agilent). Data were analyzed using GeneSprings GX software (Agilent). We excluded genes whose value fluctuated more than 2-fold between duplicated analyses.

first: Keisuke

last: Okita

first: Tomoko

last: Ichisaka


title: Temporal expression profile of granulocytic differentiation of primary CD34+ cells cultured under 5% and 20% O2 levels

status: Public on Jun 06 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary:
Little is known about the global transcriptional program underlying granulocytic (G) commitment, differentiation and maturation.  Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of G differentiation of human CD34-positive hematopoietic stem and progenitor cells cultured with interleukin-3, interleukin-6 granulocyte colony stimulating factor and stem cell factor.  The goal this study was to identify genes involved in the various facets of G differentiation including commitment, expansion, differentiation and functional capacity.

This SuperSeries is composed of the SubSeries listed below.


title: Atm-/-,mTerc-/-,p53-/- triple knock-out lymphoma vs normal mouse DNA (GPL2872)

status: Public on Jun 05 2007

city: boston

first: bin

last: feng

address: 44 binney street

institute: dfci

summary:
Highly rearranged and mutated cancer genomes present major challenges in the identification of pathogenetic events driving the cancer process.  Here, we engineered lymphoma-prone mice with chromosomal instability to assess the utility of mouse models in cancer gene discovery and the extent of cross-species overlap in cancer-associated copy number aberrations.  Integrating with targeted re-sequencing, our comparative oncogenomic studies efficiently identified FBXW7 and PTEN as commonly deleted or mutated tumor suppressors in human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL).  More generally, the murine cancers acquire widespread recurrent clonal amplifications and deletions targeting loci syntenic to alterations present in not only human T-ALL but also diverse tumors of hematopoietic, mesenchymal and epithelial types. These results thus support the view that murine and human tumors experience common biological processes driven by orthologous genetic events as they evolve towards a malignant phenotype.  The highly concordant nature of genomic events encourages the use of genome unstable murine cancer models in the discovery of biologically relevant driver events in human cancer.
Keywords: comparative genomic hybridization, genetic modification

overall_design: 18 lymphoma samples from Atm-/-, mTerc-/-, p53-/- triple knock-out mice were analyzed. 3 week old hymus RNA from healthy mice of p53 Hets was used as reference. Each sample was hybridized with dye-swap replica.

first: B

last: Feng

first: R

last: Maser

first: K

last: Wong

first: A

last: Protopopov

first: E

last: Lin

first: L

last: Chin

last: Depinho


title: In vitro cultured and Ex vivo sorted murine pro-B cells: Wild-type versus Pax5-/-

status: Public on Jul 13 2007

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

institute: Research Institute of Molecular Pathology

first: Alexandra

last: Schebesta


title: Identification of genes differentially expressed in cotton

status: Public on Jun 26 2007

city: Raleigh

first: Earl

middle: William

last: Taliercio

state: NC

address: 3127 Ligon St

institute: USDA/ARS


title: MicroRNAs in adult rodent liver and response to dioxin

status: Public on Aug 15 2007

city: Toronto

first: Ivy

last: Moffat

state: Ontario

address: 1 King's College Circle, Medical Science Building Rm.4302

department: Pharmacology

institute: University of Toronto

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

middle: D

first: Paul

last: Boutros

first: Trine

last: Celius

first: Jere

last: Lindén

first: Raimo

last: Pohjanvirta

first: Allan

last: Okey


title: Human Colon tumor vs Normal Human DNA

last: feng

summary:
Highly rearranged and mutated cancer genomes present major challenges in the identification of pathogenetic events driving the cancer process.  Here, we engineered lymphoma-prone mice with chromosomal instability to assess the utility of mouse models in cancer gene discovery and the extent of cross-species overlap in cancer-associated copy number aberrations.  Integrating with targeted re-sequencing, our comparative oncogenomic studies efficiently identified FBXW7 and PTEN as commonly deleted or mutated tumor suppressors in human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL).  More generally, the murine cancers acquire widespread recurrent clonal amplifications and deletions targeting loci syntenic to alterations present in not only human T-ALL but also diverse tumors of hematopoietic, mesenchymal and epithelial types. These results thus support the view that murine and human tumors experience common biological processes driven by orthologous genetic events as they evolve towards a malignant phenotype.  The highly concordant nature of genomic events encourages the use of genome unstable murine cancer models in the discovery of biologically relevant driver events in human cancer.
Keywords: comparative genomic hybridization

overall_design: 81 human Colon tumor samples (74 unique ones) were analyzed. Normal Human DNA was used as reference. Some samples were hybridized with dye-swap replica.

last: Martin

first: C

last: Brennan


title: Human GBM tumor vs Normal Human DNA

first: bin

overall_design: 38 human GBM samples were analyzed. Normal Human DNA was used as reference. Some samples were hybridized with dye-swap replica.

last: Feng

last: Maser

last: Wiedemeyer


title: Temporal expression profile of granulocytic differentiation of primary CD34+ cells cultured under 20% O2 levels

first: Eleftherios

last: Papoutsakis

summary:
Little is known about the global transcriptional program underlying granulocytic (G) commitment, differentiation and maturation.  Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of G differentiation of human CD34-positive hematopoietic stem and progenitor cells cultured with interleukin-3, interleukin-6 granulocyte colony stimulating factor and stem cell factor.  The goal this study was to identify genes involved in the various facets of G differentiation including commitment, expansion, differentiation and functional capacity.
Keywords: time course

overall_design: G-CSF mobilized peripheral blood CD34-positive cells were cultured with IL-3, IL-6, SCF and G-CSF under 20% O2.  Three biological replicate experiments were analyzed and approximately 15% of the samples were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

first: Huang

last: Li Ting

first: William

last: Miller

middle: T


title: Temporal expression profile of granulocytic differentiation of primary CD34+ cells cultured under 5% O2 levels

overall_design: G-CSF mobilized peripheral blood CD34-positive cells were cultured with IL-3, IL-6, SCF and G-CSF under 5% O2.  Three biological replicate experiments were analyzed and approximately 15% of the samples were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.

middle: M


title: ATM-dependent regulation of gene expression upon DNA damage in human fibroblasts

city: Morrisville

first: Tong

last: Zhou

address: 133 Southcenter Court, Suite 400

institute: Gentris Corperation

summary:
The relationships between profiles of global gene expression and DNA damage checkpoint functions were studied in cells from patients with ataxia telangiectasia (AT).  Three telomerase-expressing AT fibroblast lines displayed the expected hypersensitivity to ionizing radiation (IR) and defects in DNA damage checkpoints. Profiles of global gene expression in AT cells were determined at 2, 6 and 24 h after treatment with 1.5 Gy IR or sham-treatment, and were compared to those previously recognized in normal human fibroblasts.  Under basal conditions 160 genes or ESTs were differentially expressed in AT and normal fibroblasts, and these were associated by gene ontology with insulin-like growth factor binding and regulation of cell growth. Upon DNA damage, 1091 gene mRNAs were changed in at least two of the three AT cell lines.  When compared with the 1811 genes changed in normal human fibroblasts after the same treatment, 715 were found in both AT and normal fibroblasts, including most genes categorized by gene ontology into cell cycle, cell growth and DNA damage response pathways.  However, the IR-induced changes in these 715 genes in AT cells usually were delayed or attenuated in comparison to normal cells. The reduced change in DNA-damage-response genes and the attenuated repression of cell-cycle-regulated genes may account for the defects in cell cycle checkpoint function in AT cells.  The observation of attenuated and not ablated checkpoint responses in AT cells supports a hypothesis that the ATM- and rad3-related checkpoint kinase ATR also responds to IR-induced DNA damage and complements ATM signaling.
Keywords: ATM, cell cycle checkpoint, ionizing radiation, microarray

overall_design: Logarithmically growing cells were treated with 1.5 Gy IR or sham, and harvested at 2, 6 or 24 h after the treatment. Total RNA was isolated using Qiagen RNeasy kit. The quality of all RNA samples was confirmed using an Agilent 2100 Bioanalyzer. Microarray analysis was then performed: briefly, 1 µg of sample RNA and global reference RNA (Stratagene) were converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with either Cy3-dUTP or Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization. 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven (Robbins Scientific Model 400, 1040-60-1AG) at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap. Following hybridization, the arrays were scanned using the Agilent DNA Microarray Scanner with SureScan® Technology and microarray images were analyzed using Agilent Feature Extraction Software (v7.1). The gene expression level was presented as ratio of sample intensity against reference intensity.

first: Jeff

last: Chou

last: Kaufmann


title: Atm-/-,mTerc-/-,p53-/- triple knock-out lymphoma vs normal mouse DNA (GPL4092)

overall_design: 13 lymphoma samples from Atm-/-, mTerc-/-, p53-/- triple knock-out mice were analyzed. DNA from matched mouse of the same tumorsample was used as reference. Each sample was hybridized with dye-swap replica. 44K of 244K probes were extracted for analysis in order to combine these 13 samples with other 22 samples which are hybridized on Agilent's 44K mouse CGH arrays, GPL2884

first: B

first: R

first: K

last: Wong

first: A

last: Protopopov

first: E

last: Lin

first: L

last: Chin

last: Depinho


title: nai1-1, ER body deficient mutant, vs wild-type Col-0

status: Public on Jun 04 2007

city: Kitashirakawa, Sakyoku

first: Ikuko

last: Hara-Nishimura

state: Kyoto

address: Oiwakecho

department: Depertment of Botany

institute: Kyoto University

summary:
ER bodies are endoplasmic reticulum (ER)-derived organelles that might be involved in defense systems. The NAI1 gene regulates the development of ER bodies because mutation of NAI1 abolishes the formation of ER bodies. The nai1-1 mutant had a single nucleotide change at an intron acceptor site of At2g22770 (NAI1 gene). Because of this mutation, aberrant splicing of NAI1 mRNA occurs in the nai1-1 mutant. NAI1 encodes a transcription factor that has a basic-helix-loop-helix (bHLH) domain. Transient expression of NAI1 induced ER bodies in the nai1-1 mutant. To identify genes that are related to ER bodies, we compared the genome-wide expression profiles of Col-0 and the nai1-1 mutant using DNA microarrays. Twenty-nine genes were found to be expressed at least 2-fold more strongly in the nai1-1 mutant than in Col-0, and 341 genes were found to be expressed at least 2-fold more strongly in Col-0 than in the nai1-1 mutant. The 15 genes that showed the strongest expression in Col-0 compared to the expression in nai1-1 are shown in Table 1. Five of these genes are JAL genes (JAL22, JAL23, JAL31, JAL33 and PBP1/JAL30). The mRNA level of PYK10 was reduced in nai1-1 (4.3 fold larger in Col-0 than in nai1-1). The mRNA levels of GLL genes (GLL23 and GLL25) were also reduced in nai1-1.
Keywords: mutant vs wt comparison

overall_design: Total RNA was purified from the roots of 20-day-old plants (3 plants were pooled for each genotype). Arabidopsis plants were grown under continuous light condition at 22˚C on MS medium paltes. The control plants and the nai1-1 mutant were cultivated in the same plate. This was done to avoid any difference in plant growth conditions between the mutants and the control plants.

first: Atsushi

middle: J

last: Nagano

first: Mikio

last: Nishimura


title: Expression profile of mature normal PB neutrophils

summary:
The transcriptional patterns of mature normal PB neutrophils (granulocytes) was examined and used as a control against which the transcriptional programs of cultured granulocytes and granulocytic cells lines can be compared.
Keywords: Peripheral blood neutrophils

overall_design: RNA was extracted from peripheral blood neutrophils.  Three biological replicate experiments were analyzed and approximately 67% of the samples were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference RNA pool labeled with Cy5.


title: Human Pancreas tumor vs Normal Human DNA

last: feng

overall_design: 30 human Pancreas tumor samples were analyzed. Normal Human DNA was used as reference. Some samples were hybridized with dye-swap replica.

last: Feng


title: control males

status: Public on Jun 01 2007

first: Yuhei

address: 2309 Gonda 695 Charles E Young Dr. South

department: Neuropsychiatric Institute

institute: University of California Los Angeles

summary:
gene expression profiles of lymphoblastoid cells from control males without autism
Keywords: control males

overall_design:
Cy5; each control male
Cy3; pool of 14 unrelated individuals.

first: Daniel

middle: H

last: Geschwind


title: autism with FMR1FM

summary:
gene expression profiles of lymphoblastoid cells from individuals with autism and full mutation of FMR1
Keywords: autism with FMR1-FM

overall_design:
Cy5; each individual with autism and FMR1FM
Cy3; pool of 14 unrelated individuals.


title: Gene expression profiles of lymphoblastoid cells

overall_design: Refer to individual Series


title: autism with dup(15q)

summary:
gene expression profiles of lymphoblastoid cells from individuals with autism and  duplication of 15q11-13
Keywords: autism with dup(15q)

overall_design:
Cy5; each male with autism and dup(15q)
Cy3; pool of 14 unrelated individuals.


title: Gene expression affected by TNFa and SB203580

status: Public on May 22 2007

first: Jai

middle: Moo

last: Shin

address: 11301 Wilshire Blvd

department: Physiology

summary:
Gene expression affected by TNFa was investigated, then, p38 inhibitor SB203580 was used to investigate p38 signal pathway.
Keywords: p38 signal response

overall_design: Fibroblast-like synoviocyte culture was treated with TNFa in the presence and absence of SB203580 and compared to the gene expression not treated with TNFa.

first: George

last: Sachs

first: Cindy

last: Zer


title: Glis3: The role in osteoblast differentiation and adipocyte differentiation

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

summary:
The expression of Glis3 in C3H10T1/2 cells promotes osteoblastic differentiation as indicated by the the induction of increase in alkaline phosphatase activity, an early marker of osteoblast differentiation, and increased expression of osteopontin, a late marker of osteogenesis. Glis3 acts synergistically with bone morphogenic protein 2 (BMP-2). In contrast, expression of Glis3 inhibits the induction of adipocyte differentiation. Microarray analysis identified the fibroblast growth factor 18 (FGF18) as one of the genes induced by Glis3 in C3H10T1/2 cells directly.
Keywords: Glis3, osteoblast differentiation, adipocyte differentiation, FGF18, BMP2

overall_design: Total RNA was extracted from C3H10T1/2 cells infected with empty vector or Glis3 using Qiagen Rneasy Mini kit.  Each RNA sample was amplified and converted to fluorescently labeled cRNA, either with cyanine 3 (Cy3) or cyanine 5 (Cy5), using the Agilent Fluorescent Linear Amplification Kit. The fluorescently labeled cRNAs were mixed and hybridized simultaneously to Agilent mouse oligo arrays. The sample pair was hybridized to two arrays, employing a fluor reversal. Chips were scanned with an Agilent dual-laser scanner.  Gene expression data were generated using the Agilent feature extraction software (v7.5), with defaults for all parameters.

first: JuYoun

last: Beak

first: HongSoon

last: Kang

first: Yong-Sik

last: Kim

first: Anton

last: Jetten


title: Sch9 Is a Major Target of TORC1 in Saccharomyces cerevisiae

status: Public on Apr 28 2007

city: Princeton

first: Soyeon

last: Lippman

state: NJ

address: 301 Lewis Thomas Lab

institute: Princeton University

summary:
The Target Of Rapamycin (TOR) protein is a Ser/Thr kinase that functions in two distinct multiprotein complexes: TORC1 and TORC2. These conserved complexes regulate many different aspects of cell growth in response to intra- and extracellular cues. Here we report the first bona fide substrate of yeast TORC1: the AGC-kinase Sch9. Six amino acids in the c-terminus of Sch9 are directly phosphorylated by TORC1. Phosphorylation of these residues is lost upon rapamycin-treatment as well as carbon- or nitrogen-starvation and transiently reduced following application of osmotic, oxidative or thermal stress. TORC1-dependent phosphorylation is required for Sch9 activity and replacement of residues phosphorylated by TORC1 with Asp/Glu renders Sch9 activity TORC1-independent. Sch9 is required for TORC1 to properly regulate ribosome biogenesis, translation initiation and entry into G0 phase, but not expression of Gln3-dependent genes. Our results suggest that Sch9 functions analogously to the mammalian TORC1 substrate S6K1 rather than the mTORC2 substrate PKB/Akt.
Keywords: time course, cell type.

overall_design: Global transcriptional analysis of rapamycin response was conducted on cells expressing either a wild-type, Sch9(WT), or TOR-independent allele of Sch9, Sch9(2D3E). Reference samples used were cells collected immediately prior to rapamycin treatment for the respective cell genotypes. Test samples were collected 20, 30, 60, 90, 120, and 180min post rapamycin treatment.

first: Jorg

last: Urban

first: James

last: Broach

first: Robbie

last: Loewith


title: The influence of highly recurrent EBV reactivation on genetic copy number alterations

status: Public on May 30 2007

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary:
We proposed that the frequency of EBV reactivation may be crucial for its pathogenic role and highly recurrent EBV reactivations exert a profound influence on genome instability. Recurrent reactivations were induced in the EBV-latently infected NPC cells (NA cells) by treating with 12-o-tetradecanoylphorbol-13-acetate (TPA) and sodium n-butyrate (SB) once per passage periodically. Genome-wild oligoarray-based comparative genomic hybridization (CGH) technology was applied to investigate the copy-number aberrations in response for different frequencies of EBV reactivation. The results showed that the NR15 cells, NA cells with the highest frequency (15 times) of reactivation, exhibit extensive genomic copy-number alterations (CNAs) mostly involving chromosome 3p, 3q, 8p, 8q, 9p and 9q, whereas limited number of CNAs were observed both in NR1 cells where only the initial reactivation take place and NP15 cells which were culture in parallel with NR15 cells without EBV-reactivation. We concluded that it is the highly recurrent reactivations of EBV, but neither just a primary reactivation nor EBV-latent infection, may intimately involve in carcinogenesis of nasopharyngeal epithelial cells with the progressive genome instabilities and the accumulation of genetic mutations.
Keywords: array-based comparative genomic hybridization, reactivation of EBV, incidence, frequency, recurrent, genome instability, copy-number alterations, carcinogenesis, and nasopharyngeal carcinoma (NPC).

overall_design: Samples of four sources were analyzed. The NP1 cells denoted the EBV-latently infected nasopharyngeal carcinoma cell lines, NA cells, with low-passage-number and mock-treated. The NR1 denoted the NA cells harboring one time of EBV reactivation. The NR15 cells denoted the NA cells harboring fifteen times of EBV reactivation. The NP15 cells denoted the NA cells cultured in parallel with NR15 (experienced 15 times of passages) without EBV-reactivation. Genomic DNAs extracted from NP15, NR1 and NR15 cells were used as experimental samples and subjected to Cy5-labeling reactions. Genomic DNAs extracted from NP1 cells were used as the common reference samples subjected to Cy3-labeling reactions. All three experiments were verified by dye-swap design where the targets labeling conditions were exchanged, NP1 labeled with Cy5, and NP15, NR1 or NR15 labeled with Cy3.

first: C

middle: Y

last: Fang

first: J

last: Chen


title: Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii

status: Public on May 21 2007

city: Tampa

first: Kami

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

type: Expression profiling by genome tiling array

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

sample_organism:
Homo sapiens
Toxoplasma gondii RH

first: Mathieu

last: Gissot

first: Krystina

last: Kelly

first: Ajioka

last: Jim

first: Greally

last: John


title: Comparative profiling of Tcl1 gene disruptants and Tcl1 stable transformants.

status: Public on May 10 2007

city: Suita

first: Tatsushi

last: Miyazaki

state: Osaka

address: 2-2 Yamadaoka

department: Department of Molecular Therapeutics

institute: Osaka University Graduate School of Medicine

summary:
Tcl1 is one of embryonic stem cell specific transcripts identified by digital differential display analysis. Tcl1 is highly expressed during early embryogenesis and to some extent in embryonic stem cells. Its expression in adult tissues is restricted to testis and ovary, and is found to decline if Oct-3/4 expression is suppressed in embryonic stem cells. It is reported that the female knockout mice exhibit reduced fertility. It was first identified in human T-cell tumors and the tumorigenic property was proved by a series of transgenic studies. We have used DNA microarray to identify potential Tcl1 targets in embryonic stem cells and the influence of Tcl1 on stemness.
Keywords: genetic modification

overall_design: We analyzed two arrays, each comparing expression profiles of a Tcl1 gene disruptant and a Tcl1 stable transformant. We used different clones with their dyes swapped.(biological replication)

first: Satsuki

first: Tomofumi

last: Tanaka

first: Fumi

last: Tashiro

first: Eiji

last: Yamato

first: Jun-ichi


title: Gene expression profile of peripheral blood lymphocytes: comparison between melanoma patients and healthy controls

status: Public on May 09 2007

city: Stanford

first: Peter

middle: P.

address: CCSR room 1155, 269 Campus Drive

department: Department of Medicine

institute: Stanford University

summary:
We focused on the major peripheral blood lymphocyte populations that may be involved in anti-tumor responses and negatively impacted by cancer, specifically CD8 T cells, CD4 T cells, B cells and CD56dim natural killer cells. The pure cell subsets were stringently sorted by flow cytometry from PBMC samples. Gene expression profiles of these cell populations from melanoma patients were compared to healthy controls.
Keywords: gene expression profile

overall_design:
The raw data set contained 48 arrays: 6 healthy and 6 melanoma arrays for each of the 4 cell types. Two of the arrays had quality issues due to background noise and were excluded, leaving us with 46 arrays.

On each array we used Cy3 to label a pool of two RNA samples from a pair of age and gender matched stage IV (American Joint Committee on Cancer) melanoma patients or from a pair of age and gender matched healthy donors. We used Cy5 to label the Total Lymphocyte Reference (TLR) RNA. The TLR is a common reference specifically created for this study using the total peripheral lymphocyte fraction from 20 healthy donors.

first: Rebecca

last: Critchley-Thorne

first: Ning

last: Yan

first: Serban

last: Nacu

first: Jeffrey

last: Weber

first: Susan

middle: P

last: Holmes


title: Murine Hepatoblasts

status: Public on May 25 2007

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary:
The homeobox transcription factor Prox1 is expressed in embryonic hepatoblasts and remains expressed in adult hepatocytes. Prox1-null mice show severe deficiencies of liver development, but the underlying mechanisms are unknown. We studied the effects of Prox1 on the transcriptional profile of embryonic day-14 (ED14) met-murine-hepatocytes (ED14-MMH). These immortalized murine hepatoblasts express numerous hepatoblast markers, but not Prox1. We performed stable transfection with Prox1 cDNA, analyzed the transcriptome with Agilent mouse whole genome microarrays and validated genes by qRT-PCR. We observed more than 12-fold up-regulation of 22 genes and down-regulation of 232 genes. Numerous of these genes are involved in metabolic hepatocyte functions and may be regulated by Prox1 directly or indirectly, e.g. by down-regulation of HNF4a. Prox1 induces down-regulation of transcription factors, which are highly expressed in neighboring endodermal organs, suggesting a function during hepatoblast commitment. Prox1 does not influence proliferative activity of MMH but regulates genes involved in liver morphogenesis. We observed up-regulation of both type-IVa3 procollagen and functionally active matrix metalloproteinase-2 (MMP-2), which places Prox1 in the centre of liver matrix turnover. This is consistent with MMP-2 expression in hepatoblasts during liver development, and persistence of a basal lamina around the liver bud in Prox1-deficient mice. Our studies suggest that Prox1 is a multifunctional regulator of liver morphogenesis, hepatocyte function and commitment.

Keywords: Met murine hepatocytes - Hex - HNF4a - MMP-2 - Type-IV collagen
Keywords: Met murine hepatocytes - Hex - HNF4a - MMP-2 - Type-IV collagen

overall_design:
- two samples
- Dye Swap design with 6 arrays

first: Maria

last: Papoutsi

first: Jozsef

last: Dudas

first: Jürgen

last: Becker

first: Marco

last: Tripodi

first: Lennart

last: Opitz

first: Giuliano

last: Ramadori

first: Jörg

last: Wilting


title: Serogroup Conversion of Vibrio cholerae in Aquatic Reservoirs

status: Public on Apr 25 2007

first: Melanie

last: Blokesch

address: 279 Campus Drive

department: Medical School


status: Public on Apr 03 2007

city: Chapel Hill

first: Nancy

last: DeMore

address: 3010 Old Clinic Rd., CB 7213

department: Surgery

institute: UNC @ Chapel Hill

summary:
Molecular Characterization of Human Breast Tumor Microvessels
Keywords: breast cancer

overall_design: LCM & Microarrays


title: Microarray analysis of aortic tissue from different rat hypertensive models

status: Public on Apr 11 2007

city: Seattle

first: Lynn

last: Amon

state: WA

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

summary:
To determine if there exists a consistent gene signature associated with vascular hypertrophy among different rat hypertensive models:  treated and untreated Wistar Kyoto (WKY) rats and treated and untreated Spontaneous Hypertensive Rat (SHR) rats.
Keywords: strain comparison, treatment vs control

overall_design: Two strains of rat were studies:  WKY which are normotensive and SHR which are hypertensive.  Aortic tissue was taken from 6 untreated WKY rats and 6 WKY rats treated with angiotensin.  Aortic tissue was taken from 6 untreated SHR rats, 6 treated with nifedipine for two weeks and 5 treated with nifedipine for two weeks and then washed out for three weeks.  There was a total of 29 samples.  A pool of RNA from 6 untreated WKY rats was used as a reference.  Hybridizations were performed in duplicate with a dye-flip and always with the reference as the second color.

first: David

last: Pritchard

first: Xi

last: Wang

first: Evelyne

last: Marchand

first: Hangjun

last: Duan

first: Larry

last: Adams

first: Denis

last: deBlois

first: Stephen

last: Schwartz


title: Reoviruses MyRV1-Cp9B21 and MyRV2-CpC18 responsive genes in Cryphonectria parasitica

status: Public on Apr 20 2007

city: Rockville

first: Donald

middle: Lee

last: Nuss

state: MD

address: 9600 Gudelsky Drive

department: Center for Biosystems Research

institute: University of Maryland Biotechnology Institute


title: ACC Agilent 44K CGH

status: Public on Apr 10 2007

city: Phoenix

first: Elizabeth

middle: A

last: Stephan

state: AZ

address: 445 North 5th Street

department: Genetic Basis of Human Disease

institute: Translational Genomics Research Institute

summary:
Adrenocortical carcinoma (ACC) is a rare endocrine malignancy accounting for between 0.02 and 0.2 percent of all cancer deaths. Surgical removal offers the only current potential for cure. Unfortunately, ACC has undergone metastatic spread in approximately 40-70 percent of patients at the time of diagnosis. Standard chemotherapy with mitotane containing regimens is often ineffective and associated with intolerable side-effects. Modern molecular technologies now allow the examination of germ-line and somatic DNA for chromosomal alterations which can give biological insight into cancer processes. Using an array-based high density comparative genomic hybridization (CGH) screen, genomic aberrations within 25 ACC patients were assessed to identify genomic characteristic of this cancer. Genomes were queried with >44,000 probes on the Agilent Human Genome CGH array detecting regions of chromosomal gain and loss within the tumor population. Statistical analysis of this genetic landscape reveals a set of chromosomal aberrations strongly associated with survival in an accumulation dependent fashion. These regions may hold prognostic indicators and offer therapeutic targets that can be used to develop novel treatments for aggressive tumors.
Keywords: CGH, adrenocortical carcinoma, cancer

overall_design: Array-based high density comparative genomic hybridization (CGH) screen was utilized to identify genomic aberrations within 25 ACC patients. Thirteen tumor samples are from male and 12 are from female patients. The mean age of patients is 51.8 years (range, 23.3-77.7 years) with a median of 54.2 years. The mean tumor physical measurements for the ACC set are a mean weight of 536.3 grams (range, 20.5-2880 grams) and size of 10.7 cm (range, 3-21.5 cm). The clinical data also includes functional status of the tumor which is based on clinical parameters and confirmed by biochemical analysis. Nonfunctional tumors or those that do not over-produce hormones represent 48% of the tumor set. The localization of each tumor is a measure of the tumor metastatic characteristic at time of operation while tumor grade is a histologically based rating system for tumor progression. Sixty percent of the tumors (15 of 25) were localized to the adrenal area with no indication of metastatic spread. The majority of tumors were grade 3 and 4 at time of diagnosis (17 of 25) indicating necrosis and atypical mitosis of >21/50 hpf. Genomes were queried with >44,000 probes on the Agilent Human Genome CGH array detecting regions of chromosomal gain and loss within the tumor population.

first: Tae-Hoon

last: Chung

first: Clive

middle: S

last: Grant

first: Seungchan

last: Kim

first: Daniel

last: Von Hoff

first: Jeffrey

last: Trent

first: Michael

last: Demeure


title: Expression profiling of motor cortex in sporadic amyotrophic lateral sclerosis

status: Public on Mar 26 2007

city: Catania

first: Sebastiano

last: Cavallaro

address: Viale Regina Margherita, 6

department: Institute of Neurological Sciences

institute: Italian National Research Council

summary:
We used oligonucleotide microarrays to find differentially expressed genes between control subjects and those affected by sporadic amyotrophic lateral sclerosis.
Keywords: disease state analysis

overall_design: Complementary RNAs (cRNAs) labelled with Cy5-CTP (Perkin-Elmer) were synthesized from 1 µg of total RNA of each sample of human motor cortex using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) following the manufacturer’s protocol. A reference cRNA, labelled with Cy3-CTP (Perkin-Elmer), was synthesized from 1 µg of sample Diseased 2 RNA. Aliquots (750 ng) of Cy3 and Cy5 labelled cRNA targets were co-hybridized on Whole Human Genome Oligo Microarrays (Agilent Technologies). Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as indicated by the manufacturer (Agilent Technologies). Microarrays were scanned at 10-μm resolution using a GenePix Personal 4100A microarray scanner and the GenePix Pro 6.0 acquisition and data-extraction software (Molecular Devices, Corp.).

first: Carsten

last: Lederer

first: Antonietta

last: Torrisi

first: Niovi

last: Santama


title: Gene expression profiling of chickpea responses

status: Public on Apr 12 2007

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Bldg 223, Level 1, Plenty Road

department: Biotechnology & Environmental Biology

country: Australia

institute: RMIT University

platform_organism:
Cicer arietinum
Lathyrus sativus
Lens culinaris


title: Allergen-stimulated CD4+ T cells from hen's egg allergic patients

status: Public on Apr 18 2007

city: Toyoake

first: Nakajima

last: Yoichi

state: Aichi

address: 1-98 Dengakugakubo Kutsukake

department: Pediatrics

institute: Fujita Health University

summary:
Allergen-stimulated T cells from hen’s egg-allergic children were analyzed to identify genes that are specifically up-regulated in these cells.
Keywords: disease state analysis

overall_design: PBMCs from three hen’s egg allergic children and two non-allergic children were cultured in RPMI 1640 supplemented with 10% autologous plasma for 16 hours with or without hen’s egg white allergen (allergen concentration10 mg/ml).  To focus on specific T cells reacting with HEW, cells bearing CD4 antigen were isolated from cultured PBMCs using a Magnetic cell sorter（Miltenyi Biotec,  Bergisch Gladbach, Germany）after CD14 positive cell depletion. Total RNA was extracted from these CD4 positive cells with an RNeasy mini-kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instruction.

first: Yoichi

last: Nakajima


title: Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection

status: Public on Apr 23 2007

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary:
Histone acetylation plays an important role in regulating DNA accessibility. Multifunctional Sin3 proteins bind histone deacetylases (HDACs) to assemble silencing complexes that selectively target chromatin. We show that, in fission yeast, an essential HDAC Clr6 exists in two distinct Sin3 core complexes. Complex I contains an essential Sin3 homologue Pst1 and other factors, and predominantly targets gene promoters. Complex II contains a non-essential Sin3, Pst2, and several conserved proteins.  It preferentially targets transcribed chromosomal regions and centromere cores.  Defects in complex II abrogate global protective functions of chromatin, causing increased accessibility of DNA to genotoxic agents and widespread antisense transcripts that are processed by the exosome.  Interestingly, the two Clr6 complexes differentially repress forward and reverse centromeric repeat transcripts, suggesting that these complexes regulate transcription in heterochromatin and euchromatin in a similar manner, including suppression of spurious transcripts from cryptic start sites.

This SuperSeries is composed of the SubSeries listed below.

first: Estelle

last: Nicolas

first: Takatomi

last: Yamada

first: Hugh

last: Cam

first: Peter

middle: C

last: FitzGerald

first: Ryuji

last: Kobayashi

middle: I


title: Profiling brain and liver tissues from mice

status: Public on May 02 2007

city: Ciudad de Buenos Aires

first: Mariano

middle: Cesar

last: Salibe

address: Av. Patricias Argentinas 435

country: Argentina

institute: Gentron LLC


title: Rice plants infected by Rice dwarf virus

status: Public on Mar 14 2007

city: Tsukuba

first: Takumi

last: SHIMIZU

address: Kannondai 3-1-1

institute: National Agricultural Research Center

summary:
We investigated changes in gene expression in rice plants exposed to RDV to gain some insight into the fundamental physiological and biochemical changes that are induced by viral infection, in the hope of finding clues that might help to control the viral disease.
An analysis, using microarrays, of gene expression in rice plants infected with Rice dwarf virus revealed significant decreases in levels of expression of genes that are involved in the formation of cell walls, reflecting the stunted growth of diseased plants. The expression of plastid-related genes was also suppressed, as anticipated from the white chlorotic appearance of infected leaves. By contrast, the expression of defense- and stress-related genes was enhanced after viral infection.
Keywords: disease state analysis

overall_design: To reduce experimental variations, three sets of ten seedlings were harvested from RDV-infected and mock-inoculated plants 9 dpi. Then we pooled leaves from multiple plants as the source of RNA, and employed three sets of microarrays (GSM119715, GSM119718 and GSM119719) using RNAs from different sources and one set of dye-swapping microarrays (GSM119715 and GSM119717).

last: Shimizu

first: Kouji

last: Satoh

first: Shoshi

last: Kikuchi

first: Toshihiro

last: Omura


title: Global gene expression analysis of quercetin bioactivity in cultured rat cardiomyocytes

status: Public on Mar 31 2007

city: Bologna

first: Cristina

last: Angeloni

state: BO

address: Via Irnerio 48

department: Biochemistry

institute: University of Bologna

summary:
Despite extensive studies, the fundamental mechanisms responsible for the development and progression of heart failure have not yet been fully elucidated. Recent experimental and clinical studies have suggested that reactive oxygen species (ROS) play a major pathological role.   Quercetin, a major flavonoid present in the human diet, has been studied widely and its biological properties are consistent with its protective role in the cardiovascular system. However, it remains unknown whether the cardioprotective effects of quercetin may also occur through the modulation of genes involved in cell survival. This study was therefore designed to examine the gene expression profiling of cultured rat primary cardiomyocytes supplemented with quercetin using DNA-microarrays and relating these data to functional effects.
Keywords: nutritional intervention, dose response

overall_design: Primary heart cell cultures were obtained by isolation of cardiomyocytes from the ventricles of 2–4 day old Wistar rats and grown until complete confluence. In some dishes, 30 μM quercetin was added to the culture medium for 6, 12 or 24 h. Total RNA was extracted using Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA), following the manufacturer’s protocol. The yield and purity of the RNA were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., Rockland, Del, USA). The 28s and 18s ribosomal bands were checked using Agilent 2100 bioanalyzer with an RNA 6000 Nano LabChip Kit. For each sample, mRNA was amplified starting from 1.5 μg of totRNA by Amino Allyl MessageAmp I aRNA Kit (Ambion Inc.) to obtain amino allyl antisense RNA (aaRNA). Labeling of aaRNA was performed using NHS ester Cy3 or Cy5 dies (Amersham Biosciences, Piscataway, NJ - USA). One hybridization to Agilent 22K-gene arrays (Rat oligo array G4130A) was performed to compare quercetin supplemented cells versus unsupplemented ones.  Each analysis was replicated swapping the labeling with the two cyanine dyes.

first: Emanuela

last: Leoncini

first: Silvana

last: Hrelia


title: Expression analysis of two-round IVT-amplified LCM samples: Arabidopsis endosperm

status: Public on Apr 02 2007

city: Dunedin

first: Robert

last: Day

state: Otago

address: Cumberland Street

country: New Zealand

institute: University of Otago


title: hGRβ: Elucidation of its Role in Transcriptional Regulation and Identification of a Ligand

status: Public on Mar 02 2007

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
The human glucocorticoid receptor (GR) is expressed as two alternately spliced Cterminal isoforms: α and β. In contrast to the canonical hGRα, hGRβ is constitutively nuclear, is not thought to bind ligand, and is believed to affect gene transcription only by acting as a dominant negative to hGRα.   Microarray analysis indicated that hGRβ, expressed in the absence of hGRα, can regulate gene expression, and furthermore, occupation of hGRβ with the antagonist RU-486 diminishes that capacity.
Keywords: cell type comparison

overall_design:
RNA preparation: Total RNA was extracted from 5x10 6 U-OFF or U-2
OSβ cells treated with either ethanol vehicle or 1μM RU-486 for 6 hours using the RNAqueous Total RNA Isolation Kit (Ambion Inc. Austin, TX) according to manufacturer’s instructions.  RNA was treated with DNase using the DNA-Free DNase Treatment and Removal Reagents (Ambion Inc.) according to manufacturer’s instructions prior to use with the microarray. Four pairs of RNA (vehicle vs. RU-486 treated) were harvested for each cell type to yield four biological replicates for gene expression analysis.
Linear Amplification Label Protocol and Feature Extraction: Gene expression analysis was conducted using Agilent Human1Av2 arrays (Agilent Technologies, Palo Alto, CA). Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol
and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters.

first: Laura

last: Lewis-Tuffin

first: Christine

last: Jewell

first: Rachelle

last: Bienstock

first: Jennifer

middle: B

last: Collins

first: John

last: Cidlowski


title: Profiling of Rgt1-regulated gene transcripts in the fungal pathogen Candida albicans

status: Public on Mar 01 2007

city: Santa Barbara

first: Jessica

last: Sexton

address: UCSB/MCDB

institute: UCSB

overall_design: Refer to individual Series